bluuebunny/crossref_metadata_2025 huggingface dataset:
Unpacking sublinear growth: diversity, stability and coexistence
Authors: Aguadé-Gorgorió Guim , Lajaaiti Ismaël , Arnoldi Jean-François , Kéfi Sonia
Published: June 2024

How can many species coexist in natural ecosystems remains a fundamental question in ecology. Theory suggests that competition for space and resources should maintain the number of coexisting species far below the staggering diversity commonly found in nature. A recent model finds that, when sublinear growth rates of species are coupled with competition, species diversity can stabilize community dynamics. This, in turn, is suggested to explain the coexistence of many species in natural ecosystems. In this brief note we clarify why the sublinear growth (SG) model does not solve the long standing paradox of species coexistence. This is because in the SG model coexistence emerges from an unrealistic property, in which species per-capita growth rate diverges at low abundance, preventing species from ever going extinct. When infinite growth at low abundance is reconciled with more realistic assumptions, the SG model recovers the expected paradox: increasing diversity leads to competitive exclusion and species extinctions.
Participatory science methods to monitor water quality and ground truth remote sensing of the Chesapeake Bay
Authors: Neale Patrick , Brown Shelby , Sill Tara , Cawood Alison , Tzortziou Maria , Park Jieun , Lee Min-Sun , Paquette Beth
Published: June 2024

Measurements by volunteer scientists using participatory science methods in combination with high resolution remote sensing can improve our ability to monitor water quality changes in highly vulnerable and economically valuable nearshore and estuarine habitats. In the Chesapeake Bay (USA), tidal tributaries are a focus of watershed and shoreline management efforts to improve water quality. The Chesapeake Water Watch program seeks to enhance the monitoring of tributaries by developing and testing methods for volunteer scientists to easily measure chlorophyll, turbidity, and colored dissolved organic matter (CDOM) to inform Bay stakeholders and improve algorithms for analogous remote sensing (RS) products. In the program, trained volunteers have measured surface turbidity using a smartphone app, HydroColor, calibrated with a photographer’s gray card. In vivo chlorophyll and CDOM fluorescence were assessed in surface samples with hand-held fluorometers (Aquafluor) located at sample processing “hubs” where volunteers drop-off samples for same day processing. In validation samples, HydroColor turbidity and Aquafluor in vivo chlorophyll and CDOM fluorescence were linearly related to standard analytical measures of turbidity, chlorophyll and CDOM, respectively, with R2values ranging from 0.65 to 0.85. These methods are being used for both repeat sampling at fixed sites of interest and ad-hoc “blitzes” to synoptically sample tributaries all around the Bay in coordination with satellite overpasses. All data is accessible on a public database (serc.fieldscope.org) and can be a resource to monitor long-term trends in the tidal tributaries as well as detect and diagnose causes of events of concern such as algal blooms and storm-induced reductions in water clarity.
Evaluating Biodiversity Credits Using Metacommunity Modelling
Authors: Maczik Dominik M , Jansen Vincent A.A. , Rossberg Axel G.
Published: June 2024

Enhancing global biodiversity is one of the key pillars of the UN’s Sustainable Development Goals, widely acknowledged as necessary to mitigate climate change. Nevertheless, an annual additional of US$ 700 billions of funding is required to reach the ‘30 by 30’ target set out in the Kunming-Montreal Global Biodiversity Framework. The proposed voluntary biodiversity credit market aims to bridge this funding gap via a market-based mechanism by assigning financial value to biodiversity and ecosystem services. To capitalise on this nascent market, several voluntary biodiversity credits are emerging from independent start-ups, internationally respected NGOs, and established carbon credit companies. Projects which are primary funded by credit sales must align their objectives with their credit issuance methodology to avoid underdelivering on their commitments. In this pioneering study, the diderences in behaviour between six diderent well-established credits were investigated, to highlight the impact of methodology choice and evaluate their accuracy on representing ecosystem level changes. Our results indicate that all six credits are suitable for tracking basic restoration edorts, however there are significant diderences in their methodologies and thus their responsiveness to interventions. Furthermore, not one credit was suitable to successfully track all six distinct nature-positive or nature-loss experiments simulated, suggesting that a universal biodiversity credit remains unattainable.
Evolution and paradigm shift in forest health research: A review on global trends and knowledge gaps
Authors: Acosta-Muñoz Cristina , Navarro-Cerrillo Rafael M. , Bonet-García Francisco J. , Ruiz-Gómez Francisco J. , González-Moreno Pablo
Published: June 2024

Forests provide key ecosystem services to human society, and the ability to provide these services depends on their overall health. Forest health is an attractive and interesting concept in forestry research, which environmental, social and political interests have shaped. Assessing forest health is crucial, but finding a single definition of the concept is complex. It is determined by the aim of the forest study, different areas of knowledge, scales of work, technology, methodologies, historical moment or source of funding, among others. With almost a century of scientific evidence, the aim is to identify and contextualise temporal changes in the relevance of this key concept. Trends are analysed through the construction of three main descriptors (state variables, drivers and methods) and the main conceptual subdomains (themes). This review reveals the significant geographical bias in the research, which the Global North predominantly conducts. We observe the evolution of forest health research driven by diverse needs and interests, ranging from air pollution to the multifaceted impacts of climate change. Methodologies applied in this field have also evolved from traditional crown condition inventories to the use of advanced tools such as remote sensing or ecophysiology, improving the characterisation of forest health patterns at both global and individual scales. Forest health research has evolved towards more holistic and multidisciplinary approaches, reflected in the broadening and integration of methodologies and technologies, influenced by historical context, which influence what is being researched today and future scenarios. We identified key knowledge gaps in the scientific literature, in particular the concepts of ecosystem services, Essential Biodiversity Variables (EBVs) and the concept of ‘One Health’. These findings highlight the need for future research to incorporate these critical but often overlooked areas, potentially reshaping future directions and scenarios for forest health research.
Ratiometric fluorescence nanoscopy and lifetime imaging of novel Nile Red analogs for analysis of membrane packing in living cells
Authors: Lauritsen Line , Szomek Maria , Hornum Mick , Reinholdt Peter , Kongsted Jacob , Nielsen Poul , Brewer Jonathan R. , Wüstner Daniel
Published: June 2024

Subcellular membranes have complex lipid and protein compositions, which give rise to organelle-specific membrane packing, fluidity, and permeability. Due to its exquisite solvent sensitivity, the lipophilic fluorescence dye Nile Red has been used extensively to study membrane packing and polarity. Further improvement of Nile Red can be achieved by introducing electron-donating or withdrawing functional groups. Here, we compare the potential of derivatives of Nile Red with such functional substitutions for super-resolution fluorescence microscopy of lipid packing in model membranes and living cells. All studied Nile Red derivatives exhibit cholesterol-dependent fluorescence changes in model membranes, as shown by spectrally resolved stimulated emission depletion (STED) microscopy. STED imaging of Nile Red probes in cells reveals lower membrane packing in fibroblasts from healthy subjects compared to those from patients suffering from Niemann Pick type C1 (NPC1) disease, a lysosomal storage disorder with accumulation of cholesterol and sphingolipids in late endosomes and lysosomes. We also find small but consistent changes in the fluorescence lifetime of the Nile Red derivatives in NPC1 cells, suggesting altered hydrogen-bonding capacity in their membranes. All Nile Red derivatives are essentially non-fluorescent in water but increase their brightness in membranes, allowing for their use in MIN-FLUX single molecule tracking experiments. Our study uncovers the potential of Nile Red probes with functional substitutions for nanoscopic membrane imaging.
Representation learning for multi-modal spatially resolved transcriptomics data
Authors: Nonchev Kalin , Andani Sonali , Ficek-Pascual Joanna , Nowak Marta , Sobottka Bettina ,   Tumor Profiler Consortium, Koelzer Viktor Hendrik , Raetsch Gunnar
Published: June 2024

Spatial transcriptomics enables in-depth molecular characterization of samples on a morphology and RNA level while preserving spatial location. Integrating the resulting multi-modal data is an unsolved problem, and developing new solutions in precision medicine depends on improved methodologies. Here, we introduce AESTETIK, a convolutional deep learning model that jointly integrates spatial, transcriptomics, and morphology information to learn accurate spot representations. AESTETIK yielded substantially improved cluster assignments on widely adopted technology platforms (e.g., 10x Genomics™, NanoString™) across multiple datasets. We achieved performance enhancement on structured tissues (e.g., brain) with a 21% increase in median ARI over previous state-of-the-art methods. Notably, AESTETIK also demonstrated superior performance on cancer tissues with heterogeneous cell populations, showing a two-fold increase in breast cancer, 79% in melanoma, and 21% in liver cancer. We expect that these advances will enable a multi-modal understanding of key biological processes.
Unraveling the role of plasma proteins in dementia: insights from two cohort studies in the UK, with causal evidence from Mendelian randomization
Authors: Gong Jessica , Williams Dylan M. , Scholes Shaun , Assaad Sarah , Bu Feifei , Hayat Shabina , Zaninotto Paola , Steptoe Andrew
Published: June 2024

Population-based proteomics offer a groundbreaking avenue to predict dementia onset. This study employed a proteome-wide, data-driven approach to investigate protein-dementia associations in 229 incident all-cause dementia (ACD) among 3,249 participants from the English Longitudinal Study of Ageing (ELSA) over a median 9.8-year follow-up, then validated in 1,506 incident ACD among 52,745 individuals from the UK Biobank (UKB) over median 13.7 years. NEFL and RPS6KB1 were robustly associated with incident ACD; MMP12 was associated with vascular dementia in ELSA. Additional markers EDA2R and KIM1 (HAVCR1) were identified from sensitivity analyses. Combining NEFL and RPS6KB1 with other factors yielded high predictive accuracy (area under the curve (AUC)=0.871) for incident ACD. Replication in the UKB confirmed associations between identified proteins with various dementia subtypes. Results from reverse Mendelian Randomization also supported the role of several proteins as early dementia biomarkers. These findings underscore proteomics’ potential in identifying novel risk screening targets for dementia.
Meal Protein Quality Score: A novel tool to evaluate protein quantity and quality of meals
Authors: Grootswagers Pol , Christensen Sine Højlund , Timmer Marielle , Riley William , de Groot Lisette , Tetens Inge
Published: June 2024

Background

The recent shift towards increased plant-based protein consumption has necessitated the development of new tools to evaluate the quality and quantity of protein in meals, especially given the changing dietary guidelines and the adoption of plant-centric menus in healthcare and other settings.

Objective

To develop and test the feasibility of the Meal Protein Quality Score (MPQS), a novel metric that assesses the protein quality and quantity in meals based on essential amino acid (EAA) content, digestibility and requirements, with a focus on optimizing protein intake for vulnerable populations, particularly older adults.

Methods

The MPQS integrates digestibility-adjusted EAA intake with total protein consumed in a meal, that together with the EAA requirements provide a score from 0 to 100 to reflect EAA coverage adequacy. The score was tested for feasibility by applying it to recipe data from real life hospital meals, and to dietary data from the NU-AGE trial, involving detailed seven-day food records from 252 non-vegan participants analyzed over multiple meal moments.

Results

The analyses revealed that the higher the content of plant-protein in a meal, the lower the meal protein quality. Also, breakfast meals scored lowest on protein quality, mainly due to low contents of protein overall, and of lysine and methionine. The MPQS effectively highlighted the difference in protein quality between plant-based and animal-based meals, and across different meal types.

Conclusion

The MPQS appears to be a practical tool that facilitates the assessment of meal-based protein quality. The MPQS can be used to guide dietary transitions towards plant-rich diets, ensuring that such shifts do not compromise protein adequacy for at-risk populations. The score allows for guidance in meal-planning, leading to improvements in plant-rich meal formulation to meet both individual and public health nutritional needs.
spread.gl: visualising pathogen dispersal in a high-performance browser application
Authors: Li Yimin , Bollen Nena , Hong Samuel Leandro , Brusselmans Marius , Gambaro Fabiana , Suchard Marc A. , Rambaut Andrew , Lemey Philippe , Dellicour Simon , Baele Guy
Published: June 2024

Phylogeographic analyses are able to exploit the location data associated with sampled molecular sequences to reconstruct the spatio-temporal dispersal history of a pathogen. Visualisation software is commonly used to facilitate the interpretation of the accompanying estimation results, as these are not always easily interpretable. spread.gl is a powerful, open-source and feature-rich browser application that enables smooth, intuitive and user-friendly visualisation of both discrete and continuous phylogeographic inference results, enabling the animation of pathogen geographic dispersal through time. spread.gl can render and combine the visualisation of several data layers, including a geographic layer (e.g., a world map), multiple layers that contain information extracted from the input phylogeny, and different types of layers that represent environmental data. As such, users can explore which environmental data may have shaped pathogen dispersal patterns, that can subsequently be formally tested through more principled statistical analyses. We showcase the visualisation features of spread.gl on several representative pathogen dispersal examples, including the smooth animation of a phylogeny encompassing over 17,000 genomic sequences resulting from a large-scale SARS-CoV-2 analysis.
Radical Pericardiectomy and Use of Cardiopulmonary Bypass for Constrictive Pericarditis
Authors: Koprivanac Marijan , Bauza Karolis , Smedira Nicholas , Pettersson Gosta , Unai Shinya , Barrios Paola , Oh Nicholas , Stembal Filip , Lara-Erazo Valentina , Soltesz Edward G. , Bakaeen Faisal G. , Elgharably Haytham , Desai Milind , Wang Tom K. , Houghtaling Penny L , Svensson Lars G. , Gillinov Marc , McCurry Kenneth , Johnston Douglas R. , Blackstone Eugene H. , Klein Allan , Tong Michael Z.
Published: June 2024

Background

Pericardiectomy is definitive treatment for constrictive pericarditis. However, extent of resection (radical versus partial) and use of cardiopulmonary bypass (CPB) are debated.

Objectives

To determine the association of extent of pericardial resection and use of CPB with outcomes.

Methods

From January 2000 to January 2022, 565 patients with constrictive pericarditis underwent radical (n=445, 314 [71%] on CPB) or partial (n=120, 67 [56%] on CPB) pericardiectomy at Cleveland Clinic. Outcomes stratified by extent of pericardial resection and use of CPB were compared after propensity-score matching.

Results

Both radical pericardiectomy and CPB use (67% [381/565]) increased over time. Among 88 propensity-matched pairs (73% of possible matches), immediate postoperative cardiac index increased (P<0.001) in both groups by a median of 1.0 L•min-1•m-2. There were no significant differences between radical versus partial resection groups in occurrence of reoperation for bleeding (2.3%, [2/88] vs. 0,P=.50). Median postoperative hospital length of stay was 10 versus 8.5 days (P=.02). Operative mortality was 9.1% (8/88) versus 6.8% (6/88) (P=.58). 10-year survival was 54% versus 41%, with a higher propensity-adjusted hazard ratio after partial resection (1.9, 95% CI 1.2-3.1).

Conclusions

When surgical intervention is deemed necessary, radical — rather than partial — resection for constrictive pericarditis can be performed with low surgical mortality and morbidity. Radical pericardiectomy can be accomplished on CPB and results in better long-term survival.

CLINICAL PERSPECTIVES

Patients with constrictive pericarditis require a multidisciplinary approach involving primarily a cardiologist and cardiac surgeon, and other disciplines like gastroenterology since liver cirrhosis from increased central venous pressure and congestion is common, or immunology for evaluation of possible autoimmune etiology.

Communication is critical in managing patient expectations after pericardiectomy, especially linking etiology to short- and long-term outcomes in this complex patient population.

Radical pericardiectomy should be the gold standard for treating patients with constrictive pericarditis.

Routine use of cardiopulmonary bypass is safe and enables the radical pericardiectomy surgery and should be recommended in the guidelines.
Disability inclusion in the Brazilian health system: results of a health system assessment
Authors: Polack Sarah , Ramos Vinicius Delgado , Köptcke Luciana Sepúlveda , de Araujo Morais Indyara , Reichenberger Veronika , Scherer Nathaniel , do Socorro Veloso de Albuquerque Maria , Kuper Hannah , Lyra Tereza Maciel , de Brito Christina May Moran
Published: June 2024

Background

People with disabilities face more barriers accessing healthcare and, on average, experience worse health outcomes. Strengthening health access for people with disabilities requires coordinated action across the health system. The Missing Billion Inclusive Health System Framework is a new tool to support policy makers assess levels of disability inclusion within health systems. In this study we use the framework within the Unified Health System in Brazil. We consider the relevance and feasibility of the indicators, as part of further testing and refining the framework.

Methods

Information sources, used to complete the assessment, included Brazilian laws and policies, publically available data, published literature and interviews with people with disabilities and service providers. A workshop with stakeholders was held to co-develop key recommendations.

Findings

Overall, the framework was comprehensive and feasible to complete. It highlighted key strengths in terms of disability inclusion in the Brazilian health system as well as gaps and leverage points for action.

Interpretation

The Missing Billions framework can identify progress and opportunities to strengthen disability inclusion in health systems. In Brazil, key promotive factors include supportive policies, leadership and financing structures. There are also opportunities for strengthening data and evidence, healthcare worker training on disability and health service accessibility. Actions must be centered on, and informed by, people with disabilities.

Funding

This work was supported by the São Paulo Research Foundation, Brazilian National Council for Scientific Technological Development, Federate District Research Foundation and the Medical Research Council. Hannah Kuper is supported by a NIHR Global Research Professorship.
Effectiveness of Updated 2023–2024 (Monovalent XBB.1.5) COVID-19 Vaccination Against SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 Lineage Hospitalization and a Comparison of Clinical Severity — IVY Network, 26 Hospitals, October 18, 2023–March 9, 2024
Authors: Ma Kevin C. , Surie Diya , Lauring Adam S. , Martin Emily T. , Leis Aleda M. , Papalambros Leigh , Gaglani Manjusha , Columbus Christie , Gottlieb Robert L. , Ghamande Shekhar , Peltan Ithan D. , Brown Samuel M. , Ginde Adit A. , Mohr Nicholas M. , Gibbs Kevin W. , Hager David N. , Saeed Safa , Prekker Matthew E. , Gong Michelle Ng , Mohamed Amira , Johnson Nicholas J. , Srinivasan Vasisht , Steingrub Jay S. , Khan Akram , Hough Catherine L. , Duggal Abhijit , Wilson Jennifer G. , Qadir Nida , Chang Steven Y. , Mallow Christopher , Kwon Jennie H. , Parikh Bijal , Exline Matthew C. , Vaughn Ivana A. , Ramesh Mayur , Safdar Basmah , Mosier Jarrod , Harris Estelle S. , Shapiro Nathan I. , Felzer Jamie , Zhu Yuwei , Grijalva Carlos G. , Halasa Natasha , Chappell James D. , Womack Kelsey N. , Rhoads Jillian P. , Baughman Adrienne , Swan Sydney A. , Johnson Cassandra A. , Rice Todd W. , Casey Jonathan D. , Blair Paul W. , Han Jin H. , Ellington Sascha , Lewis Nathaniel M. , Thornburg Natalie , Paden Clinton R. , Atherton Lydia J. , Self Wesley H. , Dawood Fatimah S. , DeCuir Jennifer
Published: June 2024

Background

Assessing COVID-19 vaccine effectiveness (VE) and severity of SARS-CoV-2 variants can inform public health risk assessments and decisions about vaccine composition. BA.2.86 and its descendants, including JN.1 (referred to collectively as “JN lineages”), emerged in late 2023 and exhibited substantial genomic divergence from co-circulating XBB lineages.

Methods

We analyzed patients hospitalized with COVID-19–like illness at 26 hospitals in 20 U.S. states admitted October 18, 2023–March 9, 2024. Using a test-negative, case-control design, we estimated the effectiveness of an updated 2023–2024 (Monovalent XBB.1.5) COVID-19 vaccine dose against sequence-confirmed XBB and JN lineage hospitalization using logistic regression. Odds of severe outcomes, including intensive care unit (ICU) admission and invasive mechanical ventilation (IMV) or death, were compared for JN versus XBB lineage hospitalizations using logistic regression.

Results

585 case-patients with XBB lineages, 397 case-patients with JN lineages, and 4,580 control-patients were included. VE in the first 7–89 days after receipt of an updated dose was 54.2% (95% CI = 36.1%–67.1%) against XBB lineage hospitalization and 32.7% (95% CI = 1.9%–53.8%) against JN lineage hospitalization. Odds of ICU admission (adjusted odds ratio [aOR] 0.80; 95% CI = 0.46–1.38) and IMV or death (aOR 0.69; 95% CI = 0.34–1.40) were not significantly different among JN compared to XBB lineage hospitalizations.

Conclusions

Updated 2023–2024 COVID-19 vaccination provided protection against both XBB and JN lineage hospitalization, but protection against the latter may be attenuated by immune escape. Clinical severity of JN lineage hospitalizations was not higher relative to XBB lineage hospitalizations.
PRDX6 dictates ferroptosis sensitivity by directing cellular selenium mobilization
Authors: Ito Junya , Nakamura Toshitaka , Toyama Takashi , Doll Sebastian , Suzuki Mirai , Zhang Weijia , Zheng Jiashuo , Trümbach Dietrich , Yamada Naoya , Ono Koya , Wahida Adam , Saito Yoshiro , Nakagawa Kiyotaka , Mishima Eikan , Conrad Marcus
Published: June 2024

Selenium-dependent glutathione peroxidase 4 (GPX4) is the guardian of ferroptosis and prevents unrestrained (phospho)lipid peroxidation by directly reducing phospholipid hydroperoxides (PLOOH) to their corresponding alcohols. However, it remains unclear whether other phospholipid peroxidases can also contribute to ferroptosis prevention, albeit to a varying degree. Here we show that cells lacking GPX4 still exhibit substantial PLOOH reduction capacity, arguing for the presence of alternative PLOOH peroxidases. By scrutinizing potential candidates, we showed that while overexpression of peroxiredoxin 6 (PRDX6), a thiol-specific antioxidant enzyme with reported PLOOH-reducing activity, failed to prevent ferroptosis, its genetic loss markedly sensitizes cancer cells to ferroptosis. Mechanistically, we uncover that PRDX6 facilitates intracellular selenium handling, which is crucial for selenium incorporation into selenoproteins, including GPX4. Consequently, PRDX6 modulates GPX4 expression, thereby dictating the sensitivity of cells to undergo ferroptosis. Our study highlights PRDX6 as a critical factor in ferroptosis prevention by directing cellular selenium mobilization.
Information theoretic inference of magnitude and direction of gene flow in metapopulation networks using nyemtaay, with potential for applications in metastasizing cancer clonal cell origin analysis
Authors: Ortiz-Velez Adrian N. , Sukumaran Jeet
Published: June 2024

Background

We introducenyemtaay, a Python package for the calculation of classical population genetic statistics and inference of gene flow network connections and directionality in metapopulation networks using information theory. This genetic information flow network inference approach provided here is the only existing implementation of [1], and is applicable not only to ecological and evolutionary organism and landscape scale studies, but also has potential applications in, for example, cancer biology for analyzing clonal cell origins in metastasizing tumors.

Results

We demonstrate this potential through simulations and an analysis of metastasizing cancer cell lineages, showcasing its ability to identify the tissue site of origin in cancer networks. This work highlights the importance of considering demographic history and founder effects in interpreting gene flow directionality, and the benefits of this understanding in allowing application of this approach to gene flow network modeling to reach a broader range of domains.

Conclusions

nyemtaayis available under the MIT license from its public repository (https://github.com/aortizsax/nyemtaay), and can be installed locally using the Python package manager ‘pip’.
Geographic redistributions are insufficient to mitigate the erosion of species’ environmental niches
Authors: Cohen Jeremy , Jetz Walter
Published: June 2024

As climate change accelerates, species may survive in place thanks to niche plasticity or adaptation or must redistribute to conserve their environmental niches1. Examples of such geographical range shifts abound2–4, but to date an assessment of species’ success in retaining niches and limiting their climate change exposure is missing. Here, we develop a novel method to account for biases inherent in tens of millions of citizen science observations, allowing us to evaluate how species have mitigated their climatic niche loss using geographical redistributions. We find that over 20 years, 384 North American bird species shifted their summertime distributions 0.73° north, mitigating their expected exposure to warming by ∼1.16 °C and thus averting 44% of expected niche loss had they stayed in place. Despite these movements, species were still exposed to an average ∼1.47 °C increase in temperature and few species achieved complete niche retention. Meanwhile, species only mitigated ∼0.47 °C (11%) in winter, shifting their niches by ∼3.74 °C, with almost no species fully retaining their niches. Species moving the furthest north succeeded most in conserving niches across both seasons. As expected, but previously untested at this scale, species that have physiological characteristics associated with dispersal achieved the greatest redistributions and niche retention. Most geographical redistributions have only been partially effective towards mitigating climate change and the gap between climate change exposure and species’ historical niches is growing rapidly even in a highly mobile group such as birds, raising concerns about the ability of less mobile taxa to persist in a warmer world.
Cell-free expression and SMA copolymer encapsulation of a functional receptor tyrosine kinase disease variant, FGFR3-TACC3
Authors: Snow Alexander J D , Wijesiriwardena Tharushi , Lane Benjamin J , Farrell Brendan , Dowdle Polly C , Katan Matilda , Muench Stephen P , Breeze Alexander L
Published: June 2024

Despite their high clinical relevance, obtaining structural and biophysical data on transmembrane proteins has been hindered by challenges involved in their expression and extraction in a homogeneous, functionally-active form. The inherent enzymatic activity of receptor tyrosine kinases (RTKs) presents additional challenges. Oncogenic fusions of RTKs with heterologous partners represent a particularly difficult-to-express protein subtype due to their high flexibility, aggregation propensity and the lack of a known method for extraction within the native lipid environment. One such protein is the fibroblast growth factor receptor 3 fused with transforming acidic coiled-coil-containing protein 3 (FGFR3-TACC3), which has failed to express to sufficient quality or functionality in traditional expression systems. Cell-free protein expression (CFPE) is a burgeoning arm of synthetic biology, enabling the rapid and efficient generation of recombinant proteins. This platform is characterised by utilising an optimised solution of cellular machinery to facilitate protein synthesisin vitro. In doing so, CFPE can act as a surrogate system for a range of proteins that are otherwise difficult to express through traditional host cell-based approaches. Here, functional FGFR3-TACC3 was expressed through a novel cell-free expression system in under 48 hours. The resultant protein was reconstituted using SMA copolymers with a specific yield of 300 µg/mL of lysate. Functionally, the protein demonstrated significant kinase domain phosphorylation (t<0.0001). Currently, there is no published, high-resolution structure of any full-length RTK. These findings form a promising foundation for future research on oncogenic RTKs and the application of cell-free systems for synthesising functional membrane proteins.
Pathogenicity of Commensal Gut Biofilm In Prefrail Aging
Authors: Cosquer Guillaume Le , Pannier Melissa , Meunier Elodie , Thevenin Julie , Guyonnet Sophie , Vellas Bruno , Santin Yohan , Guiard Bruno , Parini Angelo , Buscail Louis , Bournet Barbara , Guillemet Damien , Deraison Celine , Vergnolle Nathalie , Motta Jean-Paul ,   the IHU HealthAge INSPIRE/Open Science study group
Published: June 2024

Achieving healthy aging is a global challenge requiring a deeper understanding of aging mechanisms, spanning from robustness to frailty. Although age-related alteration of the gut microbiome (microb-aging) is well studied, there is a lack of research investigating the gut microbiota during the early stages of prefrailty and understanding its behavior within the context of a natural community lifestyle, in interaction with host tissue. Therefore, we used fecal samples from the human aging cohort INSPIRE-T, to characterize polymicrobial biofilms. Intestinal tissues and feces from an aging mouse cohort were also used. Food supplement was tested for potential geroprotective effects on biofilms. Findings pointed to taxonomic and physical alterations, increased instability, and virulence with regards to intestinal epithelium, for biofilms of prefrail individuals, compared to their age-matched robust counterparts. Multiparametric analyses further linked biofilm characteristics to clinical traits, suggesting that biofilm culture could be a proxy tool for evaluating a healthy or unhealthy aging status. Exposure of biofilms to the grape pomace prebiotic partially reversed the prefail biofilm phenotype. In aged mice with prefrailty, but not in robust aged mice, gut microbiota biofilm structure was altered and caused colon damage when transplanted into antibiotic-depleted mice. These findings suggest a causal link between microb-aging in prefrailty and gut inflammation, advocating microbiota-targeted therapies to reverse prefrail phenotype and thereby promote healthspan.
Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape
Authors: Liesenfelder Sven , Mabrouk Mohamed H. Elsafi , Iliescu Jessica , Baranda Monica Varona , Mizi Athanasia , Wessiepe Martina , Papantonis Argyris , Wagner Wolfgang
Published: June 2024

Aging is reflected by genome-wide DNA methylation changes, but it is largely unclear how these epigenetic modifications are regulated. In this study, we explored the possibility to interfere with epigenetic clocks by epigenetic editing at individual CpG sites. CRISPR-guided approaches (dCas9-DNMT3A and CRISPRoff) facilitated targeted methylation at an age-associated genomic region inPDE4Cthat remained stable for more than three months. Furthermore, epigenetic editing evoked many genome-wide off-target effects, which were highly reproducible and enriched at other age-associated CpGs – thus, they are not random off-target effects, but seem to resemble coregulated epigenetic bystander modifications. 4C chromatin conformation analysis at age-associated sites revealed increased interactions with bystander modifications and other age-associated CpG sites. Subsequently, we multiplexed epigenetic modifications in HEK293T and primary T cells at five genomic regions that become either hypermethylated or hypomethylated upon aging. While epigenetic editing at age-hypomethylated CpGs appeared less stable, it also resulted in a clear enrichment of bystander modifications at other age-associated CpGs. Conversely, epigenetic clocks tend to be accelerated up to ten years after targeted DNA methylation, particularly at hypermethylated CpGs. These results demonstrate that targeted epigenome editing can modulate the epigenetic aging network in its entirety and thereby interfere with epigenetic clocks.
The human blood harbors a phageome which differs in Crohn’s disease
Authors: Lamy-Besnier Quentin , Theodorou Ilias , Billaud Maud , Zhang Hao , Brot Loïc , Culot Antoine , Abriat Guillaume , Sokol Harry , De Paepe Marianne , Petit Marie-Agnès , De Sordi Luisa
Published: June 2024

Increasing evidence suggests that the human blood hosts microbes including bacteria and eukaryotic viruses, which could have important implications for health. Bacteriophages of the blood are challenging to study and have been overlooked, but could translocate to this environment from different body-sites. We thus developed specific virome protocols and analysis methods to study the viral communities of blood samples obtained from healthy individuals and Crohn’s disease (CD) patients. We uncovered a diverse viral community in the human blood, dominated by phages infecting Pseudomonadota bacteria. We found that an important fraction of those phages overlaps with the gut virome, consolidating the idea that gut phages can translocate to the blood. Strikingly, viral communities of the blood were different between CD patients and healthy individuals, revealing a new signature of disease. This was not the case for fecal viral communities. Collectively, these results advance our knowledge of the microorganisms present in the human blood and pave the way for further studies of this environment in the context of disease.
Molecular effects of indoor tanning
Authors: Gerami Pedram , Tandukar Bishal , Deivendran Delahny , Olivares Shantel , Chen Limin , Tang Jessica , Tan Tuyet , Sharma Harsh , Bandari Aravind K , Cruz-Pacheco Noel , Chang Darwin , Marty Annika , Olshen Adam , Murad Natalia Faraj , Song Jing , Lee Jungwha , Yeh Iwei , Hunter Shain A.
Published: June 2024

Background

Tanning bed users have a significantly increased risk of melanoma, but it remains unclear how indoor tanning drives melanomagenesis. Tanning bed radiation is often thought of as a substitute for natural UV radiation despite differences in the maximum doses, UV content, body sites exposed, and patterns of melanoma that arise.

Methods

To better understand the epidemiologic trends and etiology of melanoma associated with tanning bed use, we described the patterns of melanoma in patients with quantifiable tanning bed usage and performed exome sequencing of 182 melanocytes from normal skin of a subset of these patients.

Results

Tanning bed users were more likely than non-users to have melanoma on body sites with low cumulative levels of sun damage and were more likely to have multiple melanomas. The melanocytes in normal appearing skin from tanning bed users had higher mutation burdens, a higher proportion of melanocytes with pathogenic mutations, and distinct mutational signatures. These differences were most prominent over body sites that experience comparatively less exposure to natural sunlight.

Conclusions

We conclude that tanning bed radiation induces melanoma by increasing the mutation burden of melanocytes and by mutagenizing a broader field of melanocytes than are typically exposed to natural sunlight. The unique signatures of mutations in skin cells of tanning users may be attributable to the distinct spectra of radiation emitted from solariums.
Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling
Authors: Oliveira Michelli F. , Romero Juan P. , Chung Meii , Williams Stephen , Gottscho Andrew D. , Gupta Anushka , Pilipauskas Susan E. , Mohabbat Syrus , Raman Nandhini , Sukovich David , Patterson David ,   Visium HD Development Team, Taylor Sarah E. B.
Published: June 2024

Colorectal cancer (CRC) is the second-deadliest cancer in the world, yet a deeper understanding of spatial patterns of gene expression in the tumor microenvironment (TME) remains elusive. Here, we introduce the Visium HD platform (10x Genomics) and use it to investigate human CRC and normal adjacent mucosal tissues from formalin fixed paraffin embedded (FFPE) samples. The first assay available on Visium HD is a probe-based spatial transcriptomics workflow that was developed to enable whole transcriptome single cell scale analysis. We demonstrate highly refined unsupervised spatial clustering in Visium HD data that aligns with the hallmarks of colon tissue morphology and is notably improved over earlier Visium assays. Using serial sections from the same FFPE blocks we generate a single cell atlas of our samples, then we integrate the data to comprehensively characterize the immune cell types present in the TME, specifically at the tumor periphery. We observed enrichment of two pro-tumor macrophage subpopulations with differential gene expression profiles that were localized within distinct tumor regions. Further characterization of the T cells present in one of the samples revealed a clonal expansion that we were able to localize in the tissue using in situ gene expression analysis. In situ analysis also allowed us to perform in-depth characterization of the microenvironment of the clonally expanded T cell population and we identified a third macrophage subpopulation with gene expression profiles consistent with an anti-tumor response. Our study provides a comprehensive map of the cellular composition of the CRC TME and identifies phenotypically and spatially distinct immune cell populations within it. We show that the single cell-scale resolution afforded by Visium HD and the whole transcriptome nature of the assay allows investigations into cellular function and interaction at the tumor periphery in FFPE tissues, which has not been previously possible.
Stabilization of the open conformation of Insulin-Regulated Aminopeptidase by a novel substrate-selective small molecule inhibitor
Authors: Mpakali Anastasia , Georgaki Galateia , Buson Alberto , Findlay Alison D. , Foot Jonathan S. , Mauvais Francois-Xavier , van Endert Peter , Giastas Petros , Hamprecht Dieter W. , Stratikos Efstratios
Published: June 2024

Insulin-Regulated Aminopeptidase (IRAP) is an enzyme with important biological functions and the target of several drug-discovery efforts although no clinically useful inhibitors have been reported yet. We combinedin silicoscreening with a medicinal chemistry optimization campaign to discover a nanomolar inhibitor of IRAP based on a pyrazolylpyrimidine scaffold. This compound displays an excellent selectivity profile versus homologous aminopeptidases and kinetic analysis suggests it utilizes an uncompetitive mechanism of action when inhibiting the cleavage of a typical dipeptidic substrate. Surprisingly, the compound is a poor inhibitor of the processing of the physiological cyclic peptide substrate oxytocin and a 10mer antigenic epitope precursor but displays a biphasic inhibition profile for the trimming of a 9mer antigenic peptide and is active in blocking IRAP-dependent cross-presentation of an 8mer epitope. To better understand the mechanism of action and the basis for the unusual substrate selectivity of this inhibitor, we solved the crystal structure of the compound in complex with IRAP. The structure indicated direct zinc(II) engagement by the pyrazolylpyrimidine scaffold and revealed that the compound binds to an open conformation of the enzyme in a pose that should block the conformational transition to the closed conformation previously observed with other low molecular weight inhibitors and hypothesized to be important for catalysis. This compound constitutes the first IRAP inhibitor targeting the active site that utilizes a conformation-specific mechanism of action, provides insight into the intricacies of the IRAP catalytic cycle, and highlights a novel approach to regulating IRAP activity by blocking its conformational rearrangements.
Bistable perception of symbolic numbers
Authors: Luo Junxiang , Yokoi Isao , Dumoulin Serge O. , Takemura Hiromasa
Published: June 2024

Numerals, i.e., semantic expressions of numbers, enable us to have an exact representation of the amount of things. Visual processing of numerals plays an indispensable role in the recognition and interpretation of numbers. Here, we investigate how visual information from numerals is processed to achieve semantic understanding. We first found that partial occlusion of some digital numerals introduces bistable interpretations. Next, by using the visual adaptation method, we investigated the origin of this bistability in human participants. We showed that adaptation to digital and normal Arabic numerals, as well as homologous shapes, but not Chinese numerals, biases the interpretation of a partially occluded digital numeral. We suggest that this bistable interpretation is driven by intermediate shape processing stages of vision, i.e., by features more complex than local visual orientations but more basic than the abstract concepts of numerals.
Protein recruitment to dynamic DNA-RNA host condensates
Authors: Dizani Mahdi , Sorrentino Daniela , Agarwal Siddharth , Stewart Jaimie Marie , Franco Elisa
Published: June 2024

We describe the design and characterization of artificial nucleic acid condensates that are engineered to recruit and locally concentrate proteins of interestin vitro. These condensates emerge from the programmed interactions of nanostructured motifs assembling from three DNA strands and one RNA strand that can include an aptamer domain for the recruitment of a target protein. Because condensates are designed to form regardless of the presence of target protein, they function as “host” compartments. As a model protein we consider streptavidin (SA) due to its widespread use in binding assays, thus the host condensates presented here could find immediate use for the physical separation of a variety of biotin-tagged components. In addition to demonstrating protein recruitment, we describe two approaches to control the onset of condensation and protein recruitment. The first approach uses UV irradiation, a physical stimulus that bypasses the need for exchanging molecular inputs and is particularly convenient to control condensation in emulsion droplets. The second approach uses RNA transcription, a ubiquitous biochemical reaction that is central to the development of the next generation of living materials. We finally show that the combination of RNA transcription and degradation leads to an autonomous dissipative system in which host condensates and protein recruitment occur transiently, and that the host condensate size as well as the timescale of the transient can be controlled by the level of RNA degrading enzyme.

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Multimodal mechanisms of human centriole engagement and disengagement
Authors: Ito Kei K , Matsuhashi Kyohei , Takumi Kasuga , Nagai Kaho , Fukuyama Masamitsu , Yamamoto Shohei , Chinen Takumi , Hata Shoji , Kitagawa Daiju
Published: June 2024

The DNA and the centrioles are the only cellular structures that uniquely replicate to produce identical copies, which is crucial for proper chromosome segregation in mitosis. A new centriole termed “daughter” is progressively assembled adjacent to a pre-existing, “mother” centriole. Only after the daughter centriole is structurally completed as an identical copy, it disengages from its mother to become the core of a new functional centrosome. The mechanisms preventing precocious disengagement of the immature copy have been previously unknown. Here, we identify three key centriole-associated mechanisms that maintain the mother-daughter engagement: the cartwheel, the torus, and the pericentriolar material pathways. Among these, the torus is critical for establishing the characteristic orthogonal engagement between the mother and daughter centrioles. Furthermore, we show that the engagement mediated by the cartwheel and the torus pathways is released stepwise through structural changes in the daughter centriole, known as centriole blooming and centriole distancing, respectively. Disruption at any stage of these structural transitions leads to the failure of all subsequent steps, ultimately blocking centriole disengagement and centrosome conversion at the end of mitosis. Overall, this study provides a comprehensive understanding of how the maturing daughter centriole progressively disengages from its mother through multiple maturation steps, to ensure its complete structure and conversion into an independent centrosome.
Ethosuximide: subunit- and Gβγ-dependent blocker and reporter of allosteric changes in GIRK channels
Authors: Shalomov Boris , Friesacher Theres , Yakubovich Daniel , Combista J. Carlo , Reddy Haritha P. , Dabbah Shoham , Bernsteiner Harald , Zangerl-Plessl Eva-Maria , Stary-Weinzinger Anna , Dascal Nathan
Published: June 2024

The antiepileptic drug ethosuximide (ETX) suppresses epileptiform activity in a mouse model ofGNB1syndrome, caused by mutations in Gβ1protein, likely through the inhibition of G-protein gated K+(GIRK) channels. Here we show that ETX is a subunit-selective, allosteric blocker of GIRKs. The potency of ETX block is increased by the G protein subunit dimer Gβγ, the physiological activator of GIRKs. Molecular dynamics (MD) simulations and mutagenesis locate the ETX binding site in GIRK2 to a region associated with phosphatidylinositol-4,5-bisphosphate (PIP2) regulation, and suggest that ETX acts by closing the HBC gate and altering channel’s interaction with PIP2. The apparent affinity of ETX block is highly sensitive to changes in channel gating caused by mutations in Gβ1or GIRK subunits. Our findings pose GIRK as a potential therapeutic target for ETX, and ETX as a potent allosteric GIRK blocker and a tool for probing gating-related conformational changes in GIRK.