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https://www.readbyqxmd.com/read/29684914/serum-calcium-is-related-to-the-degree-of-artery-stenosis-in-acute-ischemic-stroke
#1
Jiayan Wu, Junchao Xie, Yanxin Zhao, Li Gong, Xueyuan Liu, Wangmi Liu
BACKGROUND/AIMS: Acute ischemic stroke is caused by stenosis of artery supplying to brain. We aimed to detect some metabolites in the serum that would be related to the degree of artery stenosis and to analyze potential mechanisms. METHODS: Patients diagnosed with acute ischemic stroke were divided into two groups according to their degree of artery stenosis (which was determined by computed tomographic angiography): a mild group (stenosis ≤ 30%) and a severe group (stenosis > 30%)...
2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29684857/microrna-449a-functions-as-a-tumor-suppressor-in-pancreatic-cancer-by-the-epigenetic-regulation-of-atdc-expression
#2
Feng Li, Jing Liang, Lu Bai
A growing body of evidence has suggested that microRNAs (miRNAs) play a pivotal role in the development and progression of pancreatic cancer. miRNA-449a (miR-449a) has attracted particular interest due to its critical role in regulating cancer biology in numerous cancer types. However, whether miR-449a is involved in the regulation of pancreatic cancer development and progression remains unknown. In this study, we aimed to investigate the expression pattern and potential biological function of miR-449a in pancreatic cancer...
April 20, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29684772/identification-of-mir-22-3p-mir-92a-3p-and-mir-137-in-peripheral-blood-as-biomarker-for-schizophrenia
#3
Jie Ma, Shanshan Shang, Jihan Wang, Tianbu Zhang, Fayi Nie, Xiaobin Song, Heping Zhao, Chunhui Zhu, Rui Zhang, Dingjun Hao
MicroRNAs (miRNAs) are a class of endogenous and non-coding single-stranded RNAs with length of about 22 nucleotides, and many are evolutionarily conserved. Although postmortem brain samples provide direct evidence of miRNA dysregulation within the brain, peripheral tissue samples can be obtained from living subjects and have the potential to yield biomarkers that could be used as diagnostic tools. To verify and detect additional miRNAs differentially expressed in peripheral blood and further explore their diagnostic value and function for schizophrenia, we performed a next-generation sequencing approach in combination with a literature search to select appropriate miRNAs...
April 7, 2018: Psychiatry Research
https://www.readbyqxmd.com/read/29684641/methodological-considerations-for-the-identification-of-choline-and-carnitine-degrading-bacteria-in-the-gut
#4
REVIEW
Eleanor Jameson, Mussa Quareshy, Yin Chen
The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut...
April 19, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29684532/a-complicated-complex-ion-channels-voltage-sensing-cell-membranes-and-peptide-inhibitors
#5
REVIEW
Alan H Zhang, Gagan Sharma, Eivind A B Undheim, Xinying Jia, Mehdi Mobli
Voltage-gated ion channels (VGICs) are specialised ion channels that have a voltage dependent mode of action, where ion conduction, or gating, is controlled by a voltage-sensing mechanism. VGICs are critical for electrical signalling and are therefore important pharmacological targets. Among these, voltage-gated sodium channels (NaV s) have attracted particular attention as potential analgesic targets. NaV s, however, comprise several structurally similar subtypes with unique localisations and distinct functions, ranging from amplification of action potentials in nociception (e...
April 20, 2018: Neuroscience Letters
https://www.readbyqxmd.com/read/29684489/analysis-of-the-microrna-transcriptome-of-daphnia-pulex-during-aging
#6
Jiabao Hu, Chongyuan Lin, Mengdi Liu, Qiaoqiong Tong, Shanliang Xu, Danli Wang, Yunlong Zhao
Daphnia pulex is an important food organism that exhibits a particular mode of reproduction known as cyclical parthenogenesis (asexual) and sexual reproduction. Regulation of the aging process by microRNAs (miRNAs) is a research hotspot in miRNA studies. To investigate a possible role of miRNAs in regulating aging and senescence, we used Illumina HiSeq to sequence two miRNA libraries from 1-day-old (1d) and 25-day-old (25d) D. pulex specimens. In total, we obtained 11,218,097 clean reads and 28,569 unique miRNAs from 1d specimens and 11,819,106 clean reads and 44,709 unique miRNAs from 25d specimens...
April 20, 2018: Gene
https://www.readbyqxmd.com/read/29684483/three-dimensional-protein-shape-similarity-analysis-based-on-hybrid-features
#7
Zhong Li, Jiangjiang Yu, Hailong Hu, Shuiwang Ji
The analysis of protein similarity is a matter of concern in the bioinformatics field, since studying the protein similarity can help understand the protein structure-function relationship. To this aim, several methods have been proposed, but currently, protein similarity results are still not satisfactory. Here we presented a novel method for evaluating the similarity of 3D protein models based on hybrid features, including the local diameter (LD), the salient geometric feature (SGF) and the heat kernel signature (HKS)...
April 20, 2018: Gene
https://www.readbyqxmd.com/read/29684362/characterization-of-the-small-intestinal-lesion-in-celiac-disease-by-label-free-quantitative-mass-spectrometry
#8
Astrid E V Tutturen, Siri Dørum, Trevor Clancy, Henrik M Reims, Asbjørn Christophersen, Knut E A Lundin, Ludvig M Sollid, Gustavo A de Souza, Jorunn Stamnaes
Global characterization of tissue proteomes from small amounts of biopsy material has become feasible due to advances in mass spectrometry and bioinformatics tools. In celiac disease (CD), dietary gluten induces an immune response which is accompanied by pronounced remodeling of the small intestine. Removal of gluten from the diet abrogates the immune response and the tissue architecture normalizes. In this study differences in global protein expression of small intestinal biopsies from CD patients were quantified by analyzing formalin-fixed, paraffin-embedded material using liquid-chromatography mass spectrometry and label-free protein quantitation...
April 20, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29684330/novel-bioactive-peptides-from-pd-l1-2-a-type-1-ribosome-inactivating-protein-from-phytolacca-dioica-l-evaluation-of-their-antimicrobial-properties-and-anti-biofilm-activities
#9
Elio Pizzo, Katia Pane, Andrea Bosso, Nicola Landi, Sara Ragucci, Rosita Russo, Rosa Gaglione, Marcelo D T Torres, Cesar de la Fuente-Nunez, Angela Arciello, Alberto Di Donato, Eugenio Notomista, Antimo Di Maro
Antimicrobial peptides, also called Host Defence Peptides (HDPs), are effectors of innate immune response found in all living organisms. In a previous report, we have identified by chemical fragmentation, and characterized the first cryptic antimicrobial peptide in PD-L4, a type 1 ribosome-inactivating protein (RIP) from leaves of Phytolacca dioica L. We applied a recently developed bioinformatic approach to a further member of the differently expressed pool of type 1 RIPs from P. dioica (PD-L1/2), and identified two novel putative cryptic HDPs in its N-terminal domain...
April 20, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29684324/taxonomic-distribution-structure-function-relationship-and-metabolic-context-of-the-two-families-of-sulfide-dehydrogenases-sqr-and-fcsd
#10
Filipe M Sousa, Juliana G Pereira, Bruno C Marreiros, Manuela M Pereira
Hydrogen sulfide (H2 S) is a versatile molecule with different functions in living organisms: it can work as a metabolite of sulfur and energetic metabolism or as a signaling molecule in higher Eukaryotes. H2 S is also highly toxic since it is able to inhibit heme cooper oxygen reductases, preventing oxidative phosphorylation. Due to the fact that it can both inhibit and feed the respiratory chain, the immediate role of H2 S on energy metabolism crucially relies on its bioavailability, meaning that studying the central players involved in the H2 S homeostasis is key for understanding sulfide metabolism...
April 20, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29684280/discovery-of-a-kojibiose-phosphorylase-in-escherichia-coli-k-12
#11
Keya W Mukherjee, Tamari Narindoshvili, Frank M Raushel
The substrate profiles for three uncharacterized enzymes (YcjM, YcjT, and YcjU) that are expressed from a cluster of twelve genes (ycjM-W and ompG) of unknown function in Escherichia coli K-12 have been determined. Through a comprehensive bioinformatic and steady-state kinetic analysis, the catalytic function of YcjT was determined to be kojibiose phosphorylase. In the presence of saturating phosphate and kojibiose (α-(1,2)-D-glucose-D-glucose) this enzyme catalyzes the formation of D-glucose and β-D-glucose-1-phosphate (kcat = 1...
April 23, 2018: Biochemistry
https://www.readbyqxmd.com/read/29684140/ultra-fast-global-homology-detection-with-discrete-cosine-transform-and-dynamic-time-warping
#12
Daniele Raimondi, Gabriele Orlando, Yves Moreau, Wim F Vranken
Motivation: Evolutionary information is crucial for the annotation of proteins in bioinformatics. The amount of retrieved homologs often correlates with the quality of predicted protein annotations related to structure or function. With a growing amount of sequences available, fast and reliable methods for homology detection are essential, as they have a direct impact on predicted protein annotations. Results: We developed a discriminative, alignment-free algorithm for homology detection with quasi-linear complexity, enabling theoretically much faster homology searches...
April 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29684124/iro-3wpseknc-identify-dna-replication-origins-by-three-window-based-pseknc
#13
Bin Liu, Fan Weng, De-Shuang Huang, Kuo-Chen Chou
Motivation: DNA replication is the key of the genetic information transmission, and it is initiated from the replication origins. Identifying the replication origins is crucial for understanding the mechanism of DNA replication. Although several discriminative computational predictors were proposed to identify DNA replication origins of yeast species, they could only be used to identify very tiny parts (250 bp or 300 bp) of the replication origins. Besides, none of the existing predictors could successfully capture the "GC asymmetry bias" of yeast species reported by experimental observations...
April 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29684099/comparative-analysis-of-tissue-reconstruction-algorithms-for-3d-histology
#14
Kimmo Kartasalo, Leena Latonen, Jorma Vihinen, Tapio Visakorpi, Matti Nykter, Pekka Ruusuvuori
Motivation: Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution...
April 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29684098/binquasi-a-peak-detection-method-for-chip-sequencing-data-with-biological-replicates
#15
Emily Goren, Peng Liu, Chao Wang, Chong Wang
Motivation: ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling...
April 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29683450/targeted-next-generation-sequencing-and-bioinformatics-pipeline-to-evaluate-genetic-determinants-of-constitutional-disease
#16
Allison A Dilliott, Sali M K Farhan, Mahdi Ghani, Christine Sato, Eric Liang, Ming Zhang, Adam D McIntyre, Henian Cao, Lemuel Racacho, John F Robinson, Michael J Strong, Mario Masellis, Dennis E Bulman, Ekaterina Rogaeva, Anthony Lang, Carmela Tartaglia, Elizabeth Finger, Lorne Zinman, John Turnbull, Morris Freedman, Rick Swartz, Sandra E Black, Robert A Hegele
Next-generation sequencing (NGS) is quickly revolutionizing how research into the genetic determinants of constitutional disease is performed. The technique is highly efficient with millions of sequencing reads being produced in a short time span and at relatively low cost. Specifically, targeted NGS is able to focus investigations to genomic regions of particular interest based on the disease of study. Not only does this further reduce costs and increase the speed of the process, but it lessens the computational burden that often accompanies NGS...
April 4, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29683367/insights-into-apoptotic-proteins-in-chemotherapy-quantification-techniques-and-informing-therapy-choice
#17
Janine Naß, Thomas Efferth
INTRODUCTION: Cancer is one of the leading causes of morbidity and mortality worldwide. A hallmark of cancer is evasion of apoptosis leading to tumor progression and drug resistance. Biomarker research has become a sign of the times, and proteins involved in apoptosis may be used for clinical diagnostic or prognostic purposes in cancer treatment. The recent progress in proteomic technology has triggered an emerging number of researchers to study the molecular mechanisms that regulate the apoptotic signal transduction pathways in cancer...
April 23, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29682676/how-human-microbiome-talks-to-health-and-disease
#18
REVIEW
Jing Cong, Xiaochun Zhang
Microbes are ubiquitous in the human body. They usually live in communities, and each of these communities has a distinct taxonomical structure. Due to its close relationship with human health and disease, the human microbiome has received great attention and is probably considered to be the most valuable biomarker in preventing and solving human diseases. In this paper, we first review the value of the human microbiome. Then, we focus on the role of the human microbiome in influencing human health and disease...
April 22, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29682564/profiling-and-bioinformatic-analyses-indicate-differential-circrna-and-mirna-isomir-expression-and-interactions
#19
Li Guo, Liang Zheng, Yang Zhao, Qianyun Wang
As a novel class of noncoding RNAs, circular RNAs (circRNAs) have been reported to play a role in various biological processes. Some circRNAs may serve as microRNA (miRNA) sponges, regulating transcription or splicing. Herein, we investigated the expression profiles and interactions of miRNAs/isomiRs and circRNAs in male patients with esophageal cancer. We found that some miRNA genes generated two deregulated miRNA products (miR-#-5p and miR-#-3p), and these products were consistently abnormally expressed. Some circRNAs were predicted to be miRNA sponges for specific miRNAs...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29682420/tas3-mir390-dependent-loci-in-non-vascular-land-plants-towards-a-comprehensive-reconstruction-of-the-gene-evolutionary-history
#20
Sergey Y Morozov, Irina A Milyutina, Tatiana N Erokhina, Liudmila V Ozerova, Alexey V Troitsky, Andrey G Solovyev
Trans-acting small interfering RNAs (ta-siRNAs) are transcribed from protein non-coding genomic TAS loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants, gymnosperms, ferns and mosses. In this study, bioinformatic and experimental PCR-based approaches were used as tools to analyze TAS3 and TAS6 loci in transcriptomes and genomic DNAs from representatives of evolutionary distant non-vascular plant taxa such as Bryophyta, Marchantiophyta and Anthocerotophyta...
2018: PeerJ
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