bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glucose uptake in mammalian cells measured by ICP-MS
Authors: Norman Natalie J. , Ghali Joyce , Radzyukevich Tatiana L. , Heiny Judith A. , Landero-Figueroa Julio 
Published: October 2021

ABSTRACTWe developed a sensitive, ratiometric method to measure simultaneously 13C-labeled glucose and rubidium in biological samples using ICP-MS. The method uses probe-assisted ultra-sonication with water to extract 13C-[6C]-labeled-D-glucose and other polar analytes from mammalian tissues. It extracts >80% of the reference value for Rb and >95 % of 13C in a CRM spiked with 13C-[6C]-labeled-D-glucose in the micro-molar range. Using optimized instrument conditions, the method achieves a stable 13C/12C signal without spectral interferences. The 13C/12C signal is independent of sample composition and depends linearly on the concentration of 13C-[6C]-labeled-D-glucose in spiked samples. Overall, the method achieves a limit of detection of 10 µM for 6-C-labeled 13C glucose in biological tissues. This detection capability for carbon in biological matrices by ICP-MS opens a wider range of applications for ICP-MS in biomedical research. As proof-of-principle, we combined 13C detection with the multi-channel capability of ICP-MS to measure glucose and rubidium uptake in the same contracting skeletal muscles. Multi-isotope detection is needed to study many biological processes, including coupled membrane transport. These results demonstrate a capability for carbon detection by ICP-MS that can significantly advance studies of complex biological processes that require multi-isotope detection.
Hunting the plant surrender signal activating apoplexy in grapevines after Neofusicoccum parvum infection
Authors: Khattab Islam M. , Fischer Jochen , Kaźmierczak Andrzej , Thines Eckhard , Nick Peter 
Published: October 2021

SummaryApoplectic breakdown from Grapevines Trunk Diseases (GTDs) has become a serious challenge to viticulture in consequence to drought stress. We hypothesise that fungal aggressiveness is controlled by a chemical communication between host and colonising fungus.We introduce the new concept of a “plant surrender signal” accumulating in host plants under stress and triggering aggressive behaviour of the strain Neofusicoccum parvum (Bt-67) causing Botryosphaeriaceae-related dieback in grapevines.Using a cell-based experimental system (Vitis cells) and bioactivity-guided fractionation, we identify trans-ferulic acid, a monolignol precursor, as “surrender signal”. We show that this signal specifically activates secretion of the fungal phytotoxin Fusicoccin A. We show further that this phytotoxin, mediated by 14-3-3 proteins, activates programmed cell death in Vitis cells.We arrive at a model pinpointing the chemical communication driving apoplexy in Botryosphaeriaceae-Vitis interaction and define the channelling of phenylpropanoid pathway from the lignin precursor, trans-ferulic acid to the phytoalexin transresveratrol as target for future therapy.
Sex Differences in Cortical Morphometry during Ageing: Examining the Interplay between Lifestyle and Reproductive Factors
Authors: Costantino Manuela , Bussy Aurélie , Pigeau Grace , Blostein Nadia , Devenyi Gabriel A. , Markello Ross D. , Patel Raihaan , Gervais Nicole , Chakravarty M. Mallar 
Published: October 2021

AbstractSex differences in neurodegenerative disorder prevalence have been attributed to life expectancy, modifiable risk factors related to lifestyle and the impact of changes in sex hormones and the reproductive system. Although these factors are known to interact with one another, they are often studied in isolation. Here, we used a multivariate approach to investigate how lifestyle, along with menopause and the number of children, interacts with cortical thickness (CT) in healthy adults. Using CT measures from T1-weighted scans (MPRAGE, 1 mm3voxels; 124 participants; 67 females; 40-70 years old) from the Cam-CAN dataset. Using a partial least squares decomposition, we identified patterns of covariance between CT and lifestyle factors, menopause and the number of children. In women, we identified significant patterns that linked education, socioeconomic status, social contact and length of reproductive period to CT in the left prefrontal cortex, as well as alcohol consumption, physical activity and menopausal status to CT in the frontal poles. Contrastingly, the results in men were driven by education and anxiety, and involved increased CT in the temporal poles. Our findings suggests that sex differences in cortical anatomy during brain ageing might be driven by interactions between contrasting lifestyles and the female-specific endocrine environment.
Shared and distinct genetic features in human and canine B-cell lymphomas
Authors: Coyle Krysta M , Hillman Tiana , Cheung Matthew , Grande Bruno M. , Bushell Kevin R. , Arthur Sarah E. , Alcaide Miguel , Thomas Nicole , Dreval Kostiantyn , Wong Stephanie , Campbell Krishanna , Morin Ryan D. 
Published: October 2021

ABSTRACTAnimal models of human cancers are an important tool for the development and preclinical evaluation of therapeutics. Canine B-cell lymphoma (cBCL) is an appealing model for human mature B-cell neoplasms due to the high sequence similarity in cancer genes to humans and inactive telomerase in adult tissues. We performed targeted sequencing on 86 canine patients from the Canine Comparative Oncology Genomic Consortium, with 61 confirmed as B-cell lymphomas. We confirmed a high frequency of mutations in TRAF3 (45%) and FBXW7 (20%) as has been reported by our group and others. We also note a higher frequency of DDX3X (20%) and MYC (13%) mutations in our canine cohort.We compared the pattern and incidence of mutations in cBCL to human diffuse large B-cell lymphoma (hDLBCL) and human Burkitt lymphoma (hBL). Canine MYC mutations displayed a focal pattern with 80% of mutations affecting the conserved phosphodegron sequence in MYC box 1, which are known to stabilize MYC protein. We also note that MYC and FBXW7 mutations do not co-occur in our cBCL cohort, leading to the hypothesis that these mutations represent alternative approaches to stabilize MYC in canine lymphoma.We observed striking differences in the pattern of DDX3X mutations in canine lymphoma as compared to hBL and uncovered a sex-specific pattern of DDX3X mutations in hBL that is not consistent with those identified in canine lymphomas.In sum, we describe key differences between cBCL and human mature B-cell lymphomas which may indicate differences in the biology of these cancers. This should be considered in future studies of cBCL as a model of human lymphomas.
Dietary super-doses of cholecalciferol fed to aged laying hens illustrates limitation of 24,25-dihydroxycholecalciferol conversion
Authors: Warren Matthew F. , Pitman Pete M. , Hodgson Dellila D. , Thompson Nicholas C. , Livingston Kimberly A. 
Published: October 2021

ABSRACTBackgroundOlder humans who take high levels of vitamin D supplementation for a prolonged time may be at risk of vitamin D toxicity. It is unclear how dietary super-doses (10,000x greater than requirement) can affect vitamin D status in aged animals. Aged laying hens could be a model to compare vitamin D supplementation effects with women in peri-or postmenopausal stages of life.ObjectiveWe investigated dietary super-dose impacts of cholecalciferol (vitamin D3) on vitamin D status in aged laying hens in production.MethodsForty-eight 68 wk old Hy-Line Brown laying hens were individually housed in cages with eight hens per dietary treatment for eleven weeks. Hens were randomly assigned to one of six treatment groups of dietary vitamin D3supplementation and fedad libitum. Supplementation levels were 400, 800, 7,400, 14,000, 20,000, and 36,000 IU D3/kg of feed. At the end of the study, all hens were euthanized and tissue samples and feces were collected. Plasma and egg yolk vitamin D metabolites, calcium and phosphorus composition of multiple sites, and tissue gene expression levels were measured.ResultsWe observed that increasing dietary vitamin D3increased plasma vitamin D3and egg yolk vitamin D3(p < 0.0001 for both sites). We also observed an increase in plasma 24,25-dihydroxycholecalciferol as dietary vitamin D3levels increased (p < 0.0001). The plasma 25-hydroxycholecalciferol:24,25-dihydroxycholecalciferol ratio exhibited an asymptotic relationship starting at the 14,000 IU/kg D3treatment.ConclusionsDietary super-doses of vitamin D3led to greater plasma and egg yolk vitamin D levels to show that aged laying hens can deposit excess vitamin D in egg yolk. We suggest future research should explore how 24-hydroxylation mechanisms are affected by vitamin D supplementation. Further understanding of 24-hydroxylation can help ascertain ways to reduce risk of vitamin D toxicity.
Dysfunctional temporal stages of eye-gaze perception in adults with ADHD: a high-density EEG study
Authors: Mauriello Cheyenne , Pham Eleonore , Kumar Samika , Piguet Camille , Deiber Marie-Pierre , Aubry Jean-Michel , Dayer Alexandre , Michel Christoph M. , Perroud Nader , Berchio Cristina 
Published: October 2021

AbstractADHD have been associated with social cognitive impairments across the lifespan, but no studies have specifically addressed the presence of abnormalities in eye-gaze processing in the adult brain.This study investigated the neural basis of eye-gaze perception in adults with ADHD using event-related potentials (ERP). Twenty-three ADHD and 23 controls performed a delayed face-matching task with neutral faces that had either direct or averted gaze. ERPs were classified using microstate analyses.ADHD and controls displayed similar P100 and N170 microstates. ADHD was associated with cluster abnormalities in the attention-sensitive P200 to direct gaze, and in the N250 related to facial recognition. For direct gaze, source localization revealed reduced activity in ADHD for the P200 in the left/midline cerebellum, as well as in a cingulate-occipital network at the N250. These results suggest brain impairments involving eye-gaze decoding in adults with ADHD, suggesting that neural deficits persist across the lifespan.
Methods for analyzing continuous conformational variability of biomolecules in cryo electron subtomograms: HEMNMA-3D vs. traditional classification
Authors: Harastani Mohamad , Jonic Slavica 
Published: October 2021

AbstractCryogenic electron tomography (cryo-ET) allows studying biological macromolecular complexes in cells by three-dimensional (3D) data analysis. The complexes continuously change their shapes (conformations) to achieve biological functions. The shape heterogeneity in the samples imaged in the cryo electron microscope is a bottleneck for comprehending biological mechanisms and developing drugs. Low signal-to-noise ratio and spatial anisotropy (missing wedge artefacts) make cryo-ET data particularly challenging for resolving the shape variability. Other shape variability analysis techniques simplify the problem by considering discrete rather than continuous conformational changes of complexes. Recently, HEMNMA-3D was introduced for cryo-ET continuous shape variability analysis, based on elastic and rigid-body 3D registration between simulated shapes and cryo-ET data. The simulated motions are obtained by normal mode analysis of a high- or low-resolution 3D reference model of the complex under study. The rigid-body alignment is achieved via fast rotational matching with missing wedge compensation. HEMNMA-3D provides a visual insight into molecular dynamics by grouping and averaging subtomograms of similar shapes and by animating movies of registered motions. This article reviews the method and compares it with existing literature on a simulated dataset for nucleosome shape variability.
Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa trees reveal evolutionary mechanisms of longevity
Authors: Chakraborty Abhisek , Mahajan Shruti , Bisht Manohar Singh , Sharma Vineet K. 
Published: October 2021

ABSTRACTFicus benghalensis (Indian banyan tree) and Ficus religiosa (Peepal) trees are well-known for their long lifespan, traditional significance, and medicinal properties. Therefore, to understand the genomic and evolutionary aspect of these characteristics the whole genomes of these two Ficus species were sequenced using 10x Genomics and Oxford Nanopore sequencing platforms. The draft genome assemblies of F. benghalensis (392.89 Mbp genome containing 25,016 high-confidence coding genes), and F. religiosa (332.97 Mbp genome containing 23,929 high-confidence coding genes) were constructed. We also established the genome-wide phylogenetic position of the two Ficus trees with respect to 46 other Angiosperm plant species and studied the comparative population demographic history of these two species to show a population bottleneck event ~0.8 Mya for both the species. We also identified 7,468 orthogroups across 16 phylogenetically closer Eudicot plant species including F. benghalensis and F. religiosa. Comparative evolutionary analyses using these orthogroups, gene family expansion/contraction analysis, and gene duplication analysis showed adaptive evolution in genes involved in cellular pathways and mechanisms that are central to plant growth and development and provide genomic insights into longevity and ecological significance of these large woody trees.
Stable modulation of neuronal oscillations produced through brain-machine equilibrium
Authors: McNamara Colin G. , Rothwell Max , Sharott Andrew 
Published: October 2021

AbstractBrain stimulation is predominantly delivered independent of ongoing activity, whereas closed-loop systems can modify activity through interaction. They have the unrealised potential to continuously bind external stimulation to specific dynamics of a neural circuit. Such manipulations are particularly suited to rhythmic activities, where neuronal activity is organised in oscillatory cycles. Here, we developed a fast algorithm that responds on a cycle-by-cycle basis to stimulate basal ganglia nuclei at predetermined phases of successive cortical beta cycles in parkinsonian rats. Using this approach, we demonstrate a stable brain-machine interaction. An equilibrium emerged between the modified brain signal and feedback-dependent stimulation pattern, which led to sustained amplification or suppression of the oscillation. Sustained beta amplification slowed movement speed by altering the mode of locomotion. Integrating an external stimulus with network activity in this way could be used to correct maladaptive activities and to define the role of oscillations in fundamental brain functions.
Impact of IgG isotype on the induction of antibody-dependent cellular phagocytosis of HIV by human milk leukocytes
Authors: Fox Alisa , Liu Xiaomei , Zolla-Pazner Susan , Powell Rebecca L. 
Published: October 2021

AbstractApproximately 100,000 mother-to-child transmission (MTCT) events of HIV via human milk feeding occur each year (1). However, only about 15% of infants milk-fed by untreated HIV+ mothers become infected, suggesting a protective effect of the milk itself (1, 2). Infants ingest 105-108 maternal leukocytes daily via milk, which remain functional beyond ingestion (3–9). Such function may be elicited by maternal milk antibody (Ab). Though IgA is dominant in milk, most HIV-specific milk Abs are of the IgG subclass, highlighting the importance of investigating the function of each IgG isotype in the milk context (10–16). Though Ab effector function mediated by the constant (Fc) domain via interaction with Fc Receptors (FcRs), such as Ab-dependent cellular phagocytosis (ADCP), are critical in protecting against HIV infection, ADCP is largely unexplored as it relates to mitigation of MTCT (17–21). Presently we report the ADCP activity of milk leukocytes against HIV particles and immune complexes (ICs), using 57 unique samples from 34 women, elicited by IgG1/2/3/4 of monoclonal (m)Ab 246-D. Granulocyte ADCP of HIV was most potent compared to other phagocytes when elicited by IgG1/3/4. IgG1/3 activated granulocytes similarly, exhibiting 1.6x-4.4x greater activity compared to IgG2/4, and a preference for virus compared to ICs. Notably, CD16-monocyte ADCP of a given target were unaffected by isotype, and CD16+ monocytes were poorly stimulated by IgG1. IgG2/4 elicited potent IC ADCP, and in terms of total leukocyte IC ADCP, IgG4 and IgG3 exhibited similar function, with IgG4 eliciting 1.6x-2.1x greater activity compared to IgG1/IgG2, and CD16+ monocytes most stimulated by IgG2. These data contribute to a more comprehensive understanding of Fc-mediated functionality of milk leukocytes, which is critical in order to develop therapeutic approaches to eliminating this route of MTCT, including mucosal administration of mAbs and/or a maternal vaccination aimed to elicit a potent milk Ab response.
Using a Homeogram to Detect Sleep in Free-living Animals
Authors: Gaidica Matt , Studd Emily , Wishart Andrea E , Gonzalez William , Lane Jeffrey E , McAdam Andrew G , Boutin Stan , Dantzer Ben 
Published: October 2021

AbstractSleep is appreciated as a behavior critical to homeostasis, performance, and fitness. Yet, most of what we know about sleep comes from humans or controlled laboratory experiments. Assessing sleep in wild animals is challenging, as it is often hidden from view, and electrophysiological recordings that define sleep states are difficult to obtain. Accelerometers have offered great insight regarding gross movement, although ambiguous quiescent states like sleep have been largely ignored, limiting our understanding of this ubiquitous behavior.We developed a broadly applicable sleep detection method called a homeogram that can be applied to accelerometer data collected from wild animals. We applied our methodology to detect sleep in free-ranging North American red squirrels (Tamiasciurus hudsonicus) in a region that experiences drastic seasonal shifts in light, temperature, and behavioral demands.Our method characterized sleep in a manner consistent with limited existing studies and expanded those observations to provide evidence that red squirrels apply unique sleep strategies to cope with changing environments.Applying our analytical strategy to accelerometer data from other species may open new possibilities to investigate sleep patterns for researchers studying wild animals.
Stimulus-dependent orientation strategies in monarch butterflies
Authors: Franzke Myriam , Kraus Christian , Gayler Maria , Dreyer David , Pfeiffer Keram , Jundi Basil el 
Published: October 2021

AbstractInsects are well-known for their ability to keep track of their heading direction based on a combination of skylight cues and visual landmarks. This allows them to navigate back to their nest, disperse throughout unfamiliar environments, as well as migrate over large distances between their breeding and non-breeding habitats. The monarch butterfly (Danaus plexippus) for instance is known for its annual southward migration from North America to certain trees in Central Mexico. To maintain a constant flight route, these butterflies use a time-compensated sun compass for orientation which is processed in a region in the brain, termed the central complex. However, to successfully complete their journey, the butterflies’ brain must generate a multitude of orientation strategies, allowing them to dynamically switch from sun-compass orientation to a tactic behavior toward a certain target. To study if monarch butterflies exhibit different orientation modes and if they can switch between them, we observed the orientation behavior of tethered flying butterflies in a flight simulator while presenting different visual cues to them. We found that the butterflies’ behavior depended on the presented visual stimulus. Thus, while a dark stripe was used for flight stabilization, a bright stripe was fixated by the butterflies in their frontal visual field. If we replaced a bright stripe by a simulated sun stimulus, the butterflies switched their orientation behavior and exhibited compass orientation. Taken together, our data show that monarch butterflies rely on and switch between different orientation modes, allowing them to adjust orientation to the actual behavioral demands of the animal.
Intrinsic maturation of sleep output neurons regulates sleep ontogeny in Drosophila
Authors: Gong Naihua N. , Dang An H. , Mainwaring Benjamin , Shields Emily , Schmeckpeper Karl , Bonasio Roberto , Kayser Matthew S. 
Published: October 2021

AbstractThe maturation of sleep behavior across a lifespan (sleep ontogeny) is an evolutionarily conserved phenomenon. Mammalian studies have shown that in addition to increased sleep duration, early life sleep exhibits stark differences compared to mature sleep with regard to the amount of time spent in certain sleep states. How intrinsic maturation of sleep output circuits contributes to sleep ontogeny is poorly understood. The fruit fly Drosophila melanogaster exhibits multifaceted changes to sleep from juvenile to mature adulthood. Here, we use a non-invasive probabilistic approach to investigate changes in sleep architecture in juvenile and mature flies. Increased sleep in juvenile flies is driven primarily by a decreased probability of transitioning to wake, and characterized by more time in deeper sleep states. Functional manipulations of sleep-promoting neurons in the dFB suggest these neurons differentially regulate sleep in juvenile and mature flies. Transcriptomic analysis of dFB neurons at different ages and a subsequent RNAi screen implicate genes involved in distinct molecular processes in sleep control of juvenile and mature flies. These results reveal that dynamic transcriptional states of sleep output neurons contribute to changes in sleep across the lifespan.
A Genomic Perspective on the Evolutionary Diversification of Turtles
Authors: Gable Simone M. , Byars Michael I. , Literman Robert , Tollis Marc 
Published: October 2021

ABSTRACTTo examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa. Our results suggest that gene tree-species tree discordance in these datasets is likely driven by population-level processes such as incomplete lineage sorting. We found very little effect of substitutional saturation on species tree topologies, and no clear phylogenetic patterns in codon usage bias and compositional heterogeneity. There was no correlation between gene and site concordance, node age, and DNA substitution rate across most annotated genomic regions. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible in order to obtain accurate phylogenies for assessing conservation priorities in turtles.