bluuebunny/crossref_metadata_2025 huggingface dataset:
Disrupting hierarchical control of nitrogen fixation enables carbon-dependent regulation of ammonia excretion in soil diazotrophs
Authors: Batista Marcelo Bueno , Brett Paul , Appia-Ayme Corinne , Wang Yi-Ping , Dixon Ray
Published: March 2021

The energetic requirements for biological nitrogen fixation necessitate stringent regulation of this process in response to diverse environmental constraints. To ensure that the nitrogen fixation machinery is expressed only under appropriate physiological conditions, the dedicated NifL-NifA regulatory system, prevalent in Proteobacteria, plays a crucial role in integrating signals of the oxygen, carbon and nitrogen status to control transcription of nitrogen fixation (nif) genes. Greater understanding of the intricate molecular mechanisms driving transcriptional control ofnifgenes may provide a blueprint for engineering diazotrophs that associate with cereals. In this study, we investigated the properties of a single amino acid substitution in NifA, (NifA-E356K) which disrupts the hierarchy ofnifregulation in response to carbon and nitrogen status inAzotobacter vinelandii. The NifA-E356K substitution enabled overexpression of nitrogenase in the presence of excess fixed nitrogen and release of ammonia outside the cell. However, both of these properties were conditional upon the nature of the carbon source. Our studies reveal that the uncoupling of nitrogen fixation from its assimilation is likely to result from feedback regulation of glutamine synthetase, allowing surplus fixed nitrogen to be excreted. Reciprocal substitutions in NifA from other Proteobacteria yielded similar properties to theA. vinelandiicounterpart, suggesting that this variant protein may facilitate engineering of carbon source-dependent ammonia excretion amongst diverse members of this family.

Significance

The NifL-NifA regulatory system provides dedicated signal transduction machinery to regulate nitrogen fixation in diverse Proteobacteria. Understanding how the balance of nitrogen and carbon resources is signalled via NifL-NifA for precise control of nitrogen fixation may lead to broadly applicable translational outputs. Here, we characterize a NifA variant that bypasses nitrogen regulation but is still dependent on the carbon status to enable ammonia excretion in soil diazotrophs. Disruption of the regulatory hierarchy in response to nitrogen and carbon suggests how the integration of environmental stimuli could be harnessed to engineer conditional release of fixed nitrogen for the benefit of cereal crops.
Comparing two circular distributions: advice for effective implementation of statistical procedures in biology
Authors: Landler Lukas , Ruxton Graeme D. , Malkemper E. Pascal
Published: March 2021

Many biological variables, often involving timings of events or directions, are recorded on a circular rather than linear scale, and need different statistical treatment for that reason. A common question that is asked of such circular data involves comparison between two groups or treatments: Are the populations from which the two samples drawn differently distributed around the circle? For example, we might ask whether the distribution of directions from which a stalking predator approaches its prey differs between sunny and cloudy conditions; or whether the time of day of mating attempts differs between lab mice subject to one of two hormone treatments. An array of statistical approaches to these questions have been developed. We compared 18 of these (by simulation) in terms of both abilities to control type I error rate near the nominal value, and statistical power. We found that only eight tests offered good control of type I error in all our test situations. Of these eight, we are able to identify Watson’s U2test and MANOVA based on trigonometric functions of the data as offering the best power in the overwhelming majority of our test circumstances. There was often little to choose between these tests in terms of power, and no situation where either of the remaining six tests offered substantially better power than either of these. Hence, we recommend the routine use of either Watson’s U2test or MANOVA when comparing two samples of circular data.
Structural insights into GlcNAc-1-phosphotransferase that directs lysosomal protein transport
Authors: Du Shuo , Wang Guopeng , Zhang Zhiying , Ma Chengying , Gao Ning , Xiao Junyu
Published: March 2021

GlcNAc-1-phosphotransferase (GNPT) catalyzes the initial step in the formation of the mannose-6-phosphate tag that labels ∼60 lysosomal proteins for transport. Mutations in GNPT cause lysosomal storage disorders such as mucolipidoses. However, the molecular mechanism of GNPT remains unclear. Mammalian GNPTs are α2β2γ2 hexamers in which the core catalytic α- and β-subunits are derived from GNPTAB. Here, we present the cryo-electron microscopy structure of theDrosophila melanogasterGNPTAB homolog (DmGNPTAB). Four conserved regions located far apart in the sequence fold into the catalytic domain, which exhibits structural similarity to that of the UDP-glucose glycoprotein glucosyltransferase (UGGT). Comparison with UGGT revealed a putative donor substrate-binding site, and the functional requirements of critical residues in human GNPTAB were validated usingGNPTAB-knockout cells. DmGNPTAB forms an evolutionarily conserved homodimer, and perturbing the dimer interface undermines the maturation and activity of human GNPTAB. These results provide important insights into GNPT function and related diseases.
MEG cortical microstates: spatiotemporal characteristics, dynamic functional connectivity and stimulus-evoked responses
Authors: Tait Luke , Zhang Jiaxiang
Published: March 2021

EEG microstate analysis is a useful approach for studying brain states - nicknamed ‘atoms of thought’ - and their fast transitions in healthy cognition and disease. A key limitation of conventional microstate analysis is that it must be performed at the sensor level, and therefore gives limited anatomical insight into the cortical mechanisms underpinning these states. In this study, we generalise the microstate methodology to be applicable to source-reconstructed electrophysiological data. Using simulations of a neural-mass network model, we first established the validity and robustness of the proposed method. Using MEG resting-state data, we uncovered ten microstates with distinct spatial distributions of cortical activation. Multivariate pattern analysis demonstrated that source-level MEG microstates were associated with distinct functional connectivity patterns. Using a passive auditory paradigm, we further demonstrated that the occurrence probability of MEG microstates were altered by evoked auditory responses, exhibiting a hyperactivity of the microstate including the auditory cortex. Our results support the use of MEG source-level microstates as a data-driven method for investigating brain dynamic activity and connectivity at the millisecond scale.
Local fitness and epistatic effects lead to distinct patterns of linkage disequilibrium in protein-coding genes
Authors: Ragsdale Aaron P.
Published: March 2021

Selected mutations interfere and interact with evolutionary processes at nearby loci, distorting allele frequency trajectories and creating correlations between pairs of mutations. A number of recent studies have used patterns of linkage disequilibrium (LD) between selected variants to test for selective interference and epistatic interactions, with some disagreement over interpreting observations from data. Interpretation is hindered by a lack of analytic or even numerical expectations for patterns of variation between pairs of loci under the combined effects of selection, dominance, epistasis, and demography. Here, I develop a numerical approach to compute the expected two-locus sampling distribution under diploid selection with arbitrary epistasis and dominance, recombination, and variable population size. I use this to explore how epistasis and dominance affect expected signed LD, including for non-steadystate demography relevant to human populations. Using whole-genome sequencing data from humans, I explore genome-wide patterns of LD within protein-coding genes. I show that positive LD between missense mutations within genes is driven by strong positive allele-frequency correlations between pairs of mutations that fall within the same annotated conserved domain, pointing to compensatory mutations or antagonistic epistasis as the prevailing mode of interaction within conserved genic elements. LD between missense mutations is reduced outside of conserved domains, as would expected under Hill-Robertson interference. This variation in both mutational fitness effects and selective interactions within proteincoding genes calls for more refined inferences of the joint distribution of fitness and interactive effects, and the methods presented here should prove useful in that pursuit.
Volume-transmitted GABA waves pace epileptiform rhythms in the hippocampal network
Authors: Magloire Vincent , Savtchenko Leonid P. , Sylantyev Sergyi , Jensen Thomas P. , Cole Nicholas , Marvin Jonathan S. , Looger Loren L. , Kullmann Dimitri M. , Walker Matthew C. , Pavlov Ivan , Rusakov Dmitri A.
Published: March 2021

Mechanisms that entrain and drive rhythmic epileptiform discharges remain debated. Traditionally, this quest has been focusing on interneuronal networks driven by GABAergic connections that activate synaptic or extrasynaptic receptors. However, synchronised interneuronal discharges could also trigger a transient elevation of extracellular GABA across the tissue volume, thus raising tonic GABAAreceptor conductance (Gtonic) in multiple cells. Here, we use patch-clamp GABA ‘sniffer’ and optical GABA sensor to show that periodic epileptiform discharges are preceded by region-wide, rising waves of extracellular GABA. Neural network simulations that incorporate volume-transmitted GABA signals point to mechanistic principles underpinning this relationship. We validate this hypothesis using simultaneous patch-clamp recordings from multiple nerve cells, selective optogenetic stimulation of fast-spiking interneurons. Critically, we manipulate GABA uptake to suppress extracellular GABA waves but not synaptic GABAergic transmission, which shows a clear effect on rhythm generation. Our findings thus unveil a key role of extrasynaptic, volume-transmitted GABA actions in pacing regenerative rhythmic activity in brain networks.
Neuronal ribosomes dynamically exchange ribosomal proteins in a context-dependent manner
Authors: Fusco Claudia M. , Desch Kristina , Dörrbaum Aline R. , Wang Mantian , Staab Anja , Chan Ivy C.W. , Vail Eleanor , Villeri Veronica , Langer Julian D. , Schuman Erin M.
Published: March 2021

Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs quickly associated with translating ribosomes in the cytoplasm and that this incorporation is independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (in response to oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing remote neuronal synapses a rapid solution to the relatively slow and energy-demanding requirement of nuclear ribosome biogenesis.
Purkinje cell outputs selectively inhibit a subset of unipolar brush cells in the input layer of the cerebellar cortex
Authors: Guo Chong , Rudolph Stephanie , Neuwirth Morgan E. , Regehr Wade G.
Published: March 2021

Circuitry of the cerebellar cortex is regionally and functionally specialized. Unipolar brush cells (UBCs), and Purkinje cell (PC) synapses made by axon collaterals in the granular layer, are both enriched in areas that control balance and eye-movement. Here we find a link between these specializations: PCs preferentially inhibit mGluR1-expressing UBCs that respond to mossy fiber inputs with long lasting increases in firing, but PCs do not inhibit mGluR1-lacking UBCs. PCs inhibit about 29% of mGluR1-expressing UBCs by activating GABAAreceptors (GABAARs) and inhibit almost all mGluR1-expressing UBCs by activating GABABRs. PC to UBC synapses allow PC output to regulate the input layer of the cerebellar cortex in diverse ways. GABAAR-mediated feedback is fast, unreliable, noisy, and suited to linearizing input-output curves and decreasing gain. Slow GABABR-mediated inhibition allows elevated PC activity to sharpen the input-output transformation of UBCs, and allows dynamic inhibitory feedback of mGluR1-expressing UBCs.
Dynamic distortion of orientation representation after learning in the mouse primary visual cortex
Authors: Corbo Julien , McClure John P. , Erkat O. Batuhan , Polack Pierre-Olivier
Published: March 2021

Learning is an essential cognitive mechanism allowing behavioral adaptation through adjustments in neuronal processing. It is associated with changes in the activity of sensory cortical neurons evoked by task-relevant stimuli. However, the exact nature of those modifications and the computational advantages they may confer are still debated. Here, we investigated how learning an orientation discrimination task alters the neuronal representations of the cues orientations in the primary visual cortex (V1) of male and female mice. When comparing the activity evoked by the task stimuli in naïve mice and mice performing the task, we found that the representations of the orientation of the rewarded and non-rewarded cues were more accurate and stable in trained mice. This better cue representation in trained mice was associated with a distortion of the orientation representation space such that stimuli flanking the task-relevant orientations were represented as the task stimuli themselves, suggesting that those stimuli were generalized as the task cues. This distortion was context dependent as it was absent in trained mice passively viewing the task cues and enhanced in the behavioral sessions where mice performed best. Those modifications of the V1 population orientation representation in performing mice were supported by a suppression of the activity of neurons tuned for orientations neighboring the orientations of the task cues. Thus, visual processing in V1 is dynamically adapted to enhance the reliability of the representation of the learned cues and favor generalization in the task-relevant computational space.

Significance statement

Performance improvement in a task often requires facilitating the extraction of the information necessary to its execution. Here, we demonstrate the existence of a suppression mechanism that improves the representation of the orientations of the task stimuli in the V1 of mice performing an orientation discrimination task. We also show that this mechanism distorts the V1 orientation representation space, leading stimuli flanking the task stimuli orientations to be generalized as the task stimuli themselves.
Computational assessment of the spike protein antigenicity reveals diversity in B cell epitopes but stability in T cell epitopes across SARS-CoV-2 variants
Authors: Ge Anni , Rioux Melissa , Kelvin Alyson A.
Published: March 2021

Since its emergence into the human population at the end of 2019, SARS-CoV-2 has caused significant morbidity and mortality worldwide. Efforts to develop a protective vaccine against COVID-19 have yielded several vaccine platforms currently in distribution targeting the original SARS-CoV-2 spike protein sequence from the first cases of infection. In recent months, variants of SARS-CoV-2 have raised concerns that viral mutation may undermine vaccination efforts through viral escape of host immune memory acquired from infection or vaccination. We therefore used a computational approach to predict changes in spike protein antigenicity with respect to host B cell and CD8+ T cell immunity across six SARS-CoV-2 variants (D614G, B.1.1.7, B.1.351, P.1, B.1.429, and mink-related). Our epitope analysis using DiscoTope suggests possible changes in B cell epitopes in the S1 region of the spike protein across variants, in particular the B.1.1.7 and B.1.351 lineages, which may influence immunodominance. Additionally, we show that high-affinity MHC-I-binding peptides and glycosylation sites on the spike protein appear consistent between variants with the exception of an extra glycosylation site in the P.1 variant. Together, these analyses suggests T cell vaccine strategies have the most longevity before reformulation.
Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
Authors: Maier Wolfgang , Bray Simon , van den Beek Marius , Bouvier Dave , Coraor Nathaniel , Miladi Milad , Singh Babita , De Argila Jordi Rambla , Baker Dannon , Roach Nathan , Gladman Simon , Coppens Frederik , Martin Darren P , Lonie Andrew , Grüning Björn , Kosakovsky Pond Sergei L. , Nekrutenko Anton
Published: March 2021

The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available athttps://covid19.galaxyproject.org.
Collagen Deposition in Diabetic Kidney Disease Boosts Intercellular Signaling: A Mathematical Model
Authors: Thomas Haryana Y. , Ford Versypt Ashlee N.
Published: March 2021

Diabetic kidney disease is a health burden that is becoming more prevalent in the US and worldwide. The limited options for treating and preventing diabetic kidney disease are in part due to gaps in our understanding of the progression of diabetic kidney damage and its impacts on cellular function. An important cellular function in the kidney glomerulus is intercellular communication via the release and uptake of soluble cytokines and growth factors. In diabetic kidney disease, excess collagen deposition alters the mesangial matrix properties, which, we hypothesize, diminishes the intercellular signaling between key glomerular cells. To test our hypothesis, we utilized established mathematical models of transport to study the impact of pathological deposition on the ability of cells to communicate via intercellular signaling. Our analysis reveals that pathological collagen deposition can enhance the signaling range of the glomerular cells rather than diminishing it.

SIGNIFICANCE

The incidence of diabetes is expected to rise to over 600 million by the year 2040, one third of whom are expected to develop diabetic kidney disease. Our lack of understanding of how diabetic kidney disease progresses and affects cellular and tissue function has led to our inability to mitigate the rapidly rising burden of diabetic kidney disease. A hallmark of diabetic kidney damage is collagen deposition, yet its impact on cellular and tissue function is still not well understood. The elucidation of the impact of collagen deposition on cellular and tissue function will enable the identification of mechanisms that exacerbate the progression of diabetic kidney damage and thus provide novel avenues for preventing or slowing the progression of diabetic kidney damage.
The von Willebrand Factor stamps Plasmatic Extracellular Vesicles from Glioblastoma Patients
Authors: Sabbagh Quentin , André-Grégoire Gwennan , Alves-Nicolau Carolina , Bidère Nicolas , Jouglar Emmanuel , Guével Laëtitia , Frénel Jean-Sébastien , Gavard Julie
Published: March 2021

Glioblastoma is a devastating tumor of the central nervous system characterized by a poor survival and an extremely dark prognosis, making its diagnosis, treatment and monitoring highly challenging. Numerous studies have highlighted extracellular vesicles (EVs) as key players of tumor growth, invasiveness and resistance, as they carry and disseminate oncogenic material in the local tumor microenvironment and at distance. However, whether their quality and quantity reflect individual health status and changes in homeostasis is still not fully elucidated. Here, we separated EVs from plasma collected at different time points alongside with the clinical management of GBM patients. Our findings confirm that plasmatic EVs could be separated and characterized with standardized protocols, thereby ensuring the reliability of measuring vesiclemia,i.e. extracellular vesicle concentration in plasma. This unveils that vesiclemia is a dynamic parameter, which could be reflecting tumor burden and/or response to treatments. Further label-free liquid chromatography tandem mass spectrometry unmasks the von Willebrand Factor (VWF) as a selective protein hallmark for GBM-patient EVs. Our data thus support the notion that EVs from GBM patients showed differential protein cargos that can be further surveyed in circulating EVs, together with vesiclemia.
Target Capture Sequencing of SARS-CoV-2 Genomes Using the ONETest Coronaviruses Plus
Authors: Zhan Shing H. , Alamouti Sepideh M. , Kwok Brian S. , Lee Meng-Hsun , Khattra Jaswinder , Daneshpajouh Habib , Houck Herbert J. , Rand Kenneth H.
Published: March 2021

Background

Genomic sequencing is important to track and monitor genetic changes in SARS-CoV-2. We introduce a target capture next-generation sequencing methodology, the ONETest Coronaviruses Plus, to sequence SARS-CoV-2 genomes and select genes of other respiratory viruses simultaneously.

Methods

We applied the ONETest on 70 respiratory samples (collected in Florida, USA between May and July, 2020), in which SARS-CoV-2 had been detected by a qualitative PCR assay. For 48 (69%) of the samples, we also applied the ARTIC protocol for Illumina sequencing. All the libraries were sequenced as 2×150 nucleotide reads on an Illumina instrument. The ONETest data were analyzed using an in-house pipeline and the ARTIC data using a published pipeline to produce consensus SARS-CoV-2 genome sequences, to which lineages were assigned usingpangolin.

Results

Of the 70 ONETest libraries, 45 (64%) had a complete or near-complete SARS-CoV-2 genome sequence (> 29,000 bases and with > 90% of its bases covered by at least 10 reads). Of the 48 ARTIC libraries, 25 (52%) had a complete or near-complete SARS-CoV-2 genome sequence.

In 24 out of 34 (71%) samples in which both the ONETest and ARTIC sequences were complete or near-complete and in which lineage could be assigned to both the ONETest and ARTIC sequences, the SARS-CoV-2 lineage identified was the same.

Conclusions

The ONETest can be used to sequence the SARS-CoV-2 genomes in archived samples and thereby enable detection of circulating and emerging SARS-CoV-2 variants. Target capture approaches, such as the ONETest, are less prone to loss of sequence coverage probably due to amplicon dropouts encountered in amplicon approaches, such as ARTIC. With its added value of characterizing other major respiratory pathogens, although not assessed in this study, the ONETest can help to better understand the epidemiology of infectious respiratory disease in the post COVID-19 era.
Postural perturbation induced by electrical stimulation; A new approach to examine the mechanism of falling
Authors: Tahayori Behdad , Tahayori Bahman , Mehdizadeh Alireza , Koceja David M.
Published: March 2021

Background

Falling is a major cause of disability and death among elderly people. Therefore, a clear understanding of fall mechanism is necessary for providing preventative and treatment methods. Several fall simulation protocols have been introduced to study lost of balance in a laboratory setting.

New Method

We have explained and examined a new method to induce a sudden perturbation on standing posture to provide an insight into the mechanism of falling. The method comprises eliciting an H-reflex protocol while subjects are standing which produces a contraction in soleus and gastrocnemius muscles. We have also defined analytical techniques to provide biomarkers of balance control during perturbation. The method is easy to implement and interpret. The H-reflex or M-wave can be elicited unilaterally or bilaterally causing a forward or sideway perturbation. The vector analysis and the Equilibrium Point calculations defined here can quantify the amplitude, direction, and evolution of the perturbation.

Results

We tested this method on a group of healthy individuals and observed clear patterns of loss of balance due to stimulation. Direction and magnitude of deviation was manifested through the reconstructed vectors, with bilateral stimulation causing the largest perturbation.

Comparison and conclusion

The resultant plantarflexion torque is reminiscent of tripping over an obstacle and triggers corrective reactions to restore balance. Therefore, it is more similar to an internal perturbation. Mechanical perturbations to the torso cause a displacement in center of mass (COM) and trigger a cascade of mechanisms. Our method, does not trigger the perturbation by the displacement of COM initially and therefore, triggers fewer mechanisms for regaining balance.
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
Authors: Course Meredith M. , Sulovari Arvis , Gudsnuk Kathryn , Eichler Evan E. , Valdmanis Paul N.
Published: March 2021

There are over 55,000 variable number tandem repeats (VNTRs) in the human genome, notable for both their striking polymorphism and mutability. Despite their role in human evolution and genomic variation, they have yet to be studied collectively and in detail, partially due to their large size, variability, and predominant location in non-coding regions. Here, we examine 467 VNTRs that are human-specific expansions, unique to one location in the genome, and not associated with retrotransposons. We leverage publicly available long-read genomes – including from the Human Genome Structural Variant Consortium – to ascertain the exact nucleotide composition of these VNTRs, and compare their composition of alleles. We then confirm repeat unit composition in over 3000 short-read samples from the 1000 Genomes Project. Our analysis reveals that these VNTRs contain remarkably structured repeat motif organization, modified by frequent deletion and duplication events. While overall VNTR compositions tend to remain similar between 1000 Genomes Project super-populations, we describe a notable exception with substantial differences in repeat composition (in PCBP3), as well as several VNTRs that are significantly different in length between super-populations (in ART1, PROP1, WDR60, and LOC102723906). We also observe that most of these VNTRs are expanded in archaic human genomes, yet remain stable in length between single generations. Collectively, our findings indicate that repeat motif variability, repeat composition, and repeat length are all informative modalities to consider when characterizing VNTRs and their contribution to genomic variation.
Brain endothelial cell tissue-nonspecific alkaline phosphatase (TNAP) activity promotes maintenance of barrier integrityviathe ROCK pathway
Authors: Nwafor Divine C. , Brichacek Allison L. , Wang Wei , Bidwai Nina , Lilly Christa L. , Luis Millán José , Brown Candice M.
Published: March 2021

Blood-brain barrier (BBB) dysfunction is a key feature in many neuroinflammatory diseases. Yet, no therapies exist to effectively mitigate BBB dysfunction. A strategy to bridge this knowledge gap requires an examination of proteins localized to brain microvascular endothelial cells (BMECs) and evaluating their role in preserving barrier integrity. Tissue-nonspecific alkaline phosphatase (TNAP) is highly abundant in brain microvascular endothelial cells (BMECs); however, its function in BMECs remains unclear. We hypothesized that a loss or inhibition of TNAP activity on BMECs would impair barrier integrity through increased cytoskeletal remodeling driven by the Rho-associated protein kinase (ROCK) pathway. First, we examined barrier integrity in hCMEC/D3 cells treated with a TNAP inhibitor (TNAPi) and in primary BMECs (pBMECs)viathe conditional deletion of TNAP in endothelial cells. Our results showed that both pharmacological inhibition and genetic conditional loss of TNAP significantly worsened endothelial barrier integrity compared to controls. Next, we examined the mechanisms through which TNAP activity exerts a protective phenotype on BMECs. Our results showed that hCMEC/D3 cells treated with TNAPi displayed remarkable phalloidin and vimentin cytoskeletal remodeling compared to control. We then examined the role of ROCK, a key player in cytoskeletal remodeling. Our results showed that TNAPi increased the expression of ROCK 1/2. Furthermore, inhibition of ROCK 1/2 with fasudil mitigated TNAPi-induced and VE-cKO barrier dysfunction. Collectively, our results support a novel mechanism through which loss of TNAP activity results in cerebrovascular dysfunction, and selective modulation of TNAP activity in BMECs may be a therapeutic strategy to improve BBB function.
Hemodialysis Patients Show a Highly Diminished Antibody Response after COVID-19 mRNA Vaccination Compared to Healthy Controls
Authors: Simon Benedikt , Rubey Harald , Treipl Andreas , Gromann Martin , Hemedi Boris , Zehetmayer Sonja , Kirsch Bernhard
Published: March 2021

1.

1.1

Background and Objectives

Hemodialysis patients are prone to infection with SARS-COV2 and show a high probability of a severe course of disease and high mortality when infected. In many countries hemodialysis patients are prioritised in vaccination programs to protect this vulnerable community. However, no hemodialysis patients were included in efficacy trials of SARS CoV-2 vaccines and therefore efficacy and safety data for this patient group are lacking. These data would be critical, since hemodialysis patients showed decreased responses against various other vaccines and this could mean decreased response to SARS CoV-2 vaccines.

1.2

Design, setting, participants, and measurements

We conducted a prospective cohort study consisting of a group of 81 hemodialysis patients and 80 healthy controls who were vaccinated with mRNA vaccine BNT162b2 (BionTech/Pfizer, 2 doses with an interval of 21 days). Anti-SARS-COV-2 S antibody response in all participants was measured 21 days after the second dose. The groups were compared with univariate quantile regressions and a multiple analysis. Adverse events (AEs) of the vaccination were assessed with a standardized questionnaire. We also performed a correlation of HBs-Antibody response with the SARS-COV-2 antibody response in the hemodialysis patients.

1.3

Results

Dialysis patients had significantly lower Anti-SARS-COV-2 S antibody titres than healthy control patients 21 days after vaccination with BNT162b2 (median dialysis Patients 171 U/ml versus median controls 2500 U/ml). Age also had a significant but less pronounced influence on antibody titres. Dialysis patients showed less AEs than the control group. No significant correlation was found for Hepatitis B vaccine antibody response and SARS CoV-2 vaccine antibody response.

1.4

Conclusions

Hemodialysis patients exhibit highly diminished SARS-COV-2 S antibody titres compared to a cohort of controls. Therefore these patients could be much less protected by SARS CoV-2 mRNA vaccination than expected. Alternative vaccination schemes must be considered and preventive measures must be maintained after vaccination.
Why COVID-19 is not so spread in Africa: How does Ivermectin affect it?
Authors: Tanioka Hisaya , Tanioka Sayaka , Kaga Kimitaka
Published: March 2021

Background

Scientists have so far been unable to determine the reason for the low number of COVID-19 cases in Africa.

Objective

To evaluate the impact of ivermectin interventions for onchocerciasis on the morbidity, mortality, recovery, and fatality rates caused by COVID-19.

Method

A retrospective statistical analysis study of the impact of ivermectin against COVID-19 between the 31 onchocerciasis-endemic countries using the community-directed treatment with ivermectin (CDTI) and the non-endemic 22 countries in Africa. The morbidity, mortality, recovery rate, and fatality rate caused by COVID-19 were calculated from the WHO situation report in Africa. We investigated the onchocerciasis endemic 31 countries and the non-endemic 22 countries. Statistical comparisons used by the Welch test of them in the two groups were made.

Results

The morbidity and mortality were statistically significantly less in the 31 countries using CDTI. The recovery and fatality rates were not statistically significant difference. The average life expectancy was statistically significantly higher in the non-endemic countries.

Conclusions

The morbidity and mortality in the onchocerciasis endemic countries are lesser than those in the non-endemic ones. The community-directed onchocerciasis treatment with ivermectin is the most reasonable explanation for the decrease in morbidity and fatality rate in Africa. In areas where ivermectin is distributed to and used by the entire population, it leads to a significant reduction in mortality.
COVID-19 Vaccine’s Gender Paradox
Authors: Galasso Vincenzo , Profeta Paola , Foucault Martial , Pons Vincent
Published: March 2021

Women die less than men of COVID-19, but have been more concerned about its health consequences and more compliant with the public health rules imposed during the pandemic. Since return to normal life depends on vaccination, but delays in acceptance or outright refusals of vaccination are already evident, we investigate gender differences in attitudes and expected behaviors regarding COVID-19 vaccination. Using original data from a survey conducted in December 2020 in ten developed countries (N=13,326), we discover aCOVID-19 Vaccine’s gender paradox. Being more concerned about COVID-19 and more likely to believe to be infected and consequently to become seriously ill, women could be expected to be more supportive of vaccination than men. Instead, our findings show that women agree less than men to be vaccinated and to make vaccination compulsory. Our evidence suggests that their vaccine hesitance is partly due skepticism, since women are less likely to believe that vaccination is the only solution to COVID-19 and more likely to believe that COVID-19 was created by large corporations. Using a survey experiment performed in these ten countries, we show that information provision on the role of vaccination to become immune to COVID-19 is effective in reducing vaccine hesitance.
Clustering Lifestyle Risk Behaviors among Vietnamese Adolescents and Roles of School: A Bayesian Multilevel Analysis of Global School-Based Student Health Survey 2019
Authors: Khuong Quynh Long , Hoang Thi Ngoc-Anh , Nguyen Hong Phuong , Tran Thi Tuyet Hanh , Park Kidong , Takeuchi Momoe , Nguyen Tuan Lam , Pham Thi Quynh Nga , Le Phuong Anh , Le Van Tuan , Tran Quoc Bao , Ong Phuc Thinh , Nguyen Van Huy , Vu Thi Hoang Lan , Hoang Van Minh
Published: March 2021

Background
Adolescence is a vulnerable period for many lifestyle risk behaviors. In this study, we aimed to 1) examine a clustering pattern of lifestyle risk behaviors; 2) investigate roles of the school health promotion programs on this pattern among adolescents in Vietnam.
Methods
We analyzed data of 7,541 adolescents aged 13-17 years from the 2019 nationally representative Global School-based Student Health Survey, conducted in 20 provinces and cities in Vietnam. We applied the latent class analysis to identify groups of clustering and used Bayesian 2-level logistic regressions to evaluate the correlation of school health promotion programs on these clusters. We reassessed the school effect size by incorporating different informative priors to the Bayesian models.
Findings
The most frequent lifestyle risk behavior among Vietnamese adolescents was physical inactivity, followed by unhealthy diet, and sedentary behavior. Most of students had a cluster of at least two risk factors and nearly a half with at least three risk factors. Latent class analysis detected 23% males and 18% females being at higher risk of lifestyle behaviors. Consistent through different priors, high quality of health promotion programs associated with lower the odds of lifestyle risk behaviors (highest quality schools vs. lowest quality schools; males: Odds ratio (OR) = 0.67, 95% Highest Density Interval (HDI): 0.46 - 0.93; females: OR = 0.69, 95% HDI: 0.47 - 0.98).
Interpretation
Our findings demonstrated the clustering of specific lifestyle risk behaviors among Vietnamese in-school adolescents. School-based interventions separated for males and females might reduce multiple health risk behaviors in adolescence.
Snapshots of actin and tubulin folding inside the TRiC chaperonin
Authors: Kelly John J. , Tranter Dale , Pardon Els , Chi Gamma , Kramer Holger , Knee Kelly M. , Janz Jay M. , Steyaert Jan , Bulawa Christine , Paavilainen Ville O. , Huiskonen Juha T. , Yue Wyatt W.
Published: March 2021

The integrity of a cell’s proteome depends on correct folding of polypeptides by chaperonins. The TCP-1 ring chaperonin (TRiC) acts as obligate folder for >10% of cytosolic proteins, including cytoskeletal proteins actin and tubulin. While its architecture and how it recognises folding substrates is emerging from structural studies, the subsequent fate of substrates inside the TRiC chamber is not defined. We trapped endogenous human TRiC with substrates (actin, tubulin) and co-chaperone (PhLP2A) at different folding stages, for structure determination by cryogenic electron microscopy. The already-folded regions of client proteins are anchored at the chamber wall, positioning unstructured regions towards the central space to achieve their folding. Substrates engage with different sections of the chamber during the folding cycle, coupled to TRiC open-and-close transitions. Furthermore, the cochaperone PhLP2A modulates folding, acting as a molecular strut between substrate and TRiC chamber. Our structural snapshots piece together an emerging atomistic model of client protein folding through TRiC.
Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility
Authors: Hall Rebecca J. , Whelan Fiona J. , Cummins Elizabeth A. , Connor Christopher , McNally Alan , McInerney James O.
Published: March 2021

The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene, suggesting that cooperation is more common than conflict in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.

Data summary

All Supplementary Data files and the Python scripts used in the analyses are available at doi.org/10.17639/nott.7103.

Impact statement

The pangenome of a species encompasses the core genes encoded by all genomes, as well as the accessory genes found in only a subset. Much remains to be understood about the relationships and interactions between accessory genes; in particular, what drives pairs of genes to appear together in the same genome, or what prevents them from being in the same genome together, more often than expected by chance. How these co-occurrence and avoidance relationships develop, and what effect they have on the dynamics and evolution of the pangenome as a whole, is largely unknown. Here, we present a springboard for understanding prokaryote pangenome evolution by uncovering significant gene relationships in a model Escherichia coli pangenome. We identify mobile genetic elements and the sharing of common function as possible driving forces behind the co-occurrence of accessory genes. Furthermore, this work offers an extensive dataset from which gene relationships could be identified for any gene of interest in this E. coli accessory genome, providing a rich resource for the community.
Rapid response to emerging biomedical challenges and threats
Authors: Grabowski Marek , Macnar Joanna M. , Cymborowski Marcin , Cooper David R. , Shabalin Ivan G. , Gilski Miroslaw , Brzezinski Dariusz , Kowiel Marcin , Dauter Zbigniew , Rupp Bernhard , Wlodawer Alexander , Jaskolski Mariusz , Minor Wladek
Published: March 2021

As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.
Adaptive finite element analysis of free vibration of elastic membranes via element energy projection technique
Authors: Sun Haohan , Yuan Si
Published: March 2021

Purpose

A general strategy is developed for adaptive finite element (FE) analysis of free vibration of elastic membranes based on the element energy projection (EEP) technique.

Design/methodology/approach

By linearizing the free vibration problem of elastic membranes into a series of linear equivalent problems, reliable a posteriori point-wise error estimator is constructed via EEP super-convergent technique. Hierarchical local mesh refinement is incorporated to better deal with tough problems.

Findings

Several classical examples were analyzed, confirming the effectiveness of the EEP-based error estimation and overall adaptive procedure equipped with a local mesh refinement scheme. The computational results show that the adaptively-generated meshes reasonably catch the difficulties inherent in the problems and the procedure yields both eigenvalues with required accuracy and mode functions satisfying user-preset error tolerance in maximum norm.

Originality/value

By reasonable linearization, the linear-problem-based EEP technique is successfully transferred to two-dimensional eigenproblems with local mesh refinement incorporated to effectively and flexibly deal with singularity problems. The corresponding adaptive strategy can produce both eigenvalues with required accuracy and mode functions satisfying user-preset error tolerance in maximum norm and thus can be expected to apply to other types of eigenproblems.
Assessing the responsiveness of out-of-pocket healthcare expenditure to macro-fiscal factors and different health financing systems: evidence from the European and OECD area
Authors: Grigorakis Nikolaos , Galyfianakis Georgios , Tsoukatos Evangelos
Published: March 2021

Purpose

In this paper, the authors assess the responsiveness of OOP healthcare expenditure to macro-fiscal factors, as well as to tax-based, SHI, mixed systems and voluntary PHI financing. Although the relationship between OOP expenditure, macroeconomy, aggregate public and PHI financing is well documented in the existing empirical literature, little is known for the impact of several macro-fiscal drivers and the existing health financing arrangements associated with voluntary PHI on OOP expenditure.

Design/methodology/approach

The authors gather panel data by applying three official organizations’ databases. They elaborate static and dynamic panel data methodology to a dataset of 49 European and OECD countries from 2000 to 2015.

Findings

The authors’ findings do not indicate a considerable impact of GDP growth and general government debt as a share of GDP on OOP payments. Unemployment rate presents as a positive driver of OOP payments in all three compulsory national health systems post to the 2008 economic crisis. OOP payments are significantly influenced by countries’ fiscal capacity to increase general government expenditure to GDP in SHI and mixed health systems. Additionally, study findings present that government health financing, irrespective of the different health systems structure characteristics, and OOP healthcare payments follow different directions. Voluntary PHI financing considerably counteracts OOP payments only in tax-based health systems.

Practical implications

In the backdrop of a new economic crisis associated to the COVID-19 epidemic, health policy planners have to deal with the emerging unprecedented challenges in financing of health systems, especially for these economies that have to face the fiscal capacity constraints owing to the 2008 financial crisis and its severe recession.

Originality/value

To the best of authors’ knowledge, there is no empirical consensus on the effects of macro-fiscal parameters, different compulsory health systems financing associated with the parallel voluntary PHI institution funding on OOP expenditure, for the majority of European and OECD settings.