bluuebunny/crossref_metadata_2025 huggingface dataset:
A protocol-driven approach to reduce lengths of stay for pediatric blunt liver and spleen injury patients
Authors: Wang Chen Chia , Gupta Ashwin , Stone Michelle , Milovancev Monica , Townsend Kelsie , Zhao Shilin , Greeno Amber
Published: January 2024

BACKGROUND

Our institution updated blunt liver and spleen injury (BLSI) protocols in 2019 in adherence to updated American Pediatric Surgery Association recommendations. This retrospective study compares resource utilization for pediatric BLSI patients treated under old and updated guidelines.

METHODS

Blunt liver and spleen injury patients without severe non-abdomen injuries younger than 18 years treated with prior (April 2015 to June 2019) and updated (June 2019 to December 2022) guidelines were retrospectively reviewed and compared. Each patient received an adjusted Injury Severity Score (ISS) to control for non-BLSI injuries. Multivariate analysis examined protocol group differences while controlling for adjusted ISS and BLSI grades. Primary outcomes were intensive care unit (ICU) length of stay (LOS), hospital LOS (analyzed using Cox regression), and patient costs (linear regression). Secondary outcomes include readmission in 2 weeks and death rates (logistic regression).

RESULTS

A total of 176 and 170 BLSI patients were treated with old and updated protocols, respectively. Patient demographics, average BLSI grade, and adjusted ISS were similar in both groups. Patients treated with old protocols indicate decreased hazard, showing significantly more days before ICU discharge (coefficient, −0.3868; p < 0.0009) and hospital discharge (coefficient, −0.5507; p < 0.0001). Patient costs (coefficient, 0.0921; p = 0.1874) trend toward being lower in the new protocol. Readmission rates were significantly higher in the new protocol (coefficient, −1.1731; p = 0.0465), and death rates (coefficient, 0.0519; p = 0.9710) were comparable.

CONCLUSIONS

Blunt liver and spleen injury patients treated under new American Pediatric Surgery Association guidelines compared with old guidelines had significant decreases in ICU and hospital LOS, a decreasing trend in costs, and comparable death rates but higher readmission rates. Future studies with larger sample sizes and detailed cost analysis would explore whether updated guidelines reduce patient costs and help elucidate the veracity or potential cause of the increased readmission rates.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level III.
Caregivers of People With Mild Cognitive Impairment and Dementia
Authors: Meyer Oanh L. , Zheng Shichen , Alto Raquel , Tran Duyen , Luu San , Vu Uyen , Hinton Ladson , Harvey Danielle
Published: January 2024

Objective:

Little is known about caregiving across the spectrum of cognitive impairment [mild cognitive impairment (MCI) to dementia] and how early life and sociocultural factors affect caregiver health. In this study, we characterized differences between caregivers of those with MCI versus those with dementia.

Methods:

A total of 158 caregivers were enrolled in this cross-sectional study, most of whom were dementia caregivers (65%). Caregivers completed questionnaires on depressive symptoms, self-rated health (SRH), perceived burden and stress, as well as psychosocial and demographic measures.

Results:

Caregivers of those with MCI reported fewer depressive symptoms and lower stress and burden compared with dementia caregivers. In adjusted analyses caregivers with greater stress reported more depressive symptoms. For SRH, at lower stress levels, having a sibling die before age 18 (ie, early life adversity) was associated with poorer SRH; at higher stress levels, having early life adversity was associated with better SRH. At lower burden levels, more live births were associated with worse SRH; at higher burden levels, more live births were associated with better SRH.

Conclusions:

Early life factors are relevant for caregivers of those with cognitive impairment and targeted prevention and early intervention may be helpful in alleviating caregiver burden and stress.
Ancient occupation by humans leads to missing bird diversity in otherwise natural habitats
Authors: Murray Alexander H. , Frishkoff Luke O.
Published: January 2024

Habitat modification is responsible for substantial biodiversity declines, but communities vary in their tolerance to land-use change. One infrequently queried possibility is that historical factors determine the sensitivity of contemporary communities. We use bird community data from 54 studies across the world to test the hypothesis that pre-historic human presence reduced community sensitivity to land-use change by eliminating sensitive species in natural habitats. We find that pre-historic human population size correlates with reduced sensitivity of communities. Primary vegetation in areas with larger pre-historic human populations contain fewer species today, while species richness in structurally simple agriculture is unimpacted. The greatest signal of humans impacts dates back to 12,000 YBP suggesting that early humans may have caused even more widespread extinctions, than previously appreciated.

One-Sentence Summary

Areas with high human population 12,000 years ago have less biodiversity today, but are more tolerant of habitat modification
The endophytic fungusSerendipita indicaalters auxin distribution inArabidopsis thalianaroots through alteration of auxin transport and conjugation to promote plant growth
Authors: Ortega-Villaizán Adrián González , King Eoghan , Patel Manish K. , Alonso Marta-Marina Pérez- , Scholz Sandra S. , Sakakibara Hitoshi , Kiba Takatoshi , Kojima Mikiko , Takebayashi Yumiko , Ramos Patricio , Morales-Quintana Luis , Breitenbach Sarah , Smolko Ana , Salopek-Sondi Branka , Bauer Nataša , Ludwig-Müller Jutta , Krapp Anne , Oelmüller Ralf , Vicente-Carbajosa Jesús , Pollmann Stephan
Published: January 2024

Plants share their habitats with a multitude of different microbes. This close vicinity promoted the evolution of inter-organismic interactions between plants and many different microorganisms that provide mutual growth benefits both to the plant and the microbial partner. The symbiosis ofArabidopsis thalianawith the beneficial root colonizing endophyteSerendipita indicarepresents a well-studied system. Co-colonization of Arabidopsis roots withS. indicasignificantly promotes plant growth. Due to the notable phenotypic alterations of fungus-infected root systems, the involvement of a reprogramming of plant hormone levels, especially that of indole-3-acetic acid, has been suggested earlier. However, until now, the molecular mechanism by whichS. indicapromotes plant growth remains largely unknown. This study used comprehensive transcriptomics, metabolomics, reverse genetics, and life cell imaging to reveal the intricacies of auxin-related processes that affect root growth in the symbiosis betweenA. thalianaandS. indica. Our experiments revealed the essential role of tightly controlled auxin conjugation in the plant–fungus interaction. It particularly highlighted the importance of twoGRETCHEN HAGEN 3(GH3) genes,GH3.5andGH3.17, for the fungus infection-triggered stimulation of biomass production, thus broadening our knowledge about the function of GH3s in plants. Furthermore, we provide evidence for the transcriptional alteration of thePIN2auxin transporter gene in roots of Arabidopsis seedlings infected withS. indicaand demonstrate that this transcriptional adjustment affects auxin signaling in roots, which results in increased plant growth.
Long-readde novoassembly of the red-legged partridge (Alectoris rufa) genome
Authors: González-Prendes Rayner , Pena Ramona Natacha , Richart Cristobal , Nadal Jesús , Ros-Freixedes Roger
Published: January 2024

The red-legged partridge (Alectoris rufa) is a popular game bird species that is in decline in several regions of southwestern Europe. The introduction of farm-reared individuals of a distinct genetic make-up in hunting reserves can result in genetic swamping of wild populations. Here we present ade novogenome assembly for the red-legged partridge based on long-read sequencing technology. The assembled genome size is 1.14 Gb, with scaffold N50 of 37.6 Mb and contig N50 of 29.5 Mb. Our genome is highly contiguous and contains 97.06% of complete avian core genes. Overall, quality of this genome assembly is equivalent to those available for other close relatives such as the Japanese quail or the chicken. This genome assembly will contribute to the understanding of genetic dynamics of wild populations of red-legged partridges with releases of farm-reared reinforcements and to appropriate management decisions of such populations.
The dilemma of underestimating freshwater biodiversity: morphological and molecular approaches
Authors: Schoenle Alexandra , Scepanski Dominik , Floß Alexander , Büchel Pascal , Koblitz Ann-Kathrin , Scherwaß Anja , Arndt Hartmut , Waldvogel Ann-Marie
Published: January 2024

Background

The Lower Rhine ecosystem has been extensively shaped by human activities, destroying, modifying, and even creating novel water bodies as habitats. Freshwater systems are hotspots of biodiversity and highly complex ecosystems. However, knowledge and description of its biodiversity across all trophic levels is still incomplete and the complexity of interactions remains unresolved, especially below the micro scale. This is even true for important international inland waterways such as the River Rhine. We here document the biodiversity of the Lower Rhine and associated water bodies, spanning from the level of protists up to the level of larger invertebrate predators and herbivores organized in faunal size classes (nano-, micro, meio- and macrofauna). This study is part of a long-term ecological research project (LTER-D REES). Our study includes two riprap sections of the river’s main channel, two oxbows and two gravel-pit lakes in the river’s flood plain. Diversity was assessed through morphotype richness and metabarcoding, as well as accounting for sediment composition.

Results

We found high discrepancies between amplicon sequencing variants (ASVs) and morphotype richness in all size classes, as well as a problematic limitation of reference sequences from freshwater organisms in public databases. Irrespective of the size class, we observed habitat specific zoobenthos communities in each of the three investigated habitat types, with few taxa or taxonomic groups overlapping.

Conclusions

Our results demonstrate the importance to integrate different methodologies and extend freshwater sequencing efforts for the assessment of biodiversity across all trophic levels, as particularly relevant for long term projects.
The effects of Paternal Radiofrequency Radiation Exposure on Sperm and Testicular Integrity in F1-Male Swiss Albino Mice
Authors: Pandey Neelam , Giri Sarbani , Sharma GD
Published: January 2024

The escalating prevalence of infertility and reproductive malignancies in the youth demographic warrants thorough investigation. The escalating ubiquity of communication devices, such as mobile phones and Wi-Fi, exposes individuals to unprecedented levels of Radiofrequency Radiation (RFR), raising concerns about its potential association with reproductive issues and cancer. In this study, we endeavored to elucidate the impact of RFR exposure on the fertility of F0 male Swiss albino mice, as well as the consequential effects on sperm quality and testicular morphology in F1 male mice during adulthood. F0 male mice were subjected to RFR exposure for 3 hours per day, twice daily, over a span of 35 days, followed by mating with naïve, unexposed females, culminating in a comprehensive endpoint evaluation. The repercussions of RFR exposure included a diminution in sperm count, heightened incidence of sperm defects, augmented DNA damage in both sperm and bone marrow cells, diminished sperm viability, and aberrations in testicular histology. Subsequent mating of exposed male mice with naïve females revealed no discernible effects on pregnancy outcomes, as indicated by the fertility index, litter size, and copulation index.Nevertheless, F1 male offspring exhibited a noteworthy reduction in sperm count and depletion of the germinal epithelium within seminiferous tubules in the testes. These findings propose that RFR exposure to F0 males may precipitate diminished sperm count in subsequent F1 generations, implicating the potential role of epigenetic modulation through the male germline.
Coarse-Grained Model of Serial Dilution Dynamics in Synthetic Human Gut Microbiome
Authors: Mahajan Tarun , Maslov Sergei
Published: January 2024

Many microbial communities in nature are complex, with hundreds of coexisting strains and the resources they consume. We currently lack the ability to assemble and manipulate such communities in a predictable manner in the lab. Here, we take a first step in this direction by introducing and studying a simplified consumer resource model of such complex communities in serial dilution experiments. The main assumption of our model is that during the growth phase of the cycle, strains share resources and produce metabolic byproducts in proportion to their average abundances and strain-specific consumption/production fluxes. We fit the model to describe serial dilution experiments in hCom2, a defined synthetic human gut microbiome with a steady-state diversity of 63 species growing on a rich media, using consumption and production fluxes inferred from metabolomics experiments. The model predicts serial dilution dynamics reasonably well, with a correlation coefficient between predicted and observed strain abundances as high as 0.8. We applied our model to: (i) calculate steady-state abundances of leave-one-out communities and use these results to infer the interaction network between strains; (ii) explore direct and indirect interactions between strains and resources by increasing concentrations of individual resources and monitoring changes in strain abundances; (iii) construct a resource supplementation protocol to maximally equalize steady-state strain abundances.
Single NV in nanodiamond for quantum sensing of protein dynamics in an ABEL trap
Authors: Pérez Iván , Krueger Anke , Wrachtrup Jörg , Jelezko Fedor , Börsch Michael
Published: January 2024

Enzymes are cellular protein machines using a variety of conformational changes to power fast biochemical catalysis. Our goal is to exploit the single-spin properties of the luminescent NV (nitrogen-vacancy) center in nanodiamonds to reveal the dynamics of an active enzyme complex at physiological conditions with the highest spatio-temporal resolution. Specifically attached to the membrane enzyme FoF1-ATP synthase, the NV sensor will report the adenosine triphosphate (ATP)-driven full rotation of Fomotor subunits in ten consecutive 36° steps. Conformational dynamics are monitored using either a double electron-electron resonance scheme or NV-magnetometry with optical readout or using NV-relaxometry with a superparamagnetic nanoparticle as the second marker attached to the same enzyme. First, we show how all photophysical parameters like individual size, charge, brightness, spectral range of fluorescence and fluorescence lifetime can be determined for the NV-center in a single nanodiamond held in aqueous solution by a confocal anti-Brownian electrokinetic trap (ABEL trap). Stable photon count rates of individual nanodiamonds and the absence of blinking allow for observation times of single nanodiamonds in solution exceeding hundreds of seconds. For the proposed quantum sensing of nanometer-sized distance changes within an active enzyme, we show that local magnetic field fluctuations can be detected all-optically by analyzing fluorescence lifetime changes of the NV-center in each nanodiamond in solution.
Supervised land- and water-based exercise intervention in women with fibromyalgia: CERT- based exercise study protocol of the al-Ándalus physical activity randomised controlled trial
Authors: Álvarez-Gallardo Inmaculada C. , Gavilán-Carrera Blanca , Carbonell-Baeza Ana , Segura-Jiménez Víctor , Camiletti-Moirón Daniel , Borges-Cosic Milkana , Aparicio Virginia , Delgado-Fernández Manuel
Published: January 2024

Background

Exercise is recommended for managing fibromyalgia; however, the scant details provided about exercise programs (EP) in the available literature make standardization, replicability, and interpretation of results difficult. The aim of the present report is to provide a comprehensive CERT (Consensus on Exercise Reporting Template)-based description of the rationale and details of the land- and water-based EP implemented in the al-Ándalus Randomized Controlled Trial (RCT).

Methods

Women aged 35-65 with fibromyalgia (n=180) were planned to be recruited in Southern Spain (Andalucía). The study design was composed of three groups: the usual care (control) group, the land- and the water-based supervised exercise intervention groups (n=60 for each group). Participants allocated in the exercise intervention groups undertook a 24-week supervised multicomponent (strength, aerobic and flexibility) EP (three non-consecutive sessions per week, 45-60 min/session). The rationale of the exercise program is described in detail following the CERT criteria detailing its 16 key items.

Discussion

This study details the supervised EP of the al-Ándalus RCT project, which may serve: 1) exercise professionals who would like to implement an evidence-based supervised EP for people with fibromyalgia in land- and water-based settings, and 2) as an example of the application of the CERT criteria.

Trial registration

ClinicalTrials.gov ID:NCT01490281
Large datasets from Electronic Health Records predict seizures after ischemic strokes: A Machine Learning approach
Authors: Lekoubou Alain , Petucci Justin , Ajala Temitope Femi , Katoch Avnish , Sen Souvik , Honavar Vasant
Published: January 2024

Objective

To develop an artificial intelligence, machine learning prediction model for estimating the risk of seizures 1 year and 5 years after ischemic stroke (IS) using a large dataset from Electronic Health Records.

Background

Seizures are frequent after ischemic strokes and are associated with increased mortality, poor functional outcomes, and lower quality of life. Separating patients at high risk of seizures from those at low risk of seizures is needed for treatment and clinical trial planning, but remains challenging. Machine learning (ML) is a potential approach to solve this paradigm.

Design/Methods

We identified patients (aged ≥18 years) with IS without a prior diagnosis of seizures from 2015 until inception (08/09/22) in the TriNetX Research Network, using the International Classification of Diseases, Tenth Revision (ICD-10) I63, excluding I63.6 (venous infarction). The outcome of interest was any ICD-10 diagnosis of seizures (G40/G41) at 1 year and 5 years following the index IS. We applied a conventional logistic regression and a Light Gradient Boosted Machine algorithm to predict the risk of seizures at 1 year and 5 years. The performance of the model was assessed using the area under the receiver operating characteristics (AUROC), the area under the precision-recall curve (AUPRC), F1 statistic, model accuracy, balanced accuracy, precision, and recall, with and without anti-seizure medication use in the models.

Results

Our study cohort included 430,254 IS patients. Seizures were present in 18,502 (4.3%) and (5.3%) patients within 1 and 5 years after IS, respectively. At 1-year, the AUROC, AUPRC, F1 statistic, accuracy, balanced-accuracy, precision, and recall were respectively 0.7854 (standard error: 0.0038), 0.2426 (0.0048), 0.2299 (0.0034), 0.8236 (0.001), 0.7226 (0.0049), 0.1415 (0.0021), and 0.6122, (0.0095). Corresponding metrics at 5 years were 0.7607 (0.0031), 0.247 (0.0064), 0.2441 (0.0032), 0.8125 (0.0013), 0.7001 (0.0045), 0.155 (0.002) and 0.5745 (0.0095).

Conclusion

Our findings suggest that ML models show good model performance for predicting seizures after IS.
PPTC7 limits mitophagy through proximal and dynamic interactions with BNIP3 and NIX
Authors: Wei Lianjie , Gok Mehmet Oguz , Svoboda Jordyn D. , Forny Merima , Friedman Jonathan R. , Niemi Natalie M.
Published: January 2024

PPTC7 is a mitochondrial-localized PP2C phosphatase that maintains mitochondrial protein content and metabolic homeostasis. We previously demonstrated that knockout ofPptc7elevates mitophagy in a BNIP3– and NIX-dependent manner, but the mechanisms by which PPTC7 influences receptor-mediated mitophagy remain ill-defined. Here, we demonstrate that loss of PPTC7 upregulates BNIP3 and NIX post-transcriptionally and independent of HIF-1α stabilization. On a molecular level, loss ofPPTC7prolongs the half-life of BNIP3 and NIX while blunting their accumulation in response to proteasomal inhibition, suggesting that PPTC7 promotes the ubiquitin-mediated turnover of BNIP3 and NIX. Consistently, overexpression of PPTC7 limits the accumulation of BNIP3 and NIX protein levels in response to pseudohypoxia, a well-known inducer of mitophagy. This PPTC7-mediated suppression of BNIP3 and NIX protein expression requires an intact PP2C catalytic motif but is surprisingly independent of its mitochondrial targeting, indicating that PPTC7 influences mitophagy outside of the mitochondrial matrix. We find that PPTC7 exists in at least two distinct states in cells: a longer isoform, which likely represents full length protein, and a shorter isoform, which likely represents an imported, matrix-localized phosphatase pool. Importantly, anchoring PPTC7 to the outer mitochondrial membrane is sufficient to blunt BNIP3 and NIX accumulation, and proximity labeling and fluorescence co-localization experiments suggest that PPTC7 associates with BNIP3 and NIX within the native cellular environment. Importantly, these associations are enhanced in cellular conditions that promote BNIP3 and NIX turnover, demonstrating that PPTC7 is dynamically recruited to BNIP3 and NIX to facilitate their degradation. Collectively, these data reveal that a fraction of PPTC7 dynamically localizes to the outer mitochondrial membrane to promote the proteasomal turnover of BNIP3 and NIX.
Superior target genes and pathways for RNAi mediated pest control revealed by genome wide analysis in the red flour beetleTribolium castaneum
Authors: Buer Benjamin , Dönitz Jürgen , Milner Martin , Mehlhorn Sonja , Hinners Claudia , Siemanowski-Hrach Janna , Ulrich Julia K. , Großmann Daniela , Cedden Doga , Nauen Ralf , Geibel Sven , Bucher Gregor
Published: January 2024

An increasing human population, the emergence of resistances against pesticides and their potential impact on the environment call for the development of new eco-friendly pest control strategies. RNA interference (RNAi) based pesticides have emerged as new option with the first products entering the market. Essentially, double stranded RNAs targeting essential genes of pests are either expressed in the plants or sprayed on their surface. Upon feeding, pests mount an RNAi response and die. However, it has remained unclear, whether RNAi based insecticides should target the same pathways as classic pesticides or whether the different mode of action would favor other processes. Moreover, there is no consensus on the best genes to be targeted. We performed a genome-wide screen in the red flour beetle to identify 905 RNAi target genes. Based on a validation screen and clustering, we identified the 192 most effective target genes in that species. The transfer to oral application in other beetle pests revealed a list of 34 superior target genes, which are an excellent starting point for application in other pests. GO and KEGG analyses of our genome wide dataset revealed that genes with high efficacy belonged mainly to basic cellular processes such as gene expression and protein homeostasis – processes not targeted by classic insecticides. In summary, our work revealed the best target genes and target processes for RNAi based pest control and we propose a procedure to transfer our short list of superior target genes to other pests.
SPOT-RASTR - a cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface
Authors: Esfahani Behrouz G. , Randolph Peter S. , Peng Ruizhi , Grant Timothy , Stroupe M. Elizabeth , Stagg Scott M.
Published: January 2024

In cryogenic electron microscopy (cryo-EM), specimen preparation remains a bottleneck despite recent advancements. Classical plunge freezing methods often result in issues like aggregation and preferred orientations at the air/water interface. Many alternative methods have been proposed, but there remains a lack a universal solution, and multiple techniques are often required for challenging samples. Here, we demonstrate the use of lipid nanotubes with nickel NTA headgroups as a platform for cryo-EM sample preparation. His-tagged specimens of interest are added to the tubules, and they can be frozen by conventional plunge freezing. We show that the nanotubes protect samples from the air/water interface and promote a wider range of orientations. The reconstruction of average subtracted tubular regions (RASTR) method allows for the removal of the nanotubule signal from the cryo-EM images resulting in isolated images of specimens of interest. Testing with β-galactosidase validates the method’s ability to capture particles at lower concentrations, overcome preferred orientations, and achieve near-atomic resolution reconstructions. Since the nanotubules can be identified and targeted automatically at low magnification, the method enables fully automated data collection. Furthermore, the particles on the tubes can be automatically identified and centered using 2D classification enabling particle picking without requiring prior information. Altogether, our approach that we call specimen preparation on a tube RASTR (SPOT-RASTR) holds promise for overcoming air-water interface and preferred orientation challenges and offers the potential for fully automated cryo-EM data collection and structure determination.
Conformational changes of the ABC Transporter BmrA Depend on Membrane Curvature
Authors: Damm Alicia , Paik Su-Jin , Sadhu Raj Kumar , Di-Cicco Aurélie , Manzi John , Castellana Michele , Margeat Emmanuel , Dahan Maxime , Sens Pierre , Lévy Daniel , Bassereau Patricia
Published: January 2024

While mechanosensitive ion channels’ gating has been well documented, the effect of membrane mechanics, in particular membrane curvature, on the function of transporters remains elusive. Since conical shape transmembrane proteins locally deform membranes, conversely membrane bending could impact their conformations and their function. We tested this hypothesis using BmrA, a bacterial ABC exporter that exhibits large conformational changes upon ATP hydrolysis, switching between open and closed states with opposite V-shapes. After reconstitution in liposomes of different curvatures, we showed that BmrA ATPase activity decreases by 2.9-fold when their diameter decreases from 125 to 29 nm. Moreover, using single-molecule FRET, we observed that the fraction of closed conformations is significantly reduced in highly curved vesicles when adding ATP or non-hydrolysable AMP-PNP. Our results are well explained by a theoretical 2-states model including the effect of membrane mechanics on protein shape transition. Our work reveals that the functional cycle of conical transporters is curvature sensitive, to an extent depending on protein geometry.

Teaser

High membrane curvature strongly impacts the functional cycle of transporters.
Elucidation of chalkophomycin biosynthesis revealsN-hydroxypyrrole-forming enzymes
Authors: Crooke Anne Marie , Chand Anika K. , Cui Zheng , Balskus Emily P.
Published: January 2024

Reactive functional groups, such asN-nitrosamines, impart unique bioactivities to the natural products in which they are found. Recent work has illuminated enzymaticN-nitrosation reactions in microbial natural product biosynthesis, motivating an interest in discovering additional metabolites constructed using such reactivity. Here, we use a genome mining approach to identify over 400 cryptic biosynthetic gene clusters (BGCs) encoding homologs of theN-nitrosating biosynthetic enzyme SznF, including the BGC for chalkophomycin, a CuII-binding metabolite that contains aC-type diazeniumdiolate andN-hydroxypyrrole. Characterizing chalkophomycin biosynthetic enzymes reveals previously unknown enzymes responsible forN-hydroxypyrrole biosynthesis, including the first prolyl-N-hydroxylase, and a key step in assembly of the diazeniumdiolate-containing amino acid graminine. Discovery of this pathway enriches our understanding of the biosynthetic logic employed in constructing unusual heteroatom-heteroatom bondcontaining functional groups, enabling future efforts in natural product discovery and biocatalysis.
The voltage-gated potassium channelShal(Kv4) contributes to active hearing inDrosophila
Authors: Gregory Eli S. , Xu YiFeng Y. J. , Lee Tai-Ting , Joiner Mei-ling A. , Kamikouchi Azusa , Su Matthew P. , Eberl Daniel F.
Published: January 2024

The full complement of ion channels which influence insect auditory mechanotransduction, and the mechanisms by which their influence is exerted, remain unclear.Shal(Kv4), aShakerfamily member encoding voltage-gated potassium channels inDrosophila melanogaster, has been shown to localize to dendrites in some neuron types, suggesting a potential role forShalinDrosophilahearing, including mechanotransduction. A GFP-protein trap was used to visualize the localization of theShalchannel in Johnston’s organ neurons responsible for hearing in the antenna.Shalprotein was localized to the cell body and the proximal dendrite region of sensory neurons, suggesting its involvement not only in general auditory function, but specifically in mechanotransduction. Electrophysiological recordings conducted to assess neural responses to auditory stimuli in mutantShalflies revealed significant decreases in auditory responses. Laser Doppler Vibrometer recordings indicated abnormal antennal free fluctuation frequencies in mutant lines, indicating an effect on active antennal tuning, and thus active transduction mechanisms. This suggests thatShalparticipates in coordinating energy-dependent antennal movements inDrosophilathat are essential for tuning the antenna to courtship song frequencies.

Significance Statement

The study of fruit fly hearing has revealed mechanosensitive ion channels that participate in mechanotransduction, and as in mammalian hearing, energy-dependent mechanisms actively amplify and tune auditory processes. Identifying distinct roles played by different ion channels is essential to better understand this process. Here, we explore the influence of a specific voltage-gated potassium channel,Shal, on fly hearing, and find that it affects specific parts of the mechanotransduction process. Our research uncoversShal’slocalization in sensory dendrite regions of auditory neurons, where it contributes to shaping mechanotransduction and active antennal tuning. UnderstandingShal’s involvement in auditory function and mechanotransduction deepens our knowledge of fly hearing and unveils a key player in the coordination of energy-dependent active antennal movements.
Electrically silent KvS subunits associate with native Kv2 channels in brain and impact diverse properties of channel function
Authors: Ferns Michael , van der List Deborah , Vierra Nicholas C. , Lacey Taylor , Murray Karl , Kirmiz Michael , Stewart Robert G. , Sack Jon T. , Trimmer James S.
Published: January 2024

Voltage-gated K+channels of the Kv2 family are highly expressed in brain and play dual roles in regulating neuronal excitability and in organizing endoplasmic reticulum - plasma membrane (ER- PM) junctions. Studies in heterologous cells suggest that the two pore-forming alpha subunits Kv2.1 and Kv2.2 assemble with “electrically silent” KvS subunits to form heterotetrameric channels with distinct biophysical properties. Here, using mass spectrometry-based proteomics, we identified five KvS subunits as components of native Kv2.1 channels immunopurified from mouse brain, the most abundant being Kv5.1. We found that Kv5.1 co-immunoprecipitates with Kv2.1 and to a lesser extent with Kv2.2 from brain lysates, and that Kv5.1 protein levels are decreased by 70% in Kv2.1 knockout mice and 95% in Kv2.1/2.2 double knockout mice. Multiplex immunofluorescent labelling of rodent brain sections revealed that in neocortex Kv5.1 immunolabeling is apparent in a large percentage of Kv2.1 and Kv2.2-positive layer 2/3 neurons, and in a smaller percentage of layer 5 and 6 neurons. At the subcellular level, Kv5.1 is co-clustered with Kv2.1 and Kv2.2 at ER-PM junctions in cortical neurons, although clustering of Kv5.1-containing channels is reduced relative to homomeric Kv2 channels. We also found that in heterologous cells coexpression with Kv5.1 reduces the clustering and alters the pharmacological properties of Kv2.1 channels. Together, these findings demonstrate that the Kv5.1 electrically silent subunit is a component of a substantial fraction of native brain Kv2 channels, and that its incorporation into heteromeric channels can impact diverse aspects of Kv2 channel function.
In silicoassessment of immune cross protection between BCoV and SARS-CoV-2
Authors: Querne Lana Bazan Peters , Bastos Fernanda Zettel , dos Anjos Adur Mikaela , Cavalheiro Vitória , Beirão Breno Castello Branco
Published: January 2024

Background

Humans have long shared infectious agents with cattle, and the bovine-derived human common cold OC-43 CoV is a not-so-distant example of cross-species viral spill over of coronaviruses. Human exposure to the Bovine Coronavirus (BCoV) is certainly common, as the virus is endemic in most high-density cattle-raising regions. Since BCoVs are phylogenetically close to SARS-CoV-2, it is possible that cross-protection against COVID-19 occurs in people exposed to BCoV.

Methods

This article shows anin silicoinvestigation of human cross-protection to SARS-CoV-2 due to BCoV exposure. We determined HLA recognition and human B lymphocyte reactivity to BCoV epitopes using bioinformatics resources. A retrospective geoepidemiological analysis of COVID-19 was then performed to verify if BCoV/SARS-CoV-2 cross-protection could have occurred in the field. Brazil was used as a model for the epidemiological analysis of the impact of livestock density – as a proxy for human exposure to BCoV – on the prevalence of COVID-19 in people.

Results

As could be expected from their classification in the sameBetacoronavirusgenus, we show that several human B and T epitopes are shared between BCoV and SARS-CoV-2. This raised the possibility of cross-protection of people from exposure to the bovine coronavirus. Analysis of field data added partial support to the hypothesis of viral cross-immunity from human exposure to BCoV. There was a negative correlation between livestock geographical density and COVID-19. Whole-Brazil data showed areas in the country in which COVID-19 prevalence was disproportionally low (controlled by normalization by transport infrastructure). Areas with high cattle density had lower COVID-19 prevalence in these low-risk areas.

Conclusions

These data are hypothesis-raising indications that cross-protection is possibly being induced by human exposure to the Bovine Coronavirus.
A C-terminal motif containing a PKC phosphorylation site regulates γ-Protocadherin-mediated dendrite arborization in the cerebral cortexin vivo
Authors: Hanes Camille M. , Mah Kar Men , Steffen David M. , Marcucci Charles G. , Fuller Leah C. , Burgess Robert W. , Garrett Andrew M. , Weiner Joshua A.
Published: January 2024

ThePcdhggene cluster encodes 22 γ-Protocadherin (γ-Pcdh) cell adhesion molecules that critically regulate multiple aspects of neural development, including neuronal survival, dendritic and axonal arborization, and synapse formation and maturation. Each γ-Pcdh isoform has unique protein domains–a homophilically-interacting extracellular domain and a juxtamembrane cytoplasmic domain– as well as a C-terminal cytoplasmic domain shared by all isoforms. The extent to which isoform-specificvs.shared domains regulate distinct γ-Pcdh functions remains incompletely understood. Our previousin vitrostudies identified PKC phosphorylation of a serine residue within a shared C-terminal motif as a mechanism through which γ-Pcdh promotion of dendrite arborizationviaMARCKS is abrogated. Here, we used CRISPR/Cas9 genome editing to generate two new mouse lines expressing only non-phosphorylatable γ-Pcdhs, due either to a serine-to-alanine mutation (PcdhgS/A) or to a 15-amino acid C-terminal deletion resulting from insertion of an early stop codon (PcdhgCTD). Both lines are viable and fertile, and the density and maturation of dendritic spines remains unchanged in bothPcdhgS/AandPcdhgCTDcortex. Dendrite arborization of cortical pyramidal neurons, however, is significantly increased in both lines, as are levels of active MARCKS. Intriguingly, despite having significantly reduced levels of γ-Pcdh proteins, thePcdhgCTDmutation yields the strongest phenotype, with even heterozygous mutants exhibiting increased arborization. The present study confirms that phosphorylation of a shared C-terminal motif is a key γ-Pcdh negative regulation point, and contributes to a converging understanding of γ-Pcdh family function in which distinct roles are played by both individual isoforms and discrete protein domains.
A microglia clonal inflammatory disorder in Alzheimer’s Disease
Authors: Vicario Rocio , Fragkogianni Stamatina , Weber Leslie , Lazarov Tomi , Hu Yang , Hayashi Samantha Y. , Craddock Barbara P. , Socci Nicholas D. , Alberdi Araitz , Baako Ann , Ay Oyku , Ogishi Masato , Lopez-Rodrigo Estibaliz , Kappagantula Rajya , Viale Agnes , Iacobuzio-Donahue Christine A. , Zhou Ting , Ransohoff Richard M , Chesworth Richard ,   Netherlands Brain Bank, Abdel-Wahab Omar , Boisson Bertrand , Elemento Olivier , Casanova Jean-Laurent , Miller W. Todd , Geissmann Frederic
Published: January 2024

Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer’s Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, bothin vitroand in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.

One-Sentence Summary

A subset of Alzheimer Disease patients carry mutant microglia somatic clones which promote neuro-inflammation.
Metabolomic Profiles and Pathways in Osteoarthritic Human Cartilage: A Comparative Analysis with Healthy Cartilage
Authors: Welhaven Hope D. , Welfley Avery H. , Brahmachary Priyanka , Bergstrom Annika R. , Houske Eden , Glimm Matthew , Bothner Brian , Hahn Alyssa K. , June Ronald K.
Published: January 2024

Objective

Osteoarthritis (OA) is a chronic joint disease with heterogenous metabolic pathology. To gain insight into OA-related metabolism, healthy and end-stage osteoarthritic cartilage were compared metabolically to uncover disease-associated profiles, classify OA-specific metabolic endotypes, and identify targets for intervention for the diverse populations of individuals affected by OA.

Design

Femoral head cartilage (n=35) from osteoarthritis patients were collected post-total joint arthroplasty. Healthy cartilage (n=11) was obtained from a tissue bank. Metabolites from all cartilage samples were extracted and analyzed using liquid chromatography-mass spectrometry metabolomic profiling. Additionally, cartilage extracts were pooled and underwent fragmentation analysis for biochemical identification of metabolites.

Results

Specific metabolites and metabolic pathways, including lipid- and amino acid pathways, were differentially regulated between osteoarthritis-derived and healthy cartilage. The detected alterations of amino acids and lipids highlight key differences in bioenergetic resources, matrix homeostasis, and mitochondrial alterations in osteoarthritis-derived cartilage compared to healthy. Moreover, metabolomic profiles of osteoarthritic cartilage separated into four distinct endotypes highlighting the heterogenous nature of OA metabolism and diverse landscape within the joint between patients.

Conclusions

The results of this study demonstrate that human cartilage has distinct metabolomic profiles between healthy and end-stage osteoarthritis patients. By taking a comprehensive approach to assess metabolic differences between healthy and osteoarthritic cartilage, and within osteoarthritic cartilage alone, several metabolic pathways with distinct regulation patterns were detected. Additional investigation may lead to the identification of metabolites that may serve as valuable indicators of disease status or potential therapeutic targets.
Spyglass: a framework for reproducible and shareable neuroscience research
Authors: Lee Kyu Hyun , Denovellis Eric L. , Ly Ryan , Magland Jeremy , Soules Jeff , Comrie Alison E. , Gramling Daniel P. , Guidera Jennifer A. , Nevers Rhino , Adenekan Philip , Brozdowski Chris , Bray Samuel R. , Monroe Emily , Bak Ji Hyun , Coulter Michael E. , Sun Xulu , Broyles Emrey , Shin Donghoon , Chiang Sharon , Holobetz Cristofer , Tritt Andrew , Rübel Oliver , Nguyen Thinh , Yatsenko Dimitri , Chu Joshua , Kemere Caleb , Garcia Samuel , Buccino Alessio , Frank Loren M.
Published: January 2024

Scientific progress depends on reliable and reproducible results. Progress can also be accelerated when data are shared and re-analyzed to address new questions. Current approaches to storing and analyzing neural data typically involve bespoke formats and software that make replication, as well as the subsequent reuse of data, difficult if not impossible. To address these challenges, we createdSpyglass, an open-source software framework that enables reproducible analyses and sharing of data and both intermediate and final results within and across labs. Spyglass uses the Neurodata Without Borders (NWB) standard and includes pipelines for several core analyses in neuroscience, including spectral filtering, spike sorting, pose tracking, and neural decoding. It can be easily extended to apply both existing and newly developed pipelines to datasets from multiple sources. We demonstrate these features in the context of a cross-laboratory replication by applying advanced state space decoding algorithms to publicly available data.

New users can try out Spyglass on a Jupyter Hub hosted by HHMI and 2i2c:https://spyglass.hhmi.2i2c.cloud/.
Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake
Authors: Tan Han L. , Yin Luping , Tan Yuqi , Ivanov Jessica , Plucinska Kaja , Ilanges Anoj , Herb Brian R. , Wang Putianqi , Kosse Christin , Cohen Paul , Lin Dayu , Friedman Jeffrey M.
Published: January 2024

Leptin is an adipose tissue hormone that maintains homeostatic control of adipose tissue mass by regulating the activity of specific neural populations controlling appetite and metabolism1. Leptin regulates food intake by inhibiting orexigenic agouti-related protein (AGRP) neurons and activating anorexigenic pro-opiomelanocortin (POMC) neurons2. However, while AGRP neurons regulate food intake on a rapid time scale, acute activation of POMC neurons has only a minimal effect3–5. This has raised the possibility that there is a heretofore unidentified leptin-regulated neural population that suppresses appetite on a rapid time scale. Here, we report the discovery of a novel population of leptin-target neurons expressing basonuclin 2 (Bnc2) that acutely suppress appetite by directly inhibiting AGRP neurons. Opposite to the effect of AGRP activation, BNC2 neuronal activation elicited a place preference indicative of positive valence in hungry but not fed mice. The activity of BNC2 neurons is finely tuned by leptin, sensory food cues, and nutritional status. Finally, deleting leptin receptors in BNC2 neurons caused marked hyperphagia and obesity, similar to that observed in a leptin receptor knockout in AGRP neurons. These data indicate that BNC2-expressing neurons are a key component of the neural circuit that maintains energy balance, thus filling an important gap in our understanding of the regulation of food intake and leptin action.
Person-Centred Critical Care: Lessons from a Service Evaluation
Authors: Pearson S. , Petsas A. , Balabanovic J. , Juj M. , Harris W. , Bonnici T.
Published: January 2024

Context

‘Critical care’ encompasses ‘intensive care’, ‘intensive therapy’ and ‘high dependency’ care and is operationalised when patients require specialised monitoring and intervention following complex surgery, or a life-threatening illness or injury.

Background

During the pandemic, the Critical Care Department at UCLH formed a family liaison team to bridge the connection gap between patients, families, and clinical teams. This evolved into the Patient & Family Team (PFT), which organised several engagement events to understand patient and family experiences in critical care.

Methods

Focus group discussions were conducted online and in-person with patients and bereaved families exploring their experience of the service. Discussions revolved around pivotal moments in the critical care journey. Feedback was analysed thematically and validated with the participants.

Findings

Patients described their journey through four stages: Admission, Period of Disorientation, Re-Awakening, and Recovery. Bereaved families categorised their experiences into seven stages from ‘The Phone Call’ to ‘Bereavement.’ The need for effective and compassionate communication and support was evident for both groups.

Discussion

Feedback revealed the emotional journeys of patients and families in critical care. While many experiences align with the existing literature, they also highlight areas for improvement, emphasising the value of human connection in healthcare. This study also demonstrated the need for continuous service evaluation and strategies for understanding underserved populations.
Correlation between autistic traits and brain functional connectivity in preschoolers with autism spectrum disorder: a resting state MEG study
Authors: Taddei Matilde , Cuesta Pablo , Annunziata Silvia , Bulgheroni Sara , Esposito Silvia , Visani Elisa , Granvillano Alice , Dotta Sara , Rossi Davide Sebastiano , Panzica Ferruccio , Franceschetti Silvana , Varotto Giulia , Riva Daria
Published: January 2024

Background

Neurophysiological studies recognized that Autism Spectrum Disorder (ASD) is associated with altered patterns of over- and under-connectivity. However, few results are available about network organization in children with ASD in the early phases of development and the correlation with the severity of core autistic features.

Methods

The present study aimed at investigating the association between brain connectivity derived by MEG signals and severity of ASD traits measured with different diagnostic clinical scales, in a sample of 16 children with ASD aged 2 to 6 years.

Results

A significant correlation emerged between connectivity strength in cortical brain areas implicated in several resting state networks and the severity of communication anomalies, social interaction problems, social affect problems, and repetitive behaviors. Seed analysis revealed that this pattern of correlation was mainly caused by global rather than local effects.

Conclusions

The present results confirm that altered connectivity strength in several resting state networks is related to clinical features and may contribute to neurofunctional correlates of ASD. Future studies implementing the same method on a wider and stratified sample may further support functional connectivity as a possible biomarker of the condition.