bluuebunny/crossref_metadata_2025 huggingface dataset:
Institutional Differences in the Stewardship and Research Output of United States Herbaria
Authors: Garretson Alexis
Published: January 2021

Public policy decisions regarding institutional frameworks that govern the stewardship of biodiversity data at public and private institutions are an area of increasing importance. Museums, government agencies, and academic institutions across the United States maintain collections of biological specimens and information critical to scientific discovery. One subset of these natural history collections are herbaria, or collections of preserved plant matter and their associated data. In this study, I evaluate the current state of the digitization and databasing of herbariums contributing data to the SEInet Regional Network of North American Herbaria, and assess the impact of characteristics, particularly institution type (cultural sector institutions, public universities, private universities, or public land institutions), on the metrics of herbaria richness, digitization, and research usage. The results of this study suggest that institution type is significantly associated with the size, diversity, and digitization efforts of a herbarium collection. Specifically, cultural sector institutions tend to have larger and more diverse collections, followed by public and private universities, and finally public land institutions. Additionally, as herbarium size and richness increases, the research output of associated staff also increases. These results highlight that some institutions, particularly larger institutions located at universities or cultural sector institutions, may be better supported in the curation, stewardship, and digitization of large collections, allowing long-term access to the associated biodiversity data. Smaller institutions at public land institutions may need additional support in these endeavors, and may represent an area of unmet needs for digitization and curatorial funding and resources.
Impact of gene annotation choice on the quantification of RNA-seq data
Authors: Chisanga David , Liao Yang , Shi Wei
Published: January 2021

RNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression levels of genes from RNA-seq data is to map reads to a reference genome and then count mapped reads to each gene. Gene annotation data, which include chromosomal coordinates of exons for tens of thousands of genes, are required for this quantification process. There are several major sources of gene annotations that can be used for quantification, such as Ensembl and RefSeq databases. However, there is very little understanding of the effect that the choice of annotation has on the accuracy of gene expression quantification in an RNA-seq analysis. In this paper, we present results from our comparison of Ensembl and RefSeq human annotations on their impact on gene expression quantification using a benchmark RNA-seq dataset generated by the SEquencing Quality Control (SEQC) consortium. We show that the use of RefSeq gene annotation models led to better quantification accuracy, based on the correlation with ground truths including expression data from >800 real-time PCR validated genes, known titration ratios of gene expression and microarray expression data. We also found that the recent expansion of the RefSeq annotation has led to a decrease in its annotation accuracy. Finally, we demonstrated that the RNA-seq quantification differences observed between different annotations were not affected by the use of different normalization methods.
Molecular mechanism of ACAD9 in mitochondrial respiratory complex 1 assembly
Authors: Xia Chuanwu , Lou Baoying , Fu Zhuji , Mohsen Al-Walid , Vockley Jerry , Kim Jung-Ja P.
Published: January 2021

ACAD9 belongs to the acyl-CoA dehydrogenase family, which catalyzes the α-β dehydrogenation of fatty acyl-CoA thioesters. Thus, it is involved in fatty acid β-oxidation (FAO). However, it is now known that the primary function of ACAD9 is as an essential chaperone for mitochondrial respiratory complex 1 assembly. ACAD9 interacts with ECSIT and NDUFAF1, forming the mitochondrial complex 1 assembly (MCIA) complex. Although the role of MCIA in the complex 1 assembly pathway is well studied, little is known about the molecular mechanism of the interactions among these three assembly factors. Our current studies reveal that when ECSIT interacts with ACAD9, the flavoenzyme loses the FAD cofactor and consequently loses its FAO activity, demonstrating that the two roles of ACAD9 are not compatible. ACAD9 binds to the carboxy-terminal half (C-ECSIT), and NDUFAF1 binds to the amino-terminal half of ECSIT. Although the binary complex of ACAD9 with ECSIT or with C-ECSIT is unstable and aggregates easily, the ternary complex of ACAD9-ECSIT-NDUFAF1 (i.e., the MCIA complex) is soluble and extremely stable. Molecular modeling and SAXS studies of the MCIA complex identified the possible interaction sites between the three assembly factors and binding sites for other assembly factors, including complex 1 subunits. Furthermore, we have mapped over 40 currently known pathogenic mutation sites onto the homology-modeled ACAD9 structure, giving us the structural basis for their involvement in diseases that result from complex 1 deficiency.
Fibrinolysis influences SARS-CoV-2 infection in ciliated cells
Authors: Hou Yapeng , Ding Yan , Nie Hongguang , Ji Hong-Long
Published: January 2021

Rapid spread of COVID-19 has caused an unprecedented pandemic worldwide, and an inserted furin site in SARS-CoV-2 spike protein (S) may account for increased transmissibility. Plasmin, and other host proteases, may cleave the furin site of SARS-CoV-2 S protein and γ subunits of epithelial sodium channels (γ ENaC), resulting in an increment in virus infectivity and channel activity. As for the importance of ENaC in the regulation of airway surface and alveolar fluid homeostasis, whether SARS-CoV-2 will share and strengthen the cleavage network with ENaC proteins at the single-cell level is urgently worthy of consideration. To address this issue, we analyzed single-cell RNA sequence (scRNA-seq) datasets, and found the PLAU (encoding urokinase plasminogen activator), SCNN1G (γENaC), and ACE2 (SARS-CoV-2 receptor) were co-expressed in alveolar epithelial, basal, club, and ciliated epithelial cells. The relative expression level of PLAU, TMPRSS2, and ACE2 were significantly upregulated in severe COVID-19 patients and SARS-CoV-2 infected cell lines using Seurat and DESeq2 R packages. Moreover, the increments in PLAU, FURIN, TMPRSS2, and ACE2 were predominately observed in different epithelial cells and leukocytes. Accordingly, SARS-CoV-2 may share and strengthen the ENaC fibrinolytic proteases network in ACE2 positive airway and alveolar epithelial cells, which may expedite virus infusion into the susceptible cells and bring about ENaC associated edematous respiratory condition.
Site-directed crosslinking identifies the stator-rotor interaction surfaces in a hybrid bacterial flagellar motor
Authors: Terashima Hiroyuki , Kojima Seiji , Homma Michio
Published: January 2021

The bacterial flagellum is the motility organelle powered by a rotary motor. The rotor and stator elements of the motor are embedded in the cytoplasmic membrane. The stator units assemble around the rotor, and an ion flux (typically H+or Na+) conducted through a channel of the stator induces conformational changes that generate rotor torque. Electrostatic interactions between the stator protein PomA inVibrio(MotA inEscherichia coli) and the rotor protein FliG have been suggested by genetic analyses, but have not been demonstrated directly. Here, we used site-directed photo- and disulfide-crosslinking to provide direct evidence for the interaction. We introduced a UV-reactive amino acid,p-benzoyl-L-phenylalanine (pBPA), into the cytoplasmic region of PomA or the C-terminal region of FliG in intact cells. After UV irradiation,pBPA inserted at a number of positions formed a crosslink with FliG. PomA residue K89 gave the highest yield of crosslinks, suggesting that it is the PomA residue nearest to FliG. UV-induced crosslinking stopped motor rotation, and the isolated hook-basal body contained the crosslinked products.pBPA inserted to replace residues R281 or D288 in FliG formed crosslinks with theEscherichia colistator protein, MotA. A cysteine residue introduced in place of PomA K89 formed disulfide crosslinks with cysteine inserted in place of FliG residues R281 and D288, and some other flanking positions. These results provide the first demonstration of direct physical interaction between specific residues in FliG and PomA/MotA.
Topoisomerase 2β induces DNA breaks to regulate human papillomavirus replication
Authors: Kaminski Paul , Hong Shiyuan , Kono Takeyuki , Hoover Paul , Laimins Laimonis
Published: January 2021

Topoisomerases regulate higher order chromatin structures through the transient breaking and re-ligating of one or both strands of the phosphodiester backbone of duplex DNA. TOP2β is a type II topoisomerase that induces double strand DNA breaks at topological-associated domains (TADS) to relieve torsional stress arising during transcription or replication. TADS are anchored by CTCF and SMC1 cohesin proteins in complexes with TOP2β. Upon DNA cleavage a covalent intermediate DNA-TOP2β (TOP2βcc) is transiently generated to allow for strand passage. The tyrosyl-DNA phosphodiesterase TDP2 can resolve TOP2βcc but failure to do so quickly can lead to long-lasting DNA breaks. Given the role of CTCF/SMC1 proteins in the HPV life cycle we investigated if TOP2β proteins contribute to HPV pathogenesis. Our studies demonstrated that levels of both TOP2β and TDP2 were substantially increased in cells with high risk HPV genomes and this correlated with high amounts of DNA breaks. Knockdown of TOP2β with shRNAs reduced DNA breaks by over 50% as determined through COMET assays. Furthermore this correlated with substantially reduced formation of repair foci such as γH2AX, pCHK1 and pSMC1 indicative of impaired activation of DNA damage repair pathways. Importantly, knockdown of TOP2β also blocked HPV genome replication. Our previous studies demonstrated that CTCF /SMC1 factors associate with HPV genomes at sites in the late regions of HPV31 and these correspond to regions that also bind TOP2β. This study identifies TOP2β as responsible for enhanced levels of DNA breaks in HPV positive cells and as a regulator of viral replication.
Efficacy of propolis as an adjunct treatment for hospitalized COVID-19 patients: a randomized, controlled clinical trial
Authors: Duarte Silveira Marcelo Augusto , De Jong David , dos Santos Galvão Erica Batista , Ribeiro Juliana Caldas , Silva Thiago Cerqueira , Berretta Andresa Aparecida , Amorim Thais Chaves , San Martin Raissa Lanna Araújo , Rebelo da Conceição Luis Filipe Miranda , Dantas Gomes Marcel Miranda , Teixeira Maurício Brito , de Souza Sergio Pinto , Alves dos Santos Marcele Helena Celestino , de Oliveira Silva Márcio , Lírio Monique , Moreno Lis , Miranda Sampaio Julio Cezar , Mendonça Renata , Ultchak Silviana Salles , Amorim Fabio Santos , Rosa João Gabriel , Pena Batista Paulo Benigno , da Guarda Suzete Nascimento Farias , Mendes Ana Verena Almeida , Passos Rogerio da Hora ,   for the BeeCovid Team
Published: January 2021

Among candidate treatment options for COVID-19, propolis, produced by honey bees from bioactive plant exudates, has shown potential against viral targets and has demonstrated immunoregulatory properties. We conducted a randomized, controlled, open-label, single center trial, with a standardized propolis product (EPP-AF) on hospitalized adult COVID-19 patients. Patients received standard care plus propolis at an oral dose of 400mg/day (n=40) or 800mg/day (n=42) for seven days, or standard care alone (n=42). Standard care included all necessary interventions, as determined by the attending physician. The primary end point was the time to clinical improvement defined as the length of hospital stay or oxygen therapy dependency. Secondary outcomes included acute kidney injury and need for intensive care or vasoactive drugs. Time in the hospital after intervention was significantly shortened in both propolis groups compared to the controls; median 7 days with 400mg/day and 6 days with 800mg/day, versus 12 days for standard care alone. Propolis did not significantly affect the need for oxygen supplementation. With the higher dose, significantly fewer patients developed acute kidney injury than in the controls (2 versus 10 of 42 patients). Propolis as an adjunct treatment was safe and reduced hospitalization time. The registration number for this clinical trial is: NCT04480593 (20/07/2020).
The Conundrum of Giglio Island: unraveling the dynamics of an apparent resistance to COVID-19 – A descriptive study
Authors: Bognanni Antonio , Schiaffino Armando , Pimpinelli Fulvia , Donzelli Sara , Celesti Ilaria , Strano Sabrina , Solari Elena , Schiaffino Giorgia , Solari Gabriele , Solari Domenico , Delbue Serena , Rigoni Marta , Nollo Giandomenico , Muti Greta E. , Schünemann Giovanna E.U. Muti , Schünemann Holger J , Blandino Giovanni , Morrone Aldo , Muti Paola
Published: January 2021

Objectives

Despite an extensive risk of exposure to COVID-19, the residents of Giglio Island, Italy, did not develop any symptom of SARS-CoV-2. The present study aims to characterize the nature of exposure and to describe the local population dynamics underlying its apparent resistance to COVID-19.

Methods

We conducted seroprevalence screening from April 29 to May 3, 2020 across the three main settlements on the island. We invited the adult resident population, present on the island to undergo testing by rapid serologic assay and to provide a sample of saliva for molecular validation. We monitored the participation through the official municipality residents’ list. Serologic testing was performed using a COVID-19 IgG/IgM rapid test while molecular analyses were carried out by Allplex 2019-nCoV Assay (Seegene).

Results

A total of 634 residents out of 748 (84.8%) present at the time, and 89 non-residents underwent serological testing. 364 males and 359 females with a median age of 58.5 years. The serological screening identified one positive, asymptomatic subject. The Nucleic Acid Amplification Tests did not yield any positive result.

Conclusion

Despite extensive exposure to SARS-CoV-2, only one new asymptomatic infection occurred in this population. This may be due to unknown protective factors or chance. On the basis of this first descriptive study, using its population as a reference model, further investigations will be conducted to characterize the summer period exposure and to test the advanced hypotheses, focusing on the evaluation of a possible cross-reactivity to SARS-CoV-2 from exposure to endemic viruses.
Tuberculosis biomarkers discovered using Diversity Outbred mice
Authors: Koyuncu Deniz , Niazi M. Khalid Khan , Tavolara Thomas , Abeijon Claudia , Ginese Melanie , Liao Yanghui , Mark Carolyn , Gower Adam C , Gatti Daniel M , Kramnik Igor , Gurcan Metin , Yener Bülent , Beamer Gillian
Published: January 2021

Background

Biomarker discovery for pulmonary tuberculosis (TB) may be accelerated by modeling human genotypic diversity and phenotypic responses toMycobacterium tuberculosis(Mtb). To meet these objectives, we use the Diversity Outbred (DO) mouse population and apply novel classifiers to identify informative biomarkers from multidimensional data sets.

Method

To identify biomarkers, we infected DO mice with aerosolizedMtbconfirmed a human-like spectrum of phenotypes, examined gene expression, and inflammatory and immune mediators in the lungs. We measured 11 proteins in 453Mtb-infected and 29 non-infected mice. We have searched all combinations of six classification algorithms and 239 biomarker subsets and independently validated the selected classifiers. Finally, we selected two mouse lung biomarkers to test as candidate biomarkers of active TB, measuring their diagnostic performance in human sera acquired from the Foundation for Innovative New Diagnostics.

Findings

DO mice discovered two translationally relevant biomarkers, CXCL1 and MMP8 that accurately diagnosed active TB in humans with > 90% sensitivity and specificity compared to controls. We identified them through the two classifiers that accurately diagnosed supersusceptible DO mice with early-onset TB: Logistic Regression using MMP8 as a single biomarker, and Gradient Tree Boosting using a panel of 4 biomarkers (CXCL1, CXCL2, TNF, IL-10).

Interpretation

This work confirms that the DO population models human responses and can accelerate discovery of translationally relevant TB biomarkers.

Funding

Support was provided by NIH R21 AI115038; NIH R01 HL145411; NIH UL1-TR001430; and the American Lung Association Biomedical Research Grant RG-349504.
How can the public health impact of vaccination be estimated?
Authors: Londono Susy Echeverria , Li Xiang , Toor Jaspreet , Villiers Margaret J. de , Nayagam Shevanthi , Hallett Timothy B. , Abbas Kaja , Jit Mark , Klepac Petra , Jean Kévin , Garske Tini , Ferguson Neil M. , Gaythorpe Katy A. M.
Published: January 2021

Deaths due to vaccine preventable diseases cause a notable proportion of mortality worldwide. To quantify the importance of vaccination, it is necessary to estimate the burden averted through vaccination. The Vaccine Impact Modelling Consortium (VIMC) was established to estimate the health impact of vaccination. We describe the methods implemented by the VIMC to estimate impact by calendar year, birth year and year of vaccination (YoV). The calendar and birth year methods estimate impact in a particular year and over the lifetime of a particular birth cohort, respectively. The YoV method estimates the impact of a particular year’s vaccination activities through the use of impact ratios which have no stratification and stratification by activity type and/or birth cohort. Furthermore, we detail an impact extrapolation (IE) method for use between coverage scenarios. We compare the methods, focusing on YoV for hepatitis B, measles and yellow fever. We find that the YoV methods estimate similar impact with routine vaccinations but have greater yearly variation when campaigns occur with the birth cohort stratification. The IE performs well for the YoV methods, providing a time-efficient mechanism for updates to impact estimates. These methods provide a robust set of approaches to quantify vaccination impact.
Detection and surveillance of SARS-CoV-2 genomic variants in wastewater
Authors: Jahn Katharina , Dreifuss David , Topolsky Ivan , Kull Anina , Ganesanandamoorthy Pravin , Fernandez-Cassi Xavier , Bänziger Carola , Devaux Alexander J. , Stachler Elyse , Caduff Lea , Cariti Federica , Corzón Alex Tuñas , Fuhrmann Lara , Chen Chaoran , Jablonski Kim Philipp , Nadeau Sarah , Feldkamp Mirjam , Beisel Christian , Aquino Catharine , Stadler Tanja , Ort Christoph , Kohn Tamar , Julian Timothy R. , Beerenwinkel Niko
Published: January 2021

The emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to assess circulating viral lineages in the community. We performed genomic sequencing of 122 wastewater samples from three locations in Switzerland to analyze the B.1.1.7, B.1.351, and P.1 variants of SARS-CoV-2 on a population level. We called variant-specific signature mutations and monitored variant prevalence in the local population over time. To enable early detection of emerging variants, we developed a bioinformatics tool that uses read pairs carrying multiple signature mutations as a robust indicator of low-frequency variants. We further devised a statistical approach to estimate the transmission fitness advantage, a key epidemiological parameter indicating the speed at which a variant spreads through the population, and compared the wastewater-based findings to those derived from clinical samples. We found that the local outbreak of the B.1.1.7 variant in two Swiss cities was observable in wastewater up to 8 days before its first detection in clinical samples. We detected a high prevalence of the B.1.1.7 variant in an alpine ski resort popular among British tourists in December 2020, a time when the variant was still very rare in Switzerland. We found no evidence of local spread of the B.1.351 and P.1 variants at the monitored locations until the end of the study (mid February) which is consistent with clinical samples. Estimation of local variant prevalence performs equally well or better for wastewater samples as for a much larger number of clinical samples. We found that the transmission fitness advantage of B.1.1.7, i.e. the relative change of its reproductive number, can be estimated earlier and based on substantially fewer wastewater samples as compared to using clinical samples. Our results show that genomic sequencing of wastewater samples can detect, monitor, and evaluate genetic variants of SARS-CoV-2 on a population level. Our methodology provides a blueprint for rapid, unbiased, and cost-efficient genomic surveillance of SARS-CoV-2 variants.
Engineered RNA biosensors enable ultrasensitive SARS-CoV-2 detection in a simple color and luminescence assay
Authors: Chakravarthy Anirudh , Anirudh KN , George Geen , Ranganathan Shyamsundar , Shettigar Nishan , Suchitta U , Palakodeti Dasaradhi , Gulyani Akash , Ramesh Arati
Published: January 2021

The continued resurgence of the COVID-19 pandemic with multiple variants underlines the need for diagnostic strategies, that are easily adapatable to the changing virus. Here, we have designed and developed toehold RNA-based sensors across the SARS-CoV-2 genome for direct and ultrasensitive detection of the virus and its prominent variants. In our assay, isothermal amplification of a fragment of SARS-CoV-2 RNA coupled with activation of our biosensors leads to a conformational switch in the sensor. This leads to translation of a reporter-protein e.g. LacZ or Nano-lantern that is easily detected using color/luminescence. By optimizing RNA-amplification and biosensor-design, we have generated a highly-sensitive diagnostic assay; with sensitivity down to attomolar SARS-CoV-2 RNA. As low as 100 copies of viral RNA are detected with development of bright color that is easily visualized by the human eye, or a simple cell phone camera as well as quantified using a spectrophotometer. This makes our assay deployable all the way from a well equiped laboratory to a low-resource setting anywhere in the world. Finally, this PHAsed NASBA-Translation Optical Method (PHANTOM) using our engineered RNA biosensors efficiently detects the presence of viral RNA in human patient samples, correlating well with Ct values from RT-qPCR tests. This work presents a powerful and universally accessible strategy for detecting Covid-19 and its prominent variants. This strategy is easily adaptable to further viral evolution and brings RNA-based bioengineering to centerstage.
Comparison of algorithm-based versus single-item diagnostic measures of anxiety and depression disorders in the GLAD and COPING cohorts
Authors: Davies Molly R. , Buckman Joshua E. J. , Adey Brett N. , Armour Chérie , Bradley John R. , Curzons Susannah C. B. , Davis Katrina A. S. , Goldsmith Kimberley A. , Hirsch Colette R. , Hotopf Matthew , Hübel Christopher , Jones Ian R. , Kalsi Gursharan , Krebs Georgina , Lin Yuhao , Marsh Ian , McAtarsney-Kovacs Monika , McIntosh Andrew M. , Monssen Dina , Peel Alicia J. , Rogers Henry C. , Skelton Megan , Smith Daniel J. , Kuile Abigail ter , Thompson Katherine N. , Veale David , Walters James T. R. , Zahn Roland , Breen Gerome , Eley Thalia C.
Published: January 2021

Background

Understanding and improving outcomes for people with anxiety or depression often requires large studies. To increase participation and reduce costs, such research is typically unable to utilise “gold-standard” methods to ascertain diagnoses, instead relying on remote, self-report measures.

Aims

To assess the comparability of remote diagnostic methods for anxiety and depression disorders commonly used in research.

Method

Participants from the UK-based GLAD and COPING NBR cohorts (N= 58,400) completed an online questionnaire between 2018-2020. Responses to detailed symptom reports were compared to DSM-5 criteria to generate algorithm-based diagnoses of major depressive disorder (MDD), generalised anxiety disorder (GAD), specific phobia, social anxiety disorder, panic disorder, and agoraphobia. Participants also self-reported any prior diagnoses from health professionals, termed single-item diagnoses. “Any anxiety” included participants with at least one anxiety disorder. Agreement was assessed by calculating accuracy, Cohen’s kappa, McNemar’s chi-squared, sensitivity, and specificity.

Results

Agreement between diagnoses was moderate for MDD, any anxiety, and GAD, but varied by cohort. Agreement was slight to fair for the phobic disorders. Many participants with single-item GAD did not receive an algorithm-based diagnosis. In contrast, algorithm-based diagnoses of the phobic disorders were more common than single-item diagnoses.

Conclusions

Agreement for MDD, any anxiety, and GAD was higher for cases in the case-enriched GLAD cohort and for controls in the general population COPING NBR cohort. For anxiety disorders, single-item diagnoses classified most participants as having GAD, whereas algorithm-based diagnoses distributed participants more evenly across the anxiety disorders. Further validation against gold standard measures is required.
Inflight Transmission of COVID-19 Based on Aerosol Dispersion Data
Authors: Wang Zhaozhi , Galea Edwin R. , Grandison Angus , Ewer John , Jia Fuchen
Published: January 2021

Background

An issue of concern to the travelling public is the possibility of in-flight transmission of COVID-19 during long- and short-haul flights. The aviation industry maintain the probability of contracting the illness is small based on reported cases, modelling and data from aerosol dispersion experiments conducted on-board aircraft.

Methods

Using experimentally derived aerosol dispersion data for a B777-200 aircraft and a modified version of the Wells-Riley equation we estimate inflight infection probability for a range of scenarios involving quanta generation rate and face mask efficiency. Quanta generation rates were selected based on COVID-19 events reported in the literature while mask efficiency was determined from the aerosol dispersion experiments.

Results

The MID-AFT cabin exhibits the highest infection probability. The calculated maximum individual infection probability (without masks) for a 2-hour flight in this section varies from 4.5% for the “Mild Scenario” to 60.2% for the “Severe Scenario” although the corresponding average infection probability varies from 0.1% to 2.5%. For a 12-hour flight, the corresponding maximum individual infection probability varies from 24.1% to 99.6% and the average infection probability varies from 0.8% to 10.8%. If all passengers wear face masks throughout the 12-hour flight, the average infection probability can be reduced by approximately 73%/32% for high/low efficiency masks. If face masks are worn by all passengers except during a one-hour meal service, the average infection probability is increased by 59%/8% compared to the situation where the mask is not removed.

Conclusions

This analysis has demonstrated that while there is a significant reduction in aerosol concentration due to the nature of the cabin ventilation and filtration system, this does not necessarily mean that there is a low probability or risk of in-flight infection. However, mask wearing, particularly high-efficiency ones, significantly reduces this risk.
Polymorphisms affecting expression of the vaccine antigen factor H binding protein influence invasiveness of Neisseria meningitidis
Authors: Earle Sarah G. , Lobanovska Mariya , Lavender Hayley , Tang Changyan , Exley Rachel M. , Ramos-Sevillano Elisa , Browning Douglas , Kostiou Vasiliki , Harrison Odile B. , Bratcher Holly B. , Varani Gabriele , Tang Christoph M. , Wilson Daniel J. , Maiden Martin C. J.
Published: January 2021

Many bacterial diseases are caused by organisms that ordinarily are harmless components of the human microbiome. Effective interventions against these conditions requires an understanding of the processes whereby symbiosis or commensalism breaks down. Here, we performed bacterial genome-wide association studies (GWAS) of Neisseria meningitidis, a common commensal of the human respiratory tract despite being a leading cause of meningitis and sepsis. GWAS discovered single nucleotide polymorphisms (SNPs) and other bacterial genetic variants associated with invasive meningococcal disease (IMD) versus carriage in several loci across the genome, revealing the polygenic nature of this phenotype. Of note, we detected a significant peak around fHbp, which encodes factor H binding protein (fHbp); fHbp promotes bacterial immune evasion of human complement by recruiting complement factor H (CFH) to the meningococcal surface. We confirmed the association around fHbp with IMD in a validation GWAS, and found that SNPs identified in the validation affecting the 5’ region of fHbp mRNA alter secondary RNA structures, increase fHbp expression, and enhance bacterial escape from complement-mediated killing. This finding mirrors the known link between complement deficiencies and CFH variation with human susceptibility to IMD, highlighting the central importance of human and bacterial genetic variation across the fHbp:CFH interface in IMD susceptibility, virulence, and the transition from carriage to disease.
Expression of a miRNA targeting mutated SOD1 in astrocytes induces motoneuron plasticity and improves neuromuscular function in ALS mice
Authors: Rochat C. , Bernard-Marissal N. , Pradervand S. , Perrin F.E. , Raoul C. , Aebischer P. , Schneider B.L.
Published: January 2021

In amyotrophic lateral sclerosis (ALS) caused by SOD1 gene mutations, both cell-autonomous and non-cell-autonomous mechanisms lead to the selective degeneration of motoneurons. Here, we evaluate the therapeutic potential of gene therapy targeting mutated SOD1 in mature astrocytes using mice expressing the mutated SOD1G93A protein. An AAV-gfaABC1D vector encoding an artificial microRNA is used to deliver RNA interference against mutated SOD1 selectively in astrocytes. The treatment leads to the progressive rescue of neuromuscular junction occupancy, to the recovery of the compound muscle action potential in the gastrocnemius muscle, and significantly improves neuromuscular function. In the spinal cord, gene therapy targeting astrocytes protects a small pool of fast-fatigable motoneurons until disease end stage. In the gastrocnemius muscle of the treated SOD1G93A mice, the fast-twitch type IIb muscle fibers are preserved from atrophy. Axon collateral sprouting is observed together with muscle fiber type grouping indicative of denervation/re-innervation events. The transcriptome profiling of spinal cord motoneurons shows changes in the expression levels of factors regulating the dynamics of microtubules. Gene therapy delivering RNA interference against mutated SOD1 in astrocytes provides therapeutic effects enhancing motoneuron plasticity and improving neuromuscular function in ALS mice.
Distinct regulation of dopamine D3 receptor in the basolateral amygdala and dentate gyrus during the reinstatement of cocaine CPP induced by drug priming and social stress
Authors: Guerrero-Bautista Rocío , Franco-García Aurelio , Hidalgo Juana M. , Fernández-Gómez Francisco José , Ribeiro Do Couto Bruno , Núñez Cristina , Milanés M. Victoria
Published: January 2021

Relapse in cocaine seeking and intake is one of the main challenges when treating its addiction. Among the triggering factors for recurrence of cocaine use are the re-exposure to the drug and stressful events. Cocaine relapse engages the activity of memory-related nuclei, such as the basolateral amygdala (BLA) and the hippocampal dentate gyrus (DG), which are responsible for emotional and episodic memories. Besides, D3 receptor (D3R) antagonists have recently arisen as a potential treatment for preventing drug relapse. Thus, we have assessed the impact of D3R blockade in the expression of some dopaminergic markers and in the activity of the mTOR pathway, that is modulated by D3R, in the BLA and DG during the reinstatement of cocaine-induced CPP evoked by drug priming and social stress. Reinstatement of cocaine-CPP paralleled with a trend to increase of D3R and dopamine transporter (DAT) levels in the BLA. Social stress-but not drug-induced reactivation of cocaine memories was prevented by systemic administration of SB-277011-A (a selective D3R antagonist), that was able, however, to impede D3R and DAT up-regulation in the BLA during CPP reinstatement evoked by both stress and cocaine. Concomitantly with cocaine-CPP reactivation occurred a diminution of mTOR phosphorylation (activation) in the BLA and DG that was inhibited by D3R blockade in both nuclei before the social stress episode, and only in the BLA when CPP reinstatement was provoked by a cocaine prime. Our data, while support a main role for D3R signalling in the BLA in the reactivation of cocaine memories evoked by social stress, indicates that different neural circuits and signalling mechanisms might mediate in the reinstatement of cocaine-seeking behaviours depending upon the triggering stimuli.
Mitochondrial fusion regulates proliferation and differentiation in the type II neuroblast lineage inDrosophila
Authors: Dubal Dnyanesh , Moghe Prachiti , Uttekar Bhavin , Rikhy Richa
Published: January 2021

Optimal mitochondrial function determined by mitochondrial dynamics, morphology and activity is coupled to stem cell differentiation and organism development. However, the mechanisms of interaction of signaling pathways with mitochondrial morphology and activity are not completely understood. We assessed the role of mitochondrial fusion and fission in differentiation of neural stem cells called neuroblasts (NB) in theDrosophilabrain. Depletion of mitochondrial inner membrane fusion protein Opa1 and mitochondrial outer membrane protein Marf in theDrosophilatype II neuroblast lineage led to mitochondrial fragmentation and loss of activity. Opa1 and Marf depletion did not affect the numbers and polarity of type II neuroblasts but led to a decrease in proliferation and differentiation of cells in the lineage. On the contrary, loss of mitochondrial fission protein Drp1 led to mitochondrial fusion but did not show defects in proliferation and differentiation. Depletion of Drp1 along with Opa1 or Marf also led to mitochondrial fusion and suppressed fragmentation, loss of mitochondrial activity, proliferation and differentiation in the type II NB lineage. We found that Notch signaling depletion via the canonical pathway showed mitochondrial fragmentation and loss of differentiation similar to Opa1 mutants. An increase in Notch signaling required mitochondrial fusion for NB proliferation. Further, Drp1 mutants in combination with Notch depletion showed mitochondrial fusion and drove differentiation in the lineage suggesting that fused mitochondria can influence Notch signaling driven differentiation in the type II NB lineage. Our results implicate a crosstalk between Notch signalling, mitochondrial activity and mitochondrial fusion as an essential step in type II NB differentiation.
Design-of-Experiments In Vitro Transcription Yield Optimization of Self-Amplifying RNA
Authors: Samnuan Karnyart , Blakney Anna K. , McKay Paul F. , Shattock Robin J.
Published: January 2021

Self-amplifying RNA (saRNA) vaccines are able to induce a higher antigen-specific immune response with a more cost-effective and rapid production process compared to plasmid DNA vaccines. saRNAs are synthesized through in vitro transcription (IVT) however; this process has mainly been optimized for relatively short mRNAs. Here, we optimized the IVT process for long saRNAs, approximately 9.4 kb through a design of experiment (DoE) approach to produce a maximal RNA yield and validated the optimal IVT method on various sizes of RNA. We found that magnesium has the highest impact on RNA yield with acetate ions enabling a higher yield than chloride ions. In addition, the interaction between magnesium and nucleoside triphosphates (NTPs) is highly essential for IVT. Further addition of sodium acetate (NaOAc) during IVT provided no added benefit in RNA yield. Moreover, pyrophosphatase was not essential for productive IVT. The optimal IVT method can be used to synthesize different lengths of RNA. These findings emphasize the ability to synthesize high quality and quantity of saRNA through IVT and that the optimal amount of each component is essential for their interactions to produce a high RNA yield.
No evidence for general intelligence in a fish
Authors: Aellen Mélisande , Burkart Judith M. , Bshary Redouan
Published: January 2021

Differences in human general intelligence or reasoning ability can be quantified with the psychometric factorg, because individual performance across cognitive tasks is positively correlated.galso emerges in mammals and birds, is correlated with brain size and may similarly reflect general reasoning ability and behavioural flexibility in these species. To exclude the alternative that these positive cross-correlations may merely reflect the general biological quality of an organism or an inevitable by-product of having brains it is paramount to provide solid evidence for the absence ofgin at least some species. Here, we show that wild-caught cleaner fishLabroides dimidiatus, a fish species otherwise known for its highly sophisticated social behaviour, completely lacksgwhen tested on ecologically non-relevant tasks. Moreover, performance in these experiments was not or negatively correlated with an ecologically relevant task, and in none of the tasks did fish caught from a high population density site outperform fish from a low-density site.gis thus unlikely a default result of how brains are designed, and not an automatic consequence of variation in social complexity. Rather, the results may reflect thatgrequires a minimal brain size, and thus explain the conundrum why the average mammal or bird has a roughly 10 times larger brain relative to body size than ectotherms. Ectotherm brains and cognition may therefore be organized in fundamentally different ways compared to endotherms.
Novel functional sequences uncovered through a bovine multi-assembly graph
Authors: Crysnanto Danang , Leonard Alexander S. , Fang Zih-Hua , Pausch Hubert
Published: January 2021

Linear reference genomes are typically assembled from single individuals. They are unable to reflect the genetic diversity of populations and lack millions of bases. To overcome such limitations and make non-reference sequences amenable to genetic investigations, we build a multi-assembly graph from six reference-quality assemblies from taurine cattle and their close relatives. We uncover 70,329,827 bases that are missing in the bovine linear reference genome. The missing sequences encode novel transcripts that are differentially expressed between individual animals. Reads which were previously poorly or unmapped against the bovine reference genome now align accurately to the non-reference sequences. We show that the non-reference sequences contain polymorphic sites that segregate within and between breeds of cattle. Our efforts to uncover novel functional sequences from a multi-assembly graph pave the way towards the transition to a more representative bovine reference genome.
Aurora kinase A is essential for meiosis in mouse oocytes
Authors: Blengini Cecilia S. , Ibrahimian Patricia , Vaskovicova Michaela , Drutovic David , Solc Petr , Schindler Karen
Published: January 2021

The Aurora protein kinases are well-established regulators of spindle building and chromosome segregation in mitotic and meiotic cells. In mouse oocytes, there is significant Aurora kinase A (AURKA) compensatory abilities when the other Aurora kinase homologs are deleted. Whether the other homologs, AURKB or AURKC can compensate for loss of AURKA is not known. Using a conditional mouse oocyte knockout model, we demonstrate that this compensation is not reciprocal because female oocyte-specific knockout mice are sterile and their oocytes fail to complete meiosis I. In determining the AURKA-specific functions, we demonstrate that its first meiotic requirement is to activate Polo-like kinase 1 at microtubule organizing centers (MTOCs; meiotic spindle poles). This activation induces fragmentation of the MTOCs, a step essential for building a bipolar spindle. The next step that requires AURKA is building the liquid-like spindle domain that involves TACC3. Finally, we find that AURKA is also required for anaphase I onset to trigger cohesin cleavage in an APC/C independent manner. We conclude that AURKA has multiple functions essential to completing MI that are distinct from AURKB and AURKC.

Author Summary

Female gametes, oocytes, are uniquely prone to chromosome segregation errors in meiosis I that are associated with early miscarriages. The Aurora protein kinases are essential to control chromosome segregation in all cell types. During mitosis, Aurora kinase A (AURKA) regulates the building of the spindle, the machinery responsible for pulling chromosomes apart. Here, we use a genetic approach to demonstrate that AURKA is essential for meiosis I in mouse oocytes. AURKA is required at multiple steps in meiosis I, first to trigger fragmentation of protein structures that make up the two ends of the meiotic spindle, later to regulate building of a specialized phase-separated spindle domain, and finally to trigger efficient cleavage of cohesin, the molecular glue that holds chromosomes together until anaphase onset. These findings are the first demonstration of distinct Aurora kinase function that cannot be compensated for by the other two homologs. Therefore, this mouse model is excellent tool for pinpointing specific Aurora kinase functions and identifying AURKA target proteins critical for chromosome segregation in meiosis I.
Transposable element landscape changes are buffered by RNA silencing in agingDrosophila
Authors: Yang Nachen , Srivastav Satyam P. , Rahman Reazur , Ma Qicheng , Dayama Gargi , Chinen Madoka , Lei Elissa P. , Rosbash Michael , Lau Nelson C.
Published: January 2021

Genetic mechanisms that repress transposable elements (TEs) in young animals decline during aging, as reflected by increased TE expression in aged animals. Does increased TE expression during aging lead to more genomic TE copies in older animals? To answer this question, we quantified TE Landscapes (TLs) via whole genome sequencing of young and agedDrosophilastrains of wild-type and mutant backgrounds. We quantified TLs in whole flies and dissected brains and validated the feasibility of our approach in detecting new TE insertions in agingDrosophilagenomes when natural defenses like RNA interference (RNAi) pathways are compromised. By also incorporating droplet digital PCR to validate genomic TE loads, we confirm TL changes can occur in a single lifespan ofDrosophilawhen TEs are not suppressed. We also describe improved sequencing methods to quantify extra-chromosomal DNA circles (eccDNAs) inDrosophilaas an additional source of TE copies that accumulate during aging. Lastly, to combat the natural progression of aging-associated TE expression, we show that knocking downPAF1, a conserved transcription elongation factor that antagonizes RNAi pathways, may bolster suppression of TEs during aging and extend lifespan. Our study suggests that RNAi mechanisms generally mitigate genomic TL expansion despite the increase in TE transcripts during aging.
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle
Authors: Lee Young-Lim , Takeda Haruko , Moreira Gabriel Costa Monteiro , Karim Latifa , Mullaart Erik , Coppieters Wouter ,   The GplusE consortium, Appeltant Ruth , Veerkamp Roel F. , Groenen Martien A. M. , Georges Michel , Bosse Mirte , Druet Tom , Bouwman Aniek C. , Charlier Carole
Published: January 2021

Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM is under genetic control, and a prominent CM resistance QTL located on chromosome 6 was reported in various dairy cattle breeds. Nevertheless, the biological mechanism underpinning this QTL has been lacking. Herein, we mapped, fine-mapped, and discovered the putative causal variant underlying this CM resistance QTL in the Dutch dairy cattle population. We identified a~12 kb multi-allelic copy number variant (CNV), that is in perfect linkage disequilibrium with a GWAS lead SNP, as a promising candidate variant. By implementing a genome-wide association study (GWAS) and through expression QTL mapping, we showed that the group-specific component gene (GC), a gene encoding a vitamin D binding protein, is an excellent candidate causal gene for the QTL. The multiplicated alleles are associated with increasedGCexpression and low CM resistance. Ample evidence from functional genomics data supports the presence of an enhancer within this CNV, which would exertcis-regulatory effect onGC. We observed that strong positive selection swept the region near the CNV, and haplotypes associated with the multiplicated allele were strongly selected for. Moreover, the multiplicated allele showed pleiotropic effects for increased milk yield and reduced fertility, hinting that a shared underlying biology for these effects may revolve around the vitamin D pathway. These findings together suggest a putative causal variant of a CM resistance QTL, where acis-regulatory element located within a CNV can alter gene expression and affect multiple economically important traits.

Author summary

Clinical mastitis (CM) is an inflammatory disease that negatively influences dairy production and compromises animal welfare. Although one major genetic locus for CM resistance was mapped on bovine chromosome 6, a mechanistic description of this association has been lacking. Herein, we report a 12-kb multiallelic copy number variant (CNV), encompassing a strong enhancer for group-specific component gene (GC), as a likely causal variant for this locus. This CNV is associated with highGCexpression and low CM resistance. We speculate that upregulation ofGCleads to a large amount of vitamin D binding protein, which in turn, reduces biologically available vitamin D, resulting in vitamin D deficiency and low CM resistance. Despite the negative effect on CM resistance, the CNV contributes to increased milk production, hinting at balancing selection. Our results highlight how multiplication of a regulatory element can shape economically important traits in dairy cattle, both in favourable and unfavourable directions.