bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of cardiorespiratory exercise during rehabilitation on functional recovery early post-stroke: a cohort study
Authors: Thompson Sarah , Devasahayam Augustine J. , Danells Cynthia J. , Jagroop David , Inness Elizabeth L. , Mansfield Avril
Published: August 2024

Background

People with stroke often have low cardiorespiratory fitness, hindering daily activities and rehabilitation participation. Cardiorespiratory exercise (CRE) early post-stroke can improve fitness, facilitating participation in rehabilitation, and may promote neuroplasticity. This longitudinal observational study aimed to determine the effect of CRE during routine inpatient stroke rehabilitation on motor and cognitive function, functional ambulation, and motor impairment.

Methods

Data were collected from charts of patients (n=504) admitted to two rehabilitation hospitals in Ontario, Canada, over 14 month periods. Patients were classified into three groups: ‘Prescribed’, ‘Incidental’, or no cardiorespiratory exercise (‘None’). Functional independence Measure (FIM), Functional Ambulation Category (FAC), and Chedoke-McMaster Stroke Assessment (CMSA) scores were compared between groups at discharge from rehabilitation, controlling for age, length of stay, and scores at baseline.

Results

Patients who had cardiorespiratory exercise included in their treatment plan (i.e., Prescribed group) had higher FIM total and motor sub-scores at discharge than the None group (Site A; FIM total mean between-group difference: 13.2, p<0.0001; FIM motor mean between-group difference: 13.1, p<0.0001), or than those that completed cardiorespiratory exercise without a prescription (‘Incidental’ group; Site B; FIM Total mean between-group difference: 13.6, p=0.031; FIM motor mean between-group difference: 12.9, p=0.010). At both sites, FIM cognitive sub-scores and CMSA leg scores were higher at discharge for the Prescribed group than the None group (FIM cognitive mean between-group difference: 1.2, p=0.038; CMSA leg mean between-group difference: 0.5, p=0.0099). FAC scores were higher at discharge for the two exercise groups compared to the group that did not complete cardiorespiratory exercise at Site A only (p=0.0010).

Conclusions

Findings support that cardiorespiratory exercise as part of routine in-patient rehabilitation early post-stroke is associated with improved functional independence and ambulation. However, the observational design limits causal inferences, highlighting the need for controlled studies to confirm cardiorespiratory exercise benefits in early stroke recovery.
An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins
Authors: Ghanbarpour Alireza , Telusma Bertina , Powell Barrett M. , Zhang Jia Jia , Bolstad Isabella , Vargas Carolyn , Keller Sandro , Baker Tania , Sauer Robert T. , Davis Joseph H.
Published: August 2024

FtsH, a AAA protease, associates with HflK/C subunits to form a megadalton complex that spans the inner membrane and extends into the periplasm ofE. coli. How this complex and homologous assemblies in eukaryotic organelles recruit, extract, and degrade membrane-embedded substrates is unclear. Following overproduction of protein components, recent cryo-EM structures reveal symmetric HflK/C cages surrounding FtsH in a manner proposed to inhibit degradation of membrane-embedded substrates. Here, we present structures of native complexes in which HflK/C instead forms an asymmetric nautilus-like assembly with an entryway for membrane-embedded substrates to reach and be engaged by FtsH. Consistent with this nautilus-like structure, proteomic assays suggest that HflK/C enhances FtsH degradation of certain membrane-embedded substrates. The membrane curvature in our FtsH·HflK/C complexes is opposite that of surrounding membrane regions, a property that correlates with lipid-scramblase activity and possibly with FtsH’s function in the degradation of membrane-embedded proteins.
Tissue-specific modulation of CRISPR activity by miRNA-sensing guide RNAs
Authors: Garcia-Guerra Antonio , Sathyaprakash Chaitra , de Jong Olivier G. , Lim Wooi F. , Vader Pieter , El Andaloussi Samir , Bath Jonathan , Reine Jesus , Aoki Yoshitsugu , Turberfield Andrew J. , Wood Matthew J. A. , Rinaldi Carlo
Published: August 2024

Nucleic acid nanostructures offer unique opportunities for biomedical applications due to their sequence-programmable structures and functions, which enable the design of complex responses to molecular cues. Control of the biological activity of therapeutic cargoes based on endogenous molecular signatures holds the potential to overcome major hurdles in translational research: cell specificity and off-target effects. Endogenous microRNAs can be used to profile cell type and cell state and are ideal inputs for RNA nanodevices. Here we present CRISPR MiRAGE (miRNA-activated genome editing), a tool comprising a dynamic single-guide RNA that senses miRNA complexed with Argonaute proteins and controls downstream CRISPR activity based on the detected miRNA signature. We study the operation of the miRNA-sensing single-guide RNA and attain muscle-specific activation of gene editing through CRISPR MiRAGE in models of Duchenne muscular dystrophy. By enabling RNA-controlled gene editing activity, this technology creates opportunities to advance tissue-specific CRISPR treatments for human diseases.
Spatial localization of CD16a at the human NK cell ADCC lytic synapse
Authors: Ross Patrick , Fatima Hijab , Leaman Dan P. , Matthias Jessica , Spencer Kathryn , Zwick Michael B. , Henderson Scott C. , Mace Emily M. , Murin Charles Daniel
Published: August 2024

Natural Killer (NK) cells utilize effector functions, including antibody-dependent cellular cytotoxicity (ADCC), for the clearance of viral infection and cellular malignancies. NK cell ADCC is mediated by FcγRIIIa (CD16a) binding to the fragment crystallizable (Fc) region of immunoglobulin G (IgG) within immune complexes on a target cell surface. While antibody-induced clustering of CD16a is thought to drive ADCC, the molecular basis for this activity has not been fully described. Here we use MINFLUX nanoscopy to map the spatial distribution of stoichiometrically labeled CD16a across the NK cell membrane, revealing the presence of pairs of CD16a molecules with intra-doublet distance of approximately 17 nm. NK cells activated on supported lipid bilayers by Trastuzumab results in an increase of synaptic regions with greater CD16a density. Our results provide the highest spatial resolution yet described for CD16a imaging, offering new insight into how CD16a organization within the immune synapse could influence ADCC activity. MINFLUX holds great promise to further unravel the molecular details driving CD16a-based activation of NK cells.
Identification of Meibomian gland stem cell populations and mechanisms of aging
Authors: Zhu Xuming , Xu Mingang , Portal Celine , Lin Yvonne , Ferdinand Alyssa , Peng Tien , Morrisey Edward E. , Dlugosz Andrzej A. , Castellano Joseph M. , Lee Vivian , Seykora John T. , Iomini Carlo , Millar Sarah E
Published: August 2024

Meibomian glands secrete lipid-rich meibum, which prevents tear evaporation. Aging-related Meibomian gland shrinkage may result in part from stem cell exhaustion and is associated with evaporative dry eye disease, a common condition lacking effective treatment. The identities and niche of Meibomian gland stem cells and the signals controlling their activity are poorly defined. Using snRNA-seq, in vivo lineage tracing, ex vivo live imaging, and genetic studies in mice, we identified markers for stem cell populations that maintain distinct regions of the gland and uncovered Hh signaling as a key regulator of stem cell proliferation. Consistent with this, human Meibomian gland carcinoma exhibited increased Hh signaling. Aged glands displayed decreased Hh and EGF signaling, deficient innervation, and loss of collagen I in niche fibroblasts, indicating that alterations in both glandular epithelial cells and their surrounding microenvironment contribute to age-related degeneration. These findings suggest new approaches to treat aging-associated Meibomian gland loss.
Triple Negative Breast Cancer Cells Acquire Lymphocyte Proteins and Genomic DNA During Trogocytosis with T Cells
Authors: Sivakoses Anutr , Marcarian Haley Q. , Arias Anika M. , Lam Allison R. , Ihedioha Olivia C. , Santamaria Juan A. , Gurtner Geoffrey C. , Bothwell Alfred L.M.
Published: August 2024

Trogocytosis is the process by which a recipient cell siphons small membrane fragments and proteins from a donor cell and may be utilized by cancer cells to avoid immune detection. We observed lymphocyte specific protein expressed by TNBC cells via immunofluorescence imaging of patient samples. Image analysis of CD45RA expression, a T cell specific protein, revealed that all stages of TNBCs express CD45RA. Flow cytometry revealed TNBC cells trogocytose CD45 protein from T cells. We also showed that the acquisition of these lymphoid markers is contact dependent. Confocal and super-resolution imaging further revealed CD45+spherical structures containing T cell genomic DNA inside TNBC cells after co-culture. Trogocytosis between T cells and TNBC cells altered cancer cell gene expression. Our results revealed that CD45 is obtained by TNBC cells from T cells via trogocytosis and that TNBC cells express CD45 intracellularly and on the membrane.

Teaser

TNBC cells acquire small spherical structures from T cells containing lymphocyte-specific membrane proteins and genomic DNA.
The Phylogeny and the Evolution of Parasitic Strategies in Trematoda
Authors: Xiang Chuan-Yu , Jakovlić Ivan , Ye Tong , Song Rui , Zou Hong , Wang Gui-Tang , Li Wen-Xiang , Zhang Dong
Published: August 2024

Trematodes are obligatory parasites that generally must transmit between hosts to complete their life cycle. They parasitize varying numbers of intermediate hosts (0, 1 or 2), but the evolutionary history of these strategies and the ancestral states remain unknown. We conducted the ancestral state reconstruction of the number of intermediate hosts using mitogenomic (Trematoda) and nuclear-genomic (Neodermata) topologies. Aspidogastrea was identified as the sister-group (“basal”) to all other Trematoda using a range of approaches, so it is crucial for studying the evolutionary history of trematodes. However, there is only one transcriptome available for this lineage, and mitochondrial genomes (mitogenomes) remain unavailable. Herein, we sequenced mitogenomes of two aspidogastreans:Aspidogaster ijimaiandAspidogaster conchicola. As the ancestral state reconstruction analysis is topology-sensitive, we tested multiple phylogenetic strategies, comprising the outgroup selection, phylogenetic models, partitioning strategies, and topological constraints. These mitogenomic phylogenies exhibited pronounced topological instability, with Aspidogastrea resolved as the “basal” radiation in most, but not all, topologies. Based on our analyses, Cestoda was the optimal outgroup choice, and the “heterogeneous” CAT-GTR model in PhyloBayes was the optimal model choice. We inferred the time tree and conducted ancestral state reconstruction analyses using this “optimal” topology, as well as constrained mitogenomic and nuclear genomic topologies. Results were ambiguous for some lineages, but scenario that received the strongest support is the direct life cycle (no intermediate hosts) in the ancestors of Trematoda (proto-trematodes) and Aspidogastrea (proto-aspidogastreans), while the ancestor of Digenea (proto-digeneans) had two intermediate hosts. The inferred scenario indicates that host strategies are relatively plastic among trematodes, putatively comprising several independent host gains, and multiple host losses. We propose a timeline for these events and discuss the role that alternating sexual and asexual generations putatively played in the evolution of complex parasitic life histories in digeneans.
Confidence and insight into working memories are shaped by attention and recent performance
Authors: Chekroud Sammi R , Nobre Anna C , Kolling Nils
Published: August 2024

Working memory (WM) is capacity-limited, and our ability to access information from WM is variable, but selective attention to working memory contents can improve performance. People are able to make introspective judgements regarding the quality of their memories, and these judgements are linked to objective memory performance. However, it remains unknown whether benefits of internally directed attention on memory performance occur alongside commensurate changes in introspective judgments. Across two experiments, we used retrospective cues (retro-cues) during working-memory maintenance to direct attention to items in memory. We then examined their consequence on introspective judgements. In the second experiment, we provided trial-wise feedback on performance. We found that selective attention improved confidence judgements and not just performance of the probed item. We were also able to judge participants’ genuine insight into working-memory contents through the correlation between confidence judgements and memory quality. Neurophysiologically, alpha desynchronization correlated first with memory error and then confidence during retro-cueing, suggesting a sequential process of attentional enhancement of memory contents and introspective insight. Further, we showed that participants can use feedback on the accuracy of confidence judgements to update their beliefs across time, according to performance. Our results emphasize flexibility in working memory by showing we can selectively modulate our confidence about its contents based on internally directed attention or objective feedback.
De novogenome sequence assembly of the RNAi-tractable endosymbiosis model systemParamecium bursaria186b reveals factors shaping intron repertoire
Authors: Leonard Guy , Jenkins Benjamin H. , Savory Fiona R. , Kilias Estelle S. , Maguire Finlay , Varma Varun , Milner David S. , Richards Thomas A.
Published: August 2024

How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protistParamecium bursariahosts green algae of the order Chlorellales in a facultative photo-endosymbiosis. We have recently reported RNAi as a tool for understanding gene function inParamecium bursaria186b, CCAP strain 1660/18 [1]. To complement this work, here we report a highly complete host genome andtranscriptome sequence dataset, using both Illumina and PacBio sequencing methods to aid genome analysis and to enable the design of RNAi experiments. Our analyses demonstrateParamecium bursaria, like other ciliates such as diverse species ofParamecia, possess numerous tiny introns. These data, combined with the alternative genetic code common to ciliates, makes gene identification and annotation challenging. To explore intron evolutionary dynamics further we show that alternative splicing leading to intron retention occurs at a higher frequency among the smaller number of longer introns, identifying a source of selection against longer introns. These data will aid the investigation of genome evolution in theParameciaand provide additional source data for the exploration of endosymbiotic functions.
Niche and spatial partitioning restrain ecological equivalence among microbes along aquatic redox gradient
Authors: Kajan Katarina , Kirkegaard Rasmus , Pjevac Petra , Orlic Sandi , Mehrshad Maliheh
Published: August 2024

Microbial metabolic capabilities and interactions shape their niche hypervolume that in turn governs their ecological strategies and ecosystem services. In the context of functional redundancy or ecological equivalence, the focus has been on functional guilds in order to bypass the complex challenge faced by niche theory for disentangling the niche hypervolume. However, in some cases this simplification has been at the expense of ignoring the role of individual genotype of each microbe within a functional guild and fails to explain how the diversity within each functional guild is maintained. In this study, we inspect the metabolic profile of metagenome-assembled genomes along the pronounced redox gradient of the water column in an anchialine cave. Bridging neutral theory of biodiversity and biogeography and niche theory, our analysis uses focal metabolic capabilities while also incorporating individuality by looking into background metabolic capabilities of each individual and further includes spatial distribution of microbes to delineate their niche space. Our results emphasize that differences in background metabolic capabilities are critical for furnishing the niche hypervolume of microbes carrying the same focal metabolic capability and refute their ecological equivalence with their spatial distribution further enables niche partitioning among them.
Intra-cluster receptor density (IRD) dictates TNFR1 clusters’ signaling efficacy
Authors: Jana Subhamoy , Roy Priyanka , Das Jibitesh , Biswas Parijat , Nanda Nandana , Sinha Bidisha , Sinha Deepak Kumar
Published: August 2024

Tumor Necrosis Factor Receptor 1 (TNFR1) signaling determines cell fate during inflammation, immunopathogenesis, and tumorigenesis. TNFR1 proteins homo-oligomerize into clusters on the plasma membrane. The potential impact of TNFR1 clustering on downstream signaling remains unexplored. Homo-FRET measurements elucidate that alterations in intra-cluster receptor density (IRD) dictate the outcomes of downstream TNFR1 signaling. Soluble TNF-α (sTNF-α) elevates IRD within the TNFR1 clusters’ core while diminishing it in the rim, through intra-cluster dynamic reorganization of TNFR1. Decreasing TNFR1 IRD through increasing membrane tension, administering TNFR1 antagonist zafirlukast, actin depolymerization, or depleting cholesterol impedes sTNF-α-mediated stimulation. Conversely, increasing IRD by reducing membrane tension or exposing cells to 3D gel-like microenvironment induces ligand-independent TNFR1 signaling. These findings suggest a broader applicability of IRD in modulating signaling pathways across other receptor families, offering insights for innovative strategies in TNFR1 signaling modulation.
New tools to monitorPseudomonas aeruginosainfection and biofilmsin vivoinC. elegans
Authors: Ragno Martina , Xue Feng , Blackburn Sarah A. , Fasseas Michael , Maitra Sushmita , Tholozan Frederique , Thompson Rachel , Sellars Laura , Hall Rebecca , Saunter Chris , Weinkove David , Ezcurra Marina
Published: August 2024

Antimicrobial resistance is a growing health problem.Pseudomonas aeruginosais a pathogen of major concern because of its multidrug resistance and global threat, especially in health-care settings. The pathogenesis and drug resistance ofP. aeruginosadepends on its ability to form biofilms, making infections chronic and untreatable as the biofilm protects against antibiotics and host immunity. A major barrier to developing new antimicrobials is the lack ofin vivobiofilm models. Standard microbiological testing is usually performedin vitrousing planktonic bacteria, without representation of biofilms, reducing translatability. Here we develop tools to study both infection and biofilm formation byP. aeruginosa in vivoto accelerate development of strategies targeting infection and pathogenic biofilms. Using the nematodeCaenorhabditis elegansandP. aeruginosareporters combined within vivoimaging we show that fluorescentP. aeruginosareporters that form biofilmsin vitrocan be used to visualise tissue infection. Using automated tracking ofC. elegansmovement, we find that that the timing of this infection corresponds with a decline in health endpoints. In a mutant strain ofP. aeruginosalacking RhlR, a transcription factor that controls quorum sensing and biofilm formation, we find reduced capacity ofP. aeruginosato form biofilms, invade host tissues and negatively impact healthspan and survival. Our findings suggest that RhlR could be a new antimicrobial target to reduceP. aeruginosabiofilms and virulencein vivoandC. eleganscould be used to more effectively screen for new drugs to combat antimicrobial resistance.
Nanobody immunolabelling and three-dimensional imaging reveals spatially restricted LYVE1 expression by kidney lymphatic vessels in mice
Authors: Funk Eva Maria , Jafree Daniyal , Hansmeier Nils Rouven , Abad Baucells Claudia , Behncke Rose Yinghan , Pomeranz Gideon , Kolatsi-Joannou Maria , Mason William , Moulding Dale , Russell Lauren G , Ulferts Sascha , Wilson Laura , Long David , Haegerling Rene
Published: August 2024

Lymphatic vessels are complex three-dimensional (3D) structures that facilitate tissue fluid clearance and regulate immune responses in health and inflammatory contexts. Recent advances in wholemount immunolabelling and 3D imaging have provided insights into organ-specific heterogeneity of lymphatic structure and function. However, the visualisation of lymphatic vessels deep within an intact organ remains a challenge. We hypothesised that nanobodies, single-domain antibodies raised in camelid species, would result in improved labelling of lymphatics in intact mouse organs, without loss of information due to organ sectioning or inadequate penetration. We generated and characterised nanobody clones targeting lymphatic vessel endothelial hyaluronan receptor 1 (LYVE1), a marker of lymphatic capillaries. Nanobodies were superior at penetrating whole mouse organs and enhanced labelling of lymphatics compared with a conventional anti-LYVE1 polyclonal antibody. Utilising this new tool, we found that kidney lymphatics; an organ in which labelling of lymphatics is challenging, have spatially restricted LYVE1 expression compared with lymphatics of skin, heart, and lung. The timing of this LYVE1 spatial restriction coincides with the the early postnatal period in mice. Our findings highlight an unexpected, organ-specific characteristic of kidney lymphatic vessels, whilst providing a novel experimental tool for characterisation, isolation, or perturbation of lymphatic vessels in health and disease.
Spatio-temporal modeling of host-pathogen interactions using level set method
Authors: Permanes Sheila Rae E. , Mammeri Youcef , Leclerc Melen
Published: August 2024

Phenotyping host-pathogen interactions is crucial for understanding infectious diseases in plants. Traditionally, this process has relied on visual assessments or manual measurements, which can be subjective and labor-intensive. Recent advances in image processing and mathematical modeling enable precise and high-throughput phenotyping. In this study, we propose an innovative approach in plant pathology by combining image processing techniques with the level set method. This integrated approach leverages the strengths of both methodologies to provide accurate, robust, and detailed analysis of leaf and lesion evolution. By employing this combination, we achieve precise delineation of lesion boundaries and track their progression over time, offering clear visual feedback. This enhances the ability of the method to monitor plant health status comprehensively. The results, which track the growth of Peyronellaea pinodes on the stipules of two pea cultivars and the associated leaf deformation, provide an accurate visual representation of disease progression. This model represents a significant advancement in plant disease phenotyping, offering precise and detailed insights that can enhance our understanding of host-pathogen interactions.
Uncoupling de novo pyrimidine biosynthesis from mitochondrial electron transport by ectopic expression of cytosolic DHODH
Authors: Curtabbi Andrea , Cortés Rocío Sanz , Enríquez José Antonio
Published: August 2024

Dihydroorotate dehydrogenase (DHODH) is an enzyme involved in the biosynthesis of pyrimidine nucleotides. In most eukaryotes, this enzyme is bound to the inner mitochondrial membrane, where it couples the synthesis of orotate with the reduction of ubiquinone. As ubiquinone must be regenerated by respiratory complex III, pyrimidine biosynthesis and cellular respiration are tightly coupled. Consequently, inhibition of respiration leads to cessation of DNA synthesis and impairs cell proliferation. We show that expression ofSaccharomyces cerevisiaeURA1 gene (ScURA) in mammalian cells uncouples biosynthesis of pyrimidines from mitochondrial electron transport. ScURA forms a homodimer in the cytosol that uses fumarate instead of ubiquinone as the electron acceptor, enabling oxygen-independent pyrimidine biosynthesis. Cells expressingScURAare resistant to drugs that inhibit complex III and the mitochondrial ribosome. ScURA enables the growth of mtDNA-lacking ρ0cells in uridine-deficient medium and ameliorates the phenotype of cellular models of mitochondrial diseases. This genetic tool uncovers the contribution of pyrimidine biosynthesis to the phenotypes arising from electron transport chain defects.
Divergence of discrete- versus continuous-time calculations of the temperature dependence of maximum population growth rate in a disease vector
Authors: Huxley Paul J , Johnson Leah R , Cator Lauren , Pawar Samraat
Published: August 2024

The temperature dependence of maximal population growth rate (rm) is key to predicting how organisms respond and adapt to natural and anthropogenic changes in climate. For organisms with complex life histories, discrete-time matrix projection models (MPMs) can be used to calculate temperature-dependentrmbecause they directly capture variation in empirically-observed life-history trait values as well as the time delays inherent in those traits. However, MPM calculations can be laborious and do not capture the continuous nature of time. Temperature-dependentrmcalculated from more complex approaches based on delay-differential equation and integral projection models are more accurate but are notoriously difficult to parameterise. Ordinary differential equation-based models (ODEMs) offer a relatively tractable alternative of intermediate complexity but it is largely unknown whether ODEM-based calculations and MPMs broadly agree when the effects of time delays and altered juvenile survival trajectories on temperature-dependentrmare introduced by environmental variation. Here we investigate differences in the predicted temperature dependence ofrmobtained from an ODE-based model with those calculated from MPMs using high-resolution temperature- and resource dependent life-history trait data for the globally-distributed disease vector,Aedes aegypti. We show that the level of agreement between discrete- and continuous-time representations of temperature-dependentrmcan vary with resource availability, and is extremely sensitive to how juvenile survival is characterised. This finding suggests that analyticrmmodels can consistently provide comparablermpredictions to standard methods except for under severe resource constraints. Our study also suggests that all formulations of the intrinsic growth rate of a population may not be equally accurate for all types of organisms in all situations. Furthermore, this study's findings raise questions relating to whether existing mathematical models can be used to predict and understand population-level effects of environmental change.
In-silico identification of archaeal DNA-binding proteins
Authors: Donvil Linus , Housmans Joëlle A.J. , Peeters Eveline , Vranken Wim , Orlando Gabriele
Published: August 2024

The rapid advancement of next-generation sequencing technologies has generated an immense volume of genetic data. However, this data is unevenly distributed, with well-studied organisms being disproportionately represented, while other organisms, such as from archaea, remain significantly underexplored. The study of archaea is particularly challenging due to the extreme environments they inhabit and the difficulties associated with culturing them in the laboratory. Despite these challenges, archaea likely represent a crucial evolutionary link between eukaryotic and prokaryotic organisms, and their investigation could shed light on the early stages of life on Earth. Yet, a significant portion of archaeal proteins are annotated with limited or inaccurate information.

Among the various classes of archaeal proteins, DNA-binding proteins are of particular importance. While they represent a large portion of every known proteome, their identification in archaea is complicated by the substantial evolutionary divergence between archaeal and the other better studied organisms.

To address the challenges of identifying DNA-binding proteins in archaea, we developed Xenusia, a neural network-based tool capable of screening entire archaeal proteomes to identify DNA-binding proteins. Xenusia has proven effective across diverse datasets, including metagenomics data, successfully identifying novel DNA-binding proteins, with experimental validation of its predictions.

Xenusia is available as a PyPI package, with source code accessible athttps://github.com/grogdrinker/xenusia, and as a Google Colab web server application athttps://colab.research.google.com/drive/1c4eb4sEz8OsBqHL62XDFrqmwa7CxImww?usp=sharing.
Quantitative comparison of the structural differences between NRAS and its mutations by well-tempered metadynamics simulations
Authors: Hu Zheyao , Marti Jordi
Published: August 2024

The NRAS-mutant subset of melanoma is one of the most aggressive and lethal types associated with poor overall survival. Unfortunately, a low understanding of the NRAS-mutant dynamic behavior has lead to the lack of clinically approved therapeutic agents able to directly target NRAS oncogenes. In this work, accurate local structures of NRAS and its mutants have been fully explored through the corresponding free energy surfaces obtained by microsecond scale well-tempered metadynamics simulations. Free energy calculations are crucial to reveal the precise mechanisms of Q61 mutations at the atomic level. Considering specific atom-atom distances d and angles φ as appropriate reaction coordinates we have obtained free energy surfaces revealing local and global minima together with their main transitions states, unvealing the mechanisms of abnormal NRAS activation from atomic-level and quantitatively analyzing the corresponding stable states. This will help to advance in our understanding of the basic mechanisms of NRAS mutations, offering new opportunities for the design of potential inhibitors.
Infectious subgenomic amplicon strategies for Japanese encephalitis and West Nile viruses
Authors: Singh Prince Pal , Khanh Le Nguyen Phuong , Karniychuk Uladzimir
Published: August 2024

Classical methods for constructing infectious cDNA clones of flaviviruses are often hindered by instability and toxicity. The Infectious-Subgenomic-Amplicons (ISA) method is an advancement which utilizes overlapping DNA fragments representing viral genomic sequence and in-cell recombination to bypass bacterial plasmid assembly. However, the ISA method has limitations due to the toxicity of some ISA DNA fragments in bacteria during synthetic production. We validated modified ISA strategies for producing toxic ISA Japanese encephalitis virus (JEV) and West Nile virus (WNV) DNA fragments. Three approaches were explored including subdividing toxic DNA fragments into two sub-fragments for synthetic clonal production, using a low-copy bacterial plasmid, and subdividing the toxic DNA fragments into four short overlapping sub- fragments, each up to 1.8 kb. The latter novel approach in ISA applications enabled the synthesis of entirely bacteria-free ISA DNA fragments. Our results demonstrate that subdividing toxic fragments into sub-fragments smaller than 1.8 kb for synthesis is the efficient strategy, circumventing the need for bacterial plasmids and ensuring rapid production of synthetic flaviviruses. This method also shortens the production timeline. We also compared the efficacy of JEV and WNV ISA in zinc finger antiviral protein 1 (ZAP) wild-type and knockout cells and found that knockout cells may be more effective for ISA rescue of flaviviruses, including attenuated strains for live attenuated vaccines. The validated modified ISA strategies provide an efficient approach for producing synthetic JEV and WNV. This will enable rapid research during outbreaks of emerging flaviviruses by facilitating the quick generation of new virus variants.
Novel Insights into Post-Myocardial Infarction Cardiac Remodeling through Algorithmic Detection of Cell-Type Composition Shifts
Authors: Gural Brian , Kirkland Logan , Hockett Abbey , Sandroni Peyton , Zhang Jiandong , Rosa-Garrido Manuel , Swift Samantha K. , Chapski Douglas , Flinn Michael A , O’Meara Caitlin C , Vondriska Thomas M , Patterson Michaela , Jensen Brian C. , Rau Christoph D
Published: August 2024

Background

Recent advances in single cell sequencing have led to an increased focus on the role of cell-type composition in phenotypic presentation and disease progression. Cell-type composition research in the heart is challenging due to large, frequently multinucleated cardiomyocytes that preclude most single cell approaches from obtaining accurate measurements of cell composition. Ourin silicostudies reveal that ignoring cell type composition when calculating differentially expressed genes (DEGs) can have significant consequences. For example, a relatively small change in cell abundance of only 10% can result in over 25% of DEGs being false positives.

Methods

We have implemented an algorithmic approach that uses snRNAseq datasets as a reference to accurately calculate cell type compositions from bulk RNAseq datasets through robust data cleaning, gene selection, and multi-sample cross-subject and cross-cell-type deconvolution. We applied our approach to cardiomyocyte-specific α1A adrenergic receptor (CM-α1A-AR) knockout mice. 8-12 week-old mice (either WT or CM-α1A-KO) were subjected to permanent left coronary artery (LCA) ligation or sham surgery (n=4 per group). Transcriptomes from the infarct border zones were collected 3 days later and analyzed using our algorithm to determine cell-type abundances, corrected differential expression calculations using DESeq2, and validated these findings using RNAscope.

Results

Uncorrected DEGs for the CM-α1A-KO X LCA interaction term featured many cell-type specific genes such asTimp4(fibroblasts) andAplnr(cardiomyocytes) and overall GO enrichment for terms pertaining to cardiomyocyte differentiation (P=3.1E-4). Using our algorithm, we observe a striking loss of cardiomyocytes and gain in fibroblasts in the α1A-KO + LCA mice that was not recapitulated in WT + LCA animals, although we did observe a similar increase in macrophage abundance in both conditions. This recapitulates prior results that showed a much more severe heart failure phenotype in CM-α1A-KO + LCA mice. Following correction for cell-type, our DEGs now highlight a novel set of genes enriched for GO terms such as cardiac contraction (P=3.7E-5) and actin filament organization (P=6.3E-5).

Conclusions

Our algorithm identifies and corrects for cell-type abundance in bulk RNAseq datasets opening new avenues for research on novel genes and pathways as well as an improved understanding of the role of cardiac cell types in cardiovascular disease.
Rpt5 encodes a receptor-like protein that provides broad and effective net form net blotch (Pyrenophora teres f. teres) resistance in barley
Authors: Effertz Karl , Richards Jonathan K , Clare Shaun James , del Castillo Madeline , Sharma Poudel Roshan , Li Mengyuan , Zhang Jianwei , Moscou Matthew James , Friesen Timothy , Brueggeman Robert Saxon
Published: August 2024

The foliar disease net form net blotch (NFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt), causes significant yield and quality losses of barley worldwide. Dominant resistance conferred by the Resistance to Pyrenophora teres 5 (Rpt5) gene from barley line CI5791 is the broadest and most effective resistance reported in this pathosystem. The Rpt5 locus was identified in multiple independent genetic studies utilizing diverse host populations and Ptt isolates, and harbors both dominant Rpt5 resistance and isolate-specific susceptibility genes/alleles that are dominant in the absence of Rpt5, designated susceptibility to Pyrenophora teres 1 (Spt1). Ptt virulence and avirulence effectors from diverse pathogen isolates genetically interact with the Rpt5/Spt1 locus, suggesting a complex locus with a function targeted by the evolution of a diversity of pathogen effectors. High-resolution mapping utilizing 1,920 recombinant gametes from a CI5791 x Tifang biparental population, identified 12 candidate genes in an ~4.6 Mb delimited region in the cv Morex V3 genome assembly, but is 1.1 − 2.2 Mb in the pangenome assemblies, containing 5−12 genes. Analysis revealed a strong correlation between the CI5791 allele of a receptor-like protein (RLP), provisionally designated Rpt5 candidate gene 1, (Rcg1), and broad Rpt5−mediated resistance. Two independent transformants of the CI5791 Rcg1 allele in the susceptible cv Golden Promise background showed significantly increased resistance when challenged with Rpt5 avirulent Ptt isolates 6A, 15A, and 0−1 compared to the Golden Promise wildtype. Thus, Rpt5, encodes an RLP and is the first net blotch resistance gene cloned in barley.
TheToxoplasma gondiihomolog of ATPase inhibitory factor 1 is critical for mitochondrial cristae maintenance and stress response
Authors: Usey Madelaine M. , Ruberto Anthony A. , Huet Diego
Published: August 2024

The production of energy in the form of ATP by the mitochondrial ATP synthase must be tightly controlled. One well-conserved form of regulation is mediated via ATPase inhibitory factor 1 (IF1), which governs ATP synthase activity and gene expression patterns through a cytoprotective process known as mitohormesis. In apicomplexans, the processes regulating ATP synthase activity are not fully elucidated. Using the model apicomplexanToxoplasma gondii, we found that knockout and overexpression of TgIF1, the structural homolog of IF1, significantly affected gene expression. Additionally, TgIF1 overexpression resulted in the formation of a stable TgIF1 oligomer that increased the presence of higher order ATP synthase oligomers. We also show that parasites lacking TgIF1 exhibit reduced mitochondrial cristae density, and that while TgIF1 levels do not affect growth in conventional culture conditions, they are crucial for parasite survival under hypoxia. Interestingly, TgIF1 overexpression enhances recovery from oxidative stress, suggesting a mitohormetic function. In summary, while TgIF1 does not appear to play a role in metabolic regulation under conventional growth conditions, our work highlights its importance for adapting to stressors faced byT. gondiiand other apicomplexans throughout their intricate life cycles.

SIGNIFICANCE STATEMENT

Toxoplasma gondiiis a member of the Apicomplexa, a phylum consisting of parasites responsible for significant global morbidity and mortality. An intact mitochondrial ATP synthase is criticalT. gondiisurvival, but how this enzyme is regulated is not completely understood.

Our work demonstrates that theT. gondiihomolog of ATPase inhibitory factor 1 (TgIF1) does not impact metabolism under standard culture conditions, but plays a role in mitochondrial cristae density and stress responses.

This study reveals the role of TgIF1 in regulating ATP synthase activity under stressful conditions and increases our understanding of this divergent enzyme inT. gondii.
Development of a Novel Japanese Eel Myoblast Cell Line for Application in Cultured Meat Production
Authors: Ikeda Daisuke , Otsuka Yui , Kan-no Nobuhiro
Published: August 2024

The present study investigates the isolation, analysis, and characterization of primary cultured cells derived from the muscle tissue of Japanese eel (Anguilla japonica), culminating in establishing a spontaneously immortalized myoblast cell line, JEM1129. We isolated satellite cells from eel muscle tissue to establish a foundation for cultured eel meat production. While initial cell cultures contained myoblasts, continued passaging led to a decline in myoblast characteristics and an increase in fibroblast-like cells. RNA-Seq and RT-qPCR analyses showed significant downregulation of well-established markers for satellite cells and myoblasts, such as pax7a and myoD, over successive passages, highlighting a loss of myoblastic traits. Single-cell cloning was employed to overcome this challenge and maintain myoblast purity, leading to the successful creation of the JEM1129 cell line. These JEM1129 cells demonstrated enhanced expression of myoblast marker genes, exceeding the initial primary culture cell population. The cells showed strong myotube formation, particularly when cultured in a differentiation medium, indicating their robust potential for muscle development. The JEM1129 cell line represents a significant advancement in the cultivation of eel muscle cells, offering a promising avenue for cultured meat production. The findings contribute to a deeper understanding of muscle cell biology and provide valuable insights into using fish-derived myoblasts for cultured meat production.

Highlights

Single-cell cloning established a stable Japanese eel myoblast line, JEM1129.

Single-cell cloning aids in establishing spontaneously immortalized fish myoblasts.

JEM1129 demonstrates robust myogenic differentiation, crucial for cultured meat.

Potential for sustainable eel meat production reducing wild eel depletion.
The inattentional rhythm in audition
Authors: Lui Troby Ka-Yan , Boglietti Eva , Zoefel Benedikt
Published: August 2024

The detection of temporally unpredictable visual targets depends on the preceding phase of alpha oscillations (~7-12 Hz). In audition, however, such an effect seemed to be absent. Due to the transient nature of its input, the auditory system might be particularly vulnerable to information loss that occurs if relevant information coincides with the low excitability phase of the oscillation. We therefore hypothesised that effects of oscillatory phase in audition will be restored if auditory events are made task-irrelevant and information loss can be tolerated. To this end, we collected electroencephalography (EEG) data from 29 human participants (21F) while they detected pure tones at one sound frequency and ignored others. Confirming our hypothesis, we found that the neural response to task-irrelevant but not to task-relevant tones depends on the pre-stimulus phase of neural oscillations. Alpha oscillations modulated early stages of stimulus processing, whereas theta oscillations (~3-7 Hz) affected later components, possibly related to distractor inhibition. We also found evidence that alpha oscillations alternate between sound frequencies during divided attention. Together, our results suggest that the efficacy of auditory oscillations depends on the context they operate in, and demonstrate how they can be employed in a system that heavily relies on information unfolding over time.

Significance Statement

The phase of neural oscillations shapes visual processing, but such an effect seemed absent in the auditory system when confronted with temporally unpredictable events. We here provide evidence that oscillatory mechanisms in audition critically depend on the degree of possible information loss during the oscillation’s low excitability phase, possibly reflecting a mechanism to cope with the rapid sensory dynamics that audition is normally exposed to. We reach this conclusion by demonstrating that the processing of task-irrelevant but not task-relevant tones depends on the pre-stimulus phase of neural oscillations during selective attention. During divided attention, cycles of alpha oscillations seemed to alternate between possible acoustic targets similar to what was observed in vision, suggesting an attentional process that generalises across modalities.
Citizens' acceptance of prefabricated housing in China: the role of procedural justice and uncertainty
Authors: Zhou Zhenzong , Wei Chen , Shen Geoffrey Qiping , Xue Jin , Liu Yongyue , Wang Yaowu , Man Qingpeng
Published: August 2024

Purpose

This study explores citizens’ acceptance of prefabricated housing (PH) from the perspective of socio-demographic and psychological factors, aiming to reveal the formation of PH acceptance and realize a sustainable development of PH.

Design/methodology/approach

This study proposed hypotheses drawing on procedural justice theory and uncertainty management theory. A survey of 245 respondents was conducted, and the collected data was analyzed in a stepwise multiple regression model. Then, the psychological influencing mechanism was demonstrated using a mediation model.

Findings

Results of the data analysis manifested that citizens’ acceptance of PH was influenced by socio-demographic and psychological factors, where psychological factors had more significant effects on acceptance than socio-demographic factors. The psychological mechanism was examined by verifying the mediating role of uncertainty between procedural justice and the acceptance of PH. Furthermore, a scientific strategy for developing PH was proposed based on this empirical study.

Originality/value

This study extends the knowledge of procedural justice theory by investigating people’s acceptance in the PH context. This study is also one of the first studies to unveil the psychological mechanism toward a high-cost product with invisible technological innovation. This study contributes to the literature by introducing uncertainty management theory to a controversial issue, examining and expanding its application in a complicated context. Moreover, results highlight the positive influence of fair processes on controversial issues.
From pledge to action: integrating racial diversity into the supply chain
Authors: Kinney Yahzmine , Siegler Janaina , Fernhaber Stephanie A.
Published: August 2024

Purpose

Organizations are increasingly making commitments and equity pledges to racially diversify their supply chain. While such commitments are commendable, historical attempts at reform have experienced limited success. This suggests that there is a need for organizations to understand the hurdles and complexity that might limit impact, and then be intentional when taking action.

Design/methodology/approach

In this study, we conduct an inductive, qualitative investigation involving five organizations in Indianapolis USA. Three are corporations that had made a commitment to and are actively trying to racially diversify their supply chain. The other two are support organizations that serve as a link between suppliers and corporations.

Findings

The results identify three levels of interrelated management challenges associated with racially diversifying the supply chain at the industry, strategy, and operation levels.

Originality/value

Strategies for overcoming the challenges when integrating racial diversity into the supply chain are discussed, and a set of directional questions are provided to help organizations with their quest to racially diversify their supply chains.