bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optogenetic control of protein binding using light-switchable nanobodies
Authors: Gil Agnieszka A. , Zhao Evan M. , Wilson Maxwell Z. , Goglia Alexander G. , Carrasco-Lopez Cesar , Avalos José L. , Toettcher Jared E. 
Published: August 2019

AbstractA growing number of optogenetic tools have been developed to control binding between two engineered protein domains. In contrast, relatively few tools confer light-switchable binding to a generic target protein of interest. Such a capability would offer substantial advantages, enabling photoswitchable binding to endogenous target proteins in vivo or light-based protein purification in vitro. Here, we report the development of opto-nanobodies (OptoNBs), a versatile class of chimeric photoswitchable proteins whose binding to proteins of interest can be enhanced or inhibited upon blue light illumination. We find that OptoNBs are suitable for a range of applications: modulating intracellular protein localization and signaling pathway activity and controlling target protein binding to surfaces and in protein separation columns. This work represents a first step towards programmable photoswitchable regulation of untagged, endogenous target proteins.HighlightsOpto-Nanobodies (OptoNBs) enable light-regulated binding to a wide range of protein targets.We identify an optimized LOV domain and two loop insertion sites for light-regulated binding.OptoNBs function in vivo: when expressed in cells and fused to signaling domains, OptoNBs enable light-activated and light-inhibited Ras/Erk signaling.OptoNBs function in vitro: Target proteins can be reversibly bound to OptoNB-coated beads and separated through size-exclusion chromatography.
Prolonged tonic pain in healthy humans disrupts intrinsic brain networks implicated in pain modulation
Authors: Meeker Timothy J. , Schmid Anne-Christine , Keaser Michael L. , Khan Shariq A. , Gullapalli Rao P. , Dorsey Susan G. , Greenspan Joel D. , Seminowicz David A. 
Published: August 2019

AbstractNeural mechanisms of ongoing nociceptive processing in the human brain remain largely obscured by the dual challenge of accessing neural dynamics and safely applying sustained painful stimuli. Recently, pain-related neural processing has been measured using fMRI resting state functional connectivity (FC) in chronic pain patients. However, ongoing pain-related processing in normally pain-free humans remains incompletely understood. Therefore, differences between chronic pain patients and controls may be due to comorbidities with chronic pain. Decreased FC among regions of the descending pain modulation network (DPMN) are associated with presence and severity of chronic pain disorders. We aimed to determine if the presence of prolonged tonic pain would lead to disruption of the DPMN. High (10%) concentration topical capsaicin was combined with a warm thermode applied to the leg to create a flexible, prolonged tonic pain model to study the FC of brain networks in otherwise healthy, pain-free subjects in two separate cohorts (n=18; n=32). We contrasted seed-based FC during prolonged tonic pain with a pain-free passive task. In seed-based FC analysis prolonged tonic pain led to enhanced FC between the anterior middle cingulate cortex (aMCC) and the somatosensory leg representation. Additionally, FC was enhanced between the pregenual anterior cingulate cortex (pACC), right mediodorsal thalamus and the posterior parietal cortex bilaterally. Further, in the seed-driven PAG network, positive FC with the left DLPFC became negative FC during prolonged tonic pain. These data suggest that some altered DPMN FC findings in chronic pain could partially be explained by the presence of ongoing pain.
Modeling vaccine-induced immunotherapy: treatment scheduling and robustness with virtual mice cohorts
Authors: Bhatt Priya , Kambara Manoj , Pilon-Thomas Shari , Rejniak Katarzyna A. , Chamseddine Ibrahim M. 
Published: August 2019

AbstractTherapeutic vaccines are used to boost patients’ immune system activity by imposing signals that increase T cell proliferation or infiltration. A large population of cytotoxic T cells may then be able to reduce tumor growth. We developed here a mathematical model of vaccine-induced immunotherapy and used it to test the vaccine frequency and doses that can reduce tumor burden. Since tumors are heterogeneous, we examined if the proposed treatments are robust; i.e, are successful for a wide range of tumors. This was assessed by constructing virtual mice cohorts. Together, the optimal and most robust treatment protocol was determined through mathematical modeling.
Optimising network modelling methods for fMRI
Authors: Pervaiz Usama , Vidaurre Diego , Woolrich Mark W. , Smith Stephen M. 
Published: August 2019

AbstractA major goal of neuroimaging studies is to develop predictive models to analyse the relationship between whole brain functional connectivity patterns and behavioural traits. However, there is no single widely-accepted standard pipeline for analyzing functional connectivity. The common procedure for designing functional connectivity based predictive models entails three main steps: parcellating the brain, estimating the interaction between defined parcels, and lastly, using these integrated associations between brain parcels as features fed to a classifier for predicting non-imaging variables e.g., behavioural traits, demographics, emotional measures, etc. There are also additional considerations when using correlation-based measures of functional connectivity, resulting in three supplementary steps: utilising Riemannian geometry tangent space parameterization to preserve the geometry of functional connectivity; penalizing the connectivity estimates with shrinkage approaches to handle challenges related to short time-series (and noisy) data; and removing confounding variables from brain-behaviour data. These six steps are contingent on each-other, and to optimise a general framework one should ideally examine these various methods simultaneously. In this paper, we investigated strengths and short-comings, both independently and jointly, of the following measures: parcellation techniques of four kinds (categorized further depending upon number of parcels), five measures of functional connectivity, the decision of staying in the ambient space of connectivity matrices or in tangent space, the choice of applying shrinkage estimators, six alternative techniques for handling confounds and finally four novel classifiers/predictors. For performance evaluation, we have selected two of the largest datasets, UK Biobank and the Human Connectome Project resting state fMRI data, and have run more than 9000 different pipeline variants on a total of ∼14000 individuals to determine the optimum pipeline. For independent performance validation, we have run some best-performing pipeline variants on ABIDE and ACPI datasets (∼1000 subjects) to evaluate the generalisability of proposed network modelling methods.
Evolution of Ty1 copy number control in yeast by horizontal transfer of agaggene
Authors: Czaja Wioletta , Bensasson Douda , Ahn Hyo Won , Garfinkel David J. , Bergman Casey M. 
Published: August 2019

AbstractInsertion of mobile DNA sequences typically has deleterious effects on host fitness, and thus diverse mechanisms have evolved to control mobile element proliferation across the tree of life. Mobility of the Ty1 retrotransposon inSaccharomycesyeasts is regulated by a novel form of copy number control (CNC) mediated by a self-encoded restriction factor derived from the Ty1gagcapsid gene that inhibits virus-like particle function. Here, we survey a panel of wild and human-associated strains ofS. cerevisiaeandS. paradoxusto investigate how genomic Ty1 content influences variation in Ty1 mobility. We observe high levels of mobility for a canonical Ty1 tester element in permissive strains that either lack full-length Ty1 elements or only contain full-length copies of the Ty1’ subfamily that have a divergentgagsequence. In contrast, low levels of canonical Ty1 mobility are observed in restrictive strains carrying full-length Ty1 elements containing canonicalgag. Phylogenomic analysis of full-length Ty1 elements revealed that Ty1’ is the ancestral subfamily present in wild strains ofS. cerevisiae, and that canonical Ty1 inS. cerevisiaeis a derived subfamily that acquiredgagfromS. paradoxusby horizontal transfer and recombination. Our results provide evidence that variation in the ability ofS. cerevisiaeandS. paradoxusstrains to repress canonical Ty1 transpositionviaCNC is encoded by the genomic content of different Ty1 subfamilies, and that self-encoded forms of transposon control can spread across species boundaries by horizontal transfer.
Genome sequencing of the nine-spined stickleback (Pungitius pungitius) provides insights into chromosome evolution
Authors: Varadharajan Srinidhi , Rastas Pasi , Löytynoja Ari , Matschiner Michael , Calboli Federico C. F. , Guo Baocheng , Nederbragt Alexander J. , Jakobsen Kjetill S. , Merilä Juha 
Published: August 2019

AbstractThe Gasterostidae fish family hosts several species that are important models for eco-evolutionary, genetic and genomic research. In particular, a wealth of genetic and genomic data have been generated for the three-spined stickleback (Gasterosteus aculeatus), the ‘ecology’s supermodel’, while the genomic resources for the nine-spined stickleback(Pungitius pungitius)have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly ofP. pungitiusconsisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and ca. 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromeric-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years (MYA) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 MYA. Compared to the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
GapMind: Automated annotation of amino acid biosynthesis
Authors: Price Morgan , Deutschbauer Adam M. , Arkin Adam P. 
Published: August 2019

AbstractGapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl/gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 seconds. To avoid error-prone “transitive” annotations, GapMind relies primarily on a database of experimentally-characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for “best hit” approaches. To improve GapMind’s coverage, we examined genetic data from 35 bacteria that grow in minimal media and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates inBacteroides thetaiotaomicronand we propose thatDyella japonicasynthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. If a potential gap in the genome of interest is also a gap in a related microbe that can grow in minimal media, GapMind marks the gap as “known.”
A Toxic RNA Catalyzes the Cellular Synthesis of Its Own Inhibitor, Shunting It to Endogenous Decay Pathways
Authors: Benhamou Raphael I. , Angelbello Alicia J. , Wang Eric T. , Disney Matthew D. 
Published: August 2019

SUMMARYMyotonic dystrophy type 2 (DM2) is a genetically defined muscular dystrophy caused by a toxic expanded repeat of r(CCUG) [heretofore (CCUG)exp], harbored in intron 1 of CHC-Type Zinc Finger Nucleic Acid Binding Protein (CNBP) pre-mRNA. This r(CCUG)exp causes DM2 via a gain-of-function mechanism that results in three hallmarks of its pathology: (i) binding to RNA-binding proteins (RBPs) that aggregate into nuclear foci; (ii) sequestration of muscleblind-like-1 (MBNL1) protein, a regulator of alternative pre-mRNA splicing, leading to splicing defects; and (iii) retention of intron 1 in the CNBP mRNA. Here, we find that CNBP intron retention is caused by the r(CCUG)exp-MBNL1 complex and can be rescued by small molecules. We studied two types of small molecules with different modes of action, ones that simply bind and ones that can be synthesized by a r(CCUG)exp-templated reaction in cells, that is the RNA synthesizes its own drug. Indeed, our studies completed in DM2 patient-derived fibroblasts show that the compounds disrupt the r(CCUG)exp-MBNL1 complex, reduce intron retention, subjecting the liberated intronic r(CCUG)exp to native decay pathways, and rescue other DM2-associated cellular defects. Collectively, this study shows that small molecules can affect RNA biology by shunting toxic transcripts towards native decay pathways.HIGHLIGHTSIntron retention in RNA repeat expansions can be due to repeats binding to proteinsSmall molecules that bind RNA repeats and inhibit protein binding can trigger decayA toxic RNA repeat can catalyze the synthesis of its own inhibitor on-siteOn-site drug synthesis most potently affects disease biologyeTOC BLURBThe most common way to target RNA is to use antisense oligonucleotides to target unstructured RNAs for destruction. Here, we show for the first time that small molecules targeting structured, disease-causing RNAs can shunt them towards native decay pathways by affecting their processing.
A systematic NGS-based approach for contaminant detection and functional inference
Authors: Park Sung-Joon , Onizuka Satoru , Seki Masahide , Suzuki Yutaka , Iwata Takanori , Nakai Kenta 
Published: August 2019

AbstractBackgroundMicrobial contamination impedes successful biological and biomedical research. Computational approaches utilizing next-generation sequencing (NGS) data offer promising diagnostics to assess the presence of contaminants. However, as host cells are often contaminated by multiple microorganisms, these approaches require careful attention to intra- and interspecies sequence similarities, which have not yet been fully addressed.ResultsWe present a computational approach that rigorously investigates the genomic origins of sequenced reads, including those mapped to multiple species that have been discarded in previous studies. Through the analysis of large-scale synthetic and public NGS samples, we approximated that 1,000−100,000 microbial reads prevail when one million host reads are sequenced by RNA-seq. The microbe catalog we established included Cutibacterium as a prevalent contaminant, suggesting that contamination mostly originates from the laboratory environment. Importantly, by applying a systematic method to infer the functional impact of contamination, we revealed that host-contaminant interactions cause profound changes in the host molecular landscapes, as exemplified by changes in inflammatory and apoptotic pathways during Mycoplasma infection.ConclusionsThese findings reinforce the concept that precise determination of the origins and functional impacts of contamination is imperative for quality research and illustrate the usefulness of the proposed approach to comprehensively characterize contamination landscapes.
The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis During Planktonic Growth and Growth in Biofilms
Authors: Ritzert Jeremy T. , Minasov George , Embry Ryan , Schipma Matthew J. , Satchell Karla J. F. 
Published: August 2019

ABSTRACTCyclic adenosine monophosphate (cAMP) receptor protein (Crp) is an important transcriptional regulator of Yersinia pestis. Expression of crp increases during pneumonic plague as the pathogen depletes glucose and forms large biofilms within lungs. To better understand control of Y. pestis Crp, we determined a 1.8 Å crystal structure of the protein-cAMP complex. We found that compared to Escherichia coli Crp, C helix amino acid substitutions in Y. pestis Crp did not impact cAMP dependency of Crp to bind DNA promoters. To investigate Y. pestis Crp-regulated genes during plague pneumonia, we performed RNA-sequencing on both wild-type and Δcrp mutant bacteria growing in planktonic and biofilm states in minimal media with glucose or glycerol. Y. pestis Crp is found to dramatically alter expression of hundreds of genes dependent upon carbon source and growth state. Gel shift assays confirmed direct regulation of the malT and ptsG promoters and Crp was then linked to Y. pestis growth on maltose as a sole carbon source. Iron-regulation genes ybtA and fyuA were found to be indirectly regulated by Crp. A new connection between carbon source and quorum sensing was revealed as Crp was found to regulate production of acyl-homoserine lactones (AHLs) through direct and indirect regulation of genes for AHL synthetases and receptors. AHLs were subsequently identified in the lungs of Y. pestis infected mice when crp expression is highest in Y. pestis biofilms. Thus, in addition to well-studied pla, other Crp-regulated genes likely have important functions during plague infection.IMPORTANCEBacterial pathogens have evolved extensive signaling pathways to translate environmental signals into changes in gene expression. While Crp has long been appreciated for its role in regulating metabolism of carbon sources in many bacterial species, transcriptional profiling has revealed that this protein regulates many other aspects of bacterial physiology. The plague pathogen, Y. pestis, requires this global regulator to survive in blood, skin, and lungs. During disease progression, this organism adapts to changes within these niches. In addition to regulating genes for metabolism of non-glucose sugars, we find the Crp regulates genes for virulence, metal acquisition and quorum sensing by direct or indirect mechanisms. Thus, this single transcriptional regulator, that responds to changes in available carbon sources, can regulate multiple critical behaviors for causing disease.
Differential remodeling of the electron transport chain is required to support TLR3 and TLR4 signaling and cytokine production in macrophages
Authors: Ahmed Duale , Roy David , Jaworski Allison , Edwards Alex , Abizaid Alfonso , Kumar Ashok , Golshani Ashkan , Cassol Edana 
Published: August 2019

AbstractIncreasing evidence suggests that mitochondria play a critical role in driving innate immune responses against bacteria and viruses. However, it is unclear if differential reprogramming of mitochondrial function contributes to the fine tuning of pathogen specific immune responses. Here, we found that TLR3 and TLR4 engagement on murine bone marrow derived macrophages was associated with differential remodeling of electron transport chain complex expression. This remodeling was associated with differential accumulation of mitochondrial and cytosolic ROS, which were required to support ligand specific inflammatory and antiviral cytokine production. We also found that the magnitude of TLR3, but not TLR4, responses were modulated by glucose availability. Under conditions of low glucose conditions, TLR3 engagement was associated with increased ETC complex III expression, increased mitochondrial and cytosolic ROS and increased inflammatory and antiviral cytokine production. This amplification was selectively reversed by targeting superoxide production from the outer Q-binding site of the ETC complex III. These results suggest that ligand specific modulation of the ETC may act as a rheostat that fine-tunes innate immune responses via mitochondrial ROS production. Modulation of these processes may represent a novel mechanism to modulate the nature as well as the magnitude of antiviral versus inflammatory immune responses.
Altered immunity of laboratory mice in the natural environment is associated with fungal colonization
Authors: Yeung Frank , Chen Ying-Han , Lin Jian-Da , Leung Jacqueline M. , McCauley Caroline , Devlin Joseph C. , Hansen Christina , Cronkite Alex , Stephens Zac , Drake-Dunn Charlotte , Fulmer Yi , Shopsin Bo , Ruggles Kelly V. , Round June L. , Loke P’ng , Graham Andrea L. , Cadwell Ken 
Published: August 2019

AbstractThe immune systems of free-living mammals such as humans and wild mice display a heightened degree of activation compared with laboratory mice maintained under artificial conditions. Here, we demonstrate that releasing inbred laboratory mice into an outdoor enclosure to mimic life in a natural environment alters the state of immunity. In addition to enhancing the differentiation of T cell populations previously associated with pathogen exposure, we found that outdoor release of mice led to an increase in circulating granulocytes. However, rewilded mice were not infected by pathogens previously implicated in immune activation. Rather, changes to the immune system were associated with an altered composition of the microbiota, and fungi isolated from rewilded mice were sufficient to increase circulating granulocytes. These findings establish an experimental procedure to investigate the impact of the natural environment on immune development and identify a role for sustained fungal exposure in determining granulocyte numbers.
Progressive impairments in executive function in the APP/PS1 model of Alzheimer’s disease as measured by translatable touchscreen testing
Authors: Shepherd A. , Lim J.K.H. , Wong V.H.Y. , Zeleznikow-Johnston A.M. , Churilov L. , Nguyen C.T.O. , Bui B.V. , Hannan A.J. , Burrows E.L. 
Published: August 2019

AbstractExecutive function deficits in Alzheimer’s disease (AD) occur early in disease progression and may be predictive of cognitive decline. However, no preclinical studies have identified deficits in rewarded executive function in the commonly used APP/PS1 mouse model. To address this, we assessed 12-26 month old APP/PS1 mice on rewarded reversal and/or extinction tasks. 16-month-old, but not 13- or 26-month-old, APP/PS1 mice showed an attenuated rate of extinction. Reversal deficits were seen in 22-month-old, but not 13-month-old APP/PS1 animals. We then confirmed that impairments in reversal were unrelated to previously reported visual impairments in both AD mouse models and humans. Age, but not genotype, had a significant effect on markers of retinal health, indicating the deficits seen in APP/PS1 mice were directly related to cognition. This is the first characterisation of rewarded executive function in APP/PS1 mice, and has great potential to facilitate translation from preclinical models to the clinic.