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https://www.readbyqxmd.com/read/29168051/efficient-conformational-ensemble-generation-of-protein-bound-peptides
#1
Yumeng Yan, Di Zhang, Sheng-You Huang
Conformation generation of protein-bound peptides is critical for the determination of protein-peptide complex structures. Despite significant progress in conformer generation of small molecules, few methods have been developed for modeling protein-bound peptide conformations. Here, we have developed a fast de novo peptide modeling algorithm, referred to as MODPEP, for conformational sampling of protein-bound peptides. Given a sequence, MODPEP builds the peptide 3D structure from scratch by assembling amino acids or helix fragments based on constructed rotamer and helix libraries...
November 22, 2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29167468/transcriptome-and-metabolite-analyses-reveal-the-complex-metabolic-genes-involved-in-volatile-terpenoid-biosynthesis-in-garden-sage-salvia-officinalis
#2
Mohammed Ali, Penghui Li, Guangbiao She, Daofu Chen, Xiaochun Wan, Jian Zhao
A large number of terpenoid compounds have been extracted from different tissues of S. officinalis. However, the molecular genetic basis of terpene biosynthesis pathways is virtually unknown. In this study, approximately 6.6 Gb of raw data were generated from the transcriptome of S. officinalis leaves using Illumina HiSeq 2000 sequencing. After filtering and removing the adapter sequences from the raw data, the number of reads reached 21 million, comprising 98 million of high-quality nucleotide bases. 48,671 unigenes were assembled de novo and annotated for establishing a valid database for studying terpenoid biosynthesis...
November 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29166857/genome-analysis-of-the-foxtail-millet-pathogen-sclerospora-graminicola-reveals-the-complex-effector-repertoire-of-graminicolous-downy-mildews
#3
Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun, Ryohei Terauchi
BACKGROUND: Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches' broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S...
November 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29163600/plastome-rearrangements-in-the-adenocalymma-neojobertia-clade-bignonieae-bignoniaceae-and-its-phylogenetic-implications
#4
Luiz H M Fonseca, Lúcia G Lohmann
The chloroplast is one of the most important organelles of plants. This organelle has a circular DNA with approximately 130 genes. The use of plastid genomic data in phylogenetic and evolutionary studies became possible with high-throughput sequencing methods, which allowed us to rapidly obtain complete genomes at a reasonable cost. Here, we use high-throughput sequencing to study the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). More specifically, we use Hi-Seq Illumina technology to sequence 10 complete plastid genomes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163486/structure-and-diversity-of-the-rhesus-macaque-immunoglobulin-loci-through-multiple-de-novo-genome-assemblies
#5
Akshaya Ramesh, Sam Darko, Axin Hua, Glenn Overman, Amy Ransier, Joseph R Francica, Ashley Trama, Georgia D Tomaras, Barton F Haynes, Daniel C Douek, Thomas B Kepler
The rhesus macaque is a critically important animal model in biomedical research, most recently playing a key role in the development of vaccines against human immunodeficiency virus-1. Nevertheless, the immunoglobulin (Ig) loci of macaques are as yet incompletely determined and our understanding of differences between human and macaque humoral immunity remains deficient. We completed a high-coverage, high-quality whole genome sequencing and assembly project with a single rhesus macaque of Indian origin, and partial genome assemblies using genomic molecular targeting of the Ig loci in nine other rhesus macaques of Indian origin...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29162031/norgal-extraction-and-de-novo-assembly-of-mitochondrial-dna-from-whole-genome-sequencing-data
#6
Kosai Al-Nakeeb, Thomas Nordahl Petersen, Thomas Sicheritz-Pontén
BACKGROUND: Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. RESULTS: Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers...
November 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29161377/transmission-and-persistence-of-incf-conjugative-plasmids-in-the-gut-microbiota-of-full-term-infants
#7
Anuradha Ravi, Lorena Valdés-Varela, Miguel Gueimonde, Knut Rudi
Conjugative plasmids represent major reservoirs for horizontal transmission of antibiotic resistance (AR) and virulence genes. Our knowledge about the ecology and persistence of these plasmids in the gut microbiota remains limited. The IncF plasmids are the most widespread in clinical samples and in healthy humans. Therefore, the main aim is to study their ecology and association with the developing gut microbiota. Using a longitudinal (2, 10, 30 and 90 days) cohort of full-term infants, we investigated the transmission and persistence of IncFIA and IncFIB plasmids...
November 17, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29159068/transcriptome-analysis-of-the-chinese-giant-salamander-andrias-davidianus-using-rna-sequencing
#8
Yong Huang, Jian Li Xiong, Xiao Chan Gao, Xi Hong Sun
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/29158627/development-of-transcriptome-based-web-genomic-resources-of-yellow-mosaic-disease-in-vigna-mungo
#9
Rahul Singh Jasrotia, Mir Asif Iquebal, Pramod Kumar Yadav, Neeraj Kumar, Sarika Jaiswal, U B Angadi, Anil Rai, Dinesh Kumar
Vigna mungo (Urdbean) is cultivated in the tropical and sub-tropical continental region of Asia. It is not only important source of dietary protein and nutritional elements, but also of immense value to human health due to medicinal properties. Yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus is known to incur huge loss to crop, adversely affecting crop yield. Contrasting genotypes are ideal source for knowledge discovery of plant defence mechanism and associated candidate genes for varietal improvement...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158402/structural-insights-into-enzymatic-4-2-aza-cycloaddition-in-thiopeptide-antibiotic-biosynthesis
#10
Dillon P Cogan, Graham A Hudson, Zhengan Zhang, Taras V Pogorelov, Wilfred A van der Donk, Douglas A Mitchell, Satish K Nair
The [4+2] cycloaddition reaction is an enabling transformation in modern synthetic organic chemistry, but there are only limited examples of dedicated natural enzymes that can catalyze this transformation. Thiopeptides (or more formally thiazolyl peptides) are a class of thiazole-containing, highly modified, macrocyclic secondary metabolites made from ribosomally synthesized precursor peptides. The characteristic feature of these natural products is a six-membered nitrogenous heterocycle that is assembled via a formal [4+2] cycloaddition between two dehydroalanine (Dha) residues...
November 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29157209/transcriptome-sequencing-and-analysis-of-zinc-uptake-related-genes-in-trichophyton-mentagrophytes
#11
Xinke Zhang, Pengxiu Dai, Yongping Gao, Xiaowen Gong, Hao Cui, Yipeng Jin, Yihua Zhang
BACKGROUND: Trichophyton mentagrophytes is an important zoonotic dermatophytic (ringworm) pathogen; causing severe skin infection in humans and other animals worldwide. Fortunately, commonly used fungal skin disease prevention and treatment measures are relatively simple. However, T. mentagrophytes is primarily studied at the epidemiology and drug efficacy research levels, yet current study has been unable to meet the needs of clinical medicine. Zinc is a crucial trace element for the growth and reproduction of fungi and other microorganisms...
November 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29152671/comparative-transcriptome-analysis-provides-insights-into-differentially-expressed-genes-and-long-non-coding-rnas-between-ovary-and-testis-of-the-mud-crab-scylla-paramamosain
#12
Xiaolong Yang, Mhd Ikhwanuddin, Xincang Li, Fan Lin, Qingyang Wu, Yueling Zhang, Cuihong You, Wenhua Liu, Yinwei Cheng, Xi Shi, Shuqi Wang, Hongyu Ma
The molecular mechanism underlying sex determination and gonadal differentiation of the mud crab (Scylla paramamosain) has received considerable attention, due to the remarkably biological and economic differences between sexes. However, sex-biased genes, especially non-coding genes, which account for these differences, remain elusive in this crustacean species. In this study, the first de novo gonad transcriptome sequencing was performed to identify both differentially expressed genes and long non-coding RNAs (lncRNAs) between male and female S...
November 20, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/29146946/de-novo-transcriptome-sequencing-of-meja-induced-taraxacum-koksaghyz-rodin-to-identify-genes-related-to-rubber-formation
#13
XinWen Cao, Jie Yan, JiLiang Lei, Jin Li, JianBo Zhu, HuiYan Zhang
Increase in the consumption of natural rubber (NR) has necessitated the identification of alternative sources of NR. The quality of NR produced by Taraxacum koksaghyz Rodin (TKS) is comparable to that from Hevea brasiliensis (H.brasiliensis), and therefore, TKS is being considered as an alternative source of NR. Here, we sequenced the TKS root transcriptome after wild TKS seedlings were treated with methyl jasmonate (MeJA) for 0, 6, and 24 h. The clean reads generated for each experimental line were assembled into 127,833 unigenes...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146182/plakophilin3-increases-desmosome-assembly-size-and-stability-by-increasing-expression-of-desmocollin2
#14
Mansa Gurjar, Kumarkrishna Raychaudhuri, Snehal Mahadik, Divya Reddy, Apurva Atak, Trupti Shetty, Kruthi Rao, Mansi S Karkhanis, Prajakta Gosavi, Lalit Sehgal, Sanjay Gupta, Sorab N Dalal
Previous reports show that the desmosomal plaque protein plakophilin3 (PKP3) is essential for desmosome formation. Here, we report that PKP3 over-expression decreases calcium dependency for de novo desmosome formation and makes existing cell-cell adhesion junctions more resilient in low calcium medium due to an increase in desmocollin2 expression. PKP3 overexpression increases the stability of other desmosomal proteins independently of the increase in DSC2 levels and regulates desmosome formation and stability by a multimodal mechanism affecting transcription, protein stability and cell border localization of desmosomal proteins...
November 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29145861/hybrid-de-novo-genome-assembly-and-centromere-characterization-of-the-gray-mouse-lemur-microcebus-murinus
#15
Peter A Larsen, R Alan Harris, Yue Liu, Shwetha C Murali, C Ryan Campbell, Adam D Brown, Beth A Sullivan, Jennifer Shelton, Susan J Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C Durand, Muhammad S Shamim, Erez Lieberman Aiden, Donna M Muzny, Richard A Gibbs, Anne D Yoder, Jeffrey Rogers, Kim C Worley
BACKGROUND: The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly...
November 16, 2017: BMC Biology
https://www.readbyqxmd.com/read/29145825/assembling-large-genomes-analysis-of-the-stick-insect-clitarchus-hookeri-genome-reveals-a-high-repeat-content-and-sex-biased-genes-associated-with-reproduction
#16
Chen Wu, Victoria G Twort, Ross N Crowhurst, Richard D Newcomb, Thomas R Buckley
BACKGROUND: Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145430/de-novo-sequencing-and-analysis-of-the-transcriptome-during-the-browning-of-fresh-cut-luffa-cylindrica-fusi-3-fruits
#17
Haisheng Zhu, Jianting Liu, Qingfang Wen, Mindong Chen, Bin Wang, Qianrong Zhang, Zhuzheng Xue
Fresh-cut luffa (Luffa cylindrica) fruits commonly undergo browning. However, little is known about the molecular mechanisms regulating this process. We used the RNA-seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut fruits from luffa cultivar 'Fusi-3'. Over 90 million high-quality reads were assembled into 58,073 Unigenes, and 60.86% of these were annotated based on sequences in four public databases. We detected 35,282 Unigenes with significant hits to sequences in the NCBInr database, and 24,427 Unigenes encoded proteins with sequences that were similar to those of known proteins in the Swiss-Prot database...
2017: PloS One
https://www.readbyqxmd.com/read/29144390/rna-sequencing-and-coexpression-analysis-reveal-key-genes-involved-in-%C3%AE-linolenic-acid-biosynthesis-in-perilla-frutescens-seed
#18
Tianyuan Zhang, Chi Song, Li Song, Zhiwei Shang, Sen Yang, Dong Zhang, Wei Sun, Qi Shen, Degang Zhao
Perillafrutescen is used as traditional food and medicine in East Asia. Its seeds contain high levels of α-linolenic acid (ALA), which is important for health, but is scarce in our daily meals. Previous reports on RNA-seq of perilla seed had identified fatty acid (FA) and triacylglycerol (TAG) synthesis genes, but the underlying mechanism of ALA biosynthesis and its regulation still need to be further explored. So we conducted Illumina RNA-sequencing in seven temporal developmental stages of perilla seeds...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29142132/identification-of-a-small-molecule-that-compromises-the-structural-integrity-of-viroplasms-and-rotavirus-double-layered-particles
#19
Catherine Eichwald, Giuditta De Lorenzo, Elisabeth M Schraner, Guido Papa, Michela Bollati, Paolo Swuec, Matteo de Rosa, Mario Milani, Eloise Mastrangelo, Mathias Ackermann, Oscar R Burrone, Francesca Arnoldi
Despite the availability of two attenuated vaccines, rotavirus (RV) gastroenteritis remains an important cause of mortality among children in developing countries causing about 215,000 infant deaths annually. Currently, there are no specific antiviral therapies available. RV is a non-enveloped virus with a segmented double-stranded RNA genome. Viral genome replication and assembly of transcriptionally active double-layered particles (DLPs) take place in cytoplasmic viral structures called viroplasms. In this study, we describe strong impairment of the early stages of RV replication induced by a small molecule known as RNA polymerase III inhibitor, ML-60218 (ML)...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29140718/pem-fitter-a-coarse-grained-method-to-validate-protein-candidate-models
#20
Kamal Al Nasr, Christopher Jones, Feras Yousef, Ruba Jebril
The volumetric images produced by Cryo-Electron Microscopy (cryo-EM) technique are used to model macromolecular assemblies and machines. De novo protein modeling uses these images to computationally model the structure of the molecules. Many candidate conformations are usually generated during the intermediate step. Conventionally, each of these candidates is evaluated by time-consuming approaches such as potential energy. We introduce an initial version of a geometrical screening method that uses the skeleton of the cryo-EM images to evaluate candidate structures...
November 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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