bluuebunny/crossref_metadata_2025 huggingface dataset:
Reducing Falls in Hospitalized Children and Adolescents with Cancer and Blood Disorders: A Quality Improvement Journey
Authors: Morrissey Lisa K. , Ho Phuc , Ilowite Maya , Johnson David A. , Nixon Colleen M. , Thomas Marissa K. , Waitt Julie A. , Wierzchowski Amy , Renaud Ashley M.
Published: August 2024

Background:

Falls in hospitalized pediatric patients represent a serious patient safety concern. Children and adolescents with cancer and blood disorders have inherent risk factors that increase the likelihood of injury from falls. The Hematology/Oncology (HO) and Stem Cell Transplant (SCT) inpatient units at Boston Children’s Hospital embarked on a multiyear quality improvement journey to reduce inpatient falls in this population.

Methods:

A targeted Falls Reduction Task Force implemented key initiatives between 2020 and 2023. These include enhancing communication strategies to heighten awareness of the highest fall-risk patients, conducting a formal apparent cause analysis on every fall with injury, and initiating a physical therapy-led program to reduce deconditioning. Outcome measures were total falls, rate of preventable falls with injury per 1000 patient days, and days between preventable falls with injury. Our quality improvement team used statistical process control charts to track changes over time.

Results:

The combined rate of preventable falls with injury per 1000 patient days decreased from 0.63 in fiscal year (FY) 2020 to 0.25 in 2023. The SCT and HO units achieved a maximum of 442 days and 410 days, respectively, between preventable falls with injury in 2021–2023, compared with 124 and 117 days in 2020. The two units observed a 51% reduction in total falls over 4 years.

Conclusions:

A multifaceted fall reduction quality initiative effectively reduced preventable falls with injury on pediatric HO and SCT inpatient units, thereby reducing avoidable harm in a vulnerable patient population.
Fluid resuscitation in trauma: What you need to know
Authors: Dhillon Navpreet K. , Kwon Junsik , Coimbra Raul
Published: August 2024

There have been numerous changes in resuscitation strategies for severely injured patients over the last several decades. Certain strategies, such as aggressive crystalloid resuscitation, have largely been abandoned because of the high incidence of complications and worsening of trauma-induced coagulopathy. Significant emphasis has been placed on restoring a normal coagulation profile with plasma or whole blood transfusion. In addition, the importance of the lethal consequences of trauma-induced coagulopathy, such as hyperfibrinolysis, has been easily recognized by the use of viscoelastic testing, and its treatment with tranexamic acid has been extensively studied. Furthermore, the critical role of early intravenous calcium administration, even before blood transfusion administration, has been emphasized. Other adjuncts, such as fibrinogen supplementation with fibrinogen concentrate or cryoprecipitate and prothrombin complex concentrate, are being studied and incorporated in some of the institutional massive transfusion protocols. Finally, balanced blood component transfusion (1:1:1 or 1:1:2) and whole blood have become commonplace in trauma centers in North America. This review provides a description of recent developments in resuscitation and a discussion of recent innovations and areas for future investigation.
Actinomycetospora aeridis sp. nov., Actinomycetospora flava sp. nov. and Actinomycetospora aurantiaca sp. nov., endophytic actinobacteria isolated from wild orchid (Aerides multiflora Roxb)
Authors: Suriyachadkun Chanwit , Ngaemthao Wipaporn , Pujchakarn Tawanmol , Sakdapetsiri Chatsuda , Ayawong Chanjira , Chairote Kamonchai , Chunhametha Suwanee
Published: August 2024

Three novel mycelium-forming actinobacteria, designated OC33-EN06T, OC33-EN07T, and OC33-EN08T, were isolated from wild orchid (Aerides multiflora Roxb), collected from a hill evergreen forest in Northern Thailand. Strains OC33-EN06T and OC33-EN07T showed the highest 16S rRNA gene similarity with Actinomycetospora lutea TT00-04T, 99.17 and 99.45%, respectively. Strain OC33-EN08T showed high similarity with four species, namely ‘Actinomycetospora termitidis Odt1-22T’ (99.37%), Actinomycetospora chiangmaiensis DSM 45062T (99.02%), Actinomycetospora corticicola 014-5T (99.02%), and Actinomycetospora soli SF1T (98.81%). Comparative genome analysis of OC33-EN06T, OC33-EN07T, and OC33-EN08T with the closely related type strains showed that average nucleotide identity (ANI) based on blast, ANI based on MUMmer, and average amino acid identity values were less than 95% and the digital DNA–DNA hybridization values were less than 70%, all below the thresholds for species demarcation. The digital G+C content of OC33-EN06T, OC33-EN07T, and OC33-EN08T were 74.5, 74, and 74 mol%, respectively. These three strains developed bud-like chains of non-motile cylindrical spores with a smooth surface. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained ribose, arabinose, and galactose. The predominant menaquinone was MK-8(H4). The phospholipid profile included phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. Based on comparative analysis of genotypic, phenotypic and chemotaxonomic data, strains OC33-EN06T (=TBRC 18349T=NBRC 116543T), OC33-EN07T (=TBRC 18350T=NBRC 116544T), and OC33-EN08T (=TBRC 18318T=NBRC 116542T) represent the type strains of three novel species of the genus Actinomycetospora for which the names Actinomycetospora aeridis sp. nov., Actinomycetospora flava sp. nov., and Actinomycetospora aurantiaca sp. nov., are proposed.
Comparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae
Authors: Andrews Kimberly R. , Besser Thomas E. , Stalder Thibault , Top Eva M. , Baker Katherine N. , Fagnan Matthew W. , New Daniel D. , Schneider G. Maria , Gal Alexandra , Andrews-Dickert Rebecca , Hunter Samuel S. , Beckmen Kimberlee B. , Christensen Lauren , Justice-Allen Anne , Konetchy Denise , Lehman Chadwick P. , Manlove Kezia , Miyasaki Hollie , Nordeen Todd , Roug Annette , Cassirer E. Frances
Published: August 2024

Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.
BEHAV3D Tumor Profiler to map heterogeneous cancer cell behavior in the tumor microenvironment
Authors: Rios-Jimenez Emilio , Zomer Anoek , Collot Raphael , Román Mario Barrera , Ariese Hendrikus , van Ineveld Ravian L. , Kleinnijenhuis Michiel , Bessler Nils , Johnson Hannah , Rios Anne , Alieva Maria
Published: August 2024

Intravital microscopy (IVM) enables live imaging of animals at single-cell level, offering essential insights into cancer progression. This technique allows for the observation of single-cell behaviors within their natural 3D tissue environments, shedding light on how genetic and microenvironmental changes influence the complex dynamics of tumors. The complexity of data generated by IVM often surpasses the capabilities of conventional analyses accessible to biomedical scientists, thereby neglecting single-cell heterogeneity and limiting the exploration of microenvironmental influences on cellular behavior without bias. To address this challenge, here we introduce BEHAV3D Tumor Profiler (BEHAV3D-TP), a user-friendly computational framework designed for the comprehensive analysis of single tumor cell behaviors and their interactions with the tumor microenvironment (TME). BEHAV3D-TP facilitates unbiased profiling of cancer cell dynamics without requiring advanced computational expertise. Here, we apply BEHAV3D-TP to study diffuse midline glioma (DMG), a highly aggressive pediatric brain tumor characterized by invasive growth. Our analysis reveals that distinct migratory behaviors of DMG cells correlate with specific TME components such as tumor-associated macrophages and vasculature. This approach, initially aimed at uncovering tumor invasive patterns and their interactions with the TME, holds promise for understanding additional cancer cell behaviors like intravasation and metastasis. BEHAV3D-TP represents a significant advancement in democratizing the analysis of heterogeneous cancer cell behaviors and their TME interactions, providing accessible computational insights into tumor dynamics.
Haemolymphatic tissues of captive boa constrictor(Boa constrictor):morphological features in healthy individuals and with Boid Inclusion Body Disease
Authors: Dervas E. , Michalopoulou E. , Thiele T. , Baggio F. , Hetzel U. , Kipar A.
Published: August 2024

Knowledge on the structure and composition of the haematopoietic tissue (HT) is essential to understand the basic immune functions of the immune system in any species. For reptiles, it is extremely limited, hence we undertook an in-depth in situ investigation of the HT (bone marrow, thymus, spleen, lymphatic tissue of the alimentary tract) in the common boa (Boa constrictor). We also assessed age- and disease-related changes, with a special focus on Boid Inclusion Body Disease, a highly relevant reptarenavirus-associated disease in boid snakes. The HT was subjected to gross, histological and ultrastructural examination, including special stains, immunohistochemistry, in situ hybridization and morphometric analyses. In general, the HT was dominated by T cells and lacked a clear structural organization, such as follicle formation. BIBD was associated with significantly higher cellularity and a granulomatous response in the spleen, and the presence of virus-infected haematopoietic cells in the bone marrow, suggesting the latter as a persistent source of viremia.

Highlights

Lymphatic tissues ofB. constrictorlack organization and are dominated by T cells

The thymus ofB. constrictorshows slow age-related involution

BIBD-positiveboasshow a granulomatous response in the spleen

Reptarenaviruses infect haematopoietic cells in the bone marrow

Reptarenavirusinfectedbone marrow cells might represent a source of viremia
Plant-plant interactions in wheat mixtures modulate mean and variance of susceptibility to Septoria tritici blotch
Authors: Mathieu Laura , Ducasse Aurélie , Ballini Elsa , Morel Jean-Benoît
Published: August 2024

Varietal mixtures are a promising agro-ecological approach to stabilizing yields by reducing diseases. The effects of mixtures stem from modifications of epidemiological processes and plant-plant interactions, which could explain some of the paradoxical observations made in the field. However, the role of plant-plant interactions in modifying bread wheat and durum wheat susceptibility to septoria tritici blotch remains to be elucidated. Our study aimed to determine the effect of such plant-plant interactions, by producing full matrices of binary mixtures in the absence of epidemics, on septoria symptoms—specifically necroses (lesions) and pycnidia (spore-containing structures). We employed statistical modeling to compare the mean and variance of focal plants’ phenotype in all mixturesversuspure conditions and in each mixtureversuspure condition. Our findings demonstrate significant effects of plant-plant interactions on wheat susceptibility to septoria. Notably, these interactions had specific rather than general effects, with some but not all genotypic combinations significantly influencing focal susceptibility to septoria. Furthermore, mixtures resulted in reduced necrosis with lower variance, but increased pycnidia formation. These results reinforce the need to consider specific plant-plant interactions for their contribution to trait means and variances. Better considering these interactions could improve crop management strategies that enhance disease control.

Highlight

Wheat varietal mixtures modulate the mean and variance of septoria disease symptoms through specific plant-plant interactions. Mixtures reduce lesions and their variance but increase the formation of spore-containing bodies.
Local weakening of cell-ECM adhesion triggers basal tissue folding via changes in cell shape, actomyosin organization and E-cad levels
Authors: Valencia-Expósito Andrea , Khalilgharibi Nargess , Martínez-Abarca Millán Ana , Mao Yanlan , Martín-Bermudo María D.
Published: August 2024

Duringdevelopment, epithelial sheets sculpt organs by folding, either apically or basally, into complex 3D structures. Given the presence of actomyosin networks and cell adhesion sites on both sides of cells, a common machinery mediating apical and basal epithelial tissue folding has been proposed. However, little is known about the mechanisms regulating epithelial folding towards the basal side. Here, using theDrosophilawing imaginal disc and a multidisciplinary approach, combining genetic perturbations and computational modelling, we demonstrate opposing roles for cell-cell and cell-ECM adhesion systems during epithelial folding. Thus, while cadherin-mediated adhesion, linked to actomyosin network, regulates apical folding, a reduction on integrin-dependent adhesion, followed by changes in cell shape, organization of the basal actomyosin cytoskeleton and E-Cad levels, is necessary and sufficient to trigger basal folding. These results suggest that modulation of the cell mechanical landscape through the crosstalk between integrins and cadherins is essential for correct epithelial folding.
Conjugation of dn-OPDA with amino acids inhibits its hormonal bioactivity inMarchantia polymorpha
Authors: Liang Wenting , Zamarreño Ángel M. , Torres-Montilla Salvador , de la Torre Antonio , Totozafy Jean Chrisologue , Kaji Takuya , Ueda Minoru , Corso Massimiliano , García-Mina José M. , Solano Roberto , Chini Andrea
Published: August 2024

Jasmonates are important phytohormones activating plant tolerance to biotic and abiotic stress, as well as different development processes. A conserved signalling pathway activated by distinct hormones in different plant species mediates these responses: dinor-12-oxo-phytodienoic acid (dn-OPDA) isomers in bryophytes and lycophytes, and JA-Ile in most vascular plants. The final responses depend, in many cases, on the accumulation of specialized metabolites. To identify novel compounds regulated by the dn-OPDA pathway in Marchantia, untargeted metabolomic analyses were carried out in response to dn-OPDA-regulated stress. A novel group of molecules were identified as dn-OPDA-amino acid conjugates (dn-OPDA-aas), and their accumulation after wounding and herbivory confirmed by targeted metabolic profiling in Marchantia and all species in which we previously found dn-iso-OPDA. Mutants inGRETCHEN-HAGEN 3A(MpGH3A) failed to accumulate dn-OPDA-aa conjugates, and showed a constitutive activation of the OPDA pathway and increased resistance to herbivory. Our results show that dn-iso-OPDA bioactivity is reduced by conjugation with amino acids. Therefore, a dichotomous role of jasmonate conjugation in land plants is highlighted: jasmonic acid (JA) conjugation with isoleucine (Ile) produce the bioactive JA-Ile in tracheophytes, whereas conjugation of dn-iso-OPDA with different amino acids disactivate the hormone in bryophytes and lycophytes.
Systematic deletion of symmetricalCFTRexons reveals new therapeutic targets for exon skipping antisense oligonucleotides
Authors: Pena-Rasgado Cecilia , Manriquez Elvia , Dundr Miroslav , Bridges Robert J. , Hastings Michelle L. , Michaels Wren E.
Published: August 2024

There is a major need for therapeutics that treat diseases caused by pathogenic gene variants that disrupt protein open-reading frames. Splice-switching antisense oligonucleotides (ASOs) offer a potential solution by inducing the skipping of exons containing these variants, removing them from the mRNA and correcting the open-reading frame. Cystic fibrosis (CF), caused by disruption of the CF transmembrane regulator (CFTR) gene, is one such disease that has many chain-terminating variants, which are untreatable with standard protein-targeted modulator therapies. UsingCFTRas a model, we demonstrate the utility of ASOs in engineering protein isoforms through exon skipping to rescue protein function disrupted by truncating variants. We functionally screened all CFTR isoforms generated by the deletion of symmetrical exons, which can be skipped without disrupting the open-reading frame. We identified exons that can be removed and produce CFTR isoforms that remain functionally responsive to modulators. We screened for ASOs that induce skipping of these exons and show that they recover CFTR function in airway cells derived from individuals with terminatingCFTRvariants. This study demonstrates that systematic functional analysis of in-frame exon-deleted protein isoforms can identify targets for ASO-based splice-switching therapies, a concept that can be broadly applied to any multi-exon protein-coding gene.
Reduced neural distinctiveness of speech representations in the middle-aged brain
Authors: Guo Zhe-chen , McHaney Jacie R. , Parthasarathy Aravindakshan , Chandrasekaran Bharath
Published: August 2024

Speech perception declines independent of hearing thresholds in middle-age, and the neurobiological reasons are unclear. In line with the age-related neural dedifferentiation hypothesis, we predicted that middle-aged adults show less distinct cortical representations of phonemes and acoustic-phonetic features relative to younger adults. In addition to an extensive audiological, auditory electrophysiological, and speech perceptual test battery, we measured electroencephalographic responses time-locked to phoneme instances (phoneme-related potential; PRP) in naturalistic, continuous speech and trained neural network classifiers to predict phonemes from these responses. Consistent with age-related neural dedifferentiation, phoneme predictions were less accurate, more uncertain, and involved a broader network for middle-aged adults compared with younger adults. Representational similarity analysis revealed that the featural relationship between phonemes was less robust in middle-age. Electrophysiological and behavioral measures revealed signatures of cochlear neural degeneration (CND) and speech perceptual deficits in middle-aged adults relative to younger adults. Consistent with prior work in animal models, signatures of CND were associated with greater cortical dedifferentiation, explaining nearly a third of the variance in PRP prediction accuracy together with measures of acoustic neural processing. Notably, even after controlling for CND signatures and acoustic processing abilities, age-group differences in PRP prediction accuracy remained. Overall, our results reveal “fuzzier” phonemic representations, suggesting that age-related cortical neural dedifferentiation can occur even in middle-age and may underlie speech perceptual challenges, despite a normal audiogram.
Development of ketobenzothiazole-based peptidomimetic TMPRSS13 inhibitors with low nanomolar potency
Authors: Joushomme Alexandre , Désilets Antoine , Champagne William , Hassanzadeh Malihe , Lemieux Gabriel , Gravel-Trudeau Alice , Lepage Matthieu , Lafrenière Sabrina , Froehlich Ulrike , List Karin , Boudreault Pierre-Luc , Leduc Richard
Published: August 2024

TMPRSS13, a member of the Type II Transmembrane Serine Proteases (TTSP) family, is involved in cancer progression and in cell entry of respiratory viruses. To date, no inhibitors have been specifically developed toward this protease. In this study, a chemical library of 65 ketobenzothiazole-based peptidomimetic molecules was screened against a proteolytically active form of recombinant TMPRSS13 to identify novel inhibitors. Following an initial round of screening, subsequent synthesis of additional derivatives supported by molecular modelling, uncovered important molecular determinants involved in TMPRSS13 inhibition. One inhibitor, N-0430, achieved low nanomolar affinity towards TMPRSS13 activity in a cellular context. Using a SARS-CoV-2 pseudovirus cell entry model, we further show the ability of N-0430 to block TMPRSS13-dependent entry of the pseudovirus. The identified peptidomimetic inhibitors and the molecular insights of their potency gained from this study will aid in the development of specific TMPRSS13 inhibitors.
Immune aging impairs muscle regeneration via macrophage-derived anti-oxidant selenoprotein P
Authors: Hoang Dieu-Huong , Bouvière Jessica , Galvis Johanna , Moullé Pauline , Migliavacca Eugenia , Juban Gaëtan , Liot Sophie , Stuelsatz Pascal , Le Grand Fabien , Feige Jérôme N , Mounier Rémi , Chazaud Bénédicte
Published: August 2024

Muscle regeneration is impaired in the aged organism, due to both intrinsic defects of muscle stem cells (MuSCs) and alterations of their environmental niche. However, the latter has still been poorly explored. Here, we compared and analyzed the time course of the various cell types constituting the MuSC niche during muscle generation in young and old mice. Aging altered the amplification of all niche cells with particularly prominent phenotypes in macrophages that impaired the resolution of inflammation in the old regenerating muscle. RNAsequencing of FACs-isolated MuSCs and non-myogenic niche cells during regeneration uncovered specific profiles and kinetics of genes and molecular pathways differentially regulated in old versus young regenerating muscle, indicating that each cell type responded to aging in a specific manner. Through this, we discovered that macrophages have a strong signature of aging with altered the activation of Selenoprotein P (Sepp1) expression in macrophages during the resolution of inflammation in regenerating muscle. Macrophage-specific deletion ofSepp1gene was sufficient to impair the acquisition of the repair inflammatory profile, perturbed the support of macrophages to MuSCsin vitroandin vivo, and to cause inefficient skeletal muscle regeneration. When transplanted in aged mice, bone marrow from young WT mice, but not Sepp1 KOs, restored muscle regeneration to youthful levels. Altogether this work provides a unique resource to study the aging of the MuSC niche, reveals that aging of niche cells is asynchronous and establishes impaired macrophage dynamics/polarization and the anti-oxidant Selenoprotein P expression as drivers of age-related decline of muscle regeneration.

Teaser:Cell profiling reveals asynchronicity of aging in the muscle stem cell niche and age-dependent macrophage/stem cell interactions through anti-oxidant selenoprotein P
MINERVA FAIR assessment fosters open science & scientific crowd-sourcing in systems biomedicine
Authors: Balaur Irina , Welter Danielle , Rougny Adrien , Inau Esther Thea , Mazein Alexander , Ghosh Soumyabrata , Schneider Reinhard , Waltemath Dagmar , Ostaszewski Marek , Satagopam Venkata
Published: August 2024

1

The Disease Maps Project (https://disease-maps.org) focuses on the development of diseasespecific comprehensive structured knowledge repositories supporting translational medicine research. These disease maps require continuous interdisciplinary collaboration and should be reusable and interoperable. Adhering to the Findable, Accessible, Interoperable and Reusable (FAIR) principles enhances the utility of such digital assets.

We used the RDA FAIR Data Maturity Model and assessed the FAIRness of the Molecular Interaction NEtwoRk VisuAlization (MINERVA) Platform. MINERVA is a standalone webserver that allows users to manage, explore and analyse disease maps and their related data manually or programmatically. We exemplify the FAIR assessment on the Parkinson’s Disease Map (PD map) and the COVID-19 Disease Map, which are large-scale projects under the umbrella of the Disease Maps Project, aiming to investigate molecular mechanisms of the Parkinson’s disease and SARS-CoV-2 infection, respectively.

We discuss the FAIR features supported by the MINERVA Platform and we outline steps to further improve the MINERVA FAIRness and to better connect this resource to other ongoing scientific initiatives supporting FAIR in computational systems biomedicine.
Ultrasound-activated microbubbles mediate F-actin disruptions and endothelial gap formation during sonoporation
Authors: Meijlink Bram , van der Kooij H. Rhodé , Wang Yuchen , Li Hongchen , Huveneers Stephan , Kooiman Klazina
Published: August 2024

Locally opening up the endothelial barrier in a safe and controlled way is beneficial for drug delivery into the extravascular tissue. Although ultrasound-induced microbubble oscillations can affect endothelial barrier integrity, the mechanism remains unknown. Here we uncover a new role for F-actin in microbubble-mediated endothelial gap formation. Unique simultaneous high-resolution confocal microscopy and ultra-high-speed camera imaging (10 million frames per second) reveal that oscillating microbubbles (radius 1.3-3.8 µm) induce sonoporation in all cells in which F-actin remodeling occurred. F-actin disruption only mainly resulted in tunnel formation (75%) and F-actin stress fiber severing and recoil mainly resulted in cell-cell contact opening within 15 s upon treatment (54%) and tunnel formation (15%). Stress fiber severing occurred when fibers were within reach of the microbubble’s maximum radius during oscillation, requiring normal forces of ≥230 nN. Together, these findings reveal a novel mechanism of microbubble-mediated drug delivery, which associates with the underlying cytoskeletal organization.
Deciphering the coupling state-dependent transcription termination in theEscherichia coligalactose operon
Authors: N Monford Paul Abishek , Wang Xun , Jeon Heung Jin , Lim Heon M.
Published: August 2024

The distance between the ribosome and the RNA polymerase active center, often referred to as the mRNA loop length, is a critical determinant of transcription-translation coupling. While structural biology studies have indicated the existence of multiple expressomes with varying mRNA loop lengths, theirin vivoroles and functional significance remain largely unexplored. This study delves into the mechanisms governing transcription termination within theEscherichia coligalactose operon, revealing a crucial role in the transcription and translation coupling state. The operon employs both Rho-independent and Rho-dependent terminators. Our findings demonstrate that long-loop coupled transcription-translation complexes preferentially terminate at the upstream Rho-independent terminator. In contrast, short-loop coupled complexes bypass the Rho-independent terminator and terminate at the downstream Rho-dependent terminator. The efficiency of the Rho-independent terminator is enhanced by an extended U-track, suggesting a novel mechanism for overcoming ribosome inhibition. These results challenge the traditional view of transcription termination as a random process, highlighting a predetermined mechanism contingent on the coupling state. This study emphasizes the intricate interactions between transcription and translation in prokaryotes. Understanding how these processes affect the RNA polymerase’s selection of transcriptional terminators is critical for developing strategies to regulate gene expression.
O-glycosylation contributes to mammalian glycoRNA biogenesis
Authors: Porat Jennifer , Watkins Christopher P. , Jin Chunsheng , Xie Xixuan , Tan Xiao , Lebedenko Charlotta G. , Hemberger Helena , Shin Woojung , Chai Peiyuan , Collins James J. , Garcia Benjamin A. , Bojar Daniel , Flynn Ryan A.
Published: August 2024

There is an increasing appreciation for the role of cell surface glycans in modulating interactions with extracellular ligands and participating in intercellular communication. We recently reported the existence of sialoglycoRNAs, where mammalian small RNAs are covalently linked to N-glycans through the modified base acp3U and trafficked to the cell surface. However, little is currently known about the role for O-glycosylation, another major class of carbohydrate polymer modifications. Here, we use parallel genetic, enzymatic, and mass spectrometry approaches to demonstrate that O-linked glycan biosynthesis is responsible for the majority of sialoglycoRNA levels. By examining the O-glycans associated with RNA from cell lines and colon organoids we find known and previously unreported O-linked glycan structures. Further, we find that O-linked glycans released from small RNA from organoids derived from ulcerative colitis patients exhibit higher levels of sialylation than glycans from healthy organoids. Together, our work provides flexible tools to interrogate O-linked glycoRNAs (O-glycoRNA) and suggests that they may be modulated in human disease.
The Role of Metabolic Strategies in Determining Microbial Community Diversity along Temperature Gradients
Authors: Duan Quqiming , Clegg Tom , Smith Thomas P. , Bell Thomas , Pawar Samraat
Published: August 2024

By conservative estimates, microbes make up about 17% of the world’s biomass and are essential for most ecosystem functions. However, the mechanisms driving the variation in microbial species diversity in response to both natural and anthropogenic temperature gradients remain unclear. In this study, we integrate ecological metabolic theory with a community assembly model to predict that microbial community diversity generally follows a unimodal pattern with temperature. The position and magnitude of peak diversity are determined by interaction-driven species sorting acting on variations in the temperature dependence of carbon use efficiency (CUE) and generalist-specialist tradeoff. Specifically, trait sorting across temperatures favours communities with high mean and low variance in species-level CUEs. We provide empirical evidence supporting our qualitative predictions of the unimodal temperature-diversity pattern along the global geological temperature gradient, which peaks at about 10-15°C. Our findings indicate that the response of diversity as well as CUE to temperature of microbial communities can be predicted from relatively feasible life-history trait measurements, paving the way for interlinking microbial community diversity and carbon cycling along spatial and temporal thermal gradients.
Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems
Authors: McCullough Jenna M. , Eliason Chad M. , Hackett Shannon , Myers Corinne E. , Andersen Michael J.
Published: August 2024

The flora and fauna of island systems, especially those in the Indo-Pacific, are renowned for their high diversification rates and outsized contribution to the development of evolutionary theories. The total diversity of geographic radiations of many Indo-Pacific fauna is often incompletely sampled in phylogenetic studies due to the difficulty in obtaining single island endemic forms across the Pacific and the relatively poor performance of degraded DNA when using museum specimens for inference of evolutionary relationships. New methods for production and analysis of genome-wide datasets sourced from degraded DNA are facilitating insights into the complex evolutionary histories of these influential island faunas. Here, we leverage whole genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity withinTodiramphuskingfishers, a rapid radiation of largely island endemic ‘Great Speciators.’ We find that whole genome datasets do not outright resolve the evolutionary relationships of this clade: four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree building methods did not find a single well-supported and concordant species-level topology. We then uncover evidence of widespread incomplete lineage sorting and both ancient and contemporary gene flow and demonstrate how these factors contribute to conflicting evolutionary histories. Our complete taxonomic sampling allowed us to further identify a novel case of mitochondrial capture between two allopatric species, suggesting a potential historical (but since lost) hybrid zone as islands were successively colonized. Taken together, these results highlight how increased genomic and taxon sampling can reveal complex evolutionary patterns in rapid island radiations.
Profiling extremophile bacterial communities recovered from a mining tailing against soil ecosystems through comparative genome-resolved metagenomics and evolutionary analysis
Authors: Rojas Moises A. , Serrano Gladis , Torres Jorge , Ortega Jaime , Gálvez Gabriel , Vilches Emilio , Parra Valentina , Reyes-Jara Angélica , Maracaja-Coutinho Vinicius , Pizarro Lorena , Latorre Mauricio , Di Genova Alex
Published: August 2024

Microbial communities inhabiting mining environments harbor a diverse array of bacteria with specialized metabolic capacities adapted to extreme conditions. Here, we utilized comparative genome-resolved metagenomics of a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile. We investigate the metabolic roles and evolutionary behaviors of the resident microorganisms, focusing on capacities related to copper, iron, and sulfur metabolism. We recovered 44 medium and high-quality metagenome-assembled genomes (MAGs), primarily classified belonging to phylumActinobacteriota(21),Proteobacteria(10), andAcidobacteriota(6). These MAGs were compared to the Global Soil MAGs project (SMAG catalog), which includes bacteria from conventional or natural ecosystems, to uncover specialized properties of mining bacteria. Notably, we discovered a new phylum,Nitrospirota_A, and provided insights into the unexplored taxonomic classifications at the lowest ranks such as genus and species. Functional potential analysis revealed that the mining community has enhanced molecular capabilities associated with sulfur and copper metabolism. Evolutionary analysis revealed that mining genes involved in targeted metabolism are under strong negative selection, indicating conservative evolutionary pressure within the mining environment. In particular, it was possible to identify a MAG from the genusAcidithrixwith a global dN/dS ratio greater than 1, suggesting positive selection. Additionally, core proteins essential for bacterial survival, such as flagellar motors, cell cycle regulators, and biogenesis proteins, were also under positive selection. The latter points to the need for enhanced mobility in these microorganisms to locate resources efficiently. We demonstrate that copper mining communities are diverse and possess a significant metabolic repertoire under extreme conditions in sulfur and copper proteins. Those specialized genes appear to be in a conservative state rather than undergoing adaptive evolution. This study enhances our understanding of extremophile mining microbiomes, highlighting their high variability in classification, metabolic functions, evolution, and adaptation, which can be leveraged for further biotechnological applications.
Integer topological defects provide a new way to quantify and classify cell sheets
Authors: Zhao Zihui , Li He , Yao Yisong , Zhao Yongfeng , Serra Francesca , Kawaguchi Kyogo , Zhang Hepeng , Chaté Hugues , Sano Masaki
Published: August 2024

Sheets of confluent cells are often considered as active nematics, with accumulation attopological defects and escape fromdefects being widely recognized. However, collective dynamics surrounding integer-charge defects remain poorly understood, despite its biological importance. By using microfabricated patterns, we induce diverse+1topological defects (aster, spirals, and target) within monolayers of neural progenitor cells. Remarkably, cells are consistently attracted to the core of+1defects regardless of their type, challenging existing theories and the conventional extensile/contractile dichotomy. We trace back the origin of this accumulation behavior to previously overlooked nonlinear active forces using a combination of experiments and a continuous theory derived from a cell-level model. Our findings demonstrate that+1topological defects can reveal key features of active nematic systems and offer a new way to characterize and classify cell layers.
Mosquitoes reared in distinct insectaries within an institution in close spatial proximity possess significantly divergent microbiomes
Authors: Brettell Laura E. , Hoque Ananya F. , Joseph Tara S. , Dhokiya Vishaal , Hornett Emily A. , Hughes Grant L. , Heinz Eva
Published: August 2024

The microbiome affects important aspects of mosquito biology and differences in microbial composition can affect the outcomes of laboratory studies. To determine how the biotic and abiotic conditions in an insectary affect the composition of the bacterial microbiome of mosquitoes we reared mosquitoes from a single cohort of eggs from one genetically homogeneous inbredAedes aegypticolony, which were split into three batches, and transferred to each of three different insectaries located within the Liverpool School of Tropical Medicine. Using three replicate trays per insectary, we assessed and compared the bacterial microbiome composition as mosquitoes developed from these eggs. We also characterised the microbiome of the mosquitoes’ food sources, measured environmental conditions over time in each climate-controlled insectary, and recorded development and survival of mosquitoes. While mosquito development was overall similar between all three insectaries, we saw differences in microbiome composition between mosquitoes from each insectary. Furthermore, bacterial input via food sources, potentially followed by selective pressure of temperature stability and range, did affect the microbiome composition. At both adult and larval stages, specific members of the mosquito microbiome were associated with particular insectaries; and the insectary with less stable and cooler conditions resulted in slower pupation rate and higher diversity of the larval microbiome. Tray and cage effects were also seen in all insectaries, with different bacterial taxa implicated between insectaries. These results highlight the necessity of considering the variability and effects of different microbiome composition even in experiments carried out in a laboratory environment starting with eggs from one batch; and highlights the impact of even minor inconsistencies in rearing conditions due to variation of temperature and humidity.
SNAP-tag2: faster and brighter protein labeling
Authors: Kühn Stefanie , Nasufovic Veselin , Wilhelm Jonas , Kompa Julian , de Lange Eline M.F. , Lin Yin-Hsi , Egoldt Cornelia , Fischer Jonas , Lennoi Artem , Tarnawski Miroslaw , Reinstein Jochen , Vlijm Rifka , Hiblot Julien , Johnsson Kai
Published: August 2024

SNAP-tag is a powerful tool for labeling proteins with synthetic fluorophores in bioimaging. However, its utility in live-cell applications can be constrained by its relatively slow labeling kinetics and the limited cell permeability of its substrates. Here we introduce new labeling substrates and an engineered SNAP-tag for faster labelingin vitroand in live cells. SNAP-tag2 presents a second-order rate constant with rhodamine substrates that approaches 107s-1M-1, a 100-fold improvement over the corresponding SNAP-tag-substrate pairs. When labeled with highly fluorogenic dyes, SNAP-tag2 also shows a 5-fold increase in fluorescence brightness relative to currently used SNAP-tag. The increased labeling kinetics and brightness of SNAP-tag2 translates into a greatly improved performance in various live-cell (super-resolution) imaging applications.
Credible set is sensitive to imputation quality and missing variants
Authors: Liang Yanyu ,   23andMe Research Team, Auton Adam , Wang Xin
Published: August 2024

Bayesian fine-mapping to obtain credible sets has been widely applied post GWAS to pinpoint causal variants. The calculation of credible sets generally assumes that all variants have been equally well genotyped, which is often not the case when a GWAS has been run on imputed data. In this work, we investigate the behavior of credible sets in imputed datasets utilizing ‘held out’ genotyped variants to measure accuracy. We show, via simulation, that: i) the coverage of credible sets decreases when using imputed variants in GWAS; ii) rare causal variants often fail to be tagged in credible sets when they are not present in the GWAS variant set. We develop a reweighting approach to take imputation quality into account during fine-mapping that only requires summary statistics, and demonstrate the approach with real data.
Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses
Authors: Mendelsohn Alana I. , Nikoobakht Laudan , Bikoff Jay B. , Costa Rui M.
Published: August 2024

The basal ganglia control multiple sensorimotor behaviors though anatomically segregated and topographically organized subcircuits with outputs to specific downstream circuits. However, it is unclear how the anatomical organization of basal ganglia output circuits relates to the molecular diversity of cell types. Here, we demonstrate that the major output nucleus of the basal ganglia, the substantia nigra pars reticulata (SNr) is comprised of transcriptomically distinct subclasses that reflect its distinct progenitor lineages. We show that these subclasses are topographically organized within SNr, project to distinct targets in the midbrain and hindbrain, and receive inputs from different striatal subregions. Finally, we show that these mouse subclasses are also identifiable in human SNr neurons, suggesting that the genetic organization of SNr is evolutionarily conserved. These findings provide a unifying logic for how the developmental specification of diverse SNr neurons relates to the anatomical organization of basal ganglia circuits controlling specialized downstream brain regions.
Toward the Clinical Translation of Safe Intravenous Long Circulating Iodinated Lipid Nanoemulsion Contrast Agents for CT Imaging
Authors: Attia Mohamed F. , Marasco Ryan N. , Kwain Samuel , Foxx Charity , Whitehead Daniel C. , Kabanov Alexander , Lee Yueh Z.
Published: August 2024

Current clinical small molecule x-ray CT agents are effective but pose risks such as nephrotoxicity, short blood circulation time, limiting scan durations, potential thyroid impact, and immune responses. These challenges drive the development of kidney-safe x-ray nanoparticle (NP)-based contrast agents (CAs), though translation to clinical practice is hindered by chemical complexities and potential toxicity. We have engineered an intravenous, injectable, and safe blood pool NP-based CT CAs at a clinical-equivalent dose of ∼300 mgI/kg (∼2 mL/kg), ideal for vascular and hepatic imaging which are limited by clinical agents. Our iodinated lipid nanodroplet emulsions (ILNEs) contrast agent offers high x-ray attenuation thus improved contrast enhancement, extended stability, and exceptional batch-to-batch consistency. It also boasts a straightforward and scalable manufacturing process with minimal protein interaction, prolonged blood residency (∼4h), and hepatic clearance within 3 days, avoiding nephrotoxicity. Studies in vitro, in mice, and 16.6kg porcine animal model studies confirm its safety, cytocompatibility, and absence of tissue damage. Blood, and thyroid-stimulating hormone (TSH) analyses, and kidney and liver function tests, also support further toxicity evaluations for clinical translation.
Single-turnover kinetic analysis of non-LTR retrotransposition defines the mechanism and rate constants governing each step
Authors: Dangerfield Tyler L. , Zhou Jun , Eickbush Thomas , Johnson Kenneth A.
Published: August 2024

Site specific retrotransposon-mediated gene therapy has the potential to revolutionize medicine by allowing insertion of large gene cargos. Despite decades of effort, the reaction sequence remains to be fully elucidated limiting the ability to engineer improved activity for gene insertion. Here we provide a kinetic/mechanistic framework for R2 non-LTR retrotransposition. Single turnover measurements and global data fitting defined the rate constants for each step in the pathway involving 1st-strand DNA cleavage to provide a DNA primer, reverse transcription to copy the RNA, 2nd-strand DNA cleavage to provide the second primer, and 2nd-strand synthesis to make duplex cDNA. Sequence analysis of the cDNA confirms accurate replication of the 1400 nt RNA used in this study. This represents the only complete analysis of the reaction sequence and first observation of 2nd-strand synthesisin vitro. We provide a kinetic framework to understand non-LTR retrotransposition, which provide a basis to engineer improved activity.
Headache-specific Hyperexcitation Sensitises and Habituates on different Time Scales: An Event Related Potential study of Pattern-Glare
Authors: Dogan Cihan , Miller Claire E. , Jefferis Tom , Saranti Margarita , Tempesta Austyn J. , Schofield Andrew J. , Palaniappan Ramaswamy , Bowman Howard
Published: August 2024

Cortical hyperexcitability is a key pathophysiological feature in several neurological disorders, including migraine, epilepsy, tinnitus, and Alzheimer’s disease. We examined the temporal characteristics of Evoked Related Potentials (ERPs) in a healthy population using the Pattern Glare Test, a diagnostic tool used to assess patients with sensitivity to cortical hyperexcitability. During the experiment, participants recorded state measures with this study focussing on susceptibility to migraine. We investigated two timeframes: habituation over the course of the experiment and sensitization over the course of stimulus presentation. We found evidence of hyperexcitability in the visual cortex, for the clinically aggravating stimuli (medium). Participants who reported a higher state measure exhibited a higher degree of habituation and sensitization, which was dependent on susceptibility to migraine. These findings suggest that the same experimental paradigm and analysis should be performed on a clinically diagnosed population.