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https://www.readbyqxmd.com/read/28549159/a-non-photosynthetic-diatom-reveals-early-steps-of-reductive-evolution-in-plastids
#1
Ryoma Kamikawa, Daniel Moog, Stefan Zauner, Goro Tanifuji, Ken-Ichiro Ishida, Hideaki Miyashita, Shigeki Mayama, Tetsuo Hashimoto, Uwe-G Maier, John M Archibald, Yuji Inagaki
Non-photosynthetic plastids retain important biological functions and are indispensable for cell viability. However, the detailed processes underlying the loss of plastidal functions other than photosynthesis remain to be fully understood. In this study, we used transcriptomics, subcellular localization, and phylogenetic analyses to characterize the biochemical complexity of the non-photosynthetic plastids of the apochlorotic diatom Nitzschia sp. NIES-3581. We found that these plastids have lost isopentenyl pyrophosphate (IPP) biosynthesis and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-based carbon fixation but have retained various proteins for other metabolic pathways, including amino acid biosynthesis, and a portion of the Calvin-Benson cycle comprised only of glycolysis/gluconeogenesis, and the reductive pentose phosphate pathway (rPPP)...
May 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28548975/factor-vii-activating-protease-sex-related-association-with-coronary-artery-calcification
#2
Ramshanker Ramanathan, Jørgen B Gram, Niels Peter R Sand, Bjarne L Nørgaard, Axel C P Diederichsen, Frank Vitzthum, Herbert Schwarz, Johannes J Sidelmann
: Factor VII-activating protease (FSAP) may regulate development of cardiovascular disease (CVD). We evaluated sex differences in FSAP measures and examined the association between FSAP and coronary artery calcification (CAC) in a middle-aged population. Participants were randomly selected citizens aged 50 or 60 without CVD, diabetes mellitus, Marburg I polymorphism, or hormone replacement therapy (HRT). FSAP protein concentration (total FSAP), FSAP urokinase-activating capacity (FSAP GP), and FSAP GP/total FSAP (specific FSAP activity) were measured...
May 25, 2017: Blood Coagulation & Fibrinolysis: An International Journal in Haemostasis and Thrombosis
https://www.readbyqxmd.com/read/28548042/new-insights-into-reovirus-evolution-implications-from-a-newly-characterized-mycoreovirus
#3
Lijiang Liu, Jiasen Cheng, Yanping Fu, Huiquan Liu, Daohong Jiang, Jiatao Xie
We performed molecular cloning and complete genome sequencing of a novel mycoreovirus, Sclerotinia sclerotiorumreovirus 1 (SsReV1), isolated from an isolate of the phytopathogenic fungus Sclerotinia sclerotiorum. SsReV1 has a genome of 28 055 bp and is composed of 11 double-stranded RNA segments. With a combination of unique molecular features, virion shape and composition, and phylogenetic analysis, SsReV1 is significantly distinct from all known reoviruses and defines a novel genus in the family Reoviridae...
May 26, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28547909/identification-and-expression-of-conserved-and-novel-rna-variants-of-medaka-pax6b-gene
#4
Tiansheng Chen, Benzion Cavari, Manfred Schartl, Yunhan Hong
Gene duplication is a major driving force of evolution. How gene duplicates have evolved remains a mystery. A highly conserved gene such as Pax6 is an ideal model to study functional conservation and divergence via comparisons among diverse organisms. One pax6 gene has been characterized in the Japanese medaka (Oryzias latipes), which is annotated as pax6b on chromosome 3. Here, we report that Medaka pax6b is homolog to Pax6 of mammals in sequence, chromosomal synteny, and genomic organization. Cloning and sequencing led to the identification of up to 43 pax6b RNA variants predicting six protein isoforms, 22 of which are similar to those reported in other organisms and 21 represent novel RNA variants...
May 26, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28547747/deciphering-common-recognition-principles-of-nucleoside-mono-di-and-tri-phosphates-binding-in-diverse-proteins-via-structural-matching-of-their-binding-sites
#5
Raghu Bhagavat, Narayanaswamy Srinivasan, Nagasuma Chandra
Nucleoside triphosphate (NTP) ligands are of high biological importance and essential for all life forms. A pre-requisite for them to participate in diverse biochemical processes is their recognition by diverse proteins. It is thus of great interest to understand the basis for such recognition in different proteins. Towards this, we have employed a structural bioinformatics approach and analyse structures of 4677 NTP complexes available in PDB. Binding sites were extracted and compared exhaustively by using PocketMatch, a sensitive in-house site comparison algorithm, which resulted in grouping the entire dataset into 27 site-types...
May 25, 2017: Proteins
https://www.readbyqxmd.com/read/28545395/characterizing-the-roles-of-changing-population-size-and-selection-on-the-evolution-of-flux-control-in-metabolic-pathways
#6
Alena Orlenko, Peter B Chi, David A Liberles
BACKGROUND: Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance...
May 25, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28545255/frozen-accident-pushing-50-stereochemistry-expansion-and-chance-in-the-evolution-of-the-genetic-code
#7
Eugene V Koonin
Nearly 50 years ago, Francis Crick propounded the frozen accident scenario for the evolution of the genetic code along with the hypothesis that the early translation system consisted primarily of RNA. Under the frozen accident perspective, the code is universal among modern life forms because any change in codon assignment would be highly deleterious. The frozen accident can be considered the default theory of code evolution because it does not imply any specific interactions between amino acids and the cognate codons or anticodons, or any particular properties of the code...
May 23, 2017: Life
https://www.readbyqxmd.com/read/28545148/mitochondrial-genome-evolution-in-alismatales-size-reduction-and-extensive-loss-of-ribosomal-protein-genes
#8
Gitte Petersen, Argelia Cuenca, Athanasios Zervas, Gregory T Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant...
2017: PloS One
https://www.readbyqxmd.com/read/28545140/the-role-of-the-zinc-finger-protein-zc3h32-in-bloodstream-form-trypanosoma-brucei
#9
Cornelia Klein, Monica Terrao, Christine Clayton
Kinetoplastids rely heavily on post-transcriptional mechanisms for control of gene expression, with regulation of mRNA processing, translation and degradation by RNA-binding proteins. ZC3H32 is a cytosolic mRNA-binding protein with three non-canonical CCCH zinc finger domains. It is much more abundant in bloodstream-form Trypanosoma brucei than in procyclic forms. Tethering of ZC3H32 to a reporter mRNA suppressed translation and resulted in mRNA degradation, and deletion analysis suggested that this activity was present in both the N- and C-terminal domains, but not the central zinc finger-containing domain...
2017: PloS One
https://www.readbyqxmd.com/read/28544438/genome-wide-identification-characterization-and-evolution-of-cuticular-protein-genes-in-the-malaria-vector-anopheles-sinensis-diptera-culicidae
#10
Bai-Qi Liu, Liang Qiao, Qi-Yi He, Yong Zhou, Shuang Ren, Bin Chen
Thirteen cuticular proteins (CPs) families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified into 10 families based on motifs and phylogenetic analyses. In 11 other insect species, 9 had CP numbers > 150 while Apis mellifera and Tribolium castaneum had CP numbers less than 52. The CPs of 8 species occupied > 1.4% of the total genomic gene number whereas in 3 species the CPs occupied < 1%...
May 24, 2017: Insect Science
https://www.readbyqxmd.com/read/28544154/floral-nectar-of-the-obligate-outcrossing-canavalia-gladiata-jacq-dc-fabaceae-contains-only-one-predominant-protein-a-class-iii-acidic-chitinase
#11
Xue-Long Ma, Richard I Milne, Hong-Xia Zhou, Jiang-Yu Fang, Hong-Guang Zha
Floral nectar can affect the fitness of insect-pollinated plants, through both attraction and manipulation of pollinators. Self-incompatible insect-pollinated plants receive more insect visits than their self-compatible relatives, and the nectar of such species might face more risk to be infested by the pathogens carried by pollinators than self-compatible plants. Proteins in nectar (nectarins) play an important role in the protection of nectar, but little is known regarding nectarins in self-incompatible species...
May 20, 2017: Plant Biology
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#12
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree amongst themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28544018/next-generation-nucleic-acid-aptamers-with-two-base-modified-nucleotides-improve-the-binding-affinity-and-potency
#13
Rakesh Naduvile Veedu, Hadi AlShamaileh
Aptamers are single-stranded oligonucleotides (RNA or DNA) that can bind to their targets with high affinities and specificities because of their ability to adopt three-dimensional shapes in solution. Traditionally, aptamers are developed by SELEX (Systematic Evolution of Ligands by Exponential enrichment), a reiterative process involving selection by target molecule incubation with an oligonucleotide library and enrichment of the selected oligonucleotides by amplification. One drawback of current aptamer selection approach is the lack of diversity in the nucleic acid library with only four nucleobases compositions...
May 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28543308/exocytic-trafficking-pathways-in-plants-why-and-how-they-are-redirected
#14
REVIEW
Takehiko Kanazawa, Takashi Ueda
The membrane trafficking system is responsible for precise transportation and localization of proteins, lipids, and polysaccharides among single membrane-bound organelles, the plasma membrane, and the extracellular space. While the exocytic trafficking pathway is considered to be a default transport pathway in many organisms, including land plants, research has shown that evolutionary processes led to an increase in the number of machinery components involved in the plant exocytic pathway. This study provides an overview of the diversification of exocytic trafficking pathways in plants, which mediate the formation and maintenance of cell polarity, interaction with symbiotic and pathogenic microbes, and cytokinesis...
May 25, 2017: New Phytologist
https://www.readbyqxmd.com/read/28542629/characteristics-of-candidate-genes-associated-with-embryonic-development-in-the-cow-evidence-for-a-role-for-wbp1-in-development-to-the-blastocyst-stage
#15
M Sofia Ortega, Justin J Kurian, Robert McKenna, Peter J Hansen
The goal was to gain understanding of how 12 genes containing SNP previously related to embryo competence to become a blastocyst (BRINP3, C1QB, HSPA1L, IRF9, MON1B, PARM1, PCCB, PMM2, SLC18A2, TBC1D24, TTLL3 and WBP1) participate in embryonic development. Gene expression was evaluated in matured oocytes and embryos. BRINP3 and C1QB were not detected at any stage. For most other genes, transcript abundance declined as the embryo developed to the blastocyst stage. Exceptions were for PARM1 and WBP1, where steady-state mRNA increased at the 9-16 cell stage...
2017: PloS One
https://www.readbyqxmd.com/read/28542596/progressive-mitochondrial-protein-lysine-acetylation-and-heart-failure-in-a-model-of-friedreich-s-ataxia-cardiomyopathy
#16
Amanda R Stram, Gregory R Wagner, Brian D Fogler, P Melanie Pride, Matthew D Hirschey, R Mark Payne
INTRODUCTION: The childhood heart disease of Friedreich's Ataxia (FRDA) is characterized by hypertrophy and failure. It is caused by loss of frataxin (FXN), a mitochondrial protein involved in energy homeostasis. FRDA model hearts have increased mitochondrial protein acetylation and impaired sirtuin 3 (SIRT3) deacetylase activity. Protein acetylation is an important regulator of cardiac metabolism and loss of SIRT3 increases susceptibility of the heart to stress-induced cardiac hypertrophy and ischemic injury...
2017: PloS One
https://www.readbyqxmd.com/read/28542519/characterization-of-the-whole-chloroplast-genome-of-chikusichloa-mutica-and-its-comparison-with-other-rice-tribe-oryzeae-species
#17
Zhiqiang Wu, Cuihua Gu, Luke R Tembrock, Dong Zhang, Song Ge
Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B)...
2017: PloS One
https://www.readbyqxmd.com/read/28542325/membrane-protein-contact-and-structure-prediction-using-co-evolution-in-conjunction-with-machine-learning
#18
Pedro L Teixeira, Jeff L Mendenhall, Sten Heinze, Brian Weiner, Marcin J Skwark, Jens Meiler
De novo membrane protein structure prediction is limited to small proteins due to the conformational search space quickly expanding with length. Long-range contacts (24+ amino acid separation)-residue positions distant in sequence, but in close proximity in the structure, are arguably the most effective way to restrict this conformational space. Inverse methods for co-evolutionary analysis predict a global set of position-pair couplings that best explain the observed amino acid co-occurrences, thus distinguishing between evolutionarily explained co-variances and these arising from spurious transitive effects...
2017: PloS One
https://www.readbyqxmd.com/read/28542193/an-agent-based-model-of-leukocyte-transendothelial-migration-during-atherogenesis
#19
Rita Bhui, Heather N Hayenga
A vast amount of work has been dedicated to the effects of hemodynamics and cytokines on leukocyte adhesion and trans-endothelial migration (TEM) and subsequent accumulation of leukocyte-derived foam cells in the artery wall. However, a comprehensive mechanobiological model to capture these spatiotemporal events and predict the growth and remodeling of an atherosclerotic artery is still lacking. Here, we present a multiscale model of leukocyte TEM and plaque evolution in the left anterior descending (LAD) coronary artery...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28541477/mitochondrial-retroprocessing-promoted-functional-transfers-of-rpl5-to-the-nucleus-in-grasses
#20
Zhiqiang Wu, Daniel B Sloan, Colin W Brown, Mónica Rosenblueth, Jeffrey D Palmer, Han Chuan Ong
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus...
May 25, 2017: Molecular Biology and Evolution
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