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https://www.readbyqxmd.com/read/28643793/genomic-rearrangements-in-sporadic-lymphangioleiomyomatosis-an-evolving-genetic-story
#1
Stephen J Murphy, Simone B Terra, Faye R Harris, Aqsa Nasir, Jesse S Voss, James B Smadbeck, Sarah H Johnson, Vishnu Serla, Jay H Ryu, Eunhee S Yi, Benjamin R Kipp, George Vasmatzis, Eva M Carmona
Sporadic lymphangioleiomyomatosis is a progressive pulmonary cystic disease resulting from the infiltration of smooth muscle-like lymphangioleiomyomatosis cells into the lung. The migratory/metastasizing properties of the lymphangioleiomyomatosis cell together with the presence of somatic mutations, primarily in the tuberous sclerosis complex gene (TSC2), lead many to consider this a low-grade malignancy. As malignant tumors characteristically accumulate somatic structural variations, which have not been well studied in sporadic lymphangioleiomyomatosis, we utilized mate pair sequencing to define structural variations within laser capture microdissected enriched lymphangioleiomyomatosis cell populations from five sporadic lymphangioleiomyomatosis patients...
June 23, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28642677/a-novel-workflow-combining-plaque-imaging-plaque-and-plasma-proteomics-identifies-biomarkers-of-human-coronary-atherosclerotic-plaque-disruption
#2
Regent Lee, Roman Fischer, Philip D Charles, David Adlam, Alessandro Valli, Katalin Di Gleria, Rajesh K Kharbanda, Robin P Choudhury, Charalambos Antoniades, Benedikt M Kessler, Keith M Channon
BACKGROUND: Atherosclerotic plaque rupture is the culprit event which underpins most acute vascular syndromes such as acute myocardial infarction. Novel biomarkers of plaque rupture could improve biological understanding and clinical management of patients presenting with possible acute vascular syndromes but such biomarker(s) remain elusive. Investigation of biomarkers in the context of de novo plaque rupture in humans is confounded by the inability to attribute the plaque rupture as the source of biomarker release, as plaque ruptures are typically associated with prompt down-stream events of myocardial necrosis and systemic inflammation...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28641559/a-stepwise-approach-for-the-isolation-and-the-identification-of-chemically-reactive-exofacial-protein-thiols
#3
Gabriele Candiani, Elisa Fasoli
The plasma membrane controls the selective internalization of (macro)molecules through different mechanisms, often relaying on specialized outward-facing carriers such as exofacial proteins thiols (EPTs). Although the interchange of critical thiols and disulphides between EPTs and exogenous cargoes is the first critical event, the identification of specific cell interactors remains to be thoroughly explored. We herein devise an enabling methodology for the isolation and identification of a subset of EPTs, named chemically reactive EPS, which are potential theranostic targets...
June 20, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28633407/exploring-fungus-plant-n-transfer-in-a-tripartite-ant-plant-fungus-mutualism
#4
Céline Leroy, Alain Jauneau, Yves Martinez, Armelle Cabin-Flaman, David Gibouin, Jérôme Orivel, Nathalie Séjalon-Delmas
Background and Aims: The plant Hirtella physophora , the ant Allomerus decemarticulatus and a fungus, Trimmatostroma sp., form a tripartite association. The ants manipulate both the plant trichomes and the fungus to build galleries under the stems of their host plant used to capture prey. In addition to its structural role, the fungus also improves nutrient uptake by the host plant. But it still remains unclear whether the fungus plays an indirect or a direct role in transferring nutrients to the plant...
June 13, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28627811/energy-based-neural-networks-as-a-tool-for-harmony-based-virtual-screening
#5
Nelly I Zhokhova, Igor I Baskin
In Energy-Based Neural Networks (EBNNs), relationships between variables are captured by means of a scalar function conventionally called "energy". In this article, we introduce a procedure of "harmony search", which looks for compounds providing the lowest energies for the EBNNs trained on active compounds. It can be considered as a special kind of similarity search that takes into account regularities in the structures of active compounds. In this paper, we show that harmony search can be used for performing virtual screening...
June 19, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28622761/dated-tribe-wide-whole-chloroplast-genome-phylogeny-indicates-recurrent-hybridizations-within-triticeae
#6
Nadine Bernhardt, Jonathan Brassac, Benjamin Kilian, Frank R Blattner
BACKGROUND: Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing...
June 16, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28620939/engineering-novel-targeted-boron-10-enriched-theranostic-nanomedicine-to-combat-against-murine-brain-tumors-via-mr-imaging-guided-boron-neutron-capture-therapy
#7
Naresh Kuthala, Raviraj Vankayala, Yi-Nan Li, Chi-Shiun Chiang, Kuo Chu Hwang
Glioblastoma multiforme (GBM) is a very common type of "incurable" malignant brain tumor. Although many treatment options are currently available, most of them eventually fail due to its recurrence. Boron neutron capture therapy (BNCT) emerges as an alternative noninvasive therapeutic treatment modality. The major challenge in treating GBMs using BNCT is to achieve selective imaging, targeting, and sufficient accumulation of boron-containing drug at the tumor site so that effective destruction of tumor cells can be achieved without harming the normal brain cells...
June 16, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28617917/genomic-profiling-of-small-bowel-adenocarcinoma
#8
Alexa B Schrock, Craig E Devoe, Robert McWilliams, James Sun, Thomas Aparicio, Philip J Stephens, Jeffrey S Ross, Richard Wilson, Vincent A Miller, Siraj M Ali, Michael J Overman
Importance: Small-bowel adenocarcinomas (SBAs) are rare cancers with a significantly lower incidence, later stage at diagnosis, and worse overall survival than other intestinal-derived cancers. To date, comprehensive genomic analysis of SBA is lacking. Objective: To perform in-depth genomic characterization of a large series of SBAs and other gastrointestinal tumors to draw comparisons and identify potentially clinically actionable alterations. Design, Setting, and Participants: Prospective analysis was performed of clinical samples from patients with SBA (n = 317), colorectal cancer (n = 6353), and gastric carcinoma (n = 889) collected between August 24, 2012, and February 3, 2016, using hybrid-capture-based genomic profiling, at the request of the individual treating physicians in the course of clinical care for the purpose of making therapy decisions...
June 15, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28616133/naked-eye-detection-of-multiple-tumor-related-mrnas-from-patients-with-photonic-crystal-micropattern-supported-dual-modal-upconversion-bioprobes
#9
Xiaoxia Hu, Yingqian Wang, Haoyang Liu, Jie Wang, Yaning Tan, Fubing Wang, Quan Yuan, Weihong Tan
Development of a portable device for the detection of multiple mRNAs is a significant need in the early diagnosis of cancer. We have designed a biochip-based mRNA detection device by combining a hydrophilic-hydrophobic micropattern with upconversion luminescence (UCL) probes. The device achieves highly sensitive detection, using the naked eye, of multiple mRNAs among patient samples. The high sensitivity is attributed to enrichment of the target concentration and a fluorescence enhancement effect. In addition, since the photonic crystal (PC) dot biochip is functionalized with dual-wavelength excitation UCL probes, two kinds of mRNAs in the heterogeneous biological samples are detected simultaneously, and the corresponding luminescence signals are captured using an unmodified camera phone...
January 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28615063/lineage-specific-rediploidization-is-a-mechanism-to-explain-time-lags-between-genome-duplication-and-evolutionary-diversification
#10
Fiona M Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R Hvidsten, Anthony K Redmond, Sigbjørn Lien, Samuel A M Martin, Peter W H Holland, Simen R Sandve, Daniel J Macqueen
BACKGROUND: The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28613820/protein-modification-by-endogenously-generated-lipid-electrophiles-mitochondria-as-the-source-and-target
#11
William N Beavers, Kristie L Rose, James J Galligan, Michelle M Mitchener, Carol A Rouzer, Keri A Tallman, Connor R Lamberson, Xiaojing Wang, Salisha Hill, Pavlina T Ivanova, H Alex Brown, Bing Zhang, Ned A Porter, Lawrence J Marnett
Determining the impact of lipid electrophile-mediated protein damage that occurs during oxidative stress requires a comprehensive analysis of electrophile targets adducted under pathophysiological conditions. Incorporation of ω-alkynyl linoleic acid into the phospholipids of macrophages prior to activation by Kdo2-lipid A, followed by protein extraction, click chemistry and streptavidin affinity capture, enabled a systems-level survey of proteins adducted by lipid electrophiles generated endogenously during the inflammatory response...
June 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28611392/targeted-sequencing-of-both-dna-strands-barcoded-and-captured-individually-by-rna-probes-to-identify-genome-wide-ultra-rare-mutations
#12
Qing Wang, Xu Wang, Pheobe S Tang, Grace M O'leary, Ming Zhang
Next Generation Sequencing (NGS) has been widely implemented in biological research and has made a profound impact on patient care. One of the essential NGS applications is to identify disease-causing sequence variants, where high coverage and accuracy are needed. Here, we reported a novel NGS pipeline, termed a Sequencing System of Digitalized Barcode Encrypted Single-stranded Library from Extremely Low (quality and quantity) DNA Input with Probe-based DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28611076/learning-a-comorbidity-driven-taxonomy-of-pediatric-pulmonary-hypertension
#13
Mei-Sing Ong, Mary P Mullen, Eric D Austin, Peter Szolovits, Marc Natter, Alon Geva, Tianxi Cai, Sek Won Kong, Kenneth D Mandl
Rationale: Pediatric pulmonary hypertension (PH) is a heterogeneous condition with varying natural history and therapeutic response. Precise classification of PH subtypes is therefore crucial for individualizing care. However, gaps remain in our understanding of the spectrum of PH in children. Objective: We seek to study the manifestations of PH in children, and to assess the feasibility of applying a network-based approach to discern disease subtypes from comorbidity data recorded in longitudinal datasets...
June 13, 2017: Circulation Research
https://www.readbyqxmd.com/read/28606269/-application-of-gene-capture-technology-on-mutation-screening-of-rb1-gene-in-retinoblastoma-patients
#14
Q Y Meng, L Z Huang, B Wang, X X Li, J H Liang
Objectives: To analyze RB1 gene mutation in retinoblastoma (RB) patients using gene capture technology. Methods: Experimental research. The clinical data of 17 RB patients were collected at Department of Ophthalmology, Peking University People's Hospital from June 2010 to Jun 2014. Peripheral blood samples of seventeen RB patients and their parents were collected and genomic DNA were extracted. DNA library from RB patients was mixed with designed gene capture probe of RB1 exons and its flanking sequences. The data were analyzed using bioinformatics software...
June 11, 2017: [Zhonghua Yan Ke za Zhi] Chinese Journal of Ophthalmology
https://www.readbyqxmd.com/read/28604959/-analysis-of-tcirg1-gene-mutation-in-a-chinese-family-affected-with-infantile-malignant-osteopetrosis
#15
Min Wang, Tianping Chen, Ling Jin, Lijun Qu, Jian Wang, Yan Li, Jie Cheng, Zhe Xu, Chengjun Wang, Shan Gao
OBJECTIVE: To detect potential mutation of the TCIRG1 gene in a boy with infantile malignant osteopetrosis. METHODS: Target sequence capture and next-generation sequencing were applied for the proband and his parents to identify the causative mutation, and Sanger sequencing was used to verify the suspected mutation. RESULTS: The proband manifested at 4 months of age with symptoms including anemia, thrombocytopenia, hepatosplenomegaly, and cephalus quadratus...
June 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28600759/whole-genome-enrichment-using-rna-probes-and-sequencing-of-chlamydia-trachomatis-directly-from-clinical-samples
#16
Amanda Claire Brown, Mette T Christiansen
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow-growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28599707/a-multiplexed-immunocapture-liquid-chromatography-tandem-mass-spectrometry-assay-for-the-simultaneous-measurement-of-myostatin-and-gdf-11-in-rat-serum-using-an-automated-sample-preparation-platform
#17
Yue Zhao, Guowen Liu, Frank C Zambito, Yan J Zhang, Binodh S DeSilva, Alexander T Kozhich, Jim X Shen
Myostatin, also known as growth differentiation factor 8 (GDF-8), is a protein acting as a negative regulator in skeletal muscle growth. Inhibition of myostatin by therapeutic agents provides opportunities for current unmet medical needs. In order to better understand drug engagement to aid the drug development, we have developed a hybrid LC-MS/MS method which can differentially measure myostatin and another protein from the same GDF family, GDF-11. Although the two proteins share high homology, the LC-MS/MS assay provided the specificity based on monitoring of unique surrogate peptide generated from enzymatic digestion...
August 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28599151/comparative-evaluation-of-sea-urchin-larval-stage-sensitivity-to-ocean-acidification
#18
M C Passarelli, A Cesar, I Riba, T A DelValls
Changes in the marine carbonate system may affect various calcifying organisms. This study is aimed to compare the sensitivity of embryo-larval development of two species of sea urchins (Paracentrutos lividus and Lytechinus variegatus) collected and exposed to samples from different coastal zone (Spain and Brazil) to ocean acidification. The results showed that the larval stages are very sensitive to small changes in the seawater's pH. The larvae from P. lividus species showed to be more sensitive to acidified elutriate sediments than larvae from L...
June 6, 2017: Chemosphere
https://www.readbyqxmd.com/read/28595801/deregulation-of-hsa-mir-20b-expression-in-tnf-%C3%AE-induced-premature-senescence-of-human-pulmonary-microvascular-endothelial-cells
#19
Pooi-Fong Wong, Juliana Jamal, Kind-Leng Tong, Eng-Soon Khor, Chia-Earn Yeap, Hui-Lan Jong, Sui-Ting Lee, Mohd Rais Mustafa, Sazaly Abubakar
miRNAs are important regulators of cellular senescence yet the extent of their involvement remains to be investigated. We sought to identify miRNAs that are involved in cytokine-induced premature senescence (CIPS) in endothelial cells. CIPS was established in young human pulmonary microvascular endothelial cells (HMVEC-Ls) following treatment with a sublethal dose (20ng/ml) of tumor necrosis factor alpha (TNF-α) for 15days. In parallel, HMVEC-Ls were grown and routinely passaged until the onset of replicative senescence (RS)...
June 5, 2017: Microvascular Research
https://www.readbyqxmd.com/read/28592497/increased-power-to-dissect-adaptive-traits-in-global-sorghum-diversity-using-a-nested-association-mapping-population
#20
Sophie Bouchet, Marcus O Olatoye, Sandeep R Marla, Ramasamy Perumal, Tesfaye Tesso, Jianming Yu, Mitch Tuinstra, Geoffrey P Morris
Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]-a widely adapted cereal crop-we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing...
June 2017: Genetics
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