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https://www.readbyqxmd.com/read/28813005/identification-and-functional-divergence-analysis-of-wox-gene-family-in-paper-mulberry
#1
Feng Tang, Naizhi Chen, Meiling Zhao, Yucheng Wang, Ruiping He, Xianjun Peng, Shihua Shen
The WOX (WUSCHEL-related homeobox) is a plant-specific transcription factor involved in plant development and stress response. However, few studies have been reported on the WOX gene in woody plants. In this study, 10 BpWOX genes were isolated from paper mulberry by RACE-PCR and categorized into three clades through phylogenetic analysis, ancient, intermediate and WUS clade. Among them, five members had the transcriptional activity detected by yeast one-hybrid and seven were uniquely localized to the nucleus through green fluorescent protein (GFP) observation...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812709/adaptation-to-deep-sea-chemosynthetic-environments-as-revealed-by-mussel-genomes
#2
Jin Sun, Yu Zhang, Ting Xu, Yang Zhang, Huawei Mu, Yanjie Zhang, Yi Lan, Christopher J Fields, Jerome Ho Lam Hui, Weipeng Zhang, Runsheng Li, Wenyan Nong, Fiona Ka Man Cheung, Jian-Wen Qiu, Pei-Yuan Qian
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro-benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago...
April 3, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811569/transcriptional-response-to-stress-is-pre-wired-by-promoter-and-enhancer-architecture
#3
Anniina Vihervaara, Dig Bijay Mahat, Michael J Guertin, Tinyi Chu, Charles G Danko, John T Lis, Lea Sistonen
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. Here, to investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Our results globally show that the release of promoter-proximal paused RNA polymerase into elongation functions as a critical switch at which a gene's response to stress is determined...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811350/defining-the-dna-binding-site-recognized-by-the-fission-yeast-zn2cys6-transcription-factor-pho7-and-its-role-in-phosphate-homeostasis
#4
Beate Schwer, Ana M Sanchez, Angad Garg, Debashree Chatterjee, Stewart Shuman
Fission yeast phosphate homeostasis entails transcriptional induction of genes encoding phosphate-mobilizing proteins under conditions of phosphate starvation. Transcription factor Pho7, a member of the Zn2Cys6 family of fungal transcription regulators, is the central player in the starvation response. The DNA binding sites in the promoters of phosphate-responsive genes have not been defined, nor have any structure-function relationships been established for the Pho7 protein. Here we narrow this knowledge gap by (i) delineating an autonomous DNA-binding domain (DBD) within Pho7 that includes the Zn2Cys6 module, (ii) deploying recombinant Pho7 DBD in DNase I footprinting and electrophoretic mobility shift assays (EMSAs) to map the Pho7 recognition sites in the promoters of the phosphate-regulated pho1 and tgp1 genes to a 12-nucleotide sequence motif [5'-TCG(G/C)(A/T)xxTTxAA], (iii) independently identifying the same motif as a Pho7 recognition element via in silico analysis of available genome-wide ChIP-seq data, (iv) affirming that mutations in the two Pho7 recognition sites in the pho1 promoter efface pho1 expression in vivo, and (v) establishing that the zinc-binding cysteines and a pair of conserved arginines in the DBD are essential for Pho7 activity in vivoIMPORTANCE Fungi respond to phosphate starvation by inducing the transcription of a set of phosphate acquisition genes that comprise a phosphate regulon...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28811072/evolution-of-hemoglobin-loci-and-their-regulatory-elements
#5
REVIEW
Sjaak Philipsen, Ross C Hardison
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene...
August 9, 2017: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/28810863/multiple-essential-functions-of-plasmodium-falciparum-actin-1-during-malaria-blood-stage-development
#6
Sujaan Das, Leandro Lemgruber, Chwen L Tay, Jake Baum, Markus Meissner
BACKGROUND: The phylum Apicomplexa includes intracellular parasites causing immense global disease burden, the deadliest of them being the human malaria parasite Plasmodium falciparum, which invades and replicates within erythrocytes. The cytoskeletal protein actin is well conserved within apicomplexans but divergent from mammalian actins, and was primarily reported to function during host cell invasion. However, novel invasion mechanisms have been described for several apicomplexans, and specific functions of the acto-myosin system are being reinvestigated...
August 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28810523/reactive-oxygen-species-mediated-nf-%C3%AE%C2%BAb-p38-feedback-loop-implicated-in-proliferation-inhibition-of-hfls-ra-cells-induced-by-1-7-dihydroxy-3-4-dimethoxyxanthone
#7
Jian Zuo, De-Yu Dou, Hui-Fang Wang, Yan-Hong Zhu, Yan Li, Jia-Jie Luan
1,7-Dihydroxy-3,4-dimethoxyxanthone (XAN) is a bioactive compound isolated from Securidaca inappendiculata Hassk. and exerts the inhibitory effects on fibroblast-like synoviocytes by targeting NF-κB and p38. This study was designed to elucidate mechanisms underlying the divergent regulation on the two pathways in HFLS-RA cells by XAN. Expressions of hallmark proteins and transcription of GADD45α mRNA were determined by Western-blot and RT-qPCR methods, respectively. Fluorescence staining was employed to evaluate intracellular oxidative stress...
August 11, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28808654/genome-wide-identification-and-transcriptional-expression-analysis-of-cucumber-superoxide-dismutase-sod-family-in-response-to-various-abiotic-stresses
#8
Yong Zhou, Lifang Hu, Hao Wu, Lunwei Jiang, Shiqiang Liu
Superoxide dismutase (SOD) proteins are widely present in the plant kingdom and play important roles in different biological processes. However, little is known about the SOD genes in cucumber. In this study, night SOD genes were identified from cucumber (Cucumis sativus) using bioinformatics-based methods, including 5 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Phylogenetic analyses with SODs from cucumber and several other species revealed that these SOD proteins can be traced back to two ancestral SODs before the divergence of monocot and dicot plants...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28808356/the-gist-of-delay-of-gratification-understanding-and-predicting-problem-behaviors
#9
Valerie F Reyna, Evan A Wilhelms
Delay of gratification captures elements of temptation and self-denial that characterize real-life problems with money and other problem behaviors such as unhealthy risk taking. According to fuzzy-trace theory, decision makers mentally represent social values such as delay of gratification in a coarse but meaningful form of memory called "gist." Applying this theory, we developed a gist measure of delay of gratification that does not involve quantitative trade-offs (as delay discounting does) and hypothesize that this construct explains unique variance beyond sensation seeking and inhibition in accounting for problem behaviors...
April 2017: Journal of Behavioral Decision Making
https://www.readbyqxmd.com/read/28808066/maternal-mrnas-with-distinct-3-utrs-define-the-temporal-pattern-of-ccnb1-synthesis-during-mouse-oocyte-meiotic-maturation
#10
Ye Yang, Cai-Rong Yang, Seung Jin Han, Enrico Maria Daldello, Ara Cho, Joao P Sousa Martins, Guoliang Xia, Marco Conti
The final stages of female gamete maturation occur in the virtual absence of transcription, with gene expression driven by a program of selective unmasking, translation, and degradation of maternal mRNAs. Here we demonstrate that the timing of Ccnb1 mRNA translation in mouse oocytes is dependent on the presence of transcripts with different 3' untranslated regions (UTRs). This 3' UTR heterogeneity directs distinct temporal patterns of translational activation or repression. Inclusion or exclusion of cis-acting elements is responsible for these divergent regulations...
July 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28805714/does-osmotic-stress-affect-natural-product-expression-in-fungi
#11
David Overy, Hebelin Correa, Catherine Roullier, Wei-Chiung Chi, Ka-Lai Pang, Mostafa Rateb, Rainer Ebel, Zhuo Shang, Rob Capon, Gerald Bills, Russell Kerr
The discovery of new natural products from fungi isolated from the marine environment has increased dramatically over the last few decades, leading to the identification of over 1000 new metabolites. However, most of the reported marine-derived species appear to be terrestrial in origin yet at the same time, facultatively halo- or osmotolerant. An unanswered question regarding the apparent chemical productivity of marine-derived fungi is whether the common practice of fermenting strains in seawater contributes to enhanced secondary metabolism? To answer this question, a terrestrial isolate of Aspergillus aculeatus was fermented in osmotic and saline stress conditions in parallel across multiple sites...
August 13, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28804459/metabolic-variability-of-a-multispecies-probiotic-preparation-impacts-on-the-anti-inflammatory-activity
#12
Michele Biagioli, Luca Laghi, Adriana Carino, Sabrina Cipriani, Eleonora Distrutti, Silvia Marchianò, Carola Parolin, Paolo Scarpelli, Beatrice Vitali, Stefano Fiorucci
Background: In addition to strain taxonomy, the ability of probiotics to confer beneficial effects on the host rely on a number of additional factors including epigenetic modulation of bacterial genes leading to metabolic variability and might impact on probiotic functionality. Aims: To investigate metabolism and functionality of two different batches of a probiotic blend commercialized under the same name in Europe in models of intestinal inflammation. Methods: Boxes of VSL#3, a probiotic mixture used in the treatment of pouchitis, were obtained from pharmacies in UK subjected to metabolomic analysis and their functionality tested in mice rendered colitis by treatment with DSS or TNBS...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28802695/scarce-resource-allocation-during-disasters-a-mixed-method-community-engagement-study
#13
Elizabeth Lee Daugherty Biddison, Howard S Gwon, Monica Schoch-Spana, Alan C Regenberg, Chrissie Juliano, Ruth R Faden, Eric S Toner
BACKGROUND: During a catastrophe, health care providers may face difficult questions regarding who will receive limited life-saving resources. The ethical principles that should guide decision-making have been considered by expert panels but have not been well explored with the public or front line clinicians. The objective of this study was to characterize the public's values regarding how scarce mechanical ventilators should be allocated during an influenza pandemic, with the ultimate goal of informing a statewide scare resource allocation framework...
August 9, 2017: Chest
https://www.readbyqxmd.com/read/28802080/segmental-allotetraploidy-generates-extensive-homeologous-expression-rewiring-and-phenotypic-diversity-at-the-population-level-in-rice
#14
Yue Sun, Ying Wu, Chunwu Yang, Shuai Sun, Xiuyun Lin, Lixia Liu, Chunming Xu, Jonathan F Wendel, Lei Gong, Bao Liu
Allopolyploidization, i.e., concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genome-wide transcriptome dynamics, a phenomenon referred to as "transcriptomic shock". However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain under-investigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic, and homeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), in vitro "hybrids" (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5(th) -selfed generation (S5)...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28801915/manganese-and-1-methyl-4-phenylpyridinium-mpp-induced-neurotoxicity-indicate-differences-in-morphological-electrophysiological-and-genome-wide-alterations-implications-for-idiopathic-parkinson-s-disease
#15
Rajeswara Babu Mythri, Narayana Reddy Raghunath, Santosh Chandrakant Narwade, Mirazkar DasharathaRao Pandareesh, Kollarkandi Rajesh Sabitha, Mohamad Aiyaz, Bipin Chand, Manas Sule, Krittika Ghosh, Senthil Kumar, Bhagyalakshmi Shankarappa, Soundarya Soundararajan, Phalguni Anand Alladi, Meera Purushottam, Narayanappa Gayathri, Deepti Dileep Deobagkar, Thenkanidiyoor Rao Laxmi, Srinivas Bharath Muchukunte Mukunda
Idiopathic Parkinson's disease (iPD) and manganese-induced atypical Parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to levodopa distinguish both, differences at the neuronal level are largely unknown. We studied the morphological, neurophysiological and molecular differences in dopaminergic neurons exposed to the PD toxin 1-methyl-4-phenylpyridinium ion (MPP(+) ) and manganese (Mn) followed by validation in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and Mn mouse models...
August 12, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28801556/collective-modes-in-simple-melts-transition-from-soft-spheres-to-the-hard-sphere-limit
#16
Sergey Khrapak, Boris Klumov, Lénaïc Couëdel
We study collective modes in a classical system of particles with repulsive inverse-power-law (IPL) interactions in the fluid phase, near the fluid-solid coexistence (IPL melts). The IPL exponent is varied from n = 10 to n = 100 to mimic the transition from moderately soft to hard-sphere-like interactions. We compare the longitudinal dispersion relations obtained using molecular dynamic (MD) simulations with those calculated using the quasi-crystalline approximation (QCA) and find that this simple theoretical approach becomes grossly inaccurate for [Formula: see text]...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800300/intraventricular-vector-flow-mapping-a-doppler-based-regularized-problem-with-automatic-model-selection
#17
Kondo Claude Assi, Etienne Gay, Christophe Chnafa, Simon Mendez, Franck Nicoud, Juan F P J Abascal, Pierre Lantelme, François Tournoux, Damien Garcia
We propose a regularized least-squares method for reconstructing 2D velocity vector fields within the left ventricular cavity from single-view color Doppler echocardiographic images. Vector flow mapping is formulated as a quadratic optimization problem based on an [Formula: see text]-norm minimization of a cost function composed of a Doppler data-fidelity term and a regularizer. The latter contains three physically interpretable expressions related to 2D mass conservation, Dirichlet boundary conditions, and smoothness...
August 11, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28793262/adaptive-evolution-of-gene-expression-in-drosophila
#18
Armita Nourmohammad, Joachim Rambeau, Torsten Held, Viera Kovacova, Johannes Berg, Michael Lässig
Gene expression levels are important quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies have revealed substantial adaptive evolution at the genomic level, but the evolutionary modes of gene expression remain controversial. Here, we present evidence that adaptation dominates the evolution of gene expression levels in flies. We show that 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28793240/cultural-values-and-the-prevalence-of-mental-disorders-in-25-countries-a-secondary-data-analysis
#19
Eva Heim, Iris Wegmann, Andreas Maercker
RATIONALE: The prevalence of common mental disorders (CMDs, i.e., depression and anxiety) worldwide is substantial, and prevalence rates are higher in high-income than in low- and middle-income countries. This difference might reflect both underlying prevalence rates as well as the measurement model used in cross-national epidemiological studies. Schwartz' cultural values provide a meaningful taxonomy to describe 'culture' and to examine how culture affects both the aetiology and phenomenology of CMDs...
July 29, 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/28791907/a-one-step-procedure-for-immobilising-the-thermostable-carbonic-anhydrase-sspca-on-the-surface-membrane-of-escherichia-coli
#20
Sonia Del Prete, Rosa Perfetto, Mosè Rossi, Fatmah A S Alasmary, Sameh M Osman, Zeid AlOthman, Claudiu T Supuran, Clemente Capasso
The carbonic anhydrase superfamily (CA, EC 4.2.1.1) of metalloenzymes is present in all three domains of life (Eubacteria, Archaea, and Eukarya), being an interesting example of convergent/divergent evolution, with its seven families (α-, β-, γ-, δ-, ζ-, η-, and θ-CAs) described so far. CAs catalyse the simple, but physiologically crucial reaction of carbon dioxide hydration to bicarbonate and protons. Recently, our groups characterised the α-CA from the thermophilic bacterium, Sulfurihydrogenibium yellowstonense finding a very high catalytic activity for the CO2 hydration reaction (kcat = 9...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
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