bluuebunny/crossref_metadata_2025 huggingface dataset:
Brief Report: CYP27B1 rs10877012 T Allele Was Linked to Non-AIDS Progression in ART-Naïve HIV-Infected Patients: A Retrospective Study
Authors: Jiménez-Sousa María Angeles , Jiménez José Luis , Bellón José María , Fernández-Rodríguez Amanda , Iribarren Jose Antonio , López-Cortés Luís Fernando , Olalla-Sierra Julián , Martín-Rodrigo María Dolores , Muñoz-Fernández María Ángeles , Resino Salvador
Published: September 2020

Background:

HIV/AIDS progression is linked to vitamin D, which is regulated by several key cytochromes P450 (CYP). Single nucleotide polymorphisms (SNPs) in CYP genes influence vitamin D metabolism and serum levels. The objective of this study was to evaluate the association between CYP SNPs and the clinical AIDS progression in antiretroviral treatment (ART)-naïve HIV-infected patients.

Methods:

We performed a retrospective study in 661 ART-naïve HIV-infected patients who were stratified by their AIDS progression pattern [181 long-term nonprogressors (LTNPs), 332 moderate progressors, and 148 rapid progressors (RPs)]. Four CYP SNPs (CYP2R1 rs10500804, CYP2R1 rs1993116, CYP27B1 rs10877012, and CYP24A1 rs6013897) were genotyped using Agena Bioscience's MassARRAY platform. Correction for multiple testing was performed using the false discovery rate (Benjamini–Hochberg procedure).

Results:

The adjusted regression showed a significant association only for CYP27B1 rs10877012 SNP. When analyzing all HIV patients, the rs10877012 T allele was protective against AIDS progression (ordinal outcome) under the dominant [adjusted odds ratio (aOR) = 0.69; P = 0.021) and additive (aOR) = 0.75; P = 0.025] inheritance models. When analyzing LTNPs versus RPs, the rs10877012 T allele also showed a significant protective association under the dominant (aOR = 0.45; P = 0.004) and additive (aOR = 0.54; P = 0.008) inheritance models. P values remained significant after correcting by multiple comparisons only for the comparison of LTNPs versus RPs (extreme phenotypes).

Conclusions:

The CYP27B1 rs10877012 T allele was linked to non-AIDS progression in ART-naïve HIV-infected patients. The rs10877012 SNP seems to have an impact on the clinical AIDS progression, possibly modifying vitamin D levels, which could be relevant for the pathogenesis of HIV infection.
A Comprehensive View on MRI Techniques for Imaging Blood-Brain Barrier Integrity
Authors: Elschot Elles P. , Backes Walter H. , Postma Alida A. , van Oostenbrugge Robert J. , Staals Julie , Rouhl Rob P.W. , Jansen Jacobus F.A.
Published: September 2020

The blood-brain barrier (BBB) is the interface between the blood and brain tissue, which regulates the maintenance of homeostasis within the brain. Impaired BBB integrity is increasingly associated with various neurological diseases. To gain a better understanding of the underlying processes involved in BBB breakdown, magnetic resonance imaging (MRI) techniques are highly suitable for noninvasive BBB assessment. Commonly used MRI techniques to assess BBB integrity are dynamic contrast-enhanced and dynamic susceptibility contrast MRI, both relying on leakage of gadolinium-based contrast agents. A number of conceptually different methods exist that target other aspects of the BBB. These alternative techniques make use of endogenous markers, such as water and glucose, as contrast media. A comprehensive overview of currently available MRI techniques to assess the BBB condition is provided from a scientific point of view, including potential applications in disease. Improvements that are required to make these techniques clinically more easily applicable will also be discussed.
Intraindividual Consistency of Iodine Concentration in Dual-Energy Computed Tomography of the Chest and Abdomen
Authors: Zopfs David , Reimer Robert Peter , Sonnabend Kristina , Rinneburger Miriam , Hentschke Clemens M. , Persigehl Thorsten , Lennartz Simon , Große Hokamp Nils
Published: September 2020

Objectives

Dual-energy computed tomography (DECT)–derived quantification of iodine concentration (IC) is increasingly used in oncologic imaging to characterize lesions and evaluate treatment response. However, only limited data are available on intraindividual consistency of IC and its variation. This study investigates the longitudinal reproducibility of IC in organs, vessels, and lymph nodes in a large cohort of healthy patients who underwent repetitive DECT imaging.

Materials and Methods

A total of 159 patients, who underwent a total of 469 repetitive (range, 2–4), clinically indicated portal-venous phase DECT examinations of the chest and abdomen, were retrospectively included. At time of imaging, macroscopic tumor burden was excluded by follow-up imaging (≥3 months). Iodine concentration was measured region of interest-based (N = 43) in parenchymatous organs, vessels, lymph nodes, and connective tissue. Normalization of IC to the aorta and to the trigger delay as obtained from bolus tracking was performed. For statistical analysis, intraclass correlation coefficient and modified variation coefficient (MVC) were used to assess intraindividual agreement of IC and its variation between different time points, respectively. Furthermore, t tests and analysis of variance with Tukey-Kramer post hoc test were used.

Results

The mean intraclass correlation coefficient over all regions of interest was good to excellent (0.642–0.936), irrespective of application of normalization or the normalization technique. Overall, MVC ranged from 1.8% to 25.4%, with significantly lower MVC in data normalized to the aorta (5.8% [1.8%–15.8%]) in comparison with the MVC of not normalized data and data normalized to the trigger delay (P < 0.01 and P = 0.04, respectively).

Conclusions

Our study confirms intraindividual, longitudinal variation of DECT-derived IC, which varies among vessels, lymph nodes, organs, and connective tissue, following different perfusion characteristics; normalizing to the aorta seems to improve reproducibility when using a constant contrast media injection protocol.
Alternatives to Gadolinium-Based Contrast Agents
Authors: Tweedle Michael F.
Published: September 2020

Gadolinium-based contrast agents have been used in hundreds of millions of patients in the past 30 years, with an exemplary safety record. However, assumptions made at their inception have been recently challenged, rekindling innovation efforts. This critical review outlines the motivations, technical obstacles, problems, and the most recent published progress toward the creation of alternatives to the existing gadolinium-based contrast agent.
Pseudonocardia acidicola sp. nov., a novel actinomycete isolated from peat swamp forest soil
Authors: Klaysubun Chollachai , Lipun Kenika , Duangmal Kannika
Published: September 2020

A novel actinobacterium, designated strain K10HN5T, was isolated from a peat soil sample collected from Kantulee peat swamp forest, Surat Thani Province, Thailand and its taxonomic position was determined using a polyphasic approach. Strain K10HN5T contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose in its whole-cell hydrolysates. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C16 : 1H. Mycolic acids were not present. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, hydroxyphosphatidylmethylethanolamine and phosphatidylinositol. The 16S rRNA gene sequence analysis indicated that it was closely related to

Pseudonocardia bannensis

DSM 45300T (97.9 %) and

Pseudonocardia xinjiangensis

JCM 11839T (97.9 %). Strain K10HN5T exhibited low average nucleotide identity and digital DNA–DNA hybridization values with

P. bannensis

DSM 45300T (82.6, 28.7 %) and

P. xinjiangensis

JCM11839T (76.3, 22.2 %). The DNA G+C content of strain K10HN5T was 72.4 mol%. Based on polyphasic data, strain K10HN5T represents a novel species of the genus

Pseudonocardia

, for which the name Pseudonocardia acidicola sp. nov. is proposed. The type strain is K10HN5T (=TBRC 10048T=NBRC 113897T).
Zinc sulfate in combination with a zinc ionophore may improve outcomes in hospitalized COVID-19 patients
Authors: Carlucci Philip M. , Ahuja Tania , Petrilli Christopher , Rajagopalan Harish , Jones Simon , Rahimian Joseph
Published: September 2020

Introduction. COVID-19 has rapidly emerged as a pandemic infection that has caused significant mortality and economic losses. Potential therapies and prophylaxis against COVID-19 are urgently needed to combat this novel infection. As a result of in vitro evidence suggesting zinc sulphate may be efficacious against COVID-19, our hospitals began using zinc sulphate as add-on therapy to hydroxychloroquine and azithromycin.

Aim. To compare outcomes among hospitalized COVID-19 patients ordered to receive hydroxychloroquine and azithromycin plus zinc sulphate versus hydroxychloroquine and azithromycin alone.

Methodology. This was a retrospective observational study. Data was collected from medical records for all patients with admission dates ranging from 2 March 2020 through to 11 April 2020. Initial clinical characteristics on presentation, medications given during the hospitalization, and hospital outcomes were recorded. The study included patients admitted to any of four acute care NYU Langone Health Hospitals in New York City. Patients included were admitted to the hospital with at least one positive COVID-19 test and had completed their hospitalization. Patients were excluded from the study if they were never admitted to the hospital or if there was an order for other investigational therapies for COVID-19.

Results. Patients taking zinc sulphate in addition to hydroxychloroquine and azithromycin (n=411) and patients taking hydroxychloroquine and azithromycin alone (n=521) did not differ in age, race, sex, tobacco use or relevant comorbidities. The addition of zinc sulphate did not impact the length of hospitalization, duration of ventilation or intensive care unit (ICU) duration. In univariate analyses, zinc sulphate increased the frequency of patients being discharged home, and decreased the need for ventilation, admission to the ICU and mortality or transfer to hospice for patients who were never admitted to the ICU. After adjusting for the time at which zinc sulphate was added to our protocol, an increased frequency of being discharged home (OR 1.53, 95 % CI 1.12–2.09) and reduction in mortality or transfer to hospice among patients who did not require ICU level of care remained significant (OR 0.449, 95 % CI 0.271–0.744).

Conclusion. This study provides the first in vivo evidence that zinc sulphate may play a role in therapeutic management for COVID-19.
Ambroxol Hydrochloride Inhibits the Interaction between Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein’s Receptor Binding Domain and Recombinant Human ACE2
Authors: Olaleye Omonike A. , Kaur Manvir , Onyenaka Collins C.
Published: September 2020

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), enters the host cells through two main pathways, both involving key interactions between viral envelope-anchored spike glycoprotein of the novel coronavirus and the host receptor, angiotensin-converting enzyme 2 (ACE2). To date, SARS-CoV-2 has infected up to 26 million people worldwide; yet, there is no clinically approved drug or vaccine available. Therefore, a rapid and coordinated effort to re-purpose clinically approved drugs that prevent or disrupt these critical entry pathways of SARS-CoV-2 spike glycoprotein interaction with human ACE2, could potentially accelerate the identification and clinical advancement of prophylactic and/or treatment options against COVID-19, thus providing possible countermeasures against viral entry, pathogenesis and survival. Herein, we discovered that Ambroxol hydrochloride (AMB), and its progenitor, Bromhexine hydrochloride (BHH), both clinically approved drugs are potent effective modulators of the key interaction between the receptor binding domain (RBD) of SARS-CoV-2 spike protein and human ACE2. We also found that both compounds inhibited SARS-CoV-2 infection-induced cytopathic effect at micromolar concentrations. Therefore, in addition to the known TMPRSS2 activity of BHH; we report for the first time that the BHH and AMB pharmacophore has the capacity to target and modulate yet another key protein-protein interaction essential for the two known SARS-CoV-2 entry pathways into host cells. Altogether, the potent efficacy, excellent safety and pharmacologic profile of both drugs along with their affordability and availability, makes them promising candidates for drug repurposing as possible prophylactic and/or treatment options against SARS-CoV-2 infection.
Perceptions and Attitudes of Prison Staff towards ADHD – double jeopardy for inmates affected
Authors: Buadze Anna , Friedl Nadine , Schleifer Roman , Young Susan , Schneeberger Andres , Liebrenz Michael
Published: September 2020

Background

Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder that is associated with risk-taking behaviors, poor self-control and interpersonal difficulties. Affected individuals have an increased probability of involvement in the criminal justice system, contributing to a higher rate of arrest and imprisonment compared with the general population. Current data on the prevalence of ADHD among prisoners reports rates of 26%, but finds them inadequately treated.

Aims

Because prison staff play a central role in the identification of inmates with mental disorders, they could well be key to improving provision of care. There is however little knowledge of the conceptions, perceptions and attitudes of prison staff towards ADHD. Such information could help to identify starting points for awareness training and to further implementation of specific ADHD treatment.

Methods

To bridge this gap, we employed a qualitatively driven mixed methods design combining qualitative data collection in the form of narrative interviews with 19 prison staff from a Swiss correctional facility with quantitative data collection in the form of a survey that included the Attitudes Toward Prisoners scale. The interviews were analyzed with QSR NVIVO 11 and a qualitative content analysis approach was used to evaluate findings.

Results

Prison staff were generally aware of ADHD and its symptomology, believed it to a be “real”, but “fashionable” disorder and favored hereditary-genetic or biological explanatory models for its development. They viewed inmates with ADHD rather negatively, as complicating correctional efforts, perceived them as sticking out, as tying up more resources and as frequently being involved in confrontations. Our findings suggest that difficulties in pragmatic aspects of communication and language comprehension may be perceived “as not listening or following instructions” creating additional tensions. Consequently, inmates with ADHD are more often exposed to disciplinary sanctions, such as solitary confinement - an intervention deemed “necessary” by staff. Therefore, staff training on ADHD might need to cover evidence on adverse effects. Non-pharmacological interventions for treatment were preferred and considered to be highly efficacious. Skepticism towards pharmacological treatment prevailed, even when benefits from stimulant medication were described. Acceptance of multimodal treatment among prison staff may require customized strategies.
Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach
Authors: Beckman MF , Igba CK , Mougeot FB , Mougeot J-LC
Published: September 2020

Background

The COVID-19 pandemic has led to over 820,000 deaths for almost 24 million confirmed cases worldwide, as of August 27th, 2020, per WHO report. Risk factors include pre-existing conditions such as cancer, cardiovascular disease, diabetes, obesity, and cancer. There are currently no effective treatments. Our objective was to complete a meta-analysis to identify comorbidity-associated single nucleotide polymorphisms (SNPs), potentially conferring increased susceptibility to SARS-CoV-2 infection using a computational approach.

Results

SNP datasets were downloaded from publicly available GWAS catalog for 141 of 258 candidate COVID-19 comorbidities. Gene-level SNP analysis was performed to identify significant pathways by using MAGMA program. SNP annotation program was used to analyze MAGMA-identified genes. COVID-19 comorbidities from six disease categories were found to have significant associated pathways, which were validated by Q-Q plots (p<0.05). The top 250 human mRNA gene expressions for SNP-affected pathways, extracted from publicly accessible gene expression profiles, were evaluated for significant pathways. Protein-protein interactions of identified differentially expressed genes, visualized with STRING program, were significant (p<0.05). Gene interaction networks were found to be relevant to SARS and influenza pathogenesis.

Conclusion

Pathways potentially affected by or affecting SARS-CoV-2 infection were identified in underlying medical conditions likely to confer susceptibility and/or severity to COVID-19. Our findings have implications in COVID-19 treatment development.
Mathematical Modelling of the Spread of the Coronavirus under Social Restrictions
Authors: Al-arydah Mo’tassem , Berhe Hailay Weldegiorgis , Dib Khalid , Madhu Kalyanasundaram
Published: September 2020

Background

COVID-19 has affected most countries and declared as pandemic. Most countries have implemented some social restrictions to control it. In this work we will use mathematical modelling to assess the current social restrictions in controlling the spread of the disease.

Methods

We formulate a simple susceptible-infectious-recovery (SIR) model to describe the spread of the coronavirus under social restrictions. The transmission rate in this model is considered variable to catch social restrictions impact. We analyze this model, then fit the model to 160 days induced death data in Italy, Iran, USA, Germany, France, India, Spain and China. we estimate some factors that help in understanding not only the spread of the disease but also assess the current social restriction in controlling this disease.

Results

We find a formula for the basic reproduction function (R(t)) and the maximum number of daily infected people. Then estimate the model’s parameters with 95% confidence intervals in these countries. We notice that the model has excellent fit to the disease death data in all considered countries except Iran. The percentage of disease death estimated by the model in Germany and France are 3.8% and 1.2% respectively, which are close to reported percentages values. Finally, we estimate the time, after first reported death, spent under social restrictions to reduce the basic reproduction function (R(t)) to one unit. The times to do that in Italy, USA, Germany, France, Spain and China are 40, 50, 34,58, 31, and 15 days respectively. However, the Indian social restrictions in the 160 days were not enough to reach R(t) = 1.

Conclusion

The transmission rate is between 0.1035–1.6076 and recovery rate is between 0–0.2456. The disease death rates calculated for Germany and France are more realistic than others with average value 0.0023. Extending the same social restrictions for enough time could control the disease in Italy, USA, Germany, France, India, Spain and China. While, more social restrictions are needed to control the disease in India.
COVID-19 Mortality in Cancer Patients: A Report from a Tertiary Cancer Centre in India
Authors: Mehta Anurag , Vasudevan Smreti , Parkash Anuj , Sharma Anurag , Vashist Tanu , Krishna Vidya
Published: September 2020

Background

Cancer patients, especially those receiving cytotoxic therapy are assumed to have a higher probability of death from COVID-19. We have conducted this study to identify the Case Fatality Rate (CFR) in cancer patients with COVID-19 and have explored the relationship of various clinical factors to mortality in our patient cohort.

Methods

All active cancer cases presented to the hospital from 8th June to 24 August 2020, and developed symptoms/ radiological features suspicious of COVID-19 were tested by Real-time polymerase chain reaction assay and/or cartridge-based nucleic acid amplification test from a combination of naso-oropharyngeal swab for SARS-CoV-2. Clinical data, treatment details, and outcomes were assessed from the medical records.

Results

Of the total 3101 cancer patients admitted to the hospital, 1088 patients were tested and 186 patients were positive for SARS-CoV-2. The CFR in the cohort was 27/186 (14.5%). Univariate analysis showed that the risk of death was significantly associated with the presence of comorbidities [OR: 2.68; (95%CI: 1.13–6.32); P = 0.02], multiple comorbidities [OR: 3.01; (95%CI: 1.02–9.07); P = 0.046 for multiple vs. single], and the severity of COVID-19 presentation [OR: 27.48; (95%CI: 5.34–141.49); P = 0.0001 for severe vs. not severe]. Among all comorbidities, diabetes [OR: 3.3; (95%CI: 1.35–8.09); P = 0.008] and cardiovascular diseases [OR: 3.77; (95%CI: 1.02–13.91); P = 0.045] were significant risk factors for death. The receipt of anticancer treatments including chemotherapy, surgery, radiotherapy, targeted therapy, and immunotherapy within a month before the onset of COVID-19 symptoms had no significant effect on the mortality of cancer patients.

Conclusion

To the best of our knowledge, this is the first study from India reporting the CFR, clinical associations, and risk factors for mortality in SARS-CoV-2 infected cancer patients. Our study shows that the frequency of COVID-19 in cancer patients is high, and the CFR is 7.6 times more than the national average. Anticancer therapies did not increase the risk of death. Pre-existing comorbidities specially diabetes, multiple comorbidities, and severity of COVID-19 presenting symptoms are significantly linked with COVID-19 related death in the cohort.
Self-reassurance reduces neural and self-report reactivity to negative life events
Authors: Kim Jeffrey J. , Cunnington Ross , Kirby James N.
Published: September 2020

Background

Whilst research has shown how self-criticism may increase both neural and self-report markers of negative emotion, less well known is how self-reassurance - a compassionately-motivated cognitive self-relating style - may regulate negative emotion.

Method

Using fMRI, we invited participants to engage in self-criticism and self-reassurance toward written descriptions of negative life events (mistakes, setbacks, failures).

Results

Our results identify that neural markers of negative emotion and self-report markers of trial intensity during fMRI are suppressed under conditions of self-reassurance, relative to self-criticism.

Limitations

Future work to control for autobiographical memory during this fMRI task is needed, to explore how memory can contribute to self-reassurance and self-criticism.

Conclusions

Engagement in self-reassurance can reduce the ‘sting’ of negative life-events, both neural and self-report, which holds important implications for therapy.
The DNA Damage-Sensing NER Repair Factor XPC-RAD23B Does Not Recognize Bulky DNA Lesions with a Missing Nucleotide Opposite the Lesion
Authors: Feher Katie M. , Kolbanovskiy Alexander , Durandin Alexander , Shim Yoonjung , Min Jung-Hyun , Lee Yuan Cho , Shafirovich Vladimir , Mu Hong , Broyde Suse , Geacintov Nicholas E.
Published: September 2020

The Nucleotide Excision Repair (NER) mechanism removes a wide spectrum of structurally different lesions that critically depend on the binding of the DNA damage sensing NER factor XPC-RAD23B (XPC) to the lesions. The bulky mutagenic benzo[a]pyrene diol epoxide metabolite-derivedcis- andtrans-B[a]P-dG lesions (G*) adopt base-displaced intercalative (cis) or minor groove (trans)conformations in fully paired DNA duplexes with the canonical C opposite G* (G*:C duplexes). While XPC has a high affinity for binding to these DNA lesions in fully complementary double-stranded DNA, we show here that deleting only the C in the complementary strand opposite the lesion G* embedded in 50-mer duplexes, fully abrogates XPC binding. Accurate values of XPC dissociation constants (KD) were determined by employing an excess of unmodified DNA as a competitor; this approach eliminated the binding and accumulation of multiple XPC molecules to the same DNA duplexes, a phenomenon that prevented the accurate estimation of XPC binding affinities in previous studies. Surprisingly, a detailed comparison of XPC dissociation constantsKDof unmodified and lesion-containing G*:Del complexes, showed that theKDvalues were ∼ 2.5 – 3.6 times greater in the case of G*:Del than in the unmodified G:Del and fully base-paired G:C duplexes. The origins of this unexpected XPC lesion avoidance effect is attributed to the intercalation of the bulky, planar B[a]P aromatic ring system between adjacent DNA bases that thermodynamically stabilize the G*:Del duplexes. The strong lesion-base stacking interactions associated with the absence of the partner base, prevent the DNA structural distortions needed for the binding of the BHD2 and BHD3 β–hairpins of XPC to the deletion duplexes, thus accounting for the loss of XPC binding and the known NER-resistance of G*:Del duplexes.
A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem
Authors: Briand Samuel , Dessimoz Christophe , El-Mabrouk Nadia , Nevers Yannis
Published: September 2020

Motivation

Comparing trees is a basic task for many purposes, and especially in phylogeny where different tree reconstruction tools may lead to different trees, likely representing contradictory evolutionary information. While a large variety of pairwise measures of similarity or dissimilarity have been developed for comparing trees with no information on internal nodes, very few address the case of inner node-labeled trees. Yet such trees are common; for instance reconciled gene trees have inner nodes labeled with the type of event giving rise to them, typically speciation or duplication. Recently, we proposed a formulation of the Labeled Robinson Foulds edit distance with edge extensions, edge contractions between identically labeled nodes, and node label flips. However, this distance proved difficult to compute, in particular because shortest edit paths can require contracting “good” edges, i.e. edges present in the two trees.

Results

Here, we report on a different formulation of the Labeled Robinson Foulds edit distance — based on node insertion, deletion and label substitution — which we show can be computed in linear time. The new formulation also maintains other desirable properties: being a metric, reducing to Robinson Foulds for unlabeled trees and maintaining an intuitive interpretation. The new distance is computable for an arbitrary number of label types, thus making it useful for applications involving not only speciations and duplications, but also horizontal gene transfers and further events associated with the internal nodes of the tree. To illustrate the utility of the new distance, we use it to study the impact of taxon sampling on labeled gene tree inference, and conclude that denser taxon sampling yields better trees.
1RS.1BL molecular resolution provides novel contributions to wheat improvement
Authors: Ru Zhengang , Juhasz Angela , Li Danping , Deng Pingchuan , Zhao Jing , Gao Lifeng , Wang Kai , Keeble-Gagnere Gabriel , Yang Zujun , Li Guangrong , Wang Daowen , Bose Utpal , Colgrave Michelle , Kong Chuizheng , Zhao Guangyao , Zhang Xueyong , Liu Xu , Cui Guoqing , Wang Yuquan , Niu Zhipeng , Wu Liang , Cui Dangqun , Jia Jizeng , Appels Rudi , Kong Xiuying
Published: September 2020

Wheat-rye 1RS.1BL translocation has a significant impact on wheat yield and hence food production globally. However, the genomic basis of its contributions to wheat improvement is undetermined. Here, we generated a high-quality assembly of 1RS.1BL translocation comprising 748,715,293 bp with 4,996 predicted protein-coding genes. We found the size of 1RS is larger than 1BS with the active centromere domains shifted to the 1RS side instead of the 1BL side in Aikang58 (AK58). The gene alignment showed excellent synteny with 1BS from wheat and genes from 1RS were expressed well in wheat especially for 1RS where expression was higher than that of 1BS for the grain-20DPA stage associated with greater grain weight and negative flour quality attributes. A formin-like-domain protein FH14 (TraesAK58CH1B01G010700) was important in regulating cell division. Two PPR genes were most likely the genes for the multi fertility restoration locusRfmulti. Our data not only provide the high-resolution structure and gene complement for the 1RS.1BL translocation, but also defined targets for enhancing grain yield, biotic and abiotic stress, and fertility restoration in wheat.
The effect of E-liquid exposure onCaenorhabditis elegans
Authors: Wang Ying , Ingram Thomas L , Marshall Sophie , Shephard Freya , Chakrabarti Lisa
Published: September 2020

E-cigarettes are being promoted as a less harmful alternative to smoking tobacco. However, vaping is a new phenomenon and safety profiles have not been fully established. Model organisms can be used to examine the cellular processes that may be changed by exposure to the E-liquids used for vaping. Mitochondria are essential in eukaryotic cells for production of ATP, protein biogenesis, metabolic pathways, cellular signalling, stress responses and apoptosis. Mitochondrial health can be used as a proxy for many aspects of healthy cellular physiology. Mutations in the PINK1 gene can lead to mitochondria-specific autophagy deficiency. We exposed two strains ofCaenorhabditis elegans, CB5600 control and CC46 pink1, with 10% concentrations of nine different flavoured E liquids. We measured lifespan, movement, body size, brood size, and we examined their mitochondrial networks to investigate the effect of the E-liquids. We show that the CC46 (pink1) strain is affected by the E-liquids, even the flavours without nicotine, and that they have reduced lifespan, movement ability and mitochondrial organisation. We found that some E-liquids can dramatically shorten lifespan in this strain. Our data emphasise a need to carefully ascertain the potential harm that may be caused by the use of E-liquids.
FUS-ALS mutants alter FMRP phase separation equilibrium and impair protein translation
Authors: Birsa N. , Ule A.M. , Garone M.G. , Tsang B. , Mattedi F. , Chong P.A. , Humphrey J. , Jarvis S. , Pisiren M. , Wilkins O.G. , Nosella M. , Devoy A. , Bodo C. , Fernandez de la Fuente R. , Fisher E.M.C. , Rosa A. , Viero G. , Forman-Kay J.D. , Schiavo G. , Fratta P.
Published: September 2020

Mutations in the RNA binding protein (RBP) FUS cause amyotrophic lateral sclerosis (ALS) and result in its nuclear depletion and cytoplasmic mislocalisation, with cytoplasmic gain of function thought to be crucial in pathogenesis. Here, we show that expression of mutant FUS at physiological levels drives translation inhibition in both mouse and human motor neurons. Rather than acting directly on the translation machinery, we find that mutant FUS forms cytoplasmic condensates that promote the phase separation of FMRP, another RBP associated with neurodegeneration and robustly involved in translation regulation. FUS and FMRP co-partition and repress translationin vitro. In ourin vivomodel, FMRP RNA targets are depleted from ribosomes. Our results identify a novel paradigm by which FUS mutations favour the condensed state of other RBPs, impacting on crucial biological functions, such as protein translation.
Drivers of ESBL-producingEscherichia colidynamics in calf fattening farms: a modelling study
Authors: Bastard Jonathan , Haenni Marisa , Gay Emilie , Glaser Philippe , Madec Jean-Yves , Temime Laura , Opatowski Lulla
Published: September 2020

The contribution of bacteria in livestock to the global burden of antimicrobial resistance raises concerns worldwide. However, the dynamics of selection and diffusion of antimicrobial resistance in farm animals are not fully understood. Here, we used veal calf fattening farms as a model system, as they are a known reservoir of Extended Spectrum β-Lactamase-producingEscherichia coli(ESBL-EC). Longitudinal data of ESBL-EC carriage and antimicrobial use (AMU) were collected from three veal calf farms during the entire fattening process. We developed 18 agent-based mechanistic models to assess different hypotheses regarding the main drivers of ESBL-EC dynamics in calves. The models were independently fitted to the longitudinal data using Markov Chain Monte Carlo and the best model was selected. Within-farm transmission between individuals and sporadic events of contamination were found to drive ESBL-EC dynamics on farms. In the absence of AMU, the median carriage duration of ESBL-EC was estimated to be 19.6 days (95% credible interval: [12.7; 33.3]). In the best model, AMU was found to influence ESBL-EC dynamics, by affecting ESBL-EC clearance rather than acquisition. This effect of AMU was estimated to decrease gradually after the end of exposure and to disappear after 62.5 days [50.0; 76.9]. Moreover, using a simulation study, we quantified the efficacy of ESBL-EC mitigation strategies. Decreasing ESBL-EC prevalence by 50% on arrival at the fattening farm reduced prevalence at slaughter age by 33.3%. Completely eliminating the use of selective antibiotics had a strong effect on average ESBL-EC prevalence (relative reduction of 79.6%), but the effect was mild if this use was only decreased by 50% compared to baseline (relative reduction of 3.7%).
Flexible RSV prefusogenic fusion glycoprotein exposes multiple neutralizing epitopes that may collectively contribute to protective immunity
Authors: Patel Nita , Tian Jing-Hui , Flores Rhonda , Jacobson Kelsey , Walker Michelle , Portnoff Alyse , Gueber-Xabier Mimi , Massare Michael J. , Glenn Greg , Ellingsworth Larry , Smith Gale
Published: September 2020

Human respiratory syncytial virus (RSV) is a significant cause of lower respiratory tract infection in infants, young children, and older adults. There is no licensed vaccine and prophylactic treatment options are limited and not widely available in developing countries with the greatest disease burden. The RSV fusion (F) glycoprotein is a primary target of host immunity and thus a major focus for vaccine development. The native F glycoprotein structure is flexible and undergoes significant rearrangements from the metastable prefusion to a stable postfusion structure with neutralizing epitopes on intermediate structures. We hypothesize trimeric vaccine strategies that recapitulate the breathable F quaternary structure, and provide accessibility of B-cells to epitopes on intermediate conformations, may collectively contribute to protective immunity, while ridge prefusion F structures restrict access to key protective epitopes. To test this hypothesis, we used the near full-length native prefusogenic F as a backbone to construct three prefusion F variants with substitutions in the hydrophobic head cavity: 1) disulfide bond double mutant (DS), 2) space filling hydrophobic amino acid substitutions (Cav1), and 3) DS plus Cav1 substitutions (DS-Cav1). In this study, we compared the immunogenicity of prefusogenic F to the immunogenicity of the prefusion F variants in two animal models. Native prefusogenic F was significantly more immunogenic producing high titer antibodies to prefusogenic, prefusion, and postfusion F structures compared to animals immunized with prefusion F DS or DS-Cav1. Importantly, native prefusogenic F elicited antibodies that targeted neutralizing epitopes including prefusion-specific site zero (Ø) and V as well as conformation-independent neutralizing sites II and IV. Immunization with prefusion F DS or DS-Cav1 elicited antibodies primarily targeting antigenic sites Ø and V with little or no detectable antibodies to other key neutralizing sites. Animals immunized with native prefusogenic F also had significantly higher neutralizing antibodies that cross-neutralized RSV A and B subtypes while immunization with DS or DS-Cav1 elicited neutralizing antibodies primarily to the A subtype. We conclude that breathable trimeric vaccines that closely mimic the native F-structure, and incorporate strategies for B-cell accessibility to protective epitopes, are important considerations for vaccine design. F structures locked in a single conformation restrict B-cell access to neutralizing epitopes that may collectively contribute to destabilizing F-trimers important for broad protection. These results also have implications for vaccine strategies targeting other type 1 integral membrane proteins.
Computationally Grafting an IgE Epitope onto a Scaffold: Implications for a Pan Anti-Allergy Vaccine Design
Authors: Sabban Sari
Published: September 2020

Allergy is becoming an intensifying disease among the world population, particularly in the developed world. Once allergy develops, sufferers are permanently trapped in a hyper-immune response that makes them sensitive to innocuous substances, such as the protein cupin in peanuts. The immune pathway concerned with developing allergy is the Th2immune pathway where the IgE antibody (targeting innocuous substances) binds to its FcεRI receptor on Mast and Basophil cells. Currently, there is not a permanent treatment for allergies. This paper discusses a strategy and a protocol that could disrupt the binding between the antibody and its receptor for a potential permanent treatment. Ten proteins were computationally designed to display a human IgE motif very close in proximity to the IgE antibodies’s FcεRI receptor’s binding site in an effort for these proteins to be used as a vaccine against our own IgE antibody. The motif of interest was the FG motif and it was excised and grafted onto aStaphylococcus aureusprotein (PDB ID 1YN3). The new structures (motif + scaffold) had their sequences re-designed around the motif to find an amino acid sequence that would fold to the designed structures correctly. These ten computationally designed proteins showed successful folding when simulated using Rosetta’s AbinitioRelax folding simulation and the IgE epitope was clearly displayed in its native three-dimensional structure in all of them. These designed proteins have the potential to be used as a pan anti-allergy vaccine by guiding the immune system towards developing antibodies against the body’s own IgE antibody, thus neutralising it, and presumably permanently shutting down a major aspect of the Th2immune pathway. This work employedin silicobased methods for designing the proteins and did not include any experimental verifications.
Stationary Ca2+nanodomains in the presence of buffers with two binding sites
Authors: Chen Y. , Matveev V.
Published: September 2020

We examine closed-form approximations for the equilibrium Ca2+concentration near a point Ca2+source representing a Ca2+channel, in the presence of a mobile Ca2+buffer with 2:1 Ca2+binding stoichiometry. We consider buffers with two Ca2+binding sites activated in tandem and possessing distinct binding affinities and kinetics. This allows to model the impact on Ca2+nanodomains of realistic endogenous Ca2+buffers characterized by cooperative Ca2+binding, such as calretinin. The approximations we present involve a combination or rational and exponential functions, whose parameters are constrained using the series interpolation method that we recently introduced for the case of 1:1 Ca2+buffers. We conduct extensive parameter sensitivity analysis and show that the obtained closed-form approximations achieve reasonable qualitative accuracy for a wide range of buffer’s Ca2+binding properties and other relevant model parameters. In particular, the accuracy of the newly derived approximants exceeds that of the rapid buffering approximation in large portions of the relevant parameter space.

STATEMENT OF SIGNIFICANCE

Closed-form approximations describing equilibrium distribution of Ca2+in the vicinity of an open Ca2+channel proved useful for the modeling of local Ca2+signals underlying secretory vesicle exocytosis, muscle contraction and other cell processes. Such approximations provide an efficient method for estimating Ca2+and buffer concentrations without computationally expensive numerical simulations. However, while most biological buffers have multiple Ca2+binding sites, much of prior modeling work considered Ca2+dynamics in the presence of Ca2+buffers with a single Ca2+binding site. Here we extend modeling work on equilibrium Ca2+nanodomains to the case of Ca2+buffers with two binding sites, allowing to gain deeper insight into the impact of more realistic Ca2+buffers, including cooperative buffers, on cell Ca2+dynamics.
High fidelity reconstitution of stress granules and nucleoli in mammalian cellular lysate
Authors: Freibaum Brian D. , Messing James , Yang Peiguo , Kim Hong Joo , Taylor J. Paul
Published: September 2020

Liquid-liquid phase separation (LLPS) is an important mechanism of intracellular organization that underlies the assembly of a variety of distinct RNP granules. Fundamental biophysical principles governing LLPS during RNP granule assembly have been revealed by simple in vitro systems consisting of several components, but these systems have limitations when studying the biology of complex, multicomponent RNP granules. Visualization of RNP granules in live cells has validated key principles revealed by simple in vitro systems, but this approach presents difficulties for interrogating biophysical features of RNP granules and provides limited ability to manipulate protein, nucleic acid, or small molecule concentrations. Here we introduce a system that builds upon recent insights into the mechanisms underlying RNP granule assembly and permits high fidelity reconstitution of stress granules and the granular component of nucleoli in mammalian cellular lysate. This system fills the gap between simple in vitro systems and live cells, and allows for a wide variety of studies of membraneless organelles.
High yield preparation of outer-membrane protein efflux pumps byin vitrorefolding is concentration dependent
Authors: Budiardjo S. Jimmy , Ikujuni Ayotunde Paul , Firlar Emre , Cordova Andrés , Kaelber Jason T. , Slusky Joanna S.G.
Published: September 2020

Overexpression of tripartite efflux pump systems in gram-negative bacteria are a principal component of antibiotic resistance. High-yield purification of the outer membrane component of these systems will enable biochemical and structural interrogation of their mechanisms of action and allow testing of compounds that target them. However, preparation of these proteins is typically hampered by low yields requiring laborious large-scale efforts. If refolding conditions can be found, refolding these proteins from inclusion bodies can lead to increased yields as compared to membrane isolations. Here, we develop a concentration-dependent folding protocol for refolding TolC, the outer membrane component of the antibiotic efflux pump fromEscherichia coli. We show that by our method of re-folding, homotrimeric TolC remains folded in SDS-PAGE, retains binding to an endogenous ligand, and recapitulates the known crystal structure by single particle cryoEM analysis. We find that a key factor in successful re-folding is a concentration dependence of TolC oligomerization. We extended the scheme to CmeC, a homologous protein fromCampylobacter jejuni, and find that concentration-dependent oligomerization is a general feature of these systems. Because outer-membrane efflux pump components are ubiquitous across gram-negative species, we anticipate that incorporating a concentration step in re-folding protocols will promote correct refolding allowing for reliable, high-yield preparation of this family of proteins.
Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic Neighbors
Authors: Olgun Gulden , Tastan Oznur
Published: September 2020

The dysregulation of long non-coding RNAs’ (lncRNAs) expressions has been implicated in cancer. Since most of the lncRNAs’ are not functionally characterized well, investigating the set of perturbed lncRNAs are is challenging. Existing methods that inspect lncRNAs functionally rely on the co-expressed coding genes, which are far better characterized functionally. LncRNAs can be known to act as transcriptional regulators; they may activate or repress the neighborhood’s coding genes on the genome. Based on this, in this work, we aim to analyze the deregulated lncRNAs in cancer by taking into account their ability to regulate nearby loci on the genome. We perform functional analysis on differentially expressed lncRNAs for 28 different cancers considering their adjacent coding genes. We identify that some deregulated lncRNAs are cancer-specific, but a substantial number of lncRNAs are shared across cancers. Next, we assess the similarities of the cancer types based on the functional enrichment of the deregulated lncRNA sets. We find some cancers are very similar in the functions and biological processes related to the deregulated lncRNAs. We observe that some of the cancers for which we find similarity can be linked through primary, metastatic site relations. We investigate the similarity of enriched functional terms for the deregulated lncRNAs and the mRNAs. We further assess the enriched functions’ similarity to the functions and processes that the known cancer driver genes take place. We believe that our methodology help to understand the impact of the lncRNAs in cancer functionally.
Structural characterization and evolutionary analyses of theCoccidioides immitisandCoccidioides posadasiimitochondrial genomes
Authors: de Melo Teixeira Marcus , Lang B. Franz , Matute Daniel R. , Stajich Jason E. , Barker Bridget
Published: September 2020

Fungal mitochondrial genomes encode for genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and these genes have been used as molecular markers for population genetics studies.Coccidioides immitisandC. posadasiiare endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, almost one hundredCoccidioidesstrains have been sequenced. The focus of these studies has been exclusively to infer patterns of variation of nuclear genomes (nucDNA). However, their mitochondrial genomes (mtDNA) have not been studied. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains ofC. posadasiiandC. immitis, as well as assess population variation among 77 published genomes. The circular-mapping mtDNA molecules are 68.2 Kb inC. immitisand 75.1 Kb inC. posadasii. We identified the fourteen mitochondrial protein-coding genes common to most fungal mitochondria, including genes encoding the small and large ribosomal RNAs (rnsandrnl), the RNA subunit of RNAse P (rnpB), and 26 tRNAs organized in polycistronic transcription units, which are mostly syntenic across different populations and species ofCoccidioides. BothCoccidioidesspecies are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparison of the mtDNA and nucDNA genomes shows discordance, possibly due to differences in patterns of inheritance. In summary, this work represents the first complete assessment of mitochondrial genomes among several isolates of both species ofCoccidioides, and provides a foundation for future functional work.