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https://www.readbyqxmd.com/read/29229929/oestrogen-receptor-%C3%AE-binds-the-foxp3-promoter-and-modulates-regulatory-t-cell-function-in-human-cervical-cancer
#1
Sreenivas Adurthi, Mahesh M Kumar, H S Vinodkumar, Geetashree Mukherjee, H Krishnamurthy, K Kshitish Acharya, U D Bafna, Devi K Uma, B Abhishekh, Sudhir Krishna, A Parchure, Murali Alka, R S Jayshree
Oestrogen controls Foxp3 expression in regulatory T cells (Treg cells) via a mechanism thought to involve oestrogen receptor alpha (ERα), but the molecular basis and functional impact of ERα signalling in Treg cells remain unclear. We report that ERα ligand oestradiol (E2) is significantly increased in human cervical cancer (CxCa) tissues and tumour-infiltrating Treg cells (CD4+CD25hiCD127low), whereas blocking ERα with the antagonist ICI 182,780 abolishes FOXP3 expression and impairs the function of CxCa infiltrating Treg cells...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229825/network-analysis-identifies-chromosome-intermingling-regions-as-regulatory-hotspots-for-transcription
#2
Anastasiya Belyaeva, Saradha Venkatachalapathy, Mallika Nagarajan, G V Shivashankar, Caroline Uhler
The 3D structure of the genome plays a key role in regulatory control of the cell. Experimental methods such as high-throughput chromosome conformation capture (Hi-C) have been developed to probe the 3D structure of the genome. However, it remains a challenge to deduce from these data chromosome regions that are colocalized and coregulated. Here, we present an integrative approach that leverages 1D functional genomic features (e.g., epigenetic marks) with 3D interactions from Hi-C data to identify functional interchromosomal interactions...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29224359/a-reduced-transcriptome-approach-to-assess-environmental-toxicants-using-zebrafish-embryo-test
#3
Pingping Wang, Pu Xia, Jianghua Yang, Zhihao Wang, Ying Peng, Wei Shi, Daniel L Villeneuve, Hongxia Yu, Xiaowei Zhang
Omics approaches can monitor responses and alterations of biological pathways at genome-scale, which are useful to predict potential adverse effects by environmental toxicants. However, high throughput application of transcriptomics in chemical assessment is limited due to the high cost and lack of "standardized" toxicogenomic methods. Here, a reduced zebrafish transcriptome (RZT) approach was developed to represent the whole transcriptome and to profile bioactivity of chemical and environmental mixtures in zebrafish embryo...
December 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29224170/affinity-based-enrichment-techniques-for-the-genome-wide-analysis-of-5-hydroxymethylcytosine
#4
John P Thomson, Richard R Meehan
Since its initial characterization in 2009 there has been a great degree of interest in comparative profiling of 5-hydroxymethylcytosine (5hmC) nucleotides in vertebrate DNA. Through a host of genome-wide studies the distribution of 5hmC has been mapped in a range of cell lines, tissue types and organisms; the majority of which have been generated through affinity-based methods for 5hmC enrichment. Although recent advances in the field have resulted in the ability to investigate the levels of both methylated and hydroxymethylated cytosines at single base resolution, such studies are still relatively cost-prohibitive as well as technically challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224072/snp-discovery-from-single-and-multiplex-genome-assemblies-of-non-model-organisms
#5
Phillip A Morin, Andrew D Foote, Christopher M Hill, Benoit Simon-Bouhet, Aimee R Lang, Marie Louis
Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224067/multiplexed-targeted-sequencing-for-oxford-nanopore-minion-a-detailed-library-preparation-procedure
#6
Timokratis Karamitros, Gkikas Magiorkinis
MinION is a small form factor sequencer recently retailed by Oxford Nanopore technologies. This lighter-sized USB3.0-interfaced device uses innovative nanotechnology to generate extra-long reads from libraries prepared using only standard molecular biology lab equipment. The flexibility and the portability of the platform makes it ideal for point-of-interest and real-time surveillance applications. However, MinION's limited capacity is not enough for the study of specific targets within larger genomes. Apart from just PCR-amplifying regions of interest, the capture of long reads spanning the edges of known-unknown genomic regions is of great importance for structural studies, such as the identification of mobile elements' integrations sites, bridging over low complexity repetitive regions etc...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223956/residual-risk-of-atherosclerotic-cardiovascular-events-in-relation-to-reductions-in-very-low-density-lipoproteins
#7
Patrick R Lawler, Akintunde O Akinkuolie, Paulo Harada, Robert J Glynn, Daniel I Chasman, Paul M Ridker, Samia Mora
BACKGROUND: It is uncertain whether pharmacological reductions in very-low-density lipoproteins (VLDLs), and their component triglyceride and cholesterol could reduce residual risk of atherosclerotic cardiovascular disease (ASCVD) events among individuals in whom low-density lipoprotein cholesterol (LDL-C) has been adequately lowered. We examined whether individuals with greater on-statin reductions in VLDL-related measures-beyond reductions in LDL-C-were at further reduced risk of ASCVD...
December 9, 2017: Journal of the American Heart Association
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/29221630/enrichment-of-57fe-isotope-in-neutron-flux-of-nuclear-reactors-observed-by-m%C3%A3-ssbauer-spectroscopy
#9
Jerzy A Sawicki
The abundance of 57Fe isotope in nuclear reactor core materials can be considerably enriched by neutron-capture 56Fe(n,γ) reactions. This is demonstrated using the sections of Zr-2.5 wt.%Nb pressure tubes removed from two CANDU* reactors. The tubes contained 0.11 and 0.04wt% Fe and were irradiated for about 10 effective full power years (EFPY) up to ~1026n/m2 fast neutron (E > 1MeV) fluencies. The Mössbauer spectra of 57Fe in irradiated samples indicated up to 10 times larger areas than unirradiated off-cuts from the same pressure tubes...
November 17, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/29219439/strongly-asymmetric-spectroscopy-in-plasmon-exciton-hybrid-systems-due-to-interference-induced-energy-repartitioning
#10
Si-Jing Ding, Xiaoguang Li, Fan Nan, Yu-Ting Zhong, Li Zhou, Xudong Xiao, Qu-Quan Wang, Zhenyu Zhang
Recent intense effort has been devoted to exploring different manifestations of resonant excitations of strongly coupled plasmons and excitons, but so far such studies have been limited to situations where the Fano- or Rabi-type spectra are largely symmetric at zero detuning. Using a newly developed full quantum mechanical model, here we reveal the existence of a highly asymmetric spectroscopic regime for both the Rabi splitting and transparency dip. The asymmetric nature is inherently tied to the non-negligible exciton absorbance and is caused by substantial interference-induced energy repartitioning of the resonance peaks...
October 27, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29218538/belowground-competition-drives-invasive-plant-impact-on-native-species-regardless-of-nitrogen-availability
#11
Arthur Broadbent, Carly J Stevens, Duane A Peltzer, Nicholas J Ostle, Kate H Orwin
Plant invasions and eutrophication are pervasive drivers of global change that cause biodiversity loss. Yet, how invasive plant impacts on native species, and the mechanisms underpinning these impacts, vary in relation to increasing nitrogen (N) availability remains unclear. Competition is often invoked as a likely mechanism, but the relative importance of the above and belowground components of this is poorly understood, particularly under differing levels of N availability. To help resolve these issues, we quantified the impact of a globally invasive grass species, Agrostis capillaris, on two co-occurring native New Zealand grasses, and vice versa...
December 7, 2017: Oecologia
https://www.readbyqxmd.com/read/29211962/highly-sensitive-and-rapid-detection-of-salmonella-typhimurium-using-a-colorimetric-paper-based-analytical-device-coupled-with-immunomagnetic-separation
#12
Monpichar Srisa-Art, Katherine E Boehle, Brian J Geiss, Charles S Henry
Salmonella causes over a million foodborne illnesses per year in the United States resulting in more hospitalizations and deaths than any other foodborne bacteria pathogen. To help prevent outbreaks a rapid, portable, sensitive, and reliable method for onsite detection of bacteria that can be used in different sample matrices would be beneficial. Herein, we present a colorimetric paper-based analytical device (PAD) combined with immunomagnetic separation (IMS) for detecting Salmonella typhimurium. IMS anti-Salmonella coated magnetic beads was applied to capture and separate bacteria from the sample matrix and preconcentrated it into small volumes before testing on paper...
December 6, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29205878/exosome-modified-tissue-engineered-blood-vessel-for-endothelial-progenitor-cell-capture-and-targeted-sirna-delivery
#13
Wen Chen, Mingcan Yang, Jian Bai, Xiang Li, Xiangrui Kong, Yu Gao, Lili Bi, Li Xiao, Bingyi Shi
Instability and poor targeting causes the long-term patency of RNA-modified tissue engineering blood vessels (TEBVs) remaining unsatisfactory. RNA can be enriched in exosome and then delivered into targeted cells while whether exosome-modified TEBVs achieve RNA targeted delivery is unclear. Here, to promote the expression of klotho protein on the mesenchymal stem cell (MSC)-derived exosomes, klotho plasmids are first transfected into MSCs, and adenosine kinase (ADK) siRNA is then loaded into exosome (klotho/ADK siRNA-exosome) using electrotransfection...
December 4, 2017: Macromolecular Bioscience
https://www.readbyqxmd.com/read/29198584/aptamers-targeting-cell-surface-proteins
#14
REVIEW
Masaki Takahashi
High affinity binders targeting specific cell surface proteins are vital for developing basic and applied biosciences. However, despite sustained efforts to generate such binders by chemicals and antibodies, there are still many cell surface proteins that lack high affinity binders. Nucleic acids, referred to as aptamers, appear to be potential binders to capture cell surface proteins because single-strand DNA/RNA can form distinct structures of high affinity and specificity to a wide range of targets. Aptamers are isolated from large combinatorial libraries using a unique iterative selection-amplification process known as systematic evolution of ligands by exponential enrichment (SELEX)...
November 30, 2017: Biochimie
https://www.readbyqxmd.com/read/29191164/weighted-likelihood-inference-of-genomic-autozygosity-patterns-in-dense-genotype-data
#15
Alexandra Blant, Michelle Kwong, Zachary A Szpiech, Trevor J Pemberton
BACKGROUND: Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to infer ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns...
December 1, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29186152/high-throughput-full-length-single-cell-mrna-seq-of-rare-cells
#16
Chin Chun Ooi, Gary L Mantalas, Winston Koh, Norma F Neff, Teruaki Fuchigami, Dawson J Wong, Robert J Wilson, Seung-Min Park, Sanjiv S Gambhir, Stephen R Quake, Shan X Wang
Single-cell characterization techniques, such as mRNA-seq, have been applied to a diverse range of applications in cancer biology, yielding great insight into mechanisms leading to therapy resistance and tumor clonality. While single-cell techniques can yield a wealth of information, a common bottleneck is the lack of throughput, with many current processing methods being limited to the analysis of small volumes of single cell suspensions with cell densities on the order of 107 per mL. In this work, we present a high-throughput full-length mRNA-seq protocol incorporating a magnetic sifter and magnetic nanoparticle-antibody conjugates for rare cell enrichment, and Smart-seq2 chemistry for sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/29185012/systems-biology-of-the-imidia-biobank-from-organ-donors-and-pancreatectomised-patients-defines-a-novel-transcriptomic-signature-of-islets-from-individuals-with-type-2-diabetes
#17
Michele Solimena, Anke M Schulte, Lorella Marselli, Florian Ehehalt, Daniela Richter, Manuela Kleeberg, Hassan Mziaut, Klaus-Peter Knoch, Julia Parnis, Marco Bugliani, Afshan Siddiq, Anne Jörns, Frédéric Burdet, Robin Liechti, Mara Suleiman, Daniel Margerie, Farooq Syed, Marius Distler, Robert Grützmann, Enrico Petretto, Aida Moreno-Moral, Carolin Wegbrod, Anke Sönmez, Katja Pfriem, Anne Friedrich, Jörn Meinel, Claes B Wollheim, Gustavo B Baretton, Raphael Scharfmann, Everson Nogoceke, Ezio Bonifacio, Dorothée Sturm, Birgit Meyer-Puttlitz, Ugo Boggi, Hans-Detlev Saeger, Franco Filipponi, Mathias Lesche, Paolo Meda, Andreas Dahl, Leonore Wigger, Ioannis Xenarios, Mario Falchi, Bernard Thorens, Jürgen Weitz, Krister Bokvist, Sigurd Lenzen, Guy A Rutter, Philippe Froguel, Manon von Bülow, Mark Ibberson, Piero Marchetti
AIMS/HYPOTHESIS: Pancreatic islet beta cell failure causes type 2 diabetes in humans. To identify transcriptomic changes in type 2 diabetic islets, the Innovative Medicines Initiative for Diabetes: Improving beta-cell function and identification of diagnostic biomarkers for treatment monitoring in Diabetes (IMIDIA) consortium ( www.imidia.org ) established a comprehensive, unique multicentre biobank of human islets and pancreas tissues from organ donors and metabolically phenotyped pancreatectomised patients (PPP)...
November 28, 2017: Diabetologia
https://www.readbyqxmd.com/read/29175605/elevated-co2-leads-to-carbon-sequestration-by-modulating-c4-photosynthesis-pathway-enzyme-ppdk-in-suaeda-monoica-and-s-fruticosa
#18
Sonam Yadav, Avinash Mishra, Bhavanath Jha
The C4 halophytic species Suaeda monoica and S. fruticosa, possess the C4 photosynthesis pathway without Kranz anatomy were grown at ambient (470ppm CO2) and elevated (850ppm CO2) atmospheric CO2 under control containment facility to study the plant response under CO2 stress condition. The relative growth of both Suaeda species was enhanced with atmospheric CO2 enrichment compared to control (ambient) condition. The photosynthesis rate was found 2.5μmolCO2m-2s-1 in both species under stress condition compared to about 1...
November 16, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/29173743/clinical-correlates-of-carbon-dioxide-hypersensitivity-in-children
#19
Lance M Rappaport, Christina Sheerin, Dever M Carney, Kenneth E Towbin, Ellen Leibenluft, Daniel S Pine, Melissa A Brotman, Roxann Roberson-Nay, John M Hettema
OBJECTIVE: Hypersensitivity to carbon dioxide (CO2)-enriched air may be a promising risk marker for anxiety disorders. Among adult and adolescent samples, heterogeneity in distress response to the CO2 challenge task indexes 3 underlying classes of individuals, which distinguish between sustained and acute threat response as markers for internalizing disorders, broadly, and anxiety disorders, specifically. The present study examines latent classes in children's response to the CO2 challenge task to clarify the association of CO2 hypersensitivity with anxiety and internalizing symptomatology in childhood...
December 2017: Journal of the American Academy of Child and Adolescent Psychiatry
https://www.readbyqxmd.com/read/29173727/application-of-porous-materials-to-carbohydrate-chemistry-and-glycoscience
#20
Keith J Stine
There is a growing interest in using a range of porous materials to meet research needs in carbohydrate chemistry and glycoscience in general. Among the applications of porous materials reviewed in this chapter, enrichment of glycans from biological samples prior to separation and analysis by mass spectrometry is a major emphasis. Porous materials offer high surface area, adjustable pore sizes, and tunable surface chemistry for interacting with glycans, by boronate affinity, hydrophilic interactions, molecular imprinting, and polar interactions...
2017: Advances in Carbohydrate Chemistry and Biochemistry
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