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lipid modification and sequencing

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https://www.readbyqxmd.com/read/28622918/angiosperm-plant-desiccation-tolerance-hints-from-transcriptomics-and-genome-sequencing
#1
REVIEW
Valentino Giarola, Quancan Hou, Dorothea Bartels
Desiccation tolerance (DT) in angiosperms is present in the small group of resurrection plants and in seeds. DT requires the presence of protective proteins, specific carbohydrates, restructuring of membrane lipids, and regulatory mechanisms directing a dedicated gene expression program. Many components are common to resurrection plants and seeds; however, some are specific for resurrection plants. Understanding how each component contributes to DT is challenging. Recent transcriptome analyses and genome sequencing indicate that increased expression is essential of genes encoding protective components, recently evolved, species-specific genes and non-protein-coding RNAs...
June 13, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28620036/substrate-selectivity-in-the-zdhhc-family-of-s-acyltransferases
#2
REVIEW
Kimon Lemonidis, Christine Salaun, Marianna Kouskou, Cinta Diez-Ardanuy, Luke H Chamberlain, Jennifer Greaves
S-acylation is a reversible lipid modification occurring on cysteine residues mediated by a family of membrane-bound 'zDHHC' enzymes. S-acylation predominantly results in anchoring of soluble proteins to membrane compartments or in the trafficking of membrane proteins to different compartments. Recent work has shown that although S-acylation of some proteins may involve very weak interactions with zDHHC enzymes, a pool of zDHHC enzymes exhibit strong and specific interactions with substrates, thereby recruiting them for S-acylation...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28586389/characterization-of-the-species-malassezia-pachydermatis-and-re-evaluation-of-its-lipid-dependence-using-a-synthetic-agar-medium
#3
Laura Puig, M Rosa Bragulat, Gemma Castellá, F Javier Cabañes
The genus Malassezia includes lipophilic yeasts, which are part of the skin microbiota of various mammals and birds. Unlike the rest of Malassezia species, M. pachydermatis is described as non-lipid-dependent, as it is able to grow on Sabouraud glucose agar (SGA) without lipid supplementation. In this study we have examined the phenotypic variability within M. pachydermatis and confirmed its lipid-dependent nature using a synthetic agar medium. We used a selection of representative non-lipid-dependent strains from different animal species and three atypical lipid-dependent strains of this species, which were not able to grow after multiple passages on SGA...
2017: PloS One
https://www.readbyqxmd.com/read/28575526/reconstructing-the-suberin-pathway-in-poplar-by-chemical-and-transcriptomic-analysis-of-bark-tissues
#4
Meghan K Rains, Nayana Dilini Gardiyehewa de Silva, Isabel Molina
The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood...
June 1, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28524084/bordetella-holmesii-lipid-a-structures-and-corresponding-genomic-sequences-comparison-in-three-clinical-isolates-and-the-reference-strain-atcc-51541
#5
Valérie Bouchez, Sami AlBitar-Nehmé, Alexey Novikov, Nicole Guiso, Martine Caroff
Bordetella holmesii can cause invasive infections but can also be isolated from the respiratory tract of patients with whooping-cough like symptoms. For the first time, we describe the lipid A structure of B. holmesii reference strain ATCC 51541 (alias NCTC12912 or CIP104394) and those of three French B. holmesii clinical isolates originating from blood (Bho1) or from respiratory samples (FR4020 and FR4101). They were investigated using chemical analyses, gas chromatography-mass spectrometry (GC-MS), and matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS)...
May 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28435686/apple-dwarfing-rootstocks-exhibit-an-imbalance-in-carbohydrate-allocation-and-reduced-cell-growth-and-metabolism
#6
Toshi M Foster, Peter A McAtee, Chethi N Waite, Helen L Boldingh, Tony K McGhie
Apple dwarfing rootstocks cause earlier shoot termination and reduced root and shoot mass. To identify physiological factors responsible for rootstock-induced growth restriction, we compared vascular-enriched gene expression between two dwarfing rootstocks ('M27' and 'M9') and the vigorous rootstock 'M793' using RNA sequencing and quantitative reverse transcriptase PCR. Differentially expressed genes common to both dwarfing rootstocks belonged to five main biological processes: (1) primary metabolism, (2) cell wall synthesis and modification, (3) secondary metabolism, (4) hormone signalling and response and (5) redox homeostasis...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28433721/optimizing-the-restored-chemotactic-behavior-of-anticancer-agent-salmonella-enterica-serovar-typhimurium-vnp20009
#7
Katherine M Broadway, Seungbeum Suh, Bahareh Behkam, Birgit E Scharf
Bacteria, including strains of Salmonella, have been researched and applied as therapeutic cancer agents for centuries. Salmonella are particularly of interest due to their facultative anaerobic nature, facilitating colonization of differentially oxygenated tumor regions. Additionally, Salmonella can be manipulated with relative ease, resulting in the ability to attenuate the pathogen or engineer vectors for drug delivery. It was recently discovered that the anti-cancer Salmonella enterica serovar Typhimurium strain VNP20009 is lacking in chemotactic ability, due to a non-synonymous single nucleotide polymorphism in cheY...
April 20, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28395341/electrophilic-aldehyde-products-of-lipid-peroxidation-selectively-adduct-to-heat-shock-protein-90-and-arylsulfatase-a-in-stallion-spermatozoa%C3%A2
#8
Sally E Hall, R John Aitken, Brett Nixon, Nathan D Smith, Zamira Gibb
Oxidative stress is a major determinant of mammalian sperm function stimulating lipid peroxidation cascades that culminate in the generation of potentially cytotoxic aldehydes. The aim of this study was to assess the impact of such aldehydes on the functionality of stallion spermatozoa. The impact of exposure to exogenous acrolein (ACR) and 4-hydroxynonenal (4HNE) was manifested in a highly significant dose- and time-dependent increase in mitochondrial reactive oxygen species (ROS), total cellular ROS, a decrease in sperm motility, and a time-dependent increase in lipid peroxidation...
January 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28377111/genome-wide-identification-of-micrornas-involved-in-fatty-acid-and-lipid-metabolism-of-brassica-napus-by-small-rna-and-degradome-sequencing
#9
Zhiwei Wang, Yan Qiao, Jingjing Zhang, Wenhui Shi, Jinwen Zhang
Rapeseed (Brassica napus) is an important cash crop considered as the third largest oil crop worldwide. Rapeseed oil contains various saturation or unsaturation fatty acids, these fatty acids, whose could incorporation with TAG form into lipids stored in seeds play various roles in the metabolic activity. The different fatty acids in B. napus seeds determine oil quality, define if the oil is edible or must be used as industrial material. miRNAs are kind of non-coding sRNAs that could regulate gene expressions through post-transcriptional modification to their target transcripts playing important roles in plant metabolic activities...
July 1, 2017: Gene
https://www.readbyqxmd.com/read/28373551/identification-of-specific-posttranslational-o-mycoloylations-mediating-protein-targeting-to-the-mycomembrane
#10
Clément Carel, Julien Marcoux, Valérie Réat, Julien Parra, Guillaume Latgé, Françoise Laval, Pascal Demange, Odile Burlet-Schiltz, Alain Milon, Mamadou Daffé, Maryelle G Tropis, Marie A M Renault
The outer membranes (OMs) of members of the Corynebacteriales bacterial order, also called mycomembranes, harbor mycolic acids and unusual outer membrane proteins (OMPs), including those with α-helical structure. The signals that allow precursors of such proteins to be targeted to the mycomembrane remain uncharacterized. We report here the molecular features responsible for OMP targeting to the mycomembrane of Corynebacterium glutamicum, a nonpathogenic member of the Corynebacteriales order. To better understand the mechanisms by which OMP precursors were sorted in C...
April 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28344321/broad-spectrum-antiviral-activity-for-paramyxoviruses-is-modulated-by-biophysical-properties-of-fusion-inhibitory-peptides
#11
Cyrille Mathieu, Marcelo T Augusto, Stefan Niewiesk, Branka Horvat, Laura M Palermo, Giuseppina Sanna, Silvia Madeddu, Devra Huey, Miguel A R B Castanho, Matteo Porotto, Nuno C Santos, Anne Moscona
Human paramyxoviruses include global causes of lower respiratory disease like the parainfluenza viruses, as well as agents of lethal encephalitis like Nipah virus. Infection is initiated by viral glycoprotein-mediated fusion between viral and host cell membranes. Paramyxovirus viral fusion proteins (F) insert into the target cell membrane, and form a transient intermediate that pulls the viral and cell membranes together as two heptad-repeat regions refold to form a six-helix bundle structure that can be specifically targeted by fusion-inhibitory peptides...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28323072/impairment-of-the-class-iia-bacteriocin-receptor-function-and-membrane-structural-changes-are-associated-to-enterocin-crl35-high-resistance-in-listeria-monocytogenes
#12
Emilse Masias, Fernando G Dupuy, Paulo Ricardo da Silva Sanches, Juan Vicente Farizano, Eduardo Cilli, Augusto Bellomio, Lucila Saavedra, Carlos Minahk
BACKGROUND: Enterocin CRL35 is a class IIa bacteriocin with anti-Listeria activity. Resistance to these peptides has been associated with either the downregulation of the receptor expression or changes in the membrane and cell walls. The scope of the present work was to characterize enterocin CRL35 resistant Listeria strains with MICs more than 10,000 times higher than the MIC of the WT sensitive strain. METHODS: Listeria monocytogenes INS7 resistant isolates R2 and R3 were characterized by 16S RNA gene sequencing and rep-PCR...
March 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28301719/a-reconfigured-kennedy-pathway-which-promotes-efficient-accumulation-of-medium-chain-fatty-acids-in-leaf-oils
#13
Kyle B Reynolds, Matthew C Taylor, Darren P Cullerne, Christopher L Blanchard, Craig C Wood, Surinder P Singh, James R Petrie
Medium chain fatty acids (MCFA, C6-14 fatty acids) are an ideal feedstock for biodiesel and broader oleochemicals. In recent decades, several studies have used transgenic engineering to produce MCFA in seeds oils, though these modifications result in unbalance membrane lipid profiles that impair oil yields and agronomic performance. Given the ability to engineer non-seed organs to produce oils, we have previously demonstrated that MCFA profiles can be produced in leaves, but this also results in unbalanced membrane lipid profiles and undesirable chlorosis and cell death...
March 16, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28286565/everolimus-in-the-management-of-metastatic-neuroendocrine-tumours
#14
REVIEW
David L Chan, Eva Segelov, Simron Singh
Neuroendocrine tumours are increasing in incidence and cause a variety of symptoms. The mammalian target of rapamycin (mTOR) pathway plays a key role in neuroendocrine tumour (NET) pathogenesis, leading to increased lipid synthesis, protein synthesis and cellular growth. Upregulation of this pathway is noted in both hereditary and sporadic NETs. This understanding has led to investigations of mTOR inhibitors as therapy for metastatic NETs. After promising preclinical findings, everolimus, an mTOR inhibitor, was trialled in the RADIANT-1-4 studies on patients with advanced, well differentiated NETs...
January 2017: Therapeutic Advances in Gastroenterology
https://www.readbyqxmd.com/read/28259411/genetic-and-functional-analysis-of-the-bovine-uterine-microbiota-part-ii-purulent-vaginal-discharge-versus-healthy-cows
#15
M L S Bicalho, S Lima, C H Higgins, V S Machado, F S Lima, R C Bicalho
The aim of this study was to characterize, using metagenomic shotgun DNA sequencing, the intrauterine microbial population and its predicted functional diversity within healthy cows and cows presenting purulent vaginal discharge (PVD). Twenty Holstein dairy cows from a single farm were enrolled in the study at 25 to 35 d postpartum. Purulent vaginal discharge was diagnosed by retrieving and scoring vaginal discharge using the Metricheck device (Simcro, Hamilton, New Zealand). Intrauterine samples for metagenomic analysis were collected by the cytobrush technique from 8 cows diagnosed with PVD and 12 healthy cows...
May 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28209172/evaluation-of-the-contribution-of-the-transmembrane-region-to-the-ectodomain-conformation-of-the-human-immunodeficiency-virus-hiv-1-envelope-glycoprotein
#16
Hanh T Nguyen, Navid Madani, Haitao Ding, Emerald Elder, Amy Princiotto, Christopher Gu, Patrice Darby, James Alin, Alon Herschhorn, John C Kappes, Youdong Mao, Joseph G Sodroski
BACKGROUND: The human immunodeficiency virus (HIV-1) envelope glycoprotein (Env), a Type 1 transmembrane protein, assembles into a trimeric spike complex that mediates virus entry into host cells. The high potential energy of the metastable, unliganded Env trimer is maintained by multiple non-covalent contacts among the gp120 exterior and gp41 transmembrane Env subunits. Structural studies suggest that the gp41 transmembrane region forms a left-handed coiled coil that contributes to the Env trimer interprotomer contacts...
February 16, 2017: Virology Journal
https://www.readbyqxmd.com/read/28207798/altered-hepatic-lipid-metabolism-in-mice-lacking-both-the-melanocortin-type-4-receptor-and-low-density-lipoprotein-receptor
#17
Vera Lede, Andrej Meusel, Antje Garten, Yulia Popkova, Melanie Penke, Christin Franke, Albert Ricken, Angela Schulz, Wieland Kiess, Daniel Huster, Torsten Schöneberg, Jürgen Schiller
Obesity is often associated with dyslipidemia and hepatosteatosis. A number of animal models of non-alcoholic fatty liver disease (NAFLD) are established but they significantly differ in the molecular and biochemical changes depending on the genetic modification and diet used. Mice deficient for melanocortin type 4 receptor (Mc4rmut) develop hyperphagia, obesity, and subsequently NAFLD already under regular chow and resemble more closely the energy supply-driven obesity found in humans. This animal model was used to assess the molecular and biochemical consequences of hyperphagia-induced obesity on hepatic lipid metabolism...
2017: PloS One
https://www.readbyqxmd.com/read/28130120/trifluoroacetylated-tyrosine-rich-d-tetrapeptides-have-potent-antioxidant-activity
#18
Annamaria Sandomenico, Valeria Severino, Fabio Apone, Adriana De Lucia, Andrea Caporale, Nunzianna Doti, Anna Russo, Rosita Russo, Camilla Rega, Tiziana Del Giacco, Lucia Falcigno, Menotti Ruvo, Angela Chambery
The term "oxidative stress" indicates a set of chemical reactions unleashed by a disparate number of events inducing DNA damage, lipid peroxidation, protein modification and other effects, which are responsible of altering the physiological status of cells or tissues. Excessive Reactive Oxygen Species (ROS) levels may accelerate ageing of tissues or induce damage of biomolecules thus promoting cell death or proliferation in dependence of cell status and of targeted molecules. In this context, new antioxidants preventing such effects may have a relevant role as modulators of cell homeostasis and as therapeutic agents...
March 2017: Peptides
https://www.readbyqxmd.com/read/28122677/colistin-and-carbapenem-resistant-klebsiella-oxytoca-harboring-blavim-2-and-an-insertion-in-the-mgrb-gene-isolated-from-blood-culture
#19
Michaela Simon, Holger Melzl, Andreas Hiergeist, Katharina Richert, Linda Falgenhauer, Yvonne Pfeifer, Roman G Gerlach, Kornelius Fuchs, Udo Reischl, André Gessner, Jonathan Jantsch
A carbapenemase-producing colistin-resistant Klebsiella oxytoca isolate was recovered from a blood culture of a female patient without previous report of risk factors to obtain multidrug-resistant Gram-negative bacilli. A combination of biochemical and molecular methods was used to identify the resistance mechanism of this isolate. Carbapenemase production was mediated by Verona integron-encoded metallo-β-lactamase (VIM)-2. Colistin resistance was not due to plasmid- borne mcr-1 gene, but we found an integration of IS5-like sequence in the mgrB gene of K...
February 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28114274/akt3-is-a-privileged-first-responder-in-isozyme-specific-electrophile-response
#20
Marcus J C Long, Saba Parvez, Yi Zhao, Sanjna L Surya, Yiran Wang, Sheng Zhang, Yimon Aye
Isozyme-specific post-translational regulation fine tunes signaling events. However, redundancy in sequence or activity renders links between isozyme-specific modifications and downstream functions uncertain. Methods to study this phenomenon are underdeveloped. Here we use a redox-targeting screen to reveal that Akt3 is a first-responding isozyme sensing native electrophilic lipids. Electrophile modification of Akt3 modulated downstream pathway responses in cells and Danio rerio (zebrafish) and markedly differed from Akt2-specific oxidative regulation...
March 2017: Nature Chemical Biology
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