bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coexistence in Periodic Environments
Authors: Scott Alexa M , Bieg Carling , McMeans Bailey C , McCann Kevin S 
Published: February 2023

AbstractClimate change and other anthropogenic impacts are rapidly altering natural environmental periodicities on a variety of time scales. Despite this, a general theoretical foundation describing the role of periodic environmental variation in structuring species interactions and ecological communities is still underdeveloped. Alarmingly, this leaves us unprepared to understand and predict implications for the maintenance of biodiversity under global change. Here, we extend a two-species Lotka-Volterra competition model that incorporates periodic forcing between seasons of high and low production to investigate the effects of changing environmental patterns on species coexistence. Towards this, we define coexistence criteria for periodic environments by approximating isocline solutions akin to classical coexistence outcomes. This analytical approach illustrates that periodic environments (i.e., seasonality) in and of themselves can mediate different competitive outcomes, and these patterns are general across varying time scales. Importantly, species coexistence may be incredibly sensitive to changes in these abiotic periods, suggesting that climate change has the potential to drastically impact the maintenance of biodiversity in the future.
Why Do Hybrids Turn Down Sex?
Authors: Fyon Frederic , Berbel-Filho Waldir Miron , Schlupp Ingo , Wild Geoff , Ubeda Francisco 
Published: February 2023

ABSTRACTAsexual reproduction is ancestral in prokaryotes; the switch to sexuality in eukaryotes is one of the major transitions in the history of life. The study of the maintenance of sex in eukaryotes has raised considerable interest for decades and is still one of evolutionary biology’s most prominent question. The observation that many asexual species are of hybrid origin have led some to propose that asexuality in hybrids results from sexual processes being disturbed because of incompatibilities between the two parental species’ genomes. This proximate theory appears difficult in real life, as it requires fundamental reproductive traits to be profoundly altered without collapsing individuals’ fertility. Repeated failures to produce asexual Amazon Molly in the lab through crossing experiments show that we are still in need of an evolutionary explanation. Here, we present a mathematical model and propose an adaptive route for the evolution of asexuality from previously sexual hybrids. Under smaller reproductive alterations, we show that asexuality can evolve to rescue hybrids’ reproduction. Importantly, we highlight that when incompatibilities only affect the fusion of sperm and egg’s genomes, unreduced meiosis and paternal genome elimination can evolve separately, greatly facilitating the overall evolutionary route.
Characterization of new highly selective pyrazolo[4,3-d]pyrimidine inhibitor of CDK7
Authors: Kovalová Markéta , Havlíček Libor , Djukic Stefan , Škerlová Jana , Peřina Miroslav , Pospíšil Tomáš , Řezníčková Eva , Řezáčová Pavlína , Jorda Radek , Kryštof Vladimír 
Published: February 2023

AbstractTargeting cyclin-dependent kinase 7 (CDK7) provides an interesting therapeutic option in cancer therapy because this kinase participates in regulating the cell cycle and transcription. Here, we describe a new trisubstituted pyrazolo[4,3-d]pyrimidine derivative, LGR6768, that inhibits CDK7 in the nanomolar range and displays favourable selectivity across the CDK family. We determined the structure of fully active CDK2/cyclin A2 in complex with LGR6768 at 2.6 Å resolution using X-ray crystallography, revealing conserved interactions within the active site. Structural analysis and comparison with LGR6768 docked to CDK7 provides an explanation of the observed biochemical selectivity, which is linked to a conformational difference in the biphenyl moiety. In cellular experiments, LGR6768 affected regulation of the cell cycle and transcription by inhibiting the phosphorylation of cell cycle CDKs and the carboxy-terminal domain of RNA polymerase II, respectively. LGR6768 limited the proliferation of several leukaemia cell lines, triggered significant changes in protein and mRNA levels related to CDK7 inhibition and induced apoptosis in dose- and time-dependent experiments. Our work supports previous findings and provides further information for the development of selective CDK7 inhibitors.Graphical abstract
Diet influences resource allocation in chemical defence but not melanin synthesis in an aposematic moth
Authors: Ottocento Cristina , Rojas Bibiana , Burdfield-Steel Emily , Furlanetto Miriam , Nokelainen Ossi , Winters Sandra , Mappes Johanna 
Published: February 2023

AbstractFor animals that synthesise their chemical compoundsde novo, resources, particularly proteins, can influence investment in chemical defences and nitrogen-based wing colouration such as melanin. Competing for the same resources often leads to trade-offs in resource allocation. We manipulated protein availability in the larval diet of the wood tiger moth,Arctia plantaginis, to test how early life resource availability influences relevant life history traits, melanin production, and chemical defences. We expected higher dietary protein to result in more effective chemical defences and a higher amount of melanin in the wings. According to the resource allocation hypothesis, we also expected individuals with less melanin to have more resources to allocate to chemical defences. We found that protein-deprived moths had a slower larval development, and their chemical defences were less unpalatable for bird predators, but the expression of melanin in their wings did not differ from that of moths raised on a high-protein diet. The amount of melanin in the wings, however, unexpectedly correlated positively with chemical defences, irrespective of the diet they were raised on. Our findings demonstrate that the resources available in early life have an important role in the efficacy of chemical defences, but melanin-based warning colours are less sensitive to resource variability than other fitness-related traits.
Synergistic survival-related effects of larval exposure to an aquatic pollutant and food stress get stronger during and especially after metamorphosis and shape fitness of terrestrial adults
Authors: Jorissen Sarah , Janssens Lizanne , Verheyen Julie , Stoks Robby 
Published: February 2023

AbstractTo improve the ecological risk assessment of aquatic pollutants it is needed to study their effects not only in the aquatic larval stage, but also in the terrestrial adult stage of the many animals with a complex life cycle. This remains understudied, especially with regard to interactive effects between aquatic pollutants and natural abiotic stressors. We studied effects of exposure to the pesticide DNP (2,4-Dinitrophenol) and how these were modulated by limited food availability in the aquatic larvae, and the possible delayed effects in the terrestrial adults of the damselflyLestes viridis. Our results revealed that DNP and low food each had large negative effects on the life history, behaviour and to a lesser extent on the physiology of not only the larvae, but also the adults. Food limitation magnified the negative effects of DNP as seen by a strong decline in larval survival, metamorphosis success and adult lifespan. Notably, the synergism between the aquatic pollutant and food limitation for survival-related traits was stronger in the non-exposed adults than in the exposed larvae, likely because metamorphosis is stressful itself. Our results highlight that identifying effects of aquatic pollutants and synergisms with natural abiotic stressors, not only in the aquatic larval but also in the terrestrial adult stage, is crucial to fully assess the ecological impact of aquatic pollutants and to reveal the impact on the receiving terrestrial ecosystem through a changed aquatic-terrestrial subsidy.
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets
Authors: Yi Haidong , Plotkin Alec , Stanley Natalie 
Published: February 2023

AbstractModern single-cell data analysis relies on statistical testing (e.g. differential expression testing) to identify genes or proteins that are up-or down-regulated in relation to cell-types or clinical outcomes. However, existing algorithms for such statistical testing are often limited by technical noise and cellular heterogeneity, which lead to false-positive results. To constrain the analysis to a compact and phenotype-related cell population, differential abundance (DA) testing methods were employed to identify subgroups of cells whose abundance changed significantly in response to disease progression, or experimental perturbation. Despite the effectiveness of DA testing algorithms of identifying critical cell-states, there are no systematic benchmarking or comparative studies to compare their usages in practice. Herein, we performed the first comprehensive benchmarking study to objectively evaluate and compare the benefits and potential downsides of current state-of-the-art DA testing methods. We benchmarked six DA testing methods on several practical tasks, using both synthetic and real single-cell datasets. The task evaluated include, recognizing true DA subpopulations, appropriate handing of batch effects, runtime efficiency, and hyperparameter usability and robustness. Based on various evaluation results, this paper gives dataset-specific suggestions for the usage of DA testing methods.
Influence of Demographic, Socio-economic, and Brain Structural Factors on Adolescent Neurocognition: A Correlation Analysis in the ABCD Initiative
Authors: Hussain Mohammad Arafat , Li Grace , Grant Ellen , Ou Yangming 
Published: February 2023

ABSTRACTThe Adolescent Brain Cognitive Development (ABCD) initiative is a longitudinal study aimed at characterizing brain development from childhood through adolescence and identifying key biological and environmental factors that influence this development. The study measures neurocognitive abilities across a multidimensional array of functions, with a focus on the critical period of adolescence during which physical and socio-emotional changes occur and the structure of the cortical and white matter changes. In this study, we perform a correlation analysis to examine the linear relation of adolescent neurocognition functions with the demographic, socio-economic, and magnetic resonance imaging-based brain structural factors. The overall goal is to obtain a comprehensive understanding of how natural and nurtural factors influence adolescent neurocognition. Our results on>10,000 adolescents show many positive and negative statistical significance interrelations of different neurocognitive functions with the demographic, socioeconomic, and brain structural factors, and also open up questions inviting further future studies.
Brain Structure and Working Memory Adaptations Associated with Maturation and Aging in Mice
Authors: Clifford Kevan P. , Miles Amy E. , Prevot Thomas D. , Misquitta Keith A. , Ellegood Jacob , Lerch Jason P. , Sibille Etienne , Nikolova Yuliya S. , Banasr Mounira 
Published: February 2023

IntroductionAs the population skews toward older age, elucidating mechanisms underlying human brain aging becomes imperative. Structural MRI has facilitated non-invasive investigation of lifespan brain morphology changes, yet this domain remains uncharacterized in rodents despite increasing use as models of disordered human brain aging.MethodsYoung (2m, n=10), middle-age (10m, n=10) and old (22m, n=9) mice were utilized for maturational (young vs. middle-age) and aging-related (middle-age vs. old mice) comparisons. Regional brain volume was averaged across hemispheres and reduced to 32 brain regions. Pairwise group differences in regional volume, residualized for total brain volume, and associations between volume and cognitive performance on the Y-maze task were tested. General linear models with total brain volume as a covariate, and logistic regression for sample wide associations were employed respectively, correcting for multiple comparisons. Structural covariance networks were generated using the R package ‘igraph’. Group differences in network centrality (degree), integration (mean distance), and segregation (transitivity, modularity) were tested across network densities (5–40%), using 5,000 (1,000 for degree) permutations with significance criteria of p<0.05 at ≥5 consecutive density thresholds.ResultsWidespread significant maturational changes in volume occurred in 18 brain regions, including considerable loss in isocortex regions and increases in brainstem regions and white matter tracts. The aging-related comparison yielded 6 significant changes in brain volume, including further loss in isocortex regions and increases in white matter tracts. No significant volume changes were observed across either comparison for subcortical regions. Additionally, smaller volume of the anterior cingulate area (χ2=2.325, pbh=0.044) and larger volume of the hippocampal formation (χ2=-2.180, pbh=0.044) were associated with poorer cognitive performance. Maturational network comparisons yielded significant degree changes in 9 regions, but no aging related changes, aligning with network stabilization trends in humans. Maturational decline in modularity occurred (24-29% density), mirroring human trends of decreased segregation in young adulthood, while mean distance and transitivity remained stable.Conclusions/ImplicationsThese findings offer a foundational account of age effects on brain volume, structural brain networks, and cognition in mice, informing future work in facilitating translation between rodent models and human brain aging.
Effects of pasteurization on osteopontin levels in human breastmilk and pasteurized breastmilk products
Authors: McClanahan Kathleen G. , Reese Jeff , Weitkamp Jörn-Hendrik , Olivares-Villagómez Danyvid 
Published: February 2023

AbstractBackgroundOsteopontin (OPN) is an important breastmilk protein involved in infant intestinal, immunological, and brain development. However, little is known about how common milk pasteurization and storage techniques affect this important bioactive protein.MethodsHuman milk osteopontin concentration was measured in single-donor fresh or frozen breastmilk, pooled Holder-pasteurized donor breastmilk, and a shelf-stable (retort pasteurized) breastmilk product by ELISA. Breastmilk samples were pasteurized and/or frozen before measuring osteopontin concentrations.ResultsHolder pasteurization of breastmilk resulted in an ∼50% decrease in osteopontin levels within single-donor samples, whereas pooled donor breastmilk had comparable osteopontin levels to non-pasteurized single-donor samples. Breastmilk from mothers of preterm infants trended toward higher osteopontin concentration than mothers of term infants; however, samples from preterm mothers experienced greater osteopontin degradation upon pasteurization. Finally, freezing breastmilk prior to Holder pasteurization resulted in less osteopontin degradation than Holder pasteurization prior to freezing.ConclusionCommonly used breastmilk pasteurization and storage techniques, including freezing, Holder and retort pasteurization, decrease the levels of the bioactive protein osteopontin in human breastmilk.ImpactPasteurization of human breastmilk significantly decreases the levels of the bioactive protein osteopontinUse of both pasteurization and freezing techniques for breastmilk preservation results in greater loss of osteopontinThis study presents for the first time an analysis of osteopontin levels in single-donor pasteurized milk samples
Dynamical modeling reveals RNA decay mediates the effect of matrix stiffness on aged muscle stem cell fate
Authors: Hettinger Zachary R. , Hu Sophia , Mamiya Hikaru , Sahu Amrita , Iijima Hirotaka , Wang Kai , Gilmer Gabrielle , Miller Amanda , Nasello Gabriele , D’Amore Antonio , Vorp David A. , Rando Thomas A. , Xing Jianhua , Ambrosio Fabrisia 
Published: February 2023

SummaryLoss of muscle stem cell (MuSC) self-renewal with aging reflects a combination of influences from the intracellular (e.g., post-transcriptional modifications) and extracellular (e.g., matrix stiffness) environment. Whereas conventional single cell analyses have revealed valuable insights into factors contributing to impaired self-renewal with age, most are limited by static measurements that fail to capture nonlinear dynamics. Using bioengineered matrices mimicking the stiffness of young and old muscle, we showed that while young MuSCs were unaffected by aged matrices, old MuSCs were phenotypically rejuvenated by young matrices. Dynamical modeling of RNA velocity vector fieldsin silicorevealed that soft matrices promoted a self-renewing state in old MuSCs by attenuating RNA decay. Vector field perturbations demonstrated that the effects of matrix stiffness on MuSC self-renewal could be circumvented by fine-tuning the expression of the RNA decay machinery. These results demonstrate that post-transcriptional dynamics dictate the negative effect of aged matrices on MuSC self-renewal.Graphical AbstractGraphical abstract description:The balance of self-renewal and differentiation in young muscle stem cells (MuSCs) is robust to perturbations of the biophysical microenvironment. In contrast, aged MuSCs are highly sensitive to extrinsic perturbations, and exposure to a youthful microenvironment rejuvenates the self-renewing potential of aged MuSCs by modulating post-transcriptional RNA dynamics.
The cardiac myosin binding protein-C phosphorylation state as a function of multiple protein kinase and phosphatase activities
Authors: Kampourakis Thomas , Ponnam Saraswathi , Koch Daniel 
Published: February 2023

AbstractPhosphorylation of cardiac myosin binding protein-C (cMyBP-C) is a crucial determinant of cardiac myofilament function. Although cMyBP-C phosphorylation by various protein kinases has been extensively studied, the influence of protein phosphatases on cMyBP-C’s multiple phosphorylation sites has remained largely obscure. Here we provide a detailed biochemical characterization of cMyBP-C dephosphorylation by protein phosphatases 1 and 2A (PP1 and PP2A) and develop an integrated kinetic model for cMyBP-C phosphorylation using data for both PP1, PP2A and protein kinases A (PKA), C and RSK2. We find strong site-specificity and a hierarchical mechanism for both phosphatases, proceeding in the opposite direction of sequential phosphorylation by PKA. The model is consistent with published data from human patients and predicts complex non-linear cMyBP-C phosphorylation patterns that are validated experimentally. Our results emphasize the importance of phosphatases for cMyBP-C regulation and prompt us to propose reciprocal relationships between cMyBP-C m-motif conformation, phosphorylation state and myofilament function.
Carbonate bedrock may not alleviate DIC limitation of snow algae — a test of hypothesis in the Medicine Bow Mountains, WY, USA
Authors: Hamilton Trinity L. , Havig Jeff 
Published: February 2023

ABSTRACTSnow is a critical component of the Earth system. High elevation snow can persist into the melt season and hosts a diverse array of life including snow algae. Due in part to the presence of pigments, snow algae lower albedo and accelerate snow melt which has led to increasing interest in identifying and quantifying the environmental factors that constrain their distribution. Dissolved inorganic carbon (DIC) concentration is low in supraglacial snow on Cascade stratovolcanoes and snow algae primary productivity can be stimulated through DIC addition. Here we asked if CO2would still be a limiting nutrient for snow hosted on glacially eroded carbonate bedrock (which could provide an additional source of DIC). We assayed snow algae communities for nutrient and DIC limitation on two seasonal snowfields on glacially eroded carbonate bedrock in the Snowy Range of the Medicine Bow Mountains, Wyoming, USA. DIC stimulated snow algae primary productivity in snow with lower DIC concentration despite the presence of carbonate bedrock, which alleviated DIC limitation in the other site. Our results support the hypothesis that increased atmospheric CO2concentrations may lead to larger and more robust snow algae blooms globally, even for sites with carbonate bedrock.
Go thou to the ant: A comparative biomechanical analysis of locomotion in Hymenoptera (Hexapoda)
Authors: Regeler V. , Boudinot B.E. , Wöhrl T. 
Published: February 2023

ABSTRACTAlthough ants are conceived of as paragons of social complexity, it may be their locomotory capacity that truly sets them apart from other Hymenoptera. Based on our comparative kinematic analysis of Formicidae for level, straight-line locomotion in a broad phylogenetic context, we observe that ants are distinctly capable runners. No sampled hymenopteran paralleled the body-scaled speed of ants. Relative stride lengths for ants were longer than other sampled taxa despite short ground contact durations relative to swing durations. With respect to spatial gait patterns, ants had relatively narrow hindleg and broad midleg step-widths on average, possibly enhancing speed and turning ability. Ants were able to extend their propulsive pair of legs, those of the metathorax, extremely far posterad relative to other sampled taxa, and had a distinct locomotory posture, with a high ground clearance and the femorotibial joints raised above their backs. Despite the unique modifications of their coxotrochanteral articulations, ant forelimbs were largely unremarkable with respect to our quantified variables. Sawflies, in contrast, had extremely wide and perhaps inefficient foreleg stances, and were observed for the first time to have what appears to be a dominant tetrapodal gait pattern, which raises unexpected questions about the early evolution of the Hymenoptera. Finally, we observed variability in attachment abilities and no consistent pattern of leg liftoff sequence across the sampled taxa. Our results establish locomotory evolution in the Hymenoptera as a functionally and structurally variable system with numerous directions of future research, particularly for phylogenetic comparison across wing-monomorphic and wing-polymorphic lineages.Summary statementThis work establishes a comparative phylogenetic approach to hymenopteran kinematics, demonstrating that ant locomotory capacity is derived and observes, unexpectedly, that the sampled sawflies (symphyta) never used a tripod gait.