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https://www.readbyqxmd.com/read/28449392/osmotic-stress-decreases-complexity-underlying-the-electrophysiological-dynamic-in-soybean
#1
G F R Saraiva, A S Ferreira, G M Souza
Research rationale: Studies on plant electrophysiology are mostly focused on specific traits of single cells. Inspired by the complexity of the signaling network in plants and by analogies with neurons in human brains, we have sought for evidences of high complexity in the electrical dynamics of plant signaling and a likely relation with environmental cues. Central methods: An EEG-like standard protocol was adopted for high-resolution measurements of the electrical signal in Glycine max seedlings. The signals were continuously recorded in the same plants before and after the osmotic stimuli with a -2 MPa mannitol solution...
April 27, 2017: Plant Biology
https://www.readbyqxmd.com/read/28449065/a-homozygous-missense-mutation-in-eral1-encoding-a-mitochondrial-rrna-chaperone-causes-perrault-syndrome
#2
Iliana A Chatzispyrou, Marielle Alders, Sergio Guerrero-Castillo, Ruben Zapata Perez, Martin A Haagmans, Laurent Mouchiroud, Janet Koster, Rob Ofman, Frank Baas, Hans R Waterham, Johannes N Spelbrink, Johan Auwerx, Marcel M Mannens, Riekelt H Houtkooper, Astrid S Plomp
Perrault syndrome (PS) is a rare recessive disorder characterized by ovarian dysgenesis and sensorineural deafness. It is clinically and genetically heterogeneous, and previously mutations have been described in different genes, mostly related to mitochondrial proteostasis. We diagnosed three unrelated females with PS and set out to identify the underlying genetic cause using exome sequencing. We excluded mutations in the known PS genes, but identified a single homozygous mutation in the ERAL1 gene (c.707A>T; p...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28448959/detection-of-circulating-tumor-cells-and-circulating-tumor-microemboli-in-gastric-cancer
#3
Xiumei Zheng, Li Fan, Pengfei Zhou, Hong Ma, Shaoyi Huang, Dandan Yu, Lei Zhao, Shengli Yang, Jun Liu, Ai Huang, Congli Cai, Xiaomeng Dai, Tao Zhang
PURPOSE: Gastric cancer studies indicated a potential correlation between circulating tumor cells (CTCs) in peripheral blood and tumor relapse/metastasis. The prevalence and significance of circulating tumor microemboli (CTM) in gastric cancer remain unknown. We investigated the prevalence and prognostic value of CTCs and CTM for progression-free survival (PFS) and overall survival (OS) in gastric cancer patients. METHODS: Eighty-one gastric cancer patients consented to provide 5ml of peripheral blood before systematic therapy...
April 24, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28448556/a-highly-specific-and-sensitive-massive-parallel-sequencer-based-test-for-somatic-mutations-in-non-small-cell-lung-cancer
#4
Yoshiaki Inoue, Jun Shiihara, Hitoshi Miyazawa, Hiromitsu Ohta, Megumi Higo, Yoshiaki Nagai, Kunihiko Kobayashi, Yasuo Saijo, Masanori Tsuchida, Mitsuo Nakayama, Koichi Hagiwara
Molecular targeting therapy for non-small cell lung cancer (NSCLC) has clarified the importance of mutation testing when selecting treatment regimens. As a result, multiple-gene mutation tests are urgently needed. We developed a next-generation sequencer (NGS)-based, multi-gene test named the MINtS for investigating driver mutations in both cytological specimens and snap-frozen tissue samples. The MINtS was used to investigate the EGFR, KRAS, BRAF genes from DNA, and the ERBB2, and the ALK, ROS1, and RET fusion genes from RNA...
2017: PloS One
https://www.readbyqxmd.com/read/28448058/a-rapid-automated-protocol-for-muscle-fiber-population-analysis-in-rat-muscle-cross-sections-using-myosin-heavy-chain-immunohistochemistry
#5
Konstantin D Bergmeister, Marion Gröger, Martin Aman, Anna Willensdorfer, Krisztina Manzano-Szalai, Stefan Salminger, Oskar C Aszmann
Quantification of muscle fiber populations provides a deeper insight into the effects of disease, trauma, and various other influences on skeletal muscle composition. Various time-consuming methods have traditionally been used to study fiber populations in many fields of research. However, recently developed immunohistochemical methods based on myosin heavy chain protein expression provide a quick alternative to identify multiple fiber types in a single section. Here, we present a rapid, reliable and reproducible protocol for improved staining quality, allowing automatic acquisition of whole cross sections and automatic quantification of fiber populations with ImageJ...
March 28, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448050/single-molecule-analysis-of-laser-localized-psoralen-adducts
#6
Jing Huang, Himabindu Gali, Julia Gichimu, Marina A Bellani, Durga Pokharel, Manikandan Paramasivam, Michael M Seidman
The DNA Damage Response (DDR) has been extensively characterized in studies of double strand breaks (DSBs) induced by laser micro beam irradiation in live cells. The DDR to helix distorting covalent DNA modifications, including interstrand DNA crosslinks (ICLs), is not as well defined. We have studied the DDR stimulated by ICLs, localized by laser photoactivation of immunotagged psoralens, in the nuclei of live cells. In order to address fundamental questions about adduct distribution and replication fork encounters, we combined laser localization with two other technologies...
April 20, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448036/using-microfluidic-devices-to-measure-lifespan-and-cellular-phenotypes-in-single-budding-yeast-cells
#7
Ke Zou, Diana S Ren, Qi Ou-Yang, Hao Li, Jiashun Zheng
Budding yeast Saccharomyces cerevisiae is an important model organism in aging research. Genetic studies have revealed many genes with conserved effects on the lifespan across species. However, the molecular causes of aging and death remain elusive. To gain a systematic understanding of the molecular mechanisms underlying yeast aging, we need high-throughput methods to measure lifespan and to quantify various cellular and molecular phenotypes in single cells. Previously, we developed microfluidic devices to track budding yeast mother cells throughout their lifespan while flushing away newborn daughter cells...
March 30, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448005/open-source-single-particle-analysis-for-super-resolution-microscopy-with-virusmapper
#8
Robert D M Gray, Jason Mercer, Ricardo Henriques
Super-resolution fluorescence microscopy is currently revolutionizing cell biology research. Its capacity to break the resolution limit of around 300 nm allows for the routine imaging of nanoscale biological complexes and processes. This increase in resolution also means that methods popular in electron microscopy, such as single-particle analysis, can readily be applied to super-resolution fluorescence microscopy. By combining this analytical approach with super-resolution optical imaging, it becomes possible to take advantage of the molecule-specific labeling capacity of fluorescence microscopy to generate structural maps of molecular elements within a metastable structure...
April 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448000/high-resolution-imaging-and-analysis-of-individual-astral-microtubule-dynamics-in-budding-yeast
#9
Colby P Fees, Cassi Estrem, Jeffrey K Moore
Dynamic microtubules are fundamental to many cellular processes, and accurate measurements of microtubule dynamics can provide insight into how cells regulate these processes and how genetic mutations impact regulation. The quantification of microtubule dynamics in metazoan models has a number of associated challenges, including a high microtubule density and limitations on genetic manipulations. In contrast, the budding yeast model offers advantages that overcome these challenges. This protocol describes a method to measure the dynamics of single microtubules in living yeast cells...
April 20, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447726/a-three-caller-pipeline-for-variant-analysis-of-cancer-whole-exome-sequencing-data
#10
Ze-Kun Liu, Yu-Kui Shang, Zhi-Nan Chen, Huijie Bian
Rapid advancements in next generation sequencing (NGS) technologies, coupled with the dramatic decrease in cost, have made NGS one of the leading approaches applied in cancer research. In addition, it is increasingly used in clinical practice for cancer diagnosis and treatment. Somatic (cancer‑only) single nucleotide variants and small insertions and deletions (indels) are the simplest classes of mutation, however, their identification in whole exome sequencing data is complicated by germline polymorphisms, tumor heterogeneity and errors in sequencing and analysis...
March 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447211/paclitaxel-induced-sensory-peripheral-neuropathy-is-associated-with-an-abcb1-single-nucleotide-polymorphism-and-older-age-in-japanese
#11
Yuko Tanabe, Chikako Shimizu, Akinobu Hamada, Kenji Hashimoto, Kazutaka Ikeda, Daisuke Nishizawa, Junko Hasegawa, Akihiko Shimomura, Yukinori Ozaki, Nobuko Tamura, Harukaze Yamamoto, Mayu Yunokawa, Kan Yonemori, Toshimi Takano, Hidetaka Kawabata, Kenji Tamura, Yasuhiro Fujiwara
PURPOSE: Whether age and inter-individual variability of pharmacogenetics are risk factors for paclitaxel-induced peripheral neuropathy (PIPN) is inconclusive. This study was conducted to evaluate the influence of previously investigated single nucleotide polymorphisms (SNPs) and age, using genotype data from a prospective study of paclitaxel-related toxicity in Japanese patients with breast cancer. METHODS: Peripheral blood mononuclear cells from 127 Japanese women with breast cancer who received weekly adjuvant paclitaxel were used to genotypes SLCO1B3 T334G (rs4149117), CYP2C8 A1196G (rs10509681), ABCB1 C1236T (rs1128503), ABCB1 G2677T/A (rs2032582), and ABCB1 C3435T (rs1045642)...
April 26, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28447192/rescue-of-a-wild-type-rabies-virus-from-cloned-cdna-and-assessment-of-the-proliferative-capacity-of-recombinant-viruses
#12
Qin Tian, Yifei Wang, Qiong Zhang, Jun Luo, Mingzhu Mei, Yongwen Luo, Xiaofeng Guo
Reverse genetic systems (RGS) have been widely used for fixed rabies virus (RABV) strains. However, RGS, for wild-type (wt) strains, have been seldom reported despite the value of this approach in defining the biological characteristics of these strains. In this work, we developed a wt RGS using a swine-origin RABV strain (GD-SH-01) for the first time. In order to have a better understanding of the contribution and function of individual gene on viral proliferation for wt RABV isolates, we constructed a full-length cDNA clone of GD-SH-01 and exchanged the single genes encoding RABV protein of a highly attenuated RABV strain HEP-Flury with those of the virulent strain...
April 26, 2017: Virus Genes
https://www.readbyqxmd.com/read/28447043/comparative-genomics-of-human-stem-cell-factor-scf
#13
Moein Dehbashi, Elahe Kamali, Sadeq Vallian
Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA6 showed that human and Chimpanzee (Pan troglodytes) were placed into the same cluster. By using JBrowse, we found that SCF in Neanderthal had a single copy number similar to modern human and partly conserved nucleotide sequences...
March 2017: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28446772/large-scale-snp-screenings-identify-markers-linked-with-gcrv-resistant-traits-through-transcriptomes-of-individuals-and-cell-lines-in-ctenopharyngodon-idella
#14
Zhiwei Liao, Quanyuan Wan, Xueying Shang, Jianguo Su
Grass carp (Ctenopharyngodon idella) is an important economic species in freshwater aquaculture and its industry has been confined due to variety degeneration and frequent diseases. Marker-assisted selection is a feasible method for selective breeding of new varieties. Transcriptome data have greatly facilitated high-throughput single nucleotide polymorphism (SNP) marker discovery and phenotype association study. In this study, we gained a total of 25,981 and 5,775 high quality SNPs in two transcriptomes from individuals and cell lines, respectively...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446532/next-generation-sequencing-ngs-analysis-on-single-circulating-tumor-cells-ctcs-with-no-need-of-whole-genome-amplification-wga
#15
Raffaele Palmirotta, Domenica Lovero, Erica Silvestris, Claudia Felici, Davide Quaresmini, Paola Cafforio, Franco Silvestris
BACKGROUND: Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS)...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446192/prospective-clinical-and-radiographic-evaluation-of-an-allogeneic-bone-matrix-containing-stem-cells-trinity-evolution%C3%A2-viable-cellular-bone-matrix-in-patients-undergoing-two-level-anterior-cervical-discectomy-and-fusion
#16
Timothy A Peppers, Dennis E Bullard, Jed S Vanichkachorn, Scott K Stanley, Paul M Arnold, Erik I Waldorff, Rebekah Hahn, Brent L Atkinson, James T Ryaby, Raymond J Linovitz
BACKGROUND: Trinity Evolution® (TE), a viable cellular bone allograft, previously demonstrated high fusion rates and no safety-related concerns after single-level anterior cervical discectomy and fusion (ACDF) procedures. This prospective multicenter clinical study was performed to assess the radiographic and clinical outcomes of TE in subjects undergoing two-level ACDF procedures. METHODS: In a prospective, multicenter study, 40 subjects that presented with symptomatic cervical degeneration at two adjacent vertebral levels underwent instrumented ACDF using TE autograft substitute in a polyetherethereketone (PEEK) cage...
April 26, 2017: Journal of Orthopaedic Surgery and Research
https://www.readbyqxmd.com/read/28446163/exploratory-analysis-of-the-neutrophil-to-lymphocyte-ratio-in-patients-with-pulmonary-arterial-hypertension
#17
Lars Harbaum, Kaaja M Baaske, Marcel Simon, Tim Oqueka, Christoph Sinning, Antonia Glatzel, Nicole Lüneburg, Karsten Sydow, Carsten Bokemeyer, Hans Klose
BACKGROUND: Chronic inflammation emerges as a feature of the pathogenesis of pulmonary arterial hypertension (PAH) in experimental models. Alterations of circulating cell subsets have been observed in patients with PAH. We aimed to assess associations of the white blood cell count with disease severity and outcome in patients with PAH. METHODS: The total and differential white blood cell count was related to functional parameters, pulmonary hemodynamics and transplantation-free survival in 77 patients with PAH in an observational single center study...
April 26, 2017: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/28445246/single-delivery-of-high-diversity-fecal-microbiota-preparation-by-colonoscopy-is-safe-and-effective-in-increasing-microbial-diversity-in-active-ulcerative-colitis
#18
Vinita Jacob, Carl Crawford, Shirley Cohen-Mekelburg, Monica Viladomiu, Gregory G Putzel, Yecheskel Schneider, Fatiha Chabouni, Sarah OʼNeil, Brian Bosworth, Viola Woo, Nadim J Ajami, Joseph F Petrosino, Ylaine Gerardin, Zain Kassam, Mark Smith, Iliyan D Iliev, Gregory F Sonnenberg, David Artis, Ellen Scherl, Randy S Longman
BACKGROUND: Recent trials suggest fecal microbiota transplantation (FMT) with repeated enemas and high-diversity FMT donors is a promising treatment to induce remission in ulcerative colitis. METHODS: We designed a prospective, open-label pilot study to assess the safety, clinical efficacy, and microbial engraftment of single FMT delivery by colonoscopy for active ulcerative colitis using a 2-donor fecal microbiota preparation (FMP). Safety and clinical endpoints of response, remission, and mucosal healing at week 4 were assessed...
April 25, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28445004/cftr-dependent-chloride-efflux-in-cystic-fibrosis-mononuclear-cells-is-increased-by-ivacaftor-therapy
#19
Lorenzo Guerra, Susanna D'Oria, Maria Favia, Stefano Castellani, Teresa Santostasi, Angela M Polizzi, Maria A Mariggiò, Crescenzio Gallo, Valeria Casavola, Pasqualina Montemurro, Giuseppina Leonetti, Antonio Manca, Massimo Conese
AIM: The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) potentiator ivacaftor (Kalydeco®) improves clinical outcome in G551D cystic fibrosis (CF) patients. Here, we have investigated whether ivacaftor has a clinical impact on non-G551D gating mutations and function of circulating leukocytes as well. METHODS: Seven patients were treated with ivacaftor and evaluated at baseline, and at 1-3 and 6 months. Besides clinical and systemic inflammatory parameters, circulating mononuclear cells (MNC) were evaluated for CFTR-dependent chloride efflux by spectrofluorimetry, neutrophils for oxidative burst by cytofluorimetry and HVCN1 mRNA expression by real time PCR...
April 26, 2017: Pediatric Pulmonology
https://www.readbyqxmd.com/read/28444998/large-population-cell-characterization-using-quantitative-phase-cytometer
#20
Di Jin, Yongjin Sung, Niyom Lue, Yang-Hyo Kim, Peter T C So, Zahid Yaqoob
A major challenge in cellular analysis is the phenotypic characterization of large cell populations within a short period of time. Among various parameters for cell characterization, the cell dry mass is often used to describe cell size but is difficult to be measured directly with traditional techniques. Here, we propose an interferometric approach based on line-focused beam illumination for high-content precision dry mass measurements of adherent cells in a non-invasive fashion-we call it quantitative phase cytometry (QPC)...
April 26, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
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