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Functional analysis

Mark A Frye, Euijung Ryu, Malik Nassan, Gregory D Jenkins, Ana C Andreazza, Jared M Evans, Susan L McElroy, Devin Oglesbee, W Edward Highsmith, Joanna M Biernacka
Converging genetic, postmortem gene-expression, cellular, and neuroimaging data implicate mitochondrial dysfunction in bipolar disorder. This study was conducted to investigate whether mitochondrial DNA (mtDNA) haplogroups and single nucleotide variants (SNVs) are associated with sub-phenotypes of bipolar disorder. MtDNA from 224 patients with Bipolar I disorder (BPI) was sequenced, and association of sequence variations with 3 sub-phenotypes (psychosis, rapid cycling, and adolescent illness onset) was evaluated...
September 30, 2016: Journal of Psychiatric Research
Anja Stajnko, Ingrid Falnoga, Janja Snoj Tratnik, Darja Mazej, Marta Jagodic, Mladen Krsnik, Alfred B Kobal, Marija Prezelj, Lijana Kononenko, Milena Horvat
BACKGROUND: Urine cadmium (Cd) and renal function biomarkers, mostly analysed in urine spot samples, are well established biomarkers of occupational exposure. Their use and associations at low environmental level are common, but have recently been questioned, particularly in terms of physiological variability and normalisation bias in the case of urine spot samples. AIM: To determine the appropriateness of spot urine and/or blood Cd exposure biomarkers and their relationships with renal function biomarkers at low levels of exposure...
October 19, 2016: Environmental Research
G P Chuiko, O V Dvornik, S I Shyian, Ye A Baganov
BACKGROUND: A new computer model for systolic pulse waves within the cardiovascular system is presented. The emphasis was made on blood stroke volume (BS). The new waveform for pulse wave demands the re-computing of the BS. The authors showed the applicability of suggested model for arterial aging problem. METHODS: Suggested model is based on the well-known Korteweg-de Vries (KdV) equation. Instead of the common accepted solitary wave, the periodical cnoidal wave is used...
October 14, 2016: Computers in Biology and Medicine
Påvel G Lindberg, Maxime Térémetz, Sylvain Charron, Oussama Kebir, Agathe Saby, Narjes Bendjemaa, Stéphanie Lion, Benoît Crépon, Raphaël Gaillard, Catherine Oppenheim, Marie-Odile Krebs, Isabelle Amado
Inhibition is considered a key mechanism in schizophrenia. Short-latency intracortical inhibition (SICI) in the motor cortex is reduced in schizophrenia and is considered to reflect locally deficient γ-aminobutyric acid (GABA)-ergic modulation. However, it remains unclear how SICI is modulated during motor inhibition and how it relates to neural processing in other cortical areas. Here we studied motor inhibition Stop signal task (SST) in stabilized patients with schizophrenia (N = 28), healthy siblings (N = 21) and healthy controls (n = 31) matched in general cognitive status and educational level...
September 30, 2016: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
Sunil Nath
As the chief energy source of eukaryotic cells, it is important to determine the thermodynamic efficiency of ATP synthesis in oxidative phosphorylation (OX PHOS). Previous estimates of the thermodynamic efficiency of this vital process have ranged from Lehninger's original back-of-the-envelope calculation of 38% to the often quoted value of 55-60% in current textbooks of biochemistry, to high values of 90% from recent information theoretic considerations, and reports of realizations of close to ideal 100% efficiencies by single molecule experiments...
October 15, 2016: Biophysical Chemistry
Ming-Jie Kuang, Chao Han, Jian-Xiong Ma, Fei Li, Jie Zhao, Lin Fu, Xin-Long Ma
PURPOSE: Autologous platelet gel, developed from fresh autologous blood, is a breakthrough in the promotion and acceleration of soft tissue and bone repair. The application of autologous platelet gel has been reported to improve haemostasis and promote function recovery. We screened the randomized controlled trials and controlled clinical trials of high quality to investigate whether autologous platelet gel makes a better performance for postoperative bleeding and functional recovery in patients after total knee arthroplasty...
October 19, 2016: International Journal of Surgery
Anastasia K Atabekova, Anna V Pankratenko, Svetlana S Makarova, Ekaterina A Lazareva, Robert A Owens, Andrey G Solovyev, Sergey Y Morozov
Human B-cell receptor-associated protein BAP31 (HsBAP31) is the endoplasmic reticulum-resident protein involved in protein sorting and transport as well as pro-apoptotic signaling. Plant orthologs of HsBAP31 termed 'plant BAP-like proteins' (PBL proteins) have thus far remained unstudied. Recently, the PBL protein from Nicotiana tabacum (NtPBL) was identified as an interactor of Nt-4/1, a plant protein known to interact with plant virus movement proteins and affect the long-distance transport of potato spindle tuber viroid (PSTVd) via the phloem...
October 19, 2016: Biochimie
Olena Odnokoz, Kyle Nakatsuka, Vladimir I Klichko, Jacqueline Nguyen, Liz Calderon Solis, Kaitlin Ostling, Marziyeh Badinloo, William C Orr, Svetlana N Radyuk
Previously, we have shown that flies under-expressing the two mitochondrial peroxiredoxins (Prxs), dPrx3 and dPrx5, display increases in tissue-specific apoptosis and dramatically shortened life span, associated with a redox crisis, manifested as changes in GSH:GSSG and accumulation of protein mixed disulfides. To identify specific pathways responsible for the observed biological effects, we performed a transcriptome analysis. Functional clustering revealed a prominent group enriched for immunity-related genes, including a considerable number of NF-kB-dependent antimicrobial peptides (AMP) that are up-regulated in the Prx double mutant...
October 19, 2016: Biochimica et Biophysica Acta
Y H Cho, M E Craig, A S Januszewski, P Benitez-Aguirre, S Hing, A J Jenkins, K C Donaghue
AIM: To test the hypothesis that non-invasive skin autofluorescence, a measure of advanced glycation end products, would provide a surrogate measure of long-term glycaemia and be associated with early markers of microvascular complications in adolescents with Type 1 diabetes. METHODS: Forearm skin autofluorescence (arbitrary units) was measured in a cross-sectional study of 135 adolescents with Type 1 diabetes [mean ± sd age 15.6 ± 2.1 years, diabetes duration 8...
October 22, 2016: Diabetic Medicine: a Journal of the British Diabetic Association
Gordon X Wang, Stephen J Smith, Philippe Mourrain
The distribution of proteins within sub-synaptic compartments is an essential aspect of their neurological function. Current methodology such as electron microscopy (EM) and super-resolution imaging techniques can provide precise localization of proteins, but are often limited to a small number of one-time observations with narrow spatial and molecular coverage. The diversity of synaptic proteins and synapse types demands synapse analysis on a scale that is prohibitive with current methods. Here, we demonstrate SubSynMAP, a fast, multiplexed sub-synaptic protein analysis method using wide-field data from deconvolution array tomography (ATD)...
October 22, 2016: ELife
José Ignacio Garzón, Lei Deng, Diana Murray, Sagi Shapira, Donald Petrey, Barry Honig
We present a database, PrePPI (Predicting Protein-Protein Interactions), of more than 1.35 million predicted protein-protein interactions (PPIs). Of these at least 127,000 are expected to constitute direct physical interactions although the actual number may be much larger (~500,000). The current PrePPI, which contains predicted interactions for about 85% of the human proteome is related to an earlier version but is based on additional sources of interaction evidence and is far larger in scope. The use of structural relationships allows PrePPI to infer numerous previously unreported interactions...
October 22, 2016: ELife
Li Zhang, Zhihong Yang, Jocelyn Trottier, Olivier Barbier, Li Wang
: Bile acids (BAs) play critical physiological functions in cholesterol homeostasis and deregulation of BA metabolism causes cholestatic liver injury. Maternally expressed gene 3 (MEG3) was recently shown as a potential tumor suppressor, however its basic hepatic function remains elusive. Using RNA pull-down with biotin-labeled sense or anti-sense MEG3RNA followed by mass spectrometry, we identified RNA binding protein polypyrimidine tract-binding protein 1 (PTBP1) as a MEG3 interaction protein and validated their interaction by RNA immunoprecipitation (RIP)...
October 22, 2016: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Allison C Nugent, Bruce Luber, Frederick W Carver, Stephen E Robinson, Richard Coppola, Carlos A Zarate
Recently, independent components analysis (ICA) of resting state magnetoencephalography (MEG) recordings has revealed resting state networks (RSNs) that exhibit fluctuations of band-limited power envelopes. Most of the work in this area has concentrated on networks derived from the power envelope of beta bandpass-filtered data. Although research has demonstrated that most networks show maximal correlation in the beta band, little is known about how spatial patterns of correlations may differ across frequencies...
October 22, 2016: Human Brain Mapping
Alvaro Vidal, Nicolas Arnold, Mihai Dorin Vartolomei, Bernhard Kiss, Fiona Burkhard, George N Thalmann, Beat Roth
OBJECTIVES: To prospectively evaluate the long-term oncological and functional outcomes of postoperative total parenteral nutrition after radical cystectomy. METHODS: A total of 157 consecutive patients (≤cT3, cN0, cM0) who underwent extended pelvic lymph node dissection, radical cystectomy and ileal urinary diversion from September 2008 to March 2011 at a single center were randomized to receive either postoperative total parenteral nutrition (group A; n = 74) or oral nutrition alone (group B; n = 83)...
October 21, 2016: International Journal of Urology: Official Journal of the Japanese Urological Association
Andriy Bilichak, Andrey Golubov, Igor Kovalchuk
The discovery of small RNAs in plants and animals almost two decades ago attracted a significant interest towards epigenetic regulation of gene expression and the practical implementation of the gained knowledge in applied studies. New and sometimes unexpected functions have been ascribed to sRNAs almost every couple of years since their discovery, hence indicating that the complete role of sRNAs in plant and animal physiology is still barely understood. Next-generation sequencing technologies allow to generate high-resolution profiles of sRNAs for the consequent analysis and possibly to discover novel functions of sRNAs...
2017: Methods in Molecular Biology
Sara Hernández-Castellano, Geovanny I Nic-Can, Clelia De-la-Peña
Among the epigenetic mechanisms studied with a greater interest in the last decade are the microRNAs (miRNAs). These small noncoding RNA sequences that are approximately 17-22 nucleotides in length play an essential role in many biological processes of various organisms, including plants. The analysis of spatiotemporal expression of miRNAs provides a better understanding of the role of these small molecules in plant development, cell differentiation, and other processes; but such analysis is also an important method for the validation of biological functions...
2017: Methods in Molecular Biology
Julia Engelhorn, Franziska Turck
Genome-wide analyses of chromatin factor-binding sites or histone modification localization generate lists of up to several thousand potential target genes. For many model organisms, large annotation databases are available to help with the characterization and classification of genomic datasets. The term meta-analysis has been coined for this type of multi-database comparison. In this chapter, we describe a workflow to perform a transcriptional and functional analysis of genome-wide target genes. Sources of transcription data and clustering tools to subdivide genes according to their expression pattern are described...
2017: Methods in Molecular Biology
Hisateru Komatsu, Tomohiro Iguchi, Takaaki Masuda, Hidenari Hirata, Masami Ueda, Shinya Kidogami, Yushi Ogawa, Kuniaki Sato, Qingjiang Hu, Sho Nambara, Tomoko Saito, Shotaro Sakimura, Ryutaro Uchi, Shuhei Ito, Hidetoshi Eguchi, Keishi Sugimachi, Hidetoshi Eguchi, Yuichiro Doki, Masaki Mori, Koshi Mimori
BACKGROUND: The RND1 gene encodes a protein that belongs to the Rho GTPase family, which regulates various cellular functions. Depletion of RND1 expression activates the oncogenic Ras signaling pathway. In this study, we aimed to clarify the clinical significance of RND1 expression in predicting prognosis and to investigate its biological role in human hepatocellular carcinoma (HCC). METHODS: The association between RND1 expression and clinical outcomes in patients with HCC was analyzed in three independent cohorts: 120 cases resected in our hospital; 370 cases in The Cancer Genome Atlas (TCGA); and 242 cases in GSE14520...
October 21, 2016: Annals of Surgical Oncology
Marek Sierzega, Marzena Lenart, Magdalena Rutkowska, Marta Surman, Bozenna Mytar, Andrzej Matyja, Maciej Siedlar, Jan Kulig
BACKGROUND: Neutrophil-lymphocyte ratio (NLR), platelet-lymphocyte ratio (PLR), and lymphocyte-monocyte ratio (LMR) may serve as a simple index of the immune function. The aim of this study was to investigate the prognostic significance of NLR, PLR, and LMR in patients with resectable pancreatic ductal adenocarcinoma (PDAC) and to verify whether such biomarkers are associated with changes in populations of lymphoid cells. METHODS: The prognostic implications of blood count parameters were evaluated in a retrospective cohort of 442 subjects undergoing pancreatic resections for PDAC...
October 21, 2016: Annals of Surgical Oncology
Pei Ma, Haitao Wang, Lu Han, Wei Jing, Xin Zhou, Zhisu Liu
Small nucleolar RNAs (snoRNAs) as a novel molecular species may have significant and comprehensive influences on the development and progression of hepatocellular carcinoma (HCC). We recently characterized snoRNA transcriptome signatures in HCC tissues by small RNA sequencing and found that small nucleolar RNA 78 (SNORD78) was associated with HCC. However, little is known about the pathological role of SNORD78 in HCC patients. This study aimed to profile SNORD78 expression signature and then to explore the pathogenesis of SNORD78 in HCC...
October 21, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
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