bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyperdense Thymic Atrophy After Chemotherapy in Pediatric Patients With Extrathoracic Malignancies
Authors: Kawaguchi Masaya , Kato Hiroki , Kaneko Yo , Matsuo Masayuki
Published: September 2020

Objective

The aim of the study was to evaluate computed tomography (CT) imaging findings of hyperdense thymic atrophy after chemotherapy in pediatric patients with extrathoracic malignancies.

Methods

Seventy-eight pediatric patients with extrathoracic malignancies, who developed thymic atrophy after chemotherapy, were included in this study. All patients underwent CT imaging before and after chemotherapy. We retrospectively reviewed the CT images. Hyperdense thymic atrophy was defined as thymic atrophy with high CT attenuation (≥80 HU).

Results

Hyperdense thymic atrophy after chemotherapy was observed in 7 (9%) of 78 patients. Age (4.3 ± 2.4 vs 8.4 ± 5.4 years, P < 0.01), thymic CT attenuation before chemotherapy (70.4 ± 18.8 vs 55.2 ± 11.9 HU, P < 0.01), reduction rate in thymic area (0.76 ± 0.06 vs 0.60 ± 0.22, P < 0.01), and thymic CT attenuation change (30.3 ± 15.2 vs −16.8 ± 24.0 HU, P < 0.01) were significantly different between patients with and without hyperdense thymic atrophy after chemotherapy. Thymic CT attenuation after chemotherapy (61.2 ± 23.8 vs 33.8 ± 30.1 HU, P < 0.01) and thymic CT attenuation change (−1.3 ± 21.2 vs −19.3 ± 27.9 HU, P < 0.01) were significantly different between patients 5 years or younger (n = 29) and 6 years or older (n = 49).

Conclusions

Hyperdense thymic atrophy after chemotherapy was observed in 9% of pediatric patients with extrathoracic malignancies. It was associated with younger age, greater thymic CT attenuation before chemotherapy, larger reduction rate in thymic area, and greater thymic CT attenuation change.
The Efficacy of Antihistamines in Preventing Reactions to Infliximab in Patients With Crohn Disease/Ulcerative Colitis
Authors: Fournier Kerri Ann , Dwyer Patricia A. , Vessey Judith A. , Shea Joan , Pratt Patricia
Published: September 2020

Inflammatory bowel diseases, including Crohn disease and ulcerative colitis, are most often diagnosed during adolescence and young adulthood, with a rising incidence in pediatric populations. Infliximab is an effective treatment option for Crohn disease and ulcerative colitis. The most common adverse event with infliximab is an infusion reaction. Patients are often treated prophylactically with combinations of acetaminophen, intravenous steroid, and an antihistamine to prevent an infusion reaction. There is a high degree of practice variation regarding pretreatment for infliximab infusions, the efficacy of pretreatment with an antihistamine is unproven in preventing infusion-related reactions, and there is no national clinical standard. Unnecessary pretreatment in adolescence and young adulthood may be harmful, as this is a time to focus on developing self-care management skills. Antihistamine side effects including somnolence and dizziness may adversely affect adolescents and/or young adults' ability to complete schoolwork, drive, and transition toward autonomous management of their chronic illness. This report presents the findings of an evidence-based practice project reviewing the efficacy of pretreatment with an antihistamine in patients with Crohn disease and ulcerative colitis receiving infliximab. Practice implications are discussed.
A Multicenter International Randomized Controlled Manikin Study on Different Protocols of Cardiopulmonary Resuscitation for Laypeople
Authors: Baldi Enrico , Contri Enrico , Burkart Roman , Borrelli Paola , Ferraro Ottavia Eleonora , Paglino Martina , Pugliesi Marinella , Barbati Chiara , Bertaia Daniele , Tami Christian , Lopez Daniel , Boldarin Susi , Dénéréaz Sandrine , Terrapon Michael , Cortegiani Andrea ,   and the MANI-CPR investigators
Published: September 2020

Background

Compression-only cardiopulmonary resuscitation (CPR) is a suggested technique for laypeople facing out-of-hospital cardiac arrest (OHCA). However, it is difficult performing high-quality CPR until emergency medical services arrival with this technique. We aimed to verify whether incorporating intentional interruptions of different frequency and duration increases laypeople's CPR quality during an 8-minute scenario compared with compression-only CPR.

Methods

We performed a multicenter randomized manikin study selecting participants from 2154 consecutive laypeople who followed a basic life support/automatic external defibrillation course. People who achieved high-quality CPR in 1-minute test on a computerized manikin were asked to participate. Five hundred seventy-six were enrolled, and 59 were later excluded for technical reasons or incorrect test recording. Participants were randomized in an 8-minute OHCA scenario using 3 CPR protocols (30 compressions and 2-second pause, 30c2s; 50 compressions and 5-second pause, 50c5s; 100 compressions and 10-second pause, 100c10s) or compression-only technique. The main outcome was the percentage of chest compressions with adequate depth.

Results

Five hundred seventeen participants were evaluated. There was a statistically significant difference regarding the percentage of compressions with correct depth among the groups (30c2s, 96%; 50c5s, 96%; 100c10s, 92%; compression only, 79%; P = 0.006). Post hoc comparison showed a significant difference for 30c2s (P = 0.023) and for 50c5s (P = 0.003) versus compression only. Regarding secondary outcome, there were a higher chest compression fraction in the compression-only group and a higher rate of pauses longer than 10 seconds in the 100c10s.

Conclusions

In a simulated OHCA, 30c2s and 50c5s protocols were characterized by a higher rate of chest compressions with correct depth than compression only. This could have practical consequences in laypeople CPR training and recommendations.

Clinical Trial Registration: NCT02632500
Nuclear and mitochondrial genome sequencing of North-African Leishmania infantum isolates from cured and relapsed visceral leishmaniasis patients reveals variations correlating with geography and phenotype
Authors: Bussotti Giovanni , Benkahla Alia , Jeddi Fakhri , Souiaï Oussama , Aoun Karim , Späth Gerald F. , Bouratbine Aïda
Published: September 2020

Although several studies have investigated genetic diversity of Leishmania infantum in North Africa, genome-wide analyses are lacking. Here, we conducted comparative analyses of nuclear and mitochondrial genomes of seven L. infantum isolates from Tunisia with the aim to gain insight into factors that drive genomic and phenotypic adaptation. Isolates were from cured (n=4) and recurrent (n=3) visceral leishmaniasis (VL) cases, originating from northern (n=2) and central (n=5) Tunisia, where respectively stable and emerging VL foci are observed. All isolates from relapsed patients were from Kairouan governorate (Centre); one showing resistance to the anti-leishmanial drug Meglumine antimoniate. Nuclear genome diversity of the isolates was analysed by comparison to the L. infantum JPCM5 reference genome. Kinetoplast maxi and minicircle sequences (1 and 59, respectively) were extracted from unmapped reads and identified by blast analysis against public data sets. The genome variation analysis grouped together isolates from the same geographical origins. Strains from the North were very different from the reference showing more than 34 587 specific single nucleotide variants, with one isolate representing a full genetic hybrid as judged by variant frequency. Composition of minicircle classes within isolates corroborated this geographical population structure. Read depth analysis revealed several significant gene copy number variations correlating with either geographical origin (amastin and Hsp33 genes) or relapse (CLN3 gene). However, no specific gene copy number variation was found in the drug-resistant isolate. In contrast, resistance was associated with a specific minicircle pattern suggesting Leishmania mitochondrial DNA as a potential novel source for biomarker discovery.
Complex dynamics arising from the interplay between prey harvest saturation and predator-prey dynamics
Authors: Costa Michel Iskin da S. , dos Anjos Lucas
Published: September 2020

A study of the influence of prey harvest saturation on the dynamics of a predator-prey system is undertaken. It is shown that the augmentation of the constant intensity harvest part of this functional response can significantly change prey-predator dynamics by means of slight variations of the constant harvest intensity, rendering thus species management difficult due to, for instance, multiple attractors. Given that some management policies rely on the harvest saturation structure studied in this work, these results may have significant implications regarding renewable resource management.
Spatial proteomic characterization of HER2-positive breast tumors through neoadjuvant therapy predicts response
Authors: McNamara Katherine L. , Caswell-Jin Jennifer L. , Joshi Rohan , Ma Zhicheng , Kotler Eran , Bean Gregory R. , Kriner Michelle , Zhou Zoey , Hoang Margaret , Beechem Joseph , Zoeller Jason , Press Michael F. , Slamon Dennis J. , Hurvitz Sara A. , Curtis Christina
Published: September 2020

Addition of HER2-targeted agents to neoadjuvant chemotherapy has dramatically improved pathological complete response (pCR) rates in early-stage HER2-positive breast cancer. Still, up to 50% of patients have residual disease following treatment, while others are likely overtreated. Here, we performed multiplex spatial proteomic characterization of 122 samples from 57 HER2-positive breast tumors from the neoadjuvant TRIO-US B07 clinical trial sampled pre-treatment, after 14-21 days of HER2-targeted therapy, and at surgery. We demonstrate that proteomic changes following a single cycle of HER2-targeted therapy aids the identification of tumors that ultimately undergo pCR, outperforming pre-treatment measures or transcriptomic changes. We further developed and validated a classifier that robustly predicts pCR using a single marker, CD45, measured on-treatment, and show that CD45-positive cell counts measured via conventional immunohistochemistry perform comparably. These results demonstrate novel biomarkers to enable the stratification of sensitive tumors early during neoadjuvant HER2-targeted therapy with implications for tailoring subsequent therapy.
Impact of Personal Care Habits on Post-Lockdown COVID-19 Contagion: Insights from Agent-based Simulations
Authors: Álvarez-Pomar Lindsay , Rojas-Galeano Sergio
Published: September 2020

After the first wave of spread of the COVID-19 pandemic, countries around the world are struggling to recover their economies by slowly lifting the mobility restrictions and social distance measures enforced during the crisis. Therefore, the post-lockdown containment of the disease will depend strongly not any more on government-imposed interventions but on personal care measures, taken voluntarily by their citizens. In this respect, recent studies have shed some light regarding the effectiveness individual protection habits may have in preventing SARS-Cov-2 transmission, particularly physical contact distancing, facial mask wearing and hand-washing habits. In this paper we describe experiments performed on a simulated COVID-19 epidemic in an artificial population using an agent based model, so as to illustrate to what extent the interplay between such personal care habits contributes to mitigate the spread of the disease, assuming the lack of other population-wide non-pharmaceutical interventions or vaccines. We discuss scenarios where wide adherence to these voluntary care habits alone, can be enough to contain the unfold of the contagion. Our model purpose is illustrative and contributes to ratify the importance of disseminating the message regarding the collective benefits of mass adoption of personal protection and hygiene habits, as an exit strategy for COVID-19 in the new normal state.
Review of clinical characteristics and laboratory findings of COVID-19 in children-Systematic review and Meta-analysis
Authors: Kharoud Harmeet Kaur , Asim Rizwana , Siegel Lianne , Chahal Lovepreet , Singh Gagan Deep
Published: September 2020

OBJECTIVE

To conduct a systematic review and meta-analysis to assess the prevalence of various clinical symptoms and laboratory findings of COVID-19 in children.

METHODS

PubMed, MEDLINE, and SCOPUS databases were searched to include studies conducted between January 1, 2020, and July 15, 2020 which reported data about clinical characteristics and laboratory findings in laboratory-confirmed diagnosis of COVID-19 in pediatric patients. Random effects meta-analysis using generalized linear mixed models was used to estimate the pooled prevalence.

RESULTS

The most prevalent symptom of COVID-19 in children was 46.17% (95%CI 39.18-53.33%), followed by cough (40.15%, 95%CI 34.56-46.02%). Less common symptoms were found to be dyspnea, vomiting, nasal congestion/rhinorrhea, diarrhea, sore throat/pharyngeal congestion, headache, and fatigue. The prevalence of asymptomatic children was 17.19% (95%CI 11.02-25.82%).

The most prevalent laboratory findings in COVID-19 children were elevated Creatinine Kinase (26.86%, 95%CI 16.15-41.19%) and neutropenia (25.76%, 95%CI 13.96-42.58%). These were followed by elevated LDH, thrombocytosis, lymphocytosis, neutrophilia, elevated D Dimer, Elevated CRP, elevated ESR, leukocytosis, elevated AST and leukopenia. There was a low prevalence of elevated ALT and lymphopenia in children with COVID-19.

CONCLUSIONS AND RELEVANCE

This study provides estimates of the pooled prevalence of various symptoms and laboratory findings of COVID-19 in the pediatric population.
Tailoring the assembly of collagen fibers in alginate microspheres
Authors: Lehnert Sarah , Sikorski Pawel
Published: September 2020

The application of microspheres instead of bulk hydrogels in cell-laden biomaterials offers multiple advantages such as a high surface-to-volume-ratio and, consequently, a better nutrition and oxygen transfer to and from cells. The preparation of inert alginate microspheres is facile, quick, and well-established and the fabrication of alginate-collagen microspheres has been previously reported. However, no detailed characterization of the collagen fibrillogenesis in the alginate matrix is available. We use second-harmonic imaging microscopy reflection microscopy and turbidity assay to study assembly of collagen in alginate microspheres. We show that the assembly of collagen fibers in a gelled alginate matrix is a complex process that can be aided by addition of small polar molecules, such as glycine and by a careful selection of the gelling buffer used to prepare alginate hydrogels.

Highlights

In situcharacterization of collagen fiber assembly in a gelled alginate matrix using collagen-specific second harmonic generated microscopy

Collagen fibrillogenesis is positively influenced by the presence of small molecules in the solution prior microsphere preparation

The ratio and amount of calcium, sodium and chloride ions used for the alginate gelling has also a crucial impact on the development of a collagen fiber network
Exploring the Landscape of Ectodomain Shedding by Quantitative Protein Terminomics
Authors: Tsumagari Kazuya , Chang Chih-Hsiang , Ishihama Yasushi
Published: September 2020

Ectodomain shedding is a proteolytic process that regulates the levels and functions of membrane proteins. Dysregulated shedding is linked to severe diseases, including cancer and Alzheimer’s disease. However, the exact cleavage sites of shedding substrates remain largely unknown. Here, we explore the landscape of ectodomain shedding by generating large-scale, cell-type-specific maps of shedding cleavage sites. By means of N- and C-terminal peptide enrichment and quantitative mass spectrometry, we quantified protein termini in the culture media of 10 human cell lines and identified 411 cleavage sites on the ectodomain of 132 membrane proteins whose proteolytic terminal fragments are downregulated in the presence of a broad-spectrum metalloprotease inhibitor. A major fraction of the presented cleavage sites was identified in a cell-type-specific manner, and mapped onto receptors, cell adhesion molecules, and protein kinases and phosphatases. We confidently identified 86 cleavage sites as metalloprotease substrates by means of knowledge-based scoring.
Samplot: A Platform for Structural Variant Visual Validation and Automated Filtering
Authors: Belyeu Jonathan R. , Chowdhury Murad , Brown Joseph , Pedersen Brent S. , Cormier Michael J. , Quinlan Aaron R. , Layer Ryan M.
Published: September 2020

Visual validation is an essential step to minimize false positive predictions resulting from structural variant (SV) detection. We present Samplot, a tool for quickly creating images that display the read depth and sequence alignments necessary to adjudicate purported SVs across multiple samples and sequencing technologies, including short, long, and phased reads. These simple images can be rapidly reviewed to curate large SV call sets. Samplot is easily applicable to many biological problems such as prioritization of potentially causal variants in disease studies, family-based analysis of inherited variation, orde novoSV review. Samplot also includes a trained machine learning package that dramatically decreases the number of false positives without human review. Samplot is available via the conda package manager or athttps://github.com/ryanlayer/samplot.

Contact

Ryan Layer, Ph.D., Assistant Professor, University of Colorado Boulder,ryan.layer@colorado.edu.
Functionalized bead assay to measure 3-dimensional traction forces during T-cell activation
Authors: Aramesh Morteza , Mergenthal Simon , Issler Marcel , Plochberger Birgit , Weber Florian , Qin Xiao-Hua , Liska Robert , Duda Georg N. , Huppa Johannes B. , Ries Jonas , Schütz Gerhard J. , Klotzsch Enrico
Published: September 2020

When T-cells probe their environment for antigens, the bond between the T-cell receptor (TCR) and the peptide-loaded major histocompatibility complex (MHC) is put under tension, thereby influencing the antigen discrimination process. Yet, the quantification of such forces in the context of T-cell signaling is technically challenging. Common approaches such as traction force microscopy (TFM) employ a global readout of the force fields, e.g. by measuring the displacements of hydrogel-embedded marker beads. Recent data, however, indicated that T-cells exert tensile forces locally via TCR-enriched microvilli while scanning the surface of antigen-presenting cells. Here, we developed a traction force microscopy platform, which allows for quantifying the pulls exerted via T-cell microvilli, in both tangential and normal directions, during T-cell activation. For this, we immobilized specific T-cell activating antibodies directly on the marker beads used to read out the hydrogel deformation. Microvilli targeted the functionalized beads, as confirmed by superresolution microscopy of the local actin organization. Moreover, we found that cellular components, such as actin, TCR and CD45 reorganize upon interaction with the beads, such that actin forms a vortex-like ring structure around the beads and TCR is enriched at the bead surface, whereas, CD45 is excluded from bead-microvilli contacts.

Significance statement

During the antigen recognition process, T-cells explore and probe their environment via microvilli, which exert local pushes and pulls at the surface of the antigen presenting cell. It is currently believed that these forces influence or even enable the antigen recognition process. Here, we describe the development of a platform, which allows us to quantify the magnitude and direction of traction forces exerted locally by T cell microvilli. Simultaneous Ca2+imaging was used to link the measured forces to the overall T cell activation status. Superresolution microscopy resolved the contact sites of bead-microvilli contact at the nanoscale: cells contacted beads via actin vortex-like structures, which excluded the phosphatase CD45 from the contacts.
NIAGADS Alzheimer’s GenomicsDB: A resource for exploring Alzheimer’s Disease genetic and genomic knowledge
Authors: Greenfest-Allen Emily , Valladares Otto , Kuksa Pavel P. , Gangadharan Prabhakaran , Lee Wan-Ping , Cifello Jeffrey , Katanic Zivadin , Kuzma Amanda B. , Wheeler Nicholas , Bush William S. , Leung Yuk Yee , Schellenberg Gerard , Stoeckert Christian J. , Wang Li-San
Published: September 2020

INTRODUCTION

The NIAGADS Alzheimer’s Genomics Database (GenomicsDB) is a public knowledgebase of Alzheimer’s disease (AD) genetic datasets and genomic annotations.

METHODS

It uses a custom systems architecture to adopt and enforce rigorous standards that facilitate harmonization of AD-relevant GWAS summary statistics datasets with functional annotations, including a database of >230 million annotated variants from the AD Sequencing Project’s joint-calling efforts.

RESULTS

The knowledgebase generates genome browser tracks and interactive compiled from harmonized datasets and annotations in the underlying database. These facilitate data sharing and discovery, by contextualizing AD-risk associations in a broader functional genomic context or summarizing them in the context of functionally annotated genes and variants.

DISCUSSION

Created to make AD-genetics knowledge more accessible to AD-researchers, the GenomicsDB shares annotated AD-relevant summary statistics datasets via a web interface designed to guide users unfamiliar with genetic data in not only exploring, but also interpreting this ever-growing volume of data.
Transcriptomic Analysis of Early Stages of Intestinal Regeneration inHolothuria glaberrima
Authors: Quispe-Parra David J. , Medina-Feliciano Joshua G. , Cruz-González Sebastián , Ortiz-Zuazaga Humberto , García-Arrarás José E.
Published: September 2020

Echinoderms comprise a group of animals with impressive regenerative capabilities. They can replace complex internal organs following injury or autotomy. In holothurians or sea cucumbers, cellular processes of intestinal regeneration have been extensively studied. The molecular machinery behind this faculty, however, remains to be understood. Here we assembled and annotated a de novo transcriptome using RNA-seq data consisting of regenerating and non-regenerating intestinal tissues from the sea cucumberHolothuria glaberrima. Comparisons of differential expression were made using the mesentery as a reference against 24 hour and 3 days regenerating intestine, revealing a large number of differentially expressed transcripts. Gene ontology and pathway enrichment analysis showed evidence of increasing transcriptional activity. Further analysis of transcripts associated with transcription factors revealed diverse expression patterns with mechanisms involving developmental and cancer-related activity that could be related to the regenerative process. Our study demonstrates the broad and diversified gene expression profile during the early stages of the process using the mesentery as the focal point of intestinal regeneration. It also establishes the genes that are the most important candidates in the cellular processes that underlie regenerative responses.
Incorporation of a Biocompatible Nanozyme in Cellular Antioxidant Enzyme Cascade Reverses Huntington’s Like Disorder in Preclinical Model
Authors: Adhikari Aniruddha , Mondal Susmita , Das Monojit , Biswas Pritam , Pal Uttam , Darbar Soumendra , Bhattacharya Siddhartha Sankar , Pal Debasis , Saha-Dasgupta Tanusri , Das Anjan Kumar , Mallick Asim Kumar , Pal Samir Kumar
Published: September 2020

The potentiality of nano-enzymes in therapeutic use has directed contemporary research to develop a substitute for natural enzymes, which are suffering from several disadvantages including low stability, high cost, and difficulty in storage. However, inherent toxicity, inefficiency in the physiologicalmilieu, and incompatibility to function in cellular enzyme networks limit the therapeutic use of nanozymes in living systems. Here, we have shown that citrate functionalized manganese-based biocompatible nanoscale material (C-Mn3O4NP) efficiently mimics glutathione peroxidase enzyme in the physiologicalmilieuand easily incorporates into the cellular multienzyme cascade for H2O2scavenging. A detailed computational study reveals the mechanism of the nanozyme action. We further established thein vivotherapeutic efficacy of C-Mn3O4nanozyme in a preclinical animal model of Huntington’s disease, a prevalent progressive neurodegenerative disorder, which has no effective medication till date.

Although, nano-enzymes have shown lots of promises in the management of several diseases, two major concerns limit their clinical translation. Apart from the inherent toxicity of the constituent materials (e.g., cerium, vanadium, gold, etc.), activities of contemporary nanozymes are often inhibited in physiologicalmilieu. Furthermore, most of them are incapable of incorporation into the cellular metabolic networks for functioning in tandem and parallel with natural enzymes, a major criteria for potential therapeutics.

Here, we have shown that citrate-functionalized spherical Mn3O4nanoparticles can efficiently mimic glutathione peroxidase (GPX) enzyme without the limitations of contemporary nanozymes, and effectively manage neurodegenerative Huntington’s disease in preclinical animal model. The choice of the material in the nanozyme lies on the fact that Mn is an essential micronutrient for mammals, and the stabilizing ligand citrate helps the nanoparticles to cross the blood-brain-barrier to reach brain. We have shown that the nanozyme can easily be incorporated in cellular antioxidant enzyme cascade. The specificity and efficacy of the nanozyme in the cascade was significantly higher compared to other reported nanozymes. We have justified our experimental findings with a detailed computational study. Understanding the mode of operation and management of Huntington’s disease in preclinical animal trial using a biocompatible (non-toxic) nanozyme as a part of the metabolic network may uncover a new paradigm in nanozyme based therapeutic strategy.
Visceral Leishmaniasis-HIV coinfection as a predictor of increased leishmania transmission at the village level in Bihar, India
Authors: Cloots Kristien , Marino Pia , Burza Sakib , Gill Naresh , Boelaert Marleen , Hasker Epco
Published: September 2020

Background

Visceral leishmaniasis (VL) is on the verge of being eliminated as a public health problem in the Indian subcontinent. Although Post-kala-azar dermal leishmaniasis (PKDL) is recognized as an important reservoir of transmission, we hypothesized that patients with VL co-infected with Human Immunodeficiency Virus (HIV) may also be important reservoirs of sustained leishmania transmission. We therefore investigated to what extent cases of PKDL or VL-HIV are associated with VL incidence at the village level in Bihar, India.

Methods

VL, VL-HIV, and PKDL case data from six districts within the highly VL-endemic state of Bihar, India were collected through the Kala-Azar Management Information System for the years 2014 – 2019. Multivariate analysis was done using negative binomial regression controlling for year as a fixed effect and block (subdistrict) as a random effect.

Findings

Presence of VL-HIV and PKDL cases were both associated with a more than twofold increase in VL incidence at village level, with Incidence Rate Ratios (IRR) of 2.16 (95% CI 1.81 – 2.58) and 2.37 (95% CI 2.01 – 2.81) for VL-HIV and PKDL cases respectively. A sensitivity analysis showed the strength of the association to be similar in each of the six included subdistricts.

Conclusions

These findings indicate the importance of VL-HIV patients as infectious reservoirs, and suggest that they represent a threat equivalent to PKDL patients towards the VL elimination initiative on the Indian subcontinent, therefore warranting a similar focus.

CONTRIBUTION TO THE FIELD

Visceral leishmaniasis (VL) – also called kala azar on the Indian subcontinent - is a parasitic disease which is fatal if not treated timely. Since the elimination initiative was launched in 2005 in the Indian subcontinent, the number of cases has come down drastically in this region. However, with the regional incidence of VL decreasing, understanding the role of potentially highly infectious subgroups in maintaining refractory Leishmania transmission is becoming increasingly important. Patients with Post-Kala-Azar Dermal Leishmaniasis (PKDL) are recognized as an important reservoir of transmission. We hypothesized that VL patients co-infected with Human Immunodeficiency Virus (HIV) may also be important reservoirs of sustained leishmania transmission. In this study, we found that the presence of VL-HIV and PKDL patients are both associated with a twofold increase incidence of VL at village level, suggesting they are equally important reservoirs for leishmania transmission. Our paper suggests that VL-HIV patients pose a threat equivalent to PKDL patients towards the VL elimination initiative and that therefore they should receive a similar focus.
The 4R Genome Duplication In Salmonine Fishes: Insights From Conserved Non-Coding Elements
Authors: Castillo Anibal H.
Published: September 2020

Gene and genome duplications are essential processes in evolution. Salmonids are ideal animal model systems to study these processes, as they originated from a tetraploid ancestor. Conserved non-coding elements (CNEs) are of interest because of their highly conserved DNA consensus motifs spanning lineages as diverse and divergent as humans and fish. The main goal of this study is to test CNEs as a tool to study genome duplications and to revisit the “4R” hypothesis and phylogeny of Salmonine fishes (Salmonidae)Salmo salar,Salvelinus alpinusandOncorhynchus mykissthrough the study of copy number and nucleotide variation in six pairs of CNEs. Allele numbers for most CNE sequence pairs are consistent with the 4R hypothesis, as is the symmetric phylogenetic topology shown by some CNE pairs; the estimated date of CNE duplication is consistent with the only reported range of 25-100Mya. However, the phylogenetic relationships within Salmoninae remain unresolved.
Broad-Spectrum, Patient-Adaptable Inhaled Niclosamide-Lysozyme Particles are Efficacious Against Coronaviruses in Lethal Murine Infection Models
Authors: Brunaugh Ashlee D. , Seo Hyojong , Warnken Zachary , Ding Li , Seo Sang Heui , Smyth Hugh D.C.
Published: September 2020

Niclosamide (NIC) has demonstrated promising in vitro antiviral efficacy against SARS-CoV-2, the causative agent of the COVID-19 pandemic. Though NIC is already FDA-approved, the oral formulation produces systemic drug levels that are too low to inhibit SARS-CoV-2. As an alternative, direct delivery of NIC to the respiratory tract as an aerosol could target the primary site of for SARS-CoV-2 acquisition and spread. We have developed a niclosamide powder suitable for delivery via dry powder inhaler, nebulizer, and nasal spray through the incorporation of human lysozyme (hLYS) as a carrier molecule. This novel formulation exhibits potent in vitro and in vivo activity against MERS-CoV and SARS-CoV-2 and may protect against methicillin-resistance staphylococcus aureus pneumonia and inflammatory lung damage occurring secondary to CoV infections. The suitability of the formulation for all stages of the disease and low-cost development approach will ensure wide-spread utilization
Reappraisal of Spinach-based RNA Visualization in Plants
Authors: Yu Zhiming , Mei Fengling , Yan Haiting , Chen Qiyuan , Yao Mengqin , Liu Shuyue , Wang Yue , Zhang Xian , Zhang Pengcheng , Jackson Stephen , Shi Nongnong , Liu Yule , Hong Yiguo
Published: September 2020

RNAs can be imaged in living cells using molecular beacons, RNA-binding labeled proteins and RNA aptamer-based approaches. However, Spinach RNA-mimicking GFP (RMG) has not been successfully used to monitor cellular RNAs in plants. In this study, we re-evaluated Spinach-based RNA visualization in different plants via transient, transgenic, and virus-based expression strategies. We found that like bacterial, yeast and human cellular tRNAs, plant tRNAs such as tRNALys(K) can protect and/or stabilize the spinach RNA aptamer interaction with the fluorophore DFHBI enabling detectable levels of green fluorescence to be emitted. The tRNALys-spinach-tRNALys(KSK), once delivered into “chloroplast-free” onion epidermal cells can emit strong green fluorescence in the presence of DFHBI. Transgenic or virus-based expression of monomer KSK, in either stably transformed or virus-infectedNicotinana benthamianaplants, failed to show RMG fluorescence. However, incorporating tandem repeats of KSK into recombinant viral RNAs, enabled qualitative and quantitative detection, both in vitro and ex vivo (ex planta), of KSK-specific green fluorescence, though RMG was less obvious in vivo (in planta). These findings demonstrate Spinach-based RNA visualization has the potential forex vivoandin vivomonitoring RNAs in plant cells.

One sentence summary

Spinach-based RMG technology was reevaluated to have potential for ex vivo and in vivo monitoring RNAs in plant cells.
Phosphorylated paxillin and FAK constitute subregions within focal adhesions
Authors: Bachmann Michael , Skripka Artiom , Wehrle-Haller Bernhard , Bastmeyer Martin
Published: September 2020

Integrin-mediated adhesions are convergence points of multiple signaling pathways. Their inner structure and their diverse functions can be studied with super-resolution microscopy. We used structured illumination microscopy (SIM) to analyze spatial organization of paxillin phosphorylation (pPax) within adhesions. We found that pPax and focal adhesion kinase (FAK) form spot-like, spatially defined clusters within adhesions in several cell lines. In contrast, other adhesion proteins showed no consistent organization in such clusters. Live-cell super-resolution imaging revealed that pPax-FAK clusters persist over time but modify distance to each other dynamically. Moreover, we show that the distance between separate clusters of pPax is mechanosensitive. Thus, in this work we introduce a new structural organization within focal adhesions and demonstrate its regulation and dynamics.
Histone modifications at the transcription start site of non-coding RNA revealed regulatory patterns of activation inCaenorhabditis elegansembryo
Authors: Bandeira Megan A. , Boeck Max E.
Published: September 2020

Histone modifications play an essential role in regulating recruitment of RNA polymerase II and through this regulation of transcription itself. Which modifications are essential for regulating the transcription of non-coding RNA (ncRNA) species and how these patterns differ between the different types of ncRNA remains less studied compared to mRNA. We performed a principal component analysis (PCA) of histone modifications patterns surrounding the transcription start site (TSS) of ncRNA in an attempt to understand how histone modifications predict polymerase recruitment and transcription of ncRNA in earlyC. elegansdevelopment We found that our first PCA axis was a better predictor of polymerase recruitment and expression than any single histone modification for ncRNA and miRNA. This indicates an integrated analysis of many histone modifications is essential for predicting expression based on histone modifications and that each ncRNA species have unique regulation of RNA polymerase recruitment through histone modifications.
Perfect representation of a convex 2D contour with only one Fourier component
Authors: Harbitz Alf
Published: September 2020

Shape analysis of a closed 2D contour is an important topic within biological shape analysis, where Fourier methods to reproduce the shape with a limited number of parameters have been and still are of vital importance. An example is within marine management research on fish, where shape analysis of otolith (earstone) contours is performed for species identification as well as for stock discrimination purposes. In both cases, it is expected that the fewer parameters that are needed in a method to reproduce the contour sufficiently good, the better. This contribution outlines how a convex contour of any shape can be represented to any wanted accuracy by only one Fourier component. The key idea is to allow a flexible choice of a predetermined number ofx-values along anx-axis that goes through the two most distant points of the contour. They-variable along the perpendiculary-axis is then monotonically transformed to az-variable so that the minium and maximumz-values on the contour have the same distance from thex-axis. Thex-values of the contour points are now chosen so that the correspondingz-values on the contour follows a perfect sinusoid if thex-values were equidistant. The method is illustrated by application to lasso contours of Norwegian Coastal Cod (NCC) and North East Arctic Cod (NEAC) otolith images, where the average newx-positions for the individual otolith contours were applied to all otoliths. The results show that a considerably better fit to the original individual otolith contours were obtained by applying the invers FFT to the newy-values than by the frequently applied 2D EFDs (Elliptical Fourier Descriptors) approach, for the same number,m< 11, of frequency components. A promising classification result was also obtained by the linear Fisher discrimination method and cross validation applied to the individualx-values for the NCC and NEAC otoliths, with 82% score for NCC and 80% score for NEAC with sample sizes 367 and 240, respectively.
Computational modelling of chromosome re-replication in mutant strains of fission yeast
Authors: Novák Béla , Tyson John J
Published: September 2020

Typically cells replicate their genome only once per division cycle, but under some circumstances, both natural and unnatural, cells synthesize an overabundance of DNA, either in a disorganized fashion (‘over-replication’) or by a systematic doubling of chromosome number (‘endoreplication’). These variations on the theme of DNA replication and division have been studied in strains of fission yeast,Schizosaccharomyces pombe, carrying mutations that interfere with the function of mitotic cyclin-dependent kinase (Cdk1:Cdc13) without impeding the roles of DNA-replication licensing factor (Cdc18) and S-phase cyclin-dependent kinase (Cdk1:Cig2). Some of these mutations support endoreplication, and some over-replication. In this paper, we propose a dynamical model of the interactions among the proteins governing DNA replication and cell division in fission yeast. By computational simulations of the mathematical model, we account for the observed phenotypes of these re-replicating mutants, and by theoretical analysis of the dynamical system, we provide insight into the molecular distinctions between over-replicating and endoreplicating cells. In case of induced over-production of regulatory proteins, our model predicts that cells first switch from normal mitotic cell cycles to growth-controlled endoreplication, and ultimately to disorganized over-replication, parallel to the slow increase of protein to very high levels.
Precision design of single and multi-heme de novo proteins
Authors: Hutchins George H. , Noble Claire E. M. , Blackburn Hector , Hardy Ben , Landau Charles , Parnell Alice E. , Yadav Sathish , Williams Christopher , Race Paul R. , Oliveira A. Sofia F. , Crump Matthew P. , Berger-Schaffitzel Christiane , Mulholland Adrian J. , Anderson J. L. Ross
Published: September 2020

Thede novodesign of simplified porphyrin-binding helical bundles is a versatile approach for the construction of valuable biomolecular tools to both understand and enhance protein functions such as electron transfer, oxygen binding and catalysis. However, the methods utilised to design such proteins by packing hydrophobic side chains into a buried binding pocket for ligands such as heme have typically created highly flexible, molten globule-like structures, which are not amenable to structural determination, hindering precise engineering of subsequent designs. Here we report the crystal structure of ade novotwo-heme binding “maquette” protein, 4D2, derived from the previously designed D2 peptide, offering new opportunities for computational design and re-engineering. The 4D2 structure was used as a basis to create a range of heme binding proteins which retain the architecture and stability of the initial crystal structure. A well-structured single-heme binding variant was constructed by computational sequence redesign of the hydrophobic protein core, assessed by NMR, and utilised for experimental validation of computational redox prediction and design. The structure was also extended into a four-heme binding helical bundle resembling a molecular wire. Despite a molecular weight of only 24kDa, imaging by CryoEM illustrated a remarkable level of detail in this structure, indicating the positioning of both the secondary structure and the heme cofactors. The design and determination of atomic-level resolution in suchde novoproteins is an invaluable resource for the continued development of novel and functional protein tools.
An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic
Authors: Kumar Sudhir , Tao Qiqing , Weaver Steven , Sanderford Maxwell , Caraballo-Ortiz Marcos A. , Sharma Sudip , Pond Sergei L. K. , Miura Sayaka
Published: September 2020

We report the likely most recent common ancestor of SARS-CoV-2 – the coronavirus that causes COVID-19. This progenitor SARS-CoV-2 genome was recovered through a novel application and advancement of computational methods initially developed to reconstruct the mutational history of tumor cells in a patient. The progenitor differs from the earliest coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the USA harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide as soon as weeks after the first reported cases of COVID-19. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains, which have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic. There have been multiple replacements of predominant coronavirus strains in Europe and Asia and the continued presence of multiple high-frequency strains in Asia and North America. We provide a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/).
Hamster and ferret experimental infection with intranasal low dose of a single strain of SARS-CoV-2
Authors: Monchatre-Leroy Elodie , Lesellier Sandrine , Wasniewski Marine , Picard-Meyer Evelyne , Richomme Céline , Boué Franck , Lacôte Sandra , Murri Séverine , Pulido Coralie , Vulin Johann , Salguero Francisco J , Gouilh Meriadeg Ar , Servat Alexandre , Marianneau Philippe
Published: September 2020

Understanding the pathogenesis of the SARS-CoV-2 infection is key to develop preventive and therapeutic strategies against COVID-19, in the case of severe illness but also when the disease is mild. The use of appropriate experimental animal models remains central in the in-vivo exploration of the physiopathology of infection and antiviral strategies. This study describes SARS-CoV-2 intra-nasal infection in ferrets and hamsters with low doses of low-passage SARS-CoV-2 clinical French isolate UCN19, describing infection levels, excretion, immune responses and pathological patterns in both animal species. Individual infection with 103pfu SARS-CoV-2 induced a more severe disease in hamsters than in ferrets. Viral RNA was detected in the lungs of hamsters but not of ferrets and in the brain (olfactive and/or spinal bulbs) of both species. Overall, the clinical disease remained mild, with serological responses detected from 7 days and 10 days post inoculation in hamsters and ferrets respectively. Virus became undetectable and pathology resolved within 14 days. The kinetics and levels of infection can be used in ferrets and hamsters as experimental models for understanding the pathogenicity of SARS-CoV-2, and testing the protective effect of drugs.
Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India
Authors: Mehrotra Arnav , Bhushan Bharat , Karthikeyan A , Singh Akansha , Panda Snehasmita , Bhati Meenu , Panigrahi Manjit , Dutt Triveni , Mishra Bishnu P. , Pausch Hubert , Kumar Amit
Published: September 2020

The evolution and domestication of pigs is a complex and ongoing process. Despite its rich biodiversity and proximity to the geographical origins ofSus scrofa domesticus, the place of Indian pigs in the global phylogeny is unclear. Using microarray-derived (porcine 60K SNP chip) genotypes of 11 Ghurrah pigs from North-Western India and a public dataset comprising 2113 pigs of 146 breeds, we determined the genomic ancestry of Ghurrah pigs and compared their genetic constitution to European and Asian breeds to ascertain signatures of divergent selection. Results showed that Ghurrah pigs contain genes of Asian and European ancestry with signs of inter-species introgression. Using Admixture LD – decay statistics, the European admixture event was dated to the recent past, coinciding with the start of cross-breeding efforts in India. The complex Asian ancestry pattern of the breed resembled that of wild boars of South – Central China and Thailand, possibly suggesting introgression from an Indian wild boar relative.FSTand XP – EHH comparisons with Asian breeds highlighted divergent selection in genomic regions associated with odontogenesis and skeletal muscle development. Comparisons with European commercial breeds revealed that genomic regions governing olfaction and response to sensory stimulation were under selection in Ghurrah pigs. QTL for meat and carcass traits also showed divergent selection between European breeds and Ghurrah pigs. Our results present the first genomic characterization of an Indian pig breed using dense microarray-derived genotypes and highlight the importance of further genomic characterization of Indian domestic and wild pigs.
Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert
Authors: Reverdy Alicyn , Hathaway Daniel , Jha Jessica , Michaels Gabriel , Sullivan Jeffrey , Mac-Adoo Daniela Diaz , Riquelme Carlos , Chai Yunrong , Godoy Veronica G.
Published: September 2020

The Atacama Desert, the driest and oldest desert in the world, is a hostile environment for life. Despite the inhospitable conditions, bacterial sequences detected in this location suggest rich bacterial life. This study tested the idea that certain bacteria would thrive in this location and that some of them could be cultivated permitting further characterization. Environmental surface soil samples from 1-5 cm deep were collected from 18 diverse locations within the Atacama Desert. To assess the bacterial taxa, diversity, and abundance, Illumina 16S rRNA gene sequencing was performed directly on soil samples. Bacteria were also cultured from the samples. We have a collection of 74 unique bacterial isolates after cultivation and confirmation by 16S rRNA gene sequencing. Pigmentation, biofilm formation, antibiotic production againstEscherichia coliMG1655 andStaphylococcus aureusHG003, and antibiotic resistance were assessed on these isolates. We found that approximately a third of the colonies produced pigments, 80% of isolates formed biofilms, many isolates had antibiotic activity againstE. coliand/orS. aureus,and many were resistant to commercial antibiotics. The functional characterization of these isolates gives us insight into the adaptive bacterial strategies in harsh environments and enables us to learn about their possible use in agriculture, healthcare, or biotechnology.

Originality-Significant Statement

This study provides the first microbial diversity analysis from Atacama Desert soil, presents the cultivation and isolation of 74 unique bacterial isolates, many of which may be novel genera and species, and explores pigment production, antibiotic production and resistance, and unique biofilm development as bacterial survival strategies for living within extreme environments.