bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elongation capacity of polyunsaturated fatty acids in the annelidPlatynereis dumerilii
Authors: Ramos-Llorens Marc , Bainour Khalida , Adelmann Leonie , Hontoria Francisco , Navarro Juan C. , Raible Florian , Monroig Óscar 
Published: March 2024

AbstractIn animals, elongation of very long-chain fatty acid (Elovl) proteins play pivotal functions in the biosynthesis of fatty acids, including the physiologically essential long-chain polyunsaturated fatty acids (LC-PUFA). Polychaetes have important roles in marine ecosystems, contributing not only to nutrient recycling but also exhibiting a distinctive capacity for biosynthesising LC-PUFA, as emphasised in previous research. In order to expand our current understanding of the LC-PUFA biosynthesis in polychaetes, the present study conducted a thorough molecular and functional characterisation of Elovl occurring in the model organismPlatynereis dumerilii. In this study, we identify six Elovl proteins in the genome ofP. dumerilii. The sequence and phylogenetic analyses established that four Elovl, identified as Elovl2/5, Elovl4 (two genes) and Elovl1/7, have putative functions in the LC-PUFA biosynthesis. Functional characterisation in yeast confirmed the roles of these elongases in the LC-PUFA biosynthetic pathways, demonstrating thatP. dumeriliipossesses a varied and functionally diverse complement of Elovl enzymes that, along the enzymatic specificities of previously characterised desaturases, enableP. dumeriliito perform all the reactions required for the biosynthesis of the LC-PUFA. Importantly, we uncovered that one of the two Elovl4-encoding genes fromP. dumeriliiis remarkably long in comparison with any other animals’ Elovl, which contains a C terminal KH domain unique among Elovl enzymes. The distinctive expression pattern of this protein in photoreceptors strongly suggests a central role in vision.
Dorsomedial Striatal Glutamatergic Transmission Inhibits Binge Drinking in Selectively Bred Crossed High Alcohol Preferring Mice
Authors: Bauer Meredith R. , McVey Megan M. , Zhang Yanping , Boehm Stephen L. 
Published: March 2024

AbstractCrossed high alcohol preferring (cHAP) mice have been selectively bred to consume considerable amounts of alcohol resulting in binge drinking. The dorsal striatum (DS) is a brain region involved in action selection where the dorsomedial striatum (DMS) is involved in goal-directed action selection and dorsolateral striatum (DLS) is involved in habitual action selection. Alcohol use disorder (AUD) may involve a disruption in the balance between the DMS and DLS. While the DLS is involved in binge drinking, the reliance on the DMS and DLS in binge drinking has not been investigated in cHAP mice. We have previously demonstrated that glutamatergic activity in the DLS is necessary for binge-like alcohol drinking in C57BL/6J mice, another high drinking mouse. Because of this, we hypothesized that DLS glutamatergic activity would gate binge-like alcohol drinking in cHAP mice. cHAP mice underwent bilateral cannulation into the DMS or DLS and were allowed free-access to 20% alcohol for two-hours each day for 11 days. Mice were microinjected with the AMPA receptor (AMPAR) antagonist, NBQX, into the DMS or DLS immediately prior to alcohol access. AMPAR protein expression was also assessed in a separate group of animals in DS subregions following an 11-day drinking history. We found that intra-DMS (but not intra-DLS) NBQX, alters binge alcohol drinking, with intra-DMS NBQX increasing alcohol consumption. We also found that the ratio of GluA1 to GluA2 differs across DS subregions. Together, these findings suggest that glutamatergic activity in the DMS may serve to limit binge drinking in cHAP mice.
A bacterial type III effector hijacks plant ubiquitin proteases to evade degradation
Authors: Yu Wenjia , Li Meng , Wang Wenjun , Zhuang Haiyan , Luo Jiamin , Sang Yuying , Segonzac Cecile , Macho Alberto P. 
Published: March 2024

AbstractGram-negative bacterial pathogens inject effector proteins inside plant cells using a type III secretion system. These effectors manipulate plant cellular functions and suppress the plant immune system in order to promote bacterial proliferation. Despite the fact that bacterial effectors are exogenous threatening proteins potentially exposed to the protein degradation systems inside plant cells, effectors are relative stable and able to perform their virulence functions. In this work, we found that RipE1, an effector protein secreted by the bacterial wilt pathogen,Ralstonia solanacearum, undergoes phosphorylation of specific residues inside plant cells, and this promotes its stability. Moreover, RipE1 associates with plant ubiquitin proteases, which contribute to RipE1 deubiquitination and stabilization. The absence of those specific phosphorylation sites or specific host ubiquitin proteases leads to a substantial decrease in RipE1 protein accumulation, indicating that RipE1 hijacks plant post-translational modification regulators in order to promote its own stability. These results suggest that effector stability or degradation in plant cells constitute another molecular event subject to co-evolution between plants and pathogens.
Biophysics-based protein language models for protein engineering
Authors: Gelman Sam , Johnson Bryce , Freschlin Chase , Sharma Arnav , D’Costa Sameer , Peters John , Gitter Anthony , Romero Philip A. 
Published: March 2024

ABSTRACTProtein language models trained on evolutionary data have emerged as powerful tools for predictive problems involving protein sequence, structure, and function. However, these models overlook decades of research into biophysical factors governing protein function. We propose Mutational Effect Transfer Learning (METL), a protein language model framework that unites advanced machine learning and biophysical modeling. Using the METL framework, we pretrain transformer-based neural networks on biophysical simulation data to capture fundamental relationships between protein sequence, structure, and energetics. We finetune METL on experimental sequence-function data to harness these biophysical signals and apply them when predicting protein properties like thermostability, catalytic activity, and fluorescence. METL excels in challenging protein engineering tasks like generalizing from small training sets and position extrapolation, although existing methods that train on evolutionary signals remain powerful for many types of experimental assays. We demonstrate METL’s ability to design functional green fluorescent protein variants when trained on only 64 examples, showcasing the potential of biophysics-based protein language models for protein engineering.
Inhibition of Proteasome Activity Facilitates Definitive Endodermal Specification of pluripotent Stem Cells by influencing YAP signaling
Authors: Ashok Akshaya , Ashwathnarayan Ashwini , Bhaskar Smitha , Shekar Spandana , Prasanna Jyothi , Kumar Anujith 
Published: March 2024

AbstractUnderstanding the molecular players that control the specification of definitive endoderm is imperative to obtain the homogenous population of pancreatic β-cells from stem cells. Though the Ubiquitin proteasome system (UPS) has been envisaged as a crucial intracellular protein degradation system, its role in germ layer specification remains elusive. In this study, using a mouse embryonic stem cells model system (mESCs) we observed decreased proteasomal activity specifically during endoderm, but not in meso- or ecto-derm differentiation. Extraneous inhibition of proteasomal activity during differentiation enhanced the expression of endodermal genes specifically. Enhancing proteasomal activity by including the activator IU1 in the induction culture, inhibited definitive endodermal differentiation. Further, inhibiting proteasomal activity at the definitive endodermal stage resulted in enhanced generation of insulin-positive cells. A similar increase in endodermal gene expression by inhibiting proteasomal activity was observed in miPSC and hiPSC differentiated towards endodermal lineage. Mechanistic insight showed no contribution of endoplasmic reticulum unfolded protein response but revealed the involvement of the YAP signaling pathway in proteasome-inhibited enhanced endodermal differentiation. Unravelling the specific involvement of UPS in endodermal cell fate specification in pluripotent stem cells paves the way for obtaining better qualitative and quantitative definitive endodermal cells for plausible cellular therapy in the future.
Microbial utilisation of maize rhizodeposits applied to an agricultural soil at a range of concentrations
Authors: Niedeggen Daniela , Rüger Lioba , Oburger Eva , Santangeli Michael , Ahmed Mutez , Vetterlein Doris , Blagodatsky Sergey , Bonkowski Michael 
Published: March 2024

SummaryRhizodeposition fuels carbon (C) and nutrient cycling in soil. However, the dynamics of microbial growth on rhizodeposits in relation to the distance from the root have not been well studied. This study investigates microbial growth on individual organic components of rhizodeposits and on maize root-derived exudates and mucilage from an agricultural soil. By creating a gradient of substrate concentrations, we simulated reduced microbial access to rhizosphere C with increasing distance to the root surface. We identified distinct C-thresholds for the activation of microbial growth, and these were significantly higher for rhizodeposits compared to singular, simple sugars. In addition, testing for stoichiometric constraints of microbial growth by supplementing N and P showed accelerated and increased microbial growth by activating a larger proportion of the microbial biomass. Early and late season exudates triggered significantly different microbial growth responses. The mineralisation of early season exudates was induced at a high C-threshold, whereas the mineralisation of late season exudates showed ’sugar-like’ properties, with a low C-threshold, high substrate affinity, and a reduced maximum respiration rate. Mucilage exhibited the highest C-threshold for the activation of microbial growth, although with a short lag-period and with an efficient mucilage degradation comparable to that of sugars. By determining kinetic parameters and turnover times for different root-derived substrates, our data enable the upscaling of micro-scale processes to the whole root system, allowing more precise predictions of how rhizodeposits drive microbial C and nutrient dynamics in soil.HighlightsGrowth thresholds for rhizodeposits were significantly higher than for singular, simple sugars.No distinct microbial growth on root exudates was observed even at high concentrations.Mucilage has a short lag-phase and efficient decomposition like sugars but only above a high threshold.N and P limited microbial growth in the agricultural soil.
AGE READINGS AND ASSESSMENT IN COASTAL BATOID ELASMOBRANCHS FROM SMALL-SCALE SIZE-SELECTIVE FISHERY: THE IMPORTANCE OF DATA COMPARABILITY IN MULTISPECIFIC ASSEMBLAGES
Authors: Scacco Umberto , Zanardi Fabiana , Kroha Silvio , Mancini Emanuele , Tiralongo Francesco , Nascetti Giuseppe 
Published: March 2024

ABSTRACTAge readings and assessment of vertebral growth increments were obtained in four batoid elasmobranch species, namelyDasyatis pastinaca,Raja asterias,Torpedo marmorata, andTorpedo torpedo. Samples were obtained opportunistically from the bycatch of a size-selective fishery, such as local small-scale trammel net fishing, in the coastal waters of the Central Tyrrhenian Sea during 2019-21. We analysed the vertebrae by a simple and rapid method preventing staining phase and histological preparation to elucidate band pairs in all species studied. Consistency of age estimates was checked by controlling for agreement on band pair counts between and within observers, and by estimating the relationships between vertebral diameter and height, and body size of the animal. Based on these data, we developed a statistical routine to obtain multiple estimates of age and growth parameters for incomplete samples due to size-selective fishing. The acceptable agreement between and within readers and the increase in vertebral size with body size demonstrated the consistency of the method. Based on the results of Von Bertalanffy and Gompertz growth models, body size was a better predictor of age than vertebral size, and Gompertz models were a better estimator of age and growth parameters than Von Bertalanffy models. The estimated parameters (k and t0, kg and cg) matched the data available for the species studied in the Mediterranean Sea. In fact,D. pastinaca,T. torpedoandR. asteriasshowed the lowest (k = 0.05-0.12), intermediate (k = 0.112-0.19) and highest (k = 0.18-0.23) growth rate, respectively. Overall, the method proved effective both in delineating band pairs in vertebrae of different species by making use of only minimal optical equipment and a single reagent, and in reliably estimating the age and growth parameters of problematic samples due to size-selective fishing. The replicability of the method will help to collect comparable demographic data in similar samples from other areas of the Mediterranean, as well as in assemblages of different species from other places.
Quantitative effects of co-culture on T cell motility and cancer-T cell interactions
Authors: Li Xinyue , Jin Taoli , Wang Lisha , Li Ming , Han Weijing , Li Xuefei 
Published: March 2024

AbstractOne of the primary challenges in current cancer immunotherapy is the insufficient infiltration of cytotoxic T cells into solid tumors. Despite ongoing investigations, the mechanisms restricting T cell infiltration in immune-cold tumors remains elusive, hindered by the intricate tumor microenvironment. Here, we co-cultured mouse cancer cell lines with cancer-specific cytotoxic T cells to study the influence of cancer-T cell interactions on T cell motility, a crucial factor for effective tumor infiltration. By quantifying T cell motility patterns, we found that cancer-specific T cells exhibited extended contact time with cancer-cell clusters and higher directional persistence than non-specific T cells. Computational modelling suggested that T cells with stronger persistence could facilitate efficient searching for cancer clusters. Transcriptomic profiling revealed T cells recognizing cancer cells orchestrate accumulation on cancer cell clusters by activating adhesion proteins on both cancer cells and T cells, thereby fostering prolonged interaction on cancer cells. Furthermore, we observed that there were two distinct subpopulations of cancer cells after co-culturing with cancer-specific T cells: one expressing elevated levels of T-cell attractants and antigen-presentation molecules, while the other expressing immunosuppressive molecules and undergoing epithelial-to-mesenchymal transition. These dynamic insights into the complex interplay of cancer-T cell interactions and their impact on T cell motility hold implications for refining more efficacious cancer immunotherapy strategies.
Cycle-frequency content EEG analysis improves the assessment of respiratory-related cortical activity
Authors: Navarro-Sune Xavier , Raux Mathieu , Hudson Anna L. , Similowski Thomas , Chavez Mario 
Published: March 2024

AbstractTime-Frequency (T-F) analysis of EEG is a common technique to characterise spectral changes in neural activity. This study explores the limitations of utilizing conventional spectral techniques in examining cyclic event-related cortical activities due to challenges, including high inter-trial variability. Introducing the Cycle-Frequency (C-F) analysis, we aim to enhance the evaluation of cycle-locked respiratory events. For synthetic EEG that mimicked cycle-locked pre-motor activity, C-F had more accurate frequency and time localization compared to conventional T-F analysis, even for a significantly reduced number of trials and a variability of breathing rhythm. Preliminary validations using real EEG data during both unloaded breathing and loaded breathing (that evokes pre-motor activity) suggest potential benefits of using the C-F method, particularly in normalizing time units to cyclic activity phases and refining baseline placement and duration. The proposed approach could provide new insights for the study of rhythmic neural activities, complementing T-F analysis.
Wee1 inhibition decouples Cdk1 and Plk1 activities: a role for gradual Cdk1 activation throughout G2 phase
Authors: Akopyan Karen , Lindqvist Arne 
Published: March 2024

AbstractAt completion of DNA replication, the mitotic kinases CDK1 and PLK1 are activated. Their activities increase slowly through early G2 phase, but the reason for this low-level activity before mitotic entry is not clear. Using a combination of experiments and mathematical modelling, we find that gradual CDK1 activation through G2 phase stimulates production of mitotic factors and coordinates activation of CDK1 and PLK1. We find that inhibition of CDK1 during G2 phase limits transcription of mitotic factors.Conversely, the duration of premature mitosis by forced activation of CDK1 is inversely related to the time-point in G2 when mitosis is triggered. Forced CDK1 activation not only leads to a lack of mitotic factors, but also decouples CDK1 and PLK1 activation. Accordingly, we find that duration of forced mitosis by WEE1 inhibition can be partially rescued by expression of constitutively active PLK1. Our results show a function for slow mitotic kinase activation through G2 phase and suggests a mechanism for how the timing of mitotic entry is linked to preparation for mitosis.HighlightsSlow Cdk1 activation through G2 phase coordinates expression of mitotic proteins and activation of mitotic kinasesThe duration of forced mitosis by WEE1 inhibition depends on when in G2 mitosis is triggeredForced CDK1 activation decouples CDK1 and PLK1 activationThe duration of forced mitosis can be partially rescued by expression of constitutively active PLK1
Aedes albopictuscolonies from different geographic origins differ in their sleep and activity levels but not in the time of peak activity
Authors: Wynne Nicole E. , Applebach Emilie , Chandrasegaran Karthikeyan , Ajayi Oluwaseun M. , Chakraborty Souvik , Bonizzoni Mariangela , Lahondère Chloé , Benoit Joshua B. , Vinauger Clément 
Published: March 2024

AbstractMosquitoes occupy a wide range of habitats where they experience various environmental conditions. The ability of some species, such as the tiger mosquito,Aedes albopictus, to adapt to local conditions certainly contributes to their invasive success. Among traits that remain to be examined, mosquitoes’ ability to time their activity with that of the local host population has been suggested to be of significant epidemiological importance. However, whether different populations display heritable differences in their chronotype has not been examined. Here, we compared laboratory strains originating from 8 populations from 3 continents, monitored their spontaneous locomotor activity patterns, and analyzed their sleep-like states. Overall, all strains showed conserved diurnal activity concentrated in the hours preceding the crepuscule. Similarly, they all showed increased sleep levels during the morning and night hours. However, we observed strain-specific differences in the activity levels at each phase of the day. We also observed differences in the fraction of time that each strain spends in a sleep-like state, explained by variations in the sleep architecture across strains. Human population density and the latitude of the site of geographic origin of the tested strain showed significant effects on sleep and activity patterns. Altogether, these results suggest thatAe. albopictusmosquitoes adapt to local environmental conditions via heritable adaptations of their chronotype.
Loss of the Na+/K+cation pump CATP-1 suppressesnekl-associated molting defects
Authors: Binti Shaonil , Edeen Phil T. , Fay David S. 
Published: March 2024

ABSTRACTThe conservedC. elegansprotein kinases NEKL-2 and NEKL-3 regulate multiple steps of membrane trafficking and are required for larval molting. Through a forward genetic screen we identified a loss-of-function mutation incatp-1as a suppressor of molting defects in synthetically lethalnekl-2; nekl-3double mutants.catp-1is predicted to encode a membrane- associated P4-type ATPase involved in Na+–K+exchange. Moreover, a mutation predicted to abolish CATP-1 ion-pump activity also suppressednekl-2; nekl-3mutants. Endogenously tagged CATP-1 was primarily expressed in epidermal (hypodermal) cells within punctate structures located at or near the apical plasma membrane. Through whole genome sequencing, we identified two additionalnekl-2; nekl-3suppressor strains containing coding-altering mutations incatp-1but found that neither mutation, when introduced intonekl-2; nekl-3mutants using CRISPR methods, was sufficient to elicit robust suppression of molting defects. Our data also suggested that the twocatp-1isoforms,catp-1aandcatp-1b, may in some contexts be functionally redundant. On the basis of previously published studies, we tested the hypothesis that loss ofcatp-1may suppressnekl-associated defects by inducing partial entry into the dauer pathway. Contrary to expectations, however, we failed to obtain evidence that loss ofcatp-1suppressesnekl-2; nekl-3defects through a dauer-associated mechanism or that loss ofcatp-1leads to entry into the pre-dauer L2d stage. As such, loss ofcatp-1may suppressnekl-associated molting and membrane trafficking defects by altering electrochemical gradients within membrane-bound compartments.
MAGNETICALLY-DRIVEN HYDROGEL SURFACES FOR DYNAMIC STIFFNESS MODULATION FOR MODULATING MACROPHAGE BEHAVIOR
Authors: Li Lanhui , Alsema Els , Beijer Nick R.M. , Gumuscu Burcu 
Published: March 2024

AbstractDuring the host response towards implanted biomaterials, macrophages can shift phenotype rapidly upon changes in their microenvironment within the host tissue. Exploration of this phenomenon can gain significantly from the development of adequate tools. Creating dynamic surface alterations on classical hydrogel substrates presents challenges, particularly when integrating them with cell cultivation and monitoring processes. However, having the capability to dynamically manipulate the stiffness of biomaterial surfaces holds significant potential. We introduce magnetically actuated dynamic surfaces (MadSurface) tailored to induce reversible stiffness changes on polyacrylamide hydrogel substrates with embedded magnetic microparticles in a time-controllable manner. Our investigation focused on exploring the potential ofMadSurface in dynamically modulating macrophage behavior in a programmable manner. We achieved a consistent modulation by subjecting theMadSurface to a pulsed magnetic field with a frequency of 0.1 Hz and a magnetic field flux density of 50 mT and analyzed exposed cells using flow cytometry and ELISA. At the single cell level, we identified a sub-population for which the dynamic stiffness conditions in conjunction with the pulsed magnetic field increased the expression of CD206 in M1-activated THP-1 cells, indicating a consistent shift toward M2 anti-inflammatory phenotype onMadSurface. At the population level, this effect was mostly hindered in the first 24 hours.MadSurface approach can create controlled environments to advance our understanding of the interplay between dynamic surface mechanics and macrophage behavior.