bluuebunny/crossref_metadata_2025 huggingface dataset:
Call Me Dr. Ishmael: Trends in Electronic Health Record Notes Available at ED Visits and Admissions
Authors: Patterson Brian W. , Hekman Daniel J , Liao Frank , Hamedani Azita , Shah Manish N. , Afshar Majid
Published: February 2024

Objective

Numerous studies have identified information overload as a key issue for electronic health records (EHRs). This study describes the amount of text data across all notes available to emergency physicians in the EHR, trended over the time since EHR establishment.

Materials and Methods

We conducted a retrospective analysis of EHR data from a large healthcare system, examining the number of notes and corresponding number of total words and total tokens across all notes available to physicians during patient encounters in the emergency department (ED). We assessed the change in these metrics over a 17-year period between 2006 and 2023.

Results

The study cohort included 730,968 ED visits made by 293,559 unique patients and a total note count of 132,574,964. The median note count for all encounters in 2006 was 7 (IQR: 3 - 18), accounting for 1,894 words (IQR: 538 - 5,864). By the last full year of the study period in 2022, the median number of notes had grown to 380 (IQR: 93 - 1,008), representing 61,591 words (IQR: 13,621 - 174,152). Note and word counts were higher for admitted patients.

Conclusion

The volume of notes available for review by providers has increased by over 30-fold in the 17 years since the implementation of the EHR at a large health system. The task of reviewing these notes has become correspondingly more difficult. These data point to the critical need for new strategies and tools for filtering, synthesizing, and summarizing information to achieve the promise of the medical record.
A Cost-effectiveness analysis of Nivolumab plus chemotherapy for the first-line treatment of locally advanced or metastatic gastric/GEJ/oesophageal adenocarcinoma in the United States of America
Authors: Zhou Jin , Tang Yukai , Li Geli
Published: February 2024

Background

Nivolumab in combination with chemotherapy significantly improves survival in patients with gastric/gastroesophageal junction (G/GEJ)/esophageal adenocarcinoma.The purpose of this study was to evaluate the cost-effectiveness of Nivolumab plus chemotherapy for G/GEJ/esophageal adenocarcinoma.

Methods

A Markov model was developed on the basis of the US healthcare payers’ perspectives. We estimated the costs and summarised their effectiveness as quality-adjusted life-years (QALYs). One-way and probabilistic sensitivity analyses were conducted to explore the impact of uncertainties on the cost-effectiveness’s results.

Results

The incremental cost-effectiveness ratios (ICER) for Nivolumab plus chemotherapy($149636.97,1.24QALYs) verus chemotherapy($13941.06,0.75QALYs) is $135695.91 and the QALYs is 0.49.

Conclusions

Evidence suggests that Nivolumab plus chemotherapy a for the first-line treatment of locally advanced or metastatic gastric/GEJ/oesophageal adenocarcinoma may be not a cost-effective choice.
“If I am free from diabetes, that itself will be the happiest thing”: A convergent mixed methods study of the lived experiences of young adults with type 2 diabetes in Mysore district, India
Authors: Gopisetty Nikhita R. , Muralidhar Kiranmayee , Ningaiah Nagalambika , Chinnappa Rani , Buono Mia , Jaykrishna Poornima , Madhivanan Purnima , Ariely Sumedha G. , Puffer Eve S.
Published: February 2024

Type 2 diabetes (T2D) has been occurring at younger ages of onset around the world. India’s population accounts for nearly 20% of the global disease burden. This study investigated the occurrence of depressive symptoms and qualitatively explored the lived experiences of 20 young adults living with T2D under the age of 35. We conducted a convergent mixed-methods study with the Patient Health Questionnaire (PHQ-9) and semi-structured interviews from June 2022 to July 2022 in Mysore district, India. Guided by the World Health Organization’s Commission on Social Determinants of Health conceptual framework and biopsychosocial frameworks, areas of inquiry included knowledge and perception about T2D, accessibility of healthcare resources, T2D-related self-care activities, and the impact of the condition on their daily life. Interviews were debriefed by the research team and analyzed thematically using NVivo 12. Participants were aged between 21 and 35 (mean: 30.8, SD: 4.2) and the majority were female (75%). Overall, 55% reported mild depression symptoms, 15% reported moderate to moderately severe depression symptoms; 5 participants (25%) reported suicidality. Sex, living in rural Mysore district, socioeconomic status, T2D duration, family history of T2D, T2D-induced complications, and T2D-related self-care behaviors were associated with depressive symptoms. Thematic analysis revealed 1) low knowledge about T2D, 2) substantial interpersonal and internalized stigma for having T2D at a young age, 3) financial and time constraints to seek and receive care, 4) self-perception as burdens to family members due to the cost and stress of living with T2D, 5) competing priorities with work and family, and 6) the power of social support in managing T2D. These themes were consistent across the sample, regardless of severity of depressive symptoms. Awareness campaigns and peer support programs may help reduce depressive symptoms and increase self-efficacy in this population.
Quantitative Characterization of Retinal Features in Translated OCTA
Authors: Badhon Rashadul Hasan , Thompson Atalie Carina , Lim Jennifer I. , Leng Theodore , Alam Minhaj Nur
Published: February 2024

Purpose

This study explores the feasibility of using generative machine learning (ML) to translate Optical Coherence Tomography (OCT) images into Optical Coherence Tomography Angiography (OCTA) images, potentially bypassing the need for specialized OCTA hardware.

Methods

The method involved implementing a generative adversarial network framework that includes a 2D vascular segmentation model and a 2D OCTA image translation model. The study utilizes a public dataset of 500 patients, divided into subsets based on resolution and disease status, to validate the quality of TR-OCTA images. The validation employs several quality and quantitative metrics to compare the translated images with ground truth OCTAs (GT-OCTA). We then quantitatively characterize vascular features generated in TR-OCTAs with GT-OCTAs to assess the feasibility of using TR-OCTA for objective disease diagnosis.

Result

TR-OCTAs showed high image quality in both 3 and 6 mm datasets (high-resolution, moderate structural similarity and contrast quality compared to GT-OCTAs). There were slight discrepancies in vascular metrics, especially in diseased patients. Blood vessel features like tortuosity and vessel perimeter index showed a better trend compared to density features which are affected by local vascular distortions.

Conclusion

This study presents a promising solution to the limitations of OCTA adoption in clinical practice by using vascular features from TR-OCTA for disease detection.

Translation relevance

This study has the potential to significantly enhance the diagnostic process for retinal diseases by making detailed vascular imaging more widely available and reducing dependency on costly OCTA equipment.
Physiological effects of dual target DBS in an individual with Parkinson’s Disease and a sensing-enabled pulse generator
Authors: Cummins Daniel D. , Sandoval-Pistorius Stephanie S. , Cernera Stephanie , Fernandez-Gajardo Rodrigo , Hammer Lauren , Starr Philip A.
Published: February 2024

Introduction

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) or globus pallidus (GP) is an established therapy for Parkinson’s disease (PD). Novel DBS devices can record local field potential (LFP) physiomarkers from the STN or GP. While beta (13-30 Hz) and gamma (40-90 Hz) STN and GP LFP oscillations correlate with PD motor severity and with therapeutic effects of treatments, STN-GP interactions in electrophysiology in patients with PD are not well characterized.

Methods

Simultaneous bilateral STN and GP LFPs were recorded in a patient with PD who received bilateral STN-DBS and GP-DBS. Power spectra in each target and STN-GP coherence were assessed in various ON- and OFF-levodopa and DBS states, both at rest and with voluntary movement.

Results

OFF-levodopa and OFF-DBS, beta peaks were present at bilateral STN and GP, coincident with prominent STN-GP beta coherence. Levodopa and dual-target-DBS (simultaneous STN-DBS and GP-DBS) completely suppressed STN-GP coherence. Finely-tuned gamma (FTG) activity at half the stimulation frequency (62.5Hz) was seen in the STN during GP-DBS at rest. To assess the effects of movement on FTG activity, we recorded LFPs during instructed movement. We observed FTG activity in bilateral GP and bilateral STN during contralateral body movements while on GP-DBS and ON-levodopa. No FTG was seen with STN-DBS or dual-target-DBS.

Conclusion

Dual-target-DBS and levodopa suppressed STN-GP coherence. FTG throughout the basal ganglia was induced by GP-DBS in the presence of levodopa and movement. This bilateral STN-FTG and GP-FTG corresponded with the least severe bradykinesia state, suggesting a pro-kinetic role for FTG.
Enhancing Mental Health Condition Detection on Social Media through Multi-Task Learning
Authors: Liu Jiawen , Su Menglu
Published: February 2024

Objective

Mental health conditions are traditionally modeled individually, which ignores the complex, interconnected nature of mental health disorders, which often share overlapping symptoms. This study aims to develop an integrated multi-task learning framework to enhance the detection of mental health conditions.

Method

Utilizing datasets from Reddit’s SuicideWatch and Mental Health Collection (SWMH) and Psychiatric-disorder Symptoms (PsySym), the study develops a BERT-based multi-task learning framework. This framework leverages pre-trained embedding layers of BERT variants to capture linguistic nuances relevant to various mental health conditions from social media narratives. The approach is tested against the two datasets, comparing multitask modeling with a wide array of single-task baselines and large language models (LLM).

Results

The multi-task learning framework demonstrated higher performance in efficiently predicting mental health conditions together compared to single-task models and general-purpose LLMs. Specifically, the framework achieved higher F1 scores across multiple conditions, with notable improvements in recall and precision metrics. This indicates more accurate modeling of mental health disorders when considered together, rather than in isolation.

Conclusion

The study confirms the effectiveness of a multi-task learning approach in enhancing the detection of mental health conditions from social media data. It sets a new precedent in computational psychiatry and suggests future explorations into multi-task frameworks for deeper insights into mental health disorders.
Food Fermentation in Space Is Possible, Distinctive, and Beneficial
Authors: Coblentz Maggie , Evans Joshua D. , Kothe Caroline Isabel , Mak Tiffany , Valeron Nabila Rodriguez , Chwalek Patrick , Wejendorp Kim , Garg Shilpa , Pless Louisa , Mak Sarah , Sörensen Pia M. , Jahn Leonie Johanna , Ekblaw Ariel
Published: February 2024

Space exploration is expanding, which demands new technologies and enables new scientific questions. Food, as a bridge between disciplines, can bring these fundamental and applied goals together. Here we investigate whether food fermentation in space is possible, and if so, how it compares with fermentation on Earth. We fermented a miso, a traditional Japanese condiment, on the International Space Station over 30 days, and compared it with two earthbound controls. Using a specially-built environmental sensing box, we gathered metadata for temperature, relative humidity, pressure, and radiation. We analyzed the three misos with shotgun metagenomics to investigate the microbial communities’ composition and safety; whole genome sequencing to investigate the mutation rate ofAspergillus oryzae; untargeted metabolomics to quantify aromatic compounds, amino acids and organic acids; colorimetry to quantify color; and sensory analysis to describe the misos’ flavours and quantify liking and sensory difference. Across these datasets, we found that overall, the space miso is recognizable as a miso, suggesting fermentation in space is possible. We also found certain differences in the space miso: specifically the presence ofBacillus velezensis, a higher mutation rate ofA. oryzae, higher attributions of ‘roasted’ and ‘nutty’ flavours, and the most different sensory impression. Taken together, these observations suggest unique features of the space environment—what we might call ‘space terroir’—which could be harnessed to create more flavorful, nourishing foods for long-term space missions and to address fundamental questions about the biology of novel environments.

Significance Statement

Our study presents, to our knowledge, the first time a food product has been fermented in space. We demonstrate that fermentation in space is possible with safe and successful results, a proof of concept that offers fermentation as a new tool for space research and future long-term space exploration missions. We also document how the space environment shapes the fermentation process in unique ways, suggesting a ‘space terroir’. These findings on the feasibility and novelty of fermentation in space open up directions for further multidisciplinary research across science, health, systems design, and society and culture.
p24-Tango1 interactions ensure ER-Golgi interface stability and efficient transport
Authors: Yang Ke , Feng Zhi , Pastor-Pareja José C.
Published: February 2024

The eukaryotic p24 family, consisting of α-, β-, γ- and δ-p24 subfamilies, has long been known to be involved in regulating secretion. Despite increasing interest in these proteins, fundamental questions remain about their role. Here, we systematically investigatedDrosophilap24 proteins. We discovered that members of all four p24 subfamilies are required for general secretion, and that their localizations between ER exit site (ERES) and Golgi are interdependent in an α→βδ→γ sequence. We also found that localization of p24 proteins and ERES determinant Tango1 requires interaction through their respective GOLD and SH3 lumenal domains, with Tango1 loss sending p24 proteins to the plasma membrane and vice versa. Finally, we show that p24 loss expands the COPII zone at ERES and increases the number of ER-Golgi vesicles, supporting a restrictive role of p24 proteins on vesicle budding for efficient transport. Our results reveal Tango1-p24 interplay as central to the generation of a stable ER-Golgi interface.

Yang et al. systematically analyze inDrosophilathe function of the four p24 protein subfamilies and discover that interaction with Tango1 is essential for their concentration between ER and Golgi and for efficiency of COPII-mediated general secretory transport.
Knockout of AMPA receptor binding protein Neuron-Specific Gene 2 (NSG2) enhances associative learning and cognitive flexibility
Authors: Zimmerman Amber J. , Serrano-Rodriguez Antonio , Wilson Sandy J. , Linsenbardt David N. , Brigman Jonathan L. , Weick Jason P.
Published: February 2024

The vast majority of gene mutations and/or gene knockouts result in either no observable changes, or significant deficits in molecular, cellular, or organismal function. However, in a small number of cases, mutant animal models display enhancements in specific behaviors such as learning and memory. To date, most gene deletions shown to enhance cognitive ability generally affect a limited number of pathways such as NMDA receptor- and translation-dependent plasticity, or GABA receptor- and potassium channel-mediated inhibition. While endolysosomal trafficking of AMPA receptors is a critical mediator of synaptic plasticity, mutations in genes that affect AMPAR trafficking either have no effect or are deleterious for synaptic plasticity, learning and memory. NSG2 is one of the three-member family of Neuron-specific genes (NSG1-3), which have been shown to regulate endolysosomal trafficking of a number of proteins critical for neuronal function, including AMPAR subunits (GluA1-2). Based on these findings and the largely universal expression throughout mammalian brain, we predicted that genetic knockout of NSG2 would result in significant impairments across multiple behavioral modalities including motor, affective, and learning/memory paradigms. However, in the current study we show that loss of NSG2 had highly selective effects on associative learning and memory, leaving motor and affective behaviors intact. For instance, NSG2 KO animals performed equivalent to wild-type C57Bl/6n mice on rotarod and Catwalk motor tasks, and did not display alterations in anxiety-like behavior on open field and elevated zero maze tasks. However, NSG2 KO animals demonstrated enhanced recall in the Morris water maze, accelerated reversal learning in a touch-screen task, and accelerated acquisition and recall on a Trace Fear Conditioning task. Together, these data point to a specific involvement of NSG2 on multiple types of associative learning, and expand the repertoire of pathways that can be targeted for cognitive enhancement.
The importance of stereochemistry in the disorder-order continuum of protein-protein interactions
Authors: Newcombe Estella A. , Due Amanda D. , Sottini Andrea , Fernandes Catarina B. , Staby Lasse , Delaforge Elise , Bartling Christian R. O. , Brakti Inna , Bugge Katrine , Schuler Benjamin , Skriver Karen , Olsen Johan G. , Kragelund Birthe B.
Published: February 2024

Intrinsically disordered proteins can bindviathe formation of highly disordered protein complexes without the formation of 3D-structure. Most naturally occurring proteins are “left-handed” or levorotatory (L), made up only of L-amino acids, imprinting molecular structure and communication with stereochemistry. In contrast, their mirror image “right-handed” or dextrorotatory (D) amino acids are rare in Nature. Whether disordered protein complexes are truly independent of 3D-topology and thus of chiral constraints is not clear. To test the chiral constraints of disordered protein-protein interactions, a set of interacting protein pairs covering the disorder-order continuum was chosen as representative examples. By observing both the natural ligands and their stereochemical mirror images in free and bound states, we discovered that chirality was inconsequential in a fully disordered complex. However, if the interaction relied on the ligand undergoing coupled folding and binding, correct stereochemistry was essential. Between these extremes, binding could be observed for the D-ligand with a strength that correlated with the amount of disorder in the final complex. These findings have important implications for our understanding of protein-protein interactions, the molecular processes leading to complex formation, the use of D-peptides in drug discovery, and the chemistry of protein evolution of the first living entities on Earth.
Elevated levels of iodide promote peroxidase-mediated protein iodination and inhibit protein chlorination
Authors: Jokumsen Kathrine V. , Huhle Valerie H. , Hägglund Per M. , Davies Michael J. , Gamon Luke F.
Published: February 2024

At inflammatory sites, immune cells generate oxidants including H₂O₂. Myeloperoxidase (MPO), released by activated leukocytes employs H₂O₂ and halide/pseudohalides to form hypohalous acids that mediate pathogen killing. Hypochlorous acid (HOCl) is a major species formed. Excessive or misplaced HOCl formation damages host tissues with this linked to multiple inflammatory diseases. Previously (Redox Biology, 2020, 28, 101331) we reported that iodide (I⁻) modulates MPO-mediated protein damage by decreasing HOCl generation with concomitant hypoiodous acid (HOI) formation. HOI may however impact on protein structure, so in this study we examined whether and how HOI, from peroxidase/H₂O₂/I⁻ systems+Cl⁻, modifies proteins. Experiments employed MPO and lactoperoxidase (LPO) and multiple proteins (serum albumins, anastellin), with both chemical (intact protein and peptide mass mapping, LC-MS) and structural (SDS-PAGE) changes assessed. LC-MS analyses revealed dose-dependent iodination of anastellin and albumins by LPO/H2O2with increasing I⁻. Incubation of BSA with MPO/H2O2/Cl⁻ revealed modest chlorination (Tyr286, Tyr475, ∼4%) and Met modification. Lower levels of these species, and extensive iodination at specific Tyr and His residues (>20% modification with>10 µM I⁻) were detected with increasing I⁻. Anastellin dimerization was inhibited by increasing I⁻, but less marked changes were observed with albumins. These data confirm that I⁻ competes with Cl⁻ for MPO and is an efficient HOCl scavenger. These processes decrease protein chlorination and oxidation, but result in extensive iodination. This is consistent with published data on the presence of iodinated Tyr on neutrophil proteins. The biological implications of protein iodination relative to chlorination require further clarification.
Automated plankton monitoring suggests a key role of microzooplankton and temperature for predicting dynamics of phytoplankton size classes
Authors: Merkli Stefanie , Merz Ewa , Reyes Marta , Ntetsika Pinelopi , Dennis Stuart R. , Isles Peter D.F. , Kyathanahally Sreenath , Baity-Jesi Marco , To Sze-Wing , Merico Agostino , Pomati Francesco
Published: February 2024

The interplay between abiotic (resource supply, temperature) and biotic (grazing) factors determines growth and loss processes in phytoplankton through resource competition and trophic interactions, which are mediated by morphological traits like size. Here, we study the relative importance of grazers, water physics and chemistry on the daily net accumulation rates (AR) of individual phytoplankton from natural communities, grouped into six size classes from circa 10 to 500 μm. Using a Random Forest modelling approach and four years of daily data from a lake, we find that water temperature is generally a pivotal control of all phytoplankton AR. At the same time, nutrients and light are important for the smallest and the largest classes. Mesozooplankton abundance is a key predictor of the AR for small phytoplankton, with microzooplankton being important for the middle-size range. In our data, large and small phytoplankton have different (seasonal) blooming patterns: small forms are favoured by low temperature and grazing, and high phosphorus levels. Larger forms show positive ARs at high temperatures and low phosphorus (being relatively insensitive to zooplankton grazing). These results help us understand the opportunities and limitations of using size to explain and model phytoplankton responses to biotic and abiotic environmental change.
Odor-induced persistent neural activity in associative encoding in humans
Authors: Tarrida Joan , Moreno Manuel , Vidal Jordi , Panyella David , Marco-Pallarés Josep , Fuentemilla Lluís
Published: February 2024

This study explored the impact of brief exposure to odor cues on sustained neural activity during a 6-second delay period before memory encoding of a picture image. Combining univariate and multivariate ERP analytical approaches, our results align with nonhuman data, indicating that odor cues induced sustained neural activity in humans, persisting beyond the odor exposure throughout the nearly 6-second delay period. We observed higher amplitude of sustained ERPs for unpleasant compared to pleasant odor cues. Additionally, participants exhibited more confident memory recall for pictures preceded by unpleasant rather than pleasant odor cues during encoding, underscoring the influence of brief odor cues on memory formation for temporally distant events. In conclusion, this study revealed that brief exposure to odor cues induced sustained neural activity in humans, with distinct effects on memory formation along the pleasantness dimension, emphasizing the lasting impact of olfactory stimuli on cognitive processes.
The ciliary protein C2cd3 is required for mandibular musculoskeletal tissue patterning
Authors: Brooks Evan C. , Han Simon J.Y. , Bonatto Paese Christian Louis , Lewis Amya A. , Aarnio-Peterson Megan , Brugmann Samantha A.
Published: February 2024

The mandible is composed of several musculoskeletal tissues including bone, cartilage, and tendon that require precise patterning to ensure structural and functional integrity. Interestingly, most of these tissues are derived from one multipotent cell population called cranial neural crest cells (CNCCs). How CNCCs are properly instructed to differentiate into various tissue types remains nebulous. To better understand the mechanisms necessary for the patterning of mandibular musculoskeletal tissues we utilized the avian mutanttalpid2(ta2) which presents with several malformations of the facial skeleton including dysplastic tendons, mispatterned musculature, and bilateral ectopic cartilaginous processes extending off Meckel’s cartilage. We found an ectopic epithelial BMP signaling domain in theta2mandibular prominence (MNP) that correlated with the subsequent expansion ofSOX9+ cartilage precursors. These findings were validated with conditional murine models suggesting an evolutionarily conserved mechanism for CNCC-derived musculoskeletal patterning. Collectively, these data support a model in which cilia are required to define epithelial signal centers essential for proper musculoskeletal patterning of CNCC-derived mesenchyme.
BTK and MMP9 regulate NLRP3 inflammasome-dependent cytokine and NET responses in primary neutrophils
Authors: Leal Vinicius N. C. , Bork Francesca , von Guilleaume Juli-Christin , Greve Carsten L. , Bugl Stefanie , Danker Bettina , Bittner Zsofía A. , Grimbacher Bodo , Pontillo Alessandra , Weber Alexander N. R.
Published: February 2024

Background

Inflammation is a double-edged state of immune activation that is required to resolve threats harmful to the host but can also cause severe collateral damage. Polymorphonuclear neutrophils (PMN,) the primary leukocyte population in humans, mediate inflammation through the release of cytokines and neutrophil extracellular traps (NETs). Whilst the pathophysiological importance of NETs is unequivocal, the multiple molecular pathways driving NET release are not fully defined. Recently, NET release was linked to the NLRP3 inflammasome which is regulated by Bruton’s tyrosine kinase (BTK) in macrophages.

Objective

As NLRP3 inflammasome regulation by BTK has not been studied in neutrophils, we here explored a potential regulatory role of BTK in primary murine and human neutrophils and matched monocytes or macrophages from Btk-deficient vs WT mice or healthy donors (HD) vsBTKdeficient X-linked agammaglobulinemia (XLA) patients, respectively.

Methods

Cytokine, MPO and MMP-9 release were quantified by ELISA, NET release and inflammasome formation by immunofluorescence.

Results

Surprisingly, in both mouse and human primary neutrophils, we observed a significant increase in NLRP3 inflammasome-dependent IL-1β and NETs when BTK was absent or inhibited, whereas IL-1β release was decreased in corresponding primary mouse macrophages or human PBMC, respectively. This suggests a negative regulatory role of BTK in neutrophil NLRP3 activation. Both IL-1β and NET release in mouse and human primary neutrophils were strictly dependent on NLRP3, caspase-1 and, surprisingly, MMP-9.

Conclusion

This highlights BTK and MMP-9 as novel and versatile inflammasome regulators and may have implications for the clinical use of BTK inhibitors.

Key messages

Neutrophils contribute to inflammation by release of interleukin-1β and Neutrophil Extracellular Traps (NETs) via the NLRP3 inflammasome

Bruton’s tyrosine kinase (BTK) is a negative regulator of NLRP3-mediated primary human neutrophil functions, whereas it positively regulates NLRP3 in monocytes

MMP-9 is both effector and regulator of the neutrophil NLRP3 inflammasome

Capsule summary

Here we report that interleukin-1β and Neutrophil Extracellular Traps (NETs) release via the NLRP3 inflammasome is negatively regulated by Bruton’s tyrosine kinase (BTK) in primary neutrophils. Thus, targeting BTK using FDA-approved inhibitors might increase neutrophil functions.
Agrobacterium-mediatedCuscuta campestristransformation as a tool for understanding plant-plant interactions
Authors: Adhikari Supral , Mudalige Asha , Phillips Lydia , Lee Hyeyoung , Bernal-Galeano Vivian , Gruszewski Hope , Westwood James H. , Park So-Yon
Published: February 2024

Cuscuta campestris, a stem parasitic plant, has served as a valuable model plant for the exploration of plant-plant interactions and molecular trafficking. However, a major barrier toC. campestrisresearch is that a method to generate stable transgenic plants has not yet been developed. Here, we describe the development of aCuscutatransformation protocol using various reporter genes (GFP, GUS, or RUBY) and morphogenic genes (CcWUS2andCcGRF/GIF), ultimately leading to a robust protocol forAgrobacterium-mediatedC. campestristransformation. The stably transformed and regenerated RUBYC. campestrisplants produced haustoria, the signature organ of parasitic plants, and these were functional in forming host attachments. The locations of T-DNA integration in the parasite genome were confirmed through TAIL-PCR. TransformedC. campestrisalso produced flowers and transgenic seeds exhibiting betalain pigment, providing proof of germline transmission of the RUBY transgene. Furthermore, the RUBY reporter is not only a useful selectable marker for theAgrobacterium-mediated transformation, but also provides insight into the movement of molecules fromC. campestristo the host during parasitism. Thus, the protocol for transformation ofC. campestrisreported here overcomes a major obstacle toCuscutaresearch and opens new possibilities for studying parasitic plants and their interactions with hosts.
Contractility of cardiac and skeletal muscle tissue increases with environmental stiffness
Authors: Kah Delf , Lell Julia , Wach Tina , Spörrer Marina , Dessalles Claire A. , Wiedenmann Sandra , Gerum Richard C. , Vergarajauregui Silvia L. , Esser Tilman U. , Böhringer David , Engel Felix B. , Thievessen Ingo , Fabry Ben
Published: February 2024

The mechanical interplay between contractility and mechanosensing in striated muscles is of fundamental importance for tissue morphogenesis, load adaptation, and disease progression, but remains poorly understood. In this study, we investigate the dependence of contractile force generation of cardiac and skeletal muscle on environmental stiffness. Usingin vitroengineered muscle micro-tissues that are attached to flexible elastic pillars, we vary the stiffness of the microenvironment over three orders of magnitude and study its effect on contractility. We find that the active contractile force upon electrical stimulation of both cardiac and skeletal micro-tissues increases with environmental stiffness according to a strong power-law relationship. To explore the role of adhesion-mediated mechanotransduction processes, we deplete the focal adhesion protein β-parvin in skeletal micro-tissues. This reduces the absolute contractile force but leaves the mechanoresponsiveness unaffected. Our findings highlight the influence of external stiffness on the adaptive behavior of muscle tissue and shed light on the complex mechanoadaptation processes in striated muscle.
IFNB induced by non-lytic virus immunotherapy promotes improved survival in hepatocellular carcinoma, mediated by MHCII-independent cytotoxic CD4+ T-cells
Authors: Hughes Russell , Moran Amy , Scott Karen J , Appleton Elizabeth , Bentham Matthew J , Ilett Elizabeth , Melcher Alan , Macdonald Andrew , Samson Adel , Griffin Stephen
Published: February 2024

Hepatocellular carcinoma (HCC) is the third most common cause of cancer deaths worldwide. Combination immunotherapy is now standard of care for advanced HCC, improving patient outcomes. However, a considerable number of patients remain unresponsive, or are unable to tolerate therapy. Tyrosine kinase inhibitors (TKIs), such as the former first-line agent sorafenib, remain an option for such patients, yet provide only marginal efficacy. We hypothesised that a clinically advanced immunogenic oncolytic virus, namely, human Orthoreovirus, might improve TKI mediated therapy. Surprisingly, uv-inactivated, replication-deficient reovirus, but not live virus, significantly extended survival when combined with sorafenib in preclinical immunocompetent HCC models. Favourable responses were dependent upon adaptive immunity, mediated by IFNB-induced skewing of the infiltrating T-cell ratio in favour of cytotoxic CD4+ T-cells expressing granzyme B and perforin. Interestingly, this subset effectively killed tumours via both contact juxtacrine and paracrine processes, the former being MHCII independent. Moreover, efficacy correlated with more rapid and robust IFN production by inactivated virus due to the absence of innate viral antagonists. Thus, we reveal a means to improve TKI-HCC outcomes through an alternative virus-driven immunotherapy, underpinned by non-classical immunological mechanisms.
Comparative pollinator conservation potential of coffee agroforestry relative to coffee monoculture and tropical rainforest in the DR Congo
Authors: Jonas Depecker , Filip Vandelook , Kurt Jordaens , Achik Dorchin , Benjamin Ntumba Katshela , Ieben Broeckhoven , Benoit Dhed’a , Arne Devriese , Lien Deckers , Piet Stoffelen , Olivier Honnay
Published: February 2024

Animal-pollination is crucial in the reproduction of many crops grown in the tropics, including the self-incompatible Robusta coffee.Coffea canephoraPierre ex A. Froehner. is indigenous to the Congo basin where it is growing in the rainforest understorey yet providing very low yields. Cultivation therefore mainly occurs in either unshaded monocultures or in agroforestry systems. Here we surveyed the Diptera (true flies) and Hymenoptera (bees) communities that are putative coffee pollinating organisms in the Yangambi region in DR Congo, and we assessed the comparative benefits of coffee agroforestry and monocultures to the coffee pollinator community. To assess a base line value of pollinator conservation value of the agroforestry system, we also compared it with natural rainforest. Using white pan traps, we identified 9,597 specimens. Natural rainforest harboured a higher number of individuals, as well as a higher number of species than both agroforestry and coffee monoculture systems, with no differences between the latter two land-uses. The Simpson diversity and Pielou’s evenness on the other hand did not differ among land-uses. Furthermore, we observed different responses in species richness and diversity to land-use between Diptera and Hymenoptera. Our analyses of pollinator community composition showed a high dissimilarity between natural rainforest and the two cultivation systems, without significant differences between the latter land-uses. Specifically, the community composition of the agroforestry and coffee monoculture systems were totally different, rather than a subset of the community composition of the natural rainforest. Our study indicates that rehabilitation of agricultural land through intercropping fruit trees may not always enhance the pollinator community and that the studied agroforestry system falls short of matching the pollinator conservation potential found in natural rainforests. A more optimal selection of tree species intercropped with coffee may both enhance the conservation value of the agroforestry system and the provisioning of pollination services.
Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression
Authors: Parmar Shaifaly , Bume Desta Doro , Conelly Colleen , Boer Robert , Prestwood Peri R. , Wang Zhen , Labuhn Henning , Sinnadurai Krishshanthi , Feri Adeline , Ouellet Jimmy , Homan Philip , Numata Tomoyuki , Schneekloth John S.
Published: February 2024

Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with theThermoanaerobacter tengcongensis(Tte)-PreQ1riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1in six structurally and mechanistically diverse PreQ1riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.
Design and construction towards a pan-microbial toolkit
Authors: Gilbert Charlie , Crits-Christoph Alexander , Ledieu-Dherbécourt Elise , Kang Shinyoung Clair , Brumwell Stephanie L. , Lee Henry H. , Ostrov Nili
Published: February 2024

Establishing genetic tractability in non-model microbes requires identifying genetic parts that function in a target host. However, the paucity and purported narrow host range of available parts means that successful identification is governed by serendipity. Instead, a more comprehensive and scalable process would be desirable. Here, we describe the design principles for a pan-microbial genetic toolkit in which phylogenetically-diverse parts can be assembled and tested for function in microbes using high-throughput readouts. The architecture is based on Golden Gate Assembly, which simplifies the addition of parts and the construction of combinatorial libraries. We used this framework to develop two modules: first, thePOSSUM(PlasmidOrigins andSelection MarkerSforUndomesticatedMicrobes) module for identification of replicating plasmids in non-model microbes which includes 29 plasmid origin of replication sequences, 23 selection markers, and 30 unique DNA sequences for tracking by sequencing; second, theMACKEREL(Modular, NGS-trACKableExpRessionELement) module, for identification of functional gene expression cassettes which includes 426 bacterial promoter-RBS sequences driving fluorescent reporter expression, trackable by flow cytometry. We demonstrate the use of these libraries to screen for functional promoter-RBS variants in 6 non-model microbes. Continued efforts to expand this pan-microbial toolbox will accelerate efforts to improve genetic tractability and guide research across the tree of life.
Microtubules and actin filaments direct nuclear movement during the polarisation ofMarchantiaspore cells
Authors: Attrill Sarah , Dolan Liam
Published: February 2024

Multicellular organisms typically develop from single cells, the polarity of which establishes the first body axis of the organism. The multicellular haploid stage of land plants develops from a single haploid cell produced by meiosis – the spore. Starting from a non-polar state, these spores develop polarity and divide asymmetrically to establish the first apical-basal axis of the plant body. In the spore of the liverwort,Marchantia polymorpha, we show that the nucleus migrates from the cell centroid to the side of the cell to define the future basal pole. A microtubule organising centre leads this migration by initiating a dense microtubules array towards the cortex at the basal pole. Simultaneously, cortical microtubules disappear from the apical hemisphere but persist near the basal pole. A dense network of fine actin filaments also accumulates between the nucleus and the basal cell cortex. These data demonstrate that microtubules and actin filaments reorganise during the polarisation of theM. polymorphaspore. We speculate that signals orient microtubules and actin filaments during spore polarisation, resulting in the formation of a fine actin filament network between the nucleus and cell cortex that moves the nucleus to the future basal pole.

SUMMARY STATEMENT

Microtubules and actin filament dynamics are required for the basal movement of the nucleus which establishes cell asymmetry before cell division in theMarchantiaspore.
Characterisation of mesenchymal stromal cells in the skin of Atlantic salmon
Authors: Ruiz Daniels R. , Salisbury S.J. , Sveen L. , Taylor R.S , Vaadal M. , Tengs T. , Monaghan S.J. , Villamayor P.R. , Ballantyne M. , Penaloza C. , Fast M.D. , Bron J.E. , Houston R. , Robinson N. , Robledo D.
Published: February 2024

Background

The skin serves as the first line of defence for an organism against the external environment. Despite the global significance of salmon in aquaculture, a critical component of this first line of defence, mesenchymal stromal cells, remains unexplored. These pluripotent cells can differentiate into various tissues, including bone, cartilage, tendon, ligament, adipocytes, dermis, muscle and connective tissue within the skin. These cells are pivotal for preserving the integrity of skin tissue throughout an organism’s lifespan and actively participate in wound healing processes.

Results

In this study, we characterise mesenchymal stromal cells in detail for the first time in healthy Atlantic salmon tissue and during the wound healing process. Single-nucleus sequencing and spatial transcriptomics revealed the transcriptional dynamics of these cells, elucidating the differentiation pathways leading to osteogenic and fibroblast lineages in the skin of Atlantic salmon. We charted their activity during an in vivo wound healing time course, showing clear evidence of their active role during this process, as they become transcriptionally more active during the remodelling stage of wound healing.

Conclusions

For the first time, we chart the activity of sub-clusters of differentiating stromal cells during the process of wound healing, revealing different spatial niches of the various MSC subclusters, and setting the stage for investigations into the manipulation of MSCs to improve fish health.
Arp2/3 complex-dependent actin regulation protects the survival of tissue-resident mast cells
Authors: Kaltenbach Lukas , Mihlan Michael , Ulferts Svenja , Müsken Mathias , Glaser Katharina M. , Mittler Gerhard , Babina Magda , Innocenti Metello , Grosse Robert , Stradal Theresia E.B. , Lämmermann Tim
Published: February 2024

Actin network dynamics are pivotal in governing the motility and effector functions of immune cells. The Arp2/3 complex is a key regulator of actin filament branching, with mutations in its subunits being linked with human immunodeficiencies. While known for its role in phagocytosis and cell migration, our study uncovers a critical role of the Arp2/3 complex in safeguarding the tissue residency of mast cells (MCs), essential immune cells in allergies, venom detoxification and antigen-specific avoidance. Mechanistically, we show that MCs require Arp2/3-regulated actin filament assembly to resist their integrin-mediated mechano-coupling with their tissue niche. Arp2/3 complex depletion directs MCs into cell cycle arrest and death, which can be rescued by inhibiting their mechanical interactions with extracellular matrix. Our findings underscore the Arp2/3 complex as a mechano-protective element for maintaining MC survival and longevity in tissues, highlighting the importance of actin regulation in preserving the homeostasis of a tissue-resident immune cell population.

One Sentence Summary

Arp2/3 complex protects the tissue homeostasis of resident mast cell networks
Cortical tracking of speech is reduced in adults who stutter when listening for speaking
Authors: Gastaldon Simone , Busan Pierpaolo , Molinaro Nicola , Lizarazu Mikel
Published: February 2024

Purpose

Investigate cortical tracking of speech (CTS) in adults who stutter (AWS) compared to typically fluent adults (TFA) to test the involvement of the speech-motor network in tracking auditory information.

Method

Participants’ EEG was recorded while they either had to simply listen to sentences (listening only) or complete them by naming a picture (listening-for-speaking), thus manipulating the upcoming involvement of speech production. We analyzed speech-brain coherence and brain connectivity during listening.

Results

During the listening-for-speaking task, AWS exhibited reduced CTS in the 3-5 Hz range (theta), corresponding to the syllabic rhythm. The effect was localized in left inferior parietal and right pre-/supplementary motor regions. Connectivity analyses revealed that TFA had stronger information transfer in the theta range in both tasks in fronto-temporo-parietal regions. When considering the whole sample of participants, increased connectivity from the right superior temporal cortex to the left sensorimotor cortex was correlated with faster naming times in the listening-for-speaking task.

Conclusions

Atypical speech-motor functioning in stuttering also impacts speech perception, especially in situations requiring articulatory alertness. The involvement of frontal and (pre-) motor regions in CTS in typically fluent adults is highlighted. Speech perception in individuals with speech-motor deficits should be further investigated, especially when smooth transitioning between listening and speaking is required, such as in real-life conversational settings.
Rhodoquinone-dependent electron transport chain is essential forC. eleganssurvival in hydrogen sulfide environments
Authors: Romanelli-Cedrez Laura , vairoletti Franco , Salinas Gustavo
Published: February 2024

Hydrogen sulfide (H2S) has traditionally been considered as an environmental toxin for animal lineages; yet, it plays a signaling role in various processes at low concentrations. Mechanisms controlling H2S in animals, especially in sulfide-rich environments, are not fully understood. The main detoxification pathway involves the conversion of H2S into less harmful forms, through a mitochondrial oxidation pathway. The first step of this pathway oxidizes sulfide and reduces ubiquinone (UQ) through sulfide-quinone oxidoreductase (SQRD/SQOR). Because H2S inhibits cytochrome oxidase and hence UQ regeneration, this pathway becomes compromised at high H2S concentrations. The free-living nematodeC. elegansfeeds on bacteria and can face high sulfide concentrations in its natural environment. This organism has an alternative ETC that uses rhodoquinone (RQ) as the lipidic electron transporter and fumarate as the final electron acceptor. In this study, we demonstrate that RQ is essential for survival in sulfide. RQ-less animals (kynu-1andcoq-2eKO) cannot survive high H2S concentrations, while UQ-less animals (clk-1andcoq-2aKO) exhibit recovery, even when provided with a UQ-deficient diet. Our findings highlight thatsqrd-1uses both benzoquinones and that RQ-dependent ETC confers a key advantage (RQ regeneration) over UQ in sulfide conditions.C. elegansalso faces cyanide, another cytochrome oxidase inhibitor, whose detoxification leads to H2S production, viacysl-2. Our study reveals that RQ delays killing by the HCN-producing bacteriaPseudomonas aeruginosaPAO1. These results underscore the fundamental role that RQ-dependent ETC serves as a biochemical adaptation to H2S environments, and to pathogenic bacteria producing cyanide and H2S toxins.