- Dept. of Cell and Molecular Biology,
Faculty of Biotechnology and Biomolecular Sciences,
Universiti Putra Malaysia,
43400 UPM Serdang,
Malaysia
Soon -Guan Tan
UPM - Universiti Putra Malaysia, Cell and Molecular biology, Faculty Member
Trichoderma species are commercially applied as biocontrol agents against numerous plant pathogenic fungi due to their production of antifungal metabolites, competition for nutrients and space, and mycoparasitism. However, currently the... more
Trichoderma species are commercially applied
as biocontrol agents against numerous plant pathogenic
fungi due to their production of antifungal metabolites,
competition for nutrients and space, and mycoparasitism.
However, currently the identification of Trichoderma species
from throughout the world based on micro-morphological
descriptions is tedious and prone to error. The
correct identification of Trichoderma species is important
as several traits are species-specific. The Random Amplified
Microsatellites (RAMS) analysis done using five
primers in this study showed different degrees of the
genetic similarity among 42 isolates of this genus. The
genetic similarity values were found to be in the range of
12.50–85.11% based on a total of 76 bands scored in the
Trichoderma isolates. Of these 76 bands, 96.05% were
polymorphic, 3.95% were monomorphic and 16% were
exclusive bands. Two bands (250 bp and 200 bp) produced
by primer LR-5 and one band (250 bp) by primer P1A
were present in all the Trichoderma isolates collected from
healthy and infected oil palm plantation soils. Cluster
analysis based on UPGMA of the RAMS marker data
showed that T. harzianum, T. virens and T. longibrachiatum
isolates were grouped into different clades and lineages.
In this study we found that although T. aureoviride
isolates were morphologically different when compared to
T. harzianum isolates, the UPGMA cluster analysis showed
that the majority isolates of T. aureoviride (seven from
nine) were closely related to the isolates of T. harzianum.
as biocontrol agents against numerous plant pathogenic
fungi due to their production of antifungal metabolites,
competition for nutrients and space, and mycoparasitism.
However, currently the identification of Trichoderma species
from throughout the world based on micro-morphological
descriptions is tedious and prone to error. The
correct identification of Trichoderma species is important
as several traits are species-specific. The Random Amplified
Microsatellites (RAMS) analysis done using five
primers in this study showed different degrees of the
genetic similarity among 42 isolates of this genus. The
genetic similarity values were found to be in the range of
12.50–85.11% based on a total of 76 bands scored in the
Trichoderma isolates. Of these 76 bands, 96.05% were
polymorphic, 3.95% were monomorphic and 16% were
exclusive bands. Two bands (250 bp and 200 bp) produced
by primer LR-5 and one band (250 bp) by primer P1A
were present in all the Trichoderma isolates collected from
healthy and infected oil palm plantation soils. Cluster
analysis based on UPGMA of the RAMS marker data
showed that T. harzianum, T. virens and T. longibrachiatum
isolates were grouped into different clades and lineages.
In this study we found that although T. aureoviride
isolates were morphologically different when compared to
T. harzianum isolates, the UPGMA cluster analysis showed
that the majority isolates of T. aureoviride (seven from
nine) were closely related to the isolates of T. harzianum.
Isozyme and protein electrophoresis data from mycelial extracts of 27 isolates of Trichoderma harzianum, 10 isolates of T. aureoviride, and 10 isolates of T. longibrachiatum from Southern Peninsular Malaysia were investigated. The eight... more
Isozyme and protein electrophoresis data from mycelial extracts of 27 isolates of Trichoderma harzianum, 10 isolates of T. aureoviride, and 10 isolates of T. longibrachiatum from Southern Peninsular Malaysia were investigated. The eight enzyme and a single protein pattern systems were analyzed. Three isozyme and total protein patterns were shown to be useful for the detection of three Trichoderma species. The isozyme and protein data were analyzed using the Nei and Li Dice similarity coefficient for pairwise comparison between individual isolates, species isolate group, and for generating a distance matrix. The UPGMA cluster analysis showed a higher degree of relationship between T. harzianum and T. aureoviride than to T. longibrachiatum. These results suggested that the T.harzianum isolates had high levels of genetic variation compared with the other isolates of Trichoderma species.
Research Interests:
Research Interests:
Oil palm chloroplast is maternally inherited, making investigation of the chloroplast diversity an interesting endeavor. This paper describes a method for extracting enriched oil palm chloroplast DNA (cpDNA) done on six palms of different... more
Oil palm chloroplast is maternally inherited, making investigation of the chloroplast diversity an interesting endeavor. This paper describes a method for extracting enriched oil palm chloroplast DNA (cpDNA) done on six palms of different origins from Angola, Nigeria, Ghana, Madagascar and Suriname. Restriction enzyme digestion was used to evaluate the successful extraction of the oil palm cpDNA. The use of a mitochondrial DNA specific- universal primer revealed that most of the cpDNA were free from mitochondrial DNA contamination. Three chloroplast- specific universal primers were also used to evaluate the cpDNA. Their amplicons were cloned and sequenced to confirm that the cpDNA was indeed amplified. A search against the public databases further confirmed that the primers amplied sequences of the Elaeis guineensis Jacq. chloroplast genome. Two of them gave consistent amplifications when tested on cpDNA from the Angolan, Nigerian, Ghanian, Madagascan and Suriname palms.
Research Interests:
Research Interests:
ABSTRACT Miyun Reservoir is the main raw water source for Beijing’s domestic water supply. Flow discharge to Miyun Reservoir decreased drastically over a 50-year period, from 1956 to 2005, and had seriously affected Beijing’s water... more
ABSTRACT Miyun Reservoir is the main raw water source for Beijing’s domestic water supply. Flow discharge to Miyun Reservoir decreased drastically over a 50-year period, from 1956 to 2005, and had seriously affected Beijing’s water supply. Climate variability and human activity had been identified as the two main reasons for the decrease in flow. Here, climate variability refers to changes in precipitation and temperature. Impact of human activity includes direct withdrawal of water (referred to as “direct abstraction” in this paper) from the river (primary) or groundwater and indirect impact due to man-made changes in land use and vegetation in the upstream of the reservoir. According to the historical record, “direct abstraction” from the upstream of the reservoir has increased significantly since 1984. The study period was split into two sub-periods, from 1956 to 1983 and from 1984 to 2005. Based on the historical record, annual runoff in the upstream catchment of Miyun Reservoir (i.e., inflow into the reservoir) had decreased from 90.3 mm to 41.8 mm for the two sub-periods, a decrease of 48.5 mm. Over the same period, average annual “direct abstraction” increased from 2.2 mm to 13.4 mm, an increase of 11.2 mm. The latter accounted for 23% (11.2 mm/48.5 mm) of the decrease in inflow into the reservoir.This study utilised: (1) a distributed hydrological model (geomorphology-based hydrological model, or GBHM) and (2) a climate elasticity model to conduct a quantitative assessment of the impact of climate variability and the indirect impact of human activity on the inflow into the reservoir. Simulation results of GBHM and the climate elasticity model showed that climate impact was accountable for about 55% and 51% of the decrease in reservoir inflow, respectively. The indirect impact of human activity (mainly man-made land use and vegetation changes) accounted for 18% of the decrease in reservoir inflow.
Research Interests:
Research Interests:
Inter-simple sequence repeats (ISSRs) are regions in the genome flanked by microsatellite sequences. PCR amplification of these regions using a single primer yields multiple amplification products that can be used as a dominant multilocus... more
Inter-simple sequence repeats (ISSRs) are regions in the genome flanked by microsatellite sequences.
PCR amplification of these regions using a single primer yields multiple amplification products that can
be used as a dominant multilocus marker system for the study of genetic variation in various organisms.
ISSR markers are easy to use, low-cost, and methodologically less demanding compared to other
dominant markers, making it an ideal genetic marker for beginners and for organisms whose genetic
information is lacking. Here, we comment upon some of the intricacies often overlooked in designing an
ISSR experiment, clarify some misconceptions, and provide recommendations on using ISSR markers
in genetic variation studies.
PCR amplification of these regions using a single primer yields multiple amplification products that can
be used as a dominant multilocus marker system for the study of genetic variation in various organisms.
ISSR markers are easy to use, low-cost, and methodologically less demanding compared to other
dominant markers, making it an ideal genetic marker for beginners and for organisms whose genetic
information is lacking. Here, we comment upon some of the intricacies often overlooked in designing an
ISSR experiment, clarify some misconceptions, and provide recommendations on using ISSR markers
in genetic variation studies.
Research Interests:
Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexploitation of horseshoe crabs around the world, and the lack of information on their populations, it is crucial that genetic variation studies... more
Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexploitation of horseshoe crabs
around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to
assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here,
five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were
studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were
obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred
that most of the genetic variations were distributed at the individual level rather than among populations of the species.
Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation.
Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula
that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South
China Sea.
Key words: Dispersal, genetic monitoring, land barrier, peninsular Malaysia, population structure
around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to
assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here,
five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were
studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were
obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred
that most of the genetic variations were distributed at the individual level rather than among populations of the species.
Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation.
Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula
that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South
China Sea.
Key words: Dispersal, genetic monitoring, land barrier, peninsular Malaysia, population structure
Research Interests:
Sampling for the mangrove snails, Nerita lineata, and surface sediments was carried out from nine geographical sites of Peninsular Malaysia in April 2011. The concentrations of Lithium (Li) were determined in the shells, opercula and soft... more
Sampling for the mangrove snails, Nerita lineata, and surface sediments was carried out
from nine geographical sites of Peninsular Malaysia in April 2011. The concentrations of
Lithium (Li) were determined in the shells, opercula and soft tissues of N. lineata and in
the surface sediments by using ICP-MS. The ranges of Li concentrations (μg/g dry weight)
were found to be 0.107-0.283 for shells, 0.021-0.177 for opercula and 0.011-0.634 for
total soft tissues of N. lineata. For sediments, Li ranges were found to be between 21.84-
146.22 μg/g dry weight). The distribution of Li was found to be: sediment> ST> shell>
opercula. The Li sediment data in the present study were comparable with the results of Li
contaminated sediments which had been previously reported in the literature and higher
than those of continental crust materials and igneous rocks. There was no significant
correlation (P>0.05) for the Li levels between the sediments. The snails (shells, opercula
and soft tissues) and this indicated that Li is an essential metal for metabolism and thus is
being regulated in the body of the snail.
from nine geographical sites of Peninsular Malaysia in April 2011. The concentrations of
Lithium (Li) were determined in the shells, opercula and soft tissues of N. lineata and in
the surface sediments by using ICP-MS. The ranges of Li concentrations (μg/g dry weight)
were found to be 0.107-0.283 for shells, 0.021-0.177 for opercula and 0.011-0.634 for
total soft tissues of N. lineata. For sediments, Li ranges were found to be between 21.84-
146.22 μg/g dry weight). The distribution of Li was found to be: sediment> ST> shell>
opercula. The Li sediment data in the present study were comparable with the results of Li
contaminated sediments which had been previously reported in the literature and higher
than those of continental crust materials and igneous rocks. There was no significant
correlation (P>0.05) for the Li levels between the sediments. The snails (shells, opercula
and soft tissues) and this indicated that Li is an essential metal for metabolism and thus is
being regulated in the body of the snail.
Research Interests:
Oryctes rhinoceros, a serious pest in young oil palm replanting areas, often causes reduced plant productivity and plant death. Common control measures are species specific pheromone traps; however discrepancy in attraction toward the... more
Oryctes rhinoceros, a serious pest in young oil palm replanting areas, often causes reduced plant
productivity and plant death. Common control measures are species specific pheromone traps; however
discrepancy in attraction toward the pheromone traps has raised doubts on the possibility of cryptic
species complex in O. rhinoceros. To ascertain the possibilities of a cryptic species complex; species
specific single locus DNA microsatellite markers were used to study the genetic variation within and
between O. rhinoceros populations. Using 30 species specific single locus DNA microsatellite markers,
O. rhinoceros beetles from six populations originating from Malaysia and Indonesia revealed no isolated
gene pool. Pairwise population differentiation and gene flow values further revealed low to moderate
differentiation and a high gene flow between populations. Beetles of different population interacted
freely, permitting gene flow between closely and distantly located populations; thus ruling out the
possibility for cryptic species complex in O. rhinoce
productivity and plant death. Common control measures are species specific pheromone traps; however
discrepancy in attraction toward the pheromone traps has raised doubts on the possibility of cryptic
species complex in O. rhinoceros. To ascertain the possibilities of a cryptic species complex; species
specific single locus DNA microsatellite markers were used to study the genetic variation within and
between O. rhinoceros populations. Using 30 species specific single locus DNA microsatellite markers,
O. rhinoceros beetles from six populations originating from Malaysia and Indonesia revealed no isolated
gene pool. Pairwise population differentiation and gene flow values further revealed low to moderate
differentiation and a high gene flow between populations. Beetles of different population interacted
freely, permitting gene flow between closely and distantly located populations; thus ruling out the
possibility for cryptic species complex in O. rhinoce
Research Interests:
Abstract Background: The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human Variome Project (HVP) country-specific nodes. Since its inception in 9th October 2010, MyHVP has attracted the significant... more
Abstract
Background: The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human
Variome Project (HVP) country-specific nodes. Since its inception in 9th October 2010, MyHVP has attracted the
significant number of Malaysian clinicians and researchers to participate and contribute their data to this project.
MyHVP also act as the center of coordination for genotypic and phenotypic variation studies of the Malaysian
population. A specialized database was developed to store and manage the data based on genetic variations
which also associated with health and disease of Malaysian ethnic groups. This ethnic-specific database is called
the Malaysian Node of the Human Variome Project database (MyHVPDb).
Findings: Currently, MyHVPDb provides only information about the genetic variations and mutations found in the
Malays. In the near future, it will expand for the other Malaysian ethnics as well. The data sets are specified based
on diseases or genetic mutation types which have three main subcategories: Single Nucleotide Polymorphism
(SNP), Copy Number Variation (CNV) followed by the mutations which code for the common diseases among
Malaysians. MyHVPDb has been open to the local researchers, academicians and students through the registration
at the portal of MyHVP (http://hvpmalaysia.kk.usm.my/mhgvc/index.php?id=register).
Conclusions: This database would be useful for clinicians and researchers who are interested in doing a study on
genomics population and genetic diseases in order to obtain up-to-date and accurate information regarding the
population-specific variations and also useful for those in countries with similar ethnic background.
Keywords: Malaysian Node of the Human Variome Project, Ethnic-specific molecular variation database, SNPs,
CNVs, Disease genes and their products
Background: The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human
Variome Project (HVP) country-specific nodes. Since its inception in 9th October 2010, MyHVP has attracted the
significant number of Malaysian clinicians and researchers to participate and contribute their data to this project.
MyHVP also act as the center of coordination for genotypic and phenotypic variation studies of the Malaysian
population. A specialized database was developed to store and manage the data based on genetic variations
which also associated with health and disease of Malaysian ethnic groups. This ethnic-specific database is called
the Malaysian Node of the Human Variome Project database (MyHVPDb).
Findings: Currently, MyHVPDb provides only information about the genetic variations and mutations found in the
Malays. In the near future, it will expand for the other Malaysian ethnics as well. The data sets are specified based
on diseases or genetic mutation types which have three main subcategories: Single Nucleotide Polymorphism
(SNP), Copy Number Variation (CNV) followed by the mutations which code for the common diseases among
Malaysians. MyHVPDb has been open to the local researchers, academicians and students through the registration
at the portal of MyHVP (http://hvpmalaysia.kk.usm.my/mhgvc/index.php?id=register).
Conclusions: This database would be useful for clinicians and researchers who are interested in doing a study on
genomics population and genetic diseases in order to obtain up-to-date and accurate information regarding the
population-specific variations and also useful for those in countries with similar ethnic background.
Keywords: Malaysian Node of the Human Variome Project, Ethnic-specific molecular variation database, SNPs,
CNVs, Disease genes and their products
Research Interests:
Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexploitation of horseshoe crabs around the world, and the lack of information on their populations, it is crucial that genetic variation studies... more
Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexploitation of horseshoe crabs
around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to
assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here,
five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were
studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were
obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred
that most of the genetic variations were distributed at the individual level rather than among populations of the species.
Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation.
Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula
that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South
China Sea.
around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to
assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here,
five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were
studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were
obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred
that most of the genetic variations were distributed at the individual level rather than among populations of the species.
Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation.
Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula
that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South
China Sea.
Research Interests:
Horseshoe crabs are marine arthropods that are amongst the oldest living creatures that still exist today. Among the four extant species of horseshoe crabs, Carcinoscorpius rotundicauda differs from the other species by having poisonous... more
Horseshoe crabs are marine arthropods that are amongst the oldest living creatures that
still exist today. Among the four extant species of horseshoe crabs, Carcinoscorpius
rotundicauda differs from the other species by having poisonous eggs and lays its eggs in
sandy-mud areas near river mouths. With the rapid development of coastal areas
worldwide, C. rotundicauda habitats are decreasing. Until now, however, there has not
been any study on the species' genetic variation. Simple sequence repeat (SSR) and intersimple
sequence repeat (ISSR) markers were employed to study the genetic variation in
five C. rotundicauda populations from the east and west coasts of the Malay Peninsula. Both
markers showed differing levels of genetic variation, but concurred on the pattern of genetic
structuring among populations of the species. This includes showing that little,
although significant, genetic differentiation is present among populations, suggesting a
low rate of gene flow among populations. The results also suggested that C. rotundicauda
may be subjected to the land barrier effect of the Malay Peninsula, whereby gene flow is
limited between populations occurring on both sides of the peninsula, increasing their
genetic differentiation through time
still exist today. Among the four extant species of horseshoe crabs, Carcinoscorpius
rotundicauda differs from the other species by having poisonous eggs and lays its eggs in
sandy-mud areas near river mouths. With the rapid development of coastal areas
worldwide, C. rotundicauda habitats are decreasing. Until now, however, there has not
been any study on the species' genetic variation. Simple sequence repeat (SSR) and intersimple
sequence repeat (ISSR) markers were employed to study the genetic variation in
five C. rotundicauda populations from the east and west coasts of the Malay Peninsula. Both
markers showed differing levels of genetic variation, but concurred on the pattern of genetic
structuring among populations of the species. This includes showing that little,
although significant, genetic differentiation is present among populations, suggesting a
low rate of gene flow among populations. The results also suggested that C. rotundicauda
may be subjected to the land barrier effect of the Malay Peninsula, whereby gene flow is
limited between populations occurring on both sides of the peninsula, increasing their
genetic differentiation through time
Research Interests:
An Agrobacterium-mediated transformation method was applied to introduce the luciferase reporter gene under the control of the CaMV35S promoter in the pGreen0049 binary vector into strawberry cv. Camarosa. The in vitro regeneration system... more
An Agrobacterium-mediated transformation method was applied to introduce the
luciferase reporter gene under the control of the CaMV35S promoter in the pGreen0049
binary vector into strawberry cv. Camarosa. The in vitro regeneration system of strawberry
leaves to be used in the transformation was optimized using different TDZ concentrations in
MS medium. TDZ at 16 μM showed the highest percentage (100%) of shoot formation and
the highest mean number of shoots (24) produced per explant. Studies on the effects of
different antibiotics, namely timentin, cefotaxime, carbenicillin and ampicillin, on shoot
regeneration of strawberry leaf explants showed the best shoot regeneration in the presence
of 300 mg/L timentin and 150 mg/L cefotaxime. Assessment of the different factors affecting
Agrobacterium mediated-transformation of strawberry with the luciferase gene showed the
highest efficiency of putative transformant production (86%) in the treatment with no
preculture, bacterial OD600 of 0.6 and the addition of 150 mg/L cefotaxime in the pre-selection
and selection media. The presence of the luciferase gene in the plant genome was verified by the luciferase reporter gene assay, nested PCR amplification and dot blot of genomic
DNA isolated from the young leaves of each putatively transformed plantlet
luciferase reporter gene under the control of the CaMV35S promoter in the pGreen0049
binary vector into strawberry cv. Camarosa. The in vitro regeneration system of strawberry
leaves to be used in the transformation was optimized using different TDZ concentrations in
MS medium. TDZ at 16 μM showed the highest percentage (100%) of shoot formation and
the highest mean number of shoots (24) produced per explant. Studies on the effects of
different antibiotics, namely timentin, cefotaxime, carbenicillin and ampicillin, on shoot
regeneration of strawberry leaf explants showed the best shoot regeneration in the presence
of 300 mg/L timentin and 150 mg/L cefotaxime. Assessment of the different factors affecting
Agrobacterium mediated-transformation of strawberry with the luciferase gene showed the
highest efficiency of putative transformant production (86%) in the treatment with no
preculture, bacterial OD600 of 0.6 and the addition of 150 mg/L cefotaxime in the pre-selection
and selection media. The presence of the luciferase gene in the plant genome was verified by the luciferase reporter gene assay, nested PCR amplification and dot blot of genomic
DNA isolated from the young leaves of each putatively transformed plantlet
Research Interests:
The oil palm is badly affected by basal stem rot (BSR) disease in Southeast Asia. BSR disease is caused by the fungus Ganoderma boninense, which is a major threat to oil palm compared with other Ganoderma spp. Molecular markers associated... more
The oil palm is badly affected by basal
stem rot (BSR) disease in Southeast Asia. BSR disease
is caused by the fungus Ganoderma boninense, which
is a major threat to oil palm compared with other
Ganoderma spp. Molecular markers associated with
BSR disease will accelerate the identification process
of resistant breeding materials in screening of plants
for tolerance to the disease at the nursery stage. In this
study, 58 simple sequence repeat markers were
utilized with three progeny types, namely, KA4G1,
KA4G8, and KA14G8, to perform a comparative
molecular mapping for association with BSR. A total
of 319 alleles were identified with an average of 5.51
alleles per locus. Five markers, mEgCIR0793:180,
mEgCIR0894:200, mEgCIR03295:210, mEg-
CIR3737:146 and mEgCIR3785:299 were found to
be associated with Ganoderma disease with P values
of 0.018, 0.033, 0.037, 0.034 and 0.037, respectively,
in single progeny analysis. However, in pooled data
(KA4G1, KA4G8 and KA14G8), only two alleles,
mEgCIR0804:213 (P value = 0.001) and mEg-
CIR3292:183 (P value = 0.001), were found to be
associated with Ganoderma disease. These analyses
confirmed that progeny type KA4G1 was tolerant,
whereas the other two were susceptible progeny types.
These markers and KA4 progeny will be useful in
future works on BSR disease resistance in oil palm.
stem rot (BSR) disease in Southeast Asia. BSR disease
is caused by the fungus Ganoderma boninense, which
is a major threat to oil palm compared with other
Ganoderma spp. Molecular markers associated with
BSR disease will accelerate the identification process
of resistant breeding materials in screening of plants
for tolerance to the disease at the nursery stage. In this
study, 58 simple sequence repeat markers were
utilized with three progeny types, namely, KA4G1,
KA4G8, and KA14G8, to perform a comparative
molecular mapping for association with BSR. A total
of 319 alleles were identified with an average of 5.51
alleles per locus. Five markers, mEgCIR0793:180,
mEgCIR0894:200, mEgCIR03295:210, mEg-
CIR3737:146 and mEgCIR3785:299 were found to
be associated with Ganoderma disease with P values
of 0.018, 0.033, 0.037, 0.034 and 0.037, respectively,
in single progeny analysis. However, in pooled data
(KA4G1, KA4G8 and KA14G8), only two alleles,
mEgCIR0804:213 (P value = 0.001) and mEg-
CIR3292:183 (P value = 0.001), were found to be
associated with Ganoderma disease. These analyses
confirmed that progeny type KA4G1 was tolerant,
whereas the other two were susceptible progeny types.
These markers and KA4 progeny will be useful in
future works on BSR disease resistance in oil palm.
Research Interests:
Sampling for the mangrove snails, Nerita lineata, and surface sediments was carried out from nine geographical sites of Peninsular Malaysia in April 2011. The concentrations of Lithium (Li) were determined in the shells, opercula and... more
Sampling for the mangrove snails, Nerita lineata, and surface sediments was carried out
from nine geographical sites of Peninsular Malaysia in April 2011. The concentrations of
Lithium (Li) were determined in the shells, opercula and soft tissues of N. lineata and in
the surface sediments by using ICP-MS. The ranges of Li concentrations (μg/g dry weight)
were found to be 0.107-0.283 for shells, 0.021-0.177 for opercula and 0.011-0.634 for
total soft tissues of N. lineata. For sediments, Li ranges were found to be between 21.84-
146.22 μg/g dry weight). The distribution of Li was found to be: sediment> ST> shell>
opercula. The Li sediment data in the present study were comparable with the results of Li
contaminated sediments which had been previously reported in the literature and higher
than those of continental crust materials and igneous rocks. There was no significant
correlation (P>0.05) for the Li levels between the sediments. The snails (shells, opercula
and soft tissues) and this indicated that Li is an essential metal for metabolism and thus is
being regulated in the body of the snail.
from nine geographical sites of Peninsular Malaysia in April 2011. The concentrations of
Lithium (Li) were determined in the shells, opercula and soft tissues of N. lineata and in
the surface sediments by using ICP-MS. The ranges of Li concentrations (μg/g dry weight)
were found to be 0.107-0.283 for shells, 0.021-0.177 for opercula and 0.011-0.634 for
total soft tissues of N. lineata. For sediments, Li ranges were found to be between 21.84-
146.22 μg/g dry weight). The distribution of Li was found to be: sediment> ST> shell>
opercula. The Li sediment data in the present study were comparable with the results of Li
contaminated sediments which had been previously reported in the literature and higher
than those of continental crust materials and igneous rocks. There was no significant
correlation (P>0.05) for the Li levels between the sediments. The snails (shells, opercula
and soft tissues) and this indicated that Li is an essential metal for metabolism and thus is
being regulated in the body of the snail.
Research Interests:
Oil palm breeding has been progressing very well in Southeast Asia, especially in Malaysia and Indonesia. Despite this progress, there are still problems due to the difficulty of controlled crossing in oil palm. Contaminated/ illegitimate... more
Oil palm breeding has been progressing very
well in Southeast Asia, especially in Malaysia and Indonesia.
Despite this progress, there are still problems due to
the difficulty of controlled crossing in oil palm. Contaminated/
illegitimate progeny has appeared in some
breeding programs; late and failure of detection by the
traditional method causes a waste of time and labor. The
use of molecular markers improves the integrity of breeding
programs in perennial crops such as oil palm. Four halfsib
families with a total of 200 progeny were used in this
study. Thirty polymorphic single locus DNA microsatellites
markers were typed to identify the illegitimate individuals
and to obtain the correct parental and progeny
assignments by using the CERVUS and COLONY programs.
Three illegitimate palms (1.5 %) were found, and
16 loci proved to be sufficient for sibship assignments
without parental genotypes by using the COLONY program.
The pairwise-likelihood score (PLS) method was
better for half-sib family assignments than the full likelihood
(FL) method.
well in Southeast Asia, especially in Malaysia and Indonesia.
Despite this progress, there are still problems due to
the difficulty of controlled crossing in oil palm. Contaminated/
illegitimate progeny has appeared in some
breeding programs; late and failure of detection by the
traditional method causes a waste of time and labor. The
use of molecular markers improves the integrity of breeding
programs in perennial crops such as oil palm. Four halfsib
families with a total of 200 progeny were used in this
study. Thirty polymorphic single locus DNA microsatellites
markers were typed to identify the illegitimate individuals
and to obtain the correct parental and progeny
assignments by using the CERVUS and COLONY programs.
Three illegitimate palms (1.5 %) were found, and
16 loci proved to be sufficient for sibship assignments
without parental genotypes by using the COLONY program.
The pairwise-likelihood score (PLS) method was
better for half-sib family assignments than the full likelihood
(FL) method.
Research Interests:
Background: The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit; the... more
Background: The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins
based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit;
the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and
Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which
were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions
of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu
Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from
Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian
SNP Initiative (PASNPI) Consortium and International HapMap project database.
Results: We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan
which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98%
of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly
admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced
back to have shared a common ancestor with the Proto-Malays and Chinese.
Conclusions: These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided
valuable information on the enigmatic demographical history as well as shed some insights into the origins of the
Malays in the Malay Peninsula.
Keywords: Malays; Single nucleotide polymorphisms; Genetic structure; Admixture; Haplotypes
based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit;
the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and
Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which
were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions
of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu
Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from
Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian
SNP Initiative (PASNPI) Consortium and International HapMap project database.
Results: We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan
which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98%
of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly
admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced
back to have shared a common ancestor with the Proto-Malays and Chinese.
Conclusions: These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided
valuable information on the enigmatic demographical history as well as shed some insights into the origins of the
Malays in the Malay Peninsula.
Keywords: Malays; Single nucleotide polymorphisms; Genetic structure; Admixture; Haplotypes
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The genetic diversity of the long-tailed macaques (Macaca fascicularis) from Penang, Malaysia, including Jerejak Island and the mainland area of the state of Penang, Seberang Perai were examined using 1,042 bp control region (CR) segment... more
The genetic diversity of the long-tailed macaques (Macaca fascicularis) from Penang, Malaysia, including Jerejak Island and
the mainland area of the state of Penang, Seberang Perai were examined using 1,042 bp control region (CR) segment of the
mitochondrial DNA (mtDNA). Twenty haplotypes were described with a single haplotype sharing between the mainland and the
island which suggests that it is a remnant of the genetic makeup from the mainland. Compared to previous studies based on
the CR, all the Penang haplotypes are newly described with none shared with the other regional populations of M. fascicularis.
A single deletion mutation unique to the Penang samples (Groups I and II) could be a good indicator for the conservation of the
genetic uniqueness and possibly should be managed as a management unit (MU). A summarised phylogenetic tree (NJ, MP, ML and
Bayesian) supports the monophyletic clustering of the M. fascicularis as described in previous studies. The topology separates the
Penang haplotypes into three major groups, which generally corresponds to their geographical distribution. We also noted that the
Penang haplotypes are of the continental lineage which separated from the insular lineage at around 1.04 mya. Finally, we showed
that the CR of the mtDNA is powerful and suitable for the quantification of intraspecific diversity in M. fascicularis.
the mainland area of the state of Penang, Seberang Perai were examined using 1,042 bp control region (CR) segment of the
mitochondrial DNA (mtDNA). Twenty haplotypes were described with a single haplotype sharing between the mainland and the
island which suggests that it is a remnant of the genetic makeup from the mainland. Compared to previous studies based on
the CR, all the Penang haplotypes are newly described with none shared with the other regional populations of M. fascicularis.
A single deletion mutation unique to the Penang samples (Groups I and II) could be a good indicator for the conservation of the
genetic uniqueness and possibly should be managed as a management unit (MU). A summarised phylogenetic tree (NJ, MP, ML and
Bayesian) supports the monophyletic clustering of the M. fascicularis as described in previous studies. The topology separates the
Penang haplotypes into three major groups, which generally corresponds to their geographical distribution. We also noted that the
Penang haplotypes are of the continental lineage which separated from the insular lineage at around 1.04 mya. Finally, we showed
that the CR of the mtDNA is powerful and suitable for the quantification of intraspecific diversity in M. fascicularis.
Research Interests:
Molecular markers in oil palm characterization and breeding began two decades ago. Microsatellite markers are a system that is commonly used in oil palm research since its development. Monomorphic SSR markers have been eliminated from all... more
Molecular markers in oil palm characterization and breeding began two decades ago. Microsatellite markers are a system that is commonly used in oil palm research since its development. Monomorphic SSR markers have been eliminated from all evolutionary and population genetics studies by researchers because of their lack of genetic variability. The goals of this study were to review polymorphic DNA microsatellite marker system also known as simple sequence repeats (SSR) in oil palm research since its development and to employ a monomorphic SSR marker for detection of illegitimacy in oil palm breeding programs. Ten monomorphic SSR markers and two half-sib families were used in this study. Illegitimate offspring IDs 97 and 180 were found by four monomorphic loci mEgCIR0425, mEgCIR3477, mEgCIR3769, and mEgCIR3902 in Family-1and Family-2. In addition, five loci (mEgCIR3574, mEgCIR3607, mEgCIR3672, mEgCIR3785 and mEgCIR3807) detect one illegitimate offspring ID 180. This study showed that monomorphic SSR markers are suitable for the detection of illegitimate offsprings in oil palm breeding programs.
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The oil palm is badly affected by basal stem rot (BSR) disease in Southeast Asia. BSR disease is caused by the fungus Ganoderma boninense, which is a major threat to oil palm compared with other Ganoderma spp. Molecular markers... more
The oil palm is badly affected by basal stem rot (BSR) disease in Southeast Asia. BSR disease is caused by the fungus Ganoderma boninense, which is a major threat to oil palm compared with other Ganoderma spp. Molecular markers associated with BSR disease will accelerate the identification process of resistant breeding materials in screening of plants for tolerance to the disease at the nursery stage. In this study, 58 simple sequence repeat markers were utilized with three progeny types, namely, KA4G1, KA4G8, and KA14G8, to perform a comparative molecular mapping for association with BSR. A total of 319 alleles were identified with an average of 5.51 alleles per locus. Five markers, mEgCIR0793:180, mEgCIR0894:200, mEgCIR03295:210, mEgCIR3737:146 and mEgCIR3785:299 were found to be associated with Ganoderma disease with P-values of 0.018, 0.033, 0.037, 0.034 and 0.037, respectively, in single progeny analysis. However, in pooled data (KA4G1, KA4G8 and KA14G8), two alleles mEgCIR0804:213 (P-value =0.001) and mEgCIR3292:183 (P-value =0.001) were found to be associated with Ganoderma disease. These analyses confirmed that progeny type KA4G1 was tolerant, whereas the other two were susceptible progeny types. These markers and KA4 progeny will be useful in future work on BSR disease resistance in oil palm.
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Genetic variation due to heavy metal contamination has always been an interesting topic of study. Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion and argument as to which... more
Genetic variation due to heavy metal contamination has always been an interesting topic of study.
Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion
and argument as to which contaminant(s) caused the variations in the genetic structures of biomonitors.
This study used a Single Primer Amplification Reaction (SPAR) technique, namely Random Amplified Polymorphic
DNA (RAPD), to determine the genetic diversity of the populations of the green-lipped mussel
Perna
viridis
collected from a metal-contaminated site at Kg. Pasir Puteh and those from four relatively uncontaminated
sites (reference sites). Heavy metal levels (Cd, Cu, Pb, and Zn) were also measured in the soft tissues and
byssus of the mussels from all the sites. Cluster analyses employing UPGMA based on the RAPD markers
grouped the populations into two major clusters; the Bagan Tiang, Pantai Lido, Pontian, and Kg. Pasir Puteh
populations were in one cluster, while the Sg. Belungkor population clustered by itself. This indicated that the
genetic diversity based on bands resulting from the use of all four RAPD primers on
P. viridis
did not indicate
its potential use as a biomarker of heavy metal pollution in coastal waters. However, based on a correlation analysis
between a particular metal and a band resulting from a specific RAPD primer revealed some significant
(
P
< 0.01) correlations between the primers and the heavy metal concentrations in the byssus and soft tissues.
Thus, the correlation between a particular metal and the bands resulting from the use of a specific RAPD primer
on
P. viridis
could be used as biomonitoring tool of heavy metal pollution.
Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion
and argument as to which contaminant(s) caused the variations in the genetic structures of biomonitors.
This study used a Single Primer Amplification Reaction (SPAR) technique, namely Random Amplified Polymorphic
DNA (RAPD), to determine the genetic diversity of the populations of the green-lipped mussel
Perna
viridis
collected from a metal-contaminated site at Kg. Pasir Puteh and those from four relatively uncontaminated
sites (reference sites). Heavy metal levels (Cd, Cu, Pb, and Zn) were also measured in the soft tissues and
byssus of the mussels from all the sites. Cluster analyses employing UPGMA based on the RAPD markers
grouped the populations into two major clusters; the Bagan Tiang, Pantai Lido, Pontian, and Kg. Pasir Puteh
populations were in one cluster, while the Sg. Belungkor population clustered by itself. This indicated that the
genetic diversity based on bands resulting from the use of all four RAPD primers on
P. viridis
did not indicate
its potential use as a biomarker of heavy metal pollution in coastal waters. However, based on a correlation analysis
between a particular metal and a band resulting from a specific RAPD primer revealed some significant
(
P
< 0.01) correlations between the primers and the heavy metal concentrations in the byssus and soft tissues.
Thus, the correlation between a particular metal and the bands resulting from the use of a specific RAPD primer
on
P. viridis
could be used as biomonitoring tool of heavy metal pollution.
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The techniques for the use of the human as the source of biochemical genetic markers are described.
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lsozymes of 23 cultures of the anaerobic rumen fungi and seven cultures of aerobic chytridiomycete fungi were analysed by PAGE. A total of 14 isozyme loci were successfully typed by PAGE. They were peptidase A & C-I, peptidase A & C-2,... more
lsozymes of 23 cultures of the anaerobic rumen fungi and seven cultures of
aerobic chytridiomycete fungi were analysed by PAGE. A total of 14 isozyme
loci were successfully typed by PAGE. They were peptidase A & C-I, peptidase
A & C-2, peptidase D-I, peptidase D-2, malate dehydrogenase-I, malate
dehydrogenase-2, esterase-I, esterase-2, malic enzyme-I, malic enzyme-2,
isocitrate dehydrogenase, shikimate dehydrogenase, phosphoglucomutase and
6-phosphogluconate dehydrogenase. lsozyme analysis can be used for
studying the genetic relationships among the different anaerobic rumen fungi
and the aerobic chytridiomycete fungi and the isozyme characteristics can
serve as additional taxonomic criteria in the classification of the anaerobic
rumen fungi. A dendrogram based on the isozyme data demonstrated that the
anaerobic rumen fungi formed a cluster, indicating a monophyletic group,
distinctly separated from the aerobic chytridiomycete fungi. Piromyces
communis and P. minutus showed a close relationship but P. spiralis showed a
more distant relationship to both P. communis and P. minutus. Piromyces as a
whole was more related to Caecomyces than to Neocallimastix. Orpinomyces
was also found to be more related to Piromyces and Caecomyces than to
Neocallimastix. Orpinomyces intercalaris C 70 from cattle showed large genetic
variation from 0. joyonii, indicating that it is a different species.
aerobic chytridiomycete fungi were analysed by PAGE. A total of 14 isozyme
loci were successfully typed by PAGE. They were peptidase A & C-I, peptidase
A & C-2, peptidase D-I, peptidase D-2, malate dehydrogenase-I, malate
dehydrogenase-2, esterase-I, esterase-2, malic enzyme-I, malic enzyme-2,
isocitrate dehydrogenase, shikimate dehydrogenase, phosphoglucomutase and
6-phosphogluconate dehydrogenase. lsozyme analysis can be used for
studying the genetic relationships among the different anaerobic rumen fungi
and the aerobic chytridiomycete fungi and the isozyme characteristics can
serve as additional taxonomic criteria in the classification of the anaerobic
rumen fungi. A dendrogram based on the isozyme data demonstrated that the
anaerobic rumen fungi formed a cluster, indicating a monophyletic group,
distinctly separated from the aerobic chytridiomycete fungi. Piromyces
communis and P. minutus showed a close relationship but P. spiralis showed a
more distant relationship to both P. communis and P. minutus. Piromyces as a
whole was more related to Caecomyces than to Neocallimastix. Orpinomyces
was also found to be more related to Piromyces and Caecomyces than to
Neocallimastix. Orpinomyces intercalaris C 70 from cattle showed large genetic
variation from 0. joyonii, indicating that it is a different species.
Research Interests:
White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn (Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium rosenbergii nodavirus (MrNV). The N-terminal end of the... more
White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn
(Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium
rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in
positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and
internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20–29,
where 80% of amino acids are positively charged. Substitution of all these positively charged
residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still
assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly
domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding
region of MrNV capsid protein
(Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium
rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in
positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and
internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20–29,
where 80% of amino acids are positively charged. Substitution of all these positively charged
residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still
assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly
domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding
region of MrNV capsid protein
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Apis dorsata is a major pollinator in the rainforests of Peninsular Malaysia, which is threatened by frequent harvesting via the removal of whole comb nests from trees during the harvesting season. There is an urgent need for conservation... more
Apis dorsata is a major pollinator in the rainforests of Peninsular Malaysia, which is threatened by frequent harvesting via the removal of whole comb nests from trees during the harvesting season. There is an urgent need for conservation of this species and the long-term survival of tropical lowland forests. In this paper, the genetic relatedness of A. dorsata aggregations are addressed with a preliminary study on local populations in Malaysia. The analysis of 30 single locus DNA microsatellite markers on three aggregations at intra-aggregation level showed that the queens of different nests within an aggregation were significantly different and not related as mother-daughter (P > 0.063). At inter-aggregation level, the results demonstrated that there was no significant relatedness between the aggregations (P > 0.05) separated by a distance of 0.5 km. The results showed that adjacent aggregations were genetically different and had enough time for establishing the colonies to produce honey.
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DNA sequencing of the Y-chromosome testis-specific protein locus (TSPY) and sex-determining region (SRY) was conducted on 27 Macaca fascicularis individuals from eight insular and two peninsula localities of Penang State, Malaysia. Five... more
DNA sequencing of the Y-chromosome testis-specific protein locus (TSPY) and sex-determining region (SRY) was conducted on 27 Macaca fascicularis individuals from eight insular and two peninsula localities of Penang State, Malaysia. Five haplotypes were discovered from the Penang samples, of which four were unique for that population. These haplotypes constituted of related individuals as observed in theY-chromosomal gene flow within and between the insular and mainland regions. The
occurrence of a dominant haplotype shared amongst M. fascicularis from southern Thailand, the Malay Peninsula, and Sumatra could be the result of a recent dispersal event from the common Pleistocene refugia, which had most likely been located inthe Malay Peninsula. A combination of nucleotides at 12 sites distinguished the M.fascicularis from the northern region of the Isthmus of Kra from those of the southern region including our samples. The molecular phylogenetic tree confirmed that, unlike
conspecific populations from regions north of the Isthmus of Kra, M. fascicularis from the southern region of the isthmus were free of introgression of Y-chromosome from M. mulatta. We dated the last common ancestors shared by the fascicularis group at
approximately 1.5 million years ago (mya). Also, we estimated the bifurcation between the insular and the continental lineages of M. fascicularis as approximately 0.7 mya, which had been estimated as 0.4 mya in a previous study. Finally, similarly to the
observations on various taxa by previous authors we recognise the role of the Isthmus of Kra area as a genetic barrier to the dispersal of and to gene flow in M. fascicularis.
Keywords Macaca fascicularis – Y-chromosome – TSPY and SRY – Isthmus of Kra
– genetic barrier
occurrence of a dominant haplotype shared amongst M. fascicularis from southern Thailand, the Malay Peninsula, and Sumatra could be the result of a recent dispersal event from the common Pleistocene refugia, which had most likely been located inthe Malay Peninsula. A combination of nucleotides at 12 sites distinguished the M.fascicularis from the northern region of the Isthmus of Kra from those of the southern region including our samples. The molecular phylogenetic tree confirmed that, unlike
conspecific populations from regions north of the Isthmus of Kra, M. fascicularis from the southern region of the isthmus were free of introgression of Y-chromosome from M. mulatta. We dated the last common ancestors shared by the fascicularis group at
approximately 1.5 million years ago (mya). Also, we estimated the bifurcation between the insular and the continental lineages of M. fascicularis as approximately 0.7 mya, which had been estimated as 0.4 mya in a previous study. Finally, similarly to the
observations on various taxa by previous authors we recognise the role of the Isthmus of Kra area as a genetic barrier to the dispersal of and to gene flow in M. fascicularis.
Keywords Macaca fascicularis – Y-chromosome – TSPY and SRY – Isthmus of Kra
– genetic barrier
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Andrographis paniculata (AP) is a medicinal plant species introduced into Malaysia. To address the genetic structure and evolutionary connectedness of the Malaysian AP with the Indian AP, a DNA sequence analysis was conducted based on... more
Andrographis paniculata (AP) is a medicinal
plant species introduced into Malaysia. To address the
genetic structure and evolutionary connectedness of the
Malaysian AP with the Indian AP, a DNA sequence analysis
was conducted based on 24 microsatellite markers. Out
of the 24 primer sets, seven novel microsatellite primers
were designed and amplified intra-specifically according to
the available Indian AP sequences at the National Centre
for Biotechnology Information (NCBI), where 17 of them
were amplified using the cross-species strategy by
employing the primers belonging to Acanthus ilicifolius
Linn (Acanthaceae) and Lumnitzera racemosa Wild
(Combretaceae). The primers were then applied on the
Malaysian AP accessions. Sixteen of the new microsatellite
loci were amplified successfully. Analysis of these microsatellite
sequences, revealed some significant differences
between the Indian and Malaysian AP accessions in terms
of the size and type of the repeat motifs. These findings
depicted the cryptic feature of this species. Despite identifying
several heterozygous alleles no polymorphism was
observed in the detected loci of the selected accessions.
This situation was in concordance with the presence of
‘‘fixed heterozygosity’’ phenomenon in the mentioned loci.
Accordingly, this was fully consistent with the occurrence
of the genetic bottleneck and founder effect within
Malaysian AP population. Apart from the amplification of
new microsatellites in this species, our observations could
be in agreement with the risk of genetic depletion and
consequently extinction of this precious herb in Malaysia.
This issue should be taken into consideration in the future
studies.
Keywords Genetic bottleneck Founder effect
Microsatellite Mutation Cryptic species
plant species introduced into Malaysia. To address the
genetic structure and evolutionary connectedness of the
Malaysian AP with the Indian AP, a DNA sequence analysis
was conducted based on 24 microsatellite markers. Out
of the 24 primer sets, seven novel microsatellite primers
were designed and amplified intra-specifically according to
the available Indian AP sequences at the National Centre
for Biotechnology Information (NCBI), where 17 of them
were amplified using the cross-species strategy by
employing the primers belonging to Acanthus ilicifolius
Linn (Acanthaceae) and Lumnitzera racemosa Wild
(Combretaceae). The primers were then applied on the
Malaysian AP accessions. Sixteen of the new microsatellite
loci were amplified successfully. Analysis of these microsatellite
sequences, revealed some significant differences
between the Indian and Malaysian AP accessions in terms
of the size and type of the repeat motifs. These findings
depicted the cryptic feature of this species. Despite identifying
several heterozygous alleles no polymorphism was
observed in the detected loci of the selected accessions.
This situation was in concordance with the presence of
‘‘fixed heterozygosity’’ phenomenon in the mentioned loci.
Accordingly, this was fully consistent with the occurrence
of the genetic bottleneck and founder effect within
Malaysian AP population. Apart from the amplification of
new microsatellites in this species, our observations could
be in agreement with the risk of genetic depletion and
consequently extinction of this precious herb in Malaysia.
This issue should be taken into consideration in the future
studies.
Keywords Genetic bottleneck Founder effect
Microsatellite Mutation Cryptic species
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The bracket fungus, Ganoderma boninense Pat., causes basal stem rot (BSR) disease in oil palm plants. Previously the disease was reported only in older age palms and currently found on young stages palms as well. Therefore, Ganoderma can... more
The bracket fungus, Ganoderma boninense Pat., causes basal stem rot (BSR) disease in oil palm plants. Previously the disease was reported only in older age palms and currently found on young stages palms as well. Therefore, Ganoderma can infect all stages of oil palm plants. Disease symptoms only appear at the late stage of the disease and usually called a silent killer of oil palm. Progression of the disease is slow; however, it can destroy thousands of hectares of oil palm plantations. Basal stem rot shortens the productive life of oil palms and causes serious economic losses to the oil palm industry. Hence, BSR is considered a serious threat to the oil palm industry in South East Asian countries. To date, there is high demand for sustainable detection and control of this disease. This review paper is elaborated on the detection and ecological impact of Ganoderma and BSR disease in oil palms plantation.
Keywords: Basal stem rot disease, diagnostic, Ecological impact, Ganoderma, oil palm.
Keywords: Basal stem rot disease, diagnostic, Ecological impact, Ganoderma, oil palm.
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Indians appeared in Malaysia early in its history. Sustained contact often resulted in racial admixture. We have analyzed the biochemical genetic markers PHI, LDH, AK, hemoglobin, rhesus blood group and haptoglobin among Malays (the... more
Indians appeared in Malaysia early in its history. Sustained contact often resulted in racial admixture. We have analyzed the biochemical genetic markers PHI, LDH, AK, hemoglobin, rhesus blood group and haptoglobin among Malays (the indigenous people of Peninsular Malaysia0 and Indians to provide genetic evidence for racial admixture of these two groups. The occurrence of specific rare variants PHI 3-1, LDH Calcutta-1 and Madras-1 and Hb S, as well as the gene frequencies of adenylate kinase (AK0 and haptoglobin in Malays and Indians confirm the gene flow from Indians to Malays.
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The genetic relationships among eight ethnic groups from Malaysia and eight ethnic groups from other parts of Southeast Asia were obtained by clustering based on their genetic distances from protein level allozyme markers using UPGMA.... more
The genetic relationships among eight ethnic groups from Malaysia and eight ethnic groups from other parts of Southeast Asia were obtained by clustering based on their genetic distances from protein level allozyme markers using UPGMA. Two major clusters were obtained, one containing three non-Mongoloid ethnic groups, Indians, Senoi and Aetas (Negrito) and the other containing 13 Mongoloid ethnic groups, Kadazan, Malays, Chinese, Batak, Land Dayak (Bidayuh), Iban (Sea Dayak), Visayan, Tagalog, Paiwan, Aboriginal Malays, Ifugao, Atayal and Bunun
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Malays, Chinese, and Indians from Peninsular Malaysia; Ibans and Bidayuh from Sarawak State; Kadazans from Sabah State, Northern Borneo; and Bataks, Minangkabau, and Javanese from North Sumatra, Indonesia, were subtyped for transferrin C... more
Malays, Chinese, and Indians from Peninsular Malaysia; Ibans and Bidayuh from Sarawak State; Kadazans from Sabah State, Northern Borneo; and Bataks, Minangkabau, and Javanese from North Sumatra, Indonesia, were subtyped for transferrin C by polyacrylamide gel isoelectric focusing. All nine populations studied are polymorphic for two alleles, TfC1 and TfC2. TfC3 was polymorphic in six populations and present as a rare variant in the other three. The frequency of TfC1 ranged from 0.855 in Bidayuh to 0.711 in Javanese, that of TfC2 from 0.231 in Indians to 0.113 in Bidayuh, and that of TfC3 from 0.030 in Javanese and Chinese to 0.008 in Bidayuh. TfDchi is polymorphic in all the populations that we studied except in Minangkabau, in whom it is present as a rare variant, and in Indians, in whom it is absent.
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Cerumen types were determined in 406 Malays, 362 Chinese and 381 Indians living in Peninsular Malaysia. The gene frequencies obtained for the allele for dry cerumen are Malays=0.600±0.028, Chinese=0.840±0.020 and Indians=0.652±0.028. A... more
Cerumen types were determined in 406 Malays, 362 Chinese and 381 Indians living in Peninsular Malaysia. The gene frequencies obtained for the allele for dry cerumen are Malays=0.600±0.028, Chinese=0.840±0.020 and Indians=0.652±0.028. A significant association was found between cerumen types and axillary odour in all three races.
Research Interests:
Research Interests:
Keywords: allozymes; Asian water buffalo; Bubalus bubalis; genetic diversity; microsatellites; molecular phylogenetics Twenty-one microsatellite loci in 11 populations of Asian water buffalo (eight... more
Keywords:
allozymes;
Asian water buffalo;
Bubalus bubalis;
genetic diversity;
microsatellites;
molecular phylogenetics
Twenty-one microsatellite loci in 11 populations of Asian water buffalo (eight swamp, three river type) were analysed and, within and among populations, genetic variability was compared with results from 25 polymorphic protein-coding loci. Within-population mean heterozygosity ranged from 0·380–0·615, approximately twice that estimated from the protein-coding loci (0·184– 0·346). Only eight significant departures from Hardy–Weinberg equilibrium (involving four loci) were detected; global tests showed significant heterozygote deficiencies for these four loci. Non-amplifying alleles are likely to be segregating in some or all populations for one of these loci, and probably for the other three. There was significant differentiation between the swamp and river types of water buffalo, and among populations within each buffalo type. Estimates of θ (measure of population differentiation) for each locus for the eight swamp populations were all highly significant (mean θ = 0·168 ± 0·018). Mean θ for protein-coding loci was not significantly different (0·182 ± 0·041). The variance among protein-coding loci was significantly higher than among microsatellite loci, suggesting balancing selection affecting allele frequencies at some protein-coding loci. Genetic distances show clear separation of the swamp and river types, which were estimated to have diverged at least 10 000–15 000 years ago. The topology of the swamp populations’ microsatellite tree is consistent with their geographical distribution and their presumed spread through south-east Asia. By contrast, the tree based on the protein-coding loci distances is quite different, being clearly distorted by a bottleneck effect in one population, and possibly in at least two others. As many domestic livestock breeds are possibly descended from small numbers of founders, microsatellite-based trees are to be preferred in assessing breed genetic relationships.
allozymes;
Asian water buffalo;
Bubalus bubalis;
genetic diversity;
microsatellites;
molecular phylogenetics
Twenty-one microsatellite loci in 11 populations of Asian water buffalo (eight swamp, three river type) were analysed and, within and among populations, genetic variability was compared with results from 25 polymorphic protein-coding loci. Within-population mean heterozygosity ranged from 0·380–0·615, approximately twice that estimated from the protein-coding loci (0·184– 0·346). Only eight significant departures from Hardy–Weinberg equilibrium (involving four loci) were detected; global tests showed significant heterozygote deficiencies for these four loci. Non-amplifying alleles are likely to be segregating in some or all populations for one of these loci, and probably for the other three. There was significant differentiation between the swamp and river types of water buffalo, and among populations within each buffalo type. Estimates of θ (measure of population differentiation) for each locus for the eight swamp populations were all highly significant (mean θ = 0·168 ± 0·018). Mean θ for protein-coding loci was not significantly different (0·182 ± 0·041). The variance among protein-coding loci was significantly higher than among microsatellite loci, suggesting balancing selection affecting allele frequencies at some protein-coding loci. Genetic distances show clear separation of the swamp and river types, which were estimated to have diverged at least 10 000–15 000 years ago. The topology of the swamp populations’ microsatellite tree is consistent with their geographical distribution and their presumed spread through south-east Asia. By contrast, the tree based on the protein-coding loci distances is quite different, being clearly distorted by a bottleneck effect in one population, and possibly in at least two others. As many domestic livestock breeds are possibly descended from small numbers of founders, microsatellite-based trees are to be preferred in assessing breed genetic relationships.
Research Interests: Genetics, Zoology, Population Genetics, Molecular Evolution, Australia, and 19 moreSri Lanka, Genetic Diversity, Phylogeny, Mitochondrial DNA, Animal Genetics, Animal, Haplotypes, Animals, Asia, Polymerase Chain Reaction, Proteins, Cytochrome B, Genotype, Time Factors, Genetic variation, Veterinary Sciences, Species Specificity, Buffaloes, and Molecular Sequence Data
Research Interests: Genetics, Microbiology, Biotechnology, Plant Biology, Southeast Asia, and 28 moreMolecular Markers, Plant Breeding, Plant biotechnology, Plant breeding and genetics, Plant Molecular Biology, QTL mapping, Fatty acids, Arecaceae, Marker assisted selection, Agricultural Production, Oil palm, Agronomic Traits, Palm Oil, Molecular Marker, Linkage Group, Group, Quantitative Trait Loci, Oil Palm, Fatty Acid Compositions, Oleic Acid, Stearic Acid, Crop improvements, Genetic Markers, Palmitic Acid, Fatty Acid Composition, DNA marker, Linoleic Acid, and Quality Measures
Isolation and characterization of microsatellite loci in the Persian sturgeon (Acipenser persicus, Borodine, 1897) and cross-species amplification in four commercial sturgeons from the Caspian Sea Moghim M.1, 3∗; Heist E. J.2; Tan S. G.3; Pourkazemi M.4; Siraj S. S.5 ; Panandam J. M.6; Pourgholam R.1; Kor D.1; Laloei F1. ; Taghavi M. J.1 Received: January 2012 Accepted: March 2012more
In order to have a sustainable management on Persian sturgeon as a highly commercial species in the South Caspian Sea, we need to identify its population structure and the level as well as its conservation status in their natural habitat.... more
In order to have a sustainable management on Persian sturgeon as a highly commercial species in the South Caspian Sea, we need to identify its population structure and the level as well as its conservation status in their natural habitat. To develop a conservation program for this all Caspian Sea' sturgeon species it requires knowledge of its genetic diversity using reliable molecular marker to study population genetic structure. For these purposes, an enriched library was prepared based on a modified biotin-capture method. Approximately 1800 positive clones were screened for microsatellites in an Acipenser persicus genomic library. Of these 350 positively hybridizing clones were sequenced, and 81 clones were identified as having microsatellites with adequate flanking regions. We developed and tested 68 microsatellite primer pairs for Persian sturgeon. Out of 68 primer pairs developed, 11 pairs resulted in poor or no amplification, 13 were ambiguous, 6 were monomorphic, 20 were tetrasomic and 18 were octosomic in Persian sturgeon. While none of the markers showed disomic inheritance in Persian sturgeon and Russian sturgeon (A. gueldenstaedtii). Several of the markers appeared useful for studies stellate sturgeon (A. stellatus), ship sturgeon (A.nudiventris) and beluga (Huso huso). Nearly all the polymorphic pattern for ship, stellate and beluga displayed the simple banding patterns characteristic of disomic loci, while those for Russian sturgeon displayed banding patterns characteristic of tetraploid or higher polyploid levels. These markers may prove useful in a variety of future sturgeon population genetic studies in the Caspian Sea.
Research Interests:
Mixtures of chromosomal forms A, B, C and D in natural populations of Anopheles dirus Peyton &amp; Harrison sensu lato in Thailand show significant positive values of Wright&#39;s fixation index for six enzyme-electromorph loci.... more
Mixtures of chromosomal forms A, B, C and D in natural populations of Anopheles dirus Peyton &amp; Harrison sensu lato in Thailand show significant positive values of Wright&#39;s fixation index for six enzyme-electromorph loci. The mean value of FIS over all loci was found to be +0.28 (SD 0.02), with a range of +0.57 (Odh) to +0.10 (Idh-2). Partitioning electromorph data for the chromosomal forms reduces the mean FIS to 0.03 (SD 0.01), which suggests that positive assortative mating is a characteristic of each form. This supports the hypothesis that the chromosomal/electrophoretic forms A, B, C and D represent four distinct biological species within the An. dirus complex. An example is given of the use of enzyme electromorphs as a means of vector identification during a malaria entomological field study involving a mixture of An. dirus species A and D. Electromorph identifications of 323 sp. A and 161 sp. D were more than 98% correct when cross-referenced to specific DNA probes.
Research Interests:
Research Interests: Marine Biology, Malaysia, Marine Aquaculture, Environmental Monitoring, Molluscan Biology, and 16 moreMultidisciplinary, Heavy metals, Marine Mussels, Copper, Heavy Metal Pollution, Bivalvia, Animals, Biomonitoring, Heavy Metal, Lead, Sequential Extraction, Zinc, Cadmium, Soft Tissue, Environment, and Geologic Sediments
Horseshoe crabs are said to be declining worldwide. However, there is still no published report on the status of horseshoe crabs in Malaysia. Thus, we report here eight informative microsatellite markers that were developed using the... more
Horseshoe crabs are said to be declining
worldwide. However, there is still no published report on
the status of horseshoe crabs in Malaysia. Thus, we report
here eight informative microsatellite markers that were
developed using the 50-anchored ISSR-PCR enrichment
procedure to diagnose the population genetic structure of
the mangrove horseshoe crab, Carcinoscorpius rotundicauda
from Peninsular Malaysia. This set of markers was
tested on 127 samples and showed polymorphism in this
species. Hence they should be useful in future essential
population genetic studies of these living fossils in the
Southeast Asian region.
Keywords Mangrove horseshoe crab C. rotundicauda
50 anchored ISSR-PCR Microsatellite
worldwide. However, there is still no published report on
the status of horseshoe crabs in Malaysia. Thus, we report
here eight informative microsatellite markers that were
developed using the 50-anchored ISSR-PCR enrichment
procedure to diagnose the population genetic structure of
the mangrove horseshoe crab, Carcinoscorpius rotundicauda
from Peninsular Malaysia. This set of markers was
tested on 127 samples and showed polymorphism in this
species. Hence they should be useful in future essential
population genetic studies of these living fossils in the
Southeast Asian region.
Keywords Mangrove horseshoe crab C. rotundicauda
50 anchored ISSR-PCR Microsatellite
Research Interests:
Enroute to mapping QTLs for yield components in oil palm, we constructed the linkage map of a FELDA high yielding oil palm (Elaeis guineensis), hybrid cross. The parents of the mapping population are a Deli dura and a pisifera of Yangambi... more
Enroute to mapping QTLs for yield components in oil palm, we constructed the linkage map of a FELDA high yielding oil
palm (Elaeis guineensis), hybrid cross. The parents of the mapping population are a Deli dura and a pisifera of Yangambi
origin. The cross out-yielded the average by 8–21% in four trials all of which yielded comparably to the best current
commercial planting materials. The higher yield derived from a higher fruit oil content. SSR markers in the public domain -
from CIRAD and MPOB, as well as some developed in FELDA - were used for the mapping, augmented by locally-designed
AFLP markers. The female parent linkage map comprised 317 marker loci and the male parent map 331 loci, both in 16
linkage groups each. The number of markers per group ranged from 8–47 in the former and 12–40 in the latter. The
integrated map was 2,247.5 cM long and included 479 markers and 168 anchor points. The number of markers per linkage
group was 15–57, the average being 29, and the average map density 4.7 cM. The linkage groups ranged in length from
77.5 cM to 223.7 cM, with an average of 137 cM. The map is currently being validated against a closely related population
and also being expanded to include yield related QTLs.
palm (Elaeis guineensis), hybrid cross. The parents of the mapping population are a Deli dura and a pisifera of Yangambi
origin. The cross out-yielded the average by 8–21% in four trials all of which yielded comparably to the best current
commercial planting materials. The higher yield derived from a higher fruit oil content. SSR markers in the public domain -
from CIRAD and MPOB, as well as some developed in FELDA - were used for the mapping, augmented by locally-designed
AFLP markers. The female parent linkage map comprised 317 marker loci and the male parent map 331 loci, both in 16
linkage groups each. The number of markers per group ranged from 8–47 in the former and 12–40 in the latter. The
integrated map was 2,247.5 cM long and included 479 markers and 168 anchor points. The number of markers per linkage
group was 15–57, the average being 29, and the average map density 4.7 cM. The linkage groups ranged in length from
77.5 cM to 223.7 cM, with an average of 137 cM. The map is currently being validated against a closely related population
and also being expanded to include yield related QTLs.
Research Interests:
[Ling L. P., Adibah A. B., Tan S. G., Christianus A. and Faridah Q. Z. 2011 Isolation by the 5 anchored PCR technique and characterization of eighteen microsatellite loci in the horseshoe crab (Tachypleus gigas). J. Genet. 90, e101–e104.... more
[Ling L. P., Adibah A. B., Tan S. G., Christianus A. and Faridah Q. Z. 2011 Isolation by the 5 anchored PCR technique and characterization
of eighteen microsatellite loci in the horseshoe crab (Tachypleus gigas). J. Genet. 90, e101–e104. Online only: http://www.ias.ac.in/jgenet/
OnlineResources/90/e101.pdf]
of eighteen microsatellite loci in the horseshoe crab (Tachypleus gigas). J. Genet. 90, e101–e104. Online only: http://www.ias.ac.in/jgenet/
OnlineResources/90/e101.pdf]
Research Interests:
Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single... more
Patterns of modern human population structure are helpful in understanding the history of human migration and
admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide
single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu
Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on
these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11
other populations’ genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia
obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic
groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very
close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan
formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups.
We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their
different historical origins. Our results provide information of the genetic differentiation between these populations and a
valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia
admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide
single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu
Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on
these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11
other populations’ genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia
obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic
groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very
close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan
formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups.
We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their
different historical origins. Our results provide information of the genetic differentiation between these populations and a
valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia
Termites of the genus Odontotermes are important decomposers in the Old World tropics and are sometimes important pests of crops, timber and trees. The species within the genus often have overlapping size ranges and are difficult to... more
Termites of the genus Odontotermes are important decomposers in the Old World tropics and are sometimes important
pests of crops, timber and trees. The species within the genus often have overlapping size ranges and are difficult to
differentiate based on morphology. As a result, the taxonomy of Odontotermes in Peninsular Malaysia has not been
adequately worked out. In this study, we examined the phylogeny of 40 samples of Odontotermes from Peninsular Malaysia
using two mitochondrial DNA regions, that is, the 16S ribosomal RNA and cytochrome oxidase subunit I genes, to aid in
elucidating the number of species in the peninsula. Phylogenies were reconstructed from the individual gene and
combined gene data sets using parsimony and likelihood criteria. The phylogenies supported the presence of up to eleven
species in Peninsular Malaysia, which were identified as O. escherichi, O. hainanensis, O. javanicus, O. longignathus, O.
malaccensis, O. oblongatus, O. paraoblongatus, O. sarawakensis, and three possibly new species. Additionally, some of our
taxa are thought to comprise a complex of two or more species. The number of species found in this study using DNA
methods was more than the initial nine species thought to occur in Peninsular Malaysia. The support values for the clades
and morphology of the soldiers provided further evidence for the existence of eleven or more species. Higher resolution
genetic markers such as microsatellites would be required to confirm the presence of cryptic species in some taxa.
pests of crops, timber and trees. The species within the genus often have overlapping size ranges and are difficult to
differentiate based on morphology. As a result, the taxonomy of Odontotermes in Peninsular Malaysia has not been
adequately worked out. In this study, we examined the phylogeny of 40 samples of Odontotermes from Peninsular Malaysia
using two mitochondrial DNA regions, that is, the 16S ribosomal RNA and cytochrome oxidase subunit I genes, to aid in
elucidating the number of species in the peninsula. Phylogenies were reconstructed from the individual gene and
combined gene data sets using parsimony and likelihood criteria. The phylogenies supported the presence of up to eleven
species in Peninsular Malaysia, which were identified as O. escherichi, O. hainanensis, O. javanicus, O. longignathus, O.
malaccensis, O. oblongatus, O. paraoblongatus, O. sarawakensis, and three possibly new species. Additionally, some of our
taxa are thought to comprise a complex of two or more species. The number of species found in this study using DNA
methods was more than the initial nine species thought to occur in Peninsular Malaysia. The support values for the clades
and morphology of the soldiers provided further evidence for the existence of eleven or more species. Higher resolution
genetic markers such as microsatellites would be required to confirm the presence of cryptic species in some taxa.
Research Interests:
A total of 19 polymorphic microsatellite loci were used to analyse levels of genetic variation for 10 populations of Perna viridis L. collected from all over peninsular Malaysia. The populations involved in this study included Pulau Aman... more
A total of 19 polymorphic microsatellite loci were used to analyse levels of genetic variation for 10 populations of Perna viridis L. collected from all over peninsular Malaysia. The populations involved in this study included Pulau Aman in Penang, Tanjung Rhu in Kedah, Bagan Tiang in Perak, Pulau Ketam in Selangor, Muar, Parit Jawa, Pantai Lido and Kampung Pasir Puteh in Johore, and Kuala Pontian and Nenasi in Pahang state. The number of alleles per locus ranged from two to seven, with an average of 3.1. Heterozygote deficiencies were observed across all the 10 populations. Characterization of the populations revealed that local populations of P. viridis in peninsular Malaysia were genetically similar enough to be used as a biomonitoring agent for heavy metal contamination in the Straits of Malacca. Cluster analysis grouped the P. viridis populations according to their geographical distributions with the exception of Parit Jawa. The analysis also revealed that P. viridis from the northern parts of peninsular Malaysia were found to be the most distant populations among the populations of mussels investigated and P. viridis from the eastern part of peninsular Malaysia were closer to the central and southern populations than to the northern populations.
Research Interests:
... Yap CK;Ismail A;Tan SG;Abdul Rahim 1 Can the shell of the green-lipped mussel Perna viridis (Linnaeus) from the west coast of Peninsular Malaysia be a potential biomonitoring material for Cd,Pb and Zn? [外文期刊] 2003; ...
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... Amapola DC Generosa 85 Use of Wetland for Dye-house Waste Waters Purifying PurposesDurdica Parac-Osterman, Ana Sutlovic, Vedran Durasevic and Tjasa Griessler-Bulc ... Antonius Indarto 191 Occurrence of Natural Hazards and Outbreak of... more
... Amapola DC Generosa 85 Use of Wetland for Dye-house Waste Waters Purifying PurposesDurdica Parac-Osterman, Ana Sutlovic, Vedran Durasevic and Tjasa Griessler-Bulc ... Antonius Indarto 191 Occurrence of Natural Hazards and Outbreak of Epidemic: A Statistical Scrutiny ...
Research Interests:
Research Interests: Plant Biology, Environmental Pollution, Marine Turtles, Aquatic Ecosystem, Heavy Metal Pollution, and 13 moreFood supply, Genetic Structure, Penaeus Monodon, Species Diversity, Marine Fish, Molecular Marker, Population Genetic Structure, Green Turtle, Oreochromis niloticus, Indexation, Gross Domestic Product (GDP), Random amplified polymorphic DNA, and Chelonia mydas
The coding region of the nucleocapsid (N) gene was amplified from the viral RNA and inserted into the bacterial expression vector, pTrcHis2, for intracellular expression in three Escherichia coli strains: TOP 10, BL 21 and SG 935. The N... more
The coding region of the nucleocapsid (N) gene was amplified from the viral RNA and inserted into the bacterial expression vector, pTrcHis2, for intracellular expression in three Escherichia coli strains: TOP 10, BL 21 and SG 935. The N protein was expressed as a fusion protein containing the myc epitope and His-tag at its C-terminal end. The amount of the fusion protein expressed in strain SG 935 was significantly higher than the other two strains, and was detected by the anti-myc antibody, anti-His and swine anti-NiV serum. Hence, the N(fus) protein produced in E. coli could serve as an alternative antigen for the detection of anti-NiV in swine.
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... a, Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. ... The shell demonstrated higher concentrations of Pb (41.23±1.20 μg/g dry weight) when compared to the selected soft... more
... a, Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. ... The shell demonstrated higher concentrations of Pb (41.23±1.20 μg/g dry weight) when compared to the selected soft tissues except gill from Kuala Sg. ...
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Three human saliva genetic markers, namely, salivary peroxidase (SAPX), Pm, and Ph proteins, were investigated in the three major ethnic groups of Malaysia: Malays, Chinese, and Indians. For Pm, the allelic frequencies of Pm + for Malays,... more
Three human saliva genetic markers, namely, salivary peroxidase (SAPX), Pm, and Ph proteins, were investigated in the three major ethnic groups of Malaysia: Malays, Chinese, and Indians. For Pm, the allelic frequencies of Pm + for Malays, Chinese, and Indians are 0.385±0.030, 0.282±0.026, and 0.289±0.026 respectively. For Ph, the allelic frequencies of Ph + are 0.082±0.016 for Malays, 0.109±0.017 for Chinese, and 0.062±0.013 for Indians. For SAPX, the allelic frequencies of SAPX 1 in Malays, Chinese, and Indians are 0.762±0.027, 0.755±0.027, and 0.723±0.026 respectively.
Research Interests:
... 作 者： Chee Kong Yap Mew Seong Choh Franklin Edward Berandah Ahmad Ismail Soon GuanTan 作者单位： Department of Biology, Faculty of Science, Universiti Putra Malaysia,UPM 43400, Serdang, Selangor, Malaysia 期 刊： 湿地科学 ISTIC Journal： WETLAND... more
... 作 者： Chee Kong Yap Mew Seong Choh Franklin Edward Berandah Ahmad Ismail Soon GuanTan 作者单位： Department of Biology, Faculty of Science, Universiti Putra Malaysia,UPM 43400, Serdang, Selangor, Malaysia 期 刊： 湿地科学 ISTIC Journal： WETLAND SCIENCE ...
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It has been widely reported that heavy metal contamination in coastal waters can modify the allozyme profiles of marine organisms. Previous studies have recorded elevated metal concentrations in sediments and mussel tissues off Peninsular... more
It has been widely reported that heavy metal contamination in coastal waters can modify the allozyme profiles of marine organisms.
Previous studies have recorded elevated metal concentrations in sediments and mussel tissues off Peninsular Malaysia. In the present study,
horizontal starch gel electrophoresis was carried out to estimate the levels of allelic variation of the green-lipped mussel, Perna viridis,
collected from one contaminated and three relatively uncontaminated sites off Peninsular Malaysia. Fourteen polymorphic loci were
observed. In addition, the concentrations of cadmium, copper, lead, mercury and zinc were determined in the sediments and in the soft tissues
of the mussels. Mussels from contaminated site, evidenced by high metal pollution indices (MPI) of the sediment and the mussel tissues,
showed the highest percentage of polymorphic loci (78.6%), while those collected from the uncontaminated sites had lower MPI of the
sediment and mussel tissue, and exhibited lower percentages of polymorphic loci (35.7–57.1%). The population from the contaminated site
showed the highest excess of heterozygosity (0.289) when compared to that of the populations from the three uncontaminated sites (0.108–
0.149). Allozyme frequencies at the phosphoglucomutase (PGM; E.C. 2.7.5.1) locus also differed between the contaminated and
uncontaminated populations. Previous studies have shown that exposure to heavy metals can select or counter-select for particular alleles at
this locus. The present results suggest that allozyme polymorphism in P. viridis is a potential biomonitoring tool for heavy metal
contamination but further validation is required.
D 2003 Elsevier Science Ltd. All rights reserved.
Keywords: Perna viridis; Allozymes; Heavy metals; Malaysia
1. Introduction
Evidence is increasing to suggest that genetic polymorphism
of organisms (animals and plants) is linked to
adaptation to specific environmental parameters (Nevo et
al., 1986; Nevo, 1990; Koehn and Bayne, 1989; Hummel
and Patarnello, 1994; Gillespie and Guttman, 1999). This is
due to the fact that the use of genetic biomarkers of
environmental pollution has become a topic of interest in
the literature recently. In particular, the impact of pollutants
on the genetic structure of marine organisms has been
demonstrated by several studies (Nevo et al., 1986; Ben-
Shlomo and Nevo, 1988; Nevo, 1990; Ma et al., 2000;
Moraga et al., 2002; Mulvey et al., 2002; Ross et al., 2002;
Sokolowski et al., 2002). For example, it was found that
using artificial heavy metal pollution as an environmental
stress, potential differences between genetic variants of the
marine gastropods, Cerithium scabridum, could be identified
(Latvie and Nevo, 1986a). For each population and for
each pollutant, specific resistant alleles would become
pronounced if organisms were continually exposed to a
specific pollutant. Studies have demonstrated that the higher
the level of genetic variation in a population the greater the
chance that the population will be able to tolerate exposure
to heavy metals (Klerks and Weis, 1987).
Horizontal starch gel electrophoresis had been widely
used to investigate the relationship between heavy metal
exposure and protein allozyme variation in marine gastropods
(Latvie and Nevo, 1982, a,b) and blue mussel Mytilus
edulis (Koehn, 1991; Gosling, 1992; Beaumont and Toro,
1996). Recently, by using protein allozyme study, Yap et al.
0160-4120/$ - see front matter D 2003 Elsevier Science Ltd. All rights reserved.
doi:10.1016/S0160-4120(03)00144-2
* Corresponding author. Tel.: +60-3-89486101x3603;
fax: +60-3-89432508.
E-mail address: yapckong@hotmail.com (C.K. Yap).
www.elsevier.com/locate/envint
Environment International 30 (2004) 39– 46
Previous studies have recorded elevated metal concentrations in sediments and mussel tissues off Peninsular Malaysia. In the present study,
horizontal starch gel electrophoresis was carried out to estimate the levels of allelic variation of the green-lipped mussel, Perna viridis,
collected from one contaminated and three relatively uncontaminated sites off Peninsular Malaysia. Fourteen polymorphic loci were
observed. In addition, the concentrations of cadmium, copper, lead, mercury and zinc were determined in the sediments and in the soft tissues
of the mussels. Mussels from contaminated site, evidenced by high metal pollution indices (MPI) of the sediment and the mussel tissues,
showed the highest percentage of polymorphic loci (78.6%), while those collected from the uncontaminated sites had lower MPI of the
sediment and mussel tissue, and exhibited lower percentages of polymorphic loci (35.7–57.1%). The population from the contaminated site
showed the highest excess of heterozygosity (0.289) when compared to that of the populations from the three uncontaminated sites (0.108–
0.149). Allozyme frequencies at the phosphoglucomutase (PGM; E.C. 2.7.5.1) locus also differed between the contaminated and
uncontaminated populations. Previous studies have shown that exposure to heavy metals can select or counter-select for particular alleles at
this locus. The present results suggest that allozyme polymorphism in P. viridis is a potential biomonitoring tool for heavy metal
contamination but further validation is required.
D 2003 Elsevier Science Ltd. All rights reserved.
Keywords: Perna viridis; Allozymes; Heavy metals; Malaysia
1. Introduction
Evidence is increasing to suggest that genetic polymorphism
of organisms (animals and plants) is linked to
adaptation to specific environmental parameters (Nevo et
al., 1986; Nevo, 1990; Koehn and Bayne, 1989; Hummel
and Patarnello, 1994; Gillespie and Guttman, 1999). This is
due to the fact that the use of genetic biomarkers of
environmental pollution has become a topic of interest in
the literature recently. In particular, the impact of pollutants
on the genetic structure of marine organisms has been
demonstrated by several studies (Nevo et al., 1986; Ben-
Shlomo and Nevo, 1988; Nevo, 1990; Ma et al., 2000;
Moraga et al., 2002; Mulvey et al., 2002; Ross et al., 2002;
Sokolowski et al., 2002). For example, it was found that
using artificial heavy metal pollution as an environmental
stress, potential differences between genetic variants of the
marine gastropods, Cerithium scabridum, could be identified
(Latvie and Nevo, 1986a). For each population and for
each pollutant, specific resistant alleles would become
pronounced if organisms were continually exposed to a
specific pollutant. Studies have demonstrated that the higher
the level of genetic variation in a population the greater the
chance that the population will be able to tolerate exposure
to heavy metals (Klerks and Weis, 1987).
Horizontal starch gel electrophoresis had been widely
used to investigate the relationship between heavy metal
exposure and protein allozyme variation in marine gastropods
(Latvie and Nevo, 1982, a,b) and blue mussel Mytilus
edulis (Koehn, 1991; Gosling, 1992; Beaumont and Toro,
1996). Recently, by using protein allozyme study, Yap et al.
0160-4120/$ - see front matter D 2003 Elsevier Science Ltd. All rights reserved.
doi:10.1016/S0160-4120(03)00144-2
* Corresponding author. Tel.: +60-3-89486101x3603;
fax: +60-3-89432508.
E-mail address: yapckong@hotmail.com (C.K. Yap).
www.elsevier.com/locate/envint
Environment International 30 (2004) 39– 46
Research Interests:
Horizontal starch gel electrophoresis was used to estimate the levels of genetic variation for 8 different geographical populations (Penang, Pulau Aman, Bagan Lalang, Telok Emas, Sungai Muar, Tanjung Kupang, Pantai Lido, and Kampong Pasir... more
Horizontal starch gel electrophoresis was used to estimate the
levels of genetic variation for 8 different geographical populations (Penang, Pulau Aman, Bagan Lalang, Telok
Emas, Sungai Muar, Tanjung Kupang, Pantai Lido, and Kampong Pasir Puteh) of the mussel, Perna viridis, collected
from the waters off the west coast of Peninsular Malaysia. Fourteen polymorphic loci were observed.
The observed mean heterozygosity ranged from 0.108 to 0.334, while the expected mean heterozygosity
ranged from 0.133 to 0.301. The highest mean value for genetic distance (0.091) was found between the populations
of Penang and Telok Emas while the lowest value (0.004) was found between those of Pantai Lido and
Tanjung Kupang. The populations studied could be divided into 2 groups by the UPGMA dendrogram based on
Nei’s (1978) genetic similarities. The groupings seemed to indicate differentiation into local populations. These
results suggest that P. viridis has a tendency to split into a number of geographical populations regardless of
larval dispersal as a potential agent of gene flow. The mean FST value of 0.149 indicates that the mussel populations
show a moderate degree of genetic differentiation. However, the mean genetic distance from the present
study (0.048 0.004) falls within the range of genetic distances between conspecific populations of mussels
(0.0-0.14). Therefore, the present study supports the use of the local mussel P. viridis as a suitable biomonitoring
agent for heavy metals. The range of genetic distance values (0.004-0.091) presented here can also
serve as baseline data to which results of similar studies in the future can be compared to determine whether
genetic divergence of mussel populations from the west coast of Peninsular Malaysia is taking place
levels of genetic variation for 8 different geographical populations (Penang, Pulau Aman, Bagan Lalang, Telok
Emas, Sungai Muar, Tanjung Kupang, Pantai Lido, and Kampong Pasir Puteh) of the mussel, Perna viridis, collected
from the waters off the west coast of Peninsular Malaysia. Fourteen polymorphic loci were observed.
The observed mean heterozygosity ranged from 0.108 to 0.334, while the expected mean heterozygosity
ranged from 0.133 to 0.301. The highest mean value for genetic distance (0.091) was found between the populations
of Penang and Telok Emas while the lowest value (0.004) was found between those of Pantai Lido and
Tanjung Kupang. The populations studied could be divided into 2 groups by the UPGMA dendrogram based on
Nei’s (1978) genetic similarities. The groupings seemed to indicate differentiation into local populations. These
results suggest that P. viridis has a tendency to split into a number of geographical populations regardless of
larval dispersal as a potential agent of gene flow. The mean FST value of 0.149 indicates that the mussel populations
show a moderate degree of genetic differentiation. However, the mean genetic distance from the present
study (0.048 0.004) falls within the range of genetic distances between conspecific populations of mussels
(0.0-0.14). Therefore, the present study supports the use of the local mussel P. viridis as a suitable biomonitoring
agent for heavy metals. The range of genetic distance values (0.004-0.091) presented here can also
serve as baseline data to which results of similar studies in the future can be compared to determine whether
genetic divergence of mussel populations from the west coast of Peninsular Malaysia is taking place
Research Interests:
It has been widely reported that allozyme frequency variation is a potential indicator of heavy metal-induced impacts in aquatic populations. In the present study, wild populations of horseshoe crab (Carcinoscorpius rotundicauda) were... more
It has been widely reported that allozyme
frequency variation is a potential indicator
of heavy metal-induced impacts in aquatic populations.
In the present study, wild populations
of horseshoe crab (Carcinoscorpius rotundicauda)
were collected from contaminated and uncontaminated
sites of Peninsular Malaysia. By adopting
horizontal starch gel electrophoresis, seven enzyme
systems were used to study allozyme polymorphisms.
Nine polymorphic loci were observed
in C. rotundicauda. The relationships of allozyme
variations with the concentrations of Cd, Cu, Ni,
and Zn in sediments and in muscle tissues of
horseshoe crabs were determined. Based on genetic
distance, the lower mean value of Nei’s
D (0.017) indicated that both of the contaminated
populations of Kg. Pasir Puteh and Kuala
Juru were very closely related when compared to
the relatively uncontaminated Pantai Lido pop-
C. K. Yap (B) · C. M. Chong
Department of Biology, Faculty of Science,
Universiti Putra Malaysia, 43400 UPM,
Serdang, Selangor, Malaysia
e-mail: yapckong@hotmail.com
S. G. Tan
Department of Cell and Molecular Biology,
Faculty of Biotechnology and Biomolecular Sciences,
Universiti Putra Malaysia, 43400 UPM,
Serdang, Selangor, Malaysia
ulation. Higher heterozygosities were shown by
the contaminated populations when compared to
the uncontaminated population. Different allelic
frequencies could be observed for the aldolase
(ALD; E.C. 2.7.5.1) locus between the contaminated
and uncontaminated populations of C.
rotundicauda. The dendrogram of genetic relationships
of the three populations of C. rotundicauda
showed the same clustering pattern as the
dendrograms are based on heavy metals in the
sediments and in the horseshoe crabs’ abdominal
muscles. From the F statistics, the present study
showed that the three populations of horseshoe
crabs were considered to have undergone moderate
genetic differentiation with a mean FST value
of 0.092 .The current results suggest that allozyme
polymorphism in horseshoe crabs is a potential
biomonitoring tool for metal contamination,
although further validation is required.
Keywords Carcinoscorpius rotundicauda ·
Heavy metals · Peninsular Malaysia · Allozymes
frequency variation is a potential indicator
of heavy metal-induced impacts in aquatic populations.
In the present study, wild populations
of horseshoe crab (Carcinoscorpius rotundicauda)
were collected from contaminated and uncontaminated
sites of Peninsular Malaysia. By adopting
horizontal starch gel electrophoresis, seven enzyme
systems were used to study allozyme polymorphisms.
Nine polymorphic loci were observed
in C. rotundicauda. The relationships of allozyme
variations with the concentrations of Cd, Cu, Ni,
and Zn in sediments and in muscle tissues of
horseshoe crabs were determined. Based on genetic
distance, the lower mean value of Nei’s
D (0.017) indicated that both of the contaminated
populations of Kg. Pasir Puteh and Kuala
Juru were very closely related when compared to
the relatively uncontaminated Pantai Lido pop-
C. K. Yap (B) · C. M. Chong
Department of Biology, Faculty of Science,
Universiti Putra Malaysia, 43400 UPM,
Serdang, Selangor, Malaysia
e-mail: yapckong@hotmail.com
S. G. Tan
Department of Cell and Molecular Biology,
Faculty of Biotechnology and Biomolecular Sciences,
Universiti Putra Malaysia, 43400 UPM,
Serdang, Selangor, Malaysia
ulation. Higher heterozygosities were shown by
the contaminated populations when compared to
the uncontaminated population. Different allelic
frequencies could be observed for the aldolase
(ALD; E.C. 2.7.5.1) locus between the contaminated
and uncontaminated populations of C.
rotundicauda. The dendrogram of genetic relationships
of the three populations of C. rotundicauda
showed the same clustering pattern as the
dendrograms are based on heavy metals in the
sediments and in the horseshoe crabs’ abdominal
muscles. From the F statistics, the present study
showed that the three populations of horseshoe
crabs were considered to have undergone moderate
genetic differentiation with a mean FST value
of 0.092 .The current results suggest that allozyme
polymorphism in horseshoe crabs is a potential
biomonitoring tool for metal contamination,
although further validation is required.
Keywords Carcinoscorpius rotundicauda ·
Heavy metals · Peninsular Malaysia · Allozymes
Research Interests:
Research Interests:
Studies on hybridization, inheritance, and population genetics of brown planthoppers that infest rice and weeds were undertaken using starch gel electrophoresis to determine whether the weed-infesting population represents a biological... more
Studies on hybridization, inheritance, and population genetics of brown
planthoppers that infest rice and weeds were undertaken using starch gel electrophoresis
to determine whether the weed-infesting population represents a biological
race or a species. F1 and F2 generations were produced by crosses between parental
insects from the two populations with little indication of hybrid sterility. Gpi, Mdh,
and Idh loci were inherited in a simple Mendelian fashion in families of two
sympatric populations. Sixteen populations of Nilaparvata spp. from eight locations
were collected. The Mdh, Idh, Pgm, Gpi, 6Pgd, and Acp loci were polymorphic. The
N. lugens of rice with high esterase activity were clustered into a group and characterized
by the presence of alleles Gpi110 and Gpi120, whereas N. lugens from
weeds with low esterase activity were clustered into another group and characterized
by Gpi100 and Gpi90. There was a lack of heterozygotes between the common
alleles of the two populations. This means that the two groups of individuals belong
to different gene pools.
Keywords Hybridization Allozymes Inheritance study Genetic variability
Brown planthopper complex
planthoppers that infest rice and weeds were undertaken using starch gel electrophoresis
to determine whether the weed-infesting population represents a biological
race or a species. F1 and F2 generations were produced by crosses between parental
insects from the two populations with little indication of hybrid sterility. Gpi, Mdh,
and Idh loci were inherited in a simple Mendelian fashion in families of two
sympatric populations. Sixteen populations of Nilaparvata spp. from eight locations
were collected. The Mdh, Idh, Pgm, Gpi, 6Pgd, and Acp loci were polymorphic. The
N. lugens of rice with high esterase activity were clustered into a group and characterized
by the presence of alleles Gpi110 and Gpi120, whereas N. lugens from
weeds with low esterase activity were clustered into another group and characterized
by Gpi100 and Gpi90. There was a lack of heterozygotes between the common
alleles of the two populations. This means that the two groups of individuals belong
to different gene pools.
Keywords Hybridization Allozymes Inheritance study Genetic variability
Brown planthopper complex
A simple and rapid method for isolating tetranucleotide microsatellites in mungbean, Vigna radiata , based on the 5 ′ -anchored polymerase chain reaction technique, revealed 15 microsatellite sequences. We report on the characterization... more
A simple and rapid method for isolating tetranucleotide microsatellites in mungbean,
Vigna radiata
, based on the 5
′
-anchored polymerase chain reaction technique, revealed 15
microsatellite sequences. We report on the characterization of seven polymorphic microsatellite
loci in
V. radiata
. The number of alleles per locus ranged from 2 to 6, whereas the
observed heterozygosity ranged from 0 to 0.561. Tetranucleotide markers are useful
because they amplify fewer stutter bands thus making scoring easier. These markers will
be useful for detecting genetic variation in mungbean varieties for germplasm management
and development of the crop.
Keywords
:
microsatellites, mungbean, polymorphism, tetranucleotide,
Vigna
Vigna radiata
, based on the 5
′
-anchored polymerase chain reaction technique, revealed 15
microsatellite sequences. We report on the characterization of seven polymorphic microsatellite
loci in
V. radiata
. The number of alleles per locus ranged from 2 to 6, whereas the
observed heterozygosity ranged from 0 to 0.561. Tetranucleotide markers are useful
because they amplify fewer stutter bands thus making scoring easier. These markers will
be useful for detecting genetic variation in mungbean varieties for germplasm management
and development of the crop.
Keywords
:
microsatellites, mungbean, polymorphism, tetranucleotide,
Vigna
Research Interests:
Research Interests:
Trichoderma species are commercially applied as biocontrol agents against numerous plant pathogenic fungi due to their production of antifungal metabolites, competition for nutrients and space, and mycoparasitism. However, currently the... more
Trichoderma species are commercially applied as biocontrol agents against numerous plant pathogenic fungi due to their production of antifungal metabolites, competition for nutrients and space, and mycoparasitism. However, currently the identification of Trichoderma species from throughout the world based on micro-morphological descriptions is tedious and prone to error. The correct identification of Trichoderma species is important as several traits are species-specific. The Random Amplified Microsatellites (RAMS) analysis done using five primers in this study showed different degrees of the genetic similarity among 42 isolates of this genus. The genetic similarity values were found to be in the range of 12.50–85.11% based on a total of 76 bands scored in the Trichoderma isolates. Of these 76 bands, 96.05% were polymorphic, 3.95% were monomorphic and 16% were exclusive bands. Two bands (250 bp and 200 bp) produced by primer LR-5 and one band (250 bp) by primer P1A were present in all the Trichoderma isolates collected from healthy and infected oil palm plantation soils. Cluster analysis based on UPGMA of the RAMS marker data showed that T. harzianum, T. virens and T. longibrachiatum isolates were grouped into different clades and lineages. In this study we found that although T. aureoviride isolates were morphologically different when compared to T. harzianum isolates, the UPGMA cluster analysis showed that the majority isolates of T. aureoviride (seven from nine) were closely related to the isolates of T. harzianum.
Research Interests:
Abstract Two sympatric populations of brown planthopper (BPH), one from rice and the other from Leersia hexandra were collected from each of five locations in Malaysia. All the tested malathion-resistant individuals of the rice BPH... more
Abstract Two sympatric populations of brown planthopper (BPH), one from rice and the other from Leersia hexandra were collected from each of five locations in Malaysia. All the tested malathion-resistant individuals of the rice BPH population and F1 generation (cross between malathion-resistant [usually caught on rice] and malathion-susceptible [usually caught on Leersia]) showed high esterase activity, while all malathion-susceptible individuals on L. hexandra showed low esterase activity. In the F2 generation, all the individuals tested against malathion were approximately 75% resistant and 25% susceptible and the inheritance pattern of esterase activity (high and low esterase activity) segregated in the same manner to a 3: 1 ratio. This confirms that resistance to malathion is mono-factorial and inheritance pattern of esterase activity is also linked to malathion resistance. Carboxylesterase or total esterase activity in BPH is inherited in a simple Mendelian fashion that is encoded by a single dominant gene. For the total esterase assay, average esterase activity levels in the rice-infesting population ranged from 17.64 to 19.37 nmoles 1-napthol/mg protein while that in the Leersia-infesting population ranged from 5.29 to 6.11 nmoles 1-napthol/mg protein. In terms of esterase activity, the two sympatric Nilaparvata lugens populations separated into two distinct groups. Results based on the tube color intensity test showed 96% and 98% resistant and susceptible individuals were present in the rice- and Leersia-infesting populations, respectively. In a filter paper test, the rice-infesting population had 94% with high esterase activity while the Leersia-infesting population had 96% with low esterase activity.
Research Interests:
Research Interests:
Research Interests:
We have cloned three cDNAs encoding chitinases from oil palm, EgCHI1, EgCHI2, and EgCHI3. The abundance of transcripts encoding all three chitinases was relatively higher in oil palm root tissues treated with either Ganoderma boninense or... more
We have cloned three cDNAs encoding chitinases from oil palm, EgCHI1, EgCHI2, and EgCHI3. The abundance of transcripts encoding all three chitinases was relatively higher in oil palm root tissues treated with either Ganoderma boninense or Trichoderma harzianum singly compared to that of untreated oil palm root tissues at 5 week post inoculation (wpi). The expression of EgCHI1 and EgCHI2 was also up-regulated in oil palm roots treated with a combination of G. boninense and T. harzianum at 2, 5 and 8 wpi. The up-regulation of chitinases understudied was likely a universal response of host plant to fungal attack.► Association of host plants and fungi increased expression of defense-related enzymes. ► Chitinases are important PR proteins that degrade fungal cell wall. ► Fungi increased transcripts encoding plant chitinases. ► Universal response of host plant against fungi.
Research Interests:
This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique... more
This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification.
Research Interests: Genetics, Polymorphism, Africa, Phylogeny, Sequence alignment, and 13 moreExpressed Sequence Tags, Asia, Polymerase Chain Reaction, Arecaceae, Oil palm, South America, Genetic Differentiation, Genomic Library, Genetic variation, Oil Palm, Trinucleotide Repeat Disorders, Base Sequence, and Simple Sequence Repeat
An electrochemical DNA biosensor was developed that is based on a gold electrode modified with a nanocomposite membrane made from an ionic liquid, ZnO nanoparticles and chitosan. A single-stranded DNA probe was immobilized on this... more
An electrochemical DNA biosensor was developed that is based on a gold electrode modified with a nanocomposite membrane made from an ionic liquid, ZnO nanoparticles and chitosan. A single-stranded DNA probe was immobilized on this electrode. Acridine orange was used as the hybridization probe for monitoring the hybridization of the target DNA. The biosensor was capable of detecting target DNA in the concentration range from 1.0 × 10–14 to 1.8 × 10–4 mol L-1, with a detection limit of 1.0 × 10–15 mol L-1. The approach towards constructing a DNA biosensor allows studies on the hybridization even with crude DNA fragments and also to analyze sample obtained from real samples. The results show that the DNA biosensor has the potential for sensitive detection of a specific sequence of the Trichoderma harzianum gene and provides a quick, sensitive and convenient method for the study of microorganisms. Figure Suggested interaction mechanism of modified electrode (IL/ZnO/CHIT/AuE) between immobilization and hybridization
Research Interests: Engineering, Genetics, Analytical Chemistry, Technology, Bioelectrochemistry, and 28 moreElectrochemistry, Ionic Liquid, Biological Sciences, DNA, Infectious Disease, Calibration, Biosensor, Polymerase Chain Reaction, Physical sciences, DNA hybridization, Trichoderma Harzianum, Methylene Blue, CHEMICAL SCIENCES, Moving average, Composite Membrane, Hepatitis B virus, High Sensitivity, Modified Electrode, Organometallic Compounds, Square Wave Voltammetry, Ligands, Acridine Orange, Biosensing Techniques, Oligonucleotides, Nucleic Acid, single stranded DNA, DNA fragmentation, and DNA sequence
Research Interests:
Research Interests: Genetics, Polymorphism, Malaysia, China, India, and 7 moreHumans, Chinese, Female, Male, Saliva, Ethnic Group, and Genetic variation
Nine populations of three species ofNephotettix (Insecta: Hemiptera) from Peninsular Malaysia were analysed for nine enzymes comprising 11 loci. Nei's (Genetics 89, 583, 1978) genetic distance,D, betweenN. virescens andN. malayanus was... more
Nine populations of three species ofNephotettix (Insecta: Hemiptera) from Peninsular Malaysia were analysed for nine enzymes comprising 11 loci. Nei's (Genetics 89, 583, 1978) genetic distance,D, betweenN. virescens andN. malayanus was 0.181, that betweenN. virescens andN. nigropictus was 0.283, and that betweenN. malayanus andN. nigropictus was 0.203. The genetic distance betweenN. nigropictus from rice plant and from the weed-grassL. hexandra at Universiti Pertanian Malaysia was 0.004 and their genetic identity was 0.996, thus indicating that this insect species feeds on both host plants. The proportion of polymorphic loci and the observed heterozygosities were higher inN. nigropictus, with a wider range of host plants, than inN. virescens andN. malayanus, restricted to rice andL. hexandra, respectively.
Research Interests:
Research Interests:
Malays, Chinese and Indians from peninsular Malaysia; Ibans and Bidayuh from Sarawak state, Northern Borneo; and Bataks, Minangkabau and Javanese from North Sumatra, Indonesia, were subtyped for Gc (group-specific component) by... more
Malays, Chinese and Indians from peninsular Malaysia; Ibans and Bidayuh from Sarawak state, Northern Borneo; and Bataks, Minangkabau and Javanese from North Sumatra, Indonesia, were subtyped for Gc (group-specific component) by polyacrylamide gel isoelectric focusing. All eight populations investigated were found to be polymorphic for three common alleles, GcIF, GcIS and Gc2.
Research Interests:
Research Interests:
Research Interests:
Kadazans, the largest indigenous group in Sabah, northern Borneo, were surveyed for glyoxalase I, phosphoglucomutase I, red cell acid phosphatase, esterase D, adenosine deaminase, soluble glutamate pyruvate transaminase, soluble glutamate... more
Kadazans, the largest indigenous group in Sabah, northern Borneo, were surveyed for glyoxalase I, phosphoglucomutase I, red cell acid phosphatase, esterase D, adenosine deaminase, soluble glutamate pyruvate transaminase, soluble glutamate oxaloacetate transaminase, 6-phosphogluconate dehydrogenase, uridine monophosphate kinase, adenylate kinase, peptidase B and D, superoxide dismutase, C5, group specific component, haptoglobin and transferrin. Kadazans were found to be polymorphic for GLOI, PGMI, RCAP, esterase D, ADA, s-Gpt, 6PGD, UMPK, Gc, C5, haptoglobin and peptidase B. Rare variants were found for transferrin and peptidase D. No variant was found for s-Got, SOD and AK.
Research Interests:
Research Interests:
Research Interests:
Properdin factor B (Bf) is a polymorphic protein in the human plasma. Two common alleles, BfS, BfF, and two rare alleles, BfF1, BfS1, have been demonstrated in Caucasians. We now report that BfF can be subtyped into two alleles, BfFa and... more
Properdin factor B (Bf) is a polymorphic protein in the human plasma. Two common alleles, BfS, BfF, and two rare alleles, BfF1, BfS1, have been demonstrated in Caucasians. We now report that BfF can be subtyped into two alleles, BfFa and BfFb by isoelectrofocusing. Family studies indicate that they are inherited in a co-dominant pattern. Gene frequencies for Caucasians are: BfS 0.808, BfF1 0.019, BfS1 0.005, BfFa 0.038 and BfFb 0.128.
Research Interests:
Malaysians of Malay, Chinese, and Indian ancestries were electrophoretically phenotyped for Amy1 and saliva esterase region 1(Set-1) from saliva, Amy2 from plasma, soluble and mitochondrial GOT and PGM 3 from leukocyte and placenta.... more
Malaysians of Malay, Chinese, and Indian ancestries were electrophoretically phenotyped for Amy1 and saliva esterase region 1(Set-1) from saliva, Amy2 from plasma, soluble and mitochondrial GOT and PGM 3 from leukocyte and placenta. Kadazans and Bajaus, the indigenous people of Sabah, East Malaysia were surveyed for Amy2. Three types of variants were observed for Amy1, one type for Amy2. Only Indians were found to be polymorphic for Amy1. Two GOT s 2-1 and three GOT m 2-1 variants were found among 281 Chinese while three GOT m 2-1 variants were found among 311 Malays. Malaysian Malays, Chinese, and Indians were found to be polymorphic for Set-1 and PGM 3. The gene frequencies in Malays are Set-1F=0.601±0.021, Set-1S=0.399±0.021; PGM 31=0.788±0.020, PGM 32=0.212±0.020; in Chinese Set-1F=0.497±0.028, Set-1S=0.503±0.028; PGM 31=0.745±0.024, PGM 32=0.255±0.024; in Indians, Set-1F=0.449±0.031, Set-1S=0.551±0.031; PGM 31=0.755±0.029, PGM 32=0.245±0.029.
Research Interests:
Research Interests:
Research Interests:
The distributions of Cd, Pb and Zn in the total soft tissues and total shells of the green-lipped mussel Perna viridis were studied in field collected samples as well as from laboratory experimental samples. The results showed that Cd, Pb... more
The distributions of Cd, Pb and Zn in the total soft tissues and total shells of the green-lipped mussel Perna viridis were studied in field collected samples as well as from laboratory experimental samples. The results showed that Cd, Pb and Zn were readily accumulated in the whole shells. In mussels sampled from 12 locations along the west coast of Peninsular Malaysia, the ratios of the shell metals to the soft tissue metals were different at each sampling site. Nevertheless, the Cd and Pb levels in the shells were always higher than those in the soft tissues, while the Zn level was higher in the soft tissues than in the shells. In comparison with soft tissues, the degrees of variability for Pb and Cd concentrations in the shells were lower. The lower degrees of variability and significant (P<0.05) correlation coefficients of Cd and Pb within the shells support the use of the mussel shell as a suitable biomonitoring material for the two metals rather than the soft tissue since this indicated that there is more precision (lower CV) in the determination of metal concentrations in the shell than in the soft tissue. Experimental work showed that the pattern of depuration in the shell was not similar to that of the soft tissue although their patterns of accumulation were similar. This indicated that the depuration of heavy metals in the shell was not affected by the physiological conditions of the mussels. Although Zn could be regulated by the soft tissue, the incorporated Cd, Pb and Zn remained in the shell matrices. The present results support the use of the total shell of P. viridis as a potential biomonitoring material for long-term contamination of Cd, Pb and Zn.
Research Interests:
We have developed the methodologies for typing and family studies to establish the modes of inheritance of water buffalo red cell acid phosphatase (Acp), protease inhibitor (Pi), and group-specific component (Gc) on isoelectric focusing... more
We have developed the methodologies for typing and family studies to establish the modes of inheritance of water buffalo red cell acid phosphatase (Acp), protease inhibitor (Pi), and group-specific component (Gc) on isoelectric focusing and albumin (Alb), red cell α-esterase-3 (Est-3), and catalase (Cat) on polyacrylamide gel electrophoresis. Family studies showed that Pi, Gc, Alb, and Cat are coded by autosomal genes with two codominant alleles, while Est-3 is autosomal with two codominant alleles and a recessive null allele and Acp exhibits three codominant alleles.
Research Interests:
An assessment of the different soft tissues (STs) of Pernaviridis as biomonitoring agents of Pb has not been specifically reported in the literature. Based on the results of our laboratory studies,different rates of accumulation and... more
An assessment of the different soft tissues (STs) of Pernaviridis as biomonitoring agents of Pb has not been specifically reported in the literature. Based on the results of our laboratory studies,different rates of accumulation and depuration of Pb in the different STs werefound and this might be due to different mechanisms of metal binding andregulation. At the end of depuration, Pb levels in the different STs of P. viridis were 3–100 times higher than those before Pb exposure. The high ratio of maximum to minimum Pb levels (160) and the similar patterns (althoughdifferent rates) of accumulation and depuration in the different STs forPb indicated that P. viridis is a good biomonitoring organism for Pband our conclusion is also supported by analysis of field samples collected fromcontaminated and uncontaminated sites. The distribution of Pb in the STssuggests that gills and byssus are better for the biomonitoring of Pb than the total ST.
Research Interests:
Research Interests:
The genetic make-up of five populations of Oreochromis spp. was examined by microsatellite analysis. Eleven polymorphic microsatellite loci showed significant departures from the Hardy–Weinberg equilibrium. The mean heterozygosity ranged... more
The genetic make-up of five populations of Oreochromis spp. was examined by microsatellite analysis. Eleven polymorphic microsatellite loci showed significant departures from the Hardy–Weinberg equilibrium. The mean heterozygosity ranged from 0.6280 to 0.7040 for each population. The genetic distance values showed a clear separation between O. niloticus and O. mossambicus. The differentiation of the O. niloticus populations was then tested with various genetic measures, which are based on both the Infinite Allele and the Stepwise Mutation models. All these measures grouped the populations similarly.
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Ecotoxicological tests were conducted in the green-lipped mussel Perna viridis under laboratory conditions. Different rates of accumulation and depuration in soft tissues are found and this might be due to different mechanisms of metal... more
Ecotoxicological tests were conducted in the green-lipped mussel Perna viridis under laboratory conditions. Different rates of accumulation and depuration in soft tissues are found and this might be due to different mechanisms of metal binding and regulation. At the end of depuration, Cd levels in soft tissues of P. viridis were 10–30 times higher than before exposure, while Zn levels in soft tissues were almost similar to levels before exposure. These results indicate that P. viridis is a good biomonitoring organism for Cd but Zn levels might be actively regulated. It remains uncertain whether P. viridis is a good biomonitoring organism of environmental Zn contamination. However, the positive patterns, although different rates, of accumulation and depuration for Cd and Zn support the use of P. viridis as a biomonitoring agent for such metals.
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Electrochemical DNA sensors based on the recognition of a base single- or double-stranded DNA (ss/ds-DNA) sequence specific to a Trichoderma harzianum gene and immobilized onto a gold disk electrode are described here. The ssDNA probe was... more
Electrochemical DNA sensors based on the recognition of a base single- or double-stranded DNA (ss/ds-DNA) sequence specific to a Trichoderma harzianum gene and immobilized onto a gold disk electrode are described here. The ssDNA probe was immobilized on the modified gold electrode to measure the electrochemical response. The hybridization of the probe ssDNA with the target DNA was explored by differential pulse voltammetry (DPV) using methylene blue (MB) as an electroactive indicator. MB on a modified gold electrode was found to be more largely localized than that on a bare gold electrode. Peak currents were found to increase in the order of hybrid-modified-AuE > probe-modified-AuE > non-harzianum > non-complementary DNA. Control experiments with the non-complementary oligonucleotides were performed to assess whether the DNA biosensor responded selectively, via hybridization, to the target. The variation in redox current with the different concentrations of target DNA was linear in the range of 1–20 ppm. Various properties and characteristics of this sensor were also described in this report. A novel approaches to construct an electrochemical biosensor consisting of the probe ssDNA to hybridize with crude DNA fragments from real samples was successfully applied in the study of biological microorganisms.
Research Interests: Materials Engineering, Microbiology, Analytical Chemistry, Molecular Biology, Molecular Evolution, and 12 moreBiology, Hybridization, Nanotechnology, DNA, Nanoscience, DNA hybridization, Trichoderma Harzianum, Methylene Blue, Self Assembled Monolayer, Differential Pulse Voltammetry, DNA fragmentation, and DNA sequence
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Malaysia is now a developing country and on her way towards being an industrialised one by the year 2020. Most of her industries and urban areas are located on the west coast of Peninsular Malaysia. In addition, the offshore area of the... more
Malaysia is now a developing country and on her way towards being an industrialised one by the year 2020. Most of her industries and urban areas are located on the west coast of Peninsular Malaysia. In addition, the offshore area of the west coast is now one of the busiest shipping lanes in the world. These two phenomena make the intertidal and offshore areas of the west coast of Peninsular Malaysia interesting for scientific studies. Therefore, this study focused on both the offshore and intertidal sediments of the west coast of Peninsular Malaysia. Sampling for sediment samples were done from the northern to the southern ends of the peninsula and these sediment samples were analysed for Cu and Pb. It was found that total Cu concentrations ranged from 0.25 to 13.8 and 0.40 to 315 μg/g dry weight (dw) for offshore and intertidal sediments, respectively. For Pb, it ranged from 3.59 to 25.4 and 0.96 to 69.8 μg/g dw for the offshore and intertidal sediments, respectively. The ranges of Cu and Pb found from the west coast of Peninsular Malaysia were low in comparison to regional data. However, some intertidal areas were identified as receiving anthropogenic Cu and Pb. Geochemical studies revealed that the ‘nonresistant’ fraction for Pb contributed about 70.0% to 75.0% and 54.0% of the total Pb concentration in the offshore and intertidal sediments, respectively. As for Cu, the ‘nonresistant’ fraction contributed about 46.2% to 60.4% and 46.3% of the total Cu concentration in the offshore and intertidal sediments, respectively. The ‘nonresistant’ fraction contained mostly of anthropogenic metals besides natural origins. These ‘nonresistant’ percentages indicated that both the offshore and intertidal areas could have received anthropogenic-derived metals, which could be influenced by physico-chemical properties of the sediments. Although the present data indicated that contamination due to Cu and Pb in the west coast of Peninsular Malaysia especially in the offshore areas were not serious, regular biomonitoring studies along the west coast of Peninsular Malaysia are recommended.
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Concentrations of cadmium (Cd), lead (Pb) and zinc (Zn) in total soft tissues (ST) and byssus (BYS) of the green-lipped mussel Perna viridis from 11 different geographical locations off the west coast of Peninsular Malaysia were... more
Concentrations of cadmium (Cd), lead (Pb) and zinc (Zn) in total soft tissues (ST) and byssus (BYS) of the green-lipped mussel Perna viridis from 11 different geographical locations off the west coast of Peninsular Malaysia were determined. The metal concentrations distributed between the BYS and ST were compared. The results of this study indicated that higher levels of Cd (1.31 μg/g), Pb (38.49 μg/g) and Zn (206.52 μg/g) were accumulated in the BYS than in the total ST (Cd: 0.29 μg/g; Pb: 8.27 μg/g; Zn: 102.6 μg/g). Semi-static and short period controlled laboratory experiments were also conducted for the accumulation and depuration of Cd, Pb and Zn in the total ST and BYS of P. viridis. The ratios (BYS/ST) for Pb and Cd from the laboratory experiments showed that the total ST accumulated more metals than the BYS. Therefore, these laboratory results disagreed with those found for the field samples. However, the laboratory results for the Zn ratio (BYS/ST) agreed with those of the field samples. It was evident that when compared to the ST, the BYS was a more sensitive biomonitoring organ for Zn while it could be a complementary organ for Cd and Pb in the total ST. Since total ST of P. viridis had been reported to have regulative mechanism for Zn, its BYS can be used as a biomonitoring organ for the identification of coastal areas exposed to Zn pollution.
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DNA microsatellites have found widespread application in gene mapping, pedigree determination and population genetics. In closely related species such as bovids, heterologous polymerase chain reaction (PCR) primers may in some cases be... more
DNA microsatellites have found widespread application in gene mapping, pedigree determination and population genetics. In closely related species such as bovids, heterologous polymerase chain reaction (PCR) primers may in some cases be used, bypassing the need to isolate and characterize microsatellite-containing sequences and design PCR primers. We report on the ability of a set of eighty bovine derived DNA microsatellite primers to amplify sequences in the two types (swamp and river) of water buffalo (Bubalus bubalis). Number of alleles and per cent heterozygosities in a large number of animals were determined on a subset of microsatellite loci selected on the robustness of the primers. These loci will form the basis of a set of polymorphic DNA markers for use in water buffalo.
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A study of the impacts of anthropogenic activities on the distribution and biodiversity of benthic macroinvertebrates and water quality of the Langat River (Peninsular Malaysia) was conducted. Four pristine stations from the upstream and... more
A study of the impacts of anthropogenic activities on the distribution and biodiversity of benthic macroinvertebrates and water quality of the Langat River (Peninsular Malaysia) was conducted. Four pristine stations from the upstream and 4 stations at the downstream receiving anthropogenic impacts were selected along the river. For 4 consecutive months (March–June 1999), based on the Malaysian DOE (Malaysia Environmental Quality Report 2000, Department of Environment, Ministry of Science, Technology and Environment Malaysia. Maskha Sdn. Bhd. Kuala Lumpur, 86pp; Malaysia Environmental Quality Report 2001, Department of Environment, Ministry of Science, Technology and the Environment Malaysia) water quality index classes, the upstream stations recorded significantly (P<0.05P<0.05) higher Biological Monitoring Working Party scores and better water quality indices than those of the downstream. The total number of macrobenthic taxa and their overall richness indices and diversity indices were significantly (P<0.05P<0.05) higher at the upstream stations (54 taxa) than at the downstream stations (5 taxa). The upstream of the Langat River was dominated by Ephemeroptera and chironomid dipterans while other orders found in small quantities included Trichoptera, Diptera, Plecoptera, Odonata, Ephemeraptera, Coleoptera, and Gastropoda. On the other hand, the downstream of the river was mainly inhabited by the resistant Oligochaeta worms Limnodrilus spp. and Branchiodrilus sp. and Hirudinea in small numbers. The relationships between the physicochemical and the macrobenthic data were investigated by Pearson correlation analysis and multiple stepwise regression analysis. These statistical analyses showed that the richness and diversity indices were generally influenced by the total suspended solids and the conductivity of the river water. This study also highlighted the impacts of anthropogenic land-based activities such as urban runoff on the distribution and species diversity of macrobenthic invertebrates in the downstream of the Langat River. The data obtained in this study supported the use of the bioindicator concept for Malaysian rivers. Some sensitive (Trichopteran caddisflies and Ephemeraptera) and resistant species (Oligochaeta such as Limnodrilus spp.) are identified as potential bioindicators of clean and polluted river ecosystems, respectively, for Malaysian rivers.
Research Interests: Water quality, Ecotoxicology, Malaysia, Invertebrates, Population Dynamics, and 19 moreEnvironmental Monitoring, Rivers, Biodiversity, Environmental Sciences, River water, Animals, Water Quality Index, Species Diversity, Anthropogenic impact, CHEMICAL SCIENCES, Environmental quality, Ecosystem, Correlation Analysis, Fresh water, Water Quality, Biological Monitoring, Stepwise Regression, Diversity Indices, and Urban Runoff
Total concentrations and speciation of cadmium (Cd), copper (Cu), lead (Pb) and zinc (Zn) in surface sediment samples were correlated with the respective metal measured in the total soft tissue of the green-lipped mussel Perna viridis,... more
Total concentrations and speciation of cadmium (Cd), copper (Cu), lead (Pb) and zinc (Zn) in surface sediment samples were correlated with the respective metal measured in the total soft tissue of the green-lipped mussel Perna viridis, collected from water off the west coast of Peninsular Malaysia. The aim of this study is to relate the possible differences in the accumulation patterns of the heavy metals in P. viridis to those in the surface sediment. The sequential extraction technique was employed to fractionate the sediment into ‘freely leachable and exchangeable’ (EFLE), ‘acid-reducible,’ ‘oxidisable–organic’ and ‘resistant’ fractions. The results showed that significant (P<.05) correlations were observed between Cd in P. viridis and Cd in the sediment (EFLE fraction and total Cd), Cu in P. viridis and Cu in the sediment (EFLE and ‘acid-reducible’ fractions and total Cu) and Pb in P. viridis and Pb in the sediment (‘oxidisable–organic’ fraction and total Pb). No significant correlation (P>.05) was found between Zn in P. viridis and all the sediment geochemical fractions of Zn and total Zn in the sediment. This indicated that Zn was possibly regulated from the soft tissue of P. viridis. The present results supported the use of P. viridis as a suitable biomonitoring agent for Cd, Cu and Pb.
Research Interests: Marine Biology, Malaysia, Marine Aquaculture, Environmental Monitoring, Molluscan Biology, and 16 moreMultidisciplinary, Heavy metals, Marine Mussels, Copper, Heavy Metal Pollution, Bivalvia, Animals, Biomonitoring, Heavy Metal, Lead, Sequential Extraction, Zinc, Cadmium, Soft Tissue, Environment, and Geologic Sediments
Genetic variation at 53 protein-coding loci (25 polymorphic) was analysed for 17 water buffalo populations – 12 swamp, three Lankan and two of the Murrah breed (river type), to determine the magnitude of genetic differentiation and the... more
Genetic variation at 53 protein-coding loci (25 polymorphic) was analysed for 17 water buffalo populations – 12 swamp, three Lankan and two of the Murrah breed (river type), to determine the magnitude of genetic differentiation and the genetic relationships among the populations. In accord with previous cytological studies, the Lankan buffalo clearly are river type. Significant deviations from Hardy–Weinberg equilibrium were shown for a number of locus–population combinations, with all populations but one showing significant heterogeneity in these deviations among loci. By contrast, heterogeneity among populations for each locus was much less, indicating locus-specific deviations, which suggest selection affecting allele frequencies at some loci. There was significant genetic differentiation among populations of both the swamp and river types. The differentiation among the swamp populations may reflect the geography of south-east Asia and the presumed spread of the swamp buffalo through this region. Phylogenies derived from pairwise genetic distance estimates show the clear separation of swamp and river types, but the topology of the swamp populations shows rather poor consistency with their geographic locations. For at least one population (Australia), it is clear that bottleneck effects have distorted the phylogenetic topology. Average genetic distances for both the swamp and river types, as compared with previous studies of livestock breeds, show that the genetic differentiation of each of these sets of populations is of the same order of magnitude as that among well-recognized and established breeds of other species.
Research Interests: Genetics, Zoology, Animal Science, Population Genetics, Southeast Asia, and 16 moreMolecular Markers, Molecular Genetics, Animal Production, Phylogeny, Enzymes, Animal Genetics, Livestock, Animal breeding and genetics, Animal, Animals, Goats, Genotype, Genetic variation, Veterinary Sciences, Capra Hircus, and Buffaloes
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Research Interests: Genetics, Zoology, Population Genetics, Molecular Evolution, Australia, and 19 moreSri Lanka, Genetic Diversity, Phylogeny, Mitochondrial DNA, Animal Genetics, Animal, Haplotypes, Animals, Asia, Polymerase Chain Reaction, Proteins, Cytochrome B, Genotype, Time Factors, Genetic variation, Veterinary Sciences, Species Specificity, Buffaloes, and Molecular Sequence Data
The genetic relationships among eight ethnic groups from Malaysia and eight other ethic groups from other parts of Southeast Asia were determined based on allozyme data.Two major clustere were obtained, one grouping the non-Mongoloid... more
The genetic relationships among eight ethnic groups from Malaysia and eight other ethic groups from other parts of Southeast Asia were determined based on allozyme data.Two major clustere were obtained, one grouping the non-Mongoloid ethnic groups of Indians, Senoi and Aetas (Negrito) and the other containing 13 Mongoloid ethnic groups of Malay, Chinese, Batak,Land Dayak, Visayan, Iban, Kadazan,Tagalog, Paiwan, Aboriginal Malaysa, Ifugao, Atayal and Bunan
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Research Interests: Genetics, Methodology, Polymorphism, Population Genetics, Southeast Asia, and 16 moreThailand, Fish Biology, Aquaculture, Phylogeny, Enzymes, Animals, Biochemical, Populations, Body Weight, Genetic variation, Biochemical Genetics, Gel electrophoresis, Loci, Genetic distance, Genetic Markers, and Hemoglobins
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Research Interests: Genetics, Polymorphism, Plant biotechnology, Plant breeding and genetics, Genetic Diversity, and 13 moreBiological Sciences, Plant Genetic Resources, Biologia, Phylogenetic analysis, Oil palm, Genetic Differentiation, Genetic Divergence, Oil Palm, Oilpalm, Population Study, Genetic distance, Nucleotides, and Simple Sequence Repeat
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... 作 者： Chee Kong Yap Mew Seong Choh Franklin Edward Berandah Ahmad Ismail Soon GuanTan 作者单位： Department of Biology, Faculty of Science, Universiti Putra Malaysia,UPM 43400, Serdang, Selangor, Malaysia 期 刊： 湿地科学 ISTIC Journal： WETLAND... more
... 作 者： Chee Kong Yap Mew Seong Choh Franklin Edward Berandah Ahmad Ismail Soon GuanTan 作者单位： Department of Biology, Faculty of Science, Universiti Putra Malaysia,UPM 43400, Serdang, Selangor, Malaysia 期 刊： 湿地科学 ISTIC Journal： WETLAND SCIENCE ...
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Research Interests: Organic Chemistry, Technology, Polymorphism, Population Genetics, Molecular Evolution, and 38 morePlant Biology, China, Plant Breeding, Genetic Diversity, Molecular Ecology, Biological Sciences, Phylogeny, Plant Genome Project, Tissue culture, FingerPrinting, Expressed Sequence Tags, Microsatellites, Asia Pacific, Primer design, Cluster Analysis, DNA fingerprinting, Marker assisted selection, Sesamum, Genome Analysis, Genetic Map, Microsatellite, Oil palm, Ssr, Genetic linkage analysis, Repetitive DNA, Molecules, Linkage Group, Genetic Polymorphism, Genomic Library, SSR, Oil Palm, Genome sequence, Base Sequence, Genetic Markers, Linkage Analysis, Simple Sequence Repeat, Molecular Sequence Data, and Molecular Probe
Shell morphological characters and allozyme electrophoresis were used to study the relationships among six geographical populations of land snails collected from Peninsular Malaysia. Allozyme electrophoresis was used to study the genetic... more
Shell morphological characters and allozyme electrophoresis were used to study the relationships among six geographical populations of land snails collected from Peninsular Malaysia. Allozyme electrophoresis was used to study the genetic variations to complement the morphological features studied that included shell lengths, numbers of whorls and shell colour. Ten loci coding for six enzymes (MDH, LAP, ALP, PGM, G6PDH and EST) could be reliably scored in samples from the six populations studied. The dendrogram showed two major clusters with one cluster comprising Subulinidae populations from Perak, Selangor, Johor, Terengganu and Pahang while the other cluster included only the Streptaxidae Huttonella bicolor (red) population. The Subulinidae populations were grouped into two subclusters: one subcluster included the Subulina sp. populations from Perak, Selangor an Johor while the other subcluster included the Opeas sp. populations from Terengganu and Pahang. Morphological features can identify the different families and therefore they can complement the allozyme genetic studies on the land snail populations. Like other reports in the literature, our results also underline the importance of a genetic approach in conjunction with a morphological approach, for discriminating land snail species. The present results suggest that small land snails, which were similar in colour but different in sizes, were not of the same family/genus.
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Research Interests: Genetics, Entomology, Molecular Biology, Polymorphism, Population Genetics, and 20 moreSoutheast Asia, Malaysia, Insect-Plant Interactions, Molecular Genetics, Insect Molecular Biology, Phylogeny, Plant diseases, Female, Animals, Male, Insects, Oryza Sativa, Sterilization, Isoenzymes, Genetic variation, Biochemical Genetics, Gel electrophoresis, Genetic Variability, Inheritance Patterns, and Complex I
Genetic variation due to heavy metal contamination has always been an interesting topic of study. Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion and argument as to which... more
Genetic variation due to heavy metal contamination has always been an interesting topic of study. Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion and argument as to which contaminant(s) caused the variations in the genetic structures of biomonitors. This study used a Single Primer Amplification Reaction (SPAR) technique namely Random Amplified Polymorphic DNA (RAPD) to determine the genetic diversity of the populations of the green-lipped mussel Perna viridis collected from a metal-contaminated site at Kg. Pasir Puteh and those from four relatively&amp;amp;amp;amp;amp;amp;amp;amp;#39; uncontaminated sites (reference sites). Heavy metal levels (Cd, Cu, Pb and Zn) were also measured in the soft tissues and byssus of the mussels from all the sites. Cluster analyses employing UPGMA done based on the RAPD makers grouped the populations into two major clusters; the Bagan Tiang, Pantai Lido, Pontian and Kg. Pasir Puteh populations were in one cluster, while the Sg. Belungkor population clustered by itself. This indicated that the genetic diversity based on bands resulting from the use of all four RAPD primers on P. viridis did not indicate its potential use as a biomarker of heavy metal pollution in coastal waters. However, based on a correlation analysis between a particular metal and a band resulting from a specific RAPD primer revealed some significant (P &amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.01) correlations between the primers and the heavy metal concentrations in the byssus and soft tissues. Thus, the correlation between a particular metal and the bands resulting from the use of a specific RAPD primer on P. viridis could be used as biomonitoring tool of heavy metal pollution.
Research Interests: Genetics, Aquatic Ecology, Russian, Population Genetics, Environmental Monitoring, and 15 moreGenetic Diversity, Heavy metals, Heavy Metal Pollution, Animals, Biomonitoring, Heavy Metal, Mollusca, Perna viridis, Heavy Metal Contamination, Correlation Analysis, Genetic variation, Straits of Malacca, Genetika, Genetic Markers, and Random amplified polymorphic DNA
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Abstract： The distribution and concentrations of Cd, Cu, Pb and Zn were determined in the gills and remaining soft tissues of Perna viridis collected from 12 geographical sites ( 10 from the west and 2 from the east coastal waters) of... more
Abstract： The distribution and concentrations of Cd, Cu, Pb and Zn were determined in the gills and remaining soft tissues of Perna viridis collected from 12 geographical sites ( 10 from the west and 2 from the east coastal waters) of Peninsular Malaysia. All samples showed that ...
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Abstract： Three different aquatic ecosystems(an urban pond,Kelana Jays Pond;a polluted river,Sepang River;and the intertidal and offshore areas of the west coast of Peninsular Malaysia)with different sets of ecological backgrounds and... more
Abstract： Three different aquatic ecosystems(an urban pond,Kelana Jays Pond;a polluted river,Sepang River;and the intertidal and offshore areas of the west coast of Peninsular Malaysia)with different sets of ecological backgrounds and human activities were ...
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【摘要】：Surface drainage sediments were collected, between January and April in 2005, from 6 sampling sites in Peninsular Malaysia suspected to have received different anthropogenic sources. These drainages included sites near a... more
【摘要】：Surface drainage sediments were collected, between January and April in 2005, from 6 sampling sites in Peninsular Malaysia suspected to have received different anthropogenic sources. These drainages included sites near a petrochemical plant, an electronic factory, ...
Research Interests: Engineering, Genetics, Analytical Chemistry, Technology, Bioelectrochemistry, and 28 moreElectrochemistry, Ionic Liquid, Biological Sciences, DNA, Infectious Disease, Calibration, Biosensor, Polymerase Chain Reaction, Physical sciences, DNA hybridization, Trichoderma Harzianum, Methylene Blue, CHEMICAL SCIENCES, Moving average, Composite Membrane, Hepatitis B virus, High Sensitivity, Modified Electrode, Organometallic Compounds, Square Wave Voltammetry, Ligands, Acridine Orange, Biosensing Techniques, Oligonucleotides, Nucleic Acid, single stranded DNA, DNA fragmentation, and DNA sequence
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Macrobrachium rosenbergii nodavirus (MrNv) infects giant freshwater prawns and causes white tail disease (WTD). The coding region of the capsid protein of MrNv was amplified with RT-PCR and cloned into the pTrcHis2-TOPO vector. The... more
Macrobrachium rosenbergii nodavirus (MrNv) infects giant freshwater prawns and causes white tail disease
(WTD). The coding region of the capsid protein of MrNv was amplified with RT-PCR and cloned into
the pTrcHis2-TOPO vector. The recombinant plasmid was introduced into Escherichia coli and protein
expression was induced with IPTG. SDS-PAGE showed that the recombinant protein containing the Histag
and myc epitope has a molecular mass of about 46 kDa and it was detected by the anti-His antibody
in Western blotting. The protein was purified using immobilized metal affinity chromatography (IMAC)
and transmission electron microscopic analysis revealed that the recombinant protein assembled into
virus-like particles (VLPs) with a diameter of about 30
±
3 nm. The size of the particles was confirmed
by dynamic light scattering. Nucleic acids were extracted from the VLPs and treatment with nucleases
showed that they were mainly RNA molecules. This is the first report describing the production of MrNv
capsid protein in bacteria and its assembly into VLPs
(WTD). The coding region of the capsid protein of MrNv was amplified with RT-PCR and cloned into
the pTrcHis2-TOPO vector. The recombinant plasmid was introduced into Escherichia coli and protein
expression was induced with IPTG. SDS-PAGE showed that the recombinant protein containing the Histag
and myc epitope has a molecular mass of about 46 kDa and it was detected by the anti-His antibody
in Western blotting. The protein was purified using immobilized metal affinity chromatography (IMAC)
and transmission electron microscopic analysis revealed that the recombinant protein assembled into
virus-like particles (VLPs) with a diameter of about 30
±
3 nm. The size of the particles was confirmed
by dynamic light scattering. Nucleic acids were extracted from the VLPs and treatment with nucleases
showed that they were mainly RNA molecules. This is the first report describing the production of MrNv
capsid protein in bacteria and its assembly into VLPs