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https://www.readbyqxmd.com/read/29792949/srnaome-and-transcriptome-analysis-provide-insight-into-chilling-response-of-cowpea-pods
#1
Jinhua Zuo, Yunxiang Wang, Benzhong Zhu, Yunbo Luo, Qing Wang, Lipu Gao
Cowpea is an important horticultural crop in tropical and subtropical areas of Asia, Africa, and Latin America, as well as parts of southern Europe and Central and South America. Chilling injury is a common physiological hazard of cowpea in cold chain logistics which reduce the cowpea pod's nutritional quality and product value. However, the molecular mechanism involved in chilling injury remains unclear in cowpea pods. RNA-Seq and sRNA-Seq technologies were employed to decipher the miRNAs and mRNAs expression profiles and their regulatory networks in cowpea pods involved in chilling stress...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792712/targeted-discovery-and-combinatorial-biosynthesis-of-polycyclic-tetramate-macrolactam-combamides-a-e
#2
Yan Liu, Haoxin Wang, Rentai Song, Jining Chen, Tianhong Li, Yaoyao Li, Liangcheng Du, Yuemao Shen
Polycyclic tetramate macrolactams (PoTeMs) are a growing class of natural products with distinct structure and diverse biological activities. By promoter engineering and heterologous expression of the cryptic cbm gene cluster, four new PoTeMs, combamides A-E (1-4), were identified. Additionally, two new derivatives, combamides E (5) and F (6), were generated via combinatorial biosynthesis. Together, our findings provide a sound base for expanding the structure diversities of PoTeMs through genome mining and combinatorial biosynthesis...
May 24, 2018: Organic Letters
https://www.readbyqxmd.com/read/29792566/clues-to-an-evolutionary-mystery-the-genes-for-t-toxin-enabler-of-the-devastating-1970-southern-corn-leaf-blight-epidemic-are-present-in-ancestral-species-suggesting-an-ancient-origin
#3
Bradford J Condon, Candace E Elliott, Jonathan Gonzalez, Sung-Hwan Yun, Yasunori Akagi, Tyr Wiesner-Hanks, Motoichiro Kodama, Gillian Turgeon
The Southern Corn Leaf Blight epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern US. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T-toxin, while P. zeae-maydis produces PM-toxin, both host selective polyketide toxins necessary for supervirulence. Present abundance of genome sequences offers an opportunity to tackle the evolutionary origins of T- and PM- toxin biosynthetic genes, previously thought unique to these species...
May 24, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29792386/disparate-effects-of-shb-gene-deficiency-on-disease-characteristics-in-murine-models-of-myeloid-b-cell-and-t-cell-leukemia
#4
Maria Jamalpour, Xiujuan Li, Karin Gustafsson, Jeffrey W Tyner, Michael Welsh
The Src homology-2 domain protein B is an adaptor protein operating downstream of tyrosine kinases. The Shb gene knockout has been found to accelerate p210 Breakpoint cluster region-cAbl oncogene 1 tyrosine kinase-induced leukemia. In human myeloid leukemia were tumors with high Src homology-2 domain protein B mRNA content, tumors were, however, associated with decreased latency and myeloid leukemia exhibiting immune cell characteristics. Thus, the aim of this study was to investigate the effects of Shb knockout on the development of leukemia in three additional models, that is, colony stimulating factor 3 receptor-T618I-induced neutrophilic leukemia, p190 Breakpoint cluster region-cAbl oncogene 1 tyrosine kinase-induced B-cell leukemia, and G12D-Kras-induced T-cell leukemia/thymic lymphoma...
April 2018: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29792377/comparative-analysis-of-probiotic-bacteria-based-on-a-new-definition-of-core-genome
#5
Maria Satti, Yasuhiro Tanizawa, Akihito Endo, Masanori Arita
The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes...
March 26, 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29792237/according-to-mitochondrial-dna-evidence-parascaris-equorum-and-parascaris-univalens-may-represent-the-same-species
#6
J F Gao, X X Zhang, X X Wang, Q Li, Y Li, W W Xu, Y Gao, C R Wang
Parascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates...
May 24, 2018: Journal of Helminthology
https://www.readbyqxmd.com/read/29792165/molecular-characterization-and-differential-expression-suggested-diverse-functions-of-p-type-ii-ca-2-atpases-in-triticum-aestivum-l
#7
Mehak Taneja, Santosh Kumar Upadhyay
BACKGROUND: Plant P-type II Ca2+ ATPases are formed by two distinct groups of proteins (ACAs and ECAs) that perform pumping of Ca2+ outside the cytoplasm during homeostasis, and play vital functions during development and stress management. In the present study, we have performed identification and characterisation of P-type II Ca 2+ ATPase gene family in an important crop plant Triticum aestivum. RESULTS: Herein, a total of 33 TaACA and 9 TaECA proteins were identified from the various chromosomes and sub-genomes of Triticum aestivum...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792158/landraces-of-snake-melon-an-ancient-middle-eastern-crop-reveal-extensive-morphological-and-dna-diversity-for-potential-genetic-improvement
#8
Samer Omari, Yuri Kamenir, Jennifer I C Benichou, Sarah Pariente, Hanan Sela, Rafael Perl-Treves
BACKGROUND: Snake melon (Cucumis melo var. flexuosus, "Faqqous") is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a "Common Garden" rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers. RESULTS: The different landraces ("populations") showed extensive variation in morphology and quantitative traits such as yield and femaleness, and clustered into four horticultural varieties...
May 23, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29790944/the-reducing-clade-iib-polyketide-synthase-pks14-acts-as-a-virulence-determinant-of-the-entomopathogenic-fungus-beauveria-bassiana
#9
Chettida Srisuksam, Juntira Punya, Songsak Wattanachaisaereekul, Wachiraporn Toopaang, Supapon Cheevadhanarak, Morakot Tanticharoen, Alongkorn Amnuaykanjanasin
pks14, a reducing clade IIb polyketide synthase gene, is preserved throughout the evolution of entomopathogenic fungi. We examined the functions of pks14 in Beauveria bassiana using targeted gene disruption. pks14 disruption was verified by Southern blot and PCR analyses. The radial growth, cell dry weight and conidial germination of Δpks14 were comparable to that of the wild type. Our sequence and gene expression analyses of the pks14 biosynthetic cluster demonstrated: (i) cotranscription and constitutive expression of nearly all genes of the aforementioned cluster including C2H2 zinc finger transcription regulator gene, but not pks14 and cytochrome P450 gene; (ii) expression of pks14 gene in insect-containing culture condition only; whereby (iii) a KAR9-like gene in direct proximity with pks14 is the only gene showing co-regulation...
May 22, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29789651/analysis-of-the-genomic-landscape-of-multiple-myeloma-highlights-novel-prognostic-markers-and-disease-subgroups
#10
Niccolo Bolli, Giulia Biancon, Matahi Moarii, Silvia Gimondi, Yilong Li, Chiara de Philippis, Francesco Maura, Vijitha Sathiaseelan, Yu-Tzu Tai, Laura Mudie, Sarah O'Meara, Keiran Raine, Jon W Teague, Adam P Butler, Cristiana Carniti, Moritz Gerstung, Tina Bagratuni, Efstathios Kastritis, Meletios Dimopoulos, Paolo Corradini, Kenneth C Anderson, Philippe Moreau, Stephane Minvielle, Peter J Campbell, Elli Papaemmanuil, Herve Avet-Loiseau, Nikhil C Munshi
In multiple myeloma, next-generation sequencing (NGS) has expanded our knowledge of genomic lesions, and highlighted a dynamic and heterogeneous composition of the tumor. Here we used NGS to characterize the genomic landscape of 418 multiple myeloma cases at diagnosis and correlate this with prognosis and classification. Translocations and copy number abnormalities (CNAs) had a preponderant contribution over gene mutations in defining the genotype and prognosis of each case. Known and novel independent prognostic markers were identified in our cohort of proteasome inhibitor and immunomodulatory drug-treated patients with long follow-up, including events with context-specific prognostic value, such as deletions of the PRDM1 gene...
May 22, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29789481/concepts-and-methods-to-access-novel-antibiotics-from-actinomycetes
#11
REVIEW
Joachim J Hug, Chantal D Bader, Maja Remškar, Katarina Cirnski, Rolf Müller
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics...
May 22, 2018: Antibiotics
https://www.readbyqxmd.com/read/29789359/conserved-responses-in-a-war-of-small-molecules-between-a-plant-pathogenic-bacterium-and-fungi
#12
Joseph E Spraker, Philipp Wiemann, Joshua A Baccile, Nandhitha Venkatesh, Julia Schumacher, Frank C Schroeder, Laura M Sanchez, Nancy P Keller
Small-molecule signaling is one major mode of communication within the polymicrobial consortium of soil and rhizosphere. While microbial secondary metabolite (SM) production and responses of individual species have been studied extensively, little is known about potentially conserved roles of SM signals in multilayered symbiotic or antagonistic relationships. Here, we characterize the SM-mediated interaction between the plant-pathogenic bacterium Ralstonia solanacearum and the two plant-pathogenic fungi Fusarium fujikuroi and Botrytis cinerea We show that cellular differentiation and SM biosynthesis in F...
May 22, 2018: MBio
https://www.readbyqxmd.com/read/29789295/integration-of-protein-phosphorylation-acetylation-and-methylation-data-sets-to-outline-lung-cancer-signaling-networks
#13
Mark Grimes, Benjamin Hall, Lauren Foltz, Tyler Levy, Klarisa Rikova, Jeremiah Gaiser, William Cook, Ekaterina Smirnova, Travis Wheeler, Neil R Clark, Alexander Lachmann, Bin Zhang, Peter Hornbeck, Avi Ma'ayan, Michael Comb
Protein posttranslational modifications (PTMs) have typically been studied independently, yet many proteins are modified by more than one PTM type, and cell signaling pathways somehow integrate this information. We coupled immunoprecipitation using PTM-specific antibodies with tandem mass tag (TMT) mass spectrometry to simultaneously examine phosphorylation, methylation, and acetylation in 45 lung cancer cell lines compared to normal lung tissue and to cell lines treated with anticancer drugs. This simultaneous, large-scale, integrative analysis of these PTMs using a cluster-filtered network (CFN) approach revealed that cell signaling pathways were outlined by clustering patterns in PTMs...
May 22, 2018: Science Signaling
https://www.readbyqxmd.com/read/29789256/systems-level-analysis-of-risk-genes-reveals-the-modular-nature-of-schizophrenia
#14
Jiewei Liu, Ming Li, Xiong-Jian Luo, Bing Su
Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome...
May 19, 2018: Schizophrenia Research
https://www.readbyqxmd.com/read/29789182/geodermatophilus-chilensis-sp-nov-from-soil-of-the-yungay-core-region-of-the-atacama-desert-chile
#15
Jean Franco Castro, Imen Nouioui, Vartul Sangal, Martha E Trujillo, Maria Del Carmen Montero-Calasanz, Tara Rahmani, Alan T Bull, Juan A Asenjo, Barbara A Andrews, Michael Goodfellow
A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12T , B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus...
April 4, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29789016/unraveling-bacterial-fingerprints-of-city-subways-from-microbiome-16s-gene-profiles
#16
Alejandro R Walker, Tyler L Grimes, Somnath Datta, Susmita Datta
BACKGROUND: Microbial communities can be location specific, and the abundance of species within locations can influence our ability to determine whether a sample belongs to one city or another. As part of the 2017 CAMDA MetaSUB Inter-City Challenge, next generation sequencing (NGS) data was generated from swipe samples collected from subway stations in Boston, New York City hereafter New York, and Sacramento. DNA was extracted and Illumina sequenced. Sequencing data was provided for all cities as part of 2017 CAMDA contest challenge dataset...
May 22, 2018: Biology Direct
https://www.readbyqxmd.com/read/29788921/signatures-of-host-specialization-and-a-recent-transposable-element-burst-in-the-dynamic-one-speed-genome-of-the-fungal-barley-powdery-mildew-pathogen
#17
Lamprinos Frantzeskakis, Barbara Kracher, Stefan Kusch, Makoto Yoshikawa-Maekawa, Saskia Bauer, Carsten Pedersen, Pietro D Spanu, Takaki Maekawa, Paul Schulze-Lefert, Ralph Panstruga
BACKGROUND: Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). RESULTS: The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs)...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788916/in-silico-exploration-of-red-sea-bacillus-genomes-for-natural-product-biosynthetic-gene-clusters
#18
Ghofran Othoum, Salim Bougouffa, Rozaimi Razali, Ameerah Bokhari, Soha Alamoudi, André Antunes, Xin Gao, Robert Hoehndorf, Stefan T Arold, Takashi Gojobori, Heribert Hirt, Ivan Mijakovic, Vladimir B Bajic, Feras F Lafi, Magbubah Essack
BACKGROUND: The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788904/genetic-diversity-of-bola-drb3-in-south-american-zebu-cattle-populations
#19
Shin-Nosuke Takeshima, Claudia Corbi-Botto, Guillermo Giovambattista, Yoko Aida
BACKGROUND: Bovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolution typing methods has been poor. Here, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 421 cattle (116 Bolivian Nellore, 110 Bolivian Gir, and 195 Peruvian Nellore-Brahman). Data from 1416 Taurine and Zebu samples were also included in the analysis...
May 22, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29788535/cyp2a5-promoter-based-gene-reporter-assay-a-novel-design-of-cell-based-bioassay-for-toxicity-prediction
#20
A'edah Abu-Bakar, Hao Hu, Matti A Lang
The murine cytochrome P450 2a5 (Cyp2a5) gene is regulated by complex interactions of various stress-activated transcription factors (TFs). Elevated Cyp2a5 transcription under chemical-induced stress conditions is achieved by interplay between the various TFs-including as aryl hydrocarbon receptor (AhR) and nuclear factor (erythroid-derived 2)-like 2 wild-type (Nrf2)-at the "stress-responding" cluster of response elements on the Cyp2a5 promoter, as well as through mRNA stabilisation mediated by interaction of the stress-activated heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) with the 3'UTR of the CYP2A5 mRNA...
May 22, 2018: Basic & Clinical Pharmacology & Toxicology
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