bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macrophage-Dependent Trafficking and Remodeling of the Basement Membrane-Interstitial Matrix Interface
Authors: Bahr Julian C. , Weiss Stephen J. 
Published: July 2018

SummaryMacrophages infiltrate and remodel extracellular matrix barriers during development and disease. Bahr and Weiss demonstrate that human macrophages remodel native basement membrane barriers in an MT1-MMP-dependent fashion while retaining the ability to traverse tissue barriers by actomyosin-dependent forces alone.AbstractMacrophages dominate inflammatory environments where they modify the extracellular matrix by mobilizing complex repertoires of proteolytic enzymes. Nevertheless, the dominant proteinases used by macrophage as they confront physiologic tissue barriers remain undefined. Herein, we have characterized the molecular mechanisms that define human macrophage-extracellular matrix interactions ex vivo. Resting and immune-polarized macrophages are shown to proteolytically remodel basement membranes while infiltrating the underlying interstitial matrix. In an unbiased screen to identify key proteases, we find that the macrophage metalloproteinase, MT1-MMP, is the dominant effector of basement membrane degradation and invasion. Unexpectedly, macrophages can alternatively use actomyosin-dependent forces to transmigrate native basement membrane pores that provide cells with proteinase-independent access to the interstitial matrix. These studies not only identify MT1-MMP as a key proteolytic effector of extracellular matrix remodeling by human macrophages, but also define the invasive strategies used by macrophages to traverse physiologic tissue barriers.
Reconciling disparate estimates of viral genetic diversity during human influenza infections
Authors: Xue Katherine S. , Bloom Jesse D. 
Published: July 2018

AbstractDeep sequencing can measure viral genetic diversity within human influenza infections, but published studies disagree in their estimates of how much genetic diversity is typically present. One large-scale deep-sequencing study of human influenza reported high levels of shared viral genetic diversity among infected individuals in Hong Kong, but subsequent studies of other cohorts have reported little shared viral diversity. We re-analyze sequencing data from four studies of within-host genetic diversity encompassing more than 500 acute human influenza infections. We identify an anomaly in the Hong Kong data that provides a technical explanation for these discrepancies: read pairs from this study are often split between different biological samples, indicating that some reads are incorrectly assigned. These technical abnormalities explain the high levels of within-host variation and loose transmission bottlenecks reported by this study. Studies without these anomalies consistently report low levels of genetic diversity in acute human influenza infections.
Considerations in using recurrent neural networks to probe neural dynamics
Authors: Kao Jonathan C 
Published: July 2018

AbstractRecurrent neural networks (RNNs) are increasingly being used to model complex cognitive and motor tasks performed by behaving animals. Here, RNNs are trained to reproduce animal behavior while also recapitulating key statistics of empirically recorded neural activity. In this manner, the RNN can be viewed as an in silico circuit whose computational elements share similar motifs with the cortical area it is modeling. Further, as the RNN’s governing equations and parameters are fully known, they can be analyzed to propose hypotheses for how neural populations compute. In this context, we present important considerations when using RNNs to model motor behavior in a delayed reach task. First, by varying the network’s nonlinear activation and rate regularization, we show that RNNs reproducing single neuron firing rate motifs may not adequately capture important population motifs. Second, by visualizing the RNN’s dynamics in low-dimensional projections, we demonstrate that even when RNNs recapitulate key neurophysiological features on both the single neuron and population levels, it can do so through distinctly different dynamical mechanisms. To militate between these mechanisms, we show that an RNN consistent with a previously proposed dynamical mechanism is more robust to noise. Finally, we show that these dynamics are sufficient for the RNN to generalize to a target switch task it was not trained on. Together, these results emphasize important considerations when using RNN models to probe neural dynamics.
Structural and Functional Consequences of Age-Related Isomerization in α-Crystallins
Authors: Lyon Yana A. , Riggs Dylan L. , Collier Miranda P. , Degiacomi Matteo T. , Benesch Justin L.P. , Julian Ryan R. 
Published: July 2018

AbstractLong-lived proteins are subject to spontaneous degradation and may accumulate a range of modifications over time, including subtle alterations such as isomerization. Recently, tandem-mass spectrometry approaches have enabled the identification and detailed characterization of such peptide isomers, including those differing only in chirality. However, the structural and functional consequences of these perturbations remain largely unexplored. Here we examine the site-specific impact of isomerization of aspartic acid and epimerization of serine in human αA- and αB-crystallin. From a total of 81 sites of modification identified in aged eye lenses, four (αBSer59,αASer162,αBAsp62,αBAsp109) map to crucial oligomeric interfaces. To characterize the effect of isomerization on quaternary assembly, molecular dynamics calculations and native mass spectrometry experiments were performed on recombinant forms of αA- and αB-crystallin that incorporate, or mimic, isomerized residues. In all cases, oligomerization is significantly affected, with epimerization of a single serine residue (αASer162) sufficing to weaken inter-subunit binding dramatically. Furthermore, phosphorylation ofαBSer59, known to play an important regulatory role in oligomerization, is severely inhibited by serine epimerization and altered by isomerization of nearbyαBAsp62. Similarly, isomerization ofαBAsp109 disrupts a vital salt-bridge withαBArg120, a loss previously shown to yield aberrant oligomerization and aggregation in several disease variants. Our results illustrate how isomerization of amino-acid residues, which may seem like a minor structural perturbation, can have profound consequences on protein assembly and activity by disrupting specific hydrogen bonds and salt bridges.Significance StatementProteins play numerous critical roles in our bodies but suffer damage with increasing age. For example, isomerization is a spontaneous post-translational modification that alters the three-dimensional connectivity of an amino acid, yet remains invisible to traditional proteomic experiments. Herein, radical-based fragmentation was used for isomer identification while molecular dynamics and native mass spectrometry were utilized to assess structural consequences. The results demonstrate that isomerization disrupts both oligomeric assembly and phosphorylation in the α-crystallins, which are long-lived proteins in the lens of the eye. The loss of function associated with these modifications is likely connected to age-related diseases such as cataract and neurodegenerative disorders, while the methodologies we present represent a framework for structure-function studies on other isomerized proteins.
Adaptive strategies of the candidate probioticE. coliNissle in the mammalian gut
Authors: Crook Nathan , Ferreiro Aura , Gasparrini Andrew J. , Pesesky Mitchell , Gibson Molly K. , Wang Bin , Sun Xiaoqing , Condiotte Zevin , Dobrowolski Stephen , Peterson Daniel , Dantas Gautam 
Published: July 2018

SummaryProbiotics are living microorganisms that are increasingly used as gastrointestinal therapeutics by virtue of their innate or engineered genetic function. Unlike abiotic therapeutics, probiotics can replicate in their intended site, subjecting their genomes and therapeutic properties to natural selection. By exposing the candidate probioticE. coliNissle (EcN) to the mouse gastrointestinal tract over several weeks, we uncovered the consequences of gut transit, inter-species competition, antibiotic pressure, and engineered genetic function on the processes under selective pressure during both within-genome and horizontal evolutionary modes. We then show the utility of EcN as a chassis for engineered function by achieving the highest reported reduction in serum phenylalanine levels in a mouse model of phenylketonuria using an engineered probiotic. Collectively, we demonstrate a generalizable pipeline which can be applied to other probiotic strains to better understand their safety and engineering potential.
A Multiplex Droplet Digital PCR Assay for Quantification of HTLV-1c DNA Proviral Load and T-Cells from Blood and Respiratory Exudates Sampled in a Remote Setting
Authors: Yurick David , Khoury Georges , Clemens Bridie , Loh Liyen , Pham Hai , Kedzierska Katherine , Einsiedel Lloyd , Purcell Damian 
Published: July 2018

AbstractDuring human T-cell leukemia virus type-1 (HTLV-1) infection the frequency of cells harboring an integrated copy of viral cDNA, the proviral load (PVL), is the main risk factor for progression of HTLV-1-associated diseases. Accurate quantification of provirus by droplet digital PCR (ddPCR) is a powerful diagnostic tool with emerging uses for monitoring viral expression. Current ddPCR techniques quantify HTLV-1 PVL in terms of whole genomic cellular material, while the main target of HTLV-1 infection is the CD4+and CD8+T-cell. Our understanding of HTLV-1 proliferation and the amount of viral burden present in different compartments is limited. Recently a sensitive ddPCR assay was applied to quantifying T-cells by measuring loss of germline T-cell receptor genes as method of distinguishing non-T-cell from recombined T-cell DNA. In this study, we demonstrated and validated novel applications of the duplex ddPCR assay to quantify T-cells from various sources of human gDNA extracted from frozen material (PBMCs, bronchoalveolar lavage, and induced sputum) from a cohort of remote Indigenous Australians and then compared the T-cell measurements by ddPCR to the prevailing standard method of flow cytometry. The HTLV-1c PVL was then calculated in terms of extracted T-cell gDNA from various compartments. Because HTLV-1c preferentially infects CD4+T-cells, and the amount of viral burden correlates with HTLV-1c disease pathogenesis, application of this ddPCR assay to accurately measure HTLV-1c-infected T-cells can be of greater importance for clinical diagnostics, prognostics as well as monitoring therapeutic applications.
Genome-wide characterization of the Fur regulatory network reveals a link between catechol degradation and bacillibactin metabolism in Bacillus subtilis
Authors: Pi Hualiang , Helmann John D. 
Published: July 2018

AbstractThe ferric uptake regulator (Fur) is the global iron biosensor in many bacteria. Fur functions as an iron-activated transcriptional repressor for most of its regulated genes. There are a few examples where holo-Fur activates transcription, either directly or indirectly. Recent studies suggest that apo-Fur might also act as a positive regulator and, besides iron metabolism, the Fur regulon might encompass other biological processes such as DNA synthesis, energy metabolism, and biofilm formation. Here, we obtained a genomic view of the Fur regulatory network in Bacillus subtilis using ChIP-seq. Besides the known Fur target sites, 70 putative DNA binding sites were identified, and the vast majority had higher occupancy under iron sufficient conditions. Among the new sites detected, a Fur binding site in the promoter region of the catDE operon is of particular interest. This operon, encoding catechol 2,3-dioxygenase, is critical for catechol degradation and is under negative regulation by CatR and YodB. These three repressors function cooperatively to regulate the transcription of catDE, with Fur functioning as a sensor of iron-limitation and CatR as the major sensor of catechol stress. Genetic analysis suggests that CatDE is involved in metabolism of the catecholate siderophore bacillibactin, particularly when bacillibactin is constitutively produced and accumulates intracellularly, potentially generating endogenous toxic catechol derivatives. This study documents a role for catechol degradation in bacillibactin metabolism, and provides evidence that catechol 2,3-dioxygenase can detoxify endogenously produced catechol substrates in addition to its more widely studied role in biodegradation of environmental aromatic compounds and pollutants.ImportanceMany bacteria synthesize high affinity iron chelators (siderophores). Siderophore-mediated iron acquisition is an efficient and widely utilized strategy for bacteria to meet their cellur iron requirements. One prominent class of siderophores uses catecholate groups to chelate iron. B. subtilis bacillibactin, structurally similar to enterobactin (made by enteric bacteria), is a triscatecholate siderophore that is hydrolyzed to monomeric units after import to release iron. However, the ultimate fate of these catechol compounds and their potential toxicity have not been defined previously. Here, we performed genome-wide identification of Fur binding sites in vivo and uncovered a connection between catechol degradation and bacillibactin metabolism in B. subtilis. Beside its role in detoxification of environmental catechols, the catechol 2,3-dioxygenase encoded by catDE also protects cells from intoxication by endogeous bacillibactin-derived catechol metabolites under iron-limited conditions. These findings shed light on the degradation pathway and precursor recycling of the catecholate siderophores.
Internal noise in contrast discrimination propagates forwards from early visual cortex
Authors: Vilidaite Greta , Marsh Emma , Baker Daniel H. 
Published: July 2018

AbstractHuman contrast discrimination performance is limited by transduction nonlinearities and variability of the neural representation (noise). Whereas the nonlinearities have been well-characterised, there is less agreement about the specifics of internal noise. Psychophysical models assume that it impacts late in sensory processing, whereas neuroimaging and intracranial electrophysiology studies suggest that the noise is much earlier. We investigated whether perceptually-relevant internal noise arises in early visual areas or later decision making areas. We recorded EEG and MEG during a two-interval-forced-choice contrast discrimination task and used multivariate pattern analysis to decode target/non-target and selected/non-selected intervals from evoked responses. We found that perceptual decisions could be decoded from both EEG and MEG signals, even when the stimuli in both intervals were physically identical. Above-chance decision classification started <100ms after stimulus onset, suggesting that neural noise affects sensory signals early in the visual pathway. Classification accuracy increased over time, peaking at >500ms. Applying multivariate analysis to separate anatomically-defined brain regions in MEG source space, we found that occipital regions were informative early on but then information spreads forwards across parietal and frontal regions. This is consistent with neural noise affecting sensory processing at multiple stages of perceptual decision making. We suggest how early sensory noise might be resolved with Birdsall’s linearisation, in which a dominant noise source obscures subsequent nonlinearities, to allow the visual system to preserve the wide dynamic range of early areas whilst still benefitting from contrast-invariance at later stages. A preprint of this work is available at:http://dx.doi.org/10.1101/364612
Ad-Seq, a genome-wide DNA-adduct profiling assay
Authors: Harismendy Olivier , Howell Stephen B. 
Published: July 2018

SummaryCarcinogens form adducts with the DNA which, when not properly repaired, can lead to mutations and drive oncogenesis. The identity, sequence specificity and mutagenicity of most DNA-adducts is however poorly understood and current molecular assays are limited in their scope and scalability. We present a novel genome-wide DNA adduct sequencing (Ad-Seq) assay to map the location of DNA-adducts at single-nucleotide resolution. Ad-Seq enriches for DNA fragments containing nuclease digestion resistant DNA-adducts. The genomic location of the resulting reads is aggregated in a quantitative profile showing the DNA-adduct sequence context. Ad-Seq is quantitative and confirms known specificity of damages from Ultra-Violet light (di-pyrimidine) and cisplatin (AG and GG di-purines). Furthermore, in cells, Ad-Seq profile can be compared to chromatin segments to show that cisplatin associated adducts are depleted in open and active chromatin regions. The Ad-Seq assay can therefore generate a broad DNA signature of DNA damage and, by comparing to mutagen exposure or downstream mutational profile and signatures, be used to improve our understanding of cancer molecular etiology.
DoubletDecon: Cell-State Aware Removal of Single-Cell RNA-Seq Doublets
Authors: DePasquale Erica A.K. , Schnell Daniel J. , Valiente-Alandí Íñigo , Blaxall Burns C. , Grimes H. Leighton , Singh Harinder , Salomonis Nathan 
Published: July 2018

SUMMARYMethods for single-cell RNA sequencing (scRNA-Seq) have greatly advanced in recent years. While droplet- and well-based methods have increased the capture frequency of cells for scRNA-Seq, these technologies readily produce technical artifacts, such as doublet-cell and multiplet-cell captures. Doublets occurring between distinct cell-types can appear as hybrid scRNA-Seq profiles, but do not have distinct transcriptomes from individual cell states. We introduce DoubletDecon, an approach that detects doublets with a combination of deconvolution analyses and the identification of unique cell-state gene expression. We demonstrate the ability of DoubletDecon to identify synthetic and cell-hashing cell singlets and doublets from scRNA-Seq datasets of varying cellular complexity. DoubletDecon is able to account for cell-cycle effects and is compatible with diverse species and unsupervised population detection algorithms (e.g., ICGS, Seurat). We believe this approach has the potential to become a standard quality control step for the accurate delineation of cell states.
Repeated evolution of asexuality involves convergent gene expression changes
Authors: Parker Darren J. , Bast Jens , Jalvingh Kirsten , Dumas Zoé , Robinson-Rechavi Marc , Schwander Tanja 
Published: July 2018

AbstractAsexual reproduction has evolved repeatedly from sexual ancestors across a wide range of taxa. While the costs and benefits associated with asexuality have received considerable attention, the molecular changes underpinning the evolution of asexual reproduction remain relatively unexplored. In particular, it is completely unknown whether the repeated evolution of asexual phenotypes involves similar molecular changes, as previous studies have focused on changes occurring in single lineages. Here we investigate the extent of convergent gene expression changes across five independent transitions to asexuality in stick insects. We compared gene expression of asexual females to females of close sexual relatives in whole-bodies, reproductive tracts, and legs. We identified a striking amount of convergent gene expression change (up to 8% of genes), greatly exceeding that expected by chance. Convergent changes were also tissue-specific, and most likely driven by selection for functional changes. Genes showing convergent changes in the reproductive tract were associated with meiotic spindle formation and centrosome organization. These genes are particularly interesting as they can influence the production of unreduced eggs, a key barrier to asexual reproduction. Changes in legs and whole-bodies were likely involved in female sexual trait decay, with enrichment in terms such as sperm-storage and pigmentation. By identifying changes occurring across multiple independent transitions to asexuality, our results provide a rare insight into the molecular basis of asexual phenotypes and suggest that the evolutionary path to asexuality is highly constrained, requiring repeated changes to the same key genes.
Pseudomonas aeruginosainhibitsRhizopus microsporusgermination through sequestration of free environmental iron
Authors: Kousser Courtney , Clark Callum , Voelz Kerstin , Hall Rebecca A. 
Published: July 2018

AbstractRhizopus sppare the most common etiological agents of mucormycosis, causing over 90% mortality in disseminated infection. Key to pathogenesis is the ability of fungal spores to swell, germinate, and penetrate surrounding tissues. Antibiotic treatment in at-risk patients increases the probability of the patient developing mucormycosis, suggesting that bacteria have the potential to control the growth of the fungus. However, research into polymicrobial relationships involvingRhizopus spphas not been extensively explored. Here we show that co-culturingRhizopus microsporusandPseudomonas aeruginosaresults in the inhibition of spore germination. This inhibition was mediated via the secretion of bacterial siderophores, confirming the essential role of iron for fungal growth. Addition ofP. aeruginosasiderophores toR. microsporusspores in the zebrafish larval model of infection resulted in inhibition of fungal germination and reduced host mortality. Therefore, during infection antibacterial treatment may relieve bacterial imposed nutrient restriction resulting in secondary fungal infections.
Megadomains and superloops form dynamically but are dispensable for X-chromosome inactivation and gene escape
Authors: Froberg John E. , Pinter Stefan F. , Kriz Andrea J. , Jégu Teddy , Lee Jeannie T. 
Published: July 2018

ABSTRACTThe mammalian inactive X-chromosome (Xi) is structurally distinct from all other chromosomes and serves as a model for how the 3D genome is organized. The Xi shows weakened topologically associated domains and is instead organized into megadomains and superloops directed by the noncoding loci, Dxz4 and Firre. Their functional significance is presently unclear, though one study suggests that they permit Xi genes to escape silencing. Here, we find that megadomains do not precede Xist expression or Xi gene silencing. Deleting Dxz4 disrupts megadomain formation, whereas deleting Firre weakens intra-megadomain interactions. Surprisingly, however, deleting Dxz4 and Firre has no impact on Xi silencing and gene escape. Nor does it affect Xi nuclear localization, stability, or H3K27 methylation. Additionally, ectopic integration of Dxz4 and Xist is not sufficient to form megadomains on autosomes, further uncoupling megadomain formation from chromosomal silencing. We conclude that Dxz4 and megadomains are dispensable for Xi silencing and escape from X-inactivation.