bluuebunny/crossref_metadata_2025 huggingface dataset:
Palygorskite improves growth performance and prevents liver damage in avian pathogenic Escherichia coli-challenged broiler chickens at an early age
Authors: Tan Zichao , Chen Yueping , Zhou Yanmin
Published: October 2024

Avian pathogenic Escherichia coli (APEC) is a major bacterial infection that causes economic losses in the global poultry industry. Palygorskite (PAL) has been shown to enhance growth performance while improving antioxidative and anti-inflammatory properties of broilers. This study evaluated the protective effects of PAL on growth performance and liver function in broilers subjected to APEC challenge. A total of 320 one-day-old male Arbor Acres chicks were divided into 4 groups with 8 replicates of 10 birds each, based on a 2 × 2 factorial arrangement (basal diet or 5 g/kg PAL-supplemented diet) and inoculation (bacterial culture medium or APEC). PAL increased body weight gain (BWG) prior to APEC challenge (P < 0.05). However, APEC caused losses in BWG, feed intake (FI), and feed efficiency, along with increased relative hepatic weight, hepatic pathology scores, and hepatic-cell apoptosis rate (P < 0.05). Compared to normal birds, APEC increased interleukin (IL)-1β, interferon-γ (IFN-γ), tumor necrosis factor-α (TNF-α), malondialdehyde (MDA), and nitric oxide (NO) levels, as well as lysozyme (LZM) and myeloperoxidase (MPO) activities, while decreasing total antioxidant capacity (T-AOC) and IL-10 levels, and total superoxide dismutase (T-SOD) and catalase (CAT) activities in both serum and liver, APEC also raised alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities, but reduced total protein (TP), albumin (ALB), immunoglobulin (Ig) A, IgG, and IgM levels in serum (P < 0.05). Moreover, APEC increased hepatic mRNA level of IL-1β, IFN-γ, TNF-α, nuclear factor kappa B, and inducible nitric oxide synthase (iNOS), while inhibited mRNA level of IL-10 (P < 0.05). In contrast, PAL increased BWG and FI, and alleviated hepatic-cell apoptosis rate during the challenge period (P < 0.05). Incorporation of PAL reduced triglyceride and NO contents, ALT, and AST activities, while increasing TP, ALB, IL-10, IgG, and IgM levels in serum, enhancing serum T-SOD and CAT activities, elevating hepatic T-AOC and CAT activities, inhibiting hepatic MDA accumulation, and reducing IL-1β levels and LZM activity in both liver and serum (P < 0.05). An interactive effect was found for hepatic TNF-α and iNOS mRNA expression, in which PAL inhibited their mRNA expression in APEC-challenged birds (P < 0.05). Overall, PAL addition partially mitigated the negative impact of the APEC challenge on the growth performance and liver function of broiler chicks at an early age.
Insights into optimization of oleaginous fungi – genome-scale metabolic reconstruction and analysis ofUmbelopsissp. WA50703
Authors: Dziurzyński Mikołaj , Nowak Maksymilian E. , Furman Maria , Okrasińska Alicja , Pawłowska Julia , Fondi Marco
Published: October 2024

Oleaginous fungi, known for their high lipid content—up to 80% of their dry mass—are of significant interest for biotechnological applications, particularly in biofuel and fatty acid production. Among these, the genusUmbelopsis, a common soil saprotroph of the Mucoromycota phylum, stands out for its rapid growth, low nutritional requirements, and ability to produce substantial amounts of lipids, especially polyunsaturated fatty acids (PUFAs). Despite previous studies on lipid production inUmbelopsis, metabolic engineering has been underexplored. This study fills that gap by presenting the first comprehensive metabolic model forUmbelopsissp. WA50703, encompassing 2413 metabolites, 2216 reactions, and 1629 genes (iMD1629). The model demonstrated strong predictive accuracy, correctly predicting metabolic capabilities in 82.1% of cases when evaluated against experimental data. Using the Flux Scanning based on Enforced Objective Flux (FSEOF) algorithm, the study identified 33 genes linked to 23 metabolic reactions. Notably, reactions catalysed by acetyl-CoA carboxylase and carbonic anhydrase emerged as prime candidates for up-regulation. These findings provide a solid framework for future metabolic engineering efforts to optimize PUFA production inUmbelopsisstrains.

Importance

Umbelopsisstrains are capable of producing valuable compounds like polyunsaturated fatty acids (PUFAs). These compounds are essential for human health, found in various foods and supplements that support heart and brain function. In this study we developed a computer model to better understand how this fungus works at a metabolic level, guiding further research investigations towards optimization of PUFAs production in a cost-effective way. This research lays the groundwork for future innovations in metabolic engineering ofUmbelopsisPUFA production leading to healthier food options and a more sustainable food system, directly impacting everyday life.
Reliability and Validity of the Jumpster accelerometer-based app compared to the Vertec when completing a countermovement jump
Authors: Holman Matthew E. , Harnish Christopher R.
Published: October 2024

The reliability and validity of the Jumpster app (JA) was compared to the Vertec. Thirty-six participants completed 100 total trials using both tools simultaneously. Validity was assessed using correlation and tolerance analyses. Reliability was assessed using 95% predictive intervals (PI95) and tolerance limits (TL95) between the measures, comparing standard error of the measure (SEM) and coefficients of variation (CV) for each tool, and examining the intraclass correlation coefficient (ICC 2,K; upper and lower 95% CI) comparing both tools. The JA was weakly related to the Vertec (r = 0.24; p < 0.01). The tolerance analysis showed a moderately strong proportional bias of the JA (r = 0.45; p < 0.01). While all data fell within calculated PI95 ±TL95, the JA SEM (14.7cm) and CV (40.30%) exceeded the Vertec SEM (3.57cm) and CV (7.22%) with an ICC of 0.55 [0.79, -0.08]. These JA is neither reliable or valid.
Testing for the genomic footprint of conflict between life stages in an angiosperm and a moss species
Authors: Yuan Meng , Kollar Leslie M. , Sacchi Bianca M. , Carey Sarah B. , Choudhury Baharul I. , Jones Teresa , Grimwood Jane , Barrett Spencer C. H. , McDaniel Stuart F. , Wright Stephen I. , Stinchcombe John R.
Published: October 2024

The maintenance of genetic variation by balancing selection is of considerable interest to evolutionary biologists. An important but understudied potential driver of balancing selection is antagonistic pleiotropy between diploid and haploid stages of the plant life cycle. Despite sharing a common genome, sporophytes (2n) and gametophytes (n) may undergo differential or even opposing selection. Theoretical work suggests the antagonistic pleiotropy between life stages can generate balancing selection and maintain genetic variation. Despite the potential for far-reaching consequences of gametophytic selection, empirical tests of its pleiotropic effects (neutral, synergistic, or antagonistic) on sporophytes are generally lacking. Here, we examined the population genomic signals of selection across life stages in the angiospermRumex hastatulusand the mossCeratodon purpureus. We compared gene expression among life stages and between sexes, combined with neutral diversity statistics and the analysis of the distribution of fitness effects. In contrast to what would be predicted under balancing selection due to antagonistic pleiotropy, we found that unbiased genes between life stages are under stronger purifying selection, likely explained by a predominance of synergistic pleiotropy between life stages and strong purifying selection on broadly expressed genes. In addition, we found that 30% of candidate genes under balancing selection inR. hastatulusare located within inversion polymorphisms. Our findings provide novel insights into the genome-wide characteristics and consequences of plant gametophytic selection.

Significance

The genome-wide importance of balancing selection has been a key question in evolutionary biology. Despite theoretical support for the potential of balancing selection generated by antagonistic pleiotropy between plant life stages, no empirical studies have investigated this problem. Our results revealed genome-wide patterns more consistent with synergistic pleiotropy, with gametophyte-biased genes mostly likely to be under relaxed purifying selection in both angiosperm and moss species we investigated. In addition, our study suggests gene expression level and breadth has a greater effect on selection efficacy than differences between ploidy levels in different life stages.
Ixochymostatin, a trypsin inhibitor-like (TIL) protein fromIxodes scapularis, inhibits chymase and impairs vascular permeability
Authors: Martins Larissa Almeida , Berger Markus , Kotál Jan , Lu Stephen , Sousa-Paula Lucas C. , Smith Brian J. , Zhang Yixiang , Andersen John F. , Tirloni Lucas
Published: October 2024

Ticks, as pool feeders, obtain a blood meal by lacerating small blood vessels and ingesting the blood that flows to the feeding site, which triggers various host-derived responses. However, ticks face the challenge of wound healing, a process involving hemostasis, inflammation, cell proliferation and migration, and remodeling, hindering blood acquisition. To overcome these obstacles, tick salivary glands produce a diverse array of bioactive molecules. Here, we characterize ixochymostatin, anIxodes scapularisprotein belonging to the trypsin inhibitor-like (TIL) family. It is expressed in multiple developmental stages and in tick salivary glands and acts as a slow and tight-binding inhibitor of chymase, cathepsin G, and chymotrypsin. Predictions for the tertiary structure complex between ixochymostatin and chymase suggest a direct interaction between the inhibitor’s reactive site loop and protease active sites.In vitro, ixochymostatin protects the endothelial cell barrier against chymase degrading action, decreasing cell permeability.In vivo, it reduces vascular permeability induced by chymase and compound 48/80, a mast cell degranulator agonist, in a mouse model. Additionally, ixochymostatin inhibits the chymase-dependent generation of vasoconstrictor peptides. Antibodies against ixochymostatin neutralize its inhibitory properties, with epitope mapping identifying potential neutralization regions. Ixochymostatin emerges as a novel tick protein modulating host responses against tick feeding, facilitating blood acquisition.

Highlights

Ixochymostatin is a newly described trypsin inhibitor-like (TIL) protein fromIxodes scapularis.

Ixochymostatin inhibits chymase and reduces vascular permeability.

Ixochymostatin inhibits chymase-dependent generation of vasoconstrictive peptides.

Antibodies generated against ixochymostatin neutralize its inhibitory functions.

Potential epitopes responsible for anti-ixochymostatin neutralization were mapped.
Intrinsic molecular identifiers enable robust molecular counting in single-cell sequencing
Authors: Fontanez Kristina M. , Agam Yigal , Bevans Sophia , May-Zhang Aaron A. , Hayford Corey , Xue Yi , Ishibashi Jacob S. A. , Komuhendo Rachael , Yoder Lucas , Hettige Pabodha , Rickner Hannah D. , Zhang Jesse Q. , Osman Ahmad , D’Amato Chris , Smithers Trinity , Calkins Sarah , Rahman Muntasir , Mutafopulos Kiryakos S. , Kiani Sepehr , Meltzer Robert H.
Published: October 2024

Particle-templated instant partition sequencing (PIPseq), is an emerging approach for massively scalable single-cell gene expression studies that does not require complex instrumentation or expensive consumables. We present PIPseqTMV, a novel implementation of the PIPseq workflow with significant improvements in assay performance and sensitivity compared to prior methods. Among the innovations driving the improved performance in PIPseq V is a new approach for transcript counting using Intrinsic Molecular Identifiers (IMIs) from the captured transcript sequence, eliminating the need for traditional Unique Molecular Identifiers (UMIs). IMIs are the starting positions for molecules generated by random fragmentation after limited cycle PCR, which can be used to uniquely identify individual transcript copies of genes expressed within individual cells. To correct for experimental variation in IMI generation, we have developed a dynamic correction strategy that can adapt to different sample cell input, transcript expression, and sequencing depth without the need for external benchmarking or controls. Our results demonstrate that PIPseq V with IMI-based analysis provides biological information comparable to established UMI-based approaches while avoiding UMI-associated biases. Dynamic correction offers a robust and data-driven analysis strategy for scRNAseq.
A combination of expansion microscopy and proximity labelling reveals conserved and unique asymmetric functional hubs at the trypanosome nuclear pore
Authors: Gabiatti Bernardo Papini , Odenwald Johanna , Braune Silke , Krüger Timothy , Zoltner Martin , Kramer Susanne
Published: October 2024

Nuclear export of mRNAs requires loading the mRNP to the transporter Mex67/Mtr2 in the nucleoplasm, controlled access to the pore by the basket-localized TREX2 complex and mRNA release at the cytoplasmic site by the DEAD-box RNA helicase Dbp5. Asymmetric localisation of nucleoporins (NUPs) and transport components as well as the ATP dependency of Dbp5 ensure unidirectionality of transport. Trypanosomes possess homologues of the mRNA transporter Mex67/Mtr2, but not of TREX2 or Dbp5. Instead, nuclear export is likely fuelled by the GTP/GDP gradient created by the Ran GTPase. However, it remains unclear, how directionality is achieved since the current model of the trypanosomatid pore is mostly symmetric.

We have revisited the architecture of the trypanosome nuclear pore complex using a novel combination of expansion microscopy, proximity labelling and streptavidin imaging. We could confidently assign the NUP76 complex, a known Mex67 interaction platform, to the cytoplasmic site of the pore. The resulting availability of reference proteins for basket, inner ring and cytoplasmic site allowed mapping of all 75 trypanosome proteins with known nuclear pore localisation to a sub-region of the pore based on mass spectrometry data from proximity labelling. This approach defined many further asymmetrically localised nuclear pore components. At the nuclear site, we identified several trypanosome-unique proteins, for instance the FG-NUPs NUP64/NUP98, but also proteins with structural homology to TREX-2 components. We mapped the components of the Ran-based nuclear export system and confirm the absence of a Dbp5 homologue. Lastly, we demonstrate, by deploying an auxin degron system, that NUP76 holds an essential role in mRNA export consistent with a functional orthology to NUP82/88.

Altogether, the combination of proximity labelling with expansion microscopy revealed an asymmetric architecture of the trypanosome nuclear pore supporting inherent roles fort directed transport. Our approach delivered novel nuclear pore associated components inclusive positional information, which can now be interrogated for functional roles to explore trypanosome specific adaptions of the nuclear basket, export control and mRNP remodelling.
The FunCoup Cytoscape App: multi-species network analysis and visualization
Authors: Buzzao Davide , Steininger Lukas , Guala Dimitri , Sonnhammer Erik L.L.
Published: October 2024

Functional association networks, such as FunCoup, are crucial for analyzing complex gene interactions. To facilitate the analysis and visualization of such genome-wide networks, there is a need for seamless integration with powerful network analysis tools like Cytoscape.

The FunCoup Cytoscape App integrates the FunCoup web service API with Cytoscape, allowing users to visualize and analyze gene interaction networks for 640 species. Users can input gene identifiers and customize search parameters, employing various network expansion algorithms like group or independent gene search, MaxLink, and TOPAS. The app maintains consistent visualizations with the FunCoup website, providing detailed node and link information, including tissue and pathway gene annotations. The integration with Cytoscape plugins, such as ClusterMaker2, enhances the analytical capabilities of FunCoup, as exemplified by the identification of theMyasthenia gravisdisease module along with potential new therapeutic targets.

Availability and implementation

The FunCoup Cytoscape App is developed using the Java OSGi framework, with UI components implemented in Java Swing and build support from Maven. The App is available as a JAR file athttps://bitbucket.org/sonnhammergroup/funcoup_cytoscape/repo, and can be downloaded from the Cytoscape App storehttps://apps.cytoscape.org/.

Contact

erik.sonnhammer@scilifelab.se
Genetically encoded biosensor for fluorescence lifetime imaging of PTEN dynamics in the intact brain
Authors: Kagan Tomer , Gabay Matan , Levi Yossi , Eid Sharbel , Malchenko Nikol , Maman Maya , Nitzan Anat , Ravotto Luca , Zaidel-Bar Ronen , Gal Maayan , Laviv Tal
Published: October 2024

The phosphatase and tensin homolog (PTEN) is a vital signaling protein which maintains an inhibitory brake that is critical for cellular metabolism, proliferation, and growth. The importance of PTEN signaling is evident from the broad spectrum of human pathologies associated with its loss of function. Moreover, loss or gain of PTEN function in animal models leads to aberrant cellular morphology, function, and metabolic regulation. However, despite the important role of PTEN signaling, there is currently no method to dynamically monitor its activity with cellular specificity within intact biological systems. Here, we describe the development of a novel PTEN biosensor, optimized for two-photon fluorescence lifetime imaging microscopy (2pFLIM). This biosensor is designed to measure PTEN activity within intact cells, tissues, and organisms. Our approach is based on monitoring FRET-dependent changes in PTEN conformation, which serves as a proxy for the activity state in living cells. We identify a point mutation that allow us to express this biosensor with minimal interference to endogenous PTEN signaling and cellular function. We demonstrate the utility of imaging PTEN signaling in cell lines, developingC. elegans,and in the living mouse brain. To complement this approach, we developed a red-shifted PTEN sensor variant that permits simultaneous imaging with GFP-based sensors. Finally, we use in vivo PTEN imaging in the mouse brain to identify cell-type specific dynamics of PTEN activity in excitatory and inhibitory cortical cells. In summary, our approach enables dynamic imaging of PTEN activity in vivo with unprecedented spatial and temporal resolution.
Malaria parasite HOPS/CORVET complexes are critical for endocytosis and invasion organelles function
Authors: Mesén-Ramírez Paolo , Fuchs Gwendolin , Burmester Jonas , Farias Guilherme B. , Alape-Flores Ana-María , Singla Shamit , Alder Arne , Cubillán-Marín José , Castro-Peña Carolina , Lemcke Sarah , Sondermann Holger , Prado Mónica , Spielmann Tobias , Wilson Danny William , Gilberger Tim-Wolf
Published: October 2024

The tethering complexes HOPS/CORVET are central for vesicular fusion through the eukaryotic endolysosomal system, but the functions of these complexes in the intracellular development of malaria parasites are unknown. Here we show that early inactivation of core HOPS/CORVET complex subunits in Plasmodium falciparum leads to developmental arrest and accumulation of cytosolic vesicles, indicating a role of HOPS/CORVET in parasite endocytosis and fusion of endosomes to the digestive vacuole membrane. Late inactivation of the core HOPS/CORVET subunits led to the mislocalization of luminal rhoptry and microneme proteins, and to a severe defect in merozoite invasion. Ultra-expansion microscopy revealed a reduced rhoptry volume and the accumulation of numerous vesicles, further supporting a role of HOPS/CORVET in protein trafficking to the apical organelles. Malaria parasites have therefore repurposed HOPS/CORVET to perform dual functions consistent with a canonical endocytosis pathway for delivery of host cell material to the digestive vacuole in trophozoite stages and a parasite specific role in trafficking of protein cargo to the apical organelles required for invasion in schizont stages.
Evolutionary history with chronic malnutrition enhances pathogen susceptibility at older ages
Authors: Sarkar Saubhik , Shit Biswajit , Bose Joy , De Souvik , Kawecki Tadeusz J. , Khan Imroze
Published: October 2024

Juvenile malnutrition is a global public health concern that negatively impacts the development and maturation of the immune system, leading to increased susceptibility to infectious diseases. Such adverse effects on immunity might increase with ageing, worsening disease conditions later in life. Furthermore, malnutrition may persist across generations, imposing strong natural selection to survive the nutrient shortage. However, it is unclear how the evolutionary history of ancestral generations with chronic malnutrition could influence pathogen resistance and infection susceptibility, as well as their age-specific changes in extant generations. To address this, we usedDrosophila melanogasterpopulations adapted against chronic juvenile malnutrition and exposed them to a bacterial pathogen,Providencia rettgeri, during their early and late adulthood. Surprisingly, we observed that in populations adapted to chronic malnutrition, young flies survived infection better by tolerating the infection, while control flies displayed higher infection susceptibility despite carrying a similar pathogen load. However, this pattern in post-infection survival is reversed with ageing. There was no change in pathogen resistance, but evolved flies succumbed more to infection than control flies regardless of the input infection doses. Our study thus revealed new evolutionary insights into the development of contrasting early vs late-life immune strategies and age-specific vulnerabilities to infection as a function of early-life malnutrition.
Chemically defined lipid diets reveal the versatility of lipidome remodeling in genomically minimal cells
Authors: Safronova Nataliya , Junghans Lisa , Oertel Jana , Fahmy Karim , Saenz James P.
Published: October 2024

All cells are encapsulated in a lipid membrane that provides a responsive interface between life and its environment. Although simple membranes can be built from a single type of lipid, cellular membranes contain 10s to 100s of unique lipid species. Deciphering the significance of lipidome complexity is a central challenge in understanding the design principles of living membranes. While functions of individual lipids have been extensively studied, understanding how lipidomes collectively contribute to membrane function and cell phenotypes is experimentally challenging in most organisms. To address this challenge, we turned to the simple pathogenic organismMycoplasma mycoidesand its genomically derived “Minimal Cell” JCVI-syn3B, to establish a living minimal membrane model system in which lipidome complexity can be experimentally manipulated. By complexing lipids with cyclodextrins, we introduce a chemically defined approach to deliver lipid ‘diets’ with different chemistries to cells, resulting in cellular lipidomes with as few as seven to nearly 30 lipids species. We explored how lipidome size and composition influences cell growth, osmotic sensitivity, and membrane adaptability to changes in growth temperature. Our findings indicate that lipidome composition dictates membrane adaptation to temperature change. Moreover, we show that lipidome diversity enhances cellular robustness to hypoosmotic shock. We further show that impaired acyl chain remodeling in the minimal cell is associated with impaired membrane temperature adaptation. Finally, we demonstrate as a proof of principle, how cells with tuneable lipidomes can be used as experimental chassis for screening membrane active antimicrobial peptides. Our study introduces an experimental resource and foundation for deciphering the role of lipidome complexity in membrane function and cellular fitness.
An iterative design approach to development of an ex-vivo normothermic multivisceral perfusion platform
Authors: van Leeuwen L. Leonie , Holzner Matthew L. , McKenney Ceilidh , Todd Rachel , Frost Jamie K. , Gudibendi S. , Kim-Schluger Leona , Schiano Thomas , Florman Sander , Akhtar M. Zeeshan
Published: October 2024

Challenges in normothermic machine perfusion (NMP) remain, particularly concerning the duration for which individual organs can be safely preserved. We hypothesize that optimal preservation can be achieved by perfusing organs together in a multivisceral block. Therefore, our aim was to establish a platform forex vivomultivisceral organ perfusion.

Multivisceral grafts containing the liver, kidneys, pancreas, spleen and intestine were obtained from Yorkshire pigs. Three generation (gen) setups were tested during the iterative design process, and minor changes were made throughout. Gen1 (n=4) used a custom-designed single perfusion circuit. Gen2 (n=3) employed a dual perfusion circuit. Gen3 (n=4) featured a single perfusion circuit with an optimized basin and reservoir. Grafts underwent NMP using an autologous blood-based perfusate, while hemostatic parameters and function were assessed.

With each iteration, aortic flow improved, resistance decreased, urine output increased, oxygen consumption rose, perfusate lactate levels dropped, and pH stability improved. Cellular injury trended lower in Gen3. Histological evaluation demonstrated minimal differences in Gen2 and 3.

We demonstrate the feasibility of abdominal multivisceral NMP for up to 8 hours. Adequate arterial flow, stable perfusate pH, and high oxygen consumption in setup 3 indicate organ viability. Multivisceral perfusion may serve as a platform for long-term NMP.
Pool PaRTI: A PageRank-based Pooling Method for Robust Protein Sequence Representation in Deep Learning
Authors: Tartici Alp , Nayar Gowri , Altman Russ B
Published: October 2024

Motivation

Protein language models generate token-level embeddings for each residue, necessitating a method to pool these into a single vector representation of the entire protein. Traditional pooling methods often result in substantial information loss, impacting downstream task performance. We aim to develop a task-agnostic pooling method that preserves more information from token embeddings while offering biological interpretability.

Results

We introduce Pool PaRTI, a novel pooling method that leverages internal transformer attention matrices and PageRank to assign token importance weights. Pool PaRTI demonstrates statistically significant performance improvements across three diverse protein machine learning tasks, outperforming traditional pooling methods. It enhances accuracy, AUPRC, and MCC while offering interpretability by identifying biologically relevant regions without explicit structural training. Our approach is generalizable to encoder-containing protein language models.

Availability and Implementation

Pool PaRTI is implemented in Python with PyTorch and is available athttps://github.com/Helix-Research-Lab/Pool_PaRTI.git
Insights into the role of phosphorylation on microtubule crosslinking by PRC1
Authors: Tai Ellinor , Henglein Austin , Alfieri Angus , Saxena Gauri , Forth Scott
Published: October 2024

The mitotic spindle is composed of distinct networks of microtubules, including interpolar bundles that can bridge sister kinetochore fibers and bundles that organize the spindle midzone in anaphase. The crosslinking protein PRC1 can mediate such interactions between antiparallel microtubules. PRC1 is a substrate of mitotic kinases including CDK/cyclin-B, suggesting that it can be phosphorylated in metaphase and dephosphorylated in anaphase. How these biochemical changes to specific residues regulate its function and ability to organize bundles is not known. Here, we perform biophysical analyses on microtubule networks crosslinked by two PRC1 constructs, one a wild-type reflecting a dephosphorylated state, and one phosphomimetic construct with two threonine to glutamic acid substitutions near PRC1’s microtubule binding domain. We find that the wild-type construct builds longer and larger bundles that form more rapidly and are much less resistant to mechanical disruption than the phosphomimetic PRC1. Interestingly, microtubule pairs organized by both constructs behave similarly within the same assays. Our results suggest that phosphorylation of PRC1 in metaphase would tune the protein to stabilize smaller and more flexible bundles, while removal of these PTMs in anaphase would favor the assembly of larger more mechanically robust bundles to resist chromosome and pole separation forces at the spindle midzone.
Gum Arabic (Acacia senegal) enhances reproduction and modulates the microbiota-gut-brain axis of zebrafish in a sex-specific and dosage-dependent manner
Authors: Abi Assaf Justin , de Coriolis Jean-Charles , Godden Alice May , Redhead Eve , Bartram Jamie , Cohen-Krais Jayme , Silova Karina , Crighton Zoe , Le Gall Gwenaelle , Sami Saber , Khalid Sami Ahmed , Immler Simone
Published: October 2024

Dietary fibres (DFs) constitute a wide range of heterogeneous compounds that resist digestion and have beneficial effects on general health. Gum Arabic (GA) is a tree exudate consisting of 90% arabinogalactan, a polymer of arabinose and galactose sugars with prebiotic properties. As a dietary fibre, GA improves renal function, metabolism, and immune response in humans and animals. However, the underlying mechanisms leading to these health benefits are poorly understood. We supplemented female and male zebrafish (Danio rerio) with two concentrations of GA (6% and 60%) for two weeks. We assessed the effects of GA supplementation on the gut microbiome composition, intestinal and brain metabolic profiles, reproductive fitness, and brain gene expression. We found that GA supplementation resulted in changes to the gut microbiome with a relative increase in Fusobacteria and a relative decrease in Proteobacteria where the beneficial genusCetobacteriumwas significantly more abundant after supplementation. GA supplementation increased acetate levels, particularly in the brain, causing a decreased expression ofcart1in the brain of female zebrafish. While GA supplementation increased overall activity in male and female fish, reproductive fitness was negatively affected by GA supplementation in females. Our results suggest that while GA supplementation may have positive effects on metabolic rate and overall activity, it may come at a trade-off with reproductive fitness.

Significance Statement

Dietary fibres, found in plant-based food sources, can improve health. They include natural gums like gum Arabic, a highly sought-after food additive used as a homogeniser. Despite our better understanding of nutrition, a fibre gap is still prevalent in the Western world with efforts being made to incorporate new sources to close this gap and boost well-being. Here, we showed that when gum Arabic was supplemented into the zebrafish diet, it had a beneficial modulatory effect on the microbiota-gut-brain axis and reproductive fitness. Our findings support the benefits of dietary fibres but also link their impact to sexual dimorphism and dosage. This has implications for developing nutrition guidelines for both animals and humans.
The N-terminus of YY1 regulates DNA and RNA binding affinity for both the zinc-fingers and an unexpected nucleic acid binding domain
Authors: Elias Jimmy , Rosin Jane J. , Keplinger Amanda J. , Ruthenburg Alexander J.
Published: October 2024

Transcription factors (TFs) play central roles in dictating cellular identity and function by regulating gene expression programs. Beyond their well-folded DNA binding domains (DBDs) which recognize cognate DNA elements in the genome, TFs are enriched for intrinsically disordered regions (IDRs), which have a host of proposed functions including facilitating protein-protein interactions, aiding in binding site search, and binding RNA. Defining intrinsic regulatory properties of TFs requires further mechanistic investigation. We chose to investigate the DNA and RNA binding properties of Yin Yang 1 (YY1), a ubiquitously expressed TF directly involved in transcriptional activation, repression and genome architecture. Through systematic in vitro nucleic acid binding experiments we resolve conflicting literature defining the RNA binding interface of YY1, demonstrating that there are two RNA binding domains within YY1: its canonical 4 zinc finger DBD and a previously unannotated nucleic acid binding domain, which we term the REPO-NAB. Furthermore, we discover surprising autoinhibitory properties that the N-terminus of the protein imparts on each of these binding domains. Our results provide a new example of IDR-mediated regulation within TFs and enables future mechanistically precise functional investigations.
ADT-1004: A First-in-Class, Orally Bioavailable Selective pan-RAS Inhibitor for Pancreatic Ductal Adenocarcinoma
Authors: Reddy Bandi Dhana Sekhar , Nagaraju Ganji Purnachandra , Sarvesh Sujith , Carstens Julienne L. , Foote Jeremy B. , Graff Emily C. , Fang Yu-Hua D , Keeton Adam B. , Chen Xi , Berry Kristy L. , Bae Sejong , Akce Mehmet , Gorman Greg , Yoon Karina J. , Manne Upender , Boyd Micheal R. , Buchsbaum Donald J. , Azmi Asfar S. , Maxuitenko Yulia Y. , Piazza Gary A. , El-Rayes Bassel F.
Published: October 2024

Here, we evaluatedin vivoantitumor activity, target engagement, selectivity, and tumor specificity of ADT-1004, an orally bioavailable prodrug of ADT-007 having highly potent and selective pan-RAS inhibitory activity. ADT-1004 strongly blocked tumor growth and RAS activation in mouse PDAC models without discernable toxicity. As evidence of target engagement and tumor specificity, ADT-1004 inhibited activated RAS and ERK phosphorylation in PDAC tumors at dosages approximately 10-fold below the maximum tolerated dose and without discernable toxicity. ADT-1004 inhibited ERK phosphorylation in PDAC tumors. In addition, ADT-1004 blocked tumor growth and ERK phosphorylation in PDX PDAC models with KRASG12D, KRASG12V, KRASG12C, or KRASG13Qmutations. ADT-1004 treatment increased CD4+and CD8+T cells in the TME consistent with exhaustion and increased MHCII+M1 macrophage and dendritic cells. ADT-1004 demonstrated superior efficacy over sotorasib and adagrasib in tumor models involving human PDAC cells resistant to these KRASG12Cinhibitors. As evidence of selectivity for tumors from PDAC cells with mutant KRAS, ADT-1004 did not impact the growth of tumors from RASWTPDAC cells. Displaying broad antitumor activity in multiple mouse models of PDAC, along with target engagement and selectivity at dosages that were well tolerated, ADT-1004 warrants further development.

Significance

ADT-1004 displayed robust antitumor activity in aggressive and clinically relevant PDAC models with unique tumor specificity to block RAS activation and MAPK signaling in RAS mutant cells. As a pan-RAS inhibitor, ADT-1004 has broad activity and potential efficacy advantages over allele-specific KRAS inhibitors by averting resistance. These findings support clinical trials of ADT-1004 for KRAS mutant PDAC.
Deep Mining of the Human Antibody Repertoire Identifies Frequent and Immunogenetically Diverse CDRH3 Topologies Targetable by Vaccination
Authors: Habib Rumi , Solieva Shahlo O. , Lin Zi Jie , Ghosh Sukanya , Bayruns Kelly , Singh Maya , Agostino Colby J. , Tursi Nicholas J. , Sowers Kirsten J. , Huang Jinwei , Roark Ryan S. , Purwar Mansi , Park Younghoon , Ayyanathan Kasirajan , Li Hui , Carey John W. , Kim Amber , Park Joyce , McCanna Madison E. , Skelly Ashwin N. , Chokkalingam Neethu , Kriete Sinja , Shupin Nicholas , Huynh Alana , Walker Susanne , Laenger Niklas , Du Jianqiu , Cui Jiayan , Hahn Beatrice H. , Patel Ami , Escolano Amelia , Kwong Peter D. , Shapiro Lawrence , Bowman Gregory R. , Shaw George M. , Weiner David B. , Pallesen Jesper , Kulp Daniel W.
Published: October 2024

Many vaccination strategies against highly variable pathogens such as HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) with particular immunogenetic or structural features. The V2 apex of the HIV-1 Env protein is a promising target for a class of bnAbs that contain conserved structural motifs in the heavy chain complementarity determining region 3 (CDRH3). Here, we show that these structural motifs are targetable by vaccination by characterizing V2 apex ‘axe-like’ CDRH3s in the human repertoire and developing new immunogens capable of selectively engaging them. We determined the frequency and diversity of axe-like CDHR3s in healthy human donors using a series of structural informatics approaches finding these precursors in 86.5% of donors. Axe-targeting immunogens based on the HIV-1 Env Q23.17 were developed and bound axe-like precursors in cryo-EM structures, induced V2 apex-specific antibody responses in humanized mice, and induced axe-like heterologous neutralizing antibodies in rhesus macaques. These results unveil a new structure-guided immunoinformatic vaccine design paradigm that can be employed to elicit immunogenetically diverse yet structurally conserved classes of antibodies.
A complete account of the behavioral repertoire uncovers principles of larval zebrafish hunting behavior
Authors: Rubinstein Yoav , Moshkovitz Maayan , Ottenheimer Itay , Shapira Sapir , Tiomkin Stas , Avitan Lilach
Published: October 2024

In goal-directed behavior animals select actions from a diverse repertoire of possible movements. Accurately quantifying the complete behavioral repertoire can uncover the underlying rules that guide such goal-directed behavior. However, these movements are usually complex, high-dimensional, and lead to various outcomes, posing a challenge to fully capture the complete repertoire. By tracking freely hunting zebrafish larvae using a highspeed camera and analyzing their movements, we developed a mathematical model that accurately reproduces the complete repertoire. Using the model, we show that fish position and change in heading angle following a movement are coupled, such that the choice of one of them limits the possibilities of the other. This repertoire structure uncovered fundamental principles of movements, showing that fish rotate around an identified rotation point and then move forward or backward along straight lines. From the uncovered movement principles, we identified a new guiding rule for prey interaction: in each movement, fish turn to face the prey and then move forward or backward. This enables decoupling between orientation and distance selections of the fish during the hunt. These results provide a comprehensive and continuous description of the repertoire of movements, reveal underlying algorithmic rules that govern the behavior, and offer insights into the potential neural implementation of the repertoire.
SEXUAL-DIMORPHISM IN VISUALLY GUIDED APPROACH BEHAVIOR EMERGES UNIQUELY DURING ADOLESCENCE
Authors: Gonzalez-Olvera Rocio , Allen Kelsey , Feng Ting , Hoy Jennifer L.
Published: October 2024

Studying prey capture behavior in mice offers a fruitful platform for understanding how ecologically relevant visual stimuli are differentially processed by the brain throughout life. For example, specific visual stimuli that indicate prey and that naturally draw appetitive orienting in the adult may be interpreted differently or evoke distinct behaviors during development. What are the neural mechanisms that might allow an animal to flexibly couple the same stimulus information to distinct behavioral outcomes as a function of developmental needs? To begin to address this important question, we quantified visually evoked orienting behaviors between adolescent and adult C57BL6/J mice of both sexes under the natural prey capture context compared to responses in our established virtual motion stimulus paradigm, C-SPOT. Most surprisingly, we discovered that female versus male adolescent mice have opposing innate behavioral biases evoked by the same sweeping motion stimuli which is not present in adulthood. Further, female mice display a robust enhancement of approach towards visual motion over all other groups tested, yet they are the least aggressive in response to live prey. Thus, our work overall revealed that innate approach towards visual motion is robustly dissociated from predatory aggression in female versus male mice specifically during adolescence. This underscores the different natural behavioral goals and physiological states that uniquely apply to female versus male adolescent animals, and reveals that approach towards visual motion is a key sensory-motor process selectively augmented during female adolescence.

Highlights

Adolescent mice of both sexes innately approach insects more than adults

Adolescent males versus females have distinct response biases to visual motion

Adolescent males display the strongest hunger-related predatory aggression
Parent-offspring brain similarity: Specificities and commonalities across gender combinations - the Transmit Radiant Individuality to Offspring (TRIO) study
Authors: Matsudaira Izumi , Yamaguchi Ryo , Taki Yasuyuki
Published: October 2024

Research suggests that parent-offspring brain similarities may underlie intergenerational transmission of psychopathology. However, most studies have focused on mothers and offspring, with few including fathers. This study aimed to extend understanding of parent-offspring neural similarities by examining parent-offspring trios. The study included 152 Japanese biological parent-offspring trios who participated in the Transmit Radiant Individuality to Offspring (TRIO) study. We analyzed the parent-offspring similarities in brain structural features (cortical thickness, surface area, local gyrification index, and subcortical volume) across different parent-offspring gender combinations (father-son, father-daughter, mother-son, and mother-daughter). Additionally, we investigated the relationship between brain similarities and similarities in intelligence and personality traits in parents and offspring. Our findings confirmed that correlations in brain structural features between father-offspring or mother-offspring dyads were significantly stronger than those between unrelated individuals. Notably, both sons and daughters exhibited brain regions similar to their fathers only, mothers only, both parents, or neither parent. Furthermore, a significant association was observed between similarities in general intelligence and the surface area of auditory regions in both father-offspring and mother-offspring dyads. These results provide valuable insights into the genetic and environmental factors influencing brain development and aging across generations. This study is expected to contribute to future research elucidating the mechanisms underlying the intergenerational transmission of psychiatric disorders.
Transcriptomic Insights into Hypothalamic Aging During Menopause: A Comparative Analysis of Human and Mouse Models
Authors: Bloom Jordana C. B. , Torres Encarnacion , Pereira Sidney A. , Arvizu-Sanchez Liliana , Fontes Audrey N. , Joffe Hadine , Page David C. , Navarro Victor M.
Published: October 2024

Menopause significantly impacts women’s health, yet hypothalamic changes during this transition remain poorly understood. We analyzed gene expression in human hypothalamic samples across menopausal stages, revealing significant changes in inflammatory pathways, KNDy neuron signaling, and thermoregulatory genes. This analysis also identified novel central markers of menopause, including AKAP5 and CDKN1A (p21). To further investigate these changes, we developed a novel mouse model based on long-term (4 months) ovariectomy (OVX) that mimics the gonadotropin and temperature fluctuations of menopausal transition. Remarkably, the posterior hypothalamus of 4-month OVX mice closely mirrored the transcriptional changes observed in perimenopausal women. Both species exhibited increased inflammatory signaling and glial activation, alongside altered KNDy neuron activity. Our findings provide new insights into the central mechanisms of menopausal symptoms and offer a valuable preclinical model for testing interventions.
The effect of population size on adaptation to fluctuating temperatures
Authors: Räsänen Emmi , Nieminen Veera , Summanen Pauliina A. M. , Villalba de la Peña Mariana , Makkonen Peetu , Suisto Kaisa , Ketola Tarmo , Kronholm Ilkka
Published: October 2024

Climate change exposes populations to more frequent periods of extreme temperatures and faster temperature fluctuations. Theoretical models suggest that different types of adaptations should occur in constant versus fluctuating environments of varying frequency. Furthermore, evolutionary adaptation to one environment may weaken the adaptations to alternative environments due to antagonistically pleiotropic alleles. However, fitness trade-offs are rarely observed in experiments and it has been hypothesized that the number and severity of trade-offs evolving in fluctuating environments might depend on population size. To evaluate whether specific types of adaptations evolve at fluctuating temperatures and how population size affects the evolution of trade-offs, we performed an evolution experiment with fission yeast (Schizosaccharomyces pombe). The small and large populations evolved for 500 generations at constant and fluctuating temperatures, after which the evolved strains competed against ancestral strains in respective selection environments and in alternative environments to detect trade-offs. We observed significant adaptation and maladaptation only to constant heat, but not to fluctuating temperatures. Overall, the population size did not have significant effects on adaptation capacity or trade-offs in alternative environments. Our results suggest that constant extreme temperatures may act as stronger selective pressures than temperature variation and that trade-offs are unlikely to constrain adaptation to fluctuating temperatures.
Co-lethality ofLEU2andBAP2is carbon source dependent and is overcome byBUL1deletion inSaccharomyces cerevisiae
Authors: Maheswaran S , Bhat Paike Jayadeva
Published: October 2024

In a leucine requiringSaccharomyces cerevisiaestrain, deletion ofBAP2, a high affinity leucine permease confers lethality in presence of fermentable sugars, but not other carbon sources. Deletion ofBUL1, an adaptor overcomes this lethality.BUL1deletion augments leucine import through accumulation of Bap3 and Bap2 in the plasma membrane and reduces their turnover. We suspectBUL1as a cognate adaptor for ubiquitylation of these permeases.