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https://www.readbyqxmd.com/read/28742982/investigation-of-orthologous-pathogen-recognition-gene-rich-regions-in-solanaceous-species
#1
A Di Donato, Giuseppe Andolfo, A Ferrarini, M Delledonne, M R Ercolano
The genome architecture of pathogen receptor genes (PRGs) was extensively investigated in several plant species. However, we still know little about their elaborate reorganization arose during the plant speciation process. Using recently released pepper and eggplant genome sequences we were able to identify 1097 pathogen recognition genes in pepper Zunla-1 and 775 in eggplant Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping...
July 25, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28742821/evolution-of-the-camp-dependent-protein-kinase-pka-catalytic-subunit-isoforms
#2
Kristoffer Søberg, Line Victoria Moen, Bjørn Steen Skålhegg, Jon Kristen Laerdahl
The 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase, or protein kinase A (PKA), pathway is one of the most versatile and best studied signaling pathways in eukaryotic cells. The two paralogous PKA catalytic subunits Cα and Cβ, encoded by the genes PRKACA and PRKACB, respectively, are among the best understood model kinases in signal transduction research. In this work, we explore and elucidate the evolution of the alternative 5' exons and the splicing pattern giving rise to the numerous PKA catalytic subunit isoforms...
2017: PloS One
https://www.readbyqxmd.com/read/28741966/the-connections-of-wnt-pathway-components-with-cell-cycle-and-centrosome-side-effects-or-a-hidden-logic
#3
Vítězslav Bryja, Igor Červenka, Lukáš Čajánek
Wnt signaling cascade has developed together with multicellularity to orchestrate the development and homeostasis of complex structures. Wnt pathway components - such as β-catenin, Dishevelled (DVL), Lrp6, and Axin-- are often dedicated proteins that emerged in evolution together with the Wnt signaling cascade and are believed to function primarily in the Wnt cascade. It is interesting to see that in recent literature many of these proteins are connected with cellular functions that are more ancient and not limited to multicellular organisms - such as cell cycle regulation, centrosome biology, or cell division...
July 25, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28740726/c2h2-zinc-finger-proteins-the-largest-but-poorly-explored-family-of-higher-eukaryotic-transcription-factors
#4
A A Fedotova, A N Bonchuk, V A Mogila, P G Georgiev
The emergence of whole-genome assays has initiated numerous genome-wide studies of transcription factor localizations at genomic regulatory elements (enhancers, promoters, silencers, and insulators), as well as facilitated the uncovering of some of the key principles of chromosomal organization. However, the proteins involved in the formation and maintenance of the chromosomal architecture and the organization of regulatory domains remain insufficiently studied. This review attempts to collate the available data on the abundant but still poorly understood family of proteins with clusters of the C2H2 zinc finger domains...
April 2017: Acta Naturae
https://www.readbyqxmd.com/read/28740497/the-role-of-multiscale-protein-dynamics-in-antigen-presentation-and-t-lymphocyte-recognition
#5
R Charlotte Eccleston, Shunzhou Wan, Neil Dalchau, Peter V Coveney
T lymphocytes are stimulated when they recognize short peptides bound to class I proteins of the major histocompatibility complex (MHC) protein, as peptide-MHC complexes. Due to the diversity in T-cell receptor (TCR) molecules together with both the peptides and MHC proteins they bind to, it has been difficult to design vaccines and treatments based on these interactions. Machine learning has made some progress in trying to predict the immunogenicity of peptide sequences in the context of specific MHC class I alleles but, as such approaches cannot integrate temporal information and lack explanatory power, their scope will always be limited...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28740486/evolution-of-acinetobacter-baumannii-in-vivo-international-clone-ii-more-resistance-to-ceftazidime-mutation-in-ptk
#6
Xiaoting Hua, Zhihui Zhou, Qing Yang, Qiucheng Shi, Qingye Xu, Jianfeng Wang, Keren Shi, Feng Zhao, Long Sun, Zhi Ruan, Yan Jiang, Yunsong Yu
Acinetobacter baumannii is an important nosocomial pathogen worldwide. A more comprehensive understanding of the within-host genomic evolution of A. baumannii would provide a molecule basis for improving treatment of A. baumannii infection. To understand the evolutionary mechanism facilitating A. baumannii survived in human body, we here reported the genomic analysis of A. baumannii isolated sampled from Chinese patients. We used whole-genome sequence of A. baumannii isolates from the same patient to determine single-nucleotide variants, insertion sequence mapping, and gene change...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28739732/reduced-expression-of-ranbpm-is-associated-with-poorer-survival-from-lung-cancer-and-increased-proliferation-and-invasion-of-lung-cancer-cells-in-vitro
#7
Zehang Zhao, Shan Cheng, Catherine Zabkiewicz, Jinfeng Chen, Lijiang Zhang, Lin Ye, Wen G Jiang
BACKGROUND/AIM: Ran binding protein microtubule-organizing centre (RanBPM), also known as RanBP9, is a scaffold protein conserved through evolution. We investigated the role of RanBPM in human lung cancer. MATERIALS AND METHODS: Transcripts of RanBPM were determined in 56 human lung cancers along with paired normal lung tissues using real-time PCR. Association with prognosis was analyzed by online Kaplan-Meier survival analysis. In vitro lung cancer cell functional assays examined the impact of RanBPM-knockdown on cellular growth and invasion...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28738827/bacterial-tail-anchors-can-target-to-the-mitochondrial-outer-membrane
#8
Güleycan Lutfullahoğlu-Bal, Abdurrahman Keskin, Ayşe Bengisu Seferoğlu, Cory D Dunn
BACKGROUND: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria...
July 24, 2017: Biology Direct
https://www.readbyqxmd.com/read/28738772/molecular-docking-and-drug-discovery-in-%C3%AE-adrenergic-receptors
#9
Santiago Vilar, Eduardo Sobarzo-Sánchez, Lourdes Santana, Eugenio Uriarte
Evolution in computer engineering, availability of increasing amounts of data and the development of new and fast docking algorithms and software have led to improved molecular simulations with crucial applications in virtual high-throughput screening and drug discovery. Moreover, analysis of protein-ligand recognition through molecular docking has become a valuable tool in drug design. In this review, we focus on the applicability of molecular docking on a particular class of G protein-coupled receptors: the β-adrenergic receptors, which are relevant targets in clinic for the treatment of asthma and cardiovascular diseases...
July 24, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28738272/evolution-of-corresponding-resistance-genes-in-the-water-of-fish-tanks-with-multiple-stresses-of-antibiotics-and-heavy-metals
#10
Xiaolin He, Yanbin Xu, Jinliang Chen, Jiayin Ling, Yafei Li, Lu Huang, Xiao Zhou, Li Zheng, Guangyan Xie
Abuse of antibiotics and heavy metals in aquaculture has been widely concerned and might aggravate the spread of resistance genes in environment. To investigate the occurrence and proliferation of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs), three commonly used antibiotics (tetracycline, sulfanilamide, cefotaxime) and two heavy metals (Zn and Cu) were designed to add individually or jointly in nine fish tanks including five individual exposure tanks of tetracycline (tet), sulfanilamide (sul), cefotaxime (cef), Cu, Zn and four combination exposure tanks of tetracycline + sulfanilamide (tet + sul), tetracycline + sulfanilamide + cefotaxime (tet + sul + cef), tetracycline + sulfanilamide + Cu (tet + sul + Cu), tetracycline + sulfanilamide + Zn (tet + sul + Zn) as well as the control during the experiment period of 180 days...
July 19, 2017: Water Research
https://www.readbyqxmd.com/read/28736570/genome-wide-identification-and-functional-analysis-of-the-calcineurin-b-like-protein-and-calcineurin-b-like-protein-interacting-protein-kinase-gene-families-in-turnip-brassica-rapa-var-rapa
#11
Xin Yin, Qiuli Wang, Qian Chen, Nan Xiang, Yunqiang Yang, Yongping Yang
The calcineurin B-like protein (CBL)-CBL-interacting protein kinase (CIPK) complex has been identified as a primary component in calcium sensors that perceives various stress signals. Turnip (Brassica rapa var. rapa) has been widely cultivated in the Qinghai-Tibet Plateau for a century as a food crop of worldwide economic significance. These CBL-CIPK complexes have been demonstrated to play crucial roles in plant response to various environmental stresses. However, no report is available on the genome-wide characterization of these two gene families in turnip...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28736036/-regulation-of-the-expression-of-coenzyme-q-synthesis-complex-during-ageing
#12
Carmen Campos-Silva, Iván Reyes-Torres, Maximiliano Rivera, Catherine Meza-Torres, Juan Diego Hernández-Camacho, Elisabet Rodríguez-Bies, Plácido Navas, Guillermo López-Lluch
INTRODUCTION: Coenzyme Q is an essential component in the activity of the mitochondrial electron transport chain. Its synthesis involves, at least, a complex of ten different proteins. In this study, an attempt is made to determine the evolution of the expression of the genes involved in coenzyme Q synthesis during mouse ageing. MATERIAL AND METHODS: The messenger RNA (mRNA) of different organs, such as brain, liver, kidney and skeletal muscle from young (8 months), mature (18 months), and old (24 months) mice was extracted by using Trizol and was then analysed by real time PCR (qPCR) using specific primers for all the known components of the coenzyme Q-synthesis complex (COQ genes)...
July 20, 2017: Revista Española de Geriatría y Gerontología
https://www.readbyqxmd.com/read/28735035/the-lamin-code
#13
Nadir M Maraldi
Unicellular eukaryotes and metazoa present a nuclear envelope (NE) and metazoa express in it one or more lamins that give rise to the nuclear lamina. The expression of different types of lamins is related to the complexity of the organism and the expression of type-A lamins is related to the initial steps of tissue-specific cell differentiation. Several posttranslational modifications characterize the expression of lamin A in the course of cell differentiation, and the alteration of this expression pattern leads to impressive phenotypic diseases that are collectively referred to as laminopathies...
July 19, 2017: Bio Systems
https://www.readbyqxmd.com/read/28734049/development-of-aptamers-against-unpurified-proteins
#14
Shinichi Goto, Kaori Tsukakoshi, Kazunori Ikebukuro
SELEX (Systematic Evolution of Ligands by EXponential enrichment) has been widely used for the generation of aptamers against target proteins. However, its requirement for pure target proteins remains a major problem in aptamer selection, as procedures for protein purification from crude bio-samples are not only complicated but also time and labour consuming. This is because native proteins can be found in a large number of diverse forms because of posttranslational modifications and their complicated molecular conformations...
July 22, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28733422/differences-in-dna-binding-specificity-of-floral-homeotic-protein-complexes-predict-organ-specific-target-genes
#15
Cezary Smaczniak, Jose M Muiño, Dijun Chen, Gerco C Angenent, Kerstin Kaufmann
Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. How these factors achieve their regulatory specificities is however still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS-domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high throughput DNA sequencing (SELEX-seq) on several floral MADS-domain protein homo- and heterodimers to measure their DNA-binding specificities...
July 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28732234/computational-modelling-of-genome-scale-metabolic-networks-and-its-application-to-cho-cell-cultures
#16
REVIEW
Živa Rejc, Lidija Magdevska, Tilen Tršelič, Timotej Osolin, Rok Vodopivec, Jakob Mraz, Eva Pavliha, Nikolaj Zimic, Tanja Cvitanović, Damjana Rozman, Miha Moškon, Miha Mraz
Genome-scale metabolic models (GEMs) have become increasingly important in recent years. Currently, GEMs are the most accurate in silico representation of the genotype-phenotype link. They allow us to study complex networks from the systems perspective. Their application may drastically reduce the amount of experimental and clinical work, improve diagnostic tools and increase our understanding of complex biological phenomena. GEMs have also demonstrated high potential for the optimisation of bio-based production of recombinant proteins...
July 8, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28731826/convergently-evolved-toxic-secondary-metabolites-in-plants-drive-the-parallel-molecular-evolution-of-insect-resistance
#17
Georg Petschenka, Vera Wagschal, Michael von Tschirnhaus, Alexander Donath, Susanne Dobler
Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae)...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731533/improvement-of-d-lactic-acid-production-in-saccharomyces-cerevisiae-under-acidic-conditions-by-evolutionary-and-rational-metabolic-engineering
#18
Seung-Ho Baek, Eunice Y Kwon, Sang-Jeong Bae, Bo-Ram Cho, Seon-Young Kim, Ji-Sook Hahn
Microbial lactic acid (LA) production under acidic fermentation conditions is favorable to reduce the production cost, but circumventing LA toxicity is a major challenge. We generated D-LA-producing Saccharomyces cerevisiae strain JHY5610 by expressing D-lactate dehydrogenase gene (Lm. ldhA) from Leuconostoc mesenteroides, while deleting genes involved in ethanol production (ADH1, ADH2, ADH3, ADH4, and ADH5), glycerol production (GPD1 and GPD2), and degradation of D-LA (DLD1). Adaptive laboratory evolution of JHY5610 led to a strain JHY5710 having higher LA tolerance and D-LA-production capability...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731468/a-role-for-the-cell-wall-protein-silacidin-in-cell-size-of-the-diatom-thalassiosira-pseudonana
#19
Amy R Kirkham, Patrick Richthammer, Katrin Schmidt, Martin Wustmann, Yoshiaki Maeda, René Hedrich, Eike Brunner, Tsuyoshi Tanaka, Karl-Heinz van Pée, Angela Falciatore, Thomas Mock
Diatoms contribute 20% of global primary production and form the basis of many marine food webs. Although their species diversity correlates with broad diversity in cell size, there is also an intraspecific cell-size plasticity owing to sexual reproduction and varying environmental conditions. However, despite the ecological significance of the diatom cell size for food-web structure and global biogeochemical cycles, our knowledge about genes underpinning the size of diatom cells remains elusive. Here, a combination of reverse genetics, experimental evolution and comparative RNA-sequencing analyses enabled us to identify a previously unknown genetic control of cell size in the diatom Thalassiosira pseudonana...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28730764/mtor-deregulation-in-oral-cavity-squamous-cell-carcinoma
#20
Nicholas S Mastronikolis, Evangelos Tsiambas, Theodoros A Papadas, Panagiotis P Fotiades, Athanasios T Papadas, Stylianos N Mastronikolis, Ioannis Kastanioudakis, Vasileios Ragos
Signal transduction pathways consist of a variety of inter- and intra-cellular molecules. They act as supporting mechanisms for cell survival and homeostasis. Among them, the phosphatidylinositol 3-kinase (PI3K)/tumor suppressor phosphatase and tensin homologue deleted on chromosome ten (PTEN)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) pathway plays a crucial role in regulating normal cell growth based on growth factor receptors (GFRs) interaction, including epidermal GFR (type II-HER2) and insulin GFR (IGF)...
May 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
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