Molecular taxonomy

Six pheasant species; koklass pheasant (Pucrasia macrolopha), Himalayan monal (Lophophorus impejanus), white crested kalij (Lophura leucomelana), western tragopan (Tragopan melanocephalus), cheer pheasant (Catreus willachii) and blue peacock (Pavo cristatus) found in Pakistan were analyzed for elaborating genetic diversity and their possible phylogenetic affinities. The total genomic DNA was isolated from blood and PCR was performed by using six SSR markers. The results revealed low to medium level genetic diversity (GD = 4–57%) among the pheasant’s genotypes. Maximum GD (57%) was estimated between female of Himalayan monal and male of blue peacock while minimum GD (4%) was observed in two comparisons; one between male of monal and female of cheer pheasant and other between the male of western tragopan and female of cheer pheasant. Phylogeny was analyzed by constructing the dendrogram, based on PCR amplification profiles. Dendrogram clustered all the genotypes of pheasants into two main groups A and B. Group A was largest and subdivided into sub-groups. Some novel findings were also observed in dendrogram in which male and female of the same species were found to be clustered with male or female of other species in separate groups. This novelty needs further genetic elaborations for its clarity.

Actinomycetes is bacterial group that have similarity to Fungi. Actinomycetes contribute around 45% secondary metabolite that has been found or around 10000 secondary metabolite. Even though information about actinomycetes such as unique trait or the benefit of it is known already but chemotaxonomy analysis and molecular analysis still need to be learn. This thing happen because classification of actinomycetes always changing following the research and study that has been done. The aim for this research is to studying diversity  until genus level actinomycetes Indonesia LIPI Cibinong culture collection using chemotaxonomy and molecular methods.  This research was done in the LIPI Cibinong Bogor for 6 months. 10 isolate actinomycetes that was used in this research are being prepare for chemotaxonomy and molecular analysis. Isolate ID04-1019,ID04-1052, ID04-1066, ID04-1067, ID04-1071, ID04-1088, ID04-1093, ID04-1103 was isolated from leaves in Jambi, Isolate ID05-0653 was from soil in Timor and isolate ID06-0464 was from soil in Lombok. This research using chemotaxonomy method that is Diamino pimelic acid analysis, cell sugar analysis, fatty acid analysis, menaquinone analysis, phospholipid analysis also molecular method that is gen sequencing of 16S rRNA and G+C Content determination. Analysis result using phylogenic tree showed that isolate ID04-1071 related to species Actinoplanes rectilleneatus, isolate ID04-1066, ID04-1052 dan ID04-1033 related to species Actinoplanes ferrugineus and isolate ID04-1067, ID04-1093 and ID04-1088 related to species Actinoplanes globisporus. Result showed isolate ID04-1052, ID04-1066, ID04-1067, ID04-1071, ID04-1088, ID04-1093, ID04-1103 are genus member of Actinoplanes. Isolate ID05-0653 and ID-0464 are genus member of Actinophytocola.

Deep-sea soft sediments from trench systems and depths in the northwestern Pacific Ocean ranging from less than 300 to 10 897 m in depth have been analyzed for three target genera of actinomycetes: Micromonospora, Rhodococcus, and Streptomyces. Only culturable strains, recovered at atmospheric pressure on selective isolation media, have been examined to date. Maximum recoveries of culturable bacteria were greater that 107/ml wet g sediment, but actinomycetes comprised a small proportion of this population (usually less than 1%). The target actinomycetes were isolated at all depths except from the Mariana Trench sediments. Actinomycete colonies were defined initially on the basis of colony morphologies, and preliminary identification then was made by chemotaxonomic tests. Pyrolysis mass spectrometry (PyMS) of deep-sea mycolic acid-containing actinomycetes gave excellent correspondence with numerical (phenetic) taxonomic analyses and subsequently was adopted as a rapid procedure for assessing taxonomic diversity. PyMS analysis enabled several clusters of deep-sea rhodococci to be distinguished that are quite distinct from all type strains. 16S rRNA gene sequence analysis has revealed that several of these marine rhodococci have sequences that are very similar to certain terrestrial species of Rhodococcus and to Dietzia. There is evidence for the intrusion of terrestrial runoff into these deep trench systems, and the inconsistency of the phenotypic and molecular taxonomies may reflect recent speciation events in actinomycetes under the high-pressure conditions of the deep sea. The results of DNA-DNA pairing experiments point to the novelty of Rhodococcus strains recovered from hadal depths in the Izu Bonin Trench. Biotransformation studies of deep-sea bacteria have focused on nitrile compounds. Nitrile-metabolizing bacteria, closely related to rhodococci, have been isolated that grow well at low temperature, high salt concentrations, and high pressures, suggesting that they are of marine origin or have adapted to the deep-sea environment.

In the wide panorama of modifications and applications of Polymerase Chain Reaction (PCR), genome analysis by randomtargeted primers has been increasingly used since its proposal in 1990. In this group of techniques, here collectively referred to as Multiple Arbitrary Amplicon Profiling (MAAP), one arbitrarily designed primer is used at low stringency to amplify DNA from any source. Fingerprints of various complexity are obtained and are tested to determine their suitability for genetic analysis both in bacteria and in different eukaryotes. Since MAAP does not require prior knowledge of DNA sequence, it has been mostly used to study poorly characterized genomes. In this review, we will outline MAAP technology, current methodology (annotated with drawbacks, confoundings and pitfalls), its wide range of applications, and its potential use in the study of the phylogenetic relationships and molecular taxonomy of non-human primates.

About 50 species of sand flies have been reported to be prevalent in India. We explored the utility of the DNA barcode
approach towards species identification of these medically important insects. A total of 62 specimens belonging to seven
morphologically identified species of two genera, Phlebotomus and Sergentomyia, collected from Puducherry Union Territory, Maharashtra and Rajasthan states of India were subjected to the analysis. Neighbor-joining (NJ) analysis of DNA barcode sequences identified the individuals of seven morphological species into eight distinct species, as presented in the designed NJ tree. This methodology delineated morphologically identified species, S. bailyi, into two genetically isolated groups. Also, this study characterizes DNA barcodes of P. argentipes and P. papatasi, the vector species of leishmaniasis inIndia, for the first time.

Museum fish specimens are invaluable resources for genetic studies, but extraction of high quality DNA is often problematic. In this study, hairtail fishes of the genera Trichiurus and Lepturacanthus (family: Trichiuridae) representing a wide range of preservation histories and three different methods of preservation were analyzed for mitochondrial DNA (mtDNA) extraction, amplification and sequencing of marker genes. A total of six protocols, including a commercially available kit, were compared in this study. Amplification of conserved genes such as16S rRNA and 12S rRNA were done using polymerase chain reaction with sequence analyses using automated capillary sequencing techniques. The results show that mtDNA extraction, amplification and sequencing of conserved genes could be obtained successfully from frozen (−20°C) preserved specimens (1–5 years) and also from ethanol (95%) fixed specimens (2–5 years) but not from any of the formalin (10%) fixed specimens (3–4 years). However, specimens that have been fixed for only 7 days in buffered formalin (10% formalin with phosphate buffer containing 173 mm salt) and ethanol (95%) could yield successful mtDNA extraction, amplification and sequence information of both 16S rRNA and 12S rRNA.

I conducted herpetofaunal surveys in poorly-explored sections of Central India: The Amarkantak Plateau; The Son, Johila, and Narmada river lowlands; parts of the Maikal Mountain Range; and pockets of the core zone area of Achanakmar-Amarkantak Biosphere Reserve. I recorded a total of 61 species (17 amphibian and 44 reptilian spe¬cies). Noteworthy findings included the rediscovery of the Critically Endangered Sacred Grove Bush Frog (Philautus sanctisilvaticus)at its type locality after 54 years, new state records for Dobson’s Burrowing Frog (Sphaerotheca dobsonii) and Beddome’s Grass Skink (Eutropis beddomii), and significant new distributional records for a number of species. This study highlights the importance of landscape-level, long-term fieldwork to untangle the hidden diversity of the Amarkantak Plateau.

I conducted herpetofaunal surveys in poorly explored sections of Central India: The Amarkantak Plateau; The Son, Johila, and Narmada river lowlands; parts of the Maikal Mountain Range; and pockets of the core zone area of Achanakmar-Amarkantak Biosphere Reserve. I recorded a total of 61 species (17 amphibian and 44 reptilian). Noteworthy findings included the rediscovery of the Critically Endangered Sacred Grove Bush Frog (Philautus sanctisilvaticus) at its type locality after 54 years, new state records for Dobson’s Burrowing Frog (Sphaerotheca dobsonii) and Beddome’s Grass Skink (Eutropis beddomii), and significant new distributional records for a number of species. This study highlights the importance of landscape-level, long-term fieldwork to untangle the hidden diversity of the Amarkantak Plateau.

Advances in the analysis of expression profiles, using genomic techniques, have revealed the high heterogeneity present in breast cancers. These approaches have served to identify different breast cancer subgroups with specific molecular characteristics that could sub-classify these tumours as carcinomas expressing hormone receptors, denominated Luminal subtype, and tumours with negative expression of hormone receptors, the Basal and HER2+ phenotypes. Therefore, during recent years, identification of markers characteristic of each subtype has been the focus of many research groups. All of these breast tumour subtypes probably have specific clinical and morphological features; however, this hypothesis needs to be confirmed by analysing more homogenous series. Although this “new” classification has limitations, it could be useful in the clinical practice, allowing not only a more accurate prognosis in breast cancer patients but also a selective treatment for each predefined subtype.

© 2010 IFVC Summary: Vavilovia ( Vavilovia formosa (Stev.) Fed.) belongs to the tribe Fabeae along with peas, vetchlings, vetches and lentils. It prefers high mountain areas in Armenia, Azerbaijan, Georgia, Iran, Iraq, Lebanon, Russia, Syria and Turkey. A true success in the ex situ conservation has recently been achieved, within the display plot Flora and Vegetation of Armenia in the Yerevan Botanic Garden. The hybridization between vavilovia and other Fabeae was done in the N. I. Vavilov Institute of Plant Industry with F 1 seeds and F 1 plants that did not produce the next generation. The recent molecular research showed that vavilovia belongs to a Lathyrus-Pisum-Vavilovia clade with a clearly distinct status.

As one of the most abundant and complex groups of terrestrial insects, ants have associations with many other organismal groups, such as hemipteran insects producing honeydew. With the aim of expanding the knowledge base of ant species associated with aphids, this study analyzed mitochondrial COI barcodes of 301 ant samples for 37 aphid-associated ant species in a subtropical area of southern China. Sequence analyses revealed that the intraspecific and interspecific distances ranged from zero to 7.7%% and 0.2 to 31.7%, respectively. Three barcoding approaches-Automatic Barcode Gap Discovery, Bayesian Poisson Tree Processes and Generalized Mixed Yule-coalescent-were used to help delimit ant species based on COI sequences, and their results corresponded well with most of the morphospecies. All three approaches indicate cryptic diversity may exist within Tetramorium bicarinatum and Technomyrmex albipes, with in-traspecific genetic distances of 7.7% and 6.24%, respectively. Our analyses also reported five species for the first time from Fujian Province of China, and the COI sequences of nine species are newly added into the GenBank. This study provides information about species diversity of aphid-associated ants in subtropical China and compiles a DNA barcode reference library for future ant barcoding work.

The seed storage free amino acids of 4 taxa of Blyxa were analyzed from the fully aquatic family Hydrocharitaceae by Thin Layer Chromatography. Total 22 amino acids were found, among these 3 were not identified. Considerable amount of homology were observed in between Blyxa aubertii var. aubertii and B. aubertii var. echinosperma (60%). Also another homology observed in between B. octandra and B. quandricostata (41.17%), but B. japonica was far differ from others analyzed taxa. The major amino acids were Amino-n-butyric acid, Glutamic acid, Phenylalanine, Glycine, Tryptophan, Methionine, Isoleucine and Serine. The present observation reveals that there was a correlation in between morphology and free amino acids composition of
Blyxa analyzed taxa. Free amino amino acids can use as a taxonomic markers to draw the similarity among the plant taxa.