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https://www.readbyqxmd.com/read/29241295/in-vitro-selection-and-characterization-of-dna-aptamers-to-a-small-molecule-target
#1
Annamaria Ruscito, Erin M McConnell, Anna Koudrina, Ranganathan Velu, Christopher Mattice, Vernon Hunt, Maureen McKeague, Maria C DeRosa
Aptamers, synthetic oligonucleotide-based molecular recognition probes, have found use in a wide array of biosensing technologies based on their tight and highly selective binding to a variety of molecular targets. However, the inherent challenges associated with the selection and characterization of aptamers for small molecule targets have resulted in their underrepresentation, despite the need for small molecule detection in fields such as medicine, the environment, and agriculture. This protocol describes the steps in the selection, sequencing, affinity characterization, and truncation of DNA aptamers that are specific for small molecule targets...
December 14, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/29241203/genome-wide-transcriptome-analysis-of-estrogen-receptor-positive-and-human-epithelial-growth-factor-receptor-2-positive-breast-cancers-by-ribonucleic-acid-sequencing
#2
Pengtao Chen, Wei Song, Liangli Liu
AIM: The aim is to identify complex pathogenesis of breast cancer subtypes and disclose the whole landscape of altered transcriptional activities in these cancers. METHODS: We downloaded raw expression data from public database, and performed transcriptome analysis of 8 estrogen receptor-positive (ER+) breast cancer tissue samples, 8 human epithelial growth factor receptor 2-positive (HER2+) breast cancer tissue samples, and 3 normal breast tissues by identification, functional annotation, and prediction of upstream regulators and cell-surface biomarkers of differentially expressed genes (DEGs)...
December 14, 2017: Gynecologic and Obstetric Investigation
https://www.readbyqxmd.com/read/29241198/fam3a-protects-against-glutamate-induced-toxicity-by-preserving-calcium-homeostasis-in-differentiated-pc12-cells
#3
Qing Song, Wen-Li Gou, Yu-Liang Zou
BACKGROUND/AIMS: Stroke is the leading cause of adult disability, and glutamate-induced dysregulation of intracellular Ca2+ homeostasis is a key mechanism. FAM3A is the first member of the family with sequence similarity 3 (FAM3) gene family, and its biological function remains largely unknown. We have recently reported that FAM3A exerts protective effects against oxidative stress and mitochondrial dysfunction in HT22 cells. METHODS: Here, we investigated the protective effects of FAM3A using a glutamate-induced neuronal injury model in nerve growth factor (NGF)-differentiated PC12 cells...
December 12, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29241190/circrna-expression-profile-in-early-stage-lung-adenocarcinoma-patients
#4
Jiangmin Zhao, Le Li, Qian Wang, Hongxiu Han, Qing Zhan, Ming Xu
BACKGROUND/AIMS: Lung adenocarcinoma, a form of non-small cell lung cancer with high lethality at an advanced stage, is becoming more common in women, non- or never-smokers, and even young adults. At present, there are still no effective early diagnosis methods for patients to be cured in a timely manner. Circular RNAs (circRNAs), which are stable and conserved non-coding RNA in mammalian cells, have been reported to be widely involved in the processes of cancer disease. However, it is still a puzzle as to which specific circRNAs are involved in the development of early-stage lung adenocarcinoma...
December 12, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29241165/sc1-promotes-mir124-3p-expression-to-maintain-the-self-renewal-of-mouse-embryonic-stem-cells-by-inhibiting-the-mek-erk-pathway
#5
Qing Wei, Hongliang Liu, Zhiying Ai, Yongyan Wu, Yingxiang Liu, Zhaopeng Shi, Xuexue Ren, Zekun Guo
BACKGROUND/AIMS: Self-renewal is one of the most important features of embryonic stem (ES) cells. SC1 is a small molecule modulator that effectively maintains the self-renewal of mouse ES cells in the absence of leukemia inhibitory factor (LIF), serum and feeder cells. However, the mechanism by which SC1 maintains the undifferentiated state of mouse ES cells remains unclear. METHODS: In this study, microarray and small RNA deep-sequencing experiments were performed on mouse ES cells treated with or without SC1 to identify the key genes and microRNAs that contributed to self-renewal...
December 12, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29241140/ammonium-haloacetates-an-alternative-to-glyphosate
#6
Marika Turek, Robert Biczak, Barbara Pawłowska, Ewa Różycka-Sokołowska, Bernard Marciniak, Małgorzata Deska, Joanna Skalik, Piotr Bałczewski
This study shows the design, synthesis and evaluation of eco(phyto)toxic and herbicidal activities of quaternary ammonium salts (QASs), derived from haloacetic acids, in context of the search for safer alternatives to the commonly used herbicide, N-(phosphonomethyl)glycine (glyphosate). The structure of the investigated QASs refers to the heteroatom sequence in the anion of glyphosate in which the (P-C)-N nitrogen atom was replaced by one or more halogens (F, Cl). The ecotoxicity of the synthesized QASs was tested against luminescent marine bacteria Vibrio fischeri (Microtox® test) and the crustaceans Heterocypris incongruens (Ostracodtoxkit F™)...
December 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/29241127/high-strength-n-methyl-2-pyrrolidone-containing-process-wastewater-treatment-using-sequencing-batch-reactor-and-membrane-bioreactor-a-feasibility-study
#7
Chun Heng Loh, Bing Wu, Liya Ge, Chaozhi Pan, Rong Wang
N-methyl-2-pyrrolidone (NMP) is widely used as a solvent in polymeric membrane fabrication process, its elimination from the process wastewater (normally at a high concentration > 1000 mg/L) prior to discharge is essential because of environmental concern. This study investigated the feasibility of treating high-strength NMP-containing process wastewater in a sequencing batch reactor (SBR; i.e., batch feeding and intermittent aerobic/anoxic condition) and a membrane bioreactor (MBR; i.e., continuous feeding and aeration), respectively...
December 6, 2017: Chemosphere
https://www.readbyqxmd.com/read/29241044/cooperative-broadband-spin-echoes-through-optimal-control
#8
Wolfgang Kallies, Steffen J Glaser
The Hahn echo sequence is one of the most common building blocks in magnetic resonance, consisting of an excitation pulse and a refocusing pulse. Conventional approaches to improve the performance of echo experiments focused on the optimization of individual pulses, compensating their own imperfections. Here we present an approach to concurrently design both pulses such that they also compensate each others imperfections. The fact that for such cooperative pulses the individual pulses do not need to be perfect provides additional degrees of freedom, resulting in improved overall Hahn echo performance...
November 22, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/29241024/age-and-gender-associated-liver-physiological-t1rho-dynamics-demonstrated-with-a-clinically-applicable-single-breathhold-acquisition
#9
Yì Xiáng J Wáng, Min Deng, Jiang Lin, Anthony W L Kwok, Eric K W Liu, Weitian Chen
To understand women's and men's physiological ranges of liver T1rho relaxation time measured with a single breathhold black blood sequence, this healthy volunteer study was conducted in 62 women (mean age, 38.9 y; range, 18-75 y) and 34 men (mean age, 44.7 y; range, 24-80 y). Approval from the institutional ethics committee was obtained. Magnetic resonance imaging was performed with a 3.0T scanner with six spin-lock times of 0, 10, 20, 25, 35, and 50 ms and a single breathhold of 12 s per slice acquisition...
December 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/29240976/clopidogrel-plus-aspirin-versus-aspirin-alone-for-preventing-cardiovascular-events
#10
REVIEW
Alessandro Squizzato, Marta Bellesini, Andrea Takeda, Saskia Middeldorp, Marco Paolo Donadini
BACKGROUND: Aspirin is the prophylactic antiplatelet drug of choice for people with cardiovascular disease. Adding a second antiplatelet drug to aspirin may produce additional benefit for people at high risk and people with established cardiovascular disease. This is an update to a previously published review from 2011. OBJECTIVES: To review the benefit and harm of adding clopidogrel to aspirin therapy for preventing cardiovascular events in people who have coronary disease, ischaemic cerebrovascular disease, peripheral arterial disease, or were at high risk of atherothrombotic disease, but did not have a coronary stent...
December 14, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/29240946/chemistry-mechanism-and-clinical-status-of-antisense-oligonucleotides-and-duplex-rnas
#11
Xiulong Shen, David R Corey
RNA plays a central role in the expression of all genes. Because any sequence within RNA can be recognized by complementary base pairing, synthetic oligonucleotides and oligonucleotide mimics offer a general strategy for controlling processes that affect disease. The two primary antisense approaches for regulating expression through recognition of cellular RNAs are single-stranded antisense oligonucleotides and duplex RNAs. This review will discuss the chemical modifications and molecular mechanisms that make synthetic nucleic acid drugs possible...
December 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29240932/homogenization-of-populations-in-the-wildflower-texas-bluebonnet-lupinus-texensis
#12
Kathryn G Turner, Daisie I Huang, Quentin C B Cronk, Loren H Rieseberg
Wildflower seeds are routinely spread along highways and thoroughfares throughout North America as part of federal beautification policy, but the genetic effect of the introduction of these cultivated populations on wild populations of the same species is unknown. Interbreeding may occur between these seeded and wild populations, resulting in several possible outcomes. Here we sample 187 individuals in 12 matched pairs of neighboring wild and seeded populations of the Texas bluebonnet (Lupinus texensis), a species popular in commercially available wildflower seed mixes used by both the Texas Department of Transportation and the public...
December 12, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29240929/the-genome-and-adult-somatic-transcriptome-of-the-mormyrid-electric-fish-paramormyrops-kingsleyae
#13
Jason R Gallant, Mauricio Losilla, Chad Tomlinson, Wesley C Warren
Several studies have begun to elucidate the genetic and developmental processes underlying major vertebrate traits. Few of these traits have evolved repeatedly in vertebrates, preventing the analysis of molecular mechanisms underlying these traits comparatively. Electric organs have evolved multiple times among vertebrates, presenting a unique opportunity to understand the degree of constraint and repeatability of the evolutionary processes underlying novel vertebrate traits. As there is now a completed genome sequence representing south american electric eels, we were motivated to obtain genomic sequence from a linage that independently evolved electric organs to facilitate future comparative analyses of the evolution and development of electric organs...
December 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29240926/exocet-exonuclease-in-vitro-assembly-combined-with-recet-recombination-for-highly-efficient-direct-dna-cloning-from-complex-genomes
#14
Hailong Wang, Zhen Li, Ruonan Jia, Jia Yin, Aiying Li, Liqiu Xia, Yulong Yin, Rolf Müller, Jun Fu, A Francis Stewart, Youming Zhang
The exponentially increasing volumes of DNA sequence data highlight the need for new DNA cloning methods to explore the new information. Here, we describe 'ExoCET' (Exonuclease Combined with RecET recombination) to directly clone any chosen region from bacterial and mammalian genomes with nucleotide precision into operational plasmids. ExoCET combines in vitro exonuclease and annealing with the remarkable capacity of full length RecET homologous recombination (HR) to retrieve specified regions from genomic DNA preparations...
December 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29240920/an-appeal-for-a-more-evidence-based-approach-to-biopesticide-safety-in-the-eu
#15
Ben Raymond, Brian A Federici
EFSA responded to our perspective article on the safe use of the insect pathogen Bacillus thrurigiensis (Bt). In doing so they admitted that there is no direct evidence to suggest that B. thuringiensis can cause diarrhoea. They nevertheless continue to repeat the assertion that Bt cannot be distinguished from Bacillus cereus, even though nearly all Bt strains, and certainly all biopesticide strains, can be distinguished from B. cereus using multi-locus sequencing typing. EFSA also continue to repeat the unsupported and speculative hypothesis that Bt strains could be capable of causing cryptic infections in humans...
December 12, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29240891/primary-ovarian-insufficiency-and-azospermia-in-carriers-of-a-homozygous-psmc3ip-stop-gain-mutation
#16
Abdulmoein Eid Al-Agha, Ihab Abdulhamed Ahmed, Esther Nuebel, Mika Moriwaki, Barry Moore, Katherine A Peacock, Tim Mosbruger, Deborah W Neklason, Lynn B Jorde, Mark Yandell, Corrine K Welt
Context: The etiology of primary ovarian insufficiency (POI) remains unknown in a majority of cases. Objective: We sought to identify genes causing POI. Design: The study was a familial genetic study. Setting: The study was performed in two academic institutions. Patients: We identified a consanguineous Yemeni family in which 4 daughters had POI. A brother had azoospermia. Intervention: DNA was subjected to whole genome sequencing...
December 12, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29240889/geoboost-accelerating-research-involving-the-geospatial-metadata-of-virus-genbank-records
#17
Tasnia Tahsin, Davy Weissenbacher, Karen O'Connor, Arjun Magge, Matthew Scotch, Graciela Gonzalez-Hernandez
Summary: GeoBoost is a command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, GeoBoost extracts, integrates, and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications. In addition, to facilitate probabilistic geospatial modeling, GeoBoost assigns probability scores for each possible LOIH...
December 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29240876/machine-learning-for-classifying-tuberculosis-drug-resistance-from-dna-sequencing-data
#18
Yang Yang, Katherine E Niehaus, Timothy M Walker, Zamin Iqbal, A Sarah Walker, Daniel J Wilson, Tim E Peto, Derrick W Crook, E Grace Smith, Tingting Zhu, David A Clifton
Motivation: Correct and rapid determination of Mycobacterium tuberculosis (MTB) resistance against available tuberculosis (TB) drugs is essential for the control and management of TB. Conventional molecular diagnostic test assumes that the presence of any well-studied single nucleotide polymorphisms is sufficient to cause resistance, which yields low sensitivity for resistance classification. Methods: Given the availability of DNA sequencing data from MTB, we developed machine learning models for a cohort of 1839 UK bacterial isolates to classify MTB resistance against eight anti-TB drugs (isoniazid, rifampicin, ethambutol, pyrazinamide, ciprofloxacin, moxifloxacin, ofloxacin, streptomycin) and to classify multi-drug resistance...
December 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29240874/wheat-genetic-resources-in-the-post-genomics-era-promise-and-challenges
#19
Awais Rasheed, Abdul Mujeeb-Kazi, Francis Chuks Ogbonnaya, Zhonghu He, Sanjaya Rajaram
Background: Wheat genetic resources have been used for genetic improvement since 1876, when Stephen Wilson (Transactions and Proceedings of the Botanical Society of Edinburgh 12: 286) consciously made the first wide hybrid involving wheat and rye in Scotland. Wide crossing continued with sporadic attempts in the first half of 19th century and became a sophisticated scientific discipline during the last few decades with considerable impact in farmers' fields. However, a large diversity of untapped genetic resources could contribute in meeting future wheat production challenges...
December 12, 2017: Annals of Botany
https://www.readbyqxmd.com/read/29240841/microcystin-lr-does-not-induce-alterations-to-transcriptomic-or-metabolomic-profiles-of-a-model-heterotrophic-bacterium
#20
Robbie M Martin, Stephen P Dearth, Gary R LeCleir, Shawn R Campagna, Elizabeth M Fozo, Erik R Zinser, Steven W Wilhelm
Microcystins are secondary metabolites produced by several freshwater, bloom-forming cyanobacterial species. Microcystin-producing cyanobacteria co-occur with a complex community of heterotrophic bacteria. Though conflicting, studies suggest that microcystins affect the physiology of heterotrophic bacteria by inducing oxidative stress and increasing cell envelope permeability. Based on these observations, we hypothesized that exposure to microcystin should induce differential expression in genes responding to oxidative and envelope stress and trigger shifts in metabolite pools...
2017: PloS One
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