bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementation With Dexmedetomidine for Transsphenoidal Resection of Pituitary Adenoma: A Meta-Analysis of Randomized Controlled Trials
Authors: Liu Zhongtao , Gao Caibin , Liu Chunhong , Liu Wenqing , Xu Xingguo , Ma Tongshan , Du Xiaoxia , Shen Jianbo
Published: January 2021

Introduction

The effect of dexmedetomidine supplementation on hemodynamic stability for transsphenoidal resection of pituitary adenoma remains controversial. We conduct a systematic review and meta-analysis to explore the influence of dexmedetomidine supplementation on hemodynamic stability for transsphenoidal resection of pituitary adenoma.

Methods

We have searched PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases through August 2020 for randomized controlled trials assessing the effect of dexmedetomidine supplementation on transsphenoidal resection of pituitary adenoma.

Results

Four randomized controlled trials involving 160 patients were included in the meta-analysis. Overall, compared with the control group for transsphenoidal resection of pituitary adenoma, dexmedetomidine supplementation resulted in significantly reduced mean arterial pressure at 30 minutes [mean difference (MD), −26.62; 95% confidence interval (CI), −36.71 to −16.53; P < 0.00001], heart rate at 30 minutes (MD, −16.50; 95% CI, −32.48 to −0.53; P = 0.04), blood loss (MD, −112.57; 95% CI, −165.12 to −60.01; P < 0.0001), and fentanyl (MD, −154.13; 95% CI, −303.97 to −4.29; P = 0.04), but demonstrated similar incidence of nausea and vomiting (odds ratio, 0.37; 95% CI, 0.13–1.03; P = 0.06), and hypotension (odds ratio, 2.11; 95% CI, 0.49–9.22; P = 0.32).

Conclusions

Dexmedetomidine supplementation was effective in improving hemodynamic stability for transsphenoidal resection of pituitary adenoma.
Utilization of Whole Genome Sequencing to Understand SARS-CoV-2 Transmission Dynamics in Long-Term Care Facilities, Correctional Facilities and Meat Processing Plants in Minnesota, March – June 2020
Authors: Lehnertz Nicholas B , Wang Xiong , Garfin Jacob , Taylor Joanne , Zipprich Jennifer , VonBank Brittany , Martin Karen , Eikmeier Dana , Medus Carlota , Wiedinmyer Brooke , Bernu Carmen , Plumb Matthew , Pung Kelly , Honein Margaret A. , Carter Rosalind , MacCannell Duncan , Smith Kirk E. , Como-Sabetti Kathryn , Ehresmann Kris , Danila Richard , Lynfield Ruth
Published: January 2021

Congregate settings and high-density workplaces have endured a disproportionate impact from COVID-19. In order to provide further understanding of the transmission patterns of SARS-CoV-2 in these settings, whole genome sequencing (WGS) was performed on samples obtained from 8 selected outbreaks in Minnesota from March – June, 2020. WGS and phylogenetic analysis was conducted on 319 samples, constituting 14.4% of the 2,222 total SARS-CoV-2-positive individuals associated with these outbreaks. Among the sequenced specimens, three LTCFs and both correctional facilities had spread associated with a single genetic sequence. A fourth LTCF had outbreak cases associated with two distinct sequences. In contrast, cases associated with outbreaks in the two meat processing plants represented multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak, and early identification and cohorting of cases, along with continued vigilance with infection prevention and control measures is imperative.
IL-2 and IFN-γ are biomarkers of SARS-CoV-2 specific cellular response in whole blood stimulation assays
Authors: Pérez-Cabezas Begoña , Ribeiro Ricardo , Costa Inês , Esteves Sofia , Teixeira Ana Rafaela , Reis Teresa , Monteiro Ricardo , Afonso Alexandre , Pinheiro Vitor , Antunes Maria Isabel , Lucília Araújo Maria , Ribeiro João Niza , Cordeiro-da-Silva Anabela , Santarém Nuno , Tavares Joana
Published: January 2021

A proper description of the immune response to SARS-CoV-2 will be critical for the assessment of protection elicited after both infection and vaccination. Uncoupled T and B cell responses have been described in acute and convalescent patients and exposed individuals. We assessed the potential usefulness of whole blood stimulation assays to identify functional cellular immune responses to SARS-CoV-2. Blood from COVID-19 recovered individuals (5 months after infection) and negative subjects was stimulated for 24 hours with HLA predicted peptide “megapools” of the Spike and Nucleoprotein, or the mixture of them. After stimulation, cytokines were quantified using a beads-based multiplex assay. Interleukin-2 and IFN-γ were found to be specific biomarkers of SARS-CoV-2 cellular response. Using the Spike and Nucleoprotein mixture, 91.3% of COVID-19 recovered individuals presented an IL-2 stimulation index over the cut-off, while 82.6% showed IFN-γ. All the negative individuals presented an IL-2 response under the cut-off, while 5.3% of these subjects presented positive IFN-γ stimulation indexes. Moreover, IL-2 production correlated with IgG levels for Spike 1, RBD, and Nucleocapsid. In conclusion, we demonstrate the potential of whole blood stimulation assays and the quantification of IL-2 and IFN-γ for the analysis of SARS-CoV-2 functional cellular responses.
Identifying low risk insecticides that can enhance food production without increasing mortality of biocontrol agents for human schistosomiasis
Authors: Haggerty Christopher J E , Delius Bryan K. , Jouanard Nicolas , Ndao Pape D , De Leo Giulio A , Lund Andrea J , Lopez-Carr David , Remais Justin V , Riveau Gilles , Sokolow Susanne H , Rohr Jason R
Published: January 2021

Use of agrochemicals, including insecticides, is vital to food production and predicted to increase 2-5 fold by 2050. Previous studies have shown a positive association between agriculture and the human infectious disease schistosomiasis, which is problematic as this parasitic disease infects approximately 250 million people worldwide. Certain insecticides might runoff fields and be highly toxic to invertebrates, such as prawns in the genusMacrobrachium, that are biocontrol agents for snails that transmit the parasites causing schistosomiasis. We used a laboratory dose-response experiment and an observational field study to determine the relative toxicities of three pyrethroid (esfenvalerate, λ-cyhalothrin, and permethrin) and three organophosphate (chlorpyrifos, malathion, and terbufos) insecticides toMacrobrachiumprawns. In the lab, pyrethroids were consistently several orders of magnitude more toxic than organophosphate insecticides, and more likely to runoff fields at lethal levels according to modeling data. In the field, we found thatMacrobrachiumprawn survival at 31 water contact sites in the lower basin of the Senegal River where schistosomiasis is endemic was predicted by pyrethroid application rates to nearby crop fields after controlling for abiotic and prawn-level factors. Our findings suggest that widely used pyrethroid insecticides can have strong non-target effects onMacrobrachiumprawns that are biocontrol agents where 400 million people are at risk of human schistosomiasis. Understanding the ecotoxicology of high-risk insecticides may help improve human health in schistosomiasis-endemic regions undergoing agricultural expansion.
Thermal proteome profiling reveals distinct target selectivity for differentially oxidized oxysterols
Authors: Rossetti Cecilia , Laraia Luca
Published: January 2021

Oxysterols are produced physiologically by many species, however their distinct roles in regulating human (patho)physiology have not been studied systematically. The role of differing oxidation states and sites in mediating their biological functions is also unclear. As individual oxysterols have been associated with atherosclerosis, neurodegeneration and cancer, a better understanding of their protein targets would be highly valuable. To address this, we profiled three A- and B-ring oxidized sterols as well as 25-hydroxycholesterol using thermal proteome profiling (TPP), validating selected targets with the cellular thermal shift assay (CETSA) and isothermal dose response fingerprinting (ITDRF). This revealed that the site of oxidation has a profound impact on target selectivity, with each oxysterol possessing an almost unique set of target proteins. However, overall targets clustered in pathways relating to vesicular transport and lipid metabolism and trafficking, suggesting that while individual oxysterols bind to a unique set of proteins, the processes they modulate are highly interconnected.
Convergence of Comorbidity and COVID-19 Infection to Fatality: An Investigation Based on Health Assessment and Vaccination among Older Adults in Kerala
Authors: Joseph Sindhu , Ulahannan Jijo Pulickiyil , Parvathy A J
Published: January 2021

Objective

To investigate the impact of age, comorbidity, and vaccination in the fatality of older COVID-19 patients in the state of Kerala, India, based on their comorbidity and vaccination status.

Methods

It is a cross sectional study adopting a mixed method approach conducted among the older population in Kerala. To study the health profile, 405 older people were surveyed, and 102 people were interviewed in-depth at their households, between June to November 2020. The results of the study were triangulated with elderly COVID-19 fatality data, available from the citizen-science dashboards of the research team and Department of Health, Kerala. Vaccination data was retrieved from cowin.gov.in to study its impact. The data was analysed using the IBM SPSS version 22.0.

Results

Age is a predictor of COVID-19 fatality. Diabetes, hypertension, heart diseases, CKD and COPD are the significant predictors of elderly COVID-19 fatality. The current comorbidity profile of the total older population matches with the comorbidities of the COVID-19 elderly death cases. Vaccination has impacted COVID-19 mortality after vaccinating 65 percent (first dose) of the elderly.

Conclusions

Age and comorbidities can predict potential fatality among older COVID-19 patients. Timely and accurate health data and better knowledge of high-risk factors such as comorbidity can easily guide the healthcare system and authorities to efficient prevention and treatment methodologies. Knowledge on prevailing NCDs can drive early preparedness before it converges with an epidemic like the present zoonotic disease. Priority must be given for elderly vaccination to bring down the mortality rates.
Combination of blood biomarkers and stroke scales improves identification of large vessel occlusions
Authors: Gaude Edoardo , Nogueira Barbara , Graham Sheila , Smith Sarah , Shaw Lisa , Graziadio Sara , Mochales Gonzalo Ladreda , Mochales Marcos Ladreda , Sloan Philip , Bernstock Joshua D. , Shekhar Shashank , Gropen Toby I. , Price Christopher I.
Published: January 2021

Background and Purpose

Acute ischemic stroke caused by large vessel occlusions (LVO) is a major contributor to stroke deaths and disabilities; however, identification for emergency treatment is challenging.

Aims

To evaluate the diagnostic accuracy of a panel of biomarkers for LVO prediction.

Methods

170 patients with suspected stroke were recruited retrospectively at one hospital. We analysed the plasma levels of D-dimer, OPN, OPG, GFAP, vWF, and ADAMTS13 in LVO vs non-LVO. Diagnostic performance was estimated by using blood biomarkers alone or in combination with NIHSS-derived stroke severity scales.

Results

Our patient cohort comprised 20% stroke mimics, 11% transient ischemic attack, 11% hemorrhagic stroke, 15% LVO ischemic stroke, 28% non-LVO ischemic stroke, and 15% ischemic stroke with unknown LVO status. Multivariable analysis found that the optimal set of blood biomarkers for LVO prediction was D-dimer (OR 15.4, 95% CI 4.9 to 57.6; p-value<0.001) and GFAP (OR 0.83, 95% CI 0.90 to 0.99; p-value=0.03). The combination of D-dimer and GFAP with stroke scales significantly improved LVO prediction, compared to the stroke scales alone (p-value<0.001). The combination of biomarkers with constructed FAST-ED or EMSA scales achieved an AUC of 95% (95% CI 91-100%) or 93% (CI 95% 89-97%), a sensitivity of 91% (95% CI 71-98%) or 86 (95% CI 66-97%), and a specificity of 95% (95% CI 89-98%) or 94% (95% CI 88-98%), for LVO prediction, respectively.

Conclusions

The combination of D-dimer, GFAP, and stroke scales could provide a simple and highly accurate tool for identifying LVO patients.
Modeling the effect of vaccination strategies in an Excel spreadsheet: The rate of vaccination, and not only the vaccination coverage, is a determinant for containing COVID-19 in urban areas
Authors: Moisés Alvarez Mario , Bravo-González Sergio , Trujillo-de Santiago Grissel
Published: January 2021

We have investigated the importance of the rate of vaccination to contain COVID-19 in urban areas. We used an extremely simple epidemiological model that is amenable to implementation in an Excel spreadsheet and includes the demographics of social distancing, efficacy of massive testing and quarantine, and coverage and rate of vaccination as the main parameters to model the progression of COVID-19 pandemics in densely populated urban areas. Our model predicts that effective containment of pandemic progression in densely populated cities would be more effectively achieved by vaccination campaigns that consider the fast distribution and application of vaccines (i.e., 50% coverage in 6 months) while social distancing measures are still in place. Our results suggest that the rate of vaccination is more important than the overall vaccination coverage for containing COVID-19. In addition, our modeling indicates that widespread testing and quarantining of infected subjects would greatly benefit the success of vaccination campaigns. We envision this simple model as a friendly, readily accessible, and cost-effective tool for assisting health officials and local governments in the rational design/planning of vaccination strategies.
Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation
Authors: Maison David P. , Ching Lauren L. , Shikuma Cecilia M. , Nerurkar Vivek R.
Published: January 2021

COVID-19 pandemic has ravaged the world, caused over 1.8 million deaths in the first year, and severely affected the global economy. Hawaii is not spared from the transmission of SARS-CoV-2 in the local population, including high infection rates in racial and ethnic minorities. Early in the pandemic, we described in this journal various technologies used for the detection of SARS-CoV-2. Herein we characterize a 969-bp SARS-CoV-2 segment of the S gene downstream of the receptor-binding domain. At the John A. Burns School of Medicine Biocontainment Facility, RNA was extracted from an oropharyngeal swab and a nasal swab from two patients from Hawaii who were infected with the SARS-CoV-2 in August 2020. Following PCR, the two viral strains were sequenced using Sanger sequencing, and phylogenetic trees were generated using MEGAX. Phylogenetic tree results indicate that the virus has been introduced to Hawaii from multiple sources. Further, we decoded 13 single nucleotide polymorphisms across 13 unique SARS-CoV-2 genomes within this region of the S gene, with one non-synonymous mutation (P681H) found in the two Hawaii strains. The P681H mutation has unique and emerging characteristics with a significant exponential increase in worldwide frequency when compared to the plateauing of the now universal D614G mutation. The P681H mutation is also characteristic of the new SARS-CoV-2 variants from the United Kingdom and Nigeria. Additionally, several mutations resulting in cysteine residues were detected, potentially resulting in disruption of the disulfide bridges in and around the receptor-binding domain. Targeted sequence characterization is warranted to determine the origin of multiple introductions of SARS-CoV-2 circulating in Hawaii.
Nonadaptive radiation of the gut microbiome in an adaptive radiation ofCyprinodonpupfishes with minor shifts for scale-eating
Authors: Heras J. , Martin C.H.
Published: January 2021

Adaptive radiations offer an excellent opportunity to understand the eco-evolutionary dynamics of gut microbiota and host niche specialization. In a laboratory common garden, we compared the gut microbiota of two novel trophic specialists, a scale-eater and a molluscivore, to a set of four outgroup generalist populations from which this adaptive radiation originated. We predicted an adaptive and highly divergent microbiome composition in the specialists matching their rapid rates of craniofacial diversification in the past 10 kya. We measured gut lengths and sequenced 16S rRNA amplicons of gut microbiomes from lab-reared fish fed the same high protein diet for one month. In contrast to our predictions, gut microbiota largely reflected 5 Mya phylogenetic divergence times among generalist populations in support of phylosymbiosis. However, we did find significant enrichment ofBurkholderiaceaebacteria in both lab-reared scale-eater populations. These bacteria sometimes digest collagen, the major component of fish scales, supporting an adaptive shift. We also found some enrichment ofRhodobacteraceaeandPlanctomycetaciain lab-reared molluscivore populations, but these bacteria target cellulose. Minor shifts in gut microbiota appear adaptive for scale-eating in this radiation, whereas overall microbiome composition was phylogenetically conserved. This contrasts with predictions of adaptive radiation theory and observations of rapid diversification in all other trophic traits in these hosts, including craniofacial morphology, foraging behavior, aggression, and gene expression, suggesting that microbiome divergence proceeds as a nonadaptive radiation.
Comprehensive multi-omics study of the molecular perturbations induced by simulated diabetes on coronary artery endothelial cells
Authors: Moreno-Ulloa Aldo , Delgado-De la Herrán Hilda Carolina , Álvarez-Delgado Carolina , Mendoza-Porras Omar , Carballo-Castañeda Rommel A. , Villarreal Francisco
Published: January 2021

Coronary artery endothelial cells (CAEC) exert an important role in the development of cardiovascular disease. Dysfunction of CAEC is associated with cardiovascular disease in subjects with type 2 diabetes mellitus (T2DM). However, comprehensive studies of the effects that a diabetic environment exerts on this cellular type scarce. The present study characterized the molecular perturbations occurring on cultured bovine CAEC subjected to a prolonged diabetic environment (high glucose [HG] and high insulin [HI]). Changes at the metabolite and peptide level were assessed by untargeted metabolomics and chemoinformatics, and the results were integrated with proteomics data using published SWATH-based proteomics on the samein vitromodel. Our findings were consistent with reports on other endothelial cell types, but also identified novel signatures of DNA/RNA, aminoacid, peptide, and lipid metabolism in cells under a diabetic environment. Manual data inspection revealed disturbances on tryptophan catabolism and biosynthesis of phenylalanine-based, glutathione-based, and proline-based peptide metabolites. Fluorescence microscopy detected an increase in binucleation in cells under treatment that also occurred when human CAEC were used. This multi-omics study identified particular molecular perturbations in an induced diabetic environment that could help unravel the mechanisms underlying the development of cardiovascular disease in subjects with T2DM.
Genome-wide variability in recombination activity is associated with meiotic chromatin organization
Authors: Jin Xiaofan , Fudenberg Geoff , Pollard Katherine S.
Published: January 2021

Background

Recombination enables reciprocal exchange of genomic information between parental chromosomes and successful segregation of homologous chromosomes during meiosis. Errors in this process lead to negative health outcomes, while variability in recombination rate affects genome evolution. In mammals, most crossovers occur in hotspots defined by PRDM9 motifs, though PRDM9 binding sites are not all equally hot. We hypothesize that dynamic patterns of meiotic genome folding are linked to recombination activity.

Results

We apply an integrative bioinformatics approach to analyze how three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strandbreak (DSB) and crossover formation at PRDM9 hotspots. We show that active, spatially accessible genomic regions during meiotic prophase are associated with DSB-favoured hotspots, which further adopt a transient locally active configuration in early prophase. Conversely, crossover formation is depleted among DSBs in spatially accessible regions during meiotic prophase, particularly within gene bodies. We also find evidence that active chromatin regions have smaller average loop sizes in mammalian meiosis. Collectively, these findings establish that differences in chromatin architecture along chromosomal axes are associated with variable recombination activity.

Conclusions

We propose an updated framework describing how 3D organization of brush-loop chromosomes during meiosis may modulate recombination.
Human B cell lineages engaged by germinal centers following influenza vaccination are measurably evolving
Authors: Hoehn Kenneth B. , Turner Jackson S. , Miller Frederick I. , Jiang Ruoyi , Pybus Oliver G. , Ellebedy Ali H. , Kleinstein Steven H.
Published: January 2021

Poor efficacy of seasonal influenza virus vaccines is often attributed to pre-existing immunity interfering with the persistence and maturation of vaccine-induced B cell responses.1Consistent with this notion, no significant increase in somatic hypermutation (SHM) among circulating influenza-binding lineages was detected following seasonal vaccination in humans.2A more recent study showed that at least a subset of vaccine-induced B cell lineages are recruited into germinal centers (GCs) following vaccination, suggesting that affinity maturation of these lineages can occur.3Crucially, however, it has not been demonstrated whether these GC-engaged lineages actually accumulate additional SHM. Here, we address this point using a phylogenetic test of measurable evolution. We first validate this test through simulations and demonstrate measurable B cell evolution in known examples of affinity maturation such as the response to HIV infection. We then show that lineages in the blood are rarely measurably evolving following influenza vaccination, but that GC-engaged lineages - likely derived from memory B cells - are frequently measurably evolving. These findings confirm that seasonal influenza virus vaccination can stimulate additional SHM among responding B cell lineages.
Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder
Authors: Berto Stefano , Treacher Alex , Caglayan Emre , Luo Danni , Haney Jillian R. , Gandal Michael J. , Geschwind Daniel H. , Montillo Albert , Konopka Genevieve
Published: January 2021

Gene expression covaries with brain activity as measured by resting state functional MRI. However, it is unclear how genomic differences driven by disease state can affect this relationship. Here, we integrate brain gene expression datasets of neurotypical controls and autistic (ASD) patients with regionally matched brain activity measurements from fMRI datasets. We identify genes linked with brain activity whose association is disrupted in ASD patients. We identified a subset of genes that showed a differential developmental trajectory in ASD patients compared with controls. These genes are enriched in voltage-gated ion channels and inhibitory neurons, pointing to excitation-inhibition imbalance in ASD. We further assessed differences at the regional level showing that the primary visual cortex is the most affected region in ASD patients. Our results link disrupted brain expression patterns of individuals with ASD to brain activity and show developmental, cell type, and regional enrichment of activity linked genes.
Inherent random fluctuations in COVID-19 outbreaks may explain rapid growth of new mutated virus variants
Authors: Bodin Kenneth , Rocklöv Joacim
Published: January 2021

A new virus variant of SARS-COV-2 has had a profound impact on society while governments have taken action to limit its impacts by enforcing lockdowns and limiting spread from the UK to other countries. Variants with mutations in the virus genome are likely to occur, but do not always associate to significant changes in the biology of the virus, or the disease. For the variant VOC 202012/01 (also referred to as B.1.1.7), however, preliminary reports indicate it may be more transmissible. Here we use a simulation model calibrated to the inherent random fluctuating transmission pattern of COVID-19 to investigate what the probability may be for detecting more transmissible virus variants post facto. We find that post facto identification of successful virus variants of SARS-COV-2 are likely to exhibit growth rates that are substantially larger than the average growth rate. This finding has implications for interpreting growth rate and transmissibility of new virus variants.
MinION™, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting
Authors: Komiya Shinnosuke , Matsuo Yoshiyuki , Nakagawa So , Morimoto Yoshiharu , Kryukov Kirill , Okada Hidetaka , Hirota Kiichi
Published: January 2021

It has been suggested that the local microbiota in the reproductive organs is relevant to women’s health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read sequencers has been used to identify vaginal and endometrial microbiota, but it requires a long time to obtain the results, making it unsuitable for the rapid analysis of small samples in a clinical context. We demonstrated a simple workflow using the nanopore sequencer MinION™ that allows high-resolution and rapid differentiation of vaginal microbiota. Vaginal samples collected from 18 participants were subjected to DNA extraction and full-length 16S rRNA gene sequencing with MinION™. The principal coordinate analysis showed no differences in the bacterial compositions regardless of the sample collection method. The vaginal microbiota results could be reported within 2 days of specimen receipt. Although bacterial vaginosis (BV) was not diagnosed by the Nugent score in any cases, groups with both healthy and BV-like vaginal microbiota were clearly characterized by MinION™ sequencing. We conclude that full-length 16S rRNA gene sequencing analysis with MinION™ provides a rapid means for identifying vaginal bacteria with higher resolution. Species-level profiling of human vaginal microbiota by MinION™ sequencing can allow the analysis of associations with conditions such as genital infections, endometritis, and threatened miscarriage.
CpG-adjuvanted stable prefusion SARS-CoV-2 spike protein protected hamsters from SARS-CoV-2 challenge
Authors: Lien Chia-En , Lin Yi-Jiun , Chen Charles , Lian Wei-Cheng , Kuo Tsun-Yung , Campbell John D , Traquina Paula , Lin Meei-Yun , Liu Luke Tzu-Chi , Chuang Ya-Shan , Ko Hui-Ying , Liao Chun-Che , Chen Yen-Hui , Jan Jia-Tsrong , Sun Cheng-Pu , Lin Yin-Shiou , Wu Ping-Yi , Wang Yu-Chiuan , Tao Mi-Hua , Lin Yi-Ling
Published: January 2021

The COVID-19 pandemic presents an unprecedented challenge to global public health. Rapid development and deployment of safe and effective vaccines are imperative to control the pandemic. In the current study, we applied our adjuvanted stable prefusion SARS-CoV-2 spike (S-2P)-based vaccine, MVC-COV1901, to hamster models to demonstrate immunogenicity and protection from virus challenge. Golden Syrian hamsters immunized intramuscularly with two injections of 1 µg or 5 µg of S-2P adjuvanted with CpG 1018 and aluminum hydroxide (alum) were challenged intranasally with SARS-CoV-2. Prior to virus challenge, the vaccine induced high levels of neutralizing antibodies with 10,000-fold higher IgG level and an average of 50-fold higher pseudovirus neutralizing titers in either dose groups than vehicle or adjuvant control groups. Six days after infection, vaccinated hamsters did not display any weight loss associated with infection and had significantly reduced lung pathology and most importantly, lung viral load levels were reduced to lower than detection limit compared to unvaccinated animals. Vaccination with either 1 μg or 5 μg of adjuvanted S-2P produced comparable immunogenicity and protection from infection. This study builds upon our previous results to support the clinical development of MVC-COV1901 as a safe, highly immunogenic, and protective COVID-19 vaccine.
Assessing the Involvement of Platelet Degranulation in the Therapeutic Properties of Exosome Derived from Amniotic Epithelial Cells through Enrichment and Interaction Network Analysis
Authors: Valizadeh M. , Bangash A. Haider , Hayati D. , Jafari A. , Rajabi-Maham H.
Published: January 2021

Platelet degranulation allows the release of large secretable pools of biologically active proteins which are critical in wound healing initiation and angiogenesis. Exosomes, which can transport a diverse suite of macromolecules, derived from amniotic epithelial cells (AEC-Exo) improve wound healing and angiogenesis. However, the underlying mechanisms are still unclear. In this investigation, we performed a user-friendly bioinformatics analysis system to identify association among the angiogenic and wound healing effects of AEC-Exo treatments. To this end, FunRich software was used, and linked to the Universal Protein Resource (UniProt) as a background database. Several enrichment analyses, including biological process, cellular component, molecular function, and protein domains were conducted on AEC-Exo proteome. Furthermore, to identify the proteins involved in platelet degranulation and evaluate protein–protein association information, comparative analyses and interaction network analyses were illustrated using the NCBI BioSystems, ExoCarta, and STRING databases. Our results indicated the statistically significant association between the proteome in AEC-Exo, platelet degranulation, and their corresponding processes. Therefore, the involvement of platelet degranulation in AEC-Exo proteins may elucidate the angiogenic and wound-healing effects of AEC-Exo treatments.
Capsule network for protein ubiquitination site prediction
Authors: Huang Qiyi , Jiang Jiulei , Luo Yin , Li Weimin , Wang Ying
Published: January 2021

Ubiquitination modification is one of the most important protein posttranslational modifications used in many biological processes. Traditional ubiquitination site determination methods are expensive and time-consuming, whereas calculation-based prediction methods can accurately and efficiently predict ubiquitination sites. This study used a convolutional neural network and a capsule network in deep learning to design a deep learning model, “Caps-Ubi,” for multispecies ubiquitination site prediction. Two encoding methods, one-of-K and the amino acid continuous type were used to characterize the sequence pattern of ubiquitination sites. The proposed Caps-Ubi predictor achieved an accuracy of 0.91, a sensitivity of 0.93, a specificity of 0.89, a measure-correlate-prediction of 0.83, and an area under receiver operating characteristic curve value of 0.96, which outperformed the other tested predictors.
The intensity of the immune response to LPS andE. coliregulates the induction of preterm labor in Rhesus Macaques
Authors: Cappelletti Monica , Presicce Pietro , Ma Feyaing , Senthamaraikannan Paranthaman , Miller Lisa A. , Pellegrini Matteo , Jobe Alan H. , Divanovic Senad , Way Sing Sing , Chougnet Claire A. , Kallapur Suhas G.
Published: January 2021

Intrauterine infection/inflammation (IUI) is a major contributor to preterm labor (PTL). However, IUI does not invariably cause PTL. We hypothesized that quantitative and qualitative differences in immune response exist in subjects with or without PTL. To define the triggers for PTL, we developed Rhesus macaque models of IUI driven by lipopolysaccharyde (LPS) or liveE. coli. PTL did not occur in LPS challenged Rhesus macaque whileE. coliinfected animals frequently delivered preterm. Although LPS and liveE. coliboth caused immune cell infiltration,E. coliinfected animals showed higher levels of inflammatory mediators, particularly IL6 and prostaglandins, in the chorioamnion decidua and amniotic fluid. Neutrophil infiltration in the chorion was a common feature to both LPS andE. coli. However, neutrophilic infiltration andIL6andPTGS2expression in the amnion was specifically induced by liveE. coli. RNASeq analysis of fetal membranes revealed that specific pathways involved in augmentation of inflammation including type I interferon response, chemotaxis, sumoylation and iron homeostasis were upregulated in theE. coligroup compared to the LPS group. Our data suggest that intensity of the host immune response to IUI may determine susceptibility to PTL.
Phosphorylation of the selective autophagy receptor TAX1BP1 by canonical and noncanonical IκB kinases promotes its lysosomal localization and clearance of MAVS aggregates
Authors: Choi Young Bong , Zhang Jiawen , Vo Mai Tram , White Jesse , He Chaoxia , Harhaj Edward W.
Published: January 2021

TAX1BP1 is a selective autophagy receptor which inhibits NF-κB and RIG-I-like receptor (RLR) signaling to prevent excessive inflammation and maintain homeostasis. Selective autophagy receptors such as p62/SQSTM1 and OPTN are phosphorylated by the noncanonical IκB kinase TBK1 to stimulate their selective autophagy function. However, it is unknown if TAX1BP1 is regulated by TBK1 or other kinases under basal conditions or during RNA virus infection. Here, we found that the noncanonical IκB kinases TBK1 and IKKi phosphorylate TAX1BP1 to regulate its basal turnover, whereas the canonical IκB kinase IKKα and the core autophagy factor ATG9 play essential roles in RNA virus-mediated TAX1BP1 autophagosomal degradation. TAX1BP1 phosphorylation by canonical and noncanonical IκB kinases promotes its localization to lysosomes resulting in its degradation. Furthermore, TAX1BP1 plays a critical role in the clearance of MAVS aggregates, and phosphorylation of TAX1BP1 augments its MAVS aggrephagy function. Together, our data support a model whereby IκB kinases license TAX1BP1 selective autophagy function to inhibit MAVS and RLR signaling.

Author Summary

The RIG-I-like receptor (RLR) pathway induces type I interferon (IFN) and proinflammatory cytokines in response to RNA virus infection. MAVS is a mitochondrial adaptor protein in the RLR pathway that forms prion-like aggregates upon activation; however, how MAVS aggregates are cleared to restore homeostasis is unclear. Autophagy is a lysosomal degradation pathway important for the clearance of potentially cytotoxic protein aggregates that could induce inflammation and/or cell death. TAX1BP1 is a selective autophagy receptor that inhibits RLR signaling, but the precise mechanisms remain unknown. Here, we found that TAX1BP1 is a substrate for multi-site phosphorylation by canonical and noncanonical IκB kinases which triggered its lysosomal localization and degradation. We also found that TAX1BP1 was critical for the clearance of MAVS aggregates in a phosphorylation-dependent manner. Overall, our data suggest that phosphorylation serves a key regulatory function for TAX1BP1 to inhibit RLR signaling.
Potential biomarker of human papillomavirus 16 L1 methylation for prediction of anal intraepithelial neoplasia in men who have sex with men (MSM)
Authors: Chaiwongkot Arkom , Phanuphak Nittaya , Pankam Tippawan , Bhattarakosol Parvapan
Published: January 2021

Quantitative measurement of human papillomavirus (HPV) 16 early promoter and L1 genes methylation were analyzed in anal cells collected from men who have sex with men (MSM) to determine the potential biomarker for screening of HPV related anal cancer. The methylation patterns of the HPV16 genes including early promoter (CpG 31, 37, 43, 52 and 58) and L1 gene (CpG 5600, 5606, 5609, 5615, 7136 and 7145) were analyzed in 178 anal samples with histology diagnosed as normal, anal intraepithelial neoplasia (AIN) 1, AIN2 and AIN3 by pyrosequencing assay. Low methylation levels of early promoter (<10%) and L1 genes (<20%) were found in all detected normal anal cells, while medium to high methylation (>20-60%) in early promoter was found 1.5% (1/67) and 5% (2/40) in AIN1 and AIN2-3 samples, respectively. Interestingly, slightly increased L1 gene methylation level (>20-60%) especially at HPV16 5’L1 regions CpGs 5600 and 5609 from normal to AIN3 were demonstrated. Moreover, negative correlation between high HPV16 L1 gene methylation at CpGs 5600, 5609, 5615 and 7145 and low percentage of CD4+ was found in AIN3 HIV positive cases. When compared methylation status of AIN2-3 to those of the normal/AIN1 lesion, the results indicated potential of using HPV16 L1 gene methylation as a biomarker for HPV related cancer screening.
Milieu matters: Anin vitrowound milieu to recapitulate key features of, and probe new insights into, polymicrobial biofilms
Authors: Kadam Snehal , Madhusoodhanan Vandana , Bhide Devyani , Ugale Rutuja , Tikhole Utkarsha , Kaushik Karishma S
Published: January 2021

Bacterial biofilms are a major cause of delayed wound healing. Consequently, the study of wound biofilms, particularly in host-relevant conditions, has gained importance. Mostin vitrobiofilm studies employ refined laboratory media to study biofilms, conditions that are not relevant to the infection state. To mimic the wound milieu,in vitrobiofilm studies often incorporate serum or plasma in growth conditions, or employ clot or matrix-based biofilm models. While incorporating serum or plasma alone is a minimalistic approach, the more complexin vitrowound models are technically demanding, and poorly compatible with standard biofilm assays. Based on previous reports of clinical wound fluid composition, we have developed anin vitrowound milieu (IVWM) that includes, in addition to serum (to recapitulate wound fluid), matrix elements and biochemical factors. In comparison with Luria-Bertani broth and Fetal Bovine Serum (FBS), the IVWM was used to study planktonic growth and biofilm features, including interspecies interactions, of common wound pathogens,Staphylococcus aureusandPseudomonas aeruginosa. We demonstrate that the IVWM recapitulates widely reportedin vivobiofilm features such as metabolic activity, increased antibiotic tolerance, 3D structure, and interspecies interactions for single- and co-species biofilms. Further, the IVWM is simple to formulate, uses laboratory-grade components, and is compatible with standard biofilm assays. Given this, it holds potential as a tractable approach to study wound biofilms under host-relevant conditions.
New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2
Authors: Saramago Margarida , Bárria Cátia , Costa Vanessa , Souza Caio S. , Viegas Sandra C. , Domingues Susana , Lousa Diana , Soares Cláudio M , Arraiano Cecília M , Matos Rute G.
Published: January 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has triggered a global pandemic with devastating consequences for health-care and social-economic systems. Thus, the understanding of fundamental aspects of SARS-CoV-2 is of extreme importance.

In this work, we have focused our attention on the viral ribonuclease (RNase) nsp14, since this protein was considered one of the most interferon antagonists from SARS-CoV-2, and affects viral replication. This RNase is a multifunctional protein that harbors two distinct activities, an N-terminal 3’-to-5’ exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), both with critical roles in coronaviruses life cycle. Namely, SARS-CoV-2 nsp14 ExoN knockout mutants are non-viable, indicating nsp14 as a prominent target for the development of antiviral drugs.

Nsp14 ExoN activity is stimulated through the interaction with the nsp10 protein, which has a pleiotropic function during viral replication. In this study, we have performed the first biochemical characterization of the complex nsp14-nsp10 from SARS-CoV-2. Here we confirm the 3’-5’ exoribonuclease and MTase activities of nsp14 in this new Coronavirus, and the critical role of nsp10 in upregulating the nsp14 ExoN activityin vitro. Furthermore, we demonstrate that SARS-CoV-2 nsp14 N7-MTase activity is functionally independent of the ExoN activity. The nsp14 MTase activity also seems to be independent of the presence of nsp10 cofactor, contrarily to nsp14 ExoN.

Until now, there is no available structure for the SARS-CoV-2 nsp14-nsp10 complex. As such, we have modelled the SARS-CoV-2 nsp14-nsp10 complex based on the 3D structure of the complex from SARS-CoV (PDB ID 5C8S). We also have managed to map key nsp10 residues involved in its interaction with nsp14, all of which are also shown to be essential for stimulation of the nsp14 ExoN activity. This reinforces the idea that a stable interaction between nsp10 and nsp14 is strictly required for the nsp14-mediated ExoN activity of SARS-CoV-2, as observed for SARS-CoV.

We have studied the role of conserved DEDD catalytic residues of SARS-CoV-2 nsp14 ExoN. Our results show that motif I of ExoN domain is essential for the nsp14 function contrasting to the functionality of these conserved catalytic residues in SARS-CoV, and in the Middle East respiratory syndrome coronavírus (MERS). The differences here revealed can have important implications regarding the specific pathogenesis of SARS-CoV-2.

The nsp10-nsp14 interface is a recognized attractive target for antivirals against SARS-CoV-2 and other coronaviruses. This work has unravelled a basis for discovering inhibitors targeting the specific amino acids here reported, in order to disrupt the assembly of this complex and interfere with coronaviruses replication.
Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life
Authors: Méheust Raphaël , Huang Shuo , Rivera-Lugo Rafael , Banfield Jillian F. , Light Samuel H.
Published: January 2021

Disparate redox activities that take place beyond the bounds of the prokaryotic cell cytosol must connect to membrane or cytosolic electron pools. Proteins post-translationally flavinylated by the enzyme ApbE mediate electron transfer in several characterized extracytosolic redox systems but the breadth of functions of this modification remains unknown. Here we present a comprehensive bioinformatic analysis of 31,910 prokaryotic genomes that provides evidence of extracytosolic ApbEs within ~50% of bacteria and the involvement of flavinylation in numerous uncharacterized biochemical processes. By mining flavinylation-associated gene clusters, we identify five protein classes responsible for transmembrane electron transfer and two domains of unknown function (DUF2271 and DUF3570) that are flavinylated by ApbE. We observe flavinylation/iron transporter gene colocalization patterns that implicate functions in iron reduction and assimilation. We find associations with characterized and uncharacterized respiratory oxidoreductases that highlight roles of flavinylation in respiratory electron transport chains. Finally, we identify interspecies gene cluster variability consistent with flavinylation/cytochrome functional redundancies and discover a class of “multi-flavinylated proteins'' that may resemble multiheme cytochromes in facilitating longer distance electron transfer. These findings provide key mechanistic insight into an important facet of bacterial physiology and establish flavinylation as a functionally diverse mediator of extracytosolic electron transfer.

Impact Statement

Bioinformatic and biochemical studies find that covalently bound flavins are common and participate in wide-ranging extracytosolic redox activities throughout bacterial life.
International risk of the new variant COVID-19 importations originating in the United Kingdom
Authors: Du Zhanwei , Wang Lin , Yang Bingyi , Ali Sheikh Taslim , Tsang Tim K. , Shan Songwei , Wu Peng , Lau Eric H. Y. , Cowling Benjamin J. , Meyers Lauren Ancel
Published: January 2021

A fast-spreading SARS-CoV-2 variant identified in the United Kingdom in December 2020 has raised international alarm. We estimate that, in all 15 countries analyzed, there is at least a 50% chance the variant was imported by travelers from the United Kingdom by December 7th.
Exo-β-N-acetylmuramidase NamZ ofBacillus subtilisis the founding member of a family of exo-lytic peptidoglycan hexosaminidases
Authors: Müller Maraike , Calvert Matthew , Hottmann Isabel , Kluj Robert Maria , Teufel Tim , Balbuchta Katja , Engelbrecht Alicia , Selim Khaled A. , Xu Qingping , Borisova Marina , Titz Alexander , Mayer Christoph
Published: January 2021

Endo-β-N-acetylmuramidases, commonly known as lysozymes, are well-characterized antimicrobial enzymes that potentially lyse bacterial cells. They catalyze an endo-lytic cleavage of the peptidoglycan, the structural component of the bacterial cell wall; i.e. they hydrolyze glycosidicN-acetylmuramic acid (MurNAc)-β-1,4-N-acetylglucosamine (GlcNAc)-bonds within the heteroglycan backbone of peptidoglycan. In contrast, little is known about exo-β-N-acetylmuramidases, catalyzing an exo-lytic cleavage of β-1,4-MurNAc entities from the non-reducing ends of peptidoglycan chains. Such an enzyme was identified earlier in the bacteriumBacillus subtilis, but the corresponding gene has remained unknown so far. We identifiedybbCofB. subtilis,renamednamZ, as encoding the reported exo-β-N-acetylmuramidase. A ΔnamZmutant accumulated specific cell wall fragments and showed growth defects under starvation conditions, indicating a role of NamZ in cell wall turnover. Recombinant NamZ protein specifically hydrolyzed the artificial substrate para-nitrophenyl β-MurNAc and the peptidoglycan-derived disaccharide MurNAc-β-1,4-GlcNAc. Together with the exo-β-N-acetylglucosaminidase NagZ and the exo-muramoyl-L-alanine amidase AmiE, NamZ degraded intact peptidoglycan by sequential hydrolysis from the non-reducing ends. NamZ is a member of the DUF1343 protein family of unknown function and shows no significant sequence identity with known glycosidases. A structural model of NamZ revealed a putative active site located in a cleft within the interface of two subdomains, one of which constituting a Rossmann-fold-like domain, unusual for glycosidases. On this basis, we propose that NamZ represents the founding member of a novel family of peptidoglycan hexosaminidases, which is mainly present in the phylum Bacteroidetes and, less frequently, within Firmicutes (Bacilli, Clostridia), Actinobacteria and Gammaproteobacteria.