bluuebunny/crossref_metadata_2025 huggingface dataset:
Race and Apolipoprotein E-e4 Allele Status Differences in the Association Between Loneliness and Cognitive Decline
Authors: Desai Pankaja , Krueger Kristin R. , de Leon Carlos Mendes , Wilson Robert S. , Evans Denis A. , Rajan Kumar B.
Published: January 2023

Objective

This study aimed to examine race and apolipoprotein E-e4 allele (APOE-e4) status differences in the longitudinal associations between loneliness and cognitive decline.

Methods

The study sample is composed of participants (N = 7696, 64% Black participants and 36% White participants) from the Chicago Health and Aging Project, a population-based cohort study. Mixed-effects regression models were conducted to examine the longitudinal associations between loneliness on global cognitive function and individual tests of cognitive function. Models were also stratified by race and APOE-e4.

Results

A greater percentage of Black participants (17%) reported loneliness at baseline visit compared with White participants (12%). Black and White participants who were lonely individuals had a similar rate of decline in global cognitive function at 0.075 (95% confidence interval [CI] = −0.082 to −0.068) standard deviation unit (SDU) per year for Black participants and at 0.075 (95% CI = −0.086 to −0.063) SDU per year for White participants. Lonely participants with APOE-e4 had a higher rate of global cognitive decline at −0.102 (95% CI = −0.115 to −0.088) SDU per year than for lonely participants without APOE-e4 at −0.052 (95% CI = −0.059 to −0.045) SDU per year.

Conclusions

The burden of loneliness and its relation to cognitive decline is higher among participants with APOE-e4 compared with those without APOE-e4. Loneliness is associated with cognitive decline in both Black and White participants.
Broadly neutralizing antibody-mediated protection against simian-HIV infection among macaques with vaginal sexually transmitted infections
Authors: Garber David A. , Guenthner Patricia , Zhao Chunxia , Mitchell James , Ellis Shanon , Jia Hongwei , Manganare Marcos , Gazumyan Anna , Seaman Michael S. , Vishwanathan Sundaram Ajay , Heneine Walid , McNicholl Janet M.
Published: January 2023

Objective:

Sexually transmitted infections (STIs) increase mucosal HIV infection risk and have the potential to reduce preexposure prophylaxis efficacy. Clinical trials of a broadly neutralizing antibody (bNAb) provided proof-of-concept that passive immunization against HIV can be efficacious in people. We sought to evaluate preclinically the protective efficacy of passive bNAb immunization against simian-human immunodeficiency virus (SHIV) infection in the context of concurrent vaginal STIs.

Design:

Using a macaque model of combined ulcerative and nonulcerative vaginal STIs caused by Treponema pallidum, Chlamydia trachomatis, and Trichomonas vaginalis, we determined the protection that passively administered bNAb 10-1074 conferred against repeated vaginal SHIV challenges and compared correlates of protection to contemporaneous and historical controls without STIs.

Methods:

Plasma viremia was monitored via RT-qPCR assay. Concentrations of 10-1074 were determined longitudinally in plasma samples via TZM-bl pseudovirus neutralization assay.

Results:

Among macaques with vaginal STIs, a single subcutaneous injection of 10-1074 durably protected against vaginal SHIV acquisition, as compared with untreated controls. Interestingly, the median plasma concentration of 10-1074 at the time of SHIV breakthrough among macaques with STIs was significantly higher (10-fold) than that previously observed among 10-1074-treated macaques in the absence of STIs.

Conclusion:

Passive immunization with 10-1074 conferred significant protection against repeated vaginal SHIV challenges among macaques harboring vaginal STIs. However, our findings suggest that higher bNAb concentrations may be required for prophylaxis when STIs are present. Our findings potentially impact dose selection for the clinical development of bNAbs and highlight the importance of additional preclinical efficacy testing in STI models.
MACHINE LEARNING MODELS FOR PREDICTING ACUTE KIDNEY INJURY IN PATIENTS WITH SEPSIS-ASSOCIATED ACUTE RESPIRATORY DISTRESS SYNDROME
Authors: Zhou Yang , Feng Jinhua , Mei Shuya , Zhong Han , Tang Ri , Xing Shunpeng , Gao Yuan , Xu Qiaoyi , He Zhengyu
Published: January 2023

Background: Acute kidney injury (AKI) is a prevalent and serious complication among patients with sepsis-associated acute respiratory distress syndrome (ARDS). Prompt and accurate prediction of AKI has an important role in timely intervention, ultimately improving the patients’ survival rate. This study aimed to establish machine learning models to predict AKI via thorough analysis of data derived from electronic medical records. Method: The data of eligible patients were retrospectively collected from the Medical Information Mart for Intensive Care III database from 2001 to 2012. The primary outcome was the development of AKI within 48 hours after intensive care unit admission. Four different machine learning models were established based on logistic regression, support vector machine, random forest, and extreme gradient boosting (XGBoost). The performance of all predictive models was evaluated using the area under receiver operating characteristic curve, precision-recall curve, confusion matrix, and calibration plot. Moreover, the discrimination ability of the machine learning models was compared with that of the Sequential Organ Failure Assessment (SOFA) model. Results; Among 1,085 sepsis-associated ARDS patients included in this research, 375 patients (34.6%) developed AKI within 48 hours after intensive care unit admission. Twelve predictive variables were selected and further used to establish the machine learning models. The XGBoost model yielded the most accurate predictions with the highest area under receiver operating characteristic curve (0.86) and accuracy (0.81). In addition, a novel shiny application based on the XGBoost model was established to predict the probability of developing AKI among patients with sepsis-associated ARDS. Conclusions: Machine learning models could be used for predicting AKI in patients with sepsis-associated ARDS. Accordingly, a user-friendly shiny application based on the XGBoost model with reliable predictive performance was released online to predict the probability of developing AKI among patients with sepsis-associated ARDS.
ENDOTHELIAL GLYCOCALYX SHEDDING IN INTRA-ABDOMINAL SEPSIS: A FEASIBILITY STUDY
Authors: Carmichael Samuel P. , Appelbaum Rachel D. , Renaldo Antonio , Hauser Nathaniel , Rahbar Elaheh , Nunn Andrew M.
Published: January 2023

Background: The endothelial glycocalyx layer (EGL) is a complex meshwork of glycosaminoglycans and proteoglycans that protect the vascular endothelium. Cleavage or shedding of EGL-specific biomarkers, such as hyaluronic acid (HA) and syndecan-1 (SDC-1, CD138) in plasma, have been shown to be associated with poor clinical outcomes. However, it is unclear whether levels of circulating EGL biomarkers are representative of the EGL injury within the tissues. The objective of the present feasibility study was to describe a pathway for plasma and tissue procurement to quantify EGL components in a cohort of surgical patients with intra-abdominal sepsis. We sought to compare differences between tissue and plasma EGL biomarkers and to determine whether EGL shedding within the circulation and/or tissues correlated with clinical outcomes. Methods: This was a prospective, observational, single-center feasibility study of adult patients (N = 15) with intra-abdominal sepsis, conducted under an approved institutional review boards. Blood and resected tissue (pathologic specimen and unaffected peritoneum) samples were collected from consented subjects at the time of operation and 24–48 hours after surgery. Endothelial glycocalyx layer biomarkers (i.e., HA and SDC-1) were quantified in both tissue and plasma samples using a CD138 stain and ELISA kit, respectively. Pairwise comparisons were made between plasma and tissue levels. In addition, we tested the relationships between measured EGL biomarkers and clinical status and patient outcomes. Results: Fifteen patients with intra-abdominal sepsis were enrolled in the study. Elevations in EGL-specific circulating biomarkers (HA, SDC-1) were positively correlated with postoperative SOFA scores and weakly associated with resuscitative volumes at 24 hours. Syndecan-1 levels from resected pathologic tissue significantly correlated with SOFA scores at all time points (R = 0.69 and P < 0.0001) and positively correlated with resuscitation volumes at 24 hours (R = 0.41 and P = 0.15 for t = 24 hours). Tissue and circulating HA and SDC-1 positively correlated with SOFA >6. Conclusions: Elevations in both circulating and tissue EGL biomarkers were positively correlated with postoperative SOFA scores at 24 hours, with resected pathologic tissue EGL levels displaying significant correlations with SOFA scores at all time points. Tissue and circulating EGL biomarkers were positively correlated at higher SOFA scores (SOFA > 6) and could be used as indicators of resuscitative needs within 24 hours of surgery. The present study demonstrates the feasibility of tissue and plasma procurement in the operating room, although larger studies are needed to evaluate the predictive value of these EGL biomarkers for patients with intra-abdominal sepsis.
Genomic characterization of colistin resistance in Klebsiella spp. under the pressure of colistin
Authors: Chen Xin , Sun Zhewei , Xu Xiaogang , Jiang Jianping , Su Jiachun
Published: January 2023

Introduction. Carbapenem-resistant

Klebsiella pneumoniae

(CRKP) has become a serious threat to global public health. Colistin is regarded as the last-resort antibiotic for CRKP infections, but colistin resistance among CRKP is increasingly being reported, making clinical treatment for CRKP infections more difficult.

Hypothesis/Gap Statement. The molecular mechanisms of colistin resistance in

Klebsiella

spp. under the pressure of colistin have not been fully investigated.

Aim. We aimed to investigate the phenotypic and genetic variation in two colistin-susceptible

Klebsiella

spp. strains under selective pressure of colistin.

Methodology. One hundred microlitres of overnight cultures of the CRKP clinical strain CRKP12-130 and of ATCC 700603 was spread on five Mueller-Hinton Agar (MHA) plates with colistin concentrations of 2, 4, 8, 16 and 32 µg ml−1, and growth of colonies was observed for five consecutive days. Colonies collected from plates were passaged daily for 10 days on MHA plates without colistin and susceptibility testing of colistin was performed by broth microdilution. Thirty-four colistin-resistant strains randomly selected were submitted to whole genome sequencing (WGS). Transcriptional levels of genes involved in colistin resistance (mgrB, phoP, phoQ, pmrA, pmrB, pmrD, pmrE and pmrK) were measured by quantitative real-time PCR.

Results. A total of 114 and 119 colistin-resistant colonies were obtained from CRKP12-130 and ATCC 700603 in this study, among which 16 and 18 colonies were submitted to WGS, respectively. Among these 34 sequenced isolates, mutation in phoQ (13/16, 81.25 %) was the main genetic factor mediating colistin resistance in strains from CRKP12-130, while for strains from ATCC 700603, mutation associated with mgrB (8/18, 44.44 %) was found to be the commonest. Mutation of mgrB led to a significant increase in the MIC for colistin (from 64 to >128 µg ml−1), and a novel mutation C28R in mgrB was first reported in this study.

Conclusion. Colistin-resistant

Klebsiella

spp. could be easily selected under pressure of different concentrations of colistin. Mutations of mgrB, phoP, phoQ and pmrB genes were the main mechanisms leading to chromosomally mediated colistin resistance in

Klebsiella

spp.
The importance of increasing primary vaccinations against COVID-19 in Europe
Authors: Boëlle Pierre-Yves , Valdano Eugenio
Published: January 2023

In the European Union, mass vaccination against COVID-19 staved off the strict restrictions that had characterized early epidemic response. Now, vaccination campaigns are focusing on booster doses, and primary vaccinations have all but halted. Still, 52 million European adults are unvaccinated. We investigated if reaching the still unvaccinated population in future vaccination campaigns would substantially decrease the current burden of COVID-19, which is substantial. We focused on vaccination homophily, whereby those who are unvaccinated are mostly in contact with other unvaccinated, making COVID-19 circulation easier. We quantified vaccination homophily and estimated its impact on COVID-19 circulation.

We used an online survey of 1,055,286 people from 22 European countries during early 2022. We computed vaccination homophily as the association between reported vaccination status and perceived vaccination uptake among one’s own social contacts, using a case-referent design and a hierarchical logistic model. We used this information in an analysis of the COVID-19 reproduction ratio to determine the impact of vaccine homophily in transmission.

Vaccination homophily was present and strong everywhere: the average odds ratio of being vaccinated for a 10-percentage-point increase in coverage among contacts was 1.66 (95% CI=(1.60, 1.72)). Homophily was positively associated with the strictness of COVID-19-related restrictions in 2020 (Pearson=0.49, p-value=0.03). In the countries studied, 12%-to-18% of the reproduction ratio would be attributable to vaccine homophily.

Reducing vaccination homophily may curb the reproduction ratio substantially even to the point of preventing recurrent epidemic waves. In addition to boosting those already vaccinated, increasing primary vaccination should remain a high priority in future vaccination campaigns, to reduce vaccination homophily: this combined strategy may decrease COVID-19 burden.
Prevalence of undiagnosed hypertension and prehypertension among bankers of Bangladesh: a cross-sectional study
Authors: Munira Sira Jam , Hasan Mohammad Jahid , Rafi Md Abdur , Shaheen Shafia , Kabir Md. Iqbal
Published: January 2023

Objective

Bankers lead a sedentary and highly stressful life that often leads to developing noncommunicable diseases (NCDs) such as hypertension, diabetes, mental disorders, etc. The study aims to assess the prevalence of undiagnosed hypertension and prehypertension among bankers in Bangladesh.

Methods

Data from 365 bankers from five public and private banks in Bangladesh were collected using a pretested semistructured questionnaire. Prehypertension was defined as having systolic blood pressure of 120-139 mmHg and diastolic blood pressure of 80-89 mmHg. Multivariate logistic regression models were created to investigate the factors associated with them.

Results

The prevalence of undiagnosed hypertension and prehypertension were 22.5% and 55.3%, respectively. Most of the bankers were males and 35-44 years of age. The risk of hypertension and prehypertension was significantly higher among males (OR, 16.59; OR, 6.42), longer duration of services (F, 3.56), prolonged working hours (OR, 3.8; OR, 3.09), smoking (OR, 6.18; OR, 3.43), overweight (OR, 6.81; OR, 2.41) and obese (OR, 8.94; OR, 3.36) bankers, respectively. After controlling for all confounders, the predictors of hypertension were males (aOR, 12.8; CI, 2.73-60.02), current smokers (aOR,2.87; CI, 1.03-8), overweight (aOR,5.11; CI, 1.46-17.93), and obesity (aOR, 9.59; CI, 2.41-38.22). For prehypertension, males (aOR, 9.72; CI, 3.06-30.87) and obesity (aOR, 3.95; CI, 1.52-10.25) were found as predictors.

Conclusion

More than three fourth of bankers in Bangladesh have either undiagnosed hypertension or prehypertension associated with several contributing factors to occur. A large-scale study is recommended to understand the clear picture of the overall NCD risk factors burden among bankers in Bangladesh.

WHAT IS ALREADY KNOWN ON THIS TOPIC

The prevalence of hypertension and prehypertension are already higher in Bangladesh. Sedentary lifestyles and work stress make bankers a vulnerable community to developing these NCD risk factors.

WHAT THIS STUDY ADDS

Bankers have a higher prevalence of undiagnosed hypertension and prehypertension in Bangladesh.

Several factors gender, long duration of service, prolonged working hours, and physical inactivity leading to overweight or obesity were found to be significant predictors of developing them.

HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICY

This research suggests that it is now a national demand to conduct large scale surveys to assess the NCD risk factors burden among high risk occupational groups like bankers.
SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests
Authors: Nguyen Phuong-Vi , Carmola Ludy Registre , Wang Ethan , Bassit Leda , Rao Anuradha , Greenleaf Morgan , Sullivan Julie A. , Martin Greg S. , Lam Wilbur A. , Waggoner Jesse J. , Piantadosi Anne
Published: January 2023

Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.
Sex differences in the associations between risk for late-life AD, protective lifestyle factors and cognition in mid-life
Authors: Qi Qing , Deng Feng , Ritchie Karen , Muniz-Terrera Graciela , Koychev Ivan , Malhotra Paresh , O’Brien John T. , Ritchie Craig W. , Lawlor Brian , Naci Lorina
Published: January 2023

It is now acknowledged that Alzheimer’s Disease (AD) processes are present decades before the onset of clinical symptoms, but whether lifestyle activities can protect against these early AD processes in mid-life remains poorly understood. Furthermore, the impact of sex as a biological variable on associations between dementia risk, protective lifestyle activities and cognition is unknown. In this study, we aimed to replicate findings from our two recent studies [Deng et al. (2022) and Heneghan et al. (2022)] on the contribution of mid-life modifiable activities to cognition in individuals with dementia risk, in a larger independent cohort of the PREVENT–Dementia research program (N = 461 vs N = 208 used previously). Second, we investigated associations between biological sex, dementia risk, protective lifestyle activities and cognitive performance. Participants (40–59 years; N = 461) completed cognitive and clinical assessments cross-sectionally. Mid-life activities were measured with the Lifetime of Experiences Questionnaire. Known risk factors for sporadic late-onset AD (Apolipoprotein EƐ4 allele status, family history of dementia, and the Cardiovascular Risk Factors Aging and Dementia score [CAIDE]) were investigated. Replicating our key previous findings (Deng et al., 2022 and Heneghan et al., 2022), we found that episodic and relational memory was (a) significantly negatively associated with the CAIDE risk score, (b) positively associated with stimulating lifestyle activities, and (c) that females performed significantly better than males in episodic and relational memory. The key novel finding of this study was that inherited dementia risk (i.e., APOEƐ4 genotype) modulated the association between sex, lifestyle and cognition. Only for APOEƐ4+ females, not APOEƐ4-, higher occupational attainment was associated with better episodic and relational memory. Conversely, only for APOEƐ4+ males, not APOEƐ4-, higher occupational attainment was associated with worse episodic and relational memory. These findings suggest that modifiable lifestyle activities offset cognitive decrements due to inherited AD risk in mid-life and support the targeting of modifiable lifestyle activities for the prevention of Alzheimer’s disease. Furthermore, these findings suggest an urgent need for targeted research on female-specific risk factors, to inform personalised strategies for AD prevention and the promotion of female brain health.
Pericoronary adipose tissue radiomics from coronary CT angiography identifies vulnerable plaques characteristics in intravascular OCT
Authors: Kim Justin N. , Gomez-Perez Lia , Zimin Vladislav N. , Makhlouf Mohamed H. E. , Al-Kindi Sadeer , Wilson David L. , Lee Juhwan
Published: January 2023

Pericoronary adipose tissue (PCAT) features on CT have been shown to reflect local inflammation, and signals increased cardiovascular risk. Our goal was to determine if PCAT radiomics extracted from coronary CT angiography (CCTA) images are associated with intravascular optical coherence tomography (IVOCT)-identified vulnerable plaque characteristics (e.g., microchannels [MC] and thin-cap fibroatheroma [TCFA]). CCTA and IVOCT images of 30 lesions from 25 patients were registered. Vessels with vulnerable plaques were identified from the registered IVOCT images. PCAT radiomics features were extracted from CCTA images for the lesion region of interest (PCAT-LOI) and the entire vessel (PCAT-Vessel). We extracted 1356 radiomics features, including intensity (first-order), shape, and texture features. Features were reduced using standard approaches (e.g., high feature correlation). Using stratified three-fold cross-validation with 1000 repeats, we determined the ability of PCAT radiomics features from CCTA to predict IVOCT vulnerable plaque characteristics. In identification of TCFA lesions, PCAT-LOI and PCAT-Vessel radiomics models performed comparably (AUC±standard deviation 0.78±0.13, 0.77±0.14). For identification of MC lesions, PCAT-Vessel radiomics model (0.89±0.09) was moderately better associated than that of PCAT-LOI model (0.83±0.12). Both PCAT-LOI and PCAT-Vessel radiomics models also similarly identified coronary vessels thought to be highly vulnerable (i.e., both TCFA and MC) (0.88±0.10, 0.91±0.09). Favorable radiomics features tended to be those describing texture and size of PCAT. PCAT radiomics can identify coronary vessels with TCFA or MC, consistent with IVOCT. CCTA radiomics may improve risk stratification by noninvasively detecting vulnerable plaque characteristics that are only visible with IVOCT.
Differential COVID-19 mortality in the United States: Patterns, causes and policy implications
Authors: Stoto Michael A. , Schlageter Samantha , degl’Innocenti Duccio Gamannossi , Zollo Fabiana , Kraemer John D.
Published: January 2023

A “two Americas” narrative emerged in the summer of 2021: one with high demand for COVID-19 vaccines, and a second with widespread vaccine hesitancy and opposition to mask mandates. But our analysis of excess mortality shows that the U.S. has been a divided nation at least since the start of the pandemic. Through April, 2022, there were 1,335,292 excess deaths associated with COVID-19, 37% more than reported as such. After the first wave, death rates in the South were more than double those in the Northeast; 45% of deaths were in the South, with 38% of the population.

While some regard vaccination and other measures as matters of personal choice, the population impact is striking. If every region had the same mortality rate as the lowest regional rate in each period, more than 418,763 COVID-19 deaths were “avoidable,” more than half (58%) in the South and almost half before vaccines were available. These results show that population-based COVID-19 policies can still play an important role in protecting those most vulnerable to severe disease and death and reducing the spread of the virus.

This example illustrates the importance of excess mortality measures as part of a comprehensive surveillance system. Official mortality counts rely on complete recording of COVID-19 as a cause of death, but COVID-19 deaths are under reported for many reasons. Indeed, the proportion of COVID-19 deaths reported as such varied markedly over time, and from 67% in the West to 87% the Northeast. In 2022, some regions cut back on testing making it harder to see a re-emergence of COVID-19 in those places. More extensive surveillance based on wastewater testing and other means that do not depend on testing are needed to get a more accurate picture. Excess mortality estimates are more tenuous years beyond the pre-pandemic period.
Systematic elucidation of genetic mechanisms underlying cholesterol uptake
Authors: Hamilton Marisa C. , Fife James D. , Akinci Ersin , Yu Tian , Khowpinitchai Benyapa , Cha Minsun , Barkal Sammy , Thi Thi Tun , Yeo Grace H.T. , Barroso Juan Pablo Ramos , Francoeur Matthew Jake , Velimirovic Minja , Gifford David K. , Lettre Guillaume , Yu Haojie , Cassa Christopher A. , Sherwood Richard I.
Published: January 2023

Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we have substantially improved the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake. We use co-essentiality-based gene module analysis to show that dysfunction of the RAB10 vesicle transport pathway leads to hypercholesterolemia in humans and mice by impairing surface LDL receptor levels. Further, we demonstrate that loss of function ofOTX2leads to robust reduction in serum LDL-C levels in mice and humans by increasing cellular LDL-C uptake. Altogether, we present an integrated approach that improves our understanding of genetic regulators of LDL-C levels and provides a roadmap for further efforts to dissect complex human disease genetics.
CeLab, a Microfluidic Platform for the Study of Life History Traits, reveals Metformin and SGK-1 regulation of Longevity and Reproductive Span
Authors: Sohrabi Salman , Cota Vanessa , Murphy Coleen T.
Published: January 2023

The potential to carry out high-throughput assays in a whole organism in a small space is one of the benefits ofC. elegans, but worm assays often require a large sample size with frequent physical manipulations, rendering them highly labor-intensive. Microfluidic assays have been designed with specific questions in mind, such as analysis of behavior, embryonic development, lifespan, and motility. While these devices have many advantages, current technologies to automate worm experiments have several limitations that prevent widespread adoption, and most do not allow analyses of reproduction-linked traits. We developed a miniatureC. eleganslab-on-a-chip device,CeLab, a reusable, multi-layer device with 200 separate incubation arenas that allows progeny removal, to automate a variety of worm assays on both individual and population levels.CeLab enables high-throughput simultaneous analysis of lifespan, reproductive span, and progeny production, refuting assumptions about the Disposable Soma hypothesis. BecauseCeLab chambers require small volumes, the chip is ideal for drug screens; we found that drugs previously shown to increase lifespan also increase reproductive span, and we discovered that low-dose metformin increases both.CeLab reduces the limitations of escaping and matricide that typically limit plate assays, revealing that feeding with heat-killed bacteria greatly extends lifespan and reproductive span of mated animals.CeLab allows tracking of life history traits of individuals, which revealed that the nutrient-sensing mTOR pathway mutant,sgk-1, reproduces nearly until its death. These findings would not have been possible to make in standard plate assays, in low-throughput assays, or in normal population assays.
The splicing isoform Foxp3Δ2 releases the autoinhibitory conformation and differentially regulates tTregs and pTregs homeostasis
Authors: Gu Qianchong , Zhao Xiufeng , Guo Jie , Xu Wei , Zhang Jianhua , Zhang Wei , Zhang Fuping , Hou Baidong , Zhou Xuyu
Published: January 2023

Foxp3 is the master transcription factor for the development and function of regulatory T cells (Tregs). So far, little is known about whether the conformation change in Foxp3 could impact the Tregs biology. Alternative splicing of human Foxp3 results in the expression of two major isoforms: the full-length protein or an exon 2-deleted protein (Foxp3Δ2). Here, AlphaFold2 structure predictions andin vitroexperiments demonstrated that the N-terminal domain of Foxp3 inhibits DNA binding by moving toward the C-terminus and that this movement is mediated by exon 2. Consequently, we generated exon 2 deficient mice and found Foxp3Δ2-bearing Tregs in the peripheral lymphoid organ were less sensitive to TCR due to the enhanced binding of Foxp3Δ2 to theBatfpromoter and were unsusceptible to IL-2. In contrast, among RORγt+Tregs in the large intestine, Foxp3Δ2 Tregs expressed much more RORγt-related genes, and more strikingly, the deletion of exon 2 of Foxp3 conferred a competitive advantage over WT RORγt+Tregs. Together, our results reveal that alternative splicing of exon 2 generates a constitutively active form of Foxp3, which plays a differential role in regulating tTregs and pTregs homeostasis.

Highlights

Foxp3Δ2 broke the inhibitory loop and generated constitutive DNA-binding activity.

Foxp3 isoforms differentially regulate tTregs and pTregs homeostasis

Foxp3Δ2-bearing Tregs in the peripheral lymphoid organ were less sensitive to TCR and were unsusceptible to IL-2

Foxp3Δ2 RORγt+pTregs benefited them for better adapting to the gut environmental conditions
A cinnamyl alcohol dehydrogenase (CAD) like enzyme leads to a branch in the shikonin biosynthetic pathway inArnebia euchroma
Authors: Wang Ruishan , Liu Changzheng , Wang Sheng , Sun Jiahui , Guo Juan , Lyu Chaogeng , Kang Chuanzhi , Wan Xiufu , Shi Linyuan , Wang Jinye , Huang Luqi , Guo Lanping
Published: January 2023

Shikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such asLithospermum erythrorhizonandArnebia euchroma. Phytochemical researches utilizingL. erythrorhizonandA. euchromacultured cells both indicate the existence of a competing route branching out from the shikonin biosynthetic pathway toward benzo/hydroquinones. A previous study has shown that the branch point is a putative alcohol dehydrogenase converting (Z)-3’’-hydroxygeranylhydroquinone [(Z)-3’’-OH-GHQ] to an aldehyde intermediate (E)-3’’-oxo-GHQ. However, the enzyme involved in the branch reaction is not characterized at the molecular level yet. In this study, we clone a candidate gene belonging to the cinnamyl alcohol dehydrogenase (CAD) family,AeHGO, through coexpression analysis of transcriptome data sets of shikonin-proficient and shikonin-deficient cell lines ofA. euchroma. In biochemical assays, purified AeHGO protein reversibly oxidizes (Z)-3’’-OH-GHQ to produce (E)-3’’-oxo-GHQ followed by reversibly reducing (E)-3’’-oxo-GHQ to (E)-3’’-OH-GHQ, resulting in an equilibrium mixture of the three compounds. Time course analysis and kinetic parameters show that the reaction with (Z)-3’’-OH-GHQ is about twice as efficient as with (E)-3’’-OH-GHQ, which leads to the predominance of (E)-3’’-OH-GHQ and (E)-3’’-oxo-GHQ in the equilibrium mixture. According to a previous report, (E)-3’’-oxo-GHQ can be converted to deoxyshikonofuran, a hydroquinone metabolite produced by boraginaceous plants. Considering there is a competition for accumulation between shikonin derivatives and benzo/hydroquinones in bothL. erythrorhizonandA. euchromacultured cells, AeHGO is supposed to play an important role in the metabolic regulation of shikonin biosynthetic pathway.
General solution to inflated type I and II errors in multi-subject single-cell differential gene expression analysis
Authors: Lee Hanbin , Han Buhm
Published: January 2023

Large-scale multi-subject single-cell data have become very common. For differential gene expression (DGE) analysis of these datasets, a common practice is to choose any of the two: pseudobulk methods or cell-wise methods. However, multi-subject single-cell studies have highly heterogeneous study designs. Some studies have case/control samples to be compared and tested, and some make within-sample perturbations. In this work, we report that to prevent severely inflated errors, we must treat the two categories of study designs differently in the DGE analysis. In studies with case/control labels, pseudobulk methods work the best, and cell-wise methods produce severe inflation of type II errors. Cell-wise methods work best in studies with within-sample perturbations, and pseudobulk methods produce severe inflation of type I errors. We provide mathematical proofs to support this argument. Surprisingly, many existing studies, even published ones, often choose an inappropriate DGE method. The most common temptation is to use cell-wise methods for case/control studies, which will only make p-values falsely look significant. Our analyses and proofs warn that choosing an appropriate DGE method is not an option but a requirement.
Modular transcriptional responses to environmental changes
Authors: Beringer Marc , Mattam Bella , Choudhury Rimjhim Roy , Parisod Christian
Published: January 2023

Knowledge about the molecular underpinnings of phenotypic plasticity is still scarce and quantifying gene expression in response to abiotic and biotic factors enables to investigate transcriptional plasticity. RNAseq data on clones of the alpine plantBiscutella laevigata(Brassicaceae) subjected to control, cold, heat, drought and herbivory treatments assessed differentially expressed genes (DEGs) and transposable elements (DE-TEs) in comparison to similar experiments inArabidopsis thaliana. Synergistic and trade-off DEGs presenting parallel and antagonistic regulation among treatments were further identified and used with networks of co-expressed DEGs to characterize transcriptional plasticity in response to environmental changes. Compared toA. thaliana,B. laevigatapresented fewer DEGs that were mostly up-regulated by stronger expression shifts in response to environmental treatments.Biscutella laevigatashowed constitutive expression of half of theA. thalianaDEGs. It further presented a higher proportion of synergistic DEGs, a lower number of trade-off DEGs and a transcriptome organized in environment-specific subnetworks. Several DE-TEs were identified as activated by heat and herbivory. The stress-tolerant perennialB. laevigatapresents a highly modular transcriptional plasticity in response to environmental changes, contrasting with the more integrated transcriptome ofA. thaliana.

Significance statement

Little is known about the molecular underpinnings of phenotypic plasticity. Here, focusing on expression shifts during changes in abiotic and biotic conditions, we highlight environment-responsive genes acting synergistically or antagonistically among treatments and underlying modular transcriptional plasticity in two Brassicacea species.
T-cell derived extracellular vesicles prime macrophages for improved STING based cancer immunotherapy
Authors: Hansen Aida S. , Jensen Lea S. , Ryttersgaard Kristoffer G. , Krapp Christian , Just Jesper , Gammelgaard Kristine R. , Jønsson Kasper L. , Johansen Mogens , Etzerodt Anders , Deleuran Bent W. , Jakobsen Martin R.
Published: January 2023

A key phenomenon in cancer is the establishment of a highly immunosuppressive tumor microenvironment (TME). Despite advances in immunotherapy, where the purpose is to induce tumor recognition and hence hereof tumor eradication, the majority of patients applicable for such treatment still fail to respond. It has been suggested that high immunological activity in the tumor is essential for achieving effective response to immunotherapy, which therefore have led to exploration of strategies that triggers inflammatory pathways. Here activation of the stimulator of interferon genes (STING) signaling pathway has been considered an attractive target, as it is a potent trigger of pro-inflammatory cytokines and type I and III interferons. However, immunotherapy combined with targeted STING agonists has not yielded sustained clinical remission in humans. This suggest a need for exploring novel adjuvants to improve the innate immunological efficacy. Here, we demonstrate that extracellular vesicles (EVs), derived from activated CD4+T cells (T-EVs), sensitizes macrophages to elevate STING activation, mediated by IFNγ carried on the T-EVs. Our work support that T-EVs can disrupt the immune suppressive environment in the tumor by reprogramming macrophages to a pro-inflammatory phenotype, and priming them for a robust immune response towards STING activation.
Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation
Authors: Caspi Itamar , Meir Moran , Nun Nadav Ben , Yakhini Uri , Stern Adi , Ram Yoav
Published: January 2023

RNA viruses are particularly notorious for their high levels of genetic diversity, which is generated through the forces of mutation and natural selection. However, disentangling these two forces is a considerable challenge, and this may lead to widely divergent estimates of viral mutation rates, as well as difficulties in inferring fitness effects of mutations. Here, we develop, test, and apply an approach aimed at inferring the mutation rate and key parameters that govern natural selection, from haplotype sequences covering full length genomes of an evolving virus population. Our approach employsneural posterior estimation, a computational technique that applies simulation-based inference with neural networks to jointly infer multiple model parameters. We first tested our approach on synthetic data simulated using different mutation rates and selection parameters while accounting for sequencing errors. Reassuringly, the inferred parameter estimates were accurate and unbiased. We then applied our approach to haplotype sequencing data from a serial-passaging experiment with the MS2 bacteriophage. We estimated that the mutation rate of this phage is around 0.2 mutations per genome per replication cycle (95% highest density interval: 0.051-0.56). We validated this finding with two different approaches based on single-locus models that gave similar estimates but with much broader posterior distributions. Furthermore, we found evidence for reciprocal sign epistasis between four strongly beneficial mutations that all reside in an RNA stem-loop that controls the expression of the viral lysis protein, responsible for lysing host cells and viral egress. We surmise that there is a fine balance between over and under-expression of lysis that leads to this pattern of epistasis. To summarize, we have developed an approach for joint inference of the mutation rate and selection parameters from full haplotype data with sequencing errors, and used it to reveal features governing MS2 evolution.
Mapping the auditory space ofCulex pipiensfemale mosquito in 3D
Authors: Lapshin Dmitry. N. , Vorontsov Dmitry. D.
Published: January 2023

The task of directional hearing faces most of the animals that possess ears. They approach this task in different ways, but the common trait is the usage of the binaural cues to find the direction to the source of sound. In insects, the task is further complicated by their small size and, hence, minute temporal and level differences between two ears. A way to overcome this problem is to receive the particle velocity component of sound rather than the pressure, as the former naturally involves directionality. However, even in this case, one ear is not enough for directional hearing: a single symmetric flagellar particle velocity receiver cannot discriminate between the two opposite directions along the vector of the sound wave. Insects that use flagellar auditory organs, and mosquitoes in particular, possess a pair of receivers, which presumes the usage of binaural hearing. Its mechanisms are expected to be significantly different from the ones typical for the pressure receivers. However, the directionality of flagellar auditory organs has received little attention. Here we measured the in-flight orientation of a female mosquito antennae and obtained detailed physiological mapping of the Johnston’s organ directionality at the level of individual sensory units. By combining these data, we provided a three-dimensional model of the mosquito’s auditory space. The natural orientation of the antennae together with angular distribution of sensory units in each of the Johnston’s organs was found to be optimal for binaural hearing focused primarily in front of, above and below a flying mosquito.
Ketocarotenoid production in tomato triggers metabolic reprogramming and cellular adaptation: The quest for homeostasis?
Authors: Nogueira Marilise , Enfissi Eugenia M. A. , Price Elliott J. , Menard Guillaume N. , Venter Eudri , Eastmond Peter J. , Bar Einat , Lewinsohn Efraim , Fraser Paul D.
Published: January 2023

Plants are sessile and therefore have developed an extraordinary capacity to adapt to external signals. Here, the focus is on the plasticity of the plant cell to respond to new intracellular cues. Ketocarotenoids are high-value natural red pigments with potent antioxidant activity. In the present study, system level analyses have revealed that the heterologous biosynthesis of ketocarotenoids in tomato initiated a series of cellular and metabolic mechanisms to cope with the formation of metabolites that are non-endogenous to the plant. The broad multilevel changes were linked to, among others, (i) the remodelling of the plastidial membrane, where the synthesis and storage of ketocarotenoids occurs, (ii) the recruiting of core metabolic pathways for the generation of metabolite precursors and energy, and (iii) redox control. The role of the metabolites as regulators of cellular processes shown here, reinforces their pivotal role suggested in the remodelled “central dogma” concept.
Native Triboelectric Nanogenerator Ion Mobility-Mass Spectrometry of Egg Proteins Relevant to Objects of Cultural Heritage at Picoliter and Nanomolar Quantities
Authors: Vallejo Daniel D. , Popowich Aleksandra , Arslanoglu Julie , Tokarski Caroline , Fernández Facundo M.
Published: January 2023

Native mass spectrometry (nMS) has found widespread success in measuring native-like protein structures in the gas-phase and, when combined with ion mobility (IM), is capable of measuring protein collision cross sections (CCS) and stabilities. These methods are well validated, but often rely on samples that are abundantly available through repeated recombinant protein expression. For ultra-precious and irreplaceable samples from cultural heritage objects, protein content can be far below the micromolar and microliter levels required for robust protein experiments, a major hurdle in characterizing protein higher order structure and degradation mechanisms. Combining triboelectric nanogenerators (TENG) and IM-MS enables measuring protein size and stability rapidly from ultra-small sample quantities. Here, TENG IM-MS is implemented with standard and sub-micron emitters to characterize proteins relevant to cultural heritage objects, and demonstrates native structures can be obtained even at nanomolar concentrations and picoliter quantities.
Phosphatidylinositol-4-phosphate signaling regulates dense granule biogenesis and exocytosis inToxoplasma gondii
Authors: Arabiotorre Angela , Formanowicz Megan , Bankaitis Vytas A. , Grabon Aby
Published: January 2023

Phosphoinositide metabolism defines the foundation of a major signaling pathway that is conserved throughout the eukaryotic kingdom. The 4-OH phosphorylated phosphoinositides such as phosphatidylinositol-4-phosphate (PtdIns4P) and phosphatidylinositol-4,5-bisphosphate are particularly important molecules as these execute intrinsically essential activities required for the viability of all eukaryotic cells studied thus far. Using intracellular tachyzoites of the apicomplexan parasiteToxoplasma gondiias model for assessing primordial roles for PtdIns4P signaling, we demonstrate the presence of PtdIns4P pools in Golgi/trans-Golgi (TGN) system and in post-TGN compartments of the parasite. Moreover, we show that deficits in PtdIns4P signaling result in structural perturbation of compartments that house dense granule cargo with accompanying deficits in dense granule exocytosis. Taken together, the data report a direct role for PtdIns4P in dense granule biogenesis and exocytosis. The data further indicate that the biogenic pathway for secretion-competent dense granule formation inT. gondiiis more complex than simple budding of fully matured dense granules from the TGN.
A comparative analysis of microglial inducible Cre lines
Authors: Faust Travis E. , Feinberg Philip A. , O’Connor Ciara , Kawaguchi Riki , Chan Andrew , Strasburger Haley , Masuda Takahiro , Amann Lukas , Knobeloch Klaus-Peter , Prinz Marco , Schaefer Anne , Schafer Dorothy P.
Published: January 2023

Cre/LoxP technology has revolutionized genetic studies and allowed for spatial and temporal control of gene expression in specific cell types. The field of microglial biology has particularly benefited from this technology as microglia have historically been difficult to transduce with virus or electroporation methods for gene delivery. Here, we interrogate four of the most widely available microglial inducible Cre lines. We demonstrate varying degrees of recombination efficiency and spontaneous recombination, depending on the Cre line and loxP distance. We also establish best practice guidelines and protocols to measure recombination efficiency in microglia, which could be extended to other cell types. There is increasing evidence that microglia are key regulators of neural circuit structure and function. Microglia are also major drivers of a broad range of neurological diseases. Thus, reliable manipulation of their function in vivo is of utmost importance. Identifying caveats and benefits of all tools and implementing the most rigorous protocols are crucial to the growth of the field of microglial biology and the development of microglia-based therapeutics.