bluuebunny/crossref_metadata_2025 huggingface dataset:
Examination of the coverage of functional assessments in the OMOP common data model
Authors: French Margaret A. , Hartman Paul , Hayes Heather A. , Ling Leah , Magel John , Thackeray Anne
Published: May 2024

Background

High-value care aims to enhance meaningful patient outcomes while reducing costs. Curating data across healthcare systems with common data models (CDMs) would help these systems move towards high-value healthcare. However, meaningful patient outcomes, such as function, must be represented in commonly used CDMs, such as Observational Medical Outcomes Partnership Model (OMOP). Yet the extent that functional assessments are included in the OMOP CDM is unclear.

Objective

Examine the extent that functional assessments used in neurologic and orthopaedic conditions are included in the OMOP CDM.

Methods

After identifying functional assessments from clinical practice guideline, two reviewer teams independently mapped the neurologic and orthopaedic assessments into the OMOP CDM. After this mapping, we measured agreement with the reviewer team with the number of assessments mapped by both reviewers, one reviewer but not the other, or neither reviewer. The reviewer teams then reconciled disagreements, after which we again examined agreement and the average number of concept ID numbers per assessment.

Results

Of the 81 neurologic assessments, 48.1% were initially mapped by both reviewers, 9.9% were mapped by one reviewer but not the other, and 42% were unmapped. After reconciliation, 46.9% of neurologic assessments were mapped by both reviewers and 53.1% were unmapped. Of the 79 orthopaedic assessments, 46.8% were initially mapped by both reviewers, 12.7% were mapped by one reviewer but not the other, and 48.1% were unmapped. After reconciliation, 48.1% of orthopaedic assessments were mapped by both reviewers and 51.9% were unmapped. Most assessments that were mapped had more than one concept ID number (neurologic assessments: 2.2±1.3; orthopaedic assessments: 4.3±4.4).

Conclusions

The OMOP CDM includes a portion of functional assessments recommended for use in neurologic and orthopaedic conditions. Many assessments did not have any term in the OMOP CDM. Thus, expanding the OMOP CDM to include recommended functional assessments and creating guidelines for mapping functional assessments would improve our ability to harmonize these data across healthcare systems.
Generation of spermatogonia from pluripotent stem cells in humans and non-human primates
Authors: Whelan Eoin C. , Hwang Young Sun , Seita Yasunari , Yokomizo Ryo , Leu N. Adrian , Cheng Keren , Sasaki Kotaro
Published: May 2024

Failures in germline development drive male infertility, but the lack of model systems that recapitulate human spermatogenesis hampers therapeutic development. Here, we have developed a system to differentiate human induced pluripotent stem cells (iPSCs) into primordial germ cell-like cells that self-organize within xenogeneic reconstituted testes (xrTestes) generated from mouse fetal testicular cells. Subsequent transplant of xrTestes into immunodeficient mice resulted in efficient generation of undifferentiated and differentiated spermatogonia as well as preleptotene spermatocytes with striking similarities to theirin vivocounterparts. As future clinical application will require testing in non-human primates, we utilized a similar strategy to differentiate rhesus iPSCs through all fetal germ cell stages into spermatogonia-like cells. Together, these models will serve as steppingstone to completion of human male in vitro gametogenesis.
The impact of insecticide decay on the rate of insecticide resistance evolution for monotherapies and mixtures
Authors: Hobbs Neil Philip , Hastings Ian Michael
Published: May 2024

The issue of insecticide decay in the public health deployments of insecticides is frequently highlighted as an issue for disease control. There are additional concerns insecticide decay also impacts the selection for insecticide resistance. Despite these concerns insecticide decay is lacking from models evaluating insecticide resistance management strategies. The impact of insecticide decay is modelled using a model which assumes a polygenic basis of insecticide resistance. Single generation selection events covering the insecticide efficacy and insecticide resistance space for both monotherapies and mixtures are conducted. With the outcome being the between generation change in the bioassay survival to the insecticides. The monotherapy sequence strategy and mixture strategy were compared against each other when including insecticide decay, with the outcome being the difference in strategy lifespan. The results demonstrate that as insecticides decay, they can apply a greater selection pressure than newly deployed insecticides, a process which can occur for both monotherapies and mixtures. For mixtures, it is seen that the rate of selection is highest when both insecticides are at reduced efficacies which would occur if reduced dose mixtures were used. Inclusion of insecticide decay in simulations was found to reduce the benefit of mixtures against monotherapy sequences, and this is especially so when reduced-dose mixtures are used. Insecticide decay is often highlighted as an important consideration for mixtures. The inclusion of insecticide decay in models is often lacking, and these results indicate this is absence may be over-inflating the performance of full-dose mixtures. As insecticides decay, they still provide selection pressures with reduced ability to control transmission, replenishing worn-out insecticides more frequently should be considered.
Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions
Authors: Kotliar Dylan , Curtis Michelle , Agnew Ryan , Weinand Kathryn , Nathan Aparna , Baglaenko Yuriy , Zhao Yu , Sabeti Pardis C. , Rao Deepak A. , Raychaudhuri Soumya
Published: May 2024

T-cells recognize antigens and induce specialized gene expression programs (GEPs) enabling functions including proliferation, cytotoxicity, and cytokine production. Traditionally, different classes of helper T-cells express mutually exclusive responses – for example, Th1, Th2, and Th17 programs. However, new single-cell RNA sequencing (scRNA-Seq) experiments have revealed a continuum of T-cell states without discrete clusters corresponding to these subsets, implying the need for new analytical frameworks. Here, we advance the characterization of T-cells with T-CellAnnoTator (TCAT), a pipeline that simultaneously quantifies pre-defined GEPs capturing activation states and cellular subsets. From 1,700,000 T-cells from 700 individuals across 38 tissues and five diverse disease contexts, we discover 46 reproducible GEPs reflecting the known core functions of T-cells including proliferation, cytotoxicity, exhaustion, and T helper effector states. We experimentally characterize several novel activation programs and apply TCAT to describe T-cell activation and exhaustion in Covid-19 and cancer, providing insight into T-cell function in these diseases.
Proliferation-driven mechanical feedback regulates cell dynamics in growing tissues
Authors: Sinha Sumit , Li Xin , Malmi-Kakkada Abdul N , Thirumalai D.
Published: May 2024

Local stresses in a tissue, a collective property, regulate cell division and apoptosis. In turn, cell growth and division induce active stresses in the tissue. As a consequence, there is a feed-back between cell growth and local stresses. However, how the cell dynamics depend on local stress-dependent cell division and the feedback strength is not fully understood. Here, we probe the consequences of stress-mediated growth and cell division on cell dynamics using agent-based simulations of a two-dimensional growing tissue. We discover a rich dynamical behavior of individual cells, ranging from jamming (mean square displacement, Δ(t) ∼tαwithαless than unity), to hyperdiffusion (α >2) depending on cell division rate and the strength of the mechanical feedback. Strikingly, Δ(t) is determined by the tissue growth law, which quantifies cell proliferation (number of cellsN(t) as a function of time). The growth law (N(t) ∼tλat long times) is regulated by the critical pressure that controls the strength of the mechanical feedback and the ratio between cell division-apoptosis rates. We show thatλ∼α, which implies that higher growth rate leads to a greater degree of cell migration. The variations in cell motility are linked to the emergence of highly persistent forces extending over several cell cycle times. Our predictions are testable using cell-tracking imaging techniques.
SEQSIM – A novel bioinformatics tool for comparisons of upstream gene regions – a case study of calcium binding protein spermatid associated 1 (CABS1)
Authors: Santos Joy Ramielle L. , Sun Weijie , Befus A. Dean , Marcet-Palacios Marcelo
Published: May 2024

The regulation of gene expression is carefully overseen by upstream gene regions (UGRs) which include promoters, enhancers, and other regulatory elements. Understanding these regions is difficult using standard bioinformatic approaches due to the scale of the human genome. Here we present SEQSIM, a novel bioinformatics tool based on a modified Needleman-Wunsch algorithm that allows for fast, comprehensive, and accurate comparison of UGRs across the human genome.

In this study, we detailed the applicability and validity of SEQSIM through an extensive case study of the calcium binding protein spermatid-associated 1 (CABS1). By analyzing 2000 base pairs upstream of every human gene, SEQSIM identified distinct clusters of UGRs, revealing conserved motifs and suggesting potential regulatory interactions. Our analysis identified 41 clusters, the second largest of which contains the CABS1 UGR. Studying the other members of the CABS1 cluster could offer new insights into its regulatory mechanisms and suggest broader implications for genes involved in similar pathways or functions.

The development and implementation of SEQSIM represents a significant step forward for the genomics field, providing a powerful new tool to dissect the complexity of the human genome and gain a better understanding of how gene expression is regulated. The study not only shows that SEQSIM is an effective means to identify potential regulatory elements and gene clusters, but also opens up new lines of inquiry to understand overall genomic architecture.
Understanding early HIV-1 rebound dynamics following antiretroviral therapy interruption: The importance of effector cell expansion
Authors: Perelson Alan S. , Phan Tin , Conway Jessica M , Pagane Nicole , Kreig Jasmine , Sambaturu Narmada , Iyaniwura Sarafa , Li Jonathan Z , Ribeiro Ruy M , Ke Ruian
Published: May 2024

Most people living with HIV-1 experience rapid viral rebound once antiretroviral therapy is interrupted; however, a small fraction remain in viral remission for an extended duration. Understanding the factors that determine whether viral rebound is likely after treatment interruption can enable the development of optimal treatment regimens and therapeutic interventions to potentially achieve a functional cure for HIV-1. We built upon the theoretical framework proposed by Conway and Perelson to construct dynamic models of virus-immune interactions to study factors that influence viral rebound dynamics. We evaluated these models using viral load data from 24 individuals following antiretroviral therapy interruption. The best-performing model accurately captures the heterogeneity of viral dynamics and highlights the importance of the effector cell expansion rate. Our results show that post-treatment controllers and non-controllers can be distinguished based on the effector cell expansion rate in our models. Furthermore, these results demonstrate the potential of using dynamic models incorporating an effector cell response to understand early viral rebound dynamics post-antiretroviral therapy interruption.
Arkypallidal neurons in the external globus pallidus can mediate inhibitory control by altering competition in the striatum
Authors: Giossi Cristina , Bahuguna Jyotika , Rubin Jonathan E. , Verstynen Timothy , Vich Catalina
Published: May 2024

Reactive inhibitory control is crucial for survival. Traditionally, this control in mammals was attributed solely to the hyperdirect pathway, with cortical control signals flowing unidirectionally from the subthalamic nucleus (STN) to basal ganglia output regions. Yet recent findings have put this model into question, suggesting that the STN is assisted in stopping actions through ascending control signals to the striatum mediated by the external globus pallidus (GPe). Here we investigate this suggestion by harnessing a biologically-constrained spiking model of the corticobasal ganglia-thalamic (CBGT) circuit that includes pallidostriatal pathways originating from arkypallidal neurons. Through a series of experiments probing the interaction between three critical inhibitory nodes (the STN, arkypallidal cells, and indirect path-way spiny projection neurons), we find that the GPe acts as a critical mediator of both ascending and descending inhibitory signals in the CBGT circuit. In particular, pallidostriatal pathways regulate this process by weakening the direct pathway dominance of the evidence accumulation process driving decisions, which increases the relative suppressive influence of the indirect pathway on basal ganglia output. These findings delineate how pallidostriatal pathways can facilitate action cancellation by managing the bidirectional flow of information within CBGT circuits.
Oxygen partitioning into biomolecular condensates is governed by protein density
Authors: Garg Ankush , Brasnett Christopher , Marrink Siewert J. , Koren Klaus , Kjaergaard Magnus
Published: May 2024

Biomolecular condensates form through the self-assembly of proteins and nucleic acids to create dynamic compartments in cells. By concentrating specific molecules, condensates establish distinct microenvironments that regulate biochemical reactions in time and space. Macromolecules and metabolites partition into condensates depending on their interactions with the macromolecular constituents, however, the partitioning of gases has not been explored. We investigated oxygen partitioning into condensates formed by intrinsically disordered repeat proteins with systematic sequence variations using microelectrodes and phosphorescence lifetime imaging microscopy (PLIM). Unlike other hydrophobic metabolites, oxygen is partially excluded from the condensate with partitioning constants more strongly modulated by changes in protein length than hydrophobicity. For repeat proteins, the dense phase protein concentration drops with chain length resulting in a looser condensate. We found that oxygen partitioning is anti-correlated with dense phase protein concentration. Several mechanisms could explain such an anti-correlation including excluded volume or salting out effects. Molecular dynamics simulations suggest that oxygen does not form strong and specific interactions with the scaffold and is dynamic on the nanosecond timescale. Biomolecular condensates thus result in variation of oxygen concentrations on nanometer length-scales, which may tune the oxygen concentration available for biochemical reactions within the cell.
Acoustic target strengths and swimbladder morphology of Chub mackerelScomber japonicusin the Northwest Pacific Ocean
Authors: Yoon Euna , Lee Hyungbeen , Lee Yong-Deuk , Choo Yong Jin , Lee Jeong-Hoon , Kim Jung Nyun
Published: May 2024

The Northwest Pacific chub mackerel (Scomber japonicus) is one of the most productive, economically important fishery resources worldwide. Due to fluctuations in their abundance and distribution, there is a pressing need to accurately assess this species and to ensure total allowable catch limits are followed. Acoustic target strength (TS; dB) measurements ofScomber japonicuswere conducted at 38, 70, and 120 kHz using a split-beam echosounder of individuals from nine size groups (mean fork length, 10.8∼28.3 cm) swimming freely in a net cage within a seawater tank. An underwater camera was utilized to simultaneously measure the swimming angle. A least-squares regression analysis revealed that when the slope was constrained to 20, as per the generally applicable morphometric equation, the resulting values for the constant term (b20) were ‒67.7, ‒66.6, and – 67.3 dB at 38, 70, and 120 kHz, respectively. The mean swimming angle ofS. japonicusacross the groups was –10.5∼9.6° (standard deviation (SD), 16.3∼33.3°). In addition, the ratio of swimbladder height to swimbladder length, swimbladder length to fork length, and tilt angle of the swimbladder (mean ± SD) were 0.191 ± 0.060, 0.245 ± 0.055, and 9.6 ± 3.0°, respectively. These results can be used for the acoustic stock assessment ofS. japonicusin the Northwest Pacific Ocean.
A molecular representation to identify isofunctional molecules
Authors: Pinel Philippe , Guichaoua Gwenn , Devaux Nicolas , Gaston-Mathé Yann , Hoffmann Brice , Stoven Véronique
Published: May 2024

The challenges of drug discovery from hit identification to clinical development sometimes involve addressing scaffold hopping issues, in order to optimize biological activity or ADME properties, improve selectivity or mitigate toxicology concerns of a drug candidate, not to mention intellectual property reasons. Docking is usually viewed as the method of choice for identification of isofunctional molecules, i.e. highly dissimilar molecules that share common binding modes with a protein target. However, in cases where the protein structure has low resolution or is unknown, docking may not be suitable. In such cases, ligand-based approaches offer promise but are often inadequate to handle large-step scaffold hopping, because they usually rely on the molecular structure. Therefore, we propose the Interaction Fingerprints Profile (IFPP), a molecular representation that captures molecules binding modes based on docking experiments against a panel of diverse high-quality protein structures. Evaluation on the Large-Hops (LH) benchmark demonstrates the utility of IFPP for identification of isofunctional molecules. Nevertheless, computation of IFPPs is expensive, which limits the scalability for screening very large molecular libraries. We propose to overcome this limitation by leveraging Metric Learning approaches, allowing fast estimation of molecules’ IFPP similarities, thus providing an efficient pre-screening strategy applicable to very large molecular libraries. Overall, our results suggest that IFPP provides an interesting and complementary tool alongside existing methods, in order to address challenging scaffold hopping problems effectively in drug discovery.
The evolutionary history and functional specialization of microRNA genes inArabidopsis halleriandA. lyrata
Authors: Pavan Flavia , Azevedo Favory Jacinthe , Lacoste Eléanore , Beaumont Chloé , Louis Firas , Blassiau Christelle , Cruaud Corinne , Labadie Karine , Gallina Sophie , Genete Mathieu , Kumar Vinod , Kramer Ute , Batista Rita A. , Patiou Claire , Debacker Laurence , Ponitzki Chloé , Houzé Esther , Durand Eléonore , Aury Jean-Marc , Castric Vincent , Legrand Sylvain
Published: May 2024

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To better understand this, we first performed a detailed annotation of miRNA genes in the closely related plantsArabidopsis halleriandA. lyrataand evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of “canonical” miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Nucleotide polymorphism was lower in the mature miRNA sequence than in the other parts of the hairpin (stem, terminal loop), and the regions of coding sequences targeted by miRNAs also had reduced diversity as compared to their neighboring regions along the genes. These patterns were less pronounced for recently emerged than for evolutionarily conserved miRNA genes, suggesting a weaker selective constraint on the most recent miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary processes by which a small fraction of them eventually integrate into “core” biological processes.
In vivo CRISPR screening identifies geranylgeranyl diphosphate as a pancreatic cancer tumor growth dependency
Authors: Kubota Casie S. , Myers Stephanie L. , Seppälä Toni T. , Burkhart Richard A. , Espenshade Peter J.
Published: May 2024

Cancer cells must maintain lipid supplies for their proliferation and do so by upregulating lipogenic gene programs. The sterol regulatory element-binding proteins (SREBPs) act as modulators of lipid homeostasis by acting as transcriptional activators of genes required for fatty acid and cholesterol synthesis and uptake. SREBPs have been recognized as chemotherapeutic targets in multiple cancers, however it is not well understood which SREBP target genes are essential for tumorigenesis. Using parallel in vitro and in vivo CRISPR knockout screens, we identified terpenoid backbone biosynthesis genes as essential for pancreatic ductal adenocarcinoma (PDAC) tumor development. Specifically, we identified the non-sterol isoprenoid product of the mevalonate pathway, geranylgeranyl diphosphate (GGPP), as an essential lipid for tumor growth. Mechanistically, we observed that restricting mevalonate pathway activity using statins and SREBP inhibitors synergistically induced apoptosis and caused disruptions in small G protein prenylation that have pleiotropic effects on cellular signaling pathways. Finally, we demonstrated thatgeranylgeranyl diphosphate synthase 1(GGPS1) knockdown significantly reduces tumor burden in an orthotopic xenograft mouse model. These findings indicate that PDAC tumors selectively require GGPP over other lipids such as cholesterol and fatty acids and that this is a targetable vulnerability of pancreatic cancer cells.
IFNγ activates an immune-like regulatory network in the cardiac vascular endothelium
Authors: Arthur Timothy D. , Joshua Isaac N. , Nguyen Jennifer P. , D’Antonio-Chronowska Agnieszka , D’Antonio Matteo , Frazer Kelly A.
Published: May 2024

The regulatory mechanisms underlying the response to pro-inflammatory cytokines in cardiac diseases are poorly understood. Here, we use iPSC-derived cardiovascular progenitor cells (CVPCs) to model the response to interferon gamma (IFNγ) in human cardiac tissue. We generate RNA-seq and ATAC-seq for four CVPCs that were treated with IFNγ and compare them with paired untreated controls. Transcriptional differences after treatment show that IFNγ initiates an innate immune cell-like response, shifts the CVPC transcriptome towards coronary artery and aorta profiles, and stimulates expression of endothelial cell-specific genes. Analysis of the accessible chromatin shows that IFNγ is a potent chromatin remodeler and establishes an IRF-STAT immune-cell like regulatory network. Finally, we show that 11 GWAS risk variants for 8 common cardiac diseases overlap IFNγ-upregulated ATAC-seq peaks. Our findings reveal insights into IFNγ-induced activation of an immune-like regulatory network in the cardiac vascular endothelium and the potential role that regulatory elements in this pathway play in common cardiac diseases.

Graphical Abstract

Paired RNA-seq and ATAC-seq was generated for induced pluripotent stem cell derived cardiovascular progenitor cells (CVPCs) treated with interferon-gamma (IFNγ) and matched controls to model the effect of the pro-inflammatory cytokine on human cardiac tissue. Using the RNA-seq, transcriptomic changes were characterized by performing differential gene expression analysis, integrating gene expression data from hundreds of samples of adult cardiac tissues, and using single cell RNA-seq to evaluate cell type-specificity. Using the ATAC-seq, epigenomic changes were characterized by performing differential chromatin accessibility and transcription factor binding analyses, and annotating ATAC-seq peaks with chromatin states from over 800 tissues. Genetic variants in risk loci associated with cardiac diseases were intersected with ATAC-seq peaks to evaluate whether they were in chromatin that is only accessible after IFNγ treatment. The findings demonstrate the utility of using CVPCs to model the effects of cytokines on cardiac tissues and provide the framework for conducting large scale studies to further evaluate GWAS loci that are explained by context-specific regulatory variation.
RealtimeDecoder: A fast software module for online clusterless decoding
Authors: Chu Joshua P. , Coulter Michael E. , Denovellis Eric L. , Nguyen Trevor T. K. , Liu Daniel F. , Deng Xinyi , Eden Uri T. , Kemere Caleb T. , Frank Loren M.
Published: May 2024

Decoding algorithms provide a powerful tool for understanding the firing patterns that underlie cognitive processes such as motor control, learning, and recall. When implemented in the context of a real-time system, decoders also make it possible to deliver feedback based on the representational content of ongoing neural activity. That in turn allows experimenters to test hypotheses about the role of that content in driving downstream activity patterns and behaviors. While multiple real-time systems have been developed, they are typically implemented in C++ and are locked to a specific data acquisition system, making them difficult to adapt to new experiments.

Here we present a Python software system that implements online clusterless decoding using state space models in a manner independent of data acquisition systems. The parallelized system processes neural data with temporal resolution of 6 ms and median computational latency <50 ms for medium- to large-scale (32+ tetrodes) rodent hippocampus recordings without the need for spike sorting. It also executes auxiliary functions such as detecting sharp wave ripples from local field potential (LFP) data. Performance is similar to state-of-the-art solutions which use compiled programming languages. We demonstrate this system use in a rat behavior experiment in which the decoder allowed closed loop neurofeedback based on decoded hippocampal spatial representations . This system provides a powerful and easy-to-modify tool for real-time feedback experiments.
Daily glucocorticoids promote glioblastoma growth and circadian synchrony to the host
Authors: Gonzalez-Aponte Maria F. , Damato Anna R. , Simon Tatiana , Aripova Nigina , Darby Fabrizio , Rubin Joshua B. , Herzog Erik D.
Published: May 2024

Glioblastoma (GBM) is the most common primary brain tumor in adults with a poor prognosis despite aggressive therapy. A recent, retrospective clinical study found that administering Temozolomide in the morning increased patient overall survival by 6 months compared to evening. Here, we tested the hypothesis that daily host signaling regulates tumor growth and synchronizes circadian rhythms in GBM. We found daily Dexamethasone promoted or suppressed GBM growth depending on time of day of administration and on the clock gene,Bmal1. Blocking circadian signals, like VIP or glucocorticoids, dramatically slowed GBM growth and disease progression. Finally, mouse and human GBM models have intrinsic circadian rhythms in clock gene expressionin vitroandin vivothat entrain to the host through glucocorticoid signaling, regardless of tumor type or host immune status. We conclude that GBM entrains to the circadian circuit of the brain, which modulates its growth through clock-controlled cues, like glucocorticoids.
Quantification ofTrypanosoma Bruceisocial motility indicates different colony growth phases
Authors: Kuhn Andreas , Krueger Timothy , Schüttler Magdalena , Engstler Markus , Fischer Sabine C.
Published: May 2024

In vitrocolonies of the flagellated parasiteTrypanosoma bruceigrow in characteristic fingering instability patterns. The underlying cause of this this type of collective migration and the associated behavior called social motility remains a topic of intense debate in the scientific community. In order to study these mechanisms in detail, it is crucial to develop quantitative methods to assess and measure social motility patterns at the level of the whole colony beyond qualitative image comparisons. Here, we show a quantification of the growth process based on two scale free metrics designed to quantify the shape of two-dimensional colonies. While initially developed for yeast colonies, we adapted, modified and extended the analysis pipeline for theTrypanosomasystem. Combining the quantitative measurements with colony growth simulations based on the Eden model, we discovered two distinct growth phases in social motility showing colonies: In the first phase, the colonies shown mainly circular expansion and later switch to an almost exclusive finger growing phase. These phases are robust when increasing the number of cells as well as upon partial inhibition of the finger formation. A newly developed anisotropy index shows that upon partial inhibition the anisotropy in the colony increases over time. Our results provide objective measurements that help advance the understanding of social motility of trypanosomes. Furthermore, our approach is suitable as a blueprint for investigations of other colony forming cells such as yeast or bacteria.
Effect of Sulfate Availability on Phytoplankton Stoichiometry
Authors: Whitney Larisa , Segura-Noguera Mariona , Ruan Zuoxi , Giordano Mario
Published: May 2024

Sulfur is a key element in multiple metabolic pathways of phytoplankton cells. The effect of environmental S availability on phytoplankton elemental quotas and stoichiometry has been addressed in few studies, using a limited number of species and with contradictory results.

Using high-temperature combustion oxidation and X-ray fluorescence methods, we measured the concentrations of micro- and trace elements in monocultures of 20 phytoplankton species, grown with different sulfate concentrations representing those of early and modern oceans.

The red lineage species, with higher S requirement and metabolic S fluxes, have higher S content than those of the green lineage, resulting in lower C:S (93) and higher S:P (1.06) than the green lineage species (226 and 0.76, respectively). Zn was the only trace element affected by the environmental concentration of sulfate.

Phytoplankton cells respond to different sulfate availability by either increasing Zn or decreasing P quotas, where the P response is more characteristic in the red lineage, and the Zn response is independent of genotypic constraints or plastid type. This study sheds light on a metabolic basis for the expansion of the red lineage algae and their current dominance in ocean waters.

Plain language summary

Microalgae assimilate dissolved sulfate as a source of sulfur, an element that takes part in multiple biochemical pathways and cellular functions. Changes in the concentration of dissolved sulfate in the environment have an effect on the cellular dynamics of several essential biological elements, essencially phosphorus and zinc. The results of this study help to understand the biogeochemical cycling of these elements in the ocean and the dominance of certain phytoplankton lineages.
Oxidative Stress is a shared characteristic of ME/CFS and Long COVID
Authors: Shankar Vishnu , Wilhelmy Julie , Curtis Ellis J. , Michael Basil , Cervantes Layla , Mallajosyula Vamsee A. , Davis Ronald W. , Snyder Michael , Younis Shady , Robinson William H. , Shankar Sadasivan , Mischel Paul S. , Bonilla Hector , Davis Mark M.
Published: May 2024

More than 65 million individuals worldwide are estimated to have Long COVID (LC), a complex multisystemic condition, wherein patients of all ages report fatigue, post-exertional malaise, and other symptoms resembling myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS). With no current treatments or reliable diagnostic markers, there is an urgent need to define the molecular underpinnings of these conditions. By studying bioenergetic characteristics of peripheral blood lymphocytes in over 16 healthy controls, 15 ME/CFS, and 15 LC, we find both ME/CFS and LC donors exhibit signs of elevated oxidative stress, relative to healthy controls, especially in the memory subset. Using a combination of flow cytometry, bulk RNA-seq analysis, mass spectrometry, and systems chemistry analysis, we also observed aberrations in ROS clearance pathways including elevated glutathione levels, decreases in mitochondrial superoxide dismutase levels, and glutathione peroxidase 4 mediated lipid oxidative damage. Critically, these changes in redox pathways show striking sex-specific trends. While females diagnosed with ME/CFS exhibit higher total ROS and mitochondrial calcium levels, males with an ME/CFS diagnosis have normal ROS levels, but larger changes in lipid oxidative damage. Further analyses show that higher ROS levels correlates with hyperproliferation of T cells in females, consistent with the known role of elevated ROS levels in the initiation of proliferation. This hyperproliferation of T cells can be attenuated by metformin, suggesting this FDA-approved drug as a possible treatment, as also suggested by a recent clinical study of LC patients. Thus, we report that both ME/CFS and LC are mechanistically related and could be diagnosed with quantitative blood cell measurements. We also suggest that effective, patient tailored drugs might be discovered using standard lymphocyte stimulation assays.
CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds
Authors: Ye Bowei , Tian Wei , Wang Boshen , Liang Jie
Published: May 2024

Geometric and topological properties of protein structures, including surface pockets, interior cavities, and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a widely used web server for locating, delineating, and measuring these geometric and topological properties of protein structures. Recent developments in AI-based protein structure prediction such as AlphaFold2 (AF2) have significantly expanded our knowledge on protein structures. Here we present CASTpFold, a continuation of CASTp that provides accurate and comprehensive identifications and quantifications of protein topography. It now provides (i) results on an expanded database of proteins, including the Protein Data Bank (PDB) and non-singleton representative structures of AlphaFold2 structures, covering 183 million AF2 structures; (ii) functional pockets prediction with corresponding Gene Ontology (GO) terms or Enzyme Commission (EC) numbers for AF2-predicted structures; and (iii) pocket similarity search function for surface and protein-protein interface pockets. The CASTpFold web server is freely accessible athttps://cfold.bme.uic.edu/castpfold/.
Cloning and functional characterization of novel human neutralizing anti-interferon-alpha and anti-interferon-beta antibodies
Authors: Papasavvas Emmanouil , Lu Lily , Fair Matthew , Oliva Isabela , Cassel Joel , Majumdar Sonali , Mounzer Karam , Kostman Jay R. , Tebas Pablo , Bar-Or Amit , Muthumani Kar , Montaner Luis J.
Published: May 2024

Type I interferons (IFNs) play a pivotal role in immune response modulation, yet dysregulation is implicated in various disorders. Therefore, it is crucial to develop tools that facilitate the understanding of their mechanism of action and enable the development of more effective anti-IFN therapeutic strategies. In this study, we isolated, cloned, and characterized anti-IFN-α and anti-IFN-β antibodies (Abs) from peripheral blood mononuclear cells of individuals treated with IFN-α or IFN-β, harboring confirmed neutralizing Abs. Clones AH07856 and AH07857 were identified as neutralizing anti-IFN-α-specific with inhibition against IFN-α2a, -α2b, and -αK subtypes. Clones AH07859 and AH07866 were identified as neutralizing anti-IFN-β1a-specific signaling, and able to block Lipopolysaccharide or S100 calcium binding protein A14-induced IFN-β signaling effects. Cloned Abs bind rhesus but not murine IFNs. The specificity of inhibition between IFN-α and IFN-β suggests potential for diverse research and clinical applications.
Functional coexistence theory: a mechanistic framework linking biodiversity to ecosystem function
Authors: Wan Joe , Ke Po-Ju , Hordijk Iris , Bialic-Murphy Lalasia , Crowther Thomas W.
Published: May 2024

Theory and experiments show that diverse ecosystems often have higher levels of function (for instance, biomass production), yet it remains challenging to identify the biological mechanisms responsible. We synthesize developments in coexistence theory into a general theoretical framework linking community coexistence to ecosystem function. Our framework, which we term functional coexistence theory, identifies three components determining the total function of a community of coexisting species. The first component directly corresponds to the niche differences that enable pairwise species coexistence, and to the complementarity component from the additive partition of biodiversity effects. The second component measures whether higher functioning species also have higher competitive fitness, providing a missing link between the additive partition’s selection effect and modern coexistence theory’s concept of equalization. The third component is least well-studied: reducing functional imbalances between species increases niche difference’s positive effect on function. Using a mechanistic model of resource competition, we show that our framework can identify how traits drive the effect of competition on productivity, and confirm our theoretical expectations by fitting this model to data from a classic plant competition experiment. Furthermore, we apply our framework to simulations of communities with multiple ecosystem functions or more than two species, demonstrating that relationships between niche, fitness, and function also predict total function beyond the case studied by classical theory. Taken together, our results highlight fundamental links between species coexistence and its consequences for ecosystem function, providing an avenue towards a predictive theory of community–ecosystem feedbacks.
Unravelling Immune Cell Signatures: CIBERSORTx-assisted Construction of Signature Matrix from Single-Cell Data
Authors: Verma Madhulika
Published: May 2024

The immune system’s intricate orchestration is pivotal in combating infections and diseases, often leaving discernible signatures within circulating blood cells. Peripheral blood mononuclear cells (PBMCs), comprising diverse immune cell populations, serve as crucial indicators of immune system status and its responses to various conditions, including cancer. While traditional bulk metrics pose challenges in dissecting specific immune cell functionalities, advancements in single-cell technologies offer unprecedented insights into the dynamic activities of immune cell populations.

In this study, we analyzed single-cell data from droplet sequencing to delineate immune cell types and subtypes within PBMCs. Employing the CIBERSORTx tool, we constructed a signature matrix to comprehensively represent significant cell populations within tissue. Through iterative optimization and minimization of the condition number based on marker genes, we aimed to enhance the robustness and stability of the gene signature matrices, enabling scalable investigation of novel or poorly understood phenotypic states in bulk tissue gene expression profiles. The resultant matrix consisted of 14 immune cell types represented by 275 gene having significant highest expression for their respective cell types and the least in other cells.

This approach facilitates precise characterization of immune cell populations and their responses to diverse diseases, contributing to a deeper understanding of immunological processes and paving the way for targeted therapeutic interventions.
Haem toxicity in the aged spleen impairs T-cell immunity through iron deprivation
Authors: Ezuz David , Ombashe Heba , watted Lana , Atar Orna , Ron-Harel Noga
Published: May 2024

Ageing profoundly impacts T cell immunity, compromising vaccine responses, susceptibility to infections, and immunosurveillance. Mechanisms of T cell ageing involve cell-intrinsic alterations and interactions with other immune and stromal cells1. This study investigates how a tissue’s microenvironment influences T cell ageing trajectories, following our discovery of varying rates of T cell ageing within a single host. Spleen-derived lymphocytes exhibited functional decline compared to those from lymph nodes, with proteomic analysis revealing increased expression of haem detoxification and iron storage proteins in aged spleen-derived lymphocytes. Exposure to the aged spleen microenvironment or to haem induced multiple ageing phenotypes in young lymphocytes, characterized by reduced proliferation and upregulation of the ectonucleotidases CD39 and CD73. Mechanistically, we show that T cells survive the hostile microenvironment of the aged spleen by maintaining low labile iron pools to resist ferroptosis. Finally, vaccination responses in aged mice were enhanced by timed iron infusions. Our findings underscore a trade-off between T cell survival and function in the aged host. Recent studies show how Dysfunctional T cells induce premature ageing phenotypes in multiple solid organs of a young host2,3. Our findings highlight the bidirectional relationship between T cells and their ageing microenvironment. Understanding these mechanisms will inform strategies to enhance immune responses in the elderly.
Mitochondrial Oxidative Phosphorylation Capacity in Skeletal Muscle Measured by Ultrafast Z-Spectroscopy (UFZ) MRI at 3T
Authors: Ju Licheng , Schär Michael , Wang Kexin , Li Anna , Wu Yihan , Samuel T. Jake , Ganji Sandeep , van Zijl Peter C. M. , Yadav Nirbhay N. , Weiss Robert G. , Xu Jiadi
Published: May 2024

Background

To investigate the feasibility of rapid CEST MRI acquisition for evaluating oxidative phosphorylation (OXPHOS) in human skeletal muscle at 3 Tesla, utilizing ultrafast Z-spectroscopy (UFZ) MRI combined with the Polynomial and Lorentzian line-shape Fitting (PLOF) technique.

Methods

UFZ MRI on muscle was evaluated with turbo spin echo (TSE) and segmented 3D EPI readouts. Five healthy subjects performed in-magnet plantar flexion exercise (PFE) and subsequent changes of amide, phosphocreatine (PCr) and partial PCr mixed creatine (Cr+) CEST dynamic signals post-exercise were enabled by PLOF fitting. PCr/Cr CEST signal was further refined through pH correction by using the ratios between PCr/Cr and amide signals, named PCAR/CAR, respectively.

Results

UFZ MRI with TSE readout significantly reduces acquisition time, achieving a temporal resolution of <50 seconds for collecting high-resolution Z-spectra. Following PFE, the recovery/decay times (τ) for both PCr and Cr in the gastrocnemius muscle of the calf were notably longer when determined using PCr/Cr CEST compared to those after pH correction with amideCEST, namelys andτPCr= 98.1 ± 20.4 s versusτCAR=36.4 ± 18.6 s andτPCAR= 43.0 ± 13.0 s, respectively. Literature values ofτPCrobtained via31P MRS closely resemble those obtained from pH-corrected PCr/Cr CEST signals.

Conclusion

The outcomes suggest potential of UFZ MRI as a robust tool for non-invasive assessment of mitochondrial function in skeletal muscles. pH correction is critical for the reliable OXPHOS measurement by CEST.
Recombinant manufacturing of multispecies biolubricants
Authors: Colville Marshall J. , Huang Ling-Ting , Schmidt Samuel , Chen Kevin , Vishwanath Karan , Su Jin , Williams Rebecca M. , Bonassar Lawrence J. , Reesink Heidi L. , Paszek Matthew J.
Published: May 2024

Lubricin, a lubricating glycoprotein abundant in synovial fluid, forms a low-friction brush polymer interface in tissues exposed to sliding motion including joints, tendon sheaths, and the surface of the eye. Despite its therapeutic potential in diseases such as osteoarthritis and dry eye disease, there are few sources available. Through rational design, we developed a series of recombinant lubricin analogs that utilize the species-specific tissue-binding domains at the N- and C-termini to increase biocompatibility while replacing the central mucin domain with an engineered variant that retains the lubricating properties of native lubricin. In this study, we demonstrate the tissue binding capacity of our engineered lubricin product and its retention in the joint space of rats. Next, we present a new bioprocess chain that utilizes a human-derived cell line to produceO-glycosylation consistent with that of native lubricin and a purification strategy that capitalizes on the positively charged, hydrophobic N- and C-terminal domains. The bioprocess chain is demonstrated at 10 L scale in industry-standard equipment utilizing commonly available ion exchange, hydrophobic interaction and size exclusion chromatography resins. Finally, we confirmed the purity and lubricating properties of the recombinant biolubricant. The biomolecular engineering and bioprocessing strategies presented here are an effective means of lubricin production and could have broad applications to the study of mucins in general.
kinact/KIValue Determination for Penicillin-Binding Proteins in Live Cells
Authors: Shirley Joshua D. , Nauta Kelsie M. , Gillingham Jacob R. , Diwakar Shivani , Carlson Erin E.
Published: May 2024

Penicillin-binding proteins (PBPs) are an essential family of bacterial enzymes that are inhibited by the β-lactam class of antibiotics. PBP inhibition disrupts cell wall biosynthesis, which results in deficient growth and proliferation, and ultimately leads to lysis. IC50values are often employed as descriptors of enzyme inhibition and inhibitor selectivity but can be misleading in the study of time-dependent, irreversible inhibitors. Due to this disconnect, the second order rate constantkinact/KIis a more appropriate metric of covalent inhibitor potency. Despite being the gold standard measurement of potency,kinact/KIvalues are typically obtained fromin vitroassays, which limits assay throughput if investigating an enzyme family with multiple homologs (such as the PBPs). Therefore, we developed a whole-cellkinact/KIassay to define inhibitor potency for the PBPs inStreptococcus pneumoniaeusing the fluorescent activity-based probe Bocillin-FL. Our results align within vitro kinact/KIdata and show a comparable relationship to previously established IC50values. These results support the validity of ourin vivo kinact/KImethod as a means of obtaining a full picture of β-lactam potency for a suite of PBPs.

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