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https://www.readbyqxmd.com/read/27922122/identification-of-critical-paralog-groups-with-indispensable-roles-in-the-regulation-of-signaling-flow
#1
Dezso Modos, Johanne Brooks, David Fazekas, Eszter Ari, Tibor Vellai, Peter Csermely, Tamas Korcsmaros, Katalin Lenti
Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in human signaling networks, we developed a signaling network-based method using cross-talk annotation and tissue-specific signaling flow analysis. 75 CPGs were found with higher degree, betweenness centrality, closeness, and 'bowtieness' when compared to other paralogs or other proteins in the signaling network...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922095/co-expression-network-analyses-identify-functional-modules-associated-with-development-and-stress-response-in-gossypium-arboreum
#2
Qi You, Liwei Zhang, Xin Yi, Kang Zhang, Dongxia Yao, Xueyan Zhang, Qianhua Wang, Xinhua Zhao, Yi Ling, Wenying Xu, Fuguang Li, Zhen Su
Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922066/de-novo-transcriptome-characterization-of-dracaena-cambodiana-and-analysis-of-genes-involved-in-flavonoid-accumulation-during-formation-of-dragon-s-blood
#3
Jia-Hong Zhu, Tian-Jun Cao, Hao-Fu Dai, Hui-Liang Li, Dong Guo, Wen-Li Mei, Shi-Qing Peng
Dragon's blood is a red resin mainly extracted from Dracaena plants, and has been widely used as a traditional medicine in East and Southeast Asia. The major components of dragon's blood are flavonoids. Owing to a lack of Dracaena plants genomic information, the flavonoids biosynthesis and regulation in Dracaena plants remain unknown. In this study, three cDNA libraries were constructed from the stems of D. cambodiana after injecting the inducer. Approximately 266.57 million raw sequencing reads were de novo assembled into 198,204 unigenes, of which 34,873 unique sequences were annotated in public protein databases...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920155/sos2-and-acp1-loci-identified-through-large-scale-exome-chip-analysis-regulate-kidney-development-and-function
#4
Man Li, Yong Li, Olivia Weeks, Vladan Mijatovic, Alexander Teumer, Jennifer E Huffman, Gerard Tromp, Christian Fuchsberger, Mathias Gorski, Leo-Pekka Lyytikäinen, Teresa Nutile, Sanaz Sedaghat, Rossella Sorice, Adrienne Tin, Qiong Yang, Tarunveer S Ahluwalia, Dan E Arking, Nathan A Bihlmeyer, Carsten A Böger, Robert J Carroll, Daniel I Chasman, Marilyn C Cornelis, Abbas Dehghan, Jessica D Faul, Mary F Feitosa, Giovanni Gambaro, Paolo Gasparini, Franco Giulianini, Iris Heid, Jinyan Huang, Medea Imboden, Anne U Jackson, Janina Jeff, Min A Jhun, Ronit Katz, Annette Kifley, Tuomas O Kilpeläinen, Ashish Kumar, Markku Laakso, Ruifang Li-Gao, Kurt Lohman, Yingchang Lu, Reedik Mägi, Giovanni Malerba, Evelin Mihailov, Karen L Mohlke, Dennis O Mook-Kanamori, Antonietta Robino, Douglas Ruderfer, Erika Salvi, Ursula M Schick, Christina-Alexandra Schulz, Albert V Smith, Jennifer A Smith, Michela Traglia, Laura M Yerges-Armstrong, Wei Zhao, Mark O Goodarzi, Aldi T Kraja, Chunyu Liu, Jennifer Wessel, Eric Boerwinkle, Ingrid B Borecki, Jette Bork-Jensen, Erwin P Bottinger, Daniele Braga, Ivan Brandslund, Jennifer A Brody, Archie Campbell, David J Carey, Cramer Christensen, Josef Coresh, Errol Crook, Gary C Curhan, Daniele Cusi, Ian H de Boer, Aiko P J de Vries, Joshua C Denny, Olivier Devuyst, Albert W Dreisbach, Karlhans Endlich, Tõnu Esko, Oscar H Franco, Tibor Fulop, Glenn S Gerhard, Charlotte Glümer, Omri Gottesman, Niels Grarup, Vilmundur Gudnason, Tamara B Harris, Caroline Hayward, Lynne Hocking, Albert Hofman, Frank B Hu, Lise Lotte N Husemoen, Rebecca D Jackson, Torben Jørgensen, Marit E Jørgensen, Mika Kähönen, Sharon L R Kardia, Wolfgang König, Charles Kooperberg, Jennifer Kriebel, Lenore J Launer, Torsten Lauritzen, Terho Lehtimäki, Daniel Levy, Pamela Linksted, Allan Linneberg, Yongmei Liu, Ruth J F Loos, Antonio Lupo, Christine Meisinger, Olle Melander, Andres Metspalu, Paul Mitchell, Matthias Nauck, Peter Nürnberg, Marju Orho-Melander, Afshin Parsa, Oluf Pedersen, Annette Peters, Ulrike Peters, Ozren Polasek, David Porteous, Nicole M Probst-Hensch, Bruce M Psaty, Lu Qi, Olli T Raitakari, Alex P Reiner, Rainer Rettig, Paul M Ridker, Fernando Rivadeneira, Jacques E Rossouw, Frank Schmidt, David Siscovick, Nicole Soranzo, Konstantin Strauch, Daniela Toniolo, Stephen T Turner, André G Uitterlinden, Sheila Ulivi, Dinesh Velayutham, Uwe Völker, Henry Völzke, Melanie Waldenberger, Jie Jin Wang, David R Weir, Daniel Witte, Helena Kuivaniemi, Caroline S Fox, Nora Franceschini, Wolfram Goessling, Anna Köttgen, Audrey Y Chu
Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L; PStage1<3...
December 5, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27919758/the-chemokinome-superfamily-in-channel-catfish-i-cxc-subfamily-and-their-involvement-in-disease-defense-and-hypoxia-responses
#5
Qiang Fu, Qifan Zeng, Yun Li, Yujia Yang, Chao Li, Shikai Liu, Tao Zhou, Ning Li, Jun Yao, Chen Jiang, Daoji Li, Zhanjiang Liu
Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in regulating cell migration and activation. They are defined by the presence of four conserved cysteine residues and are divided into four subfamilies depending on the arrangement of the first two conserved cysteines residues: CXC, CC, C and CX3C. In this study, a complete set of 17 CXC chemokine ligand (CXCL) genes was systematically identified and characterized from channel catfish genome through data mining of existing genomic resources...
December 2, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27918468/transcriptome-analysis-of-the-tadpole-shrimp-triops-longicaudatus-by-illumina-paired-end-sequencing-assembly-annotation-and-marker-discovery
#6
Jiyeon Seong, Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Mi Young Noh, Seung-Hwan Park, Gwang Joo Jeon, Hong Sik Kong, Soonok Kim, Ui Wook Hwang, Hong Seog Park, Yeon Soo Han, Yong Seok Lee
The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs...
December 2, 2016: Genes
https://www.readbyqxmd.com/read/27918112/validation-of-adam10-metalloprotease-as-a-bacillus-thuringiensis-cry3aa-toxin-functional-receptor-in-colorado-potato-beetle-leptinotarsa-decemlineata
#7
V M Ruiz-Arroyo, I García-Robles, C Ochoa-Campuzano, G A Goig, E Zaitseva, G Baaken, A C Martínez-Ramírez, C Rausell, M D Real
Bacillus thuringiensis parasporal crystal proteins (Cry proteins) are insecticidal pore-forming toxins that bind to specific receptor molecules on the brush border membrane of susceptible insect midgut cells to exert their toxic action. In the Colorado potato beetle (CPB), a coleopteran pest, we previously proposed that interaction of Cry3Aa toxin with a CPB ADAM10 metalloprotease is an essential part of the mode of action of this toxin. Here, we annotated the gene sequence encoding an ADAM10 metalloprotease protein (CPB-ADAM10) in the CPB genome sequencing project, and using RNA interference gene silencing we demonstrated that CPB-ADAM10 is a Cry3Aa toxin functional receptor in CPB...
December 5, 2016: Insect Molecular Biology
https://www.readbyqxmd.com/read/27917315/the-first-complete-plastid-genomes-of-melastomataceae-are-highly-structurally-conserved
#8
Marcelo Reginato, Kurt M Neubig, Lucas C Majure, Fabian A Michelangeli
BACKGROUND: In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. METHODS: Genome skimming was performed for 16 species spread across the Melastomataceae...
2016: PeerJ
https://www.readbyqxmd.com/read/27917288/towards-an-open-grapevine-information-system
#9
REVIEW
A-F Adam-Blondon, M Alaux, C Pommier, D Cantu, Z-M Cheng, G R Cramer, C Davies, S Delrot, L Deluc, G Di Gaspero, J Grimplet, A Fennell, J P Londo, P Kersey, F Mattivi, S Naithani, P Neveu, M Nikolski, M Pezzotti, B I Reisch, R Töpfer, M A Vivier, D Ware, H Quesneville
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www...
2016: Horticulture Research
https://www.readbyqxmd.com/read/27917166/temporal-metagenomic-and-metabolomic-characterization-of-fresh-perennial-ryegrass-degradation-by-rumen-bacteria
#10
Olga L Mayorga, Alison H Kingston-Smith, Eun J Kim, Gordon G Allison, Toby J Wilkinson, Matthew J Hegarty, Michael K Theodorou, Charles J Newbold, Sharon A Huws
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27916935/genome-wide-survey-reveals-transcriptional-differences-underlying-the-contrasting-trichome-phenotypes-of-two-sister-desert-poplars
#11
Jianchao Ma, Xiaodong He, Xiaotao Bai, Zhimin Niu, Bingbing Duan, Ningning Chen, Xuemin Shao, Dongshi Wan
Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica-which have, respectively, dense and sparse trichomes-to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P...
December 1, 2016: Genes
https://www.readbyqxmd.com/read/27916797/pseudogenes-and-their-genome-wide-prediction-in-plants
#12
REVIEW
Jin Xiao, Manoj Kumar Sekhwal, Pingchuan Li, Raja Ragupathy, Sylvie Cloutier, Xiue Wang, Frank M You
Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes)...
November 28, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27916258/the-apicoplast-genomes-of-two-taxonomic-units-of-babesia-from-sheep
#13
Tao Wang, Guiquan Guan, Pasi K Korhonen, Anson V Koehler, Ross S Hall, Neil D Young, Hong Yin, Robin B Gasser
The apicoplast (ap) is a unique, non-photosynthetic organelle found in most apicomplexan parasites. Due to the essential roles that this organelle has, it has been widely considered as target for drugs against diseases caused by apicomplexans. Exploring the ap genomes of such parasites would provide a better understanding of their systematics and their basic molecular biology for therapeutics. However, there is limited information available on the ap genomes of apicomplexan parasites. In the present study, the ap genomes of two operational taxonomic units of Babesia (known as Babesia sp...
November 6, 2016: Veterinary Parasitology
https://www.readbyqxmd.com/read/27915291/the-landscape-of-microbial-phenotypic-traits-and-associated-genes
#14
Maria Brbić, Matija Piškorec, Vedrana Vidulin, Anita Kriško, Tomislav Šmuc, Fran Supek
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913905/proteins-immunologically-related-to-map65-1-accumulate-and-localize-differentially-during-bud-development-in-vitis-vinifera-l
#15
Luigi Parrotta, Claudia Faleri, Mauro Cresti, Giampiero Cai
Various arrays of microtubules are present throughout the plant cell cycle and are involved in distinct functions. Microtubule-associated proteins (MAPs) regulate microtubule dynamics by acting as stabilizers, destabilizers, and promoters of microtubule dynamics. The MAP65 family is a specific group of cross-linkers required for structural maintenance of microtubules. In plants, different isoforms of MAP65 are differentially expressed according to their developmental program. In this work, we analyzed the differential distribution of proteins immunologically related to MAP65-1 during bud development in grapevine (Vitis vinifera L...
December 2, 2016: Protoplasma
https://www.readbyqxmd.com/read/27913725/in-vivo-expression-technology-and-5-end-mapping-of-the-borrelia-burgdorferi-transcriptome-identify-novel-rnas-expressed-during-mammalian-infection
#16
Philip P Adams, Carlos Flores Avile, Niko Popitsch, Ivana Bilusic, Renée Schroeder, Meghan Lybecker, Mollie W Jewett
Borrelia burgdorferi, the bacterial pathogen responsible for Lyme disease, modulates its gene expression profile in response to the environments encountered throughout its tick-mammal infectious cycle. To begin to characterize the B. burgdorferi transcriptome during murine infection, we previously employed an in vivo expression technology-based approach (BbIVET). This identified 233 putative promoters, many of which mapped to un-annotated regions of the complex, segmented genome. Herein, we globally identify the 5' end transcriptome of B...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27912842/the-rapid-spread-of-carbapenem-resistant-enterobacteriaceae
#17
REVIEW
Robert F Potter, Alaric W D'Souza, Gautam Dantas
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids...
November 2016: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/27912769/three-novel-bacteriophages-isolated-from-the-east-african-rift-valley-soda-lakes
#18
Leonardo Joaquim van Zyl, Shonisani Nemavhulani, James Cass, Donald Arthur Cowan, Marla Trindade
BACKGROUND: Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. METHODS: Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays...
December 3, 2016: Virology Journal
https://www.readbyqxmd.com/read/27911958/advantages-of-an-improved-rhesus-macaque-genome-for-evolutionary-analyses
#19
Julien S Gradnigo, Abhishek Majumdar, Robert B Norgren, Etsuko N Moriyama
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct...
2016: PloS One
https://www.readbyqxmd.com/read/27911803/genomic-sequencing-based-mutational-enrichment-analysis-identifies-motility-genes-in-a-genetically-intractable-gut-microbe
#20
Sena Bae, Olaf Mueller, Sandi Wong, John F Rawls, Raphael H Valdivia
A major roadblock to understanding how microbes in the gastrointestinal tract colonize and influence the physiology of their hosts is our inability to genetically manipulate new bacterial species and experimentally assess the function of their genes. We describe the application of population-based genomic sequencing after chemical mutagenesis to map bacterial genes responsible for motility in Exiguobacterium acetylicum, a representative intestinal Firmicutes bacterium that is intractable to molecular genetic manipulation...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
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