bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensing the shape of a surface by intracellular filaments
Authors: Shi Handuo , Nguyen Jeffrey , Gitai Zemer , Shaevitz Joshua , Bratton Benjamin P. , Gopinathan Ajay , Grason Gregory , Huang Kerwyn Casey
Published: November 2024

Understanding the mechanisms that dictate the localization of cytoskeletal filaments is crucial for elucidating cell shape regulation in prokaryotes. The actin homolog MreB plays a pivotal role in maintaining the shape of many rod-shaped bacteria such asEscherichia coliby directing cell-wall synthesis according to local curvature cues. However, the basis of MreB’s curvature-dependent localization has remained elusive. Here, we develop a biophysical model for the energetics of filament binding to a surface that integrates the complex interplay between filament twist and bending and the two-dimensional surface geometry. Our model predicts that the spatial localization of a filament like MreB with substantial intrinsic twist is governed by both the mean and Gaussian curvatures of the cell envelope, which strongly covary in rod-shaped cells. Using molecular dynamics simulations to estimate the mechanical properties of MreB filaments, we show that their thermodynamic preference for regions with lower mean and Gaussian curvatures matches experimental observations for physiologically relevant filament lengths of ∼50 nm. We find that the experimentally measured statistical curvature preference is maintained in the absence of filament motion and after a cycle of depolymerization, repolymerization, and membrane rebinding, indicating that equilibrium energetics can explain MreB localization. These findings provide critical insights into the physical principles underlying cytoskeletal filament localization, and suggest new design principles for synthetic shape sensing nanomaterials.

Significance statement

The protein MreB, a homolog of eukaryotic actin, regulates the shape of bacteria likeEscherichia coliby guiding new cell-wall insertion based on local curvature cues. However, the mechanism by which a nanometer-scale MreB filament “senses” the micron-scale curvature of the cell wall has remained a mystery. We introduce a biophysical model of the energetics of twisted and bent filaments bound to curved surfaces, which predicts that localization of filaments like MreB is sensitive to both mean and Gaussian curvature. The model captures experimentally measured curvature enrichment patterns and explains how MreB naturally localizes to saddle-shaped regions without energy-consuming processes. Beyond cell shape regulation, our work suggests design principles for synthetic systems that can sense and respond to surface shape.
Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis
Authors: Xue Jin , Allaband Celeste , Zuffa Simone , Poulsen Orit , Meadows Jason , Zhou Dan , Dorrestein Pieter C. , Knight Rob , Haddad Gabriel G.
Published: November 2024

Background

Obstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have implicated gut microbiota and metabolites in atherogenesis, we dissected their contributions to OSA-induced atherosclerosis.

Results

Atherosclerotic lesions were compared between conventionally-reared specific pathogen free (SPF) and germ-free (GF)ApoE-/-mice following a high fat high cholesterol diet (HFHC), with and without IHC conditions. The fecal microbiota and metabolome were profiled using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry (LC-MS/MS) respectively. Phenotypic data showed that HFHC significantly increased atherosclerosis as compared to regular chow (RC) in both aorta and pulmonary artery (PA) of SPF mice. IHC exacerbated lesions in addition to HFHC. Differential abundance analysis of gut microbiota identified an enrichment of Akkermansiaceae and a depletion of Muribaculaceae (formerly S24-7) family members in the HFHC-IHC group. LC-MS/MS showed a dysregulation of bile acid profiles with taurocholic acid, taurodeoxycholic acid, and 12-ketodeoxycholic acid enriched in the HFHC-IHC group, long-chain N-acyl amides, and phosphatidylcholines. Interestingly, GFApoE-/-mice markedly reduced atherosclerotic formation relative to SPFApoE-/-mice in the aorta under HFHC/IHC conditions. In contrast, microbial colonization did not show a significant impact on the atherosclerotic progression in PA.

Conclusions

In summary, this research demonstrated that (1) IHC acts cooperatively with HFHC to induce atherosclerosis; (2) gut microbiota modulate atherogenesis, induced by HFHC/IHC, in the aorta not in PA; (3) different analytical methods suggest that a specific imbalance between Akkermansiaceae and Muribaculaceae bacterial families mediate OSA-induced atherosclerosis; and (4) derived bile acids, such as deoxycholic acid and lithocholic acid, regulate atherosclerosis in OSA. The knowledge obtained provides novel insights into the potential therapeutic approaches to prevent and treat OSA-induced atherosclerosis.
Rethinking cholera diagnostic test performance, interpretation and evaluation: a field-based latent-class analysis in Bangladesh
Authors: Perez-Saez Javier , Bhuiyan Taufiqur Rahman , Hegde Sonia T , Khan Ishtiakul Islam , Islam Md Taufiqul , Khan Zahid Hasan , Amin Mohammad Ashraful , Dent Hulse Juan , Ahmed Shakeel , Rashid Mamunur , Rashid Rumana , Hossain Md Zakir , Khan Ashraful Islam , Qadri Firdausi , Azman Andrew S
Published: November 2024

Background

Accurate and reliable diagnostics, including rapid diagnostic tests (RDTs), are critical components of cholera control programs, though their performance has varied greatly across studies. While poorly understood, this variability may be due to the reference assay choice, patient-level and/or sampling characteristics, which hinder test result interpretation and performance evaluation.

Methods

We enrolled all suspected cholera cases seeking care at two healthcare facilities in Sitakunda, Bangladesh over 19 months. All stool samples were tested with the Cholkit RDT, and a subset by PCR and culture. Test performance was estimated using a latent-class Bayesian framework accounting for imperfect test performance, incomplete PCR and culture testing, and time-varying changes in cholera incidence. Patient-level (including age, antibiotic use) and sampling (season, testing delays) factor effects were estimated, and simulations were used to assess the bias in RDT performance estimates when using traditional reference assays.

Findings

We enrolled 3,744 suspected cases, 692 of whom were RDT-positive. Among the RDT-positives, 573 were PCR-positive and 450 culture-positive. For RDT, PCR and culture, we estimated a sensitivity of 93.5% (95% Credible Intervals, CrI: 91.3-95.4), 90.3% (88.4-92.1), and 73.7% (70.8-76.5), and a specificity of 97.3% (96.7-97.8), 97.2% (96.6-97.8), and 100% (culture specificity assumed perfect), respectively. We found that younger age (≤ 5), antibiotic use, and testing delays decreased culture sensitivity, but RDT performance remained relatively constant. The RDT positive predictive value ranged from <15% in children <5 years to >80% in adults, varying greatly across seasons. Simulations demonstrated underestimation of RDT sensitivity and specificity in low and high cholera prevalence settings, respectively, when evaluated against PCR or culture.

Interpretation

Our results shed light on the potential mechanisms leading to heterogeneous cholera RDT performance estimates in previous studies, including the use of culture as a reference assay. Across various patient and sampling characteristics, Cholkit RDT had high performance in this cholera-endemic setting, supporting its use for cholera surveillance and control. Accounting for epidemiologic context is crucial both for individual-level clinical test interpretation, and for the future evaluation of diagnostics like RDTs.

Funding

The work was supported by the Bill & Melinda Gates Foundation (INV-021879).
Improved Data Alignment Between National HIV Reporting Systems, Mozambique, 2017–2023
Authors: Tiberi Orrin , Templin Lindsay , Ferreira Ferreira , Nhaguiombe Herminio , Couto Aleny , Lara Joe , Keating Ryan , Mizela Jose , Matsimbe Lucio , Magaia Helio , da Cunha Morais
Published: November 2024

Introduction

Data quality improvements have aimed to align national reporting systems for Ministry of Health (MISAU) and PEPFAR. For example, in 2019 the patient Master Card improved systematic data collection process and sites were selected for intensified support including data quality activities (AJUDA). This study aims to compare reported data between MISAU and PEPAFR to understand data alignment trends.

Methods

The annual number of PLHIV on ART, newly initiating ART and HIV status in first ANC visit as reported by MISAU and PEPFAR were compared for 2017-2023. The absolute difference was calculated as MISAU-reported number minus PEPFAR-reported number; proportional absolute difference as the absolute difference over the MISAU-reported number and assessed the slope of the difference over time.

Results

During 2017–2023, median absolute difference for PLHIV on ART was 104,940 (range = 154,901 [2018] to 1,598 [2020]), and median proportional difference was 5.0% (range = 0.1% [2020] to 12.8% [2018]), with a trend towards improved concordance. A similar trend was found in positive HIV status at first ANC (10.4% [2017] to 0.0% [2023]), as well as with newly initiated on ART (2.7% [2017] to 0.3% [2023]).

Conclusion

In the three indicators analyzed, there were improvements in data alignment between the years of 2017 and 2023, with increased alignment in different years and for different reasons. Continued improvements will support programming and increase certainty for tracking progress toward the UNAIDS 95-95-95 goals to end HIV.
Segmentation and Measurements of Major Blood Vessels from CT Pulmonary Angiography Using Deep Learning
Authors: Kahraman Ali Teymur , Fröding Tomas , Toumpanakis Dimitris , Gustafsson Christian Jamtheim , Sjöblom Tobias
Published: November 2024

Background

Measuring major blood vessels from CT pulmonary angiography examinations (CTPAs) to assess cardiovascular diseases has the potential to improve overall patient outcomes. However, this process is time-consuming and prone to errors. Deep learning (DL) approaches offer the potential to enhance accuracy, speed, and consistency.

Objectives

To develop and train a deep learning-based algorithm capable of automatically and accurately segmenting and measuring major blood vessels in CTPAs.

Methods

Seven hundred CTPAs from 652 patients were retrospectively collected at a single center. The dataset was split into two subsets, one for training and cross-validation (n = 490) and one for assessing model performance (n = 210). The segmentation masks for the descending aorta (DAo), ascending aorta (AAo), and pulmonary trunk (PT) were generated by our previously developed segmentation model and were quantitatively validated by two radiologists. These validated masks were subsequently used as ground truth for model training. An U-Net deep learning model was created using the nnU-Net framework and trained on 490 CTPAs with 5-fold cross-validation. Following the training, the model was applied to volumes of interest in the images to generate a pool of candidate regions containing potential vessels. A vessel detection algorithm was developed and used on the candidate pool to identify vessels followed by measurement. The final model was evaluated on 210 and 47 CTPAs from internal and external datasets, respectively.

Results

Assessing model segmentation performance on the internal evaluation set, the median Dice scores were 0.95 for the DAo, 0.96 for the AAo, and 0.95 for the PT. The model measurements showed a strong correlation with those made by the radiologist, with Pearson’s r values of 0.91 for image noise, 0.98 for intravenous contrast concentration in the PT, 0.93 for AAo diameter, and 0.55 for PT diameter (P< .001). Additionally, the AAo segmentation (median Dice score 0.94) and the PT diameter measurement (r = 0.77) were evaluated in two external datasets.

Conclusions

The fully automated, deep learning-based algorithm accurately segmented and measured major blood vessels in real-world CTPAs.
Efficacy and Safety of Transcranial Temporal Interference Stimulation for Treating Bipolar Disorder with Depressive Episodes
Authors: Zhou Hetong , Wang Minmin , Qi Shuangyu , Chen Qianfeng , Lai Jianbo , Wu Zhengping , Liu Ruobing , Wang Liang , Tang Junxian , Zhang Shaomin , Hu Shaohua
Published: November 2024

Background

Bipolar disorder (BD) presents significant challenges in clinical management, often characterized by persistent depressive symptoms and cognitive deficits. Transcranial temporal interference stimulation (tTIS) has shown promise in targeting deep brain structures with minimal invasiveness. This study aimed to assess the efficacy and safety of tTIS in newly diagnosed or medication-washout BD patients.

Methods

We conducted a single-arm clinical trial with 36 BD patients who underwent 10 sessions of tTIS targeting the left nucleus accumbens over one week, with two sessions per day. Each tTIS session lasted 20 minutes, utilizing a maximum current intensity of 2 mA and an envelope stimulation frequency of 40 Hz. Depressive symptoms were assessed pre- and post-intervention using validated scales, including HAMD, QIDS, MADRS, and HAMA, while cognitive functions were evaluated using standardized neuropsychological tests. Safety was monitored through adverse event reporting.

Results

Among 36 participants, 25 completed the full intervention protocol. Significant reductions were observed in depressive symptom scores: HAMD decreased from 23.36 to 16.16 (P< 0.0001), QIDS from 13.52 to 9.68 (P< 0.001), MADRS from 39.12 to 31.28 (P< 0.01), and HAMA from 19.68 to 15.44 (P< 0.05). Cognitive evaluations demonstrated notable improvements in memory and executive function. Adverse events were mild, primarily limited to transient scalp discomfort.

Conclusions

This study provides preliminary evidence supporting the efficacy and safety of tTIS in alleviating depressive symptoms and improving cognitive function in BD patients.
HIV Antiretroviral Therapy Scale-Up in Mozambique and Estimated Averted HIV Infections and Related Deaths, 2004–2023
Authors: Chilundo Sónia , Gaspar Irénio , Keating Ryan , Fortmann Joshua , Filimão Dércio , Nguimfack Alexandre , Pereira Isabel , Alfredo Charity , Gudo Paula Samo , Langa António , Dirlikov Emilio , Greenberg Seth , Pathmanathan Ishani , Couto Aleny
Published: November 2024

Introduction

Mozambique is a HIV high-burden country. In 2004, Mozambique had an estimated HIV prevalence of 15.6% and 1.5 million people living with HIV (PLHIV). During same year the country started antiretroviral therapy (ART) scale-up supported by the U.S. President’s Emergency Plan for AIDS Relief (PEPFAR). We describe the ART scale-up and estimate averted HIV infections and HIV-related deaths.

Methods

We analyzed PEPFAR Monitoring, Evaluation, and Reporting program data from fiscal year 2004 to 2023. Before October 2018, PLHIV on ART were defined as clients with ≤90 days since last missed visit; in October 2018, this changed to ≤28 days. Viral load suppression (VLS) rate was calculated as PLHIV at PEPFAR-supported sites with VLS (<1,000 viral copies/mL) among those tested in previous 12 months. We used the 2024 United Nations Programme on HIV/AIDS (UNAIDS) Spectrum AIDS Impact Model and Goals Age Structured Model (ASM) to estimate HIV infections and HIV-related deaths averted.

Results

By September 2023, 2.1 million PLHIV in Mozambique were receiving PEPFAR-supported ART (1.4 million women [66%]; 1.9 million aged ≥15 years [95%]), a 650-fold increase from 3,226 in March 2004. The VLS rate increased from 62% (78,808/126,212) in 2017 to 94% (1,235,626/1,318,544) in 2023. During 2004–2023, ART scale-up helped avert an estimated 1.6 million HIV infections, including over 350,000 infections among HIV-exposed infants, and 1,070,295 HIV-related deaths.

Conclusion

The over 20 years of Mozambique’s scaled up ART effort has greatly expanded effective treatment and averted many new infections and HIV-related deaths. While progress has been impressive, gaps remain toward ending HIV as a public health threat.
Factors influencing healthcare providers’ knowledge and skills retention following helping mothers survive and helping babies survive training in Tanzania: A mixed methods cross-sectional study
Authors: Mwilike Beatrice Erastus , Rimoy Martha , Mabada Lucy , Komba Nicodem , Mwanga Feddy , Gosse Rashid , Ambikile Joel
Published: November 2024

The Tanzanian Midwives Association (TAMA), in collaboration with development partners, implemented a project (50,000 Happy Birthdays)from 2018 to 2020 to improve providers’ knowledge and skills in saving lives at birth. The project was implemented under two training modules namelyHelping Mothers Survive(HMS) andHelping Babies Survive(HBS). Through a mixed-methods cross-sectional design, knowledge retention was assessed by comparing follow-up and post-test knowledge scores among healthcare providers in the selected health facilities in Tanga, Geita, and Katavi regions. Four knowledge areas were evaluated using a written test and five skills areas were assessed using skills observation checklists for each. Quantitative data was analyzed using IBM SPSS version 25 by performing descriptive analysis,t-test and One-Way ANOVA with the level of significance determined at p< 0.05. Qualitative analysis was conducted through a thematic analysis approach and themes were generated to describe the factors influencing retention. 210 respondents participated in the study with more than half holding diploma (n=116; 55.2%) and working in urban area (n=123; 58.6%). There was a statistically significant drop in mean knowledge scores for controlling bleeding after birth (t=15.404,p<0.001), in helping babies breathe (t=8.580,p<0.001), and in essential care for small babies (t=19.620,p<0.001). Working in a rural area had a statistical significant higher drop in mean knowledge scores for managing pre-eclampsia (F=4.491,p=0.035) and for helping babies breathe (F=5.005,p=0.026). Education level also showed a significant difference in the mean knowledge score for managing pre-eclampsia (F=4.850,p=0.003).

There was poor knowledge retention following receiving training on HMS and HBS. The level of professional education and residential area significantly influenced knowledge retention. Frequent refresher training and other relevant training among healthcare workers may be helpful in knowledge retention regarding maternal and neonatal care, with much emphasis on providers working in rural areas and those with lower level of professional education.
Healthy Dietary Patterns and Lower Atherosclerosis in High-Risk Individuals
Authors: Cherian Laurel , Agarwal Puja , Agrawal Sonal , James Bryan D. , Yang Dixon , Wagner Maude , Leurgans Sue , Bennett David , Aggarwal Neelum , Schneider Julie
Published: November 2024

Background

This study investigates associations between diet patterns and the risk of intracranial atherosclerosis (ICAD) in individuals with preexisting hypertension (HTN) or myocardial infarction (MI).

Method

676 autopsied participants (mean age at death =91.1±6.1, 71% women) of a longitudinal clinical neuropathological cohort study, with complete dietary and neuropathology data, were included. Diet scores were computed (median interval to death = 5.9 (3.0, 8.7 years). HTN and MI history was self-reported. Large vessel atherosclerosis was evaluated at the circle of Willis, and severity of intracranial atherosclerosis was assessed based on number of atherosclerotic plaques, extent of vessel involvement, and degree of vessel occlusion to create a 4-level grading system (0-3). All regression models were adjusted for age, sex, education, caloric intake, and APOE4.

Results

Of the 676 subjects, 361 (53%) had mild, 142 (21%) had moderate, and 29 (5%) had severe atherosclerosis. There was no direct relationship between diet and atherosclerosis. The relationship between ICAD and MI (OR = 1.38, 95% CI = 0.95, 2.00) showed a nonsignificant trend. HTN (OR = 1.598, 95% CI = 1.15, 2.18) was positively associated with intracranial atherosclerosis. The association of diet with intracranial atherosclerosis differed by history of MI (MIND (p=0.007), MedDiet (p=0.006)). The association between ICAD and the MIND diet also differed by whether HTN was reported (β=-0.212, SE= 0.111, p=0.055) as did the relationship between ICAD and the MedDiet (β = -0.077, SE= 0.035, p=0.029). In stratified analysis, among individuals with preexisting MI (N=130), those with a better diet had lower odds of intracranial atherosclerosis (MedDiet: OR = 0.88, 95% CI = 0.81, 0.96; MIND: OR = 0.69, 95% CI = 0.53, 0.90).

Conclusion

A healthy dietary pattern is associated with lower odds of severe intracranial large vessel atherosclerosis in high-risk older adults. In-vivo studies of dietary habits and brain health, specifically in those at high vascular risk are needed.
The impact of knowledge, attitudes, and practices on hypertension Control and associated Comorbidities among workers of a beverage company in Bangladesh
Authors: Saleh Abu Sayeed Md. , Rahman Monjur , Mashreky S M Saidur Rahman
Published: November 2024

Hypertension is well known globally as a major health issue because of its high magnitude and further complications of cardiovascular and kidney diseases. Bangladesh has witnessed a gradual epidemiological transition where communicable diseases especially the chronic ones are dominating including the rural area where people have least access to the health care services. As is evident from aforementioned complications, hypertension if not well managed, equally has dire consequences hence calls early diagnosis and intervention. Consequently, hypertension prevalence in low-income countries rises due to certain lifestyle aspects; for instance, Afghanistan. In regard to this, Knowledge, Attitude, and Practice (KAP) questionnaires facilitate in assessing gaps in the approach toward managing hypertension. The same issues are seen in Benin: China, Egypt: Ethiopia, Ghana: India: Iran, Lebanon, Malaysia: and Mongolia where the government acknowledges that solutions should be specific to increase awareness, act on lifestyle factors and therapy compliance. Thus, management of hypertension must address general approaches to reducing the burden of hypertension and its effects on the affected individuals and healthcare facilities across the world.
Investigating immune amnesia after measles virus infection in two West African countries: A study protocol Short Title - Investigating immune amnesia in two West African countries
Authors: Fouth Tchos Karine , Ridzon Renée , Haidara Mory Cherif , Dabitao Djeneba , Akpa Esther , Camara Daouda , Vallée David , Coulibaly Mariam , Camara Sekou , Aboulhab Jamila , Diakité Mahamadou , Diarra Bassirou , Diarra Samba , Dicko Ilo , Francis Alyson , Kolié Cécé Francis , Koropogui Michel , Lim Caeul , Samaké Seydou , Hunsberger Sally , Sidibé Moussa , Chen Ray Y. , Konate Issa , Doumbia Seydou , Beavogui Abdoul Habib , Shaw-Saliba Kathryn
Published: November 2024

“Investigation of Immune Amnesia Following Measles Infection in Select African Regions” (ClinicalTrials.govIdentifier:NCT06153979) is a prospective, observational, longitudinal study being conducted in two West African countries, Guinea, and Mali. The overall goal is to investigate the impact of measles virus (MeV) infection on pre-existing immunity, vaccine response, and susceptibility to subsequent illness. A total of 256 children aged 1 to 15 years are being enrolled into one of two study arms: those with acute MeV infection (cases) and without (controls). Acute MeV is confirmed by RT-PCR testing on upper respiratory specimens or IgM detection on blood samples at screening. Blood samples are collected at multiple time points at screening (Day 0), at an optional visit to repeat IgM serology for inconclusive or negative Day 0 results (Day 7-10), and during follow-up visits on Day 14, Week 13, and Week 52. These blood samples will be tested to evaluate both humoral and cellular immune responses to endemic pathogens to measure variations in antibody diversity and antibody secreting cells (ASCs). To explore how recent MeV infection may affect the child’s ability to respond to a controlled immune stimulus, all participants will receive rabies vaccine pre-exposure prophylaxis (PrEP) using Verorab inactivated rabies vaccine. Three doses of 0.5 ml of VERORAB vaccine are administered on Days 0, 7, and 28. Biological samples will be collected after vaccination to assess if the rabies vaccine response differs: 1) between cases and controls, and 2) based on the timing of the rabies vaccination after acute measles infection. In addition, the study team will collect information on healthcare encounters during the year-long follow-up will be collected to determine if there is a difference in the number of encounters by study group. The findings of this study will further the understanding of the MeV immune amnesia phenotype.
From protection of sacrificial self to critical turning points and growth: Nurses’ experiences on the frontline during the COVID-19 pandemic
Authors: Creedon Sinéad , Trace Anna
Published: November 2024

The mental health and wellbeing of nurses has been a concern, long before the arrival of the COVID-19 pandemic. Working on the frontline under such challenging circumstances, for extended periods of time, has resulted in negative psychological responses. The current study aims to examine nurses’ resilience in acute hospitals in Ireland, during a period of adversity (pandemic), to explore it’s impact on their personal and professional identity, and their perception of meaningful supports and coping. An interpretative phenomenological analysis was carried out to gain insight into how nurses adapted to the changing work environment during the pandemic. Online semi-structured interviews were carried out with six experienced female nurses, who were redeployed to the frontline from their own roles. Three experiential themes representing the nurses’ journey were generated: Protection of Sacrificial Self; The Fortifying Effect of Us, and Critical Turning Points & Growth. Nurses made significant sacrifices and had to find ways to detach to cope. They revitalized themselves by creating a sense of ‘us’ to help them face a harsh climate against others, which enabled critical turning points and growth. This study has strongly highlighted the emotional effects on nurses due to feeling isolated, undervalued, and excluded during redeployment to the frontline. It has also featured how well nurses coped while faced with an existential crisis and has given voice to all nurses who faced this pandemic despite exposure to risk of burnout and threats to their mental health and wellbeing. This study has further enriched our understanding of personal growth and trauma in adverse work conditions by including an exploration of what sacrificial commitment adds to our understanding of physical and moral courage. Future provision of supports for nurses must be ongoing both during and after crisis events.
Obesity-associated MRAP2 variants impair multiple MC4R-mediated signaling pathways
Authors: Wyatt Rachael A. , Jamaluddin Aqfan , Mistry Vinesh , Quinn Caitlin , Gorvin Caroline M.
Published: November 2024

The melanocortin-4 receptor (MC4R) is a G protein-coupled receptor expressed at hypothalamic neurons that has an important role in appetite suppression and food intake. Mutations in MC4R are the most common cause of monogenic obesity and can affect multiple signaling pathways including Gs-cAMP, Gq, ERK1/2, β-arrestin recruitment, internalization and cell surface expression. The melanocortin-2 receptor accessory protein 2 (MRAP2), is a single-pass transmembrane protein that interacts with and regulates signaling by MC4R. Variants in MRAP2 have also been identified in overweight and obese individuals. However, functional studies that have only measured the effect of MRAP2 variants on MC4R-mediated cAMP signaling have produced inconsistent findings and most do not reduce MC4R function. Here we investigated the effect of twelve of these previously reported MRAP2 variants and showed that all variants that have been identified in overweight or obese individuals impair MC4R function. When expressed at equal concentrations, seven MRAP2 variants impaired MC4R-mediated cAMP signaling, while nine variants impaired IP3 signaling. Four mutations in the MRAP2 C-terminus affected internalization. MRAP2 variants had no effect on total or cell surface expression of either the MRAP2 or MC4R proteins. Structural models predicted that MRAP2 interacts with MC4R transmembrane helices 5 and 6, and mutations in two MRAP2 residues in putative contact sites impaired the ability of MRAP2 to facilitate MC4R signaling. In summary, our studies demonstrate that human MRAP2 variants associated with obesity impair multiple MC4R signaling pathways and that both Gs-cAMP and Gq-IP3 pathways should be assessed to determine variant pathogenicity.
Targeting GOF p53 and c-MYC through LZK Inhibition or Degradation Suppresses Head and Neck Tumor Growth
Authors: Funk Amy L. , Katerji Meghri , Afifi Marwa , Nyswaner Katherine , Woodroofe Carolyn C. , Edwards Zoe C. , Lindberg Eric , Bergman Knickole L. , Gough Nancy R. , Rubin Maxine R. , Karpińska Kamila , Trotter Eleanor W. , Dash Sweta , Ries Amy L. , James Amy , Robinson Christina M. , Difilippantonio Simone , Karim Baktiar O. , Chang Ting-Chia , Chen Li , Xu Xin , Doroshow James H. , Ahel Ivan , Marusiak Anna A. , Swenson Rolf E. , Cappell Steven D. , Brognard John
Published: November 2024

The worldwide frequency of head and neck squamous cell carcinoma (HNSCC) is approximately 800,000 new cases, with 430,000 deaths annually. We determined that LZK (encoded byMAP3K13) is a therapeutic target in HNSCC and showed that inhibition with small molecule inhibitors decreases the viability of HNSCC cells with amplifiedMAP3K13. A drug-resistant mutant of LZK blocks decreases in cell viability due to LZK inhibition, indicating on-target activity by two separate small molecules. Inhibition of LZK catalytic activity suppressed tumor growth in HNSCC PDX models with amplifiedMAP3K13. We found that the kinase activity of LZK stabilized c-MYC and that LZK stabilized gain-of-function (GOF) p53 through a kinase-independent mechanism. Therefore, we designed proteolysis-targeting chimeras (PROTACs) and demonstrate that our lead PROTAC promotes LZK degradation and suppresses expression of GOF p53 and c-MYC leading to impaired viability of HNSCC cell lines. This research provides a strong basis for development of therapeutics targeting LZK in HNSCCs with amplification of the gene.

One Sentence Summary

This study establishes the kinase LZK as a therapeutic target for HNSCC through regulation of c-MYC expression.
Enhanced encephalitic tropism of bovine H5N1 compared to the Vietnam H5N1 isolate in mice
Authors: Goldin Kerry , van Tol Sarah , Johnson Randall C. , Mukesh Reshma Koolaparambil , Gallogly Shane , Schulz Jonathan E. , Prado-Smith Jessica , Saturday Greg , Yinda Kwe Claude , Munster Vincent J. , de Wit Emmie , van Doremalen Neeltje
Published: November 2024

In recent years, the landscape of highly pathogenic avian influenza (HPAI) virus infections has shifted, as evidenced by an increase in infections among mammals. This includes the recent circulation of H5N1 in dairy cattle herds in the USA and a rise in associated human cases. In this study, we investigated differences in tissue tropism of two HPAI H5N1 strains, the isolate A/Vietnam/1203/2004 (VN1203) isolated from a fatal human case in 2004 and the bovine isolate A/Bovine/Ohio/B24osu-342/2024 (Bov342) isolated in 2024, in C57BL/6J mice. Infection with either HPAI H5N1 isolate was uniformly lethal in mice. However, tissue tropism differed significantly: while VN1203 replication was largely restricted to the respiratory tract, Bov342 successfully replicated in the respiratory tract as well as various regions of the brain. Bov342-challenged animals exhibited clinical signs consistent with central nervous system (CNS) infection, and infectious virus was detected in brain tissue. Correspondingly, cytokine profiles in the brain differed significantly between the isolates. Notably, in addition to abundant evidence of CNS infection in Bov342-challenged mice via immunohistochemistry, sporadic intranuclear and intracytoplasmic immunoreactivity was observed in other tissues in the head, including the choroid plexus, retina, and inner ear. This study demonstrates that while both HPAI H5N1 isolates are uniformly lethal in C57BL/6J mice upon aerosol exposure, significant differences exist in tissue tropism, with Bov342 resulting in respiratory disease as well as increased neurotropism and inflammation in the brain and nasal turbinates compared to VN1203, which predominantly induces respiratory disease.

Significance statement

The rise in HPAI H5N1 infections among mammals, including humans in the USA, highlights an emerging One Health concern. Understanding the phenotypic changes of HPAI H5N1 and associated increase in infection of mammalian hosts is critical. In this study, we investigated the tissue tropism in mice of a bovine HPAI H5N1 strain isolated in 2024 and compared it to a strain isolated from a human patient in 2004. Our findings reveal that the bovine isolate exhibits enhanced neurotropism, unlike the respiratory-restricted replication observed with the HPAI H5N1 isolate from 2004. This difference in tissue tropism, accompanied by distinct cytokine responses in the brain, underscores the potential for altered disease outcomes in other mammalian hosts.
Boltz-1: Democratizing Biomolecular Interaction Modeling
Authors: Wohlwend Jeremy , Corso Gabriele , Passaro Saro , Reveiz Mateo , Leidal Ken , Swiderski Wojtek , Portnoi Tally , Chinn Itamar , Silterra Jacob , Jaakkola Tommi , Barzilay Regina
Published: November 2024

Understanding biomolecular interactions is fundamental to advancing fields like drug discovery and protein design. In this paper, we introduce Boltz-1, an open-source deep learning model incorporating innovations in model architecture, speed optimization, and data processing achieving AlphaFold3-level accuracy in predicting the 3D structures of biomolecular complexes. Boltz-1 demonstrates a performance on-par with state-of-the-art commercial models on a range of diverse benchmarks, setting a new benchmark for commercially accessible tools in structural biology. By releasing the training and inference code, model weights, datasets, and benchmarks under the MIT open license, we aim to foster global collaboration, accelerate discoveries, and provide a robust platform for advancing biomolecular modeling.
Critical assessment of nanopore sequencing for the detection of multiple forms of DNA modifications
Authors: Kong Yimeng , Zhang Yanchun , Mead Edward A. , Chen Hao , Loo Christian E. , Fan Yu , Ni Mi , Zhang Xue-Song , Kohli Rahul M. , Fang Gang
Published: November 2024

While nanopore sequencing is increasingly used for mapping DNA modifications, it is important to recognize false positive calls as they can mislead biological interpretations. To assist biologists and methods developers, we describe a framework for rigorous evaluation that highlights the use of false discovery rate with rationally designed negative controls capturing both general background and confounding modifications. Our critical assessment across multiple forms of DNA modifications highlights that while nanopore sequencing performs reliably for high-abundance modifications, including 5-methylcytosine (5mC) at CpG sites in mammalian cells and 5-hydroxymethylcytosine (5hmC) in mammalian brain cells, it makes a significant proportion of false positive detections for low-abundance modifications, such as 5mC at CpH sites, 5hmC and N6-methyldeoxyadenine (6mA) in most mammal cell types. This study highlights the urgent need to incorporate this framework in future methods development and biological studies, and advocates prioritizing nanopore sequencing for mapping abundant over rare modifications in biomedical applications.
The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation
Authors: Piscitelli Silvia , Cascone Emanuela , D’Ambrosio Chiara , Divisato Giuseppina , De Lisio Laura , Leoni Guido , Matassa Danilo Swann , Lanzuolo Chiara , Rosti Valentina , Zizolfi Maria Chiara , Matuozzo Monica , di Patrizio Soldateschi Emanuele , Maiuri Paolo , Scaloni Andrea , Passaro Fabiana , Parisi Silvia
Published: November 2024

The transition of embryonic stem cells (ESCs) from pluripotency to lineage commitment is regulated by multiple mechanisms, including chromatin dynamics and both transcriptional and post-transcriptional processes. Recent advances have highlighted that these mechanisms often interact, forming intricate multi-layered regulatory networks that require detailed characterization. In this study, we demonstrate that the RNA-binding protein LIN28A plays a pivotal role in neuronal differentiation by mediating RNA-dependent interactions with the Polycomb repressive complex 2 (PRC2). This interaction facilitates the eviction of PRC2 from chromatin, thereby activating a neuronal lineage-specific transcriptional program. Proteomic analyses revealed that the LIN28A interactome undergoes substantial remodeling during differentiation, corresponding to changes in LIN28A localization. In ESCs, LIN28A is predominantly nuclear and interacts with several components of the PRC2 complex in an RNA-dependent manner, assisting in chromatin dynamics. Our findings show that in the absence of LIN28A, PRC2 remains associated with chromatin, impairing the expression of genes critical for neuronal differentiation in ESCs. Chromatin immunoprecipitation sequencing (ChIP-seq) further confirmed that loss of LIN28A results in preferential PRC2 occupancy at the promoters of differentiation-associated genes. This study uncovers a novel role for LIN28A in epigenetic remodeling, which is essential for the proper differentiation of ESCs into the neuronal lineage.
Comparative single-cell lineage bias in human and murine hematopoietic stem cells
Authors: Shamie Isaac , Bliss-Moreau Meghan , Lee Jamie Casey , Mathieu Ronald , Hoffman Harold M. , Geng Bob , Lewis Nathan E. , Zhu Yanfang Peipei , Croker Ben A.
Published: November 2024

The commitment of hematopoietic stem cells (HSC) to myeloid, erythroid, and lymphoid lineages is influenced by microenvironmental cues, and governed by cell-intrinsic and epigenetic characteristics that are unique to the HSC population. To investigate the nature of lineage commitment bias in human HSC, mitochondrial single cell (sc) ATAC-Sequencing (mt-scATAC-Seq) was used to identify somatic mutations in mitochondrial DNA to act as natural genetic barcodes for tracking theex vivodifferentiation potential of HSC to mature cells. Clonal lineages of human CD34+cells and their mature progeny were normally distributed across the hematopoietic lineage tree without evidence of significant skewing. To investigate commitment biasin vivo, mice were transplanted with limited numbers of long-term HSC (LT-HSC). Variation in the ratio of myeloid and lymphoid cells between donors, although suggestive of a skewed output, was not altered by increasing numbers of LT-HSC. These data suggest that the variation in myeloid and lymphoid engraftment is a stochastic process influenced by the irradiated recipient niche and not a cell-intrinsic lineage bias of LT-HSC.
Uncertainty mapping and probabilistic tractography using Simulation-Based Inference in diffusion MRI: A comparison with classical Bayes
Authors: Manzano-Patrón J.P. , Deistler Michael , Schröder Cornelius , Kypraios Theodore , Gonçalves Pedro J. , Macke Jakob H. , Sotiropoulos Stamatios S.N.
Published: November 2024

Simulation-Based Inference (SBI) has recently emerged as a powerful framework for Bayesian inference: Neural networks are trained on simulations from a forward model, and learn to rapidly estimate posterior distributions. We here present an SBI framework for parametric spherical deconvolution of diffusion MRI data of the brain. We demonstrate its utility for estimating white matter fibre orientations, mapping uncertainty of voxel-based estimates and performing probabilistic tractography by spatially propagating fibre orientation uncertainty. We conduct an extensive comparison against established Bayesian methods based on Markov-Chain Monte-Carlo (MCMC) and find that: a) in-silico training can lead to calibrated SBI networks with accurate parameter estimates and uncertainty mapping for both single and multi-shell diffusion MRI, b) SBI allows amortised inference of the posterior distribution of model parameters given unseen observations, which is orders of magnitude faster than MCMC, c) SBI-based tractography yields reconstructions that have a high level of agreement with their MCMC-based counterparts, equal to or higher than scan-rescan reproducibility of estimates. We further demonstrate how SBI design considerations (such as dealing with noise, defining priors and handling model selection) can affect performance, allowing us to identify optimal practices. Taken together, our results show that SBI provides a powerful alternative to classical Bayesian inference approaches for fast and accurate model estimation and uncertainty mapping in MRI.
Cell-type specific prediction of RNA stability from RNA-protein interactions
Authors: Saran Sepideh , Lebedeva Svetlana , Hirsekorn Antje , Ohler Uwe
Published: November 2024

RNA-binding proteins (RBPs) are important contributors to post-transcriptional regulatory processes. The combinatorial action of expressed RBPs and non-coding factors bound to the same transcript determines post-transcriptional properties of the mRNA in a context-dependent manner. To gain a better understanding of RNA stability and translational activity across different conditions, we have compiled and analyzed a set of ribosome profiling datasets for four human cell lines and used existing and newly generated metabolic labeling data to determine matching RNA degradation rates. We then used machine learning methods to predict RNA degradation rate and translation level from RBP binding information, which comprised existing in vivo binding datasets and computationally predicted binding sites. Utilizing this new RNA stability resource, we predicted RNA degradation rate and translation level from RBP binding alone. In vivo binding sites had higher importance for prediction compared to computationally predicted binding sites, likely due to confounding effects. We further explored the feature importance of different RBPs for stability prediction in the context of differential stability conferred by 3’UTR isoforms. Taken together, an RNA stability machine learning model trained on one context successfully generalizes but is impacted by the availability and reliability of current data.
HUMAN SPINAL CORD ORGANOIDS REVEAL CELL INTERCALATION AS A CONSERVED MECHANISM FOR SECONDARY NEURULATION
Authors: Blanco-Ameijeiras José , García-Valero Mar , El Majzoub Yara , Rebollo Elena , Macho-Rendón Javier , Corbacho Jorge , Martínez-Morales Juan Ramón , Martí Elisa
Published: November 2024

The spinal cord originates from bipotent stem cells called neuromesodermal progenitors, which are organized in a transient embryonic structure called the neural tube. The development of neural organoids is offering unprecedented tools to advance in the limited understanding of the initial construction and subsequent maturation of the human neural tube. In this study, we have generated human neural tube organoids with defined anterior and posterior identities. Through transcriptome profiling, we identified that the posterior organoids possessed a spinal cord identity. By modifying the culture conditions, we recapitulated the morphogenetic events for secondary neurulation in vivo, and revealed that de novo lumen formation in the spinal cord organoids involves a conserved Yap-dependent cell intercalation process. We believe that these findings will contribute to our understanding of the mechanisms required for building the human spinal cord in the embryo, and to understand the biological basis of neurodevelopmental disorders, which are among the most common birth defects.

INCLUSION AND DIVERSITY

We support inclusive, diverse, and equitable conduct of research
Host origin of microbiota drives functional recovery andClostridioides difficileclearance in mice
Authors: Millard Sophie A. , Vendrov Kimberly C. , Young Vincent B. , Seekatz Anna M.
Published: November 2024

Colonization resistance provided by the gut microbiota is essential for resisting both initialClostridioides difficileinfection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearingC. difficilecompared to a mouse-derived microbiota, despite successful microbial engraftment and recovery of bacterial functional potential. Metabolomic analysis revealed deficits in secondary metabolites, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors involved in FMT-based recovery from rCDI.

Importance

Clostridioides difficileis a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain largely underexplored. This study reveals that effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for CDI and other conditions.
Vertebrate vision is ancestrally based on competing cone circuits
Authors: Fornetto Chiara , Euler Thomas , Baden Tom
Published: November 2024

Vision first evolved in the water, where light becomes increasingly monochromatic with viewing distance. The presence of spectrally broad (′white′) light is therefore the exclusive remit of the visual foreground. However, if and how aquatic visual systems exploit this ′white effect′ as an inductive bias, for example to judge distance, remains unknown. By combining two-photon imaging with hyperspectral stimulation, genetic cone-type ablation, and behaviour, we here show that zebrafish suppress neural responses to the visual background by contrasting ′greyscale′ and ′colour′ circuits that emerge at the first synapse of vision. To do so, zebrafish use an early retinal architecture that fundamentally differs from that of mammals: Rather than combining cone signals to drive the retinal output leading to behaviour, zebrafish vision is built around competing ancestral cone systems: Red/UV versus green/blue. Of these, the non-opponent red and UV cones, which are retained in mammals, are necessary and sufficient for vision. By contrast, the colour opponent green and blue cones, which are lost in mammals, form a net-suppressive ′auxiliary′ system that shape the ′core′ drive from red and UV cones. Our insights challenge the long–held notions that cones act in concert to drive visual behaviour, and that their spectral diversity primarily serves colour vision. Instead, we posit that vertebrate vision is ancestrally built upon opposing cone systems that emerged to exploit the strong spectral interactions of light with water. This alternative view points at terrestrialisation, not nocturnalisation, as the leading driver for visual circuit reorganisation in mammals.