bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pan-plant protein complex map reveals deep conservation and novel assemblies
Authors: McWhite Claire D. , Papoulas Ophelia , Drew Kevin , Cox Rachael M. , June Viviana , Dong Oliver Xiaoou , Kwon Taejoon , Wan Cuihong , Salmi Mari L. , Roux Stanley J. , Browning Karen S. , Chen Z. Jeffrey , Ronald Pamela C. , Marcotte Edward M. 
Published: October 2019

SUMMARYPlants are foundational to global ecological and economic systems, yet most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. Using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified novel interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical to agriculture. We also uncovered plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers the first cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.
Quantification of DNA methylation using methylation-sensitive restriction enzymes and multiplex digital PCR
Authors: Nell R.J. , van Steenderen D. , Menger N.V. , Weitering T.J. , Versluis M. , van der Velden P.A. 
Published: October 2019

ABSTRACTEpigenetic regulation is important in human health and disease, but the exact mechanisms remain largely enigmatic. DNA methylation represents one well-studied aspect of epigenetic regulation, but is challenging to quantify accurately. In this study, we introduce a digital approach for the absolute quantification of the amount, density and allele-specificity of DNA methylation. Combining the efficiency of methylation-sensitive restriction enzymes with the quantitative power of digital PCR, DNA methylation is measured accurately without the need to treat the DNA samples with sodium bisulphite. Moreover, as the combination of PCR amplicon and restriction enzyme is flexible, the context and density of DNA methylation can be taken into account. Additionally, by extending the experimental setup to a multiplex digital PCR, methylation markers may be analysed together with physically linked genetic markers to determine the allele-specificity of the methylation. In-silico simulations demonstrated the mathematical validity of the experimental setup. Next the approach was validated in a variety of healthy and malignant reference samples in the context of RASSF1A promotor methylation. RASSF1A is an established tumour suppressor gene, that is aberrantly methylated in many human cancers. A dilution series of well-characterized reference samples cross-validated the sensitivity and dynamic range of the approach. Compared to conventional PCR based methods, digital PCR provides a more accurate and more sensitive approach to quantify DNA methylation. As no sodium bisulphite conversion is needed, also analysis of minute amounts of DNA could be carried out efficiently.
Genomic Outcomes of Haploid Induction Crosses in Potato (Solanum tuberosumL.)
Authors: Amundson Kirk R , Ordoñez Benny , Santayana Monica , Tan Ek Han , Henry Isabelle M , Mihovilovich Elisa , Bonierbale Merideth , Comai Luca 
Published: October 2019

AbstractThe challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination withS. tuberosumAndigenum Group (formerlyS. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports described aneuploid and euploid progeny, which, in some cases, displayed genetic markers from the haploid inducer. Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the haploid inducer, and for small-scale introgression of genetic markers. In 19 progeny, we detected ten of the twelve possible trisomies and, in all cases, demonstrated the non-inducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing of haploid inducer origin were better explained as technical artifacts. Leveraging recurring CNV patterns, we documented sub-chromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.
Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Cancers
Authors: Nair Asha A. , Tang Xiaojia , Thompson Kevin J. , Kalari Krishna R. , Subramanian Subbaya 
Published: October 2019

ABSTRACTComplex interactions between mRNAs and microRNAs influence cellular functions. The interactions between mRNA and microRNAs also determine the post-transcriptional availability of free mRNAs and unbound microRNAs. The microRNAs bind to one or more microRNA Response Elements (MREs) predominantly located on the 3’untranslated regions (3’UTR) of mRNAs. In this study, we leveraged MRE sites and their frequencies in transcriptomes of cancer and matched normal tissues to obtain insights into disease-specific interactions between mRNAs and microRNAs. Toward this, we developed a novel bioinformatics method called ‘ReMIx’ that utilizes RNA-Seq data to quantify MRE frequencies at 3’UTR of genes across the transcriptome. We applied ReMIx to The Cancer Genome Atlas (TCGA) Triple Negative (TN) breast cancer tumor-normal adjacent pairs (N=13) and identified distinctly and differentially expressed MREs specific to the TN tumors. Novel data generated by ReMIx identified candidate mRNAs and microRNAs in the MAPK signaling cascade of the TN tumors. We further analyzed the MAPK endogenous RNA network to establish regulatory microRNA partners, along with interacting protein-coding mRNAs that influence and modulate MAPK signaling in TN breast cancers.
Decoupling Genetics from Attainments: The Role of Social Environments
Authors: Fletcher Jason 
Published: October 2019

AbstractThis paper examines the extent to which growing up in a socially mobile environment might decouple genetic endowments related to educational attainment with actual attainments. Many models of intergenerational transmission of advantage contain both a transmission channel through endowments (i.e. genetics) from parents to children as well as from parental investments and “luck”. Indeed, many scholars consider the intergenerational links due to the transmission of genetically based advantage to place a lower bound on plausible levels of social mobility—genetics may be able to “lock in” advantage across generations. This paper explores this idea by using new genetic measurements in the Health and Retirement Study to examine potential interactions between social environments and genetics related to attainments. The results suggest evidence of gene environment interactions: children born in high mobility states have lower genetic penetrance—the interaction between state-level mobility and the polygenic score for education is negative. These results suggest a need to incorporate gene-environment interactions in models of attainment and mobility and to pursue the mechanisms behind the interactions.
Monitoring of Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea
Authors: Kattenberg Johanna Helena , Razook Zahra , Keo Raksmei , Koepfli Cristian , Jennison Charlie , Lautu-Ninda Dulcie , Fola Abebe A. , Ome-Kaius Maria , Barnadas Céline , Siba Peter , Felger Ingrid , Kazura James , Mueller Ivo , Robinson Leanne J. , Barry Alyssa E. 
Published: October 2019

ABSTRACTMonitoring the genetic structure of malaria parasite populations has been proposed as a novel and sensitive approach to quantify the impact of malaria control and elimination efforts. Here we describe the first population genetic analysis of sympatric Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from serial cross-sectional studies pre-(2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially in these communities (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. P. falciparum diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow between provinces. P. vivax prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, the emergence of clonal transmission and significant multilocus linkage disequilibrium (mLD) due to increased focal inbreeding post-LLIN was a strong indicator of impact on the parasite population using these markers. After eight years of intensive malaria control in PNG and substantial prevalence decline the impact on parasite population diversity and structure detectable by microsatellite genotyping was limited.
Manganese uptake, mediated by SloABC and MntH, is essential for the fitness ofStreptococcus mutans
Authors: Kajfasz Jessica K. , Katrak Callahan , Ganguly Tridib , Vargas Jonathan , Wright Logan , Peters Zachary T. , Spatafora Grace A. , Abranches Jacqueline , Lemos José A. 
Published: October 2019

ABSTRACTEarly epidemiological studies implicated manganese (Mn) as a possible caries-promoting agent while laboratory studies have indicated that manganese stimulates the expression of virulence-related factors in the dental pathogenStreptococcus mutans. To better understand the importance of manganese homeostasis toS. mutanspathophysiology, we first used RNA sequencing to obtain the global transcriptional profile ofS. mutansUA159 grown under Mn-restricted conditions. Among the most highly expressed genes were the entiresloABCoperon, encoding a dual iron/manganese transporter, and an uncharacterized gene, hereinmntH, that codes for a protein bearing strong similarity to Nramp-type transporters. While inactivation ofsloC, which encodes the lipoprotein receptor of the SloABC system, ormntHalone had no major consequence on the overall fitness ofS. mutans, simultaneous inactivation ofsloCandmntH(ΔsloCΔmntH) impaired growth and survival under Mn-restricted conditions, including in human saliva or in the presence of calprotectin. Further, disruption of Mn transport resulted in diminished stress tolerance and reduced biofilm formation in the presence of sucrose. These phenotypes were markedly improved when cells were provided with excess Mn. Metal quantifications revealed that the single mutant strains contain similar intracellular levels of Mn as the parent strain, whereas Mn was nearly undetectable in the ΔsloCΔmntHstrain. Collectively, these results reveal that SloABC and MntH work independently and cooperatively to promote cell growth under Mn-restricted conditions, and that mauitanence of Mn homeostasis is essential for the expression of major virulence attributes inS. mutans.IMPORTANCEAs trace biometals such as manganese (Mn) are important for all forms of life, the ability to regulate biometals availability during infection is an essential trait of successful bacterial pathogens. Here, we showed that the caries pathogenStreptococcus mutansutilizes two Mn transport systems, namely SloABC and MntH, to acquire Mn from the environment, and that the ability to maintain the cellular levels of Mn is important for the manifestation of characteristics that associateS. mutanswith dental caries. Our results indicate that the development of strategies to depriveS. mutansof Mn hold promise in the combat against this important bacterial pathogen.
Divergent sperm traits in Carabidae ground beetles (Insecta: Coleoptera)
Authors: Sasakawa Kôji 
Published: October 2019

AbstractSperm exhibit marked morphological diversity, and investigations into sperm diversity can further the understanding of many areas of evolutionary biology. In this study, using light microscopy, sperm morphology was examined in 39 species of Carabidae from eight subfamilies, including five subfamilies in which sperm morphology has not previously been examined. In all but one of the subfamilies, the subfamily members shared the same type of sperm: single sperm were observed in Cicindelinae, Nebriinae, and Trechinae; sperm conjugates, in which numerous sperm adhere together, were observed in Elaphrinae, Patrobinae, and Brachinae; and both single sperm and sperm conjugates were observed in Broscinae. In the remaining subfamily, Harpalinae, most species formed sperm conjugates, but some species formed single sperm. Some noteworthy sperm were also observed: the shortest single sperm in the order Coleoptera was found; multiflagellated sperm were observed, which had previously been reported from only one species in the class Insecta; and size variation of sperm conjugates, which may represent size dimorphism, was observed. Based on the results of this and previous studies, the evolutionary pattern of sperm traits and the phylogenetic utility of sperm morphologies in Carabidae are discussed.
Improve Protein Solubility and Activity based on Machine Learning Models
Authors: Han Xi , Ning Wenbo , Ma Xiaoqiang , Wang Xiaonan , Zhou Kang 
Published: October 2019

AbstractImproving catalytic ability of protein biocatalysts leads to reduction in the production cost of biocatalytic manufacturing process, but the search space of possible proteins/mutants is too large to explore exhaustively through experiments. To some extent, highly soluble recombinant proteins tend to exhibit high activity. Here, we demonstrate that an optimization methodology based on machine learning prediction model can effectively predict which peptide tags can improve protein solubility quantitatively. Based on the protein sequence information, a support vector machine model we recently developed was used to evaluate protein solubility after randomly mutated tags were added to a target protein. The optimization algorithm guided the tags to evolve towards variants that can result in higher solubility. Moreover, the optimization results were validated successfully by adding the tags designed by our optimization algorithm to a model protein, expressing it in vivo and experimentally quantifying its solubility and activity. For example, solubility of a tyrosine ammonium lyase was more than doubled by adding two tags to its N- and C-terminus. Its protein activity was also increased nearly 3.5 fold by adding the tags. Additional experiments also supported that the designed tags were effective for improving activity of multiple proteins and are better than previously reported tags. The presented optimization methodology thus provides a valuable tool for understanding the correlation between amino acid sequence and protein solubility and for engineering protein biocatalysts.Contactkang.zhou@nus.edu.sg, chewxia@nus.edu.sg
The perinuclear ER scales nuclear size independently of cell size in early embryos
Authors: Mukherjee Richik Nilay , Sallé Jérémy , Dmitrieff Serge , Nelson Katherine , Oakey John , Minc Nicolas , Levy Daniel L. 
Published: October 2019

SUMMARYNuclear size plays pivotal roles in gene expression, embryo development, and disease. A central hypothesis in organisms ranging from yeast to vertebrates is that nuclear size scales to cell size. This implies that nuclei may reach steady state sizes set by limiting cytoplasmic pools of size-regulating components. By monitoring nuclear dynamics in early sea urchin embryos, we found that nuclei undergo substantial growth in each interphase, reaching a maximal size prior to mitosis that declined steadily over the course of development. Manipulations of cytoplasmic volume through multiple chemical and physical means ruled out cell size as a major determinant of nuclear size and growth. Rather, our data suggest that the perinuclear endoplasmic reticulum, accumulated through dynein activity, serves as a limiting membrane pool that sets nuclear surface growth rate. Partitioning of this local pool at each cell division modulates nuclear growth kinetics and dictates size scaling throughout early development.
Work time and well-being for workers at home: evidence from the American Time Use Survey
Authors: Giménez-Nadal José Ignacio , Molina José Alberto , Velilla Jorge 
Published: October 2019

Purpose
The purpose of this paper is to analyze the time-allocation decisions of individuals who work from home (i.e. teleworkers), and compare them with their commuter counterparts.

Design/methodology/approach
Using data from the American Time Use Survey for the years 2003–2015, the authors analyze the time spent working, and the timing of work, of both commuters and teleworkers.

Findings
Results show that teleworkers devote 40 percent less time to market work activities than do commuters, and less than 60 percent of teleworkers work at “regular hours,” vs around 80 percent of their commuter counterparts. Using information from the Well-being Module for the years 2012 and 2013, the authors find that male teleworkers experience lower levels of negative feelings while working than do commuters.

Originality/value
This paper addresses the timing of work of workers working from home; and the instant well-being experienced, exploiting information at diary level.
Geographical diversification and bank performance: evidence from Indian banks
Authors: Sharma Shweta , Anand Anand 
Published: October 2019

PurposeGeographic diversification results in the improvement of firm value through an increase in scale and scope of economies, gains in synergy, reduction in cost and improved corporate governance, however, the capabilities of financial institutions get heavily affected due to information asymmetries, varied macro and microeconomic factors across economies. In this context, the purpose of this paper is to empirically analyze the impact of geographical diversification on the performance of Indian Banks.Design/methodology/approachFor an unbalanced panel data set of Indian Banks over the period 2001–2016, fixed effect model (FEM) with a distributed lag is used and tested for firm and time fixed effects. Further, the study also examines the role of bank size and ownership on the above association.FindingsFindings of the study suggests that geographical diversification helps in increasing bank returns for the overall sample but does not have any significant impact on bank risk. For foreign and public banks, geographical diversification helps in increasing bank returns but does not have any significant impact on bank risk. This indicates toward the adverse selection, poor monitoring incentives in new markets and suggesting a lack of managerial skills.Originality/valueThe study indicates that while formulating the policies regarding branching and expansion these findings can serve as a guiding tool for managers and regulators. Findings have important implications for financial institution and policymakers in globalized financial markets.
Antecedents of innovative work behaviour in healthcare: does efficacy play a role?
Authors: Oppi Chiara , Bagheri Afsaneh , Vagnoni Emidia 
Published: October 2019

PurposeExploring how to enhance innovative work behaviour (IWB) has been the main concern of top managers and researchers, particularly in knowledge-intensive and public organizations. Yet, studies investigating factors that shape innovative behaviour at work are scarce. Focussing on the healthcare setting, the purpose of this paper is to hypothesize a direct relationship between individuals’ perceived creative self-efficacy (CSE), creative collective efficacy (CCE) and IWB.Design/methodology/approachThe research used survey data from 446 clinical managers working in public healthcare organizations in six different Italian regions and a set of previously validated questionnaires to measure the study variables.FindingsFindings suggest that clinical managers’ perceptions of their CSE and their perceived CCE significantly influence their self-reported IWB.Research limitations/implicationsFindings highlight the importance of constructing and developing clinical managers’ efficacy in creativity at both an individual and team level in order to incentivize the emergence of innovation behaviour. Further research is needed to assess the existence of mediating and/or moderating mechanisms underlying the relationships emerging from this study in order to support decision makers in diffusing innovation and creativity in healthcare organizations.Originality/valueThe research adds to the debate on improving IWB by introducing perceived individual and team creative efficacy as determinants of IWB in healthcare organizations. The research is among the first attempts to contribute to healthcare organizations’ management through exploring clinical managers’ characteristics that influence their IWB.
Capital-constrained bi-objective newsvendor model with risk-averse preference and bankruptcy threshold
Authors: Yang Chen , Wu Desheng , Fang Weiguo 
Published: October 2019

Purpose
The purpose of this paper is to investigate the major factors influencing retailer’s optimal ordering strategy in a supply chain consisting of one supplier and one retailer, where the retailer is newsvendor-like and capital-constrained, and further explore the issue of supply chain coordination.

Design/methodology/approach
Based on bi-objective programming which is modeled under the mean-variance framework, the retailer’s optimal ordering strategy is derived. Furthermore, through comparative analysis between decentralized system and centralized system along with a numerical simulation, this study examines the theoretical conclusions about supply chain coordination.

Findings
This study shows that a poor retailer with a high Expected Terminal Wealth Target Threshold (ETWTT) would ignore bankruptcy risk and order more, whereas a rich retailer is relatively conservative. It also reveals that in some cases, the optimal order quantity and performance of decentralized system could be both improved. However, the centralized system can always get more profit than the decentralized one.

Originality/value
This study uses a bankruptcy threshold to describe retailer’s bankruptcy risk, and considers retailer’s wealth status to formulate the model as an innovative bi-objective programming. The type of retailer as rich or poor in terms of his wealth status and asset structure is distinguished. Moreover, the impacts of retailer’s type and ETWTT on ordering strategy are examined.