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https://www.readbyqxmd.com/read/29351892/identification-and-functional-analysis-of-cassava-della-proteins-in-plant-disease-resistance-against-cassava-bacterial-blight
#1
Xiaolin Li, Wen Liu, Bing Li, Guoyin Liu, Yunxie Wei, Chaozu He, Haitao Shi
Gibberellin (GA) is an essential plant hormone in plant growth and development as well as various stress responses. DELLA proteins are important repressors of GA signal pathway. GA and DELLA have been extensively investigated in several model plants. However, the in vivo roles of GA and DELLA in cassava, one of the most important crops and energy crops in the tropical area, are unknown. In this study, systematic genome-wide analysis identified 4 MeDELLAs in cassava, as evidenced by the evolutionary tree, gene structures and motifs analyses...
December 26, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29351742/herv-w-group-evolutionary-history-in-non-human-primates-characterization-of-erv-w-orthologs-in-catarrhini-and-related-erv-groups-in-platyrrhini
#2
Nicole Grandi, Marta Cadeddu, Jonas Blomberg, Jens Mayer, Enzo Tramontano
BACKGROUND: The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology...
January 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29351733/glutamate-synthases-from-conifers-gene-structure-and-phylogenetic-studies
#3
Ángel García-Gutiérrez, Francisco M Cánovas, Concepción Ávila
BACKGROUND: Plants synthesize glutamate from ammonium by the combined activity of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) through the glutamate synthase cycle. In plants, there are two forms of glutamate synthases that differ in their electron donors, NADH-GOGAT (EC 1.4.1.14) and Fd-GOGAT (EC 1.4.7.1), which have differential roles either in primary ammonia assimilation or in the reassimilation of ammonium from different catabolic processes. Glutamate synthases are complex iron-sulfur flavoproteins containing functional domains involved in the control and coordination of their catalytic activities in annual plants...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351731/a-chelicerate-specific-burst-of-nonclassical-dscam-diversity
#4
Guozheng Cao, Yang Shi, Jian Zhang, Hongru Ma, Shouqing Hou, Haiyang Dong, Weiling Hong, Shuo Chen, Hao Li, Yandan Wu, Pengjuan Guo, Xu Shao, Bingbing Xu, Feng Shi, Yijun Meng, Yongfeng Jin
BACKGROUND: The immunoglobulin (Ig) superfamily receptor Down syndrome cell adhesion molecule (Dscam) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for both nervous and immune systems in insects. However, further information is required to develop a comprehensive view of Dscam diversification across the broad spectrum of Chelicerata clades, a basal branch of arthropods and the second largest group of terrestrial animals. RESULTS: In this study, a genome-wide comprehensive analysis of Dscam genes across Chelicerata species revealed a burst of nonclassical Dscams, categorised into four types-mDscam, sDscamα, sDscamβ, and sDscamγ-based on their size and structure...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351588/sorghum-root-system-classification-in-contrasting-p-environments-reveals-three-main-rooting-types-and-root-architecture-related-marker-trait-associations
#5
Sebastian Parra-Londono, Mareike Kavka, Birgit Samans, Rod Snowdon, Silke Wieckhorst, Ralf Uptmoor
Background and Aims: Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions...
January 17, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29351194/involvement-of-bax-and-bcl-2-in-induction-of-apoptosis-by-essential-oils-of-three-lebanese-salvia-species-in-human-prostate-cancer-cells
#6
Alessandra Russo, Venera Cardile, Adriana C E Graziano, Rosanna Avola, Maurizio Bruno, Daniela Rigano
Prostate cancer is one of the most common forms of cancer in men, and research to find more effective and less toxic drugs has become necessary. In the frame of our ongoing program on traditionally used Salvia species from the Mediterranean Area, here we report the biological activities of Salvia aurea, S. judaica and S. viscosa essential oils against human prostate cancer cells (DU-145). The cell viability was measured by 3(4,5-dimethyl-thiazol-2-yl)2,5-diphenyl-tetrazolium bromide (MTT) test and lactate dehydrogenase (LDH) release was used to quantify necrosis cell death...
January 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29350283/epigenetic-regulation-of-neuroblastoma-development
#7
REVIEW
Durinck Kaat, Speleman Frank
In recent years, technological advances have enabled a detailed landscaping of the epigenome and the mechanisms of epigenetic regulation that drive normal cell function, development and cancer. Rather than merely a structural entity to support genome compaction, we now look at chromatin as a very dynamic and essential constellation that is actively participating in the tight orchestration of transcriptional regulation as well as DNA replication and repair. The unique feature of chromatin flexibility enabling fast switches towards more or less restricted epigenetic cellular states is, not surprisingly, intimately connected to cancer development and treatment resistance, and the central role of epigenetic alterations in cancer is illustrated by the finding that up to 50% of all mutations across cancer entities affect proteins controlling the chromatin status...
January 19, 2018: Cell and Tissue Research
https://www.readbyqxmd.com/read/29349810/medicago-truncatula-copper-transporter-1-mtcopt1-delivers-copper-for-symbiotic-nitrogen-fixation
#8
Marta Senovilla, Rosario Castro-Rodríguez, Isidro Abreu, Viviana Escudero, Igor Kryvoruchko, Michael K Udvardi, Juan Imperial, Manuel González-Guerrero
Copper is an essential nutrient for symbiotic nitrogen fixation. This element is delivered by the host plant to the nodule, where membrane copper (Cu) transporter would introduce it into the cell to synthesize cupro-proteins. COPT family members in the model legume Medicago truncatula were identified and their expression determined. Yeast complementation assays, confocal microscopy and phenotypical characterization of a Tnt1 insertional mutant line were carried out in the nodule-specific M. truncatula COPT family member...
January 19, 2018: New Phytologist
https://www.readbyqxmd.com/read/29348648/specific-cyclic-adp-ribose-phosphohydrolase-obtained-by-mutagenic-engineering-of-mn2-dependent-adp-ribose-cdp-alcohol-diphosphatase
#9
João Meireles Ribeiro, José Canales, Alicia Cabezas, Joaquim Rui Rodrigues, Rosa María Pinto, Iralis López-Villamizar, María Jesús Costas, José Carlos Cameselle
Cyclic ADP-ribose (cADPR) is a messenger for Ca2+ mobilization. Its turnover is believed to occur by glycohydrolysis to ADP-ribose. However, ADP-ribose/CDP-alcohol diphosphatase (ADPRibase-Mn) acts as cADPR phosphohydrolase with much lower efficiency than on its major substrates. Recently, we showed that mutagenesis of human ADPRibase-Mn at Phe37, Leu196 and Cys253 alters its specificity: the best substrate of the mutant F37A + L196F + C253A is cADPR by a short difference, Cys253 mutation being essential for cADPR preference...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348327/genome-instability-as-a-consequence-of-defects-in-the-resolution-of-recombination-intermediates
#10
Stephen C West, Ying Wai Chan
The efficient processing of homologous recombination (HR) intermediates, which often contain four-way structures known as Holliday junctions (HJs), is required for proper chromosome segregation at mitosis. Eukaryotic cells possess three distinct pathways of resolution: (i) HJ dissolution mediated by BLM-topoisomerase IIIα-RMI1-RMI2 (BTR) complex, and HJ resolution catalyzed by either (ii) SLX1-SLX4-MUS81-EME1-XPF-ERCC1 (SMX complex) or (iii) GEN1. The BTR pathway acts at all times throughout the cell cycle, whereas the actions of SMX and GEN1 are restrained in S phase and become elevated late in the cell cycle to ensure the resolution of persistent recombination intermediates before mitotic division...
January 18, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29347912/genome-wide-analysis-of-the-potato-hsp20-gene-family-identification-genomic-organization-and-expression-profiles-in-response-to-heat-stress
#11
Peng Zhao, Dongdong Wang, Ruoqiu Wang, Nana Kong, Chao Zhang, Chenghui Yang, Wentao Wu, Haoli Ma, Qin Chen
BACKGROUND: Heat shock proteins (Hsps) are essential components in plant tolerance mechanism under various abiotic stresses. Hsp20 is the major family of heat shock proteins, but little of Hsp20 family is known in potato (Solanum tuberosum), which is an important vegetable crop that is thermosensitive. RESULTS: To reveal the mechanisms of potato Hsp20s coping with abiotic stresses, analyses of the potato Hsp20 gene family were conducted using bioinformatics-based methods...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29346775/brd4-promotes-dna-repair-and-mediates-the-formation-of-tmprss2-erg-gene-rearrangements-in-prostate-cancer
#12
Xiangyi Li, GuemHee Baek, Susmita G Ramanand, Adam Sharp, Yunpeng Gao, Wei Yuan, Jon Welti, Daniel N Rodrigues, David Dolling, Ines Figueiredo, Semini Sumanasuriya, Mateus Crespo, Adam Aslam, Rui Li, Yi Yin, Bipasha Mukherjee, Mohammed Kanchwala, Ashley M Hughes, Wendy S Halsey, Cheng-Ming Chiang, Chao Xing, Ganesh V Raj, Sandeep Burma, Johann de Bono, Ram S Mani
BRD4 belongs to the bromodomain and extraterminal (BET) family of chromatin reader proteins that bind acetylated histones and regulate gene expression. Pharmacological inhibition of BRD4 by BET inhibitors (BETi) has indicated antitumor activity against multiple cancer types. We show that BRD4 is essential for the repair of DNA double-strand breaks (DSBs) and mediates the formation of oncogenic gene rearrangements by engaging the non-homologous end joining (NHEJ) pathway. Mechanistically, genome-wide DNA breaks are associated with enhanced acetylation of histone H4, leading to BRD4 recruitment, and stable establishment of the DNA repair complex...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346668/rad51-and-rtel1-compensate-telomere-loss-in-the-absence-of-telomerase
#13
Margaux Olivier, Cyril Charbonnel, Simon Amiard, Charles I White, Maria E Gallego
Replicative erosion of telomeres is naturally compensated by telomerase and studies in yeast and vertebrates show that homologous recombination can compensate for the absence of telomerase. We show that RAD51 protein, which catalyzes the key strand-invasion step of homologous recombination, is localized at Arabidopsis telomeres in absence of telomerase. Blocking the strand-transfer activity of the RAD51 in telomerase mutant plants results in a strikingly earlier onset of developmental defects, accompanied by increased numbers of end-to-end chromosome fusions...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346554/functional-roles-of-sex-biased-growth-hormone-regulated-micrornas-mir-1948-and-mir-802-in-young-adult-mouse-liver
#14
Pengying Hao, David J Waxman
Sex-specific temporal patterns of pituitary GH secretion determine the sex-biased transcription of hundreds of genes in the liver and impart significant sex differences in liver physiology, metabolism and disease. Sex differences in hepatic gene expression vary widely, ranging from <2-fold to >1,000-fold in the mouse. Here, we use small RNA sequencing to discover 24 sex-biased mouse liver miRNAs, and then investigate the roles of two of these miRNAs in GH-regulated liver sex differences. Studies in pre-pubertal and young adult mice, and in mice where pituitary hormones are ablated or where sex-specific hepatic GH signaling is dysregulated, demonstrated that the male-biased miR-1948 and the female-biased miR-802 are both regulated by sex-specific pituitary GH secretory patterns, acquire sex specificity at puberty, and are dependent on the GH-activated transcription factor STAT5 for their sex-specific expression...
January 16, 2018: Endocrinology
https://www.readbyqxmd.com/read/29346513/pancancer-analysis-identifies-prognostic-high-apobec1-expression-level-implicated-in-cancer-in-frame-insertions-and-deletions
#15
Ahmadreza Niavarani, Asieh Shahrabi Farahani, Maryam Sharafkhah, Minoo Rassoulzadegan
Genome insertions and deletions (indels) show tremendous functional impacts despite they are much less common than single nucleotide variants, which are at the center of studies assessing cancer mutational signatures. We studied 8,891 tumor samples of 32 types from The Cancer Genome Atlas in order to explore those genes which are potentially implicated in cancer indels. Survival analysis identified in-frame indels as the most important variants predicting adverse outcome. Transcriptome-wide association study identified 16 genes overexpressed in both tumor samples and tumor types with high number of in-frame indels, of whom four (APOBEC1, BCL2L15, FOXL1, and PDX1) were identified with gene products distributed within the nucleus...
January 13, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29346437/tissue-specific-transcriptome-analyses-provide-new-insights-into-gpcr-signalling-in-adult-schistosoma-mansoni
#16
REVIEW
Steffen Hahnel, Nic Wheeler, Zhigang Lu, Arporn Wangwiwatsin, Paul McVeigh, Aaron Maule, Matthew Berriman, Timothy Day, Paula Ribeiro, Christoph G Grevelding
Schistosomes are blood-dwelling trematodes with global impact on human and animal health. Because medical treatment is currently based on a single drug, praziquantel, there is urgent need for the development of alternative control strategies. The Schistosoma mansoni genome project provides a platform to study and connect the genetic repertoire of schistosomes to specific biological functions essential for successful parasitism. G protein-coupled receptors (GPCRs) form the largest superfamily of transmembrane receptors throughout the Eumetazoan phyla, including platyhelminths...
January 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29344951/the-rise-of-a-novel-classification-system-for-endometrial-carcinoma-integration-of-molecular-subclasses
#17
REVIEW
Jessica McAlpine, Alicia Leon-Castillo, Tjalling Bosse
Endometrial cancer is a clinically heterogeneous disease and it is becoming increasingly clear that this heterogeneity may be a function of the diversity of the underlying molecular alterations. Recent large scale genomic studies have revealed that endometrial cancer can be divided into at least four distinct molecular subtypes, with well described underlying genomic aberrations. These subtypes can be reliably delineated and carry significant prognostic as well as predictive information; embracing and incorporating them into clinical practice is thus attractive...
January 17, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344903/nuclear-genes-involved-in-mitochondrial-diseases-caused-by-instability-of-mitochondrial-dna
#18
REVIEW
Joanna Rusecka, Magdalena Kaliszewska, Ewa Bartnik, Katarzyna Tońska
Mitochondrial diseases are defined by a respiratory chain dysfunction and in most of the cases manifest as multisystem disorders with predominant expression in muscles and nerves and may be caused by mutations in mitochondrial (mtDNA) or nuclear (nDNA) genomes. Most of the proteins involved in respiratory chain function are nuclear encoded, although 13 subunits of respiratory chain complexes (together with 2 rRNAs and 22 tRNAs necessary for their translation) encoded by mtDNA are essential for cell function...
January 17, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29344864/laser-capture-microdissection-in-traumatic-brain-injury-research-obtaining-hippocampal-subregions-and-pools-of-injured-neurons-for-genomic-analyses
#19
Deborah R Boone, Harris A Weisz, Stacy L Sell, Helen L Hellmich
The methods presented here are based on our laboratory's 15 years of experience using laser capture microdissection to obtain samples for the study of gene expression after traumatic brain injury (TBI) using a well-established rat model of experimental TBI. Here, we describe how to use the ArcturusXT laser capture microdissection system to capture swaths of specific regions of the rat hippocampus as well as specific neuronal populations defined by Fluoro-Jade C staining. Staining with Fluoro-Jade C identifies a neuron that is in the process of degeneration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29343579/identification-of-poxvirus-genome-uncoating-and-dna-replication-factors-with-mutually-redundant-roles
#20
Baoming Liu, Debasis Panda, Jorge D Mendez-Rios, Sundar Ganesan, Linda S Wyatt, Bernard Moss
Genome uncoating is essential for replication of most viruses. For poxviruses, the process is divided into two stages: removal of the envelope allowing early gene expression, and breaching of the core wall allowing DNA release, replication and late gene expression. Subsequent studies showed that the host proteasome and the viral D5 protein, which has an essential role in DNA replication, are required for vaccinia virus (VACV) genome uncoating. In a search for additional VACV uncoating proteins, we noted a report that described a defect in DNA replication and late expression when the gene encoding a 68 kDa ankyrin-repeat/F box protein (68k-ank), associated with the cellular SCF ubiquitin ligase complex, was deleted from the attenuated modified vaccinia virus Ankara (MVA)...
January 17, 2018: Journal of Virology
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