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Capture enrichment

Natsuko Hama, Yasushi Totoki, Fumihito Miura, Kenji Tatsuno, Mihoko Saito-Adachi, Hiromi Nakamura, Yasuhito Arai, Fumie Hosoda, Tomoko Urushidate, Shoko Ohashi, Wakako Mukai, Nobuyoshi Hiraoka, Hiroyuki Aburatani, Takashi Ito, Tatsuhiro Shibata
The accumulations of different types of genetic alterations such as nucleotide substitutions, structural rearrangements and viral genome integrations and epigenetic alterations contribute to carcinogenesis. Here, we report correlation between the occurrence of epigenetic features and genetic aberrations by whole-genome bisulfite, whole-genome shotgun, long-read, and virus capture sequencing of 373 liver cancers. Somatic substitutions and rearrangement breakpoints are enriched in tumor-specific hypo-methylated regions with inactive chromatin marks and actively transcribed highly methylated regions in the cancer genome...
April 24, 2018: Nature Communications
Junior Tayou
BACKGROUND: Lung cancer is the leading cause of cancer-related death in both men and women. KRAS mutations occur in ~ 25% of patients with lung cancer, and the presence of these mutations is associated with a poor prognosis. Unfortunately, efforts to directly target KRAS or its associated downstream MAPK or PI3K/AKT/mTOR pathways have seen little or no benefits. Here, I hypothesize that KRAS-mutant tumors do not respond to KRAS pathway therapies due to the co-occurrence of other activated cell survival pathways and/or mechanisms...
April 20, 2018: Cellular Oncology (Dordrecht)
Reuben M Buckley, R Daniel Kortschak, David L Adelson
The forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation. Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events in their respective genomic contexts. To further understand this connection we used comparative genomics to identify genome-wide individual DNA gain and loss events in the human and mouse genomes. Focusing on the distribution of DNA gains and losses, relationships to important structural features and potential impact on biological processes, we found that in autosomes, DNA gains and losses both followed separate lineage-specific accumulation patterns...
April 20, 2018: PLoS Computational Biology
David Z Pan, Kristina M Garske, Marcus Alvarez, Yash V Bhagat, James Boocock, Elina Nikkola, Zong Miao, Chelsea K Raulerson, Rita M Cantor, Mete Civelek, Craig A Glastonbury, Kerrin S Small, Michael Boehnke, Aldons J Lusis, Janet S Sinsheimer, Karen L Mohlke, Markku Laakso, Päivi Pajukanta, Arthur Ko
Increased adiposity is a hallmark of obesity and overweight, which affect 2.2 billion people world-wide. Understanding the genetic and molecular mechanisms that underlie obesity-related phenotypes can help to improve treatment options and drug development. Here we perform promoter Capture Hi-C in human adipocytes to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We find that promoter-interacting elements in human adipocytes are enriched for adipose-related transcription factor motifs, such as PPARG and CEBPB, and contribute to heritability of cis-regulated gene expression...
April 17, 2018: Nature Communications
Xiaoqin Zhang, Yuting Zhang, Caiyun Fang, Lei Zhang, Pengyuan Yang, Changchun Wang, Haojie Lu
Palmitoylation, a type of fatty acylation, has vital roles in many biological processes. For ultra-deep identification of protein palmitoylation, an enrichment approach based on a novel magnetic microsphere modified with 2,2'-dithiodipyridine (Fe3O4/SiO2-SSPy microsphere) was presented in this study. The Fe3O4/SiO2-SSPy microspheres were synthesized by directly coating thiol-containing silane coupling agent onto the magnetic supraparticles in aqueous solution at room temperature. Due to the intrinsic magnetic properties, high surface-to-volume ratios and abundant reactive functional groups on surface, these microspheres enabled direct capture of palmitoylated targets and convenient isolation, contributing to remarkable enrichment selectivity (purifying palmitoylated peptides from mixtures with non-palmitoylated peptides even at a 1:500 molar ratio) and sensitivity (the detection limit was at fmol level), thus enables a global annotation of protein palmitoylation for complex biological samples...
April 16, 2018: Analytical Chemistry
Choong Eun Jin, Bonhan Koo, Eun Yeong Lee, Ji Yeun Kim, Sung-Han Kim, Yong Shin
Diseases caused by pathogenic microorganisms including bacteria and viruses can cause serious medical issues including death and result in huge economic losses. Despite the myriad of recent advances in the rapid and accurate detection of pathogens, large volume clinical samples with a low concentration of pathogens continue to present challenges for diagnosis and surveillance. We here report a simple and label-free approach via homobifunctional imidoesters (HIs) with a microfluidic platform (SLIM) to efficiently enrich and extract pathogens at low concentrations from clinical samples...
April 3, 2018: Biosensors & Bioelectronics
Michael J Madsen, Stacey Knight, Carol Sweeney, Rachel E Factor, Mohamed E Salama, Inge J Stijleman, Venkatesh Rajamanickam, Bryan E Welm, Sasi Arunachalam, Brandt Jones, Rakesh Rachamadugu, Kerry Rowe, Melissa Cessna, Alun Thomas, Lawrence H Kushi, Bette Caan, Philip S Bernard, Nicola J Camp
BACKGROUND: Breast tumor subtyping has failed to provide impact in susceptibility genetics. The PAM50 assay categorizes breast tumors into: Luminal A, Luminal B, HER2-enriched and Basal-like. However, tumors are often more complex than simple categorization can describe. The identification of heritable tumor characteristics has potential to decrease heterogeneity and increase power for gene-finding. METHODS: We used 911 sporadic breast tumors with PAM50 expression data to derive tumor dimensions using principal components (PC)...
April 12, 2018: Cancer Epidemiology, Biomarkers & Prevention
Soo Hwan Suh, Soo Jung Choi, Hari P Dwivedi, Matthew D Moore, Blanca I Escudero-Abarca, Lee-Ann Jaykus
A single stranded (ss) DNA aptamer, specific to members of Listeria genus, was used to develop a two-site binding sandwich assay for capture and detection of L. monocytogenes. Antibody-immobilized immunomagnetic beads were used to capture L. monocytogenes, followed by their exposure to the aptamer detector. Detection was achieved by amplification of the cell-bound aptamer by qPCR. The lower limit of detection for the combined assay was 2.5 CFU L. monocytogenes in 500 μl buffer. This is juxtaposed to a detection limit of 2...
April 9, 2018: Analytical Biochemistry
Joel Cutinho, Boyce S Chang, Stephanie Oyola-Reynoso, Jiahao Chen, S Sabrina Akhter, Ian D Tevis, Nelson J Bello, Andrew Martin, Michelle C Foster, Martin M Thuo
Droplets capture an environment-dictated equilibrium state of a liquid material. Equilibrium, however, often necessitates nanoscale interface organization, especially with formation of a passivating layer. Herein, we demonstrate that this kinetics-driven organization may predispose a material to autonomous thermal-oxidative composition inversion (TOCI) and texture reconfiguration under felicitous choice of trigger. We exploit inherent structural complexity, differential reactivity, and metastability of the ultrathin (∼0...
April 16, 2018: ACS Nano
Chu-Wei Kuo, Shih-Yun Guu, Kay-Hooi Khoo
High sensitivity identification of sulfated glycans carried on specific sites of glycoproteins is an important requisite for investigation of molecular recognition events involved in diverse biological processes. However, aiming for resolving site-specific glycosylation of sulfated glycopeptides by direct LC-MS2 sequencing is technically most challenging. Other than the usual limiting factors such as lower abundance and ionization efficiency compared to analysis of non-glycosylated peptides, confident identification of sulfated glycopeptides among the more abundant non-sulfated glycopeptides requires additional considerations in the selective enrichment and detection strategies...
April 11, 2018: Journal of the American Society for Mass Spectrometry
Kyla A L Collins, Timothy J Stuhlmiller, Jon S Zawistowski, Michael P East, Trang T Pham, Claire R Hall, Daniel R Goulet, Samantha M Bevill, Steven P Angus, Sara H Velarde, Noah Sciaky, Tudor I Oprea, Lee M Graves, Gary L Johnson, Shawn M Gomez
Multiplexed small molecule inhibitors covalently bound to Sepharose beads (MIBs) were used to capture functional kinases in luminal, HER2-enriched and triple negative (basal-like and claudin-low) breast cancer cell lines and tumors. Kinase MIB-binding profiles at baseline without perturbation proteomically distinguished the four breast cancer subtypes. Understudied kinases, whose disease associations and pharmacology are generally unexplored, were highly represented in MIB-binding taxonomies and are integrated into signaling subnetworks with kinases that have been previously well characterized in breast cancer...
March 20, 2018: Oncotarget
Katelyn A Walzer, Danielle M Kubicki, Xiaohu Tang, Jen-Tsan Ashley Chi
Sexual reproduction is an obligate step in the Plasmodium falciparum life cycle, with mature gametocytes being the only form of the parasite capable of human-to-mosquito transmission. Development of male and female gametocytes takes 9 to 12 days, and although more than 300 genes are thought to be specific to gametocytes, only a few have been postulated to be male or female specific. Because these genes are often expressed during late gametocyte stages and for some, male- or female-specific transcript expression is debated, the separation of male and female populations is technically challenging...
April 25, 2018: MSphere
Jun-Seok Bae, Yonggang Jin, Chi Huynh, Shi Su
Ventilation air methane (VAM), which is the main source of greenhouse gas emissions from coal mines, has been a great challenge to deal with due to its huge flow rates and dilute methane levels (typically 0.3-1.0 vol%) with almost 100% humidity. As part of our continuous endeavor to further improve the methane adsorption capacity of carbon composites, this paper presents new carbon composites derived from macadamia nut shells (MNSs) and incorporated with carbon nanotubes (CNTs). These new carbon composites were fabricated in a honeycomb monolithic structure to tolerate dusty environment and to minimize pressure drop...
April 3, 2018: Journal of Environmental Management
Colin M Court, Shuang Hou, Paul Winograd, Nicholas H Segel, Qingyu Wilda Li, Yazhen Zhu, Saeed Sadeghi, Richard S Finn, Ekambaram Ganapathy, Min Song, Samuel W French, Bita V Naini, Shonan Sho, Fady M Kaldas, Ronald W Busuttil, James S Tomlinson, Hsian-Rong Tseng, Vatche G Agopian
Current clinicopathologic staging systems and serum biomarkers poorly discriminate tumor biology in hepatocellular carcinoma (HCC), with high recurrence rates following curative-intent surgical resection and liver transplantation (LT). Identification of accurate biomarkers for improved prognostication and treatment selection is a critical unmet need. We sought to develop a novel "liquid-biopsy" assay capable of detecting HCC circulating tumor cells (CTCs), and characterizing phenotypic subpopulations with prognostic significance...
April 6, 2018: Liver Transplantation
Liju Nie, Fulai Li, Xiaolin Huang, Zoraida Aguilar, Yongqiang Andrew Wang, Yonghua Xiong, Fen Fu, Hengyi Xu
Studies regarding circulating tumor cells (CTCs) have great significance for cancer prognosis, treatment monitoring, and metastasis diagnosis. However, due to their extremely low concentration in peripheral blood, isolation and enrichment of CTCs are the key steps for early detection. To this end, targeting the folic acid receptors (FR) on the CTCs surface for capture with folic acid (FA) using bovine serum albumin (BSA)-tether for multibiotin enhancement in combination with streptavidin coated magnetic nanoparticles (MNPs-SA) was developed for ovarian cancer CTCs isolation...
April 5, 2018: ACS Applied Materials & Interfaces
Ruqin Kou, Jian Zhao, Priya Gogoi, Shannon Carskadon, Will Chow, Clara Hwang, Nallasivam Palanisamy, Conrad Leung, Yixin Wang
The potential of circulating tumor cells (CTCs) in the diagnosis and prognosis of cancer patients has become increasingly attractive. However, molecular analysis of CTCs is hindered by low sensitivity and a high level of background leukocytes in CTC enrichment technologies. We have developed a novel protocol using a microfluidic device, which enriches and retrieves CTCs from blood samples. The principle of CTC capturing is that tumor cells are larger and less deformable than normal blood cells. To evaluate the potential of utilizing Celsee PREP100 in CTC molecular analysis, we prepared prostate cancer cell lines PC3 and LNCaP, retrieved the captured cells and analyzed them using PCR amplicon sequencing...
March 30, 2018: Oncology Reports
Diego Cerrudo, Shiliang Cao, Yibing Yuan, Carlos Martinez, Edgar Antonio Suarez, Raman Babu, Xuecai Zhang, Samuel Trachsel
To increase genetic gain for tolerance to drought, we aimed to identify environmentally stable QTL in per se and testcross combination under well-watered (WW) and drought stressed (DS) conditions and evaluate the possible deployment of QTL using marker assisted and/or genomic selection (QTL/GS-MAS). A total of 169 doubled haploid lines derived from the cross between CML495 and LPSC7F64 and 190 testcrosses (tester CML494) were evaluated in a total of 11 treatment-by-population combinations under WW and DS conditions...
2018: Frontiers in Plant Science
Bogdan Bernevic, Ahmed H El-Khatib, Norbert Jakubowski, Michael G Weller
OBJECTIVE: The human copper-protein ceruloplasmin (Cp) is the major copper-containing protein in the human body. The accurate determination of Cp is mandatory for the reliable diagnosis of several diseases. However, the analysis of Cp has proven to be difficult. The aim of our work was a proof of concept for the determination of a metalloprotein-based on online immunocapture ICP-MS. The immuno-affinity step is responsible for the enrichment and isolation of the analyte from serum, whereas the compound-independent quantitation with ICP-MS delivers the sensitivity, precision, and large dynamic range...
April 2, 2018: BMC Research Notes
Francesco Tiezzi, Maria E Arceo, John B Cole, Christian Maltecca
BACKGROUND: Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. Different dairy cattle breeds have different incidence of calving difficulty, with Holstein having the highest dystocia rates and Jersey the lowest. Genomic selection becomes important especially for complex traits with low heritability, where the accuracy of conventional selection is lower...
April 2, 2018: BMC Genetics
Philippe Lherminier
We distinguish two types of predations: the predation of matter-energy equals the food chain, and the informative predation is the capture of the information brought by the sexual partners. The cell or parent consumes energy and matter to grow, multiply and produce offspring. A fixed amount of resources is divided by the number of organisms, so individual growth and numerical multiplication are limited by depletion resources of the environment. Inversely, fertilization does not destroy information, but instead produces news...
March 29, 2018: Comptes Rendus Biologies
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