bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiac metabolic imaging using hyperpolarized [1-13C]lactate as a substrate
Authors: Lau Angus Z , Chen Albert P , Cunningham Charles H 
Published: December 2020

AbstractHyperpolarized [1-13C]lactate is an attractive alternative to [1-13C]pyruvate as a substrate to investigate cardiac metabolism in vivo; it can be administered safely at a higher dose and can be polarized to a similar degree as pyruvate via dynamic nuclear polarization. While13C cardiac experiments using HP lactate have been performed in small animal models, it has not been demonstrated in large animal models or humans. Utilizing the same hardware and data acquisition methods used in the first human HP13C cardiac study, 13C metabolic images were acquired following injections of HP [1-13C]lactate in porcine hearts. Data were also acquired using HP [1-13C]pyruvate for comparison. The13C bicarbonate signal was localized to the myocardium and had a similar appearance with both substrates for all animals. No13C pyruvate signal was detected in the experiments following injection of hyperpolarized13C lactate. The SNR of injected lactate was 88 +/-14% of the SNR of injected pyruvate, and the SNR of bicarbonate in the experiments using lactate as the substrate was 52+/-19% of the SNR in the experiments using pyruvate as the substrate. The lower SNR was likely due to the shorter T1 of [1-13C]lactate as compared to [1-13C]pyruvate and the additional enzyme-catalyzed metabolic conversion step before the 13C nuclei from [1-13C]lactate were detected as13C bicarbonate. While challenges remain, the potential of HP lactate as a substrate for clinical metabolic imaging of human heart was demonstrated.
Assessing bird collisions in the United Kingdom: Modelling frequency of bird-strike from road and rail mortality using a Bayesian hierarchical approach
Authors: Freire Silvia , Read Lee , Lewis Todd R. 
Published: December 2020

AbstractRoads are an important way to transport people and goods, but they sometimes have negative impacts on wildlife. One of the leading causes of mortality for several species is identified as road strikes, and the most significant remains bird-vehicle collisions. This study aimed to investigate what species of birds are most affected, and what other factors impact in their susceptibility in road collisions, such as age, sex, season, and type of transports. A total of N=5413 records, and 140 bird species were documented by BTO ringers. For analysis four Bayesian Hierarchical Models were used, with random effects results showing that Barn owls were most affected by collisions. Road mortality presents the highest cause of mortality among species when contrasted with rail mortality. Age and sexual bias was detected across all species, however juveniles and males did appear to be prominent in relation to other age classes. Winter and early spring were the months with most reported casualties and 2016 had lower abundance of mortality across the 10-year period. 75% of birds were found within a week, which may indicate some bias interference from scavenging animals, as true figures could be up to 16 times more. This study discusses some mitigation measures found in current research, that could dramatically reduce numbers of birds affected each year by road mortality.
Harnessing Colon Chip technology to identify commensal bacteria that promote host tolerance to infection
Authors: Gazzaniga Francesca S. , Camacho Diogo M. , Wu Meng , Palazzo Matheus , Dinis Alexandre , Grafton Francis N. , Cartwright Mark J. , Super Michael , Kasper Dennis L. , Ingber Donald E. 
Published: December 2020

ABSTRACTCommensal bacteria within the gut microbiome contribute to development of host tolerance to infection, however, identifying specific microbes responsible for this response is difficult. Here we describe methods for developing microfluidic organ-on-a-chip models of small and large intestine lined with epithelial cells isolated from duodenal, jejunal, ileal, or colon organoids derived from wild type or transgenic mice. To focus on host-microbiome interactions, we carried out studies with the mouse Colon Chip and demonstrated that it can support co-culture with living gut microbiome and enable assessment of effects on epithelial adhesion, tight junctions, barrier function, mucus production, and cytokine release. Moreover, infection of the Colon Chips with the pathogenic bacterium,Salmonella typhimurium, resulted in epithelial detachment, decreased tight junction staining, and increased release of cytokines (CXCL1, CXCL2, and CCL20) that closely mimicked changes previously seen in mice. Symbiosis between microbiome bacteria and the intestinal epithelium was also recapitulated by populating Colon Chips with complex living mouse or human microbiome. By taking advantage of differences in the composition between complex microbiome samples cultured on each chip using 16s sequencing, we were able to identifyEnterococcus faeciumas a positive contributor to host tolerance, confirming past findings obtained in mouse experiments. Thus, mouse Intestine Chips may represent new experimentalin vitroplatforms for identifying particular bacterial strains that modulate host response to pathogens, as well as for investigating the cellular and molecular basis of host-microbe interactions.
Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations
Authors: He Guanglin , Liu Jing , Wang Mengge , Zou Xing , Ming Tianyue , Zhu Sumin , Yeh Hui-Yuan , Wang Chuanchao , Wang Zheng , Hou Yiping 
Published: December 2020

AbstractAncestry informative markers (AIMs), which are distributed throughout the human genome, harbor significant allele frequency differences among diverse ethnic groups. The use of sets of AIMs to reconstruct population history and genetic relationships is attracting interest in the forensic community, because biogeographic ancestry information for a casework sample can potentially be predicted and used to guide the investigative process. However, subpopulation ancestry inference within East Asia remains in its infancy due to a lack of population reference data collection and incomplete validation work on newly developed or commercial AIM sets. In the present study, 316 Chinese persons, including 85 Sinitic-speaking Haikou Han, 120 Qiongzhong Hlai and 111 Daozhen Gelao individuals belonging to Tai-Kadai-speaking populations, were analyzed using the Precision ID Ancestry Panel (165 AISNPs). Combined with our previous 165-AISNP data (375 individuals from 6 populations), the 1000 Genomes Project and forensic literature, comprehensive population genetic comparisons and ancestry inference were further performed via ADMIXTURE, TreeMix, PCA,f-statistics and N-J tree. Although several nonpolymorphic loci were identified in the three southern Chinese populations, the forensic parameters of this ancestry inference panel were better than those for the 23 STR-based Huaxia Platinum System, which is suitable for use as a robust tool in forensic individual identification and parentage testing. The results based on the ancestry assignment and admixture proportion evaluation revealed that this panel could be used successfully to assign individuals at a continental scale but also possessed obvious limitations in discriminatory power in intercontinental individuals, especially for European-Asian admixed Uyghurs or in populations lacking reference databases. Population genetic analyses further revealed five continental population clusters and three East Asian-focused population subgroups, which is consistent with linguistic affiliations. Ancestry composition and multiple phylogenetic analysis further demonstrated that the geographically isolated Qiongzhong Hlai harbored a close phylogenetic relationship with Austronesian speakers and possessed a homogenous Tai-Kadai-dominant ancestry, which could be used as the ancestral source proxy in population history reconstruction of Tai-Kadai-speaking populations and as one of the representatives for forensic database establishment. In summary, more population-specific AIM sets focused on East Asian subpopulations, comprehensive algorithms and high-coverage population reference data should be developed and validated in the next step.
Genomics of altitude-associated wing shape in two tropical butterflies
Authors: Montejo-Kovacevich Gabriela , Salazar Patricio A. , Smith Sophie H. , Gavilanes Kimberly , Bacquet Caroline N. , Chan Yingguang Frank , Jiggins Chris D. , Meier Joana I. , Nadeau Nicola J. 
Published: December 2020

AbstractUnderstanding how organisms adapt to their local environment is central to evolution. With new whole-genome sequencing technologies and the explosion of data, deciphering the genomic basis of complex traits that are ecologically relevant is becoming increasingly feasible. Here we study the genomic basis of wing shape in two Neotropical butterflies that inhabit large geographical ranges.Heliconiusbutterflies at high elevations have been shown to generally have rounder wings than those in the lowlands. We reared over 1100 butterflies from 71 broods ofH. eratoandH. melpomenein common-garden conditions and show that wing aspect ratio, i.e. elongatedness, is highly heritable in both species and elevation-associated wing shape differences are maintained. Genome-wide associations with a published dataset of 666 whole genomes from across a hybrid zone, uncovered a highly polygenic basis to wing shape variation in the wild. We identify several genes that have roles in wing morphogenesis or wing shape variation inDrosophilaflies, making them promising candidates for future studies. There was little evidence for molecular parallelism in the two species, with only one shared candidate gene, nor for a role of the four known colour pattern loci, except foroptixinH. erato. Thus, we present the first insights into the heritability and genomic basis of within-species wing shape in twoHeliconiusspecies, adding to a growing body of evidence that polygenic adaptation may underlie many ecologically relevant traits.
Functional maps of the primate cortex revealed by through-skull wide-field optical imaging
Authors: Song Xindong , Guo Yueqi , Li Hongbo , Chen Chenggang , Schmidt Zachary , Wang Xiaoqin 
Published: December 2020

ABSTRACTThe primate cerebral cortex is organized into specialized areas representing different functional modalities (e.g., vision, audition, touch) and their associations along a continuous surface. The functional maps of these areas, however, are often investigated in a single modality at a time. Here, we developed and applied to awake primates a polarization-enhanced wide-field optical imaging method for measuring cortical hemodynamics through the intact skull. Adjacent somatosensory, auditory, and visual cortices were noninvasively localized and rapidly parcellated in awake marmosets (Callithrix jacchus), a primate model featuring a smooth cortex. Detailed somatotopy, tonotopy, and retinotopy were also mapped out on an individual-subject basis, with a new pure-tone-responsive tonotopic gradient discovered outside the auditory core. Moreover, the motion-sensitive extent surrounding the primate-specific MT/V5 and the location of a face-sensitive patch were both revealed with respect to retinotopy. This approach provides a powerful tool for mapping the functional landscape across modalities in a single non-human primate subject, and thus opens new opportunities for probing how primate cortical system is organized to enable real-world behaviors.
Ucp2-dependent microglia-neuronal coupling controls ventral hippocampal circuit function and anxiety-like behavior
Authors: Yasumoto Yuki , Stoiljkovic Milan , Kim Jung Dae , Sestan-Pesa Matija , Gao Xiao-Bing , Diano Sabrina , Horvath Tamas L. 
Published: December 2020

AbstractMicroglia have been implicated in synapse remodeling by phagocytosis of synaptic elements in the adult brain. However, the underlying mechanism of such process is ill-defined. By examining microglia-neuronal interaction in the ventral hippocampus, we found a significant reduction in spine synapse number during the light phase of the light/dark cycle accompanied by increased microglial phagocytosis. This was followed by a transient rise in microglial production of reactive oxygen species (ROS) and uncoupling protein 2 (Ucp2) expression, which is a regulator of mitochondrial ROS generation. Conditional ablation of microglialUcp2hindered phasic elimination of spine synapses, increased accumulations of ROS and lysosome-lipid droplet complexes leading to hippocampal circuitry disruption assessed by electrophysiology, and, altered anxiety-like behavior. These observations unmasked a novel and chronotypical interaction between microglia and neurons involved in control of brain functions.
Marine Bacteria Associated with the Green SeaweedUlvasp. for the Production of Polyhydroxyalkanoates
Authors: Gnaim Rima , Polikovsky Mark , Unis Razan , Sheviryov Julia , Gozin Michael , Golberg Alexander 
Published: December 2020

AbstractThe biosynthesis of polyhydroxyalkanoate (PHA) biopolymers from certain marine microbes, associated with green macroalgaeUlvasp., has attracted significant attention. TheUlvasp. is abundant biomass in numerous locations around the world and could be easily cultivated by marine farming. The variety of sugars found inUlvasp. homogenate could be used as a carbon source for microbial growth and PHA production. In this work, we isolated and explored a series of bacterial strains that function as potential producers of P(3HB), utilizing a range of common sugars found inUlvasp. Analysis of 16S rDNA gene-sequence revealed that the PHA-producing bacteria were phylogenetically related to species of the genusCobetia, Bacillus, Pseudoaltermonas, andSulfito-bacter. The highest-yield of P(3HB) was observed in the case of newCobetiastrain,C. amphilecti, with up to 61% (w/w) in the presence of mannitol and 12% (w/w) onUlvasp. acid hydrolysate as a substrate.
Whole Genome Sequencing for Revealing the Point Mutations of SARS-CoV-2 Genome in Bangladeshi Isolates and their Structural Effects on Viral Proteins
Authors: Hossain Mohammad Uzzal , Ahammad Ishtiaque , Hossain Emon Md. Tabassum , Bhattacharjee Arittra , Chowdhury Zeshan Mahmud , Mosaib Md. Golam , Das Keshob Chandra , Keya Chaman Ara , Salimullah Md. 
Published: December 2020

AbstractCoronavirus disease-19 (COVID-19) is the recent global pandemic caused by the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The virus has already killed more than one million people worldwide and billions are at risk of getting infected. As of now, there is neither any drug nor any vaccine in sight with conclusive scientific evidence that it can cure or provide protection against the illness. Since novel coronavirus is a new virus, mining its genome sequence is of crucial importance for drug/vaccine(s) development. Whole genome sequencing is a helpful tool in identifying genetic changes that occur in a virus when it spreads through the population. In this study, we performed complete genome sequencing of SARS-CoV-2 to unveil the genomic variation and indel, if present. We discovered thirteen (13) mutations in Orf1ab, S and N gene where seven (7) of them turned out to be novel mutations from our sequenced isolate. Besides, we found one (1) insertion and seven (7) deletions from the indel analysis among the 323 Bangladeshi isolates. However, the indel did not show any effect on proteins. Our energy minimization analysis showed both stabilizing and destabilizing impact on viral proteins depending on the mutation. Interestingly, all the variants were located in the binding site of the proteins. Furthermore, drug binding analysis revealed marked difference in interacting residues in mutants when compared to the wild type. Our analysis also suggested that eleven (11) mutations could exert damaging effects on their corresponding protein structures. The analysis of SARS-CoV-2 genetic variation and their impacts presented in this study might be helpful in gaining a better understanding of the pathogenesis of this deadly virus.
A Grad-seq view of RNA and protein complexes inPseudomonas aeruginosaunder standard and bacteriophage predation conditions
Authors: Gerovac Milan , Wicke Laura , Chihara Kotaro , Schneider Cornelius , Lavigne Rob , Vogel Jörg 
Published: December 2020

ABSTRACTThe Gram-negative rod-shaped bacteriumPseudomonas aeruginosais not only a major cause of nosocomial infections but also serves as a model species of bacterial RNA biology. While its transcriptome architecture and post-transcriptional regulation through the RNA-binding proteins Hfq, RsmA and RsmN have been studied in detail, global information about stable RNA–protein complexes is currently lacking in this human pathogen. Here, we implement Gradient profiling by sequencing (Grad-seq) in exponentially growingP. aeruginosacells to comprehensively predict RNA and protein complexes, based on glycerol gradient sedimentation profiles of >73% of all transcripts and ∼40% of all proteins. As to benchmarking, our global profiles readily reported complexes of stable RNAs ofP. aeruginosa, including 6S RNA with RNA polymerase and associated pRNAs. We observe specific clusters of non-coding RNAs, which correlate with Hfq and RsmA/N, and provide a first hint thatP. aeruginosaexpresses a ProQ-like FinO domain containing RNA-binding protein. To understand how biological stress may perturb cellular RNA/protein complexes, we performed Grad-seq after infection by the bacteriophage ΦKZ. This model phage, which has a well-defined transcription profile during host takeover, displayed efficient translational utilization of phage mRNAs and tRNAs, as evident from their increased co-sedimentation with ribosomal subunits. Additionally, Grad-seq experimentally determines previously overlooked phage-encoded non-coding RNAs. Taken together, thePseudomonasprotein and RNA complex data provided here will pave the way to a better understanding of RNA-protein interactions during viral predation of the bacterial cell.IMPORTANCEStable complexes by cellular proteins and RNA molecules lie at the heart of gene regulation and physiology in any bacterium of interest. It is therefore crucial to globally determine these complexes in order to identify and characterize new molecular players and regulation mechanisms. Pseudomonads harbour some of the largest genomes known in bacteria, encoding ∼5,500 different proteins. Here, we provide a first glimpse on which proteins and cellular transcripts form stable complexes in the human pathogenPseudomonas aeruginosa. We additionally performed this analysis with bacteria subjected to the important and frequently encountered biological stress of a bacteriophage infection. We identified several molecules with established roles in a variety of cellular pathways, which were affected by the phage and can now be explored for their role during phage infection. Most importantly, we observed strong co-localization of phage transcripts and host ribosomes, indicating the existence of specialized translation mechanisms during phage infection. All data are publicly available in an interactive and easy to use browser.
Global elongation and high shape flexibility as an evolutionary hypothesis of accommodating mammalian brains into skulls
Authors: Weisbecker Vera , Rowe Timothy , Wroe Stephen , Macrini Thomas E. , Garland Kathleen L. S. , Travouillon Kenny J. , Black Karen , Archer Michael , Hand Suzanne J. , Berlin Jeri , Beck Robin M.D. , Ladevèze Sandrine , Sharp Alana C. , Mardon Karine , Sherratt Emma 
Published: December 2020

AbstractLittle is known about how the large brains of mammals are accommodated into the dazzling diversity of their skulls. It has been suggested that brain shape is influenced by relative brain size, that it evolves or develops according to extrinsic or intrinsic mechanical constraints, and that its shape can provide insights into its proportions and function. Here, we characterise the shape variation among 84 marsupial cranial endocasts of 57 species including fossils, using 3D geometric morphometrics and virtual dissections. Statistical shape analysis revealed four main patterns: over half of endocast shape variation ranges between elongate and straight to globular and inclined; little allometric variation with respect to centroid size, and none for relative volume; no association between locomotion and endocast shape; limited association between endocast shape and previously published histological cortex volumes. Fossil species tend to have smaller cerebral hemispheres. We find divergent endocast shapes in closely related species and within species, and diverse morphologies superimposed over the main variation. An evolutionarily and individually malleable brain with a fundamental tendency to arrange into a spectrum of elongate-to-globular shapes – possibly mostly independent of brain function - may explain the accommodation of brains within the enormous diversity of mammalian skull form.
Genetically Engineered Proportional-Integral Feedback Controllers for Robust Perfect Adaptation in Mammalian Cells
Authors: Frei T. , Chang C.-H. , Filo M. , Arampatzis A. , Khammash M. 
Published: December 2020

AbstractTo support their survival, cells adapt to environmental disturbances by maintaining a constant internal milieu. Robust perfect adaptation is a strategy that utilizes integral feedback to promote adaptation by robustly driving regulated physiological variables to their pre-disturbance levels. Present in natural systems, this stringent regulatory strategy promises to enable the engineering of sophisticated genetic programs with diverse applications. Here, we present the first synthetic implementations of integral and proportional-integral feedback controllers in mammalian cells. We show that the integral controller robustly and precisely maintains a desired level of a transcription factor, in spite of induced disturbances and network perturbations. Augmenting proportional feedback reduces stochastic variability while maintaining robust perfect adaptation. We demonstrate the benefits of these controllers in mitigating the impact of resource burden and investigate their use in cell therapy. The synthetic biological realization of robust perfect adaptation holds promise for substantial advances in industrial biotechnology and cell-based therapies.
The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
Authors: Gomes-dos-Santos André , Lopes-Lima Manuel , Machado André M. , Ramos António Marcos , Usié Ana , Bolotov Ivan N. , Vikhrev Ilya V. , Breton Sophie , Castro L. Filipe C. , da Fonseca Rute R. , Geist Juergen , Österling Martin E. , Prié Vincent , Teixeira Amílcar , Gan Han Ming , Simakov Oleg , Froufe Elsa 
Published: December 2020

AbstractSince historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2,4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species’ unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.