bluuebunny/crossref_metadata_2025 huggingface dataset:
Digital Health Tools Applications in Frail Older Adults - A Review Article
Authors: Isaradech Natthanaphop , Sirikul Wachiranun
Published: February 2024

Background

Frailty is a common degenerative condition highly prevalent in adults over 60 years old. A frail person has a higher risk of morbidities and mortality when exposed to health-related stressors. However, frailty is a reversible state when it is early diagnosed. Studies have shown that frail people who participated in an exercise prescription have a greater chance to transition from frail to fit. Additionally, with a rapid advancement of technology, a vast majority of studies are supporting evidence regarding the digital health tools application on frail population in recent years.

Objectives

This review comprehensively summarizes and discusses about technology application in frail persons to capture the current knowledge gaps and propose future research directions to support additional research in this field.

Methods

We used PubMed to search literature (2012-2023) with pre-specified terms. Studies required older adults (≥40 years) using digital tools for frailty comparison, association, or prediction and we excluded non-English studies and those lacking frailty comparison or digital tool use.

Findings

Our review found potential etiognostic factors in trunk, gait, upper-extremity, and physical activity parameters for diagnosing frailty using digital tools in older adults.

Conclusion

Studies suggest exercise improves frailty status, emphasizing the need for integrated therapeutic platforms and personalized prevention recommendations.
Patient Centric Summarization of Radiology Findings using Large Language Models
Authors: Tariq Amara , Fathizadeh Sam , Ramaswamy Gokul , Trivedi Shubham , Urooj Aisha , Tan Nelly , Stib Matthew T. , Patel Bhavik N. , Banerjee Imon
Published: February 2024

Objective

Develop automated AI models for patient-sensitive summarization of radiology reports. Level of medical education or socio-economic background of a patient may dictate their level of understanding of medical jargon. Inability to understand primary findings from a radiology report may lead to unnecessary anxiety among patients or result in missed follow up.

Materials and Methods

Computed tomography exams of chest were selected as a use-case for this study. Approximately 7K chest CT reports were collected from Mayo Clinic Enterprise. Summarization model was built on the T5 large language model (LLM) as its text-to-text transfer architecture is intuitively suited for abstractive text summarization, resulting in a model size of ~0.77B. Noisy groundtruth for model training was collected by prompting LLaMA 13B model.

Results

We recruited both experts (board-certified radiologists) and laymen to manually evaluate summaries generated by model. Model-generated summaries rarely missed information as marked by majority opinion of radiologists. Laymen indicated 63% improvement in their understanding by reading layman summaries generated by the model. Comparative study with zero-shot performance of LLaMA indicated that LLaMA hallucinated and missed information 3 and 4 times more often, respectively, than the proposed model.

Discussion

The proposed patient-sensitive summarization model can generate summaries for radiology reports understandable by patients with vastly different levels of medical knowledge. In addition, task-specific training allows for more reliable performance compared to much larger off-the-shelf models.

Conclusions

The proposed model could improve adherence to follow up treatment suggested by radiology reports by increasing patients’ level of understanding of these reports.
SYNERGISTIC ANTITUMOR EFFECT OF NAPROXEN AND SORAFENIB IN HEPATOCELLULAR CARCINOMA
Authors: Akar Etkin , Beyge Seyma Unsal , Kahraman Deniz Cansen
Published: February 2024

Hepatocellular carcinoma (HCC) is one of the most prevalent and deadliest cancer types in the world. Due to the inevitable development of resistance to classical chemotherapy and current targeted therapies, combination therapy became an important strategy. Recently drug repurposing studies have emphasized the potential of non-steroidal anti-inflammatory drugs (NSAIDs) in exhibiting anti-tumor activities in different cancer types, including HCC. In this study we explored the synergistic bioactivity of naproxen in combination with sorafenib in HCC cell lines. Network reconstruction analysis, performed to identify key factors mediating the synergistic therapeutic effects of sorafenib and naproxen revealed apoptosis pathways enriched in both sorafenib and naproxen networks. CAPN2 emerged as the common gene shared between the two networks.In vitrostudies on Huh7 and Mahlavu cells revealed that induction of apoptosis was associated mainly with the PI3K/AKT pathway inhibition. Furthermore, combined treatment of naproxen and sorafenib led to the downregulation of CAPN2 expression, suggesting a potential link to apoptosis and PI3K/AKT pathway regulation, which needs further investigation. In conclusion, combining sorafenib with naproxen presents a promising strategy with potential synergistic therapeutic benefits in HCC.
Limb, not touch location, is coded in 3D space
Authors: Heed Tobias , Burbach Julia , Rödenbeck Nele , Habets Boukje , Fuchs Xaver
Published: February 2024

Skin location of touch is said to be recoded, by default, into a 3D-spatial location. Here, human participants received tactile stimulus pairs on a common or on two different limbs and judged either whether stimuli had occurred on the same limb, or on a common side of space. Misaligning skin and 3D-spatial codes through limb crossing had a stronger effect on spatial than on limb judgments, contradicting the notion that the 3D location of touch is readily available. Additionally, crossing effects were significantly reduced when stimulus pairs lay in a common dermatome, suggesting that limb choice was based on anatomical, not 3D-spatial, stimulus information. These results suggest that it is limbs, not touch, which are coded in 3D space. Commonly observed errors in reporting where touch occurred on the body depend on confusion due to where the touched limb usually resides with the spatial layout of the currently action-relevant limbs.
Substrate Stiffness Reshapes Layer Architecture and Biophysical Features of Human Induced Pluripotent Stem Cells to Modulate their Differentiation Potential
Authors: Llewellyn Jack , Charrier Anne , Helfer Emmanuèle , Dono Rosanna
Published: February 2024

Lineage-specific differentiation of human induced pluripotent stem cells (hiPSCs) relies on complex interactions between biochemical and physical cues. Here we investigated the ability of hiPSCs to undergo lineage commitment in response to inductive signals and assessed how this competence is modulated by substrate stiffness. We showed that Activin A-induced hiPSC differentiation into mesendoderm and its derivative, definitive endoderm is enhanced on gel-based substrates softer than glass. This correlated with changes in tight junction formation and extensive cytoskeletal remodeling. Further, live imaging andin silicostudies suggested changes in cell motility, shape, forces and pressures, underlie hiPSC layer reshaping on soft substrates. Finally, we repurposed an ultra-soft silicone gel, which may provide a suitable substrate for culturing hiPSCs at physiological stiffnesses. Our results provide mechanistic insight into how epithelial mechanics dictate the hiPSC response to chemical signals, and provide a tool for their efficient differentiation in emerging stem cell therapies.
OPA1and disease-causing mutants perturb mitochondrial nucleoid distribution
Authors: Macuada J. , Molina-Riquelme I. , Vidal G. , Pérez-Bravo N. , Vásquez-Trincado C. , Aedo G. , Lagos D. , Horvath R. , Rudge T.J. , Cartes-Saavedra B. , Eisner V.
Published: February 2024

Optic atrophy protein 1 (OPA1) mediates inner mitochondrial membrane (IMM) fusion and cristae organization. Mutations in OPA1 cause autosomal dominant optic atrophy (ADOA), a leading cause of blindness. Cells from ADOA patients show impaired mitochondrial fusion, cristae structure, bioenergetic function, and mitochondrial DNA (mtDNA) integrity. The mtDNA encodes electron transport chain subunits and is packaged into nucleoids spread within the mitochondrial population. Nucleoids interact with the IMM, and their distribution is tightly linked to mitochondrial fusion and cristae shaping. Yet, little is known about the physio-pathological relevance of nucleoid distribution. We studied the effect of OPA1 and ADOA-associated mutants on nucleoid distribution using high-resolution confocal microscopy. We applied a novel model incorporating the mitochondrial context, separating nucleoid distribution into the array in the mitochondrial population and intramitochondrial longitudinal distribution. Opa1-null cells showed decreased mtDNA levels and nucleoid abundance. Also, loss of Opa1 lead to an altered distribution of nucleoids in the mitochondrial population, loss of cristae periodicity, and altered nucleoids to cristae proximity partly rescued by OPA1 isoform 1. Overexpression of WT OPA1 or ADOA-causing mutants c.870+5G>A or c.2713C>T in WT cells, showed perturbed nucleoid array in the mitochondria population associated with cristae disorganization. Opa1-null and cells overexpressing ADOA mutants accumulated mitochondria without nucleoids. Interestingly, intramitochondrial nucleoid distribution was only altered in Opa1-null cells. Altogether, our results highlight the relevance of OPA1 in nucleoid distribution in the mitochondrial landscape and at a single-organelle level and shed light on new components of ADOA etiology.
Hypoxia and TNF-alpha modulate extracellular vesicle release from human induced pluripotent stem cell-derived cardiomyocytes
Authors: Viola Margarida , Bebelman Maarten P. , Maas Renee G. C. , Verweij Frederik J. , Seinen Cor S. , de Jager Saskia C. A. , Vader Pieter , Pegtel D. Michiel , Sluijter Joost P. G.
Published: February 2024

Extracellular vesicles (EVs) have emerged as important mediators of intercellular communication in the heart under homeostatic and pathological conditions, such as myocardial infarction (MI). However, the basic mechanisms driving cardiomyocyte-derived EV (CM-EV) production following stress are poorly understood. In this study, we generated human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) that express NanoLuc-tetraspanin reporters. These modified hiPSC-CMs allow for robust quantification of CM-EV secretion from small numbers of cells without the need for time-consuming EV isolation techniques. We subjected these cells to a panel of small molecules to study their effect on CM-EV biogenesis and secretion under basal and stress-associated conditions. We observed that EV biogenesis is context-dependent in hiPSC-CMs. Nutrient starvation decreases CM-EV secretion while hypoxia increases the production of CM-EVs in a nSmase2-dependent manner. Moreover, the inflammatory cytokine TNF-α increased CM-EV secretion through a process involving NLRP3 inflammasome activation and mTOR signaling. Here, we detailed for the first time the regulatory mechanisms of EV biogenesis in hiPSC-CMs upon MI-associated stressors.
Multiplex Single-Cell Bioprinting for Engineering of Heterogeneous Tissue Constructs with Subcellular Spatial Resolution
Authors: Helms Haylie R. , Oyama Kody A. , Ware Jason P. , Ibsen Stuart D. , Bertassoni Luiz E.
Published: February 2024

Tissue development, function, and disease are largely driven by the spatial organization of individual cells and their cell-cell interactions. Precision engineered tissues with single-cell spatial resolution, therefore, have tremendous potential for next generation disease models, drug discovery, and regenerative therapeutics. Despite significant advancements in biofabrication approaches to improve feature resolution, strategies to fabricate tissues with the exact same organization of individual cells in their native cellular microenvironment have remained virtually non-existent to date. Here we report a method to spatially pattern single cells with up to eight cell phenotypes and subcellular spatial precision. As proof-of-concept we first demonstrate the ability to systematically assess the influence of cellular microenvironments on cell behavior by controllably altering the spatial arrangement of cell types in bioprinted precision cell-cell interaction arrays. We then demonstrate, for the first time, the ability to produce high-fidelity replicas of a patient’s annotated cancer biopsy with subcellular resolution. The ability to replicate native cellular microenvironments marks a significant advancement for precision biofabricated in-vitro models, where heterogenous tissues can be engineered with single-cell spatial precision to advance our understanding of complex biological systems in a controlled and systematic manner.
Quantifying Fit-for-Purpose in Real World Data: Data Grading and FitQ Scores
Authors: Jackson Michael L. , Manickam Raj , Derieg Dan , Gombar Saurabh , Low Yen S
Published: February 2024

Real-world evidence (RWE), derived from analysis of RWD, is increasingly used to guide decisions in drug development, regulatory oversight, and clinical decision-making. Evaluating the fitness-for-purpose of RWD sources is one key component to generating transparent RWE. Here, we demonstrate tools that fill two gaps in the data grading literature. These are the need for quantitative data grading scores, and the need for scoring mechanisms that can be run in automated fashion and at scale. The Real World Data Score (RWDS) rates the overall quality and completeness of a RWD source across a range of customizable metrics. The Fitness Quotient (FitQ) grades how well a specific data source fits a specific RWE query. In concert, these tools give producers and consumers of RWE evidence to assess the quality of the underlying RWD.
Investigation of the Relationship Between Calpain and HMGB1/TLR4/NF-KB Signalling Pathway in Multiple Sclerosis and Other Demyelinating Diseases
Authors: Uluc Firdevs , Turkoglu Sule Aydin , Celik Bihter Gokce , Karabork Seyda , Kayis Seyit Ali
Published: February 2024

Background

To develop more effective treatments for demyelinating diseases, it is essential to identify the associated signaling pathways and factors. The objective of this study was to investigate the possible correlation between Calpain-1 (CAPN1) and Calpain-2 (CAPN2) with the HMGB1/TLR4/NF-κB signaling pathway and to evaluate the influence of these proteins on Interleukin 17A (IL-17A) and Interleukin 37 (IL-37) cytokines in individuals with newly diagnosed and untreated Multiple Sclerosis (MS) and Neuromyelitis Optica Spectrum Disorder (NMOSD).

Methods

In this pilot study, a total of 73 newly diagnosed patients were recruited, including 36 with MS, 9 with NMOSD, and an unhealthy control group composed of 28 individuals with Pseudotumour cerebri (PTC). To ensure accuracy and transparency, all groups’ demographic and clinical characteristics were meticulously described. ELISA technique was utilized to compare levels of CAPN1, CAPN2, HMGB1, TLR4, and NF-KB, as well as IL-17A and IL-37 cytokines, between the case and the unhealthy control groups. The expectation from these findings is to provide valuable insights into the pathophysiological mechanisms of these neurological disorders, possibly opening the door to novel therapeutic perspectives.

Results

In patients with MS, the levels of CAPN1 were found to be higher than those in patients with NMOSD and PTC. Similarly, the level of CAPN2 was significantly higher in patients with MS than in patients with NMOSD and higher in patients with PTC than in patients with NMOSD. There were no differences in the levels of HMGB1, TLR4, NF-κB, IL-17A, and IL-37 between the groups. Age and gender did not affect any of the parameters. In the MS group, both CAPN1 and CAPN2 showed positive correlation with HMGB1, TLR4, and NF-κB levels.

Conclusions

It may be suggested that CAPN1 may exhibit greater efficacy than CAPN2 during the initial stages of neuroinflammation. To obtain deeper and more guiding results of the varying levels of CAPN1 and CAPN2, and their relationship with the HMGB1/TLR4/NF-κB signaling pathway, it is advisable to conductin-vivoandin-vitroprospective studies featuring CAPN1-specific inhibitors with larger study groups.
Tumor-derived hypoxic small extracellular vesicles promote endothelial cell migration and tube formation via ALS2/Rab5/β-catenin signaling
Authors: Silva Patricio , Hernández Nadia , Tapia Héctor , Gaete-Ramírez Belén , Flores Tania , Herrera Daniela , Cáceres-Verschae Albano , Varas-Godoy Manuel , Torres Vicente A.
Published: February 2024

Tumor hypoxia has been associated with cancer progression, angiogenesis, and metastasis via modifications in the release and cargo composition of extracellular vesicles secreted by tumor cells. Indeed, hypoxic extracellular vesicles are known to trigger a variety of angiogenic responses via different mechanisms. We recently showed that hypoxia promotes endosomal signaling in tumor cells via HIF-1α-dependent induction of the guanine exchange factor ALS2, which activates Rab5, leading to downstream events involved in cell migration and invasion. Since Rab5-dependent signaling is required for endothelial cell migration and angiogenesis, we explored the possibility that hypoxia promotes the release of small extracellular vesicles containing ALS2, which in turn activate Rab5 in recipient endothelial cells leading to pro-angiogenic properties. In doing so, we found that hypoxia promoted ALS2 expression and incorporation as cargo within small extracellular vesicles, leading to subsequent transfer to recipient endothelial cells, promoting cell migration, tube formation and downstream Rab5 activation. Consequently, ALS2-containing small extracellular vesicles increased early endosome size and number in recipient endothelial cells, which was followed by subsequent sequestration of components of the β-catenin destruction complex within endosomal compartments, leading to stabilization and nuclear localization of β-catenin. These events converged in the expression of β-catenin target genes involved in angiogenesis. Knockdown of ALS2 in donor-tumor cells, which precluded its incorporation into small extracellular vesicles, prevented Rab5-downstream events and endothelial cell responses, which depended on Rab5 activity and guanine exchange factor activity of ALS2. These findings indicate that vesicular ALS2, secreted in hypoxia, promotes endothelial cell events leading to angiogenesis. Finally, these events might explain how tumor angiogenesis proceeds in hypoxic conditions.
High Shear Stress Reduces ERG Causing Endothelial-Mesenchymal Transition and Pulmonary Arterial Hypertension
Authors: Shinohara Tsutomu , Moonen Jan-Renier , Chun Yoon Hong , Lee-Yow Yannick C. , Okamura Kenichi , Szafron Jason M. , Kaplan Jordan , Cao Aiqin , Wang Lingli , Taylor Shalina , Isobe Sarasa , Dong Melody , Yang Weiguang , Guo Katherine , Franco Benjamin D , Pacharinsak Cholawat , Pisani Laura J. , Saitoh Shinji , Mitani Yoshihide , Marsden Alison L. , Engreitz Jesse M. , Körbelin Jakob , Rabinovitch Marlene
Published: February 2024

Pathological high shear stress (HSS, 100 dyn/cm2) is generated in distal pulmonary arteries (PA) (100-500 μm) in congenital heart defects and in progressive PA hypertension (PAH) with inward remodeling and luminal narrowing. Human PA endothelial cells (PAEC) were subjected to HSS versus physiologic laminar shear stress (LSS, 15 dyn/cm2). Endothelial-mesenchymal transition (EndMT), a feature of PAH not previously attributed to HSS, was observed. H3K27ac peaks containing motifs for an ETS-family transcription factor (ERG) were reduced, as was ERG-Krüppel-like factors (KLF)2/4 interaction and ERG expression. Reducing ERG by siRNA in PAEC during LSS caused EndMT; transfection of ERG in PAEC under HSS prevented EndMT. An aorto-caval shunt was preformed in mice to induce HSS and progressive PAH. Elevated PA pressure, EndMT and vascular remodeling were reduced by an adeno-associated vector that selectively replenished ERG in PAEC. Agents maintaining ERG in PAEC should overcome the adverse effect of HSS on progressive PAH.
Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment
Authors: Leech Vivienne , Kenny Fiona N , Marcotti Stefania , Shaw Tanya J , Stramer Brian M , Manhart Angelika
Published: February 2024

Collective alignment of cell populations is a commonly observed phenomena in biology. An important example are aligning fibroblasts in healthy or scar tissue. In this work we derive and simulate a mechanistic agent-based model of the collective behaviour of actively moving and interacting cells, with a focus on understanding collective alignment. The derivation strategy is based on energy minimisation. The model ingredients are motivated by data on the behaviour of different populations of aligning fibroblasts and include: Self-propulsion, overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces. We find that there is an optimal ratio of self-propulsion speed and overlap avoidance that maximises collective alignment. Further we find that deformability aids alignment, and that cell-cell junctions by themselves hinder alignment. However, if cytoskeletal forces are transmitted via cell-cell junctions we observe strong collective alignment over large spatial scales.
The Recurrent Temporal Restricted Boltzmann Machine Captures Neural Assembly Dynamics in Whole-Brain Activity
Authors: Quiroz Monnens Sebastian , Peters Casper , Hesselink Luuk Willem , Smeets Kasper , Englitz Bernhard
Published: February 2024

Animal behaviour alternates between stochastic exploration and goal-directed actions, which are generated by the underlying neural dynamics. Previously, we demonstrated that the compositional Restricted Boltzmann Machine (cRBM) can decompose whole-brain activity of larval zebrafish data at the neural level into a small number (∼100-200) of assemblies that can account for the stochasticity of the neural activity (van der Plas et al., eLife, 2023). Here we advance this representation by extending to a combined stochastic-dynamical representation to account for both aspects using the Recurrent Temporal RBM (RTRBM) and transfer-learning based on the cRBM estimate. We demonstrate that the functional advantage of the RTRBM is captured in the temporal weights on the hidden units, representing neural assemblies, for both simulated and experimental data. Our results show that the temporal expansion outperforms the stochastic-only cRBM in terms of generalisation error and achieves a more accurate representation of the moments in time. Lastly, we demonstrate that we can identify the original time-scale of assembly dynamics by estimating multiple RTRBMs at different temporal resolutions. Together, we propose that RTRBMs are a valuable tool for capturing the combined stochastic and time-predictive dynamics of large-scale data sets.
Prefrontal cortex temporally multiplexes slow and fast dynamics in value learning and memory
Authors: Hashemirad Seyed Reza , Abbaszadeh Mojtaba , Ghazizadeh Ali
Published: February 2024

Previous studies have revealed segregated circuitries in basal ganglia for fast learning that enables value adaptability and slow forgetting which underlies stable value memories. However, the mechanisms mediating the conflict between value adaptability vs stability remain unknown. Using a reinforcement learning paradigm involving a brief value reversal for objects with previously stable values, we predicted and confirmed a novel behavioral manifestation of the conflict between adaptability vs stability namely the spontaneous recovery of old values in macaque monkeys. Furthermore, we found that individual neurons in ventrolateral prefrontal cortex (vlPFC) temporally multiplexed slow and fast processes in their early and late responses to objects. The local field potential in vlPFC also reflected the two-rate system. These findings implicate vlPFC as a plexus for the interactions between adaptability vs stability in reinforcement learning and suggest spontaneous recovery of past values caused by a two-rate system to mediate relapse to old habits.
Microgroove substrates unveil topography-driven, dynamic 3D nuclear deformations
Authors: Leclech Claire , Roellinger Bettina , Frederick Joni , Mamchaoui Kamel , Coirault Catherine , Barakat Abdul I.
Published: February 2024

Navigating complex extracellular environments requires extensive deformation of cells and their nuclei. Nuclear deformations are intricately linked to nuclear structure and mechanical properties, and abnormalities in nuclear mechanics contribute to various diseases including laminopathies and cancer. Mostin vitrosystems used to study nuclear deformations are typically designed to generate strong whole-cell confinement relevant for specific cell types such as immune or cancer cells. Here, we use microgroove substrates as a model of anisotropic basement membrane topography and we report that adherent cells including endothelial cells and myoblasts exhibit significant 3D (in-plane and out-of-plane) nuclear deformations, with partial to complete penetration into the microgrooves. These deformations are dynamic with nuclei cyclically entering and exiting the microgrooves. AFM measurements show that these deformation cycles are accompanied by transient changes in nuclear mechanical properties. We also show that nuclear penetration into the grooves is principally driven by cell-substrate adhesion, without the need for cytoskeleton-associated forces. Finally, we demonstrate that myoblasts from patients withLMNAmutations exhibit abnormal nuclear deformations which can be rapidly identified and quantified using automated image analysis. We therefore propose the use of microgrooves as a novel simple, tunable, and high throughput system to study nuclear deformations in adherent cells, with the potential to serve as a functional diagnostic platform for pathological alterations in nuclear mechanics.
BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III
Authors: Chen Brandon , Stark Drew C. , Jadhav Pankaj V. , Lynn-Nguyen Theophilus M. , Halligan Benjamin S. , Rossiter Nicholas J. , Sindoni Nicole , Shin Myunsun , Paulo Joao A. , Chang Matthew , Koo Imhoi , Koshkin Sergei , Eyunni Sanjana , Ronchi Paolo , Paulsen Michelle T. , Morlacchi Pietro , Hanna David A. , Lin Jason , Guerra Rachel M. , Pagliarini David J. , Banerjee Ruma , Parolia Abhijit , Ljungman Mats E. , Patterson Andrew D. , Mancias Joseph D. , Mosalaganti Shyamal , Sexton Jonathan Z. , Calì Tito , Lyssiotis Costas A. , Shah Yatrik M.
Published: February 2024

Inter-organellar communication is critical for cellular metabolic homeostasis. One of the most abundant inter-organellar interactions are those at the endoplasmic reticulum and mitochondria contact sites (ERMCS). However, a detailed understanding of the mechanisms governing ERMCS regulation and their roles in cellular metabolism are limited by a lack of tools that permit temporal induction and reversal. Through unbiased screening approaches, we identified fedratinib, an FDA-approved drug, that dramatically increases ERMCS abundance by inhibiting the epigenetic modifier BRD4. Fedratinib rapidly and reversibly modulates mitochondrial and ER morphology and alters metabolic homeostasis. Moreover, ERMCS modulation depends on mitochondria electron transport chain complex III function. Comparison of fedratinib activity to other reported inducers of ERMCS revealed common mechanisms of induction and function, providing clarity and union to a growing body of experimental observations. In total, our results uncovered a novel epigenetic signaling pathway and an endogenous metabolic regulator that connects ERMCS and cellular metabolism.
Single-cell and bulk transcriptional profiling of mouse ovaries reveals novel genes and pathways associated with DNA damage response in oocytes
Authors: Mills Monique , Emori Chihiro , Kumar Parveen , Boucher Zachary , George Joshy , Bolcun-Filas Ewelina
Published: February 2024

Immature oocytes enclosed in primordial follicles stored in female ovaries are under constant threat of DNA damage induced by endogenous and exogenous factors. Checkpoint kinase 2 (CHEK2) is a key mediator of the DNA damage response in all cells. Genetic studies have shown that CHEK2 and its downstream targets, p53 and TAp63, regulate primordial follicle elimination in response to DNA damage, however the mechanism leading to their demise is still poorly characterized. Single-cell and bulk RNA sequencing were used to determine the DNA damage response in wildtype andChek2-deficient ovaries. A low but oocyte-lethal dose of ionizing radiation induces a DNA damage response in ovarian cells that is solely dependent on CHEK2. DNA damage activates multiple ovarian response pathways related to apoptosis, p53, interferon signaling, inflammation, cell adhesion, and intercellular communication. These pathways are differentially employed by different ovarian cell types, with oocytes disproportionately affected by radiation. Novel genes and pathways are induced by radiation specifically in oocytes, shedding light on their sensitivity to DNA damage, and implicating a coordinated response between oocytes and pre-granulosa cells within the follicle. These findings provide a foundation for future studies on the specific mechanisms regulating oocyte survival in the context of aging, as well as therapeutic and environmental genotoxic exposures.
A genome-wide screen links peroxisome regulation with Wnt signaling through RNF146 and tankyrase
Authors: Vu Jonathan T. , Tavasoli Katherine U. , Mandjikian Lori , Sheedy Connor J. , Bacal Julien , Morrissey Meghan A. , Richardson Chris D. , Gardner Brooke M.
Published: February 2024

Peroxisomes are membrane-bound organelles harboring metabolic enzymes. In humans, peroxisomes are required for normal development, yet the genes regulating peroxisome function remain unclear. We performed a genome-wide CRISPRi screen to identify novel factors involved in peroxisomal homeostasis. We found that inhibition of RNF146, an E3 ligase activated by poly(ADP-ribose), reduced the import of proteins into peroxisomes. RNF146-mediated loss of peroxisome import depended on the stabilization and activity of the poly(ADP-ribose) polymerase tankyrase, which binds the peroxisomal membrane protein PEX14. We propose that RNF146 and tankyrase regulate peroxisome import efficiency by PARsylation of proteins at the peroxisome membrane. Interestingly, we found that the loss of peroxisomes increased tankyrase and RNF146-dependent degradation of non-peroxisomal substrates, including the beta-catenin destruction complex component AXIN1, which was sufficient to alter the amplitude of beta-catenin transcription. Together, these observations not only suggest previously undescribed roles for RNF146 in peroxisomal regulation, but also a novel role in bridging peroxisome function with Wnt/beta-catenin signaling during development.
APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census
Authors: Wenk Elizabeth , Cornwell William , Fuchs Anne , Kar Fonti , Monro Anna , Sauquet Hervé , Stephens Ruby , Falster Daniel S
Published: February 2024

Here we present “APCalign”, an R package and accompanying browser-sourced application to align and update scientific names for Australian vascular plants to the most likely currently accepted name using the Australian Plant Census (APC) or a name in the Australian Plant Names Index (APNI). Scientific names are the label assigned to unique taxon concepts by the scientific community, but this common terminology is most useful if a taxon concept is consistently referred to by the same name. These links can be broken due to either spelling mistakes or taxonomic changes. Automated tools are required to resolve taxon lists, aligning and updating long lists of possibly erroneous scientific names to the most likely currently accepted names. It is essential that tools specific to the APC/APNI be developed, as these lists specify an endorsed national-level nomenclature used in government legislation and include the uniquely Australian concept of phrase names, absent in global taxonomic datasets. To align input names to names within the APC or APNI, “APCalign” works progressively through a sequence of checks that combine different permutations of the input name, exact versus fuzzy matches, matches that consider the entire name input versus a subset of words, and character strings that indicate a name can only be resolved to a genus or family. The aligned names are then, when possible, updated to a currently accepted taxon concept within the APC. This package should facilitate all research outputs that require diverse scientific name lists to be merged or outdated lists to be updated.
Long-term gut colonization with ESBL-producingEscherichia coliin participants without known risk factors from the southeastern United States
Authors: Garcia Coralis Rodriguez , Norfolk William A. , Howard Amanda K. , Glatter Amanda L. , Beaudry Megan S. , Mallis Nicholas A. , Welton Michael , Glenn Travis C. , Lipp Erin K. , Ottesen Elizabeth A.
Published: February 2024

We evaluated gut carriage of extended spectrum beta lactamase producingEnterobacteriaceae(ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, which found carriage rates of 2.5-3.9% in healthy U.S. residents.

All ESBL-E confirmed isolates (n=25) were identified asEscherichia coli. Isolates belonged to 11 sequence types, with 48% classified as ST131. Ninety six percent of ESBL-E isolates carried ablaCTX-Mgene. Isolated ESBL-Es frequently carried virulence genes as well as multiple classes of antibiotic resistance genes. Long-term colonization was common, with 64% of ESBL-E positive participants testing positive when rescreened three months later. One participant yielded isolates belonging to two differentE. colisequence types that carriedblaCTX-M-1genes on near-identical plasmids, suggesting intra-gut plasmid transfer.

Isolation ofE. colion media without antibiotics revealed that ESBL-E. colitypically made up a minor fraction of the overall gutE. colipopulation, although in some cases they were the dominant strain. ESBL-E carriage was not associated with a significantly different stool microbiome composition. However, some microbial taxa were differentially abundant in ESBL-E carriers. Together, these results suggest that a small subpopulation of US residents are long-term, asymptomatic carriers of ESBL-Es, and may serve as an important reservoir for community spread of these ESBL genes.

Importance

Antibiotic resistant bacteria, especiallyEnterobacteriaceaecarrying ESBLs, have become an increasing public health threat. Increasing numbers of community-associated infections (47% of ESBL-E infections in the U.S.) in participants without healthcare exposure is particularly concerning. This study found that 4.5% of a southeastern United States study population, without in-patient healthcare exposure, were asymptomatically colonized with ESBL-E, and 64% of ESBL-E positive participants were still positive when rescreened 3 months later. This suggests that the gut microbiome of healthy participants may represent an understudied community reservoir of ESBL genes and ESBLEscherichia coliin the U.S.
Metatranscriptomic analysis of wastewater sites reveals a high abundance of antimicrobial resistance genes from hospital wastewater
Authors: Musundi Sebastian , Ng’ang’a Samuel , Wanjiru Esther Wangui , Sagoe Kate , Wandera Ernest , Kanoi Bernard , Gitaka Jesse
Published: February 2024

Objective

This study analyzed the metatranscriptome of wastewater samples from different sites with a focus of identifying antibiotic resistance genes and the bacterial community.

Methods

Twenty-four wastewater samples were collected from a hospital, university sewer, and the influent and effluent of a wastewater treatment plant (WWTP). The metatranscriptome was sequenced to identify antimicrobial resistance genes (ARGs), mobile genetic elements, and bacterial community composition.

Results

Metatranscriptome analysis revealed varying abundances of ARG transcripts across different sites, with 84, 27, 14, and 9 ARG transcripts identified in wastewater collected from the hospital, university, influent, and effluent of a WWTP, respectively. Notably, hospital wastewater contained clinically relevant beta-lactam ARGs, includingbla-NDM-1and severalblaOXAtranscripts. Four core ARGs, against sulfonamidessul1andsul2and aminoglycosidesaph(6)-ldandaph(’3’)-lbwere also identified. The predominant bacterial community comprised ofGammaproteobacteria,with priority pathogens likeNeisseria gonorrheaandHelicobacter pyloripresent in hospital wastewater and WWTP influent.

Conclusion

These findings provide insights into the wastewater resistome and how meta-transcriptomic data can be utilized for the surveillance of antibiotic resistance. Overall, our study highlights the utility of wastewater surveillance in understanding and addressing the dissemination of antibiotic resistance and emphasizes the crucial role of proper wastewater management in protecting public and environmental health.
Improving rice drought tolerance through host-mediated microbiome selection
Authors: Styer Alex , Pettinga Dean , Caddell Daniel , Coleman-Derr Devin
Published: February 2024

Plant microbiome engineering remains a significant challenge due to challenges associated with accurately predicting microbiome assembly and function in complex, heterogeneous soil environments. However, host-mediated selection can simplify the process by using plant host phenotype as a reporter of microbiome function; by iteratively selecting microbiomes from hosts with desired phenotypes and using them to inoculate subsequent cohorts of hosts, artificial selection can steer the microbiome towards a composition producing optimized plant phenotypes. In this study, we inoculated rice with wild microbial communities from fallow rice field, desert, and serpentine seep field soils. By challenging these plants with drought and iteratively selecting microbiomes from the least drought stressed plants across multiple generations, we derived simplified microbiomes that enhanced both the growth and drought tolerance of rice. Across selection cycles, microbiomes within and between soil treatments became increasingly similar, implicating both dispersal and selection as drivers of community composition. With amplicon sequencing data we identified specific bacterial taxa associated with improved rice drought phenotypes; while many of these taxa have been previously described as plant growth promoters, we also identified novel taxa exhibiting strong positive correlation with improved drought performance. Lastly, we resolved 272 metagenome-assembled genomes (MAGs) and used these MAGs to identify functions enriched in bacteria driving enhanced drought tolerance. The most significantly enriched functions—particularly glycerol-3-phosphate and iron transport—have been previously implicated as potential mediators of plant-microbe interactions during drought. Altogether, these data demonstrate that host-mediated selection provides an efficient framework for microbiome engineering through the identification of both individual taxa and simplified communities associated with enhanced plant phenotypes.
P. aeruginosatRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in Cystic Fibrosis
Authors: Li Zhongyou , Barnaby Roxanna , Nymon Amanda , Roche Carolyn , Koeppen Katja , Ashare Alix , Hogan Deborah A. , Gerber Scott A. , Taatjes Douglas J. , Hampton Thomas H. , Stanton Bruce A.
Published: February 2024

Although tobramycin increases lung function in people with cystic fibrosis (pwCF), the density ofPseudomonas aeruginosa (P. aeruginosa)in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves lung function is not completely understood. Here, we demonstrate that tobramycin increases 5′ tRNA-fMet halves in outer membrane vesicles (OMVs) secreted by laboratory and CF clinical isolates ofP. aeruginosa. The 5′ tRNA-fMet halves are transferred from OMVs into primary CF human bronchial epithelial cells (CF-HBEC), decreasing OMV-induced IL-8 and IP-10 secretion. In mouse lung, increased expression of the 5′ tRNA-fMet halves in OMVs attenuated KC secretion and neutrophil recruitment. Furthermore, there was less IL-8 and neutrophils in bronchoalveolar lavage fluid isolated from pwCF during the period of exposure to tobramycin versus the period off tobramycin. In conclusion, we have shown in mice andin vitrostudies on CF-HBEC that tobramycin reduces inflammation by increasing 5′ tRNA-fMet halves in OMVs that are delivered to CF-HBEC and reduce IL-8 and neutrophilic airway inflammation. This effect is predicted to improve lung function in pwCF receiving tobramycin forP. aeruginosainfection.

New and noteworthy

The experiments in this report identify a novel mechanim whereby tobramycin reduces inflammation in two models of CF. Tobramycin increased the secretion of tRNA-fMet haves in OMVs secreted byP. aeruginiosa, which reduced the OMV-LPS induced inflammatory response in primary cultures of CF-HBEC and in mouse lung, an effect predicted to reduce lung damage in pwCF.

Graphical abstract

The anti-inflammatory effect of tobramycin mediated by 5′ tRNA-fMet halves secreted inP. aeruginosaOMVs.(A)P. aeruginosacolonizes the CF lungs and secrets OMVs. OMVs diffuse through the mucus layer overlying bronchial epithelial cells and induce IL-8 secretion, which recruits neutrophils that causes lung damage. (B) Tobramycin increases 5′ tRNA-fMet halves in OMVs secreted byP. aeruginosa. 5′ tRNA-fMet halves are delivered into host cells after OMVs fuse with lipid rafts in CF-HBEC and down-regulate protein expression of MAPK10, IKBKG, and EP300, which suppresses IL-8 secretion and neutrophils in the lungs. A reduction in neutrophils in CF BALF is predicted to improve lung function and decrease lung damage.
Genomic and environmental controls onCastellaniellabiogeography in an anthropogenically disturbed subsurface
Authors: Goff Jennifer L. , Szink Elizabeth G. , Durrence Konnor L. , Lui Lauren M. , Nielsen Torben N. , Kuehl Jennifer V. , Hunt Kristopher A. , Chandonia John-Marc , Huang Jiawen , Thorgersen Michael P. , Poole Farris L. , Stahl David A. , Chakraborty Romy , Deutschbauer Adam M. , Arkin Adam P. , Adams Michael W. W.
Published: February 2024

Castellaniellaspecies have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of theCastellaniellagenus concurrent to increased denitrification rates. Thus, we asked how genomic and abiotic factors control theCastellaniellabiogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. ORRCastellaniellastrains showed a higher degree of genetic diversification than those originating from non-ORR sites, which we attribute to the multitude of extreme stressors faced in the ORR subsurface. We report the isolation and characterization of severalCastellaniellastrains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to twoCastellaniellaamplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least two decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.
Time resolved multi-omics reveals diverse metabolic strategies ofSalmonelladuring diet-induced inflammation
Authors: Kokkinias Katherine , Sabag-Daigle Anice , Kim Yongseok , Leleiwi Ikaia , Shaffer Michael , Kevorkian Richard , Daly Rebecca A. , Wysocki Vicki H. , Borton Mikayla A. , Ahmer Brian M. M. , Wrighton Kelly C.
Published: February 2024

With a rise in antibiotic resistance and chronic infection, the metabolic response ofSalmonella entericaserovar Typhimurium to various dietary conditions over time remains an understudied avenue for novel, targeted therapeutics. Elucidating how enteric pathogens respond to dietary variation not only helps us decipher the metabolic strategies leveraged for expansion but also assists in proposing targets for therapeutic interventions. Here, we use a multi-omics approach to identify the metabolic response ofSalmonella entericaserovar Typhimurium in mice on both a fibrous diet and high-fat diet over time. When comparingSalmonellagene expression between diets, we found a preferential use of respiratory electron acceptors consistent with increased inflammation of the high-fat diet mice. Looking at the high-fat diet over the course of infection, we noticed heterogeneity of samples based onSalmonellaribosomal activity, which separated into three infection phases: early, peak, and late. We identified key respiratory, carbon, and pathogenesis gene expression descriptive of each phase. Surprisingly, we identified genes associated with host-cell entry expressed throughout infection, suggesting sub-populations ofSalmonellaor stress-induced dysregulation. Collectively, these results highlight not only the sensitivity ofSalmonellato its environment but also identify phase-specific genes that may be used as therapeutic targets to reduce infection.

Importance

Identifying novel therapeutic strategies forSalmonellainfection that occur in relevant diets and over time is needed with the rise of antibiotic resistance and global shifts towards Western diets that are high in fat and low in fiber. Mice on a high-fat diet are more inflamed compared to those on a fibrous diet, creating an environment that results in more favorable energy generation forSalmonella. Over time on a high-fat diet, we observed differential gene expression across infection phases. Together, these findings reveal the metabolic tuning ofSalmonellato dietary and temporal perturbations. Research like this, exploring the dimensions of pathogen metabolic plasticity, can pave the way for rationally designed strategies to control disease.