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https://www.readbyqxmd.com/read/29031119/index-analysis-and-human-health-risk-model-application-for-evaluating-ambient-air-heavy-metal-contamination-in-chemical-valley-sarnia
#1
Richard Olawoyin, Linda Schweitzer, Kuangyuan Zhang, Oladapo Okareh, Kevin Slates
The impacts of air emissions as a consequence of industrial activities around communities of human habitation have been extensively reported. This study is the first to assess potential adverse human health effects in the Chemical Valley Sarnia (CVS) area, around the St. Clair River, using health risk models, ecological and pollution indices. Large quantities of particulate matters (PM) are generated from anthropogenic activities, which contain several heavy metals in trace quantities with potentially adverse effects to humans and environmental health...
October 11, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29031100/discovery-of-a-new-mechanism-for-regulation-of-plant-triacylglycerol-metabolism-the-peanut-diacylglycerol-acyltransferase-1-gene-family-transcriptome-is-highly-enriched-in-alternative-splicing-variants
#2
Ling Zheng, Jay Shockey, Feng Guo, Lingmin Shi, Xinguo Li, Lei Shan, Shubo Wan, Zhenying Peng
Triacylglycerols (TAGs) are the most important energy storage form in oilseed crops. Diacylglycerol acyltransferase (DGAT) catalyzes the rate-limiting step of the Kennedy pathway of TAG biosynthesis. To date, little is known about the regulation of DGAT activity in peanut (Arachis hypogaea), an agronomically important oilseed crop that is cultivated in many parts of the world. In this study, seven distinct forms of type 1 DGAT (AhDGAT1.1-AhDGAT1.7) were identified, cloned, and characterized. Comparisons of the nucleotide sequences and gene structures revealed many different splicing variants of AhDGAT1, some of which displayed different organ-specific expression patterns...
October 6, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29031077/4-quinolone-hybrids-and-their-antibacterial-activities
#3
Yuan-Qiang Hu, Shu Zhang, Zhi Xu, Zao-Sheng Lv, Ming-Liang Liu, Lian-Shun Feng
The emergence and wide-spread of drug-resistant bacteria including multi-drug resistant and pan-drug resistant pathogens which are associated with considerable mortality, represent a significant global health threat. 4-Quinolones which are exemplified by fluoroquinolones are the second largest chemotherapy agents used in clinical practice for the treatment of various bacterial infections. However, the resistance of bacteria to 4-quinolones develops rapidly and spreads widely throughout the world due to the long-term, inappropriate use and even abuse...
September 28, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29029339/targeted-enrichment-of-large-gene-families-for-phylogenetic-inference-phylogeny-and-molecular-evolution-of-photosynthesis-genes-in-the-portullugo-clade-caryophyllales
#4
Abigail J Moore, Jurriaan M de Vos, Lillian P Hancock, Eric Goolsby, Erika J Edwards
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis...
September 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029172/dnasp-6-dna-sequence-polymorphism-analysis-of-large-datasets
#5
Julio Rozas, Albert Ferrer-Mata, Juan Carlos Sánchez-DelBarrio, Sara Guirao-Rico, Pablo Librado, Sebastián E Ramos-Onsins, Alejandro Sánchez-Gracia
We present version 6 of the DnaSP (DNA Sequence Polymorphism) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyse large datasets, such as those generated by high-throughput sequencing (HTS) technologies. Among other features, DnaSP 6 implements: i) modules for reading and analysing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, ii) faster methods scalable for HTS data, and iii) summary statistics for the analysis of multi-locus population genetics data...
September 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029115/whole-genome-next-generation-sequencing-to-study-within-host-evolution-of-chronic-norovirus-infection-among-immunocompromised-patients
#6
J van Beek, M de Graaf, S L Smits, C M E Schapendonk, G M G M Verjans, H Vennema, A A van der Eijk, M V T Phan, M L Cotten, M P G Koopmans
Background: The genus Norovirus comprises large genetic diversity and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods: Faecal samples (n=65) from immunocompromised patients (n=16) were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform...
September 27, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29028941/dysregulation-of-cortical-neuron-dna-methylation-profile-in-autism-spectrum-disorder
#7
Stefano Nardone, Dev Sharan Sams, Antonino Zito, Eli Reuveni, Evan Elliott
Autism Spectrum Disorder (ASD) is a complex neuropsychiatric syndrome whose etiology includes genetic and environmental components. Since epigenetic marks are sensitive to environmental insult, they may be involved in the development of ASD. Initial brain studies have suggested a dysregulation of epigenetic marks in ASD. However, due to cellular heterogeneity in the brain, these studies have not determined if there is a true change in the neuronal epigenetic signature. Here, we report a genome-wide methylation study on fluorescence-activated cell sorting-sorted neuronal nuclei from the frontal cortex of 16 male ASD and 15 male control subjects...
September 28, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/29028909/the-systematic-analysis-of-ultraconserved-genomic-regions-in-the-budding-yeast
#8
Zhi-Kai Yang, Feng Gao
Motivation: In the evolution of species, a kind of special sequences, termed ultraconserved sequences (UCSs), have been inherited without any change, which strongly suggests those sequences should be crucial for the species to survive or adapt to the environment. However, the UCSs are still regarded as mysterious genetic sequences so far. Here, we present a systematic study of ultraconserved genomic regions in the budding yeast based on the publicly available genome sequences, in order to reveal their relationship with the adaptability or fitness advantages of the budding yeast...
September 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028844/a-polyphenol-enriched-diet-and-ascaris-suum-infection-modulate-mucosal-immune-responses-and-gut-microbiota-composition-in-pigs
#9
Andrew R Williams, Lukasz Krych, Hajar Fauzan Ahmad, Peter Nejsum, Kerstin Skovgaard, Dennis S Nielsen, Stig M Thamsborg
Polyphenols are a class of bioactive plant secondary metabolites that are thought to have beneficial effects on gut health, such as modulation of mucosal immune and inflammatory responses and regulation of parasite burdens. Here, we examined the interactions between a polyphenol-rich diet supplement and infection with the enteric nematode Ascaris suum in pigs. Pigs were fed either a basal diet or the same diet supplemented with grape pomace (GP), an industrial by-product rich in polyphenols such as oligomeric proanthocyanidins...
2017: PloS One
https://www.readbyqxmd.com/read/29028600/physico-chemical-characterization-of-playground-sand-dust-inhalable-and-bioaccessible-fractions
#10
Iris H Valido, Elio Padoan, Teresa Moreno, Xavier Querol, Oriol Font, Fulvio Amato
Dust is a mixture of natural and anthropogenic particles originated from multiple sources, which can represent an hazard for human health. Playgrounds are a site of particularly concern, due to sand dust ingestion by toddlers and inhalation. In this study, 37 sands used in public playgrounds in the city of Barcelona were physico-chemically characterized also in relation to routine maintenance activities such as disinfection and sand renewal. The analyzed sands show a felsic mineralogy dominated by Na-feldspar, quartz, and, to a lesser extent, K-feldspar, with minor amounts of clay minerals, carbonates and hematite...
September 25, 2017: Chemosphere
https://www.readbyqxmd.com/read/29028494/surfactants-selectively-reallocated-the-bacterial-distribution-in-soil-bioelectrochemical-remediation-of-petroleum-hydrocarbons
#11
Xiaojing Li, Qian Zhao, Xin Wang, Yongtao Li, Qixing Zhou
Soil contaminated by aged petroleum hydrocarbons is faced with scarcity of electron acceptors, low activity of functional microbes and inefficient electron transfer, which hinder the bioremediation application. The soil microbial fuel cell (MFC) simultaneously solves these problems with bioelectricity production. In this study, five types of surfactants were introduced to enhance the bioavailability of aged petroleum hydrocarbon in soils. The ampholytic surfactant (lecithos) was optimal due to the highest bioelectricity generation (0...
October 7, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29028448/characterization-of-the-stool-microbiome-in-hispanic-preschool-children-by-weight-status-and-time
#12
Emily B Hollister, Byron A Foster, Mahmoud Dahdouli, Jesica Ramirez, Zhao Lai
BACKGROUND: Variations in gut microbiota composition and diversity have been associated with childhood adiposity, although most studies describing this have been cross-sectional in nature. Our objective was to evaluate associations between body weight and the gut microbiota over time in obese preschool-age children. METHODS: Obese, preschool-age, Hispanic children provided stool samples at baseline and following a 6-month behavioral intervention. Normal-weight (NW) children also provided stool samples...
October 13, 2017: Childhood Obesity
https://www.readbyqxmd.com/read/29028405/evaluation-of-plasma-peptides-extraction-methods-by-high-resolution-mass-spectrometry
#13
N V Zakharova, A Y Shornikova, A E Bugrova, V V Baybakova, M I Indeykina, A S Kononikhin, I A Popov, O I Kechko, A A Makarov, E N Nikolaev
Monitoring of peptides offers a promising approach for the discovery of novel biomarkers, which might be valuable for detection, treatment and prevention of large variety of diseases. Development of highly effective methods for plasma peptide extraction remains an important task. In the current study, we applied different types of plasma peptide extraction approaches to reveal efficient methods which would provide the highest peptide yield. We used different combinations of plasma treatment with acetonitrile and/or urea/guanidine, protein precipitation by acetone, gel-filtration, ultrafiltration, and two types of solid phase extraction...
August 2017: European Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29028263/epigenomic-annotation-based-interpretation-of-genomic-data-from-enrichment-analysis-to-machine-learning
#14
Mikhail G Dozmorov
Motivation: One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The interpretation of these genome-wide ROIs represents a challenge as the majority of them lie outside of functionally well-defined protein coding regions. Recent efforts by the members of the International Human Epigenome Consortium have generated volumes of functional/regulatory data (reference epigenomic datasets), effectively annotating the genome with epigenomic properties...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028197/multi-task-vehicle-detection-with-region-of-interest-voting
#15
Wenqing Chu, Yao Liu, Chen Shen, Deng Cai, Xian-Sheng Hua
Vehicle detection is a challenging problem in autonomous driving systems, due to its large structural and appearance variations. In this paper, we propose a novel vehicle detection scheme based on multi-task deep convolutional neural networks (CNN) and region-of-interest (RoI) voting. In the design of CNN architecture, we enrich the supervised information with subcategory, region overlap, bounding-box regression and category of each training RoI as a multi-task learning framework. This design allows the CNN model to share visual knowledge among different vehicle attributes simultaneously, thus detection robustness can be effectively improved...
October 12, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/29028004/geobiological-feedbacks-and-the-evolution-of-thermoacidophiles
#16
Daniel R Colman, Saroj Poudel, Trinity L Hamilton, Jeff R Havig, Matthew J Selensky, Everett L Shock, Eric S Boyd
Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027900/rna-polymerase-ii-stalling-at-pre-mrna-splice-sites-is-enforced-by-ubiquitination-of-the-catalytic-subunit
#17
Laura Milligan, Camille Sayou, Alex Tuck, Tatsiana Auchynnikava, Jane E A Reid, Ross Alexander, Flavia de Lima Alves, Robin Allshire, Christos Spanos, Juri Rappsilber, Jean D Beggs, Grzegorz Kudla, David Tollervey
Numerous links exist between co-transcriptional RNA processing and the transcribing RNAPII. In particular, pre-mRNA splicing was reported to be associated with slowed RNAPII elongation. Here we identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. Ubiquitination was increased in the absence of the Bre5-Ubp3 ubiquitin protease complex. Bre5 binds RNA in vivo, with a preference for exon 2 regions of intron-containing pre-mRNAs and poly(A) proximal sites. Ubiquitinated RNAPII showed similar enrichment...
October 13, 2017: ELife
https://www.readbyqxmd.com/read/29027787/detection-of-t4-polynucleotide-kinase-via-allosteric-aptamer-probe-platform
#18
Mingxuan Gao, Jingjing Guo, Yanling Song, Zhi Zhu, Chaoyong James Yang
As a vital enzyme in DNA phosphorylation and restoration, T4 polynuceotide kinase (T4 PNK) has aroused great interest in recent years. Numerous strategies have been established for highly sensitive detection of T4 PNK based on diverse signal amplification techniques. However, they often need sophisticated design, a variety of auxiliary reagents and enzymes, or cumbersome manipulations. Herein, we have designed a new kind of allosteric aptamer probe consisting of streptavidin aptamer (SA aptamer) and the complementary DNA (cDNA) for simple detection of T4 PNK without signal amplification and with minimized interference in complex biological samples...
October 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29027762/fresh-noncultured-endothelial-progenitor-cells-improve-neonatal-lung-hyperoxia-induced-alveolar-injury
#19
Alexandra B Firsova, A Daniel Bird, Degu Abebe, Judy Ng, Richard Mollard, Timothy J Cole
Treatment of preterm human infants with high oxygen can result in disrupted lung alveolar and vascular development. Local or systemic administration of endothelial progenitor cells (EPCs) is reported to remedy such disruption in animal models. In this study, the effects of both fresh (enriched for KDR) and cultured bone marrow (BM)-derived cell populations with EPC characteristics were examined following hyperoxia in neonatal mouse lungs. Intraperitoneal injection of fresh EPCs into five-day-old mice treated with 90% oxygen resulted in full recovery of hyperoxia-induced alveolar disruption by 56 days of age...
October 13, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/29027729/application-of-bayesian-analysis-to-the-doubly-labelled-water-method-for-total-energy-expenditure-in-humans
#20
Yue Ruan, Les Bluck, James Smith, Adrian Mander, Priya Singh, Michelle Venables
RATIONALE: The doubly labelled water (DLW) method is the reference method for the estimation of free-living total energy expenditure (TEE). In this method, where both (2) H and (18) O are employed, different approaches have been adopted to deal with the non-conformity observed regarding the distribution space for the labels being non-coincident with total body water. However, the method adopted can have a significant effect on the estimated TEE. METHODS: We proposed a Bayesian reasoning approach to modify an assumed prior distribution for the space ratio using experimental data to derive the TEE...
October 13, 2017: Rapid Communications in Mass Spectrometry: RCM
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