bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymorphic fungus-specific microsatellite markers ofBactrospora dryinareveal multiple colonizations of trees
Authors: NADYEINA Olga , ZARABSKA-BOŻEJEWICZ Daria , WIEDMER Andrea , CORNEJO Carolina , SCHEIDEGGER Christoph 
Published: November 2017

AbstractBactrospora dryinais an epiphytic lichen-forming fungus specifically related to old-growth floodplain forests, which have dramatically declined in Europe over the past centuries. In order to promote conservation management of such forest remnants, we aimed to study population genetics of this rare and threatened lichen. The newly developed 16 microsatellite markers are specific for the mycobiont ofB. dryinaand reliably amplify either single fruiting bodies or a sterile thallus. This allows the use of these markers for the identification of sterile crusts and for quantification of recent dispersal of the species into restored habitats. We tested the markers in 264 samples collected from 10 pedunculate oak trees growing in three localities in north-eastern Switzerland. All markers were polymorphic and showed two to five alleles per locus, and unbiased gene diversity varied from 0·06 to 0·71 over three populations. The relatively low number of alleles inB. dryinais possibly the consequence of colonization of secondary habitats created by forest management. Although oaks were largely covered with a single, continuousB. dryinacolony, the microsatellite markers identified single or complex multi-genotype colonizations per tree. For future population genetic studies, we recommend collection of 5–15 specimens from one tree which would enable detection of 60–80% of the multilocus genotypes present. Hierarchical AMOVA revealed high variation (70%) on host trees, and a relatively high differentiation (12%) among the three locations in NE Switzerland indicated limited gene flow between those regions. Thus, the newly developed markers showed their applicability in population genetics at different spatial scales. They will play an important role in monitoring habitat restoration for the conservation ofB. dryinaand associated forests and riverscapes.
Build your own soil: exploring microfluidics to create microbial habitat structures
Authors: Aleklett Kristin , Kiers E Toby , Ohlsson Pelle , Shimizu Thomas S , Caldas Victor E A , Hammer Edith C 
Published: November 2017

Abstract
Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.
Development of corticostriatal connectivity constrains goal-directed behavior during adolescence
Authors: Insel Catherine , Kastman Erik K. , Glenn Catherine R. , Somerville Leah H. 
Published: November 2017

AbstractWhen pursuing high-value goals, mature individuals typically titrate cognitive performance according to environmental demands. However, it remains unclear whether adolescents similarly integrate value-based goals to selectively enhance goal-directed behavior. We used a value-contingent cognitive control task during fMRI to assess how stakes—the value of a prospective outcome—modulate flexible goal-directed behavior and underlying neurocognitive processes. Here we demonstrate that while adults enhance performance during high stakes, adolescents perform similarly during low and high stakes conditions. The developmental emergence of value-contingent performance is mediated by connectivity between the striatum and prefrontal cortex; this connectivity selectively increases during high stakes and with age. These findings suggest that adolescents may not benefit from high stakes to the same degree adults do—a behavioral profile that may be constrained by ongoing maturation of corticostriatal connectivity. We propose that late development of corticostriatal connectivity sets the stage for optimal goal-directed behavior.
Structural basis for the assembly of the Ragulator-Rag GTPase complex
Authors: Yonehara Ryo , Nada Shigeyuki , Nakai Tomokazu , Nakai Masahiro , Kitamura Ayaka , Ogawa Akira , Nakatsumi Hirokazu , Nakayama Keiichi I. , Li Songling , Standley Daron M. , Yamashita Eiki , Nakagawa Atsushi , Okada Masato 
Published: November 2017

AbstractThe mechanistic target of rapamycin complex 1 (mTORC1) plays a central role in regulating cell growth and metabolism by responding to cellular nutrient conditions. The activity of mTORC1 is controlled by Rag GTPases, which are anchored to lysosomes via Ragulator, a pentameric protein complex consisting of membrane-anchored p18/LAMTOR1 and two roadblock heterodimers. Here we report the crystal structure of Ragulator in complex with the roadblock domains of RagA-C, which helps to elucidate the molecular basis for the regulation of Rag GTPases. In the structure, p18 wraps around the three pairs of roadblock heterodimers to tandemly assemble them onto lysosomes. Cellular and in vitro analyses further demonstrate that p18 is required for Ragulator-Rag GTPase assembly and amino acid-dependent activation of mTORC1. These results establish p18 as a critical organizing scaffold for the Ragulator-Rag GTPase complex, which may provide a platform for nutrient sensing on lysosomes.
Programmable DNA looping using engineered bivalent dCas9 complexes
Authors: Hao Nan , Shearwin Keith E. , Dodd Ian B. 
Published: November 2017

AbstractDNA looping is a ubiquitous and critical feature of gene regulation. Although DNA looping can be efficiently detected, tools to readily manipulate DNA looping are limited. Here we develop CRISPR-based DNA looping reagents for creation of programmable DNA loops. Cleavage-defective Cas9 proteins of different specificity are linked by heterodimerization or translational fusion to create bivalent complexes able to link two separate DNA regions. After model-directed optimization, the reagents are validated using a quantitative DNA looping assay in E. coli. Looping efficiency is ~15% for a 4.7 kb loop, but is significantly improved by loop multiplexing with additional guides. Bivalent dCas9 complexes are also used to activate endogenous norVW genes by rewiring chromosomal DNA to bring distal enhancer elements to the gene promoters. Such reagents should allow manipulation of DNA looping in a variety of cell types, aiding understanding of endogenous loops and enabling creation of new regulatory connections.
Gallstone Disease and the Risk of Type 2 Diabetes
Authors: Lv Jun , Yu Canqing , Guo Yu , Bian Zheng , Yang Ling , Chen Yiping , Li Shanpeng , Huang Yuelong , Fu Yan , He Pan , Tang Aiyu , Chen Junshi , Chen Zhengming , Qi Lu , Li Liming 
Published: November 2017

AbstractGallstone disease (GSD) is related to several diabetes risk factors. The present study was to examine whether GSD was independently associated with type 2 diabetes in the China Kadoorie Biobank study. After excluding participants with prevalent diabetes and prior histories of cancer, heart disease, and stroke at baseline, 189,154 men and 272,059 women aged 30–79 years were eligible for analysis. The baseline prevalence of GSD was 5.7% of the included participants. During 4,138,687 person-years of follow-up (median, 9.1 years), a total of 4,735 men and 7,747 women were documented with incident type 2 diabetes. Compared with participants without GSD at baseline, the multivariate-adjusted hazard ratios (HRs) for type 2 diabetes for those with GSD were 1.09 (95% CI: 0.96–1.24; P = 0.206), 1.21 (95% CI: 1.13-1.30; P < 0.001), and 1.17 (95% CI: 1.10-1.25; P < 0.001) in men, women, and the whole cohort respectively. There was no statistically significant heterogeneity between men and women (P = 0.347 for interaction). The association between GSD and type 2 diabetes was strongest among participants who reported ≥5 years since the first diagnosis and were still on treatment at baseline (HR = 1.48; 95% CI: 1.16-1.88; P = 0.001). The present study highlights the importance of developing a novel prevention strategy to mitigate type 2 diabetes through improvement of gastrointestinal health.
Accurate thermal conductivities from optimally short molecular dynamics simulations
Authors: Ercole Loris , Marcolongo Aris , Baroni Stefano 
Published: November 2017

AbstractThe evaluation of transport coefficients in extended systems, such as thermal conductivity or shear viscosity, is known to require impractically long simulations, thus calling for a paradigm shift that would allow to deploy state-of-the-art quantum simulation methods. We introduce a new method to compute these coefficients from optimally short molecular dynamics simulations, based on the Green-Kubo theory of linear response and the cepstral analysis of time series. Information from the full sample power spectrum of the relevant current for a single and relatively short trajectory is leveraged to evaluate and optimally reduce the noise affecting its zero-frequency value, whose expectation is proportional to the corresponding conductivity. Our method is unbiased and consistent, in that both the resulting bias and statistical error can be made arbitrarily small in the long-time limit. A simple data-analysis protocol is proposed and validated with the calculation of thermal conductivities in the paradigmatic cases of elemental and molecular fluids (liquid Ar and H2O) and of crystalline and glassy solids (MgO and a-SiO2). We find that simulation times of one to a few hundred picoseconds are sufficient in these systems to achieve an accuracy of the order of 10% on the estimated thermal conductivities.
Treatment of Myocardial Infarction with Gene-modified Mesenchymal Stem Cells in a Small Molecular Hydrogel
Authors: Wu Zhiye , Chen Guoqin , Zhang Jianwu , Hua Yongquan , Li Jinliang , Liu Bei , Huang Anqing , Li Hekai , Chen Minsheng , Ou Caiwen 
Published: November 2017

AbstractThe effect of transplanted rat mesenchymal stem cells (MSCs) can be reduced by extracellular microenvironment in myocardial infarction (MI). We tested a novel small-molecular hydrogel (SMH) on whether it could provide a scaffold for hepatocyte growth factor (HGF)-modified MSCs and alleviate ventricular remodeling while preserving cardiac function after MI. Overexpression of HGF in MSCs increased Bcl-2 and reduced Bax and caspase-3 levels in response to hypoxia in vitro. Immunocytochemistry demonstrated that cardiac troponin (cTnT), desmin and connexin 43 expression were significantly enhanced in the 5-azacytidine (5-aza) with SMH group compared with the 5-aza only group in vitro and in vivo. Bioluminescent imaging indicated that retention and survival of transplanted cells was highest when MSCs transfected with adenovirus (ad-HGF) were injected with SMH. Heart function and structure improvement were confirmed by echocardiography and histology in the Ad-HGF-SMHs-MSCs group compared to other groups. Our study showed that: HGF alleviated cell apoptosis and promoted MSC growth. SMHs improved stem cell adhesion, survival and myocardial cell differentiation after MSC transplantation. SMHs combined with modified MSCs significantly decreased the scar area and improved cardiac function.
Photoacoustic stimulation promotes the osteogenic differentiation of bone mesenchymal stem cells to enhance the repair of bone defect
Authors: Huang Zebin , Xu Jiankun , Chen Jiebin , Chen Hongjiang , Wang Hailong , Huang Zhonglian , Chen Youbin , Lu Xiaolin , Lu Fushen , Hu Jun 
Published: November 2017

AbstractThe aim of this study was to evaluate the direct photoacoustic (PA) effect on bone marrow mesenchymal stem cells (BMSCs) which is a key cell source for osteogenesis. As scaffold is also an indispensable element for tissue regeneration, here we firstly fabricated a composited sheet using polylactic-co-glycolic acid (PLGA) mixing with graphene oxide (GO). BMSCs were seeded on the PLGA-GO sheets and received PA treatment in vitro for 3, 9 and 15 days, respectively. Then the BMSCs were harvested and subjected to assess alkaline phosphatase (ALP) activity, calcium content and osteopontin (OPN) on 3, 9 and 15 days. For in vivo study, PLGA-GO sheet seeded with BMSCs after in vitro PA stimulation for 9 days were implanted to repair the bone defect established in the femoral mid-shaft of Sprague-Dawley rat. PLGA-GO group with PA pretreatment showed promising outcomes in terms of the expression of ALP, OPN, and calcium content, thus enhanced the repair of bone defect. In conclusion, we have developed an alternative approach to enhance the repair of bone defect by making good use of the beneficial effect of PA.
Epidemiology, pathology and identification of Colletotrichum including a novel species associated with avocado (Persea americana) anthracnose in Israel
Authors: Sharma Gunjan , Maymon Marcel , Freeman Stanley 
Published: November 2017

AbstractAnthracnose disease caused by Colletotrichum species is a major constraint for the shelf-life and marketability of avocado fruits. To date, only C. gloeosporioides sensu lato and C. aenigma have been reported as pathogens affecting avocado in Israel. This study was conducted to identify and characterize Colletotrichum species associated with avocado anthracnose and to determine their survival on different host-structures in Israel. The pathogen survived and over-wintered mainly on fresh and dry leaves, as well as fresh twigs in the orchard. A collection of 538 Colletotrichum isolates used in this study was initially characterized based on morphology and banding patterns generated according to arbitrarily primed PCR to assess the genetic diversity of the fungal populations. Thereafter, based on multi-locus phylogenetic analyses involving combinations of ITS, act, ApMat, cal, chs1, gapdh, gs, his3, tub2 gene/markers; eight previously described species (C. aenigma, C. alienum, C. fructicola, C. gloeosporioides sensu stricto, C. karstii, C. nupharicola, C. siamense, C. theobromicola) and a novel species (C. perseae) were identified, as avocado anthracnose pathogens in Israel; and reconfirmed after pathogenicity assays. Colletotrichum perseae sp. nov. and teleomorph of C. aenigma are described along with comprehensive morphological descriptions and illustrations, for the first time in this study.
Expression of SRY-related HMG Box Transcription Factors (Sox) 2 and 9 in Craniopharyngioma Subtypes and Surrounding Brain Tissue
Authors: Thimsen Vivian , John Nora , Buchfelder Michael , Flitsch Jörg , Fahlbusch Rudolf , Stefanits Harald , Knosp Engelbert , Losa Marco , Buslei Rolf , Hölsken Annett 
Published: November 2017

AbstractStem cells have been discovered as key players in the genesis of different neoplasms including craniopharyngioma (CP), a rare tumour entity in the sellar region. Sox2 and Sox9 are well-known stem cell markers involved in pituitary development. In this study we analysed the expression of both transcription factors using immunohistochemistry in a large cohort of 64 adamantinomatous (aCP) and 9 papillary CP (pCP) and quantitative PCR in 26 aCP and 7 pCP. Whereas immunohistochemically Sox2+ cells were verifiable in only five aCP (7.8%) and in 39.1% of the respective surrounding cerebral tissue, pCP specimens appeared always negative. In contrast, Sox9 was detectable in all tumours with a significantly higher expression in aCP compared to pCP (protein, p < 0.0001; mRNA p = 0.0484) This was also true for the respective tumour adjacent CNS where 63 aCP (98.4%) and six pCP (66.7%) showed Sox9+ cells. We further confirmed absence of Sox9 expression in nuclear β-catenin accumulating cells of aCP. Our results point to the conclusion that Sox2 and Sox9, seem to play essential roles not only in the specific formation of aCP, but also in processes involving the cerebral tumour environment, which needs to be illuminated in the future.
Genome-wide identification of long non-coding RNA genes and their association with insecticide resistance and metamorphosis in diamondback moth, Plutella xylostella
Authors: Liu Feiling , Guo Dianhao , Yuan Zhuting , Chen Chen , Xiao Huamei 
Published: November 2017

AbstractLong non-coding RNA (lncRNA) is a class of noncoding RNA >200 bp in length that has essential roles in regulating a variety of biological processes. Here, we constructed a computational pipeline to identify lncRNA genes in the diamondback moth (Plutella xylostella), a major insect pest of cruciferous vegetables. In total, 3,324 lncRNAs corresponding to 2,475 loci were identified from 13 RNA-Seq datasets, including samples from parasitized, insecticide-resistant strains and different developmental stages. The identified P. xylostella lncRNAs had shorter transcripts and fewer exons than protein-coding genes. Seven out of nine randomly selected lncRNAs were validated by strand-specific RT-PCR. In total, 54–172 lncRNAs were specifically expressed in the insecticide resistant strains, among which one lncRNA was located adjacent to the sodium channel gene. In addition, 63–135 lncRNAs were specifically expressed in different developmental stages, among which three lncRNAs overlapped or were located adjacent to the metamorphosis-associated genes. These lncRNAs were either strongly or weakly co-expressed with their overlapping or neighboring mRNA genes. In summary, we identified thousands of lncRNAs and presented evidence that lncRNAs might have key roles in conferring insecticide resistance and regulating the metamorphosis development in P. xylostella.
Yeast display biopanning identifies human antibodies targeting glioblastoma stem-like cells
Authors: Zorniak Michael , Clark Paul A. , Umlauf Benjamin J. , Cho Yongku , Shusta Eric V. , Kuo John S. 
Published: November 2017

AbstractGlioblastoma stem-like cells (GSC) are hypothesized to evade current therapies and cause tumor recurrence, contributing to poor patient survival. Existing cell surface markers for GSC are developed from embryonic or neural stem cell systems; however, currently available GSC markers are suboptimal in sensitivity and specificity. We hypothesized that the GSC cell surface proteome could be mined with a yeast display antibody library to reveal novel immunophenotypes. We isolated an extensive collection of antibodies that were differentially selective for GSC. A single domain antibody VH-9.7 showed selectivity for five distinct patient-derived GSC lines and visualized orthotopic GBM xenografts in vivo after conjugation with a near-infrared dye. These findings demonstrate a previously unexplored high-throughput strategy for GSC-selective antibody discovery, to aid in GSC isolation, diagnostic imaging, and therapeutic targeting.
miRNAs in bone tissue correlate to bone mineral density and circulating miRNAs are gender independent in osteoporotic patients
Authors: Kelch Sarah , Balmayor Elizabeth R. , Seeliger Claudine , Vester Helen , Kirschke Jan S. , van Griensven Martijn 
Published: November 2017

AbstractWe previously demonstrated the aberrant expression of nine specific miRNAs in serum from osteoporotic patients. In the present study, we further evaluated the expression of these miRNAs in bone tissue, osteoblasts, and osteoclasts from 28 patients. We hypothesize that miRNA expression in serum from osteoporotic patients may be gender-independent. A further hypothesis is that the miRNA expression in bone could be correlated with BMD values. Moreover, intracellular expression of these osteoporosis-related miRNAs may indicate the role of these molecules during osteoporosis. Our results indeed show that miRNA expression in serum was gender-independent except for miR125b-5p. A correlation with BMD was confirmed for miR-21-5p, miR-24-3p, miR-93-5p, miR-100-5p and miR125b-5p with linear correlation coefficients r > 0.9. Intracellular studies revealed a simultaneous up-regulation of miR-21-5p, miR-93-5p, miR-100-5p and miR125b-5p in osteoblasts and in osteoclasts. miR-148a-3p up-regulation in cells was specific for osteoporotic osteoclasts. Altogether, miR-21-5p, miR-93-5p, miR-100-5p, and miR-125b-5p showed significant upregulation in serum, tissue and bone cells of osteoporotic patients. All except miR-125b-5p showed gender independent expression and good correlation to BMD values. Our results suggest that these miRNAs may be important for an earlier diagnosis of osteoporosis.
Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline
Authors: Hobbs Matthew , King Andrew , Salinas Ryan , Chen Zhiliang , Tsangaras Kyriakos , Greenwood Alex D. , Johnson Rebecca N. , Belov Katherine , Wilkins Marc R. , Timms Peter 
Published: November 2017

AbstractThe koala retrovirus (KoRV) is implicated in several diseases affecting the koala (Phascolarctos cinereus). KoRV provirus can be present in the genome of koalas as an endogenous retrovirus (present in all cells via germline integration) or as exogenous retrovirus responsible for somatic integrations of proviral KoRV (present in a limited number of cells). This ongoing invasion of the koala germline by KoRV provides a powerful opportunity to assess the viral strategies used by KoRV in an individual. Analysis of a high-quality genome sequence of a single koala revealed 133 KoRV integration sites. Most integrations contain full-length, endogenous provirus; KoRV-A subtype. The second most frequent integrations contain an endogenous recombinant element (recKoRV) in which most of the KoRV protein-coding region has been replaced with an ancient, endogenous retroelement. A third set of integrations, with very low sequence coverage, may represent somatic cell integrations of KoRV-A, KoRV-B and two recently designated additional subgroups, KoRV-D and KoRV-E. KoRV-D and KoRV-E are missing several genes required for viral processing, suggesting they have been transmitted as defective viruses. Our results represent the first comprehensive analyses of KoRV integration and variation in a single animal and provide further insights into the process of retroviral-host species interactions.
mRNAs containing NMD-competent premature termination codons are stabilized and translated under UPF1 depletion
Authors: Kim Won Kyu , Yun SeongJu , Kwon Yujin , You Kwon Tae , Shin Nara , Kim Jiyoon , Kim Hoguen 
Published: November 2017

AbstractmRNAs containing premature termination codons (PTCs) are rapidly degraded through nonsense-mediated mRNA decay (NMD). However, some PTC-containing mRNAs evade NMD, and might generate mutant proteins responsible for various diseases, including cancers. Using PTC-containing human genomic β-globin constructs, we show that a fraction (~30%) of PTC-containing mRNAs expressed from NMD-competent PTC-containing constructs were as stable as their PTC-free counterparts in a steady state. These PTC-containing mRNAs were monosome-enriched and rarely contributed to expression of mutant proteins. Expression of trace amounts of mutant proteins from NMD-competent PTC-containing constructs was not affected by inhibition of eIF4E-dependent translation and such expression was dependent on a continuous influx of newly synthesized PTC-containing mRNAs, indicating that truncated mutant proteins originated primarily in the pioneer round of translation. The generation of mutant proteins was promoted by UPF1 depletion, which induced polysome association of PTC-containing mRNAs, increased eIF4E-bound PTC-containing mRNA levels, and subsequent eIF4E-dependent translation. Our findings suggest that PTC-containing mRNAs are potent and regulatable sources of mutant protein generation.