bluuebunny/crossref_metadata_2025 huggingface dataset:
SARS-CoV-2 variants: levels of neutralisation required for protective immunity
Authors: Cromer Deborah , Steain Megan , Reynaldi Arnold , Schlub Timothy E , Wheatley Adam K , Juno Jennifer A , Kent Stephen J , Triccas James A , Khoury David S , Davenport Miles P
Published: August 2021

A number of SARS-CoV-2 variants of concern (VOC) have been identified that partially escape serum neutralisation activity elicited by current vaccines. Recent studies have also shown that vaccines demonstrate reduced protection against symptomatic infection with SARS-CoV-2 variants. Here we integrate published data on in vitro neutralisation and clinical protection to understand and predict vaccine efficacy against existing SARS-CoV-2 variants. We find that neutralising activity against the ancestral SARS-CoV-2 is highly predictive of neutralisation of the VOC, with all vaccines showing a similar drop in neutralisation to the variants. Neutralisation levels remain strongly correlated with protection from infection with SARS-CoV-2 VOC (r=0.81, p=0.0005). We apply an existing model relating in vitro neutralisation to protection (parameterised on data from ancestral virus infection) and find this remains predictive of vaccine efficacy against VOC once drops in neutralisation to the VOC are taken into account. Modelling of predicted vaccine efficacy against variants over time suggests that protection against symptomatic infection may drop below 50% within the first year after vaccination for some current vaccines. Boosting of previously infected individuals with existing vaccines (which target ancestral virus) has been shown to significantly increase neutralising antibodies. Our modelling suggests that booster vaccination should enable high levels of immunity that prevent severe infection outcomes with the current SARS-CoV-2 VOC, at least in the medium term.
Serological detection of SARS-CoV-2 IgG using commercially available immunoassays on dried blood spots collected from patients
Authors: Walker Gregory J , Davis Rebecca , Naing Zin , McEntee Brad , Lu Yonghui , Denadija Tatijana , Rawlinson William D
Published: August 2021

Serological testing for SARS-CoV-2 antibodies provides important research and diagnostic information relating to COVID-19 immune response and surveillance. A major challenge when addressing protection post-infection or vaccination is the difficulty of specimen collection from infants and children. Dried blood spots (DBS) collected by finger prick or heel prick are a minimally invasive sample collection alternative previously used to detect antibodies to other viruses. In this study we evaluated DBS for the detection of SARS-CoV-2 antibodies on three commercially available enzyme (EIA) and chemiluminescent (CLIA) immunoassays by analysing paired DBS and serum samples collected from 54 subjects. We demonstrate that testing of DBS samples was highly sensitive and specific, and quantitative results strongly correlated with those of paired serum. These results suggest that DBS derived blood is a viable alternative to plasma or serum for use in EIAs and CLIAs, and has particular utility as a minimally invasive collection tool for COVID-19 serological testing of infants and children.
Molecular and serological investigation of the 2021 COVID-19 case surge in Mongolian vaccinees
Authors: Dashdorj Naranjargal J. , Dashdorj Naranbaatar D. , Mishra Mitali , Danzig Lisa , Briese Thomas , Lipkin W. Ian , Mishra Nischay
Published: August 2021

A surge in Covid-19 cases in Mongolia in March 2021 resulted in a government-mandated shutdown. This shutdown was relaxed in May 2021 as case numbers decreased and nationwide vaccination rates using Sinopharm, Covishield/AstraZeneca, Sputnik V, and Pfizer/BioNTech vaccines exceeded 50% of the population. Case rates increased again in early June 2021 in both vaccinated and non-vaccinated individuals. To determine whether the surge was due to the emergence of Delta or another variant, or vaccine failure, a rapid, opportunistic investigation was conducted that comprised virus sequence analysis of nasal swab samples from breakthrough cases and antibody assays of plasma from healthy vaccinees. More than 90% of breakthrough infections during the second case surge were due to the Alpha variant. Spike protein ELISA and SARS-CoV-2 neutralization assays data revealed large differences in plasma titers of antibodies to SARS-CoV-2, with mRNA vaccines eliciting higher titers than adenovirus-vectored or killed virus vaccines.
Assessing the sustainability of an integrated rural sanitation and hygiene approach: A repeated cross-sectional evaluation in 10 countries
Authors: Apanga Paschal A. , Freeman Matthew C. , Sakas Zoe , Garn Joshua V.
Published: August 2021

Introduction

While many studies have implemented programs to increase sanitation coverage throughout the world, there are limited rigorous studies on the sustainability of these sanitation programs.

Methods

Between 2014 and 2018, the rural Sustainable Sanitation and Hygiene for All (SSH4A) approach was implemented by SNV in Sub-Saharan Africa and Asia. Repeated cross-sectional household surveys were administered annually throughout program implementation, and 1-to-2-years following completion of program activities. We characterize to what extent sanitation coverage was sustained 1-2 years after implementation of this SSH4A intervention.

Results

Surveys were conducted in 12 program areas in 10 countries, with 22,666 households receiving a post-implementation survey. Six of 12 program areas (Bhutan, Ghana, Kenya, both Nepal sites, and Tanzania) had similar coverage levels of basic sanitation 1-to-2-years post-implementation, whereas there were varied levels of slippage in the other program areas (both Ethiopia sites, Indonesia, Mozambique, Uganda, and Zambia), ranging from a drop of 63 percentage points in coverage in Ethiopia to a drop of only 4 percentage points in Indonesia. In countries that experienced losses in the coverage of household sanitation, generally sanitation sharing among neighbors did not increase, whereas open defecation did increase. In each of the areas where slippage occurred, the sanitation coverage levels at the final time point were all still higher than the initial time point before SNV started working in these areas. We found a number of factors to be associated with the sustainability of sanitation coverage, including household socio-economic status, having household members with disabilities, baseline sanitation coverage levels of the program areas, and rate of change of coverage during program activities.

Conclusions

Data revealed sustained gains in sanitation coverage in some program areas, yet slippage in other areas. This work may serve to benchmark sustainability of sanitation interventions in Sub-Saharan Africa and Asia.
Mathematical modeling of vaccination rollout and NPIs lifting on COVID-19 transmission with VOC: a case study in Toronto, Canada
Authors: Aruffo Elena , Yuan Pei , Tan Yi , Gatov Evgenia , Moyles Iain , Bélair Jacques , Watmough James , Collier Sarah , Arino Julien , Zhu Huaiping
Published: August 2021

Background

Since December 2020, public health agencies have implemented a variety of vaccination strategies to curb the spread of SARS-CoV-2, along with pre-existing Nonpharmaceutical Interventions (NPIs). Initial strategy focused on vaccinating the elderly to prevent hospitalizations and deaths. With vaccines becoming available to the broader population, we aimed to determine the optimal strategy to enable the safe lifting of NPIs while avoiding virus resurgence.

Methods

We developed a compartmental deterministic SEIR model to simulate the lifting of NPIs under different vaccination rollout scenarios. Using case and vaccination data from Toronto, Canada between December 28, 2020 and May 19, 2021, we estimated transmission throughout past stages of NPI escalation/relaxation to compare the impact of lifting NPIs on different dates on cases, hospitalizations, and deaths, given varying degrees of vaccine coverages by 20-year age groups, accounting for waning immunity.

Results

We found that, once coverage among the elderly is high enough (80% with at least one dose), the main age groups to target are 20-39 and 40-59 years, whereby first-dose coverage of at least 70% by mid-June 2021 is needed to minimize the possibility of resurgence if NPIs are to be lifted in the summer. While a resurgence was observed for every scenario of NPI lifting, we also found that under an optimistic vaccination coverage (70% by mid-June, postponing reopening from August 2021 to September 2021can reduce case counts and severe outcomes by roughly 80% by December 31, 2021.

Conclusions

Our results suggest that focusing the vaccination strategy on the working-age population can curb the spread of SARS-CoV-2. However, even with high vaccination coverage in adults, lifting NPIs to pre-pandemic levels is not advisable since a resurgence is expected to occur, especially with earlier reopening.
Cognition-oriented treatments and physical exercise on cognitive function in Huntington’s disease: Protocol for systematic review
Authors: Huynh Katharine , Nategh Leila , Jamadar Sharna , Georgiou-Karistianis Nellie , Lampit Amit
Published: August 2021

Introduction

Cognitive impairments are prevalent in Huntington’s disease (HD), occurring many years prior to clinical diagnosis and are the most impactful on quality of life of patients. Cognitive interventions and exercise have been found to be efficacious in improving cognitive function in several clinical populations (e.g., older adults with mild cognitive impairment and dementia). However, the utility of cognitive interventions has not been systematically reviewed in HD. This systematic review aims to examine the efficacy of cognitive and physical interventions on cognitive function in HD.

Methods

Electronic databases (MEDLINE, EMBASE, PsycINFO, CENTRAL) were searched through till 10 May 2021 for interventional studies investigating the effect of cognition-oriented treatments and physical exercise on cognitive function in individuals with HD, compared to any control or no control. The primary outcome is change on objective measures of cognition. Additional outcomes include change in psychosocial, functional and neuroimaging measures. Variations of effects based on population and study factors will be considered. Risk of bias will be assessed using the Cochrane RoB 2 tool and ROBINS-I tool. Where appropriate, outcomes will be pooled using random-effects meta-analyses, heterogeneity will be examined using tau2and I2statistics, and moderators will be examined using meta-regression models.

Discussion

This review will systematically evaluate the efficacy of cognitive and physical interventions on improving cognitive function in HD. The eligibility criteria and planned analyses will allow for a comprehensive assessment of certainty in the evidence that will inform future trials and clinical practice.

Registration

This protocol was registered on PROSPERO (CRD42021259152).
Genetic compensation of triacylglycerol biosynthesis in the green microalga Chlamydomonas reinhardtii
Authors: Lee Yi-Ying , Park Rudolph , Miller Stephen M. , Li Yantao
Published: August 2021

Genetic compensation through transcriptional adaptation has been proposed to explain phenotypic differences between gene knockouts and knockdowns. With the rapid development of reverse genetic tools such as CRISPR/Cas9 and RNAi in microalgae, it is increasingly important to assess whether genetic compensation affects the phenotype of engineered algal mutants. While exploring triacylglycerol (TAG) biosynthesis pathways in Chlamydomonas reinhardtii, it was discovered that knockout of certain genes catalyzing rate-limiting steps of TAG biosynthesis, type-2 diacylglycerol acyltransferase genes (DGTTs), triggered genetic compensation under abiotic stress conditions. Genetic compensation of a DGTT1 null mutation by a related PDAT gene was observed regardless of the strain background or mutagenesis approach, e.g., CRISPR/Cas 9 or insertional mutagenesis. However, no compensation was found in the PDAT knockout mutant. The effect of PDAT knockout was evaluated in a Δvtc1 mutant, in which PDAT was up-regulated under stress. Knockout of PDAT in the Δvtc1 background induced a 12.8-fold upregulation of DGTT1 and a 272.3% increase in TAG content in Δvtc1/pdat1 cells, while remaining viable. These data suggest that genetic compensation contributes to the genetic robustness of microalgal TAG biosynthetic pathways, maintaining lipid and redox homeostasis in the knockout mutants under abiotic stress with a mechanism distinct from that found in plants. This work demonstrates examples of genetic compensation in microalgae, implies the physiological relevance of genetic compensation in TAG biosynthesis, and provides guidance for future genetic engineering and mutant characterization efforts.
Genome sequencing of the vermicompost strainStenotrophomonas maltophiliaUENF-4GII and population structure analysis of theS. maltophiliaSm3 genogroup
Authors: Pedrosa-Silva Francisnei , Matteoli Filipe P. , Passarelli-Araujo Hemanoel , Olivares Fabio L. , Venancio Thiago M.
Published: August 2021

TheStenotrophomonas maltophiliacomplex (Smc) is a cosmopolitan bacterial group that has been proposed an emergent multidrug-resistant pathogen. Taxonomic studies support the genomic heterogeneity of Smc, which comprises genogroups exhibiting a range of phenotypically distinct strains from different sources. Here, we report the genome sequencing and in-depth analysis ofS. maltophiliaUENF-4GII, isolated from vermicompost. This genome harbors a unique region encoding a penicillin-binding protein (pbpX) that was carried by a transposon, as well as horizontally-transferred genomic islands involved in anti-phage defense via DNA modification, and pili glycosylation. We also analyzed all available Smc genomes to investigate genes associated with resistance and virulence, niche occupation, and population structure.S. maltophiliaUENF-4GII belongs to genogroup 3 (Sm3), which comprises three phylogenetic clusters (PC). Pan-GWAS analysis uncovered 471 environment-associated and 791 PC-associated genes, including antimicrobial resistance (e.g.blaL1 andblaR1) and virulence determinants (e.g.treS andkatG) that provide insights on the resistance and virulence potential of Sm3 strains. Together, the results presented here provide the grounds for more detailed clinical and ecological investigations ofS. maltophilia.
Aged mouse ovarian immune milieu shows a shift towards adaptive immunity and attenuated cell function
Authors: Yaakov Tal Ben , Wasserman Tanya , Savir Yonatan
Published: August 2021

The immune system plays a major role in maintaining many physiological processes in the reproductive system. However, a complete characterization of the immune milieu in the ovary, and particularly how it is affected by maternal aging, is still lacking. In this work, we utilize single-cell RNA sequencing and flow cytometry to construct a complete description of the murine ovarian immune system and its changes along with pre-estropause aging. We show that the ovarian immune cells composition undergoes an extensive shift with age towards adaptive immunity. We analyze the effect of aging on gene expression and chemokine and cytokine networks and show an overall decreased expression of inflammatory mediators together with an increased senescent cells recognition. Our results reveal the changes in the aging ovarian immune system of the fertile female as it copes with the inflammatory stimulations during repeated cycles and the increasing need for clearance of accumulating atretic follicles.
Cooperation between CYB5R3 and NOX4 via coenzyme Q mitigates endothelial inflammation
Authors: Yuan Shuai , Hahn Scott A. , Miller Megan P. , Sanker Subramaniam , Calderon Michael J , Sullivan Mara , Dosunmu-Ogunbi Atinuke M. , Fazzari Marco , Li Yao , Reynolds Michael , Wood Katherine C , St. Croix Claudette M. , Stolz Donna , Cifuentes-Pagano Eugenia , Navas Placido , Shiva Sruti , Schopfer Francisco J. , Pagano Patrick J. , Straub Adam C.
Published: August 2021

NADPH oxidase 4 (NOX4) regulates endothelial inflammation by producing reactive oxygen species. Since coenzyme Q (CoQ) mimics affect NOX4 activity, we hypothesize that cytochrome b5 reductase 3 (CYB5R3), a CoQ reductase abundant in vascular endothelial cells, modulates inflammatory activation.

Mice lacking endothelial CYB5R3 (R3 KO), under lipopolysaccharides (LPS) challenge, showed exacerbated hypotension, decreased acetylcholine-induced vasodilation, and elevated vascular adhesion molecule 1 (Vcam-1) mRNA in aorta. In vitro, silencingCyb5r3enhanced LPS-induced VCAM-1 protein in a NOX4 dependent manner. APEX2- based electron microscopy and proximity biotinylation demonstrated CYB5R3’s localization on the mitochondrial outer membrane and its interaction with NOX4, which was further confirmed by the proximity ligation assay. Notably,Cyb5r3silenced HAECs had less total H2O2but more mitochondrial O2•-. Using inactive or non-membrane bound active CYB5R3, we found CYB5R3 activity and membrane translocation were needed for optimal generation of H2O2by NOX4. Lastly, CoQ deficient cells showed decreased NOX4-derived H2O2, indicating a requirement for endogenous CoQ in NOX4 activity.

In conclusion, CYB5R3 mitigates endothelial inflammatory activation by assisting in NOX4-dependent H2O2generation via CoQ.

NOVELTY AND SIGNIFICANCE

What Is Known?

NADPH oxidase 4 (NOX4) reportedly produces primarily hydrogen peroxide (H2O2) and, to a lesser extent, superoxide (O2•-) and has been shown to have both beneficial and deleterious effects in the cardiovascular system.

NOX4 activity can be affected by NAD(P)H quinone oxidoreductase 1 (NQO1), a CoQ reductase, and synthetic quinone compounds used to mimic CoQ.

Cytochrome b5 reductase 3 (CYB5R3) is known to reduce CoQ and is highly expressed in endothelial cells.

What New Information Does This Article Contribute?

In vivo, the lack of endothelial CYB5R3 causes exacerbated lipopolysaccharides (LPS)-induced inflammatory signaling, endothelial dysfunction, and hypotension.

Endothelial CYB5R3 mitigates inflammatory signaling by LPS and tumor necrosis factor α (TNF-α) in a NOX4 dependent manner.

In endothelial cells, CYB5R3 and NOX4 reside in close proximity on the mitochondrial outer membrane.

NOX4’s ability to generate H2O2depends on the membrane translocation and activity of CYB5R3 and the presence of endogenous CoQ.

NONSTANDARD Abbreviations and Acronyms

Protein names are abbreviated as capital letters (e.g., CYB5R3), while the corresponding gene names are annotated as in italic lower cases (e.g.,Cyb5r3).
Integrin signalingviaactin cytoskeleton activates MRTF/SRF to entrain circadian clock
Authors: Xiong Xuekai , Li Weini , Nam Jin , Ma Ke
Published: August 2021

The circadian clock is entrained to daily environmental cues. Integrin-linked intracellular signalingviaactin cytoskeleton dynamics transduces cellular niche signals to induce Myocardin-related Transcription Factor (MRTF)/Serum Response Factor (SRF)-mediated transcription. So far, how the integrin-associated signaling cascade may transmit cellular physical cues to entrain circadian clock remains to be defined. Using combined pharmacological and genetic approaches, here we show that the transcription factors mediating integrin to actin cytoskeleton signaling, MRTF-A and SRF, exert direct transcriptional control of core clock components, and that this signaling cascade modulates key properties of clock circadian activity. Pharmacological inhibition of MRTF/SRF activity by disrupting actin polymerization significantly augmented clock amplitude with period shortening, whereas an actin polymerizing compound attenuated oscillation amplitude with period lengthening. Genetic loss-of-function ofSrforMrtfmimics that of actin-depolymerizing agents, validating the role of actin dynamics in driving clock function. Furthermore, integrin-mediated focal adhesion with extracellular matrix and its downstream signaling modulates the circadian clock, as blockade of integrin, focal adhesion kinase or Rho-associated kinase (ROCK) increased clock amplitude and shortened period length. Mechanistically, we identify specific core clock transcription regulators,Per1, Per2andNr1d1, as direct target genes of MRTF-A/SRF. Collectively, our findings uncovered an integrin-actin cytoskeleton-MRTF/SRF signaling cascade in linking clock entrainment to its extracellular microenvironment, which may mediate cellular adaptation to its physical niche.

Author Summary

The circadian clock anticipates and adapts to environmental changes. Interestingly, serum, as a universal clock synchronizing signal, drives intracellular actin cytoskeleton reorganization through modulation of MRTF/SRF activity. However, mechanisms that may transduce extracellular niche signals to circadian clock remains to be defined. We hypothesize that integrin-mediated intracellular signaling to actin cytoskeleton links extracellular microenvironment with MRTF/SRF transcriptional regulation to control clock function. Using small molecules and genetic approaches targeting distinct steps of integrin-actin cytoskeleton-MRTF/SRF signaling cascade, we uncover the effects of this pathway in controlling circadian clock oscillation. We also identify specific core clock regulators as direct gene target genes of MRTF and SRF-mediated transcriptional control. Our study revealed how integrin-mediated cellular interaction with its physical environment influences its intrinsic clock properties through signaling transductionviaactin cytoskeleton remodeling, and that this mechanism may facilitate circadian clock adaptation to cellular physical niche.
Paramecium Polycomb Repressive Complex 2 physically interacts with the small RNA binding PIWI protein to repress transposable elements
Authors: Pina Caridad Miró , Kawaguchi Takayuki , Charmant Olivia , Michaud Audrey , Cohen Isadora , Humbert Adeline , Jaszczyszyn Yan , Del Maestro Laurence , Holoch Daniel , Ait-Si-Ali Slimane , Arnaiz Olivier , Margueron Raphaël , Duharcourt Sandra
Published: August 2021

Polycomb Repressive Complex 2 (PRC2) maintains transcriptionally silent genes in a repressed state via deposition of histone H3 K27 trimethyl (me3) marks. PRC2 has also been implicated in silencing transposable elements (TEs) yet how PRC2 is targeted to TEs remains unclear. To address this question, we performed tandem affinity purification combined with mass spectrometry and identified proteins that physically interact with the Paramecium Enhancer-of-zeste Ezl1 enzyme, which catalyzes H3K9me3 and H3K27me3 deposition at TEs. We show that the Paramecium PRC2 core complex comprises four subunits, each required in vivo for catalytic activity. We also identify PRC2 cofactors, including the RNA interference (RNAi) effector Ptiwi09, which are necessary to target H3K9me3 and H3K27me3 to TEs. We find that the physical interaction between PRC2 and the RNAi pathway is mediated by a RING finger protein and that small RNA recruitment of PRC2 to TEs is analogous to the small RNA recruitment of H3K9 methylation SU(VAR)3-9 enzymes.
Uncertainty avoidance versus conditioned reinforcement: exploring paradoxical choice in rats
Authors: Ajuwon Victor , Ojeda Andrés , Murphy Robin A. , Monteiro Tiago , Kacelnik Alex
Published: August 2021

Paying a cost to reduce uncertainty can be adaptive, because better informed decision-makers can align their preferences to opportunities. However, birds and mammals display an appetite for information that they cannot use to functionally alter behaviour or its outcomes. We explore two putative motivational mechanisms for this paradoxical behaviour. The ‘information hypothesis’, proposes that reducing uncertainty is reinforcing per se, consistent with the concept of curiosity: a motivation to know, in the absence of instrumental benefits. In contrast, the ‘conditioned reinforcement hypothesis’ sees information-seeking as a consequence of asymmetries in secondarily acquired reinforcement: responding increments caused by post-choice stimuli announcing positive outcomes (S+) exceed decrements caused by stimuli signalling absence of reward (S−). We contrast these hypotheses experimentally. Rats chose between two equally profitable options delivering food probabilistically after a fixed delay. In the informative option (Info), the outcome (food/no food) was signalled immediately after choice, whereas in the non-informative option (NoInfo) outcomes were uncertain until the delay lapsed. Subjects preferred Info when (1) outcomes were signalled by salient auditory cues, (2) only the absence of reward was signalled, and (3) only reward was signalled, though acquisition was slower when rewards were not explicitly signalled. Our results show that a salient good news signal is not required as a conditioned reinforcer to generate paradoxical preferences. Terminal preferences support the information hypothesis but the slower acquisition of Info preference when S+ is not present is consistent with the conditioning account. We conclude that both uncertainty reduction and conditioned reinforcement influence choice.
Stoney vs. Histed: Quantifying the Spatial Effects of Intracortical Microstimulation
Authors: Kumaravelu Karthik , Sombeck Joseph , Miller Lee E. , Bensmaia Sliman J. , Grill Warren M.
Published: August 2021

Background

Intracortical microstimulation (ICMS) is used to map neural circuits and restore lost sensory modalities such as vision, hearing, and somatosensation. The spatial effects of ICMS remain controversial: Stoney and colleagues proposed that the volume of somatic activation increased with stimulation intensity, while Histed et al. suggested activation density, but not somatic activation volume, increases with stimulation intensity.

Objective

We used computational modeling to quantify the spatial effects of ICMS intensity and unify the apparently paradoxical findings of Histed and Stoney.

Methods

We implemented a biophysically-based computational model of a cortical column comprising neurons with realistic morphology and representative synapses. We quantified the spatial effects of single pulse ICMS, including the radial distance to activated neurons and the density of activated neurons as a function of stimulation intensity.

Results

At all amplitudes, the dominant mode of somatic activation was by antidromic propagation to the soma following axonal activation, rather than via trans-synaptic activation. There were no occurrences of direct activation of somata or dendrites. The volume over which antidromic action potentials were initiated grew with stimulation amplitude, while the volume of somatic activations did not. However, the density of somatic activation within the activated volume increased with stimulation amplitude.

Conclusions

The results resolve the apparent paradox between Stoney and Histed’s results by demonstrating that the volume over which action potentials are initiated grows with ICMS amplitude, consistent with Stoney. However, the volume occupied by the activated somata remains approximately constant, while the density of activated neurons within that volume increase, consistent with Histed.

HIGHLIGHTS

Implemented a biophysically-based computational model of cortical column comprising cortical neurons with realistic morphology and representative synapses.

Quantified the spatial patterns of neural activation by intracortical microstimulation to resolve the paradoxical findings of Stoney et al., 1968 and Histed et al., 2009.

The dominant mode of neural activation near the electrode was direct (i.e., via antidromic propagation from direct activation of the axon) and not trans-synaptic.

The dominant effect of increased ICMS intensity was to increase the density of activated neurons but not the volume of activation.
Improving GWAS discovery and genomic prediction accuracy in Biobank data
Authors: Orliac Etienne J. , Banos Daniel Trejo , Ojavee Sven E. , Läll Kristi , Mägi Reedik , Visscher Peter M. , Robinson Matthew R.
Published: August 2021

Genetically informed and deep-phenotyped biobanks are an important research resource. The cost of phenotyping far outstrips that of genotyping, and therefore it is imperative that the most powerful, versatile and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. On average, GMRM accuracies were 15% (SE 7%) greater than prediction models run in the LDAK software with SNP annotation marker groups, 18% (SE 3%) greater than a baseline BayesR model without SNP markers grouped into MAF-LD-annotation categories, and 106% (SE 9%) greater than polygenic risk scores calculated from mixed-linear model association (MLMA) estimates. For height, the prediction accuracy R2 was 47% in a UK Biobank hold-out sample, which was 76% of the estimated . We then extend our GMRM prediction model to provide MLMA SNP marker estimates for GWAS discovery, which increased the independent loci detected to 7,910 in unrelated UK Biobank individuals, as compared to 5,521 from BoltLMM and 5,727 from Regenie, a 43% and 38% increase respectively. The average χ2 value of the leading markers was 34% (SE 5.11) higher for GMRM as compared to Regenie, and increased by 17% for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modelling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and for discovery in large-scale individual-level biobank-scale studies.
BubR1 recruitment to the kinetochore via Bub1 enhances Spindle Assembly Checkpoint signaling
Authors: Banerjee Anand , Chen Chu , Humphrey Lauren , Tyson John J. , Joglekar Ajit P.
Published: August 2021

During mitosis, unattached kinetochores in a dividing cell activate the Spindle Assembly Checkpoint (SAC) and delay anaphase onset by generating the anaphase-inhibitory Mitotic Checkpoint Complex (MCC). These kinetochores generate the MCC by recruiting MCC constituent proteins, including BubR1. In principle, BubR1 recruitment to signaling kinetochores should increase its local concentration and promote MCC formation. However, in human cells BubR1 is mainly thought to sensitize the SAC to silencing; whether BubR1 localization to signaling kinetochores per se enhances SAC signaling activity remains unknown. Therefore, we used ectopic SAC activation systems (eSAC) to isolate two molecules that recruit BubR1 to the kinetochore: the checkpoint protein Bub1 and the KI and MELT motifs in the kinetochore protein KNL1, and observed their contribution to eSAC signaling. Our quantitative analyses and mathematical modeling show that the Bub1-mediated BubR1 recruitment to the human kinetochore promotes SAC signaling and highlight BubR1’s dual role of directly strengthening the SAC and indirectly silencing it.
A low-cost greenhouse-based high-throughput phenotyping platform for genetic studies: a case study in maize under inoculation with plant growth-promoting bacteria
Authors: Yassue Rafael Massahiro , Galli Giovanni , Junior Ronaldo Borsato , Cheng Hao , Morota Gota , Fritsche-Neto Roberto
Published: August 2021

Greenhouse-based high-throughput phenotyping (HTP) presents a useful approach for studying novel plant growth-promoting bacteria (PGPB). Despite the potential of this approach to leverage genetic variability for breeding new maize cultivars exhibiting highly stable symbiosis with PGPB, greenhouse-based HTP platforms are not yet widely used because they are highly expensive; hence, it is challenging to perform HTP studies under a limited budget. In this study, we built a low-cost greenhouse-based HTP platform to collect growth-related image-derived phenotypes. We assessed 360 inbred maize lines with or without PGPB inoculation under nitrogen-limited conditions. Plant height, canopy coverage, and canopy volume obtained from photogrammetry were evaluated five times during early maize development. A plant biomass index was constructed as a function of plant height and canopy coverage. Inoculation with PGPB promoted plant growth. Phenotypic correlations between the image-derived phenotypes and manual measurements were at least 0.6. The genomic heritability estimates of the image-derived phenotypes ranged from 0.23 to 0.54. Moderate-to-strong genomic correlations between the plant biomass index and shoot dry mass (0.24–0.47) and between HTP-based plant height and manually measured plant height (0.55–0.68) across the developmental stages showed the utility of our HTP platform. Collectively, our results demonstrate the usefulness of the low-cost HTP platform for large-scale genetic and management studies to capture plant growth.

Core ideas

A low-cost greenhouse-based HTP platform was developed.

Image-derived phenotypes presented moderate to high genomic heritabilities and correlations.

Plant growth-promoting bacteria can improve plant resilience under nitrogen-limited conditions.
Carbon Fiber Electrodes for Intracellular Recording and Stimulation
Authors: Huan Yu , Gill Jeffrey P. , Fritzinger Johanna B. , Patel Paras R. , Richie Julianna M. , Valle Elena della , Weiland James D. , Chestek Cynthia A. , Chiel Hillel J.
Published: August 2021

To understand neural circuit dynamics, it is critical to manipulate and record from many neurons, ideally at the single neuron level. Traditional recording methods, such as glass microelectrodes, can only control a small number of neurons. More recently, devices with high electrode density have been developed, but few of them can be used for intracellular recording or stimulation in intact nervous systems, rather than on neuronal cultures. Carbon fiber electrodes (CFEs) are 8 micron-diameter electrodes that can be organized into arrays with pitches as low as 80 µm. They have been shown to have good signal-to-noise ratios (SNRs) and are capable of stable extracellular recording during both acute and chronic implantationin vivoin neural tissue such as rat motor cortex. Given the small fiber size, it is possible that they could be used in arrays for intracellular stimulation. We tested this using the large identified and electrically compact neurons of the marine molluskAplysia californica. The cell bodies of neurons inAplysiarange in size from 30 to over 250 µm. We compared the efficacy of CFEs to glass microelectrodes by impaling the same neuron’s cell body with both electrodes and connecting them to a DC coupled amplifier. We observed that intracellular waveforms were essentially identical, but the amplitude and SNR in the CFE were lower than in the glass microelectrode. CFE arrays could record from 3 to 8 neurons simultaneously for many hours, and many of these recordings were intracellular as shown by recording from the same neuron using a glass microelectrode. Stimulating through CFEs coated with platinum-iridium had stable impedances over many hours. CFEs not within neurons could record local extracellular activity. Despite the lower SNR, the CFEs could record synaptic potentials. Thus, the stability for multi-channel recording and the ability to stimulate and record intracellularly make CFEs a powerful new technology for studying neural circuit dynamics.
Loss of the extracellular matrix protein DIG-1 causes glial fragmentation, dendrite breakage, and dendrite extension defects
Authors: Chong Megan K. , Cebul Elizabeth R. , Mizeracka Karolina , Heiman Maxwell G.
Published: August 2021

The extracellular matrix (ECM) guides and constrains the shape of the nervous system. InC. elegans, DIG-1 is a giant ECM component that is required for fasciculation of sensory dendrites during development and for maintenance of axon positions throughout life. We identified four novel alleles ofdig-1in three independent screens for mutants affecting disparate aspects of neuronal and glial morphogenesis. First, we find that disruption of DIG-1 causes fragmentation of the amphid sheath glial cell in larvae and young adults. Second, it causes severing of the BAG sensory dendrite from its terminus at the nose tip, apparently due to breakage of the dendrite as animals reach adulthood. Third, it causes embryonic defects in dendrite fasciculation in inner labial (IL2) sensory neurons, as previously reported, as well as rare defects in IL2 dendrite extension that are enhanced by loss of the apical ECM component DYF-7, suggesting that apical and basolateral ECM contribute separately to dendrite extension. Our results highlight novel roles for DIG-1 in maintaining the cellular integrity of neurons and glia, possibly by creating a barrier between structures in the nervous system.
A B cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation
Authors: Wang Jia C. , Yim Yang-In , Wu Xufeng , Jaumouillé Valentin , Cameron Andrew , Waterman Clare M. , Kehrl John H. , Hammer John A.
Published: August 2021

B-cell activation and immune synapse (IS) formation with membrane-bound antigens are actin-dependent processes that scale positively with the strength of antigen-induced signals. Importantly, ligating the B-cell integrin, LFA-1, with ICAM-1 promotes IS formation when antigen is limiting. Whether the actin cytoskeleton plays a specific role in integrin-dependent IS formation is unknown. Here we show using super-resolution imaging of mouse primary B cells that LFA-1: ICAM-1 interactions promote the formation of an actomyosin network that dominates the B-cell IS. This network is created by the formin mDia1, organized into concentric, contractile arcs by myosin 2A, and flows inward at the same rate as B-cell receptor (BCR): antigen clusters. Consistently, individual BCR microclusters are swept inward by individual actomyosin arcs. Under conditions where integrin is required for synapse formation, inhibiting myosin impairs synapse formation, as evidenced by reduced antigen centralization, diminished BCR signaling, and defective signaling protein distribution at the synapse. Together, these results argue that a contractile actomyosin arc network plays a key role in the mechanism by which LFA-1 co-stimulation promotes B-cell activation and IS formation.
mebipred: identifying metal-binding potential in protein sequences.
Authors: Aptekmann Ariel A , Buongiorno Joy , Giovannelli Donato , Glamoclija Mihaela , Ferreiro Diego U , Bromberg Yana
Published: August 2021

Metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. We developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is nearly 90% accurate in recognizing proteins that bind metal ions and ion containing ligands. Moreover, the identity of ten ubiquitously present metal ions and ion-containing ligands can be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and outperforms other prediction methods, both in speed and accuracy. mebipred can also identify protein metal-binding capabilities from short sequence stretches and, thus, may be useful for the annotation of metagenomic samples metal requirements inferred from translated sequencing reads. We performed an analysis of microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human-hosted microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results are highlight mebipreds utility in analyzing microbiome metal requirements. mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/
Nano-scale Architecture of Blood-Brain Barrier Tight-Junctions
Authors: Sasson Esther , Anzi Shira , Bell Batia , Yakovian Oren , Zorsky Meshi , Deutsch Urban , Engelhardt Britta , Sherman Eilon , Vatine Gad D. , Dzikowski Ron , Ben-Zvi Ayal
Published: August 2021

Tight junctions (TJs) between blood-brain barrier (BBB) endothelial cells construct a robust physical barrier, whose damage underlies BBB dysfunctions related to several neurodegenerative diseases. What makes these highly specialized BBB-TJs extremely restrictive remains unknown. Here, we use super-resolution microscopy (dSTORM) to uncover new structural and functional properties of BBB TJs. Focusing on three major components, Nano-scale resolution revealed sparse (occludin) vs. clustered (ZO1/claudin-5) molecular architecture. Developmentally, permeable TJs become first restrictive to large molecules, and only later to small molecules, with claudin-5 proteins arrangement compacting during this maturation process. Mechanistically, we reveal that ZO1 clustering is independent of claudin-5 in-vivo. In contrast to accepted knowledge, we found that in the developmental context, total levels of claudin-5 inversely correlate with TJ functionality. Our super-resolution studies provide a unique perspective of BBB TJs and open new directions for understanding TJ functionality in biological barriers, ultimately enabling restoration in disease or modulation for drug delivery.
High molecular weight hyaluronan – a potential adjuvant to fluid resuscitation in porcine abdominal sepsis
Authors: Tenhunen Annelie Barrueta , van der Heijden Jaap , Weigl Wojciech , Frithiof Robert , Skorup Paul , Larsson Anders , Larsson Anders , Tenhunen Jyrki
Published: August 2021

While fluid resuscitation is fundamental in the treatment of sepsis-induced tissue hypo-perfusion, a sustained positive fluid balance is associated with excess mortality. Crystalloids are the mainstay of fluid resuscitation and use of either synthetic colloids or albumin is controversial. Hyaluronan, an endogenous glycosaminoglycan with high affinity to water, has not been tested as adjuvant in fluid resuscitation.

We sought to evaluate the effects of hyaluronan as an adjuvant to fluid resuscitation in peritonitis induced sepsis. In a prospective, parallel-grouped, blinded model of porcine peritonitis-sepsis, we randomized animals to intervention with adjuvant hyaluronan (add-on to standard therapy) (n=8) or 0.9% saline (n=8). After the onset of hemodynamic instability the animals received an initial bolus of 0.1 % hyaluronan 1 mg/kg/10 min or placebo (saline) followed by a continuous infusion of 0.1% hyaluronan (1 mg/kg/h) or saline during the experiment. We hypothesized that the administration of hyaluronan would reduce the volume of fluid administered (aiming at stroke volume variation <13%) and/or attenuate the inflammatory reaction.

Total volumes of intravenous fluids infused were 17.5 ± 11 ml/kg/h vs. 19.0 ± 7 ml/kg/h in intervention and control groups, respectively (p= 0.442). Plasma IL-6 increased to 2450 (1420 – 6890) pg/ml and 3700 (1410 – 11960) pg/ml (18 hours of resuscitation) in the intervention and control groups (NS). In a post-hoc analysis, modified shock index remained lower in intervention group (p= 0.011 - 0.037).

In conclusion adjuvant hyaluronan did not reduce the volume needed for fluid administration or decrease the inflammatory reaction. Adjuvant hyaluronan was, however, associated with lower modified shock index. Bearing in mind that the experiment has a limited group-size we suggest that further studies on hyaluronan in sepsis are warranted.
Distinguishing and employing sister species of fish in assessment of stream quality
Authors: Van Dyke Fred , van Ee Benjamin W. , Harju Seth , Budi Joshua W. , Sokolowski Thomas B. , Keas Brian
Published: August 2021

Biological indicators (bioindicators) can be individual species or species groups used to assess habitat quality. Unfortunately, conservationists often lack information on species distribution, how to differentiate between similar species, and environmental conditions associated with the presence of a species. We addressed these problems using two “sister” species of fish, the Mottled Sculpin (Cottus bairdii) and the Slimy Sculpin (Cottus cognatus), as stream quality indicators in the Manistee River watershed in the Huron-Manistee National Forests in Michigan, USA. We determined the abundance and distribution of these species and related their presence to concurrent in-stream measurements of temperature, dissolved oxygen, pH, conductivity, turbidity, and stream quality score based on macroinvertebrate diversity. To be certain of identification, we sequenced the Cytochrome c Oxidase Subunit I (CO1) molecular marker for specimens and used it as a DNA barcode to determine a specimen’s species. Cladistic analyses of CO1 unambiguously supported recognition of Mottled Sculpin and Slimy Sculpin as distinct species, confirming initial 87.5% correct identification using morphological characteristics, with uncertainty limited to juvenile fish. Field determinations increased to 100% correct identification as investigators gained more experience. Both species were most abundant in headwater regions, decreased downstream, and were sympatric at several locations. Mottled Sculpin were more likely to be found at stream locations with lower conductivity, pH, and stream quality scores, whereas Slimy Sculpin presence was more strongly associated higher levels of DO and lower levels of turbidity. Such findings are important because Mottled Sculpin are a designated management indicator species of the US Forest Service in the Huron-Manistee National Forests, but may be ineffective as a habitat quality indicator when used alone. Concurrent use of Mottled Sculpin and Slimy Sculpin as a management indicator sister-species complex could allow sufficient landscape coverage to permit habitat assessment if species-specific differences in environmental tolerances are precisely determined.
Mechanisms of Coupling between Angiotensin Converting Enzyme 2 and Nicotinic Acetylcholine Receptors
Authors: Kabbani Nadine , Brumfield Kyle D. , Sinclair Patricia , Ramanathan Arvind , Leddy Menu , Colwell Rita R. , Olds James L
Published: August 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an RNA virus encapsulated by a spike (S) glycoprotein envelope, binds with high affinity to angiotensin converting enzyme 2 (ACE2) during cell entry of a susceptible host. Recent studies suggest nicotinic acetylcholine receptors (nAChRs) play a role in functional ACE2 regulation and nicotine may contribute to the progression of coronavirus disease 2019 (COVID-19). Here, we present evidence for coupling between ACE2 and nAChR through bioinformatic analysis and cell culture experiments. Following molecular and structural protein comparison of over 250 ACE2 vertebrate orthologues, a region of human ACE2 at positions C542-L554 was identified to have sequence similarity to nAChR-binding neurotoxin and rabies virus glycoproteins (RBVG). Furthermore, experiments conducted in PC12 cells indicate a potential for physical interaction between ACE2 and α7 nAChR proteins. Our findings support a model of nAChR involvement in in COVID-19.