Genomics and morphometrics reveal the adaptive evolution of pikas.

Pikas (Lagomorpha: Ochotonidae) are small mouse-like lagomorphs. To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang (Tibet) Plateau (QTP), we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information. We also sequenced the genome of 81 specimens, representing 27 putative pika species.

Temperature and Diet Acclimation Modify the Acute Thermal Performance of the Largest Extant Amphibian.

The Chinese giant salamander (), one of the largest extant amphibian species, has dramatically declined in the wild. As an ectotherm, it may be further threatened by climate change. Therefore, understanding the thermal physiology of this species should be the priority to formulate related conservation strategies.

The complete mitochondrial genome of (Passeriformes: Fringillidae).

The Himalayan Beautiful Rosefinch , belongs to the family Fringillidae, distributed in central Himalayas from India (Himachal Pradesh) to southwest China and Bhutan. The conservation status of this species is least concern (LC) in IUCN. In this study, the complete mitogenome of was determined.

The complete mitochondrial genome of (Passeriformes: Muscicapidae).

The Blue-fronted Redstart (Muscicapidae) belongs to the family Muscicapidae, distributed in central China, Qinghai-Tibet plateau and the Himalayas. The conservation status of this species is Least Concern (LC) in IUCN. In this study, the complete mitogenome of was determined.

Effects of aging on gene expression in blood of captive Tibetan macaques ( ) and comparisons with expression in humans.

Changes in gene expression occur as animals, including primates, age. Macaques have long been used as a model species for primate evolution and biomedical studies. Here, to study gene expression in Tibetan macaques (, TMs) and its differences to humans, we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs.

Blood transcriptome analysis reveals gene expression features of breast-feeding rhesus macaque ( ) infants.

During the breast-feeding period, infants undergo remarkable changes, including rapid physiological and developmental growth. However, little is known about gene expression features and sex-specific gene expression in breast-feeding infants. In this study, we sequenced 32 blood transcriptomes from 16 breast-feeding rhesus macaque ( ) infants and their lactating mothers.

Distribution patterns of microsatellites and development of its marker in different genomic regions of forest musk deer genome based on high throughput sequencing.

Forest musk deer (, FMD) is an endangered artiodactyl species, male FMD produce musk. We have sequenced the whole genome of FMD, completed the genomic assembly and annotation, and performed bioinformatic analyses. Our results showed that microsatellites (SSRs) displayed nonrandomly distribution in genomic regions, and SSR abundances were much higher in the intronic and intergenic regions compared to other genomic regions.

Reassessment of the taxonomic status of Craseomys and three controversial species of Myodes and Alticola (Rodentia: Arvicolinae).

The genera Myodes (red-backed voles) and Alticola (mountain voles) appear to be sister taxa based on morphological similarities, but molecular analyses fail to resolve them as monophyletic genera owing to the uncertain taxonomic status of Craseomys and Phaulomys. As a result of incomplete sampling of related specimens, ongoing controversies on the taxonomic positions of several generic and specific taxa necessitate further clarifications. Herein, we combined molecular, morphometric, and geometric morphometric approaches to analyze 217 specimens of 10 taxa of Myodes and Alticola systematically.

Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes.

As the first examination of distribution, guanine-cytosine (GC) pattern, and variation analysis of microsatellites (SSRs) in different genomic regions of six bovid species, SSRs displayed nonrandomly distribution in different regions. SSR abundances are much higher in the introns, transposable elements (TEs), and intergenic regions compared to the 3'-untranslated regions (3'UTRs), 5'UTRs and coding regions. Trinucleotide perfect SSRs (P-SSRs) were the most frequent in the coding regions, whereas, mononucleotide P-SSRs were the most in the introns, 3'UTRs, TEs, and intergenic regions.

Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data.

The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies.

Bioactivity-Guided Screening of Wound-Healing Active Constituents from American Cockroach (Periplaneta americana).

Ethanol extract (EE) from (PA) is the main ingredient of Kangfuxin, which is a popular traditional chinese medicine (TCM) and has long been used for the clinical treatment of burns, wounds and ulcers. We compared the wound-healing activities of three extracts of PA using cutaneous wound-healing in mice as the bioactivity model. These three extracts were EE, total polysaccharide and total protein.

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes.

As the first systematic examination of simple sequence repeats (SSRs) and guanine-cytosine (GC) distribution in intragenic and intergenic regions of ten primates, our study showed that SSRs and GC displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation. Our results suggest that the majority of SSRs are distributed in non-coding regions, such as the introns, TEs, and intergenic regions. In these primates, trinucleotide perfect (P) SSRs were the most abundant repeats type in the 5'UTRs and CDSs, whereas, mononucleotide P-SSRs were the most in the intron, 3'UTRs, TEs, and intergenic regions.

Comparison of microsatellite distribution in genomes of Centruroides exilicauda and Mesobuthus martensii.

In this study, we characterized the distribution of microsatellites in the genomes and genes of Centruroides exilicauda and Mesobuthus martensii, carried out Gene Ontology (GO) analysis and GO enrichment analysis of coding sequences (CDSs) with microsatellite (SSR). In addition, over-represented GO functions related to environmental interactions, development process and methylation were identified to develop functional markers and facilitate further analysis of microsatellite function in the genes of scorpions. Location analysis indicated that microsatellites were predominantly concentrated at both ends of genes.

Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species.

Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced genomes of the Bovidae. We analyzed and compared the number of SSRs, relative abundance, relative density, guanine-cytosine (GC) content and proportion of SSRs in six taxonomically different bovid species: Bos taurus, Bubalus bubalis, Bos mutus, Ovis aries, Capra hircus, and Pantholops hodgsonii.

The Complete Mitochondrial Genome of the Beet Webworm, Spoladea recurvalis (Lepidoptera: Crambidae) and Its Phylogenetic Implications.

The complete mitochondrial genome (mitogenome) of the beet webworm, Spoladea recurvalis has been sequenced. The circular genome is 15,273 bp in size, encoding 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes and containing a control region with gene order and orientation identical to that of other ditrysian lepidopteran mitogenomes. The nucleotide composition of the mitogenome shows a high A+T content of 80.

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system.

Background: The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda.

Dynamic change in spring habitat use by the brown eared pheasant (Crossptilon mantchuricum) in the Huanglong mountains, Yanan City, Shaanxi Province, China.

Characterization of foraging-site preferences of threatened and endangered species is a key component of effective habitat conservation. We studied foraging-site selection by the brown eared pheasant (Crossoptilon mantchuricum) in the Huanglongshan Nature Reserve, Yanan City, Shaanxi Province, China, from early February to end of May 2011. We identified feeding sites by locating tracks and scratches characteristic of the birds, and compared habitat characteristics at these sites to those at randomly selected sites across the study area.

Modeling, docking and dynamics simulations of a non-specific lipid transfer protein from Peganum harmala L.

Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure.

A systems biology analysis of autophagy in cancer therapy.

Autophagy, which degrades redundant or damaged cellular constituents, is intricately relevant to a variety of human diseases, most notably cancer. Autophagy exerts distinct effects on cancer initiation and progression, due to the intrinsic overlapping of autophagic and cancer signalling pathways. However, due to the complexity of cancer as a systemic disease, the fate of cancer cells is not decided by any one signalling pathway.

Ecological genetics of Chinese rhesus macaque in response to mountain building: all things are not equal.

Background: Pliocene uplifting of the Qinghai-Tibetan Plateau (QTP) and Quaternary glaciation may have impacted the Asian biota more than any other events. Little is documented with respect to how the geological and climatological events influenced speciation as well as spatial and genetic structuring, especially in vertebrate endotherms. Macaca mulatta is the most widely distributed non-human primate.

Taxonomic position of Eothenomys wardi (Arvicolinae: Cricetidae) based on morphological and molecular analyses with a detailed description of the species.

Ward's Red-backed Vole (Eothenomys wardi) is a rodent from the family Cricetidae. This endemic species occurs only in extreme northwestern Yunnan province, China in the Mekong and Salween river divide. It occupies steep cliffs at 2,800 to 4,250 m above sea level on the remote Qinghai-Tibetan plateau.

GenScalpel: an application for sequence retrieval and extraction from the GenBank flatfile.

GenScalpel is a program designed for the retrieval and extraction of specified sequences from large-scale sequence sets in NCBI GenBank flatfile format. This routine task in bioinformatics analysis is a pressing need for laboratory biologists. Another objective of application development is to respond to the new form of the NCBI Nucleotide Sequence Database, which was updated in November 2011.

Detection and characterization of antibiotic-resistance genes in Arcanobacterium pyogenes strains from abscesses of forest musk deer.

Arcanobacterium pyogenes is commonly isolated from ruminant animals as an opportunistic pathogen that co-infects with other bacteria, normally causing surface or internal abscesses. Twenty-eight strains of A. pyogenes isolated from forest musk deer suppurative samples were identified by their 16S rRNA gene sequences, and confirmed by amplification of the pyolysin-encoding gene (plo) in all isolates.

The reproductive performance of female Forest musk deer (Moschus berezovskii) in captivity.

Reproductive performance of 750 adult female Forest musk deer (FMD, Moschus berezovskii) was monitored (from 2005 to 2009) on two Forest musk deer farms in Sichuan province, China. The mean (± SEM) lengths of the estrous cycle, pregnancy, and consecutive fawning intervals were 17.5 ± 0.

[Behavior ethogram and PAE coding system of Cervus nippon sichuanicus].

A monthly 5-day periodic observation at 06:00-18:00 from March to November 2007 was conducted to record the behavioral processes, contents, and results, and the surrounding habitats of Sichuan sika deer (Cervus nippon sichuanicus) in Donglie, Chonger, and Reer villages of Tiebu Natural Reserve of Sichuan Province. The behavioral ethogram, vigilance behaviors ethogram and its PAE (posture, act, and environment) coding system of the Sichuan sika deer were established, which filled the gap of the PAE coding of ungulates vigilance behaviors. A total of 11 kinds of postures, 83 acts, and 136 behaviors were recorded and distinguished, with the relative frequency of each behavior in relation to gender, age, and season described.