bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of elevated branched chain amino acids in the potent effects of vertical sleeve gastrectomy to reduce weight and improve glucose regulation in mice
Authors: Kramer Nadejda Bozadjieva , Evers Simon S. , Shin Jae Hoon , Silverwood Sierra , Wang Yibin , Burant Charles F. , Sandoval Darleen A. , Seeley Randy J. 
Published: June 2020

AbstractObesity and type 2 diabetes mellitus (T2D) are growing epidemics resulting in increased morbidity and mortality. An emerging body of evidence has shown that elevated levels of branched-chain amino acids (BCAA) and their metabolites are strongly positively associated with obesity, insulin-resistance and T2D. Bariatric surgery is among the best treatments for weight loss and the alleviation of T2D. Additionally, clinical studies have reported that bariatric surgery decreases the circulating levels of BCAA. The objective of these studies was to test the hypothesis that reduced BCAA levels contribute to the metabolic improvements after VSG. We find that, as in humans, circulating BCAA levels are significantly lower in VSG rats and mice compared to Sham controls. In order to increase circulating BCAA levels, we tested mice with either increased dietary intake of BCAA or impaired BCAA catabolism by total body deletion of mitochondrial phosphatase 2C, Pp2cm, a key enzyme in the rate-limiting step in BCAA catabolism. Our results show that a decrease in circulating BCAA levels is not necessary for sustained body weight loss and improved glucose tolerance after VSG. While it is clear that circulating levels of BCAAs are excellent biomarkers for metabolic status, the current data do not support a causal role in determining metabolic regulation and the response to VSG.
Characterization of small molecule induced changes in Parkinson’s-related trafficking via the Nedd4 ubiquitin signaling cascade
Authors: Hatstat A. Katherine , Ahrendt Hannah D. , Foster Matthew W. , Mayne Leland , Moseley M. Arthur , Englander S. Walter , McCafferty Dewey G. 
Published: June 2020

SummaryThe benzdiimidazole NAB2 rescues α-synuclein-associated trafficking defects associated with early onset Parkinson’s disease in a Nedd4-dependent manner. Despite identification of E3 ubiquitin ligase Nedd4 as a putative target of NAB2, its molecular mechanism of action has not been elucidated. As such, the effect of NAB2 on Nedd4 activity and specificity was interrogated through biochemical, biophysical, and proteomic analyses. NAB2 was found to bind Nedd4 (KDapp= 42 nM), but this binding is side chain mediated and does not alter its conformation or ubiquitination kineticsin vitro. Nedd4 co-localizes with trafficking organelles, and NAB2 exposure did not alter its colocalization. Ubiquitin-enrichment coupled proteomics revealed that NAB2 stimulates ubiquitination of trafficking and transport associated proteins, most likely through modulating the substrate specificity of Nedd4, providing a putative protein network involved in the NAB2 mechanism.
Diversity analysis of amp gene sequences in the ‘CandidatusPhytoplasma meliae’
Authors: Fernández Franco D. , Conci Luis R. 
Published: June 2020

AbstractPhytoplasmas are plant pathogenic bacteria transmitted by insects. As endosymbiotic bacteria that lack a cell wall, their membrane proteins are in direct contact with host cytoplasm. In phytoplasmas the immunodominant membrane proteins (IDPs), are the most abundant proteins of the cell membrane. The antigenic membrane protein (Amp), one of the three types of IDPs, is characterized by a positive selection pressure acting in their extracellular domain. In South America, the ‘CandidatusPhytoplasma meliae’ has been associated to chinaberry yellows disease. In the present work, we describe for the first time the structure, phylogeny and selection pressure of amp gene in sixteen ‘CandidatusPhytoplasma meliae’ isolates. Our results indicate that amp gene sequences preserve the structure, large extracellular domain flanked by to hydrophobic domains in the N- (signal peptide) and C-termini (transmembrane), previously described in its orthologues and high divergence in the amino acids residues from extracellular domain. Moreover, a positive selection pressure was detected predominantly in this region confirming previous reports.
ICOS signaling limits regulatory T cell accumulation and function in visceral adipose tissue
Authors: Mittelsteadt Kristen L. , Hayes Erika T. , Campbell Daniel J. 
Published: June 2020

AbstractA unique population of Foxp3+regulatory T cells (TR) resides in visceral adipose tissue (VAT) that regulates adipose inflammation and helps preserve insulin sensitivity. The costimulatory molecule ICOS is highly expressed on effector (e)TRthat migrate to nonlymphoid tissues, and contributes to their maintenance and function in models of autoimmunity. In this study, we report an unexpected cell-intrinsic role for ICOS expression and downstream PI3K signaling in limiting the abundance, VAT-associated phenotype, and function of TRspecifically in VAT.Icos−/−mice and mice expressing a knock-in form of ICOS that cannot activate PI3K had increased VAT-TRabundance and elevated expression of canonical VAT-TRmarkers. Loss of ICOS signaling facilitated enhanced accumulation of TRto VAT associated with elevated CCR3 expression, and resulted in reduced adipose inflammation and heightened insulin sensitivity in the context of high-fat diet. Thus, we have uncovered a new and surprising molecular pathway that regulates VAT-TRaccumulation and function.SummaryThe authors demonstrate that loss of ICOS-dependent PI3-kinase signaling supports visceral adipose tissue (VAT) TRabundance and function, and this correlates with reduced adipose inflammation and improved insulin sensitivity after high-fat diet. This work highlights a new molecular pathway that regulates VAT-TRaccumulation and activity.
Binding of DNA origami to lipids: maximising yield and switching via strand-displacement
Authors: Daljit Singh Jasleen Kaur , Darley Es , Ridone Pietro , Gaston James P , Abbas Ali , Wickham Shelley FJ , Baker Matthew AB 
Published: June 2020

ABSTRACTLiposomes are widely used as synthetic analogues of cell membranes and for drug delivery. Lipid-binding DNA nanostructures can modify the shape, porosity and reactivity of liposomes, mediated by cholesterol-modifications. DNA nanostructures can also be designed to switch conformations by DNA strand displacement. However, the optimal conditions to facilitate stable, high-yield DNA-lipid binding while allowing controlled switching by strand-displacement are not known. Here we characterised the effect of cholesterol arrangement, DNA structure, buffer and lipid composition on DNA-lipid binding and strand displacement. We observed that binding was inhibited below pH 4, and above 200 mM NaCl or 40 mM MgCl2, was independent of lipid type, and increased with membrane cholesterol content. For simple motifs, binding yield was slightly higher for double-stranded DNA than single-stranded. For larger DNA origami tiles, 4 – 8 cholesterol modifications were optimal, while edge positions and longer spacers increased yield of lipid-binding. Strand displacement achieved controlled removal of DNA tiles from membranes, but was inhibited by overhang domains, which are used to prevent cholesterol aggregation. These findings provide design guidelines for integrating strand-displacement switching with lipid-binding DNA nanostructures. This paves the way for achieving dynamic control of membrane morphology, enabling broader applications in nanomedicine and biophysics.
Collecting large datasets of rotational electron diffraction with ParallEM and SerialEM
Authors: Takaba Kiyofumi , Maki-Yonekura Saori , Yonekura Koji 
Published: June 2020

AbstractA semi-automated protocol has been developed for rotational data collection of electron diffraction patterns by combined use of SerialEM and ParallEM, where SerialEM is used for positioning of sample crystals and ParallEM for rotational data collection. ParallEM calls standard camera control software through an AutoIt script, which adapts to software operational changes and to new GUI programs guiding other cameras. Development included periodic flashing and pausing of data collection during overnight or day-long recording with a cold field-emission beam. The protocol proved to be efficient and accurate in data collection of large-scale rotational series from two JEOL electron microscopes, a general-purpose JEM-2100 and a high-end CRYO ARM 300. Efficiency resulted from simpler steps and task specialization. It is possible to collect 12–20 rotational series from ∼ −68º to ∼ 68º at a rotation speed of 1º /s in one hour without human supervision.
Characterizing and Forecasting Emergency Department Visits Related to COVID-19 Using Chief Complaints and Discharge Diagnoses
Authors: Koshute Phillip , Holtry Rekha , Wojcik Richard , Loschen Wayne , Lewis Sheri 
Published: June 2020

AbstractIn response to the unprecedented public health challenge posed by the SARS CoV-2 virus (COVID-19) in the United States, we and our colleagues at the Johns Hopkins University Applied Physics Laboratory (JHU/APL) have developed a model of COVID-19 progression using emergency department (ED) visit data from the National Capital Region (NCR). We obtained ED visits counts through targeted queries of the NCR Electronic Surveillance System for the Early Notification of Community-Based Epidemics (ESSENCE). To focus on ED visits by COVID-19 patients, we adjusted the query results for typical ED visit volumes and for reductions in ED volumes due to COVID-19 precautions. With these ED visit data, we fitted a logistic growth model to characterize and forecast the increase in cumulative COVID-19 ED visits. Our model achieves the best fit when we assume that the first NCR visit occurred in early January. We estimate that approximately 15,000 COVID-19 ED visits occurred prior to May 2020 and that approximately 17,000 more visits will occur in subsequent months. We plan to deploy an operational pilot of this model in the NCR ESSENCE environment, assisting local public health authorities as they brace for a second wave of COVID-19. Additionally, we will iteratively assess potential model refinements, aiming to maximize our model’s relevance for local public health authorities’ situational awareness and decision-making.
Ramularia leaf spot disease of barley is highly host genotype-dependent and suppressed by continuous drought stress in the field
Authors: Hoheneder Felix , Hofer Katharina , Groth Jennifer , Herz Markus , Heß Michael , Hückelhoven Ralph 
Published: June 2020

AbstractSince the 1980s, Ramularia leaf spot (RLS) is an emerging barley disease world-wide. The control of RLS is increasingly aggravated by a recent decline in fungicide efficacy and a lack of RLS-resistant cultivars. Furthermore, climate change increases drought periods in Europe, enhances variable weather conditions and thus will have an impact on severity of plant diseases. Hence, identification of RLS-resistant cultivars and understanding of disease progression under abiotic stress are important aims in integrated disease management under climate change. In the present study, we evaluated quantitative RLS resistance of 15 spring barley genotypes under drought, controlled irrigation and field conditions between 2016 and 2019 and monitored microclimatic conditions within the canopy. We identified genotypes that show robust quantitative resistance to RLS in different field environments. Our findings suggest that long-lasting drought periods create unfavourable conditions for the disease and supports that the extent and duration of leaf wetness is a key factor for RLS epidemics.
Optimizing nucleic acid extraction and transcriptome evaluation from low-input, fixed clinical samples
Authors: Campbell Katie M. , Medina Egmidio , Carretero Ignacio Baselga , Teper Yaroslav , Elumalai Rangasamy , Miller Raymond , Pal Kasturi , Pitzer Jessica , Daviso Eugenio , Carstens Carsten , Laugharn James , Hugo Willy , Chen Jia Ming , Vega-Crespo Agustin , Jilani Sameeha , Garcilazo Ivan Perez , Dong Ling , Li Xinmin , Hu-Lieskovan Siwen , Ribas Antoni 
Published: June 2020

AbstractTumor biopsies are commonly formalin-fixed and paraffin-embedded (FFPE) for long-term and efficient storage. However, FFPE preservation can greatly compromise the quality of samples, the extraction of nucleic acids, and feasibility of downstream studies, including RNA sequencing. These challenges are especially evident in the studies of clinical trial samples, where the sizes of biopsies often limit the amount of material available for study. Here, we evaluate two nucleic acid extraction kits (Covaris truXTRAC FFPE tNA Plus, QIAGEN miRNeasy FFPE) and three hybridized-capture-based RNA sequencing library preparations (Agilent SureSelect XT RNA Direct, Agilent SureSelect XT HS, and Illumina TruSeq RNA Exome) to evaluate the impact of these sample processing steps on transcriptome evaluation in a melanoma biopsy procured in a clinical setting and preserved by FFPE. While there exist many options for extraction and library preparation that are appropriate for RNA sequencing from FFPE samples, we observed that combinations of experimental approaches may have subtle impacts on downstream analysis, including gene expression quantification and fusion detection.
Pleiotropy allows recovery of phenotypic plasticity in constant environments
Authors: Kingma Enzo , Diepeveen Eveline T. , de la Cruz Leila Iñigo , Laan Liedewij 
Published: June 2020

AbstractPhenotypic plasticity confers a fitness advantage to an organism by tailoring phenotype to environmental circumstances. The extent to which phenotypic plasticity emerges as an adaptive response is still unknown, however it is predicted that the emergence and maintenance of phenotypic plasticity occurs only during evolution in fluctuating environments. Interestingly, experimental studies have shown that phenotypic plasticity can be preserved for several generations during evolution in a constant environment. Here, we evolve a mutant strain ofSaccharomyces cerevisiaethat has reduced plasticity in a constant and fluctuating environment. Subsequently we compared the adaptive response of the evolved cell, both at the phenotype and genotype level. As predicted by current theory, we find that evolution in a fluctuating environment results in a recovery of phenotypic plasticity. Surprisingly, evolution in a constant environment can lead to a similar recovery of plasticity due to a pleiotropic coupling of different traits. Thus, plasticity can emerge in both fluctuating and constant environments and its prevalence may mainly be determined by network structure. In addition, pleiotropic interactions may be an important structural component of biological networks that can facilitate the recovery of phenotypic plasticity without the requirement to continuously encounter environmental fluctuations.
Adaptive evolution of phenotypic switching during environmental change
Authors: Trivedi Urvish , Rebsdorf Maria R. , Cueva Angel R. , Rumbaugh Kendra P. , Burmølle Mette , Sørensen Søren J. , Madsen Jonas S. 
Published: June 2020

AbstractMicrobes are faced with environmental fluctuations and it is therefore important to understand how change affects bacterial evolution and population dynamics. Here, we evolved a model bacterium,Pseudomonas aeruginosaPA14, under both constant and changing conditions where settlement by biofilm formation or migration by swimming motility was induced. In changing environments, a heterogeneous population evolved with both specialists and generalists. Interestingly, over time, generalists were outcompeted despite being better at both phenotypes compared to the ancestor. However, generalists became dominant when faced with local competition after resettlement. Reintroduction into a burn wound model, the environment PA14 originally was isolated from, further suggested a tradeoff between niche breadth and peak fitness in agreement with the evolution experiments. Mutations in the c-di-GMP system were key for adaptation of the phenotypes. No mutants lost their ability to regulate c-di-GMP, but generalists acquired mutations that optimized their phenotypic response by efficiently adjusting c-di-GMP levels.
Comprehensive and Integrated Genomic Characterization of Human Immunome in Cancer
Authors: Li Yongsheng , Triplett Todd , Burgman Brandon , Sun Ming , McGrail Daniel J. , Qi Dan , Shukla Sachet , Wu Erxi , Wu Catherine J. , Capasso Anna , Eckhardt S. Gail , Georgiou George , Li Bo , Sahni Nidhi , Yi S. Stephen 
Published: June 2020

AbstractGenetic alterations in immune-related pathways are common hallmarks of cancer. However, to realize the full potential of immunotherapy, a comprehensive understanding of immune networks and how mutations impact network structure and functional output across cancer types is instrumental. Herein we systematically interrogated somatic mutations that could express neoantigens and alter immune responses in cancer patients compared to wild-type controls. To do so, we developed a network-based immunogenomics model (NIPPER) with scoring systems to prioritize critical genes and mutations eliciting differential HLA binding affinity and alternate responses to immunotherapy. These mutations are enriched in essential protein domains and often alter tumor infiltration by immune cells, affecting T cell receptor repertoire and B cell clonal expansion. Furthermore, we devised an interactome network propagation framework integrated with drug associated gene signatures to identify potential immunomodulatory drug candidates. Together, our systems-level analysis results help interpret the heterogeneous immune responses among patients, and serve as a resource for future functional studies and targeted therapeutics.SignificanceCancer cells induce specific immune-related pathway perturbations by mutations, transcriptional dysregulation, and integration of multi-omics data can help identify critical molecular determinants for effective targeted therapeutics.
Circadian clock neurons maintain phase control over daily behavioral activity patterns under diverse environmental conditions
Authors: Lorber Clara , Stanewsky Ralf , Lamaze Angélique 
Published: June 2020

AbstractProper timing of rhythmic locomotor behavior is the consequence of integrating environmental conditions and internal time within the circadian clock. The 150 clock neurons in theDrosophila melanogasterbrain are organized in various clusters, controlling different aspects of the daily activity rhythms. For example, during regular 12 hr light : 12 hr dark cycles at constant temperature (LD), so called Morning (M) neurons control the activity peak in the morning, while Evening (E-) neurons regulate the activity increase at the end of the day. During the remaining times of day and night, flies are inactive, giving rise to the crepuscular behavior observed in LD. Here, we investigate if the same neuronal groups also control behavioral activity under very different environmental conditions of constant light and temperature cycles (LLTC). While the morning activity is completely absent in LLTC, a single pronounced activity peak occurs at the end of the thermophase. We show that the same E-neurons operating in LD, also regulate the evening peak in LLTC. Interestingly, neuronal activity of E-neurons is inversely correlated with behavioral activity, suggesting an inhibitory action on locomotion. Surprisingly, the E-cells responsible for synchronization to temperature cycles belong to the clock neurons containing the circadian photoreceptor Cryptochrome, previously suggested to be more important for synchronization to LD. Our results therefore support a more deterministic function of the different clock neuronal subgroups, independent of specific environmental conditions.Significance statementMaster circadian clocks in the brains of mammals and fruit fly are composed of neurons expressing varying types of neuropeptides and transmitters. This diversity along with anatomical differences indicate diverse functions of different clock neurons. InDrosophila, so-called Morning (M) and Evening (E) neurons control locomotor activity at the respective time of day during normal day/night (LD) cycles. Recent reports point to a certain degree of plasticity with regard to circadian clock neuron function, depending on specific environmental conditions. Here we show that one neuronal group, the E-neurons, instead behave as if hard-wired to their output targets. Surprisingly they direct activity to occur during the evening both under LD conditions, as well as during temperature cycles in constant light.
Promiscuous esterases counterintuitively are less flexible than specific ones
Authors: Nutschel Christina , Coscolín Cristina , Mulnaes Daniel , David Benoit , Ferrer Manuel , Jaeger Karl-Erich , Gohlke Holger 
Published: June 2020

AbstractUnderstanding mechanisms of promiscuity is increasingly important from a fundamental and application point of view. As to enzyme structural dynamics, more promiscuous enzymes generally have been recognized to also be more flexible. However, examples for the opposite received much less attention. Here, we exploit comprehensive experimental information on the substrate promiscuity of 147 esterases tested against 96 esters together with computationally efficient rigidity analyses to understand the molecular origin of the observed promiscuity range. Unexpectedly, our data reveal that promiscuous esterases are significantly less flexible than specific ones, are significantly more thermostable, and have a significantly increased specific activity. These results may be reconciled with a model according to which structural flexibility in the case of specific esterases serves for conformational proofreading. Our results signify that esterase sequence space can be screened by rigidity analyses for promiscuous esterases as starting points for further exploration in biotechnology and synthetic chemistry.
Temperature restriction in entomopathogenic bacteria
Authors: Hapeshi Alexia , Healey Joseph R.J. , Mulley Geraldine , Waterfield Nicholas R. 
Published: June 2020

AbstractTemperature plays an important role in bacteria-host interactions and can be a determining factor for host switching. In this study we sought to investigate the reasons behind growth temperature restriction in the entomopathogenic enterobacteriumPhotorhabdus. Photorhabdushas a complex dual symbiotic and pathogenic life cycle. The genus consists of 19 species but only one subgroup, previously all classed together asP. asymbiotica, have been shown to cause human disease. These clinical isolates necessarily need to be able to grow at 37 °C, whilst the remaining species are largely restricted to growth temperatures below 34 °C and are therefore unable to infect mammalian hosts. Here, we have isolated spontaneous mutant lines ofP. laumondiiDJC that were able to grow up to 36 °C-37 °C. Following whole genome sequencing of 29 of these mutants we identified a single gene, encoding a protein with a RecG-like helicase domain, that for the majority of isolates contained single nucleotide polymorphisms. Importantly, provision of the wild-type allele of this gene intransrestored the temperature restriction, confirming the mutations are recessive, and the dominant effect of the protein product of this gene. The gene appears to be part of a short three cistron operon, which we have termed the Temperature Restricting Locus (TRL). Transcription reporter strains revealed that this operon is induced upon the switch from 30 °C to 37 °C, leading to replication arrest of the bacteria. TRL is absent from all of the human pathogenic species so far examined, although its presence is not uniform in different strains of theP. luminescenssubgroup. In a wider context, the presence of this gene is not limited toPhotorhabdus, being found in phylogenetically diverse proteobacteria. We therefore suggest that this system may play a more fundamental role in temperature restriction in diverse species, relating to as yet cryptic aspects of their ecological niches and life cycle requirements.