bluuebunny/crossref_metadata_2025 huggingface dataset:
Modified Intravascular Stent for Microvascular Suture in a Rat Superficial Femoral Artery
Authors: Maeda Kosuke , Suzuki Taku , Masugi Yohei , Tsuji Osahiko , Iwamoto Takuji , Nakamura Masaya
Published: October 2024

Background

Intravascular stent (IVaS) is sometimes used for suturing small vessels, but removing the stent after suturing is difficult. To overcome this problem, we developed an IVaS that integrates a stent and a manipulating string. This study aimed to investigate the usefulness of the modified IVaS (M-IVaS) by comparing it with conventional sutures (CS) and conventional IVaS (C-IVaS).

Methods

Forty-five superficial femoral arteries from rats were resected and sutured. The rats were randomly divided into the following 3 groups: CS, M-IVaS, and C-IVaS, with 15 rats per group. Patency rate, operating time, and ultrasonographic blood flow dynamics were examined immediately after suturing. Patency tests, ultrasonographic evaluations, and histological investigations were performed 1 week (n = 5), 2 weeks (n = 5), and 6 weeks (n = 5) after surgery.

Results

The 3 groups showed vessel patency in all cases immediately after suturing and at 1 week, 2 weeks, and 6 weeks after surgery. The mean operative time was 22.6 minutes for the CS group, 21.5 minutes for the M-IVaS group, and 25.9 minutes for the C-IVaS group. There were no significant differences in peak flow velocity and stenosis rate among the 3 groups as evaluated by ultrasonography. Histopathological evaluation revealed a similar recovery process of endothelial cells and no damage to the vascular wall.

Conclusion

The surgical time using M-IVaS was significantly shorter compared to that using C-IVaS. The M-IVaS reduced the inconvenience of C-IVaS removal. M-IVaS showed the same effectiveness as did the CS in terms of patency rate, operating time, ultrasonographic blood flow dynamics, and histological evaluation. M-IVaS can be used in the field of microsurgery.
Predicting the Impact of Dialyzer Choice and Binder Dialysate Flow Rate on Bilirubin Removal
Authors: Novokhodko Alexander , Du Nanye , Hao Shaohang , Wang Ziyuan , Shu Zhiquan , Ahmad Suhail , Gao Dayong
Published: October 2024

Liver failure is the 12thleading cause of death worldwide. Protein bound toxins such as bilirubin are responsible for many complications of the disease. Binder dialysis systems use albumin dialysate and detoxifying sorbent columns to remove these toxins. Systems like the Molecular Adsorbent Recirculating System (MARS) and BioLogic-DT have existed since the 1990s, but survival benefit in randomized controlled trials have not been consistent. Thus, a new generation of binder dialysis systems, including Open Albumin Dialysis (OPAL) and the Advanced Multi-Organ Replacement System (AMOR) are being developed. Optimal conditions for binder dialysis have not been established. We developed and validated a computational model of bound solute dialysis using established thermodynamic theories. Our objective is to improve AMOR therapy. We confirmed our model’s validity by predicting the impact of changing between two benchtop dialysis setups using different polysulfone dialyzers (F3 and F6HPS). We then applied it to predict the impact of varying dialysate flow rate on toxin removal. We found that bilirubin removal is independent of dialysate flow rate within the clinically relevant range (20 mL/min – 800 mL/min), matching our model’s predictions. At very low dialysate flow rates (2 mL/min), bilirubin removal declines, deviating from the thermodynamic model. This model may be useful to achieving optimal clinical outcomes by setting optimal dialyzer and flow rate conditions. Further improvement is possible by accounting for toxin adsorption onto the dialyzer membrane.
Effect of Futsal-Based Game Training on Performance, Self-Efficacy, Motivation, and Exercise Addiction in Adolescent Non-Athlete Girls
Authors: Beik Sahar , Dehghanizadeh Jalal
Published: October 2024

This study examined the effects of futsal-based game training on performance, self-efficacy, motivation, and exercise addiction in adolescent non-athlete girls. Thirty female students with no prior futsal experience were randomly assigned to either a traditional training group (n=15) or a game-based training group (n=15). Performance was assessed using a futsal skills test, while self-efficacy, sports motivation, and exercise addiction were measured via questionnaires. Both groups underwent separate 12-week training protocols. Analysis of covariance revealed significant differences between the game-based and traditional training groups in performance (P=0.0001), self-efficacy (P=0.0001), and sports motivation (P=0.0001). However, no significant difference was observed in exercise addiction between the two groups (P=0.531). These findings suggest that game-based training has a substantial impact on performance, self-efficacy, and motivation in adolescent non-athlete girls and may serve as an effective training strategy. The type of training method, whether game-based or traditional, does not appear to be a determining factor in the development or prevention of exercise addiction tendencies.
The Impact of Pulmonary Fibrosis on Sex and Sexual Function – A Multinational Mixed Methods Study
Authors: Avitzur Na’ama , Knaub Madelyn , Thornton-Wood Francesca , Johnson Simon R. , Ryerson Christopher J. , Jenkins R. Gísli , Stewart Iain , Johannson Kerri A.
Published: October 2024

Background

Sex is an important part of life for many adults, yet sexual function may be impacted by chronic respiratory diseases such as pulmonary fibrosis (PF). This multinational study sought to characterize the impact of PF on sex and sexual function, using mixed quantitative and qualitative methodology.

Methods

Patients were retrospectively included from a prospective registry and prospective clinical cohort if they had completed UCSD-SOBQ or SPARC questionnaire, respectively. An online multi-lingual survey used the Changes in Sexual Function Questionnaire (CSFQ) to assess sexual dysfunction, and qualitative evaluation of individual patient interviews was conducted using thematic analysis.

Results

Dyspnea with sexual activity affected 2,054/2,759 (74%) of registry patients, associated with male sex, lower FVC%, lower DLCO%, and worse cough. Distress due to the effect of PF on their sex life was reported in 52/225 (23%) of the clinical cohort, associated with younger age, male sex, lower DLCO%, and worse cough. Sexual dysfunction was common, affecting 56/67 (83%) of female and 63/73 (86%) male survey respondents. Qualitative analysis of patient interviews identified several themes including sex life limitations, changes in inter-personal relationships, quality of life, and emotions. All patients wanted to discuss sex with trusted healthcare providers.

Conclusion

In this multinational study, patients with PF reported engaging in sex and sexual activities but were adversely impacted by the effect of PF on sex life, with both physical and psychological limitations. Sexual dysfunction was common, driven by multiple disease domains. Sexual health appears to be an important component of comprehensive patient care.

Funding

The Canadian Registry for Pulmonary Fibrosis is sponsored by Boehringer Ingelheim, but had no input on any aspect of this study.
A new stegosaur (Dinosauria: Ornithischia) from the Upper Jurassic Qigu Formation of Xinjiang, China and a revision on Chinese stegosaurs phylogeny
Authors: Ning Li , Guozhong Chen , Mateus Octávio , Tao Jiang , Yan Xie , Daqing Li , Hailu You , Guangzhao Peng
Published: October 2024

Stegosaurs are a small but iconic clade of ornithischian dinosaurs. They and their sister taxa, the ankylosaurs, formed the clade Eurypoda which means ‘broad-footed’. Here, we describe a stegosaur from the Upper Jurassic Qigu Formation of Xinjiang, China, based on an associated partial skeleton that includes axial, pectoral girdle, pelvic girdle, limb and armor elements. It can be diagnosed as a new taxon,Angustungui, based on numerous autapomorphies. Some morphologies ofAngustunguiare more similar to the taxa from Europe, Africa and North America than to those from Asia. Our phylogenetic analysis recovers it as the sister taxon ofLoricatosaurus. More importantly, the narrow and claw-shaped ungual ofAngustunguiproves that Eurypoda, at least stegosaur, has claw-shaped unguals. Besides, we revised the character scores for Chinese stegosaurs based on observations of the specimens.
Female Sex Worker Preferences for HIV Pre-Exposure Prophylaxis Delivery in Uganda: A Discrete Choice Experiment
Authors: Mpirirwe Ruth , Makabayi‑Mugabe Rita , Muteebwa Laban , Kamacooko Onesmus , Wamono Felix , Kajumba Mayanja M. , Nangendo Joan , Semitala Fred C. , Kyambadde Peter , Davis Katumba James , Kalyango Joan , Karamagi Charles , Kiragga Agnes , Armstrong-Hough Mari , Moor Sarah EG , Katahoire Anne R. , Kamya Moses R , Mujugira Andrew
Published: October 2024

Background

Cisgender female sex workers (FSWs) in sub-Saharan Africa have a high risk of HIV acquisition, highlighting the need for innovative approaches to expand coverage of evidence-based HIV prevention methods, including oral pre-exposure prophylaxis (PrEP). Our study aimed to identify FSWs’ preferences for a PrEP delivery model with structured choices for delivery location, services offered, and adherence support.

Methods

We conducted a discrete choice experiment (DCE) among FSWs ≥18 years recruited from the Most At-Risk Population Initiative (MARPI) clinic in Kampala, Uganda, between October and November 2023. FSWs were recruited using consecutive sampling. To determine the most effective PrEP delivery method for FSWs, we created eight choice sets, each with three alternative combinations of PrEP service attributes and an opt-out using a D-efficient experimental design. Participants were presented with three alternatives, the fourth being an opt-out (no model selected), and asked to make selections based on four distinct attributes: the PrEP provider, place of delivery, delivery channel, and support services. We assessed FSW preferences and attribute trade-offs using a panel data mixed model and identified the preferred PrEP delivery model using the highest median utility score.

Results

Overall, 203 participants completed the DCE. The median age was 24 years (interquartile range [IQR] 20-32). Most FSWs preferred receiving PrEP from a healthcare worker at the clinic with short message service (SMS) reminders for adherence support (median utility score 0.87; interquartile range [IQR] 0.82, 0.94). This preference remained consistent across all age groups, with a median utility score of 0.88 for ages 15-19, 0.87 for ages 20-24, and 0.85 for ages ≥25.

Conclusion

FSWs preferred to receive PrEP care directly from providers at healthcare facilities and highlighted the need for additional support in the form of SMS reminders to improve adherence and prevent HIV acquisition. This preferred model, if implemented, could increase prevention coverage and inform future approaches to delivering PrEP through the Uganda National PrEP Program.
Cxcl10 is required for survival during SARS-CoV-2 infection in mice
Authors: Majumdar Shamik , Weaver Joseph D. , Pontejo Sergio M. , Minai Mahnaz , Lu Xinping , Gao Ji-Liang , Holmes Gibran , Johnson Reed , Zhang Hongwei , Kelsall Brian L. , Farber Joshua M. , Alves Derron A. , Murphy Philip M.
Published: October 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic, remains endemic worldwide ∼5 years since the first documented case. Severe COVID-19 is widely considered to be caused by a dysregulated immune response to SARS-CoV-2 within the respiratory tract. Circulating levels of the chemokine CXCL10 are strongly positively associated with poor outcome; however, its precise role in pathogenesis and its suitability as a therapeutic target have remained undefined. Here, we challenged 4-6 month old C57BL/6 mice genetically deficient inCxcl10with a mouse-adapted strain of SARS-CoV-2. Infected male, but not female,Cxcl10-/-mice displayed increased mortality compared to wild type controls. Histopathological damage, inflammatory gene induction and virus load in the lungs of male mice 4 days post infection and before death were not broadly influenced by Cxcl10 deficiency. However, accumulation of B cells and both CD4+and CD8+T cells in the lung parenchyma of infected mice was reduced in the absence of Cxcl10. Thus, during acute SARS-CoV-2 infection, Cxcl10 regulates lymphocyte infiltration in the lung and confers protection against mortality. Our preclinical model results do not support targeting CXCL10 therapeutically in severe COVID-19.
Identification and characterization of tertiary lymphoid structures in brain metastases
Authors: Mughal Sadaf S. , Reiss Yvonne , Felsberg Jörg , Meyer Lasse , Macas Jadranka , Schlue Silja , Starzetz Tatjana , Köhrer Karl , Fehm Tanja , Müller Volkmar , Lamszus Katrin , Schadendorf Dirk , Helfrich Iris , Wikman Harriet , Berghoff Anna , Brors Benedikt , Plate Karl H. , Reifenberger Guido
Published: October 2024

Brain metastases (BrM) are the most common cancers in the brain. We performed transcriptome-wide gene expression profiling combined with spatial immune cell profiling to characterize the tumor immune microenvironment in BrM from different primary tumors. We found that BrM from lung carcinoma and malignant melanoma showed overall higher immune cell infiltration as compared to BrM from breast carcinoma. RNA sequencing-based immune cell deconvolution revealed gene expression signatures indicative of tertiary lymphoid structures (TLS) in subsets of BrM, mostly from lung cancer and melanoma. This finding was corroborated by multiplex immunofluorescence staining of immune cells in BrM tissue sections. Detection of TLS signatures was more common in treatment-naïve BrM and associated with prolonged survival after BrM diagnosis in lung cancer patients. Our findings highlight the cellular diversity of the tumor immune microenvironment in BrM of different cancer types and suggest a role of TLS formation for BrM patient outcome.
Evidence for Powassan virus deletions and defective RNA in field collected ticks
Authors: Langsjoen Rose M. , Courtney Samantha J. , Trammell Chasity E. , Robich Rebecca M. , Goethert Heidi K. , McMinn Rebekah J. , Telford Sam R. , Ebel Gregory D. , Piantadosi Anne
Published: October 2024

Powassan virus (POWV) is a tick-borne flavivirus in the tick-borne encephalitis virus (TBEV) serogroup endemic to the United States, Canada, and parts of Russia. POWV remains an under-studied pathogen, despite the potential for serious and life-threatening neurologic complications following infection. While prior studies have characterized viral diversity due to single nucleotide polymorphisms, little is known about POWV recombination, defective RNAs (D-RNAs), and functional structural variants (SVs). Understanding POWV recombination in its natural vector can provide important insights into its replication and evolution. Thus, we analyzed POWV sequence data from 51 ticks collected from the Northeast United States to characterize deletion expression levels and patterns in naturally infected ticks, and we compared these results to single-passage isolates. We found that deletions were common in POWV RNA from ticks and that several areas of the genome were enriched for recombination junctions. Deletions were often associated with areas of microhomology. While most deletions were sample-specific, two major deletion archetypes were observed across multiple tick samples. The first consisted of small 19-50 base deletions in the methyltransferase domain of the ns5 RNA-dependent RNA-polymerase gene, resulting in a mixture of putative SVs and D-RNAs. The second consisted of approximately 1600 base deletions spanning the ns2a-ns3 genes, resulting in putative D-RNAs with abrogated viral protease function. Protease deletions were significantly enriched after one passage in baby hamster kidney cells despite a decrease in overall deletion expression. These results demonstrate the proclivity of POWV for recombination, with potential implications for immune evasion and persistence in ticks.

IMPORTANCE

Powassan virus is a tick-borne flavivirus that can cause serious, life-threatening neurological disease. Understanding how Powassan virus replicates and evolves within its tick vector may elucidate factors important in persistence, transmission, and human disease. Defective RNAs are replication-incompetent viral genomes generated through internal deletions, which have been associated with disease severity and persistent infection in other viruses but have not been described for Powassan virus. Here, we show that Powassan virus produces abundant defective RNAs in field-caught ticks, and that expression patterns of these defective RNAs changes after one passage in mammalian cells. Although the function of these defective RNAs remains unknown, this work establishes a critical framework for investigating the role of defective RNAs in Powassan virus replication and transmission.
Functional classification of tauopathy strains reveals the role of protofilament core residues
Authors: Vaquer-Alicea Jaime , Manon Victor A. , Bommareddy Vaibhav , Kunach Peter , Gupta Ankit , Monistrol Jim , Perez Valerie A. , Tran Hung Tri , Saez-Calveras Nil , Du Siling , Batra Sushobhna , White Charles L. , Joachimiak Lukasz A. , Shahmoradian Sarah H. , Diamond Marc I.
Published: October 2024

Distinct tau amyloid assemblies underlie diverse tauopathies but defy rapid classification. Cell and animal experiments indicate tau functions as a prion, as different strains propagated in cells cause unique, transmissible neuropathology after inoculation. Strain amplification requires compatibility of the monomer and amyloid template. We used cryo-EM to study one cell-based YFP-tagged strain, resolving its amyloid nature. We then used sequential alanine (Ala) substitution (scan) within tau repeat domain (RD) to measure incorporation to pre-existing tau RD-YFP aggregates. This robustly discriminated strains, defining sequences critical for monomer incorporation. We then created 3R/4R or 4R WT RD (aa 246-408) biosensors. Ala scan of recombinant tau seeds with the Alzheimer’s Disease fold matched that of AD homogenate. We scanned 22 brain lysates comprising 4 tauopathies. This clustered cases by neuropathological syndrome, revealed the role of amino acids in protofilament folds, and allowed strain discrimination based on amino acid requirements for prion replication.

Teaser

Discrimination of tau strains based on the relative contribution of each amino acid to templated propagation of the amyloid.
Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes
Authors: Chan Chun Kit , Nguyen Jonathan , Hryc Corey F. , Gupta Chitrak , Redding Kevin , Dowhan William , Baker Matthew L. , Perez Alberto , Mileykovskaya Eugenia , Singharoy Abhishek
Published: October 2024

The biological significance of protein supercomplexes have remained contentious, particularly how they tune the shuttling of charge-carrier redox proteins across cell membranes during biological energy conversion. We employ multiscale modeling and single particle cryo-electron microscopy (cryo-EM) to determine the mechanisms of diffusive electron transfer in mitochondrial supercomplexes, composed of respiratory complexes III and IV (CIII and CIV). Using a combination of bioinformatic and entropy maximization tools, we model an ensemble of structures representing the conformational space of CIII’s disordered QCR6 ‘hinge’ within the yeast CIII2CIV2supercomplex. Molecular and Brownian Dynamics simulations of the entire supercomplex reveal a mechanism for electrostatic coupling between these negatively charged hinge conformations, and binding and directional diffusion of the redox proteins on the mitochondrial membrane, which is simulated over the millisecond timescale. Anionic lipids reinforce this conformationally-coupled recognition of the supercomplex by retaining a pool of the redox proteins in the vicinity of the membrane when the hinges are of a critical length. Cryo-EM models reveal a large-scale rearrangement of the ΔQCR6 supercomplex, which retains a surprisingly robust electrostatic environment for recognition of the redox protein, despite compromise in the supercomplex’s negative charge, still enabling a surface-mediated electron transfer in this CIII2CIV2variant. Altogether, the evolutionary need of confining electron carriers on the surface of bioenergetic membranes is found to give rise to a refolding-guided diffusion model of the redox proteins, which improves the energy conversion efficiency within the supercomplex by nearly 30%.
Single Nuclei Sequencing Reveals Intratumoral Cellular Heterogeneity and Replication Stress in Adrenocortical Carcinoma
Authors: Popova Liudmila V. , Garfinkle Elizabeth A. R. , Chopyk Daniel M. , Navarro Jaye B. , Rivaldi Adithe , Shu Yaoling , Lomonosova Elena , Phay John E. , Miller Barbra S. , Sattuwar Swati , Mullen Mary , Mardis Elaine R. , Miller Katherine E. , Dedhia Priya H.
Published: October 2024

Adrenocortical carcinoma (ACC) is a rare endocrine malignancy with a poor prognosis and limited treatment options. Bulk genomic characterization of ACC has not yielded obvious therapeutic or immunotherapeutic targets, yet novel therapies are needed. We hypothesized that elucidating the intratumoral cellular heterogeneity by single nuclei RNA sequencing analyses would yield insights into potential therapeutic vulnerabilities of this disease. In addition to characterizing the immune cell and fibroblast landscape, our analyses of single nuclei gene expression profiles identified an adrenal cortex cell cluster exhibiting a program of replication stress and DNA damage response in primary and metastatic ACC.In vitroassessment of replication stress and DNA damage response using an ACC cell line and a series of newly-derived hormonally active patient-derived tumor organoids revealed ATR sensitivity. These findings provide novel mechanistic insight into ACC biology and suggest that an underlying dependency on ATR may be leveraged therapeutically in advanced ACC.
Linking microscopy to diffusion MRI with degenerate biophysical models: an application of the Bayesian EstimatioN of CHange (BENCH) framework
Authors: Kor Daniel Z.L. , Rafipoor Hossein , Huszar Istvan N. , Smart Adele , Daubney Greg , Jbabdi Saad , Cottaar Michiel , Miller Karla L. , Howard Amy F.D.
Published: October 2024

Biophysical modelling of diffusion MRI (dMRI) is used to non-invasively estimate microstructural features of tissue, particularly in the brain. However, meaningful description of tissue requires many unknown parameters, resulting in a model that is often ill-posed. The Bayesian EstimatioN of CHange (BENCH) framework was specifically designed to circumvent parameter fitting for ill-conditioned models when one is simply interested in interpreting signal changes related to some variable of interest. To understand the biological underpinning of some observed change in MR signal between different conditions, BENCH predicts which model parameter, or combination of parameters, best explains the observed change, without having to invert the model. BENCH has been previously used to identify which biophysical parameters could explain group-wise dMRI signal differences (e.g. patients vs. controls); here, we adapt BENCH to interpret dMRI signal changes related to continuous variables. We investigate how parameters from the dMRI standard model of white matter, with an additional sphere compartment to represent glial cell bodies, relate to tissue microstructure quantified from histology. We validate BENCH using synthetic dMRI data from numerical simulations. We then apply it to ex-vivo macaque brain data with dMRI and microscopy metrics of glial density, axonal density, and axonal dispersion in the same brain. We found that (i) increases in myelin density are primarily associated with an increased intra-axonal volume fraction and (ii) changes in the orientation dispersion derived from myelin microscopy are linked to variations in the orientation dispersion index. Finally, we found that the dMRI signal is sensitive to changes in glial cell soma in the WM, but that no parameter in the extended standard model was able to explain this observed signal change, suggesting model inadequacy.
Do pollinators play a role in shaping the essential amino acids found in nectar?
Authors: Parkinson Rachel H. , Power Eileen F. , Walter Kieran , McDermott-Roberts Alex E. , Pattrick Jonathan G. , Wright Geraldine A.
Published: October 2024

Plants produce floral nectar as a reward for pollinators, which contains carbohydrates and amino acids (AAs). We designed experiments to test whether pollinators could exert selection pressure on the profiles of AAs in nectar.

We used HPLC to measure the free amino acids and sugars in the nectar of 102 UK plant species. Six distinct profiles of essential amino acids (EAAs) were defined using the relative proportions of AAs with a clustering algorithm; we then tested bumblebee (Bombus terrestris) preferences for the EAA profiles and proline using a two-choice assay.

We found a phylogenetic signal for the proportions of phenylalanine, methionine and proline as well as the total concentrations of essential and non-essential AAs. However, there was no phylogenetic signal for EAA profile. Bumblebees did not exhibit a preference for any of the six EAA nectar profiles, however, four of the EAA profiles stimulated feeding. In contrast, bumblebees avoided proline in an inverse concentration-dependent manner.

Our data indicate that bees are likely to have mechanisms for the post-ingestive evaluation of free AAs in solution but are unlikely to taste EAAs at nectar-relevant quantities. We predict that EAAs increase nectar value to bumblebees post-ingestively.
Inferring Time-Varying Internal Models of Agents Through Dynamic Structure Learning
Authors: James Ashwin , Bethus Ingrid , Muzy Alexandre
Published: October 2024

Reinforcement learning (RL) models usually assume a stationary internal model structure of agents, which consists of fixed learning rules and environment representations. However, this assumption does not allow accounting for real problem solving by individuals who can exhibit irrational behaviors or hold inaccurate beliefs about their environment. In this work, we present a novel framework called Dynamic Structure Learning (DSL), which allows agents to adapt their learning rules and internal representations dynamically. This structural flexibility enables a deeper understanding of how individuals learn and adapt in real-world scenarios. The DSL framework reconstructs the most likely sequence of agent structures—sourced from a pool of learning rules and environment models—based on observed behaviors. The method provides insights into how an agent’s internal structure model evolves as it transitions between different structures throughout the learning process. We applied our framework to study rat behavior in a maze task. Our results demonstrate that rats progressively refine their mental map of the maze, evolving from a suboptimal representation associated with repetitive errors to an optimal one that guides efficient navigation. Concurrently, their learning rules transition from heuristic-based to more rational approaches. These findings underscore the importance of both credit assignment and representation learning in complex behaviors. By going beyond simple reward-based associations, our research offers valuable insights into the cognitive mechanisms underlying decision-making in natural intelligence. DSL framework allows better understanding and modeling how individuals in real-world scenarios exhibit a level of adaptability that current AI systems have yet to achieve.
Computational Analysis of Zn2+Mediated Non-Competitive Inhibition to Caspase-3
Authors: Tian Xinyu Erya , Zang Min , Wang Xiaoyu , Dong Hao
Published: October 2024

Caspase-3, a critical mediator of apoptosis, is implicated in neurodegenerative diseases and cancer, making it an attractive therapeutic target. Here, we elucidated the molecular mechanisms of caspase-3 inhibition through computational methods. We first investigated the binding of the canonical substrate DEVD and novel peptidomimetic inhibitors, characterizing their competitive inhibition mechanisms. Using AlphaFold3 and molecular dynamics simulations, we then identify Zn2+-binding sites and characterize conformational changes induced by Zn2+chelation, revealing a mechanism for non-competitive inhibition. Our results provide atomic-level insights into both competitive and Zn2+-mediated non-competitive inhibition of caspase-3, enhancing our understanding of apoptotic pathways. These findings could help guide the development of targeted therapies for apoptosis-related disorders, encompassing both competitive inhibitors and non-competitive modulators.
Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning
Authors: Ferraz Matheus V. F. , Adan W. Camilla S. , Lima Tayná E. , Santos Adriele J. C. , de Paula Sérgio O. , Dhalia Rafael , Wallau Gabriel L. , Wade Rebecca C. , Viana Isabelle F. T. , Lins Roberto D.
Published: October 2024

The design of proteins capable to effectively bind to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a complementarity-determining regions (CDRs)-grafting approach for designing nanobodies (Nbs) that target specific epitopes, with the aid of computer simulation and machine learning. As a proof-of-concept, we designed, evaluated, and characterized a high-affinity Nb against the spike protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. The designed Nb, referred to as Nb Ab.2, was synthesized and displayed high-affinity for both the purified receptor-binding domain protein and to the virus-like particle, demonstrating affinities of 9 nM and 60 nM, respectively, as measured with microscale thermophoresis. Circular dichroism showed the designed protein’s structural integrity and its proper folding, whereas molecular dynamics simulations provided insights into the internal dynamics of Nb Ab.2. This study shows that our computational pipeline can be used to efficiently design high affinity Nbs with diagnostic and prophylactic potential, which can be tailored to tackle different viral targets.

Author summary

In this study, we present a pipeline for designing a high-affinity nanobody (Nb) targeting the SARS-CoV-2 spike protein using enhanced sampling molecular dynamics simulations and CDR-grafting. To address the challenges of CDR grafting in Nbs, including the need for structural similarity between the CDR motif of interest and the scaffold region, we utilized the Nb scaffold cAbBCII10, known for its versatility in accommodating various CDRs. We generated a library based on the cAbBCII10 framework with diverse, unrelated CDRs and applied machine learning to identify the most promising candidates. Our approach enabled successful engineering of a Nb that binds to the SARS-CoV-2 spike protein with high affinity, demonstrating the effectiveness of our design pipeline for potential therapeutic applications.
Detection of positive selection driving antimicrobial resistance in the core genome ofStaphylococcus epidermidis
Authors: Rimmer Callum O. , Thomas Jonathan C.
Published: October 2024

Staphylococcus epidermidisis a commensal skin organism and leading cause of medical-device associated infections. Although previous research has investigated the phylogenetic diversity of the species, the level of positive selection on the core genome has yet to be explored. Here, we present the first core genome-wide screen of positive selection in the species. A curated dataset of 1003 whole-genome sequences (WGS) was created which represented the global diversity of the species, including all previously identified clades and genetic clusters (GCs). A 100-strain subset, which retained the diversity of the collection, was created by pruning the species-level tree with treemmer; core genes present in all genomes were extracted with Roary and used for positive selection analysis (n = 826). Site-level analysis was performed using PAML with omegaMap for confirmation. Selection along branches separating clades A and B were also investigated using PAML branch-site models and HyPhy. PAML site analysis revealed 17 genes under selection, including six hypothetical genes, most of which were linked to metabolism or transport. Several genes were associated with antimicrobial resistance, such asileSwhich confers resistance to mupirocin.cysGandsirC, which catalyse the first two steps in the synthesis of siroheme, were also under selection. Two genes were found to be under selection at the branch-site level by both PAML and HyPhy, of which only one,rhtC, has been functionally characterised. Our analysis reveals the extent to which positive selection is operating on the core genome and identifies candidate genes which may have important roles in the fitness of the species.
Modulation of the ATP-adenosine signaling axis combined with radiotherapy facilitates anti-cancer immunity in brain metastasis
Authors: Salamero-Boix Anna , Schulz Michael , Anthes Julian , Mayer Jens , Möckl Aylin , Tsoukala Ioanna , Menger Dominic , Mosa Mohammed H. , Hetzer Jenny , Macas Jadranka , Hehlgans Stephanie , Schuck Jonas , Roller Bastian , Reiss Yvonne , Hochart Guillaume , Bonnel David , Medyouf Hind , Rodriguez Mariana Barcenas , Broggini Thomas , Czabanka Marcus , Plate Karl H. , Heikenwälder Mathias , Rödel Franz , Harter Patrick N. , Imkeller Katharina , Sevenich Lisa
Published: October 2024

The immunosuppressive microenvironment in the brain poses a major limitation to successful therapy for brain metastases. Here we report that blockade of the ATP-to-adenosine-converting enzymes CD39 and CD73 and the adenosine receptor A2AR in combination with radiotherapy attenuates tumor progression in a breast-to-brain metastasis model by facilitating anti-cancer immunity. Immunophenotyping revealed loss of exhausted T cells and higher abundance of anti-cancer effector T cell populations. This effect was accompanied by a decrease of immunosuppressive lipid-laden macrophages and an expansion of CD14CD33high macrophages associated with antigen presentation. Analyses of human brain metastases samples supports a role of the ATP-adenosine signaling axis in modulating tumor inflammation and identified expression of CD39 and adenosine deaminase as predictive markers for patient survival and/or immune infiltration. Our findings demonstrate that the adenosine axis represents a druggable pathway to achieve local immunomodulation and treatment response, opening a new therapeutic avenue for brain metastases patients.
Sporadic distribution of a new archaeal genetic code with all TAG codons as pyrrolysine
Authors: Kivenson Veronika , Peters Samantha L. , Borrel Guillaume , Kivenson Aleksandr , Roe Leah T. , Hamlish Noah X. , Fadhlaoui Khaled , Schepartz Alanna , Gribaldo Simonetta , Hettich Robert L. , Banfield Jillian F.
Published: October 2024

Numerous genetic codes developed during the evolution of Eukaryotes and three are known in Bacteria, yet no alternative genetic code has been established for Archaea. Some bacterial and archaeal proteins include selenocysteine or pyrrolysine, the 21stand 22ndamino acids, but no evidence establishes the adoption of a genetic code in which a stop codon universally encodes either amino acid. Here, we used proteomics to confirm the prediction that certain Archaea consistently incorporate pyrrolysine at TAG codons, supporting a new archaeal genetic code which we designate Genetic Code 34. This genetic code has 62 sense codons encoding 21 amino acids, and only two stop codons. In contrast with monophyletic genetic code distributions in bacteria, Code 34 occurs sporadically. This, combined with evidence for lateral gene transfer of the code change machinery and anticipated barriers to code reversal, suggests Code 34 arose independently in multiple lineages. TAG codon distribution patterns in Code 34 genomes imply a wide range in time since code switch. We identified many new enzymes containing Pyl residues, raising questions about potential roles of this amino acid in protein structure and function. We used five new PylRS/tRNAPylpairs from Code 34 archaea to introduce new-to-nature pyrrolysine analogs into proteins inE. coli, demonstrating their utility for genetic code expansion.

Graphical abstract
Multi-omics analysis reveals the mechanism of BnC07MYB3a is involved in seed coat color inBrassica napusL
Authors: Hu Ran , Zhang Mengzhen , Shen Shulin , Liu Haijing , Gao Lei , Tian Mengjiao , Liu Yiwei , Wan Huafang , Zhao Huiyan , Yin Nengwen , Du Hai , Liu Liezhao , Lu Kun , Li Jiana , Qu Cunmin
Published: October 2024

In rapeseed (Brassica napus), yellow-seeded varieties accumulate less flavonoid pigments (anthocyanins/proanthocyanidins) in their seed coats compared with black-seeded varieties. The yellow-seeded trait is associated with greatly improved seed oil yield, quality, and commercial value. Many R2R3 MYB activators have been characterized in rapeseed, but how MYB-type repressors affect pigment biosynthesis is not yet fully understood. In this study, we performed transcriptome sequencing and metabolomic analysis ofB. napusvarieties with extreme differences in seed coat color, combined with weighted gene co-expression network analysis. This analysis identified an R2R3-MYB-type transcription factor, BnC07MYB3a (BnaC07G0178800ZS), as a candidate regulator of the yellow-seeded trait inB. napus. OverexpressingBnC07MYB3ainArabidopsis thalianaandB. napusdownregulated the expression of flavonoid biosynthetic genes, resulting in significantly lower anthocyanin and proanthocyanidin accumulation than in the wild-type and a lighter seed coat color in transgenic plants. BnC07MYB3a directly binds to the promoter of theTRANSPARENT TESTA(TT) geneBnTT6and represses its expression. BnC07MYB3a also physically interacts with BnA06bHLH92a and the WD40 transcription factor TRANSPARENT TESTA GLABRA1 (BnTTG1), suggesting that they might form a previously unidentified MYB–bHLH–WD40 transcription factor complex. Our results reveal the molecular mechanism and regulatory network of BnC07MYB3a in determining seed coat color inB. napusand provide a genetic resource for breeding yellow-seeded cultivars ofB. napus.
Dimensionality Reduction of Genetic Data using Contrastive Learning
Authors: Thor Filip , Nettelblad Carl
Published: October 2024

We introduce a framework for using contrastive learning for dimensionality reduction on genetic datasets to create PCA-like population visualizations. Contrastive learning is a self-supervised deep learning method that uses similarities between samples to train the neural network to discriminate between samples. Much of the advances in these types of models have been made for computer vision, but many of the heuristics developed do not translate well from image to genetic data. We define a loss function that outperforms other basic loss functions used in contrastive learning in our experiments, and a data augmentation scheme tailored specifically towards SNP genotype datasets. We compare the performance of our method to PCA and contemporary non-linear methods with respect to how well they preserve local and global structure, and how well they generalize to new data. Our method displays good preservation of global structure and has improved generalization properties over t-SNE, UMAP, and popvae, while preserving relative distances between individuals to a high extent. A strength of the deep learning framework is the possibility of projecting new samples and fine-tuning to new datasets using a pre-trained model without access to the original training data, and the ability to incorporate more domain-specific information in the model. We show examples of population classification on two datasets of dog and human genotypes.
3D genome organization under extreme metabolic adaptation shows variations in genome compartmentalization and looping
Authors: Biswas Tathagata , Li Hua , Rohner Nicolas
Published: October 2024

Three-dimensional (3D) genome organization plays a crucial role in gene regulation by influencing cellular functions, such as bringing regulatory elements like enhancers into proximity with their target genes. In this study, we explore variations in 3D genome organization within different morphs of the fishAstyanax mexicanus, which includes a river-dwelling surface fish and multiple cave-dwelling morphs. The cave morphs, also known as cavefish, have adapted to the dark and nutrient-scarce cave environments, resulting in distinct metabolic reprogramming that has made them persistently hyperglycemic, resilient to starvation, and prone to fat accumulation. Focusing on metabolic evolution in cavefish, we used liver tissue to conduct genome-wide contact mapping through Hi-C experiments. Comparing the 3D genome architecture of two cave morphs – Pachón and Tinaja – with that of surface fish, we observed significant changes in genome compartmentalization and genomic loops. Some of these changes were common in both Pachón and Tinaja and were classified as cave-specific looping and compartmental switches. By integrating liver Hi-C data with RNA-seq, ATAC-seq, and histone ChIP-seq datasets, we gained deeper insight into the relationship between cave-specific 3D genome features and the transcriptional activity at associated loci. Additionally, we identified structural variations in the form of common genomic inversions in Pachón and Tinaja compared to surface fish. Therefore, this study is the first to define the 3D genome organization ofAstyanax mexicanusin livers and highlights how adaptation to extreme environments is associated with significant variations in 3D genome architecture, even within the same species.
Robust Detection of Brain Stimulation Artifacts in iEEG Using Autoencoder-Generated Signals and ResNet Classification
Authors: Saal Jeremy , Khambhati Ankit N. , Chang Edward F. , Shirvalkar Prasad
Published: October 2024

Background

Intracranial EEG (iEEG) is crucial for understanding brain function, but stimulation-induced noise complicates data interpretation. Traditional artifact detection methods require manual user input or struggle with noise variability, especially with limited labeled data.

Objective

We developed a supervised method to automatically detect stimulation-induced noise in human iEEG recordings using synthetic data generated by Variational Autoencoders (VAEs) to train a ResNet-18 classifier.

Methods

Multi-lead iEEG data were collected, preprocessed, and used to train VAEs for generating synthetic clean and noisy signals. The ResNet-18 model was trained on images of spectra generated from these synthetic signals and validated on real iEEG data from five participants.

Results

The classifier, trained exclusively on synthetic data, demonstrated high accuracy, precision, and recall when applied to real iEEG recordings, with AUC values greater than 0.99 across all participants.

Conclusion

We present a novel approach to effectively detect stimulation-induced noise in iEEG, offering a robust solution for improving data interpretation in scenarios with limited labeled data. Additionally, the pre-trained ResNet-18 model is available for the community to use, facilitating further research and application in similar datasets.
Assessing sustained attention processes and related cerebral activations in typically developing adolescents using the gradual-onset continuous performance task (gradCPT)
Authors: Awada J. , Fernandez NB. , Siffredi V. , Liverani MC. , Miehlbradt J. , Borradori-Tolsa C. , Leuchter R. Ha-Vinh
Published: October 2024

Introduction

Sustained attention and inhibition processes are fundamental components of attention that mature during adolescence, a transitive period between childhood and adulthood characterized by a rapid behavioral and cognitive development. The current study aimed to provide a better understanding of sustained attention and inhibition processes in typically developing adolescents (n = 26) aged 11-18.

Methods

Functional magnetic resonance images (fMRI) were acquired during two different modalities (thefaceand thescene) from a previously validated gradual□onset continuous (gradCPT) paradigm to evaluate sustained attention performances. In addition, we performed linear regression analyses to investigate how cerebral activation varied as a function of covariates of interest.

Results

We showed a bilateral fronto-parieto-occipito brain activation during response inhibition regardless the type of task. Participants demonstrated better behavioral performances during thescenegradCPT. We observed a mainly left-lateralized pattern of activation in a fronto-cingulo-cerebellum area during thefacegradCPT and an extended bilateral fronto-temporo-parieto-occipital activation during thescenegradCPT. Finally, we found associations between brain activity and behavioral attentional responses.

Conclusion

This study gives a better understanding of the neural correlates of sustained attention and inhibition in a typically developing adolescent population.