bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-specific regulation of monocyte surface IL7R expression and soluble receptor secretion by a common autoimmune risk allele
Authors: Al-Mossawi Hussein , Yager Nicole , Taylor Chelsea , Lau Evelyn , Danielli Sara , de Wit Jelle , Gilchrist James , Nassiri Isar , Mahe Elise A , Lee Wanseon , Rizvi Laila , Makino Seiko , Cheeseman Jane , Neville Matt , Knight Julian C , Bowness Paul , Fairfax Benjamin P 
Published: February 2018

AbstractIL-7 is a key factor in T-cell immunity and IL7R polymorphisms are implicated in autoimmune pathogenesis. IL7R mRNA is induced in stimulated monocytes in a genetically determined manner, yet a role for IL7R in monocyte biology remains unexplored. Here we characterize genetic regulation of IL7R at the protein level across multiple cell subsets and conditions in healthy individuals. We find monocyte surface and soluble IL7R (sIL7R) protein are markedly expressed in response to lipopolysaccharide (LPS). We further demonstrate alleles of rs6897932, a non-synonymous IL7R polymorphism associated with susceptibility to Multiple Sclerosis, Ankylosing Spondylitis and Primary Biliary Cirrhosis, form the key determinant of both surface IL7R and sIL7R in the context of inflammation. No effect of this allele was observed in unstimulated monocytes or across lymphoid subsets. Production of sIL7R by monocytes greatly exceeded that of CD4+ T-cells, and was strongly associated with both rs6897932 genotype and expression of the splicing factor gene DDX39A. Stimulated monocytes were sensitive to exogenous IL-7, which elicits a defined transcriptional signature. Flow cytometry and single-cell sequencing of synovial fluid derived monocytes from patients with spondyloarthritis showed an enlarged subset of IL7R+ monocytes with a unique transcriptional profile that markedly overlaps that induced by IL-7 in-vitro and shows similarity to the previously described ‘Mono4’ subset. These data demonstrate disease-associated genetic variants at IL7R specifically impact monocyte surface IL7R and sIL7R following innate immune stimulation, suggesting a previously unappreciated key role for monocytes in IL-7 pathway biology and IL7R-associated diseases.
Functional Improbable Antibody Mutations Critical for HIV Broadly Neutralizing Antibody Development
Authors: Wiehe Kevin , Bradley Todd , Meyerhoff R. Ryan , Hart Connor , Williams Wilton , Easterhoff David , Faison William J. , Kepler Thomas B. , Saunders Kevin , Alam S. Munir , Bonsignori Mattia , Haynes Barton F. 
Published: February 2018

SUMMARYHIV-1 broadly neutralizing antibodies (bnAbs) require high levels of activation-induced cytidine deaminase (AID) catalyzed somatic mutations for optimal neutralization potency. Probable mutations occur at sites of frequent AID activity, while improbable mutations occur where AID activity is infrequent. One bottleneck for induction of bnAbs is the evolution of viral envelopes (Envs) that can select bnAb B cell receptors (BCR) with improbable mutations. Here we define the probability of bnAb mutations and demonstrate the functional significance of key improbable mutations in three bnAb B cell lineages. We show that bnAbs are enriched for improbable mutations, implying their elicitation will be critical for successful vaccine induction of potent bnAb B cell lineages. We outline a mutation-guided vaccine strategy for identification of Envs that can select B cells with BCRs with key improbable mutations required for bnAb development. Our analysis suggests that through generations of viral escape, Env trimers evolved to hide in low probability regions of antibody sequence space.
Properties of Gene Expression and Chromatin Structure with Mechanically Regulated Transcription
Authors: Sevier Stuart A. , Levine Herbert 
Published: February 2018

The mechanical properties of transcription have emerged as central elements in our understanding of gene expression. Recent work has been done introducing a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase (RNAP) rotation and DNA supercoiling are coupled [1]. Here we generalize this framework to accommodate the behavior of many RNAPs operating on multiple genes on a shared piece of DNA. The resulting framework is combined with well-established stochastic processes of transcription resulting in a model which characterizes the impact of the mechanical properties of transcription on gene expression and DNA structure. Transcriptional bursting readily emerges as a common phenomenon with origins in the geometric nature of the genetic system and results in the bounding of gene expression statistics. Properties of a multiple gene system are examined with special attention paid to role that genome composition (gene orientation, size, and intergenic distance) plays in the ability of genes to transcribe. The role of transcription in shaping DNA structure is examined and the possibility of transcription driven domain formation is discussed.PACS numbers:
Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase
Authors: Craggs Timothy D. , Sustarsic Marko , Plochowietz Anne , Mosayebi Majid , Kaju Hendrik , Cuthbert Andrew , Hohlbein Johannes , Domicevica Laura , Biggin Philip C. , Doye Jonathan P. K. , Kapanidis Achillefs N. 
Published: February 2018

AbstractDNA-binding proteins utilise different recognition mechanisms to locate their DNA targets. Some proteins recognise specific nucleotide sequences, while many DNA repair proteins interact with specific (often bent) DNA structures. While sequence-specific DNA binding mechanisms have been studied extensively, structure-specific mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I (Pol) substrates both alone and in Pol-DNA complexes. Using a rigid-body docking approach based on a network of 73 distance restraints collected using single-molecule FRET, we determined a novel solution structure of the singlenucleotide-gapped DNA-Pol binary complex. The structure was highly consistent with previous crystal structures with regards to the downstream primer-template DNA substrate; further, our structure showed a previously unobserved sharp bend (~120°) in the DNA substrate; we also showed that this pronounced bending of the substrate is present in living bacteria. All-atom molecular dynamics simulations and single-molecule quenching assays revealed that 4-5 nt of downstream gap-proximal DNA are unwound in the binary complex. Coarsegrained simulations on free gapped substrates reproduced our experimental FRET values with remarkable accuracy (<ΔFRET> = -0.0025 across 34 independent distances) and revealed that the one-nucleotide-gapped DNA frequently adopted highly bent conformations similar to those in the Pol-bound state (ΔG < 4 kT); such conformations were much less accessible to nicked (> 7 kT) or duplex (>> 10 kT) DNA. Our results suggest a mechanism by which Pol and other structure-specific DNA-binding proteins locate their DNA targets through sensing of the conformational dynamics of DNA substrates.Significance StatementMost genetic processes, including DNA replication, repair and transcription, rely on DNA-binding proteins locating specific sites on DNA; some sites contain a specific sequence, whereas others present a specific structure. While sequence-specific recognition has a clear physical basis, structure-specific recognition mechanisms remain obscure. Here, we use single-molecule FRET and computer simulations to show that the conformational dynamics of an important repair intermediate (1nt-gapped DNA) act as central recognition signals for structure-specific binding by DNA polymerase I (Pol). Our conclusion is strongly supported by a novel solution structure of the Pol-DNA complex wherein the gapped-DNA is significantly bent. Our iterative approach combining precise single-molecule measurements with molecular modelling is general and can elucidate the structure and dynamics for many large biomachines.
A plug-and-play system for enzyme production at commercially viable levels in fed-batch cultures of Escherichia coli BL21 (DE3)
Authors: Sohoni Sujata Vijay , Kundalia Paras Harendra , Shetty Adarsh G. , Sunder Avinash Vellore , Gaikaiwari Raghavendra P. , Wangikar Pramod P. 
Published: February 2018

AbstractCommercial exploitation of enzymes in biotransformation necessitates a robust method for enzyme production that yields high enzyme titer. Nitrilases are a family of hydrolases that can transform nitriles to enantiopure carboxylic acids, which are important pharmaceutical intermediates. Here, we report a fed-batch method that uses a defined medium and involves growth under carbon limiting conditions using DO-stat feeding approach combined with an optimized post-induction strategy, yielding high cell densities and maximum levels of active and soluble enzyme. This strategy affords strict control of nutrient feeding and growth rates, and ensures sustained protein synthesis over a longer period. The method was optimized for highest titer of nitrilase reported so far (247 kU/l) using recombinant E. coli expressing the Alcaligenes sp. ECU0401 nitrilase. The fed-batch protocol presented here can also be employed as template to produce a wide variety of enzymes with minimal modification, as demonstrated for alcohol dehydrogenase and formate dehydrogenase.
Efficient Zygotic Genome Editing via RAD51-Enhanced Interhomolog Repair
Authors: Wilde Jonathan J. , Aida Tomomi , Wienisch Martin , Zhang Qiangge , Qi Peimin , Feng Guoping 
Published: February 2018

AbstractRecent advances in genome editing have greatly improved knock-in (KI) efficiency1–9. Searching for factors to further improve KI efficiency for therapeutic use and generation of non-human primate (NHP) models, we found that the strand exchange protein RAD51 can significantly increase homozygous KI using CRISPR/Cas9 in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is well-described in the context of meiosis10, but only occurs at low frequencies in mitotic cells11,12 and its existence in zygotes is controversial. Using a variety of approaches, we provide evidence for an endogenous IHR mechanism in zygotes that can be enhanced by RAD51. We show that this process can be harnessed for generating homozygous KI animals from wildtype zygotes based on exogenous donors and for converting heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we elucidate additional factors that contribute to zygotic IHR and identify a RAD51 mutant capable of insertion-deletion (indel)-free stimulation of IHR. Thus, our study provides conclusive evidence for the existence of zygotic IHR and demonstrates methods to enhance IHR for potential use in gene drives, gene therapy, and biotechnology.
Conserved Roles of C. elegans and Human MANFs in Sulfatide Binding and Cytoprotection
Authors: Bai Meirong , Vozdek Roman , Hnízda Aleš , Jiang Chenxiao , Wang Bingying , Kuchar Ladislav , Li Tiejun , Zhang Yuefan , Wood Chase , Feng Liang , Dang Yongjun , Ma Dengke K. 
Published: February 2018

AbstractMesencephalic Astrocyte-Derived Neurotrophic Factor (MANF) is an endoplasmic reticulum (ER) protein that can be secreted and protect dopamine neurons and cardiomyocytes from ER stress and apoptosis. The mechanism of action of extracellular MANF has long been elusive. From a genetic screen for mutants with abnormal ER stress response, we identified the gene Y54G2A.23 as the evolutionarily conserved C. elegans MANF orthologue. We find that MANF binds to the lipid sulfatide, also known as 3-O-sulfogalactosylceramide present in serum and outer-cell membrane leaflets, directly in isolated forms and in reconstituted lipid micelles. Sulfatide binding promotes cellular MANF uptake and cytoprotection from hypoxia-induced cell death. Heightened ER stress responses of MANF-null C. elegans mutants and mammalian cells are alleviated by human MANF in a sulfatide-dependent manner. Our results demonstrate conserved roles of MANF in sulfatide binding and ER stress response, supporting sulfatide as a long-sought lipid mediator of MANF’s cytoprotection.
Epigenomic plasticity of Arabidopsismsh1mutants under prolonged cold stress
Authors: Kenchanmane Raju Sunil Kumar , Shao Mon-Ray , Wamboldt Yashitola , Mackenzie Sally 
Published: February 2018

ABSTRACTDynamic transcriptional and epigenetic changes enable rapid adaptive benefit to environmental fluctuations. However, the underlying mechanisms and the extent to which this occurs are not well known.MutS Homolog 1(MSH1) mutants cause heritable developmental phenotypes accompanied by modulation of defense, phytohormone, stress-response and circadian rhythm genes, as well as heritable changes in DNA methylation patterns. Consistent with gene expression changes,msh1mutants display enhanced tolerance for abiotic stress including drought and salt stress, while showing increased susceptibility to freezing temperatures and bacterial pathogenP syringae. Our results suggest that chronic cold and low light stress (10 °C, 150 μE) influences non-CG methylation to a greater degree inmsh1mutants compared to wild type Col-0. Furthermore, CHG changes are more closely pericentromeric, whereas CHH changes are generally more dispersed. This increased variation in non-CG methylation pattern does not significantly affect themsh1-derived enhanced growth behavior after mutants are crossed with isogenic wild type, reiterating the importance of CG methylation changes inmsh1-derived enhanced vigor. These results indicate thatmsh1methylome is hyper-responsive to environmental stress in a manner distinct from the wild type response, but CG methylation changes are potentially responsible for growth vigor changes in the crossed progeny.
Ancestry and Genetic Associations with Bronchopulmonary Dysplasia in Preterm Infants
Authors: Torgerson Dara G. , Ballard Philip L. , Keller Roberta L. , Oh Sam S. , Huntsman Scott , Hu Donglei , Eng Celeste , Burchard Esteban G. , Ballard Roberta A. 
Published: February 2018

ABSTRACTBronchopulmonary dysplasia in premature infants is a common and often severe lung disease with long term sequelae. A genetic component is suspected but not fully defined. We performed an ancestry and genome-wide association study to identify variants, genes and pathways associated with survival without bronchopulmonary dysplasia in 387 high-risk infants treated with inhaled nitric oxide in the Trial of Late Surfactant study. Global African genetic ancestry was associated with increased survival without bronchopulmonary dysplasia among infants of maternal self-reported Hispanic White race/ethnicity (OR=4.5, p=0.01). Admixture mapping found suggestive outcome associations with local African ancestry at 18q21 and 10q22 among infants of maternal self-reported African American race/ethnicity. For all infants, the top individual variant identified was within the intron ofNBL1, which is expressed in mid-trimester lung and is an antagonist of bone morphogenetic proteins (rs372271081, OR=0.17, p=7.4 × 10−7). The protective allele of this variant was significantly associated with lower nitric oxide metabolites in the urine of non-Hispanic white infants (p= 0.006), supporting a role in the racial differential response to nitric oxide. Interrogating genes upregulated in bronchopulmonary dysplasia lungs indicated association with variants inCCL18, a cytokine associated with fibrosis and interstitial lung disease, and pathway analyses implicated variation in genes involved in immune/inflammatory processes in response to infection and mechanical ventilation. Our results suggest that genetic variation related to lung development, drug metabolism, and immune response contribute to individual and racial/ethnic differences in respiratory outcomes following inhaled nitric oxide treatment of high-risk premature infants.
The variability of song variability in wild and domesticated zebra finchesTaeniopygia guttata
Authors: Lansverk Allison L. , London Sarah E. , Griffith Simon C. , Clayton David F. , Balakrishnan Christopher N. 
Published: February 2018

ABSTRACTBirdsong is a classic example of a learned social behavior. Like many traits of interest, however, song production is also influenced by genetic factors and understanding the relative contributions of genetic and environmental influences remains a major research goal. In this study we take advantage of genetic variation among captive zebra finch populations to examine variation in a population-level song trait: song variability. We find that zebra finch populations differ in levels of song variability. DomesticatedT. g. castanotispopulations displayed higher song diversity than more recently wild-derived populations of both zebra finch subspeciesT. g. castanotisandT. g. guttata, the Timor zebra finch. To determine whether these differences could have a genetic basis, we cross-fostered domesticatedT. g. castanotisand Timor zebra finches to Bengalese finchesLonchura striata domestica. Following cross-fostering, domesticatedT. g. castanotismaintained a higher level of song diversity thanT. g. guttata. We suggest that the high song variability of domesticated zebra finches may be a consequence of reduced purifying selection acting on song traits. Intraspecific differences in the mechanisms underlying song variability therefore represent an untapped opportunity for probing the mechanisms of song learning and production.
miRNA profiling of primate cervicovaginal lavage and extracellular vesicles reveals miR-186-5p as a potential retroviral restriction factor in macrophages
Authors: Zhao Zezhou , Muth Dillon C. , Mulka Kathleen , Liao Zhaohao , Powell Bonita H. , Hancock Grace V. , Metcalf Pate Kelly A. , Witwer Kenneth W. 
Published: February 2018

AbstractThe goal of this study was to characterize extracellular vesicles (EVs) and miRNAs of primate cervicovaginal lavage (CVL) during the menstrual cycle and simian immunodeficiency virus (SIV) infection, and to determine if differentially regulated CVL miRNAs might influence retrovirus replication. CVL and peripheral blood were collected from SIV-infected and uninfected macaques. EVs were enriched by stepped ultracentrifugation and characterized thoroughly. miRNA profiles were assessed with a medium-throughput stem-loop/hydrolysis probe qPCR platform and validated by single qPCR assays. Hormone cycling was abnormal in infected subjects, but EV concentration correlated with progesterone concentration in uninfected subjects. miRNAs were present predominantly in the EV-depleted CVL supernatant. Only a small number of CVL miRNAs were found to vary during the menstrual cycle or SIV infection. Among them was miR-186-5p, which was depleted in retroviral infection. In experiments with infected macrophages in vitro, this miRNA inhibited HIV replication. These results provide further evidence for the potential of EVs and small RNAs as biomarkers or effectors of disease processes in the reproductive tract.
A model for assessment of uncertainty in tacit knowledge acquisition
Authors: Akhavan Peyman , Shahabipour Ali , Hosnavi Reza 
Published: February 2018

Purpose
Expert systems have come to the forefront in the modeling of problems. One of the major problems facing the expert system designers is to develop an accurate knowledge base and a meaningful model of uncertainty associated with complex models. Decision-making is based on knowledge, and decision system support needs a knowledge base as well. An adequate knowledge acquisition (KA) process leads to accurate knowledge and improves the decision-making process. To manage the risk of a medical service (twin pregnancy in this case) a knowledge management system was created. The captured knowledge may be associated with an uncertainty. This study aims to introduce a method for evaluating the reliability of a tacit KA model. It assisted engineering managers in assessing and prioritizing risks. The study tried to use this method in risk management and new case in the health domain.

Design/methodology/approach
In this study, relevant variables were identified in the knowledge management literature reviews and the domain of expertise management. They are validated by a group of domain experts. Kendall’s W indicator was used to assess the degree of consensus. On the basis of combined cognitive maps, a cognitive network was constructed. Using Bayesian belief networks and fuzzy cognitive maps, an uncertainty assessment method of tacit KA was introduced. To help managers focus on major variables, a sensitivity analysis was conducted. Reliability of model was calculated for optimistic and pessimistic values. The applicability and efficacy of the proposed method were verified and validated with data from a medical university.

Findings
Results show that tacit KA uncertainty can be defined by independent variables, including environmental factors, personality and acquisition process factors. The reliability value shows the accuracy of the captured knowledge and the effectiveness of the acquisition process. The proposed uncertainty assessment method provides the reliability value of the acquisition model for knowledge engineers, so it can be used to implement the project and prevent failures in vital factors through necessary actions. If there is not a satisficed level of reliability, the KA project reliability can be improved by risk factors. The sensitivity analysis can help to select proper factors based on the resources. This approach mitigated some of the disadvantages of other risk evaluation methods.

Originality/value
The contribution of this study is to combine the uncertainty assessment with tacit KA based on fuzzy cognitive maps and the Bayesian belief networks approach. This approach used the capabilities of both narrative and computational approaches.
Key drivers of SMEs export performance: the mediating effect of competitive advantage
Authors: Rua Orlando , França Alexandra , Fernández Ortiz Rubén 
Published: February 2018

PurposeWith its focus on the context of small firm internationalization, this paper aims to assess the important contribution of strategic determinants that influence export performance (EP), considering the mediating effect of competitive strategy.Design/methodology/approachBased on survey data from 247 Portuguese small and medium-sized enterprises (SMEs) exporting textiles, members of the Portugal’s Textile Association (ATP), this research adopted a quantitative methodological approach, conducting an exploratory and transversal empirical study.FindingsThe paper finds suggest that entrepreneurial orientation (EO) has a positive and significant influence on differentiation and EP. Moreover, the results also highlight the role of intangible resources (IR) in the design of both differentiation and cost leadership strategies, which drives EP. Finally, absorptive capabilities (ACAPs) are highly related with EP.Practical implicationsThe paper provides empirical evidence that EO, IR and ACAPs are predictors of competitive strategies and EP. Moreover, and alongside with firm’s resources, this study validates that competitive strategy does matters for small firm managers and the development of one type of competitive advantage is also a major performance enhancer.Originality/valueThis study provides fresh insights into entrepreneurship and strategic management literature, as it considers the importance of multiple factors to SMEs business growth. Moreover, this paper presents empirical evidences of the strategies that small firm managers should pursue and policy makers should support. Finally, this is an original study applied to the Portuguese textile industry.