bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphatases are predicted to govern prolactin-mediated JAK–STAT signaling in pancreatic beta cells
Authors: Simoni Ariella D , Huber Holly A , Georgia Senta K , Finley Stacey D
Published: April 2022

Patients with diabetes are unable to produce a sufficient amount of insulin to properly regulate their blood glucose levels. One potential method of treating diabetes is to increase the number of insulin-secreting beta cells in the pancreas to enhance insulin secretion. It is known that during pregnancy, pancreatic beta cells proliferate in response to the pregnancy hormone, prolactin (PRL). Leveraging this proliferative response to PRL may be a strategy to restore endogenous insulin production for patients with diabetes. To investigate this potential treatment, we previously developed a computational model to represent the PRL-mediated JAK–STAT signaling pathway in pancreatic beta cells. Here, we applied the model to identify the importance of particular signaling proteins in shaping the response of a population of beta cells. We simulated a population of 10 000 heterogeneous cells with varying initial protein concentrations responding to PRL stimulation. We used partial least squares regression to analyze the significance and role of each of the varied protein concentrations in producing the response of the cell. Our regression models predict that the concentrations of the cytosolic and nuclear phosphatases strongly influence the response of the cell. The model also predicts that increasing PRL receptor strengthens negative feedback mediated by the inhibitor suppressor of cytokine signaling. These findings reveal biological targets that can potentially be used to modulate the proliferation of pancreatic beta cells to enhance insulin secretion and beta cell regeneration in the context of diabetes.
Evaluating the impact of neurosurgical rotation experience in Africa on the interest and perception of medical students towards a career in neurosurgery: a protocol for a continental, cross-sectional study
Authors: Ooi Setthasorn Zhi Yang , Dada Olaoluwa Ezekiel , Bukenya George William , Kenfack Yves Jordan , Le Chi , Ohonba Efosa , Adeyemo Emmanuel , Narain Kapil , Awad Ahmed Khaled , Barrie Umaru , Sichimba Dawin , Ogunfolaji Oloruntoba , Kitonga Lilian Mwende , Oriaku Adaeze Juanita , Bamimore Michael Abayomi , Okor Douglas Emeka , Rominiyi Ola
Published: April 2022

Introduction

Africa has the second highest neurosurgical workforce deficit globally. Despite the many recent advancements in increasing neurosurgical access in Africa, published reports have shown that the vast majority of undergraduate students have little or no exposure to neurosurgery. The lack of exposure may pose a challenge in reducing the neurosurgical workforce deficit, which is one of the long-term strategies of tackling the unmet burden of disease. Students may also miss the opportunity to appreciate the specialty and its demands as well as nurture their interest in the field. This study aims to assess the impact of a neurosurgical rotation during medical school in shaping the perception and interest of students towards a career in neurosurgery.

Methods

The cross-sectional study will be conducted through the dissemination of a self-administered e-survey hosted on Google Forms from 21st February 2021 to 20th March 2021. The survey will contain five-point Likert scale, multiple-choice and free-text questions. The structured questionnaire will have four sections with 27 items: (i) socio-demographic background, (ii) neurosurgical experience, (iii) perception towards a neurosurgical career and (iv) interest in a neurosurgical career. All consenting medical students in African medical schools who are in their clinical years (defined as fourth to sixth years or higher years of study) will be eligible. Odds ratios and their 95% confidence intervals, Wilcoxon rank-sum test, Welch t-test and adjusted logistic regression models will be used to test for associations between independent and dependent variables. Statistical significance will be accepted at P < 0.05.
Tobacco Smoking and Risk of SARS-CoV-2 Infection and Disease Severity Among Adults in an Integrated Healthcare System in California
Authors: Young-Wolff Kelly C , Slama Natalie , Alexeeff Stacey E , Sakoda Lori C , Fogelberg Renee , Myers Laura C , Campbell Cynthia I , Adams Alyce S , Prochaska Judith J
Published: April 2022

Introduction

The relationship between tobacco smoking status and SARS-CoV-2 infection and coronavirus disease 2019 (COVID-19) severity is highly debated. We conducted a retrospective cohort study of >2.4 million adults in a large healthcare system to evaluate whether smoking is associated with SARS-CoV-2 infection and disease severity.

Aims and Methods

This retrospective cohort study of 2,427,293 adults in KPNC from March 5, 2020 (baseline) to December 31, 2020 (pre-vaccine) included smoking status (current, former, never), socio-demographics, and comorbidities from the electronic health record. SARS-CoV-2 infection (identified by a positive PCR test) and COVID-19 severity (hospitalization, ICU admission or death ≤ 30 days of COVID-19 diagnosis) were estimated in time-to-event analyses using Cox proportional hazard regression models adjusting for covariates. Secondary analyses examined COVID-19 severity among patients with COVID-19 using logistic regression.

Results

During the study, 44,270 patients had SARS-CoV-2 infection. Current smoking was associated with lower adjusted rates of SARS-CoV-2 infection (aHR = 0.64 95% CI: 0.61–0.67), COVID-19-related hospitalization (aHR = 0.48 95% CI: 0.40–0.58), ICU admission (aHR = 0.62 95% CI: 0.42–0.87), and death (aHR = 0.52 95% CI: 0.27–0.89) than never-smoking. Former smoking was associated with a lower adjusted rate of SARS-CoV-2 infection (aHR = 0.96 95% CI: 0.94–0.99) and higher adjusted rates of hospitalization (aHR = 1.10 95% CI: 1.03–1.08) and death (aHR = 1.32 95% CI: 1.11–1.56) than never-smoking. Logistic regression analyses among patients with COVID-19 found lower odds of hospitalization for current versus never-smoking and higher odds of hospitalization and death for former versus never-smoking.

Conclusions

In the largest US study to date on smoking and COVID-19, current and former smoking showed lower risk of SARS-CoV-2 infection than never-smoking, while a history of smoking was associated with higher risk of severe COVID-19.

Implications

In this cohort study of 2.4 million adults, adjusting for socio-demographics and medical comorbidities, current tobacco smoking was associated with a lower risk of both SARS-CoV-2 infection and severe COVID-19 illness compared to never-smoking. A history of smoking was associated with a slightly lower risk of SARS-CoV-2 infection and a modestly higher risk of severe COVID-19 illness compared to never-smoking. The lower observed COVID-19 risk for current versus never-smoking deserves further investigation. Results support prioritizing individuals with smoking-related comorbidities for vaccine outreach and treatments as they become available.
Time to Blood Culture Positivity: An Independent Predictor of Mortality in Streptococcus Pyogenes Bacteremia
Authors: Bläckberg Anna , Svedevall Stina , Lundberg Katrina , Nilson Bo , Kahn Fredrik , Rasmussen Magnus
Published: April 2022

Background

Streptococcus pyogenes bacteremia is a severe condition with high mortality. Time to blood culture positivity (TTP) is known to predict the outcome in bacteremia with other pathogens. This study aimed to determine the association between TTP and outcome in S pyogenes bacteremia.

Methods

This retrospective observational cohort study comprised adults with S pyogenes bacteremia, identified through the laboratory database between 2015 and 2018, in the Region of Skåne, Sweden. Correlations between TTP and outcomes were investigated. Primary outcome was death within 30 days, and secondary outcomes were presence of sepsis or disease deterioration within the first 48 hours.

Results

A total of 347 episodes of S pyogenes bacteremia were identified, of which 61 were excluded, resulting in 286 included episodes. Median TTP was 10.4 (interquartile range, 8.4–11.4) hours. Thirty-day mortality was 10%. Median TTP was shorter in patients who died within 30 days compared to survivors (8.6 vs 10.4 hours; P < .001). In a multivariable logistic regression, shorter TTP was associated with 30-day mortality when adjusting for age, Charlson Comorbidity Index, and focus of infection (odds ratio, 3.7 [95% confidence interval, 1.2–11.3]; P = .02). There was no statistically significant difference in TTP between patients with sepsis within 48 hours and those who did not have sepsis. Additionally, there was no statistically significant difference in TTP between patients with disease deterioration compared to those who did not deteriorate.

Conclusions

Knowledge on TTP might be a tool to determine the prognosis of a given patient with S pyogenes bacteremia.
An overview of international genetic evaluations of show jumping in sport horses
Authors: Doyle Jennifer L , Carroll Christopher J , Corbally Alison F , Fahey Alan G
Published: April 2022

The breeding of sport horses to compete in the Olympic disciplines of show jumping, eventing, and dressage is fast becoming a global industry with the increased use of reproductive technologies, including artificial insemination and embryo transfer. Reproductive technologies have facilitated the dissemination of genetics from elite horses across multiple countries and breeds as breeders are no longer limited by location. Due to this increased level of crossbreeding, there is an increased need for estimated breeding values (EBVs) for sport horse performance that can be compared across breeds and countries. However, the implementation of across-breed or across-country genetic evaluations has been limited by the differences in each studbook’s individual breeding programs and genetic evaluations. Consequently, the aim of this review was to compare the genetic evaluations for show jumping of sport horse studbooks worldwide. The top sport horse studbooks in the world according to the World Breeding Federation for Sport Horses Studbook Rankings 2019 were contacted by email to request information on their current breeding programs and genetic evaluations. Twenty-six of the 51 studbooks contacted replied to this request but only 18 of these studbooks conducted their own genetic evaluations or were part of a larger genetic evaluation in their country of origin. The other eight studbooks were not involved in genetic evaluations at present but expressed an interest in the implementation of such in the future. Overall, many differences were identified among the genetic evaluations of each studbook or each country. The definition of show jumping performance differed within each evaluation and the methods and models utilized also differed. Despite some stallions and mares being registered in multiple studbooks or having progeny in multiple studbooks, these differences make comparison of EBVs across studbooks difficult. Further transparency and collaboration of sport horse studbooks with organizations such as Interstallion, will be essential to facilitate any future implementation of international genetic evaluations for show jumping performance.
Feedlot pens with greenhouse roofs improve beef cattle performance in temperate weather
Authors: Hidalgo Jorge , García Muñiz José G , Cesarani Alberto , Larios Neon , Atzori Alberto S , Sánchez Fernando , Espino Marco , Gorocica Milton , Salcedo Roberto , Gonzalez John
Published: April 2022

Muddy pens can negatively affect welfare and performance of feedlot beef cattle. In some regions with temperate weather, plastic greenhouse covers, above the entire pens are used to fatten cattle in a clean and dry environment. The objective of this research was to investigate effects of greenhouse roofed pens on beef cattle feedlot performance in temperate weather. Data were collected from a feedlot located in Central Mexico between 2016 and 2019. The study included 1,062 closeouts of pens with 68,305 crossbred bulls fed in pens with or without a greenhouse roof. Feeding ranged from 82 to 210 d, depending on the initial weight of cattle, which ranged from 255 to 511 kg. For each pen, average daily dry matter intake (DMI; kg of DMI·animal−1·d−1), average daily gain (ADG, kg·animal−1·d−1), and feed efficiency (G:F, ADG/DMI) were measured. Factorial analyses were performed to test the interaction and main effects of initial weight grouping (light, medium, and heavy), roof, and season as fixed effects, and year as a random effect. None of the three-way interactions were significant (P > 0.51). There was no initial weight grouping × roof interactions for DMI and ADG (P > 0.31). There was (P = 0.03) an initial weight grouping × roof interaction for G:F, as pens of all initial weight groups had greater (P < 0.01) G:F in pens with greenhouse roof than its counterpart in pens without greenhouse roof, but the advantage was greater for pens with light cattle (0.178 vs. 0.166; P < 0.01). There was no initial weight grouping × season interactions for all variables (P > 0.39). There was no roof × season interaction for DMI (P = 0.47), but there were interactions for ADG and G:F (P < 0.01). The ADG was not different (P > 0.13) during summer and autumn based on the roofing system, but pens with greenhouse roofs had greater ADG during spring (1.70 vs. 1.61) and winter (1.68 vs. 1.64; P ≤ 0.01). The G:F was greater (P < 0.01) in all seasons for pens with a greenhouse roof, with the most prominent advantage during spring (0.173 vs. 0.160). There were main effects for cattle initial weight grouping and roof for all variables (P < 0.01). Season affected DMI and G:F (P < 0.01). Pens with greenhouse roofs had decreased DMI (9.70 vs. 9.86), greater ADG (1.67 vs. 1.63), and increased G:F (0.173 vs. 0.166) compared to pens without greenhouse roofs (P < 0.01). Pens with greenhouse roofs in feedlots located in temperate regions positively affect beef cattle performance.
Demonstration of antibodies against SARS-CoV-2, neutralizing or binding, in seroconversion panels after mRNA-1273, BNT-162b2 and Ad26.COV2.S vaccine administration
Authors: Belda Francisco , Mora Oscar , Lopez-Martinez Monica , Torres Nerea , Vivanco Ana , Marfil Silvia , Pradenas Edwards , Massanella Marta , Blanco Julià , Christie Rebecca , Crowley Michael
Published: April 2022

Seroconversion panels were collected before and after vaccination with three COVID-19 vaccines: two mRNA vaccines (mRNA-1273 and BNT-162b2) and one adenovirus vector vaccine (Ad26.COV2.S). The panels were tested for antibody activity by chemiluminescent immunoassay, ELISA and one was tested in a pseudovirus neutralization assay. Participants positive for anti-SARS-CoV-2 antibodies before vaccination (18.6%) had a higher response to the first vaccine dose than participants who tested negative. For two-dose vaccines, older participants showed a lower response to the first dose than younger participants. All participants showed positive antibody responses after the second vaccine. For the adenovirus vector vaccine, two participants did not generate antibody responses two weeks and two months after vaccination. Three participants were negative at two weeks but positive at two months. Pseudovirus neutralization showed good correlation with antibody activity (correlation coefficient =0.78, p<0.0001). Antibody responses in participants over 45 years old tended to be less robust.
Prediction of serious complications in patients with cancer and pulmonary thromboembolism: validation of the EPIPHANY Index in a prospective cohort of patients from the PERSEO Study
Authors: Sánchez-Cánovas Manuel , Jimenez-Fonseca Paula , Garay David Fernández , Solís Mónica Cejuela , Elía Diego Casado , Salvans Eva Coma , de la Haba Vacas Irma , Sánchez David Gómez , Montés Ana Fernández , Giménez Roberto Morales , de Tejada Mercedes Biosca Gómez , Arrula Virginia Arrazubi , López Silvia Sequero , Candelera Remedios Otero , Cendra Cristina Sánchez , de la Peña Marina Justo , Muñoz Diana Moreno , Sarmiento Mayra Orillo , de Castro Eva Martínez , Escobar Ignacio García , Vidal Alejandro Bernal , Moran Laura Ortega , Muñoz Martín Andrés J. , Bayona Rodrigo Sánchez , Martínez Ortiz María José , de la Peña Francisco Ayala , Vicente Vicente , Carmona-Bayonas Alberto
Published: April 2022

Introduction

There is currently no validated score capable of classifying cancer-associated pulmonary embolism (PE) in its full spectrum of severity. This study has validated the EPIHANY Index, a new tool to predict serious complications in cancer patients with suspected or unsuspected PE.

Method

The PERSEO Study prospectively recruited individuals with PE and cancer from 22 Spanish hospitals. The estimation of the relative frequency θ of complications based on the EPIPHANY Index categories was made using the Bayesian alternative for the binomial test.

Results

Nine hundred patients diagnosed with PE between 2017/2020 were recruited. The rate of serious complications at 15 days was 11.8%, 95% highest density interval [HDI], 9.8-14.1%. Of the EPIPHANY low-risk patients, 2.4% (95% HDI, 0.8-4.6%) had serious complications, as did 5.5% (95% HDI, 2.9-8.7%) of the moderate-risk participants and 21.0% (95% HDI, 17.0-24.0%) of those with high-risk episodes. The EPIPHANY Index correlated with overall survival. Both the EPIPHANY Index and the Hestia criteria exhibited greater negative predictive value and a lower negative likelihood ratio than the remaining models. The incidence of bleeding at 6 months was 6.2% (95% HDI, 2.9-9.5%) in low/moderate-risk vs 12.7% (95% HDI, 10.1-15.4%) in high-risk (p-value=0.037) episodes. Of the outpatients, complications at 15 days were recorded in 2.1% (95% HDI, 0.7-4.0%) of the cases with EPIPHANY low/intermediate-risk vs 5.3% (95% HDI, 1.7-11.8%) in high-risk cases.

Conclusion

We have validated the EPIPHANY Index in patients with incidental or symptomatic cancer-related PE. This model can contribute to standardize decision-making in a scenario lacking quality evidence.

We have validated the EPIPHANY Index in patients with acute, incidental, or symptomatic cancer-related PE. This predictive model of complications can contribute to standardize decision-making in a scenario lacking quality evidence.
Motor signatures in digitized cognitive and memory tests enhances characterization of Parkinson’s disease
Authors: Ryu Jihye , Torres Elizabeth B
Published: April 2022

Background

Although there is a growing interest in using wearable sensors to characterize movement disorders, there is a lack of methodology for developing clinically interpretable kinematics biomarkers. Such digital biomarkers would provide a more objective diagnosis, capturing finer degrees of motor deficits, while retaining the information of traditional clinical tests.

Objectives

We aim at digitizing traditional tests of cognitive and memory performance to derive motor biometrics of pen-strokes and voice, thereby complementing clinical tests with objective criteria, while enhancing the overall motor characterization of Parkinson’s disease (PD).

Methods

35 participants including patients with PD, healthy young and age-matched controls performed a series of drawing and memory tasks, while their pen movement and voice were digitized. We examined the moment-to-moment variability of time-series reflecting the pen speed and voice amplitude.

Results

The stochastic signatures of the fluctuations in pen drawing speed and voice amplitude of patients with PD show lower noise-to-signal ratio compared to those derived from the younger and age-matched neurotypical controls. It appears that contact motions of the pen strokes on the tablet evokes sensory feedback for more immediate and predictable control in PD, compared to controls, while voice amplitude loses its neurotypical richness.

Conclusions

We offer new standardized data types and analytics to help advance our understanding of hidden motor aspects of cognitive and memory clinical assays commonly used in Parkinson’s disease.
Detection of a BA.1/BA.2 recombinant in travelers arriving in Hong Kong, February 2022
Authors: Gu Haogao , Ng Daisy YM , Liu Gigi YZ , Cheng Samuel SM , Krishnan Pavithra , Chang Lydia DJ , Cheuk Sammi SY , Hui Mani MY , Lam Tommy TY , Peiris Malik , Poon Leo
Published: April 2022

We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong from November-2021 to February-2022. Apart from detecting Omicron (BA.1, BA1.1. and BA.2) and Delta variants, we detected a BA.1/BA.2 recombinant in two epidemiologically linked cases. This recombinant has a breakpoint near the 5’ end of Spike gene (nucleotide position 20055-21618).
Socioeconomic inequality in the double burden of child malnutrition in the Eastern and Southern African Region
Authors: Caleyachetty Rishi , Kumar Niraj , Bekele Hana , Manaseki-Holland Semira
Published: April 2022

Socioeconomic inequalities in the double burden of child malnutrition threatens global nutrition targets 2025, especially in Eastern and Southern Africa. We aimed to quantify these inequalities from nationally representative household surveys in 13 Eastern and Southern African countries between 2000 and 2018. 13 of the latest Demographic and Health Surveys including 72,231 children under five year olds were studied. Prevalence of stunting, wasting and overweight (including obesity) were disagregated by wealth quintiles, maternal education categories and urban-rural residence for visual inspection of inequalities, and the slope index of inequality (SII) and the relative index of inequality (RII) were estimated for each country. Country-specific estimates were pooled using random-effects meta-analyses. Regional stunting and wasting prevalence was higher among children living in the poorest households, with mother’s with the lowest educational level and in rural areas. In contrast, regional overweight (including obesity) prevalence was higher among children living in the richest households, with mother’s with the highest educational level and urban areas. Tackling social inequalities in the distribution of the double burden of malnutrition among children in the Eastern and Southern African region will require strategies that address the reasons socially disadvantaged children become more exposed to stunting or wasting.
Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles
Authors: Olm Matthew R. , Dahan Dylan , Carter Matthew M. , Merrill Bryan D. , Yu Brian , Jain Sunit , Meng Xian Dong , Tripathi Surya , Wastyk Hannah , Neff Norma , Holmes Susan , Sonnenburg Erica D. , Jha Aashish R. , Sonnenburg Justin L.
Published: April 2022

Infant microbiome assembly is intensely studied in infants from industrialized nations, but little is known about this process in populations living non-industrialized lifestyles. In this study we deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with over twenty percent of genomes detected in the Hadza infant gut representing phylogenetically diverse novel species. Industrialized infants, even those who are breastfed, have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early-life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.

Recognition of work on indigenous communities

Research involving indigenous communities is needed for a variety of reasons including to ensure that scientific discoveries and understanding appropriately represent all populations and do not only benefit those living in industrialized nations. Special considerations must be made to ensure that this research is conducted ethically and in a non-exploitative manner. In this study we performed deep metagenomic sequencing on fecal samples that were collected from Hadza hunter-gatherers in 2013/2014 and were analyzed in previous publications using different methods (1, 2). A material transfer agreement with the National Institute for Medical Research in Tanzania ensures that stool samples collected are used solely for academic purposes, permission for the study was obtained from the National Institute of Medical Research (MR/53i 100/83, NIMR/HQ/R.8a/Vol.IX/1542) and the Tanzania Commission for Science and Technology, and verbal consent was obtained from the Hadza after the study’s intent and scope was described with the help of a translator. The publications that first described these samples included several scientists and Tanzanian field-guides as co-authors for the critical roles they played in sample collection, but as no new samples were collected in this study, only scientists who contributed to the analyses described here were included as co-authors in this publication. It is currently not possible for us to travel to Tanzania and present our results to the Hadza people, however we intend to do so once the conditions of the COVID-19 pandemic allow it.
Unifying genetic association tests via regression: Prospective and retrospective, parametric and non-parametric, and genotype- and allele-based tests
Authors: Zhang Lin , Sun Lei
Published: April 2022

Genetic association analysis, evaluating the relationship between genetic markers and complex and heritable traits, is the basis of genome-wide association studies. In response, many association tests have been developed, and they are generally classified as prospective vs. retrospective, parametric vs. non-parametric, and genotype- vs. allele-based association tests. While method classification is useful, it is confusing and challenging for practitioners to decide on the ‘optimal’ test to use for their data. Although there are known differences between some of the popular association tests, we provide new results that show the analytical connections between the different tests for both population- and family-based study designs.

Insérer votre résumé ici. We will supply a French abstract for those authors who can’t prepare it themselves.
A dual mechanism of APC/C inhibition by MAP kinases
Authors: Sun Li , Bai Shuang , Chen Jia-li , Deng Da-jie , Luo Zhou-qing , Wang Yamei , Jin Quan-wen
Published: April 2022

Mitotic anaphase onset is a key cellular process that is tightly regulated by multiple kinases. The involvement of mitogen-activated protein kinases (MAPKs) in this process has been established long ago in Xenopus egg extracts. However, despite its importance, it is still unclear which MAPK(s) is actually involved, this impedes the further understanding of the regulatory cascade. In this study, we first demonstrated that the involvement of MAPKs in mitotic anaphase onset regulation is evolutionarily conserved in the fission yeast (Schizosaccharomyces pombe). Then, we found that two of the three fission yeast MAPK signaling pathways act in concert to restrain anaphase-promoting complex/cyclosome (APC/C) activity upon activation of the spindle assembly checkpoint (SAC). The first pathway involves the phosphorylation of Mad2, a component of the core mitotic check complex (MCC), by MAPK Sty1, which enhances the tight binding of MCC to APC/C. The second pathway involves MAPK Pmk1 phosphorylation of Slp1Cdc20, the fission yeast homologue of Cdc20 and the co-activator of APC/C, which promotes the degradation of Slp1Cdc20. Both phosphorylation events are required to sustain mitotic arrest in response to spindle defects. These results clarified a detailed regulation cascade of the ubiquitous MAPK signaling in spindle checkpoint activation, APC/C inhibition and anaphase entry, which is vital for accurate chromosome segregation and cell viability.
Mmp14 is required for matrisome homeostasis and circadian rhythm in fibroblasts
Authors: Chloé Yeung Ching-Yan , Garva Richa , Pickard Adam , Lu Yinhui , Mallikarjun Venkatesh , Swift Joe , Taylor Susan H. , Rai Jyoti , Eyre David R. , Chaturvedi Mayank , Itoh Yoshifumi , Meng Qing-Jun , Mauch Cornelia , Zigrino Paola , Kadler Karl E.
Published: April 2022

The circadian clock in tendon regulates the daily rhythmic synthesis of collagen-I and the appearance and disappearance of small-diameter collagen fibrils in the extracellular matrix. How the fibrils are assembled and removed is not fully understood. Here, we first showed that the collagenase, membrane type I-matrix metalloproteinase (MT1-MMP, encoded byMmp14), is regulated by the circadian clock in postnatal mouse tendon. Next, we generated tamoxifen-inducedCol1a2-Cre-ERT2::Mmp14KO mice (Mmp14conditional knockout (CKO)). The CKO mice developed hind limb dorsiflexion and thickened tendons, which accumulated narrow-diameter collagen fibrils causing ultrastructural disorganization. Mass spectrometry of control tendons identified 1195 proteins of which 212 showed time-dependent abundance. InMmp14CKO mice 19 proteins had reversed temporal abundance and 176 proteins lost time dependency. Among these, the collagen crosslinking enzymes lysyl oxidase-like 1 (LOXL1) and lysyl hydroxylase 1 (LH1; encoded byPlod2) were elevated and had lost time-dependent regulation. High-pressure chromatography confirmed elevated levels of hydroxylysine aldehyde (pyridinoline) crosslinking of collagen in CKO tendons. As a result, collagen-I was refractory to extraction. We also showed that CRISPR-Cas9 deletion ofMmp14from cultured fibroblasts resulted in loss of circadian clock rhythmicity of period 2 (PER2), and recombinant MT1-MMP was highly effective at cleaving soluble collagen-I but less effective at cleaving collagen pre-assembled into fibrils. In conclusion, our study shows that circadian clock-regulatedMmp14controls the rhythmic synthesis of small diameter collagen fibrils, regulates collagen crosslinking, and its absence disrupts the circadian clock and matrisome in tendon fibroblasts.
Reduced mitochondria provide an essential function for the cytosolic methionine cycle
Authors: Zítek Justyna , Füssy Zoltán , Treitli Sebastian C. , Peña-Diaz Priscila , Vaitová Zuzana , Zavadska Daryna , Harant Karel , Hampl Vladimír
Published: April 2022

It has been long hypothesised that mitochondrial reduction is intrinsically related to the remodelling of Fe-S clusters assembly. Yet as our knowledge of divergent free-living protists broadens, so does the spectrum of variability within the range of mitochondrial-related organelles (MROs) fundamental functions. We resolved to high precision the MRO proteome of Paratrimastix pyriformis using Localisation of Organelle Proteins by Isotope Tagging (LOPIT) and demonstrate its role in the synthesis of folate derivates bearing one-carbon (1C) units, its link to the glycine cleavage system (GCS) and their only conceivable role as suppliers for the cytosolic methionine cycle, involved in recycling of S-adenosine methionine. This observation provides congruity to the presence of GCS in MROs of free-living anaerobes and its absence in endobionts, which typically lose the methionine cycle and, in the case of oxymonads, also mitochondria.
Oncogenic mutations in the DNA-binding domain of FOXO1 disrupt folding: quantitative insights from experiments and molecular simulations
Authors: Novack Dylan , Qian Lei , Acker Gwyneth , Voelz Vincent A. , Baxter Richard H. G.
Published: April 2022

FOXO1, a member of the family of winged-helix motif Forkhead box (FOX) transcription factors, is the most abundantly expressed FOXO member in mature B-cells. Sequencing of diffuse large B-cell lymphoma (DLBCL) tumors and cell lines identified specific mutations in the forkhead domain linked to loss of function. Differential scanning calorimetry and thermal shift assays were used to characterize how eight of these mutations affect the stability of the FOX domain. Mutations L183P and L183R were found to be particularly destabilizing. Electrophoresis mobility shift assays show these same mutations also disrupt FOXO1 binding to their canonical DNA sequences, suggesting the loss of function is due to destabilization of the folded structure. Computational modeling of the effects of mutations on FOXO1 folding was performed using alchemical FEP, and a Markov model of the entire folding reaction was constructed from massively parallel molecular simulations, which predicts folding pathways involving the late folding of helix α3. Although FEP is able to qualitatively predict the destabilization from L183 mutations, we find that a simple hydrophobic transfer model, combined with estimates of unfolded-state solvent accessible surface areas from molecular simulation, is able to more accurately predict changes in folding free energies due to mutations. These results suggest that atomic detail provided from simulation is important for accurate prediction of mutational effects on folding stability. Corresponding disease-associated mutations in other FOX family members support further experimental and computational studies of the folding mechanism of FOX domains.
Surface curvature and basal hydraulic stress induce spatial bias in cell extrusion
Authors: Huang Cheng-Kuang , Yong Xianbin , She David T. , Lim Chwee Teck
Published: April 2022

Epithelial cell extrusion is employed in maintaining a healthy epithelium. It remains unclear how environmental conditions specific to various epithelial tissues, such as geometry and fluid osmolarity, affect cell extrusions. We found that, over curved surfaces, epithelial monolayers exhibited higher extrusion rates in concave regions than convex ones. This difference, and overall extrusions, decreased when osmotically induced basal hydraulic stress was reduced by increasing media osmolarity or by culturing monolayers on hydrogels. Mechanistically, basal fluid accumulation antagonized cell-substrate adhesions and the subsequent FAK-Akt survival pathway, leading to apoptotic cell death. Convex surfaces induced cellular forces that acted against osmosis, thereby promoting adhesions and lowering apoptosis. This effect was reversed in concave regions, and together, resulted in a curvature induced spatial bias in cell extrusions.
Reduced cutaneous CD200:CD200R1 signalling in psoriasis enhances neutrophil recruitment to skin
Authors: Linley Holly , Jaigirdar Shafqat , Mohamed Karishma , Griffiths Christopher EM , Saunders Amy
Published: April 2022

The skin immune system is tightly regulated to prevent inappropriate inflammation in response to harmless environmental substances. This regulation is actively maintained by mechanisms including cytokines and cell surface receptors and its loss results in inflammatory disease. In the case of psoriasis, inappropriate immune activation leads to IL-17-driven chronic inflammation, but molecular mechanisms underlying this loss of regulation are not well understood.

We reveal that immunoglobulin superfamily member CD200, and signalling via its receptor, CD200R1 are reduced in non-lesional psoriasis skin. To examine the consequences of this, CD200R1 was blocked in a mouse model of psoriasis demonstrating that the receptor limits psoriasis-like inflammation. Specifically, CD200R1 blockade enhances acanthosis, CCL20 production and neutrophil recruitment but surprisingly, macrophage function and IL-17 production were not affected, and neutrophil reactive oxygen species production was reduced.

Collectively, our data show that CD200R1 affects neutrophil function and limits inflammatory responses in healthy skin by restricting neutrophil recruitment. However, the CD200 pathway is reduced in psoriasis, resulting in a loss of immune control, and increased neutrophil recruitment in mouse models. In conclusion, we highlight a pathway that might be targeted to dampen inflammation in patients with psoriasis.
Artificial selection methods from evolutionary computing show promise for directed evolution of microbes
Authors: Lalejini Alexander , Dolson Emily , Vostinar Anya E. , Zaman Luis
Published: April 2022

Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a general purpose search engine for solutions to challenging computational problems. Despite their overlapping approaches, artificial selection methods from evolutionary computing are not commonly applied to living systems in the laboratory. In this work, we ask if parent selection algorithms—procedures for choosing promising progenitors—from evolutionary computation might be useful for directing the evolution of microbial populations when selecting for multiple functional traits. To do so, we introduce an agent-based model of directed microbial evolution, which we used to evaluate how well three selection algorithms from evolutionary computing (tournament selection, lexicase selection, and non-dominated elite selection) performed relative to methods commonly used in the laboratory (elite and top-10% selection). We found that multi-objective selection techniques from evolutionary computing (lexicase and non-dominated elite) generally outperformed the commonly used directed evolution approaches when selecting for multiple traits of interest. Our results motivate ongoing work transferring these multi-objective selection procedures into the laboratory. Additionally, our findings suggest that more sophisticated artificial selection methods from evolutionary computation should also be evaluated for use in directed microbial evolution.
Pleiotrophin signals through ALK receptor to enhance growth of neurons in the presence of inhibitory CSPGs
Authors: Gupta Somnath J , Churchward Matthew A , Todd Kathryn G , Winship Ian R
Published: April 2022

Chondroitin sulfate proteoglycans (CSPGs), one of the major extracellular matrix components of the glial scar that surrounds central nervous system (CNS) injuries, are known to inhibit the regeneration of neurons. This study investigated whether pleiotrophin (PTN), a growth factor upregulated during early CNS development, can overcome the inhibition mediated by CSPGs and promote the neurite outgrowth of neurons in vitro. The data showed that a CSPG matrix inhibited the outgrowth of neurites in primary cortical neuron cultures compared to a control matrix. PTN elicited a dose dependent increase in the neurite outgrowth even in the presence of the growth inhibitory CSPG matrix, with optimal growth at 15 ng mL-1 of PTN (114.8% of neuronal outgrowth relative to laminin control). The growth promoting effect of PTN was blocked by inhibition of the receptor anaplastic lymphoma kinase (ALK) by alectinib in a dose dependent manner. Neurite outgrowth in the presence of this CSPG matrix was induced by activation of the protein kinase B (AKT) pathway, a key downstream mediator of ALK activation. This study identified PTN as a dose-dependent regulator of neurite outgrowth in primary cortical neurons cultured in the presence of a CSPG matrix, and identified ALK activation as a key driver of PTN-induced growth.

Summary statement

Function in the central nervous system (CNS) is attributed to the complex interactions of neurons and glia. These cells are anchored in extracellular matrix (ECM) which constitutes about 10% - 20% of brain volume. Cells in the brain produce different components of the ECM in brain including chondroitin sulfate proteoglycans (CSPGs). After a nervous system injury, glial cells produce excess CSPGs that restrict the regeneration of neurons, thus limiting functional recovery. This study examines the role of the endogenous growth factor pleiotrophin (PTN) in driving the growth of neurons even in the presence of inhibitory CSPGs, and anaplastic lymphoma kinase (ALK) receptor as a key mediator by which PTN potentiates growth.
Modulation of C5a-C5aR1 signaling alters the dynamics of AD progression
Authors: Carvalho Klebea , Schartz Nicole D. , Balderrama-Gutierrez Gabriela , Liang Heidi Y. , Chu Shu-Hui , Selvan Purnika , Gomez-Arboledas Angela , Petrisko Tiffany J. , Fonseca Maria I. , Mortazavi Ali , Tenner Andrea J.
Published: April 2022

Background

The complement system is part of the innate immune system that clears pathogens and cellular debris. In the healthy brain, complement influences neurodevelopment and neurogenesis, synaptic pruning, clearance of neuronal blebs, recruitment of phagocytes, and protects from pathogens. However, excessive downstream complement activation that leads to generation of C5a, and C5a engagement with its receptor C5aR1, instigates a feed-forward loop of inflammation, injury, and neuronal death, making C5aR1 a potential therapeutic target for neuroinflammatory disorders. C5aR1 ablation in the Arctic (Arc) model of Alzheimer’s disease protects against cognitive decline and neuronal injury without altering amyloid plaque accumulation.

Methods

To elucidate the effects of C5a-C5aR1 signaling on AD pathology, we crossed Arc mice with a C5a overexpressing mouse (ArcC5a+) and tested hippocampal memory. RNA-seq was performed on hippocampus and cortex from Arc, ArcC5aR1KO, and ArcC5a+ mice at 2.7-10 months and age-matched controls to assess mechanisms involved in each system. Immunohistochemistry was used to probe for protein markers of microglia and astrocytes activation states.

Results

ArcC5a+ mice had accelerated cognitive decline compared to Arc. Deletion of C5ar1 delayed or prevented the expression of some, but not all, AD-associated genes in the hippocampus and a subset of pan-reactive and A1 reactive astrocyte genes, indicating a separation between genes induced by amyloid plaques alone and those influenced by C5a-C5aR1 signaling.. Biological processes associated with AD and AD mouse models, including inflammatory signaling, microglial cell activation, and astrocyte migration, were delayed in the ArcC5aR1KO hippocampus. Interestingly, C5a overexpression also delayed the increase of some AD-, complement-, and astrocyte-associated genes, suggesting the possible involvement of neuroprotective C5aR2. However, these pathways were enhanced in older ArcC5a+ mice compared to Arc. Immunohistochemistry confirmed that C5a-C5aR1 modulation in Arc mice delayed the increase in CD11c-positive microglia, while not affecting other pan-reactive microglial or astrocyte markers.

Conclusion

C5a-C5aR1 signaling in AD largely exerts its effects by enhancing microglial activation pathways that accelerate disease progression. While C5a may have neuroprotective effects via C5aR2, engagement of C5a with C5aR1 is detrimental in AD models. These data support specific pharmacological inhibition of C5aR1 as a potential therapeutic strategy to treat AD.
Xport-A functions as a chaperone by stabilizing the first 5 transmembrane domains of Rhodopsin-1
Authors: Gaspar Catarina J , Martins Joana C , Melo Manuel N , Cordeiro Tiago N , Adrain Colin , Domingos Pedro M
Published: April 2022

Rhodopsin-1 (Rh1), the main photo-sensitive protein ofDrosophila, is a seven transmembrane domain protein, which is inserted co-translationally in the endoplasmic reticulum (ER) membrane. Maturation of Rh1 occurs in the ER, where various chaperones interact with Rh1 to aid in its folding and subsequent transport in the secretory pathway. Xport-A has been shown to be a chaperone/ transport factor for Rh1, but the exact molecular mechanism for Xport-A activity upon Rh1 is not known. Here, based on computational predictions, we propose a model where Xport-A functions as a chaperone in the biosynthesis of Rh1 by stabilizing the first 5 transmembrane domains of Rh1, but not the full length Rh1 protein.
IMC10 and LMF1 mediate membrane contact between the mitochondrion and the inner membrane complex in Toxoplasma gondii
Authors: Souza Rodolpho Ornitz Oliveira , Jacobs Kylie N. , Arrizabalaga Gustavo
Published: April 2022

The single mitochondrion of Toxoplasma gondii is highly dynamic, being predominantly in a peripherally distributed lasso-shape in intracellular parasites and collapsed in extracellular ones. The peripheral positioning of the mitochondrion is associated with apparent contacts between the mitochondrion membrane and the parasite pellicle. The outer mitochondrial membrane-associated protein LMF1 is critical for the correct positioning of the mitochondrion, and in its absence, intracellular parasites fail to form the lasso-shaped mitochondrion. To identify other proteins that participate in tethering the parasite’s mitochondrion to the pellicle, we performed a yeast two-hybrid screen for LMF1 interactors. We identified 70 putative interactors, six of which are known to localize to the apical end of the parasite, two to the mitochondrial membrane, and three localize to the inner membrane complex (IMC), a component of the parasite pellicle. Using reciprocal immunoprecipitation and proximity ligation assays, we confirmed the interaction of LMF1 with the pellicle protein IMC10, with a hypothetical protein known to be part of the conoid, and with an ATPase-Guanylyl Cyclase. Conditional knockdown of IMC10 does not affect parasite viability but severely affects mitochondrial morphology in intracellular parasites and mitochondrial distribution to the daughter cells during division. In effect, IMC10 knockdown phenocopies disruption of LMF1, suggesting that these two proteins define a novel membrane tether between Toxoplasma’s mitochondrion and the inner membrane complex.

IMPORTANCE

Toxoplasma gondii is an opportunistic parasite that can cause life-threatening disease in immunocompromised patients and those infected congenitally. As current therapies against this parasite can be poorly tolerated and are not effective against the latent stage of the parasite, there is an urgent need to identify new drug targets. The single mitochondrion of this parasite is a validated drug target, but little is known about the machinery that controls its division and structure, information that would be critical for a thorough exploration of the mitochondrion as a drug target. We have identified parasite-specific proteins that are essential to maintain the normal structure of the mitochondrion. We have discovered a complex of two proteins that tether the mitochondrion to the periphery of the parasite. Loss of this connection results in changes in mitochondrial morphology and cell division defects. Our results provide important insight into the molecular mechanisms regulating Toxoplasma mitochondrial morphology.
Appia: simpler chromatography analysis and visualization
Authors: Posert Richard , Baconguis Isabelle
Published: April 2022

Chromatography is an essential family of assays for molecular biology and chemistry. Typically, only a qualitative assessment of peak height, position, and shape are sufficient to proceed. However, there are more advanced forms of chromatography that require integration of peak width, baseline subtraction, and precise peak position calling. To handle these precise workflows, instrument manufacturer software is complicated and arcane; this makes simpler day-to-day analyses inefficient. Additionally, each manufacturer reports the data in their own proprietary format, requiring that analysis is performed at instrument computers and making data sharing between labs difficult. Here we present Appia, a free, open-source chromatography processing and visualization package focused on making analysis, collaboration, and publication quick and easy.