bluuebunny/crossref_metadata_2025_split huggingface dataset:
You can do it!–Using published undergraduate research onHydramouth opening to train undergraduates
Authors: Hackler S. , Goel T. , Pacis J. , Collins E.-M. S. 
Published: December 2024

AbstractBiophysical research is both exciting and challenging. It is exciting because physical approaches to biology can provide novel insights, and it is challenging because it requires knowledge and skills from multiple disciplines. We have developed an undergraduate biophysical laboratory module that is accessible to both biology and physics majors, teaches fundamental skills such as time-lapse microscopy, image analysis, programming, critical reading of scientific literature, and basics of scientific writing and peer-review. This module uses published research on the biomechanics ofHydramouth opening as its framework because this work was co-first authored by an undergraduate student and featured in the public press, thus providing two anchors that make this research accessible and exciting to undergraduates. Students start with a critical reading and discussion of the publication. Then they execute some of the experiments and analysis from the paper, thereby learning fluorescence time-lapse microscopy and image analysis using ImageJ and/or MATLAB/Python, and compare their data to the literature. The module culminates in the students writing a short paper about their results following theMicropublicationjournal style, a blinded peer-review, and final paper submission. Here, we describe one possible implementation of this module with the necessary resources to reproduce it, and summarize student feedback from a pilot run. We also provide suggestions for more advanced exercises. Several students expressed that repeating a published study done by an undergraduate student inspired and motivated them, thus creating buy-in and assurance that they “can do it”, which we expect to help with confidence and retention.
Effects of the DailyColors™ Polyphenol Supplement on Serum Proteome, Cognitive Function, and Health in Older Adults at Risk of Cognitive and Functional Decline
Authors: O’Leary Mary , Bowtell Joanna L , Richards Megan , Bozbaş Esra , Palmer Abbie , Stych Kate , Meng Monica , Bloomfield Adam , Struszczak Lauren , Pritchard Jack , Lugtmeijer Celeste , Vere George , Yücel Raif , Mateos Ana Rodriguez , Zhang Zicheng , Tang Jonathan CY , Ballard Clive , Corbett Anne 
Published: December 2024

AbstractThe Mediterranean diet is associated with reduced mortality and cognitive decline, largely due to its polyphenol content. However, Western populations often do not meet recommended fruit and vegetable intakes. Polyphenols exert anti-inflammatory effects and may influence extracellular vesicle (EV) dynamics. DailyColors™ is a polyphenol-rich blend inspired by the Mediterranean Diet, containing extracts from 16 fruits, vegetables, and herbs. This 60-day, double-blind, placebo-controlled, randomised trial involved 150 UK adults aged 50+ with a BMI ≥ 25, recruited to complete cognitive and physical fitness assessments via the PROTECT-UK online platform. Participants received either a medium (750mg) or high (2000mg) dose of DailyColors™ (∼300mg and ∼750mg polyphenols, respectively) or a placebo. A sub-group (n=15 per group) underwent additional assessments, including blood pressure measurements, characterisation of circulating EVs and tandem-mass-tagged serum proteomics. Significant cognitive benefits were observed, with improvements in reaction time for the high-dose group and accuracy for both active supplement groups. The high-dose group also showed significant physical fitness gains on the Timed Stand Test (P<0.001). All groups improved on the Chair Stand Test. Proteomic analysis showed significantly reduced serum protein expression in immune and pre-β1-HDL pathways, suggesting anti-inflammatory effects. Pre-β1-HDL proteins are typically elevated in obesity; their reduction suggests a reversal of this obesity-related effect. No significant changes were noted in EV concentration or size. DailyColors™ supplementation, may enhance cognitive function, physical fitness, and systemic health in older, overweight adults, potentially mimicking the anti-inflammatory effects of the Mediterranean diet. These findings warrant investigation in larger trials.
Cardiometabolic Risk Factors in South Asians: An Epidemiological and Anthropological Study in an Urban Populace of Eastern India
Authors: Yasmin Karishma 
Published: December 2024

AbstractBackgroundThis study examines cardiometabolic (CM) risk factors in an urban South Asian population, integrating medical and Anthropological perspectives to explore the effects of socio-economic, lifestyle, gender-specific factors, and cultural norms on health outcomes.ResultsAnalysis indicates a high prevalence of MetS and Pre-MetS, particularly among females, with significant predictors including BMI, triglycerides, total cholesterol, and waist circumference, alongside socio-genetic and lifestyle factors. Employing Elastic Net logistic regression, the researcher rigorously validated models to evaluate their predictive performance while also describing the associations and prevalence of known risk factors. The use of this method underlines the importance of combining traditional risk factors with socio-genetic, biological, economic and lifestyle variables, while Anthropological insights reveal the impact of urbanization and socio-cultural norms on health behaviors.ConclusionThe study advocates for a multidisciplinary approach in public health strategies, emphasizing the complex interplay between genetic, environmental, biological and socio-cultural influences on cardiometabolic health. This dual approach aligns with descriptive and predictive model goals. The future research should further integrate biomedical sciences with socio-cultural studies to develop culturally sensitive interventions, aiming to address the growing challenge of CM diseases in urban South Asian contexts.
Honestly exaggerated: howler monkey roars are reliable signals of body size and behaviourally relevant to listeners
Authors: Dunn Jacob C. , Pederson Eloise , Farmer Holly , Dobbs Philippa , Fitch W. Tecumseh , Reby David , Charlton Benjamin 
Published: December 2024

AbstractAcoustic signals are key components of animal social behaviour, potentially conveying fitness relevant information about signallers. Howler monkeys produce extremely loud, low frequency roars, which exaggerate the acoustic impression of body size relative to other species. However, it remains unclear whether howler monkey roars contain reliable information about body size within species, and whether conspecific listeners use this information and adjust their responses accordingly. Here, we investigate whether the roars of black and gold howler monkeys (Alouatta caraya) function as an honest signal of body size by examining the relationship between formant spacing and body mass in 11 adult males. We found a strong negative correlation, indicating that larger males produce roars with lower formant spacing. To test the behavioural relevance of variation in formant spacing, we then conducted playback experiments with 23 conspecific listeners, simulating the roars of unknown males of small, average, and large body size. Listeners showed significantly different responses to calls of different body sizes, spending longer orientated towards the playback speaker and being more likely to approach calls simulating larger males. There was no significant impact of simulated body size on the likelihood of listeners vocalising in response, although males spent significantly more time vocalising in response to playbacks than females. Overall, these findings suggest that formant spacing in howler monkey roars serves as an honest indicator of body size and plays a critical role in mediating social interactions. Our study highlights the adaptive significance of acoustic cues to body size, which can provide receivers with accurate information that can be used to assess rivals or choose mates.
Vγ1+γδ T cell-derived IL-4 initiates CD8 T cell immunity
Authors: Le Shirley , Murphy Declan , Liu Shangyi , Ge Zhengyu , May Rose , Cozijnsen Anton , Burn Thomas , Jennison Charlie , Bachem Annabell , Xu Calvin , Koay Hui-Fern , Schröder Jan , Gras Stephanie , Cockburn Ian A. , Bedoui Sammy , Mackay Laura K. , McFadden Geoffrey I , Fernandez-Ruiz Daniel , Heath William R , Beattie Lynette 
Published: December 2024

AbstractDendritic cells (DC) are pivotal for initiating adaptive immunity, a process triggered by the activation of DC via pathogen products or damage. Here, we describe an additional layer to this process, essential when pathogen-derived signals alone cannot directly achieve full DC activation. Immunisation with sporozoites fromPlasmodiumleads to CD8 T cell priming in a complex response that is initiated by a collaboration between conventional type 1 DC (cDC1) and γδ T cells. We unveil a pivotal initiating role for Vγ1+γδ T cells, as they directly supply IL-4 to DC and CD8 T cells. IL-4 synergises with a CD4 T cell-derived CD40L signal to induce IL-12 production by cDC1. Both IL-12 and IL-4 then directly signal CD8 T cells, with synergy between these cytokines driving enhanced IL-12 receptor expression and expansion of responding CD8 T cells. This study reveals a key role for Vγl+γδ T cells in initiating CD8 T cell immunity toPlasmodium. More broadly, it shows that responses to some pathogens require help from innate-like T cells to pass an initiation threshold and further amplify the response in a process underscored by IL-4 production.
Lifespan trajectory of chimpanzee brains characterized by magnetic resonance imaging histology
Authors: Lipp I. , Kirilina E. , Jäger C. , Morawski M. , Jauch A. , Pine K.J. , Edwards L.J. , Helbling S. , Rose D. , Helms G. , Eichner C. , Deschner T. , Gräßle T. ,   EBC Consortium, Gunz P. , Anwander A. , Friederici A.D. , Wittig R.M. , Crockford C. , Weiskopf N. 
Published: December 2024

AbstractChimpanzee brain maturation provides an invaluable framework for understanding the evolution of the human brain. We performed ultra-high resolution quantitative magnetic resonance imaging (qMRI) with histological validation onpost mortembrains from captive and wild chimpanzees with a broad age range. We mapped developmental myelination and age-related iron accumulation across regions and layers of the neocortex. Compared to humans, chimpanzees showed more myelination and iron deposition in motor and premotor cortices, while the auditory cortex was more strongly myelinated in humans. Our model suggests that chimpanzees’ cortical myelination was largely completed by the age of nine years, while iron accumulation continued throughout the lifespan. The regions with highest adult levels of myelin and iron took the longest to mature, challenging the widespread assumption that highly myelinated regions complete their development first. The reported maps and developmental curves provide a foundation for comparative neuroscience research and understanding of human brain evolution.
Improved Efficiency of Two-Step Amplicon PCR Using an Acoustic Liquid Handler
Authors: Benz Brooke R. , Lopez Echartea Eglantina , Whitaker Briana K. , Baldwin Thomas , Geddes Barney A. 
Published: December 2024

2.AbstractThe improvement in next-generation sequencing technologies has reduced the costs of sequencing significantly. However, library preparation costs for amplicon sequencing have remained largely unchanged – which is ultimately the cost-limiting step in processing large numbers of microbiome samples. Acoustic liquid handlers can transfer volumes as low as 2.5 nL and have been used to miniaturize several different molecular and cellular assays, including single-step polymerase chain reaction (PCR) amplicon library preparations. However, there are no current methods available for a two-step library preparation process using an acoustic liquid handler. In this study, we tested the efficiency of an acoustic liquid handler to automate the PCRs and library quantification while also incorporating automated library bead cleanup. We compared the material usage and costs for library preparation and sequencing results of this automated method to the standard, manual method. The automated protocol was able to reduce both PCR reaction volumes five-fold and increased efficiency for library preparation by ∼32% without affecting bacterial community compositions. The associated increase in efficiency of our automated method will allow for greater throughput in sequencing hundreds of microbiome samples without affecting the quality of those sequences.3.Impact statementLibrary preparation for amplicon sequencing in microbiome studies remains a significant cost constraint, even while sequencing costs have decreased in the last few decades. Acoustic liquid handling robots have been utilized to miniaturize several different assays, including a one-step PCR library preparation process, to reduce costs. However, there are currently no methods available for utilizing acoustic liquid handlers for two-step PCR library preparation. Here, we show that the incorporation of an acoustic liquid handler and automated purification instruments into a two-step library preparation protocol led to a reduction in costs and time to prepare libraries. This method is comparable to the standard manual method and will lead to significant cost savings for the preparation of hundreds of samples required for microbiome studies.4.Data summaryAll protocols, sequence data, and analysis codes have been made publicly available in open-access repositories. The authors confirm all supporting data, code, and protocols have been provided within the article or through supplementary data files.Sequencing data was deposited in the NCBI SRA under the BioProject PRJNA1190462.R scripts used for data analysis are available athttps://github.com/NDSU-Geddes-Lab/brb-libprepdoi: 10.5281/zenodo.14194699.Protocols for automated library preparation have been published on protocols.io and are available at dx.doi.org/10.17504/protocols.io.e6nvwb5r2vmk/v2 and dx.doi.org/10.17504/protocols.io.e6nvwb5w2vmk/v2.
Spatiotemporal analysis of dystrophin expression during muscle repair
Authors: Hildyard John C.W. , Roskrow Liberty E. , Wells Dominic J. , Piercy Richard J. 
Published: December 2024

AbstractDystrophin mRNA is produced from a very large genetic locus and transcription of a single mRNA requires approximately 16 hours. This prolonged interval between transcriptional initiation and completion results in unusual transcriptional behaviour: in skeletal muscle, myonuclei express dystrophin continuously and robustly, yet degrade mature transcripts shortly after completion, such that most dystrophin mRNA is nascent, not mature. This implies dystrophin expression is principally controlled post-transcriptionally, a mechanism that circumvents transcriptional delay, allowing rapid responses to change in demand. Dystrophin protein is however highly stable, with slow turnover: in healthy muscle, despite constant production of dystrophin mRNA, demand is low and the need for responsive expression is minimal. We reasoned this system instead exists to control dystrophin expression during rare periods of elevated but changing demand, such as during muscle development or repair, when newly formed fibres must establish sarcolemmal dystrophin rapidly. By assessing dystrophin mRNA and protein expression in regenerating skeletal muscle following injury, we reveal a complex program that suggests control at multiple levels: nascent transcription begins even prior to myoblast fusion, effectively ‘paying in advance’ to minimise subsequent delay. During myotube differentiation and maturation, when sarcolemmal demands are high, initiation increases only modestly while mature transcript stability increases markedly to generate high numbers of mature dystrophin transcripts, a state that persists until repair is complete, when a state of oversupply and degradation resumes. Our data demonstrate that dystrophin mRNA is indeed chiefly controlled by turnover, not initiation: degradation consequently represents a potential therapeutic target for maximising efficacy of even modest dystrophin restoration.
Knockout of all nematode-specific NSPC genes expressed exclusively in the excretory gland cell results in transcriptomic signatures indicating an affected insulin signaling
Authors: Mackiewicz Zuzanna , Liudkovska Vladyslava , Dziembowski Andrzej 
Published: December 2024

AbstractThe nematodeCaenorhabditis elegansis one of the best-studied model organisms in molecular biology; however, many aspects of its physiology and the functions of many genes remain poorly understood. In this study, we investigated the role of nematode-specific NSPC proteins, whose mRNAs were recently identified as primary targets of the poly(A) polymerase TENT-5. Surprisingly, we found that NSPCs are exclusively expressed in the excretory gland cell, a cell with still unclear functionality. Using an optogenetic approach, we precisely ablated the excretory gland cell and observed that nematodes exhibited no transcriptomic or physiological changes in its absence. Additionally, we generated and thoroughly studied a strain with a deletion of all 18nspcgenes, which revealed that, despite previous indications, NSPCs do not influence the worm’s defense response. Instead, the transcriptomic analysis showed that the absence of NSPCs strongly impacts DAF-2/DAF-16 insulin signaling, suggesting that NSPCs may function as neuropeptides influencing keyC. eleganssignaling pathways. Although further studies are required to elucidate the physiological effects of this regulation, our findings provide new insights into this unexplored part of nematode physiology.
A One-Pot Biocatalytic Cascade to Access Diverse L-Phenylalanine Derivatives from Aldehydes or Carboxylic Acids
Authors: Anderson Shelby R. , Gopal Madan R. , Spangler Abigail P. , Jones Michaela A. , Wyllis D’Jana R. , Kunjapur Aditya M. 
Published: December 2024

AbstractNon-standard amino acids (nsAAs) that are L-phenylalanine derivatives with aryl ring functionalization have long been harnessed in natural product synthesis, therapeutic peptide synthesis, and diverse applications of genetic code expansion. Yet, to date these chiral molecules have often been the products of poorly enantioselective and environmentally harsh organic synthesis routes. Here, we reveal the broad specificity of multiple natural pyridoxal 5’-phosphate (PLP)-dependent enzymes, specifically an L-threonine transaldolase, a phenylserine dehydratase, and an aminotransferase, towards substrates that contain aryl side chains with diverse substitutions. We exploit this tolerance to construct a one-pot biocatalytic cascade that achieves high-yield synthesis of 18 diverse L-phenylalanine derivatives from aldehydes under mild aqueous reaction conditions. We demonstrate addition of a carboxylic acid reductase module to this cascade to enable the biosynthesis of L-phenylalanine derivatives from carboxylic acids that may be less expensive or less reactive than the corresponding aldehydes. Finally, we investigate the scalability of the cascade by developing a lysate-based route for preparative-scale synthesis of 4-formyl-L-phenylalanine, a nsAA with a bio-orthogonal handle that is not readily market-accessible. Overall, this work offers an efficient, versatile, and scalable route with the potential to lower manufacturing cost and democratize synthesis for many valuable nsAAs.
Reduced expression of PER2 protein contrbutes to β1-AA induced cardiac autophagy rhythm disorder
Authors: Li Peng-Jia , Feng Jia-Yan , Guo Jiao , Xue Jin , Li Yang , Wen Shi-Yuan , Wang Xiao-Hui , Liu Hui-Rong , Wang Li 
Published: December 2024

AbstractIt has been confirmed that heart failure may be linked to fluctuations in autophagy rhythm of cardiomyocytes throughout the day. It is known that circadian rhythms depend on the regulation of core biological clock proteins, with PER2 playing a crucial role. Our previous research has confirmed the presence of β1-Adrenergic receptor autoantibodies (β1-AA) could induce inhibition of myocardial autophagy, leading to cell death and heart failure. However, it remains unclear whether β1-AA induces cardiac autophagy rhythm disorder by affecting PER2 expression. This study find that β1-AA disrupts the autophagy rhythm in cardiomyocytes, primarily indicates by the decreased expression of the autophagy marker protein LC3; β1-AA induces disruption of the rhythmic expression of PER2 protein in myocardial cells, mainly manifests by a decrease in PER2 protein expression; Metoprolol is employed to verify that the β1-adrenergic receptor contributes to the reduction of Per2 protein caused by β1-AA. Knocking down Per2 with lentivirus reduces the inhibition of LC3 expression caused by β1-AA, while overexpressing Per2 in cardiomyocytes using lentivirus significantly restores β1-AA-induced decline in LC3 expression. At the same time, mTORC1 activation is found to participate in β1-AA-induced autophagy inhibition of cardiomyocytes after pretreatment with the mTORC1 inhibitor rapamycin. Furthermore, it is confirmed that the decreased expression of PER2 protein caused by β1-AA disrupts the myocardial autophagy rhythm by promoting mTORC1 activation through lentiviruses that knock down or overexpress the Per2 gene. This study provides experimental basis for the precision treatment of cardiovascular diseases from the perspective of biological rhythm.
Mechanistic Insights into FNBP4-Mediated Regulation of non-diaphanous formin FMN1 in Actin Cytoskeleton Dynamics
Authors: Das Shubham , Das Saikat , Maity Amrita , Maiti Sankar 
Published: December 2024

ABSTRACTFormin1 (FMN1), a member of the non-diaphanous formin family, is essential for development and neuronal function. Unlike diaphanous-related formins, FMN1 is not subject to canonical autoinhibition through the DID and DAD domains, nor is it activated by Rho GTPase binding. Recent studies suggest that formins also play roles in the nucleus, influencing DNA damage response and transcriptional regulation. However, the mechanisms regulating nuclear formins particularly non-diaphanous ones like FMN1 remain poorly understood. Our previous research identified the interaction between FMN1 and FNBP4, prompting further investigation into its functional role in regulating actin dynamics. Results reveal that FNBP4 inhibits FMN1-mediated actin assembly in vitro. It is shown that FNBP4 prevents FMN1 from displacing the capping protein CapZ at the growing barbed end of actin filaments. Additionally, FNBP4 inhibits FMN1’s bundling activity in a concentration-dependent manner. Further analysis indicates that FNBP4 interacts with the FH1 domain and the interdomain connector between the FH1 and FH2 domains, creating spatial constraints on the FH2 domain. We propose that FNBP4 acts as a stationary inhibitor of FMN1. In addition, we identify a monopartite nuclear localization signal (NLS) in FNBP4, and subcellular localization studies show that FNBP4 colocalizes with FMN1. This study provides new insights into the regulatory role of FNBP4 in modulating FMN1-mediated actin dynamics, suggesting that FNBP4 may function as a nuclear inhibitor of actin polymerization and shedding light on regulatory mechanisms specific to non-diaphanous formins.