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https://www.readbyqxmd.com/read/29149285/draft-genome-analysis-provides-insights-into-the-fiber-yield-crude-protein-biosynthesis-and-vegetative-growth-of-domesticated-ramie-boehmeria-nivea-l-gaud
#1
Chan Liu, Liangbin Zeng, Siyuan Zhu, Lingqing Wu, Yanzhou Wang, Shouwei Tang, Hongwu Wang, Xia Zheng, Jian Zhao, Xiaorong Chen, Qiuzhong Dai, Touming Liu
Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58...
November 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29145196/aqp2-abundance-is-regulated-by-the-e3-ligase-chip-via-hsp70
#2
Mariangela Centrone, Marianna Ranieri, Annarita Di Mise, Sante Princiero Berlingerio, Annamaria Russo, Peter M T Deen, Olivier Staub, Giovanna Valenti, Grazia Tamma
BACKGROUND/AIMS: AQP2 expression is mainly controlled by vasopressin-dependent changes in protein abundance which is in turn regulated by AQP2 ubiquitylation and degradation, however the proteins involved in these processes are largely unknown. Here, we investigated the potential role of the CHIP E3 ligase in AQP2 regulation. METHODS: MCD4 cells and kidney slices were used to study the involvement of the E3 ligase CHIP on AQP2 protein abundance by cell homogenization and immunoprecipitation followed by immunoblotting...
November 17, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29139580/novel-carbohydrate-binding-modules-in-the-surface-anchored-%C3%AE-amylase-of-eubacterium-rectale-provide-a-molecular-rationale-for-the-range-of-starches-used-by-this-organism-in-the-human-gut
#3
Darrell W Cockburn, Carolyn Suh, Krizia Perez Medina, Rebecca M Duvall, Zdzislaw Wawrzak, Bernard Henrissat, Nicole M Koropatkin
Gut bacteria recognize accessible glycan substrates within a complex environment. Carbohydrate binding modules (CBMs) of cell-surface glycoside hydrolases often drive binding to the target substrate. Eubacterium rectale, an important butyrate-producing organism in the gut, consumes a limited range of substrates, including starch. Host consumption of resistant starch increases the abundance of E. rectale in the intestine, likely because it successfully captures the products of resistant starch degradation by other bacteria...
November 15, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29134801/adsorbed-polyzwitterion-copolymer-layers-designed-for-protein-repellency-and-interfacial-retention
#4
S Kalasin, R A Letteri, T Emrick, M M Santore
Poly(2-methacryloyloxyethyl phosphorylcholine) (pMPC), when end-tethered to surfaces by the adsorption of copolymeric cationic segments, forms adsorbed layers that substantially reduce protein adsorption. This study examined variations in the molecular architecture of copolymers containing cationic poly(trimethylammonium ethyl methacrylate (pTMAEMA) anchor blocks that adsorbed strongly to negative surfaces. With appropriate copolymer design, the pTMAEMA blocks were shielded, by pMPC tethers, from solution-phase proteins...
November 14, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29134008/a-genome-wide-phylogeny-of-jumping-spiders-araneae-salticidae-using-anchored-hybrid-enrichment
#5
Wayne P Maddison, Samuel C Evans, Chris A Hamilton, Jason E Bond, Alan R Lemmon, Emily Moriarty Lemmon
We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida...
2017: ZooKeys
https://www.readbyqxmd.com/read/29127281/structural-and-functional-insight-of-sphingosine-1-phosphate-mediated-pathogenic-metabolic-reprogramming-in-sickle-cell-disease
#6
Kaiqi Sun, Angelo D'Alessandro, Mostafa H Ahmed, Yujin Zhang, Anren Song, Tzu-Ping Ko, Travis Nemkov, Julie A Reisz, Hongyu Wu, Morayo Adebiyi, Zhangzhe Peng, Jing Gong, Hong Liu, Aji Huang, Yuan Edward Wen, Alexander Q Wen, Vladimir Berka, Mikhail V Bogdanov, Osheiza Abdulmalik, Leng Han, Ah-Lim Tsai, Modupe Idowu, Harinder S Juneja, Rodney E Kellems, William Dowhan, Kirk C Hansen, Martin K Safo, Yang Xia
Elevated sphingosine 1-phosphate (S1P) is detrimental in Sickle Cell Disease (SCD), but the mechanistic basis remains obscure. Here, we report that increased erythrocyte S1P binds to deoxygenated sickle Hb (deoxyHbS), facilitates deoxyHbS anchoring to the membrane, induces release of membrane-bound glycolytic enzymes and in turn switches glucose flux towards glycolysis relative to the pentose phosphate pathway (PPP). Suppressed PPP causes compromised glutathione homeostasis and increased oxidative stress, while enhanced glycolysis induces production of 2,3-bisphosphoglycerate (2,3-BPG) and thus increases deoxyHbS polymerization, sickling, hemolysis and disease progression...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29125472/membrane-vesiculation-induced-by-proteins-of-the-dengue-virus-envelope-studied-by-molecular-dynamics-simulations
#7
Ricardo de Oliveira Dos Santos Soares, Leandro Oliveira Bortot, David van der Spoel, Antonio Caliri
Biological membranes are continuously remodeled in the cell by specific membrane-shaping machineries to form, for example, tubes and vesicles. We examine fundamental mechanisms involved in the vesiculation processes induced by a cluster of envelope (E) and membrane (M) proteins of the Dengue Virus (DENV) using molecular dynamics simulations and a coarse-grained model. We show that an arrangement of three E-M heterotetramers (EM3) works as a bending unit and an ordered cluster of five such units generates a closed vesicle, reminiscent of the virus budding process...
November 10, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29123973/cholera-toxin-b-subunit-induces-local-curvature-on-lipid-bilayers
#8
Weria Pezeshkian, Lina J Nåbo, John H Ipsen
The B subunit of the bacterial cholera toxin (CTxB) is responsible for the toxin binding to the cell membrane and its intracellular trafficking. CTxB binds to the monosialotetrahexosyl ganglioside at the plasma membrane of the target cell and mediates toxin internalization by endocytosis. CTxB induces a local membrane curvature that is essential for its clathrin-independent uptake. Using all-atom molecular dynamics, we show that CTxB induces local curvature, with the radius of curvature around 36 nm. The main feature of the CTxB molecular structure that causes membrane bending is the protruding alpha helices in the middle of the protein...
November 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/29123114/structural-basis-for-ragulator-functioning-as-a-scaffold-in-membrane-anchoring-of-rag-gtpases-and-mtorc1
#9
Tianlong Zhang, Rong Wang, Zhijing Wang, Xiangxiang Wang, Fang Wang, Jianping Ding
Amino acid-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) is mediated by Rag GTPases, which are recruited to the lysosome by the Ragulator complex consisting of p18, MP1, p14, HBXIP and C7orf59; however, the molecular mechanism is elusive. Here, we report the crystal structure of Ragulator, in which p18 wraps around the MP1-p14 and C7orf59-HBXIP heterodimers and the interactions of p18 with MP1, C7orf59, and HBXIP are essential for the assembly of Ragulator. There are two binding sites for the Roadblock domains of Rag GTPases: helix α1 of p18 and the two helices side of MP1-p14...
November 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/29119499/an-integrative-approach-toward-biology-organisms-and-cancer
#10
Carlos Sonnenschein, Ana M Soto
Over the last two decades, we have challenged the hegemony of the somatic mutation theory of carcinogenesis (SMT) based on the lack of theoretical coherence of the premises adopted by its followers. We offered instead a theoretical alternative, the tissue organization field theory (TOFT), that is based on the premises that cancer is a tissue-based disease and that proliferation and motility is the default state of all cells. We went on to use a theory-neutral experimental protocol that simultaneously tested the TOFT and the SMT...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29117478/design-synthesis-and-self-assembly-of-polymers-with-tailored-graft-distributions
#11
Alice B Chang, Tzu-Pin Lin, Niklas B Thompson, Shao-Xiong Luo, Allegra Lauren Liberman-Martin, Hsiang-Yun Chen, Byeongdu Lee, Robert H Grubbs
Grafting density and graft distribution impact the chain dimensions and physical properties of polymers. However, achieving precise control over these structural parameters presents long-standing synthetic challenges. In this report, we introduce a versatile strategy to synthesize polymers with tailored architectures via grafting-through ring-opening metathesis polymerization (ROMP). One-pot copolymerization of an ω-norbornenyl macromonomer and a discrete norbornenyl co-monomer (diluent) provides opportunities to control the backbone sequence and therefore the side chain distribution...
November 8, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29110208/expression-of-gas1-in-mouse-brain-release-and-role-in-neuronal-differentiation
#12
Elizabeth Bautista, Natanael Zarco, Nicolás Aguirre-Pineda, Manuel Lara-Lozano, Paula Vergara, Juan Antonio González-Barrios, Raúl Aguilar-Roblero, José Segovia
Growth arrest-specific 1 (Gas1) is a pleiotropic protein that induces apoptosis of tumor cells and has important roles during development. Recently, the presence of two forms of Gas1 was reported: one attached to the cell membrane by a GPI anchor; and a soluble extracellular form shed by cells. Previously, we showed that Gas1 is expressed in different areas of the adult mouse CNS. Here, we report the levels of Gas1 mRNA protein in different regions and analyzed its expressions in glutamatergic, GABAergic, and dopaminergic neurons...
November 6, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/29109887/usefulness-of-sacral-sublaminar-wire-for-low-transverse-sacral-fractures-two-cases-report
#13
Tatsuro Sasaji, Hideki Imaizumi, Taishi Murakami
Low transverse sacral fractures are rare, with only two published reports regarding their surgery. The complication associated with surgery for sacral fractures is the prominence of implants. In addition, screw fixation below S3 is impractical. We performed posterior sacral fixation using S2 alar iliac (S2AI) screws and sacral sublaminar wires for low transverse sacral fractures. Case 1 was 65-year-old male with an S2-3 transverse sacral fracture. We performed laminectomy (S2-3) and passed ultrahigh molecular weight polyethylene (UHMWPE) cables from laminectomy area to the third posterior sacral foramina...
2017: Case Reports in Orthopedics
https://www.readbyqxmd.com/read/29107812/proteolytic-maturation-of-drosophila-neuroligin-3-by-tumor-necrosis-factor-%C3%AE-converting-enzyme-in-the-nervous-system
#14
Jun Wu, Nana Tao, Yao Tian, Guanglin Xing, Huihui Lv, Junhai Han, Chengqi Lin, Wei Xie
BACKGROUND: The functions of autism-associated Neuroligins (Nlgs) are modulated by their post-translational modifications, such as proteolytic cleavage. A previous study has shown that there are different endogenous forms of DNlg3 in Drosophila, indicating it may undergo proteolytic processing. However, the molecular mechanism underlying DNlg3 proteolytic processing is unknown. Here, we report a novel proteolytic mechanism that is essential for DNlg3 maturation and function in the nervous system...
October 28, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29107701/b-%C3%A2-subtilis-lytr-cpsa-psr-enzymes-transfer-wall-teichoic-acids-from-authentic-lipid-linked-substrates-to-mature-peptidoglycan-in%C3%A2-vitro
#15
Robert T Gale, Franco K K Li, Tianjun Sun, Natalie C J Strynadka, Eric D Brown
Gram-positive bacteria endow their peptidoglycan with glycopolymers that are crucial for viability and pathogenesis. However, the cellular machinery that executes this function is not well understood. While decades of genetic and phenotypic work have highlighted the LytR-CpsA-Psr (LCP) family of enzymes as cell-wall glycopolymer transferases, their in vitro characterization has been elusive, largely due to a paucity of tools for functional assays. In this report, we synthesized authentic undecaprenyl diphosphate-linked wall teichoic acid (WTA) intermediates and built an assay system capable of monitoring LCP-mediated glycopolymer transfer...
October 12, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/29106606/increased-affinity-for-rna-targets-evolved-early-in-animal-and-plant-dicer-lineages-through-different-structural-mechanisms
#16
Haiyan Jia, Oralia Kolaczkowski, James Rolland, Bryan Kolaczkowski
Understanding the structural basis for evolutionary changes in protein function is central to molecular evolutionary biology and can help determine the extent to which functional convergence occurs through similar or different structural mechanisms. Here, we combine ancestral sequence reconstruction with functional characterization and structural modeling to directly examine the evolution of sequence-structure-function across the early differentiation of animal and plant Dicer/DCL proteins, which perform the first molecular step in RNA interference by identifying target RNAs and processing them into short interfering products...
July 5, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29098723/establishing-a-novel-pig-a-gene-mutation-assay-in-l5178ytk-mouse-lymphoma-cells
#17
Yiying Wang, Javier Revollo, Page McKinzie, Mason G Pearce, Azra Dad, Berran Yucesoy, Hans Rosenfeldt, Robert H Heflich, Vasily N Dobrovolsky
The X-linked Pig-a gene encodes an enzyme required for the biosynthesis of glycosyl phosphatidylinositol (GPI) anchors. Pig-a mutant cells fail to synthesize GPI and to express GPI-anchored protein markers (e.g., CD90) on their surface. Marker deficiency serves as a phenotypic indicator of Pig-a mutation in various in vivo assays. Here, we describe an in vitro Pig-a mutation assay in L5178YTk(+/-) mouse lymphoma cells, in which mutant-phenotype cells are measured by flow cytometry using a fluorescent anti-CD90 antibody...
November 2, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/29097751/microfluidic-preparation-of-anchored-cell-membrane-sheets-for-in-vitro-analyses-and-manipulation-of-the-cytoplasmic-face
#18
Shin Izuta, Satoshi Yamaguchi, Ryuji Misawa, Shinya Yamahira, Modong Tan, Masahiro Kawahara, Tomoko Suzuki, Tomoko Takagi, Kae Sato, Motonao Nakamura, Teruyuki Nagamune, Akimitsu Okamoto
Molecular networks on the cytoplasmic faces of cellular plasma membranes are critical research topics in biological sciences and medicinal chemistry. However, the selective permeability of the cell membrane restricts the researchers from accessing to the intact intracellular factors on the membrane from the outside. Here, a microfluidic method to prepare cell membrane sheets was developed as a promising tool for direct examination of the cytoplasmic faces of cell membranes. Mammalian cells immobilized on a poly(ethylene glycol)-lipid coated substrate were rapidly and efficiently fractured, with the sheer stress of laminar flow in microchannels, resulting in isolation of the bottom cell membrane sheets with exposed intact cytoplasmic faces...
November 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29097323/molecular-identification-and-expression-analysis-of-a-novel-cyclophilin-a-gene-in-the-red-swamp-crayfish-procambarus-clarkii
#19
Junjie Zhu, Feng Lin, Fei Li, Yan Wang
Cyclophilin A (Cyp A) is the main intracellular receptor of cyclosporin A (CsA) belonging to the immunophilin family, which is known as an effective immunosuppressive drug. This study aimed to gain insights into the structure and biological function of cyclophilin A in the red swamp crayfish, Procambarus clarkii (PcCypA). We cloned PcCypA by homology cloning and anchored polymerase chain reaction (PCR), and assessed its mRNA and protein expression levels in different tissues using quantitative real-time PCR and western blot analysis, respectively...
October 31, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29092894/mitochondrial-reactive-oxygen-species-in-lipotoxic-hearts-induces-post-translational-modifications-of-akap121-drp1-and-opa1-that-promote-mitochondrial-fission
#20
Kensuke Tsushima, Heiko Bugger, Adam R Wende, Jamie Soto, Gregory A Jenson, Austin R Tor, Rose McGlauflin, Helena C Kenny, Yuan Zhang, Rhonda Souvenir, Xiao X Hu, Crystal L Black, Renata O Pereira, Vitor A Lira, Kenneth Spitzer, Terry L Sharp, Kooresh I Shoghi, Genevieve C Sparagna, Eva A Rog-Zielinska, Peter Kohl, Oleh Khalimonchuk, Jean E Schaffer, E Dale Abel
Rationale: Cardiac lipotoxicity, characterized by increased uptake, oxidation and accumulation of lipid intermediates, contributes to cardiac dysfunction in obesity and diabetes. However, mechanisms linking lipid overload and mitochondrial dysfunction are incompletely understood. Objective: To elucidate the mechanisms for mitochondrial adaptations to lipid overload in postnatal hearts in vivo. Methods and Results: Using a transgenic mouse model of cardiac lipotoxicity overexpressing long-chain acyl-CoA synthetase 1 in cardiomyocytes, we show that modestly increased myocardial fatty acid uptake leads to mitochondrial structural remodeling with significant reduction in minimum diameter...
November 1, 2017: Circulation Research
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