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https://www.readbyqxmd.com/read/27933712/the-importance-of-mrna-structure-in-determining-the-pathogenicity-of-synonymous-and-non-synonymous-mutations-in-haemophilia
#1
N Hamasaki-Katagiri, B C Lin, J Simon, R C Hunt, T Schiller, E Russek-Cohen, A A Komar, H Bar, C Kimchi-Sarfaty
INTRODUCTION: Mutational analysis is commonly used to support the diagnosis and management of haemophilia. This has allowed for the generation of large mutation databases which provide unparalleled insight into genotype-phenotype relationships. Haemophilia is associated with inversions, deletions, insertions, nonsense and missense mutations. Both synonymous and non-synonymous mutations influence the base pairing of messenger RNA (mRNA), which can alter mRNA structure, cellular half-life and ribosome processivity/elongation...
December 9, 2016: Haemophilia: the Official Journal of the World Federation of Hemophilia
https://www.readbyqxmd.com/read/27933490/alterations-in-the-cerebral-microvascular-proteome-expression-profile-after-transient-global-cerebral-ischemia-in-rat
#2
Stine Spray, Sara E Johansson, Alistair V G Edwards, Martin R Larsen, Aneta Radziwon-Balicka, Gro K Povlsen, Lars Edvinsson
This study aimed at obtaining an in-depth mapping of expressional changes of the cerebral microvasculature after transient global cerebral ischemia (GCI) and the impact on these GCI-induced expressional changes of post-GCI treatment with a mitogen-activated protein kinase kinase (MEK1/2) inhibitor. GCI was induced in male Wistar rats followed by treatment with either vehicle or the MEK1/2 inhibitor U0126 every 12 h post-GCI. Seventy-two hours after GCI or sham surgery, the cerebral microvasculature was isolated and the protein content analysed with state-of-the-art mass spectrometry...
December 8, 2016: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/27932586/nup100-regulates-saccharomyces-cerevisiae-replicative-life-span-by-mediating-the-nuclear-export-of-specific-trnas
#3
Christopher L Lord, Ophir Ospovat, Susan R Wente
Nuclear pore complexes (NPCs), which are composed of nucleoporins (Nups) and regulate transport between the nucleus and cytoplasm, significantly impact the replicative life span (RLS) of Saccharomyces cerevisiae We previously reported that deletion of the non-essential gene NUP100 increases RLS, although the molecular basis for this effect was unknown. In this study, we find that nuclear tRNA accumulation contributes to increased longevity in nup100Δ cells. Fluorescence in situ hybridization (FISH) experiments demonstrate several specific tRNAs accumulate in the nuclei of nup100Δ mutants...
December 8, 2016: RNA
https://www.readbyqxmd.com/read/27932543/members-of-the-zinc-cluster-factor-family-alters-virulence-in-candida-albicans
#4
Luca Issi, Rhys A Farrer, Kelly Pastor, Benjamin Landry, Toni Delorey, George W Bell, Dawn A Thompson, Christina A Cuomo, Reeta P Rao
Virtually all humans are colonized with Candida albicans However, in immunocompromised individuals this benign commensal organism becomes a serious, life-threatening pathogen. Here, we describe and analyze the regulatory networks that modulate innate responses in the host niches. We identified Zcf15 and Zcf29, two Zinc Cluster transcription Factors (ZCF) that are required for C. albicans virulence. Previous sequence analysis of clinical C. albicans isolates from immunocompromised patients indicates that both ZCF genes diverged during clonal evolution...
December 7, 2016: Genetics
https://www.readbyqxmd.com/read/27932527/mechanisms-of-in-vivo-ribosome-maintenance-change-in-response-to-nutrient-signals
#5
Andrew D Mathis, Bradley C Naylor, Richard H Carson, Eric Evans, Justin Harwell, Jared Knect, Eric Hexem, Fredrick Peelor, Benjamin F Miller, Karyn L Hamilton, Mark K Transtrum, Benjamin T Bikman, John C Price
Control of protein homeostasis is fundamental to the health and longevity of all organisms. Because the rate of protein synthesis by ribosomes is a central control point in this process, regulation and maintenance of ribosome function could have amplified importance in the overall regulatory circuit. Indeed, ribosomal defects are commonly associated with loss of protein homeostasis, aging and disease, whereas improved protein homeostasis, implying optimal ribosomal function, is associated with disease resistance and increased lifespan...
December 8, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27932458/the-impact-of-recent-improvements-in-cryo-electron-microscopy-technology-on-the-understanding-of-bacterial-ribosome-assembly
#6
Aida Razi, Robert A Britton, Joaquin Ortega
Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process...
December 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27932387/the-long-non-coding-rna-transcriptome-of-dictyostelium-discoideum-development
#7
Rafael D Rosengarten, Balaji Santhanam, Janez Kokosar, Gad Shaulsky
Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long non-coding RNAs in D. discoideum To characterize the antisense and long intergenic non-coding RNA transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing library preparation method that selectively depletes ribosomal RNAs...
December 7, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27930727/airway-microbiota-in-bronchoalveolar-lavage-fluid-from-clinically-well-infants-with-cystic-fibrosis
#8
Theresa A Laguna, Brandie D Wagner, Cynthia B Williams, Mark J Stevens, Charles E Robertson, Cole W Welchlin, Catherine E Moen, Edith T Zemanick, Jonathan K Harris
BACKGROUND: Upper airway cultures guide the identification and treatment of lung pathogens in infants with cystic fibrosis (CF); however, this may not fully reflect the spectrum of bacteria present in the lower airway. Our objectives were to characterize the airway microbiota using bronchoalveolar lavage fluid (BALF) from asymptomatic CF infants during the first year of life and to investigate the relationship between BALF microbiota, standard culture and clinical characteristics. METHODS: BALF, nasopharyngeal (NP) culture and infant pulmonary function testing data were collected at 6 months and one year of age during periods of clinical stability from infants diagnosed with CF by newborn screening...
2016: PloS One
https://www.readbyqxmd.com/read/27929740/role-for-padi6-in-securing-the-mrna-msy2-complex-to-the-oocyte-cytoplasmic-lattices
#9
Xiaoqiu Liu, Eric Morency, Tingting Li, Hao Qin, Xiaoqian Zhang, Xuesen Zhang, Scott Coonrod
The oocyte cytoplasmic lattices (CPLs) have long been predicted to function as a storage form for the maternal contribution of ribosomes to the early embryo. Our previous studies have demonstrated that ribosomal component S6 is stored in the oocyte CPLs and peptidylarginine deiminase 6 (PADI6) is critical for CPLs formation. Additionally, we found that depletion of PADI6 reduced de novo protein synthesis prior to the maternal-to-embryonic transition, therefore causing embryos to arrest at the two-cell stage...
December 8, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27929418/yeast-reporter-assay-to-identify-cellular-components-of-ricin-toxin-a-chain-trafficking
#10
Björn Becker, Tina Schnöder, Manfred J Schmitt
RTA, the catalytic A-subunit of the ribosome inactivating A/B toxin ricin, inhibits eukaryotic protein biosynthesis by depurination of 28S rRNA. Although cell surface binding of ricin holotoxin is mainly mediated through its B-subunit (RTB), sole application of RTA is also toxic, albeit to a significantly lower extent, suggesting alternative pathways for toxin uptake and transport. Since ricin toxin trafficking in mammalian cells is still not fully understood, we developed a GFP-based reporter assay in yeast that allows rapid identification of cellular components required for RTA uptake and subsequent transport through a target cell...
December 6, 2016: Toxins
https://www.readbyqxmd.com/read/27929371/prefabrication-of-a-ribosomal-protein-subcomplex-essential-for-eukaryotic-ribosome-formation
#11
Cohue Peña, Sabina Schütz, Ute Fischer, Yiming Chang, Vikram G Panse
Spatial clustering of ribosomal proteins (r-proteins) through tertiary interactions is a striking structural feature of the eukaryotic ribosome. However, the functional importance of these intricate inter-connections, and how they are established is currently unclear. Here, we reveal that a conserved ATPase, Fap7, organizes interactions between neighboring r-proteins uS11 and eS26 prior to their delivery to the earliest ribosome precursor, the 90S. In vitro, uS11 only when bound to Fap7 becomes competent to recruit eS26 through tertiary contacts found between these r-proteins on the mature ribosome...
December 8, 2016: ELife
https://www.readbyqxmd.com/read/27929073/rna-sequencing-of-chorionic-villi-from-recurrent-pregnancy-loss-patients-reveals-impaired-function-of-basic-nuclear-and-cellular-machinery
#12
Siim Sõber, Kristiina Rull, Mario Reiman, Piret Ilisson, Pirkko Mattila, Maris Laan
Recurrent pregnancy loss (RPL) concerns ~3% of couples aiming at childbirth. In the current study, transcriptomes and miRNomes of 1(st) trimester placental chorionic villi were analysed for 2 RPL cases (≥6 miscarriages) and normal, but electively terminated pregnancies (ETP; n = 8). Sequencing was performed on Illumina HiSeq 2000 platform. Differential expression analyses detected 51 (27%) transcripts with increased and 138 (73%) with decreased expression in RPL compared to ETP (DESeq: FDR P < 0...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27928961/darpins-bioengineering-and-its-theranostic-approaches-emerging-trends-in-protein-engineering
#13
Mahmood Rasool, Arif Malik, Mubashir Hussain, Kalsoom A Haq, Kiran Butt, Abdul Basit, Muhammad Imran Naseer, Muhammad Asif, Rozena Shaikh, Mohammad Zahid Mustafa, Qamre Alam, Ghulam Rasool, Waseem Ahmad, Absarul L Haque, Mohammad Amjad Kamal
The therapeutic significance of bioengineering proteins has increased dramatically as a new generation of pharmacological drug with a great potential in medical treatment. Protein engineering has improved the use of new non immunoglobulin affinity proteins. The designed ankyrin repeat proteins abbreviated as DARPins is an example. The molecules have smaller structural size, unlike immunoglobulins, but similar target affinity is of great significance. Such molecules get more binding specificity and greater thermodynamic stability...
December 8, 2016: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/27928909/using-proteomics-to-discover-novel-biomarkers-for-fatty-liver-development-and-response-to-cb1r-antagonist-treatment-in-an-obese-mouse-model
#14
Chin-Chang Chen, Tzung-Yan Lee, Ching-Fai Kwok, Yung-Pei Hsu, Kuang-Chung Shih, Yan-Jie Lin, Low-Tone Ho
Over activity of cannabinoid receptor type 1 (CB1R) plays a key role in increasing the incidence of obesity-induced nonalcoholic fatty liver disease. Tissue proteome analysis has been applied to investigate the bioinformatics regarding the mode of action and therapeutic mechanism. The aim of this study was to explore the potential pathways altered with CB1R in obesity-induced fatty liver. Male C57BL/6 mice were fed either a standard chow diet (STD) or a high-fat diet (HFD) with or without 1-week treatment of CB1R inverse agonist AM251 at 5 mg/kg...
December 8, 2016: Proteomics
https://www.readbyqxmd.com/read/27928682/morphological-and-genetic-characterization-of-kudoa-whippsi-myxosporea-multivalvulida-from-cheilodactylus-zonatus-in-the-western-pacific-ocean-off-japan-and-two-new-kudoa-spp-k-akihitoi-n-sp-and-k-empressmichikoae-n-sp-from-acanthogobius-hasta-in-the-sea-of
#15
Akihiro Kasai, Aogu Setsuda, Hiroshi Sato
Molecular genetic characterization using the ribosomal RNA (rDNA) gene accrues a wealth of knowledge regarding the true nature of species diversity of Kudoa Meglitsch, 1947 (Myxozoa: Myxosporea: Multivalvulida) and the biogeographical relationships of isolates from different host fish and sea areas. In the present study, we characterized morphologically and genetically three Kudoa spp. with four shell valves and polar capsules (SV/PC), forming pseudocysts in the myofiber of trunk muscles of Cheilodactylus zonatus or Acanthogobius hasta in the natural seawater around Japan...
December 7, 2016: Parasitology Research
https://www.readbyqxmd.com/read/27928482/frequency-of-genes-encoding-erythromycin-ribosomal-methylases-among-staphylococcus-aureus-clinical-isolates-with-different-d-phenotypes-in-tehran-iran
#16
Sareh Sadat Hosseini, Mohammad Niakan, Horieh Saderi, Mitra Motallebi, Morovat Taherikalani, Khairollah Asadollahi, Mohammad Emaneini
BACKGROUND AND OBJECTIVES: Macrolide, lincosamide and streptogramin type B (MLSB) antibiotics are important in the treatment of Staphylococcus aureus infections and existence of isolates with ability to resist against MLSB antibiotics is worrisome. MATERIALS AND METHODS: In this cross sectional study, 101 S. aureus isolates were collected from patients of five selected hospitals in Tehran over a period of five months. Disk diffusion tests and differentiation between constitutive and inducible resistances were carried out by D-test...
June 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/27928088/comparison-of-babesia-microti-real-time-polymerase-chain-reaction-assays-for-confirmatory-diagnosis-of-babesiosis
#17
Samaly S Souza, Henry S Bishop, Patrick Sprinkle, Yvonne Qvarnstrom
Babesiosis is an emerging tick-borne disease caused by apicomplexan parasites of the genus Babesia Most human infections in the United States are caused by Babesia microti, but other infection-causing Babesia parasites have been documented as well. Polymerase chain reaction (PCR)-based methods can be used to identify this parasite to the species level. In this study, published real-time PCR assays for the specific detection of B. microti were evaluated against conventional PCR for their analytical performance...
December 7, 2016: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/27927249/the-af-1-deficient-estrogen-receptor-er%C3%AE-46-isoform-is-frequently-expressed-in-human-breast-tumors
#18
Elodie Chantalat, Frédéric Boudou, Henrik Laurell, Gaëlle Palierne, René Houtman, Diana Melchers, Philippe Rochaix, Thomas Filleron, Alexandre Stella, Odile Burlet-Schiltz, Anne Brouchet, Gilles Flouriot, Raphaël Métivier, Jean-François Arnal, Coralie Fontaine, Françoise Lenfant
BACKGROUND: To date, all studies conducted on breast cancer diagnosis have focused on the expression of the full-length 66-kDa estrogen receptor alpha (ERα66). However, much less attention has been paid to a shorter 46-kDa isoform (ERα46), devoid of the N-terminal region containing the transactivation function AF-1. Here, we investigated the expression levels of ERα46 in breast tumors in relation to tumor grade and size, and examined the mechanism of its generation and its specificities of coregulatory binding and its functional activities...
December 7, 2016: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/27926932/epsin-family-member-3-and-ribosome-related-genes-are-associated-with-late-metastasis-in-estrogen-receptor-positive-breast-cancer-and-long-term-survival-in-non-small-cell-lung-cancer-using-a-genome-wide-identification-and-validation-strategy
#19
Birte Hellwig, Katrin Madjar, Karolina Edlund, Rosemarie Marchan, Cristina Cadenas, Anne-Sophie Heimes, Katrin Almstedt, Antje Lebrecht, Isabel Sicking, Marco J Battista, Patrick Micke, Marcus Schmidt, Jan G Hengstler, Jörg Rahnenführer
BACKGROUND: In breast cancer, gene signatures that predict the risk of metastasis after surgical tumor resection are mainly indicative of early events. The purpose of this study was to identify genes linked to metastatic recurrence more than three years after surgery. METHODS: Affymetrix HG U133A and Plus 2.0 array datasets with information on metastasis-free, disease-free or overall survival were accessed via public repositories. Time restricted Cox regression models were used to identify genes associated with metastasis during or after the first three years post-surgery (early- and late-type genes)...
2016: PloS One
https://www.readbyqxmd.com/read/27926829/caught-on-camera-intermediates-of-ribosome-recycling
#20
Clarence Ling, Dmitri N Ermolenko
Following termination of protein synthesis, bacterial ribosomes are split into subunits by the joint action of elongation factor G and ribosome recycling factor in the process called ribosome recycling. In this issue of Structure, Fu et al. (2016) describe visualization of transient intermediates of ribosome recycling using time-resolved cryogenic electron microscopy.
December 6, 2016: Structure
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