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Xiaoling Guo, Yong Chen, Tingting Hong, Xianwu Chen, Yue Duan, Chao Li, Renshan Ge
Leydig cell transplantation is a better alternative in the treatment of androgen-deficient males. The main purpose of this study was to investigate the effects of induced pluripotent stem cell-derived conditioned medium (iPS-CM) on the anti-apoptosis, proliferation and function of immature Leydig cells (ILCs), and illuminate the underlying mechanisms. ILCs were exposed to 200 μmol/L hydrogen peroxide (H2 O2 ) for 24 hours with or without iPS-CM treatments. Cell apoptosis was detected by flow cytometric analysis...
April 18, 2018: Journal of Cellular and Molecular Medicine
Jun-Jie Wang, Yu Tian, Kai-Lin Xu, Rui-Xue Fu, Ming-Shan Niu, Kai Zhao
OBJECTIVE: To investigate the effect of Statins on proliferation and apoptosis in human acute T lymphocytic leukemia (T-ALL) cells and its possible mechanism. METHODS: Jurkat and CCRF-CEM cells were cultured in different concentrations of Fluvastatin and Simvastatin for 24 h respectively. Then, the cell growth inhibition level was defected by CCK-8; the DNA replication was analyzed by EdU; the cell apoptosis was analyzed by Annexin V/7-AAD double labeling; the cell cycle changes were analyzed by flow cytometry; the expressions of Cyclin D1, p21, p27, BAX, BCL-2 and p-Akt were determined by Western blot...
April 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
Wenting Song, Qian S Liu, Zhendong Sun, Xiaoxi Yang, Qunfang Zhou, Guibin Jiang
Polyfluorinated iodine alkanes (PFIs) are a kind of emerging chemicals with endocrine disrupting effects. Based on the different binding preferences of PFIs to estrogen receptor alpha and beta isoforms (ERα and β), two representative PFIs, dodecafluoro-1,6-diiodohexane (PFHxDI) and tridecafluorohexyl iodide (PFHxI), were selected to evaluate their effects on the proliferation of two kinds of breast cancer cells with different ERα/β expression levels, MCF-7 and T47D. The cell viability assay showed PFHxDI could cause higher cellular toxicity than did PFHxI in both MCF-7 and T47D...
April 14, 2018: Environmental Pollution
Nan Zhou, Shuang Hao, Zongqiang Huang, Weiwei Wang, Penghui Yan, Wei Zhou, Qihang Zhu, Xiaokang Liu
Objective Neural stem cells play an important role in the recovery and regeneration of peripheral nerve injury, and the microRNA-7 (miR-7) regulates differentiation of neural stem cells. This study aimed to explore the role of miR-7 in neural stem cells homing and proliferation and its influence on peripheral nerve injury repair. Methods The mice model of peripheral nerve injury was created by segmental sciatic nerve defect (sciatic nerve injury), and neural stem cells treatment was performed with a gelatin hydrogel conduit containing neural stem cells inserted into the sciatic nerve injury mice...
January 2018: Molecular Pain
Gileno Edu Lameira de Melo, Ana Francisca Rozin Kleiner, Jamile Benite Palma Lopes, Arislander Jonathan Lopes Dumont, Roberta Delasta Lazzari, Manuela Galli, Claudia Santos Oliveira
OBJECTIVE: To evaluate the effects of gait training with virtual reality (VR) on walking distance and physical fitness in individuals with Parkinson's Disease (PD). METHODS: Thirty-seven individuals with PD participated in this prospective, randomized, controlled clinical trial. They were randomly allocated to a control group submitted to conventional training (n = 12), a treadmill group submitted to gait training on a treadmill (n = 13) and a VR group submitted to gait training using the XboxTM (n = 12)...
April 7, 2018: NeuroRehabilitation
Amanda Birmingham, Adam M Mark, Carlo Mazzaferro, Guorong Xu, Kathleen M Fisch
Summary: With the growing availability of population-scale whole-exome and whole-genome sequencing, demand for reproducible, scalable variant analysis has spread within genomic research communities. To address this need, we introduce the Python package VAPr (Variant Analysis and Prioritization). VAPr leverages existing annotation tools ANNOVAR and with MongoDB-based flexible storage and filtering functionality. It offers biologists and bioinformatics generalists easy-to-use and scalable analysis and prioritization of genomic variants from large cohort studies...
April 6, 2018: Bioinformatics
Yuxing Liao, R Dustin Schaeffer, Jimin Pei, Nick V Grishin
Motivation: The ECOD database classifies protein domains based on their evolutionary relationships, considering both remote and close homology. The family group in ECOD provides classification of domains that are closely related to each other based on sequence similarity. Due to different perspectives on domain definition, direct application of existing sequence domain databases, such as Pfam, to ECOD struggles with several shortcomings. Results: We created multiple sequence alignments and profiles from ECOD domains with the help of structural information in alignment building and boundary delineation...
April 5, 2018: Bioinformatics
H Robert Frost
Motivation: Gene set testing, or pathway analysis, has become a critical tool for the analysis of highdimensional genomic data. Although the function and activity of many genes and higher-level processes is tissue-specific, gene set testing is typically performed in a tissue agnostic fashion, which impacts statistical power and the interpretation and replication of results. Results: To address this challenge, we have developed a bioinformatics approach to compute tissuespecific weights for individual gene sets using information on tissue-specific gene activity from the Human Protein Atlas (HPA)...
April 6, 2018: Bioinformatics
Simone Rizzetto, David N P Koppstein, Jerome Samir, Mandeep Singh, Joanne H Reed, Curtis H Cai, Andrew R Lloyd, Auda A Eltahla, Christopher C Goodnow, Fabio Luciani
Motivation: The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic hypermutation (SHM) necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing (scRNA-seq) presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature. Results: We developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains and extract somatic mutations on the VDJ region...
April 5, 2018: Bioinformatics
Ji Hyen Lee, Han Wool Kim, Kyung Hyo Kim
BACKGROUND: Invasive Streptococcus agalactiae (group B streptococcus, GBS) infection most commonly occurs in infants; however, cases of GBS infection in adults, particularly in the elderly with significant underlying diseases, are being increasingly reported. We analyzed the serotype specific opsonophagocytic antibodies (the major mechanism of protection against GBS) in infants, adults, and the elderly. METHODS: The opsonization indices (OIs) of antibodies against serotype Ia, Ib, II, III, and V GBS were studied in 89 infants, 35 adults (age, 30-50 years), and 62 elderly individuals (age, 65-85 years) according to the University of Alabama at Birmingham GBS opsonophagocytic killing assay protocol (www...
April 16, 2018: Journal of Korean Medical Science
Minjae Yoo, Jimin Shin, Hyunmin Kim, Jihye Kim, Jaewoo Kang, Aik Choon Tan
BACKGROUND AND OBJECTIVE: Traditional Chinese Medicine (TCM) has been practiced over thousands of years in China and other Asian countries for treating various symptoms and diseases. However, the underlying molecular mechanisms of TCM are poorly understood, partly due to the "multi-component, multi-target" nature of TCM. To uncover the molecular mechanisms of TCM, we perform comprehensive gene expression analysis using connectivity map. METHODS: We interrogated gene expression signatures obtained 102 TCM components using the next generation Connectivity Map (CMap) resource...
April 4, 2018: Computer Methods and Programs in Biomedicine
Kathrin K Geyer, Sabrina E Munshi, Martin Vickers, Michael Squance, Toby J Wilkinson, Daniel Berrar, Cristian Chaparro, Martin T Swain, Karl F Hoffmann
Uncontrolled host immunological reactions directed against tissue-trapped eggs precipitate a potentially lethal, pathological cascade responsible for schistosomiasis. Blocking schistosome egg production, therefore, presents a strategy for simultaneously reducing immunopathology as well as limiting disease transmission in endemic or emerging areas. We recently demonstrated that the ribonucleoside analogue 5-azacytidine (5-AzaC) inhibited Schistosoma mansoni oviposition, egg maturation and ovarian development...
April 1, 2018: International Journal for Parasitology, Drugs and Drug Resistance
Ming Zhang, Yan Xu, Lei Li, Zi Liu, Xibei Yang, Dong-Jun Yu
RNA 5-methylcytosine (m5 C) is an important post-transcriptional modification that plays an indispensable role in biological processes. The accurate identification of m5 C sites from primary RNA sequences is especially useful for deeply understanding the mechanisms and functions of m5 C. Due to the difficulty and expensive costs of identifying m5 C sites with wet-lab techniques, developing fast and accurate machine-learning-based prediction methods is urgently needed. In this study, we proposed a new m5 C site predictor, called M5C-HPCR, by introducing a novel heuristic nucleotide physicochemical property reduction (HPCR) algorithm and classifier ensemble...
April 9, 2018: Analytical Biochemistry
Tien-Chueh Kuo, Yufeng Jane Tseng
Motivation: Lipids are divided into fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, sterols, prenol lipids and polyketides. Fatty acyls and glycerolipids are commonly used as energy storage, whereas glycerophospholipids, sphingolipids, sterols and saccharolipids are common used as components of cell membranes. Lipids in fatty acyls, glycerophospholipids, sphingolipids and sterols classes play important roles in signaling. Although more than 36 million lipids can be identified or computationally generated, no single lipid database provides comprehensive information on lipids...
April 10, 2018: Bioinformatics
Michael K K Leung, Andrew Delong, Brendan J Frey
Motivation: Processing of transcripts at the 3'-end involves cleavage at a polyadenylation site followed by the addition of a poly(A)-tail. By selecting which site is cleaved, the process of alternative polyadenylation enables genes to produce transcript isoforms with different 3'-ends. To facilitate the identification and treatment of disease-causing mutations that affect polyadenylation and to understand the sequence determinants underlying this regulatory process, a computational model that can accurately predict polyadenylation patterns from genomic features is desirable...
April 10, 2018: Bioinformatics
Andrew Ching-Yuet To, David Ho Ting Chu, Angela Ruoning Wang, Frances Cheuk-Yau Li, Alan Wai-On Chiu, Daisy Yuwei Gao, Chung Hang Jonathan Choi, Siu-Kai Kong, Ting-Fung Chan, King-Ming Chan, Kevin Y Yip
Background: Toehold switches are a class of RNAs with a hairpin loop that can be unfolded upon binding a trigger RNA, thereby exposing a ribosome binding site (RBS) and permitting translation of the reporter protein. They have been shown very useful in detecting a variety of targets including RNAs from Zika and Ebola viruses. The base complementation between the toehold switch and the trigger RNA also makes it sensitive to sequence variations. Design of toehold switches involves a series of considerations related to their sequence properties, structures and specificities...
April 10, 2018: Bioinformatics
Alex K Wu, Xiaoyu Zhang, Jianwen Wang, Hongxiu Ning, Uwais Zaid, Jaqueline D Villalta, Guifang Wang, Lia Banie, Guiting Lin, Tom F Lue
Background: To investigate the outcomes and mechanisms of low-intensity extracorporeal shock wave therapy (Li-ESWT) on stress urinary incontinence (SUI) in a vaginal balloon dilation (VBD) rat model. Methods: Thirty Sprague-Dawley rats were randomly grouped into normal controls, VBD only, and VBD with Li-ESWT. Li-ESWT was administered twice per week for 3 weeks. Afterward, all 30 rats were assessed with functional and histological studies. To explore the acute effect of Li-ESWT, another 25 rats, given intraperitoneal 5-ethynyl-2-deoxyuridine (EdU) at birth, were treated with Li-ESWT followed by assessment of vascular endothelial growth factor (VEGF) expression and endogenous progenitor cells distribution at 24 hours or 1 week after the last Li-ESWT therapy...
March 2018: Translational Andrology and Urology
Lu Zhang, Yasutomo Hoshika, Elisa Carrari, Kent O Burkey, Elena Paoletti
Tropospheric ozone (O3 ) is a major air pollutant and causes serious injury to vegetation. To protect sensitive plants from O3 damage, several agrochemicals have been assessed, including cytokinin (e.g., kinetin, KIN) and ethylenediurea (EDU) with cytokinin-like activity. In higher plant, leaves are primarily injured by O3 and protective agrochemicals are often applied by leaf spraying. To our knowledge, the mitigating abilities of EDU and KIN have not been compared directly in a realistic setup. In the present research, impacts of elevated O3 (2× ambient O3 , 24hr per day, for 8days) on an O3 sensitive line (S156) of snap bean (Phaseolus vulgaris), which is often used for biomonitoring O3 pollution, were studied in a free air controlled exposure system...
April 2018: Journal of Environmental Sciences (China)
G Barmparas, P H Navsaria, D Serna-Gallegos, A J Nicol, S Edu, A A Sayari, D R Margulies, E J Ley
BACKGROUND: Blunt pharyngoesophageal injuries pose a management challenge to the trauma surgeon. The purpose of this study was to explore whether these injuries can be managed expectantly without neck exploration. METHODS: The National Trauma Databank datasets 2007-2011 were reviewed for blunt trauma patients who sustained a pharyngeal injury, including an injury to the cervical esophagus. Patients who survived over 24 h and were not transferred from other institutions were divided into two groups based on whether a neck exploration was performed...
April 1, 2018: Scandinavian Journal of Surgery: SJS
Jake Rosenberg, W Ryan Parker, Michael B Cammarata, Jennifer S Brodbelt
UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications...
April 6, 2018: Journal of the American Society for Mass Spectrometry
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