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Functional analysis

Huihui Sun, Naijun Wan, Xinli Wang, Liang Chang, Dazhi Cheng
18p deletion syndrome is a rare chromosomal disease caused by deletion of the short arm of chromosome 18. By using cytogenetic and SNP array analysis, we identified a girl with 18p deletion syndrome exhibiting craniofacial anomalies, intellectual disability, and short stature. G-banding analysis of metaphase cells revealed an abnormal karyotype 46,XX,del(18)(p10). Further, SNP array detected a 15.3-Mb deletion at 18p11.21p11.32 (chr18:12842-15375878) including 61 OMIM genes. Genotype-phenotype correlation analysis showed that clinical manifestations of the patient were correlated with LAMA1, TWSG1, and GNAL deletions...
March 16, 2018: Cytogenetic and Genome Research
Jinyu Wang, Haitao Zhang, Mohammed Al Shibar, Belinda Willard, Alo Ray, Kurt W Runge
Telomeres, the ends of eukaryotic chromosomes, consist of repetitive DNA sequences and their bound proteins that protect the end from the DNA damage response. Short telomeres with fewer repeats are preferentially elongated by telomerase. Tel1, the yeast homolog of human ATM kinase, is preferentially recruited to short telomeres and Tel1 kinase activity is required for telomere elongation. Rif1, a telomere-binding protein, negatively regulates telomere length by forming a complex with two other telomere binding proteins, Rap1 and Rif2, to block telomerase recruitment...
March 7, 2018: DNA Repair
Wei Tse Li, Hao Zheng, Vincent Nguyen, Jessica Wang-Rodriguez, Weg M Ongkeko
Though bladder urothelial carcinoma is the most common form of bladder cancer, advances in its diagnosis and treatment have been modest in the past few decades. To evaluate miRNAs as putative disease markers for bladder urothelial carcinoma, this study develops a process to identify dysregulated miRNAs in cancer patients and potentially stratify patients based on the association of their microRNAome phenotype to genomic alterations. Using RNA sequencing data for 409 patients from the Cancer Genome Atlas, we examined miRNA differential expression between cancer and normal tissues and associated differentially expressed miRNAs with patient survival and clinical variables...
March 12, 2018: Neoplasia: An International Journal for Oncology Research
Mathias Reisbeck, Lukas Richter, Michael Johannes Helou, Stephan Arlinghaus, Birgit Anton, Ignas van Dommelen, Mario Nitzsche, Michael Baßler, Barbara Kappes, Oliver Friedrich, Oliver Hayden
Time-of-flight (TOF) magnetic sensing of rolling immunomagnetically-labeled cells offers great potential for single cell function analysis at the bedside in even optically opaque media, such as whole blood. However, due to the spatial resolution of the sensor and the low flow rate regime required to observe the behavior of rolling cells, the concentration range of such a workflow is limited. Potential clinical applications, such as testing of leukocyte function, require a cytometer which can cover a cell concentration range of several orders of magnitude...
March 12, 2018: Biosensors & Bioelectronics
Dustin A Bruening, Kota Z Takahashi
BACKGROUND: Kinematic multi-segment foot models have been increasingly used to study foot function. The addition of kinetics to these models may enhance their utility; however, this been hindered by limitations in measuring ground reaction forces (GRFs) under individual foot segments. PURPOSE: To determine the accuracy of partitioning segment GRFs from a single force platform on foot joint kinetics. METHODS: Two potential partitioning methods were applied to a previously published three-segment kinetic foot model...
March 6, 2018: Gait & Posture
Michela Balconi, Laura Gatti, Maria Elide Vanutelli
Cooperation behavior is a core question of study on social neuroscience. In the present study, inter-brain functional connectivity and cognitive performance were considered during joint which was failing. The cognitive performance and the EEG (brain oscillations from delta to beta) underlying the execution of joint-actions were recorded when dyads of participants executed synchronicity game and received reinforcing negative feedbacks A pre-feedback condition (cooperation) and a control condition (individual task, T0) were provided as well as a check for possible learning effect (time series analysis)...
March 12, 2018: Consciousness and Cognition
Manuela Lavelli, Marinella Majorano, Letizia Guerzoni, Alessandra Murri, Chiara Barachetti, Domenico Cuda
This study examined (a) the functions and modalities of maternal and child communication during interaction between mothers and children with cochlear implants (CIs), comparing them with mothers and normally hearing (NH) children, and (b) the effectiveness of maternal support strategies in eliciting adequate answers in children with CI. Twenty preschoolers with CIs (M = 40 months) and 40 NH children - 20 matched by chronological age (CANH, M = 40 months) and 20 matched by hearing age (HANH, M = 25 months) - were videotaped during shared book reading and toy play with their mothers...
March 5, 2018: Journal of Communication Disorders
John K Fallon, Nicole Houvig, Catherine L Booth-Genthe, Philip C Smith
Information is needed on the expression of transporters in lung to inform drug development and therapeutic decisions. Much of the information currently available is from semiquantitative gene expression or immunometric densitometry studies reported in the literature. NanoLC-MS/MS (MRM mode) isotope dilution targeted quantitative proteomics was used here to quantify twelve selected transporters in fresh human lung membrane fraction samples and in the membrane fraction of selected immortalized human lung epithelial cell line samples...
February 22, 2018: Journal of Pharmaceutical and Biomedical Analysis
Urmi Bajpai, Abhishek Kumar Mehta, Kandasamy Eniyan, Avni Sinha, Ankita Ray, Simran Virdi, Shazeb Ahmad, Aridni Shah, Deepanksha Arora, Devyani Marwaha, Gunjan Chauhan, Prarthna Saraswat, Punita Bathla, Ruchi Singh
Bacteriophages are being considered as a promising natural resource for the development of alternative strategies against mycobacterial diseases, especially in the context of the wide spread occurrence of drug-resistance amongst the clinical isolates of M. tuberculosis. However, there isn't much information documented on mycobacteriophages from India. Here, we report the isolation of 17 mycobacteriophages using M. smegmatis as the bacterial host where 9 phages also lyse M. tuberculosis H37Rv. We present detailed analysis of one of these mycobacteriophage (PDRPv)...
March 15, 2018: Canadian Journal of Microbiology
Samiul M Ansari, David S Palmer
Recently, Güssregen et al. used solute-solvent distribution functions calculated by the 3D Reference Interaction Site Model (3DRISM) in a 3D-QSAR approach to model activity data for a set of serine protease inhibitors; this approach was referred to as Comparative Analysis of 3D RISM MAps (CARMa). [J. Chem. Inf. MODEL: , 2017, 57, 1652-1666] Here we extend this idea by introducing probe atoms into the 3DRISM solvent model in order to directly capture other molecular interactions in addition to those related to hydration/dehydration...
March 15, 2018: Journal of Chemical Information and Modeling
Thanh D Do, Joseph F Ellis, Elizabeth K Neumann, Troy J Comi, Emily G Tillmaand, Ashley E Lenhart, Stanislav S Rubakhin, Jonathan Sweedler
The mammalian dorsal root ganglia (DRG) are located on the dorsal roots of the spinal nerves and contain cell bodies of primary sensory neurons. DRG cells have been classified into subpopulations based on their size, morphology, intracellular markers, response to stimuli, and neuropeptides. To understand the connections between DRG chemical heterogeneity and cellular function, we performed optically guided, high-throughput single cell profiling using sequential matrix-assisted laser desorption/ionization mass spectrometry (MS) to detect lipids, peptides, and several proteins in individual DRG cells...
March 15, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Sang Min Yoon, Baek-Yeol Ryoo, So Jung Lee, Jong Hoon Kim, Ji Hoon Shin, Ji Hyun An, Han Chu Lee, Young-Suk Lim
Importance: Patients with hepatocellular carcinoma showing macroscopic vascular invasion have a poor prognosis. Sorafenib is the sole treatment option for these patients, with unsatisfactory response and survival benefit. Combined treatment with transarterial chemoembolization (TACE) plus external beam radiotherapy (RT) has shown promising results for these patients in observational studies. Objective: To evaluate the efficacy and safety of TACE plus RT compared with sorafenib for patients with hepatocellular carcinoma and macroscopic vascular invasion...
March 15, 2018: JAMA Oncology
Cherian K Kandathil, Emily A Spataro, Katri Laimi, Sami P Moubayed, Sam P Most, Mikhail Saltychev
Importance: While functional rhinoplasty has been broadly studied, to our knowledge no systematic review and meta-analysis of lateral wall repair has been done previously. Objective: To evaluate the effectiveness of repair of the lateral nasal wall in adult patients with nasal airway obstruction. Data Sources: Medline, Embase, Cinahl, Central, Scopus, and Web of Science databases and reference lists were searched for clinical and observational studies...
March 15, 2018: JAMA Facial Plastic Surgery
Kim C M Bul, Lisa L Doove, Ingmar H A Franken, Saskia Van der Oord, Pamela M Kato, Athanasios Maras
OBJECTIVE: The aim of the current study was to identify which subgroups of children with Attention Deficit Hyperactivity Disorder (ADHD) benefitted the most from playing a Serious Game (SG) intervention shown in a randomized trial to improve behavioral outcomes. METHOD: Pre-intervention characteristics [i.e., gender, age, intellectual level of functioning, medication use, computer experience, ADHD subtype, severity of inattention problems, severity of hyperactivity/impulsivity problems, comorbid Oppositional Defiant Disorder (ODD) and Conduct Disorder (CD) symptoms] were explored as potential moderators in a Virtual Twins (VT) analysis to identify subgroups for whom the SG intervention was most effective...
2018: PloS One
Olivier Poupel, Caroline Proux, Bernd Jagla, Tarek Msadek, Sarah Dubrac
The success of Staphylococcus aureus, as both a human and animal pathogen, stems from its ability to rapidly adapt to a wide spectrum of environmental conditions. Two-component systems (TCSs) play a crucial role in this process. Here, we describe a novel staphylococcal virulence factor, SpdC, an Abi-domain protein, involved in signal sensing and/or transduction. We have uncovered a functional link between the WalKR essential TCS and the SpdC Abi membrane protein. Expression of spdC is positively regulated by the WalKR system and, in turn, SpdC negatively controls WalKR regulon genes, effectively constituting a negative feedback loop...
March 2018: PLoS Pathogens
Mai Ishimiya, Hiroyuki Nakamura, Yutaka Kobayashi, Moeko Noguchi-Shinohara, Chiemi Abe, Chiaki Dohmoto, Yoshihisa Ikeda, Kahori Tokuno, Kazuhiro Ooi, Masami Yokokawa, Kazuo Iwasa, Kiyonobu Komai, Shuichi Kawashiri, Masahito Yamada
Although several studies have demonstrated a potential correlation of dietary patterns with cognitive function, the relationship between tooth loss and dietary patterns and cognitive function have not been identified. In this cross-sectional study, we used a reduced rank regression (RRR) analysis, a technique used previously to observe dietary patterns based on the intakes of nutrients or levels of biomarkers associated with the condition of interest, to identify tooth loss-related dietary patterns and investigate the associations of such patterns with cognitive impairment in 334 community-dwelling Japanese subjects aged ≥ 60 years...
2018: PloS One
Dilyana Filipova, Margit Henry, Tamara Rotshteyn, Anna Brunn, Mariana Carstov, Martina Deckert, Jürgen Hescheler, Agapios Sachinidis, Gabriele Pfitzer, Symeon Papadopoulos
In skeletal muscle the coordinated actions of two mechanically coupled Ca2+ channels-the 1,4-dihydropyridine receptor (Cav1.1) and the type 1 ryanodine receptor (RYR1)-underlie the molecular mechanism of rapid cytosolic [Ca2+] increase leading to contraction. While both [Ca2+]i and contractile activity have been implicated in the regulation of myogenesis, less is known about potential specific roles of Cav1.1 and RYR1 in skeletal muscle development. In this study, we analyzed the histology and the transcriptomic changes occurring at E14...
2018: PloS One
Maroua Ben Amira, Robin Mom, David Lopez, Hatem Chaar, Ali Khouaja, Valérie Pujade-Renaud, Boris Fumanal, Aurélie Gousset-Dupont, Gisèle Bronner, Philippe Label, Jean-Louis Julien, Mohamed Ali Triki, Daniel Auguin, Jean-Stéphane Venisse
Major intrinsic proteins (MIP) are characterized by a transmembrane pore-type architecture that facilitates transport across biomembranes of water and a variety of low molecular weight solutes. They are found in all parts of life, with remarkable protein diversity. Very little is known about MIP from fungi. And yet, it can legitimately be stated that MIP are pivotal molecular components in the privileged relationships fungi enjoy with plants or soil fauna in various environments. To date, MIP have never been studied in a mycoparasitism situation...
2018: PloS One
Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
Michael J Fay, Lauren A C Alt, Dominika Ryba, Ribhi Salamah, Ryan Peach, Alexander Papaeliou, Sabina Zawadzka, Andrew Weiss, Nil Patel, Asad Rahman, Zyaria Stubbs-Russell, Peter C Lamar, Joshua R Edwards, Walter C Prozialeck
Cadmium (Cd) is a nephrotoxic environmental pollutant that causes a generalized dysfunction of the proximal tubule characterized by polyuria and proteinuria. Even though the effects of Cd on the kidney have been well-characterized, the molecular mechanisms underlying these effects have not been fully elucidated. MicroRNAs (miRNAs) are small non-coding RNAs that regulate cellular and physiologic function by modulating gene expression at the post-transcriptional level. The goal of the present study was to determine if Cd affects renal cortex miRNA expression in a well-established animal model of Cd-induced kidney injury...
March 15, 2018: Toxics
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