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https://www.readbyqxmd.com/read/29244788/dual-modulation-of-human-hepatic-zonation-via-canonical-and-non-canonical-wnt-pathways
#1
Laura McEnerney, Kara Duncan, Bo-Ram Bang, Sandra Elmasry, Meng Li, Toshio Miki, Sadeesh K Ramakrishnan, Yatrik M Shah, Takeshi Saito
The hepatic lobule is divided into three zones along the portal-central vein axis. Hepatocytes within each zone exhibit a distinctive gene expression profile that coordinates their metabolic compartmentalization. The zone-dependent heterogeneity of hepatocytes has been hypothesized to result from the differential degree of exposure to oxygen, nutrition and gut-derived toxins. In addition, the gradient of Wnt signaling that increases towards the central vein seen in rodent models is believed to play a critical role in shaping zonation...
December 15, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29236847/protocol-for-chromosome-specific-probe-construction-using-prins-micromanipulation-and-dop-pcr-techniques
#2
Paulo Z Passamani, Carlos R Carvalho, Fernanda A F Soares
Chromosome-specific probes have been widely used in molecular cytogenetics, being obtained with different methods. In this study, a reproducible protocol for construction of chromosome-specific probes is proposed which associates in situ amplification (PRINS), micromanipulation and degenerate oligonucleotide-primed PCR (DOP-PCR). Human lymphocyte cultures were used to obtain metaphases from male and female individuals. The chromosomes were amplified via PRINS, and subcentromeric fragments of the X chromosome were microdissected using microneedles coupled to a phase contrast microscope...
December 7, 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29234067/the-human-blood-nerve-barrier-transcriptome
#3
Steven P Palladino, E Scott Helton, Preti Jain, Chaoling Dong, Michael R Crowley, David K Crossman, Eroboghene E Ubogu
The blood-nerve barrier (BNB), formed by tight junction-forming microvessels within peripheral nerve endoneurium, exists to regulate its internal microenvironment essential for effective axonal signal transduction. Relatively little is known about the unique human BNB molecular composition. Such knowledge is crucial to comprehend the relationships between the systemic circulation and peripheral nerves in health, adaptations to intrinsic or extrinsic perturbations and alterations that may result in disease. We performed RNA-sequencing on cultured early- and late-passage adult primary human endoneurial endothelial cells and laser-capture microdissected endoneurial microvessels from four cryopreserved normal adult human sural nerves referenced to the Genome Reference Consortium Human Reference 37 genome browser, using predefined criteria guided by known transcript or protein expression in vitro and in situ...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29231925/expression-profiling-of-the-retina-of-pde6c-a-zebrafish-model-of-retinal-degeneration
#4
Liyun Zhang, Xinlian Zhang, Gaonan Zhang, Chi Pui Pang, Yuk Fai Leung, Mingzhi Zhang, Wenxuan Zhong
Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. The molecular basis of the retinal defect can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. This retinal-degeneration model not only displays cone degeneration caused by a cone-specific mutation, but also other secondary cellular changes starting from 4 days postfertilization (dpf)...
December 12, 2017: Scientific Data
https://www.readbyqxmd.com/read/29229646/nhe-and-diffusion-dependent-proton-fluxes-across-the-tubular-system-membranes-of-fast-twitch-muscle-fibers-of-the-rat
#5
Bradley S Launikonis, Tanya R Cully, Laszlo Csernoch, D George Stephenson
The complex membrane structure of the tubular system (t-system) in skeletal muscle fibers is open to the extracellular environment, which prevents measurements of H+ movement across its interface with the cytoplasm by conventional methods. Consequently, little is known about the t-system's role in the regulation of cytoplasmic pH, which is different from extracellular pH. Here we describe a novel approach to measure H+-flux measurements across the t-system of fast-twitch fibers under different conditions. The approach involves loading the t-system of intact rat fast-twitch fibers with a strong pH buffer (20 mM HEPES) and pH-sensitive fluorescent probe (10 mM HPTS) before the t-system is sealed off...
December 11, 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/29229583/integrative-genomic-analysis-of-coincident-cancer-foci-implicates-ctnnb1-and-pten-alterations-in-ductal-prostate-cancer
#6
Marc Gillard, Justin Lack, Andrea Pontier, Divya Gandla, David Hatcher, Adam G Sowalsky, Jose Rodriguez-Nieves, Donald Vander Griend, Gladell Paner, David VanderWeele
BACKGROUND: Ductal adenocarcinoma of the prostate is an aggressive subtype, with high rates of biochemical recurrence and overall poor prognosis. It is frequently found coincident with conventional acinar adenocarcinoma. The genomic features driving evolution to its ductal histology and the biology associated with its poor prognosis remain unknown. OBJECTIVE: To characterize genomic features distinguishing ductal adenocarcinoma from coincident acinar adenocarcinoma foci from the same patient...
December 8, 2017: European Urology Focus
https://www.readbyqxmd.com/read/29224050/maldi-imaging-combined-with-laser-microdissection-based-microproteomics-for-protein-identification-application-to-intratumor-heterogeneity-studies
#7
Rémi Longuespée, Deborah Alberts, Dominique Baiwir, Gabriel Mazzucchelli, Nicolas Smargiasso, Edwin De Pauw
Matrix-assisted laser desorption ionization (MALDI) imaging is widely used for in situ proteomic mapping and finds multiple applications in pathology. However, low fragmentation yields in MALDI avoid an optimal identification of peptides from tissues. On the other hand, LMD-based microproteomic analyses allow for the identification of hundreds to thousands of proteins from small tissue regions. Herein, we present the combination of MALDI imaging and LMD-based microproteomic approaches for parallel identification...
December 10, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223109/genome-wide-analysis-of-barrett-s-adenocarcinoma-a-first-step-towards-identifying-patients-at-risk-and-developing-therapeutic-paths
#8
Yiyang Dai, Qing Wang, Adrian Gonzalez Lopez, Mario Anders, Peter Malfertheiner, Michael Vieth, Wolfgang Kemmner
BACKGROUND: Barrett's esophagus metaplasia is the key precursor lesion of esophageal adenocarcinoma. The aim of this study was to find a subset of markers that may allow the identification of patients at risk for esophageal adenocarcinoma, and to determine genes differentially expressed in esophageal squamous cell carcinoma. METHODS: Laser capture microdissection technique was applied to procure cells from defined regions. Genome-wide RNA profiling was performed on esophageal adenocarcinoma (n = 21), Barrett's esophagus (n = 20), esophageal squamous carcinoma (n = 9) and healthy esophageal biopsies (n = 18) using the Affymetrix Human Genome U133plus 2...
December 6, 2017: Translational Oncology
https://www.readbyqxmd.com/read/29222172/proximal-aberrant-crypt-foci-associate-with-synchronous-neoplasia-and-are-primed-for-neoplastic-progression
#9
David A Drew, Allen Mo, James J Grady, Richard G Stevens, Joel B Levine, Bruce M Brenner, Joseph C Anderson, Faripour Forouhar, Michael J O'Brien, Thomas J Devers, Daniel W Rosenberg
Aberrant crypt foci (ACF) are the earliest morphologically identifiable lesion found within the human colon. Despite their relatively high frequency in the distal colon, few studies have examined the molecular characteristics of ACF within the proximal colon. In the following study, clinical participants (n=184) were screened for ACF using high-definition chromoendoscopy with contrast dye-spray. Following pathological confirmation, ACF biopsies were subjected to laser-capture microdissection (LCM) and epithelial cells were evaluated for somatic mutations with a customized colorectal cancer mutation panel using DNA-mass spectrometry...
December 8, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29214365/profiling-differential-microrna-expression-between-in-situ-infiltrative-and-lympho-vascular-space-invasive-breast-cancer-a-pilot-study
#10
Patsy S Soon, Pamela J Provan, Edward Kim, Nirmala Pathmanathan, Dinny Graham, Christine L Clarke, Rosemary L Balleine
Ductal carcinoma in situ (DCIS), invasive breast cancer (IBC) and lympho-vascular invasion (LVI) represent distinct stages in breast cancer progression with different clinical implications. Altered microRNA (miRNA) expression may play a role in mediating the progression of DCIS to IBC and LVI. The aim of this pilot study was to investigate whether differential miRNA expression could play a role in breast cancer progression. Cancer cells from DCIS, IBC and LVI were microdissected from formalin fixed paraffin embedded (FFPE) tissue of five breast cancer samples...
December 6, 2017: Clinical & Experimental Metastasis
https://www.readbyqxmd.com/read/29209985/frequent-and-yet-unreported-gnaq-and-gna11-mutations-are-found-in-uveal-melanomas
#11
Bjoern Schneider, Katrin Riedel, Andrey Zhivov, Maja Huehns, Heike Zettl, Rudolf F Guthoff, Anselm Jünemann, Andreas Erbersdobler, Annette Zimpfer
Malignant melanoma of the uvea is the most common primary malignant tumor in the eye. We aimed to analyze GNAQ and GNA11 mutations in uveal melanomas using formalin-fixed, paraffin-embedded material and correlate the results with clinicopathological parameters. Tumor tissue was microdissected followed by amplification of GNAQ exon 4 and 5, GNA11 exon 4 and 5, and finally analyzed by Sanger sequencing. A total of 64.4 GNA11/GNAQ mutations, including ten yet unreported, were found. Two cases showed multiple mutations...
December 5, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/29204705/rankl-rank-opg-cytokine-receptor-system-mrna-expression-pattern-in-bph-primary-and-metastatic-prostate-cancer-disease
#12
Frank Christoph, Frank König, Steffen Lebentrau, Burkhard Jandrig, Hans Krause, Romy Strenziok, Martin Schostak
BACKGROUND: The cytokine system RANKL (receptor activator of NF-κB ligand), its receptor RANK and the antagonist OPG (osteoprotegerin) play a critical role in bone turnover. Our investigation was conducted to describe the gene expression at primary tumour site in prostate cancer patients and correlate the results with Gleason Score and PSA level. METHODS: Seventy-one samples were obtained from prostate cancer patients at the time of radical prostatectomy and palliative prostate resection (n = 71)...
December 4, 2017: World Journal of Urology
https://www.readbyqxmd.com/read/29196881/gata-6-expression-is-decreased-in-diaphragmatic-and-pulmonary-mesenchyme-of-fetal-rats-with-nitrofen-induced-congenital-diaphragmatic-hernia
#13
Toshiaki Takahashi, Florian Friedmacher, Julia Zimmer, Prem Puri
PURPOSE: Congenital diaphragmatic hernia (CDH) and associated pulmonary hypoplasia are thought to be caused by a malformation of the underlying diaphragmatic and airway mesenchyme. GATA binding protein 6 (Gata-6) is a zinc finger-containing transcription factor that plays a crucial role during diaphragm and lung development. In the primordial diaphragm, Gata-6 expression is restricted to mesenchymal compartments of the pleuroperitoneal folds (PPFs). In addition, Gata-6 is essential for airway branching morphogenesis through upregulation of mesenchymal signaling...
December 2, 2017: Pediatric Surgery International
https://www.readbyqxmd.com/read/29193461/site-specific-gene-expression-analysis-from-archived-human-intestine-samples-combining-laser-capture-microdissection-and-multiplexed-color-coded-probes
#14
A Braun, C Martinez, S Schmitteckert, R Röth, F Lasitschka, B Niesler
BACKGROUND: Alterations of site-specific gene expression profiles in disease-relevant networks within the different layers of the intestinal wall may contribute to the onset and clinical course of gastrointestinal disorders. To date, no systematic analysis has assessed and compared sub-regional gene expression patterns in all distinct layers of the gut using fresh frozen human samples. Our aim was to establish an optimized protocol for site-specific RNA isolation in order to achieve maximum RNA quality and amount for subsequent gene expression analysis combining laser-capture microdissection (LCM) with a probe-based technology, the NanoString nCounter Analysis system...
November 28, 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/29190033/single-cell-dissociation-and-characterization-in-the-murine-retina-and-optic-nerve
#15
Hee Joo Choi, Rui Wang, Tatjana C Jakobs
Recent technological advances have extended the range of analytic tools to very small samples. It is now possible to assay the transcriptome, and in some cases even the proteome, of single cells reliably. This allows addressing novel questions, such as the genotype/phenotype relationships of single neurons, heterogeneity within individual cells of the same type, or the basis of differential vulnerability to injury. An important prerequisite for these kinds of studies is the ability to isolate well-defined individual cells without contamination by adjacent tissue...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29187566/stage-specific-gene-profiling-of-germinal-cells-helps-delineate-the-mitosis-meiosis-transition
#16
Tinglu Yuan, Wei-Jie Huang, Juan He, Dong Zhang, Weihua Tang
In flowering plants, germ lines are induced from somatic meristems within reproductive organs. Within anthers, germinal cell initials first undergo several rounds of mitotic proliferation before synchronously entering meiosis. Our understanding of the progression and the molecular basis of this mitosis to meiosis transition is still limited. Taking advantage of the correlation between anther length and pre-meiotic germinal cell development in maize, we studied the transcriptome dynamics of germinal cells at three sequential stages, i...
November 29, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29185012/systems-biology-of-the-imidia-biobank-from-organ-donors-and-pancreatectomised-patients-defines-a-novel-transcriptomic-signature-of-islets-from-individuals-with-type-2-diabetes
#17
Michele Solimena, Anke M Schulte, Lorella Marselli, Florian Ehehalt, Daniela Richter, Manuela Kleeberg, Hassan Mziaut, Klaus-Peter Knoch, Julia Parnis, Marco Bugliani, Afshan Siddiq, Anne Jörns, Frédéric Burdet, Robin Liechti, Mara Suleiman, Daniel Margerie, Farooq Syed, Marius Distler, Robert Grützmann, Enrico Petretto, Aida Moreno-Moral, Carolin Wegbrod, Anke Sönmez, Katja Pfriem, Anne Friedrich, Jörn Meinel, Claes B Wollheim, Gustavo B Baretton, Raphael Scharfmann, Everson Nogoceke, Ezio Bonifacio, Dorothée Sturm, Birgit Meyer-Puttlitz, Ugo Boggi, Hans-Detlev Saeger, Franco Filipponi, Mathias Lesche, Paolo Meda, Andreas Dahl, Leonore Wigger, Ioannis Xenarios, Mario Falchi, Bernard Thorens, Jürgen Weitz, Krister Bokvist, Sigurd Lenzen, Guy A Rutter, Philippe Froguel, Manon von Bülow, Mark Ibberson, Piero Marchetti
AIMS/HYPOTHESIS: Pancreatic islet beta cell failure causes type 2 diabetes in humans. To identify transcriptomic changes in type 2 diabetic islets, the Innovative Medicines Initiative for Diabetes: Improving beta-cell function and identification of diagnostic biomarkers for treatment monitoring in Diabetes (IMIDIA) consortium ( www.imidia.org ) established a comprehensive, unique multicentre biobank of human islets and pancreas tissues from organ donors and metabolically phenotyped pancreatectomised patients (PPP)...
November 28, 2017: Diabetologia
https://www.readbyqxmd.com/read/29184999/lc-ms-ms-imaging-with-thermal-film-based-laser-microdissection
#18
Michiko Oya, Hiromi Suzuki, Andrea Roxanne J Anas, Koichi Oishi, Kenji Ono, Shun Yamaguchi, Megumi Eguchi, Makoto Sawada
Mass spectrometry (MS) imaging is a useful tool for direct and simultaneous visualization of specific molecules. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used to evaluate the abundance of molecules in tissues using sample homogenates. To date, however, LC-MS/MS has not been utilized as an imaging tool because spatial information is lost during sample preparation. Here we report a new approach for LC-MS/MS imaging using a thermal film-based laser microdissection (LMD) technique. To isolate tissue spots, our LMD system uses a 808-nm near infrared laser, the diameter of which can be freely changed from 2...
November 28, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29180763/identification-of-genes-expressed-in-a-mesenchymal-subset-regulating-prostate-organogenesis-using-tissue-and-single-cell-transcriptomics
#19
Nadia Boufaied, Claire Nash, Annie Rochette, Anthony Smith, Brigid Orr, O Cathal Grace, Yu Chang Wang, Dunarel Badescu, Jiannis Ragoussis, Axel A Thomson
Prostate organogenesis involves epithelial growth controlled by inductive signalling from specialised mesenchymal subsets. To identify pathways active in mesenchyme we used tissue and single cell transcriptomics to define mesenchymal subsets and subset-specific transcript expression. We documented transcript expression using Tag-seq and RNA-seq in female rat Ventral Mesenchymal Pad (VMP) as well as adjacent urethra comprised of smooth muscle and peri-urethral mesenchyme. Transcripts enriched in female VMP were identified with Tag-seq of microdissected tissue, RNA-seq of cell populations, and single cells...
November 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29179259/roles-of-histone-h3-5-in-human-spermatogenesis-and-spermatogenic-disorders
#20
K Shiraishi, A Shindo, A Harada, H Kurumizaka, H Kimura, Y Ohkawa, H Matsuyama
Histone H3.5 (H3.5) is a newly identified histone variant highly expressed in the human testis. We have reported the crystal structure, instability of the H3.5 nucleosome and accumulation around transcription start sites, mainly in primary spermatocytes, but its role in human spermatogenesis remains poorly understood. Testicular biopsy specimens from 30 men (mean age: 35 years) with non-obstructive azoospermia (NOA) who underwent microdissection testicular sperm extraction and 23 men with obstructive azoospermia (OA) were included...
November 27, 2017: Andrology
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