bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeated evolution of circadian clock dysregulation in cavefish populations
Authors: Mack Katya L. , Jaggard James B. , Persons Jenna L. , Passow Courtney N. , Stanhope Bethany A. , Ferrufino Estephany , Tsuchiya Dai , Smith Sarah E. , Slaughter Brian D. , Kowalko Johanna , Rohner Nicolas , Keene Alex C. , McGaugh Suzanne E. 
Published: January 2020

AbstractCircadian rhythms are nearly ubiquitous throughout nature, suggesting they are critical for survival in diverse environments. Organisms inhabiting environments with arrhythmic days, such as caves, offer a unique opportunity to study the evolution of circadian rhythms in response to changing ecological pressures. Here we demonstrate that the cave environment has led to the repeated disruption of the biological clock across multiple populations of Mexican cavefish, with the circadian transcriptome showing widespread reductions in rhythmicity and changes to the timing of the activation/repression of genes in the core pacemaker. Then, we investigate the function of two genes with decreased rhythmic expression in cavefish. Mutants of these genes phenocopy reductions in sleep seen in multiple cave populations, suggesting a link between circadian dysregulation and sleep reduction. Altogether, our results reveal that evolution in an arrhythmic environment has resulted in dysregulation to the biological clock across multiple populations by diverse molecular mechanisms.
metan: an R package for multi-environment trial analysis
Authors: Olivoto Tiago , Dal’Col Lúcio Alessandro 
Published: January 2020

AbstractMulti-environment trials (MET) are crucial steps in plant breeding programs that aim increasing crop productivity to ensure global food security. The analysis of MET data requires the combination of several approaches including data manipulation, visualization, and modeling. As new methods are proposed, analyzing MET data correctly and completely remains a challenge, often intractable with existing tools.Here we describe themetan Rpackage, a collection of functions that implement a workflow-based approach to (a) check, manipulate and summarise typical MET data; (b) analyze individual environments using both fixed and mixed-effect models; (c) compute parametric and non-parametric stability statistics; (c) implement biometrical models widely used in MET analysis; and (d) plot typical MET data quickly.In this paper, we present a summary of the functions implemented inmetanand how they integrate into a workflow to explore and analyze MET data. We guide the user along a gentle learning curve and show how adding only a few commands or options at a time, powerfull analyzes can be implemented.metanoffers a flexible, intuitive, and richly documented working environment with tools that will facilitate the implementation of a complete analysis of MET data sets.
WHIMP links the actin nucleation machinery to Src-family kinase signaling during protrusion and motility
Authors: Kabrawala Shail , Zimmer Margaret D. , Campellone Kenneth G. 
Published: January 2020

ABSTRACTCell motility is governed by cooperation between the Arp2/3 complex and nucleation factors from the Wiskott-Aldrich Syndrome Protein (WASP) family, which together assemble actin filament networks to drive membrane protrusion. Here we identify WHIMP (WAVE Homology In Membrane Protrusions) as a new member of the WASP family. The Whimp gene is encoded on the X-chromosome of multiple animals, including mice. Murine WHIMP promotes Arp2/3-dependent actin assembly, but is less potent than other nucleation factors. Nevertheless, WHIMP-mediated Arp2/3 activation enhances both plasma membrane ruffling and wound healing migration, whereas WHIMP depletion impairs protrusion and slows motility. WHIMP expression also increases Src-family kinase activity, and WHIMP-induced ruffles contain the additional nucleation factors WAVE1, WAVE2, and N-WASP, but not JMY or WASH. Perturbing the function of Src-family kinases, WAVE proteins, or Arp2/3 complex inhibits WHIMP-driven ruffling. These results suggest that WHIMP-mediated actin assembly plays a direct role in membrane protrusion, but also results in feedback control of tyrosine kinase signaling to modulate the activation of multiple WASP-family proteins.AUTHOR SUMMARYThe actin cytoskeleton is a collection of protein polymers that assemble and disassemble within cells at specific times and locations. Sophisticated cytoskeletal regulators called nucleation factors ensure that actin polymerizes when and where it is needed, and most nucleation factors are members of the Wiskott-Aldrich Syndrome Protein (WASP) family. Several of the 8 known WASP-family proteins function in cell motility, but how the different factors collaborate with one another is not well understood. In this study, we identified WHIMP, a new WASP-family member which is encoded on the X chromosome of a variety of animals. In mouse cells, WHIMP enhances cell motility by assembling actin filaments that push the cell membrane forward. Unexpectedly, WHIMP also activates tyrosine kinase enzymes, proteins that stimulate multiple WASP-family members during motility. Our results open new avenues of research into how nucleation factors cooperate during movement and how the molecular activities that underlie motility differ in distinct cell types and organisms.
Species-specific, age-varying plant traits affect herbivore growth and survival
Authors: Yang Louie H. , Cenzer Meredith L. , Morgan Laura J. , Hall Griffin W. 
Published: January 2020

AbstractSeasonal windows of opportunity represent intervals of time within a year during which organisms have improved prospects of achieving life history aims such as growth or reproduction, and may be commonly structured by temporal variation in abiotic factors, bottom-up factors, and top-down factors. Although seasonal windows of opportunity are likely to be common, few studies have examined the factors that structure seasonal windows of opportunity in time. Here, we experimentally manipulated host plant age in two milkweed species (Asclepias fascicularisandAsclepias speciosa) in order to investigate the role of plant species-specific and plant age-varying traits on the survival and growth of monarch caterpillars (Danaus plexippus). We show that the two plant species showed diverging trajectories of defense traits with increasing age. These species-specific and age-varying host plant traits significantly affected the growth and survival of monarch caterpillars through both resource quality- and resource quantity-based constraints. The effects of plant age on monarch developmental success were comparable to and sometimes larger than those of plant species identity. We conclude that species-specific and age-varying plant traits are likely to be important factors with the potential to structure seasonal windows of opportunity for monarch development, and examine the implications of these findings for both broader patterns in the ontogeny of plant defense traits and the specific ecology of milkweed-monarch interactions in a changing world.
Transport Phenomena in Fluid Films with Curvature Elasticity
Authors: Mahapatra Arijit , Saintillan David , Rangamani Padmini 
Published: January 2020

AbstractCellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of the membrane. Experiments have shown that lipid flow in the plane of the membrane is closely coupled with the diffusion of proteins. Thus there is a need for a comprehensive framework that accounts for the interplay between these processes. Here, we present a theory for the coupled in-plane viscous flow of lipids, diffusion of transmembrane proteins, and curvature elastic deformation of lipid bilayers. The proteins in the membrane are modeled such that they influence membrane bending by inducing a spontaneous curvature. We formulate the free energy of the membrane with a Helfrich-like curvature elastic energy density function modified to account for the chemical potential energy of proteins. We derive the conservation laws and equations of motion for this system. Finally, we present results from dimensional analysis and numerical simulations and demonstrate the effect of coupled transport processes in governing the dynamics of membrane bending and protein diffusion.
Sox2 modulation increases naïve pluripotency plasticity
Authors: Tremble Kathryn , Stirparo Giuliano G. , Bates Lawrence E. , Maskalenka Katsiaryna , Stuart Hannah T. , Jones Kenneth , Andersson-Rolf Amanda , Radzisheuskaya Aliaksandra , Koo Bon-Kyoung , Bertone Paul , Silva José C. R. 
Published: January 2020

AbstractInduced pluripotency provides a tool to explore the molecular mechanisms underlying the establishment, maintenance and differentiation of naïve pluripotent stem cells (nPSCs). Here, we report that self-renewal of nPSCs requires minimal Sox2 expression (Sox2-low). Sox2-low nPSCs do not show impaired neuroectoderm specification and differentiate efficientlyin vitrointo all embryonic germ lineages. Strikingly, Sox2-low cells also differentiate towards the trophoblast lineage bothin vitroandin vivo. At the single-cell level self-renewing Sox2-low nPSCs exhibit a homogeneous naïve molecular signature. However, they also display a basal trophoblast molecular signature and decreased ability of Oct4 to bind naïve-associated regulatory sequences compared to control cells. These features underlie observed enhanced cell potency upon the removal of self-renewing cues. In sum, this work defines Sox2 as a restrictor of developmental potential and suggests perturbation of the naïve pluripotent network as an underlying cause of increased cell potency.HighlightsLow Sox2 expression is sufficient for naïve pluripotent stem cell self-renewalLow Sox2 expression does not impair neurectoderm differentiationin vitroLow Sox2 expression impairs Oct4 genomic occupancyLow Sox2 expression increases naïve pluripotent cell plasticityin vitroandin vivo
TOP the Transcription Orientation Pipeline and its use to investigate the transcription of non-coding regions: assessment with CRISPR direct repeats and intergenic sequences
Authors: Houenoussi Kimberley , Boukheloua Roudaina , Vernadet Jean-Philippe , Gautheret Daniel , Vergnaud Gilles , Pourcel Christine 
Published: January 2020

AbstractA large proportion of non-coding sequences in prokaryotes are transcribed, playing an important role in the cell metabolism and defense against exogenous elements. This is the case of small RNAs and of clustered regularly interspaced short palindromic repeats “CRISPR” arrays. The CRISPR-Cas system is a defense mechanism that protects bacterial and archaeal genomes against invasions by mobile genetic elements such as viruses and plasmids. The CRISPR array, made of repeats separated by unique sequences called spacers, is transcribed but the nature of the promoter and of the transcription regulation is not well known. We describe the Transcription Orientation Pipeline (TOP) which makes use of transcriptome sequence reads to recover those corresponding to a selected sequence, and determine the direction of the transcription. CRISPR repeat sequences extracted from CRISPRCasdb were used to test the performances of the program. Statistical tests show that CRISPR elements can be reliably oriented with as little as 100 mapped reads. TOP was applied to all the available RNA-Seq Illumina sequencing archives from species possessing a CRISPR array, allowing comparisons with programs dedicated to the orientation of CRISPR repeats. In addition TOP was used to analyze small non-coding RNAs inStaphylococcus aureus, demonstrating that it is a valuable and convenient tool to investigate the transcription orientation of any sequence of interest.Availability and implementationTOPs is implemented in Python and is freely available via the I2BC github repository athttps://github.com/i2bc/TOP.
Age-related DNA methylation changes are sex-specific: a comprehensive assessment
Authors: Yusipov Igor , Bacalini Maria Giulia , Kalyakulina Alena , Krivonosov Mikhail , Pirazzini Chiara , Gensous Noémie , Ravaioli Francesco , Milazzo Maddalena , Giuliani Cristina , Vedunova Maria , Fiorito Giovanni , Gagliardi Amedeo , Polidoro Silvia , Garagnani Paolo , Ivanchenko Mikhail , Franceschi Claudio 
Published: January 2020

AbstractIn humans, females live longer than males but experience a worse longevity, as genome-wide autosomal DNA methylation differences between males and females have been reported. So far, few studies have investigated if DNA methylation is differently affected by aging in males and females. We performed a meta-analysis of 4 large whole blood datasets, comparing 4 aspects of epigenetic age-dependent remodeling between the two sexes: differential methylation, variability, epimutations and entropy. We reported that a large fraction (43%) of sex-associated probes undergoes age-associated DNA methylation changes, and that a limited number of probes shows age-by-sex interaction. We experimentally validated 2 regions mapping inFIGNandPRR4genes, and showed sex-specific deviations of their methylation patterns in models of decelerated (centenarians) and accelerated (Down syndrome) aging. While we did not find sex differences in the age-associated increase in epimutations and in entropy, we showed that the number of probes showing age-related increase in methylation variability is 15 times higher in males compared to females. Our results can offer new epigenetic tools to study the interaction between aging and sex and can pave the way to the identification of molecular triggers of sex differences in longevity and age-related diseases prevalence.
Hedgehog signaling is required for endomesodermal patterning and germ cell development inNematostella vectensis
Authors: Chen Cheng-Yi , McKinney Sean A. , Ellington Lacey R. , Gibson Matthew C. 
Published: January 2020

AbstractTwo distinct mechanisms for primordial germ cell (PGC) specification are observed within Bilatera: early determination by maternal factors or late induction by zygotic cues. Here we investigate the molecular basis for PGC specification inNematostella, a representative pre-bilaterian animal where PGCs arise as paired endomesodermal cell clusters during early development. We first present evidence that the putative PGCs delaminate from the endomesoderm upon feeding, migrate into the gonad primordia, and mature into germ cells. We then show that the PGC clusters arise at the interface betweenhedgehog1andpatcheddomains in the developing mesenteries and use gene knockdown, knockout and inhibitor experiments to demonstrate that Hh signaling is required for both PGC specification and general endomesodermal patterning. These results provide evidence that theNematostellagermline is specified by inductive signals rather than maternal factors, and support the existence of zygotically-induced PGCs in the eumetazoan common ancestor.
Deletion of RsmE 16S rRNA methyltransferase leads to low level increase in aminoglycoside resistance inMycobacterium smegmatis
Authors: Bijpuria Shipra , Sharma Rakesh , Taneja Bhupesh 
Published: January 2020

AbstractOwing to its central role in cellular function, ribosome is one of the most common targets of antibiotics in bacteria. Mutations inrrsgene, ribosomal protein genes, methyltransfersases or drug influx/efflux are often found to overcome the drug response. Despite modulation of methylation pattern in the ribosome through mutations in the methyltransferases as one of key modulators of drug response,rsmG (gidB)is the only conserved methyltransferase associated with low-level drug resistance in large number of mycobacterial isolates. Here, we present the first evidence of association of methylation by mycobacterial RsmE, that methylates U1498 of 16S rRNA, with low levels of drug resistance. Deletion of the RsmE-homolog ofMycobacterium smegmatisleads to at least two-fold increase in the inhibitory concentration of aminoglycosides that bind in the decoding center proximal to U1498 in the 30S subunit. The change in inhibitory concentrations was highly specific and does not show any cross-resistance to drugs of other classes. Surprisingly, Rv2372c, the RsmE-homolog ofMycobacterium tuberculosishas the largest number of mutations among conserved ribosomal methyltransfersases, aftergidB, highlighting the role of mutations in the RsmE methyltransferase as a key emerging mechanism of drug resistance in clinical strains ofM. tuberculosis. Our work underlies the association of methylation by the RsmE-homolog with drug resistance and lays the groundwork to tackle this emerging mechanism of drug resistane in mycobacteria.
Despite of DNA repair ability the Fanconi anemia mutant protein FANCGR22P destabilizes mitochondria and leads to genomic instability via FANCJ helicase
Authors: Bose K Jagadeesh Chandra , Kapoor Bishwajit Singh , Mondal Kamal , Ghosh Subhrima , Mokhamatam Raveendra B. , Manna Sunil K. , Mukhopadhyay Sudit S. 
Published: January 2020

SummaryFanconi anemia (FA) is a unique DNA damage repair pathway. Almost twenty-two genes have been identified which are associated with the FA pathway. Defect in any of those genes causes genomic instability, and the patients bear the mutation become susceptible to cancer. In our earlier work, we have identified that Fanconi anemia protein G (FANCG) protects the mitochondria from oxidative stress. In this report, we have identified eight patients having mutation (C.65G>C; p.Arg22Pro) in the N-terminal of FANCG. The mutant protein hFANCGR22P is able to repair the DNA and able to retain the monoubiquitination of FANCD2 in FANCGR22P/FGR22P cell. However, it lost mitochondrial localization and failed to protect mitochondria from oxidative stress. Mitochondrial instability in the FANCGR22P cell causes the transcriptional down-regulation of mitochondrial iron-sulphur cluster biogenesis protein Frataxin (FXN) and resulting iron deficiency of FA protein FANCJ, an iron-sulphur containing helicase involved in DNA repair.
Open innovation and the formation of university–industry links in the food manufacturing and technology sector
Authors: Johnston Andrew 
Published: January 2020

PurposeDespite typically being regarded as “low tech”, the food manufacturing and technology sector is increasingly turning to open innovation practices involving collaboration with universities in order to innovate. Given the broad range of activities undertaken by this sector and the fact that it utilises analytical, synthetic and symbolic knowledge for innovation, it makes an interesting case study on the factors that influence the formation of university–industry (U–I) links. The paper aims to discuss this issue.Design/methodology/approachUsing data from 249 collaborative projects that occurred between UK universities and food manufacturing and technology firms, the analysis utilises a logistic regression model based on a “synthetic counterfactual approach” to modelling the probability a collaborative link will be established with one university and not others.FindingsThe results suggest that organisational proximity, conceptualised through the presence of prior ties between actors, has the largest influence on the formation of U–I links. In addition, spatial and technological proximities between actors also have a positive influence on link formation. This result suggests that the specificity of knowledge of the food sector is important in the formation of these U–I links.Research limitations/implicationsThe results suggest that the open innovation practices of food manufacturing and technology firms are like other sectors, even though their innovation practices are considered to be different. However, the limitations of the paper mean that these findings may be specific to firms in the food manufacturing and technology sector in the UK.Originality/valueThe food sector is under-represented in empirical studies on university collaboration; this paper addresses this and provides new insights into the formation of these links.
Development of helmet mold design system using 3D anthropometric analysis
Authors: Kang Yeonghoon , Kim Sungmin 
Published: January 2020

Purpose
The purpose of this paper is to develop a software can generate helmet mold from three-dimensional (3D) human body scan data.

Design/methodology/approach
An algorithm has been developed to divide data into arbitrary number of groups considering the width, length and height of head using the standard normal distribution theory. A basic helmet mold is generated automatically based on the shape of representative convex hull for each group.

Findings
It is possible to analyze the 3D human body scan data of groups with various characteristics and apply them to mass customized production of helmet.

Practical implications
This methodology can be applied for designing other products related to the head shape such as goggles and masks by varying the measurement items of the head.

Social implications
This methodology will enable mass customized production centered on consumers in the production and design of various equipment and goods to be worn on the head.

Originality/value
An algorithm has been developed to define the vertex point, which is the limit of scan data, for the analysis of 3D human body scan data scan data. In addition, a system was developed that can mass-produce customized products by effectively dividing groups while taking into account the physical characteristics of consumers.
Economic freedom and Hofstede’s cultural dimensions
Authors: DeBode Jason D. , Haggard Dana L. , Haggard K. Stephen 
Published: January 2020

Purpose
The purpose of this paper is to investigate the influence of broad cultural dimensions, as well as those of religion and legal origin, on countries’ economic freedom, i.e., trade freedom, investment freedom, business freedom, labor freedom, monetary freedom, as well as a composite measure of economic freedom.

Design/methodology/approach
Linear regression of publicly available data regarding economic freedom (Miller et al., 2018) on cultural dimensions (Hofstede, 2009), legal origin and religion (LaPorta et al., 1999) for 52 countries was performed to determine the impact of these factors on economic freedom.

Findings
Results indicated femininity was the cultural dimension associated with the most measures of economic freedom. Short-term-oriented cultures were predictive of greater business freedom, while more restrained cultures were associated with greater business and monetary freedoms. Higher individualism was predictive of greater monetary freedom. Catholicism positively predicted investment freedom and negatively predicted business freedom. French civil law negatively predicted labor freedom, while socialist legal origins positively predicted trade freedom, but negatively predicted business freedom.

Originality/value
This is the first study to examine the impacts of culture, law and religion on economic freedom. One practical implication of this research is that countries would be wise to emphasize more feminine aspects in their cultures, as these are associated with greater economic freedom. Even minor adjustments that move in the direction of cooperation and fair processes might help increase economic freedoms and the many benefits that stem from such freedoms.