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https://www.readbyqxmd.com/read/28449211/operational-tolerance-in-kidney-transplantation-and-associated-biomarkers
#1
REVIEW
Annick Massart, Lidia Ghisdal, Marc Abramowicz, Daniel Abramowicz
In the 1960s, our predecessors won a historical battle against acute rejection and ensured that transplantation became a common life-saving treatment. In parallel to this success, or perhaps because of it, we lost the battle for long-lived transplants, being overwhelmed with chronic immune insults and the toxicities of immunosuppression. It is likely that current powerful treatments block acute rejection, but at the same time condemn the few circulating donor cells that would have been able to elicit immunoregulatory host responses towards the allograft...
April 27, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28449120/sigseeker-a-peak-calling-ensemble-approach-for-constructing-epigenetic-signatures
#2
Jens Lichtenberg, Laura Elnitski, David M Bodine
Motivation: Epigenetic data are invaluable when determining the regulatory programs governing a cell. Based on use of next-generation sequencing data for characterizing epigenetic marks and transcription factor binding, numerous peak-calling approaches have been developed to determine sites of genomic significance in these data. Such analyses can produce a large number of false positive predictions, suggesting that sites supported by multiple algorithms provide a stronger foundation for inferring and characterizing regulatory programs associated with the epigenetic data...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449110/veqtl-mapper-variance-association-mapping-for-molecular-phenotypes
#3
Andrew Anand Brown
Motivation: Genetic loci associated with the variance of phenotypic traits have been of recent interest as they can be signatures of genetic interactions, gene by environment interactions, parent of origin effects and canalisation. We present a fast efficient tool to map loci affecting variance of gene expression and other molecular phenotypes in cis. Results: Applied to the publicly available Geuvadis gene expression dataset, we identify 816 loci associated with variance of gene expression using an additive model, and 32 showing differences in variance between homozygous and heterozygous alleles, signatures of parent of origin effects...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#4
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448960/utility-of-genomic-analysis-in-differentiating-synchronous-and-metachronous-lung-adenocarcinomas-from-primary-adenocarcinomas-with-intrapulmonary-metastasis
#5
Jad Saab, Hamid Zia, Susan Mathew, Michael Kluk, Navneet Narula, Helen Fernandes
Distinguishing synchronous and metachronous primary lung adenocarcinomas from adenocarcinomas with intrapulmonary metastasis is essential for optimal patient management. In this study, multiple lung adenocarcinomas occurring in the same patient were evaluated using comprehensive histopathologic evaluation supplemented with molecular analysis. The cohort included 18 patients with a total of 52 lung adenocarcinomas. Eleven patients had a new diagnosis of multiple adenocarcinomas in the same lobe (n=5) or different lobe (n=6)...
April 24, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28448926/mass-spectra-features-of-biomass-burning-boiler-and-coal-burning-boiler-emitted-particles-by-single-particle-aerosol-mass-spectrometer
#6
Jiao Xu, Mei Li, Guoliang Shi, Haiting Wang, Xian Ma, Jianhui Wu, Xurong Shi, Yinchang Feng
In this study, single particle mass spectra signatures of both coal burning boiler and biomass burning boiler emitted particles were studied. Particle samples were suspended in clean Resuspension Chamber, and analyzed by ELPI and SPAMS simultaneously. The size distribution of BBB (biomass burning boiler sample) and CBB (coal burning boiler sample) are different, as BBB peaks at smaller size, and CBB peaks at larger size. Mass spectra signatures of two samples were studied by analyzing the average mass spectrum of each particle cluster extracted by ART-2a in different size ranges...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28448802/ddk-promotes-tumor-chemoresistance-and-survival-via-multiple-pathways
#7
Nanda Kumar Sasi, Arjun Bhutkar, Nathan J Lanning, Jeffrey P MacKeigan, Michael Weinreich
DBF4-dependent kinase (DDK) is a two-subunit kinase required for initiating DNA replication at individual origins and is composed of CDC7 kinase and its regulatory subunit DBF4. Both subunits are highly expressed in many diverse tumor cell lines and primary tumors, and this is correlated with poor prognosis. Inhibiting DDK causes apoptosis of tumor cells, but not normal cells, through a largely unknown mechanism. Firstly, to understand why DDK is often overexpressed in tumors, we identified gene expression signatures that correlate with DDK high- and DDK low-expressing lung adenocarcinomas...
April 24, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28448552/transcriptomic-analysis-of-the-hepatic-response-to-stress-in-the-red-cusk-eel-genypterus-chilensis-insights-into-lipid-metabolism-oxidative-stress-and-liver-steatosis
#8
Sebastian Naour, Brisa M Espinoza, Jorge E Aedo, Rodrigo Zuloaga, Jonathan Maldonado, Macarena Bastias-Molina, Herman Silva, Claudio Meneses, Cristian Gallardo-Escarate, Alfredo Molina, Juan Antonio Valdés
Teleosts exhibit a broad divergence in their adaptive response to stress, depending on the magnitude, duration, and frequency of stressors and the species receiving the stimulus. We have previously reported that the red cusk-eel (Genypterus chilensis), an important marine farmed fish, shows a physiological response to stress that results in increased skeletal muscle atrophy mediated by over-expression of components of the ubiquitin proteasome and autophagy-lysosomal systems. To better understand the systemic effects of stress on the red cusk-eel metabolism, the present study assessed the transcriptomic hepatic response to repetitive handling-stress...
2017: PloS One
https://www.readbyqxmd.com/read/28448519/zika-infection-of-neural-progenitor-cells-perturbs-transcription-in-neurodevelopmental-pathways
#9
Lynn Yi, Harold Pimentel, Lior Pachter
BACKGROUND: A recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and identified cell cycle-related pathways that are affected by infection. However deeper exploration of the information present in the RNA-Seq data can be used to further elucidate the manner in which Zika infection of hNPCs affects the transcriptome, refining pathway predictions and revealing isoform-specific dynamics. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed data published by Tang et al...
2017: PloS One
https://www.readbyqxmd.com/read/28448253/a-map-of-abstract-relational-knowledge-in-the-human-hippocampal-entorhinal-cortex
#10
Mona M Garvert, Raymond J Dolan, Timothy Ej Behrens
The hippocampal-entorhinal system encodes a map of space that guides spatial navigation. Goal-directed behaviour outside of spatial navigation similarly requires a representation of abstract forms of relational knowledge. This information relies on the same neural system, but it is not known whether the organisational principles governing continuous maps may extend to the implicit encoding of discrete, non-spatial graphs. Here, we show that the human hippocampal-entorhinal system can represent relationships between objects using a metric that depends on associative strength...
April 27, 2017: ELife
https://www.readbyqxmd.com/read/28447903/low-grade-sinonasal-sarcoma-with-neural-and-myogenic-features-a-recently-discovered-entity-with-unique-features-and-diagnostic-challenge
#11
Meriam Triki, Lobna Ayadi
Low-grade sinonasal sarcoma with neural and myogenic features is an entity recently described in the literature. Little is known about its etiopathogenesis, natural history, or optimal treatment. In fact, it has relatively unique findings: it has a distinctive cytogenetic signature, and it expresses both smooth muscle actin and S100 protein. However, its diagnosis is challenging on biopsies showing negative staining for these 2 markers. The differential diagnoses include fibrosarcoma, malignant peripheral nerve sheath tumors, and other benign and malignant lesions...
May 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28447615/millions-of-boreal-shield-lakes-can-be-used-to-probe-archaean-ocean-biogeochemistry
#12
S L Schiff, J M Tsuji, L Wu, J J Venkiteswaran, L A Molot, R J Elgood, M J Paterson, J D Neufeld
Life originated in Archaean oceans, almost 4 billion years ago, in the absence of oxygen and the presence of high dissolved iron concentrations. Early Earth oxidation is marked globally by extensive banded iron formations but the contributing processes and timing remain controversial. Very few aquatic habitats have been discovered that match key physico-chemical parameters of the early Archaean Ocean. All previous whole ecosystem Archaean analogue studies have been confined to rare, low sulfur, and permanently stratified lakes...
April 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28447543/human-egf-derived-direct-and-reverse-short-linear-motifs-conformational-dynamics-insight-into-the-receptor-binding-residues
#13
Nurbubu T Moldogazieva, Konstantin V Shaitan, Mikhail Yu Antonov, Innokenty M Mokhosoev, Olga V Levtsova, Аlexander A Terentiev
Short linear motifs (SLiMs) have been recognized to perform diverse functions in a variety of regulatory proteins through the involvement in protein-protein interactions, signal transduction, cell cycle regulation, protein secretion, etc. However, detailed molecular mechanisms underlying their functions including roles of definite amino acid residues remain obscure. In our previous studies, we demonstrated that conformational dynamics of amino acid residues in oligopeptides derived from regulatory proteins such as alpha-fetoprotein (AFP), carcino-embryonic antigen (CEA) and pregnancy specific β1-glycoproteins (PSGs) contributes greatly to their biological activities...
April 27, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28447460/effects-of-histidine-supplementation-on-global-serum-and-urine-1h-nmr-based-metabolomics-and-serum-amino-acid-profiles-in-obese-women-from-a-randomized-controlled-study
#14
Shanshan Du, Shuhong Sun, Liyan Liu, Qiao Zhang, Fuchuan Guo, Chunlong Li, Rennan Feng, Changhao Sun
The aim of current study was to investigate the metabolic changes associated with histidine supplementation in serum and urine metabolic signatures and serum amino acid (AA) profiles. Serum and urine 1H NMR-based metabolomics and serum AAs profiles were employed in thirty two and thirty seven obese women with metabolic syndrome (MetS) intervened with placebo or histidine for 12 weeks. Multivariable statistical analysis were conducted to define characteristic metabolites. In serum 1H NMR metabolic profiles, increases in histidine, glutamine, aspartate, glycine, choline, and trimethylamine-N-oxide (TMAO) were observed, meanwhile, decreases in cholesterol, triglycerides, fatty acids and unsaturated lipids, acetone, and α/β-Glucose were exhibited after histidine supplement...
April 27, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28447289/electroencephalographic-evidence-of-abnormal-anticipatory-uncertainty-processing-in-gambling-disorder-patients
#15
Alberto Megías, Juan F Navas, Ana Perandrés-Gómez, Antonio Maldonado, Andrés Catena, José C Perales
Putting money at stake produces anticipatory uncertainty, a process that has been linked to key features of gambling. Here we examined how learning and individual differences modulate the stimulus preceding negativity (SPN, an electroencephalographic signature of perceived uncertainty of valued outcomes) in gambling disorder patients (GDPs) and healthy controls (HCs), during a non-gambling contingency learning task. Twenty-four GDPs and 26 HCs performed a causal learning task under conditions of high and medium uncertainty (HU, MU; null and positive cue-outcome contingency, respectively)...
April 26, 2017: Journal of Gambling Studies
https://www.readbyqxmd.com/read/28447232/distribution-seasonal-variation-and-inhalation-risks-of-polychlorinated-dibenzo-p-dioxins-and-dibenzofurans-polychlorinated-biphenyls-and-polybrominated-diphenyl-ethers-in-the-atmosphere-of-beijing-china
#16
Yanfen Hao, Yingming Li, Thanh Wang, Yongbiao Hu, Huizhong Sun, Julius Matsiko, Shucheng Zheng, Pu Wang, Qinghua Zhang
Spatial distribution, seasonal variation and potential inhalation risks of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) were investigated in the atmosphere of Beijing, using passive air samplers equipped with polyurethane foam disks. Concentrations of ΣPCDD/Fs, ΣPCBs and ΣPBDEs ranged from 8.4 to 179 fg WHO2005-TEQ/m(3), 38.6-139 and 1.5-176 pg/m(3), respectively. PCDFs showed higher air concentrations than those of PCDDs, indicating the influence of industrial activities and other combustion processes...
April 26, 2017: Environmental Geochemistry and Health
https://www.readbyqxmd.com/read/28446964/strategies-for-the-acquisition-of-transcriptional-and-epigenetic-information-in-single-cells
#17
REVIEW
Guang Li, Elda Dzilic, Nick Flores, Alice Shieh, Sean M Wu
As the basic unit of living organisms, each single cell has unique molecular signatures and functions. Our ability to uncover the transcriptional and epigenetic signature of single cells has been hampered by the lack of tools to explore this area of research. The advent of microfluidic single cell technology along with single cell genome-wide DNA amplification methods had greatly improved our understanding of the expression variation in single cells. Transcriptional expression profile by multiplex qPCR or genome-wide RNA sequencing has enabled us to examine genes expression in single cells in different tissues...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28446723/up-regulation-of-long-non-coding-rna-spry4-it1-promotes-tumor-cell-migration-and-invasion-in-lung-adenocarcinoma
#18
Xia Zhang, Qingyan Chi, Zhenhua Zhao
Long non-coding RNAs (lncRNAs) play important role in a variety of biological processes, and are tightly associated with tumorigenesis and cancer prognosis. However, the potential power of lncRNA signatures in predicting survival of patients with lung adenocarcinoma (LUAD) has not been investigated. Here, we identified a four-lncRNA signature (SPRY4-IT1, LINC00941,GPR158-AS1 and KCNK15-AS1) displaying prognostic values for LUAD using The Cancer Genome Atlas (TCGA) dataset. Based on the four-lncRNA signature, the LUAD patients can be classified into high-risk and low-risk groups with significantly different survival...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28446596/dicer-loss-and-recovery-induce-an-oncogenic-switch-driven-by-transcriptional-activation-of-the-oncofetal-imp1-3-family
#19
Courtney K JnBaptiste, Allan M Gurtan, Kevin K Thai, Victoria Lu, Arjun Bhutkar, Mei-Ju Su, Asaf Rotem, Tyler Jacks, Phillip A Sharp
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression critical for organismal viability. Changes in miRNA activity are common in cancer, but how these changes relate to subsequent alterations in transcription and the process of tumorigenesis is not well understood. Here, we report a deep transcriptional, oncogenic network regulated by miRNAs. We present analysis of the gene expression and phenotypic changes associated with global miRNA restoration in miRNA-deficient fibroblasts. This analysis uncovers a miRNA-repressed network containing oncofetal genes Imp1, Imp2, and Imp3 (Imp1-3) that is up-regulated primarily transcriptionally >100-fold upon Dicer loss and is resistant to resilencing by complete restoration of miRNA activity...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28446508/enrichment-of-pik3-akt-mtor-pathway-activation-in-hepatic-metastases-from-breast-cancer
#20
Mariaelena Pierobon, Corrine Ramos, Shukmei Wong, K Alex Hodge, Jessica Aldrich, Sara A Byron, Stephen P Anthony, Nicholas J Robert, Donald W Northfelt, Mohammad Jahanzeb, Linda Vocila, Julia D Wulfkuhle, Guido Gambara, Rosa Isela Gallagher, Bryant Dunetz, Nicholas Hoke, Ting Dong, David W Craig, Massimo Cristofanilli, Brian Leyland Jones, Lance Liotta, Joyce A O'Shaughnessy, John D Carpten, Emanuel F Petricoin
Purpose: Little is known about the molecular signatures associated with specific metastatic sites in breast cancer. Using comprehensive multi-omic molecular profiling, we assessed whether alterations or activation of the PI3K-AKT-mTOR pathway is associated with specific sites of breast cancer metastasis. <p>Experimental Design: NGS-based whole exome sequencing was coupled with Reverse Phase Protein Microarray (RPPA) functional signaling network analysis to explore the PI3K-AKT-mTOR axis in 32 pretreated breast cancer metastases...
April 26, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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