bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating computational efforts and physiological resolution of mathematical models of cardiac tissue
Authors: Jæger Karoline Horgmo , Trotter James D. , Cai Xing , Arevalo Hermenegild , Tveito Aslak
Published: March 2024

Computational techniques have significantly advanced our understanding of cardiac electrophysiology, yet they have predominantly concentrated on averaged models that do not represent the intricate dynamics near individual cardiomyocytes. Recently, accurate models representing individual cells have gained popularity, enabling analysis of the electrophysiology at the micrometer level. Here, we evaluate five mathematical models to determine their computational efficiency and physiological fidelity. Our findings reveal that cell-based models introduced in recent literature offer both efficiency and precision for simulating small tissue samples (comprising thousands of cardiomyocytes). Conversely, the traditional bidomain model and its simplified counterpart, the monodomain model, are more appropriate for larger tissue masses (encompassing millions to billions of cardiomyocytes). For simulations requiring detailed parameter variations along individual cell membranes, the EMI model emerges as the only viable choice. This model distinctively accounts for the extracellular (E), membrane (M), and intracellular (I) spaces, providing a comprehensive framework for detailed studies. Nonetheless, the EMI model's applicability to large-scale tissues is limited by its substantial computational demands for subcellular resolution.
Endothelial features along the pulmonary vascular tree in chronic thromboembolic pulmonary hypertension: distinctive or shared facets?
Authors: Verhaegen Janne , Willems Lynn , Wagenaar Allard , Spreuwers Ruben , Dahdah Nessrine , Aversa Lucia , Verbelen Tom , Delcroix Marion , Quarck Rozenn
Published: March 2024

Chronic thromboembolic pulmonary hypertension (CTEPH) is a rare complication of pulmonary embolism, characterized by the presence of organized fibro-thrombotic material that partially or fully obstructs the lumen of large pulmonary arteries, microvasculopathy, and enlargement of the bronchial systemic vessels. The precise mechanisms underlying CTEPH remain unclear. However, defective angiogenesis and altered pulmonary arterial endothelial cell (PAEC) function may contribute to disease progression. Despite the observation of differences in histological features, shear stress and ischemia along the pulmonary vascular tree, the potential contribution of PAEC phenotype and function to these disparate aspects remains unexplored. Based on these observations, we postulated that angiogenic capacities and endothelial barrier function may contribute to disparities in histological features observed along the pulmonary vascular tree.

We thus explored the histological characteristics of the pulmonary vascular tree using pulmonary arterial lesions obtained during pulmonary endarterectomy (PEA). We focused on the angiogenic vascular endothelial growth factor (VEGF)-A/VEGF receptor-2 (VEGFR2) axis and collagen 15A1 (COL15A1), a potential marker of endothelial cells of the systemic circulation. Concurrently, we examinedin vitroangiogenic properties and barrier function of PAECs derived from large and (sub)-segmental pulmonary arterial lesions. (Sub)-segmental pulmonary arterial lesions were abundantly recanalized by neovessels, paralleled by an enriched expression of VEGFR2. VEGF-A expression was more pronounced in large pulmonary arterial lesions. Nevertheless, no significant difference was discerned inin vitroangiogenic capacities and barrier integrity of PAECs isolated from large and (sub)- segmental pulmonary arterial lesions. Importantly, our findings revealed the presence of endothelial cells (CD31+) expressing COL15A1, as well as CD31+cells that did not express COL15A1. This suggests that endothelial cells from both systemic and pulmonary circulation contribute to lesion recanalization.

Despite disparatein situangiogenic cues in VEGF-A/VEGFR2 axis between large and (sub)- segmental pulmonary arterial lesions in CTEPH,in vitroangiogenic capacities and barrier function remain unaltered.
Subcellular thermal profiling enables the deep functional exploration of the mitochondrial proteome
Authors: Rivera-Mejías Pablo , Le Sueur Cécile , Kurzawa Nils , Becher Isabelle , Savitski Mikhail M
Published: March 2024

Mitochondria are membrane-bound organelle hubs of cellular metabolism and signaling. The dysregulation of mitochondria is related to the genesis of several highly prevalent diseases, including cancer and cardiovascular disorders, urging the development of novel technologies to systematically study this organelle and its dynamics. Thermal proteome profiling (TPP) allows the unbiased study of the interactions of proteins with drugs, metabolites, and other proteins, providing a unique understanding of the state of the proteome. Here, we develop and introduce an optimized TPP workflow, mito-TPP, for the direct and extensive study of this organelle. We demonstrate that our approach detects both direct mitochondrial small molecule-protein and metabolite-protein interactions, as well as indirect downstream effects. We also show that mito-TPP preserves features from whole-cell systems, such as the coaggregation of interacting proteins. Finally, we explore the mitochondrial proteoform map, detecting more than 180 proteins with multiple proteoform groups. Overall, we demonstrate that mito-TPP is a powerful new tool for the functional study of the mitochondrial proteome.
Functional overlap between the mammalianSar1aandSar1bparalogs in vivo
Authors: Tang Vi T. , Xiang Jie , Chen Zhimin , McCormick Joseph , Abbineni Prabhodh S. , Chen Xiao-Wei , Hoenerhoff Mark , Emmer Brian T. , Khoriaty Rami , Lin Jiandie D. , Ginsburg David
Published: March 2024

Proteins carrying a signal peptide and/or a transmembrane domain enter the intracellular secretory pathway at the endoplasmic reticulum (ER) and are transported to the Golgi apparatus via COPII vesicles or tubules. SAR1 initiates COPII coat assembly by recruiting other coat proteins to the ER membrane. Mammalian genomes encode twoSAR1paralogs,SAR1AandSAR1B. While these paralogs exhibit ∼90% amino acid sequence identity, it is unknown whether they perform distinct or overlapping functions in vivo. We now report that genetic inactivation ofSar1ain mice results in lethality during mid-embryogenesis. We also confirm previous reports that complete deficiency of murineSar1bresults in perinatal lethality. In contrast, we demonstrate that deletion ofSar1brestricted to hepatocytes is compatible with survival, though resulting in hypocholesterolemia that can be rescued by adenovirus-mediated overexpression of either SAR1A or SAR1B. To further examine the in vivo function of these 2 paralogs, we genetically engineered mice with theSar1acoding sequence replacing that ofSar1bat the endogenousSar1blocus. Mice homozygous for this allele survive to adulthood and are phenotypically normal, demonstrating complete or near-complete overlap in function between the two SAR1 protein paralogs in mice. These data also suggest upregulation ofSAR1Agene expression as a potential approach for the treatment of SAR1B deficiency (chylomicron retention disease) in humans.
Dual agonism of sodium iodide symporter functionin vivo
Authors: Brookes Katie , Thornton Caitlin M. , Zha Ling , Kim Jana , Small Benjamin , Manivannan Selvambigai , Nieto Hannah R. , Adcock Holly , Bottegoni Giovanni , Cox Liam R. , Kannappan Vinodh , Wang Weiguang , Gorvin Caroline M. , Jhiang Sissy , Ringel Matthew D. , Campbell Moray J. , Sunassee Kavitha , Blower Philip J. , Boelaert Kristien , Smith Vicki E. , Read Martin L. , McCabe Christopher J.
Published: March 2024

New approaches are urgently needed to enhance the radioiodide (RAI) ablation of aggressive and metastatic thyroid cancer. We recently discovered that valosin-containing protein inhibitors (VCPi) such as clotrimazole and disulfiram transiently block sodium iodide symporter (NIS) proteasomal degradation, hence promoting RAI uptake. However, poor bioavailability diminishes their potential impactin vivo. Following 3D modelling and iterative drug design we appraised 26 novel analogues of clotrimazole, as well as albumin nano-encapsulated copper-diethyldithiocarbamate [Cu(DDC)2-alb] – a stabilised reformulation of a disulfiram metabolite. While several clotrimazole analogues specifically increased RAI uptake, the greatest impact was observed with Cu(DDC)2-alb in thyroid cancer cells as well as human primary thyrocytes from patients with thyroid hyperplasia. NanoBRET assays revealed that Cu(DDC)2enhanced the plasma membrane accumulation of NIS in living cells. In BALB/c mice, both intraperitoneal and intravenous administration of Cu(DDC)2-alb significantly enhanced thyroidal99mTc-uptake. RNA-Seq revealed the surprising observation that Cu(DDC)2-alb induced key thyroid transcription factors. Accordingly, expression of PAX8 and NKX2.1 was upregulated in thyroid glands from drug treated mice, with NIS levels correlating closely to99mTc-uptake. As Cu(DDC)2inhibits the VCP cofactor NPL4, with VCP being critical to the proteostatic processing of NIS protein, we identify a new dual agonist of RAI uptakein vivo, with the potential to directly impact RAI therapy for patients with aggressive thyroid cancer.
Genome-wide association study reveals multiple loci for nociception and opioid consumption behaviors associated with heroin vulnerability in outbred rats
Authors: Kuhn Brittany N. , Cannella Nazzareno , Chitre Apurva S. , Nguyen Khai-Minh H. , Cohen Katarina , Chen Denghui , Peng Beverly , Ziegler Kendra S. , Lin Bonnie , Johnson Benjamin B. , Missfeldt Sanches Thiago , Crow Ayteria D. , Lunerti Veronica , Gupta Arkobrato , Dereschewitz Eric , Soverchia Laura , Hopkins Jordan L. , Roberts Analyse T. , Ubaldi Massimo , Abdulmalek Sarah , Kinen Analia , Hardiman Gary , Chung Dongjun , Polesskaya Oksana , Solberg Woods Leah C. , Ciccocioppo Roberto , Kalivas Peter W. , Palmer Abraham A.
Published: March 2024

The increased prevalence of opioid use disorder (OUD) makes it imperative to disentangle the biological mechanisms contributing to individual differences in OUD vulnerability. OUD shows strong heritability, however genetic variants contributing to vulnerability remain poorly defined. We performed a genome-wide association study using over 850 male and female heterogeneous stock (HS) rats to identify genes underlying behaviors associated with OUD such as nociception, as well as heroin-taking, extinction and seeking behaviors. By using an animal model of OUD, we were able to identify genetic variants associated with distinct OUD behaviors while maintaining a uniform environment, an experimental design not easily achieved in humans. Furthermore, we used a novel non-linear network-based clustering approach to characterize rats based on OUD vulnerability to assess genetic variants associated with OUD susceptibility. Our findings confirm the heritability of several OUD-like behaviors, including OUD susceptibility. Additionally, several genetic variants associated with nociceptive threshold prior to heroin experience, heroin consumption, escalation of intake, and motivation to obtain heroin were identified.Tom1, a microglial component, was implicated for nociception. Several genes involved in dopaminergic signaling, neuroplasticity and substance use disorders, includingBrwd1,Pcp4, Phb1l2andMmp15were implicated for the heroin traits. Additionally, an OUD vulnerable phenotype was associated with genetic variants for consumption and break point, suggesting a specific genetic contribution for OUD-like traits contributing to vulnerability. Together, these findings identify novel genetic markers related to the susceptibility to OUD-relevant behaviors in HS rats.
Epigenetic programming of host lipid metabolism associates with resistance to TST/IGRA conversion after exposure toMycobacterium tuberculosis
Authors: Dill-McFarland Kimberly A , Simmons Jason D , Peterson Glenna J , Nguyen Felicia K , Campo Monica , Benchek Penelope , Stein Catherine M , Vaisar Tomas , Mayanja-Kizza Harriet , Boom W Henry , Hawn Thomas R
Published: March 2024

Mycobacterium tuberculosis(Mtb) exposure leads to a range of outcomes including clearance, latent TB infection (LTBI), and pulmonary tuberculosis (TB). Some heavily exposed individuals resist tuberculin skin test (TST) and interferon gamma release assay (IGRA) conversion (RSTR), which suggests that they employ IFNγ-independent mechanisms of Mtb control. Here, we compare monocyte epigenetic profiles of RSTR and LTBI from a Ugandan household contact cohort. Chromatin accessibility did not differ between uninfected RSTR and LTBI monocytes. In contrast, methylation significantly differed at 174 CpG sites and across 63 genomic regions. Consistent with previous transcriptional findings in this cohort, differential methylation was enriched in lipid and cholesterol associated pathways including in the genes APOC3, KCNQ1, and PLA2G3. In addition, methylation was enriched in Hippo signaling, which is associated with cholesterol homeostasis and includes CIT and SHANK2. Lipid export and Hippo signaling pathways were also associated with gene expression in response to Mtb in RSTR as well as IFN stimulation in monocyte-derived macrophages (MDMs) from an independent healthy donor cohort. Moreover, serum-derived HDL from RSTR had elevated ABCA1-mediated cholesterol efflux capacity (CEC) compared to LTBI. Our findings suggest that resistance to TST/IGRA conversion is linked to regulation of lipid accumulation in monocytes, which could facilitate early Mtb clearance among RSTR subjects through IFNγ-independent mechanisms.

IMPORTANCE

Tuberculosis (TB) remains an enduring global health challenge with millions of deaths and new cases each year. Despite recent advances in TB treatment, we lack an effective vaccine or a durable cure. While heavy exposure toMycobacterium tuberculosisoften results in latent TB latent infection (LTBI), subpopulations exist who are either resistant to infection or contain Mtb with IFNγ-independent mechanisms not indicative of LTBI. These resisters provide an opportunity to investigate mechanisms of TB disease and discover novel therapeutic targets. Here, we compare monocyte epigenetic profiles of RSTR and LTBI from a Ugandan household contact cohort. We identify methylation signatures in host lipid and cholesterol pathways with potential relevance to early TB clearance before the sustained IFN responses indicative of LTBI. This adds to a growing body of literature linking TB disease outcomes to host lipids.
High-dimensional mass cytometry reveals stemness state heterogeneity in pancreatic ductal adenocarcinoma
Authors: Ervin Egle Helene , Ahern David , Liu Feng , Rendek Aniko , Soonawalla Zahir , Oppermann Udo , Hulley Philippa , Pauklin Siim
Published: March 2024

Stem-like cancer cells harbour high self-renewal capacity, exhibit enhanced tumourigenicity and have been associated with therapy resistance, metastasis and tumour relapse. Therefore, understanding the molecular features of stem-like cells is critical for targeting them effectively and improving treatment outcomes for cancer patients. Several markers have been used to isolate and study the putative stem-like cells of pancreatic ductal adenocarcinoma (PDAC), but the patterns of marker co-expression and overlap between identified individual subpopulations are yet to be comprehensively studied. Here we developed a mass cytometry antibody panel for simultaneous analysis of 33 stemness-associated markers at single-cell resolution. High-dimensional mass cytometry analysis of PDAC cell lines revealed molecularly heterogeneous stemness states and highlighted the role of genotype in determining the cell line-specific stemness signature. Stemness marker expression lie along a continuum in PDAC cell lines and patient samples indicative of stepwise phenotypic transitions. We also identified a subset of PDAC cells co-expressing high levels of Musashi-2, DCLK1 and CXCR4, and harbouring basal-like and EMT transcriptional programmes associated with highly plastic phenotype. This multiplexed analysis uncovers nuance and complexities of the stemness state in the PDAC.
Virus-derived Synthetic Riboswitches for Real-time Coronaviruses Sensing in Live Cells
Authors: Zeng Leiping , Qi Lei S.
Published: March 2024

Real-time sensing of viral infection in live cells are crucial for virology research and antiviral development. However, existing methods face challenges of low signal sensitivity and the necessity for viral manipulation and cell fixation. Here, we develop aviralriboswitch (vRibo) approach that employs the viral replicase to induce transgene expression upon viral infection. The vRibo is designed to detect viral real-time transcription and replication in live cells, which in response triggers the translation of reporter and therapeutic genes. By integrating a viral packaging sequence, vRibo can be transmitted to neighboring cells through progeny virions, effectively acting as a ‘Trojan Horse’. The negative-strand vRibo elements demonstrated effective detection of several coronaviruses, including 229E and OC43, due to the conservation of cis-acting RNA structures across coronaviruses. Notably, vRibo functions as a dual-purpose system, acting both as an infection detector and inducible antiviral system. vRibo has the potential for basic virology research applications and can be adopted in improving the inducible expression of mRNA medicines for future coronaviruses.
Evaluating the impacts of tiered restrictions introduced in England in December 2020 on covid-19 hospitalisations: a synthetic control study
Authors: Zhang Xingna , Hungerford Daniel , Green Mark A. , García-Fiñana Marta , Buchan Iain E. , Barr Ben
Published: March 2024

Objectives

To assess the impact of Tier 3 covid-19 restrictions implemented in December 2020 in England on covid-19 hospital admissions compared to Tier 2 restrictions, and its potential variations by neighbourhood deprivation levels and the prevalence of the Alpha variant (B.1.1.7).

Design

Observational study utilising a synthetic control approach. Comparison of changes in weekly hospitalisation rates in Tier 3 areas to a synthetic control group derived from Tier 2 areas.

Setting

England between 4thOctober 2020 and 21stFebruary 2021.

Participants

23 million people under Tier 3 restrictions, compared to a synthetic control group derived from 29 million people under Tier 2 restrictions.

Interventions

Implementation of Tier 3 covid-19 restrictions in designated areas on 7thDecember 2020, with additional constraints on indoor and outdoor meetings and the hospitality sector compared to less stringent Tier 2 restrictions.

Main Outcome Measures

Weekly covid-19 related hospital admissions for neighbourhoods in England over a 12-week period following the interventions.

Results

The introduction of Tier 3 restrictions was associated with a 17% average reduction in hospital admissions compared to Tier 2 areas (95% CI 13% to 21%; 8158 (6286 to 9981) in total)). The effects were similar across different levels of neighbourhood deprivation and prevalence of the Alpha variant (B.1.1.7).

Conclusions

Regionally targeted Tier 3 restrictions in England had a moderate but significant effect on reducing hospitalisations. The impact did not exacerbate socioeconomic inequalities during the pandemic. Our findings suggest that regionally targeted restrictions can be effective in managing infectious diseases.

SUMMARY BOXES

What is already known on this topic

— Previous studies of localised non-pharmaceutical interventions (NPIs) found that they could be effective in reducing covid-19 transmissions.

— covid-19 hospitalisation was a key indicator of healthcare resource dynamics, encompassing supply, demand, burden, and allocation, during the pandemic.

— There is a need for a detailed examination of the impact of specific localised restrictions in the UK, such as Tier 3 measures, on hospital admissions to inform targeted public health strategies.

What this study adds

— This study found that additional localised restrictions on outdoor gatherings and in the hospitality sector were effective in mitigating hospital admissions during the pandemic.

How this study might affect research, practice or policy

— This study provides evidence for future public health policies and preparedness strategies supporting the use of differential regional restrictions during pandemics.
B-OK: A Visual and Tactile Tool for HIV Treatment Adherence Support in a United States Urban Center
Authors: Richterman Aaron , Klaiman Tamar , Palma Daniel , Ryu Eric , Schmucker Laura , Villarin Katherine , Grosso Gabrielle , Brady Kathleen A , Thirumurthy Harsha , Buttenheim Alison
Published: March 2024

Lack of adherence to antiretroviral therapy (ART) and poor retention in care are significant barriers to ending HIV epidemics. Treatment adherence support (TAS) effectiveness may be constrained by limited awareness and understanding of the benefits of ART, particularly the concepts of treatment as prevention and Undetectable=Untransmittable (U=U), for which substantial knowledge gaps persist. We used mixed methods to evaluate a straightforward visual and tactile tool, the B-OK Bottles (“B-OK”), that incorporates human-centered design and behavioral economics principles and is designed to change and strengthen mental models about HIV disease progression and transmission. We enrolled 118 consenting adults living with HIV who were clients of medical case managers at one of four case management agencies in Philadelphia. All participants completed a pre-intervention survey, a B-OK intervention, and a post-intervention survey. A subset (N=52) also completed qualitative interviews before (N=20) or after (N=32) B-OK. Participants had a median age of 55 years (IQR 47-60), about two-thirds were male sex (N=77, 65%), nearly three-quarters identified as non-Hispanic Black (N=85, 72%), and almost all reported receiving ART (N=116, 98%). Exposure to B-OK was associated with improved awareness and understanding of HIV terminology, changes in attitudes about HIV treatment, and increased intention to rely on HIV treatment for transmission prevention. Insights from qualitative interviews aligned with the quantitative findings as respondents expressed a better understanding of U=U and felt that B-OK clearly explained concepts of HIV treatment and prevention. These findings provide a strong rationale to further evaluate the potential for B-OK to improve TAS for PLWH.
RFC1repeat expansion analysis from whole genome sequencing data simplifies screening and increases diagnostic rates
Authors: Sullivan Roisin , Chen Sai , Saunders Christopher T , Yau Wai Yan , Goh Yee Yen , O’Connor Emer , Dominik Natalia , Deforie Valentina Galassi , Morsy Heba , Cortese Andrea , Houlden Henry , Eberle Michael A. , Vandrovcova Jana
Published: March 2024

Biallelic expansions and a motif change inRFC1are a common cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome. Molecular diagnosis relies on a complicated combination of repeat primed PCR and Southern blotting. We developed a whole genome sequencing based method forRFC1repeat detection.

The combination of sequence motifs and allele length analysis in 29,478 individuals showed that 92.5% of samples have no expanded allele or have expansions of known benign motifs on one allele. In total, 103 samples were classified as biallelic carriers of pathogenic expansions and the frequency of the most common pathogenic allele AAGGG was estimated as 3.9%. OurRFC1classification method was validated by molecular diagnostic methods achieving sensitivity and specificity of 100% and 97.4%, respectively. Additionally, we catalogued 8 rare repeat motifs, further elucidating the high sequence complexity within theRFC1locus.

In this study we report a new method to identify patients carryingRFC1pathogenic repeat expansions from WGS data, reducing the need for the inefficient molecular workflow currently used for clinical diagnoses. This method correctly identifies recessive pathogenic repeat expansions inRFC1and allows screening of existing large scale WGS datasets of unsolved cases.
Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery
Authors: Tan Jessica Karielle , Servellita Venice , Stryke Doug , Kelly Emily , Streithorst Jessica , Sumimoto Nanami , Foresythe Abiodun , Huh Hee Jae , Nguyen Jenny , Oseguera Miriam , Brazer Noah , Tang Jack , Ingebrigtsen Danielle , Fung Becky , Reyes Helen , Hillberg Melissa , Chen Alice , Guevara Hugo , Yagi Shigeo , Morales Christina , Wadford Debra A. , Mourani Peter M. , Langelier Charles R. , de Lorenzi-Tognon Mikael , Benoit Patrick , Chiu Charles Y.
Published: March 2024

Tools for rapid identification of novel and/or emerging viruses are urgently needed for clinical diagnosis of unexplained infections and pandemic preparedness. Here we developed and clinically validated a largely automated metagenomic next-generation sequencing (mNGS) assay for agnostic detection of respiratory viral pathogens from nasopharyngeal swab, bronchoalveolar lavage and tracheal aspirate samples in <24 hours. The mNGS assay achieved mean limits of detection of 543 copies/mL, viral load quantification with 100% linearity, and 93.6% sensitivity, 93.8% specificity, and 93.7% accuracy compared to gold-standard clinical multiplex RT-PCR. Performance increased to 97.9% overall predictive agreement after discrepancy testing and clinical adjudication, which was superior to that of RT-PCR (95.0% agreement). To enable discovery of novel, sequence-divergent human viruses with pandemic potential,de novoassembly and translated nucleotide algorithms were incorporated into the automated SURPI+ computational pipeline used by the mNGS assay for pathogen detection. Usingin silicoanalysis, we showed after removal of all human viral sequences from the reference database that 70 (100%) of 70 representative human viral pathogens could still be identified based on homology to related animal or plant viruses. Our assay, which was granted breakthrough device designation from the US Food and Drug Administration (FDA) in August of 2023, demonstrates the feasibility of routine mNGS testing in clinical and public health laboratories, thus enabling a robust and rapid response to the next viral respiratory pandemic.
Insight into the regulatory mechanism of the MFS transporter, SCO4121 by the MarR regulator, SCO4122
Authors: Nag Ankita , Sharma Shiksha , Rani Pittu Sandhya , Mehra Sarika
Published: March 2024

MarR group of transcriptional regulators are ubiquitous in bacteria and found to be involved in regulation of efflux pumps that confer multidrug resistance phenotype. While most characterized MarR regulators act as transcriptional repressors, we earlier identified a MarR regulator SCO4122 inStreptomyces coelicolor, playing an essential role in transcriptional activation of the MFS transporter SCO4121 in response to multiple substrates of the latter, including streptomycin, ciprofloxacin and chloramphenicol. In this study, using Surface Plasmon Resonance, we demonstrate that SCO4122 interacts directly with the diverse substrates of SCO4121 with the highest affinity for streptomycin with a KD of 0.73 μM. Further, in-vitro and in-vivo studies reveal that SCO4122 also binds to the intergenic region betweensco4121andsco4122,where the interaction is dependent on the cooperative binding of SCO4122 to three motifs in this region. A conserved Methionine, M93, in SCO4122 is identified to be an integral amino acid residue that is involved in activation of SCO4121 in response to ciprofloxacin, streptomycin and EtBr but not chloramphenicol. Furthermore, our studies also indicate that upon binding to different substrates, the affinity of SCO4122 to thesco4121promoter increases 50-1000 fold, thereby leading to enhanced expression of the transporter, SCO4121. This study thus highlights that SCO4122 is a novel MarR regulator that functions as a strong transcriptional activator of an efflux pump, SCO4121, through intricate molecular mechanisms in presence of structurally dissimilar substrates.

Graphical abstract
Spatial heterogeneity in collective electrotaxis: continuum modelling and applications to optimal control
Authors: Martina-Perez Simon F. , Breinyn Isaac B. , Cohen Daniel J. , Baker Ruth E.
Published: March 2024

Collective electrotaxis is a phenomenon that occurs when a cellular collective, for example an epithelial monolayer, is subjected to an electric field. Biologically, it is well known that the velocity of migration during the collective electrotaxis of large epithelia exhibits significant spatial heterogeneity. In this work, we demonstrate that the heterogeneity of velocities in the electrotaxing epithelium can be accounted for by a continuum model of cue competition in different tissue regions. Having established a working model of competing migratory cues in the migrating epithelium, we develop and validate a reaction-convection-diffusion model that describes the movement of an epithelial monolayer as it undergoes electrotaxis. We use the model to predict how tissue size and geometry affect the collective migration of MDCK monolayers, and to propose several ways in which electric fields can be designed such that they give rise to a desired spatial pattern of collective migration. We conclude with two examples that demonstrate practical applications of the method in designing bespoke stimulation protocols.
RCE-IFE: Recursive Cluster Elimination with Intra-cluster Feature Elimination
Authors: Kuzudisli Cihan , Bakir-Gungor Burcu , Qaqish Bahjat , Yousef Malik
Published: March 2024

The computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a major challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniques that seek to detect strong correlations among features and the existence of irrelevant features. In this work, we develop Recursive Cluster Elimination with Intra-Cluster Feature Elimination (RCE-IFE), a method that iterates clustering and elimination steps in a supervised context. Recursively, feature clusters are formed, then scored, and less contributing clusters are eliminated. Next, low-scoring features in retained clusters are eliminated. Intra-cluster feature elimination aims to reduce noisy features while keeping a minimum number of predictive features. The performance of RCE-IFE is evaluated and compared to other FS techniques in several datasets. The results show that the proposed strategy effectively reduces the size of the feature set and also improves the model performance.
Pouch microbiome changes during lactation in the short-beaked echidna (Tachyglossus aculeatus)
Authors: Wilson Isabella , Perry Tahlia , Eisenhofer Raphael , Rismiller Peggy , Shaw Michelle , Grutzner Frank
Published: March 2024

Monotreme and marsupial early development is characterised by a short gestation, the birth of the young at an early stage of development, and a long lactation in the pouch or pseudo-pouch. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich world. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiome during different stages of the reproductive cycle and whether this differs between wild and captive animals. Swab samples were obtained from wild and captive echidna pouches outside of breeding season, during courtship and breeding, and during lactation. 16S rRNA gene metabarcoding revealed that the pouch microbiome undergoes dramatic changes during lactation, with a reduction in bacterial taxa that may be pathogenic. These changes were not observed in samples taken outside of breeding season or during courtship and mating. This showed that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. This study pioneers pouch microbiome research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform captive breeding in the future.
MultiMatch: Geometry-Informed Colocalization in Multi-Color Super-Resolution Microscopy
Authors: Naas Julia , Nies Giacomo , Li Housen , Stoldt Stefan , Schmitzer Bernhard , Jakobs Stefan , Munk Axel
Published: March 2024

With recent advances in multi-color super-resolution light microscopy it has become possible to simultaneously visualize multiple subunits within complex biological structures at nanometer resolution. To opti-mally evaluate and interpret spatial proximity of stainings on such an image, colocalization analysis tools have to be able to integrate prior knowledge on the local geometry of the recorded biological complex. Here, we presentMultiMatchto analyze the abundance and location of chain-like particle arrangements in multi-color microscopy based on multi-marginal optimal unbalanced transport methodology. Our object-based colocalization model statistically addresses the effect of incomplete labeling efficiencies enabling inference on existent, but not fully observ-able particle chains. We showcase that MultiMatch is able to consistently recover all existing chain structures in three-color STED images of DNA origami nanorulers and outperforms established geometry-uninformed triplet colocalization methods in this task in a simulation study. Further-more, MultiMatch also excels in the evaluation of simulated four-color STED images and generalizations to even more color channels can be immediately derived from our analysis. MultiMatch is provided as a user-friendly Python package comprising intuitive colocalization visual-izations and a computationally efficient network flow implementation.
PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks
Authors: Peng Zhangzhi , Schussheim Benjamin , Chatterjee Pranam
Published: March 2024

Abstract

Proteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their amino acids greatly influence the structural and functional diversity of different protein types and uphold proteostasis, allowing cells to swiftly respond to environmental changes and intricately regulate complex biological processes. To this point, efforts to model the complex features of proteins have involved the training of large and expressive protein language models (pLMs) such as ESM-2 and ProtT5, which accurately encode structural, functional, and physicochemical properties of input protein sequences. However, the over 200 million sequences that these pLMs were trained on merely scratch the surface of proteomic diversity, as they neither input nor account for the effects of PTMs. In this work, we fill this major gap in protein sequence modeling by introducing PTM tokens into the pLM training regime. We then leverage recent advancements in structured state space models (SSMs), specifically Mamba, which utilizes efficient hardware-aware primitives to overcome the quadratic time complexities of Transformers. After adding a comprehensive set of PTM tokens to the model vocabulary, we train bidirectional Mamba blocks whose outputs are fused with state-of-the-art ESM-2 embeddings via a novel gating mechanism. We demonstrate that our resultant PTM-aware pLM,PTM-Mamba, improves upon ESM-2’s performance on various PTM-specific tasks. PTM-Mamba is the first and only pLM that can uniquely input and represent both wild-type and PTM sequences, motivating downstream modeling and design applications specific to post-translationally modified proteins. To facilitate PTM-aware protein language modeling applications, we have made our model available at:https://huggingface.co/ChatterjeeLab/PTM-Mamba.
Structural basis ofFusobacterium nucleatumadhesin Fap2 interaction with receptors on cancer and immune cells
Authors: Schöpf Felix , Marongiu Gian L. , Milaj Klaudia , Sprink Thiemo , Kikhney Judith , Moter Annette , Roderer Daniel
Published: March 2024

The intestinal microbiome (IM) is decisive for the human host’s health. Numerous microbiota drive the progression of colorectal cancer (CRC), the third-most common cancer worldwide. The Gram-negativeFusobacterium nucleatum(Fn) is overrepresented in the IM of CRC patients and has been correlated with the emergence, progression, and metastasis of tumors. A key pathogenic factor of Fn is the adhesin Fap2, an autotransporter protein that facilitates association to cancer and immune cells via two receptors, the glycan Gal-GalNAc and the T-cell protein TIGIT, respectively. The latter interaction leads to deactivation of immune cells. Mechanistic details of the Fap2/TIGIT interaction remain elusive due to the lack of high-resolution structural data. Here, we report a system to recombinantly express functional Fap2 on theEscherichia colisurface, which interacts with Gal-GalNAc on cancer cells and with purified TIGIT with submicromolar affinity. Cryo-EM structures of Fap2, alone and in complex with TIGIT, show that the ∼50 nm long rod-shaped Fap2 extracellular region binds to TIGIT on its membrane-distal tip via an extension of a β-helix domain. Moreover, by combining structure predictions, cryo-EM, docking and MD simulations, we identified a binding pit for Gal-GalNAc on the tip of Fap2. Our data represent the first purification and high-resolution structural analysis of a Fn autotransporter adhesin and its receptor association.
Translation coupled mRNA-decay is a function of both structural and codon level characteristics
Authors: Basu Sudipto , Hait Suman , Kundu Sudip
Published: March 2024

The majority of mRNA degradation occurs co-translationally. Several works in the past elucidated the role of codon composition in regulating co-translational mRNA decay. Integration of mRNA sequence, structure and ribosomal density unravels common regulatory factors of translational and degradation and helps in understanding the intricate association between these two important processes. Co-translational degradation is a two-step process, involving translational stalling and mRNA release for degradation. Our findings highlight the role of Codon Adaptation Index, a sequence-level feature that serves as the primary determinant of translation rates facilitating transcript release from translational machinery upon stalling. Concurrently, cellular endonucleases targeting Internal Unstructured Segments, facilitating easy degradation of the stalled mRNA transcripts, influencing their half-lives across the genome and over evolutionary timescales.
Multimodal intrinsic activation of GPCRs in ultrastable plasma membrane nanodomains
Authors: Kockelkoren Gabriele , Carstensen Jens , Lauritsen Line , Kazepidou Eleftheria , Tonnesen Asger , Shuttle Christopher G. , Kaas Paulina S. , Gupta Ankur , Breuer Artù , Rasmussen Søren G. F. , Duffet Loïc , Warne Tony , Patriarchi Tommaso , Tate Christopher G. , Uline Mark , Stamou Dimitrios
Published: March 2024

G protein-coupled receptors (GPCRs) mediate many physiological functions and are key targets in drug development1-3. A long-held tenet of molecular pharmacology is that GPCRs can spontaneously sample preexisting active conformations. This concept is pivotal to our understanding of ligand pharmacology4, however, direct evidence supporting it has only been obtained with reconstituted receptors5-12. Here, we introduce a method for quantitatively imaging the intrinsic activation probability of GPCRs directly at the plasma membrane of live cells, utilizing fluorescent conformational biosensors13,14. Our findings unveil a remarkable spatial multimodality in intrinsic activation probability, with a significant majority (up to 99%) of plasma membrane-expressed receptors showing negligible spontaneous activation. In contrast, the remaining minority of receptors exhibits spontaneous activation up to 22-fold higher than previously estimated. Experiments and theoretical calculations revealed that receptors diffuse into and out of ultralong-lived (∼5 minutes) nanodomains where the local membrane curvature allosterically enhances activation in the absence and presence of ligands. Extensive testing across five prototypic GPCRs indicates spatial nanoscale multimodality is ubiquitous, but varying in magnitude depending on the receptor and cell type. Upending conventional wisdom, this study reveals that drug efficacy is not a constant number but a spatiotemporal function ε(x, y, z, t)whose properties define and multiplex the signaling potency and efficacy of ternary complexes of GPCRs and likely other plasma membrane-receptors.

Graphical Abstract

GPCR spontaneous activation and intrinsic efficacy are not uniform across the plasma membrane but exhibit ultralong-lived spatial multimodality. Spatial variations in the curvature and composition of the plasma membrane, lead to the emergence of ultralong-lived nanodomains with contrasting physicochemical properties that allosterically regulate GPCR conformations. This results in a multimodal landscape of intrinsic efficacyϵ (x, y, z, t)that ultimately governs cell signaling. XY scalebar: 500 nm. Z-range: 100 nm.
Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models
Authors: Martínez-Redondo Gemma I. , Barrios-Núñez Israel , Vázquez-Valls Marçal , Rojas Ana M. , Fernández Rosa
Published: March 2024

Background

Understanding how coding genes and their functions evolve over time is a key aspect of evolutionary biology. Protein coding genes poorly understood or characterized at the functional level may be related to important evolutionary innovations, potentially leading to incomplete or inaccurate models of evolutionary change, and limiting the ability to identify conserved or lineage-specific features. Homology-based methodologies often fail to transfer functional annotations in a large fraction of the coding gene repertoire in non-model organisms. This is particularly relevant in animals, where a large number of their coding genes yield no functional annotation.

Results

Here, we leverage homology, deep learning, and protein language models to investigate functional annotation in the ‘dark proteome’ (defined as the unknown functional landscape’) of ca. 1,000 gene repertoires of virtually all animal phyla, totaling ca. 23.2 million coding genes. We then explored the ‘dark proteome’ of all animal phyla revealing an enrichment in functions related to immune response, viral infection, response to stimuli, development, or signaling, among others. Furthermore, we provide an open-source pipeline - FANTASIA - to implement and benchmark these methodologies in any dataset.

Conclusions

Our results uncover the putative functions of poorly understood protein-coding genes across the Animal Tree of Life that were inaccessible before due to the limitations in homology inference, contributing to a more comprehensive understanding of the molecular basis of animal evolution, and providing a new tool for the functional annotation of protein-coding genes in newly generated genomes.
The Structure of ApoB100 from Human Low-density Lipoprotein
Authors: Berndsen Zachary T. , Cassidy C. Keith
Published: March 2024

Low-density lipoprotein (LDL) plays a central role in lipid and cholesterol metabolism and is a key molecular agent involved in the development and progression of atherosclerosis, a leading cause of mortality worldwide. Apolipoprotein B100 (apoB100), one of the largest proteins in the genome, is the primary structural and functional component of LDL, yet its size and complex lipid associations have posed major challenges for structural studies. Here we overcome those challenges and present the first structure of apoB100 from human LDL using an integrative approach of cryo-electron microscopy, AlphaFold2, and molecular dynamics-based refinement. The structure consists of a large globular N-terminal domain that leads into a ∼58 nm long x 4 nm wide continuous amphipathic β-sheet that wraps completely around the circumference of the particle, holding it together like a belt. Distributed symmetrically across the two sides of the β-belt are 9 strategically located inserts that vary in size from ∼30-700 residues and appear to have diverse functions. The largest two form long flexible strings of paired amphipathic helices that extend across the lipid surface to provide additional structural support through specific long-range interactions. These results suggest a mechanism for how the various domains of apoB100 act in concert to maintain LDL shape and cohesion across a wide range of particle sizes. More generally, they advance our fundamental understanding of LDL form and function and will help accelerate the design of potential new therapeutics.
Metabolic and age-associated epigenetic barriers during direct reprogramming of mouse fibroblasts into induced cardiomyocytes
Authors: Santos Francisco , Correia Magda , Dias Rafaela , Bola Bárbara , Noberini Roberta , Ferreira Rita S. , Domingues Pedro , Teixeira José , Bonaldi Tiziana , Oliveira Paulo J. , Bär Christian , Bernardes de Jesus Bruno , Nóbrega-Pereira Sandrina
Published: March 2024

Heart disease is the leading cause of mortality in developed countries novel regenerative procedures are warranted for improving patients well fare. Direct cardiac conversion (DCC) can create induced cardiomyocytes (iCMs) and besides holding great promise, lacks clinical effectiveness for cardiac regeneration as metabolic and age-associated barriers remains elusive. Here, we identify by histone post-translational analysis that DCC triggers major age-dependent alterations in the epigenetic landscape. Metabolomics revealed decrease abundance of anabolic metabolites related to TCA cycle and glutaminolysis and profound mitochondrial network remodeling, with increased elongation and interconnectivity and reliance in mitochondrial respiration in iCMs.

Importantly, adult-derived iCMs present increase accumulation of oxidative stress in the mitochondria and pharmacological activation of mitophagy increase DCC of adult fibroblastsin vitro. Metabolic modulationin vitroand dietary manipulationsin vivoimproves DCC efficiency and are accompanied by significant alterations in the histone acetylation and methylation landscape and mitochondria homeostasis. Our study provides evidence that metaboloepigenetics as a direct role in cell fate transitions driving direct cardiac conversion into iCMs, highlighting the potential use of metabolic modulation in increasing cardiac regenerative strategies.
Architecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast
Authors: Barrero Daniel J. , Wijeratne Sithara S. , Zhao Xiaowei , Cunningham Grace F. , Yan Rui , Nelson Christian R. , Arimura Yasuhiro , Funabiki Hironori , Asbury Charles L. , Yu Zhiheng , Subramanian Radhika , Biggins Sue
Published: March 2024

Eukaryotic chromosome segregation requires kinetochores, multi-megadalton protein machines that assemble on the centromeres of chromosomes and mediate attachments to dynamic spindle microtubules. Kinetochores are built from numerous complexes, and understanding how they are arranged is key to understanding how kinetochores perform their multiple functions. However, an integrated understanding of kinetochore architecture has not yet been established. To address this, we purified functional, native kinetochores fromKluyveromyces marxianusand examined them by electron microscopy, cryo-electron tomography and atomic force microscopy. The kinetochores are extremely large, flexible assemblies that exhibit features consistent with prior models. We assigned kinetochore polarity by visualizing their interactions with microtubules and locating the microtubule binder Ndc80c. This work shows that isolated kinetochores are more dynamic and complex than what might be anticipated based on the known structures of recombinant subassemblies, and provides the foundation to study the global architecture and functions of kinetochores at a structural level.