bluuebunny/crossref_metadata_2025 huggingface dataset:
Bimodal distributions of anti-Trypanosoma cruziantibody levels in blood donors are associated with parasite detection and antibody waning in peripheral blood
Authors: Remesar Mirta C. , Sabino Ester C. , Buss Lewis F. , Merlo Claudio D. , López Mónica G. , Humeres Sebastián L. , Héctor Pavón A. , Clara Di Germanio C. , Coco Sonia Bakkour , Oliveira-da Silva Léa C. , Filho Marcelo Martins Pinto , Ribeiro Antonio Luiz P. , Busch Michael P. , del Pozo Ana E.
Published: November 2024

Background

In our previous study of blood donors in the Argentinian Chaco Province, we documented bimodal distributions of anti-Trypanosoma cruziantibody (Ab) levels, suggesting potential self-cure in donors with low-reactive samples. This study aimed to correlate “high” and “low” Ab level groups, defined by a mathematical model, with parasitemia and electrocardiogram findings. Ab decline over time was also assessed.

Methodology / Principal Findings

We invitedT. cruziAb reactive blood donors to enroll in the study from October 2018 to November 2019 with a follow up visit two years later. Blood samples were tested forT cruziAb by: Chagatest ELISA Lisado and Chagatest ELISA Recombinante v.4.0 (Wiener Lab, Argentina); VITROS Immunodiagnostic Products Anti-T.cruzi (Chagas) (Ortho-Clinical Diagnostics Inc., UK), and Architect Chagas (Abbott Laboratories, Germany). Target capture PCR was performed on lysed whole blood samples from enrollment visits and electrocardiograms on second visits.

Four hundred fifty donors were recruited, but 68 were excluded due to negative results on all study Ab assays. Ab level distributions were bimodal and classified as “high” or “low” at a calculated threshold for each of four assays. There were 160 donors with low and 179 with high Ab results on all assays. The remainder 43 were discordant reactive. Ninety-seven percentage of the PCR positive donors were among the concordant high Ab group. During the 2-4 year follow-up interval, relative Ab declines by three assays were significantly greater among those classified as low Ab and with negative PCR results.

Conclusions / Significance

Ab reactivity is associated with PCR-detectable parasitemia. Greater Ab declines were detected among donors with low and/or discordant Ab reactivity and negative PCR results, suggesting spontaneous parasite clearance in these donors.
Cross-dataset pan-cancer detection: Correlating cell-free DNA fragment coverage with open chromatin sites across cell types
Authors: Olsen Ludvig Renbo , Odinokov Denis , Holsting Jakob Qvortrup , Kondrup Karoline , Iisager Laura , Rusan Maria , Buus Simon , Laursen Britt Elmedal , Borre Michael , Jochumsen Mads Ryø , Bouchelouche Kirsten , Frydendahl Amanda , Rasmussen Mads Heilskov , Henriksen Tenna Vesterman , Nesic Marijana , Demuth Christina , Lindskrog Sia Viborg , Nordentoft Iver , Lamy Philippe , Therkildsen Christina , Dyrskjøt Lars , Sørensen Karina Dalsgaard , Andersen Claus Lindbjerg , Skanderup Anders Jakobsen , Besenbacher Søren
Published: November 2024

The fragmentation patterns of whole genome sequenced cell-free DNA are promising features for tumor-agnostic cancer detection. However, systematic biases challenge their cross-cohort generalization. We introduce LIONHEART, a novel, open source cancer detection method specifically optimized to generalize across datasets. The method correlates bias-corrected cfDNA fragment coverage across the genome with the locations of accessible chromatin regions from 487 cell and tissue types. We use these correlations to detect changes in the cell-free DNA cell type composition caused by cancer. We test LIONHEART on eight datasets and twelve cancer types (1083 non-cancer controls, 1251 cancers) obtained from different studies and show that it can distinguish cancer samples from non-cancer controls across cohorts with ROC AUC scores ranging from 0.59-0.91 (mean = 0.80, std = 0.11). We further validate the method on an external dataset, achieving a ROC AUC of 0.859.
Assessment of the implementation of iron and folic acid tablets supplementation to in-school girls in Nanumba South District of Northern Region, Ghana
Authors: Razak Nayina Bakunboa Isaac , Kogi Robert , Ndayishimiye Jean Claude , Opoku Samuel Yaw
Published: November 2024

Iron deficiency is a leading cause of morbidity and mortality among adolescent girls 10– 19 years of age globally. Despite the free weekly iron and folic acid supplementation, prevalence of anaemia among adolescent females still between 24% to 64.6%. This study sought to identify the factors affecting the implementation of iron and folic acid program to a school-based anaemia reduction in the Nanumba South District, Northern Region, Ghana.

A cross-sectional analytical study was carried out. And a simple random sampling method was used to select the schools and the adolescent girls, while purposive sampling was used to select school health coordinators and health staff. The outcome variable was IFA compliance and exposures were knowledge on anaemia and IFAS program, as well as socio-demographic factors (Age, marital status, level of education, gestational age, parity, gestation age, and occupation). Adolescent girls who consumed at least five tablets of the expected dose in the previous 7 weeks (1 tablet per week) which is equivalent to consuming 70% of the expected dose before the day of the data collection were considered compliant. Respondents who were able to get “1” in all the four knowledge questions were considered to have good level of knowledge. Occupation level of parents was self-identified by the respondents. Multivariable logistic regression analysis was performed to identify the predictors of the outcome variable. Significance level was set at p<0.05.

The level of knowledge about benefits of iron and folic acid supplementation was generally high in this study (88.0%). Overall, the majority (65.7%) of the respondents complied with iron and folic acid supplementation. Father’s occupational level was the only variable, which was significantly associated with adolescent girls’ IFA consumption compliance (p=0.002). The odds of compliance among respondents who were 17-25 years was significantly 56% times lower compared to those who were 10-16 years (AOR = 0.44 (95% CI: 0.21-0.96) p = 0.038). Adolescent girls of Kokomba ethnic group were also 83% less likely to comply with iron and folic acid consumption (AOR = 0.17 (95% CI: 0.03-0.89) p = 0.036).

In conclusion, the study highlighted high compliance with the IFA among respondents, emphasizing the critical roles of teachers and health workers in counseling, monitoring, and supervision, while identifying age 17-25 years and Kokomba ethnic group being less significant factors influencing compliance. It is recommended that the role of teachers and health workers in the IFAS program should be strengthened, while addressing barriers to compliance among older adolescents and engaging families.
Evaluating malaria elimination strategies in military forces in Cambodia: a cluster-randomized clinical trial comparing monthly prophylaxis with focused screening and treatment
Authors: Wojnarski Mariusz , Chaudhury Sidhartha , Boonchan Threechada , Bun Rathvicheth , Chann Soklyda , Gosi Panita , Soveasna Kin , Song Sokhun , Buathong Nillawan , Ittiverakul Mali , Sriwichai Sabaithip , Arsanok Montri , Kuntawunginn Worachet , Saingam Piyaporn , Chaisatit Chaiyaporn , Ponlawat Alongkot , Fansiri Thanyalak , Vanachayangkul Pattaraporn , Jaichapor Boonsong , Sinoun Muth , Chuor Char Meng , Kheangheng Thay , So Mary , Wanja Elizabeth , Davidson Silas , Spring Michele , Rekol Huy , Dysoley Lek , Saly Kong , Livezey Jeffrey R. , Lin Jessica T. , Smith Philip L. , Satharath Prom , Manning Jessica E. , Sok Somethy , Saunders David L.
Published: November 2024

Background

Identifying effective malaria elimination strategies for remote forested regions in Southeast Asia is challenging given limited resources. In this study, two malaria elimination strategies were evaluated in partnership with the Royal Cambodian Armed Forces - monthly malaria prophylaxis (MMP) and focused screening and treatment (FSAT).

Methods

Eight primarily military clusters (1,050 volunteers total) along the Cambodian-Thai border were randomized to 3 months of MMP or FSAT with monthly malaria testing by RDT, PCR, and microscopy for six months. Clusters were sub-randomized to permethrin treated (ITU) or sham water-treated clothing (sITU). Volunteers in MMP clusters were given three full monthly dihydroartemisinin-piperaquine (DP) treatment courses with 12 weekly 22.5mg primaquine. Volunteers in FSAT clusters were treated with appropriate first-line antimalarials if malaria-positive by microscopy or PCR.

Results

Pfpositivity in MMP clusters was reduced by 90% (10% at enrollment to 1% at 6 months; absolute risk reduction (ARR) 9%) at 6 months. However, 32% ofPfcases treated with DP as MMP at baseline recrudesced, requiring rescue treatment at 1 month with artesunate-mefloquine.Pfpositivity in FSAT clusters declined 66% over 6 months (7.6% to 2.7%; ARR 4.9%). MMP reducedPvpositivity from 9% to 0% at 3 months, butPvrebounded to 6.7% at 6 months. FSAT failed to significantly reducePvpositivity during the study. The 22.5mg weekly primaquine MMP regimen was safe, even for the 15% of volunteers with G6PD-deficiency. Those wearing ITU had additionalPvparasitemia reductions compared to sITU in the FSAT but not MMP groups. PCR was more sensitive than microscopy and RDT for detecting both species.

Conclusions

MMP was safe, and superior to FSAT to reducePfandPv, suggesting greater utility to achieve malaria elimination in Cambodia. Low dose (22.5mg) weekly primaquine was a safe adjunct in this setting, even for those with G6PD-deficiency. Permethrin-treated clothing further reducedPvparasitemia for FSAT but not MMP. MMP may be more easily scaled to eliminate malaria. The military may provide substantial support for regional elimination efforts.
Env from EIAV vaccine delicately regulates NLRP3 activation via attenuating NLRP3-NEK7 interaction
Authors: Guo Xing , Liu Cong , Wang Yuhong , Li Hongxin , Ma Saiwen , Na Lei , Ren Huiling , Lin Yuezhi , Wang Xiaojun
Published: November 2024

The current equine infectious anemia virus (EIAV) vaccine causes attenuation of the inflammatory response to an appropriate level, compared to that produced by virulent EIAV. However, how the EIAV vaccine finely regulates the inflammatory response remains unclear. Using a constructed NLRP3-IL-1β screening system, viral proteins from two EIAV strains (the attenuated vaccine and its virulent mother strain) were examined separately. Firstly, EIAV-Env was screened to direct binding P2X7(R) with notable K+efflux trans-cellularly. Secondly, EIAV-Env was found to bind NLRP3 and/or NEK7 to trigger aggregation of NLRP3-NEK7 to form NLRP3-NEK7 complex in cells. Comparison of the two strains, we observed a significant reduction on vaccine-Env-initiated NLRP3-NEK7 complex formation, with no difference in Env triggering P2X7(R)-mediated ion fluxes. Thirdly, reciprocally mutation on four stable varied amino acids between two strains produced an anticipated outcome on NLRP3-IL-1β-axis activation. As the attenuated vaccine was shown evolved as a natural quasispecies of the virulent EIAV, its precise and adaptable regulation via spatial proximity-dependent intracellular activation might present a “win-win” virus-host adaption, offering an alternative strategy on HIV vaccine development.

Author Summary

Here, we report that EIAV-Env mediates NLRP3 inflammasome activation through two distinct pathways. The first pathway involves a transcellular mechanism driven by K+ flux, which couples Env-P2X7 interaction. The second pathway entails direct intracellular binding between Env and NLRP3, promoting the assembly of NLRP3-NEK7 and subsequent inflammasome formation. Notably, we observed a marked difference in NLRP3 inflammasome activation between the vaccine and virulent strains, which was reflected in the extent of Env-mediated NLRP3-NEK7 aggregation. This study not only enhances our understanding of lentivirus-host immune interactions but also contributes to the broader discourse on virus evolution and host-induced inflammation.
The Growth Hormone-IGF-1 axis is a risk factor for Long-Term Kidney Allograft Failure
Authors: Cusick Matthew , Nair Viji , Fermin Damian , Hartman John , Beamish Jeffrey A. , Sun Zeguo , Zhang Zhongyang , Otto Edgar , Menon Rajasree , Nadimidla Sudha , Demchuk Nicholas , Shaffer Kelly , Heeger Peter , Zhang Weija , Menon Madhav C. , Kretzler Matthias , Wiggins Roger C. , Naik Abhijit S.
Published: November 2024

Introduction

Maladaptive hypertrophy and podocyte stress and depletion contribute to kidney function decline. Although IGF-1 plays a key role in early hypertrophic responses in the single kidney state, its impact on KTx outcomes remains uncertain. This report tests the hypothesis that early IGF-1 exposure reduces KTx survival.

Methods

Population datasets compared incident Death Censored Graft Failure (DCGF) rates by age at KTx (n=366,404) with IGF-1 levels by age (n=15,014). A clinical study of 216 KTx recipients evaluated the association of IGF-1 exposure with DCGF and secondary outcomes of proteinuria and Biopsy-Proven Acute Rejection. IGF-1 exposure was modeled using pre-KTx IGF-1 levels and donor kidney dose estimated from the donor:recipient body surface area ratio reflecting allograft hyperfiltration. The association of DCGF with an IGF1 SNP linked to high IGF-1 levels was assessed in 724 genotyped allograft recipients. Single-cell transcriptomic data from first-year post-KTx patients (n=14) and binephric donors (n=18) were compared to assess intrarenal cellular expression ofIGF1, IGF1R, and GHRtranscripts.

Results

DCGF risk by age at KTx paralleled IGF-1 levels by age. Higher IGF-1 exposure was associated with significantly increased risks of DCGF, proteinuria and T-Cell mediated rejection. Genotypic analysis showed a 50% increase in DCGF risk per risk allele at IGF1 eQTLrs35767. First-year biopsy results revealed no increase in intrarenalIGF1transcript, whileGHRandIGF-1Rtranscripts were suppressed, consistent with circulating IGF-1 (vs. graft-derived IGF-1) being the primary source of IGF-1 exposure.

Conclusion

We identify a novel role for the GH-IGF-1 axis in reducing KTx survival.
Knowledge of healthcare workers in the domain of oncogenetics
Authors: Jabbour Jad , Habibian Léa , Martin Christine Anne-Marie , Diab Ernest , Kourié Hampig Raphaël
Published: November 2024

Background

Cancer is the second leading cause of mortality globally. 5-10% of cancer cases involve a genetic factor. Oncogenetics studies the role of genetic mutations in the development of cancer and plays a crucial role in understanding cancer pathogenesis and developing targeted therapies. Despite the critical nature of this field, the knowledge level among healthcare workers regarding oncogenetics, particularly in breast cancer, remains underexplored.

Objective

This study aimed to assess the knowledge of healthcare workers in oncogenetics, with a specific focus on breast cancer, to identify gaps and potential areas for educational intervention.

Methods

A cross-sectional, web-based survey was conducted at a University Hospital. A questionnaire consisting of general and breast cancer-specific oncogenetics questions was distributed to nurses, medical interns, residents, and doctors. Responses were scored and analyzed to potentially identify statistically significant differences based on professional roles and experience.

Results

184 answers were recorded from which 89.67% confirmed familiarity with the term oncogenetics. Medical interns, residents, and doctors demonstrated significantly higher knowledge compared to nurses (p<0.001). The average scores indicated better general oncogenetics knowledge (mean=4.83/6) than breast cancer-specific knowledge (mean=3.77/6). Familiarity with oncogenetics correlated with higher scores across both sections (p<0.001). Notably, male participants outperformed females in breast cancer oncogenetics (p=0.02).

Conclusion

Healthcare workers displayed a satisfactory general knowledge of oncogenetics but showed significant gaps in breast cancer-specific knowledge. These findings highlight the need for targeted educational programs to enhance oncogenetics competency among healthcare workers, ensuring improved patient care. Future studies should evaluate the impact of such educational interventions on healthcare workers’ knowledge and practice.
Joint contact forces during barefoot, minimal and conventional shod running are highly individual
Authors: Kloock Lena , Arensmann Andrea , de Graaf Myriam , Gerlach Meike , Boström Kim , Wagner Heiko
Published: November 2024

The supposed benefits of barefoot running are an often debated topic, with many studies investigating footwear influences on the kinematics and kinetics of running. Few studies, however, have analysed the effect on joint contact forces (JCFs). In this study, we investigated the influence of different footwear on the JCFs of the hip, knee, and ankle during running using a 3D musculoskeletal model. Kinematics were recorded from 16 volunteers while running on a treadmill at two speeds (2.0m/s and 2.5m/s) either barefoot (BF), wearing minimal shoes (MM), or normal shoes (NS). Alongside the JCFs, stride parameters and joint angles were examined using a generalised linear mixed model. Results showed a decrease in the hip JCF from BF to MM to NS, no consistent changes in the knee and an increase from BF to MM to NS at the ankle. However, these changes mostly had small effect sizes, so it’s unclear how relevant they are. The individual responses were much larger and showed opposite effects, indicating that the effects of footwear are highly individual and probably depend on the running style and characteristics of each runner.
A scoping review of guidelines on reporting and assessing dynamic mathematical models of infectious diseases
Authors: Chaturvedi Madhav , Bartz Antonia , Denkinger Claudia M , Klett-Tammen Carolina , Kretzschmar Mirjam , Kuhlmann Alexander , Lange Berit , Marx Florian M. , Mikolajczyk Rafael , Monsef Ina , Nguyen Hoa Thi , Suer Janik , Skoetz Nicole , Jaeger Veronika K , Karch André
Published: November 2024

Background

Mathematical models are essential for guiding public health policy decisions to combat the spread of infectious diseases. Nevertheless, there are no widely-used quality assessment tools that can be used to assess the quality of infectious disease modelling studies. There is also a lack of commonly accepted and used reporting guidelines that researchers can follow to improve the comprehensibility, transparency, and credibility of their publication. This scoping review identified common themes in existing reporting and quality assessment guidance for infectious disease modelling studies and adjacent fields of research.

Methods

We conducted temporally-unrestricted searches on Medline (via Ovid), Web of Science, medRxiv, and bioRxiv on January 4th, 2024 to find articles that provide guidance on writing or assessing modelling studies within infectious disease modelling and adjacent fields like health economics. Articles were double-screened for eligibility via title-and-abstract screening and full-text screening. Recommendations made by eligible articles were classified into 33 subdimensions which were categorised into seven dimensions (applicability; model structure; parameterisation and calibration; validity; uncertainty; interpretation; and reproducibility, clarity, and transparency). We followed the PRISMA extension for reporting scoping reviews.

Results

Fifty-two articles were included in our final review. All dimensions except for interpretation were covered by most articles (79%-98%). However, we found substantial heterogeneity in the frequency with which subdimensions were addressed (12%-96%). Subdimensions pertaining to study design, assumptions about model structure, handling of parameter uncertainty, and transparency about parameter values were mentioned in most articles (85%-96%); conversely, discussions about auxiliary details regarding publication, software implementation, parsimony, and predictive validity were covered less frequently (23%-31%).

Conclusion

This review reaffirms the lack of commonly used guidelines on reporting and assessing infectious disease models. Furthermore, it identifies common topics and recommendations from neighbouring fields which can inform the development of standardised guidelines for infectious disease modelling.
Convergent molecular signatures across eating disorders and obsessive-compulsive disorder in the human brain
Authors: Breen Michael , Tao Ran , Yang Andy , Wang Xuran , Amini Pardis , Rodriguez de los Santos Miguel , Brandtjen Anna , Deep-Soboslay Amy , Kaye Walter H. , Hyde Thomas M. , Kleinman Joel E , Buxbaum Joseph D , Grice Dorothy E.
Published: November 2024

Eating disorders (ED) and obsessive-compulsive disorder (OCD) exhibit significant clinical and genetic overlap, yet their shared molecular mechanisms remain unclear. We conducted a transcriptomic investigation of the dorsolateral prefrontal cortex (DLPFC) and caudate from 86 controls, 57 ED, and 27 OCD cases. ED was associated with robust differentially expressed genes (DEGs): 102 DEGs the DLPFC and 222 in the caudate (FDR < 1%) and replicated in an independent cohort. For OCD, no DEGs reached significance; however, meta-analysis with extant data identified 57 DEGs in the caudate. High concordance in transcriptomic changes was observed between ED and OCD in both regions (DLPFC r=0.67, caudate r=0.75). A combined ED+OCD analysis uncovered 233 DEGs in the DLPFC and 816 in the caudate, implicating disrupted GABAergic neuron function, neuroendocrine pathways, metabolism, and synaptic processes. Genetically regulated expression analysis identified nine genes with strong evidence for increasing ED risk, further validating these pathways. These findings reveal a shared molecular basis for ED and OCD, offering new insights into their pathobiology and potential therapeutic targets.
Early Measurable Residual Disease Detection after CAR-T is Associated with Poor Outcome Large B-cell Lymphoma Patients
Authors: Krasnow Nira , Maurer Katie , Song Catherine , Rhoades Justin , Xiong Kan , Crnjac Andela , Blewett Timothy , Gao Lily , Jacene Heather , Merryman Reid , Gohil Satyen H. , Duffy Caitlyn , Guerrero Liliana I. , Cruz Jamie Dela , McDonough Mikaela , Wolff Jacquelyn O. , Redd Robert , Mattie Mike , Miles Brodie , Makrigiorgos G. Mike , Neuberg Donna S. , Rodig Scott J. , Armand Philippe , Jacobson Caron , Adalsteinsson Viktor A. , Wu Catherine J.
Published: November 2024

Despite responses of chimeric antigen receptor (CAR)-T cells in relapsed/refractory (R/R) large B cell lymphoma (LBCL) patients, over half of patients eventually relapse. Methods to detect early disease persistence are needed to identify patients at high-risk of treatment failure. We recently developed MAESTRO, an ultrasensitive, tumor-informed measurable residual disease (MRD) assay, which can detect parts-per-million (ppm) levels of circulating tumor DNA (ctDNA) using minimal sequencing. We applied MAESTRO to 140 samples from 28 patients (15 durable responders at 12 months, 13 nonresponders) to identify treatment failure following axicabtagene ciloleucel (axi-cel) administered at our institution between 2018 and 2022. Responder and nonresponder patients had similar baseline tumor burden. By 1 week after infusion, responders had marked ctDNA reduction compared to nonresponders, p<0.001. At weeks 2 and 4, responders had ctDNA levels approaching 0 ppm, while nonresponders had persistence of ctDNA, each p<0.001. At day 0, 21% of patients had ctDNA fractions below 0.01%, hence these individuals would not have qualified for ctDNA monitoring with a less sensitive test. Our results confirm feasibility of highly sensitive MRD detection by ctDNA for early identification of patients at high risk of disease progression from axi-cel.
The IL-33/ST2 signaling axis drives pathogenesis in acute SARS-CoV-2 infection
Authors: Fleming Claire , McSorley Henry J , Allen Judith E , Petri William A
Published: November 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), remains a significant threat to global public health. Immunopathological damage plays a role in driving pneumonia, acute respiratory distress syndrome (ARDS), and multiorgan failure in severe COVID-19. Therefore, dissecting the pulmonary immune response to SARS-CoV-2 infection is critical to understand disease pathogenesis and identify immune pathways targetable by therapeutic intervention. Considering that the type 2 cytokine IL-13 enhances COVID-19 disease severity, therapeutic targeting of upstream signals that drive type 2 immunity may confer further protection. In this study, we investigate the role of the IL-33/ST2 signaling axis, a potent inducer of type 2 immunity in the lung, in a mouse model of COVID-19. Upon infection with mouse-adapted SARS-CoV-2 MA10, ST2-/-mice had significantly improved weight loss and survival (69.2% vs 13.3% survival; P = 0.0005), as compared to wild-type mice. In a complementary pharmacologic approach, IL-33/ST2 signaling was inhibited using HpBARI_Hom2, a helminth derived protein that binds to mouse ST2 and blocks IL-33 signaling. In SARS-CoV-2 MA10 infection, HpBARI_Hom2-treated mice had significantly improved weight loss and survival (60% vs 10% survival; P = 0.0035), as compared to inert control-treated mice. These data demonstrate that loss of IL-33/ST2 signaling confers protection during acute SARS-CoV-2 MA10 infection, implicating the IL-33/ST2 signaling axis as an enhancer of COVID-19 disease severity. The protection conferred by pharmacologic blockade of IL-33/ST2 signaling was independent of viral control, as HpBARI_Hom2-treated mice had no reduction in viral titers. This finding suggests an immunopathogenic role for IL-33/ST2 signaling. One potential mechanism through which IL-33/ST2 signaling may drive severe disease is through enhancement of type 2 immune pathways including IL-5 production, as pulmonary IL-5 concentrations were found to depend on IL-33/ST2 signaling in acute SARS-CoV-2 MA10 infection.
Structural and functional role of residues undergoing hereditary spastic paraplegias-linked mutations: insights from a simulation of the spiral to ring transition in katanin
Authors: Kelly Maria S. , Capelli Riccardo , Dima Ruxandra I. , Carloni Paolo
Published: November 2024

Several dozen mutations in the large human spastin enzyme assembly have been associated with mobility impairment in hereditary spastic paraplegias. Some of them impact the structural determinants of two functional conformations of the protein, spiral and ring. Here we investigate the possible effect of the mutations on the transition between the two conformations, which is essential for the enzymatic function. By performing a variety of molecular simulations (including metadynamics) on the closely related protein katanin, we suggest that about one fourth of the known disease-associated mutations affect the transition and/or the stability of a previously unrecognized intermediate. The protocol used here can be applied to the study of conformational changes in other large biomolecular complexes.

Significance Statement

By combining molecular dynamics and enhanced sampling simulations with custom-designed collective variables, we explore transient intermediate states in a large protein assembly, the severing enzyme katanin. This enzyme plays a critical role in neuronal microtubule remodeling. By targeting the transition between the spiral and ring conformations of the protein, we reveal mechanisms associated with neurodegenerative mutations that impair the function of spastin, a structurally and functionally similar enzyme. These findings provide insights that may inform future therapeutic strategies. They also expand our ability to simulate molecular processes relevant to health and disease, as our approach can be readily applied to study structural changes in other complex biological systems.
Motor protein-assisted glycan translocation and sequencing using nanopores
Authors: Ke Wenjun , Wu Pengcheng , Ma Shengzhou , Yang Yuting , Zhang Yiwei , Zhang Qingqing , Lu Xiaojie , Xia Bingqing , Wen Liuqing , Bai Jingwei , Gao Zhaobing
Published: November 2024

The glycan sequencing remains a significant bottleneck in glycoscience. While nanopore platforms have achieved substantial progress in single-molecule nucleic acid sequencing, their application to glycan sequencing has faced considerable challenges, with limited advancements to date. In this study, we propose a novel strategy for controlling glycan translocation through the MspA nanopore as an initial step toward glycan sequencing. By conjugating the target glycan with a helicase-controlled single-stranded DNA, we successfully achieved sequencing reads of up to eleven glycans. For the first time, we isolated glycan-associated electrical signals, enabling the translocation, stretching, and controlled speed of neutral glycans through the nanopore. This method provides a platform for obtaining glycan read lengths and identifying different glycan modifications, demonstrating the capability to resolve monosaccharide composition and glycosidic linkages. To further improve resolution, we propose engineered M2-MspA to reduce the pore constriction size and enhance precision by minimizing the random thermal motion of the translocating glycan. These modifications are expected to increase the sequencing accuracy and reliability. This work represents the first proof-of-concept demonstration of glycan chain nanopore sequencing and lays a promising foundation for the development of single-molecule glycan fingerprinting and sequencing technologies. We anticipate that this approach will significantly advance the development and commercialization of nanopore-based glycan sequencing techniques.
Genome Organization with CUT and Tag (GO-CaT) identifies substructure and maturation of lamina-associated domains in neurons of the developing human brain
Authors: Zhang Chujing , Gil Eugene , Ahanger Sajad Hamid , Li Lynn Mingcong , Wang Li , Li Jingjing , Kriegstein Arnold R. , Lim Daniel A.
Published: November 2024

Approximately 30-40% of the human genome is anchored to the nuclear lamina through variably sized (10 kb–10 Mb) lamina-associated domains (LADs). Previous work in cultured murine and human cell lines indicate that LADs are not homogenous but can be classified into two subtypes (T1 and T2) based on levels of lamina-association. Due in part to technical limitations, the LAD substructure of neurons maturingin vivois poorly understood. Here, we developed Genome Organization with CUT and Tag (GO-CaT) to map LAD substructure in neurons isolated from the midgestational human cortex and adult human brain. GO-CaT with LaminB1 antibodies mapped LADs with high efficiency as compared to other methods, and in prenatal neurons, we distinguished T1- and T2-LADs based on levels of LaminB1 enrichment. While T1-LADs had the transcriptional and epigenomic characteristics of cell type-invariant LADs including strong transcriptional repression, T2-LADs had a distinct epigenomic state that included enrichment of promoter-enhancer DNA interactions and intermediate levels of gene expression. In prenatal neurons, T2-LADs defined genomic regions that play key roles in neuronal development and were enriched for neurological GWAS phenotypes including those of human cognitive disorders. In a population of adult brain neurons, most prenatal T2-LADs were repositioned to either inter-LAD regions or further sequestered into T1-LADs, perhaps representing the completed, life-long spatial genome architecture of human neurons. These studies highlight the utility of GO-CaT for LAD subdomain mapping in cells isolated from human tissues and illustrate how the substructure of LADs may contribute to neural development, neuronal maturation, and human brain disease.
Postprandial glycaemic response in different ethnic groups in East London and its association with vitamin D status: study protocol for an acute randomised crossover trial
Authors: Dong Honglin , Reynolds Christian , Islam AFM Saiful , Sarkar Swrajit , Turner Sophie
Published: November 2024

In the UK, black African-Caribbeans (ACs) and South Asians (SAs) have 3–6 times greater risks of developing diabetes than white Caucasians do. East London is among the areas with the highest prevalence of type 2 diabetes and the highest proportion of minority groups. This ethnic health inequality is ascribed to socioeconomic standing, dietary habits, culture, and attitudes, while biological diversity has rarely been investigated. The evidence shows that the postprandial glucose peak values in SAs are 2–3 times greater than those in white Caucasians after the same carbohydrate loads; however, the mechanism is poorly understood. In the UK, 50% of SAs and 33% of ACs have vitamin D (vitD) deficiency, whereas 18% of white Caucasians have vitamin D deficiency. There is evidence that vitD status is inversely associated with insulin resistance in healthy adults and diabetic patients and that vitD supplementation may help improve glycaemic control and insulin resistance in type 2 diabetes patients. However, little evidence is available on minority groups or East London. This study will investigate the postprandial glycaemic response (PGR) in three ethnic groups (white Caucasians, SAs and ACs) in East London and link PGR to plasma 25(OH)D (an indicator of vitD status). Ninety-six healthy adults (n=32 per group) will be recruited. Two test drinks will be provided to the participants (300 ml of glucose drink containing 75 g glucose, and 300 ml of pure orange juice) on different occasions. PGR is monitored before and after drinking every 30 min for up to 2 hours via finger prick. A fasting blood sample obtained via phlebotomy will be used for 25(OH)D and relevant tests. A knowledge/perception questionnaire about vitD and a 4-day food diary (analysing vitD dietary intake) will also be collected. The findings of the study will be shared with participants, published in journals, disseminated via social media, and used to inform a randomized controlled trial of the effects of vitD supplementation on PGR in minority groups.

The study complies with the Helsinki Declaration II and was approved by the Senate Research Ethics Committee at City, University of London (ETH2223-2000). The study findings will be published in open access peer-reviewed journals and disseminated at national and international conferences.ClinicalTrials.govIdentifier:NCT06241976
Prevalence and etiology of strabismus in Down syndrome: A systematic review and meta-analysis with a focus on ethnic differences in the esotropia/exotropia ratio
Authors: von Bartheld Christopher S. , Chand Avishay , Wang Lingchen
Published: November 2024

Purpose

We sought to determine the prevalence of strabismus and the esotropia/exotropia ratio in Down syndrome. Wide ranges of an increased strabismus prevalence have been reported and it is unclear by how much esotropia exceeds exotropia in people with Down syndrome.

Methods

We compiled in a systematic review and meta-analysis the results of over 100 studies that report the strabismus prevalence and ratio of esotropia/exotropia in cohorts of Down syndrome. We calculated the pooled global prevalence and established the geographical distribution of the strabismus prevalence and the esotropia/exotropia ratio.

Results

The ethnically-adjusted global prevalence of strabismus in Down syndrome is 30.2%. In subjects 15 years and older, the global prevalence is 53.2%, and the lifetime prevalence is 51.0%. In populations which normally have more esotropia than exotropia (e.g., Caucasians), Down syndrome subjects have a further increased bias towards esotropia. In populations which normally have more exotropia (e.g., West Africans, Asians and Hispanics), Down syndrome subjects have a significantly lower esotropia/exotropia ratio (3.21) than reported in Caucasians with Down syndrome (9.98).

Conclusion

Worldwide, about 1.81 million people with Down syndrome have strabismus: 1.42 million of them have esotropia, and 0.37 million have exotropia. Differences in the esotropia/exotropia ratio between ethnicities point to the orbital anatomy as a major contributing factor to the etiology of strabismus in Down syndrome. The narrow-set eyes (reduced orbital width) in Down syndrome favor esotropia over exotropia, especially in Caucasians, thus explaining why Down syndrome patients from different ethnicities have different prevalences of esotropia and exotropia.
Optogenetic manipulation of nuclear Dorsal reveals temporal requirements and consequences for transcription
Authors: Pimmett Virginia L , McGehee James , Trullo Antonio , Douaihy Maria , Radulescu Ovidiu , Stathopoulos Angelike , Lagha Mounia
Published: November 2024

Morphogen gradients convey essential spatial information during tissue patterning. While both concentration and timing of morphogen exposure are crucial, how cells interpret these graded inputs remains challenging to address. We employed an optogenetic system to acutely and reversibly modulate the nuclear concentration of the morphogen Dorsal (DL), homologue of NF-κB, which orchestrates dorso-ventral patterning in theDrosophilaembryo. By controlling DL nuclear concentration while simultaneously recording target gene outputs in real time, we identified a critical window for DL action that is required to instruct patterning, and characterized the resulting effect on spatio-temporal transcription of target genes in terms of timing, coordination, and bursting. We found that a transient decrease in nuclear DL levels at nuclear cycle 13 leads to reduced expression of the mesoderm-associated genesnail (sna)and partial derepression of the neurogenic ectoderm-associated targetshort gastrulation(sog)in ventral regions. Surprisingly, the mispatterning elicited by this transient change in DL is detectable at the level of single cell transcriptional bursting kinetics, specifically affecting long inter-burst durations. Our approach of using temporally-resolved and reversible modulation of a morphogenin vivo, combined with mathematical modeling, establishes a framework for understanding the stimulus-response relationships that govern embryonic patterning.
Modeling and measuring how codon usage modulates the relationship between burden and yield during protein overexpression in bacteria
Authors: Roots Cameron T. , Hill Alexis M. , Wilke Claus O. , Barrick Jeffrey E.
Published: November 2024

Excess utilization of translational resources is a critical source of burden on cells engineered to over-express exogenous proteins. To improve protein yields and genetic stability, researchers often use codon optimization strategies that improve translational efficiency by matching an exogenous gene’s codon usage with that of the host organism’s highly expressed genes. Despite empirical data that shows the benefits of codon optimization, little is known quantitatively about the relationship between codon usage bias and the burden imposed by protein overexpression. Here, we develop and experimentally evaluate a stochastic gene expression model that considers the impact of codon usage bias on the availability of ribosomes and different tRNAs in a cell. In agreement with other studies, our model shows that increasing exogenous protein expression decreases production of native cellular proteins in a linear fashion. We also find that the slope of this relationship is modulated by how well the codon usage bias of the exogenous gene and the host’s genes match. Strikingly, we predict that an overoptimization domain exists where further increasing usage of optimal codons worsens yield and burden. We test our model by expressing sfGFP and mCherry2 from constructs that have a wide range of codon optimization levels inEscherichia coli. The results agree with our model, including for an mCherry2 gene sequence that appears to lose expression and genetic stability from codon overoptimization. Our findings can be leveraged by researchers to predict and design more optimal cellular systems through the use of more nuanced codon optimization strategies.
Deciphering Structural Complexity of Brain, Joint, and Muscle Tissues Using Fourier Ptychographic Scattered Light Microscopy
Authors: van Staalduine Simon E. , Bianco Vittorio , Ferraro Pietro , Menzel Miriam
Published: November 2024

Fourier Ptychographic Microscopy (FPM) provides high-resolution imaging and morphological information over large fields of view, while Computational Scattered Light Imaging (ComSLI) excels at mapping interwoven fiber organization in unstained tissue sections. This study introduces Fourier Ptychographic Scattered Light Microscopy (FP-SLM), a new multi-modal approach that combines FPM and ComSLI analyses to create both high-resolution phase-contrast images and fiber orientation maps from a single measurement. The method is demonstrated on brain sections (frog, monkey) and sections from thigh muscle and knee (mouse). FP-SLM delivers high-resolution images while revealing fiber organization in nerve, muscle, tendon, cartilage, and bone tissues. The approach is validated by comparing the computed fiber orientations with those derived from structure tensor analysis of the high-resolution images. The comparison shows that FPM and ComSLI are compatible with each other and yield fully consistent results. Remarkably, this combination surpasses the sum of its parts, so that applying ComSLI analysis to FPM recordings and vice-versa outperforms both methods alone. This cross-analysis approach can be retrospectively applied to analyze any existing FPM or ComSLI dataset (acquired with LED array and low numerical aperture), significantly expanding the application range of both techniques and enhancing the study of complex tissue architectures in biomedical research.
Evolution of drug-binding residues in eukaryotic ribosomes
Authors: Chan Lewis I. , Ekemezie Chinenye L. , Helena-Bueno Karla , Brown Charlotte R. , Williams Tom A. , Melnikov Sergey V.
Published: November 2024

Drugs that target eukaryotic ribosomes are becoming increasingly important as research tools and potential therapies against cancer and pathogenic eukaryotes. However, in the absence of comparative studies, we currently do not know how many eukaryotes possess ribosomal drug-binding sites identical to those in humans, and how many significantly differ from humans. To address this, we traced the evolutionary history of individual ribosomal drug-binding residues from the emergence of eukaryotes to the present day. We found that ribosomal drug-binding sites are divergent across eukaryotic clades, with some of the clades exhibiting more substitutions in their ribosomal drug-binding sites compared to humans than humans do compared to bacteria. Overall, our work provides a resource for understanding the evolutionary divergence of drug-binding sites in eukaryotic ribosomes, which may inform the use of ribosome inhibitors as research tools and lineage-specific drugs against eukaryotic parasites.
Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanism
Authors: Sidorov Sviatoslav , Pal Koustav , Lenhard Boris , Luscombe Nicholas M.
Published: November 2024

Many human genes, including transcription factor (TF) genes, produce alternative coding isoforms. Although some alternative coding TF isoforms have been experimentally studied, a genome-wide characterisation of all such isoforms in normal human physiology is still lacking. Here, we integrate RNA sequencing and protein domain data to reveal the expression levels, tissue specificity and putative functional classes of alternative coding isoforms of human TF genes. We found that isoforms lacking a DNA-binding domain (DBD) are annotated for almost a third of known TF genes, comprise 17% of all annotated TF isoforms and likely reverse the regulatory effects of DBD-containing isoforms. Considering all coding TF isoforms, we uncovered 536 switches between the highest-expressed alternative isoforms produced by 360 TF genes across 43 adult tissues. We predicted functional consequences of these switches using a functional annotation of structural domains present in switching isoforms. Furthermore, we found 45 isoform switches between the brain and non-brain tissues and interpreted six of these switches in detail. Finally, we assembled a literature-based compendium of human TF genes with experimentally studied alternative isoforms. In total, our results suggest that the switches of alternative coding TF isoforms between adult tissues represent a widespread, yet understudied, functional mechanism.
Mountain roads across the globe significantly alter local soil microclimates
Authors: Lejeune Renée , Fuentes-Lillo Eduardo , Haesen Stef , Pirée Amber , Wiegmans Dymphna , Hostens Lore , Lenoir Jonathan , Pergl Jan , Vítková Michaela , Seipel Tim , Kutlvašr Josef , Nuñez Martin A. , Dimarco Romina D. , Alexander Jake , Backes Amanda Ratier , Haider Sylvia , Pauchard Aníbal , Nijs Ivan , Lembrechts Jonas J.
Published: November 2024

Mountain roads have repeatedly shown to host significantly different plant species communities compared to the adjacent natural vegetation. Besides the effect of propagule pressure, altered disturbance regime and soil processes, one of the reasons given for the strong influence of mountain roads on species distributions is a significantly altered microclimate in the roadside compared to the adjacent vegetation, a direct consequence of the altered disturbance regime. However, the microclimatic differences between roadside and natural vegetation have rarely been quantified, particularly lacking global analyses, hampering a better understanding of their importance for mountain biodiversity. In this study, we analysed in-situ measured soil temperatures along mountain roads in seven mountain regions across the globe, in order to assess the impact of mountain roads on a range of bioclimatic variables across the elevational gradient. Our results undeniably show the importance of roadsides as unique microhabitats, even in heterogeneous mountain environments. In most regions, roadside soils had warmer maxima (3.95 ± 2.35°C warmer) and colder minima (0.85 ± 1.11 °C colder) than the soil in the adjacent vegetation, with higher frost risks in winter. Therefore, we recommend future research to incorporate the notion that the local microclimates created by mountain roads could play a critical role in species redistributions in space and time.
The repurposed STAT3 inhibitor pyrimethamine controls mycobacterial infection-induced vascular permeability and mycobacterial burden
Authors: Han Darryl JY , Sui Xiangyu , Sorayah Ria , Hoeppner Luke H , Oehlers Stefan H
Published: November 2024

Infection-induced vascular pathologies are a side effect of the immune response to contact with a range of pathogens. Mycobacteria, including Mycobacterium tuberculosis, are particularly adept at co-opting vascular leakiness as a survival mechanism to shape the host immune response and impede the delivery of antibiotics to sites of infection. Here using the zebrafish-Mycobacterium marinum infection model, we confirm a critical role for Signal transducer and activator of transcription 3 (STAT3) in mediating infection-induced vascular permeability, and demonstrate the ability of FDA-approved drugs atovaquone and pyrimethamine to restore vascular barrier function without compromising immune control of mycobacterial infection. Additionally, we find an antibiotic effect of pyrimethamine against Mycobacterium marinum via inhibition of bacterial dihydrofolate reductase. Together our findings suggest pyrimethamine could be used as adjunctive therapy against mycobacterial infection.