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https://www.readbyqxmd.com/read/29224158/methylation-specific-pcr
#1
João Ramalho-Carvalho, Rui Henrique, Carmen Jerónimo
Cytosine methylation is a DNA modification generally associated with transcriptional silencing. Factors that regulate methylation have been linked to human disease, yet how they contribute to malignancies remains largely unknown. Methylation of DNA can change the functional state of regulatory regions, but does not change the Watson-Crick base pairing of cytosine. Moreover, sequence symmetry of CpGs enables propagation of the methyl mark through cell division. This potential for inheritance coupled with the fact that DNA methylation patterns change during development and disease partially explains the interest in DNA methylation as a memory module...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223702/rapid-and-highly-efficient-capture-and-release-of-cancer-cells-using-polymeric-microfibers-immobilized-with-enzyme-cleavable-peptides
#2
Akifumi Yoshihara, Ryota Sekine, Takayuki Ueki, Yasuhito Kondo, Yoshiyuki Sunaga, Tadashi Nakaji-Hirabayashi, Yuji Teramura, Madoka Takai
Circulating tumor cells (CTCs) are tumor cells present in the blood. CTCs have attracted much attention as a new tumor marker, because their analysis provides useful information for monitoring cancer progress. In this study, we developed cell-capture and release methods using three-dimensional (3D) microfiber fabrics without damaging the cells. Using functional peptides containing sequences from a polystyrene-binding site and a cleavable site for collagenase type IV, immobilized antibodies on the peptides were able to specifically capture MCF-7 cells in a few minutes and release the captured cells from 3D microfiber fabrics incorporating a vacuum system...
December 6, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/29223400/a-new-comprehensive-method-for-detection-of-livestock-related-pathogenic-viruses-using-a-target-enrichment-system
#3
Mami Oba, Shinobu Tsuchiaka, Tsutomu Omatsu, Yukie Katayama, Konosuke Otomaru, Teppei Hirata, Hiroshi Aoki, Yoshiteru Murata, Shinji Makino, Makoto Nagai, Tetsuya Mizutani
We tested usefulness of a target enrichment system SureSelect, a comprehensive viral nucleic acid detection method, for rapid identification of viral pathogens in feces samples of cattle, pigs and goats. This system enriches nucleic acids of target viruses in clinical/field samples by using a library of biotinylated RNAs with sequences complementary to the target viruses. The enriched nucleic acids are amplified by PCR and subjected to next generation sequencing to identify the target viruses. In many samples, SureSelect target enrichment method increased efficiencies for detection of the viruses listed in the biotinylated RNA library...
December 6, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29223336/association-of-candidate-genes-with-heading-date-in-a-diverse-dactylis-glomerata-population
#4
Xinxin Zhao, B Shaun Bushman, Xinquan Zhang, Matthew D Robbins, Steven R Larson, Joseph G Robins, Aaron Thomas
Flowering occurs in response to cues from both temperature and photoperiod elicitors in cool-season, long-day forage grasses, and genes involved in sensing the elicitors and inducing downstream flowering responses have been associated with heading date and flowering time in perennial forage grasses as well as cereal grasses. In this study we test for association between orchardgrass (Dactylis glomerata L.) heading date and polymorphisms in the CONSTANS (DgCO1), FLOWERING TIME (DgFT1), a VRN1 like MADS-box (DgMADS), and PHOTOPERIOD (DgPPD1-like) containing genes...
December 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29223157/self-organization-of-recombinant-membrane-porin-ompf-from-yersinia-pseudotuberculosis-in-aqueous-environments
#5
E V Sidorin, V A Khomenko, N Yu Kim, P S Dmitrenok, A M Stenkova, O D Novikova, T F Solov'eva
Recombinant porin OmpF (an integral protein of bacterial outer membrane) from Yersinia pseudotuberculosis was synthesized in Escherichia coli cells as inclusion bodies. By combining the methods of anion-exchange and gel filtration chromatographies, recombinant OmpF (rOmpF) was isolated as an individual protein in its denatured state, and its characteristic properties (molecular mass, N-terminal amino acid sequence, and hydrodynamic radius of the protein in 8 M urea solution) were determined. According to the data of gel filtration, dynamic light scattering, optical spectroscopy, and binding of the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid, the rOmpF is fully unfolded in 8 M urea and exists in random coil conformation...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29222759/techniques-for-large-scale-bacterial-genome-manipulation-and-characterization-of-the-mutants-with-respect-to-in-silico-metabolic-reconstructions
#6
George C diCenzo, Turlough M Finan
The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222749/the-mongoose-rational-arithmetic-toolbox
#7
Christopher Le, Leonid Chindelevitch
The modeling of metabolic networks has seen a rapid expansion following the complete sequencing of thousands of genomes. The constraint-based modeling framework has emerged as one of the most popular approaches to reconstructing and analyzing genome-scale metabolic models. Its main assumption is that of a quasi-steady-state, requiring that the production of each internal metabolite be balanced by its consumption. However, due to the multiscale nature of the models, the large number of reactions and metabolites, and the use of floating-point arithmetic for the stoichiometric coefficients, ensuring that this assumption holds can be challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222063/evolutionary-dynamism-in-bryophytes-phylogenomic-inferences-confirm-rapid-radiation-in-the-moss-family-funariaceae
#8
Rafael Medina, Matthew Johnson, Yang Liu, Nicholas Wilding, Terry A Hedderson, Norman Wickett, Bernard Goffinet
Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture...
December 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29221908/how-to-maintain-active-zone-integrity-during-high-frequency-transmission
#9
REVIEW
Niklas Byczkowicz, Andreas Ritzau-Jost, Igor Delvendahl, Stefan Hallermann
In the central nervous system, the frequency at which reliable synaptic transmission can be maintained varies strongly between different types of synapses. Several pre- and postsynaptic processes must interact to enable high-frequency synaptic transmission. One of the mechanistically most challenging issues arises during repetitive neurotransmitter release, when synaptic vesicles fuse in rapid sequence with the presynaptic plasma membrane within the active zone (AZ), potentially interfering with the structural integrity of the AZ itself...
December 5, 2017: Neuroscience Research
https://www.readbyqxmd.com/read/29221774/sleep-dependent-motor-sequence-memory-consolidation-in-individuals-with-periodic-limb-movements
#10
Valya Sergeeva, Jeremy Viczko, Laura B Ray, Adrian M Owen, Stuart M Fogel
Periodic limb movements (PLMs) during sleep increase with age and are associated with striatal neurodegeneration and dopamine deficiency. Limb movements are often associated with disruptions to non-rapid eye movement (NREM) sleep. Motor skill memory consolidation recruits the striatum, and learning-dependent striatal activation is associated with NREM sleep. Therefore, we investigated whether de novo individuals who significantly experience elevated levels of PLMs but have not been formally diagnosed with periodic limb movement disorder had learning and sleep-related memory deficits and whether these deficits were related to sleep quality and symptom severity...
December 2017: Sleep Medicine
https://www.readbyqxmd.com/read/29220515/busco-applications-from-quality-assessments-to-gene-prediction-and-phylogenomics
#11
Robert M Waterhouse, Mathieu Seppey, Felipe A Simão, Mosè Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V Kriventseva, Evgeny M Zdobnov
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic datasets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29220489/diversity-of-translation-initiation-mechanisms-across-bacterial-species-is-driven-by-environmental-conditions-and-growth-demands
#12
Adam J Hockenberry, Aaron J Stern, Luís A N Amaral, Michael C Jewett
The Shine-Dalgarno (SD) sequence motif is frequently found upstream of protein coding genes and is thought to be the dominant mechanism of translation initiation used by bacteria. Experimental studies have shown that the SD sequence facilitates start codon recognition and enhances translation initiation by directly interacting with the highly conserved anti-Shine-Dalgarno sequence on the 30S ribosomal subunit. However, the proportion of SD-led genes within a genome varies across species and the factors governing this variation in translation initiation mechanisms remain largely unknown...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29219068/predicting-enhancers-with-deep-convolutional-neural-networks
#13
Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang
BACKGROUND: With the rapid development of deep sequencing techniques in the recent years, enhancers have been systematically identified in such projects as FANTOM and ENCODE, forming genome-wide landscapes in a series of human cell lines. Nevertheless, experimental approaches are still costly and time consuming for large scale identification of enhancers across a variety of tissues under different disease status, making computational identification of enhancers indispensable. RESULTS: To facilitate the identification of enhancers, we propose a computational framework, named DeepEnhancer, to distinguish enhancers from background genomic sequences...
December 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29218886/clingen-cancer-somatic-working-group-standardizing-and-democratizing-access-to-cancer-molecular-diagnostic-data-to-drive-translational-research
#14
Subha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew Mccoy, Malachi Griffith, Obi L Griffith, Peter Mcgarvey, Shashikant Kulkarni
A growing number of academic and community clinics are conducting genomic testing to inform treatment decisions for cancer patients (1). In the last 3-5 years, there has been a rapid increase in clinical use of next generation sequencing (NGS) based cancer molecular diagnostic (MolDx) testing (2). The increasing availability and decreasing cost of tumor genomic profiling means that physicians can now make treatment decisions armed with patient-specific genetic information. Accumulating research in the cancer biology field indicates that there is significant potential to improve cancer patient outcomes by effectively leveraging this rich source of genomic data in treatment planning (3)...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218879/an-ultra-fast-and-scalable-quantification-pipeline-for-transposable-elements-from-next-generation-sequencing-data
#15
Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M Shulman, Zhandong Liu
Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative disease, and aging. Rapid development in RNA-sequencing technology has enabled us, for the first time, to study the activity of TE at the systems level.However, efficient TE analysis tools are not yet developed. In this work, we developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218271/magnetic-resonance-imaging-in-precision-radiation-therapy-for-lung-cancer
#16
REVIEW
Hannah Bainbridge, Ahmed Salem, Rob H N Tijssen, Michael Dubec, Andreas Wetscherek, Corinne Van Es, Jose Belderbos, Corinne Faivre-Finn, Fiona McDonald
Radiotherapy remains the cornerstone of curative treatment for inoperable locally advanced lung cancer, given concomitantly with platinum-based chemotherapy. With poor overall survival, research efforts continue to explore whether integration of advanced radiation techniques will assist safe treatment intensification with the potential for improving outcomes. One advance is the integration of magnetic resonance imaging (MRI) in the treatment pathway, providing anatomical and functional information with excellent soft tissue contrast without exposure of the patient to radiation...
December 2017: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/29216242/the-oxyr-regulated-phnw-gene-encoding-2-aminoethylphosphonate-pyruvate-aminotransferase-helps-protect-pseudomonas-aeruginosa-from-tert-butyl-hydroperoxide
#17
Warunya Panmanee, Nisanart Charoenlap, Sopapan Atichartpongkul, Aekkapol Mahavihakanont, Matthew D Whiteside, Geoff Winsor, Fiona S L Brinkman, Skorn Mongkolsuk, Daniel J Hassett
The LysR member of bacterial transactivators, OxyR, governs transcription of genes involved in the response to H2O2 and organic (alkyl) hydroperoxides (AHP) in the Gram-negative pathogen, Pseudomonas aeruginosa. We have previously shown that organisms lacking OxyR are rapidly killed by <2 or 500 mM H2O2 in planktonic and biofilm bacteria, respectively. In this study, we first employed a bioinformatic approach to elucidate the potential regulatory breadth of OxyR by scanning the entire P. aeruginosa PAO1 genome for canonical OxyR promoter recognition sequences (ATAG-N7-CTAT-N7-ATAG-N7-CTAT)...
2017: PloS One
https://www.readbyqxmd.com/read/29215816/efficacy-of-afatinib-in-a-previously-treated-patient-with-non-small-cell-lung-cancer-harboring-her2-mutation-case-report
#18
Cheol Kyu Park, Jae Young Hur, Chang Min Choi, Tae Ok Kim, Hyun Ju Cho, Hong Joon Shin, Jung Hwan Lim, Yoo Duk Choi, Young Chul Kim, In Jae Oh
Human epidermal growth factor receptor 2 (HER2) mutation in non-small cell lung cancer (NSCLC) is an oncogenic driver that possibly becomes a druggable target to HER2-targeted therapy. The benefit of HER2-targeted therapy is much less defined especially in eastern populations. We provide evidence of clinical benefit of afatinib in a 50-year-old Asian woman with HER2-mutant NSCLC who previously failed cytotoxic chemotherapy and gefitinib treatment. Next-generation sequencing of the tumor tissue revealed a HER2 exon 20 mutation (c...
January 1, 2018: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/29215605/cone-snails-a-big-store-of-conotoxins-for-novel-drug-discovery
#19
REVIEW
Bingmiao Gao, Chao Peng, Jiaan Yang, Yunhai Yi, Junqing Zhang, Qiong Shi
Marine drugs have developed rapidly in recent decades. Cone snails, a group of more than 700 species, have always been one of the focuses for new drug discovery. These venomous snails capture prey using a diverse array of unique bioactive neurotoxins, usually named as conotoxins or conopeptides. These conotoxins have proven to be valuable pharmacological probes and potential drugs due to their high specificity and affinity to ion channels, receptors, and transporters in the nervous systems of target prey and humans...
December 7, 2017: Toxins
https://www.readbyqxmd.com/read/29214758/comparison-of-four-human-papillomavirus-genotyping-methods-next-generation-sequencing-inno-lipa-electrochemical-dna-chip-and-nested-pcr
#20
Pornjarim Nilyanimit, Jira Chansaenroj, Witthaya Poomipak, Kesmanee Praianantathavorn, Sunchai Payungporn, Yong Poovorawan
BACKGROUND: Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. METHODS: Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS)...
March 2018: Annals of Laboratory Medicine
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