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https://www.readbyqxmd.com/read/29777708/identification-of-a-repressor-and-an-activator-of-azoreductase-gene-expression-in-pseudomonas-putida-and-xanthomonas-oryzae
#1
Wirongrong Whangsuk, Neal Toewiwat, James Dubbs, Ratiboot Sallabhan, Skorn Mongkolsuk, Suvit Loprasert
Genes responsible for the production of azoreductase enzymes in 2 g negative bacteria, the soil bacterium Pseudomonas putida (AzoP) and the plant pathogen Xanthomonas oryzae (AzoX), were identified. The deduced amino acid sequences of AzoP and AzoX, share 46% amino acid identity to each other. Two different bacterial transcription factors, a repressor (AzoPR) and an activator (AzoXR), in P. putida and X. oryzae, respectively, were found to be divergently oriented to their respective azoreductase genes. Both regulators are LysR-type transcriptional regulators (LTTR) that respond to the azo dye inducer, methyl red (MR)...
May 16, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29777493/transgenic-mice-carrying-glud2-as-a-tool-for-studying-the-expressional-and-the-functional-adaptation-of-this-positive-selected-gene-in-human-brain-evolution
#2
Andreas Plaitakis, Dimitra Kotzamani, Zoe Petraki, Maria Delidaki, Vagelis Rinotas, Ioannis Zaganas, Eleni Douni, Kyriaki Sidiropoulou, Cleanthe Spanaki
Human evolution is characterized by brain expansion and up-regulation of genes involved in energy metabolism and synaptic transmission, including the glutamate signaling pathway. Glutamate is the excitatory transmitter of neural circuits sub-serving cognitive functions, with glutamate-modulation of synaptic plasticity being central to learning and memory. GLUD2 is a novel positively-selected human gene involved in glutamatergic transmission and energy metabolism that underwent rapid evolutionary adaptation concomitantly with prefrontal cortex enlargement...
May 18, 2018: Neurochemical Research
https://www.readbyqxmd.com/read/29775608/regulation-of-the-gyr-operon-of-mycobacterium-tuberculosis-by-overlapping-promoters-dna-topology-and-reiterative-transcription
#3
Rajiv Kumar Jha, Priyanka Tare, Valakunja Nagaraja
DNA gyrase introduces negative supercoils into DNA to maintain topological homeostasis. The genes encoding gyrase, gyrB and gyrA, form a dicistronic operon in Mycobacterium tuberculosis (Mtb) and other actinobacteria. Earlier work indicated that DNA relaxation stimulates the expression of the gyr genes, a phenomenon termed relaxation-stimulated transcription (RST). The present study addresses the underlying mechanism of gyr operon regulation. The operon is regulated by overlapping and divergently oriented promoters located upstream of gyrB...
May 15, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29774426/plant-physical-and-chemical-defence-variation-along-elevation-gradients-a-functional-trait-based-approach
#4
Alan Kergunteuil, Patrice Descombes, Gaetan Glauser, Loïc Pellissier, Sergio Rasmann
Predicting variation in plant functional traits related to anti-herbivore defences remains a major challenge in ecological research, considering that multiple traits have evolved in response to both abiotic and biotic conditions. Therefore, understanding variation in plant anti-herbivore defence traits requires studying their expression along steep environmental gradients, such as along elevation, where multiple biotic and abiotic factors co-vary. We expand on plant defence theory and propose a novel conceptual framework to address the sources of variations of plant resistance traits at the community level...
May 17, 2018: Oecologia
https://www.readbyqxmd.com/read/29774338/trace-metals-in-oysters-molecular-and-cellular-mechanisms-and-ecotoxicological-impacts
#5
REVIEW
Wen-Xiong Wang, Jie Meng, Nanyan Weng
Oysters are important benthic bivalves in coastal and estuarine environments. They are widely farmed due to their rapid growth and taste; they are also widely applied in environmental monitoring of coastal pollution due to their accumulation of contaminants. Most importantly, oysters are among the few marine organisms that are considered to be hyper-accumulators of many toxic metals, such as cadmium, copper and zinc. As such, there is a tremendous call to study the interactions between metals and oysters, especially due to the increasing metal pollution in many coastal and estuarine waters...
May 18, 2018: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/29773862/nanojunction-effects-on-water-flow-in-carbon-nanotubes
#6
Fatemeh Ebrahimi, Farzaneh Ramazani, Muhammad Sahimi
We report on the results of extensive molecular dynamics simulation of water imbibition in carbon nanotubes (CNTs), connected together by converging or diverging nanojunctions in various configurations. The goal of the study is to understand the effect of the nanojunctions on the interface motion, as well as the differences between what we study and water imbibition in microchannels. While the dynamics of water uptake in the entrance CNT is the same as that of imbibition in straight CNTs, with the main source of energy dissipation being the friction at the entrance, water uptake in the exit CNT is more complex due to significant energy loss in the nanojunctions...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29772825/identification-and-characterization-of-the-wox-family-genes-in-five-solanaceae-species-reveal-their-conserved-roles-in-peptide-signaling
#7
Xiaoxu Li, Madiha Hamyat, Cheng Liu, Ahmad Salman, Xiaoming Gao, Cun Guo, Yuanying Wang, Yongfeng Guo
Members of the plant-specific WOX (WUSCHEL-related homeobox) transcription factor family have been reported to play important roles in peptide signaling that regulates stem cell maintenance and cell fate specification in various developmental processes. Even though remarkable advances have been made in studying WOX genes in Arabidopsis , little is known about this family in Solanaceae species. A total of 45 WOX members from five Solanaceae species were identified, including eight members from Solanum tuberosum , eight from Nicotiana tomentosiformis , 10 from Solanum lycopersicum , 10 from Nicotiana sylvestris and nine from Nicotiana tabacum ...
May 17, 2018: Genes
https://www.readbyqxmd.com/read/29772086/physcomitrella-patens-reute-mcherry-as-a-tool-for-efficient-crossing-within-and-between-ecotypes
#8
Pierre-François Perroud, Rabea Meyberg, Stefan A Rensing
Physcomitrella patens is a monoicous moss that is predominantly selfing in the wild. Laboratory crossing techniques have been established and crosses between the sequenced Gransden ecotype and the genetically divergent Villersexel ecotype were used for genetic mapping. The recently introduced ecotype Reute displays a high fertility rate and is genetically more closely related to the Gransden reference genome than the Villersexel ecotype. The Reute sexual reproduction phenology is similar to Gransden, which should allow successful crossing...
May 17, 2018: Plant Biology
https://www.readbyqxmd.com/read/29771926/evolutionary-and-genomic-analysis-of-the-caleosin-peroxygenase-clo-pxg-gene-protein-families-in-the-viridiplantae
#9
Farzana Rahman, Mehedi Hassan, Rozana Rosli, Ibrahem Almousally, Abdulsamie Hanano, Denis J Murphy
Bioinformatics analyses of caleosin/peroxygenases (CLO/PXG) demonstrated that these genes are present in the vast majority of Viridiplantae taxa for which sequence data are available. Functionally active CLO/PXG proteins with roles in abiotic stress tolerance and lipid droplet storage are present in some Trebouxiophycean and Chlorophycean green algae but are absent from the small number of sequenced Prasinophyceaen genomes. CLO/PXG-like genes are expressed during dehydration stress in Charophyte algae, a sister clade of the land plants (Embryophyta)...
2018: PloS One
https://www.readbyqxmd.com/read/29771147/gpf15-promotes-epithelial-to-mesenchymal-transition-in-colorectal-carcinoma
#10
Yifei Zhang, Xixun Wang, Menglai Zhang, Zhenbin Zhang, Lixin Jiang, Leping Li
Growth differentiation factor 15 (GDF15) is a divergent member of the transforming growth factor-β (TGF-β) superfamily that has been associated with colorectal cancers (CRC). However, the role of GDF15 in the progression of CRC remains unknown. We demonstrated that GDF15 expression was higher in fresh CRC tissues than in adjacent normal tissues. Moreover, we found that GDF15 overexpression significantly facilitated cell viability, cell invasion and migration (p < .01 or p < .05). The protein expression of N-cadherin, vimentin and Twist1 were up-regulated by GDF15 overexpression, while E-cadherin was down-regulated...
May 17, 2018: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/29769532/aid-apobec-like-cytidine-deaminases-are-ancient-innate-immune-mediators-in-invertebrates
#11
Mei-Chen Liu, Wen-Yun Liao, Katherine M Buckley, Shu Yuan Yang, Jonathan P Rast, Sebastian D Fugmann
In the course of both innate and adaptive immunity, cytidine deaminases within the activation induced cytidine deaminase (AID)/apolipoprotein B editing complex (APOBEC) family modulate immune responses by mutating specific nucleic acid sequences of hosts and pathogens. The evolutionary emergence of these mediators, however, seems to coincide precisely with the emergence of adaptive immunity in vertebrates. Here, we show a family of genes in species within two divergent invertebrate phyla-the echinoderm Strongylocentrotus purpuratus and the brachiopod Lingula anatina-that encode proteins with similarities in amino acid sequence and enzymatic activities to the vertebrate AID/APOBECs...
May 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29769334/reovirus-nonstructural-protein-%C3%AF-ns-acts-as-an-rna-stability-factor-promoting-viral-genome-replication
#12
Paula F Zamora, Liya Hu, Jonathan J Knowlton, Roni M Lahr, Rodolfo A Moreno, Andrea J Berman, B V Venkataram Prasad, Terence S Dermody
Viral nonstructural proteins, which are not packaged into virions, are essential for replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. Reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, activities of σNS during individual steps of the reovirus replication cycle are poorly understood...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29769290/assessment-of-an-organ-specific-de-novo-transcriptome-of-the-nematode-trap-crop-solanum-sisymbriifolium
#13
Alexander Q Wixom, N Carol Casavant, Joseph C Kuhl, Fangming Xiao, Louise-Marie Dandurand, Allan B Caplan
Solanum sisymbriifolium , also known as "Litchi Tomato" or "Sticky Nightshade," is an undomesticated and poorly researched plant related to potato and tomato. Unlike the latter species, S. sisymbriifolium induces eggs of the cyst nematode, Globodera pallida , to hatch and migrate into its roots, but then arrests further nematode maturation. In order to provide researchers with a partial blueprint of its genetic make-up so that the mechanism of this response might be identified, we used single molecule real time (SMRT) sequencing to compile a high quality de novo transcriptome of 41,189 unigenes drawn from individually sequenced bud, root, stem, and leaf RNA populations...
May 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29767366/expression-profiling-of-differentially-regulated-genes-in-fanconi-anemia
#14
Binita Zipporah E, Kavitha Govarthanan, Pavithra Shyamsunder, Rama S Verma
Gene expression analysis mainly helps to study gene quantification methods by using various downstream detection approaches like imaging, amplification, probe hybridization, or sequencing. With respect to DNA, which is less static, mRNA levels vary over time, between cell types under divergent conditions. Gene expression analysis is principally focused on determination of mRNA levels transcribed from DNA. DNA microarrays are one of the robust and powerful tools to detect changes in multiple transcripts in larger cohorts in parallel...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29764463/lncmapk6-drives-mapk6-expression-and-liver-tic-self-renewal
#15
Guanqun Huang, Hui Jiang, Yueming He, Ye Lin, Wuzheng Xia, Yuanwei Luo, Min Liang, Boyun Shi, Xinke Zhou, Zhixiang Jian
BACKGROUND: Liver tumor initiating cells (TICs) have self-renewal and differentiate capacities, and largely contribute to tumor initiation, metastasis and drug resistance. MAPK signaling is a critical pathway in many biological processes, while its role in liver TICs hasn't been explored. METHODS: Online-available dataset was used for unbiased screening. Liver TICs were examined CD133 FACS or oncosphere formation. TIC self-renewal was detected by oncosphere formation and tumor initiation assay...
May 15, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29764367/papain-like-and-legumain-like-proteases-in-rice-genome-wide-identification-comprehensive-gene-feature-characterization-and-expression-analysis
#16
Wei Wang, Xue-Mei Zhou, Han-Xian Xiong, Wan-Ying Mao, Peng Zhao, Meng-Xiang Sun
BACKGROUND: Papain-like and legumain-like proteases are proteolytic enzymes which play key roles in plant development, senescence and defense. The activities of proteases in both families could be inhibited by a group of small proteins called cystatin. Cystatin family genes have been well characterized both in tobacco and rice, suggesting their potential roles in seed development. However, their potential targets, papain-like and legumain-like proteases, have not been well characterized in plants, especially in rice, a model plant for cereal biology...
May 15, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29764289/divergent-induction-of-branched-chain-aminotransferases-and-phosphorylation-of-branched-chain-keto-acid-dehydrogenase-is-a-potential-mechanism-coupling-bcka-mediated-astrocyte-activation-to-bcaa-depletion-mediated-cognitive-deficit-after-tbi
#17
Guoqiang Xing, Ming Ren, Ajay Verma
Deficient branched chain amino acids (BCAAs) are implicated in cognitive dysfunction after traumatic brain injury (TBI). The mechanism remains unknown. BCAAs are catabolized by neuron-specific cytosolic and astrocyte-specific mitochondrial branched chain aminotransferases (BCATc, BCATm) to generate glutamate and branched-chain keto-acids (BCKAs) that are metabolized via the mitochondrial branched-chain-keto-acid dehydrogenase (BCKD) whose activity is regulated by its phosphorylation state. BCKD phosphorylation by BCKD kinase (BCKDK) inactivates BCKD and cause neuro-cognitive dysfunction, whereas de-phosphorylation by specific phosphatase restores BCKD activity...
May 15, 2018: Journal of Neurotrauma
https://www.readbyqxmd.com/read/29761415/effects-of-genetic-distance-on-heterosis-in-a-drosophila-melanogaster-model-system
#18
Charlotte Jensen, Michael Ørsted, Torsten Nygaard Kristensen
Habitat fragmentation and small population sizes can lead to inbreeding and loss of genetic variation, which can potentially cause inbreeding depression and decrease the ability of populations to adapt to altered environmental conditions. One solution to these genetic problems is the implementation of genetic rescue, which re-establishes gene flow between separated populations. Similar techniques are being used in animal and plant breeding to produce superior production animals and plants. To optimize fitness benefits in genetic rescue programs and to secure high yielding domestic varieties in animal and plant breeding, knowledge on the genetic relatedness of populations being crossed is imperative...
May 14, 2018: Genetica
https://www.readbyqxmd.com/read/29760079/selection-and-environmental-adaptation-along-a-path-to-speciation-in-the-tibetan-frog-nanorana-parkeri
#19
Guo-Dong Wang, Bao-Lin Zhang, Wei-Wei Zhou, Yong-Xin Li, Jie-Qiong Jin, Yong Shao, He-Chuan Yang, Yan-Hu Liu, Fang Yan, Hong-Man Chen, Li Jin, Feng Gao, Yaoguang Zhang, Haipeng Li, Bingyu Mao, Robert W Murphy, David B Wake, Ya-Ping Zhang, Jing Che
Tibetan frogs, Nanorana parkeri , are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29757242/hybrid-transverse-polar-navigation-for-high-precision-and-long-term-inss
#20
Ruonan Wu, Qiuping Wu, Fengtian Han, Rong Zhang, Peida Hu, Haixia Li
Transverse navigation has been proposed to help inertial navigation systems (INSs) fill the gap of polar navigation ability. However, as the transverse system does not have the ability of navigate globally, a complicated switch between the transverse and the traditional algorithms is necessary when the system moves across the polar circles. To maintain the inner continuity and consistency of the core algorithm, a hybrid transverse polar navigation is proposed in this research based on a combination of Earth-fixed-frame mechanization and transverse-frame outputs...
May 12, 2018: Sensors
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