Da-yong Zhang
Beijing Normal University, Institute of Ecology, Faculty Member
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Recently, researchers advocate to shift the focus of Pleistocene refugia studies from documenting the presence of microrefugia towards studying the ecological and evolutionary implications of survival in microrefugia. While we can endorse... more
Recently, researchers advocate to shift the focus of Pleistocene refugia studies from documenting the presence of microrefugia towards studying the ecological and evolutionary implications of survival in microrefugia. While we can endorse this movement wholeheartedly, we feel that an appropriate characterization of the differences between microrefugia and macrorefugia should not ignore population structure or subdivision altogether. When a population is subdivided into smaller subpopulations, two levels of random genetic drift take place simultaneously. There is a drift process within each subpopulation, which takes place relatively rapidly, and another drift in the population as a whole, which takes place more slowly. Since the regional population of a species surviving in microrefugia is usually more subdivided than that in macrorefugia, it should be commonplace to observe that microrefugial populations have higher genetic diversity than macrorefugial populations, a prediction tha...
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Phylogenies can be constructed in many ways, including using shared complex characters known as rare genomic changes (RGCs), such as insertions and deletions (indels), retroposon integrations and intron positions. Here, we demonstrate... more
Phylogenies can be constructed in many ways, including using shared complex characters known as rare genomic changes (RGCs), such as insertions and deletions (indels), retroposon integrations and intron positions. Here, we demonstrate that distance-based phylogenies, which were determined by shared overlapping genes from 13 completely sequenced gamma-Proteobacteria genomes, are consistent with phylogenies based on 16S rRNAs and other robust markers. These findings suggest that overlapping genes could provide interesting additional insights into the phylogenomics of completely sequenced microbial genomes.
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Currently, most researches on the properties of interacting proteins, hubs in particular, are mainly based on an aggregated network of binary interactions. Here, by projecting a yeast-aggregated cell cycle network into four phase (G1, S,... more
Currently, most researches on the properties of interacting proteins, hubs in particular, are mainly based on an aggregated network of binary interactions. Here, by projecting a yeast-aggregated cell cycle network into four phase (G1, S, G2 and M) sub-networks, we explored the properties of the hubs of the aggregated network. We found, as expected that only 69% (103 of 149) of hubs still act as hubs in at least one of the four sub-networks. Interestingly, those (19%) that are not hubs in any phase tend to perform multiple functions and differ from the others in their network positions. We also analyzed the potential biological features among the dynamic and static hubs. Finally, we investigated the dynamic properties of two complexes, the anaphase-promoting complex and the chromatin-remodeling complex. The dynamic function of the anaphase-promoting complex is represented by its interactions with CDC28 at different stages of mitotic cell cycle. The chromatin-remodeling complex is ass...
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The neutral theory of biodiversity has been criticized for its neglect of species differences. Yet it is much less heeded that S. P. Hubbell's definition of neutrality allows species to differ in their birth and death rates as long as... more
The neutral theory of biodiversity has been criticized for its neglect of species differences. Yet it is much less heeded that S. P. Hubbell's definition of neutrality allows species to differ in their birth and death rates as long as they have an equal per capita fitness. Using the lottery model of competition we find that fitness equalization through birth-death trade-offs can make species coexist longer than expected for demographically identical species, whereas the probability of monodominance for a species under zero-sum neutral dynamics is equal to its initial relative abundance. Furthermore, if newly arising species in a community survive preferentially they are more likely to slip through the quagmire of rareness, thus creating a strong selective bias favoring their community membership. On the other hand, high-mortality species, once having gained a footing in the community, are more likely to become abundant due to their compensatory high birth rates. This unexpected ...
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BACKGROUND: Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been... more
BACKGROUND: Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers
Research Interests: Bioinformatics, Evolutionary Biology, Genetics, Molecular Biology, Genomics, and 14 moreComputational Biology, Molecular Evolution, Evolution, Biological Sciences, Software, Phylogeny, Mathematical Sciences, BMC Bioinformatics, Tree of Life, Computer User Interface Design, Online Interaction, Phylogenetic Tree, Distance Matrix, and Internet
In this work, 21 completely sequenced eukaryotic genomes were analyzed using an intragene compar- ison approach. We found that all of these genomes show a significant 50-biased distribution of introns of protein-coding genes. Our findings... more
In this work, 21 completely sequenced eukaryotic genomes were analyzed using an intragene compar- ison approach. We found that all of these genomes show a significant 50-biased distribution of introns of protein-coding genes. Our findings are different from previous studies based on the intergene method, where introns are biased towards the 50 end of genes only in intron-poor genomes, but
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Ideally, only proteins that exhibit highly similar domain architectures should be compared with one another as homologues or be classified into a single family. By combining three different indices, the Jaccard index, the Goodman-Kruskal... more
Ideally, only proteins that exhibit highly similar domain architectures should be compared with one another as homologues or be classified into a single family. By combining three different indices, the Jaccard index, the Goodman-Kruskal gamma function and the domain duplicate index, into a single similarity measure, we propose a method for comparing proteins based on their domain architectures. Evaluation of the method using the eukaryotic orthologous groups of proteins (KOGs) database indicated that it allows the automatic and efficient comparison of multiple-domain proteins, which are usually refractory to classic approaches based on sequence similarity measures. As a case study, the PDZ and LRR_1 domains are used to demonstrate how proteins containing promiscuous domains can be clearly compared using our method. For the convenience of users, a web server was set up where three different query interfaces were implemented to compare different domain architectures or proteins with domain(s), and to identify the relationships among domain architectures within a given KOG from the Clusters of Orthologous Groups of Proteins database. The approach we propose is suitable for estimating the similarity of domain architectures of proteins, especially those of multidomain proteins. http://cmb.bnu.edu.cn/pdart/.
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Both DNA replication and transcription are structurally asymmetric processes. An asymmetric nucleotide substitution pattern has been observed between the leading and the lagging strand, and between the coding and the noncoding strand, in... more
Both DNA replication and transcription are structurally asymmetric processes. An asymmetric nucleotide substitution pattern has been observed between the leading and the lagging strand, and between the coding and the noncoding strand, in eubacterial, viral, and organelle genomes. Similar studies in eukaryotes have been rare, because the origins of replication in nuclear genomes are mostly unknown and the replicons are
Research Interests: Evolutionary Biology, Genetics, Caenorhabditis elegans, Molecular Evolution, DNA replication, and 20 moreDrosophila melanogaster, Arabidopsis thaliana, DNA, Saccharomyces cerevisiae, Humans, Mutation, Animals, Homo Sapiens, Genome, Anopheles gambiae, nuclear DNA, Schizosaccharomyces Pombe, Degeneration, Plasmodium falciparum, Codon, Eukaryotic Cells, Mus Musculus, Nucleotides, Biochemistry and cell biology, and single stranded DNA
Recent discovery of cryptic species in fig-pollinating wasps creates a puzzle for the ecological competition theory: how do two or more apparently identical species coexist? Conventional theory predicts that they should not. Chesson... more
Recent discovery of cryptic species in fig-pollinating wasps creates a puzzle for the ecological competition theory: how do two or more apparently identical species coexist? Conventional theory predicts that they should not. Chesson (Trends Ecol. Evol., 1991, 6, 26-28) identified one exception which he considered unlikely to occur in reality: coexistence might be possible if appropriate social behaviour was discriminately
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Synthesis of Photoresist Particles: MMA (Aldrich, >99%) and GMA (Aldrich, > 95 %) were used as supplied. Potassium persulfate (KPS) was used as an initiator for emulsion polymerization. A 100 mL two-necked round-bottom flask was... more
Synthesis of Photoresist Particles: MMA (Aldrich, >99%) and GMA (Aldrich, > 95 %) were used as supplied. Potassium persulfate (KPS) was used as an initiator for emulsion polymerization. A 100 mL two-necked round-bottom flask was filled with KPS dissolved in ...
Research Interests: Engineering, Functional Materials, Advanced Materials, Emulsion polymerization, Silica, and 14 morePhysical sciences, Atmospheric Pressure, Spatial Organization, Nitrogen, Potassium, CHEMICAL SCIENCES, Glass Transition Temperature, Room Temperature, Differential Scanning Calorimeter, Distilled Water, Length scale, Advanced, Batch Reactor, and Water Vapor
Phytophthora root and stem rot of soybean [Glycine max (L.) Merr.], caused by Phytophthora sojae Kaufmann and Gerdemann, is a destructive disease throughout the soybean planting regions in the world. Here, we report insights into the... more
Phytophthora root and stem rot of soybean [Glycine max (L.) Merr.], caused by Phytophthora sojae Kaufmann and Gerdemann, is a destructive disease throughout the soybean planting regions in the world. Here, we report insights into the function and underlying mechanisms of a novel ethylene response factor (ERF) in soybean, namely GmERF5, in host responses to P. sojae. GmERF5-overexpressing transgenic soybean exhibited significantly enhanced resistance to P. sojae and positively regulated the expression of the PR10, PR1-1, and PR10-1 genes. Sequence analysis suggested that GmERF5 contains an AP2/ERF domain of 58 aa and a conserved ERF-associated amphiphilic repression (EAR) motif in its C-terminal region. Following stress treatments, GmERF5 was significantly induced by P. sojae, ethylene (ET), abscisic acid (ABA), and salicylic acid (SA). The activity of the GmERF5 promoter (GmERF5P) was upregulated in tobacco leaves with ET, ABA, Phytophthora nicotianae, salt, and drought treatments, ...
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Plant phylogeographic studies in East Asia have provided support for the biogeographic hypothesis that the complex landforms and climate of this region have provided substantial opportunities for allopatric speciation. However, most of... more
Plant phylogeographic studies in East Asia have provided support for the biogeographic hypothesis that the complex landforms and climate of this region have provided substantial opportunities for allopatric speciation. However, most of these studies have been based on maternally inherited chloroplast DNA (cpDNA) markers and were therefore unable to reveal the role of pollen-mediated gene flow in preventing population divergence. Here, we investigate the phylogeography of the Chinese walnut Juglans cathayensis, a temperate deciduous tree widely distributed across disjunct montane sites in subtropical China. We genotyped 19 populations using seven cpDNA fragments and ten nuclear microsatellite loci and modeled the ecological niche of J. cathayensis. CpDNA analysis identified a total of nine haplotypes, and each of the 19 sampled populations was fixed for a single haplotype, displaying a prominent phylogeographic structure. The results of ecological niche modeling indicated that J. cat...
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Flexistyly is a sexual dimorphism where there are two morphs that differ in the temporal expression of sexual function and also involve reciprocal movement of the stigmatic surface through a vertical axis during the flowering period. The... more
Flexistyly is a sexual dimorphism where there are two morphs that differ in the temporal expression of sexual function and also involve reciprocal movement of the stigmatic surface through a vertical axis during the flowering period. The adaptive significance of flexistyly has been interpreted as a floral mechanism for outcrossing, but it may also function to reduce sexual interference in which styles and stigmas impede the pollen export. Here these two explanations of flexistyly were tested in Alpinia blepharocalyx through a hand-pollination experiment. Hand-pollinations were performed in two temporal morphs and consisted of two sequential pollination treatments, namely self-pollination in the morning and inter-morph pollination in the afternoon (treatment 1) or conversely inter-morph pollination in the morning and self-pollination in the afternoon (treatment 2), and two simultaneous self- and inter-morph cross-pollination treatments either in the morning (treatment 3) or in the af...
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Heterodichogamy differs from normal dichogamy, in that it involves two mating types (protogyny and protandry) that occur at a 1 : 1 ratio in a population. Flowering phases of the two mating types are synchronized and reciprocal, which was... more
Heterodichogamy differs from normal dichogamy, in that it involves two mating types (protogyny and protandry) that occur at a 1 : 1 ratio in a population. Flowering phases of the two mating types are synchronized and reciprocal, which was considered to ensure between-type outcrossing. This study aims to quantify the flowering pattern and pollination efficacy in Juglans mandshurica, a wind-pollinated heterodichogamous tree. The pattern of flowering phenology was monitored within individual trees and pollen traps were used to measure air-borne pollen loads during the spring in 2003 and 2004. Pollen longevity was determined by staining technique. Also a pollen supplementation experiment was performed in 2004 to assess pollen limitation of fruit production. There was no overlap between sexual functions within individual trees. Flowering periods of the two mating types were reciprocal and synchronous in both 2003 and 2004. Air-borne pollen loads were large, and protogynous and protandrou...
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Reduction in female fitness in large clones can occur as a result of increased geitonogamous self-fertilization and its influence through inbreeding depression. This possibility was investigated in the self-compatible, bee-pollinated... more
Reduction in female fitness in large clones can occur as a result of increased geitonogamous self-fertilization and its influence through inbreeding depression. This possibility was investigated in the self-compatible, bee-pollinated perennial herb Aconitum kusnezoffii which varies in clone size. Field investigations were conducted on pollinator behaviour, flowering phenology and variation in seed set. The effects of self-pollination following controlled self- and cross-pollination were also examined. Selfing rates of differently sized clones were assessed using allozyme markers. High rates of geitonogamous pollination were associated with large display size. Female fitness at the ramet level decreased with clone size. Fruit and seed set under cross-pollination were significantly higher than those under self-pollination. The pre-dispersal inbreeding depression was estimated as 0.502 based on the difference in seed set per flower between self- and cross-pollinated flowers. Selfing ra...
Research Interests: Plant Biology, Ecology, Pollination, Bees, Animals, and 5 moreFlowers, Reproductive Success, Fruit, Inbreeding, and Annals
The HD-Zip transcription factors, which are unique to plant kingdom, belong to Homeobox proteins. They are composed of highly conserved HD (Homeodomain) and Leu zipper (Zip) element. The former binds specifically to DNA and the later... more
The HD-Zip transcription factors, which are unique to plant kingdom, belong to Homeobox proteins. They are composed of highly conserved HD (Homeodomain) and Leu zipper (Zip) element. The former binds specifically to DNA and the later mediates the formation of dimerization. Based on the structure features, HD-Zip transcription factors can be classified into four subfamilies HD-Zip I - IV, which are involved in different biological processes of plants including growth and development, photomorphogenesis, flowering, fruit ripening, and adaptation response to environmental stresses. HD-Zip transcription factors act as the integrators of development and environmental cues and endogenous hormone signal pathway to regulate targeted gene expression and plants adaptation response. In this review, the most advanced researches on biological functions of HD-Zip were summarized based on the researches of Arabidopsis HD-Zip transcription factors and the results from other species. The aim of this...
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To investigate the effects of Toll/interleukin 1 receptor domain-containing protein(TcpC)on macrophages and its mechanisms. Murine macrophage J774A cells were co-cultured with TcpC producing wild type E. coli strain CFT073 (TcpC(wt)) or... more
To investigate the effects of Toll/interleukin 1 receptor domain-containing protein(TcpC)on macrophages and its mechanisms. Murine macrophage J774A cells were co-cultured with TcpC producing wild type E. coli strain CFT073 (TcpC(wt)) or tcpc gene-deleted CFT073 mutant (TcpC(mut)) in Transwell system, respectively. Apoptosis of J774A cells co-cultured with TcpC(wt) or TcpC(mut) was analyzed by Annexin/PI double staining. The levels of reactive oxygen species (ROS) in J774A cells were determined by DCFH-DA staining after treatment with TcpC(wt) or TcpC(mut) at 6 h, 12 h,24 h or 36 h. After the ROS was scavenged by N-acetylcysteine (NAC), the changes of J774A cell apoptosis were also examined. The expression of caspase-3 in J774A cells co-cultured with TcpC(wt) or TcpC(mut) in the presence or absence of 0.1 mmol NAC was detected by Western blot. J774A cells co-cultured with TcpC(wt) for 24 h or 36 h showed significantly increased apoptosis (27.39% ± 4.05% and 28.45% ± 4.55%,respectivel...
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ABSTRACT
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The beam quality factors (or M2 parameter) of coherent and incoherent superposition of the several lower-order LP modes emerging from a step-index fiber have been calculated by using the second-order moment method. The results indicate... more
The beam quality factors (or M2 parameter) of coherent and incoherent superposition of the several lower-order LP modes emerging from a step-index fiber have been calculated by using the second-order moment method. The results indicate that, for an individual LP mode, the M2 parameter takes its maximum value when the normalized frequency V of the step-index fiber approaches the cut-off frequency, and it gradually becomes constant as V increases. In the case of incoherent superposition, the larger the fraction intensity carried by the higher-order mode, the larger the beam quality factor M2. Under certain circumstances, the value of the M2 parameter of the mixed mode that comprises several LP-modes contents may become even smaller and closer to the ideal Gaussian beam than that of the fundamental mode in a step-index fiber. However, in the case of the coherent superposition, the value of the M2 parameter of the mixed mode may be greater than that of the higher-order constituent mode. The results reported here could be helpful for the application of the high-power fiber laser systems.
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A map of protein-protein interactions provides valuable insight into the cellular function and machinery of a proteome. By measuring the similarity between two Gene Ontology (GO) terms with a relative specificity semantic relation, here,... more
A map of protein-protein interactions provides valuable insight into the cellular function and machinery of a proteome. By measuring the similarity between two Gene Ontology (GO) terms with a relative specificity semantic relation, here, we proposed a new method of reconstructing a yeast protein-protein interaction map that is solely based on the GO annotations. The method was validated using high-quality interaction datasets for its effectiveness. Based on a Z-score analysis, a positive dataset and a negative dataset for protein-protein interactions were derived. Moreover, a gold standard positive (GSP) dataset with the highest level of confidence that covered 78% of the high-quality interaction dataset and a gold standard negative (GSN) dataset with the lowest level of confidence were derived. In addition, we assessed four high-throughput experimental interaction datasets using the positives and the negatives as well as GSPs and GSNs. Our predicted network reconstructed from GSPs consists of 40,753 interactions among 2259 proteins, and forms 16 connected components. We mapped all of the MIPS complexes except for homodimers onto the predicted network. As a result, approximately 35% of complexes were identified interconnected. For seven complexes, we also identified some nonmember proteins that may be functionally related to the complexes concerned. This analysis is expected to provide a new approach for predicting the protein-protein interaction maps from other completely sequenced genomes with high-quality GO-based annotations.
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It is intuitively clear that the average time required for competitive exclusion increases as the competitive abilities of species become closer to equal. To emphasize the importance of this point for understanding diversity patterns,... more
It is intuitively clear that the average time required for competitive exclusion increases as the competitive abilities of species become closer to equal. To emphasize the importance of this point for understanding diversity patterns, Hubbell and his colleagues modeled tropical rainforest dynamics under the extreme assumption of competitive equivalency. In this study, we aim to extend Hubbell's community drift model
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Research Interests: Genetics, Sex Allocation, Life history, Resource Allocation, Life History Theory, and 16 moreConflict of Interest, Life History Evolution, Theoretical biology, Biological Sciences, Parental care, Mathematical Sciences, Density dependence, Pollen limitation, Population Growth, Offspring Size, Plant population ecology, Integrated Approach, Seed size, Reproductive Strategy, Parent-Offspring Conflict, and Reproductive Effort
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The following sections are included: Charmed Particle Production Cross Sections D-Meson Tagging
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Recent studies have demonstrated the importance of cellular extrinsic factors in the aging of adult stem cells. However, the effects of an aged cell-extrinsic environment on mesenchymal stem cell (MSC) aging and the factors involved... more
Recent studies have demonstrated the importance of cellular extrinsic factors in the aging of adult stem cells. However, the effects of an aged cell-extrinsic environment on mesenchymal stem cell (MSC) aging and the factors involved remain unclear. In the current study, we examine the effects of old rat serum (ORS) on the aging of MSCs, and explore the effects and mechanisms of Wnt/β-catenin signaling on MSC aging induced by ORS treatment. Senescence-associated changes in the cells are examined with SA-β-galactosidase staining and ROS staining. The proliferation ability is detected by MTT assay. The surviving and apoptotic cells are determined using AO/EB staining. The results suggest that ORS promotes MSC senescence and reduces the proliferation and survival of cells. The immunofluorescence staining shows that the expression of β-catenin increases in MSCs of old rats. To identify the effects of Wnt/β-catenin signaling on MSC aging induced with ORS, the expression of β-catenin, GSK-...
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Research Interests: Fertility, Ecology, Population Dynamics, Biodiversity, Dispersion, and 12 moreAnimals, Population Density, Species Diversity, Asymmetry, Population Growth, Biological evolution, Null Model, Ecosystem, Conservation of Natural Resources, Species Specificity, Ecological Applications, and Likelihood Functions
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To discover more active and water-soluble derivatives of tetracyclic diterpenoids containing an exo-methylene cyclopentanone or an α-methylenelactone moiety. All of the key intermediates were synthesized from stevioside, and the target... more
To discover more active and water-soluble derivatives of tetracyclic diterpenoids containing an exo-methylene cyclopentanone or an α-methylenelactone moiety. All of the key intermediates were synthesized from stevioside, and the target compounds were obtained through glycosylation of the 4-carboxyl group. The cytotoxicity of the target compounds against six human cancer cell lines, HepG2, Bel-7402, A549, U251, MCF-7 and MDA-MB-231, were evaluated by the MTT assay. Compound 1b was more effective than the positive control adriamycin against the HepG2, Bel-7402, A549, MCF-7, and MDA-MB-231 cell lines with IC50 values of 0.12, 0.91, 0.35, 0.08, and 0.07 μmol·L(-1), respectively. Moreover, compound 3c exhibited the most potent and selective cytotoxic activity against the HepG2 cell line (IC50, 0.01 μmol·L(-1)). Compounds 1b and 3c could be considered as potential anticancer candidates for further study.
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The factors which affected the formation of bubble in dehydrogenated RTV silicone rubber were studied, including catalysts, crosslinking agent and filler. The amount and type of catalysts had significant effects on curing and foaming... more
The factors which affected the formation of bubble in dehydrogenated RTV silicone rubber were studied, including catalysts, crosslinking agent and filler. The amount and type of catalysts had significant effects on curing and foaming velocity of silicone rubber, and furthermore affected the morphology of silicon rubber. With increasing the dosage of catalyst, the amount of bubble raised. With increasing the dosage of crosslinking agent, the gel time of silicone rubber decreased, the amount of bubble increased. The effect of filler ...
High power laser induced nonlinear optical effects in liquid crystal are prone to deteriorate the optical properties of liquid crystal device. The self diffraction phenomenon was observed when high power Gaussian profile laser beam... more
High power laser induced nonlinear optical effects in liquid crystal are prone to deteriorate the optical properties of liquid crystal device. The self diffraction phenomenon was observed when high power Gaussian profile laser beam propagate in 5CB liquid crystal, which was taken by high speed camera. The dynamical evolution of the diffraction phenomenon was studied to analyze the nonlinear optical properties of the liquid crystal. Kirchhoff's diffraction integral was applied to study the diffraction rings induced by Gaussian profile laser beam ...
Liquid crystal optical elements have important applications in laser facility, and the indium tin oxide (ITO) films are generally used in liquid crystal optical elements as transparent conductive electrodes. Laser induced damage of ITO... more
Liquid crystal optical elements have important applications in laser facility, and the indium tin oxide (ITO) films are generally used in liquid crystal optical elements as transparent conductive electrodes. Laser induced damage of ITO films leads to failure of liquid crystal optical elements. The laser damage model of ITO films which simulates the temperature distribution and thermal stress distribution was established. The laser damage of ITO films was experimented through pump-probe technology, and the power density producing ...
Synthesis of Photoresist Particles: MMA (Aldrich, >99%) and GMA (Aldrich, > 95 %) were used as supplied. Potassium persulfate (KPS) was used as an initiator for emulsion polymerization. A 100 mL two-necked round-bottom flask was... more
Synthesis of Photoresist Particles: MMA (Aldrich, >99%) and GMA (Aldrich, > 95 %) were used as supplied. Potassium persulfate (KPS) was used as an initiator for emulsion polymerization. A 100 mL two-necked round-bottom flask was filled with KPS dissolved in ...