bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast computation of principal components of genomic similarity matrices
Authors: Hahn Georg , Lutz Sharon M. , Hecker Julian , Prokopenko Dmitry , Cho Michael H. , Silverman Edwin K. , Weiss Scott T. , Lange Christoph
Published: October 2022

The computation of a similarity measure for genomic data, for instance using the (genomic) covariance matrix, the Jaccard matrix, or the genomic relationship matrix (GRM), is a standard tool in computational genetics. The principal components of such matrices are routinely used to correct for biases in, for instance, linear regressions. However, the calculation of both a similarity matrix and its singular value decomposition (SVD) are computationally intensive. The contribution of this article is threefold. First, we demonstrate that the calculation of three matrices (the genomic covariance matrix, the weighted Jaccard matrix, and the genomic relationship matrix) can be reformulated in a unified way which allows for an exact, faster SVD computation. An exception is the Jaccard matrix, which does not have a structure applicable for the fast SVD computation. An exact algorithm is proposed to compute the principal components of the genomic covariance, weighted Jaccard, and genomic relationship matrices. The algorithm is adapted from an existing randomized SVD algorithm and ensures that all computations are carried out in sparse matrix algebra. Second, an approximate Jaccard matrix is introduced to which the fast SVD computation is applicable. Third, we establish guaranteed theoretical bounds on the distance (in L2 norm and angle) between the principal components of the Jaccard matrix and the ones of our proposed approximation, thus putting the proposed Jaccard approximation on a solid mathematical foundation. We illustrate all computations on both simulated data and data of the 1000 Genome Project, showing that the approximation error is very low in practice.
A SI3-σ arch stabilizes cyanobacteria transcription initiation complex
Authors: Shen Liqiang , Lai Giorgio , You Linlin , Shi Jing , Wu Xiaoxian , Puiu Maria , Gu Zhanxi , Feng Yu , Yuzenkova Yulia , Zhang Yu
Published: October 2022

Multi-subunit RNA polymerases (RNAPs) associate with initiation factors (σ in bacteria) to start transcription. The σ factors are responsible for recognizing and unwinding promoter DNA in all bacterial RNAPs. Here, we report two cryo-EM structures of cyanobacterial transcription initiation complexes at near-atomic resolutions. The structures show that cyanobacterial RNAP forms an ‘SI3-σ’ arch interaction between domain 2 of σA (σ2) and the sequence insertion 3 (SI3) in the mobile catalytic domain Trigger Loop (TL). The ‘SI3-σ’ arch facilitates transcription initiation from promoters of different classes through sealing the main cleft and thereby stabilizing RNAP-promoter DNA open complex. Disruption of the ‘SI3-σ’ arch disturbs cyanobacteria growth and stress response. Our study reports the structure of cyanobacterial RNAP and unique mechanism for its transcription initiation. Our data suggest functional plasticity of SI3 and provide foundation for further research into cyanobacteria and chloroplasts transcription.
Arabidopsis CPK6 regulates drought tolerance under high nitrogen by the phosphorylation of NRT1.1
Authors: Ma Qijun , Zhao Chunyan , Hu Shi , Zuo Kaijing
Published: October 2022

Nitrogen is an essential macronutrient for plant growth and development, and its availability to some extent is regulated by drought stress. Calcium-dependent protein kinases (CPKs) are a unique family of Ca2+ sensors with diverse functions in nitrogen and drought signaling pathways. However, which and how CPKs involve in the crosstalk between drought stress and nitrogen transportation remains largely unknown. Here we identified the drought tolerant function of Arabidopsis CPK6 under high nitrogen condition. The CPK6 expression is induced by the treatments of ABA and drought. The mutant cpk6 is insensitive to the ABA treatment, but sensitive to drought only under high nitrogen condition. CPK6 interacts with and phosphorylates the Thr571 in NRT1.1 protein, and thus represses its NO3− transporting activity under drought stress. Taken together, we showed the evidences that CPK6 regulates Arabidopsis drought tolerance through the phosphorylation of NRT1.1, and that enriches the knowledge of nitrogen uptake in plants during drought stress.
A Multi-Granular Stacked Regression for Forecasting Long-Term Demand in Emergency Departments
Authors: James Charlotte , Wood Richard , Denholm Rachel
Published: October 2022

Background

In the United Kingdom, Emergency Departments (EDs) are under significant pressure due to an ever-increasing number of attendances. Understanding how the capacity of other urgent care services and the health of a population may influence ED attendances is imperative for commissioners and policy makers to develop long-term strategies for reducing this pressure and improving quality and safety.

Methods

We developed a novel Multi-Granular Stacked Regression (MGSR) model using publicly available data to predict future mean monthly ED attendances within Clinical Commissioning Group regions in England. The MGSR combines measures of population health and health service capacity in other related settings. We assessed model performance using the R-squared statistic, measuring variance explained, and the Mean Absolute Percentage Error (MAPE), measuring forecasting accuracy. We used the MGSR to forecast ED demand over a 4-year period under hypothetical scenarios where service capacity is increased, or population health is improved.

Results

Measures of service capacity explain 41 ± 4% of the variance in monthly ED attendances and measures of population health explain 61 ± 25%. The MGSR leads to an overall improvement in performance, with an R-squared of 0.75 ± 0.03 and MAPE of 4% when forecasting mean monthly ED attendances per CCG. Using the MGSR to forecast long-term demand under different scenarios, we found improving population health would reduce peak ED attendances per CCG by approximately 600 per month after 2 years.

Conclusions

Combining models of population health and wider urgent care service capacity for predicting monthly ED attendances leads to an improved performance compared to each model individually. Policies designed to improve population health will reduce ED attendances and enhance quality and safety in the long-term.
Spatial and hierarchical Bayesian analysis to identify factors associated with caesarean delivery use in Ethiopia: evidence from national population and health facility data
Authors: Tegegne Teketo Kassaw , Chojenta Catherine , Getachew Theodros , Smith Roger , Loxton Deborah
Published: October 2022

Background

Caesarean section has a significant role in reducing maternal and neonatal mortality. A linked analysis of population and health facility data is valuable to map and identify caesarean section use and associated factors. This study aimed to identify geographic variation and associated factors of caesarean delivery in Ethiopia.

Method

Linked data analysis of the 2016 Ethiopia Demographic and Health Survey (EDHS) and the 2014 Ethiopian Service Provision Assessment Plus (ESPA+) survey was performed. Spatial analysis was conducted to identify geographic variations and factors associated with caesarean delivery. Hierarchical Bayesian analysis was also performed to identify factors associated with caesarean delivery using the SAS MCMC procedure.

Results

Women’s age and education, household wealth, parity, antenatal care (ANC) visits, and distance to caesarean section facility were associated with caesarean delivery use. Women who had ≥4 ANC visits were 4.67 (95% Credible Interval (CrI): 2.17, 9.43) times more likely to have caesarean delivery compared to those who had no ANC visits. Women who had education and were from rich households were also 2.80 (95% CrI: 1.83, 4.19) and 1.80 (95% CrI: 1.08, 2.84) times more likely to have caesarean deliveries relative to women who had no education and were from poor households, respectively. A one-kilometer increase in distance to a caesarean section facility was associated with an 88% reduction in the odds of caesarean delivery (Adjusted Odds Ratio (AOR) = 0.12, 95% CrI: 0.01, 0.78). Hotspots of high caesarean section rates were observed in Addis Ababa, Dire Dawa, and the Harari region. In addition, women’s age at first childbirth and ≥4 ANC visits showed significant spatially varying relations between caesarean delivery use across Ethiopia.

Conclusion

Caesarean section is a lifesaving procedure, and it is essential to narrow disparities to reduce maternal and neonatal mortality and avoid unnecessary procedures.
Impact of the COVID-19 Vaccination Program on Case Incidence, Emergency Department Visits, and Hospital Admissions among Children Aged 5–17 Years during the Delta and Omicron Periods —United States, December 2020 to April 2022
Authors: Topf Katherine G , Sheppard Michael , Marx Grace E. , Wiegand Ryan E , Link-Gelles Ruth , Binder Alison M , Cool Andrea J , Lyons B. Casey , Park Sohyun , Fast Hannah E , Presnetsov Arthur , Azondekon G Roseric , Soetebier Karl A , Adjemian Jennifer , Barbour Kamil E
Published: October 2022

Background

In the United States, national ecological studies suggest a positive impact of COVID-19 vaccination coverage on outcomes in adults. However, the national impact of the vaccination program on COVID-19 in children remains unknown. To determine the association of COVID-19 vaccination with U.S. case incidence, emergency department visits, and hospital admissions for pediatric populations during the Delta and Omicron periods.

Methods

We conducted an ecological analysis among children aged 5–17 and compared incidence rate ratios (RRs) of COVID-19 cases, emergency department visits, and hospital admissions by pediatric vaccine coverage, with jurisdictions in the highest vaccine coverage quartile as the reference.

Results

RRs comparing states with lowest pediatric vaccination coverage to the highest pediatric vaccination coverage were 2.00 and 0.64 for cases, 2.96 and 1.11 for emergency department visits, and 2.76 and 1.01 for hospital admissions among all children during the Delta and Omicron periods, respectively. During the 3-week peak period of the Omicron wave, only children aged 12–15 and 16–17 years in the states with the lowest versus highest coverage, had a significantly higher rate of emergency department visits (RR=1.39 and RR=1.34, respectively).

Conclusions

COVID-19 vaccines were associated with lower case incidence, emergency department visits and hospital admissions among children during the Delta period but the association was weaker during the Omicron period. Pediatric COVID-19 vaccination should be promoted as part of a program to decrease COVID-19 impact among children; however, vaccine effectiveness may be limited when available vaccines do not match circulating viral variants.
Barriers and facilitators to anti-retroviral therapy adherence among adolescents aged 10 to 19 years living with HIV in sub-Saharan Africa: A mixed-methods systematic review
Authors: Hlophe Londiwe D. , Tamuzi Jacques L. , Shumba Constance S. , Nyasulu Peter S.
Published: October 2022

Background

Human Immunodeficiency Virus (HIV) significantly affects adolescents globally, with the sub-Saharan Africa (SSA) reporting a high burden of the disease. HIV testing, treatment, and retention to care are low among adolescents. We conducted a mixed-method systematic review to assess anti-retroviral therapy (ART) adherence; barriers and facilitators to ART adherence and ART outcomes among adolescents living with HIV and on ART in sub-Saharan Africa.

Methods

We conducted searches in four scientific databases for studies conducted between 2010 and March 2022 to identify relevant primary studies. Studies were screened against inclusion criteria and assessed for quality, and data was extracted. Meta-analysis of rates and odd ratios was used to plot the quantitative studies and meta-synthesis summarized the evidence from qualitative studies.

Results

A total of 10 431 studies were identified and screened against the inclusion/ exclusion criteria. Sixty-six studies met the inclusion criteria (41 quantitative, 16 qualitative, and 9 mixed-methods study designs). Fifty-three thousand two hundred and seventeen (53 217) adolescents (52 319 in quantitative studies and 899 in qualitative studies) were included in the review. Thirteen support focused interventions for improved ART adherence were identified from quantitative studies. The plotted results from the meta-analysis found an ART adherence rate of 65% (95%CI 56-74), viral load suppression was 55% (95%CI 46-64), un-suppressed viral load rate of 41% (95%CI 32-50), and loss to follow up of 17% (95%CI 10-24) among adolescents. Meta-synthesis found six themes of barriers to ART (social, patient-based, economic, health system-based, therapy-based, and cultural barriers) in both the qualitative and quantitative studies, and three themes of facilitators to ART were also identified (social support, counselling, and ART education and secrecy or confidentiality) from qualitative studies.

Conclusion

ART adherence remains low among adolescents in SSA despite multiple interventions implemented to improve ART adherence. The low adherence rate may hinder the attainment of the UNAIDS 2030 targets. Additionally, various barriers to ART adherence due to lack of support have been reported among this age group. However, interventions aimed at improving social support, educating, and counselling adolescents may improve and sustain ART adherence.

Systematic review registration

PROSPERO CRD42021284891
Mitigating the Severity of COVID-19 Illness in the Primary Care Patient Population through Early Identification and Close Monitoring of Underlying Comorbidities
Authors: Parikh Payal , Greenberg Patricia , Halpert Shmuel , Abrishami Allison , Rabizadeh Liora , Shayefar Hannah , Tetelbaun Lauren , Friedman Dovid , Kaminetzky Jeffrey
Published: October 2022

Purpose

Prior studies have identified risk factors which prognosticate severity of SARS-CoV-2 illness among hospitalized patients. Since the majority of patients first present to ambulatory care sites, there is a need to identify early predictors of disease progression in this population.

Methods

This retrospective cohort study investigated the impact of underlying comorbid conditions on SARS-CoV-2 infection severity in the ambulatory setting. All patients who presented to a single federally qualified health center (FQHC) between March-May 2020 with a positive SARS-CoV-2 test were reviewed for inclusion. Patient demographics, symptomology, prior medical history, and outcomes were collected.

Results

301 patients were included, with nearly equal numbers of patients with (n=151) and without (n=150) underlying comorbidities. Overall, 269 patients (89%) had a mild outcome and 32 patients (11%) had a severe outcome. Advanced age (OR: 9.4 [95% CI: 3.4-27.4], p < 0.001) and male gender (OR: 3.2 [95% CI: 1.2-9.8], p = 0.02) were significant predictors of severe outcomes. Additionally, every obesity category (1: BMI = 30.0–34.9; 2: BMI = 35–39.9; 3: BMI = 40.0+) was associated with more severe outcomes compared to non-obese (OR: 3.5, p = 0.05; OR: 5.2, p = 0.03; OR: 13.9, p = 0.01). Compared to an HbA1C < 6, an HbA1C of 7.1–8.0 showed a clinically significant association.

Conclusion

SARS-CoV-2 severity can be prognosticated in the ambulatory population by the presence and severity of pre-existing comorbidities. Early identification and risk stratification of these comorbidities will allow clinicians to develop plans for closer monitoring to prevent severe illness.
Health care workers’ self-perceived infection risk and COVID-19 vaccine uptake: a mixed methods study
Authors: Nyamuryekung’e Kasusu , Amour Maryam , Mboya Innocent , Ndumwa Harrieth , Kengia James , Njiro Belinda J , Mhamilawa Lwidiko , Shayo Elizabeth , Ngalesoni Frida , Kapologwe Ntuli , Kalolo Albino , Metta Emmy , Msuya Sia
Published: October 2022

Background

Vaccination is the most cost-effective way of preventing COVID-19 disease although there was a considerable delay in its institution in Tanzania. This study aimed to assess healthcare workers’ (HCWs) self-perceived infection risk and uptake of COVID-19 vaccines.

Methods

A concurrent embedded, mixed methods research design was utilized to collect data among HCWs in seven Tanzanian regions. Quantitative data was collected using a validated, pre-piloted, interviewer administered questionnaire whereas in-depth interviews and focus group discussions gathered qualitative data. Descriptive analyses were performed, and chi-square test used to test for associations across categories. Thematic analysis was used to analyze the qualitative data.

Results

A total of 1,386 HCWs responded to the quantitative tool, 26 participated in the in-depth interviews and 74 in the focus-group discussions. About half of the HCW (53.6%) reported to have been vaccinated and three quarters (75.5%) self-perceived to be at a high risk of acquiring COVID-19 infection. Participants perceived that the nature of their work and the working environment in the health facilities increases their risk to infection. Limited availability and use of personal protective equipment was reported to elevate the perceived risks to the infection. Respondents belonging in the oldest age group and from low and mid-level health care facilities had higher proportions with a high-risk perception of acquiring COVID-19 infection compared to their counterparts.

Conclusions

Only about half of the HCWs reported to be vaccinated albeit the majority recounted higher perception of risk to contracting COVID-19 due to their working environment, including limited availability and use of personal protective equipment. Efforts to address heightened perceived-risks should include improving the working environment, availability of PPEs and continue updating HCWs on the benefits of COVID-19 vaccine to limit their risks to the infection and consequent transmission to their patients and public.
Towards the biogeography of butyrate-producing bacteria
Authors: Brame Joel E , Liddicoat Craig , Abbott Catherine A , Edwards Robert A , Robinson Jake M , Gauthier Nicolas E , Breed Martin F
Published: October 2022

Aim

Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, few (if any) studies have examined the macroecological influences on their large-scale biogeographical distribution. Here we aimed to characterise their global biogeography together with key explanatory climatic, geographic, and physicochemical variables.

Location

Global, and the Australian continent

Time period

2005-2020

Major taxa studied

Butyrate-producing bacteria

Methods

We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n=13,078) and Australia-wide soil 16S rRNA (n=1,331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations.

Results

The highest BPC scores were found in anoxic and fermentative environments, including the human and non-human animal gut, and in some plant-soil systems. Within plant-soil systems, roots and rhizospheres had the highest BPC scores. Among soil samples, geographic and climatic variables had the strongest overall influence on BPC scores, with human influence also making key contributions. Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas, and sites with moderate-to-high soil iron concentrations.

Main conclusions

Abundances of butyrate-producing bacteria in outdoor soils follow complex ecological patterns influenced by geography, climate, soil chemistry, and hydrological fluctuations. Human population density and soil iron also play substantial roles, and their effects are dependent on a combination of ecological variables. These new biogeographical insights further our understanding of the global ecology patterns of butyrate-producing bacteria, with implications for emerging microbially-focussed ecological and human health policies.
Triac treatment prevents neurodevelopmental and locomotor impairments in thyroid hormone transporter Mct8/Oatp1c1 deficient mice
Authors: Chen Jiesi , Salveridou Eva , Liebmann Lutz , Sundaram Sivaraj M. , Doycheva Denica , Markova Boyka , Hübner Christian A. , Boelen Anita , Visser W. Edward , Heuer Heike , Mayerl Steffen
Published: October 2022

Background

Patients with inactive thyroid hormone (TH) transporter MCT8 display intellectual disability due to an insufficient TH transport and action in the CNS. As a therapeutic strategy, application of Triac (3, 5, 3’-triiodothyroacetic acid) and Ditpa (3, 5 -diiodo-thyropropionic acid) have been proposed as both thyromimetic compounds are not dependent on MCT8 for cellular entry. Here, we tested and directly compared the thyromimetic actions of Triac versus Ditpa in Mct8/Oatp1c1 double knockout mice (Dko), a mouse model for human MCT8 deficiency.

Methods

Newborn Dko mice were daily injected during the first three postnatal weeks with either Triac (50 ng/g or 400 ng/g) or Ditpa (400 ng/g or 4000 ng/g) and compared with Wt and Dko mice receiving saline injections. A second cohort of Dko mice was daily injected with Triac (400 ng/g) only between postnatal week 3 and 6. Thyromimetic effects in the CNS and peripheral tissues were monitored at different postnatal time points by immunofluorescence stainings for neural marker proteins, in situ hybridization and quantitative real time PCR. Locomotor performance was assessed in rotarod and hanging wire test. Acute brain slices of Triac treated Dko mice and their respective controls were used for electrophysiological recordings.

Results

Only Dko mice injected with Triac (400 ng/g) during the first three postnatal weeks showed normalized myelination, differentiation of cortical GABAergic interneurons as well as locomotor performance. Electrophysiological recordings revealed an increased frequencies of cortical spontaneous miniature inhibitory postsynaptic currents in Dko mice and a normalization of this parameter in Triac treated Dko mice. In comparison, treatment of Dko mice with Ditpa at 4000 ng/g during the first three postnatal weeks resulted in normal myelination and cerebellar development but was less effective in restoring neuronal parameters and locomotor function. Finally, Triac was more potent than Ditpa in suppressingTrhandTshbexpression, respectively, and exerts stronger thyromimetic effects in liver and kidneys.

Conclusions

In newborn Dko deficient mice, Triac is highly effective and more efficient than Ditpa in promoting CNS maturation and function. Yet, Triac treatment needs to be initiated directly after birth to achieve the most beneficial effects.
Ritualistic use of ayahuasca enhances a shared functional connectome identity with others
Authors: Mallaroni Pablo , Mason Natasha L. , Kloft Lilian , Reckweg Johannes T. , van Oorsouw Kim , Toennes Stefan W. , Tolle Hanna M. , Amico Enrico , Ramaekers Johannes G.
Published: October 2022

The knowledge that brain functional connectomes are both unique and reliable has enabled behaviourally relevant inferences at a subject level. However, it is unknown whether such “fingerprints” persist under altered states of consciousness. Ayahuasca is a potent serotonergic psychedelic which elicits a widespread dysregulation of functional connectivity. Used communally in religious ceremonies, its shared use may highlight relevant novel interactions between mental state and FC inherency. Using 7T fMRI, we assessed resting-state static and dynamic FCs for 21 Santo Daime members after collective ayahuasca intake in an acute, within-subject study. Here, connectome fingerprinting revealed a shared functional space, accompanied by a spatiotemporal reallocation of keypoint edges. Importantly, we show that interindividual differences in higher-order FCs motifs are relevant to experiential phenotypes, given that they can predict perceptual drug effects. Collectively, our findings offer an example as to how individualised connectivity markers can be used to trace a subject’s functional connectome across altered states of consciousness.
Integrated transcriptome and proteome analysis in human brain organoids reveals posttranscriptional regulation of ribosomal genes
Authors: Sidhaye Jaydeep , Trepte Philipp , Sepke Natalie , Novatchkova Maria , Schutzbier Michael , Dürnberger Gerhard , Mechtler Karl , Knoblich Jürgen A.
Published: October 2022

During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. Investigations of the transcriptome and epigenome have revealed important gene regulatory networks underlying this crucial developmental event. However, the post-transcriptional control of gene expression and protein abundance during human corticogenesis remains poorly understood. We addressed this issue by using human telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons and performed cell class and developmental stage-specific transcriptome and proteome analysis. Integrating the two datasets revealed modules of gene expression during human corticogenesis. Investigation of one such module uncovered mTOR-mediated regulation of translation of the 5’TOP element-enriched translation machinery in early progenitor cells. We show that in early progenitors partial inhibition of the translation of ribosomal genes prevents precocious translation of differentiation markers. Overall, our multiomics approach reveals novel posttranscriptional regulatory mechanisms crucial for the fidelity of cortical development.
S-nitrosylation of Aux/IAA protein represses auxin signaling
Authors: Jing Hongwei , Yang Xiaolu , Feng Jian , Zhang Jian , Strader Lucia C. , Zuo Jianru
Published: October 2022

Auxin plays crucial roles in nearly every aspect of plant growth and development. Auxin signaling activation is mediated through degradation of Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) family. Nitric oxide (NO) regulates diverse cellular bioactivities through S-nitrosylation of target protein at specific cysteine residues. NO-auxin interplay has an important role in regulation plant growth. However, little is known about the molecular mechanism of how NO effects Aux/IAA proteins stability. Here we show that NO negatively regulates the IAA17 protein stability to repress auxin signaling. We found that NO directly inhibits IAA17 protein degradation. S-nitrosylation of IAA17 at Cys-70 represses the TIR-IAA17 co-receptor interaction to attenuate auxin responsiveness. Our data suggest a model in which S-nitrosylation of IAA17 at Cys-70 negatively regulates auxin signaling to effect plant development, providing a mechanism for redox-phytohormones networks.
Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius
Authors: Gambelli Lavinia , McLaren Mathew , Conners Rebecca , Sanders Kelly , Gaines Matthew C. , Clark Lewis , Gold Vicki , Kattnig Daniel , Sikora Mateusz , Hanus Cyril , Isupov Michail N. , Daum Bertram
Published: October 2022

Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single particle cryo electron microscopy (cryoEM), cryo electron tomography (cryoET) and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesize that jackknife-like conformational changes, as well as pH-induced alterations in the surface charge of SlaA, play important roles in S-layer assembly.
Sex-specific acute cerebrovascular response to photothrombotic stroke in mice requires rho-kinase
Authors: Raman-Nair Joanna , Cron Gregory , McLeod Kathleen , Lacoste Baptiste
Published: October 2022

With high energy consumption and low energy storage, the brain is highly reliant on continuous cerebral blood flow (CBF) that delivers substrates to maintain proper function, which is compromised after a stroke. The current study explores the overlapping roles played by two important modulators of cerebrovascular tone, rho-kinase (ROCK) and endogenous sex hormones, in the acute CBF responses to a photothrombotic (PT) model of ischemic stroke in ROCK2+/- mice and wild-type (WT) littermates. To remove endogenous hormones, male mice were gonadectomized and female mice were ovariectomized, whereas control (“intact”) animals received a sham surgery prior to stroke induction. Intact WT males showed a delayed drop in CBF compared to intact WT females, where maximal CBF drop was observed 48 hours following stroke. Gonadectomy in males did not alter this response, however ovariectomy in females produced a “male-like” response. Intact ROCK2+/- males also showed such phenotypic response, which was not altered by gonadectomy. Alternatively, intact ROCK2+/- females showed a striking difference in CBF values compared to intact WT females, where they displayed higher CBF values immediately post-stroke and also showed a maximal CBF drop 48 hours post-stroke, which was not altered by ovariectomy. Overall, there is a marked sex difference in acute CBF responses to PT stroke, which appears to be mediated by endogenous female sex hormones and ROCK2. This study reveals important sex-differences and the involvement of ROCK2 in acute CBF responses to PT stroke in mice.

Significance Statement

There are very few mechanistic investigations on disparities between sexes in post-stroke CBF outcome. Rho-kinase, an important regulator of vascular tone, has only been explored in males in terms of its modulation of CBF following stroke. Both rho-kinase and endogenous female sex hormones have a converging role on the regulation of endothelial nitric oxide synthase (eNOS), an important modulator of vascular tone. Rho-kinase is thought to elicit its neuroprotective effects against ischemic stroke through eNOS, however this has never been investigated in both sexes. Elucidating the cellular and molecular bases of sex differences in cerebrovascular pathophysiology is vital for understanding the origins of stroke outcomes, and for designing novel therapeutic strategies to promote functional recovery in both women and men.
An alternative mechanism for skeletal muscle dysfunction in long-term post-viral lung disease
Authors: Martin Ryan A. , Keeler Shamus P. , Wu Kangyun , Shearon William J. , Patel Devin , Hoang My , Hoffmann Christy M. , Hughes Michael E. , Holtzman Michael J.
Published: October 2022

Chronic lung disease is often accompanied by disabling extrapulmonary symptoms, notably skeletal muscle dysfunction and atrophy. Moreover, the severity of respiratory symptoms correlates with decreased muscle mass and in turn lowered physical activity and survival rates. Previous models of muscle atrophy in chronic lung disease often modeled COPD and relied on cigarette smoke exposure and LPS-stimulation, but these conditions independently affect skeletal muscle even without accompanying lung disease. Moreover, there is an emerging and pressing need to understand the extrapulmonary manifestations of long-term post-viral lung disease (PVLD) as found in Covid-19. Here, we examine the development of skeletal muscle dysfunction in the setting of chronic pulmonary disease using a mouse model of PVLD caused by infection due to the natural pathogen Sendai virus. We identify a significant decrease in myofiber size when PVLD is maximal at 49 d after infection. We find no change in the relative types of myofibers, but the greatest decrease in fiber size is localized to fast-twitch type IIB myofibers based on myosin heavy chain immunostaining. Remarkably, all biomarkers of myocyte protein synthesis and degradation (total RNA, ribosomal abundance, and ubiquitin-proteasome expression) were stable throughout the acute infectious illness and chronic post-viral disease process. Together, the results demonstrate a distinct pattern of skeletal muscle dysfunction in a mouse model of long-term PVLD. The findings thereby provide new insight into prolonged limitations in exercise capacity in patients with chronic lung disease after viral infections and perhaps other types of lung injury.
Limited roles of Piezo mechanosensing channels in articular cartilage development and osteoarthritis progression
Authors: Young Cameron , Kobayashi Tatsuya
Published: October 2022

Osteoarthritis (OA) is a prevalent disease characterized by degeneration of the joint and pain. Mechanical stress plays a central role in OA development. It is hypothesized that cells in the OA joints produce OA-promoting molecules upon mechanical stress, and therefore, the mechanosensing systems are a theoretical target for OA treatment. Piezo mechanosensing channels mediate high-level mechanical stress in chondrocytes and have been suggested to play an important role during OA progression. To test this hypothesis, we ablated Piezo1 and Piezo2 in joint tissues using Gdf5-Cre transgenic mice [Piezo1 and 2 doubly conditional knockout (cKO) mice, cKO mice]. cKO mice showed normal development of knee joints. Both control and cKO mice developed modest to severe OA 12 weeks after the induction of OA, although some cKO mice showed milder OA. We did not find significant differences in pain in mice or gene expression after fluid flow stress in primary cells between control and cKO. Our data demonstrate the limited role of Piezo channels in joint development and OA progression.

Objective

To investigate the role of Piezo1 and Piezo 2 in surgically induced osteoarthritis (OA) in mice.

Design

Male conditional knockout (cKO) mice missing Piezo1 and Piezo2 in the joint via Gdf5-Cre transgenic mice were induced post-traumatic osteoarthritis (OA) by destabilization of the medial meniscus (DMM) of the right knee joint at 12 weeks of age. The severity of OA was assessed at 24 weeks of age using a modified Osteoarthritis Research Society International (OARSI) scoring system. OA-associated pain was evaluated by static weight bearing analysis at 4, 8, and 12 weeks post-operation. Additionally, articular chondrocytes isolated from cKO mice were exposed to fluid flow shear stress (FFSS) to evaluate the expression of OA-associated genes.

Results

Mice with conditional deletion of Piezo1 and Piezo 2 showed normal joint development with no overt histological changes in the knee joint at 12 weeks and 24 weeks. DMM surgery induced moderate to severe OA in both control and cKO mice, although a few cKO mice showed milder OA. Pain assessment by static weight-bearing analysis suggested Piezo ablation in the joint has no beneficial effects on pain. FFSS increased the expression of OA-related genes both in control and cKO mice to similar extents.

Conclusion

Piezo1 and Piezo2 are not essential for normal joint development. Genetic ablation of Piezo channels did not confer evident protective effects on OA progression in mice. In vitro data suggests that different mechanotransducers other than Piezo channels mediate FFSS in mechanical stress-induced gene expression.
Rap1 coordinates cell-cell adhesion and cytoskeletal reorganization to drive collective cell migration in vivo
Authors: Rothenberg Katheryn E. , Chen Yujun , McDonald Jocelyn , Fernandez-Gonzalez Rodrigo
Published: October 2022

Collective cell movements contribute to tissue development and repair, and spread metastatic disease. In epithelia, cohesive cell movements require reorganization of adherens junctions and the actomyosin cytoskeleton. However, the mechanisms that coordinate cell-cell adhesion and cytoskeletal remodelling during collective cell migration in vivo are unclear. We investigated the mechanisms of collective cell migration during wound healing in the Drosophila embryonic epidermis. Upon wounding, the cells adjacent to the wound internalize cell-cell adhesion molecules and polarize actin and the motor protein myosin II to form a supracellular cable around the wound that coordinates cell movements. The cable anchors at former tricellular junctions (TCJs) along the wound edge, and TCJs are reinforced during wound closure. We found that the small GTPase Rap1 was both necessary and sufficient for rapid wound repair. Rap1 promoted actomyosin polarization to the wound edge and E-cadherin accumulation at TCJs. Using embryos expressing a mutant form of the Rap1 effector Canoe/Afadin that cannot bind Rap1, we found that Rap1 signals through Canoe for adherens junction remodelling, but not for actomyosin cable assembly. Rap1 was necessary and sufficient for RhoA/Rho1 activation at the wound edge. Consistent with this, the RhoGEF Ephexin localized to the wound edge in a Rap1-dependent manner, and Ephexin was necessary for myosin polarization and rapid wound repair, but not for E-cadherin redistribution. Together, our data show that Rap1 coordinates the molecular rearrangements that drive embryonic wound healing and independently drives actomyosin cable assembly through Ephexin-Rho1, and E-cadherin redistribution through Canoe, thus enabling rapid collective cell migration in vivo.
A Canine Model of Chronic Ischemic Heart Failure
Authors: Khan Muhammad S. , Smego Douglas , Ishidoya Yuki , Hirahara Annie M. , Offei Emmanuel , Castillo Sofia R. , Gharbia Omar , Palatinus Joseph A. , Krueger Lauren , Hong TingTing , Hoareau Guillaume L. , Ranjan Ravi , Selzman Craig , Shaw Robin , Dosdall Derek J.
Published: October 2022

Background

There is a paucity of novel therapeutics for chronic heart failure (HF). Preclinical large animal models of chronic HF are crucial to translating fundamental discoveries. Canine models of ischemic cardiomyopathy are frequently utilized but are severely limited by competing needs to both induce sufficient muscle injury which results in an appropriately severe degree of left ventricular dysfunction yet to also minimize early mortality.

Methods

Twenty-eight healthy adult dogs (30±4 kg, 15/28 male) underwent thoracotomy procedures followed by one of three types of left anterior descending (LAD) coronary artery ligations: Simple LAD (proximal and distal LAD ligation), LAD and Lateral (proximal and distal LAD, distal first diagonal, and proximal first obtuse marginal), and Total LAD Devascularization (TLD including the proximal and distal LAD, proximal aspects of the first, second, and third diagonals, and proximal aspects of first and second epicardial right ventricular branches of the LAD). Invasive and non-invasive hemodynamics were followed until attainment of chronic severe HF, which was achieved when left ventricular ejection fraction (LVEF) was <40% and N-terminal prohormone B-type Natriuretic peptide (NT-proBNP) >900 pmol/L, both for two consecutive measurements.

Results

Overall post-ligation early mortality (within 48 h of coronary ligation) was 18% (n=5/28), and the overall survival rate at 5 weeks post-ligation was 68% (n=19/28). At post-ligation week 1, LVEF was acutely reduced in all animals, from 54±4 to 38±1%, p<0.001. Beyond week 1, systolic function recovered over 3-4 weeks and then slowly declined as the left ventricle dilated and both systolic and diastolic function worsened. The magnitude of the initial decline in LVEF predicted ultimate HF development. Dogs with Simple LAD and LAD plus Lateral had excellent and limited survival at 48 hours (100% and 47%, respectively), yet the second group more likely developed chronic HF at 9 – 14 weeks (50% versus 57%, respectively). Dogs with TLD had both improved survival at 48 hours (90%) and excellent development of chronic HF (100%).

Conclusions

By focusing on the LAD only and limiting collateral flow to it by ligating all side branches, optimal survival and attainment of chronic ischemic HF can be achieved in the canine heart.
Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus
Authors: Heffel Matthew G. , Zhou Jingtian , Zhang Yi , Lee Dong-Sung , Hou Kangcheng , Alonso Oier Pastor , Abuhanna Kevin , Schmitt Anthony D. , Li Terence , Haeussler Maximilian , Wick Brittney , Zhang Martin Jinye , Xie Fangming , Ziffra Ryan S. , Mukamel Eran A. , Eskin Eleazar , Pasaniuc Bogdan , Ecker Joseph R. , Dixon Jesse , Nowakowski Tomasz J , Paredes Mercedes F. , Luo Chongyuan
Published: October 2022

The human frontal cortex and hippocampus play critical roles in learning and cognition. We investigated the epigenomic and 3D chromatin conformational reorganization during the development of the frontal cortex and hippocampus, using more than 53,000 joint single-nucleus profiles of chromatin conformation and DNA methylation (sn-m3C-seq). The remodeling of DNA methylation predominantly occurs during late-gestational to early-infant development and is temporally separated from chromatin conformation dynamics. Neurons have a unique Domain-Dominant chromatin conformation that is different from the Compartment-Dominant conformation of glial cells and non-brain tissues. We reconstructed the regulatory programs of cell-type differentiation and found putatively causal common variants for schizophrenia strongly overlap with chromatin loop-connected, cell-type-specific regulatory regions. Our data demonstrate that single-cell 3D-regulome is an effective approach for dissecting neuropsychiatric risk loci.
Horizontally transferred genes as RNA interference targets for aphid and whitefly control
Authors: Feng Honglin , Chen Wenbo , Hussain Sonia , Shakir Sara , Tzin Vered , Adegbayi Femi , Ugine Todd , Fei Zhangjun , Jander Georg
Published: October 2022

RNA interference (RNAi)-based technologies are starting to be commercialized as a new approach for agricultural pest control. Horizontally transferred genes (HTGs), which have been transferred into insect genomes from viruses, bacteria, fungi, or plants, are attractive targets for RNAi-mediated pest control. HTGs are often unique to a specific insect family or even genus, making it unlikely that RNAi constructs targeting such genes will have negative effects on ladybugs, lacewings, and other beneficial predatory insect species. In this study, we sequenced the genome of a red, tobacco-adapted isolate ofMyzus persicae(green peach aphid) and bioinformaticaly identified 30 HTGs. We then used plant-mediated virus-induced gene silencing (VIGS) to show that several HTGs of bacterial and plant origin are important for aphid growth and/or survival. Silencing the expression of fungal HTGs did not affect aphid survivorship, but decreased aphid reproduction. Importantly, although there was uptake of plant-expressed RNA byCoccinella septempunctata(seven-spotted ladybugs) via the aphids that they consumed, we did not observe negative effects on ladybugs from aphid-targeted VIGS constructs. In other experiments, we targeted fiveBemisia tabaci(whitefly) HTGs using VIGS and demonstrated that knockdown of some of these genes affected whitefly survival. As functional HTGs have been identified in the genomes of numerous pest species, we propose that these HTGs should be explored further as efficient and safe targets for control of insect pests using plant-mediated RNA interference.
Altered GC- and AT-biased genotypes ofOphiocordyceps sinensisin the stromal fertile portions and ascospores of naturalCordyceps sinensis
Authors: Li Yu-Ling , Gao Ling , Yao Yi-Sang , Li Xiu-Zhang , Wu Zi-Mei , Tan Ning-Zhi , Luo Zhou-Qing , Xie Wei-Dong , Wu Jian-Yong , Zhu Jia-Shi
Published: October 2022

Objective

To examine multiple genotypes ofOphiocordyceps sinensisin a semi-quantitative manner in the stromal fertile portion (SFP) densely covered with numerous ascocarps and ascospores of naturalCordyceps sinensisand to outline the dynamic alterations of the coexistingO. sinensisgenotypes in different developmental phases.

Methods

MatureCordyceps sinensisspecimens were harvested and continuously cultivated in our laboratory (altitude 2,254 m). The SFPs (with ascocarps) and fully and semi-ejected ascospores were collected for histological and molecular examinations. Biochip-based single nucleotide polymorphism (SNP) MALDI-TOF mass spectrometry (MS) was used to genotype multipleO. sinensismutants in the SFPs and ascospores.

Results

Microscopic analysis revealed distinct morphologies of the SFPs (with ascocarps) before and after ascospore ejection and SFP of developmental failure, which, along with the fully and semi-ejected ascospores, were subjected to SNP MS genotyping analysis. Mass spectra showed the coexistence of GC- and AT-biased genotypes ofO. sinensisthat were genetically and phylogenetically distinct in the SFPs before and after ejection and of developmental failure and in fully and semi-ejected ascospores. The intensity ratios of MS peaks were dynamically altered in the SFPs and the fully and semi-ejected ascospores. Mass spectra also showed transversion mutation alleles of unknown upstream and downstream sequences with altered intensities in the SFPs and ascospores. Genotype #5 of AT-biased Cluster-A maintained a high intensity in all SFPs and ascospores. An MS peak with a high intensity containing AT-biased Genotypes #6 and #15 in pre-ejection SFPs was significantly attenuated after ascospore ejection. The abundance of Genotypes #5–6 and #16 of AT-biased Cluster-A was differentially altered in the fully and semi-ejected ascospores that were collected from the sameCordyceps sinensisspecimens.

Conclusion

MultipleO. sinensisgenotypes coexisted in different combinations with altered abundances in the SFPs prior to and after ejection, the SFP of developmental failure, and the two types of ascospores ofCordyceps sinensis, demonstrating their genomic independence. Metagenomic fungal members present in different combinations and with dynamic alterations play symbiotic roles in different compartments of naturalCordyceps sinensis.
Tight control of the APP-Mint1 interaction in regulating amyloid production
Authors: Henry Shawna M. , Bartling Christian R. O. , Strømgaard Kristian , Beffert Uwe , Ho Angela
Published: October 2022

Generation of amyloid-beta (Aβ) peptides through the proteolytic processing of the amyloid precursor protein (APP) is one pathogenic event in Alzheimer’s disease (AD). APP is a type I transmembrane protein and endocytosis of APP mediated by the endocytic YENPTY sequence is a key step in Aβ generation. We and others have found that Mints, a family of cytosolic adaptor proteins, directly binds to the YENPTY motif of APP via phosphotyrosine binding (PTB) domain of Mints, facilitates APP trafficking and processing. We also show mutation of Tyr633 of Mint1 (Mint1Y633A) enhances APP binding and processing. Now, we created a low-affinity Mint1 mutant that targets two conserved residues, Tyr549 and Phe610 (Mint1Y549A/F610A), that reduced APP binding. Here, we investigate how perturbing the APP-Mint1 interaction alters APP and Mint1 cellular dynamics as well as Mint1’s interaction with its other binding partners. We show that Mint1Y633A increased binding affinity specifically for APP and presenilin1, enhanced APP endocytosis, and Aβ secretion in primary neurons. Conversely, Mint1Y549A/F610A exhibited reduced APP affinity and Aβ secretion. In fact, the effect of Mint1Y549A/F610A on Aβ release was greater compared to knocking down all three Mint proteins, supporting targeting APP-Mint1 interaction as a potential AD therapeutic.