bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclin B1 scaffolds MAD1 at the corona to activate the spindle assembly checkpoint
Authors: Allan Lindsey A , Reis Magda , Liu Yahui , Huis in ’t Veld Pim , Kops Geert JPL , Musacchio Andrea , Saurin Adrian T 
Published: August 2019

ABSTRACTThe Cyclin B:CDK1 kinase complex is the master regulator of mitosis that phosphorylates hundreds of proteins to coordinate mitotic progression. We show here that, in addition to these kinase functions, Cyclin B also scaffolds a localised signalling pathway to help preserve genome stability. Cyclin B1 localises to an expanded region of the outer kinetochore, known as the corona, where it scaffolds the spindle assembly checkpoint (SAC) machinery by binding directly to MAD1. In vitro reconstitutions map the key binding interface to a few acidic residues in the N-terminus of MAD1, and point mutations in this region remove corona MAD1 and weaken the SAC. Therefore, Cyclin B1 is the long-sought-after scaffold that links MAD1 to the corona and this specific pool of MAD1 is needed to generate a robust SAC response. Robustness, in this context, arises because Cyclin B1-MAD1 localisation becomes MPS1-independent after the corona has been established. We demonstrate that this allows corona-MAD1 to persist at kinetochores when MPS1 activity falls, ensuring that it can still be phosphorylated on a key C-terminal catalytic site by MPS1. Therefore, this study explains how corona MAD1 generates a robust SAC signal and why stripping of this pool by dynein is essential for SAC silencing. It also reveals that the key mitotic kinase, Cyclin B1-Cdk1, scaffolds the pathway that inhibits its own degradation.
Resilience to multiple stressors in an aquatic plant and its microbiome
Authors: O’Brien Anna M. , Yu Zhu Hao , Luo Dian-ya , Laurich Jason , Passeport Elodie , Frederickson Megan 
Published: August 2019

AbstractPremiseEnvironments are changing rapidly, and outcomes of species interactions, especially mutualisms, are notoriously dependent on the environment. A growing number of studies have investigated responses of mutualisms to anthropogenic changes, yet most studies have focused on nutrient pollution or climate change, and tested single stressors. Relatively little is known about impacts of simultaneous chemical contaminants, which may differ fundamentally from nutrient or climate stressors, and are especially widespread in aquatic habitats.MethodsWe investigated the impacts of two common contaminants on interactions between the common duckweed Lemna minor and its microbiome. Sodium chloride (salt) and benzotriazole (a corrosion inhibitor) negatively affect aquatic organisms individually, yet commonly co-occur in runoff to duckweed-inhabited sites. We tested three L. minor genotypes with and without the culturable portion of their microbiome across field realistic gradients of salt (3 levels) and benzotriazole (4 levels) in a fully factorial experiment (72 treatments), and measured plant and microbial growth.Key ResultsWe found that stressors had conditional effects. Salt decreased both plant and microbial growth, but decreased plant survival more as benzotriazole concentrations increased. In contrast, benzotriazole did not affect microbial abundance, and benefited plants when salt and microbes were absent, perhaps due to the biotrans-formation we observed without salt. Microbes did not ameliorate duckweed stressors, as microbial inoculation increased plant growth, but not at high salt concentrations.ConclusionsOur results suggest that multistressor effects matter when predicting responses of mutualisms to global change, but that mutualisms may not buffer organisms from stressors.
Protein yield is tunable by synonymous codon changes of translation initiation sites
Authors: Bhandari Bikash K. , Lim Chun Shen , Remus Daniela M. , Chen Augustine , van Dolleweerd Craig , Gardner Paul P. 
Published: August 2019

ABSTRACTRecombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. To address this problem, we modified up to the first nine codons of messenger RNAs with synonymous substitutions and showed that protein levels can be tuned. These modifications alter the ‘accessibility’ of translation initiation sites. We also reveal the dynamics between accessibility, gene expression, and turnovers using a coarse-grained simulation.
Unraveling the genetic structure of the coconut scale insect pest (Aspidiotus rigidusReyne) outbreak populations in the Philippines
Authors: Serrana Joeselle M. , Ishitani Naoto , Carvajal Thaddeus M. , Almarinez Billy Joel M. , Barrion Alberto T. , Amalin Divina M. , Watanabe Kozo 
Published: August 2019

AbstractThe Philippines suffered from a devastating outbreak of the coconut scale insect pest,Aspidiotus rigidusReyne inflicting significant economic losses to the country’s coconut industry. Despite the massive outbreak, little is known about the population and dispersal history of this invasive pest in the Philippines. Here, we examined the genetic diversity, structure and demographic history ofA. rigidussampled from localities with reported outbreaks from 2014 to 2017. We analyzed the genetic structure of sevenA. rigidusoutbreak populations using mitochondrialCOIand nuclearEF-1α markers. Both markers and all methods of population genetic structure analyses indicate clear differentiation among theA. rigiduspopulations separating the northern (i.e., Luzon provinces) from the southern (i.e., Basilan and Zamboanga Peninsula) regions of the Philippines. Very low or no genetic differentiation was observed within and amongst the populations per geographic region indicating two unrelated outbreak events of the pest originating from two genetically uniform populations isolated in each respective region. Historical data supports the resurgence of an establishedA. rigiduspopulation in the south which could have been driven by sudden climatic changes or human-induced habitat imbalance. Given no historical information, we disregard the possible resurgence from the northern population and infer that the outbreak could have resulted from a recent introduction of a non-nativeA. rigidusin the region. Our study provides valuable information on the genetic differentiation of the twoA. rigidusgroups that would be useful for developing and implementing biological control strategies against this pest in the Philippines.
Polygenic and clinical risk scores and their impact on age at onset of cardiometabolic diseases and common cancers
Authors: Mars Nina J. , Koskela Jukka T. , Ripatti Pietari , Kiiskinen Tuomo T.J. , Havulinna Aki S. , Lindbohm Joni V. , Ahola-Olli Ari , Kurki Mitja , Karjalainen Juha , Palta Priit ,   FinnGen, Neale Benjamin M. , Daly Mark , Salomaa Veikko , Palotie Aarno , Widén Elisabeth , Ripatti Samuli 
Published: August 2019

ABSTRACTBackgroundPolygenic risk scores (PRS) have shown promise in predicting susceptibility to common diseases. However, the extent to which PRS and clinical risk factors act jointly and identify high-risk individuals for early onset of disease is unknown.MethodsWe used large-scale biobank data (the FinnGen study; n=135,300), with up to 46 years of prospective follow-up, and the FINRISK study with standardized clinical risk factor measurements to build genome-wide PRSs with >6M variants for coronary heart disease (CHD), type 2 diabetes (T2D), atrial fibrillation (AF), and breast and prostate cancer. We evaluated their associations with first disease events, age at disease onset, and impact together with routinely used clinical risk scores for predicting future disease.ResultsCompared to the 20-80thpercentiles, a PRS in the top 2.5% translated into hazard ratios (HRs) for incident disease ranging from 2.03 to 4.28 (p-values 1.96×10−59to <1.00×10−100) and the bottom 2.5% into HRs ranging from 0.20 to 0.61. The estimated difference in age at disease onset between top and bottom 2.5% of PRSs was 6 to 13 years. Among early-onset cases, 21.3-32.9% had a PRS in the highest decile and in CHD and AF.ConclusionsThe properties of PRS were similar in all five diseases. PRS identified a considerable proportion early-onset cases, and for all ages the performance of PRS was comparable to established clinical risk scores. These findings warrant further clinical studies on application of polygenic risk information for stratified screening or for guiding lifestyle and preventive medical interventions.
Uncoating of COPII from ER exit site membranes precedes cargo accumulation and membrane fission
Authors: Shomron Olga , Nevo-Yassaf Inbar , Aviad Tamar , Yaffe Yakey , Zahavi Eitan Erez , Dukhovny Anna , Perlson Eran , Brodsky Ilya , Yeheskel Adva , Pasmanik-Chor Metsada , Mironov Anna , Beznoussenko Galina V. , Mironov Alexander A. , Sklan Ella H. , Patterson George H. , Yonemura Yoji , Kaether Christoph , Hirschberg Koret 
Published: August 2019

SummaryCOPII and COPI are considered to be analogous sets of vesicle coat protein heterocomplexes. Coupled to cargo selection, they mediate the formation of membrane vesicles translocating in opposite directions to differ rent destinations within the secretory pathway. Here, live cell and electron microscopy provided evidence for a different localization and mode of function of the COPII coat during protein export from the endoplasmic reticulum (ER). Pharmaceutical and genetic perturbations of ER-Golgi transport were used to demonstrate that COPII is recruited to membranes defining the boundary of ER-ER Exit Sites (ERES) where it facilitates selective cargo concentration. Uncoating of COPII membranes precedes cargo accumulation and fission of Golgi-bound carriers. Moreover, we report what may be direct transfer of cargo to the Golgi apparatus from Golgi-associated BFA sensitive ERESs. Finally, in ldlF cells the stably expressed functional ε-COPI-EYFP labeled both ERESs and anterograde carriers. These findings change our understanding of the role of coat proteins in ER to Golgi transport.
Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow
Authors: Borrell James S. , Zohren Jasmin , Nichols Richard A. , Buggs Richard J. A. 
Published: August 2019

AbstractWhen populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide single nucleotide polymorphism (SNP) data we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA, and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.
Spatial and temporal variation in small mammal abundance and diversity under protection, pastoralism and agriculture in the Serengeti Ecosystem, Tanzania
Authors: Shilereyo Monica T. , Magige Flora J. , Ogutu Joseph O. , Røskaft Eivin 
Published: August 2019

AbstractLand use is an important factor influencing animal abundance, species richness and diversity in both protected and human-dominated landscapes. Increase in human population and activities intensify changes in habitat structure and hence abundance, species richness and diversity. We investigated the influences of land use and seasonality on small mammal abundance, species richness and diversity in 10 habitat types distributed over protected, agricultural and pastoral landscapes in the Serengeti ecosystem in Tanzania. We used live traps (n= 141) and capture-recapture methods in each of 10 fixed plots distributed across three landscapes for a total of 28,200 trap nights of effort. Trapping was carried out in the wet and dry seasons for two consecutive years (April 2017 to October 2018). Small mammal abundance was higher in the pastoral than in the protected and in the agricultural landscape. Abundance was higher in the dry than the wet season across all the three landscapes. Species richness and diversity were higher in the protected, middling in the agricultural and lowest in the pastoral landscape. The high abundance in the pastoral landscape was due to the numerical dominance of two species, namely A.niloticusin the shrubland andM. natalensisin the cropland habitat, resulting in low species richness and diversity. Abundance was more evenly distributed across all habitats in the protected area due to less disturbance. The low abundance in the agricultural landscape, likely reflects disturbance from cultivation. High species richness and diversity in the protected area indicate high habitat heterogeneity while high species diversity in the agricultural landscape was likely due to high food availability during and soon after harvests. These findings emphasize the importance of protection in maintaining habitat heterogeneity for wildlife. They also reaffirm the need for buffer zones around protected areas to cushion them from intensifying human activities.
Global genomic population structure of Clostridioides difficile
Authors: Frentrup Martinique , Zhou Zhemin , Steglich Matthias , Meier-Kolthoff Jan P. , Göker Markus , Riedel Thomas , Bunk Boyke , Spröer Cathrin , Overmann Jörg , Blaschitz Marion , Indra Alexander , von Müller Lutz , Kohl Thomas A. , Niemann Stefan , Seyboldt Christian , Klawonn Frank , Kumar Nitin , Lawley Trevor D. , García-Fernández Sergio , Cantón Rafael , del Campo Rosa , Zimmermann Ortrud , Groß Uwe , Achtman Mark , Nübel Ulrich 
Published: August 2019

AbstractClostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce EnteroBase, a publicly accessible database (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that the identification of highly related genomes is 89% consistent between cgMLST and single-nucleotide polymorphisms. EnteroBase currently contains 13,515 quality-controlled genomes which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. Hierarchical clustering can be used to identify populations of C. difficile at all epidemiological levels, from recent transmission chains through to pandemic and endemic strains, and is largely compatible with prior ribotyping. Hierarchical clustering thus enables comparisons to earlier surveillance data and will facilitate communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile.
Light might suppress both types of sound-evoked anti-predator flight in moths
Authors: Hügel Theresa , Goerlitz Holger R. 
Published: August 2019

ABSTRACTUrbanization exposes wild animals to increased levels of light, affecting particularly nocturnal animals. Artificial light at night might shift the balance of predator-prey interactions, for example of nocturnal echolocating bats and eared moths. Moths exposed to light show less last-ditch manoeuvres in response to attacking close-by bats. In contrast, the extent to which negative phonotaxis, moths’ first line of defence against distant bats, is affected by light is unclear. Here, we aimed to quantify the overall effect of light on both types of sound-evoked anti-predator flight, last-ditch manoeuvres and negative phonotaxis. We caught moths at two light traps, which were alternately equipped with loudspeakers that presented ultrasonic playbacks to simulate hunting bats. The light field was omnidirectional to attract moths equally from all directions. In contrast, the sound field was directional and thus, depending on the moth’s approach direction, elicited either only negative phonotaxis, or negative phonotaxis and last-ditch manoeuvres. We did not observe an effect of sound playback on the number of caught moths, suggesting that light might suppress both types of anti-predator flight, as either type would have caused a decline in the number of caught moths. As control, we confirmed that our playback was able to elicit evasive flight in moths in a dark flight room. Showing no effect of a treatment, however, is difficult. We discuss potential alternative explanations for our results, and call for further studies to investigate how light interferes with animal behaviour.
Developmental regulation of Canonical and small ORF translation from mRNAs
Authors: Patraquim Pedro , Mumtaz Muhammad Ali S. , Pueyo Jose I. , Aspden Julie L. , Couso J.P. 
Published: August 2019

ABSTRACTRibosomal profiling has revealed the translation of thousands of sequences outside of annotated protein-coding genes, including small Open Reading Frames of less than 100 codons, and the translational regulation of many genes. Here we have improved Poly-Ribo-Seq and applied it toDrosophila melanogasterembryos to extend the catalogue ofin-vivotranslated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis. We obtain highly correlated samples across five embryonic stages, with close to 500 million putative ribosomal footprints mapped to mRNAs, and compared them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time inDrosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation, and we propose a simple binomial probability metric to ascertain translation probability. However, our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5’ mRNA Leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal to zygotic transition. We suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding, and to defective ribosomal scanning of ORFs outside periods of productive translation. Finally, we show that the main function of upstream short ORFs is to buffer the translation of canonical ORFs, and that in general small ORFs in mRNAs display Poly-Ribo-Seq and bioinformatics markers compatible with an evolutionary transitory state towards full coding function.
Enhancement of the performance of bubble absorber using hybrid nanofluid as a cooled absorption system
Authors: Ben Jaballah Rawya , Ben Hamida Mohamed Bechir , Saleh Jehad , Almeshaal Mohammed A. 
Published: August 2019

Purpose
The purpose of this paper is to investigate the enhancement of the performance of bubble absorber using hybrid nanofluid as a cooled NH3/H2O absorption system to reduce their size and to find the best fitting model. A numerical model for ammonia-water bubble absorber was developed to show the influence of operating conditions and design parameters on the absorber performance.

Design/methodology/approach
A finite difference numerical method is used to solve the numerical model. The model is subjected to the inlet conditions of liquid, vapor and coolant flow regimes. The absorber modeling was divided into small elements along the absorber length.

Findings
The model proposed is validated with previously published works. Then agreement between the both is considered as good.

Research limitations/implications
Numerical results/The use of hybrid nanofluids.

Originality/value
The results showed that the hybrid nanofluid is the best cooling medium. Very high heat transfer rates are obtained because of the high thermal conductivity and specific heat of hybrid nanofluid, and consequently, the absorber size decreases. It was also found that the absorber thermal load and the mass absorption flux increase with increasing of solid volume fraction. Also, the existence of an optimal absorber length was revealed, required for complete absorption when using hybrid nanofluid as a cooling medium. It is recommended that using hybrid nanofluid to remove the heat from the absorber is the best candidate for NH3/H2O absorption performance enhancement.
Consumer acceptance toward takaful in Pakistan
Authors: Ali Muhammad , Raza Syed Ali , Puah Chin Hong , Amin Hanudin 
Published: August 2019

Purpose
The purpose of this paper is to determine the factors influencing customer adoption toward takaful products in Pakistan.

Design/methodology/approach
The study used five attributes of diffusion innovation theory (DOI), namely, relative advantage, compatibility, trialability, observability and complexity. Furthermore, the authors introduced two additional constructs, namely, consumer awareness and religiosity to analyze the adoption behavior of customers. A total of 365 questionnaires were distributed among the participants of the study. The survey was conducted in the Karachi city where the respondents were the existing and potential users of takaful products. The theoretical model of DOI theory was tested using structural equation modeling.

Findings
The findings report that complexity has a negative impact on the adoption of takaful, whereas relative advantage, compatibility, trialability, observability, religiosity and consumer awareness shows a positive and significant influence.

Originality/value
It is a noteworthy point that past literature is quite limited to investigate the determinants of consumer intentions to adopt takaful products. Based on this argument, the authors build the study to provide a scope and coverage in the field of Islamic insurance. The authors also expect that the research will encourage and provide a venue for forthcoming studies to help policy makers and academicians in this emerging business.