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https://www.readbyqxmd.com/read/29046922/selection-and-identification-of-transferrin-receptor-specific-peptides-as-recognition-probes-for-cancer-cells
#1
Yuyu Tan, Wenli Liu, Zhi Zhu, Lijun Lang, Junxia Wang, Mengjiao Huang, Mingxia Zhang, Chaoyong Yang
Since the transferrin receptor (CD71 or TFRC) is known to be highly expressed in numerous cancers, CD71 has become an attractive target in cancer research. Acquiring specific molecular probes for CD71, such as small molecular ligands, aptamers, peptides, or antibodies, is of great importance for cancer cell recognition and capture. In this work, we chose CD71 as the target for phage display, and after four rounds of positive selection and one round of negative selection, the specific phage library was enriched...
October 18, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29045505/surfaceome-profiling-enables-isolation-of-cancer-specific-exosomal-cargo-in-liquid-biopsies-from-pancreatic-cancer-patients
#2
J Castillo, V Bernard, F A San Lucas, K Allenson, M Capello, D U Kim, P Gascoyne, F C Mulu, B M Stephens, J Huang, H Wang, A A Momin, R O Jacamo, M Katz, R Wolff, M Javle, G Varadhachary, I I Wistuba, S Hanash, A Maitra, H Alvarez
Background: Detection of circulating tumor DNA (ctDNA) can be limited due to their relative scarcity in circulation, particularly while patients are actively undergoing therapy. Exosomes provide a vehicle through which cancer-specific material can be enriched from the compendium of circulating non-neoplastic tissue-derived nucleic acids. We performed a comprehensive profiling of the pancreatic ductal adenocarcinoma (PDAC) exosomal "surfaceome" in order to identify surface proteins that will render liquid biopsies amenable to cancer-derived exosome enrichment for downstream molecular profiling...
September 25, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29043292/phyllodes-tumors-with-and-without-fibroadenoma-like-areas-display-distinct-genomic-features-and-may-evolve-through-distinct-pathways
#3
Fresia Pareja, Felipe C Geyer, Rahul Kumar, Pier Selenica, Salvatore Piscuoglio, Charlotte K Y Ng, Kathleen A Burke, Marcia Edelweiss, Melissa P Murray, Edi Brogi, Britta Weigelt, Jorge S Reis-Filho
Breast fibroepithelial lesions (fibroadenomas and phyllodes tumors) are underpinned by recurrent MED12 exon 2 mutations, which are more common in fibroadenomas and benign phyllodes tumors. TERT promoter hotspot mutations have been documented in phyllodes tumors, and found to be more frequent in borderline and malignant lesions. Several lines of evidence suggest that a subset of phyllodes tumors might arise from fibroadenomas. Here we sought to investigate the genetic differences between phyllodes tumors with fibroadenoma-like areas vs...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/29042549/mechanoresponsive-lipid-protein-nanoglobules-facilitate-reversible-fibre-formation-in-velvet-worm-slime
#4
Alexander Baer, Stephan Schmidt, Sebastian Haensch, Michaela Eder, Georg Mayer, Matthew J Harrington
Velvet worms eject a fluid capture slime that can be mechanically drawn into stiff biopolymeric fibres. Remarkably, these fibres can be dissolved by extended exposure to water, and new regenerated fibres can be drawn from the dissolved fibre solution-indicating a fully recyclable process. Here, we perform a multiscale structural and compositional investigation of this reversible fabrication process with the velvet worm Euperipatoides rowelli, revealing that biopolymeric fibre assembly is facilitated via mono-disperse lipid-protein nanoglobules...
October 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#5
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29038864/improved-detection-of-genetic-loci-in-estimated-glomerular-filtration-rate-and-type-2-diabetes-using-a-pleiotropic-cfdr-method
#6
Hui-Min Liu, Jing-Yang He, Qiang Zhang, Wan-Qiang Lv, Xin Xia, Chang-Qing Sun, Wei-Dong Zhang, Hong-Wen Deng
Genome-wide association studies (GWAS) have been shown to have the potential of explaining more of the "missing heritability" of complex human phenotypes by improving statistical approaches. Here, we applied a genetic-pleiotropy-informed conditional false discovery rate (cFDR) to capture additional polygenic effects associated with estimated glomerular filtration rate (creatinine) (eGFRcrea) and type 2 diabetes (T2D). The cFDR analysis improves the identification of pleiotropic variants by incorporating potentially shared genetic mechanisms between two related traits...
October 16, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29038154/deactivated-crispr-associated-protein-9-for-minor-allele-enrichment-in-cell-free-dna
#7
Amin Aalipour, Jonathan C Dudley, Seung-Min Park, Surya Murty, Jacob J Chabon, Evan A Boyle, Maximilian Diehn, Sanjiv S Gambhir
BACKGROUND: Cell-free DNA (cfDNA) diagnostics are emerging as a new paradigm of disease monitoring and therapy management. The clinical utility of these diagnostics is relatively limited by a low signal-to-noise ratio, such as with low allele frequency (AF) mutations in cancer. While enriching for rare alleles to increase their AF before sample analysis is one strategy that can greatly improve detection capability, current methods are limited in their generalizability, ease of use, and applicability to point mutations...
October 16, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/29024395/deep-eutectic-solvent-based-magnetic-nanofluid-in-the-development-of-stir-bar-sorptive-dispersive-microextraction-an-efficient-hyphenated-sample-preparation-for-ultra-trace-nitroaromatic-explosives-extraction-in-wastewater
#8
Ali Reza Zarei, Maryam Nedaei, Sohrab Ali Ghorbanian
A deep eutectic solvent based magnetic nanofluid was coupled with stir bar sorptive dispersive microextraction as a hyphenated sample preparation technique. The neodymium core magnetic stir bar was coated physically with nanofluid of magnetic carbon nanotube nanocomposites and deep eutectic solvents. The prepared nanofluid has magnetic and strong sorbing properties and is compatible with gas chromatography. In this nanofluid, the deep eutectic solvent acts simultaneously as both carrier and stabilizer for magnetic nanotubes...
October 12, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/29021288/co-expression-networks-reveal-the-tissue-specific-regulation-of-transcription-and-splicing
#9
Ashis Saha, Yungil Kim, Ariel D H Gewirtz, Brian Jo, Chuan Gao, Ian C McDowell, Barbara E Engelhardt, Alexis Battle
Gene co-expression networks capture biologically important patterns in gene expression data, enabling functional analyses of genes, discovery of biomarkers, and interpretation of genetic variants. Most network analyses to date have been limited to assessing correlation between total gene expression levels in a single tissue or small sets of tissues. Here, we built networks that additionally capture the regulation of relative isoform abundance and splicing, along with tissue-specific connections unique to each of a diverse set of tissues...
October 11, 2017: Genome Research
https://www.readbyqxmd.com/read/29021152/evaluation-of-the-clinical-performance-of-the-hpv-risk-assay-using-the-valgent-3-panel
#10
N J Polman, A Oštrbenk, L Xu, P J F Snijders, C J L M Meijer, M Poljak, D A M Heideman, M Arbyn
Human papillomavirus (HPV) testing is being increasingly incorporated into cervical cancer screening. VALGENT (VALidation of HPV GENotyping Tests) is a framework designed to evaluate the clinical performance of various HPV tests relative to the validated and accepted comparator test in a formalized and uniform manner. The aim of this study was to evaluate the clinical performance of the HPV-Risk assay within the VALGENT-3 panel, and to compare its performance to the clinically validated Hybrid Capture 2 assay (HC2)...
October 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28991398/in-situ-tem-studies-of-nanostructured-thermoelectric-materials-an-application-to-mg-doped-zn4sb3-alloy
#11
Duc-The Ngo, Hung Thanh Le, Nong Van Ngo
We demonstrate an advanced approach using advanced in-situ transmission electron microscopy (TEM) to understand the interplay between nanostructures and thermoelectric (TE) properties of high-performance Mg-doped Zn4Sb3 TE system. With the technique, microstructure and crystal evolutions of TE material have been dynamically captured as a function of temperature from 300 K to 573 K. On heating, we have observed clearly precipitation and growth of a Zn-rich secondary phase as nanoinclusions in the matrix of primary Zn4Sb3 phase...
October 9, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28984999/direct-immunofluorescence-testing-in-vasculitis-a-single-institution-experience-with-henoch-sch%C3%A3-nlein-purpura
#12
Patrick Feasel, Steven D Billings, Wilma F Bergfeld, Melissa P Piliang, Anthony P Fernandez, Jennifer S Ko
BACKGROUND: Direct immunofluorescence (DIF) panels (IgG, IgA, IgM, C3 and fibrinogen) are ordered for clinically suspected vasculitis, with frequently negative results. METHODS: Cases submitted for DIF and histology (2010-2014) with "vasculitis" in the clinical data were examined, and the electronic medical record reviewed for clinical suspicion of HSP. Peri/intravascular IgA was considered "positive," other reactants "non-specific," and no immunoreactivity "negative...
October 6, 2017: Journal of Cutaneous Pathology
https://www.readbyqxmd.com/read/28981560/dna-sampling-from-eggshells-and-microsatellite-genotyping-in-rare-tropical-birds-case-study-on-brazilian-merganser
#13
Thais Augusta Maia, Sibelle Torres Vilaça, Luciana Resende da Silva, Fabricio Rodrigues Santos, Gisele Pires de Mendonça Dantas
This study shows that sampling maternal DNA from hatched and abandoned eggshells is a viable noninvasive strategy for studying the genetics of rare or endangered tropical birds, as exemplified here by the Brazilian Merganser (Mergus octosetaceus). Eighteen microsatellites were isolated from enriched libraries and nine heterologous loci from related species were tested. Seven loci were amplified successfully, with five of them being polymorphic. These loci exhibited amplicons ranging from 110 to 254 bp for 132 samples, with 60 from eggshells and 72 from blood or muscle samples...
October 2, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28979670/quantitative-proteomics-analysis-of-mitochondrial-proteins-in-lung-adenocarcinomas-and-normal-lung-tissue-using-itraq-and-tandem-mass-spectrometry
#14
Wei Li, Xuede Zhang, Wei Wang, Ruiying Sun, Boxuan Liu, Yuefeng Ma, Wei Zhang, Li Ma, Yaofeng Jin, Shuanying Yang
Lung adenocarcinoma is the most common type of lung cancer. Unfortunately, lung adenocarcinoma has a poor prognosis and the pathogenesis remains unclear. Mitochondria are important mediators of tumorigenesis. However, the proteomics profile of lung adenocarcinoma mitochondrial proteins has not been elucidated. In this study, we investigated differences in the mitochondrial protein profiles between lung adenocarcinomas and normal tissue. Laser capture microdissection (LCM) was used to isolate the target cells from lung adenocarcinomas and normal tissue...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28979289/recon-rice-environment-coexpression-network-for-systems-level-analysis-of-abiotic-stress-response
#15
Arjun Krishnan, Chirag Gupta, Madana M R Ambavaram, Andy Pereira
Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource - RECoN - that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice transcriptome datasets generated by a researcher...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28977750/data-independent-mass-spectrometry-approach-for-screening-and-identification-of-dna-adducts
#16
Jingshu Guo, Peter W Villalta, Robert J Turesky
Long-term exposures to environmental toxicants and endogenous electrophiles are causative factors for human diseases including cancer. DNA adducts reflect the internal exposure to genotoxicants and can serve as biomarkers for risk assessment. Liquid chromatography-multistage mass spectrometry (LC-MS(n)) is the most common method for biomonitoring DNA adducts, generally targeting single exposures and measuring up to several adducts. However, the data often provide limited evidence for a role of a chemical in the etiology of cancer...
October 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28972148/time-course-negative-stain-electron-microscopy-based-analysis-for-investigating-protein-protein-interactions-at-the-single-molecule-level
#17
Bartek Nogal, Charles A Bowman, Andrew B Ward
Several biophysical approaches are available to study protein-protein interactions. Most approaches are conducted in bulk solution, and are therefore limited to an average measurement of the ensemble of molecular interactions. Here, we show how single-particle EM can enrich our understanding of protein-protein interactions at the single-molecule level and potentially capture states that are unobservable with ensemble methods because they are below the limit of detection or not conducted on an appropriate timescale...
September 29, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28967663/deterministic-droplet-based-co-encapsulation-and-pairing-of-microparticles-via-active-sorting-and-downstream-merging
#18
Meng Ting Chung, Daniel Núñez, Dawen Cai, Katsuo Kurabayashi
Co-encapsulation of two distinct particles within microfluidic droplets provides the means to achieve various high-throughput single-cell assays, such as biochemical reactions and cell-cell interactions in small isolated volumes. However, limited by the Poisson statistics, the co-encapsulation rate of the conventional co-flow approach is low even under optimal conditions. Only up to 13.5% of droplets precisely contain a pair of two distinct particles, while the rest, either being empty or encapsulating unpaired particles become wastes...
October 2, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28964259/three-dimensional-genome-architecture-and-emerging-technologies-looping-in-disease
#19
REVIEW
Arpit Mishra, R David Hawkins
Genome compaction is a universal feature of cells and has emerged as a global regulator of gene expression. Compaction is maintained by a multitude of architectural proteins, long non-coding RNAs (lncRNAs), and regulatory DNA. Each component comprises interlinked regulatory circuits that organize the genome in three-dimensional (3D) space to manage gene expression. In this review, we update the current state of 3D genome catalogues and focus on how recent technological advances in 3D genomics are leading to an enhanced understanding of disease mechanisms...
September 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28963489/demographically-framing-trade-offs-between-sensitivity-and-specificity-illuminates-selection-on-immunity
#20
C Jessica E Metcalf, Ann T Tate, Andrea L Graham
A fundamental challenge faced by the immune system is to discriminate contexts meriting activation from contexts in which activation would be harmful. Selection pressures on this ability are likely to be acute: the penalty of mis-identification of pathogens (therefore failure to attack them) is mortality or morbidity linked to infectious disease, which could reduce fitness by reducing lifespan or fertility; the penalty associated with mis-identification of host (therefore self-attack) is immunopathology, whose fitness costs can also be extreme...
September 25, 2017: Nature ecology & evolution
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