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https://www.readbyqxmd.com/read/28748551/identification-of-a-dimeric-kdg-aldolase-from-agrobacterium-tumefaciens
#1
Tatiana P Soares da Costa, Madhvi Patel, Sebastien Desbois, Ruchi Gupta, Pierre Faou, Matthew A Perugini
Agrobacterium tumefaciens is a Gram-negative bacterium and causative agent of Crown Gall disease that infects a variety of economically-important plants. The annotated A. tumefaciens genome contains 10 putative dapA genes, which code for dihydrodipicolinate synthase (DHDPS). However, we have recently demonstrated that only one of these genes (dapA7) encodes a functional DHDPS. The function of the other nine putative dapA genes is yet to be determined. Here, we demonstrate using bioinformatics that the product of the dapA5 gene (DapA5) possesses all the catalytic residues canonical to 2-keto-3-deoxygluconate (KDG) aldolase, which is a class I aldolase involved in glucose metabolism...
July 27, 2017: Proteins
https://www.readbyqxmd.com/read/28748527/the-prevalence-of-dicer1-pathogenic-variation-in-population-databases
#2
Jung Kim, Amanda Field, Kris Ann P Schultz, D Ashley Hill, Douglas R Stewart
The DICER1 syndrome is associated with a variety of rare benign and malignant tumors, including pleuropulmonary blastoma (PPB), cystic nephroma (CN) and Sertoli-Leydig cell tumor (SLCT). The prevalence and penetrance of pathogenic DICER1 variation in the general population is unknown. We examined three publicly-available germline whole exome sequence datasets: Exome Aggregation Consortium (ExAC), 1000 Genomes (1000G), and the Exome Sequencing Project (ESP). To avoid over-estimation of pathogenic DICER1 variation from cancer-associated exomes, we excluded The Cancer Genome Atlas (TCGA) variants from ExAC...
July 27, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28748187/de-novo-assembly-and-characterization-of-cajanus-scarabaeoides-l-thouars-transcriptome-by-paired-end-sequencing
#3
Deepti Nigam, Swati Saxena, G Ramakrishna, Archana Singh, N K Singh, Kishor Gaikwad
Pigeonpea [Cajanus cajan (L.) Millsp.] is a heat and drought resilient legume crop grown mostly in Asia and Africa. Pigeonpea is affected by various biotic (diseases and insect pests) and abiotic stresses (salinity and water logging) which limit the yield potential of this crop. However, resistance to all these constraints is not readily available in the cultivated genotypes and some of the wild relatives have been found to withstand these resistances. Thus, the utilization of crop wild relatives (CWR) in pigeonpea breeding has been effective in conferring resistance, quality and breeding efficiency traits to this crop...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28747494/bam35-tectivirus-intraviral-interaction-map-unveils-new-function-and-localization-of-phage-orfan-proteins
#4
Mónica Berjón-Otero, Ana Lechuga, Jitender Mehla, Peter Uetz, Margarita Salas, Modesto Redrejo-Rodríguez
Tectiviridae comprises a group of tail-less, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria.In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28744812/in-vivo-effects-of-dexamethasone-on-blood-gene-expression-in-ataxia-telangiectasia
#5
Michele Menotta, Sara Biagiotti, Sara Orazi, Luigia Rossi, Luciana Chessa, Vincenzo Leuzzi, Daniela D'Agnano, Alessandro Plebani, Annarosa Soresina, Mauro Magnani
Ataxia telangiectasia (AT) is a rare incurable genetic disease caused by biallelic mutations in the Ataxia telangiectasia-mutated gene. Intra-erythrocyte infusion of dexamethasone improves clinical outcomes in AT patients; however, the molecular mechanisms that lead to this improvement remain unknown. Hence, to gain a better understanding of these mechanisms, we assessed the effects of glucocorticoid administration on gene expression in the blood of AT patients. Whole blood was obtained from nine children enrolled in a phase two clinical trial, who were being treated with dexamethasone (AT Dexa), from six untreated AT patients (AT) and from six healthy volunteers (WT)...
July 25, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28743951/genome-wide-analysis-and-expression-divergence-of-the-trihelix-family-in-brassica-rapa-insight-into-the-evolutionary-patterns-in-plants
#6
Wenli Wang, Peng Wu, TongKong Liu, Haibo Ren, Ying Li, Xilin Hou
Trihelix gene family is an important transcription factor (TF) family involved in plants' growth and development. This extensive study of trihelix genes from Arabidopsis thaliana to Brassica rapa could shed light on the evolution in plants and support crop breeding. In this study, a total of 52 trihelix genes were identified in B.rapa. Whole-genome annotation, molecular-evolution and gene-expression analyses of all known trihelix genes were conducted. By statistics of the number of trihelix genes in each species, we found the expansion of trihelix gene family started with angiosperm evolution...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743101/in-silico-locating-the-immune-reactive-segments-of-lepidium-draba-peroxidase-and-designing-a-less-immune-reactive-enzyme-derivative
#7
Yaser Fattahian, Ali Riahi-Madvar, Reza Mirzaee, Gholamreza Asadikaram, Mohammad Reza Rahbar
Peroxidases have broad applications in industry, environmental as well as pharmaceutical and diagnosis. Recently applicability of peroxidases in cancer therapy was mentioned. In the present study, a horseradish peroxidase homologue from Lepidium draba was subjected to in silico analyzes aiming at identifying and locating immune-reactive regions. A derivative sequence with decreased immunogenicity and increased stability also suggested. The tertiary structure of the enzyme was predicted. The functional and structural importance of residues was annotated as well as the conservatory status of each residue...
July 17, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28742084/systematic-tissue-specific-functional-annotation-of-the-human-genome-highlights-immune-related-dna-elements-for-late-onset-alzheimer-s-disease
#8
Qiongshi Lu, Ryan L Powles, Sarah Abdallah, Derek Ou, Qian Wang, Yiming Hu, Yisi Lu, Wei Liu, Boyang Li, Shubhabrata Mukherjee, Paul K Crane, Hongyu Zhao
Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types. However, synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge. Here, we present GenoSkyline-Plus, an extension of our previous work through integration of an expanded set of epigenomic and transcriptomic annotations to produce high-resolution, single tissue annotations...
July 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28741996/transcriptome-changes-associated-with-tomato-spotted-wilt-virus-infection-in-various-life-stages-of-its-thrips-vector-frankliniella-fusca-hinds
#9
Anita Shrestha, Donald E Champagne, Albert K Culbreath, Dorith Rotenberg, Anna E Whitfield, Rajagopalbabu Srinivasan
Persistent propagative viruses maintain intricate interactions with their arthropod vectors. In this study, we investigated the transcriptome-level responses associated with a persistent propagative phytovirus infection in various life stages of its vector using an Illumina HiSeq sequencing platform. The pathosystem components included a Tospovirus, Tomato spotted wilt virus (TSWV), its insect vector, Frankliniella fusca (Hinds), and a plant host, Arachis hypogaea (L.). We assembled (de novo) reads from three developmental stage groups of virus-exposed and non-virus-exposed F...
July 26, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28741124/characterization-of-a-low-density-lipoprotein-receptor-lrp13-in-chinese-tongue-sole-cynoglossus-semilaevis-and-medaka-oryzias-latipes
#10
Na Wang, Ruoqing Wang, Qiaomu Hu, Wenteng Xu, Ying Zhu, Fang Yan, Songlin Chen
As an important economic marine species cultured in China, Chinese tongue sole (Cynoglossus semilaevis) has interested us due to its sexual dimorphism and ZW/ZZ sex determination system. In a previous study, dmrt1 was identified as a dosage-dependent male-determining gene. In the present study, a female-specific expressed gene, cse0440, initially annotated as lrp1b-like, was identified from chromosome W of C. semilaevis. In view of the differences between cse0440 and lrp1b in terms of expression pattern, a phylogenetic analysis containing 85 LRP proteins was constructed and provided an evidence to re-annotate cse0440 as cseLRP13...
July 24, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/28741036/network-based-subcellular-proteomics-in-monocyte-membrane-revealed-novel-candidate-genes-involved-in-osteoporosis
#11
Y Zeng, L Zhang, W Zhu, H He, H Sheng, Q Tian, F-Y Deng, L-S Zhang, H-G Hu, H-W Deng
In this study, label-free-based quantitative subcellular proteomics integrated with network analysis highlighted several candidate genes including P4HB, ITGB1, CD36, and ACTN1 that may be involved in osteoporosis. All of them are predicted as significant membrane proteins with high confidence and enriched in bone-related biological process. The results were further verified in transcriptomic and genomic levels. INTRODUCTION: Osteoporosis is a metabolic bone disease mainly characterized by low bone mineral density (BMD)...
July 24, 2017: Osteoporosis International
https://www.readbyqxmd.com/read/28739399/a-variant-on-chromosome-2p13-3-is-associated-with-atopic-dermatitis-in-chinese-han-population
#12
Xin-Ying Cai, Xiao-Dong Zheng, Ling Fang, Fu-Sheng Zhou, Yu-Jun Sheng, Yan-Yan Wu, Chong-Xian Yu, Jun Zhu, Feng-Li Xiao
BACKGROUND: Multi-ancestry genome-wide association study (GWAS) has recently identified 11 new susceptibility loci for Atopic dermatitis (AD). The replication of these new susceptibility loci in different populations should not be ignored. OBJECTIVE: To examine whether these 11 new identified susceptibility loci are also associated with AD in the Chinese Han population. METHODS: These 11 variants were imputed using our genome-wide array dataset...
July 21, 2017: Gene
https://www.readbyqxmd.com/read/28739138/the-in-silico-zebrafish-matrisome-a-new-tool-to-study-extracellular-matrix-gene-and-protein-functions
#13
Pauline Nauroy, Sandrine Hughes, Alexandra Naba, Florence Ruggiero
Extracellular matrix (ECM) proteins are major components of most tissues and organs. In addition to their crucial role in tissue cohesion and biomechanics, they chiefly regulate various important biological processes during embryonic development, tissue homeostasis and repair. In essence, ECM proteins were defined as secreted proteins that localized in the extracellular space. The characterization of the human and mouse matrisomes provided the first definition of ECM actors by comprehensively listing ECM proteins and classified them into categories...
July 21, 2017: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/28737900/accumulation-of-charantin-and-expression-of-triterpenoid-biosynthesis-genes-in-bitter-melon-momordica-charantia
#14
Do Manh Cuong, Jin Jeon, Abubaker M A Morgan, Changsoo Kim, Jae Kwang Kim, Sook Young Lee, Sang Un Park
Charantin, a natural cucurbitane type triterpenoid, has been reported to have beneficial pharmacological functions such as anticancer, antidiabetic, and antibacterial activities. However, accumulation of charantin in bitter melon has been little studied. Here, we performed a transcriptome analysis to identify genes involved in the triterpenoid biosynthesis pathway in bitter melon seedlings. Total of 88,703 transcripts with an average length of 898 bp were identified in bitter melon seedlings. Based on a functional annotation, we identified 15 candidate genes encoding enzymes related to triterpenoid biosynthesis and analyzed their expression in different organs of mature plants...
July 24, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28737829/expression-profile-of-circular-rnas-in-human-gastric-cancer-tissues
#15
You-Sheng Huang, Na Jie, Ke-Jian Zou, Yang Weng
Circular RNAs (circRNAs) represent a newly identified class of non‑coding RNA molecules, which interfere with gene transcription by adsorbing microRNAs (miRNAs). CircRNAs serve important roles in disease development and have the potential to serve as a novel class of biomarkers for clinical diagnosis. However, the role of circRNAs in the occurrence and development of gastric cancer (GC) remains unclear. In the present study, the expression profiles of circRNAs were compared between GC and adjacent normal tissues using a circRNA microarray, following which quantitative polymerase chain reaction (qPCR) was used to confirm the results of the circRNA microarray...
September 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28737213/identification-of-methylated-gnti-dependent-n-glycans-in-botryococcus-brauni
#16
Stefan Schulze, Eugen Urzica, Maarten J M F Reijnders, Henri van de Geest, Sven Warris, Linda V Bakker, Christian Fufezan, Vitor A P Martins Dos Santos, Peter J Schaap, Sander A Peters, Michael Hippler
In contrast to mammals and vascular plants, microalgae show a high diversity in the N-glycan structures of complex N-glycoproteins. Although homologues for β1,2-N-acetylglucosaminyltransferase I (GnTI), a key enzyme in the formation of complex N-glycans, have been identified in several algal species, GnTI-dependent N-glycans have not been detected so far. We have performed an N-glycoproteomic analysis of the hydrocarbon oils accumulating green microalgae Botryococcus braunii. Thereby, the analysis of intact N-glycopeptides allowed the determination of N-glycan compositions...
July 24, 2017: New Phytologist
https://www.readbyqxmd.com/read/28736702/cultivar-specific-transcriptome-prediction-and-annotation-in-ficus-carica-l
#17
Liceth Solorzano Zambrano, Gabriele Usai, Alberto Vangelisti, Flavia Mascagni, Tommaso Giordani, Rodolfo Bernardi, Andrea Cavallini, Riccardo Gucci, Giovanni Caruso, Claudio D'Onofrio, Mike Frank Quartacci, Piero Picciarelli, Barbara Conti, Andrea Lucchi, Lucia Natali
The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28736437/dissecting-evolution-and-disease-using-comparative-vertebrate-genomics
#18
REVIEW
Jennifer R S Meadows, Kerstin Lindblad-Toh
With the generation of more than 100 sequenced vertebrate genomes in less than 25 years, the key question arises of how these resources can be used to inform new or ongoing projects. In the past, this diverse collection of sequences from human as well as model and non-model organisms has been used to annotate the human genome and to increase the understanding of human disease. In the future, comparative vertebrate genomics in conjunction with additional genomic resources will yield insights into the processes of genome function, evolution, speciation, selection and adaptation, as well as the quantification of species diversity...
July 24, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28735504/low-genetic-diversity-and-functional-constraint-of-mirna-genes-participating-pollen-pistil-interaction-in-rice
#19
Kun Wang, Xin Wang, Ming Li, Tao Shi, Pingfang Yang
In this study, we sequenced and analyzed the expression and evolution of rice miRNA genes participating pollen-pistil interaction that is crucial to rice yield. Pollen-pistil interaction is an essential reproductive process for all flowering plants. While microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNA levels in eukaryotic cells, there is little knowledge about which miRNAs involved in the early stages of pollen-pistil interaction in rice and how they evolve under this conserved process...
July 22, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28734934/analysis-of-rna-protein-interactions-in-vertebrate-embryos-using-uv-crosslinking-approaches
#20
Vladimir Despic, Mario Dejung, Falk Butter, Karla M Neugebauer
A decade ago, we believed that at least 300 RNA binding proteins (RBPs) were encoded in our genomes based on annotations of known or predicted RNA binding domains. Deciphering the roles of those RBPs in regulated gene expression was a vast frontier awaiting exploration. Since then, the field has developed a number of key tools that navigate the landscape of cellular RNA. These rely principally on UV crosslinking to create covalent bonds between RBPs and target RNAs in vivo, revealing not only target identities but also local binding sites upon RNA-Seq...
July 19, 2017: Methods: a Companion to Methods in Enzymology
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