bluuebunny/crossref_metadata_2025 huggingface dataset:
A Brain Reward Circuit Inhibited By Next-Generation Weight Loss Drugs
Authors: Godschall Elizabeth N. , Gungul Taha Bugra , Sajonia Isabelle R. , Buyukaksakal Aleyna K. , Ogilvie Sophia , Keeler Austin B. , Zhang YuChen , Deutsch Tyler C. J. , Shi Yu , Conley Nicholas J. , Webster Addison N. , Calhan O. Yipkin , Akkoub Amani , Malik Karan , West Kaleigh I. , Karthikeyan Arun , van Gerven Grace , Patel Manoj K. , Campbell John N. , Deppmann Christopher D. , Güler Ali D.
Published: December 2024

Glucagon-like peptide-1 receptor agonists (GLP1RAs) effectively reduce body weight and improve metabolic outcomes, yet established peptide-based therapies require injections and complex manufacturing. Small-molecule GLP1RAs promise oral bioavailability and scalable manufacturing, but their selective binding to human versus rodent receptors has limited mechanistic studies. The neural circuits through which these emerging therapeutics modulate feeding behavior remain undefined, particularly in comparison to established peptide-based GLP1RAs. Here, we developed humanized GLP1R mouse models to investigate how small- molecule GLP1RAs influence feeding behavior. Integrating genetic manipulations, calcium imaging, and behavior profiling, we discovered that these compounds regulate both homeostatic and hedonic feeding through parallel neural circuits. Beyond engaging canonical hypothalamic and hindbrain networks that control metabolic homeostasis, GLP1RAs recruit a discrete population of Glp1r-expressing neurons in the central amygdala, which selectively suppress the consumption of palatable foods by reducing dopamine release in the nucleus accumbens. Stimulating these central amygdalar neurons curtail hedonic feeding, whereas targeted deletion of the receptor in this cell population specifically diminishes the anorectic efficacy of GLP1RAs for reward-driven intake. These findings reveal a dedicated neural circuit through which small molecule GLP1RAs modulate reward processing, suggesting broad therapeutic potential in conditions of dysregulated dopamine signaling including substance use disorder and binge eating.
A Commander-independent function of COMMD3 in endosomal trafficking
Authors: Squiers Galen T. , Wan Chun , Gorder James , Puscher Harrison , Shen Jingshi
Published: December 2024

Endosomal recycling is a branch of intracellular membrane trafficking that retrieves endocytosed cargo proteins from early and late endosomes to prevent their degradation in lysosomes. A key player in endosomal recycling is the Commander complex, a 16-subunit protein assembly that cooperates with other endosomal factors to recruit cargo proteins and facilitate the formation of tubulo-vesicular carriers. While the crucial role of Commander in endosomal recycling is well established, its molecular mechanism remains poorly understood. Here, we genetically dissected the Commander complex using unbiased genetic screens and comparative targeted mutations. Unexpectedly, our findings revealed a Commander-independent function for COMMD3, a subunit of the Commander complex, in endosomal recycling. COMMD3 regulates a subset of cargo proteins independently of the other Commander subunits. The Commander-independent function of COMMD3 is mediated by its N-terminal domain (NTD), which binds and stabilizes ADP- ribosylation factor 1 (ARF1), a small GTPase regulating endosomal recycling. Mutations disrupting the COMMD3-ARF1 interaction diminish ARF1 expression and impair COMMD3- dependent cargo recycling. These data provide direct evidence that Commander subunits can function outside the holo-complex and raise the intriguing possibility that components of other membrane trafficking complexes may also possess functions beyond their respective complexes.
How does Gloger’s rule predict near- and mid-infrared radiation in birds?
Authors: Lee Thomas , Barrett Meghan , Pilon Laurent , Shultz Allison J. , McGlynn Terrence P
Published: December 2024

Animal coloration has diverse functions such as camouflage, communication, thermoregulation, protection from UV damage and more, and can be shaped by environmental selective pressures. Some climactic selective pressures are strong enough to produce consistent patterns in many species across large-scale geographic gradients. One pattern in endothermic animals is Gloger’s rule, which predicts that populations in hot, humid areas will be darker than those in cool, dry areas. This pattern has been demonstrated in several species across latitudinal gradients and is expected to relate to the selective effects of both local thermoregulatory pressures and humidity. However, shortwave radiation from sunlight extends beyond the visible spectrum [400-700 nm] into the near-infrared; thus, thermal pressures often result in changes in surface reflectance characteristics beyond the visible [e.g., 700-2500 nm]. Further, heat exchange with the environment extends into the mid-infrared, including MIR heat loss through the atmospheric transmission window [7.5 - 14 um]. Here, we examine both UV-NIR absorption and MIR emittance in five species of birds that have been shown to follow, or not follow, Gloger’s rule. We show that NIR absorption varies by species and population in ways that correspond to their habitat and thermoregulatory strategies. MIR emittance, by contrast, was very stable across both species and populations but differed across populations of Northern Bobwhites. We conclude by highlighting the importance of extending coloration research into the NIR and MIR. Further consideration of infrared radiation is necessary for a complete view of animals’ phenotypic diversity and possible responses to thermal challenge.
Chronic Behavioral and Seizure Outcomes following Experimental Traumatic Brain Injury and ComorbidKlebsiella pneumoniaeLung Infection in Mice
Authors: Rewell Sarah S. J. , Shad Ali , Chen Lingjun , Chu Erskine , Wang Jiping , Chen Ke , O’Brien Terence J. , Li Jian , Casillas Espinosa Pablo M. , Semple Bridgette D.
Published: December 2024

Traumatic brain injury (TBI) is a leading cause of long-term disability, and infections such as pneumonia represent a common and serious complication for TBI patients in the acute and subacute post-injury period. While the acute effects of infections have been documented, their long-term consequences on neurological and behavioral recovery as well as the potential precipitation of seizures after TBI remain unclear. This study aimed to investigate the chronic effects ofKlebsiella pneumoniaeinfection following TBI, focusing on post-traumatic seizure development and neurobehavioral changes. Using a mouse model, we assessed the long-term effects of TBI andK. pneumoniaeinfection both in isolation and in combination. We found that, while infection withK. pneumoniaeresulted in loss of body weight and increased mortality compared to vehicle-inoculated mice, there was no additional mortality in TBI animals. Further, although TBI alone induced chronic hyperactivity and reduced anxiety-like behaviors,K. pneumoniaelung infection had no lasting effect on these long-term outcomes. Thirdly, while TBI resulted in both spontaneous and evoked seizures long-term post-injury, early post-injuryK. pneumoniaeinfection did not affect late onset seizure susceptibility. Together with recent findings on acute outcomes in this combined insult model of TBI andK. pneumoniaeinfection, this study suggests thatK. pneumoniaedoes not significantly alter long-term neurobehavioral outcomes or the development of post-traumatic epilepsy. This research highlights the need to further explore the interplay between additional immune insults such as infection that may influence long-term recovery.
Percutaneous assessment of the relationship between Homologous and Non-homologous bones of Upper and Lower limbs among Ghanaian tertiary students
Authors: Okwan Daniel Kobina , Abaidoo Chrissie Stansie , Robertson Juliet , Bempah Samuel Kwadwo Peprah , Wepeba Pet-Paul , Asante Thomas Kwaku , Obeng Priscilla , Domfeh Ethel Akua Achiaa , Afriyie Sarah Owusu
Published: December 2024

Background

Natural disasters and accidents may result in loss of some part of the upper and or lower limbs. In such situations, there is the need to design appropriate best fit prostheses for such victims. There is the need to have sex-and side-specific models that can be applied conveniently to design appropriate prosthesis for maximum benefit to the patient.

Aim

Therefore, this study was designed to determine the relationship between homologous and non-homologous bones of upper and lower limbs among Ghanaians using a percutaneous approach.

Methodology

Ethical approval for this cross-sectional study was sought from the Committee on Human Research, Publication and Ethics, KNUST and 242 participants were sampled via a purposive sampling technique after seeking their consent.

Results

Males significantly recorded greater percutaneous long bones for both the upper and lower limbs than the female participants. With the exception of radial length among the females, for both sexes bilateral asymmetry was observed in the remaining percutaneous limb dimensions where the upper limb parameters were greater on the left side than the right side, but showed right dominance for the lower limb parameters. Although several useful equations were derived, most of them utilized humeral length in the prediction of lower limb length estimation.

Conclusion

Findings of the present study are useful for the biological profiling of humans with dismembered body parts involved in various disasters such as automobile accidents. The formulae derived would be useful for the design of appropriate prostheses. This study has also reaffirmed the existence of sexual and bilateral dimorphism in body dimensions.
Octadecanoids as emerging lipid mediators in cnidarian-dinoflagellate symbiosis
Authors: Botana Marina T. , Lewis Robert E. , Quaranta Alessandro , Salamin Olivier , Revol-Cavalier Johanna , Oakley Clint A. , Feussner Ivo , Hamberg Mats , Grossman Arthur R. , Suggett David J. , Weis Virginia M. , Wheelock Craig E. , Davy Simon K.
Published: December 2024

Oxylipin signaling has been suggested as a potential mechanism for the inter-partner recognition and homeostasis regulation of cnidarian-dinoflagellate symbiosis, which maintains the ecological viability of coral reefs. Here we assessed the effects of symbiosis and symbiont identity on a model cnidarian, the sea anemoneExaiptasia diaphana, using mass spectrometry to quantify octadecanoid oxylipins (i.e.,18-carbon-derived oxygenated fatty acids). A total of 84 octadecanoids were reported, and distinct stereospecificity was observed for the synthesis ofR-andS-enantiomers for symbiont-free anemones and free-living cultured dinoflagellate symbionts, respectively. Symbiont-derived 13(S)-hydroxy-octadecatetraenoic acid (13(S)- HOTE) linked to a 13S-lipoxygnase was translocated to the host anemone with a 32-fold increase, suggesting it as a biomarker of symbiosis and as a potential agonist of host receptors that regulate inflammatory transcription. Only symbiosis with the native symbiontBreviolum minutumdecreased the abundance of pro-inflammatory 9(R)-hydroxy-octadecadienoic acid (9(R)-HODE) in the host. In contrast, symbiosis with the non-native symbiontDurusdinium trenchiiwas marked by higher abundance of autoxidation-derived octadecanoids, corroborating previous evidence for cellular stress in this association. The putative octadecanoid signaling pathways reported here suggest foundational knowledge gaps that can support the bioengineering and selective breeding of more optimal host-symbiont pairings to enhance resilience and survival of coral reefs.
Could Quantum-Mediated Bacterial Signaling Explain Adaptive Mutation?
Authors: Ross Patrick
Published: December 2024

The phenomenon of adaptive mutation in bacteria presents several challenges to classical models of evolution, particularly regarding the observed coordination of mutation patterns across populations. Here, we examine statistical evidence from evolved Escherichia coli populations showing mutation enrichment up to 256-fold above background rates in key metabolic genes, with remarkable temporal stability that appears to transcend known bacterial communication mechanisms. We propose a theoretical framework suggesting that bacteria may utilize quantum coherent oscillations, potentially mediated through synchronized membrane potential fluctuations, to achieve this degree of coordination in adaptive mutation. Building on Sprouffske et al.’s findings that high mutation rates can limit adaptive evolution in E. coli, we examined mutation patterns in four key metabolic genes (pykF, topA, cspC, and rpoC) previously identified as targets of selection. While Sprouffske found that extremely high mutation rates impaired adaptation, our analysis reveals that these genes show non-random enrichment patterns (p < 1.76×10-34 for pykF) that maintain remarkable temporal stability across multiple timepoints. Recent advances in quantum biology have demonstrated sustained quantum coherence in biological systems, we present a model for how quantum-mediated bacterial signaling could potentially contribute to adaptive mutation. The framework makes several experimentally testable predictions about mutation patterns, population dynamics, and coherence times in bacterial populations under stress conditions. While substantial experimental validation remains necessary, this work provides specific approaches for investigating potential quantum contributions to bacterial adaptation, with implications for understanding evolutionary mechanisms and bacterial stress responses.
Evidence of supratentorial white matter injury prior to treatment in children with posterior fossa tumours using diffusion MRI
Authors: Drabek-Maunder Emily R. , Gains Jenny , Hargrave Darren R. , Mankad Kshitij , Aquilina Kristian , Dean Jamie A. , Nisbet Andrew , Clark Chris A.
Published: December 2024

Background

Paediatric brain tumour survivors can have neurocognitive deficits that negatively impact their quality of life, but it is unclear if deficits are primarily caused by treatments, such as radiotherapy, or manifest earlier due to the tumour and related complications. The aim of this work is to characterise white matter injury caused by brain tumours, unrelated to treatment effects, and explore heterogeneity in these white matter abnormalities between individual patients.

Methods

We used diffusion tensor imaging (DTI) and Neurite Orientation Dispersion Diffusion Imaging (NODDI) to assess white matter injury in 8 posterior fossa tumour patients. A novel one-against-many approach was used by comparing an individual patient to 20 age- and sex-matched healthy controls to assess variability in white matter abnormalities between the posterior fossa tumour patients. White matter was analysed at presentation (prior to treatment), post-surgery (24-72 hours after surgery), and at follow-up (3-18 months after surgery).

Results

We demonstrate white matter abnormalities in 5 posterior fossa tumour patients before treatment, likely related to tumour-induced hydrocephalus, which persisted after treatment. White matter changes were complex and patient-specific, and group-based comparisons with control sub-jects may fail to detect these individual abnormalities.

Conclusions

Identifying pre-treatment white matter injury in posterior fossa tumour patients highlights the importance of personalised assessment of brain microstructure, which should be considered in minimising neurocognitive deficits to improve patient quality of life.
EDEPS (Early Detection of ExtraPyramidal Symptoms): supervised machine learning models to detect antipsychotics-induced extrapyramidal hand tremor from a mobile device built-in sensors
Authors: Wysokiński Adam , Zwierzchowska-Kieszek Aleksandra
Published: December 2024

Introduction

Approximately 30% of patients treated with antipsychotics develops extrapyramidal side effects, among which hand tremor is not only common, but also significantly impacting daily activities. No tool for remote assessment of hand tremor is available.

Materials and methods

We collected SAS and AIMS scores and digital recordings of health tremor from healthy and schizophrenia patients on antipsychotics. Next, we created and tested a supervised machine learning models for detecting and measuring severity of antipsychotics-induced hand tremor.

Results

We present model details, accuracy measures (R2and RMSE for regressors; log loss, AUC, misclassification, rate, accuracy, sensitivity and specificity for classifiers) and analysis of hand tremor spectral analysis.

Conclusions

Our model offers a satisfactory accuracy (0.95 to 1.0) and performance, even if only 10 second data is available. Result of the spectral analysis indicate that the dominating frequency of hand tremor in antipsychotics-induced EPS is approximately 5.0 Hz.
Non-Caloric Sweeteners combined with glucose affect hypothalamic glucose sensing-induced insulin secretion, food re-intake through neuronal cellular metabolism: Anin vivoandin vitroapproaches
Authors: Haydar J. , Fenech C. , Liénard F. , Abed B. , Grall S. , Briand Loïc , Walther G. , Leloup C.
Published: December 2024

1

Changes in brain activity associated with deleterious metabolic effects of non-caloric sweeteners (NCS) have been demonstrated in humans, particularly when their intake is concomitant with that of glucose. Here, we have focused on hypothalamic glucose sensing in rats, detecting increases in circulating glucose levels and in turn triggering various physiological controls. The identification of sweet-taste receptors in the hypothalamus has suggested that they participate in glucosensing mechanism, but the existence of a dialogue between different pathways has never been studied. Here, we tested the acute effects of hypothalamic glucosensing combined with a NCS (sucralose or acesulfame potassium (aceK)), the latter binding only to sweet-taste receptors, without producing energy. Our working hypothesis was that the concomitance of two contradictory signals (energetic, sweet glucose vs. non-energetic, sweet NCS) could be responsible for deleterious physiological effects. After validation that sweet taste receptors and their signaling expressions were indeed present in the rat hypothalamus, insulin secretion induced by hypothalamic glucosensing (increased glucose level) in the presence of sucralose and aceK was examined. Insulin release was reduced compared to glucose alone, while the two NCS alone have no effect. Regarding the satiety-inducing effect of glucose, concomitant injection of each NCS with glucose produced the opposite effect to that observed with glucose alone, with food intake being increased, an effect also present with NCS injected alone. Using the GT1-7 hypothalamic cell line expressing sweet-taste receptors, we showed that the ATP concentration which normally increases with rising glucose levels was dose-dependently decreased in the presence of NCS, an effect which is inhibited in the presence of gurmarin, a specific inhibitor of sweet-taste receptors. The increase in ROS production in response to rising glucose levels was enhanced in the presence of NCS, an effect that was blocked in the presence of gurmarin. In both cases, NCS have an inhibitory effect on stimulated mitochondrial respiration. Taken together, these results suggest that NCS via sweet-taste receptors interfere with mitochondrial signaling and/or energy production during hypothalamic glucose sensing.
Maize inbreds show allelic variation for diel transcription patterns
Authors: Gage Joseph L. , Romay M. Cinta , Buckler Edward S.
Published: December 2024

Circadian entrainment and external cues can cause gene transcript abundance to oscillate throughout the day, and these patterns of diel transcript oscillation vary across genes and plant species. Less is known about within-species allelic variation for diel patterns of transcript oscillation, or about how regulatory sequence variation influences diel transcription patterns. In this study, we evaluated diel transcript abundance for 24 diverse maize inbred lines. We observed extensive natural variation in diel transcription patterns, with two-fold variation in the number of genes that oscillate over the course of the day. A convolutional neural network trained to predict oscillation from promoter sequence identified sequences previously reported as binding motifs for known circadian clock genes in other plant systems. Genes showing diel transcription patterns that cosegregate with promoter sequence haplotypes are enriched for associations with photoperiod sensitivity and may have been indirect targets of selection as maize was adapted to longer day lengths at higher latitudes. These findings support the idea that cis-regulatory sequence variation influences patterns of gene expression, which in turn can have effects on phenotypic plasticity and local adaptation.
Variability of axon initial segment geometry and its impact on hippocampal pyramidal cell function
Authors: Stevens Nikolas Andreas , Achilles Maximilian , Monath Juri , Engelhardt Maren , Both Martin , Thome Christian
Published: December 2024

Action potentials, the primary information units of the nervous system, are usually generated at the axon initial segment (AIS). Changes in the length and position of the AIS are associated with alterations in neuronal excitability but there is only limited information about the baseline structural variability of the AIS. This work provides a comprehensive atlas of the diversity of proximal cell geometries across all anatomical axes of the murine hippocampus, encompassing dorsal-ventral, superficial-deep, and proximal-distal regions. We analyzed the morphology of 3,936 hippocampal pyramidal neurons in 12 animals of both sexes, focusing on AIS length, position, and their association with proximal cellular features such as the soma and dendritic geometries. Notably, neurons with axon-carrying dendrites were significantly more common in ventral compared to dorsal hippocampal areas, suggesting a functional adaptation to regional demands. Validation of this finding in human samples confirms the translational relevance of our murine model. We employed NEURON simulations to assess the functional implications of this variability. Here, variation in proximal geometry only minimally contributed to neuronal homeostasis, but instead increased heterogeneity of response patterns across neurons.
Disparate co-evolution and prevalence of sulfadoxine and pyrimethamine resistance alleles and haplotypes atdhfranddhpsgenes across Africa
Authors: White Nina F. D. , Whitton Georgia , Wasakul Varanya , Amenga-Etego Lucas , Dara Antoine , Andrianaranjaka Voahangy , Randrianarivelojosia Milijaona , Miotto Olivo , D’Alessandro Umberto , Djimdé Abdoulaye , Ariani Cristina V. , Pearson Richard D. , Amambua-Ngwa Alfred
Published: December 2024

Sulfadoxine-pyrimethamine (SP), despite the emergence and spread of mutations indhfranddhpsgenes associated with lower treatment efficacy, is still recommended alone or in combination by the WHO for preventive treatment in pregnant women, children and infants. Therefore, it is important to understand the evolution ofP. falciparum dhfranddhpsgenes. Here, we used a subset of the MalariaGEN Pf7 dataset to describe haplotype frequencies across 22 African countries, including changes over time in The Gambia, Mali, Ghana and Kenya. We show that the triple mutant ofdhfr,N51I/C59R/S108N, has remained the dominant haplotype across the continent with limited evidence of additional mutations. There is greater variation fordhps, with a total of 51 different haplotypes present. Thedhpsresistance mutation A437G has risen close to fixation across most of Africa, although at a lower frequency in the northwest malaria-endemic part of the continent (Gambia, Senegal and Mali). The A437G mutation is usually found together with K540E in East Africa, but K540E is still very rare in West Africa. Although samples from Madagascar have low genetic differentiation from samples from mainland East Africa at the whole genome level, we show thatdhpsK540E is highly differentiated between the two populations, being at very low frequency in Madagascar (4%). We used whole genome data to show that only 12 SNPs are more highly differentiated than K540E between Madagascar and East Africa, withaat1and a possible novel drug resistance locus approximately 20kb 3’ ofmdr1having even higher FST. We highlight the value of longitudinal sampling and whole genome sequence data for understanding the heterogeneity and ongoing changes in anti-malarial drug resistance genetic markers.
Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of H5N1 into agriculture in North America
Authors: Damodaran Lambodhar , Jaeger Anna , Moncla Louise H.
Published: December 2024

Since late 2021, a panzootic of highly pathogenic H5N1 avian influenza virus has driven significant morbidity and mortality in wild birds, domestic poultry, and mammals. In North America, infections in novel avian and mammalian species suggest the potential for changing ecology and establishment of new animal reservoirs. Outbreaks among domestic birds have persisted despite aggressive culling, necessitating a re-examination of how these outbreaks were sparked and maintained. To recover how these viruses were introduced and disseminated in North America, we analyzed 1,818 Hemagglutinin (HA) gene sequences sampled from North American wild birds, domestic birds and mammals from November 2021-September 2023 using Bayesian phylodynamic approaches. Using HA, we infer that the North American panzootic was driven by ∼8 independent introductions into North America via the Atlantic and Pacific Flyways, followed by rapid dissemination westward via wild, migratory birds. Transmission was primarily driven by Anseriformes, shorebirds, and Galliformes, while species such as songbirds, raptors, and owls mostly acted as dead-end hosts. Unlike the epizootic of 2015, outbreaks in domestic birds were driven by ∼46-113 independent introductions from wild birds, with some onward transmission. Backyard birds were infected ∼10 days earlier on average than birds in commercial poultry production settings, suggesting that they could act as “early warning signals” for transmission upticks in a given area. Our findings support wild birds as an emerging reservoir for HPAI transmission in North America and suggest continuous surveillance of wild Anseriformes and shorebirds as crucial for outbreak inference. Future prevention of agricultural outbreaks may require investment in strategies that reduce transmission at the wild bird/agriculture interface, and investigation of backyard birds as putative early warning signs.
Different liposomal formulations of 5-Fluorouracil result in variations to gastrointestinal toxicities
Authors: Thorpe Daniel , Wang Wen , Milne Robert , Stringer Andrea
Published: December 2024

5-Fluorouracil (5FU) treatment can induce severe mucositis, gastrointestinal toxicity. New formulations of 5-FU increase cancer cytotoxicity, such as neutral liposomes (NL), cationic liposomes (CL), and polyethylenimine copper (PEI-Cu) complexes. However, gastrointestinal toxicity for these new formulations remains unclear. We aim to determine if new formulations in 5FU reduce mucositis by reducing intestinal goblet cell and nerve integrity.

Sprague Dawley rats were randomly assigned to groups: saline (n=6), 5FU (n=6 ), NL-5FU (n=5), CL-5FU (n=5), PEI-CU-5FU (n=6), NL-PEI-Cu-5FU (n=5) CL-PEI-Cu-5FU (n=5) (Formulations were equivalent to 10mg/kg 5FU in saline). Treatment was administered daily for 5 days. Rats where humanely killed 2 days after treatment. Haematoxylin and Eosin staining for histological change, Alcian Blue-PAS staining for mucin composition, and immunohistochemistry with S100 antibody for nerve integrity were performed. Statistical analysis using Kruskal-Wallis test with Dunns post-test and Mann Whitney U test d were performed. Effect size was determined using Cohen’s D test.

In the jejunum, inflammatory infiltrate increased in PEI-Cu-5FU rats compared to 5-FU controls (p=0.0011). S100 positive nerve bundles increased in NL-5FU rats compared to saline control (p<0.05). S100 positive cells increased in CL-PEI-Cu-5FU rats compared to saline controls.

PEI-Cu-5FU formulation was associated with increased inflammatory infiltrate potentially in response to damage in the jejunum. However, liposomal formulations increased S100 positive neural cells, which may offer protection through increased gastrointestinal motility and contraction. While these formulations of 5FU increase cancer cytotoxicity, the gastrointestinal toxicity remains similar. However, further close monitoring of 5FU formulations for gastrointestinal toxicity is warranted.
Recombinant Expression of Photo-crosslinkable 26S Proteasome Base Subcomplex
Authors: Restrepo Santiago Yori , Martin Andreas
Published: December 2024

The 26S proteasome complex is the hub for regulated protein degradation in the cell. It is composed of two biochemically distinct complexes: the 20S core particle with proteolytic active sites in an internal chamber and the 19S regulatory particle, consisting of a lid and base subcomplex. The base contains ubiquitin receptors and an AAA+ (ATPases associated with various cellular activities) motor that unfolds substrates prior to degradation. TheS. cerevisiaebase subcomplex can be expressed recombinantly inE. coliand reconstituted into functional 26S proteasomesin vitro, which allows the introduction of unnatural amino acids with novel functions or other mutations that may not be permissiblein vivo. Here, we present a method for the introduction of the photo-induced crosslinking amino acid p-benzoyl-L-phenylalanine into the proteasomal base subcomplex. This approach has exciting implications for the study of protein-protein interactions of this complex that mediates the degradation of an incredibly diverse protein pool.
An early-stage cost and implementation feasibility study of the administration of pro/synbiotics to infants 0-5 months in rural Kenya
Authors: McCallum Beth , Otiti Iwaret , Achieng Florence , Allen Stephen , Worral Eve
Published: December 2024

Background

Undernutrition underlies approximately 45% of global deaths among children less than five years old, making it one of the most concerning global child health issues. ThePRObiotics andSYNbiotics in infants inKenya (PROSYNK) trial is assessing whether supervised doses of pro/synbiotics daily for the first 10 days and then weekly to age 6 months (total of 32 doses), has a positive impact on gut health and thereby growth and nutrition. This study is an early-stage cost and implementation feasibility study defining unit costs for the PROSYNK trial and estimating programmatic cost and feasibility of delivering the intervention to infants in rural Kenya.

Methods

This provider perspective costing study uses a combination of ingredients approach, activity-based costing and microcosting. First, an empirical cost analysis of the PROSYNK trial was conducted by review of trial documentation and time and motion observations. Next, semi-structured interviews with key informants informed a thematic analysis of implementation feasibility and the development of a theoretical programme structure which formed the basis for estimation of total economic programme costs.

Results

The economic cost of delivering the full pro/synbiotics course under trial conditions was measured as $757.32 per participant. Experience gained during PROSYNK and discussions with key informants revealed that it was feasible for the Ministry of Health (MoH) to implement programmatic delivery of the pro/synbiotics, particularly through community-based delivery, without a cold chain and with pro/synbiotic administered directly into infant’s mouths. Incremental economic costs to the MoH of delivering the pro/synbiotic programmatically were estimated to be $9.15 per infant per full course under the base case scenario.

Conclusion

Pro/synbiotic administration in early life may be feasible and bear similar costs to existing nutrition interventions. This study will provide policy makers and stakeholders with vital cost and feasibility information to inform effective programmatic implementation in Kenya and similar settings.
Structure-based Design of Chimeric Influenza Hemagglutinins to Elicit Cross-group Immunity
Authors: Castro Karla M. , Ayardulabi Reyhaneh , Wehrle Sarah , Cui Hongrui , Georgeon Sandrine , Schmidt Joseph , Xiao Shuhao , Seraj Nishat , Harshbarger Wayne , Mallett Corey P. , Vassilev Ventzislav , Saelens Xavier , Correia Bruno E.
Published: December 2024

Antigenic variability among influenza virus strains poses a significant challenge to developing broadly protective, long-lasting vaccines. Current annual vaccines target specific strains, requiring accurate prediction for effective neutralization. Despite sequence diversity across phylogenetic groups, the hemagglutinin (HA) head domain’s structure remains highly conserved. Utilizing this conservation, we designed cross-group chimeric HAs that combine antigenic surfaces from distant strains. By structure-guided transplantation of receptor-binding site (RBS) residues, we displayed an H3 RBS on an H1 HA scaffold. These chimeric immunogens elicit cross-group polyclonal responses capable of neutralizing both base and distal strains. Additionally, the chimeras integrate heterotrimeric immunogens, enhancing modular vaccine design. This approach enables the inclusion of diverse strain segments to generate broad polyclonal responses. In the future, such modular immunogens may serve as tools for evaluating immunodominance and refining immunization strategies, offering potential to bridge and enhance immune responses in individuals with pre-existing immunity. This strategy holds promise for advancing universal influenza vaccine development.

Graphical abstract: Overview of cross-group RBS transplantation approach

Phylogenetically diverse HA strains can be incorporated into chimeric immunogens by RBS transplantation. The chimera are evaluated for cross-reactivity to subtype-specific antibodies and the ability to elicit neutralizing antibodies to multiple strains.
A low-cost FPGA-based approach for pile-up corrected high-speed in vivo FLIM imaging
Authors: Moros Felipe Velasquez , Amiet Dorian , Meister Rachel Megan , von Faber-Castell Alexandra , Wyss Matthias , Saab Aiman S. , Zbinden Paul , Weber Bruno , Ravotto Luca
Published: December 2024

Intensity-based two-photon microscopy (2PM) is a cornerstone of biomedical research but lacks the ability to measure concentrations, a pivotal task for longitudinal studies and quantitative comparisons. Fluorescence Lifetime Imaging (FLIM) based on Time-Correlated Single Photon Counting (TCSPC) can overcome those limits but suffers from “pile-up” distortions at high photon count rates, severely limiting acquisition speed. We introduce the “laser period blind time” (LPBT) method to correct pile-up distortions in photon counting electronics, enabling reliable low-cost TCSPC-FLIM at high count rates. The correction was implemented on low-cost hardware based on a field programable gate array (FPGA) and validated using a combination of in silico simulations and in vitro, ex vivo and in vivo measurements. The LBPT approach achieves <3% error in lifetime measurements at count rates more than ten times higher than traditional limits, allowing robust FLIM imaging of sub-second metabolite dynamics with subcellular resolution. Our work enables high-precision, cost-effective FLIM imaging at rates comparable to commercial systems and at a fraction of the cost, facilitating the adoption of FLIM across all areas of research needing affordable, quantitative live imaging solutions.
Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations
Authors: Aditham Arjun K. , Radford Caelan E. , Carr Caleb R. , Jasti Naveen , King Neil P. , Bloom Jesse D.
Published: December 2024

Rabies virus causes nearly 60,000 human deaths annually. Antibodies that target the rabies glycoprotein (G) are being developed as post-exposure prophylactics, but mutations in G can render such antibodies ineffective. Here, we use pseudovirus deep mutational scanning to measure how all single amino-acid mutations to G affect cell entry and neutralization by a panel of antibodies. These measurements identify sites critical for rabies G’s function, and define constrained regions that are attractive epitopes for clinical antibodies, including at the apex and base of the protein. We provide complete maps of escape mutations for eight monoclonal antibodies, including some in clinical use or development. Escape mutations for most antibodies are present in some natural rabies strains. Overall, this work provides comprehensive information on the functional and antigenic effects of G mutations that can help inform development of stabilized vaccine antigens and antibodies that are resilient to rabies genetic variation.
Independence of Centromeric and Pericentromeric Chromatin Stability on CCAN Components
Authors: Biggs Ronald J. , Sundararajan Kousik , Sun Mingxuan , Hendrix Eline , Straight Aaron F. , Marko John F.
Published: December 2024

The chromatin of the centromere provides the assembly site for the mitotic kinetochore that couples microtubule attachment and force production to chromosome movement in mitosis. The chromatin of the centromere is specified by nucleosomes containing the histone H3 variant CENP-A. The constitutive centromeric-associated network (CCAN) and kinetochore are assembled on CENP-A chromatin to enable chromosome separation. CENP-A chromatin is surrounded by pericentromeric heterochromatin and bound by the sequence specific binding protein CENP-B. We performed mechanical experiments on mitotic chromosomes while tracking CENP-A and CENP-B to observe the centromere’s stiffness and the role of the CCAN. We degraded CENP-C and CENP-N using auxin-inducible degrons, which we verified compromises the CCAN via observation of CENP-T loss. Chromosome stretching revealed that the CENP-A domain does not visibly stretch, even in the absence of CENP-C and/or CENP-N. Pericentromeric chromatin deforms upon force application, stretching approximately 3-fold less than the entire chromosome. CENP-C and/or CENP-N loss has no impact on pericentromere stretching. Chromosome-disconnecting nuclease treatments showed no structural effects on CENP-A. Our experiments show that the core-centromeric chromatin is more resilient and likely mechanically disconnected from the underlying pericentromeric chromatin, while the pericentric chromatin is deformable yet stiffer than the chromosome arms.
Linkage-based ortholog refinement in bacterial pangenomes with CLARC
Authors: González Ojeda Indra , Palace Samantha G. , Martinez Pamela P. , Azarian Taj , Grant Lindsay R. , Hammitt Laura L. , Hanage William P. , Lipsitch Marc
Published: December 2024

Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) [https://github.com/IndraGonz/CLARC] improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8,000+Streptococcus pneumoniaegenomes, CLARC reduced accessory gene estimates by more than 30% and improved evolutionary predictions based on accessory gene frequencies. By refining COG definitions, CLARC offers critical insights into bacterial evolution, aiding genetic studies across diverse populations.
Promoting helmet usage in undergraduates with electric and non-electric bicycles and scooters: a single-site survey and intervention
Authors: Dorsey Alanna , Li Gabrielle , Cha Spencer , Ritter Victor , Flao Enora Le , Camarillo David B.
Published: December 2024

College students report alarmingly low helmet usage while riding bikes and other open-wheeled forms of transportation (OWTs), increasing risk of brain injury and skull fracture. Despite prior interventions, this problem persists, necessitating an updated examination of the current barriers to helmet usage, and how to effectively mitigate them. This study aimed to determine the effect of class year on helmet usage in American college students, and explore emerging trends with electric bikes, skateboards, and scooters. We created and distributed an online survey to undergraduate students at Stanford University in California (N = 400) who regularly used electric or non-electric bikes, skateboards, or scooters. This survey collected information on helmet usage, attitudes on bike safety, and demographics, and the findings were used to design a pilot intervention. Students who regularly wore helmets were recruited as peer agents (N=3) and were trained to ask friends and classmates to pledge to wear a helmet. We observed bike, scooter, and skateboard rides (N = 4885), and followed up with students who pledged to analyze their behavior change. We confirmed prior trends that most college students never or rarely wear a helmet, and the most common reasons for not wearing a helmet were “Helmets mess up my hair” (44%), “I don’t see others wearing helmets” (43%), and “It’s unlikely I will fall/crash” (34%). We also found that helmet usage was similarly low (48% of participants reported never wearing a helmet) across class years, but class years reported different reasons for not wearing a helmet. Lastly, there was no difference in helmet usage between electric and non-electric OWT users for any of the frequency categories (p=0.43 for daily, p=0.44 for a few times a week, p=0.77 for a few times a month, p=0.23 for rarely, p=0.15 for never), revealing that previous trends in helmet behavior also apply to American college students with electric OWTs. The pilot intervention resulted in a non-significant yet positive trend, and students who pledged demonstrated a behavior change (as measured by follow-up surveys about helmet usage) that persisted 3 weeks after the conclusion of the intervention. In addition to finding that past trends about helmet behavior in college students are still present, we discovered new trends on electric OWTs and class years in American college students. We also found that our peer agent program shows promise in modifying the behavior of college students.
Spatial Perturb-Seq: Single-Cell Functional Genomics within Intact Tissue Architecture
Authors: Shen Kimberle , Seow Wan Yi , Keng Choong Tat , Shern Daryl Lim , Guo Ke , Meliani Amine , Hajis Irfan Muhammad Bin , Chen Kok Hao , Chew Wei Leong
Published: December 2024

We develop Spatial Perturb-Seq, anin vivoCRISPR technology that interrogates multiple genes within single cells of intact tissues. We apply Spatial Perturb-Seq to screen risk genes for neurodegenerative diseases in the mouse brain, uncovering cell autonomous and cell-cell microenvironmental effects within the spatially intact tissue. Spatial Perturb-Seq functionally screens multiple genesin situandin vivo, identifying candidate genes underlying dysregulated neuronal intercellular communication pathways in Lrp1 signalling and ephrin-Eph receptor interactions.
Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS
Authors: Kiewisz Robert , Fabig Gunar , Conway Will , Johnston Jake , Kostyuchenko Victor A. , Bařinka Cyril , Clarke Oliver , Magaj Magdalena , Yazdkhasti Hossein , Vallese Francesca , Lok Shee-Mei , Redemann Stefanie , Müller-Reichert Thomas , Bepler Tristan
Published: December 2024

It is now possible to generate large volumes of high-quality images of biomolecules at near-atomic resolution and in near-native states using cryogenic electron microscopy/electron tomography (Cryo-EM/ET). However, the precise annotation of structures like filaments and membranes remains a major barrier towards applying these methods in high-throughput. To address this, we present TARDIS (Transformer-basedRapidDimensionlessInstanceSegmentation), a machine-learning framework for fast and accurate annotation of micrographs and tomograms. TARDIS combines deep learning for semantic segmentation with a novel geometric model for precise instance segmentation of various macromolecules. We develop pre-trained models within TARDIS for segmenting microtubules and membranes, demonstrating high accuracy across multiple modalities and resolutions, enabling segmentation of over 13,000 tomograms from the CZI Cryo-Electron Tomography data portal. As a modular framework, TARDIS can be extended to new structures and imaging modalities with minimal modification. TARDIS is open-source and freely available athttps://github.com/SMLC-NYSBC/TARDIS, and accelerates analysis of high-resolution biomolecular structural imaging data.
Phosphatidylinositol-3,5-bisphosphate mediated vacuolar morphology modulation is integral to ethanol stress response
Authors: Mandal Pritha , Hazra Babai , Ghosh Trisha , Patra Nabanita , Sarkar Srimonti
Published: December 2024

Vacuoles enlarge in response to ethanol. We used quantitative imaging to show that even brief exposure to ethanol causes a rapid transition from multilobed vacuoles to a single compartment. Vacuole unlobing is essential as mutants restricted for vacuole fusion exhibit greater ethanol sensitivity. This response involves the inhibition of vacuole fission via downregulation of the activity of Fab1, a lipid kinase generating the signaling lipid phosphatidylinositol-3,5-bisphosphate. Ethanol exposure results in the redistribution of a phosphatidylinositol-3,5-bisphosphate sensor from the perivauolar dots to the cytoplasm and the dissociation of the effector of this lipid, Atg18, from the vacuolar membrane to the cytoplasm. Impaired Atg18 membrane recruitment also entails a loss of interaction between a scaffold of the Fab1 complex, Vac14, and Atg18. A hyperactive Fab1 mutant, with elevated pools of phosphatidylinositol-3,5-bisphosphate, shows delayed vacuole enlargement; the partial relocation of the phosphatidylinositol-3,5-bisphosphate probe to the perivacuolar dots and of Atg18 to the vacuole membrane. Since Atg18 is responsible for vacuole fragmentation, our results show that, under ethanol stress, cells actively regulate vacuole morphology by modulating phosphatidylinositol-3,5-bisphosphate levels.
Neuronal activation in the axolotl brain promotes spinal cord regeneration
Authors: Walker SE , Yu K , Burgess S , Echeverri K
Published: December 2024

The axolotl retains a remarkable capacity for regenerative repair and is one of the few vertebrate species capable of regenerating its brain and spinal cord after injury. To date, studies investigating axolotl spinal cord regeneration have placed particular emphasis on understanding how cells immediately adjacent to the injury site respond to damage to promote regenerative repair. How neurons outside of this immediate injury site respond to an injury remains unknown. Here, we identify a population of dpErk+/etv1+glutamatergic neurons in the axolotl telencephalon that are activated in response to tail amputation. Importantly, the activation of these neurons facilitates successful tail regeneration by promoting axon extension into the newly regenerated tissue. We demonstrate that these dpErk+neurons extend axons into the hypothalamus, which has a well-established role in hormone production. Furthermore, these neurons upregulate the neuropeptide neurotensin in response to injury, which in turn stimulates the production of multiple hormones in the hypothalamus to promote regenerative repair. Together, these findings identify a unique population of neurons in the axolotl brain whose activation is necessary for successful spinal cord regeneration, and sheds light on how neurons outside of the immediate injury site respond to a spinal cord injury.