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https://www.readbyqxmd.com/read/28810710/testing-convergent-evolution-in-auditory-processing-genes-between-echolocating-mammals-and-the-aye-aye-a-percussive-foraging-primate
#1
Richard J Bankoff, Michael Jerjos, Baily Hohman, M Elise Lauterbur, Logan Kistler, George H Perry
Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagascariensis) are nocturnal lemurs with a specialized auditory processing system. Aye-ayes tap rapidly along the surfaces of trees, listening to reverberations to identify the mines of wood-boring insect larvae; this behavior has been hypothesized to functionally mimic echolocation...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28809552/characterization-of-2-oxindole-forming-heme-enzyme-mare-expanding-the-functional-diversity-of-the-tryptophan-dioxygenase-superfamily
#2
Yuyang Zhang, Yi Zou, Nelson L Brock, Tingting Huang, Yingxia Lan, Xiaozheng Wang, Zixin Deng, Yi Tang, Shuangjun Lin
3-Substituted 2-oxindoles are important structural motifs found in many biologically active natural products and pharmaceutical lead compounds. Here, we report an enzymatic formation of the 3-substituted 2-oxindoles catalyzed by MarE in the maremycin biosynthetic pathway in Streptomyces sp. B9173. MarE is a homologue of Fe(II)/heme-dependent tryptophan 2,3-dioxygenases (TDOs). Typical TDOs usually catalyze the insertion of two oxygen atoms from O2 into an indole ring to generate N-formylkynurenine (NFK)-like products...
August 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28806064/conditional-displacement-hybridization-assay-for-multiple-snp-phasing
#3
Tsz Wing Fan, Henson L Lee Yu, I-Ming Hsing
The two chromosomal copies of the human genome are highly polymorphic, and the allelic content on each strand can dictate a person's biological outcomes. While many of the current diagnostic tools are able to detect the presence of multiple mutations at the same time, most cannot determine the phase of these mutations unless long-range PCR or sequencing techniques are used or if templates are compartmentalized into single copies prior to amplification. Here, an enzyme-coupled hybridization assay, named Conditional Displacement Hybridization Assay (CDHA), is described for the concurrent and rapid determination of the presence and phase of SNP variants...
August 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28802076/single-cell-sequencing-unveils-the-lifestyle-and-crispr-based-population-history-of-hydrotalea-sp-in-acid-mine-drainage
#4
J D Medeiros, L R Leite, V S Pylro, F S Oliveira, V M Almeida, G R Fernandes, A C M Salim, F M G Araújo, A C Volpini, G Oliveira, S Cuadros-Orellana
Acid mine drainage (AMD) is characterized by an acid and metal-rich runoff that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early-stage AMD sample. These cells belong to the genus Hydrotalea, and is closely related to H. flava. The phylogeny and average nucleotide identity analysis suggest that all single-amplified genomes (SAGs) form two clades that may represent different strains...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28802024/the-cereal-pathogen-fusarium-pseudograminearum-produces-a-new-class-of-active-cytokinins-during-infection
#5
Jens Laurids Sørensen, Aurelie H Benfield, Rasmus Dam Wollenberg, Klaus Westphal, Reinhard Wimmer, Mikkel Rank Nielsen, Kristian Fog Nielsen, Jason Carere, Lorenzo Covarelli, Giovanni Beccari, Jonathan Powell, Takafumi Yamashino, Herbert Kogler, Teis Esben Sondergaard, Donald Max Gardiner
The fungal pathogen Fusarium pseudograminearum causes important diseases of wheat and barley. During a survey of secondary metabolites produced by this fungus, a novel class of cytokinins, herein termed Fusarium cytokinins, was discovered. Cytokinins are known for their growth promoting and anti-senescence activities and the production of a cytokinin mimic by what was once considered a necrotrophic pathogen that promotes cell death and senescence challenges the simple view that this pathogen invades its hosts by employing a barrage of lytic enzymes and toxins...
August 12, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28798873/a-novel-viral-lineage-distantly-related-to-herpesviruses-discovered-within-fish-genome-sequence-data
#6
Amr Aswad, Aris Katzourakis
Pathogenic viruses represent a small fraction of viral diversity, and emerging diseases are frequently the result of cross-species transmissions. Therefore, we need to develop high-throughput techniques to investigate a broader range of viral biodiversity across a greater number of species. This is especially important in the context of new practices in agriculture that have arisen to tackle the challenges of global food security, including the rising number of marine and freshwater species that are used in aquaculture...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/28798494/identification-and-functional-characterization-of-the-sex-determining-gene-doublesex-in-the-sawfly-athalia-rosae%C3%A2-hymenoptera-tenthredinidae
#7
Shotaro Mine, Megumi Sumitani, Fugaku Aoki, Masatsugu Hatakeyama, Masataka G Suzuki
Sexual fate of the sawfly, Athalia rosae (Hymenoptera: Tenthredinidae) is determined by the complementary sex determination (CSD) mechanism as is the case in honeybees. However, to date, genes involved in sex determination have not been identified in this species. In this study, we attempted to identify orthologs of complementary sex-determiner (csd), feminizer (fem), and doublesex (dsx) from the A. rosae genome, all of which are crucial components of the sex determination cascade in the honeybee. As a result, we identified a sawfly ortholog of dsx (designated as Ardsx)...
2017: Applied Entomology and Zoology
https://www.readbyqxmd.com/read/28798167/complete-genome-sequence-of-sulfuriferula-sp-strain-ah1-a-sulfur-oxidizing-autotroph-isolated-from-weathered-mine-tailings-from-the-duluth-complex-in-minnesota
#8
Daniel S Jones, Elizabeth W Roepke, An An Hua, Beverly E Flood, Jake V Bailey
We report the closed and annotated genome sequence of Sulfuriferula sp. strain AH1. Strain AH1 has a 2,877,007-bp chromosome that includes a partial Sox system for inorganic sulfur oxidation and a complete nitrogen fixation pathway. It also has a single 39,138-bp plasmid with genes for arsenic and mercury resistance.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28794266/multi-scale-tracking-reveals-scale-dependent-chromatin-dynamics-after-dna-damage
#9
Judith Miné-Hattab, Vincent Recamier, Ignacio Izeddin, Rodney Rothstein, Xavier Darzacq
The dynamic organization of genes inside the nucleus is an important determinant for their function. Using fast DNA tracking microscopy in S. cerevisiae cells and improved analysis of mean square displacements, we quantified DNA motion at time scales ranging from 10 milliseconds to minute and found that following DNA damage, DNA exhibits distinct sub-diffusive regimes. In response to double-strand breaks, chromatin is more mobile at large time scales but, surprisingly, its mobility is reduced at short time scales...
August 9, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28793856/mining-sequence-variations-in-representative-polyploid-sugarcane-germplasm-accessions
#10
Xiping Yang, Jian Song, Qian You, Dev R Paudel, Jisen Zhang, Jianping Wang
BACKGROUND: Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions...
August 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28791417/diverse-gene-expression-patterns-in-response-to-anticancer-drugs-between-human-and-mouse-cell-lines-revealed-by-a-comparative-transcriptomic-analysis
#11
Yong Guo, Zhuoran Liang, Xiaoliang Hou, Zhi Zhang
The aim of the present study was to perform comparative genomics using gene expression profile datasets of mice and humans who had been treated with anticancer drugs, to determine the similarities and differences in the antitumor mechanisms in the two mammals. This involved data mining of antitumor gene expression regulation, and screening of genetic loci from experimental mouse models of antitumor targets, to provide a theoretical basis of drug design. Subsequently, 9 overlapping genes with opposite expression patterns were identified across mouse and human cell lines that were treated with a specific cyclin‑dependent kinase 4/6 inhibitor, PD0332991...
August 4, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28790851/identification-of-the-anticancer-effects-of-a-novel-proteasome-inhibitor-ixazomib-on-colorectal-cancer-using-a-combined-method-of-microarray-and-bioinformatics-analysis
#12
Qiaowei Fan, Bingrong Liu
PURPOSE: The study aimed to explore the anticancer effects of a novel proteasome inhibitor, ixazomib, on colorectal cancer (CRC) using a combined method of microarray and bioinformatics analysis. MATERIALS AND METHODS: Cell proliferation was tested by Cell Counting Kit-8 (CCK-8) assay for SW620 cells treated with different concentrations of ixazomib and different treatment times. The microarray analysis was conducted for six samples, including three samples of SW620 cells untreated with ixazomib and three samples of SW620 cells treated with ixazomib...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28781807/amplification-of-the-nsd3-brd4-chd8-pathway-in-pelvic-high-grade-serous-carcinomas-of-tubo-ovarian-and-endometrial-origin
#13
Derek H Jones, Douglas I Lin
Identification of novel therapeutics in pelvic high-grade serous carcinoma (HGSC) has been hampered by a paucity of actionable point mutations in target genes. The aim of the present study was to investigate the extent of amplification of the therapeutically targetable NSD3-CHD8-BRD4 pathway in pelvic HGSC, and to determine whether amplification is associated with worse prognosis. The Cancer Genome Atlas (TCGA) ovarian and endometrial cancer cohorts were retrospectively analyzed via online data-mining tools to test the association of NSD3, CHD8 and BRD4 genomic alterations with survival of pelvic HGSC patients...
August 2017: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/28776041/hiding-in-plain-sight-mining-bacterial-species-records-for-phenotypic-trait-information
#14
Albert Barberán, Hildamarie Caceres Velazquez, Stuart Jones, Noah Fierer
Cultivation in the laboratory is essential for understanding the phenotypic characteristics and environmental preferences of bacteria. However, basic phenotypic information is not readily accessible. Here, we compiled phenotypic and environmental tolerance information for >5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) with all information made publicly available in an updatable database. Although the data span 23 different bacterial phyla, most entries described aerobic, mesophilic, neutrophilic strains from Proteobacteria (mainly Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes isolated from soils, marine habitats, and plants...
July 2017: MSphere
https://www.readbyqxmd.com/read/28765985/translational-genomics-of-grain-size-regulation-in-wheat
#15
REVIEW
Wanlong Li, Bing Yang
Identifying and mapping grain size candidate genes in the wheat genome greatly empowers reverse genetics approaches to improve grain yield potential of wheat. Grain size (GS) or grain weight is believed to be a major driving force for further improvement of wheat yield. Although the large, polyploid genome of wheat poses an obstacle to identifying GS determinants using map-based cloning, a translational genomics approach using GS regulators identified in the model plants rice and Arabidopsis as candidate genes appears to be effective and supports a hypothesis that a conserved genetic network regulates GS in rice and wheat...
August 1, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28751895/a-multiple-qtl-seq-strategy-delineates-potential-genomic-loci-governing-flowering-time-in-chickpea
#16
Rishi Srivastava, Hari D Upadhyaya, Rajendra Kumar, Anurag Daware, Udita Basu, Philanim W Shimray, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
Identification of functionally relevant potential genomic loci using an economical, simpler and user-friendly genomics-assisted breeding strategy is vital for rapid genetic dissection of complex flowering time quantitative trait in chickpea. A high-throughput multiple QTL-seq strategy was employed in two inter (Cicer arietinum desi accession ICC 4958 × C reticulatum wild accession ICC 17160)- and intra (ICC 4958 × C. arietinum kabuli accession ICC 8261)-specific RIL mapping populations to identify the major QTL genomic regions governing flowering time in chickpea...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28749477/mapping-the-genomic-landscape-of-inherited-retinal-disease-genes-prioritizes-genes-prone-to-coding-and-noncoding-copy-number-variations
#17
Kristof Van Schil, Sarah Naessens, Stijn Van de Sompele, Marjolein Carron, Alexander Aslanidis, Caroline Van Cauwenbergh, Anja Kathrin Mayer, Mattias Van Heetvelde, Miriam Bauwens, Hannah Verdin, Frauke Coppieters, Michael E Greenberg, Marty G Yang, Marcus Karlstetter, Thomas Langmann, Katleen De Preter, Susanne Kohl, Timothy J Cherry, Bart P Leroy, Elfride De Baere
PurposePart of the hidden genetic variation in heterogeneous genetic conditions such as inherited retinal diseases (IRDs) can be explained by copy-number variations (CNVs). Here, we explored the genomic landscape of IRD genes listed in RetNet to identify and prioritize those genes susceptible to CNV formation.MethodsRetNet genes underwent an assessment of genomic features and of CNV occurrence in the Database of Genomic Variants and literature. CNVs identified in an IRD cohort were characterized using targeted locus amplification (TLA) on extracted genomic DNA...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28743231/genome-wide-comparative-analysis-of-putative-pth11-related-g-protein-coupled-receptors-in-fungi-belonging-to-pezizomycotina
#18
Xihui Xu, Guopeng Li, Lu Li, Zhenzhu Su, Chen Chen
BACKGROUND: G-protein coupled receptors (GPCRs) are the largest family of transmembrane receptors in fungi, where they play important roles in signal transduction. Among them, the Pth11-related GPCRs form a large and divergent protein family, and are only found in fungi in Pezizomycotina. However, the evolutionary process and potential functions of Pth11-related GPCRs remain largely unknown. RESULTS: Twenty genomes of fungi in Pezizomycotina covering different nutritional strategies were mined for putative Pth11-related GPCRs...
July 25, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28742845/evaluation-of-k-ras-and-p53-expression-in-pancreatic-adenocarcinoma-using-the-cancer-genome-atlas
#19
Liming Lu, Jingchun Zeng
Genetic alterations in K-ras and p53 are thought to be critical in pancreatic cancer development and progression. However, K-ras and p53 expression in pancreatic adenocarcinoma have not been systematically examined in The Cancer Genome Atlas (TCGA) Data Portal. Information regarding K-ras and p53 alterations, mRNA expression data, and protein/protein phosphorylation abundance was retrieved from The Cancer Genome Atlas (TCGA) databases, and analyses were performed by the cBioPortal for Cancer Genomics. The mutual exclusivity analysis showed that events in K-ras and p53 were likely to co-occur in pancreatic adenocarcinoma (Log odds ratio = 1...
2017: PloS One
https://www.readbyqxmd.com/read/28739819/leaf-photosynthetic-parameters-related-to-biomass-accumulation-in-a-global-rice-diversity-survey
#20
Mingnan Qu, Guangyong Zheng, Jemma Essmine, Saber Hamdani, Qingfeng Song, Hongru Wang, Chengcai Chu, Xavier Sirault, Xin-Guang Zhu
Mining natural variations is a major approach to identify new options to improve crop light use efficiency. So far, successes in identifying photosynthetic parameters positively related to crop biomass accumulation through this approach are scarce possibly due to the earlier emphasis on properties related to leaf instead of canopy photosynthetic efficiency. This study aims to uncover rice natural variations to identify leaf physiological parameters that are highly correlated with biomass accumulation, a surrogate of canopy photosynthesis...
July 24, 2017: Plant Physiology
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