Publications by authors named "Long-Hui Lin"

26 Publications

  • Page 1 of 1

Venom-gland transcriptomic, venomic, and antivenomic profiles of the spine-bellied sea snake (Hydrophis curtus) from the South China Sea.

BMC Genomics 2021 Jul 8;22(1):520. Epub 2021 Jul 8.

Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.

Background: A comprehensive evaluation of the -omic profiles of venom is important for understanding the potential function and evolution of snake venom. Here, we conducted an integrated multi-omics-analysis to unveil the venom-transcriptomic and venomic profiles in a same group of spine-bellied sea snakes (Hydrophis curtus) from the South China Sea, where the snake is a widespread species and might generate regionally-specific venom potentially harmful to human activities. The capacity of two heterologous antivenoms to immunocapture the H. curtus venom was determined for an in-depth evaluation of their rationality in treatment of H. curtus envenomation. In addition, a phylogenetic analysis by maximum likelihood was used to detect the adaptive molecular evolution of full-length toxin-coding unigenes.

Results: A total of 90,909,384 pairs of clean reads were generated via Illumina sequencing from a pooled cDNA library of six specimens, and yielding 148,121 unigenes through de novo assembly. Sequence similarity searching harvested 63,845 valid annotations, including 63,789 non-toxin-coding and 56 toxin-coding unigenes belonging to 22 protein families. Three protein families, three-finger toxins (3-FTx), phospholipase A (PLA), and cysteine-rich secretory protein, were detected in the venom proteome. 3-FTx (27.15% in the transcriptome/41.94% in the proteome) and PLA (59.71%/49.36%) were identified as the most abundant families in the venom-gland transcriptome and venom proteome. In addition, 24 unigenes from 11 protein families were shown to have experienced positive selection in their evolutionary history, whereas four were relatively conserved throughout evolution. Commercial Naja atra antivenom exhibited a stronger capacity than Bungarus multicinctus antivenom to immunocapture H. curtus venom components, especially short neurotoxins, with the capacity of both antivenoms to immunocapture short neurotoxins being weaker than that for PLAs.

Conclusions: Our study clarified the venom-gland transcriptomic and venomic profiles along with the within-group divergence of a H. curtus population from the South China Sea. Adaptive evolution of most venom components driven by natural selection appeared to occur rapidly during evolutionary history. Notably, the utility of commercial N. atra and B. multicinctus antivenoms against H. curtus toxins was not comprehensive; thus, the development of species-specific antivenom is urgently needed.
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http://dx.doi.org/10.1186/s12864-021-07824-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8268360PMC
July 2021

Complete mitochondrial genome of the Bingzhi's stout newt ( Chang, 1933) and its phylogenetic placement.

Mitochondrial DNA B Resour 2021 Feb 11;6(2):524-525. Epub 2021 Feb 11.

Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, China.

The Bingzhi's stout newt ( Chang, 1933) is distributed in mountainous areas of Zhejiang, China. The first complete mitochondrial genome (mitogenome) of was determined by next-generation sequencing. The size of the assembled mitogenome for was 16,293 bp, which included 13 protein coding genes, 22 tRNAs, 2 rRNAs, a non-coding region, and a control region (D-loop). The phylogenetic analysis using Bayesian Inference validated the taxonomic status of , showing the close relationship with the other two species from the genus .
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http://dx.doi.org/10.1080/23802359.2021.1872448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889176PMC
February 2021

The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota.

PeerJ 2020 29;8:e10271. Epub 2020 Oct 29.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.

Background: The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle () and the invasive red-eared slider turtle () are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected.

Methods: We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform.

Results: The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in , whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in . In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in than in , as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in than in , presumably suggesting an enhanced potential to colonize new habitats in the former species.
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http://dx.doi.org/10.7717/peerj.10271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603792PMC
October 2020

Captivity affects diversity, abundance, and functional pathways of gut microbiota in the northern grass lizard Takydromus septentrionalis.

Microbiologyopen 2020 09 14;9(9):e1095. Epub 2020 Jul 14.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.

Animals in captivity undergo a range of environmental changes from wild animals. An increasing number of studies show that captivity significantly affects the abundance and community structure of gut microbiota. The northern grass lizard (Takydromus septentrionalis) is an extensively studied lacertid lizard and has a distributional range covering the central and southeastern parts of China. Nonetheless, little is known about the gut microbiota of this species, which may play a certain role in nutrient and energy metabolism as well as immune homeostasis. Here, we examined the differences in the gut microbiota between two groups (wild and captive) of lizards through 16S rRNA sequencing using the Illumina HiSeq platform. The results demonstrated that the dominant microbial components in both groups consisted of Proteobacteria, Firmicutes, and Tenericutes. The two groups did not differ in the abundance of these three phyla. Citrobacter was the most dominant genus in wild lizards, while Morganella was the most dominant genus in captive lizards. Moreover, gene function predictions showed that genes at the KEGG pathway levels2 were more abundant in wild lizards than in captive lizards but, at the KEGG pathway levels1, the differences in gene abundances between wild and captive lizards were not significant. In summary, captivity exerted a significant impact on the gut microbial community structure and diversity in T. septentrionalis, and future work could usefully investigate the causes of these changes using a comparative approach.
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http://dx.doi.org/10.1002/mbo3.1095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520994PMC
September 2020

Shell-Isolated Nanoparticle-Enhanced Luminescence of Metallic Nanoclusters.

Anal Chem 2020 05 28;92(10):7146-7153. Epub 2020 Apr 28.

College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Energy, Department of Physics, Xiamen University, Xiamen 361005, China.

Metallic nanoclusters (NCs) have molecular-like structures and unique physical and chemical properties, making them an interesting new class of luminescent nanomaterials with various applications in chemical sensing, bioimaging, optoelectronics, light-emitting diodes (LEDs), etc. However, weak photoluminescence (PL) limits the practical applications of NCs. Herein, an effective and facile strategy of enhancing the PL of NCs was developed using Ag shell-isolated nanoparticle (Ag SHIN)-enhanced luminescence platforms with tuned SHINs shell thicknesses. 3D-FDTD theoretical calculations along with femtosecond transient absorption and fluorescence decay measurements were performed to elucidate the enhancement mechanisms. Maximum enhancements of up to 231-fold for the [AuAg(C≡CBu)] cluster and 126-fold for DNA-templated Ag NCs (DNA-Ag NCs) were achieved. We evidenced a novel and versatile method of achieving large PL enhancements with NCs with potential for practical biosensing applications for identifying target DNA in ultrasensitive surface analysis.
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http://dx.doi.org/10.1021/acs.analchem.0c00600DOI Listing
May 2020

The geographical diversification in varanid lizards: the role of mainland versus island in driving species evolution.

Curr Zool 2020 Apr 27;66(2):165-171. Epub 2020 Jan 27.

Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.

Monitor lizards (Varanidae) inhabit both the mainland and islands of all geological types and have diversified into an exceptionally wide range of body sizes, thus providing an ideal model for examining the role of mainland versus island in driving species evolution. Here we use phylogenetic comparative methods to examine whether a link exists between body size-driven diversification and body size-frequency distributions in varanid lizards and to test the hypothesis that island lizards differ from mainland species in evolutionary processes, body size, and life-history traits (offspring number and size). We predict that: 1) since body size drives rapid diversification in groups, a link exists between body size-driven diversification and body size-frequency distributions; 2) because of various environments on island, island species will have higher speciation, extinction, and dispersal rates, compared with mainland species; 3) as a response to stronger intraspecific competition, island species will maximize individual ability associated with body size to outcompete closely-related species, and island species will produce smaller clutches of larger eggs to increase offspring quality. Our results confirm that the joint effect of differential macroevolutionary rates shapes the species richness pattern of varanid lizards. There is a link between body size-driven diversification and body size-frequency distributions, and the speciation rate is maximized at medium body sizes. Island species will have higher speciation, equal extinction, and higher dispersal rates compared with mainland species. Smaller clutch size and larger hatchling in the island than in mainland species indicate that offspring quality is more valuable than offspring quantity for island varanids.
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http://dx.doi.org/10.1093/cz/zoaa002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7083093PMC
April 2020

Can snakes use yolk reserves to maximize body size at hatching?

Curr Zool 2019 Dec 27;65(6):627-631. Epub 2018 Dec 27.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.

We experimentally miniaturized freshly laid eggs of the Chinese cobra (Elapidae) by removing ∼10% and ∼20% of original yolk. We tested if yolk-reduced eggs would produce 1) normal-sized hatchlings with invariant yolk-free body mass (and thus invariant linear size) but dramatically reduced or even completely depleted residual yolk, 2) smaller hatchlings with normal-sized residual yolk but reduced yolk-free body mass, or 3) smaller hatchlings of which both yolk-free body mass and residual yolk are proportionally reduced. Yolk quantity affected hatchling linear size (both snout-vent length and tail length) and body mass. However, changes in yolk quantity did not affect incubation length or any hatchling trait examined after accounting for egg mass at laying (for control and sham-manipulated eggs) or after yolk removal (for manipulated eggs). Specifically, yolk-reduced eggs produced hatchlings of which all major components (carcass, residual yolk, and fat bodies) were scaled down proportionally. We show that snakes cannot use yolk reserves to maximize their body size at hatching. Furthermore, our data also suggest that the partitioning of yolk in embryonic snakes is species-specific.
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http://dx.doi.org/10.1093/cz/zoy098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6911849PMC
December 2019

Background-Free Quantitative Surface Enhanced Raman Spectroscopy Analysis Using Core-Shell Nanoparticles with an Inherent Internal Standard.

Anal Chem 2019 Nov 14. Epub 2019 Nov 14.

College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Energy, College of Materials , Xiamen University , Xiamen 361005 , China.

Surface enhanced Raman spectroscopy (SERS) is an ultrasensitive label-free analytical technique that can provide unique chemical and structural fingerprint information. However, gaining reliable quantitative analysis with SERS remains a huge challenge because of poor reproducibility and the instability of nanostructured SERS active surfaces. Herein, an effective strategy of coating Au nanoparticles (NPs) with ultrathin and uniform Prussian blue (PB) shell ([email protected] NPs) was developed for quantitative detection of dopamine (DA) concentrations in blood serum and crystal violet (CV) contaminants in lake water. The only intense PB Raman signal at 2155 cm served as an ideal and interference-free internal standard (IS) for correcting fluctuations in the Raman intensities of analytes. Also, the stability of [email protected] NPs was investigated, exhibiting good functionality in strong acid solutions and thermal stability at 100 °C. This work demonstrates a convenient and fast quantitative SERS technique for detecting analyte concentrations in complex systems and has a great number of potential applications for use in analytical chemistry.
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http://dx.doi.org/10.1021/acs.analchem.9b03703DOI Listing
November 2019

Age-related reproduction of female Mongolian racerunners (Eremias argus; Lacertidae): Evidence of reproductive senescence.

J Exp Zool A Ecol Integr Physiol 2019 06 4;331(5):290-298. Epub 2019 Apr 4.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.

The reproductive maturation hypothesis, the terminal investment hypothesis, and the senescence hypothesis are the most extensively evaluated hypotheses proposed to explain age-related patterns of reproduction in iteroparous organisms. Here, we evaluated these hypotheses for the Mongolian racerunner (Eremias argus), a short-lived lacertid lizard, by comparing reproductive traits between females that completed reproductive cycles under the same laboratory conditions in two consecutive years (2008 and 2009). Reproductive females gained linear size (snout-vent length) not only as they got 1 year older but also during the breeding season. Larger females generally laid eggs earlier and invested more in reproduction than did smaller ones. Females switched from laying smaller eggs in the first clutch to larger eggs in the subsequent clutches but kept clutch size and postpartum body mass constant between successive clutches in a breeding season and between years. Females that laid more clutches or eggs in 2008 did not lay fewer clutches or eggs in 2009. Of the traits examined, only clutch frequency, annual fecundity, and annual reproductive output were susceptible to ageing. Specifically, the clutch frequency was reduced by 1.1 clutches, annual fecundity by 3.1 eggs and annual reproductive output by 1.0 g in 2009 compared with 2008. Our results suggest that the reproductive maturation hypothesis better explains patterns of reproduction in young or prime-aged females of E. argus, whereas the senescence hypothesis better explains reproductive patterns in old females. The terminal investment hypothesis does not apply to any trait examined because no trait value was maximized in old females.
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http://dx.doi.org/10.1002/jez.2264DOI Listing
June 2019

Global, regional, and cladistic patterns of variation in climatic niche breadths in terrestrial elapid snakes.

Curr Zool 2019 Feb 6;65(1):1-9. Epub 2018 Apr 6.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.

We obtained geo-referenced occurrence and climatic data from individual localities for 59 species of terrestrial elapid snakes, used phylogenetic generalized least squares regression to investigate spatial and cladistic patterns of variation in climatic niche breadths, and compared patterns within and across regions and clades to see if they parallel or differ from each other. Specifically, we test (1) whether a species' climatic niche breadth on a given niche axis relates to its position along that axis, and to its climatic niche breadth on another niche axis, and (2) whether variation in niche breadths among species is explained by within-locality variation in climatic conditions or by among-locality variation. We found that: (1) there is an overall global pattern, and patterns in individual regions or clades generally parallel each other and global patterns; (2) species in warmer environments have narrower temperature niche breadths (TNBs); (3) precipitation niche breadth (PNB) and position are positively related; (4) TNB and PNB are not related; and (5) within-locality variation in climatic conditions explains most variation in TNBs, whereas among-locality variation explains most variation in PNBs. Our results are consistent with those reported for lizards of the families Phrynosomatidae and Varanidae, confirm the importance of within-locality niche breadth to species niche breadth, and show a more important role of among-locality niche breadth in affecting species niche breadth in terrestrial elapids than in lizards.
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http://dx.doi.org/10.1093/cz/zoy026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347059PMC
February 2019

Shell-Isolated Nanoparticle-Enhanced Phosphorescence.

Anal Chem 2018 09 5;90(18):10837-10842. Epub 2018 Sep 5.

MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Department of Physics, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China.

The emerging field of plasmonics has promoted applications of optical technology, especially in plasmon-enhanced spectroscopy (PES). However, in plasmon-enhanced fluorescence (PEF), "metal loss" could significantly quench the fluorescence during the process, which dramatically limits its applications in analysis and high-resolution imaging. In this report, silver core silica shell-isolated nanoparticles ([email protected] NPs or SHINs) with a tunable thickness of shell are used to investigate the interactions between NPs and emitters by constructing coupling and noncoupling modes. The plasmonic coupling mode between [email protected] NPs and Ag film reveals an exceeding integrating spectral intensity enhancement of 330 and about 124 times that of the radiative emission rate acceleration for shell-isolated nanoparticle enhanced phosphorescence (SHINEP). The experimental findings are supported by theoretical calculations using the finite-element method (FEM). Hence, the SHINEP may provide a novel approach for understanding the interaction of plasmon and phosphorescence, and it holds great potential in surface detection analysis and singlet-oxygen-based clinical therapy.
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http://dx.doi.org/10.1021/acs.analchem.8b02109DOI Listing
September 2018

Evolutionary transitions in body plan and reproductive mode alter maintenance metabolism in squamates.

BMC Evol Biol 2018 04 3;18(1):45. Epub 2018 Apr 3.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.

Background: Energy (resources) acquired by animals should be allocated towards competing demands, maintenance, growth, reproduction and fat storage. Reproduction has the second lowest priority in energy allocation and only is allowed after meeting the energetic demands for maintenance and growth. This hierarchical allocation of energy suggests the hypothesis that species or taxa with high maintenance costs would be less likely to invest more energy in reproduction or to evolve an energetically more expensive mode of reproduction. Here, we used data on standard metabolic rate so far reported for 196 species of squamates to test this hypothesis.

Results: We found that maintenance costs were lower in snakes than in lizards, and that the costs were lower in viviparous species than in oviparous species. As snakes generally invest more energy per reproductive episode than lizards, and viviparity is an energetically more expensive mode of reproduction than oviparity, our results are consistent with the hypothesis tested.

Conclusion: The transition from lizard-like to snake-like body form and the transition from oviparity to viviparity are major evolutionary transitions in vertebrates, which likely alter many aspects of biology of the organisms involved. Our study is the first to demonstrate that evolutionary transitions in body plan and reproductive mode alter maintenance metabolism in squamates.
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http://dx.doi.org/10.1186/s12862-018-1166-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883405PMC
April 2018

The complete mitochondrial genome of Acanthosaura lepidogaster (Squamata: Agamidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2017 03 28;28(2):182-184. Epub 2015 Dec 28.

a Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, School of Life Sciences , Hangzhou Normal University , Hangzhou , Zhejiang , PR China.

In this paper, we report the complete mitochondrial genome of Acanthosaura lepidogaster (Squamata, Agamidae), which is a circular molecule of 16 899 bp in size and consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The overall base composition is as follows: T (22.8%), C (30.5%), A (32.3%), and G (14.4%). We constructed a phylogeny that included for 10 species of Leiolepidinae lizards and one outgroup Leiocephalus personatus constructed in BEAST, based on 15 mitochondrial genes (12S, 16S, ND1, ND2, COI, COII, ATP8, ATP6, COIII, ND3, ND4L, ND4, ND5, ND6, and cytochrome b). The topology of the phylogenetic tree is broadly similar to that mentioned by Pyron et al.
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http://dx.doi.org/10.3109/19401736.2015.1115500DOI Listing
March 2017

The complete mitochondrial genome of Eremias przewalskii (Squamata: Lacertidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 05 16;27(3):1918-9. Epub 2014 Oct 16.

a Hangzhou Key Laboratory of Animal Adaptation and Evolution , School of Life Sciences, Hangzhou Normal University , Hangzhou , Zhejiang , P.R. China and.

In this paper, the complete mitochondrial genome of Eremias przewalskii (Squamata: Lacertidae) is reported, which is a circular molecule of 18,225 bp in size. The base composition of mtDNA is as follows: 30.3% A, 27.9% T, 27.9% C and 13.9% G. The genome consists of 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNA genes and one putative control region.
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http://dx.doi.org/10.3109/19401736.2014.971286DOI Listing
May 2016

The nearly complete mitochondrial genome of the rapid racerunner Eremias velox (Squamata: Lacertidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 05 29;27(3):1781-2. Epub 2014 Sep 29.

a Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University , Nanjing , Jiangsu , P.R. China and.

We report the nearly complete mitochondrial genome of the rapid racerunner, Eremias velox (Lacertidae), which is a circular molecule of 18,033 bp in size and consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a partial control region (2627 bp). The A + T content of overall base composition of H-strand is 58.0% (T: 27.7%, C: 28.3%, A: 30.3%, G: 13.7%). Some short microsatellite-like repeat regions (polyA and polyT) are scattered in the control region. All the results provide powerful data for further study of the molecular systematics, species identification and conservation genetics in this species and its congenators.
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http://dx.doi.org/10.3109/19401736.2014.963810DOI Listing
May 2016

The complete mitochondrial genome of Eremias multiocellata (Squamata: Lacertidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 05 11;27(3):1654-5. Epub 2014 Sep 11.

b Jiangsu Key Laboratory for Biodiversity and Biotechnology , College of Life Sciences, Nanjing Normal University , Nanjing , Jiangsu , P.R. China.

In this paper, the complete mitochondrial genome of Eremias multiocellata (Squamata: Lacertidae) is reported, which is a circular molecule of 19,385 bp in size. The nucleotides composition are 31.2% A, 28.9% T, 27.1% C and 13.4% G. The genome consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNA genes and 1 putative control region.
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http://dx.doi.org/10.3109/19401736.2014.958714DOI Listing
May 2016

The phylogeographical pattern and conservation of the Chinese cobra (Naja atra) across its range based on mitochondrial control region sequences.

PLoS One 2014 3;9(9):e106944. Epub 2014 Sep 3.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.

The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two "star" clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106944PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4153689PMC
November 2015

The complete mitochondrial genome of Eremias vermiculata (Squamata: Lacertidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 27;27(2):1447-8. Epub 2014 Aug 27.

b Jiangsu Key Laboratory for Biodiversity and Biotechnology , College of Life Sciences, Nanjing Normal University , Nanjing , Jiangsu , P.R. China.

In this paper, we report the complete mitochondrial genome of Eremias vermiculata (Squamata: Lacertidae), which is a circular molecule of 19,914 bp in size and consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 putative control region. The A + T content of overall base of the composition of H-strand is 59.8% (T: 28.9%, C: 27.2%, A: 30.9%, G: 13.0%). All of the results provide powerful data to further study of the molecular systematics, species identification and conservation genetics.
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http://dx.doi.org/10.3109/19401736.2014.953086DOI Listing
October 2016

The complete mitochondrial genome of Leiolepis reevesii (Sauria, Agamidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 8;27(1):541-2. Epub 2014 Apr 8.

c Jiangsu Key Laboratory for Biodiversity and Biotechnology , College of Life Sciences, Nanjing Normal University , Nanjing , Jiangsu , China.

In this paper, we report the complete mitochondrial genome of Leiolepis reevesii (Sauria, Agamidae), which is a circular molecule of 16,908 bp in size and consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The A+T content of overall base composition of H-strand is 59.8% (T: 25.1%, C: 27.5%, A: 34.7%, G: 12.7%). Some short microsatellite-like repeat regions (polyA and polyT) are scattered in the control region. All the results provide powerful data to further study of the molecular systematics, species identification and conservation genetics.
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http://dx.doi.org/10.3109/19401736.2014.905848DOI Listing
September 2016

Proteomic and biochemical analyses of short-tailed pit viper (Gloydius brevicaudus) venom: age-related variation and composition-activity correlation.

J Proteomics 2014 Jun 31;105:307-22. Epub 2014 Jan 31.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, Jiangsu, China. Electronic address:

Unlabelled: We conducted an in-depth analysis of the proteomic and biochemical profiles of the venom of neonate and adult short-tailed pit vipers (Gloydius brevicaudus). Identified proteins were assigned to a few main toxin families. Disintegrin, phospholipase A2 (PLA2), serine proteinase, cysteine-rich secretory protein, C-type lectin-like protein, l-amino acid oxidase and snake venom metalloproteinase (SVMP) were detected in both venoms, while 5'-nucleotidase was detected only in the adult venom. SVMP was the predominant protein family in both venoms (neonate: 65.7%; adult: 64.4%), followed by PLA2 (neonate: 13.4%; adult: 25.0%). Antivenomic analysis revealed that commercial G. brevicaudus antivenom almost neutralized the chromatographic peaks with medium and high molecular masses in both venoms, but did not completely recognize peaks with low molecular mass. Toxicological and enzymatic activities show remarkable age-related variation in G. brevicaudus venom, probably resulting from variation in venom composition. Our data demonstrate age-related variation across venomics, antivenomics and biochemical profiles of G. brevicaudus venom, and have implications for the management of G. brevicaudus bites, including improving antivenom preparation by combining both venoms.

Biological Significance: This study investigates the composition and biochemical activity of neonate and adult Gloydius brevicaudus venoms. We found remarkable age-related variation in venom biological activity, likely the result of variation in venom composition. Antivenomics analysis was used to explore difference in neonate and adult G. brevicaudus venoms. Our findings have implications for the diagnosis and clinical management of G. brevicaudus bites, and the design of venom mixtures that will increase the efficacy of commercial antivenom. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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http://dx.doi.org/10.1016/j.jprot.2014.01.019DOI Listing
June 2014

Genetic structure and demographic history should inform conservation: Chinese cobras currently treated as homogenous show population divergence.

PLoS One 2012 27;7(4):e36334. Epub 2012 Apr 27.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.

An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a "star" cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0036334PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338645PMC
September 2012

Isolation and characterization of microsatellite loci in the Chinese Cobra Naja atra (Elapidae).

Int J Mol Sci 2011 7;12(7):4435-40. Epub 2011 Jul 7.

Hangzhou Key Laboratory for Animal Adaptation and Evolution, School of Life Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China; E-Mail:

We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong'an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4-12 alleles per locus) and heterozygosity (Ho ranged from 0.213-0.854 and He ranged from 0.301-0.838). Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001) proportion (16.0%) of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low N(m) (1.31) value in the two populations from mainland China. Thus, the Yong'an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs). The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.
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http://dx.doi.org/10.3390/ijms12074435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155360PMC
January 2015

Phylogeography and population structure of the Reevese's Butterfly Lizard (Leiolepis reevesii) inferred from mitochondrial DNA sequences.

Mol Phylogenet Evol 2010 Aug 28;56(2):601-7. Epub 2010 Apr 28.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, Jiangsu, China.

Butterfly lizards of the genus Leiolepis (Agamidae) are widely distributed in coastal regions of Southeast Asia and South China, with the Reevese's Butterfly Lizard Leiolepis reevesii having a most northerly distribution that ranges from Vietnam to South China. To assess the genetic diversity within L. reevesii, and its population structure and evolutionary history, we sequenced 1004 bp of cytochrome b for 448 individuals collected from 28 localities covering almost the whole range of the lizard. One hundred and forty variable sites were observed, and 93 haplotypes were defined. We identified three genetically distinct clades, of which Clade A includes haplotypes mainly from southeastern Hainan, Clade B from Guangdong and northern Hainan, and Clade C from Vietnam and the other localities of China. Clade A was well distinguished and divergent from the other two. The Wuzhishan and Yinggeling mountain ranges were important barriers limiting gene exchange between populations on the both sides of the mountain series, whereas the Gulf of Tonkin and the Qiongzhou Strait were not. One plausible scenario to explain our genetic data is a historical dispersion of L. reevesii as proceeding from Vietnam to Hainan, followed by a second wave of dispersal from Hainan to Guangdong and Guangxi. Another equally plausible scenario is a historically widespread population that has been structured by vicariant factors such as the mountains in Hainan and sea level fluctuations.
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http://dx.doi.org/10.1016/j.ympev.2010.04.032DOI Listing
August 2010

Conservation genetics of the Chinese cobra (Naja atra) investigated with mitochondrial DNA sequences.

Zoolog Sci 2008 Sep;25(9):888-93

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, Jiangsu, China.

We collected Chinese cobras (Naja atra) from one island (Dinghai) and four mainland (Huangshan, Lishui, Quanzhou, and Baise) populations in southeastern China, and used sequence data derived from the ND2 (1032 bp) and cytochrome b (1117 bp) genes and molecular variance estimates to investigate the population genetic structure of the species. Our sequence data show that: (1) the three eastern (Dinghai, Huangshan, and Lishui) populations are genetically segregated from the two southern (Quanzhou and Baise) populations; (2) the Quanzhou and Baise populations consist of two well-defined subclades, suggesting that the two populations have been well differentiated; (3) N. atra from the Huangshan population do not differ from those from the Lishui population, and lineage sorting in the northeastern part of the cobra's distributional range has not yet been completed because of the young age of Zhoushan Islands. The three eastern populations, the Quanzhou population, and the Baise population should be regarded as different management units (MUs). For these MUs, we suggest that in-situ protection measures should be taken because of their genetic uniqueness. Re-introductions or translocations are required to protect or re-establish natural populations of N. atra , but great care should be taken to enhance or retain local genetic variation.
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http://dx.doi.org/10.2108/zsj.25.888DOI Listing
September 2008

Nonlinear continuum of egg size-number trade-offs in a snake: is egg-size variation fitness related?

Oecologia 2009 Apr 9;159(4):689-96. Epub 2009 Jan 9.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210046, People's Republic of China.

The relationship between offspring size and offspring number is crucial to life history evolution. To examine how these two life history variables are coupled and whether an altered balance between them will result in changes in maternal fitness, we manipulated clutch size of the Chinese cobra (Naja atra) by using the techniques of hormonal manipulation and follicle ablation. Females receiving exogenous follicle-stimulating hormone produced more but smaller eggs, and females undergoing follicle ablation produced fewer but larger eggs. Neither body size (body mass and snout-vent length) at hatching nor egg mass at oviposition had a role in determining hatchling survival and growth. Female hatchlings were more likely to die in early post-hatching days and grew more slowly than male hatchlings. Our data show that: (1) there is a nonlinear continuum of egg size-number trade-offs in N. atra within which there is a single inflexion where the rate at which egg size decreases with increasing clutch size, or clutch size increases with decreasing egg size, is maximized; (2) there is a fixed upper limit to egg size for a given-sized female, and the limit is not determined by her body volume; (3) egg size has no role in determining hatchling survival and growth; and (4) the extent to which females may enjoy reproductive benefits in a given reproductive episode depends on how well egg size and egg number are balanced.
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http://dx.doi.org/10.1007/s00442-008-1252-2DOI Listing
April 2009

Experimentally reducing clutch size reveals a fixed upper limit to egg size in snakes, evidence from the king ratsnake, Elaphe carinata.

Comp Biochem Physiol A Mol Integr Physiol 2006 Aug 28;144(4):474-8. Epub 2006 Apr 28.

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210097, Jiangsu, PR China.

Snakes are free of the pelvic girdle's constraint on maximum offspring size, and therefore present an opportunity to investigate the upper limit to offspring size without the limit imposed by the pelvic girdle dimension. We used the king ratsnake (Elaphe carinata) as a model animal to examine whether follicle ablation may result in enlargement of egg size in snakes and, if so, whether there is a fixed upper limit to egg size. Females with small sized yolking follicles were assigned to three manipulated, one sham-manipulated and one control treatments in mid-May, and two, four or six yolking follicles in the manipulated females were then ablated. Females undergoing follicle ablation produced fewer, but larger as well as more elongated, eggs than control females primarily by increasing egg length. This finding suggests that follicle ablation may result in enlargement of egg size in E. carinata. Mean values for egg width remained almost unchanged across the five treatments, suggesting that egg width is more likely to be shaped by the morphological feature of the oviduct. Clutch mass dropped dramatically in four- and six-follicle ablated females. The function describing the relationship between size and number of eggs reveals that egg size increases with decreasing clutch size at an ever-decreasing rate, with the tangent slope of the function for the six-follicle ablation treatment being -0.04. According to the function describing instantaneous variation in tangent slope, the maximum value of tangent slope should converge towards zero. This result provides evidence that there is a fixed upper limit to egg size in E. carinata.
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http://dx.doi.org/10.1016/j.cbpa.2006.04.013DOI Listing
August 2006
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