Table1_Computational approaches for predicting variant impact: An overview from resources, principles to applications.docx

One objective of human genetics is to unveil the variants that contribute to human diseases. With the rapid development and wide use of next-generation sequencing (NGS), massive genomic sequence data have been created, making personal genetic information available. Conventional experimental evidence is critical in establishing the relationship between sequence variants and phenotype but with low efficiency. Due to the lack of comprehensive databases and resources which present clinical and experimental evidence on genotype-phenotype relationship, as well as accumulating variants found from NGS, different computational tools that can predict the impact of the variants on phenotype have been greatly developed to bridge the gap. In this review, we present a brief introduction and discussion about the computational approaches for variant impact prediction. Following an innovative manner, we mainly focus on approaches for non-synonymous variants (nsSNVs) impact prediction and categorize them into six classes. Their underlying rationale and constraints, together with the concerns and remedies raised from comparative studies are discussed. We also present how the predictive approaches employed in different research. Although diverse constraints exist, the computational predictive approaches are indispensable in exploring genotype-phenotype relationship.</p

Comparative Transcriptome Analysis of the Accessory Sex Gland and Testis from the Chinese Mitten Crab (<em>Eriocheir sinensis</em>)

<div><p>The accessory sex gland (ASG) is an important component of the male reproductive system, which functions to enhance the fertility of spermatozoa during male reproduction. Certain proteins secreted by the ASG are known to bind to the spermatozoa membrane and affect its function. The ASG gene expression profile in Chinese mitten crab (<em>Eriocheir sinensis</em>) has not been extensively studied, and limited genetic research has been conducted on this species. The advent of high-throughput sequencing technologies enables the generation of genomic resources within a short period of time and at minimal cost. In the present study, we performed <em>de novo</em> transcriptome sequencing to produce a comprehensive transcript dataset for the ASG of <em>E. sinensis</em> using Illumina sequencing technology. This analysis yielded a total of 33,221,284 sequencing reads, including 2.6 Gb of total nucleotides. Reads were assembled into 85,913 contigs (average 218 bp), or 58,567 scaffold sequences (average 292 bp), that identified 37,955 unigenes (average 385 bp). We assembled all unigenes and compared them with the published testis transcriptome from <em>E. sinensis</em>. In order to identify which genes may be involved in ASG function, as it pertains to modification of spermatozoa, we compared the ASG and testis transcriptome of <em>E. sinensis</em>. Our analysis identified specific genes with both higher and lower tissue expression levels in the two tissues, and the functions of these genes were analyzed to elucidate their potential roles during maturation of spermatozoa. Availability of detailed transcriptome data from ASG and testis in <em>E. sinensis</em> can assist our understanding of the molecular mechanisms involved with spermatozoa conservation, transport, maturation and capacitation and potentially acrosome activation.</p> </div

COG classification of all unigenes from ASG and testis in <i>E. sinensis</i>.

<p>COG classification of all unigenes from ASG and testis in <i>E. sinensis</i>.</p

Summary of transcriptomes from the accessory sex gland (ASG) and testis (T) in <i>E. sinensis</i>.

<p>Summary of transcriptomes from the accessory sex gland (ASG) and testis (T) in <i>E. sinensis</i>.</p

Assembly quality statistics of the ASG, testis and all unigenes from Illumina sequencing.

<p>The length distribution of <i>de novo</i> assemblies of unigenes are shown (X-axis indicates the sequence size (nt), and the Y-axis indicates the number of assembled unigenes).</p

All unigenes KEGG metabolic pathway analysis in <i>E. sinensis</i>.

<p>All unigenes KEGG metabolic pathway analysis in <i>E. sinensis</i>.</p

GO classification of all unigenes from ASG and testis in <i>E. sinensis</i>.

<p>GO classification of all unigenes from ASG and testis in <i>E. sinensis</i>.</p

Vocal repertoire of adult captive red pandas (Ailurus fulgens)

Vocal signals are a common communication tool used to recognize different individuals, advertise fertile phases or discriminate amongst potential mates. Therefore, a thorough understanding of vocal repertoires forms the basis for investigating the role of acoustic signaling in the sexual and social behavior of any animal. Red pandas (<i>Ailurus fulgens</i>) are classified as a vulnerable species and have declined by as much as 40% over the past 50 years in China. Adult red pandas are known to call frequently during mating and aggressive encounters; however, no quantitative description of their vocalizations has been attempted. Here, the vocal repertoire of captive red pandas was investigated. Acoustical and statistical analyses indicated seven vocalization types during the breeding season: “growl”, “bark”, “squeal”, “bleat”, “hoot”, “grunt” and “twitter”; the spectrogram for each vocalization type was extracted. The type of vocalizations produced varied with behavioral state and implies different functional contexts. Future studies are needed to uncover the functions of red panda vocalizations in individual recognition, sexual selection and social interaction

External Exposure to Short- and Medium-Chain Chlorinated Paraffins for the General Population in Beijing, China

Chlorinated paraffins (CPs) are a class of compounds that are currently produced and used in large amounts in commercial products worldwide. In this study, food, indoor air, indoor dust, and drinking water samples were collected to evaluate the external exposure levels of CPs and possible pathway for the general population in Beijing, China. Short chain CPs (SCCPs) and medium chain CPs (MCCPs) in 199 samples were analyzed using a gas chromatography tandem time-of-flight high-resolution mass spectrometry (GC-TOF-HR-MS) method. High levels of CPs were observed in the indoor environment from residential houses, offices, and student dormitories. The geometric mean concentrations (GM) of ∑SCCPs and ∑MCCPs in indoor dust were 92 μg g^–1 and 82 μg g^–1, respectively, while in indoor air, the concentrations were 80 ng m^–3 and 3.4 ng m^–3, respectively. The GM of ∑SCCPs and ∑MCCPs in the diet were 83 ng g^–1 dry weight (dw) and 56 ng g^–1 dw, respectively. The most important external exposure routes to CPs to the general populations in Beijing were food intake and indoor dust ingestion. Indoor dust and indoor air posed higher risks for toddlers and infants than for adults

The Complete Mitochondrial Genome of <i>Gossypium hirsutum</i> and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

<div><p>Background</p><p>Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (<i>Gossypium hirsutum</i> L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes.</p><p>Methodology/Principal Findings</p><p>We utilized 454 technology for sequencing and combined with Fosmid library of the <i>Gossypium hirsutum</i> mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on <i>Cycas taitungensis</i> and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of <i>G. hirsutum</i> was obtained. The completed <i>G.hirsutum</i> mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes.</p><p>Conclusion</p><p>The <i>G. hirsutum</i> mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.</p></div