bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zymobacter palmaepyruvate decarboxylase is less efficient than that ofZymomonas mobilisfor ethanol production in metabolically engineeredSynechocystissp PCC6803
Authors: Quinn Lorraine , Armshaw Patricia , Soulimane Tewfik , Sheehan Con , Ryan Michael P , Pembroke J Tony 
Published: July 2019

AbstractPyruvate decarboxylase (PDC) fromZymobacter palmae(ZpPDC) has been reported to have a lower Km theZymomonas mobilisPDC (ZmPDC). ZpPDC was combined with nativeslr1192alcohol dehydrogenase (adh) in an attempt to increase ethanol production in the photoautotrophic cyanobacteriumSynechocystissp. PCC 6803 over constructs created with Zmpdc. Native (Zppdc) and codon optimised (ZpOpdc) versions of the ZpPDC were cloned into a construct where thepdcexpression was controlled via thepsbA2light inducible promoter fromSynechocystisPCC 6803. These constructs were transformed into wildtypeSynechocystisPCC 6803. Ethanol levels were then compared with identical constructs containing the Zmpdc. While strains with the Zppdc(UL071) and ZpOpdc(UL072) constructs did produce ethanol, levels were lower compared to a control strain (UL004) expressing thepdcfromZymomonas mobilis. The utilisation of a PDC with a lower Km fromZymobacter palmaedid not result in enhanced ethanol production inSynechocystisPCC 6803.
Rumen Bacteria and Serum Metabolites Predictive of Feed Efficiency Phenotypes in Beef Cattle
Authors: Clemmons Brooke A , Martino Cameron , Powers Joshua B , Campagna Shawn R , Voy Brynn H , Donohoe Dallas R. , Gaffney James , Embree Mallory M , Myer Phillip R 
Published: July 2019

AbstractThe rumen microbiome is critical in ruminant nutrition and contributes to nutrient utilization and feed efficiency in cattle. Therefore, the objective of this study was to interrogate microbial and biochemical factors affecting divergences in feed efficiency in Angus steers using 16S amplicon sequencing and untargeted metabolomics. Average residual feed intake (RFI) was calculated, and steers were divided into low- and high-RFI groups. Features were ranked in relation to RFI through supervised machine learning on microbial and metabolite compositions. Residual feed intake was associated with several attributes of the rumen bacterial community. Low-RFI steers were associated with decreased bacterial α- (P=0.03) and β-diversity (P<0.001). Several serum metabolites were associated with RFI. Based on fold change (high/low RFI), low-RFI steers had greater abundances of pantothenate (P=0.02). Machine learning on RFI was predictive of both serum metabolomic signature and rumen bacterial composition (AUC ≥0.7). Log-ratio proportions of the bacterial classes Flavobacteriia over Fusobacteriia were enriched in low-RFI steers (F=6.8, P=.01). Greater proportions of pantothenate-producing bacteria, such as Flavobacteriia, and/or reductions in Fusobacteriia may result in improved nutrient utilization in low-RFI steers. Pantothenate and Flavobacteriia may serve as potentially novel biomarkers to assess or predict feed efficiency in Angus steers.
Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity
Authors: Ngou Bruno Pok Man , Ahn Hee-Kyung , Ding Pingtao , Redkar Amey , Brown Hannah , Ma Yan , Youles Mark , Tomlinson Laurence , Jones Jonathan DG 
Published: July 2019

AbstractPlant nucleotide-binding domain, leucine-rich repeat receptor (NLR) proteins play important roles in recognition of pathogen-derived effectors. However, the mechanism by which plant NLRs activate immunity is still largely unknown. The paired Arabidopsis NLRs RRS1-R and RPS4, that confer recognition of bacterial effectors AvrRps4 and PopP2, are well studied, but how the RRS1/RPS4 complex activates early immediate downstream responses upon effector detection is still poorly understood. To study RRS1/RPS4 responses without the influence of cell-surface receptor immune pathways, we generated an Arabidopsis line with inducible expression of effector AvrRps4. Induction does not lead to hypersensitive cell death response (HR) but can induce electrolyte leakage, which often correlates with plant cell death. Activation of RRS1 and RPS4 without pathogens cannot activate mitogen-associated protein kinase cascades, but still activates upregulation of defense genes, and therefore resistance against bacteria.HighlightInducible expression of AvrRps4 activates RRS1/RPS4-mediated effector-triggered immunity without the presence of pathogens, allowing us to characterise downstream immune responses triggered by TIR-NLRs without cell-surface receptor-mediated immunity.
A Statistical Pipeline for Identifying Physical Features that Differentiate Classes of 3D Shapes
Authors: Wang Bruce , Sudijono Timothy , Kirveslahti Henry , Gao Tingran , Boyer Douglas M. , Mukherjee Sayan , Crawford Lorin 
Published: July 2019

AbstractThe recent curation of large-scale databases with 3D surface scans of shapes has motivated the development of tools that better detect global patterns in morphological variation. Studies which focus on identifying differences between shapes have been limited to simple pairwise comparisons and rely on pre-specified landmarks (that are often known). We present SINATRA: the first statistical pipeline for analyzing collections of shapes without requiring any correspondences. Our novel algorithm takes in two classes of shapes and highlights the physical features that best describe the variation between them. We use a rigorous simulation framework to assess our approach. Lastly, as a case study, we use SINATRA to analyze mandibular molars from four different suborders of primates and demonstrate its ability recover known morphometric variation across phylogenies.
Oxygen supply capacity in animals evolves to meet maximum demand at the current oxygen partial pressure regardless of size or temperature
Authors: Seibel Brad A. , Deutsch Curtis 
Published: July 2019

AbstractPhysiological oxygen supply capacity is associated with athletic performance and cardiovascular health and is thought to cause hypometabolic scaling in diverse species. Environmental oxygen is widely believed to be limiting of metabolic rate and aerobic scope, setting thermal tolerance and body size limits with implications for species diversity and biogeography. Here we derive a quantifiable linkage between maximum and basal metabolic rate and their temperature, size and oxygen dependencies. We show that, regardless of size or temperature, the capacity for oxygen supply precisely matches the maximum evolved demand at the highest persistently available oxygen pressure which, for most species assessed, is the current atmospheric pressure. Any reduction in oxygen partial pressure from current values will result in a decrement in maximum metabolic performance. However, oxygen supply capacity does not constrain thermal tolerance and does not cause hypometabolic scaling. The critical oxygen pressure, typically viewed as an indicator of hypoxia tolerance, instead reflects adaptations for aerobic scope. This simple new relationship redefines many important physiological concepts and alters their ecological interpretation.One sentence summary: Metabolism is not oxygen limited
Uncovering Photolyase/Cryptochrome Genes Diversity in Aquatic Microbiomes Exposed to Diverse UV-B Regimes
Authors: Alonso-Reyes Daniel G. , Farias Maria Eugenia , Albarracín Virginia Helena 
Published: July 2019

ABSTRACTDuring evolution, microorganisms exposed to high UV-B doses developed a fine-tuned photo-enzymes called “photolyases” to cope with DNA damage by UV-B. These photoreceptors belonging to the Cryptochrome/Photolyase Family (CPF) were well characterized at the genomic and proteomic level in bacteria isolated from a wide range of environments. In this work, we go further towards studying the abundance of CPF on aquatic microbial communities from different geographic regions across the globe. Metagenomics data combined with geo-referenced solar irradiation measurements indicated that the higher the UV-B dose suffered by the microbiome’s environment, the higher the abundance of CPF genes and lower the microbial diversity. A connection between CPF abundance and radiation intensity/photoperiod was reported. Likewise, cryptochrome-like genes were found abundant in most exposed microbiomes, indicating a complementary role to standard photolyases. Also, we observed that CPFs are more likely present in dominant taxa of the highly irradiated microbiomes, suggesting an evolutionary force for survival and dominance under extreme solar exposure. Finally, this work reported three novel CPF clades not identified so far, proving the potential of global metagenomic analyses in detecting novel proteins.
A reference library for the identification of Canadian invertebrates: 1.5 million DNA barcodes, voucher specimens, and genomic samples
Authors: deWaard Jeremy R. , Ratnasingham Sujeevan , Zakharov Evgeny V. , Borisenko Alex V. , Steinke Dirk , Telfer Angela C. , Perez Kate H.J. , Sones Jayme E. , Young Monica R. , Levesque-Beaudin Valerie , Sobel Crystal N. , Abrahamyan Arusyak , Bessonov Kyrylo , Blagoev Gergin , deWaard Stephanie L. , Ho Chris , Ivanova Natalia V. , Layton Kara K. S. , Lu Liuqiong , Manjunath Ramya , McKeown Jaclyn T.A. , Milton Megan A. , Miskie Renee , Monkhouse Norm , Naik Suresh , Nikolova Nadya , Pentinsaari Mikko , Prosser Sean W.J. , Radulovici Adriana E. , Steinke Claudia , Warne Connor P. , Hebert Paul D.N. 
Published: July 2019

AbstractThe reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet’s land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
Microarray Gene Expression Dataset Re-Analysis Reveals Variability in Influenza Infection and Vaccination
Authors: Rogers Lavida R. K. , de los Campos Gustavo , Mias George I. 
Published: July 2019

ABSTRACTInfluenza, a communicable disease, affects thousands of people worldwide. Young children, elderly, immunocompromised individuals and pregnant women are at higher risk for being infected by the influenza virus. Our study aims to highlight differentially expressed genes in influenza disease compared to influenza vaccination. We also investigate genetic variation due to the age and sex of samples. To accomplish our goals, we conducted a meta-analysis using publicly available microarray expression data. Our inclusion criteria included subjects with influenza, subjects who received the influenza vaccine and healthy controls. We curated 18 microarray datasets for a total of 3,481 samples (1,277 controls, 297 influenza infection, 1,907 influenza vaccination). We pre-processed the raw microarray expression data in R using packages available to pre-process Affymetrix and Illumina microarray platforms. We used a Box-Cox power transformation of the data prior to our down-stream analysis to identify differentially expressed genes. Statistical analyses were based on linear mixed effects model with all study factors and successive likelihood ratio tests (LRT) to identify differentially-expressed genes. We filtered LRT results by disease (Bonferroni adjusted p-value<0.05) and used a two-tailed 10% quantile cutoff to identify biologically significant genes. Furthermore, we assessed age and sex effects on the disease genes by filtering for genes with a statistically significant (Bonferroni adjusted p-value<0.05) interaction between disease and age, and disease and sex. We identified 4,889 statistically significant genes when we filtered the LRT results by disease factor, and gene enrichment analysis (gene ontology and pathways) included innate immune response, viral process, defense response to virus, Hematopoietic cell lineage and NF-kappa B signaling pathway. Our quantile filtered gene lists comprised of 978 genes each associated with influenza infection and vaccination. We also identified 907 and 48 genes with statistically significant (Bonferroni adjusted p-value<0.05) disease-age and disease-sex interactions respectively. Our meta-analysis approach highlights key gene signatures and their associated pathways for both influenza infection and vaccination. We also were able to identify genes with an age and sex effect. This gives potential for improving current vaccines and exploring genes that are expressed equally across ages when considering universal vaccinations for influenza.
Comparative analysis of intracellular and extracellular antibiotic resistance gene abundance in anaerobic membrane bioreactor effluent
Authors: Wang Phillip , Harb Moustapha , Zarei-Baygi Ali , Stadler Lauren B. , Smith Adam L. 
Published: July 2019

AbstractThe growing practice of wastewater reuse poses a significant risk to further dissemination of antibiotic resistance due to the abundance of antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) in wastewater effluents. Anaerobic membrane bioreactors (AnMBRs) are an emerging wastewater treatment technology capable of reducing the total ARGs and ARB load discharged to receiving environments compared to conventional aerobic treatment processes. While size exclusion is effective at retaining ARB and its associated intracellular ARGs, the abundance and fate of extracellular ARGs in an AnMBR effluent have not been examined. This study elucidates the effect of combined antibiotics loading (ampicillin, erythromycin, and sulfamethoxazole) on the abundance of intracellular and extracellular ARGs in an AnMBR effluent over a period of five weeks. Quantification of targeted genes revealed an overall enrichment of intracellular ARGs (iARGs) and depletion of extracellular (exARGs) in response to antibiotics addition, which suggests exARG uptake as a significant mode of horizontal gene transfer in AnMBR effluents. Comparison of the iARG and exARG abundance profiles showed a potential bias for exARG uptake located on small plasmids compared to large plasmids.ImportanceAntibiotic resistance dissemination is facilitated through horizontal gene transfer (HGT) of ARGs. Currently, conjugation is considered to be the dominant mechanism during wastewater treatment. However, recent studies have detected high abundances of exARGs, implying that transformation may play a greater role in dissemination. While previous studies quantified iARGs and exARGs in wastewater treatment facilities, they did not evaluate temporal changes between the two forms. Further, almost no research has differentiated between iARGs and exARGs in anaerobic processes, which are being considered to replace aerobic activated sludge processes. This study specifically investigates the abundance of targeted iARGs and exARGs in AnMBRs in response to antibiotic pressure to quantify potential exchange of ARGs between intracellular and extracellular compartments. Our findings suggest that exARGs located on small plasmids are preferentially taken up by cells under antibiotic pressure compared to large plasmids, which implies heterogenous HGT mechanisms among the plasmid community.
Brain network dynamics correlate with personality traits
Authors: Kabbara Aya , Paban Veronique , Weill Arnaud , Modolo Julien , Hassan Mahmoud 
Published: July 2019

AbstractIntroductionIdentifying the neural substrates underlying the personality traits is a topic of great interest. On the other hand, it is now established that the brain is a dynamic networked system which can be studied using functional connectivity techniques. However, much of the current understanding of personality-related differences in functional connectivity has been obtained through the stationary analysis, which does not capture the complex dynamical properties of brain networks.ObjectiveIn this study, we aimed to evaluate the feasibility of using dynamic network measures to predict personality traits.MethodUsing the EEG/MEG source connectivity method combined with a sliding window approach, dynamic functional brain networks were reconstructed from two datasets: 1) Resting state EEG data acquired from 56 subjects. 2) Resting state MEG data provided from the Human Connectome Project. Then, several dynamic functional connectivity metrics were evaluated.ResultsSimilar observations were obtained by the two modalities (EEG and MEG) according to the neuroticism, which showed a negative correlation with the dynamic variability of resting state brain networks. In particular, a significant relationship between this personality trait and the dynamic variability of the temporal lobe regions was observed. Results also revealed that extraversion and openness are positively correlated with the dynamics of the brain networks.ConclusionThese findings highlight the importance of tracking the dynamics of functional brain networks to improve our understanding about the neural substrates of personality.
Adult crowding induces sexual dimorphism in chronic stress-response inDrosophila melanogaster
Authors: Lall Shraddha , Mudunuri Akhila , Santhosh S. , Malwade Akshay , Thadi Aarcha , Kondakath Gayathri , Dey Sutirth 
Published: July 2019

ABSTRACTStress-induced mood disorders such as depression and anxiety are sexually dimorphic in human beings. Studying behavioural stress-responses in non-human animal models can help better understand the behavioural manifestations of these disorders and the dimorphism in their prevalence. Here we explore how sexes show differential behavioural responses to different chronic stressors, both abiotic and biotic, by using outbred populations ofDrosophila melanogaster. The behaviours studied – namely, anhedonia, motivation to explore a novel habitat, locomotor activity and sleep levels – have been well-investigated in human and rodent-based models of stress disorders. These behaviours were studied in the context of two different stressors – mechanical perturbation and adult crowding. Responses to stress were found to be sexually dimorphic, and stressed females showed more behavioural changes, such as a reduced motivation to explore a novel habitat. Furthermore, adult crowding caused a greater number of sexually dimorphic behavioural changes than mechanical perturbation. For instance, while mechanical perturbation caused anhedonia across sexes, only females were anhedonic after crowding. We thus make a case forDrosophila melanogasteras a model system for studying sexual dimorphism in stress-induced mood disorders in humans.SUMMARY STATEMENTFemale fruit flies, like their human counterparts, are more prone to chronic stress-induced mood disorders like anhedonia or reduced activity. This sexual dimorphism was more evident in a biotic stress.
Increased temperatures reduce the vectorial capacity ofAedesmosquitoes for Zika virus
Authors: Gorreti Onyango Maria , Sean Bialosuknia , Ann Payne , Nicholas Mathias , Lilli Kuo , Aurelien Vigneron , Matthew DeGennaro , Alexander T Ciota , Laura D Kramer 
Published: July 2019

AbstractRapid and significant range expansion of both ZIKV and itsAedeshost species has resulted in ZIKV being declared a global health threat. Mean temperatures are projected to increase globally, likely resulting in alterations of the transmission potential of mosquito-borne pathogens. The relationship between temperature and ZIKV transmission has not been well characterised forAedes aegyptiandAedes albopictus.To understand the effect of diurnal temperature range on the vectorial capacity ofAedes aegyptiandAedes albopictusfor ZIKV, factors contributing to transmission potential were measured at different temperature regimens. Their longevity and blood feeding rates were assessed, and vector competence was determined following feeding on blood meals with 8.3 log10PFU/ml ZIKV.Higher temperature resulted in decreased longevity ofAe. aegypti[Log-rank (Mantel-Cox) Test, Chi-square, df 35.66, 5 P (<0.0001)] and a significant decrease in blood feeding rates across groups [Z score (−5.8478) P (0.0444)]. Temperature had a population and species-specific impact on ZIKV infection rates. Overall,Ae. albopictusreared at the lowest temperature regimen demonstrated the highest vectorial capacity (1.63) and the highest transmission efficiency (57%). Temperature increases decreased vectorial capacity across groups, yet the largest decreases were measured forAe. aegypti.The results of this study suggest that future climate change could significantly impact vector competence, blood feeding behavior and longevity, and therefore decrease the overall vectorial capacity ofAedesmosquitoes. It is also clear that this impact is likely to be both species and population-specific.
RNAPosers: Machine Learning Classifiers For RNA-Ligand Poses
Authors: Chhabra Sahil , Xie Jingru , Frank Aaron T. 
Published: July 2019

ABSTRACTDetermining the 3-dimensional (3D) structures of ribonucleic acid (RNA)-small molecule complexes is critical to understanding molecular recognition in RNA. Computer docking can, in principle, be used to predict the 3D structure of RNA-small molecule complexes. Unfortunately, retrospective analysis has shown that the scoring functions that are typically used to rank poses tend to misclassify non-native poses as native, andvice versa. This misclassification of non-native poses severely limits the utility of computer docking in the context pose prediction, as well as in virtual screening. Here, we use machine learning to train a set of pose classifiers that estimate the relative “nativeness” of a set of RNA-ligand poses. At the heart of our approach is the use of a pose “fingerprint” that is a composite of a set of atomic fingerprints, which individually encode the local “RNA environment” around ligand atoms. We found that by ranking poses based on the classification scores from our machine learning classifiers, we were able to recover native-like poses better than when we ranked poses based on their docking scores. With a leave-one-out training and testing approach, we found that one of our classifiers could recover poses that were within 2.5 Å of the native poses in ∼80% of the 88 cases we examined, and similarly, on a separate validation set, we could recover such poses in ∼70% of the cases. Our set of classifiers, which we refer to as RNAPosers, should find utility as a tool to aid in RNA-ligand pose prediction and so we make RNAPosers open to the academic community viahttps://github.com/atfrank/RNAPosers.