bluuebunny/crossref_metadata_2025_split huggingface dataset:
Droplet microfluidic screening to engineer angiotensin-converting enzyme 2 (ACE2) catalytic activity
Authors: Okal Evelyn F , Romero Philip A. , Heinzelman Pete 
Published: October 2024

AbstractBackgroundAngiotensin-Converting Enzyme 2 (ACE2) is a crucial peptidase in human peptide hormone signaling, catalyzing the conversion of Angiotensin-II to Angiotensin-(1-7), which activates the Mas receptor and elicits vasodilation, increased blood flow, reduced inflammation, and decreased pathological tissue remodeling. This study leverages protein engineering to enhance ACE2’s therapeutic potential for treating conditions such as respiratory viral infections, acute respiratory distress syndrome, and diabetes. Surrogate substrates used in traditional high-throughput screening methods for peptidases often fail to accurately mimic native substrates, leading to less effective enzyme variants. Here, we developed an ultra-high-throughput droplet microfluidic platform to screen peptidases on native peptide substrates. Our assay detects substrate cleavage via free amino acid release, providing a precise measurement of biologically relevant peptidase activity.ResultsUsing this new platform, we screened a large library of ACE2 variants, identifying position 187 as a hotspot for enhancing enzyme activity. Further focused screening revealed the K187T variant, which exhibited a fourfold increase in catalytic efficiency (kcat/KM) over wild-type ACE2.ConclusionsThis work demonstrates the potential of droplet microfluidics for therapeutic peptidase engineering, offering a robust and accessible method to optimize enzyme properties for clinical applications.
Electrogenic Dynamics of Biofilm Formation: Correlation Between Genetic Expression and Electrochemical Activity inBacillus subtilis
Authors: Yavarinasab Adel , He Jerry , Mookherjee Abhirup , Krishnanc Nikhil , Pestana Luis Ruiz , Fusco Diana , Bizzotto Dan , Tropini Carolina 
Published: October 2024

AbstractBacterial biofilms are structured microbial communities that play a big role in diverse processes such as nutrient cycling and bacterial pathogenesis. Biofilms are known for their electron transfer properties which are essential for metabolic processes, microbial survival, and maintaining redox balance. In this study, we investigated the electrogenic properties ofBacillus subtilis, a bacterial producer of electron-donating biofilms. Interdigitated gold electrodes were utilized to continuously measure the electrochemical activity of biofilm-formingB. subtiliscells as well as genetic mutants unable to create them (biofilm-deficient), over three days of growth. The formation of extracellular polymeric substances (EPS) and filamentous appendages was monitored via scanning electron microscopy (SEM). Chronoamperometry was used to assess electrochemical activity, which showed fluctuations in electrical current at specific time points in biofilm-forming cells. In contrast, biofilm-deficient cells showed no corresponding changes in current. Cyclic voltammetry (CV) revealed significant differences between the voltammograms of biofilm-forming and biofilm-deficient cells that were hypothesized to be a result of the reduction of secreted flavodoxin only in biofilm-forming cells. Electrochemical impedance spectroscopy (EIS) was also performed at various intervals and analyzed using an equivalent circuit model. We identified the presence of a charge transfer resistance (Rct) exclusively in biofilm-forming cells which correlated to the time of increased electrochemical activity measured using choronoamperometry. Finally, through confocal microscopy, we found that the expression of a gene involved in biofilm matrix formation,tasA, was correlated with the time where electrochemical charge transfer was measured. Altogether, these results indicate that electrochemical activity is primarily present in biofilm-forming cells rather than in biofilm-deficient mutants. By combining electrochemical and microscopic methods, a methodology was developed to continuously monitor the stages of biofilm formation through measurement of electrochemical activity, substantiating a correlation between the expression of biofilm genes and their electrochemical or redox activities. These data show that electrochemical activities within biofilms vary over time and there is a temporal relationship between these processes and the expression of genes responsible for biofilm development.
Prevalence and Dynamics of Genome Rearrangements in Bacteria and Archaea
Authors: Martinez-Gutierrez Carolina A. , Bobay Louis-Marie 
Published: October 2024

ABSTRACTThe genetic material of bacteria and archaea is organized into various structures and set-ups, attesting that genome architecture is dynamic in these organisms. However, strong selective pressures are also acting to preserve genome organization, and it remains unclear how frequently genomes experience rearrangements and what mechanisms lead to these processes. Here, we assessed the dynamics and the drivers of genomic rearrangements across 121 microbial species. We show that synteny is highly conserved within most species, although several species present exceptionally flexible genomic layouts. Our results show a rather variable pace at which genomic rearrangements occur across bacteria and archaea, pointing to different selective constraints driving the accumulation of genomic changes across species. Importantly, we found that not only inversions but also translocations are highly enriched near the origin of replication (Ori), which suggests that many rearrangements may confer an adaptive advantage to the cell through the relocation of genes that benefit from gene dosage effects. Finally, our results support the view that mobile genetic elements—in particular transposable elements—are the main drivers of genomic translocations and inversions. Overall, our study shows that microbial species present largely stable genomic layouts and identifies key patterns and drivers of genome rearrangements in prokaryotes.Significance statementBacterial and archaeal genomes display stable architectures which ensures the preservation of fundamental cellular processes. However, large genomic rearrangements occasionally occur. Although most of these events are thought to be highly deleterious, they have the potential to lead to adaptive events. Here, we examined the general trends of the dynamic of prokaryotic genomes by exploring the occurrence of genome rearrangements across a broad diversity of bacterial and archaeal species. We find that genomes remain highly syntenic in most species over short evolutionary timescales, although some species appear particularly dynamic. Rearrangements are strongly biased, and most gene blocks are relocated near the origin of replication. We also measured remarkably variables rates at which genome rearrangements occur across species, and transposons and other mobile genetic elements appear to be the main drivers of these variations. Overall, this study provides a comprehensive picture of the dynamic of genome architecture across many microbial species.
Heterogeneous distribution of inhibitory inputs among motor units as a key mechanism for motor adaptations to pain
Authors: Hug François , Dernoncourt François , Avrillon Simon , Thorstensen Jacob , Besomi Manuela , van den Hoorn Wolbert , Tucker Kylie 
Published: October 2024

AbstractPain significantly influences movement, yet the precise neural mechanisms underlying the wide range of observed motor adaptations remain unclear. This study combined experimental data andin silicomodels to investigate the contribution of inhibitory and neuromodulatory inputs to motor unit behaviour during submaximal contractions performed in the presence of pain. Specifically, we aimed to unravel the distribution pattern of inhibitory inputs to the motor unit pool. Seventeen participants performed isometric knee extension tasks under three conditions: Control, Pain (induced by injecting hypertonic saline into the infra-patellar fat pad), and Washout. We identified large samples of motor units in the vastus lateralis (up to 53/participant) from high-density electromyographic signals, which led to three key observations. First, while motor unit discharge rates significantly decreased during Pain, a substantial proportion of motor units (14.8-24.8%) did not show this decrease and, in some cases, even exhibited an increase. Second, using complementary approaches we showed that pain did not alter the amplification and prolongation effects of persistent inward currents on motor unit discharge, providing evidence that neuromodulatory drive to motor neurons remained unchanged. Third, we observed a significant reduction in the proportion of common inputs to motor units during Pain. To explore potential neurophysiological mechanisms underlying these experimental results, we simulated the behaviour of motor unit pools with varying distribution patterns of inhibitory inputs. Our simulation supports the hypothesis of a non-homogeneous distribution of inhibitory inputs, independent of motor unit size, as a key neural mechanism underlying motor adaptations to experimental pain.Significance statementOur study challenges the traditional view of homogeneous inhibition of motor units during noxious stimulation and strongly supports contemporary pain theories that propose a non-homogeneous distribution of inhibitory inputs across the motor unit pool. Although previous research has observed differential motor unit responses to pain - some with decreased discharge rates and others with increased discharge rates - these findings alone cannot distinguish between homogeneous and non-homogeneous inhibition. By combining experimental data within silicomodelling, we provide compelling evidence of increased inhibition that is non-uniformly distributed across motor units, independent of motor unit size, as a key neural mechanism underlying motor adaptations to pain.
Automated, Stress-Free, and Precise Measurement of Songbird Weight in Neuroscience Experiments
Authors: Bonneh Yuval , Tuval Avishag , Ben-Shitrit Ido , Goffer Lilia , Cohen Yarden 
Published: October 2024

AbstractMonitoring the health and well-being of research animals is essential for both ethical and scientific purposes. In songbirds, body weight is one of the main indicators for their overall condition, yet traditional weighing methods can be intrusive and stress-inducing, which could decrease their song rate. We developed a novel, automated system designed to continuously monitor the weight of untethered and tethered birds without disrupting their natural behavior in neuroscience experiments. We used the system to track weight fluctuations in six canaries over several weeks, revealing physiological patterns such as overnight weight loss, with one bird losing approximately 5.17% of its body weight during a 9.5-hour period of inactivity. Our system’s high sensitivity detected weight changes below 1% of body mass, validating its reliability for long-term studies. Control experiments confirmed that weight fluctuations observed were physiological rather than due to equipment deviations. By eliminating the need for manual handling, this system offers a non-invasive, hands-free approach that reduces stress and improves the accuracy of health assessments. This study demonstrates the system’s potential for expanding research on how environmental factors, diet, and other variables influence bird physiology and behavior. Future applications could integrate additional health metrics, providing a more comprehensive understanding of animal welfare in neuroscience and behavioral studies.
Seasonal dynamics in microbial trace metals transporters during phytoplankton blooms in the Southern Ocean
Authors: Kong Yanhui , Zhang Rui , Blain Stéphane , Obernosterer Ingrid 
Published: October 2024

AbstractTrace metals are required as cofactors in metalloproteins that are essential in microbial metabolism and growth. The microbial requirements of diverse metals and the capabilities of prokaryotic taxa to acquire these metals remain poorly understood. We present here results from metagenomic observations over an entire productive season in the region off Kerguelen Island (Indian Sector of the Southern Ocean). We observed seasonal patterns in the abundance of prokaryotic transporters of seven trace elements (zinc [Zn], manganese [Mn], nickel [Ni], molybdenum [Mo], tungsten [W], copper [Cu] and cobalt [Co]) and the consecutive spring and summer phytoplankton blooms were strong drivers of these temporal trends. Taxonomic affiliation of the functional genes revealed that Rhodobacteraceae had a broad repertoire of trace metal transporters (Mn, Zn, Ni, W and Mo) and a more restricted set was observed for other prokaryotic groups, such as Flavobacteriaceae (Zn), Nitrincolaceae (Ni and W) and Thioglobaceae (Mo). The prevalence of trace metal transporters within a prokaryotic group, as determined on the family level, was overall confirmed in representative metagenome‐assembled genomes. We discuss the potential involvement of prokaryotic groups in processes related to organic matter utilisation that require these metals and the consequences on carbon and trace metal cycling in surface waters of the Southern Ocean.
Variations in media framing of movements in China, France, and the U.S.: An intersectional approach
Authors: Li Yao , Cassard Marion , Holmes Brooke , Wu Huixuan 
Published: October 2024

AbstractCurrent literature often links contentious protests with media hostility, showing that news outlets typically portray protests involving disruption or violence in a negative light. Contesting this literature, this work introduces an intersectional approach—focusing on geopolitics, protest goals and actions—to theorize divergences in the media framing of protests that entail violence. To illustrate these divergences, we use mixed methods—network analysis and content analysis—to examine an original dataset on U.S. media coverage of three large movements in different countries. These movements share similarities in their anti‐status quo goals and contentious actions but differ in geopolitical locations: one taking place in the U.S., the second in a U.S. ally country, and the third in a non‐ally country. As the first to apply network analysis in movement‐media studies, this comparative study contributes to a systematic examination of media framing variations both within and across social movements. This work also complicates our understanding of violence and media representation by introducing a theoretically‐informed approach that considers multiple factors simultaneously.
Application of nondestructive techniques for peach (Prunus persica) quality inspection: A review
Authors: Qi Hengnian , Luo Jiahao , Wu Xiaoping , Zhang Chu 
Published: October 2024

AbstractPeaches are highly valued for their rich nutritional content. Traditional fruit quality accessing methods (i.e., manual squeezing the fruit for firmness) are both subjective and destructive, which tend to diminish the integrity of fruit samples, consequently undermining their market value. Compared to traditional detection methods, nondestructive technology offers efficient and noninvasive solutions for rapidly and accurately assessing internal external quality of peaches. This can significantly enhance product classification and quality assurance while reducing the need for extensive human resources and minimizing potential physical damage to peaches. This review provided a comprehensive overview of nondestructive techniques for peach quality evaluation, including visible/near‐infrared spectroscopy, machine vision technology, hyperspectral imaging, dielectric and optical properties, fluorescence spectroscopy, electronic nose/tongue, and acoustic vibration methods. It also evaluates the effectiveness of each technique in assessing internal quality, maturity, and disease detection of peaches. The advantages and limitations of each method were also summarized. This study focuses specifically on peaches and encompasses all existing nondestructive testing methods, providing valuable insights and references for future studies in the field of peach quality analysis using nondestructive testing methods.
Enhancement of exercise‐induced fatigue alleviation and liver selenium regulation through in situ nanoselenium synthesis by Lactobacillus rhamnosus cells, empowered by Ganoderma lucidum spore loading
Authors: Shi Dingyu , Xu Fengqin , Li Yinghui , Shang Xinzhe , Liao Ning , Jin Han , Liu Guanwen , Shao Dongyan 
Published: October 2024

AbstractGiven the increasing awareness of the negative effects of fatigue on daily activities, mental health, and quality of life, antifatigue supplements are becoming increasingly popular among consumers. Selenium has been found to have antifatigue potential in high dosage, but may cause toxicity effects to the body. In this study, inorganic selenium was first converted to nanoselenium particles via in situ synthesis by Lactobacillus rhamnosus SHA113 (Se‐LRS), and then loaded by Ganoderma lucidum spores (GLS). The resulting products were not only assessed for their antioxidant activities, but also the antifatigue potential in mice. As a result, both Se‐LRS and the Se‐LRS/GLS complex exhibited higher antioxidant and antibacterial activities in simulated gastrointestinal fluids compared to isolated selenium nanoparticles. The Se‐LRS/GLS complex demonstrated sustained release of selenium in simulated gastrointestinal fluids and showed significant alleviation of exercise‐induced fatigue indicators, but relatively lower liver selenium accumulation in the mice, surpassing the effects of isolated nanoselenium. No toxicity was found to Caco‐2 cells for Se‐LRS/GLS complex at 2 µg/mL. This is a novel approach to enhance the antifatigue potential of selenium without causing extra toxicity.
Enhancing dietary analysis: Using machine learning for food caloric and health risk assessment
Authors: Adjuik Toby A. , Boi‐Dsane Naa Adzoa A. , Kehinde Bababode A. 
Published: October 2024

AbstractIn the wake of growing concerns regarding diet‐related health issues, this study investigates the application of machine learning methods to estimate the energy content and classify the health risks of foods based on the USDA National Nutrient Database. The caloric content of foods was estimated using the nutritional composition (i.e., carbohydrates, protein, total lipid, and total sugar content) and classified based on their weighted health risks, considering their carbohydrate, lipid, and glycemic index levels. The algorithms used for modeling include multiple linear regression (MLR), K‐nearest neighbors, support vector machine, random forest regression (RFR), gradient‐boosted regression, decision trees (DT), and deep neural networks. The MLR model demonstrated high accuracy on the training dataset (R2 = 0.99, mean absolute error [MAE] = 7.71 kcal, and root mean squared error [RMSE] = 17.89 kcal) and testing dataset (R2 = 0.99, MAE = 7.75 kcal, and RMSE = 18 kcal) in energy estimation, indicating its effectiveness in dietary assessment. The RFR and DT models were useful in categorizing foods into low‐health‐risk foods, but their performance was reduced in medium and high‐health‐risk groups. This research contributes to developing tools that could aid in personalized dietary planning and public health interventions to mitigate diet‐related health risks.Practical ApplicationThis study applies machine learning to estimate how many calories are in food and to understand the health risks different foods might have. By investigating the fats, cholesterol, and sugars in food items listed in a public database, we can better plan diets or develop apps that help people make healthier eating choices. This work aims to improve public access to nutritional information, supporting efforts to combat diet‐related diseases through educational materials and applications that guide dietary choices in various settings.
Optimization of microbial consortia and materials composition enhances gluconic acid content in kombucha
Authors: Jeong Ah‐Young , Hong Seong‐Jin , Jang Da‐Eun , Kim Eunhye , Ko Sugju , Kim Young‐Min 
Published: October 2024

AbstractThe objective of this study was to optimize the microbial and ingredient composition of kombucha for enhanced production of gluconic acid (GA). Fourteen strains of Komagataeibacter spp. and one yeast strain of Dekkera sp. were isolated from kombucha. Among them, Komagataeibacter swingsii SS1 (SS1) and Komagataeibacter saccharivorans SS11 (SS11) were selected for their high GA production. A rapid reduction of pH, high GA content relative to acetic acid, and high cellulose production were observed in the tea infusion fermented by the microbial consortium (SS1 + SS11 + Dekkera bruxellensis Y24). From the correlation between the materials composition and quality indicators of kombucha, the decrease in pH was the most critical quality indicator of kombucha and the most closely related to GA content. Maximal GA production (11.7 mg/mL) was obtained under the conditions of 1% (w/v) tea extract, 8.5% (w/v) glucose, and 1.5% (v/v) ethanol through the optimization of materials composition by response surface methodology. The GA content of kombucha was enhanced threefold in comparison to general kombucha by fermentation with Komagataeibacter spp. and optimization of the composition of the ingredients. Overall, this study showed that a specific microbial consortium and materials composition could be established by correlation analysis among the ingredients, which results in increased GA levels in kombucha. These findings offer valuable foundational data for both commercial production and quality control of kombucha.
Whole cell affinity for 4‐amino‐5‐hydroxymethyl‐2‐methylpyrimidine (HMP) in the marine bacterium CandidatusPelagibacter st. HTCC7211 explains marine dissolved HMP concentrations
Authors: Brennan Elizabeth , Noell Stephen , Davis Edward W. , Giovannoni Stephen J. , Suffridge Christopher P. 
Published: October 2024

AbstractVitamin B1 is a universally required coenzyme in carbon metabolism. However, most marine microorganisms lack the complete biosynthetic pathway for this compound and must acquire thiamin, or precursor molecules, from the dissolved pool. The most common version of Vitamin B1 auxotrophy is for thiamin's pyrimidine precursor moiety, 4‐amino‐5‐hydroxymethyl‐2‐methylpyrimidine (HMP). Frequent HMP auxotrophy in plankton and vanishingly low dissolved concentrations (approximately 0.1–50 pM) suggest that high‐affinity HMP uptake systems are responsible for maintaining low ambient HMP concentrations. We used tritium‐labelled HMP to investigate HMP uptake mechanisms and kinetics in cell cultures of Candidatus Pelagibacter st. HTCC7211, a representative of the globally distributed and highly abundant SAR11 clade. A single protein, the sodium solute symporter ThiV, which is conserved across SAR11 genomes, is the likely candidate for HMP transport. Experimental evidence indicated transport specificity for HMP and mechanistically complex, high‐affinity HMP uptake kinetics. Km values ranged from 9.5 pM to 1.2 nM and were dramatically lower when cells were supplied with a carbon source. These results suggest that HMP uptake in HTCC7211 is subject to complex regulation and point to a strategy for high‐affinity uptake of this essential growth factor that can explain natural HMP levels in seawater.