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https://www.readbyqxmd.com/read/28738508/modelling-of-airborne-particulate-matter-concentration-in-underground-stations-using-a-two-size-class-conservation-model
#1
E Walther, M Bogdan, R Cohen
This study presents an attempt of predictive modelling of airborne particulate matter in underground railway stations. The aerosol is represented by a set of simple, ordinary differential equations that describe apparent emission of two particles size-classes in relation with train traffic, ventilation and deposition. The parameters of the equations are identified numerically by a genetic algorithm and comply with their respective expected order of magnitude. A quantitative comparison of numerical results with experimental data from Paris underground station exhibits a good accordance...
July 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28738077/consequences-of-severe-habitat-fragmentation-on-density-genetics-and-spatial-capture-recapture-analysis-of-a-small-bear-population
#2
Sean M Murphy, Ben C Augustine, Wade A Ulrey, Joseph M Guthrie, Brian K Scheick, J Walter McCown, John J Cox
Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades...
2017: PloS One
https://www.readbyqxmd.com/read/28738062/analysis-of-novel-runx2-mutations-in-chinese-patients-with-cleidocranial-dysplasia
#3
Xianli Zhang, Yang Liu, Xiaozhe Wang, Xiangyu Sun, Chenying Zhang, Shuguo Zheng
Cleidocranial dysplasia (CCD) is an autosomal dominant inheritable skeletal disorder characterized by cranial dysplasia, clavicle hypoplasia and dental abnormalities. This disease is mainly caused by heterozygous mutations in RUNX2, a gene that encodes an osteoblast-specific transcription factor. In the present study, mutational analyses of RUNX2 gene were performed on four unrelated Chinese patients with CCD. Four different RUNX2 mutations were detected in these patients, including one nonsense mutation (c...
2017: PloS One
https://www.readbyqxmd.com/read/28736756/advancing-the-science-of-myocardial-recovery-with-mechanical-circulatory-support-a-working-group-of-the-national-heart-lung-and-blood-institute
#4
Stavros G Drakos, Francis D Pagani, Martha S Lundberg, J Timothy Baldwin
The medical burden of heart failure (HF) has spurred interest in clinicians and scientists to develop therapies to restore the function of a failing heart. To advance this agenda, the National Heart Lung Blood Institute (NHLBI) convened a Working Group of experts on June 2-3, 2016 in Bethesda Maryland to develop recommendations for the NHLBI aimed at advancing the science of cardiac recovery in the setting of mechanical circulatory support (MCS). MSC devices effectively reduce volume and pressure overload that drives the cycle of progressive myocardial dysfunction, thereby triggering structural and functional reverse remodeling...
June 2017: JACC. Basic to Translational Science
https://www.readbyqxmd.com/read/28735504/low-genetic-diversity-and-functional-constraint-of-mirna-genes-participating-pollen-pistil-interaction-in-rice
#5
Kun Wang, Xin Wang, Ming Li, Tao Shi, Pingfang Yang
In this study, we sequenced and analyzed the expression and evolution of rice miRNA genes participating pollen-pistil interaction that is crucial to rice yield. Pollen-pistil interaction is an essential reproductive process for all flowering plants. While microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNA levels in eukaryotic cells, there is little knowledge about which miRNAs involved in the early stages of pollen-pistil interaction in rice and how they evolve under this conserved process...
July 22, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28734179/computational-analysis-for-the-determination-of-deleterious-nssnps-in-human-mthfd1-gene
#6
Mansi Desai, J B Chauhan
Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol...
July 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28734069/pathogen-richness-and-abundance-predict-patterns-of-adaptive-mhc-variation-in-insular-amphibians
#7
Supen Wang, Conghui Liu, Anthony B Wilson, Na Zhao, Xianping Li, Wei Zhu, Xu Gao, Xuan Liu, Yiming Li
The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process, and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black-spotted pond frog (Pelophylax nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the Zhoushan Archipelago and 3 nearby mainland sites...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28733541/a-validated-transitional-and-translational-porcine-model-of-hepatocellular-carcinoma
#8
Kyle M Schachtschneider, Regina M Schwind, Kwame A Darfour-Oduro, Arun K De, Lauretta A Rund, Kuldeep Singh, Daniel R Principe, Grace Guzman, Charles E Ray, Howard Ozer, Ron C Gaba, Lawrence B Schook
Difficult questions are confronting clinicians attempting to improve hepatocellular carcinoma (HCC) outcomes. A large animal model with genetic, anatomical, and physiological similarities to humans is required to transition from mouse models to human clinical trials to address unmet clinical needs. To validate our previously reported inducible porcine cancer model (Oncopig) as a transitional HCC model, Oncopig hepatocyte cultures were transformed using Cre recombinase. The resulting porcine HCC cells (pHCC) expressed oncogenic TP53R167H and KRASG12D, and displayed nuclear pleomorphisms with pale to granular cytoplasm arranged in expanded plates similar to human HCC histopathology...
June 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28733420/sg2-type-r2r3-myb-transcription-factor-myb15-controls-defense-induced-lignification-and-basal-immunity-in-arabidopsis
#9
William R Chezem, Altamash Memon, Fu-Shuang Li, Jing-Ke Weng, Nicole Kho Clay
Lignification of cell wall appositions is a conserved basal defense mechanism in the plant innate immune response. However, the genetic pathway controlling defense-induced lignification remains unknown. Here, we demonstrate the Arabidopsis thaliana SG2-type R2R3-MYB transcription factor MYB15 as a regulator of defense-induced lignification and basal immunity. Loss of MYB15 reduces the content but not the composition of defense-induced lignin, whereas constitutive expression of MYB15 increases lignin content independently of immune activation...
July 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28733402/analysis-of-dna-metabolism-in-fission-yeast
#10
Francisco Antequera, Timothy C Humphrey
The fission yeast Schizosaccharomyces pombe is an excellent model organism to study DNA metabolism, in which the DNA replication and repair mechanisms are evolutionarily conserved. In this introduction we describe a range of methods commonly used to study aspects of DNA metabolism in fission yeast, focusing on approaches used for the analysis of genome stability, DNA replication, and DNA repair. We describe the use of a minichromosome, Ch(16), for monitoring different aspects of genome stability. We introduce two-dimensional gel electrophoresis and immunofluorescent visualization of combed DNA molecules for the analysis of DNA replication...
July 21, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28733386/mir-99-regulates-normal-and-malignant-hematopoietic-stem-cell-self-renewal
#11
Mona Khalaj, Carolien M Woolthuis, Wenhuo Hu, Benjamin H Durham, S Haihua Chu, Sarah Qamar, Scott A Armstrong, Christopher Y Park
The microRNA-99 (miR-99) family comprises a group of broadly conserved microRNAs that are highly expressed in hematopoietic stem cells (HSCs) and acute myeloid leukemia stem cells (LSCs) compared with their differentiated progeny. Herein, we show that miR-99 regulates self-renewal in both HSCs and LSCs. miR-99 maintains HSC long-term reconstitution activity by inhibiting differentiation and cell cycle entry. Moreover, miR-99 inhibition induced LSC differentiation and depletion in an MLL-AF9-driven mouse model of AML, leading to reduction in leukemia-initiating activity and improved survival in secondary transplants...
July 21, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28732471/gene-expression-patterns-of-chicken-neuregulin-3-in-association-with-copy-number-variation-and-frameshift-deletion
#12
Hideaki Abe, Daiki Aoya, Hiro-Aki Takeuchi, Miho Inoue-Murayama
BACKGROUND: Neuregulin 3 (NRG3) plays a key role in central nervous system development and is a strong candidate for human mental disorders. Thus, genetic variation in NRG3 may have some impact on a variety of phenotypes in non-mammalian vertebrates. Recently, genome-wide screening for short insertions and deletions in chicken (Gallus gallus) genomes has provided useful information about structural variation in functionally important genes. NRG3 is one such gene that has a putative frameshift deletion in exon 2, resulting in premature termination of translation...
July 21, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#13
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732460/novel-efficient-genome-wide-snp-panels-for-the-conservation-of-the-highly-endangered-iberian-lynx
#14
Daniel Kleinman-Ruiz, Begoña Martínez-Cruz, Laura Soriano, Maria Lucena-Perez, Fernando Cruz, Beatriz Villanueva, Jesús Fernández, José A Godoy
BACKGROUND: The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so far have been based on 36 STRs, but their limited variability and the more complex situation of current populations demand more efficient molecular markers. The recent characterization of the Iberian lynx genome identified more than 1...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732173/exploring-the-potential-of-gametic-reconstruction-of-parental-genotypes-by-f-sub-1-sub-hybrids-as-a-bridge-for-rapid-introgression
#15
Charles H Cannon, C Lane Scher
Interspecific hybridization and genetic introgression are commonly observed in natural populations of many species, especially trees. Among oaks, gene flow between closely-related species has been well documented. And yet, hybridization does not lead to a 'melting pot', i.e. the homogenization of phenotypic traits. Here, we explore how the combination of several common reproductive traits and genomic biology could create an avenue for interspecific gene flow that partially explains this apparent paradox. During meiosis, F<sub>1</sub> hybrids will produce approximately (½)<sup>n</sup> 'reconstructed' parental gametes, where n equals the number of chromosomes...
July 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28731831/toward-a-predictive-framework-for-convergent-evolution-integrating-natural-history-genetic-mechanisms-and-consequences-for-the-diversity-of-life
#16
Anurag A Agrawal
A charm of biology as a scientific discipline is the diversity of life. Although this diversity can make laws of biology challenging to discover, several repeated patterns and general principles govern evolutionary diversification. Convergent evolution, the independent evolution of similar phenotypes, has been at the heart of one approach to understand generality in the evolutionary process. Yet understanding when and why organismal traits and strategies repeatedly evolve has been a central challenge. These issues were the focus of the American Society of Naturalists Vice Presidential Symposium in 2016 and are the subject of this collection of articles...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731545/genome-scale-data-reveals-that-endemic-poecilia-populations-from-small-sulfidic-springs-display-no-evidence-of-inbreeding
#17
Anthony P Brown, Ryan Greenway, Samuel Morgan, Corey R Quackenbush, Luca Giordani, Lenin Arias-Rodriguez, Michael Tobler, Joanna L Kelley
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulfide rich springs in southern Mexico, are examples of such populations with inherently small habitats...
July 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28730713/investigation-of-genetic-diversity-and-inbreeding-in-a-japanese-native-horse-breed-for-suggestions-on-its-conservation
#18
Akio Onogi, Kouichi Shirai, Tomoko Amano
Because native breeds can serve as genetic resources for adapting to environment changes, their conservation is important for future agroecosystems. Using pedigree analysis, we investigated genetic diversity and inbreeding in Japanese Hokkaido native horses, which have adapted to a cold climate and roughage diet. Genetic diversity was measured as the number of founders and the effective number of founders, ancestors and genomes. All metrics imply a decrease in genetic diversity. A comparison of these metrics suggested that pedigree bottlenecks contributed more than did random gene losses to the reduction of genetic diversity...
July 21, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28730343/age-at-maturation-has-sex-and-temperature-specific-effects-on-telomere-length-in-a-fish
#19
Kristina Noreikiene, Anna Kuparinen, Juha Merilä
Telomeres are highly conserved nucleoprotein structures which protect genome integrity. The length of telomeres is influenced by both genetic and environmental factors, but relatively little is known about how different hereditary and environmental factors interact in determining telomere length. We manipulated growth rates and timing of maturation by exposing full-sib nine-spined sticklebacks (Pungitius pungitius) to two different temperature treatments and quantified the effects of temperature treatments, sex, timing of maturation, growth rate and family (genetic influences) on telomere length...
July 20, 2017: Oecologia
https://www.readbyqxmd.com/read/28729957/decline-of-heterozygosity-in-a-large-but-isolated-population-a-45-year-examination-of-moose-genetic-diversity-on-isle-royale
#20
Renae L Sattler, Janna R Willoughby, Bradley J Swanson
Wildlife conservation and management approaches typically focus on demographic measurements to assess population viability over both short and long periods. However, genetic diversity is an important predictor of long term population vitality. We investigated the pattern of change in genetic diversity in a large and likely isolated moose (Alces alces) population on Isle Royale (Lake Superior) from 1960-2005. We characterized samples, partitioned into five different 5-year periods, using nine microsatellite loci and a portion of the mtDNA control region...
2017: PeerJ
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