印刷柔性塑料芯片的病毒载量的测量通过血浆和唾液中病毒的定量检测

We report a biosensing platform for viral load measurement through electrical sensing of viruses on a flexible plastic microchip with printed electrodes. Point-of-care (POC) viral load measurement is of paramount importance with significant impact on a broad range of applications, including infectious disease diagnostics and treatment monitoring specifically in resource-constrained settings. Here, we present a broadly applicable and inexpensive biosensing technology for accurate quantification of bioagents, including viruses in biological samples, such as plasma and artificial saliva, at clinically relevant concentrations. Our microchip fabrication is simple and mass-producible as we print microelectrodes on flexible plastic substrates using conductive inks. We evaluated the microchip technology by detecting and quantifying multiple Human Immunodeficiency Virus (HIV) subtypes (A, B, C, D, E, G, and panel), Epstein-Barr Virus (EBV), and Kaposi’s Sarcoma-associated Herpes Virus (KSHV) in a fingerprick volume (50 µL) of PBS, plasma, and artificial saliva samples for a broad range of virus concentrations between 102 copies/mL and 107 copies/mL. We have also evaluated the microchip platform with discarded, de-identified HIV-infected patient samples by comparing our microchip viral load measurement results with reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) as the gold standard method using Bland-Altman Analysis.

• http://feeds.nature.com/~r/srep/rss/current/~3/S3OmPcbehF8/srep09919

[详细]

有机质的来源和退化的元阳梯田农业土壤的分子生物标志物的发现

Three soils with different tillage activities were collected and compared for their organic matter sources and degradation. Two soils (TD and TP) with human activities showed more diverse of chemicals in both free lipids and CuO oxidation products than the one (NS) without human activities. Branched alkanoic acids only accounted for less than 5% of lipids, indicating limited microbial inputs in all three investigated soils. The degradation of lignin in NS and TD was relatively higher than TP, probably because of the chemical degradation, most likely UV light-involved photodegradation. Lignin parameters obtained from CuO oxidation products confirmed that woody gymnosperm tissue (such as pine trees) may be the main source for NS, while angiosperm tissues from vascular plant may be the predominant source for the lignins in TD and TP. Analysis of BPCAs illustrated that BC in NS may be mainly originated from soot or other fossil carbon sources, whereas BC in TD and TP may be produced during corn stalk and straw burning. BC was involved in mineral interactions for TD and TP. The dynamics of organic matter needs to be extensively examined for their nonideal interactions with contaminants.

• http://feeds.nature.com/~r/srep/rss/current/~3/lJMS_aSU9RA/srep11074

[详细]

在rRNA转录逐渐减少触发p53的乙酰化和细胞凋亡通过mybbp1a

The nucleolus, whose primary function is ribosome biogenesis, plays an essential role in p53 activation. Ribosome biogenesis is inhibited in response to cellular stress and several nucleolar proteins translocate from the nucleolus to the nucleoplasm, where they activate p53. In this study, we analysed precisely how impaired ribosome biogenesis regulates the activation of p53 by depleting nucleolar factors involved in rRNA transcription or rRNA processing. Nucleolar RNA content decreased when rRNA transcription was inhibited. In parallel with the reduced levels of nucleolar RNA content, the nucleolar protein Myb-binding protein 1 A (MYBBP1A) translocated to the nucleoplasm and increased p53 acetylation. The acetylated p53 enhanced p21 and BAX expression and induced apoptosis. In contrast, when rRNA processing was inhibited, MYBBP1A remained in the nucleolus and nonacetylated p53 accumulated, causing cell cycle arrest at the G1 phase by inducing p21 but not BAX. We propose that the nucleolus functions as a stress sensor to modulate p53 protein levels and its acetylation status, determining cell fate between cell cycle arrest and apoptosis by regulating MYBBP1A translocation.

• http://feeds.nature.com/~r/srep/rss/current/~3/9amZBFZitKM/srep10854

[详细]

全球的时空格局中流感大流行后时期

We study the global spatio-temporal patterns of influenza dynamics. This is achieved by analysing and modelling weekly laboratory confirmed cases of influenza A and B from 138 countries between January 2006 and January 2015. The data were obtained from FluNet, the surveillance network compiled by the the World Health Organization. We report a pattern of skip-and-resurgence behavior between the years 2011 and 2013 for influenza H1N1pdm, the strain responsible for the 2009 pandemic, in Europe and Eastern Asia. In particular, the expected H1N1pdm epidemic outbreak in 2011/12 failed to occur (or “skipped”) in many countries across the globe, although an outbreak occurred in the following year. We also report a pattern of well-synchronized wave of H1N1pdm in early 2011 in the Northern Hemisphere countries, and a pattern of replacement of strain H1N1pre by H1N1pdm between the 2009 and 2012 influenza seasons. Using both a statistical and a mechanistic mathematical model, and through fitting the data of 108 countries, we discuss the mechanisms that are likely to generate these events taking into account the role of multi-strain dynamics. A basic understanding of these patterns has important public health implications and scientific significance.

• http://feeds.nature.com/~r/srep/rss/current/~3/36hZJ3RZGJY/srep11013

[详细]

中黑盲蝽（半翅目：蝽科）表征不同发育阶段转录

Adelphocoris suturalis is one of the most serious pest insects of Bt cotton in China, however its molecular genetics, biochemistry and physiology are poorly understood. We used high throughput sequencing platform to perform de novo transcriptome assembly and gene expression analyses across different developmental stages (eggs, 2nd and 5th instar nymphs, female and male adults). We obtained 20 GB of clean data and revealed 88,614 unigenes, including 23,830 clusters and 64,784 singletons. These unigene sequences were annotated and classified by Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases. A large number of differentially expressed genes were discovered through pairwise comparisons between these developmental stages. Gene expression profiles were dramatically different between life stage transitions, with some of these most differentially expressed genes being associated with sex difference, metabolism and development. Quantitative real-time PCR results confirm deep-sequencing findings based on relative expression levels of nine randomly selected genes. Furthermore, over 791,390 single nucleotide polymorphisms and 2,682 potential simple sequence repeats were identified. Our study provided comprehensive transcriptional gene expression information for A. suturalis that will form the basis to better understanding of development pathways, hormone biosynthesis, sex differences and wing formation in mirid bugs.

• http://feeds.nature.com/~r/srep/rss/current/~3/7GrAMVtLXd8/srep11042

[详细]

R2R3-MYB蛋白在真核生物的进化史：为50亚科的分类和拓展的新见解

R2R3-MYB proteins (2R-MYBs) are one of the main transcription factor families in higher plants. Since the evolutionary history of this gene family across the eukaryotic kingdom remains unknown, we performed a comparative analysis of 2R-MYBs from 50 major eukaryotic lineages, with particular emphasis on land plants. A total of 1548 candidates were identified among diverse taxonomic groups, which allowed for an updated classification of 73 highly conserved subfamilies, including many newly identified subfamilies. Our results revealed that the protein architectures, intron patterns, and sequence characteristics were remarkably conserved in each subfamily. At least four subfamilies were derived from early land plants, 10 evolved from spermatophytes, and 19 from angiosperms, demonstrating the diversity and preferential expansion of this gene family in land plants. Moreover, we determined that their remarkable expansion was mainly attributed to whole genome and segmental duplication, where duplicates were preferentially retained within certain subfamilies that shared three homologous intron patterns (a, b, and c) even though up to 12 types of patterns existed. Through our integrated distributions, sequence characteristics, and phylogenetic tree analyses, we confirm that 2R-MYBs are old and postulate that 3R-MYBs may be evolutionarily derived from 2R-MYBs via intragenic domain duplication.

• http://feeds.nature.com/~r/srep/rss/current/~3/O0X_n-9JEUY/srep11037

[详细]

HAB1 PP2C的ABA依赖pyl10交互抑制

PYL10 is a monomeric abscisic acid (ABA) receptor that inhibits protein phosphatase 2C (PP2C) activity in Arabidopsis thaliana. Previous studies reported that the PP2C phosphatase inhibition by PYL10 was ABA-independent. Here, systematic PYL10 biochemical studies demonstrated that PYL10 activity was ABA-dependent, and the previously reported studies was interfered by the presence of BSA in the commercial kit. To investigate dynamic mechanism of how ABA binding to PYL10 induces PP2C phosphatase inhibiting activity, solution NMR relaxation analysis of apo-PYL10 and PYL10/ABA were conducted following backbone resonance assignments. Reduced spectrum density mapping of the backbone relaxation data revealed that PYL10 was more flexible in ABA bound form than apo-PYL10, indicating an increased conformational entropy upon ligand binding. Moreover, to illustrate conformation exchanges of PYL10 upon ABA binding, NMR line shape analysis was performed with increasing concentrations of ABA, and the results indicated that PYL10 backbone conformational changes occur at different time scales.

• http://feeds.nature.com/~r/srep/rss/current/~3/bROyqGrvmUI/srep10890

[详细]

radiomic特征聚类和预后特征肺头比

Radiomics provides a comprehensive quantification of tumor phenotypes by extracting and mining large number of quantitative image features. To reduce the redundancy and compare the prognostic characteristics of radiomic features across cancer types, we investigated cancer-specific radiomic feature clusters in four independent Lung and Head & Neck (H&N) cancer cohorts (in total 878 patients). Radiomic features were extracted from the pre-treatment computed tomography (CT) images. Consensus clustering resulted in eleven and thirteen stable radiomic feature clusters for Lung and H&N cancer, respectively. These clusters were validated in independent external validation cohorts using rand statistic (Lung RS = 0.92, p < 0.001, H&N RS = 0.92, p < 0.001). Our analysis indicated both common as well as cancer-specific clustering and clinical associations of radiomic features. Strongest associations with clinical parameters: Prognosis Lung CI = 0.60 ± 0.01, Prognosis H&N CI = 0.68 ± 0.01; Lung histology AUC = 0.56 ± 0.03, Lung stage AUC = 0.61 ± 0.01, H&N HPV AUC = 0.58 ± 0.03, H&N stage AUC = 0.77 ± 0.02. Full utilization of these cancer-specific characteristics of image features may further improve radiomic biomarkers, providing a non-invasive way of quantifying and monitoring tumor phenotypic characteristics in clinical practice.

• http://feeds.nature.com/~r/srep/rss/current/~3/DqbCR2JB-_4/srep11044

[详细]

在边缘共享BO4四面体单向膨胀中kznb3o6

Borates are among a class of compounds that exhibit rich structural diversity and find wide applications. The formation of edge-sharing (es-) BO4 tetrahedra is extremely unfavored according to Pauling’s third and fourth rules. However, as the first and the only es-borate obtained under ambient pressure, es-KZnB3O6 shows an unexpected high thermal stability up to its melting point. The origin of this extraordinary stability is still unclear. Here, we report a novel property in KZnB3O6: unidirectional thermal expansion, which plays a role in preserving es-BO4 from disassociation at elevated temperatures. It is found that this unusual thermal behavior originates from cooperative rotations of rigid groups B6O12 and Zn2O6, driven by anharmonic thermal vibrations of K atoms. Furthermore, a detailed calculation of phonon dispersion in association with this unidirectional expansion predicts the melting initiates with the breakage of the link between BO3 and es-BO4. These findings will broaden our knowledge of the relationship between structure and property and may find applications in future.

• http://feeds.nature.com/~r/srep/rss/current/~3/fUe8Xoc6_iM/srep10996

[详细]

cclasso：通过套索成分数据相关推理

Motivation: Direct analysis of microbial communities in the environment and human body has become more convenient and reliable owing to the advancements of high-throughput sequencing techniques for 16S rRNA gene profiling. Inferring the correlation relationship among members of microbial communities is of fundamental importance for genomic survey study. Traditional Pearson correlation analysis treating the observed data as absolute abundances of the microbes may lead to spurious results because the data only represent relative abundances. Special care and appropriate methods are required prior to correlation analysis for these compositional data.

Results: In this article, we first discuss the correlation definition of latent variables for compositional data. We then propose a novel method called CCLasso based on least squares with ₁ penalty to infer the correlation network for latent variables of compositional data from metagenomic data. An effective alternating direction algorithm from augmented Lagrangian method is used to solve the optimization problem. The simulation results show that CCLasso outperforms existing methods, e.g. SparCC, in edge recovery for compositional data. It also compares well with SparCC in estimating correlation network of microbe species from the Human Microbiome Project.

Availability: CCLasso is open source and freely available from https://github.com/huayingfang/CCLasso under GNU LGPL v3.

Contact: dengmh@pku.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

• http://bioinformatics.oxfordjournals.org/cgi/content/short/btv349v1?rss=1

[详细]

稀疏的多视图矩阵因子分解：多组织比较多变量方法

Motivation: Within any given tissue, gene expression levels can vary extensively among individuals. Such heterogeneity can be caused by genetic and epigenetic variability and may contribute to disease. The abundance of experimental data now enables the identification of features of gene expression profiles that are shared across tissues, and those that are tissue-specific. While most current research is concerned with characterising differential expression by comparing mean expression profiles across tissues, it is also believed that a significant difference in a gene expression’s variance across tissues may also be associated with molecular mechanisms that are important for tissue development and function.

Results: We propose a sparse multi-view matrix factorisation (sMVMF) algorithm to jointly analyse gene expression measurements in multiple tissues, where each tissue provides a different "view" of the underlying organism. The proposed methodology can be interpreted as an extension of principal component analysis in that it provides the means to decompose the total sample variance in each tissue into the sum of two components: one capturing the variance that is shared across tissues, and one isolating the tissue-specific variances. sMVMF has been used to jointly model mRNA expression profiles in three tissues obtained from a large and well-phenotyped twins cohort, TwinsUK. Using sMVMF, we are able to prioritise genes based on whether their variation patterns are specific to each tissue. Furthermore, using DNA methylation profiles available, we provide supporting evidence that adipose-specific gene expression patterns may be driven by epigenetic effects.

Availability: Python code is available at http://www2.imperial.ac.uk/~gmontana/.

Contact: giovanni.montana@kcl.ac.uk

• http://bioinformatics.oxfordjournals.org/cgi/content/short/btv344v1?rss=1

[详细]

定量分析的框架和GC丰富的注释（和其他）的原核基因组。一个应用程序功能的dehalogenans

Motivation: Graphical representations of contrasts in GC usage among codon frame positions (frame analysis) provide evidence of genes missing from the annotations of prokaryotic genomes of high GC content but the qualitative approach of visual frame analysis prevents its applicability on a genomic scale.

Results: We developed two quantitative methods for the identification and statistical characterization in sequence regions of 3-base periodicity (hits) associated with ORF structures. The methods were implemented in the N-Profile Analysis Computational Tool (NPACT), which highlights in graphical representations inconsistencies between newly identified ORFs and pre-existing annotations of coding-regions. We applied the NPACT procedures to two recently annotated strains of the deltaproteobacterium Anaeromyxobacter dehalogenans, identifying in both genomes numerous conserved ORFs not included in the published annotation of coding regions.

Availability and implementation: NPACT is available as a web-based service and for download at http://genome.ufl.edu/npact.

Contact: lucianob@ufl.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

• http://bioinformatics.oxfordjournals.org/cgi/content/short/btv339v1?rss=1

[详细]

对corizus tetraspilus完整的线粒体基因组（半翅目：姬缘蝽科）和蝽次目系统发育分析

by Ming-Long Yuan, Qi-Lin Zhang, Zhong-Long Guo, Juan Wang, Yu-Ying Shen

Insect mitochondrial genome (mitogenome) are the most extensively used genetic information for molecular evolution, phylogenetics and population genetics. Pentatomomorpha (>14,000 species) is the second largest infraorder of Heteroptera and of great economic importance. To better understand the diversity and phylogeny within Pentatomomorpha, we sequenced and annotated the complete mitogenome of Corizus tetraspilus (Hemiptera: Rhopalidae), an important pest of alfalfa in China. We analyzed the main features of the C. tetraspilus mitogenome, and provided a comparative analysis with four other Coreoidea species. Our results reveal that gene content, gene arrangement, nucleotide composition, codon usage, rRNA structures and sequences of mitochondrial transcription termination factor are conserved in Coreoidea. Comparative analysis shows that different protein-coding genes have been subject to different evolutionary rates correlated with the G+C content. All the transfer RNA genes found in Coreoidea have the typical clover leaf secondary structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm and possesses a unusual anticodon stem (9 bp vs. the normal 5 bp). The control regions (CRs) among Coreoidea are highly variable in size, of which the CR of C. tetraspilus is the smallest (440 bp), making the C. tetraspilus mitogenome the smallest (14,989 bp) within all completely sequenced Coreoidea mitogenomes. No conserved motifs are found in the CRs of Coreoidea. In addition, the A+T content (60.68%) of the CR of C. tetraspilus is much lower than that of the entire mitogenome (74.88%), and is lowest among Coreoidea. Phylogenetic analyses based on mitogenomic data support the monophyly of each superfamily within Pentatomomorpha, and recognize a phylogenetic relationship of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))).

• http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0129003

[详细]

从头组装，对基因的SSR标记在黑豆[豇豆蒙戈未成熟种子的转录组和发展表征（L.）Hepper ]

by J. Souframanien, Kandali Sreenivasulu Reddy

Black gram [V. mungo (L.) Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS) were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO) functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were identified, of which majority of TCS are grouped into purine metabolism (678) followed by pyrimidine metabolism (263). A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35%) followed by di-nucleotide repeats (32%). PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Tri-nucleotide repeats (57.3%) were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.

• http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0128748

[详细]

德三疣梭子蟹卵巢和睾丸的RNA序列从头转录组分析：参与性腺发育相关基因的鉴定

by Xian-liang Meng, Ping Liu, Fu-long Jia, Jian Li, Bao-Quan Gao

The swimming crab Portunus trituberculatus is a commercially important crab species in East Asia countries. Gonadal development is a physiological process of great significance to the reproduction as well as commercial seed production for P. trituberculatus. However, little is currently known about the molecular mechanisms governing the developmental processes of gonads in this species. To open avenues of molecular research on P. trituberculatus gonadal development, Illumina paired-end sequencing technology was employed to develop deep-coverage transcriptome sequencing data for its gonads. Illumina sequencing generated 58,429,148 and 70,474,978 high-quality reads from the ovary and testis cDNA library, respectively. All these reads were assembled into 54,960 unigenes with an average sequence length of 879 bp, of which 12,340 unigenes (22.45% of the total) matched sequences in GenBank non-redundant database. Based on our transcriptome analysis as well as published literature, a number of candidate genes potentially involved in the regulation of gonadal development of P. trituberculatus were identified, such as FAOMeT, mPRγ, PGMRC1, PGDS, PGER4, 3β-HSD and 17β-HSDs. Differential expression analysis generated 5,919 differentially expressed genes between ovary and testis, among which many genes related to gametogenesis and several genes previously reported to be critical in differentiation and development of gonads were found, including Foxl2, Wnt4, Fst, Fem-1 and Sox9. Furthermore, 28,534 SSRs and 111,646 high-quality SNPs were identified in this transcriptome dataset. This work represents the first transcriptome analysis of P. trituberculatus gonads using the next generation sequencing technology and provides a valuable dataset for understanding molecular mechanisms controlling development of gonads and facilitating future investigation of reproductive biology in this species. The molecular markers obtained in this study will provide a fundamental basis for population genetics and functional genomics in P. trituberculatus and other closely related species.

• http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0128659

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对食源性寄生虫病原菌环孢子虫的线粒体基因组全序列

by Hediye Nese Cinar, Gopal Gopinath, Karen Jarvis, Helen R. Murphy

Cyclospora cayetanensis is a human-specific coccidian parasite responsible for several food and water-related outbreaks around the world, including the most recent ones involving over 900 persons in 2013 and 2014 outbreaks in the USA. Multicopy organellar DNA such as mitochondrion genomes have been particularly informative for detection and genetic traceback analysis in other parasites. We sequenced the C. cayetanensis genomic DNA obtained from stool samples from patients infected with Cyclospora in Nepal using the Illumina MiSeq platform. By bioinformatically filtering out the metagenomic reads of non-coccidian origin sequences and concentrating the reads by targeted alignment, we were able to obtain contigs containing Eimeria-like mitochondrial, apicoplastic and some chromosomal genomic fragments. A mitochondrial genomic sequence was assembled and confirmed by cloning and sequencing targeted PCR products amplified from Cyclospora DNA using primers based on our draft assembly sequence. The results show that the C. cayetanensis mitochondrion genome is 6274 bp in length, with 33% GC content, and likely exists in concatemeric arrays as in Eimeria mitochondrial genomes. Phylogenetic analysis of the C. cayetanensis mitochondrial genome places this organism in a tight cluster with Eimeria species. The mitochondrial genome of C. cayetanensis contains three protein coding genes, cytochrome (cytb), cytochrome C oxidase subunit 1 (cox1), and cytochrome C oxidase subunit 3 (cox3), in addition to 14 large subunit (LSU) and nine small subunit (SSU) fragmented rRNA genes.

• http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0128645

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全基因组排序的恶性疟原虫疟疾寄生虫，WDR蛋白超家族揭示特定功能

by Priyanka Chahar, Manjeri Kaushik, Sarvajeet Singh Gill, Surendra Kumar Gakhar, Natrajan Gopalan, Manish Datt, Amit Sharma, Ritu Gill

Despite a significant drop in malaria deaths during the past decade, malaria continues to be one of the biggest health problems around the globe. WD40 repeats (WDRs) containing proteins comprise one of the largest and functionally diverse protein superfamily in eukaryotes, acting as scaffolds for assembling large protein complexes. In the present study, we report an extensive in silico analysis of the WDR gene family in human malaria parasite Plasmodium falciparum. Our genome-wide identification has revealed 80 putative WDR genes in P. falciparum (PfWDRs). Five distinct domain compositions were discovered in Plasmodium as compared to the human host. Notably, 31 PfWDRs were annotated/re-annotated on the basis of their orthologs in other species. Interestingly, most PfWDRs were larger as compared to their human homologs highlighting the presence of parasite-specific insertions. Fifteen PfWDRs appeared specific to the Plasmodium with no assigned orthologs. Expression profiling of PfWDRs revealed a mixture of linear and nonlinear relationships between transcriptome and proteome, and only nine PfWDRs were found to be stage-specific. Homology modeling identified conservation of major binding sites in PfCAF-1 and PfRACK. Protein-protein interaction network analyses suggested that PfWDRs are highly connected proteins with ~1928 potential interactions, supporting their role as hubs in cellular networks. The present study highlights the roles and relevance of the WDR family in P. falciparum, and identifies unique features that lay a foundation for further experimental dissection of PfWDRs.

• http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0128507

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CRISPR，Disruptor

A powerful gene-editing technology is the biggest game changer to hit biology since PCR. But with its huge potential come pressing concerns.

• http://feeds.nature.com/~r/nature/rss/current/~3/HUxi2pR5Et4/522020a

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线粒体系统发育和遗传关系密切相关的松毛虫（枯叶蛾科：< > > < /松毛虫）物种在中国，使用完整的线粒体基因组

Background: Pine moths (Lepidoptera; Bombycoidea; Lasiocampidae: Dendrolimus spp.) are among the most serious insect pests of forests, especially in southern China. Although COI barcodes (a standardized portion of the mitochondrial cytochrome c oxidase subunit I gene) can distinguish some members of this genus, the evolutionary relationships of the three morphospecies Dendrolimus punctatus, D. tabulaeformis and D. spectabilis have remained largely unresolved. We sequenced whole mitochondrial genomes of eight specimens, including D. punctatus wenshanensis. This is an unambiguous subspecies of D. punctatus, and was used as a reference for inferring the relationships of the other two morphospecies of the D. punctatus complex. We constructed phylogenetic trees from this data, including twelve published mitochondrial genomes of other Bombycoidea species, and examined the relationships of the Dendrolimus taxa using these trees and the genomic features of the mitochondrial genome. Results: The eight fully sequenced mitochondrial genomes from the three morphospecies displayed similar genome structures as other Bombycoidea species in terms of gene content, base composition, level of overall AT-bias and codon usage. However, the Dendrolimus genomes possess a unique feature in the large ribosomal 16S RNA subunits (rrnL), which are more than 60 bp longer than other members of the superfamily and have a higher AC proportion. The eight mitochondrial genomes of Dendrolimus were highly conservative in many aspects, for example with identical stop codons and overlapping regions. But there were many differences in start codons, intergenic spacers, and numbers of mismatched base pairs of tRNA (transfer RNA genes).Our results, based on phylogenetic trees, genetic distances, species delimitation and genomic features (such as intergenic spacers) of the mitochondrial genome, indicated that D. tabulaeformis is as close to D. punctatus as is D. punctatus wenshanensis, whereas D. spectabilis evolved independently from D. tabulaeformis and D. punctatus. Whole mitochondrial DNA phylogenies showed that D. spectabilis formed a well-supported monophyletic clade, with a clear species boundary separating it from the other congeners examined here. However, D. tabulaeformis often clustered with D. punctatus and with the subspecies D. punctatus wenshanensis. Genetic distance analyses showed that the distance between D. tabulaeformis and D. punctatus is generally less than the intraspecific distance of D. punctatus and its subspecies D. punctatus wenshanensis. In the species delimitation analysis of Poisson Tree Processes (PTP), D. tabulaeformis, D. punctatus and D. punctatus wenshanensis clustered into a putative species separated from D. spectabilis. In comparison with D. spectabilis, D. tabulaeformis and D. punctatus also exhibit a similar structure in intergenic spacer characterization. These different types of evidence suggest that D. tabulaeformis is very close to D. punctatus and its subspecies D. punctatus wenshanensis, and is likely to be another subspecies of D. punctatus. Conclusions: Whole mitochondrial genomes possess relatively rich genetic information compared with the traditional use of single or multiple genes for phylogenetic purposes. They can be used to better infer phylogenetic relationships and degrees of relatedness of taxonomic groups, at least from the aspect of maternal lineage: caution should be taken due to the maternal-only inheritance of this genome. Our results indicate that D. spectabilis is an independent lineage, while D. tabulaeformis shows an extremely close relationship to D. punctatus.

• http://www.biomedcentral.com/1471-2164/16/428

[详细]

斑马鱼胚胎发育过程中卵黄部分消耗变化蛋氨酸循环和代谢基因的动力学

Background: Limited nutrient availability during development is associated with metabolic diseases in adulthood. The molecular cause for these defects is unclear. Here, we investigate if transcriptional changes caused by developmental malnutrition reveal an early response that can be linked to metabolism and metabolic diseases. Results: We limited nutrient availability by removing yolk from zebrafish (Danio rerio) embryos. We then measured genome expression after 8, 24, 32 h post-fertilization (hpf) by RNA sequencing and 48 hpf by microarray profiling. We assessed the functional impact of deregulated genes by enrichment analysis of gene ontologies, pathways and CpG sites around the transcription start sites. Nutrient depletion during embryogenesis does not affect viability, but induces a bias towards female development. It induces subtle expression changes of metabolic genes: lipid transport, oxidative signaling, and glycolysis are affected during earlier stages, and hormonal signaling at 48 hpf. Co-citation analysis indicates association of deregulated genes to the metabolic syndrome, a known outcome of early-life nutrient depletion. Notably, deregulated methionine cycle genes indicate altered methyl donor availability. We find that the regulation of deregulated genes may be less dependent on methyl donor availability. Conclusions: The systemic response to reduced nutrient availability in zebrafish embryos affects metabolic pathways and can be linked to metabolic diseases. Further exploration of the reported zebrafish model system may elucidate the consequences of reduced nutrient availability during embryogenesis.

• http://www.biomedcentral.com/1471-2164/16/427

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RNA序列分析揭示了大豆臭氧暴露遗传反应和耐受机制

Background: Oxidative stress caused by ground level ozone is a contributor to yield loss in a number of important crop plants. Soybean (Glycine max) is considered to be ozone sensitive, and current research into its response to oxidative stress is limited. To better understand the genetic response in soybean to oxidative stress, an RNA-seq analysis of two soybean cultivars was performed comparing an ozone intolerant cultivar (Mandarin-Ottawa) and an ozone resistant cultivar (Fiskeby III) following exposure to ozone. Results: Analysis of the transcriptome data revealed cultivar-specific expression level differences of genes previously implicated in oxidative stress responses, indicating unique cultivar-specific responses. Both Fiskeby III and Mandarin (Ottawa) exhibit an increased expression of oxidative response genes as well as glutathiones, phenylpropanoids, and phenylalanine ammonia-lyases. Mandarin (Ottawa) exhibited more general stress response genes whereas Fiskeby III had heightened expression of metabolic process genes. An examination of the timing of gene responses over the course of ozone exposure identified significantly more differentially expressed genes across all time points in Mandarin (Ottawa) than in Fiskeby III. The timing of expression was also considered to identify genes that may be indicative of a delayed response to ozone stress in Fiskeby III, We found that Mandarin (Ottawa) exhibits an higher level of expression in early time points for oxidative and general stress response genes while Fiskeby III seems to maintain expression of defense and stress response genes. Of particular interest was the expression of wax and cutin biosynthetic genes that we found to be expressed in Mandarin (Ottawa) in all sampled time points, whereas the expression of this pathway is only in the first time point for Fiskeby III. Conclusions: We were able to identify differentially expressed genes that correspond to each of the known or expected categories of genes previously implicated in other species for ozone stress. Our study shows evidence that at least part of the observed ozone tolerance of Fiskeby III may be due to its thicker, denser leaves providing passive resistance thereby limiting the degree of ozone exposure. The observed diminished genetic response is then likely a consequence of this reduced exposure.

• http://www.biomedcentral.com/1471-2164/16/426

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表面等离子体共振成像揭示了农杆菌转化中介VirE2多结合模式的ssDNA

VirE2 is the major secreted protein of Agrobacterium tumefaciens in its genetic transformation of plant hosts. It is co-expressed with a small acidic chaperone VirE1, which prevents VirE2 oligomerization. After secretion into the host cell, VirE2 serves functions similar to a viral capsid in protecting the single-stranded transferred DNA en route to the nucleus. Binding of VirE2 to ssDNA is strongly cooperative and depends moreover on protein–protein interactions. In order to isolate the protein–DNA interactions, imaging surface plasmon resonance (SPRi) studies were conducted using surface-immobilized DNA substrates of length comparable to the protein-binding footprint. Binding curves revealed an important influence of substrate rigidity with a notable preference for poly-T sequences and absence of binding to both poly-A and double-stranded DNA fragments. Dissociation at high salt concentration confirmed the electrostatic nature of the interaction. VirE1–VirE2 heterodimers also bound to ssDNA, though by a different mechanism that was insensitive to high salt. Neither VirE2 nor VirE1–VirE2 followed the Langmuir isotherm expected for reversible monomeric binding. The differences reflect the cooperative self-interactions of VirE2 that are suppressed by VirE1.

• http://nar.oxfordjournals.org/cgi/content/short/gkv571v1?rss=1

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打瞌睡：一个工具来编译，分析和统计的中和抗体的面板

CATNAP (Compile, Analyze and Tally NAb Panels) is a new web server at Los Alamos HIV Database, created to respond to the newest advances in HIV neutralizing antibody research. It is a comprehensive platform focusing on neutralizing antibody potencies in conjunction with viral sequences. CATNAP integrates neutralization and sequence data from published studies, and allows users to analyze that data for each HIV Envelope protein sequence position and each antibody. The tool has multiple data retrieval and analysis options. As input, the user can pick specific antibodies and viruses, choose a panel from a published study, or supply their own data. The output superimposes neutralization panel data, virus epidemiological data, and viral protein sequence alignments on one page, and provides further information and analyses. The user can highlight alignment positions, or select antibody contact residues and view position-specific information from the HIV databases. The tool calculates tallies of amino acids and N-linked glycosylation motifs, counts of antibody-sensitive and -resistant viruses in conjunction with each amino acid or N-glycosylation motif, and performs Fisher's exact test to detect potential positive or negative amino acid associations for the selected antibody. Website name: CATNAP (Compile, Analyze and Tally NAb Panels). Website address: http://hiv.lanl.gov/catnap.

• http://nar.oxfordjournals.org/cgi/content/short/gkv404v1?rss=1

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顺式编码sRNA，蛋白和mRNA二级结构独立行动抑制IS200换位

IS200 is found throughout Enterobacteriaceae and transposes at a notoriously low frequency. In addition to the transposase protein (TnpA), IS200 encodes an uncharacterized Hfq-binding sRNA that is encoded opposite to the tnpA 5'UTR. In the current work we asked if this sRNA represses tnpA expression. We show here that the IS200 sRNA (named art200 for antisense regulator of transposase IS200) basepairs with tnpA to inhibit translation initiation. Unexpectedly, art200-tnpA pairing is limited to 40 bp, despite 90 nt of perfect complementarity. Additionally, we show that Hfq and RNA secondary structure in the tnpA 5'UTR each repress tnpA expression in an art200-independent manner. Finally, we show that disrupting translational control of tnpA expression leads to increased IS200 transposition in E. coli. The current work provides new mechanistic insight into why IS200 transposition is so strongly suppressed. The possibility of art200 acting in trans to regulate a yet-unidentified target is discussed as well as potential applications of the IS200 system for designing novel riboregulators.

• http://nar.oxfordjournals.org/cgi/content/short/gkv584v1?rss=1

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