bluuebunny/crossref_metadata_2025 huggingface dataset:
Coevolution analysis of amino-acids reveals diversified drug-resistance solutions in viral sequences: a case study of hepatitis B virus
Authors: Teppa Elin , Nadalin Francesca , Combet Christophe , Zea Diego Javier , David Laurent , Carbone Alessandra
Published: January 2020

The study of mutational landscapes of viral proteins is fundamental for the understanding of the mechanisms of cross-resistance to drugs and the design of effective therapeutic strategies based on several drugs. Antiviral therapy with nucleos(t)ide analogues targeting the hepatitis B virus (HBV) polymerase protein (Pol) can inhibit disease progression by suppression of HBV replication and makes it an important case study. In HBV, treatment may fail due to the emergence of drug-resistant mutants. Primary and compensatory mutations have been associated with lamivudine resistance, whereas more complex mutational patterns are responsible for resistance to other HBV antiviral drugs. So far, all known drug-resistance mutations are located in one of the four Pol domains, called reverse transcriptase. We demonstrate that sequence covariation identifies drug-resistance mutations in viral sequences. A new algorithmic strategy, BIS2TreeAnalyzer, is designed to apply the coevolution analysis method BIS2, successfully used in the past on small sets of conserved sequences, to large sets of evolutionary related sequences. When applied to HBV, BIS2TreeAnalyzer highlights diversified viral solutions by discovering thirty-seven positions coevolving with residues known to be associated with drug resistance and located on the four Pol domains. These results suggest a sequential mechanism of emergence for some mutational patterns. They reveal complex combinations of positions involved in HBV drug resistance and contribute with new information to the landscape of HBV evolutionary solutions. The computational approach is general and can be applied to other viral sequences when compensatory mutations are presumed.
Exploring the Views of Desk-Based Office Workers and Their Employers’ Beliefs Regarding Strategies to Reduce Occupational Sitting Time, With an Emphasis on Technology-Supported Approaches
Authors: Stephenson Aoife , McDonough Suzanne M. , Murphy Marie H. , Nugent Chris D. , Wilson Iseult M. , Mair Jacqueline L.
Published: January 2020

Objective:

Employee and employer views regarding how technology-supported strategies can best meet their needs to reduce occupational sitting are not well known. This study explored target user and key stakeholder beliefs regarding strategies to reduce occupational sitting focusing on technology-supported approaches.

Methods:

Nine focus groups and two interviews (employees, n = 27; employers, n = 19; board members, n = 2) were conducted, transcribed, and analyzed thematically.

Results:

The main barrier to reducing sitting was job-related tasks taking primary priority. Intervention designers should consider individual preferences, environmental factors, judgmental culture, productivity concerns, and staff knowledge. Technology-supported strategies such as smartphone applications, computer software, wearables, and emails were deemed to be useful tools to provide prompts and allow behavioral self-monitoring in an easily individualized manner.

Conclusions:

Technology-supported strategies were seen to be valuable approaches and might fruitfully be incorporated into future interventions to reduce sitting time.
The Impact of Massachusetts Health Reform on Colorectal and Breast Cancer Stage at Diagnosis
Authors: Sabik Lindsay M. , Eom Kirsten Y. , Dahman Bassam , Li Jie , Yao Nengliang , van Londen G. J. , Bradley Cathy J.
Published: January 2020

Background:

This study examines the expansion of health insurance coverage in Massachusetts under state health reform as a natural experiment to investigate whether expanded insurance coverage reduced the likelihood of advanced stage colorectal cancer (CRC) and breast cancer (BCA) diagnosis.

Methods:

Our study populations include CRC or BCA patients aged 50–64 years observed in the Massachusetts Cancer Registry and Surveillance Epidemiology and End Results (SEER) registries for 2001–2013. We use difference-in-differences regression models to estimate changes in the likelihood of advanced stage diagnosis after Massachusetts health reform, relative to comparison states without expanded coverage (Connecticut, New Jersey, Georgia, Kentucky, and Michigan).

Results:

We find some suggestive evidence of a decline in the proportion of advanced stage CRC cases. Approximately half of the CRC patients in Massachusetts and control states were diagnosed at advanced stages pre reform; there was a 2 percentage-point increase in this proportion across control states and slight decline in Massachusetts post reform. Adjusted difference-in-difference estimates suggest a 3.4 percentage-point (P=0.005) or 7% decline, relative to Massachusetts baseline, in the likelihood of advanced stage diagnosis after the reform in Massachusetts, though this result is sensitive to years included in the analysis. We did not find a significant effect of reform on BCA stage at diagnosis.

Conclusions:

The decline in the likelihood of advanced stage CRC diagnosis after Massachusetts health reform may suggest improvements in access to health care and CRC screening. Similar declines were not observed for BCA, perhaps due to established BCA-specific safety-net programs.
Change in Defense Mechanisms and Depression in a Pilot Study of Antidepressive Medications Plus 20 Sessions of Psychotherapy for Recurrent Major Depression
Authors: Perry J. Christopher , Banon Elisabeth , Bond Michael
Published: January 2020

Treatment studies of major depression commonly focus on symptoms, leaving aside change in putative psychological risk factors. This pilot study examines the relationship between changes in eight depressive defenses and depressive symptoms. Twelve adults with acute recurrent major depression were given antidepressive medications and randomized to 20 sessions of either cognitive behavioral therapy or dynamic psychotherapy and followed for 1 year. Defenses were assessed using the Defense Mechanism Rating Scales (DMRS) and Defense Style Questionnaire (DSQ) at intake, termination, and 1-year follow-up. Depression improved highly significantly on both the Hamilton Rating Scale for Depression and Beck Depression Inventory, respectively, eight (67%) and nine (75%) patients attained recovery by 1 year. Depressive defenses improved significantly by termination (mean ES = 0.97; 95% confidence interval, 0.30–2.16), but retrogressed somewhat by 1 year. A mean of 12.17% (SD = 10.60) depressive defenses remained; only five subjects (50%) attained normative levels. Although causal relationships were not established, depressive defenses are promising candidates for mediating treatment effects on outcome of major depression.
Simple Way of Facilitating Reduction the Fragment for Fractures With Condyle
Authors: Liu Kai , Zhi Yin , Wang Ze , Zhang Wenbin , Shi Jun
Published: January 2020

To describe a technique that uses a fixation screw with a steel wire ring which is implanted into the mandibular to facilitate the condylar fracture reduction. This technique has been used on 382 patients over the last 8 years from the Department of Oral and Cranio-Maxillofacial Science of Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. No complication has been encountered. Applying this approach, the displaced proximal condylar fragment can be found quickly, and then the fragment can be effectively prevented from being broken again in the reduction process.
The extent and drivers of gender imbalance in neuroscience reference lists
Authors: Dworkin Jordan D. , Linn Kristin A. , Teich Erin G. , Zurn Perry , Shinohara Russell T. , Bassett Danielle S.
Published: January 2020

Like many scientific disciplines, neuroscience has increasingly attempted to confront pervasive gender imbalances within the field. While much of the conversation has centered around publishing and conference participation, recent research in other fields has called attention to the prevalence of gender bias in citation practices. Because of the downstream effects that citations can have on visibility and career advancement, understanding and eliminating gender bias in citation practices is vital for addressing inequity in a scientific community. In this study, we sought to determine whether there is evidence of gender bias in the citation practices of neuroscientists. Using data from five top neuroscience journals, we find that reference lists tend to include more papers with men as first and last author than would be expected if gender were not a factor in referencing. Importantly, we show that this overcitation of men and undercitation of women is driven largely by the citation practices of men, and is increasing over time as the field becomes more diverse. We develop a co-authorship network to assess homophily in researchers’ social networks, and we find that men tend to overcite men even when their social networks are representative. We discuss possible mechanisms and consider how individual researchers might address these findings in their own practices.
Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide
Authors: Michaels Thomas C. T. , Šarić Andela , Curk Samo , Bernfur Katja , Arosio Paolo , Meisl Georg , Dear Alexander J. , Cohen Samuel I. A. , Vendruscolo Michele , Dobson Christopher M. , Linse Sara , Knowles Tuomas P. J.
Published: January 2020

Oligomeric aggregates populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach combining theory, experiment, and simulation, we reveal in molecular detail the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we find that most Aβ42 oligomers dissociate to their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar species. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases.
Characterization of novel Actinobacteriophage Giantsbane reveals unexpected cluster AU relationships
Authors: Chen Pei Ying , Liu Christopher , Dang Preston , Zhang Michael , Kapinos Andrew , Ngo Ryan , Reddi Krisanavane , Parker Jordan Moberg , Freise Amanda C.
Published: January 2020

Bacteriophages that infectArthrobacter, a genus of bacteria which play key ecological roles in soil, warrant further study. Giantsbane, a novel Actinobacteriophage, was isolated usingArthrobacter globiformisas a host. Transmission electron microscopy and whole-genome sequencing revealed aSiphoviridaemorphology and a genome length of 56,734 bp. Genome annotation identified 94 putative genes, such as a duplicated major tail protein and a major capsid and protease fusion protein. No genes were associated with lysogeny, indicating a lytic phage. Giantsbane was assigned to the phage cluster AU. Batch average nucleotide identity analysis and phylogenetic networks constructed from shared genes revealed unexpected nucleotide and gene content similarities within cluster AU. These findings have resulted in the creation of two new AU subclusters and the resubclustering of three AU bacteriophages. Analysis using Phamerator and MEME identified repeated motifs and a gene cassette present in all evaluated cluster AU phages which may promote recombination. These findings offer the first intra-cluster analysis of cluster AU phages and further our understanding of the relationships between closely related bacteriophages.
Population sequencing data reveal a compendium of mutational processes in human germline
Authors: Seplyarskiy Vladimir B. , Soldatov Ruslan A. , McGinty Ryan J. , Goldmann Jakob M. , Hernandez Ryan , Barnes Kathleen , Correa Adolfo , Burchard Esteban G. , Ellinor Patrick T. , McGarvey Stephen T. , Mitchell Braxton D. , Ramachandran Vasan S. , Redline Susan , Silverman Edwin , Weiss Scott T. , Arnett Donna K. , Blangero John , Boerwinkle Eric , He Jiang , Montgomery Courtney , Rao D.C. , Rotter Jerome I. , Brody Jennifer A , Ida Chen Yii-Der , de las Fuentes Lisa , Hwu Chii-Min , Rich Stephen S. , Manichaikul Ani W. , Mychaleckyj Josyf C. , Palmer Nicholette D. , Smith Jennifer A. , Kardia Sharon L.R. , Peyser Patricia A. , Bielak Lawrence F. , O’Connor Timothy D. , Emery Leslie S. ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,   TOPMed Population Genetics Working Group, Gilissen Christian , Wong Wendy S.W. , Kharchenko Peter V. , Sunyaev Shamil
Published: January 2020

Mechanistic processes underlying human germline mutations remain largely unknown. Variation in mutation rate and spectra along the genome is informative about the biological mechanisms. We statistically decompose this variation into separate processes using a blind source separation technique. The analysis of a large-scale whole genome sequencing dataset (TOPMed) reveals nine processes that explain the variation in mutation properties between loci. Seven of these processes lend themselves to a biological interpretation. One process is driven by bulky DNA lesions that resolve asymmetrically with respect to transcription and replication. Two processes independently track direction of replication fork and replication timing. We identify a mutagenic effect of active demethylation primarily acting in regulatory regions. We also demonstrate that a recently discovered mutagenic process specific to oocytes can be localized solely from population sequencing data. This process is spread across all chromosomes and is highly asymmetric with respect to the direction of transcription, suggesting a major role of DNA damage.
RNA splicing alterations induce a cellular stress response associated with poor prognosis in AML
Authors: Anande Govardhan , Deshpande Nandan P. , Mareschal Sylvain , Batcha Aarif M. N. , Hampton Henry R. , Herold Tobias , Lehmann Soren , Wilkins Marc R. , Wong Jason W.H. , Unnikrishnan Ashwin , Pimanda John E.
Published: January 2020

RNA splicing is a fundamental biological process that generates protein diversity from a finite set of genes. Recurrent somatic mutations of splicing factor genes are relatively uncommon in Acute Myeloid Leukemia (AML, < 20%). We examined whether RNA splicing differences exist in AML even in the absence of splicing factor mutations. Analyzing RNA-seq data from two independent cohorts of AML patients, we identified recurrent differential alternative splicing between patients with poor and good prognosis. These alternative splicing events occurred even in patients without any discernible splicing factor mutations. The alternative splicing events recurrently occurred in genes involved in specific molecular functions, primarily related to protein translation. Developing informatics tools to predict the functional impact of alternative splicing on the translated protein, we discovered that ~45% of the splicing events directly affected highly conserved protein domains. Several splicing factors were themselves misspliced in patients, and the splicing of their target transcripts were also altered. By studying differential gene expression in the same patients, we identified that alternative splicing of protein translation genes in ELNAdv patients resulted in the induction of an integrated stress response and up- regulation of inflammation-related genes. Lastly, using machine learning techniques, we identified a set of four genes whose alternative splicing can refine the accuracy of existing risk prognosis schemes and validated it in a completely independent cohort. Our discoveries therefore identify aberrant alternative splicing as a molecular feature of adverse AML with clinical relevance.
Geometric Analysis of Regime Shifts in Coral Reef Communities
Authors: Tekwa Edward W. , McManus Lisa C. , Greiner Ariel , Colton Madhavi A. , Webster Michael S. , Pinsky Malin L.
Published: January 2020

Coral reefs are among the many communities believed to exhibit regime shifts between alternative stable states, single-species dominance, and coexistence. Proposed drivers of regime shifts include changes in grazing, spatial clustering, and ocean temperature. Here we distill the dynamic regimes of coral-macroalgal interaction into a three-dimensional geometry, akin to thermodynamic phase diagrams of state transitions, to facilitate analysis. Specific regime-shifting forces can be understood as bifurcation vectors through the cubic regime geometry. This geometric perspective allows us to understand multiple forces simultaneously in terms of the stability and persistence of interacting species. For example, in a coral-macroalgae community, grazing on macroalgae can lead to alternative stable states when there is no spatial clustering (e.g., high habitat connectivity). However, with spatial clustering, grazing can lead to coexistence because of elevated local intraspecific competition. The geometrical analysis of regime shifts is applicable to any two-species communities and can help conservation efforts navigate complexity and abrupt changes.
Presynaptic PTPσ organizes neurotransmitter release machinery at excitatory synapses
Authors: Han Kyung Ah , Lee Hee-Yoon , Lim Dongseok , Shin Jungsu , Yoon Taek Han , Lee Chooungku , Rhee Jeong-Seop , Liu Xinran , Um Ji Won , Choi Se-Young , Ko Jaewon
Published: January 2020

Leukocyte common antigen-related receptor tyrosine phosphatases (LAR-RPTPs) are evolutionarily conserved presynaptic organizers. The synaptic role of vertebrate LAR-RPTPsin vivo, however, remains unclear. This study systematically analyzed the effects of genetic deletions of LAR-RPTP genes by generating single conditional knockout (cKO) mice targeting PTPσ and PTPδ. Although the numbers of synapses were reduced in cultured neurons deficient in individual PTPs, abnormalities in synaptic transmission, synaptic ultrastructures, and vesicle localization were observed only in PTPσ-deficient neurons. Strikingly, loss of presynaptic PTPσ reduced neurotransmitter release prominently at excitatory synapses, concomitant with drastic reductions in excitatory innervations onto postsynaptic target areasin vivo. However, postsynaptic PTPσ deletion had no effect on excitatory synaptic strength. Furthermore, conditional deletion of PTPσ in ventral CA1 specifically altered anxiety-like behaviors. Taken together, these results demonstrate that PTPσ is abona fidepresynaptic adhesion molecule that controls neurotransmitter release and excitatory inputs.
Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer
Authors: Uhlitz Florian , Bischoff Philip , Peidli Stefan , Sieber Anja , Obermayer Benedikt , Blanc Eric , Trinks Alexandra , Lüthen Mareen , Ruchiy Yana , Sell Thomas , Mamlouk Soulafa , Arsie Roberto , Wei Tzu-Ting , Klotz-Noack Kathleen , Schwarz Roland F , Sawitzki Birgit , Kamphues Carsten , Beule Dieter , Landthaler Markus , Sers Christine , Horst David , Blüthgen Nils , Morkel Markus
Published: January 2020

In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to define colorectal cancer cell types and signals controlling their development. More than 30,000 epithelial single cell transcriptomes of tumors and matched non-cancerous tissues of twelve colorectal cancer patients were clustered into six patient-overarching groups defined by differential activities of oncogenic signaling pathways such as mitogen-activated protein kinase and oncogenic traits such as replication stress. RNA metabolic labeling and assessment of RNA velocity in patient-derived organoids revealed developmental trajectories of colorectal cancer cells organized along a mitogen-activated protein kinase activity gradient. This was in contrast to normal colon organoid cells developing along graded Wnt activity. Experimental targeting of EGFR-BRAF-MEK in cancer organoids affected signaling and gene expression contingent on predictive KRAS/BRAF mutations and induced cell plasticity overriding default developmental trajectories, providing a basis for non-genetic resistance to targeted therapies.
ideal: an R/Bioconductor package for Interactive Differential Expression Analysis
Authors: Marini Federico , Linke Jan , Binder Harald
Published: January 2020

Background

RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking.

Results

We developed theidealsoftware package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpretation. ideal is implemented in R using the Shiny framework, and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of the differential expression analysis work-flow in an assisted way, and generate a broad spectrum of publication-ready outputs, including diagnostic and summary visualizations in each module, all the way down to functional analysis. ideal also offers the possibility to seamlessly generate a full HTML report for storing and sharing results together with code for reproducibility.

Conclusion

ideal is distributed as an R package in the Bioconductor project (http://bioconductor.org/packages/ideal/), and provides a solution for performing interactive and reproducible analyses of summarized RNA-seq expression data, empowering researchers with many different profiles (life scientists, clinicians, but also experienced bioinformaticians) to make theidealuse of the data at hand.
A Learning-Based Formulation of Parametric Curve Fitting for Bioimage Analysis
Authors: Mandal Soham , Uhlmann Virginie
Published: January 2020

Parametric curve models are convenient to describe and quantitatively characterize the contour of objects in bioimages. Unfortunately, designing algorithms to fit smoothly such models onto image data classically requires significant domain expertise. Here, we propose a convolutional neural network-based approach to predict a continuous parametric representation of the outline of biological objects. We successfully apply our method on the Kaggle 2018 Data Science Bowl dataset composed of a varied collection of images of cell nuclei. This work is a first step towards user-friendly bioimage analysis tools that extract continuously-defined representations of objects.
Concepts and Software Package for Efficient Quality Control in Targeted Metabolomics Studies – MeTaQuaC
Authors: Kuhring Mathias , Eisenberger Alina , Schmidt Vanessa , Kränkel Nicolle , Leistner David M. , Kirwan Jennifer , Beule Dieter
Published: January 2020

Targeted quantitative mass spectrometry metabolite profiling is the workhorse of metabolomics research. Robust and reproducible data is essential for confidence in analytical results and is particularly important with large-scale studies. Commercial kits are now available which use carefully calibrated and validated internal and external standards to provide such reliability. However, they are still subject to processing and technical errors in their use and should be subject to a laboratory’s routine quality assurance and quality control measures to maintain confidence in the results. We discuss important systematic and random measurement errors when using these kits and suggest measures to detect and quantify them. We demonstrate how wider analysis of the entire dataset, alongside standard analyses of quality control samples can be used to identify outliers and quantify systematic trends in order to improve downstream analysis. Finally we present the MeTaQuaC software which implements the above concepts and methods for Biocrates kits and creates a comprehensive quality control report containing rich visualization and informative scores and summary statistics. Preliminary unsupervised multivariate analysis methods are also included to provide rapid insight into study variables and groups. MeTaQuaC is provided as an open source R package under a permissive MIT license and includes detailed user documentation.
TALC: Transcript-level Aware Long Read Correction
Authors: Broseus Lucile , Thomas Aubin , Oldfield Andrew J. , Severac Dany , Dubois Emeric , Ritchie William
Published: January 2020

Motivation

Long-read sequencing technologies are invaluable for determining complex RNA transcript architectures but are error-prone. Numerous “hybrid correction” algorithms have been developed for genomic data that correct long reads by exploiting the accuracy and depth of short reads sequenced from the same sample. These algorithms are not suited for correcting more complex transcriptome sequencing data.

Results

We have created a novel reference-free algorithm called TALC (Transcription Aware Long Read Correction) which models changes in RNA expression and isoform representation in a weighted De-Bruijn graph to correct long reads from transcriptome studies. We show that transcription aware correction by TALC improves the accuracy of the whole spectrum of downstream RNA-seq applications and is thus necessary for transcriptome analyses that use long read technology.

Availability and Implementation

TALC is implemented in C++ and available athttps://gitlab.igh.cnrs.fr/lbroseus/TALC.

Contact

william.ritchie@igh.cnrs.fr
The synthetically produced predator odor 2,5-dihydro-2,4,5-trimethylthiazoline increases alcohol self-administration and alters basolateral amygdala response to alcohol in rats
Authors: Makhijani Viren H. , Franklin Janay P. , Voorhies Kalynn Van , Fortino Brayden , Besheer Joyce
Published: January 2020

Post-traumatic stress disorder (PTSD) is a psychiatric illness that can increase the risk for developing an alcohol use disorder (AUD). While clinical data has been useful in identifying similarities in the neurobiological bases of these disorders, preclinical models are essential for understanding the mechanism(s) by which PTSD increases the risk of developing AUD. The purpose of these studies was to examine if exposure of male Long-Evans rats to the synthetically produced predator odor 2,5-dihydro-2,4,5-trimethylthiazoline (TMT) would increase alcohol self-administration, potentially by facilitating transfer of salience towards cues, and alter neuronal response to alcohol as measured by the immediate early gene c-Fos. In Experiment 1 rats exposed to repeated (4x) TMT showed reductions in goal-tracking behavior in Pavlovian conditioned approach, and increases in alcohol self-administration. In Experiment 2 rats exposed to repeated TMT showed blunted basolateral amygdala c-Fos response to alcohol, and increased correlation between medial prefrontal cortex and amygdala subregions. In Experiment 3 rats exposed to single, but not repeated TMT showed increases in alcohol self-administration, and no change in anxiety-like behavior or hyperarousal. In Experiment 4, rats showed no habituation of corticosterone response after 4 TMT exposures. In summary, exposure of male rats to TMT can cause escalations in alcohol self-administration, reductions in goal-tracking behavior, and reduction in BLA response to alcohol. These studies outline and utilize a novel preclinical model that can be used to further neurobiological understanding of the relationship between PTSD and AUD.
Development of Systemic Immune Dysregulation in a Rat Trauma Model with Biomaterial-Associated Infection
Authors: Vantucci Casey E. , Ahn Hyunhee , Schenker Mara L. , Pradhan Pallab , Wood Levi B. , Guldberg Robert E. , Roy Krishnendu , Willett Nick J.
Published: January 2020

Orthopedic biomaterial-associated infections remain a large clinical challenge, particularly with open fractures and segmental bone loss. Invasion and colonization of bacteria within immune-privileged canalicular networks of the bone can lead to local, indolent infections that can persist for years without symptoms before eventual catastrophic hardware failure. Host immunity is essential for bacterial clearance and an appropriate healing response, and recent evidence has suggested an association between orthopedic trauma and systemic immune dysregulation and immunosuppression. However, the impact of a local infection on this systemic immune response and subsequent effects on the local response is poorly understood and has not been a major focus for addressing orthopedic injuries and infections. Therefore, this study utilized a model of orthopedic biomaterial-associated infection to investigate the effects of infection on the long-term immune response. Here, despite persistence of a local, indolent infection lacking outward symptoms, there was still evidence of long-term immune dysregulation with systemic increases in MDSCs and decreases in T cells compared to non-infected trauma. Further, the trauma only group exhibited a regulated and coordinated systemic cytokine response, which was not present in the infected trauma group. Locally, the infection group had attenuated macrophage infiltration in the local soft tissue compared to the non-infected group. Our results demonstrate widespread impacts of a localized orthopedic infection on the systemic and local immune responses. Characterization of the immune response to orthopedic biomaterial-associated infection may identify key targets for immunotherapies that could optimize both regenerative and antibiotic interventions, ultimately improving outcomes for these patients.
The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication but essential for the production of infectious virus
Authors: Ward Joseph C. , Lasecka-Dykes Lidia , Neil Chris , Adeyemi Oluwapelumi , Gold Sarah , McLean Niall , Wright Caroline , Herod Morgan R. , Kealy David , Warner Emma , King Donald P. , Tuthill Tobias J. , Rowlands David J. , Stonehouse Nicola J.
Published: January 2020

The positive stranded RNA genomes of picornaviruses comprise a single large open reading frame flanked by 5′ and 3′ untranslated regions (UTRs). Foot-and-mouth disease virus (FMDV) has an unusually large 5′ UTR (1.3 kb) containing five structural domains. These include the internal ribosome entry site (IRES), which facilitates initiation of translation, and the cis-acting replication element (cre). Less well characterised structures are a 5′ terminal 360 nucleotide stem-loop, a variable length poly-C-tract of approximately 100-200 nucleotides and a series of two to four tandemly repeated pseudoknots (PKs). We investigated the structures of the PKs by selective 2′ hydroxyl acetylation analysed by primer extension (SHAPE) analysis and determined their contribution to genome replication by mutation and deletion experiments. SHAPE and mutation experiments confirmed the importance of the previously predicted PK structures for their function. Deletion experiments showed that although PKs are not essential for replication, they provide genomes with a competitive advantage. However, although replicons and full-length genomes lacking all PKs were replication competent, no infectious virus was rescued from genomes containing less than one PK copy. This is consistent with our earlier report describing the presence of putative packaging signals in the PK region.
Open syntaxin overcomes synaptic transmission defects in diverseC. elegansexocytosis mutants
Authors: Tien Chi-Wei , Yu Bin , Huang Mengjia , Stepien Karolina P. , Sugita Kyoko , Xie Xiaoyu , Han Liping , Monnier Philippe P. , Zhen Mei , Rizo Josep , Gao Shangbang , Sugita Shuzo
Published: January 2020

Assembly of SNARE complexes that mediate neurotransmitter release requires opening of a ‘closed’ conformation of UNC-64/syntaxin. Rescue ofunc-13/Munc13phenotypes by overexpressed open UNC-64/syntaxin suggested a specific function of UNC-13/Munc13 in opening UNC-64/ syntaxin. Here, we revisit the effects of openunc-64/syntaxin by generating knockin (KI) worms. The KI animals exhibited enhanced spontaneous and evoked exocytosis compared to wild-type animals. Unexpectedly, the open syntaxin KI partially suppressed exocytosis defects of various mutants, includingsnt-1/synaptotagmin,unc-2/P/Q/N-type Ca2+channel alpha-subunit, andunc-31/CAPS in addition tounc-13/Munc13 andunc-10/RIM, and enhanced exocytosis intom-1/Tomosyn mutants. However, open syntaxin aggravated the defects ofunc-18/Munc18 mutants. Correspondingly, open syntaxin partially bypasses the requirement of Munc13 but not Munc18 for liposome fusion. Our results show that facilitating opening of syntaxin enhances exocytosis in a wide range of genetic backgrounds, and may provide a general means to enhance synaptic transmission in normal and disease states.
A Physiological Characterization in Controlled Bioreactors Reveals a Novel Survival Strategy forDebaryomyces hanseniiat High Salinity and Confirms its Halophilic Behavior
Authors: Navarrete Clara , Frost August T. , Ramos-Moreno Laura , Krum Mette R. , Martínez José L.
Published: January 2020

Debaryomyces hanseniiis traditionally described as a halotolerant non-conventional yeast, being the model organism for the study of osmo- and salt tolerance mechanisms in eukaryotic systems for the past 30 years.

However, unravelling ofD. hansenii’sbiotechnological potential has always been difficult due to the persistent limitations in the availability of efficient molecular tools described for this yeast. Additionally, there is a lack of consensus and contradictory information along the recent years that limits a comprehensive understanding of its central carbon metabolism, mainly due to a lack of physiological studies in controlled and monitored environments. Moreover, there is controversy about the diversity in the culture conditions (media composition, temperature and pH among others) used by different groups, which makes it complicated when trying to get significant conclusions and behavioural patterns.

In this work, we present for the first time a physiological characterization ofD. hanseniiin batch cultivations using highly instrumented and controlled lab-scale bioreactors. Our findings contribute to a more complete picture of the central carbon metabolism and the external pH influence on the yeast ability to tolerate high Na+and K+concentrations. Finally, the controversial halophilic/halotolerant character of this yeast is further clarified.
Topologically associating domain (TAD) boundaries stable across diverse cell types are evolutionarily constrained and enriched for heritability
Authors: McArthur Evonne , Capra John A.
Published: January 2020

Topologically associating domains (TADs) are fundamental units of three-dimensional (3D) nuclear organization. The regions bordering TADs—TAD boundaries—contribute to the regulation of gene expression by restricting interactions of cis-regulatory sequences to their target genes. TAD and TAD boundary disruption have been implicated in rare disease pathogenesis; however, we have a limited framework for integrating TADs and their variation across cell types into the interpretation of common trait-associated variants. Here, we investigate an attribute of 3D genome architecture—the stability of TAD boundaries across cell types—and demonstrate its relevance to understanding how genetic variation in TADs contribute to complex disease. By synthesizing TAD maps across 37 diverse cell types with 41 genome-wide association studies (GWAS), we investigate the differences in functionality and evolutionary pressure on variation in TADs versus TAD boundaries. We quantify their contribution to trait heritability and sequence-level evolutionary constraint and demonstrate that genetic variation in TAD boundaries contributes more to complex trait heritability, especially for immunologic, hematologic, and metabolic traits. We also show that TAD boundaries are more evolutionarily constrained than TADs. Next, stratifying boundaries by their stability across cell types, we find substantial differences. Boundaries stable across cell types are further enriched for complex trait heritability, evolutionary constraint, CTCF binding, and housekeeping genes compared to boundaries unique to a specific cell type. This suggests greater functional importance for stable boundaries. Thus, considering TAD boundary stability across cell types provides valuable context for understanding the genome’s functional landscape and enabling 3D-structure aware variant interpretation.
Similar time course of fast familiarity and slow recollection processes for recognition memory in humans and macaques
Authors: Wu Zhemeng , Kavanova Martina , Hickman Lydia , Lin Fiona , Buckley Mark J.
Published: January 2020

According to dual-process theory, recognition memory performance draws upon two processes, familiarity and recollection. The relative contribution to recognition memory are commonly distinguished in humans by analyzing receiver-operating-characteristics (ROC) curves; analogous methods are more complex and very rare in animals but fast familiarity and slow recollective-like processes (FF/SR) have been detected in non-human primates (NHPs) based on analyzing recognition error response time profiles. The relative utility of these methods to investigate familiarity and recollection/recollection-like processes across species is uncertain; indeed, even how comparable the FF/SR measures are across humans and NHPs remains unclear. Therefore in this study a broadly similar recognition memory task was exploited in both humans and NHPs to investigate the time course of the two recognition processes. We first show that the FF/SR dissociation exists in this task in human participants and then we demonstrate a similar profile in NHPs which suggests that FF/SR processes are comparable across species. We then verified, using ROC-derived indices for each time-bin in the FF/SR profile, that the ROC and FF/DR measures are related. Hence we argue that the FF/SR approach, procedurally easier in animals, can be used as a decent proxy to investigate these two recognition processes in future animal studies, important given that scant data exists as to the neural basis underlying recollection yet many of the most informative techniques primarily exist in animal models.
The dynamic surface proteomes of allergenic fungal conidia
Authors: Blango Matthew G. , Pschibul Annica , Rivieccio Flora , Krüger Thomas , Rafiq Muhammad , Jia Lei-Jie , Zheng Tingting , Goldmann Marie , Voltersen Vera , Li Jun , Panagiotou Gianni , Kniemeyer Olaf , Brakhage Axel A.
Published: January 2020

Fungal spores and hyphal fragments play an important role as allergens in respiratory diseases. In this study, we performed trypsin shaving and secretome analyses to identify the surface-exposed proteins and secreted/shed proteins ofAspergillus fumigatusconidia, respectively. We investigated the surface proteome under different conditions, including temperature variation and germination. We found that the surface proteome of restingA. fumigatusconidia is not static, but instead unexpectedly dynamic, as evidenced by drastically different surface proteomes under different growth conditions. Knockouts of two abundantA. fumigatussurface proteins, ScwA and CweA, were found to function only in fine-tuning the cell wall stress response, implying that the conidial surface is very robust against perturbations. We then compared the surface proteome ofA. fumigatusto other allergy-inducing molds, includingAlternaria alternata, Penicillium rubens, andCladosporium herbarum, and performed comparative proteomics on resting and swollen conidia, as well as secreted proteins from germinating conidia. We detected 125 protein ortholog groups, including 80 with putative catalytic activity, in the extracellular region of all four molds, and 42 nonorthologous proteins produced solely byA. fumigatus. Ultimately, this study highlights the dynamic nature of theA. fumigatusconidial surface and provides targets for future diagnostics and immunotherapy.
Contrasting population genetics of cattle- and buffalo-derivedTheileria annulatacausing tropical theileriosis
Authors: Chaudhry Umer , Ali Qasim , Zheng Lynn , Rashid Imran , Shabbir Muhammad Zubair , Nauman Muhammad , Ashraf Kamran , Evans Mike , Rafiq Shahzad , Oneeb Muhammad , Morrison Ivan , Sargison Neil D.
Published: January 2020

The present study was designed to improve understanding ofTheileria annulatain sympatric water buffalo and cattle in the Punjab province of Pakistan. The prevalence of tropical theileriosis is high, buparvaquone resistance is widespread, and vaccine protection is poor in the field. Better understanding is, therefore, needed of the factors that influence the genetics ofT. annulatapopulations both within its hosts and in its overall populations. Here we utilise a panel of six satellites and a mitochondrial cytochrome b marker to explore the multiplicity ofT. annulatainfection and patterns of emergence and spread of different parasite genotypes. Parasite materials were collected from infected animals in defined regions, where water buffalo and cattle are kept together. Our results show thatT. annulatais genetically more diverse in cattle- than in water buffalo-derived populations (the mean numbers of unique satellite alleles were 13.3 and 1.8 and numbers of unique cytochrome b locus alleles were 65 and 27 in cattle- and water buffalo-derived populations, respectively). The data show a high level of genetic diversity among the individual host-derived populations (the overall heterozygosity (He) indices were 0.912 and 0.931 in cattle, and 0.874 and 0.861 in buffalo, based on satellite and cytochrome b loci, respectively). When considered in the context of high parasite transmission rates and frequent animal movements between different regions, the predominance of multipleT. annulatagenotypes, with multiple introductions of infection in the hosts from which the parasite populations were derived, may have practical implications for the spread of parasite genetic adaptations; such as those conferring vaccine cross-protection against different strains affecting cattle and buffalo, or resistance to antiprotozoal drugs.
Cul3regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development
Authors: Morandell Jasmin , Schwarz Lena A. , Basilico Bernadette , Tasciyan Saren , Nicolas Armel , Sommer Christoph , Kreuzinger Caroline , Dotter Christoph P. , Knaus Lisa S. , Dobler Zoe , Cacci Emanuele , Danzl Johann G. , Novarino Gaia
Published: January 2020

De novoloss of function mutations in the ubiquitin ligase-encoding geneCullin3(CUL3)lead to autism spectrum disorder (ASD). Here, we usedCul3mouse models to evaluate the consequences ofCul3mutationsin vivo.Our results show thatCul3haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments.Cul3mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization,Cul3haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show thatCul3regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins inCul3mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development,Cul3deficiency appears less relevant at adult stages. In fact, induction ofCul3haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutiveCul3haploinsufficient animals. Taken together, our data indicate thatCul3has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due toCul3functions at early developmental stages.
Using Natural Language Processing to Learn the Grammar of Glycans
Authors: Bojar Daniel , Camacho Diogo M. , Collins James J.
Published: January 2020

While nucleic acids and proteins receive ample attention, progress on understanding the structural and functional roles of carbohydrates has lagged behind. Here, we develop a language model for glycans, SweetTalk, taking into account glycan connectivity and composition. We use this model to investigate motifs in glycan substructures, classify them according to their O-/N-linkage, and predict their immunogenicity with an accuracy of ∼92%, opening up the potential for rational glycoengineering.
Intestine-specific deletion of metal transporterZip14 (Slc39a14)causes brain manganese overload and locomotor defects of manganism
Authors: Aydemir Tolunay B. , Thorn Trista L. , Ruggiero Courtney H. , Pompilus Marjory , Febo Marcelo , Cousins Robert J.
Published: January 2020

Impaired manganese (Mn) homeostasis can result in excess Mn accumulation in specific brain regions and neuropathology. Maintaining Mn homeostasis and detoxification is dependent on effective Mn elimination. Specific metal transporters control Mn homeostasis. Human carriers of mutations in the metal transporter ZIP14 and whole-bodyZip14KO (WB-KO) mice display similar phenotypes, including spontaneous systemic and brain Mn overload, and motor dysfunction. Initially, it was believed that Mn accumulation due toZIP14mutations caused by impaired hepatobiliary Mn elimination. However, liver-specificZip14KO mice (L-KO) did not show systemic Mn accumulation or motor deficits. ZIP14 is highly expressed in the small intestine and is localized to the basolateral surface of enterocytes. Thus we hypothesized that basolaterally-localized ZIP14 in enterocytes provides another route for elimination of Mn. Using wild type and intestine-specific ZIP14 KO (I-KO) mice, we have shown that ablation of intestinalZip14is sufficient to cause systemic and brain Mn accumulation. The lack of intestinal ZIP14- mediated Mn excretion was compensated for by the hepatobiliary system; however, it was not sufficient to maintain Mn homeostasis. When supplemented with extra dietary Mn, I-KO mice displayed some motor dysfunctions, brain Mn accumulation based on both MRI imaging and chemical analysis, thus demonstrating the importance of intestinal ZIP14 as a route of Mn excretion. A defect in intestinalZip14expresssion likely could contribute to the Parkinson-like Mn accumulation of manganism.

New & Noteworthy

Mn-induced parkinsonism is recognized as rising in frequency due to both environmental factors and genetic vulnerability, yet currently, there is no cure. We provide evidence in an integrative animal model that basolaterally localized ZIP14 regulates Mn excretion and detoxification and that deletion of intestinal ZIP14 leads to systemic and brain Mn accumulation, providing robust evidence for the indispensable role of intestinal ZIP14 on Mn excretion.