bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population
Authors: Auvray Frédéric , Perrat Alexandre , Arimizu Yoko , Chagneau Camille V. , Bossuet-Greif Nadège , Massip Clémence , Brugère Hubert , Nougayrède Jean-Philippe , Hayashi Tetsuya , Branchu Priscilla , Ogura Yoshitoshi , Oswald Eric
Published: May 2021

The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of

Escherichia coli

strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine

E. coli

isolates, we identified 109 strains carrying a highly conserved pks island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of pks acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, pks was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the asnW tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, pks inserted at the asnU or asnV tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, pks was acquired, independently of the HPI, at a non-tRNA locus. All the pks-positive strains except 18 produced colibactin. Sixteen strains contained mutations in clbB or clbD, or a fusion of clbJ and clbK and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the pks island. One strain was fully metabolically inactive without pks alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the pks island is not restricted to human pathogenic B2 strains and is more widely distributed in the

E. coli

population, while preserving its functionality.
Intentional and unintentional non-adherence to social distancing measures during COVID-19: A mixed-methods analysis
Authors: Eraso Yolanda , Hills Stephen
Published: May 2021

Social distancing measures implemented by governments worldwide during the COVID-19 pandemic have proven an effective intervention to control the transmission of SARS-CoV-2. There is a growing literature on predictors of adherence behaviours to social distancing measures, however, there are no comprehensive insights into the nature and types of non-adherence behaviours. To address this gap in the literature, we studied non-adherence in terms of counts of infringements and people’s accounts on their behaviours in a representative sample of North London residents. We focused on the following social distancing rules: keeping 2 mts. distancing, meeting family and friends, and going out for non-essential reasons.

A mixed-methods explanatory sequential design was used comprising an online survey (1st– 31stMay 2020) followed by semi-structured in-depth interviews held with a purposive sample of survey respondents (5thAugust – 21stSeptember 2020). A negative binomial regression model (quantitative) and Framework Analysis (qualitative) were undertaken.

681 individuals completed the survey, and 30 individuals were interviewed. We integrated survey and interview findings following three levels of the Social Ecological model: individual, interpersonal and community levels. We identified non-adherence behaviours as unintentional (barriers beyond individual’s control) and intentional (deliberate decision). Unintentional adherence was associated with and reported as emotional inability to stay at home, lack of controllability in keeping 2 mts. distancing, social responsibility towards the community and feeling low risk. Intentional non-adherence included individual risk assessment and decision-making on the extent to following the rules, support from friends, and perceived lack of adherence in the local area. Our findings indicate that unintentional and intentional non-adherence should be improved by Government partnerships with local communities to build trust in social distancing measures; tailored messaging to young adults emphasising the need of protecting others whilst clarifying the risk of transmission; and ensuring COVID-secured environments by working with environmental health officers.
Investigating trait variability of gene co-expression network architecture in brain by manipulating genomic signatures of schizophrenia risk
Authors: Radulescu Eugenia , Chen Qiang , Pergola Giulio , Eagles Nicholas J , Stolz Joshua M , Shin Joo Heon , Hyde Thomas M , Kleinman Joel E , Weinberger Daniel R
Published: May 2021

While the role of genomic risk for schizophrenia on brain gene co-expression networks has been described, the patterns of its manifestations are varied and complex. To acquire a deeper understanding of this issue, we implemented a novel approach to network construction by manipulating the RNA-Seq expression input to “integrate” or “remove” the “modulatory” effects of genomic risk for schizophrenia. We created co-expression networks in DLPFC from the adjusted expression input and compared them in terms of gene overlap and connectivity. We used linear regression models to remove variance explained by RNA quality, cell type proportion, age, sex and genetic ancestry. We also created co-expression networks based on the genomic profile of a normative trait, height, as a “negative control”; we also applied the same analytical approach in two independent samples: LIBD Human Brain Repository (HBR) (N=78 brains, European ancestry) and Common Mind Consortium (CMC) (N=116 brains, European ancestry). In addition to direct comparisons, we explored the biological plausibility of the differential gene clusters between co-expression networks by testing them for enrichment in relevant gene ontologies and gene sets of interest (PGC2-CLOZUK GWAS significant loci genes, height GWAS significant loci genes, genes in synaptic ontologies-SynGO and genes of the “druggable genome”). We identify several key aspects of the role of genomic risk for schizophrenia in brain co-expression networks: 1) Variability of co-expression modules with “integration” or “removal” of genomic profiles of complex traits (normal or pathological); 2) Biological plausibility of gene sets represented in the differential co-expression contrasts and potential relevance for illness etiopathogenesis; 3) Non-preferential mapping of schizophrenia GWAS loci genes to network areas apparently influenced by the genomic risk score. Overall, our study supports the notion that genomic risk for schizophrenia has an extensive and non-linear effect on brain gene co-expression networks that possibly manifests as a molecular background for gene-gene, gene-environment interactions that affect various biological pathways.
Are the Items of the Starkstein Apathy Scale Fit for the Purpose of Measuring Apathy Post-Stroke?
Authors: Hum Stanley , Fellows Lesley K. , Lourenco Christiane , Mayo Nancy E.
Published: May 2021

Given the importance of apathy for stroke, we felt it was time to scrutinize the commonly used Starkstein Apathy Scale (SAS) for psychometric evidence that it is fit for this purpose. The objectives were to: (i) estimate the extent to which the SAS items fit a hierarchical continuum of the Rasch Model; and (ii) estimate the strength of the relationships between the Rasch analysed SAS and converging constructs related to stroke outcomes.

Methods

Data on 238 people with stroke (mean age=63.1 years (SD=12.1) women=37.4%) from a clinical trial of a community-based intervention targeting participation were available at 5 time points yielding 856 SAS questionnaires. SAS has 14 items, rated on a 4-point scale with higher values indicating more apathy. Psychometric properties were tested using Rasch partial-credit model, correlation, and regression. The construct was modeled as motivation with items rescored as high is better.

Results

Rasch analysis indicated that the response options were disordered for 8/14 items, pointing to unreliability in the interpretation of the response options; they were consequently reduced from 4 to 3. Only 9/14 items fit the Rasch model and therefore suitable for creating a total score. The new rSAS was deemed unidimensional (residual correlations: < 0.3), reasonably reliable (person separation index: 0.74), with item-locations uniform across time, age, sex, and education. However, 30% of scores were >2 SD above the standardized mean but only 2/9 items covered this range (construct mistargeting).

Apathy (rSAS/SAS) was correlated weakly with anxiety/depression and uncorrelated with physical capacity. Regression showed that the effect of apathy on participation and health perception was similar for rSAS/SAS versions: R2 participation measures ranged from 0.11 to 0.29; R2 for health perception was ∼0.25.

When placed on the same scale (0-42), rSAS value was 6.5 units lower than SAS value with minimal floor/ceiling effects. Estimated change over time was identical (0.12 units/month) which was not substantial (1.44 units/year) but greater than expected assuming no change (t: 3.6 and 2.4).

Conclusion

The retained items of the rSAS targeted behaviours more than beliefs and results support the rSAS as a robust measure of apathy in people with chronic stroke.
How can risk of COVID-19 transmission be minimised in domiciliary care for older people: development, parameterisation and initial results of a simple mathematical model
Authors: Kiss István Z. , Blyuss Konstantin B. , Kyrychko Yuliya N. , Middleton Jo , Roland Daniel , Bertini Lavinia , Bogen-Johnston Leanne , Wood Wendy , Sharp Rebecca , Forder Julien , Cassell Jackie
Published: May 2021

This paper proposes and analyses a stochastic model for the spread of an infectious disease that is transmitted between clients and care workers in the UK domiciliary care setting. Interactions between clients and care workers are modelled using specially generated networks, with network parameters reflecting realistic patterns of care needs and visit allocation. These networks are then used to simulate and SEIR-type epidemic dynamics with different numbers of infectious and recovery stages. The results indicate that with the same overall capacity provided by care workers, the minimum peak proportion of infection, and the smallest overall size of infection are achieved for the highest proportion of overlap between visit allocation, i.e. when care workers have the highest chances of being allocated a visit to the same client they have visited before. An intuitive explanation of this is that while providing the required care coverage, maximising overlap in visit allocation reduces the possibility of an infectious care worker inadvertently spreading the infection to other clients. The model is quite generic and can be adapted to any particular directly transmitted infectious disease, such as, more recently, COVID-19, provided accurate estimates of disease parameters can be obtained from real data.
Circadian Regulation of Vertebrate Cone Photoreceptor Function
Authors: Zang Jingjing , Gesemann Matthias , Keim Jennifer , Samardzija Marijana , Grimm Christian , Neuhauss Stephan C.F.
Published: May 2021

Eukaryotes generally display a circadian rhythm as an adaption to the reoccurring day/night cycle. This is particularly true for visual physiology that is directly affected by changing light conditions. Here we investigate the influence of the circadian rhythm on the expression and function of visual transduction cascade regulators in diurnal zebrafish and nocturnal mice. We focused on regulators of shut-off kinetics such asrecoverins, arrestins, opsin kinases, andGTPase-accelerating proteinthat have direct effects on temporal vision. Transcript as well as protein levels of most analyzed genes show a robust circadian rhythm dependent regulation, which correlates with changes in photoresponse kinetics. Electroretinography demonstrates that photoresponse recovery in zebrafish is delayed in the evening and accelerated in the morning. This physiological rhythmicity is mirrored in visual behaviors, such as optokinetic and optomotor responses. Functional rhythmicity persists in continuous darkness, it is reversed by an inverted light cycle and disrupted by constant light. This is in line with our finding that orthologous gene transcripts from diurnal zebrafish and nocturnal mice are often expressed in an anti-phasic daily rhythm.
Targeting Integrated Stress Response by ISRIB combined with imatinib attenuates STAT5 signaling and eradicates therapy-resistant Chronic Myeloid Leukemia cells
Authors: Dudka Wioleta , Hoser Grażyna , Mondal Shamba S. , Turos-Korgul Laura , Swatler Julian , Kusio-Kobiałka Monika , Wołczyk Magdalena , Klejman Agata , Brewińska-Olchowik Marta , Kominek Agata , Wiech Milena , Machnicki Marcin M , Seferyńska Ilona , Stokłosa Tomasz , Piwocka Katarzyna
Published: May 2021

Integrated Stress Response (ISR) facilitates cellular adaptation to variable environmental conditions by reprogramming cellular response. Activation of ISR was reported in neurological disorders and solid tumours, but its function in hematological malignancies remains largely unknown. Previously we showed that ISR is activated in chronic myeloid leukemia (CML) CD34+ cells, and its activity correlates with disease progression and imatinib resistance. Here we demonstrate that inhibition of ISR by small molecule ISRIB, but not by PERK inhibitor GSK2656157, restores sensitivity to imatinib and eliminates CM Blast Crisis (BC) D34+ resistant cells. We found that in Patient Derived Xenograft (PDX) mouse model bearing CD34+ imatinib/dasatinib-resistant CML blasts withPTPN11gain-of-function mutation, combination of imatinib and ISRIB decreases leukemia engraftment. Furthermore, genes related to SGK3, RAS/RAF/MAPK, JAK2 and IFNγ pathways were downregulated upon combined treatment. Remarkably, we confirmed that ISRIB and imatinib combination decreases STAT5 phosphorylation and inhibits expression of STAT5-target genes responsible for proliferation, viability and stress response. Thus, our data point to a substantial effect of imatinib and ISRIB combination, that results in transcriptomic deregulation and eradication of imatinib-resistant cells. Our findings suggest such drug combination might improve therapeutic outcome of TKI-resistant leukemia patients exhibiting constitutive STAT5 activation.
Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting
Authors: Heyse Jasmine , Schattenberg Florian , Rubbens Peter , Müller Susann , Waegeman Willem , Boon Nico , Props Ruben
Published: May 2021

Microbiome management research and applications rely on temporally-resolved measurements of community composition. Current technologies to assess community composition either make use of cultivation or sequencing of genomic material, which can become time consuming and/or laborious in case high-throughput measurements are required. Here, using data from a shrimp hatchery as an economically relevant case study, we combined 16S rRNA gene amplicon sequencing and flow cytometry data to develop a computational workflow that allows the prediction of taxon abundances based on flow cytometry measurements. The first stage of our pipeline consists of a classifier to predict the presence or absence of the taxon of interest, with yields an average accuracy of 88.13±4.78 % across the top 50 OTUs of our dataset. In the second stage, this classifier was combined with a regression model to predict the relative abundances of the taxon of interest, which yields an average R2of 0.35±0.24 across the top 50 OTUs of our dataset. Application of the models on flow cytometry time series data showed that the generated models can predict the temporal dynamics of a large fraction of the investigated taxa. Using cell-sorting we validated that the model correctly associates taxa to regions in the cytometric fingerprint where they are detected using 16S rRNA gene amplicon sequencing. Finally, we applied the approach of our pipeline on two other datasets of microbial ecosystems. This pipeline represents an addition to the expanding toolbox for flow cytometry-based monitoring of bacterial communities and complements the current plating- and marker gene-based methods.

Importance

Monitoring of microbial community composition is crucial for both microbiome management research and applications. Existing technologies, such as plating and amplicon sequencing, can become laborious and expensive when high-throughput measurements are required. Over the recent years, flow cytometry-based measurements of community diversity have been shown to correlate well to those derived from 16S rRNA gene amplicon sequencing in several aquatic ecosystems, suggesting there is a link between the taxonomic community composition and phenotypic properties as derived through flow cytometry. Here, we further integrated 16S rRNA gene amplicon sequencing and flow cytometry survey data in order to construct models that enable the prediction of both the presence and the abundance of individual bacterial taxa in mixed communities using flow cytometric fingerprinting. The developed pipeline holds great potential to be integrated in routine monitoring schemes and early warning systems for biotechnological applications.
Detection of persistent SARS-CoV-2 IgG antibodies in oral mucosal fluid and upper respiratory tract specimens following COVID-19 mRNA vaccination
Authors: Mades Aubree , Chellamathu Prithivi , Lopez Lauren , Kojima Noah , MacMullan Melanie A. , Denny Nicholas , Angel Aaron N. , Casian Joseph G. , Brobeck Matthew , Nirema Nina , Klausner Jeffrey D , Turner Frederick , Slepnev Vladimir I. , Ibrayeva Albina
Published: May 2021

Previous studies have shown that mRNA COVID-19 vaccines are highly effective at preventing SAR-CoV-2 infection by generating an immune response, which in part produces SARS-CoV-2 IgG antibodies in serum. In this study, we hypothesized that COVID-19 vaccines may elicit production of SARS-CoV-2 IgG antibodies in the upper respiratory tract, such as in oral and nasal mucosal fluid. To test that hypothesis, we enrolled 114 participants within 3-7 days of receiving the first dose of the Moderna mRNA COVID-19 vaccine and collected oral mucosal fluid samples on days 5, 10, 15, and 20 after each vaccine dose. Of participants naive to SARS-CoV-2 (n = 89), 79 (85.4%) tested positive for SARS-CoV-2 IgG antibodies by time point 2 (10 days +/-2 days after first vaccine dose), and 100% tested positive for SARS-CoV-2 IgG by time point 3 (15 days +/-2 days after first vaccine dose). Additionally, we collected paired oral mucosal fluid and anterior nares samples from 10 participants who had received both vaccine doses. We found that participants had an average SARS-CoV-2 IgG antibody concentration of 2496.0 +/-2698.0ng/mL in nasal mucosal fluid versus 153.4 +/-141.0ng/mL in oral mucosal fluid. Here, we demonstrate detection and longitudinal persistence of SARS-CoV-2 IgG antibodies in upper respiratory tract specimens following COVID-19 mRNA vaccination.
Short-term effects of BNT162b2 mRNA COVID-19 vaccination on physiological measures: a prospective study
Authors: Gepner Yftach , Mofaz Merav , Oved Shay , Yechezkel Matan , Constantini Keren , Goldstein Nir , Shmueli Erez , Yamin Dan
Published: May 2021

Background

Clinical trial guidelines for assessing the safety of vaccines, including the FDA criteria, are primarily based on subjective, self-reported questionnaires. Despite the tremendous technological advances in recent years, objective, continuous assessment of physiological measures post-vaccination is rarely performed.

Methods

To evaluate the short-term effects of the BNT162b2 COVID-19 vaccine on physiological measures, we conducted a prospective observational study during the mass vaccination campaign in Israel. 160 individuals >18 years who were not previously found to be COVID-19 positive and who received the second dose of the COVID-19 vaccine between 1 January, 2021, and 13 March, 2021 were equipped with a chest-patch sensor and a dedicated mobile application. The chest-patch sensor continuously measured 13 physiological vitals one day before the inoculation (baseline), for four days: heart rate, blood oxygen saturation, respiratory rate, systolic and diastolic blood pressure, pulse pressure, mean arterial pressure, heart rate variability, stroke volume, cardiac output, cardiac index, systemic vascular resistance, and body temperature. The mobile application collected daily self-reported questionnaires starting one day before the inoculation, for 15 days on local and systemic reactions, sleep quality, stress levels, physical activity, and mood levels.

Findings

Within the first 48 hours post-vaccination, we identified significant changes (p-value <0.05) in nearly all 13 chest-patch indicators compared to their baseline levels. 48.5% (n=78) reported no local or systemic reaction. Nevertheless, we identified considerable changes in chest-patch indicators during the first 48 hours post-vaccination also in this group of presumably asymptomatic participants. Within three days from vaccination, these measures returned to baseline levels in both groups, further supporting the safety of the vaccine.

Interpretation

Our work underscores the importance of obtaining objective physiological data in addition to self-reported questionnaires when performing clinical trials, particularly in ones conducted in very short time frames.

Funding

The European Research Council (ERC) project #949850.
Relationships of diversity and evenness in adaptation strategies of the effect of protective coloration of animals
Authors: Bespalov Yu. , Kabalyants P. , Zuev S.
Published: May 2021

This study aims to investigate the relationship between the diversity and uniformity of the protective coloration of animals. The protective coloration of animals is the result of the formation of adaptation strategies. The aim of this study is to identify the colorimetric parameters that characterize the adaptive properties of the protective coloration of animals in relation to their natural habitat. The relevance of this study is related to the importance of the tasks of remote collection of information about various biological species; in particular, animals that carry dangerous infections. This is all the more important in light of the current epidemic problems facing humanity. The revealed colorimetric characteristics can be used to describe digital images and their further recognition. They can be classifying features in machine learning algorithms. We give an example of digital image processing of a duck (Anas platyrhynchos). The analysis of the distribution of the found colorimetric parameter makes it possible to identify the image segments corresponding to theAnas platyrhynchos. The results thus obtained are also of interest from the point of view of the problem of the adaptive role of the diversity of biological systems in relation to the problem of the mechanisms of functioning of the protective coloration of animals.
The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair
Authors: McCowan Jack , Kirkwood Phoebe M. , Fercoq Frédéric , T’Jonck Wouter , Mawer Connar M. , Cunningham Richard , Mirchandani Ananda S. , Hoy Anna , Jones Gareth-Rhys , Hansen Carsten G. , Hirani Nik , Jenkins Stephen J. , Henri Sandrine , Malissen Bernard , Walmsley Sarah R. , Dockrell David H. , Saunders Philippa T. K. , Carlin Leo M. , Bain Calum C.
Published: May 2021

Alveolar macrophages are the most abundant macrophages in the healthy lung where they play key roles in homeostasis and immune surveillance against air-borne pathogens. Tissue-specific differentiation and survival of alveolar macrophages relies on niche-derived factors, such as colony stimulating factor 2 (CSF-2) and transforming growth factor beta (TGF-β). However, the nature of the downstream molecular pathways that regulate the identity and function of alveolar macrophages and their response to injury remains poorly understood. Here, we identify that the transcriptional factor EGR2 is an evolutionarily conserved feature of lung alveolar macrophages and show that cell-intrinsic EGR2 is indispensable for the tissue-specific identity of alveolar macrophages. Mechanistically, we show that EGR2 is driven by TGF-β and CSF-2 in a PPAR-γ-dependent manner to control alveolar macrophage differentiation. Functionally, EGR2 was dispensable for lipid handling, but crucial for the effective elimination of the respiratory pathogenStreptococcus pneumoniae. Finally, we show that EGR2 is required for repopulation of the alveolar niche following sterile, bleomycin-induced lung injury and demonstrate that EGR2-dependent, monocyte-derived alveolar macrophages are vital for effective tissue repair following injury. Collectively, we demonstrate that EGR2 is an indispensable component of the transcriptional network controlling the identity and function of alveolar macrophages in health and disease.

One Sentence Summary

EGR2 controls alveolar macrophage function in health and disease
Reinforcement alone does not explain increased reproductive isolation in sympatry
Authors: Matute Daniel R. , Cooper Brandon S.
Published: May 2021

Comparative studies of reproductive isolation (RI) by Coyne and Orr (1, 2) and others indicate a significant role for reinforcing natural selection inDrosophilaspeciation. The reinforcement hypothesis predicts increased prezygotic, but not postzygotic, RI between sympatric species pairs in response to maladaptive hybridization. We revisit this hypothesis and others using additionalDrosophila, Lepidopteran, and toad(Bufo)data. In contrast to the predictions of reinforcement, we find increased premating and postzygotic RI between sympatricDrosophilaspecies, including between recently diverged species pairs, as defined by Coyne and Orr (1) and others (i.e.,DNei< 0.5). However, at slightly lower divergence thresholds increased postzygotic RI in sympatry is not statistically significant, while increased premating RI is, generally in agreement with the predictions of reinforcement. While premating data are unavailable, postzygotic RI is also increased between sympatric Lepidopteran and toad (Bufo) species. We find only modest support for “concordant asymmetries” in premating and postzygotic RI between sympatricDrosophila, described by others as uniquely supporting reinforcement. Finally, the proportion of geographic range overlap shared by species is positively associated with the magnitude of premating RI as predicted by reinforcement, but it is also positively associated with postzygotic RI, which cannot be explained by reinforcement. Taken together, our results demonstrate that comparisons of premating and postzygotic RI in sympatry depend greatly on divergence time, and suggest that fusion, extinction, and/or other mechanisms must combine with reinforcement to generate these patterns.

Significance Statement

Understanding mechanisms underlying the origin of species remains a central goal of biology. By combining laboratory estimates of premating and postzygotic reproductive isolation (RI) with phylogenetic hypotheses, geographic range data, and genetic divergence estimates, the fundamental meta-analyses of Coyne and Orr provided compelling support that reinforcement contributes significantly toDrosophilaspeciation. Using additionalDrosophiladata, we demonstrate increased premating and postzygotic RI in sympatry. Postzygotic RI is also increased in sympatry between Lepidopteran and toad species. We also find only modest support for patterns previously described as uniquely supporting reinforcement. Together, our analyses demonstrate that comparisons of premating and postzygotic RI depend on divergence time, and suggest that fusion, extinction, and/or other mechanisms combine with reinforcement to produce these patterns.
Classical macrophage polarisation is limited by human β-defensin-3 via an autocrine IL-4 dependent process
Authors: Candela Maria E. , Allsop David J.P. , Carter Roderick N. , Semple Fiona , Kilanowski Fiona , Webb Sheila , Taggart David , Mullan Henry J.W , McHugh Brian J. , Dockrell David H. , Davidson Donald J. , Allen Judith E. , Jenkins Stephen J. , Morton Nicholas M. , Dorin Julia R.
Published: May 2021

Human β-defensin 3 (HBD3), is an anti-microbial host-defence peptide, that can rapidly enter macrophages to modulate TLR4 responses to lipopolysaccharide. However, the molecular mechanisms by which HBD3 exerts this anti-inflammatory influence remain unclear. Here, we show mice deleted for the orthologue of HBD3 have an increased acute lipopolysaccharide responsein vivo. Furthermore, we found that HBD3 limited the response of macrophages to classical activation, and contemporaneously drove expression of IL-4. An increase in markers of alternative activation, and a change in metabolic flux was also observed. Consistent with these results, HBD3 enhanced the IL-4 mediated polarisation of naïve macrophages. Finally, we demonstrate that the ability of HBD3 to limit macrophage classical activation requires IL-4Rα. These data reveal a previously unrecognised role for HBD3 in influencing the polarisation state of macrophages to enable a state conducive for repair and resolution.

SYNOPSIS

The anti-microbial host-defence peptide, Human β-defensin 3 (HBD3), is shown here to modulate the inflammatory response to classical activation by promoting alternative activation through IL-4Rα, to enable a state conducive for repair and resolution.

Knockout mice for the orthologous gene for HBD3, demonstrate increased acute lipopolysaccharide inflammatory response.

HBD3 limited the classical activation of macrophages polarised with LPS/IFNγ and drove expression of IL-4. Cells also displayed increase in alternative activation markers and promotion of oxidative phosphorylation.

HBD3 enhanced the IL-4-mediated activation of naïve macrophages.

The ability of HBD3 to limit macrophage classical activation and contemporaneously promote alternative activation required IL-4Rα.
Cortical granularity shapes the organization of afferent paths to the amygdala and its striatal targets in nonhuman primate
Authors: McHale AC , Cho YT , Fudge JL
Published: May 2021

The prefrontal cortex (PFC) and insula, amygdala, and striatum form interconnected networks that drive motivated behaviors. We previously found a connectional trend in which granularity of the ventromedial and orbital PFC/insula predicted connections to the amygdala, and also the breadth of amygdalo-striatal efferents, including projections beyond the ’classic’ ventral striatum. To further interrogate connectional relationships among the cortex, amygdala, and striatum, and to further define the ’limbic (amygdala-recipient) striatum’, we conducted tract tracing studies in two cohorts ofMacaques(Male n = 14, Female n = 1). We focused on the cortico-amygdalo-striatal (indirect) and cortico-‘limbic’ striatal (direct) paths originating in the entire PFC and insula. Larger data sets and a quantitative approach revealed ’cortical rules’ in which cortical granularity predicts the complexity and location of projections toboththe basal nucleus of the amygdala and striatum. Remarkably, projections from ’cortical-like’ basal nucleus to the striatum followed similar patterns. In both ’direct’ and ’indirect’ paths to the ’limbic’ striatum, agranular cortices formed a ’foundational’, broad projection, and were joined by inputs from progressively more differentiated cortices. In amygdalo-striatal paths, the ventral basal nucleus was the ‘foundational’ input, with progressively more dorsal basal nucleus regions gradually adding inputs as the ’limbic striatum’ extended caudally. Together, the ‘indirect’ and ‘direct’ paths followed consistent principles in which cortical granularity dictated the strength and complexity of projections at their targets. Cluster analyses independently confirmed these connectional trends, and also highlighted connectional features that predicted termination in specific subregions of the basal nucleus and ’limbic’ striatum.

Significance Statement

The ’limbic system’ broadly refers to brain circuits that coordinate emotional responses. Here, we investigate circuits of the amygdala, which are involved in coding the emotional value of external cues, and their influence on the striatum. Regions of prefrontal cortex and insula form gradients of overlapping inputs to the amygdala’s basal nucleus, which feed forward to the striatum. Direct cortical inputs to these ’amygdala-recipient’ striatal areas are surprisingly organized according to similar principles, but subtly shift from the classic ventral striatum to the caudal ventral striatum. Together, these distinct subsystems—cortico-amygdala-striatal circuits and direct cortico-striatal circuits— provide substantial opportunity for different levels of internal, sensory, and external experiences to be integrated within the striatum, a major motor-behavioral interface.
Capturing the nature of events and event context using Hierarchical Event Descriptors (HED)
Authors: Robbins Kay , Truong Dung , Appelhoff Stefan , Delorme Arnaud , Makeig Scott
Published: May 2021

Event-related data analysis plays a central role in EEG and MEG (MEEG) and other neuroimaging modalities such as fMRI. Choices about which events to report and how to annotate their full natures significantly influence the value, reliability, and reproducibility of neuroimaging datasets for further analysis and meta- ormega-analysis. A powerful annotation strategy using the new third-generation formulation of the Hierarchical Event Descriptors (HED) framework and tools (hedtags.org) combines robust event description with details of experiment design and metadata in a human-readable as well as machine-actionable form, making event annotation relevant to the full range of neuroimaging and other time series data. This paper considers the event design and annotation process using as a case study the well-known multi-subject, multimodal dataset of Wakeman and Henson made available by its authors as a Brain Imaging Data Structure (BIDS) dataset (bids.neuroimaging.io). We propose a set of best practices and guidelines for event annotation integrated in a natural way into the BIDS metadata file architecture, examine the impact of event design decisions, and provide a working example of organizing events in MEEG and other neuroimaging data. We demonstrate how annotations using HED can document events occurring during neuroimaging experiments as well as their interrelationships, providing machine-actionable annotation enabling automated within- and across-experiment analysis and comparisons. We discuss the evolution of HED software tools and have made an accompanying HED-annotated BIDS-formatted edition of the MEEG data of the Wakeman and Henson dataset (openneuro.org, ds003645).
An intramolecular scrambling path controlled by a gatekeeper in Xkr8 phospholipid scramblase
Authors: Sakuragi Takaharu , Kanai Ryuta , Tsutsumi Akihisa , Narita Hirotaka , Onishi Eriko , Miyazaki Takuya , Baba Takeshi , Nakagawa Atsushi , Kikkawa Masahide , Toyoshima Chikashi , Nagata Shigekazu
Published: May 2021

Xkr8-Basigin is a phospholipid scramblase at plasma membranes that is activated by kinase or caspase. We investigated its structure at a resolution of 3.8Å. Its membrane-spanning region had a cuboid-like structure stabilized by salt bridges between hydrophilic residues in helices in the lipid layer. The molecule carried phosphatidylcholine in a cleft on the surface that may function as an entry site for phospholipids. Five charged residues placed from top to bottom inside the molecule were essential for providing a path for scrambling phospholipids. A tryptophan residue was present at the extracellular end of the pathway and its mutation made the Xkr8-Basigin complex constitutively active, indicating its function as a gatekeeper. The structure of Xkr8-Basigin provides novel insights into the molecular mechanisms underlying phospholipid scrambling.
Ser/Thr phospho-regulation by PknB and Stp mediates bacterial quiescence and antibiotic persistence inStaphylococcus aureus
Authors: Huemer Markus , Shambat Srikanth Mairpady , Pereira Sandro , Van Gestel Lies , Bergada-Pijuan Judith , Gómez-Mejia Alejandro , Chang Chun-Chi , Vulin Clement , Bär Julian , Dworkin Jonathan , Zinkernagel Annelies S.
Published: May 2021

Staphylococcus aureuscolonizes 30 to 50% of healthy adults and can cause a variety of diseases, ranging from superficial to life-threatening invasive infections such as bacteraemia and endocarditis. Often, these infections are chronic and difficult-to-treat despite adequate antibiotic therapy. Most antibiotics act on metabolically active bacteria in order to eradicate them. Thus, bacteria with minimized energy consumption resulting in metabolic quiescence, have increased tolerance to antibiotics. The most energy intensive process in cells – protein synthesis – is attenuated in bacteria entering into quiescence. Eukaryote-like serine/threonine kinases (STKs) and phosphatases (STPs) can fine-tune essential cellular processes, thereby enabling bacteria to quickly respond to environmental changes and to modulate quiescence. Here, we show that deletion of the only annotated functional STP, named Stp, inS. aureusleads to increased bacterial lag-phase and phenotypic heterogeneity under different stress challenges, including acidic pH, intracellular milieu andin vivoabscess environment. This growth delay was associated with reduced intracellular ATP levels and increased antibiotic persistence. Using phosphopeptide enrichment and mass spectrometry-based proteomics, we identified possible targets of Ser/Thr phosphorylation that regulate cellular processes and bacterial growth, such as ribosomal proteins including the essential translation elongation factor EF-G. Finally, we show that acid stress leads to a reduced translational activity in thestpdeletion mutant indicating metabolic quiescence correlating with increased antibiotic persistence.

One-sentence summary

Phospho-regulation mediates quiescence and antibiotic persistence inStaphylococcus aureus.
Heat Shock Factor 1 (HSF1) as a new tethering factor for ESR1 supporting its action in breast cancer
Authors: Vydra Natalia , Janus Patryk , Kuś Paweł , Stokowy Tomasz , Mrowiec Katarzyna , Toma-Jonik Agnieszka , Krzywon Aleksandra , Cortez Alexander Jorge , Wojtaś Bartosz , Gielniewski Bartłomiej , Jaksik Roman , Kimmel Marek , Widłak Wiesława
Published: May 2021

Heat shock factor 1 (HSF1), a key regulator of transcriptional responses to proteotoxic stress, was recently linked to estrogen (E2) signaling through ESR1. We found that an HSF1 deficiency could lead to the inhibition of the mitogenic action of E2 in breast cancer cells. The stimulatory effect of E2 on the transcriptome is weaker in HSF1-deficient cells, in part due to the higher basal expression of E2-dependent genes, which correlates with the enhanced binding of unliganded ESR1 to chromatin. HSF1 and ESR1 can cooperate directly in E2-stimulated regulation of transcription, and HSF1 potentiates the action of ESR1 through a mechanism involving chromatin reorganization. Analyses of data from the TCGA database indicate that HSF1 increases the transcriptome diversity in ER-positive breast cancer and can enhance the genomic action of ESR1. Moreover,ESR1andHSF1are only prognostic when analyzed together (the worst prognosis for ER−/HSF1highcancers).
A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2
Authors: Richard Damien , Shaw Liam P , Lanfear Rob , Corbett-Detig Russell , Hinrichs Angie , McBroome Jakob , Turakhia Yatish , Acman Mislav , Owen Christopher J , Tan Cedric CS , van Dorp Lucy , Balloux François
Published: May 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and spread globally to cause the COVID-19 pandemic. Despite the constant accumulation of genetic variation in the SARS-CoV-2 population, there was little evidence for the emergence of significantly more transmissible lineages in the first half of 2020. Starting around November 2020, several more contagious and possibly more virulent ‘Variants of Concern’ (VoCs) were reported in various regions of the world. These VoCs share some mutations and deletions that haven arisen recurrently in distinct genetic backgrounds. Here, we build on our previous work modelling the association of mutations to SARS-CoV-2 transmissibility and characterise the contribution of individual recurrent mutations and deletions to estimated viral transmissibility. We then assess how patterns of estimated transmissibility in all SARS-CoV-2 clades have varied over the course of the COVID-19 pandemic by summing transmissibility estimates for all individual mutations carried by any sequenced genome analysed. Such an approach recovers the Delta variant (21A) as the most transmissible clade currently in circulation, followed by the Alpha variant (20I). By assessing transmissibility over the time of sampling, we observe a tendency for estimated transmissibility within clades to slightly decrease over time in most clades. Although subtle, this pattern is consistent with the expectation of a decay in transmissibility in mainly non-recombining lineages caused by the accumulation of weakly deleterious mutations. SARS-CoV-2 remains a highly transmissible pathogen, though such a trend could conceivably play a role in the turnover of different global viral clades observed over the pandemic so far.

Caveats

This work is not about the severity of disease. We do not analyse the severity of disease. We do not present any evidence that SARS-CoV-2 has decreased in severity.

Lineage replacement dynamics are affected by many factors. The trend we recover for a decrease in inferred transmissibility of a clade over time is a small effect. We caution against over-interpretation. This result would not affect the management of the SARS-CoV-2 pandemic: for example, we make no claims about any impact on the efficacy of particular non-pharmaceutical interventions (NPIs).

Our phylogeny-based method to infer changes in estimated transmissibility due to recurrent mutations and deletions makes a number of simplifying assumptions. These may not all be valid. The consistent trend for the slight decrease we report might be due to an as-yet-unidentified systematic bias.
Discovery of the fastest myosin, its amino acid sequence, and structural features
Authors: Haraguchi Takeshi , Tamanaha Masanori , Suzuki Kano , Yoshimura Kohei , Imi Takuma , Tominaga Motoki , Sakayama Hidetoshi , Nishiyama Tomoaki , Murata Takeshi , Ito Kohji
Published: May 2021

Cytoplasmic streaming with extremely high velocity (~70 μm s−1) occurs in cells of the characean algae (Chara). Because cytoplasmic streaming is caused by organelle-associated myosin XI sliding along actin filaments, it has been suggested that a myosin XI, which has a velocity of 70 μm s−1, the fastest myosin measured so far, exists inCharacells. However, the previously clonedChara corallinamyosin XI (CcXI) moved actin filaments at a velocity of around 20 μm s−1, suggesting that an unknown myosin XI with a velocity of 70 μm s−1may be present inChara. Recently, the genome sequence ofChara brauniihas been published, revealing that this alga has four myosin XI genes. In the work reported in this paper, we cloned these four myosin XIs (CbXI-1, 2, 3, and 4) and measured their velocities. While the velocities ofCbXI-3 andCbXI-4 were similar to that ofCcXI, the velocities ofCbXI-1 andCbXI-2 were estimated to be 73 and 66 μm s−1, respectively, suggesting thatCbXI-1 andCbXI-2 are the main contributors to cytoplasmic streaming inCharacells and showing thatCbXI-1 is the fastest myosin yet found. We also report the first atomic structure (2.8 Å resolution) of myosin XI using X-ray crystallography. Based on this crystal structure and the recently published cryo-EM structure of acto-myosin XI at low resolution (4.3 Å), it appears that the actin-binding region contributes to the fast movement ofCharamyosin XI. Mutation experiments of actin-binding surface loop 2 support this hypothesis.

Significance statement

It has been suggested for more than 50 years that the fastest myosin in the biological world, with a velocity of 70 μm s−1, exists in the algaCharabecause cytoplasmic streaming with a velocity of 70 μm s−1occurs inCharacells. However, a myosin with that velocity has not yet been identified. In this work, we succeeded in cloning a myosin XI with a velocity of 73 μm s−1, the fastest myosin so far measured. We also successfully crystallized myosin XI for the first time. Structural analyses and mutation experiments suggest that the central regions that define the fast movement ofCharamyosin XI are the actin-binding sites.
A murine model of the human CREBRFR457Qobesity-risk variant does not influence energy or glucose homeostasis in response to nutritional stress
Authors: Kanshana Jitendra S. , Mattila Polly E. , Ewing Michael C. , Wood Ashlee N. , Schoiswohl Gabriele , Meyer Anna C. , Kowalski Aneta , Rosenthal Samantha L. , Gingras Sebastien , Kaufman Brett A. , Lu Ray , Weeks Daniel E. , McGarvey Stephen T. , Minster Ryan L. , Hawley Nicola L. , Kershaw Erin E.
Published: May 2021

Obesity and diabetes have strong heritable components, yet the genetic contributions to these diseases remain largely unexplained. In humans, a missense variant in Creb3 regulatory factor (CREBRF) [rs373863828 (p.Arg457Gln); CREBRFR457Q] is strongly associated with increased odds of obesity but decreased odds of diabetes. Although virtually nothing is known about CREBRF’s mechanism of action, emerging evidence implicates it in the adaptive transcriptional response to nutritional stress downstream of TORC1. The objectives of this study were to generate a murine model with knockin of the orthologous variant in mice (CREBRFR458Q) and to test the hypothesis that this CREBRF variant promotes obesity and protects against diabetes by regulating energy and glucose homeostasis downstream of TORC1. To test this hypothesis, we performed extensive phenotypic analysis of CREBRFR458Qknockin mice at baseline and in response to acute (fasting/refeeding), chronic (low- and high-fat diet feeding), and extreme (prolonged fasting) nutritional stress as well as with pharmacological TORC1 inhibition. The results demonstrate that the murine CREBRFR458Qmodel of the human CREBRFR457Qvariant does not influence energy/glucose homeostasis in response to these interventions. Alternative preclinical models and/or studies in humans will be required to decipher the mechanisms linking this variant to human health and disease.