bluuebunny/crossref_metadata_2025 huggingface dataset:
Family-based genome-wide association study of leprosy in Vietnam
Authors: Gzara Chaima , Dallmann-Sauer Monica , Orlova Marianna , Van Thuc Nguyen , Thai Vu Hong , Fava Vinicius M. , Bihoreau Marie-Thérèse , Boland Anne , Abel Laurent , Alcaïs Alexandre , Schurr Erwin , Cobat Aurélie
Published: February 2020

Leprosy is a chronic infectious disease of the skin and peripheral nerves with a strong genetic predisposition. Recent genome-wide approaches have identified numerous common variants associated with leprosy, almost all in the Chinese population. We conducted the first family-based genome-wide association study of leprosy in 622 affected offspring from Vietnam, followed by replication in an independent sample of 1189 leprosy cases and 671 controls of the same ethnic origin. The most significant results were observed within the HLA region, in which six SNPs displayed genome-wide significant associations, all of which were replicated in the independent case/control sample. We investigated the signal in the HLA region in more detail, by conducting a multivariate analysis on the case/control sample of 319 GWAS-suggestive HLA hits for which evidence for replication was obtained. We identified three independently associated SNPs, two located in the HLA class I region (rs1265048: OR=0.69 [0.58-0.80], combined p-value = 5.53×10−11; and rs114598080: OR=1.47 [1.46-1.48], combined p-value = 8.77×10−13), and one located in the HLA class II region (rs3187964 (OR=1.67 [1.55-1.80], combined p-value = 8.35×10−16). We also validated two previously identified risk factors for leprosy: the missense variant rs3764147 in the LACC1 gene (OR=1.52 [1.41-1.63], combined p-value = 5.06×10−14), and the intergenic variant rs6871626 located close to the IL12B gene (OR=0.73 [0.61-0.84], combined p-value = 6.44×10−8). These results shed new light on the genetic control of leprosy, by dissecting the influence of HLA SNPs, and validating the independent role of two additional variants in a large Vietnamese sample.
Deep Learning for pericardial fat extraction and evaluation on a population study
Authors: Santini Gianmarco , Latta Daniele Della , Vatti Alessio , Ripoli Andrea , Chiappino Sara , Piagneri Valeria , Chiappino Dante , Martini Nicola
Published: February 2020

Objectives

The pericardial fat represents a powerful (promising) index which has been seen to correlate with several cardiovascular events. We propose a novel approach to automatically measure it from CT scans and we seek to explore how it is distributed in a study population.

Methods

We studied a population of 1528 patients where 47 (3%) showed a cardiac event. The fat segmentation model was based on a deep neural network to identify the heart and from it, the pericardial fat was extract by threshold. Statistical analysis was finally computed to stratify the population according the quantity of pericardial fat.

Results

The high segmentation quality was reported with a Dice index (92.5%) and a Pearson coefficient (0.990, p<0.001). Notably, normalized pericardial fat volume was significantly higher in patients with cardiac event (73.46±30.84 vs 60.06±25.38 cm3/m2, p=0.005) with a AUC of 63,44% for discrimination of cardiac event.

Conclusions

The proposed approach reached accurate and fast performance for the evaluation of the pericardial fat making it reliable for a population analysis.
Quantitatively Evaluating the Cross-Sectoral and One Health Impact of Interventions: A Scoping Review and Application to Antibiotic Resistance
Authors: Naylor Nichola R. , Lines Jo , Waage Jeff , Wieland Barbara , Knight Gwenan M.
Published: February 2020

Current published guidance on how to evaluate antibiotic resistance (ABR) from a One Health perspective has focussed on the evaluation of intervention design and of the intervention implementation process. For efficient resource allocation, it is also important to consider quantitative measures of intervention impact. In particular, there has been little discussion of how to practically evaluate ABR-related agri- and aquaculture interventions from a public health perspective. Lessons can be learned from other One Health and cross-sectoral intervention impact evaluations.

WebofScience, EconLit, PubMed and grey literature were searched for literature quantitatively evaluating interventions across humans, animals and/or the environment. The review included 90 studies: 73 individual evaluations (from 72 papers) and 18 reviews, all including some measure of human impact, but only 29 papers covered all three One Health perspectives (human, animal and environmental). To provide decision makers with expected outcome estimates that are related to their objective functions, evaluations should provide outcome estimates from different perspectives. These include individual, microeconomic and/or macroeconomic perspectives across the One Health system. Based on the methods found in this review, a multi-level compartmental modelling approach for ABR-related intervention evaluation is proposed. The outcomes of such models can then feed into multi-criteria-decision analyses that weigh respective impact estimates alongside other chosen outcome estimates (for example equity or uncertainty). It is key that future quantitative evaluation models of ABR-related interventions are shared (for example through open source code sharing websites) to avoid duplication of effort and to enable more comprehensive estimates of intervention impact to be modelled in the future.
Genetically determined body mass index mediates the effect of smoking on type 2 diabetes risk, but not coronary artery disease risk
Authors: Thom Christopher S , Ding Zhuoran , Levin Michael G , Damrauer Scott M , Voight Benjamin F
Published: February 2020

Clinical observations have linked tobacco smoking with increased type 2 diabetes risk (1–5), a major public health concern (6). Mendelian randomization analysis has recently suggested smoking may be a causal risk factor for type 2 diabetes (7). However, this initial association could be mediated by additional causal risk factors correlated with smoking behavior, which have not been investigated to date. We hypothesized that body mass index (BMI) could explain the association between smoking and diabetes risk. First, we confirmed previous reports that genetically determined smoking behavior increased risk for both type 2 diabetes (OR=1.21, 95% CI: 1.15-1.27, P=1×10−12) and coronary artery disease (CAD; OR=1.21, 95% CI: 1.16-1.26, P=2×10−20). Additionally, a 2-fold increased smoking risk is positively associated with body mass index (BMI; ∼0.8 kg/m2, 95% CI: 0.54-0.98 kg/m2, P=1.8×10−11). In multivariable Mendelian randomization analysis, including BMI accounted for nearly all of the risk of smoking on type 2 diabetes (OR 1.06, 95% CI: 1.01-1.11, P=0.03). In contrast, the independent association between smoking and CAD persisted (OR 1.12, CI: 1.08-1.17, P=3×10−8) despite controlling for BMI. Causal mediation analyses agreed with these estimates. Our findings support a model whereby smoking initiation increases obesity, which in turn increases type 2 diabetes risk, with minimal if any direct effects from smoking on diabetes risk. Patients should be advised to stop smoking to limit both type 2 diabetes and CAD risk, and therapeutic efforts should consider pathophysiology relating smoking and obesity.
Oral, intestinal, and pancreatic microbiomes are correlated and exhibit co-abundance in patients with pancreatic cancer and other gastrointestinal diseases
Authors: Chung Mei , Zhao Naisi , Meier Richard , Koestler Devin C. , Del Castillo Erika , Wu Guojun , Paster Bruce J. , Charpentier Kevin , Izard Jacques , Kelsey Karl T. , Michaud Dominique S.
Published: February 2020

Oral microbiota are believed to play important roles in systemic diseases, including cancer. We collected oral swabs and at least one pancreatic tissue or intestinal samples from 52 subjects, and characterized 16S ribosomal RNA genes using high-throughput DNA sequencing in a total 324 samples. We identified a total of 73 unique Amplicon Sequence Variants (ASVs) that were shared between oral and pancreatic or intestinal samples. Accounting for pairing and within-subject correlation, 7 ASVs showed significant concordance (Kappa statistics) and 5 ASVs exhibited significant or marginally significant Pairwise Stratified Association (PASTA) between oral samples and pancreatic tissue or intestinal samples. Of these, two specific bacterial species (Gemella morbillorum and Fusobacterium nucleatum subsp. vincentii) showed consistent presence or absence patterns between oral and intestinal or pancreatic samples. Lastly, our microbial co-abundance analyses showed several distinct ASVs clusters and complex correlation-networks between ASV clusters in buccal, saliva, duodenum, jejunum, and pancreatic tumor samples. Toghether, our findings suggest that oral, intestinal, and pancreatic microbiomes are correlated and bacteria of oral origin exhibit co-abundance relationships and demonstrate complex correlation patterns in the intestinal and pancreatic tumor samples. Future prospective studies should aim to uncover the co-abundance of specific microbial communities for studying etiology of microbiota-driven carcinogenesis.
Added Value and Clinical Significance of Nonlinear Variability Indices of Walking Stride Interval in Neurodegenerative Diseases
Authors: Frédéric Dierick , Charlotte Vandevoorde , Frédéric Chantraine , Olivier White , Fabien Buisseret
Published: February 2020

Though self-paced walking is highly stereotyped, the stride interval fluctuates from one stride to the next around an average value with a measurable statistical variability. In clinical gait analysis, this variability is usually assessed with indices such the standard deviation or the coefficient of variation (CV). The aim of this study is to understand the added value that nonlinear indices of walking stride interval variability, such as Hurst exponent (H) and Minkowski fractal dimension (D), can provide in a clinical context and to suggest a clinical significance of these indices in the most common neurodegenerative diseases: Parkinson, Huntington, and amyotrophic lateral sclerosis. Although evidence have been accumulated that the stride interval organization at long range displays a more random, less autocorrelated, gait pattern in neurodegenerative diseases compared with young healthy individuals, it is today necessary to recompute CV, H, and D indices in a unified way and to take into account aging impact on these indices. In fact, computed nonlinear indices of variability are mainly dependent on stride interval time series length and algorithms used, making quantitative comparisons between different studies difficult or even impossible. Here, we recompute these indices from available stride interval time series, either coming from our lab or from online databases, or made available to us by the authors of previously conducted research. We confirm that both linear and nonlinear variability indices are relevant indicators of aging process and neurodegenerative diseases. CV is sensitive to aging process and pathology but does not allow to discriminate between specific neurodegenerative diseases. D shows no significative change in pathological groups. However, since H index is correlated with Hoehn & Yahr scores and significantly lowered in patients suffering from Huntington’s disease, we recommend it as a relevant supplement to CV.
Status of water sources, hygiene and sanitation and its impact on the health of households of Makwane Village, Limpopo Province, South Africa
Authors: Budeli P , Moropeng RC , Mpenyana-Monyatsi L , Kamika I , Momba MNB
Published: February 2020

The key to reducing or even eradicating the burden of waterborne diseases is through appropriate sanitation facilities and piped water systems. Installation of centralised system may take decades to be established, especially in impoverished rural communities of African countries. A survey of 88 households representing Makwane, a scattered settlement in South Africa, Limpopo Province, was conducted to assess the status of basic services. A questionnaire was designed to obtain the required information, such as improved water sources, improved sanitation facilities, hygiene practices and incidence of diarrhoeal diseases in the community. A house-to-house survey was conducted from July to August in 2014 and data were collected from the heads of each household. Results of the survey revealed a complete absence of improved drinking water sources in the community (100%). People rely on any available water sources such stream water, or on rainwater harvesting. Safe hygiene practices were observed in most households with regards to water storage as they store water in 25 L plastic buckets (57%), vessels stored inside a room (76%), use storage containers covered with a lid (76%) and wash these containers at any time prior to storing water (39%). Results also indicated a high percentage of households not treating water (81%) prior to use, disposing wastewater in the yard (97%), lacking access to improved sanitation facilities (41%), and not allowing children under 12 years old to use the toilets (62%). As a result, they practise open defecation as an alternative sanitation facility (86%). The main water source for the community was found to be the stream (31%) and this source is used for adequate personal hygiene in terms of full body bath (94%). In terms of health outcomes, the most prevalent health problem was found to be diarrhoea (75%), which occurred mostly in children less than 5 years old and was found to persist up to 3 days (34%). The community generally visited the clinic (75%) in cases of health problems. The implementation of point-of-use household drinking water treatment in Makwane households for the production of safe drinking water is highly recommended. In addition to this, a special education with emphasis on drinking water storage, cleaning of water storage containers and safe disposal of wastewater should be offered. Open defecation should also be discouraged to mitigate the bacterial contamination of water sources and transmission of diseases.
Context matters: Contrasting behavioral and residential risk factors for Lyme disease between two high-incidence regions in the Northeastern and Midwestern U.S
Authors: Bron Gebbiena M. , Fernandez Maria del P. , Larson Scott R. , Maus Adam , Gustafson Dave , Tsao Jean I. , Diuk-Wasser Maria A. , Bartholomay Lyric C. , Paskewitz Susan M.
Published: February 2020

The dynamics of zoonotic vector-borne diseases are determined by a complex set of parameters including human behavior that may vary with socio-ecological contexts. Lyme disease is the most common vector-borne disease in the United States and the Northeast and upper Midwest are the regions most affected - two areas with differing levels of urbanization and sociocultural settings. The probability of being diagnosed with Lyme disease is related to the risk of encounters with an infected blacklegged tick, which reflects both the environmental tick hazard and human behaviors. Herein, we compare behavioral and peridomestic risk factors associated with human-tick encounters between high-incidence states in the Northeast (New York and New Jersey) and Midwest (Wisconsin) of the United States. We used a smartphone application, The Tick App, as a novel survey tool, during spring and summer of 2018. Adaptive human behavior was identified in the relationship between outdoor activities and the use of preventive methods. More frequent recreational outdoor activities and gardening (a peridomestic activity) were associated with an increased likelihood of using personal protective measures. Weekly participation in non-seasonal recreational and peridomestic outdoor activities in spring and summer was associated with an increased likelihood of finding a tick in the fall or winter. Most outdoor activities were more frequently reported by participants from the Midwest than the Northeast. Participants in the Northeast reported less use of personal protective measures, but they reported more interventions to reduce the presence of peridomestic deer and ticks (i.e. pesticide applications on their property) than participants in the Midwest. Participants from the Midwest were more likely to kill rodents on their property. Context mattered, and our study illustrates the need for the assessment of personal behavior and tick exposure in these two Lyme disease-endemic regions to aid in targeted public health messaging to reduce tick-borne diseases.

Highlights

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Use of personal tick prevention was associated with more frequent outdoor activity

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Personal protective measure use was higher in the Midwest than Northeast

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Interventions reducing peridomestic deer and ticks more common in the Northeast
The impact of brain lesion characteristics and the corticospinal tract wiring pattern on mirror movement characteristics in unilateral cerebral palsy
Authors: Simon-Martinez Cristina , Zielinski Ingar , Hoare Brian , Decraene Lisa , Williams Jacqueline , Mailleux Lisa , Steenbergen Bert , Ortibus Els , Feys Hilde , Klingels Katrijn
Published: February 2020

Background

Mirror movements (MM) influence bimanual performance in children with unilateral cerebral palsy (uCP). Whilst MM are related to brain lesion characteristics and the corticospinal tract (CST) wiring pattern, the combined impact of these neurological factors remains unknown.

Objective

To investigate the combined impact of neurological factors on MM.

Methods

Forty-nine children with uCP (mean age 10y6mo) performed a repetitive squeezing task to quantify similarity between MM activity (MM-similarity) and strength of the MM activity (MM-intensity). We used MRI to evaluate lesion type (periventricular white matter, N=30) cortico-subcortical, N=19), the extent of ipsilesional damage and damage to basal ganglia, thalamus and corpus callosum. The CST wiring pattern (17 CSTcontralateral, 16 CSTipsilateral, 16 CSTbilateral) was assessed with Transcranial Magnetic Stimulation. Data was analyzed with simple and multiple regression analyses.

Results

MM-similarity in the more-affected hand was higher with more damage to the corpus callosum. MM-intensity was higher in children with CSTcontralateral with damage to the basal ganglia and thalamus. In the less-affected hand, MM-similarity was explained by the interaction between lesion type and CST wiring pattern, with higher MM-similarity in children with cortico-subcortical lesions in the CSTcontralateral group. MM-intensity was higher with larger damage to the corpus callosum and unilateral lesions.

Conclusions

A complex combination of neurological factors influences MM characteristics and the mechanisms differ between hands.
Elucidation of novel miRNA candidates and their role in unraveling the pathology of Non-Alcoholic Fatty Liver Disease
Authors: Biju Bincy Mary , Chhabra Saheb Singh , Sarkar Chiradeep
Published: February 2020

Non-Alcoholic Fatty Liver Disease (NAFLD) is a chronic liver disease which is observed in people who do not abuse alcohol. Main cause of NAFLD is Non-Alcoholic Steatohepatitis (NASH) where there is accumulation of fats such as triglyceride in liver and the disease progression ranges from simple steatosis to fibrosis and cirrhosis. MicroRNAs are critical players in post-transcriptional gene regulation of diseases with complex etiology. In this study, we have elucidated the role of microRNAs (miRNAs) in the pathophysiology of NAFLD/NASH and unravelled molecular markers for diagnosis of NAFLD. A subset of genes (n=10) responsible for NAFLD/NASH were selected and detailedin silicoanalysis carried out using multiple tools. miRDB and DIANA-microT were used to find putative miRNA binding sites followed by analysis using miRTarBase which is an experimentally validated database of miRNA-target interactions. The study elucidated a number of statistically significant predictions for both miRDB (scores >80) and DIANA-microT (values >0.90) and also strong experimental validation in miRTarBase. The analysis revealed that certain miRNAs like miR-7 & miR-548 family members are found in both the programmes, miRDB and DIANA-microT, targeting genes involved in liver function. They were also identified in the experimental validation database miRTarBase. These miRNAs probably play an important role in the pathophysiology of this disease. They can also be used as prognostic/diagnostic markers for assessment of NAFLD.
BiCoN: Network-constrained biclustering of patients and omics data
Authors: Lazareva Olga , Van Do Hoan , Canzar Stefan , Yuan Kevin , Baumbach Jan , Blumenthal David B. , Tieri Paolo , Kacprowski Tim , List Markus
Published: February 2020

Motivation

Unsupervised learning approaches are frequently employed to identify patient subgroups and biomarkers such as disease-associated genes. Thus, clustering and biclustering are powerful techniques often used with expression data, but are usually not suitable to unravel molecular mechanisms along with patient subgroups. To alleviate this, we developed the network-constrained biclustering approach BiCoN (Biclustering Constrained by Networks) which (i) restricts biclusters to functionally related genes connected in molecular interaction networks and (ii) maximizes the difference in gene expression between two subgroups of patients.

Results

Our analyses of non-small cell lung and breast cancer gene expression data demonstrate that BiCoN clusters patients in agreement with known cancer subtypes while discovering gene subnetworks pointing to functional differences between these subtypes. Furthermore, we show that BiCoN is robust to noise and batch effects and can distinguish between high and low load of tumor-infiltrating leukocytes while identifying subnetworks related to immune cell function. In summary, BiCoN is a powerful new systems medicine tool to stratify patients while elucidating the responsible disease mechanism.

Availability

PyPI package:https://pypi.org/project/bicon

Web interface:https://exbio.wzw.tum.de/bicon

Contact

olga.lazareva@tum.de

Supplementary information

Supplementary data are available atBioinformaticsonline.
A Combination of Two Human Monoclonal Antibodies Limits Fetal Damage by Zika Virus in Macaques
Authors: Van Rompay Koen K.A. , Coffey Lark L. , Kapoor Tania , Gazumyan Anna , Keesler Rebekah I. , Jurado Andrea , Peace Avery , Agudelo Marianna , Watanabe Jennifer , Usachenko Jodie , Singapuri Anil , Immareddy Ramya , Ardeshir Amir , Stuart Jackson B. , Bournazos Stylianos , Ravetch Jeffrey V. , Balderes Paul J. , Lorenz Ivo C. , Esswein Shannon R. , Keeffe Jennifer , Bjorkman Pamela J. , Wang Qiao , Rice Charles M. , MacDonald Margaret R. , Nussenzweig Michel C. , Robbiani Davide F.
Published: February 2020

Human infection by Zika virus (ZIKV) during pregnancy can lead to vertical transmission and fetal aberrations, including microcephaly. Prophylactic administration of antibodies can diminish or prevent ZIKV infection in animal models, but whether passive immunization can protect nonhuman primates and their fetuses during pregnancy has not been determined. Z004 and Z021 are neutralizing monoclonal antibodies to domain III of the envelope (EDIII) of ZIKV. Together the two antibodies protect nonpregnant macaques against infection even after Fc modifications to prevent antibody-dependent enhancementin vitro(ADE) and extend their half-lives. Here we report on prophylactic co-administration of the Fc-modified antibodies to pregnant rhesus macaques challenged 3 times with ZIKV during first and second trimester. The two antibodies did not entirely eliminate maternal viremia but limited vertical transmission protecting the fetus from neurologic damage. Thus, maternal passive immunization with two antibodies to EDIII can shield primate fetuses from the harmful effects of ZIKV.

Significance statement

Zika virus (ZIKV) infection during pregnancy can cause fetal abnormalities. Vaccines against ZIKV are under development, but because of potential safety concerns due to disease enhancing antibodies, and the time required by active immunization to induce protective antibodies, there is a need to explore alternative strategies. Recombinant monoclonal antibodies can be modified to prevent enhancement of infection, and thus could be an efficacious and safe alternative to vaccines to confer rapid protection. We show that prophylactic administration of two engineered antibodies, Z004 and Z021, to pregnant macaques partially protects against fetal neurologic damage and limits vertical transmission of ZIKV.
Non-invasive, Real-time Detection of Vascular Disorders in Mice using Bright SWIR-emitting Gold Nanoclusters and Monte Carlo Image Analysis
Authors: Yu Zhixi , Musnier Benjamin , Henry Maxime , Wegner K. David , Chovelon Benoit , Desroches-Castan Agnès , Fertin Arnold , Resch-Genger Ute , Bailly Sabine , Coll Jean-luc , Usson Yves , Josserand Véronique , Le Guével Xavier
Published: February 2020

We present here a new approach for non-invasive high resolution whole-body vascular imaging in depth by combining water-soluble and bright SWIR-emitting gold nanoclusters revealing an anisotropic surface charge with Monte Carlo image processing of the images. We applied and validated this approach to quantify vessel complexity in transgenic mice presenting vascular disorders.
Stochastic logistic models reproduce experimental time series of microbial communities
Authors: Descheemaeker Lana , de Buyl Sophie
Published: February 2020

We analyze properties of experimental microbial time series, from plankton and the human microbiome, and investigate whether stochastic generalized Lotka-Volterra models could reproduce those properties. We show that the noise term should be large and that it is a linear function of the species abundance, while the strength of the self-interactions should vary over multiple orders of magnitude. We stress the fact that all the observed stochastic properties can be obtained from a logistic model, i.e. without interactions, even the niche character of the experimental time series. Linear noise is associated with growth rate stochasticity, which is related to changes in the environment. This suggests that fluctuations in the sparsely sampled experimental time series are caused by extrinsic sources.
ADAR1 editing dependency in triple-negative breast cancer
Authors: Kung Che-Pei , Cottrell Kyle A. , Ryu Sua , Bramel Emily R. , Kladney Raleigh D. , Bross Emily A. , Maggi Leonard , Weber Jason D.
Published: February 2020

Triple-negative breast cancer (TNBC) is the deadliest form of breast cancer. Unlike other types of breast cancer that can be effectively treated by targeted therapies, no such targeted therapy exists for all TNBC patients. The ADAR1 enzyme carries out A-to-I editing of RNA to prevent sensing of cellular double-stranded RNAs (dsRNA). ADAR1 is highly expressed in breast cancer including TNBC. Here, we demonstrate that ADAR1 expression and editing activity is required in TNBC cell lines but not in ER+ and/or Her2+ cells. In TNBC cells, knockdown of ADAR1 attenuates proliferation and tumorigenesis. PKR expression is elevated in TNBC and its activity is induced upon ADAR1-knockdown, which correlates with a decrease in translation. ADAR1-dependent TNBC cell lines also exhibit elevated IFN stimulated gene expression. IFNAR1 reduction significantly rescues the proliferative defects of ADAR1 loss. These findings establish ADAR1 as a novel therapeutic target for TNBC tumors.
Phylogenomic resolution of sea spider diversification through integration of multiple data classes
Authors: Ballesteros Jesús A. , Setton Emily V.W. , Santibáñez López Carlos E. , Arango Claudia P. , Brenneis Georg , Brix Saskia , Cano-Sánchez Esperanza , Dandouch Merai , Dilly Geoffrey F. , Eleaume Marc P. , Gainett Guilherme , Gallut Cyril , McAtee Sean , McIntyre Lauren , Moran Amy L. , Moran Randy , López-González Pablo J. , Scholtz Gerhard , Williamson Clay , Woods H. Arthur , Wheeler Ward C. , Sharma Prashant P.
Published: February 2020

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and three nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.
Glial type specific regulation of CNS angiogenesis by HIFα-activated different signaling pathways
Authors: Zhang Sheng , Kim Bokyung , Zhu Xiaoqing , Gui Xuehong , Wang Yan , Lan Zhaohui , Prabhu Preeti , Fond Kenneth , Wang Aijun , Guo Fuzheng
Published: February 2020

The mechanisms by which oligodendroglia modulate CNS angiogenesis remain elusive. Previousin vitrodata suggest that oligodendroglia regulate CNS endothelial cell proliferation and blood vessel formation through hypoxia inducible factor alpha (HIFα)-activated Wnt (but not VEGF) signaling. Usingin vivogenetic models, we show that HIFα in oligodendroglia is necessary and sufficient for angiogenesis independent of CNS regions. At the molecular level, HIFα stabilization in oligodendroglia does not perturb Wnt signaling but remarkably activates VEGF. At the functional level, genetically blocking oligodendroglia-derived VEGF but not Wnt significantly decreases oligodendroglial HIFα-regulated CNS angiogenesis. Interestingly, blocking astroglia-derived Wnt signaling reduces astroglial HIFα-regulated CNS angiogenesis. Together, ourin vivodata clearly demonstrate that oligodendroglial HIFα regulates CNS angiogenesis through Wnt-independent and VEGF-dependent signaling. Our findings represent an alternative mechanistic understanding of CNS angiogenesis by postnatal glial cells and unveil a glial cell type-dependent HIFα-Wnt axis in regulating CNS vessel formation.
Molecular Modeling Evaluation of the Binding Effect of Ritonavir, Lopinavir and Darunavir to Severe Acute Respiratory Syndrome Coronavirus 2 Proteases
Authors: Lin Shen , Shen Runnan , He Jingdong , Li Xinhao , Guo Xushun
Published: February 2020

Three anti-HIV drugs, ritonavir, lopinavir and darunavir, might have therapeutic effect on coronavirus disease 2019 (COVID-19). In this study, the structure models of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteases, coronavirus endopeptidase C30 (CEP_C30) and papain like viral protease (PLVP), were built by homology modeling. Ritonavir, lopinavir and darunavir were then docked to the models, respectively, followed by energy minimization of the protease-drug complexes. In the simulations, ritonavir can bind to CEP_C30 most suitably, and induce significant conformation changes of CEP_C30; lopinavir can also bind to CEP_C30 suitably, and induce significant conformation changes of CEP_C30; darunavir can bind to PLVP suitably with slight conformation changes of PLVP. It is suggested that the therapeutic effect of ritonavir and lopinavir on COVID-19 may be mainly due to their inhibitory effect on CEP_C30, while ritonavir may have stronger efficacy; the inhibitory effect of darunavir on SARS-CoV-2 and its potential therapeutic effect may be mainly due to its inhibitory effect on PLVP.
Generation of Xylose-inducible promoter tools forPseudomonasspecies and their use in implicating a role for the Type II secretion system protein XcpQ in inhibition of corneal epithelial wound closure
Authors: Callaghan Jake D. , Stella Nicholas A. , Lehner Kara M. , Treat Benjamin R. , Brothers Kimberly M. , St. Leger Anthony J. , Shanks Robert M. Q.
Published: February 2020

Tunable control of gene expression is an invaluable tool for biological experiments. In this study, we describe a new xylose-inducible promoter system and evaluate it in bothPseudomonas aeruginosaandP. fluorescens. ThePxutpromoter derived from theP. flurorescens xutoperon was incorporated into a broad host-range pBBR1-based plasmid and compared to theEscherichia coli-derivedPBADpromoter usinggfpas a reporter. GFP-fluorescence from thePxutpromoter was inducible in bothPseudomonasspecies, but not inE. coli,which may facilitate cloning of toxic genes usingE. colito generate plasmids. ThePxutpromoter was expressed at a lower inducer concentration thanPBADinP. fluorescensand highergfplevels were achieved usingPxut. Flow cytometry analysis indicated thatPxutwas more leaky thanPBADin the testedPseudomonasspecies, but was expressed in a higher proportion of cells when induced. D-xylose did not support growth ofP. aeruginosaorP. fluorescensas a sole carbon source and is less expensive than many other commonly used inducers which could facilitate large scale applications. The efficacy of this system aided in demonstrating a role for theP. aeruginosatype II secretion system gene fromxcpQin bacterial inhibition of corneal epithelial cell wound closure. This study introduces a new inducible promoter system for gene expression for use inPseudomonasspecies.

Importance

Pseudomonasspecies are enormously important in human infections, biotechnology, and as a model system for interrogating basic science questions. In this study we have developed a xylose-inducible promoter system and evaluated it inP. aeruginosaandP. fluorescensand found it to be suitable for the strong induction of gene expression. Furthermore, we have demonstrated its efficacy in controlled gene expression to show that a type 2 secretion system protein fromP. aeruginosa, XcpQ, is important for host-pathogen interactions in a corneal wound closure model.
Relative contribution of non-structural protein 1 in dengue pathogenesis
Authors: Lee Pei Xuan , Ting Donald Heng Rong , Boey Clement Peng Hee , Tan Eunice Tze Xin , Chia Janice Zuo Hui , Ong Li Ching , Chua Yen Leong , Hapuarachchi Chanditha , Ng Lee Ching , Alonso Sylvie
Published: February 2020

Dengue is a major public health concern in the tropical and sub-tropical world with no effective treatment. The controversial live attenuated virus vaccine Dengvaxia has boosted the pursuit of sub-unit vaccine approaches, and the non-structural protein 1 (NS1) has recently emerged as a promising candidate. However, we found that NS1 immunization or passive transfer of NS1 antibodies failed to confer protection in symptomatic dengue mouse models using two non mouse-adapted DENV2 strains from the Cosmopolitan genotype that currently circulates in South-East Asia. Furthermore, exogenous administration of purified NS1 did not worsenin vivovascular leakage in sub-lethally infected mice, thereby supporting that NS1 does not play a critical role in the pathogenesis of these DENV2 strains. Virus chimerization approaches indicated that the prME structural region, but not NS1, plays a critical role in drivingin vivofitness and virulence of the virus, through induction of key pro-inflammatory cytokines. This work highlights that the pathogenic role of NS1 is DENV strain-dependent, which warrants re-evaluation of NS1 as a universal dengue vaccine candidate.
Sorting liposomes of distinct sizes by DNA-brick assisted centrifugation
Authors: Yang Yang , Wu Zhenyong , Wang Laurie , Zhou Kaifeng , Xia Kai , Xiong Qiancheng , Xiong Yong , Melia Thomas J , Karatekin Erdem , Gu Hongzhou , Lin Chenxiang
Published: February 2020

The “tiny bubbles of fluid” wrapped by lipid-bilayer membranes, termed vesicles, are abundant in cells and extracellular space, performing critical tasks including nutrient uptake, cargo transport, and waste confinement. Vesicles on different missions and transport routes are often distinct both in size and in chemical composition, which confers specificity to their interactions with other membranous compartments. Therefore, to accurately recapitulate the vesicles’ structure and behavior, it is important to use homogeneous liposomes (vesicles made of synthetic components) with precisely defined attributes as model membranes. Although existing methods can generate liposomes of selected sizes with reasonable homogeneity, the scalable production of uniformly-sized liposomes across a wide range of dimensions and compositions remains challenging. Here we report a streamlined, high-throughput sorting technique that uses cholesterol-modified “nanobricks” made of a few DNA oligonucleotides to differentiate hetero-sized liposomes by their buoyant densities. After DNA-brick coating, milligrams of liposomes of different origins (e.g., produced via extrusion or sonication, and reconstituted with membrane proteins) can be separated by centrifugation into six to eight homogeneous populations with mean diameters from 30 to 130 nm. In proof of concept experiments, we show that these uniform, leak-free liposomes are ideal substrates to study, with an unprecedented resolution, how membrane curvature influences the activity of peripheral (ATG3) and integral (SNARE) membrane proteins. We anticipate that our sorting technique will facilitate the quantitative understanding of membrane curvature in vesicular transport. Furthermore, adding a facile and standardized separation step to the conventional liposome preparation pipeline may benefit the formulation and prototyping of liposomal drug-carrying vehicles.
Gut lymph purification regulates monocyte activity in rats with ischemia-reperfusion injury-induced sepsis
Authors: Zhang Wei , Chen Jie , Jin Can , Zhang Shuncheng , Gu Juan , Shi Meimei
Published: February 2020

Objective

To confirm that gut lymph purification (GLP) based on oXiris regulates monocyte activity by targeting the removal of ischemia-reperfusion injury (IRI)-induced intestinal toxic substances (ITSs) in rats.

Methods

Sepsis was induced by intestinal IRI in 24 adult male Sprague-Dawley rats that were randomly divided into the control, intestinal IRI, and IRI+GLP groups. The gut lymph fluid (GLF) was drained for 180 minutes. The ITSs levels and the proliferation, apoptosis and positive expression rates of MHC-II molecules of monocytes coincubated with the GLF were detected.

Results

Endotoxin, TNF-α, IL-4, IL-6 and IL-10 levels in the lymph and plasma of the IRI group were significantly higher than those of the control group (p< 0.01). Compared with the IRI group, GLP treatment significantly decreased the ITS levels (p< 0.05). Monocyte proliferation and the positive expression rate of MHC-□ molecules were significantly reduced after co-culturing with GLF upon IRI (p< 0.01), and the apoptotic rate was significantly increased (p< 0.01). However, culturing monocytes with GLP significantly enhanced the monocyte proliferation, increased the positive expression rate of MHC-□ monocytes (p< 0.01), and reduced the apoptotic rate (p< 0.01).

Conclusions

GLP therapy based on oXiris effectively removed ITSs from the GLF after IRI, thereby blocking the main process of multiple organ dysfunction syndrome by regulating monocyte activity.
Expanding the phenotypic spectrum in RDH12-associated retinal disease
Authors: Scott Hilary A. , Place Emily M. , Ferenchak Kevin , Zampaglione Erin , Wagner Naomi E. , Chao Katherine R. , DiTroia Stephanie P. , Navarro-Gomez Daniel , Mukai Shizuo , Huckfeldt Rachel M. , Pierce Eric A. , Bujakowska Kinga M.
Published: February 2020

Retinol dehydrogenase 12, RDH12, plays a pivotal role in the visual cycle to ensure the maintenance of normal vision. Alterations in activity of this protein result in photoreceptor death and decreased vision beginning at an early age and progressing to substantial vision loss later in life. Here we describe 11 patients with retinal degeneration that underwent next-generation sequencing (NGS) with a targeted panel of all currently known inherited retinal degeneration (IRD) genes and whole-exome sequencing to identify the genetic causality of their retinal disease. These patients display a range of phenotypic severity prompting clinical diagnoses of macular dystrophy, cone-rod dystrophy, retinitis pigmentosa, and early-onset severe retinal dystrophy all attributed to biallelic recessive mutations in RDH12. We report 15 causal alleles and expand the repertoire of known RDH12 mutations with four novel variants: c.215A > G (p.Asp72Gly); c.362T > C (p.Ile121Thr); c.440A > C (p.Asn147Thr); and c.697G > A (p.Val233Ille). The broad phenotypic spectrum observed with biallelic RDH12 mutations has been observed in other genetic forms of IRDs, but the diversity is particularly notable here given the prior association of RDH12 primarily with severe early-onset disease. This breadth emphasizes the importance of broad genetic testing for inherited retinal disorders and extends the pool of individuals who may benefit from imminent gene-targeted therapies.
Undifferentiated small round cell sarcoma in a young male: a case report
Authors: Ricker Cora A. , Berlow Noah E. , Crawford Kenneth A. , Georgopapadakos Todd , Huelskamp Audrey N. , Woods Andrew D. , Dhimolea Eugen , Ramkissoon Shakti H. , Spunt Sheri L. , Rudzinski Erin R. , Keller Charles
Published: February 2020

CIC-rearranged sarcomas (CRSs) have recently been characterized as a distinct sarcoma subgroup with a less favorable prognosis compared to other small round cell sarcomas. CRSs share morphologic features with Ewing's sarcoma and prior to 2013 were grouped under undifferentiated sarcomas with round cell phenotype by the WHO classification. In this report, whole-genome sequencing and RNA sequencing were performed for an adolescent male patient with CRS who was diagnosed with undifferentiated pleomorphic sarcoma (UPS) by three contemporary institutions. Somatic mutation analysis identified mutations in IQGAP1, CCNC, and ATXN1L in pre- and post-treatment tissue samples, as well as a CIC–DUX4 fusion that was confirmed by qPCR and DUX4 immunohistochemistry. Of particular interest was the overexpression of the translation factor eEF1A1, which has oncogenic properties and has recently been identified as a target of the investigational agent plitidepsin. This case may provide a valuable waypoint in the understanding and classification of CRSs and may provide a rationale for targeting eEF1A1 in similar soft tissue sarcoma cases.
Phenotypic expansion of autosomal dominant retinitis pigmentosa associated with the D477G mutation in RPE65
Authors: Jauregui Ruben , Cho Ahra , Oh Jin Kyun , Tanaka Akemi J. , Sparrow Janet R. , Tsang Stephen H.
Published: February 2020

Mutations in the gene RPE65 (OMIM: 180069) are recessively inherited and known to cause Leber congenital amaurosis. Recently, the mutation D477G in RPE65 has been identified as a cause of autosomal dominant retinitis pigmentosa (RP). Variable expressivity of this disease has been reported, as carrier individuals can present with mild, nonpenetrant, or, most commonly, a severe chorioretinal phenotype that resembles choroideremia. We report the case of a 57-yr-old male who presented to our clinic with nyctalopia and decreasing visual acuity for 1 yr. Dilated fundus examination revealed retinal atrophy and peripheral mottling of the retinal pigment epithelium (RPE). SW-AF revealed patchy hypoautofluorescence throughout the posterior pole with separate lacunae-like areas in the macula of severe RPE atrophy along with foveal sparing. Full-field electroretinogram suggested a rod–cone dystrophy. Whole-exome sequencing revealed the heterozygous mutation c.1430A > G (p.D477G) in the RPE65 gene. This phenotype of peripheral RPE mottling and severe macular lacunae-like atrophy has not been previously reported with RPE65 autosomal dominant RP, supporting the variable expressivity of the disease and expanding the known phenotypic presentations.
Enrichment of Fully Packaged Virions in Column-Purified Recombinant Adeno-Associated Virus (rAAV) Preparations by Iodixanol Gradient Centrifugation Followed by Anion-Exchange Column Chromatography
Authors: Sena-Esteves Miguel , Gao Guangping
Published: February 2020

This rapid and efficient method to prepare highly purified recombinant adeno-associated viruses (rAAVs) is based on binding of negatively charged rAAV capsids to an anion-exchange resin that is pH dependent.
Denaturing Lysis of Cells for Immunoprecipitation
Authors: DeCaprio James , Kohl Thomas O.
Published: February 2020

The only way to solubilize many antigens for immunoprecipitation is by denaturation. This cell lysis protocol is ideally suited for this purpose to release proteins from complex structures or reveal antibody epitopes hidden within native proteins. Short linear epitopes may not be accessible to antibodies within the native tertiary and quaternary protein structures, but they become exposed upon the unraveling of proteins, exposing their secondary structure. Antibodies otherwise not suitable for the immunoprecipitation of proteins prepared under nondenaturing conditions are now able to bind these antigens of interest in cell lysates prepared under denaturing conditions. These antibodies may also work well for immunoblotting purposes when the protein target is completely denatured. Harvested cells in this protocol are washed in tris-buffered saline (TBS) before lysis in 2% sodium dodecyl sulfate (SDS)-containing Lysis buffer for 10 min at 100°C. The resulting sample is diluted 20-fold in TBS to reduce the SDS concentration to ≤0.1% before the addition of an antibody for immunoprecipitation. Addition of 2% bovine serum albumin (BSA) or 0.1% Nonidet P-40 to the TBS before an immunoprecipitation, respectively, ensures either removal of SDS from the target protein or retaining denatured proteins in solution.
The structure of MP-4 from Mucuna pruriens at 2.22 Å resolution
Authors: Jain Abha , Kumar Amit , Shikhi Meha , Kumar Ashish , Nair Deepak T. , Salunke Dinakar M.
Published: February 2020

The structure of the MP-4 protein was previously determined at a resolution of 2.8 Å. Owing to the unavailability of gene-sequence information at the time, the side-chain assignment was carried out on the basis of a partial sequence available through Edman degradation, sequence homology to orthologs and electron density. The structure of MP-4 has now been determined at a higher resolution (2.22 Å) in another space group and all of the structural inferences that were presented in the previous report of the structure were validated. In addition, the present data allowed an improved assignment of side chains and enabled further analysis of the MP-4 structure, and the accuracy of the assignment was confirmed by the recently available gene sequence. The study reinforces the traditional concept that conservative interpretations of relatively low-resolution structures remain correct even with the availability of high-resolution data.