bluuebunny/crossref_metadata_2025 huggingface dataset:
A minimally guided organoid model for cross-species comparisons of cerebellar development
Authors: Guglielmi Luca , Lloyd-Davies-Sánchez Daniel , González Martínez José , Lancaster Madeline A.
Published: October 2024

The human cerebellum has undergone significant evolutionary expansion compared to other species, contributing to both motor and cognitive skills. However, the mechanisms underlying this process remain largely unknown as interrogating human cerebellar development alongside other species has to date been unfeasible. To address this, we developed a minimally guided cerebellar organoid protocol that combines unguided neural induction with precise temporal calibration of posteriorizing morphogens. This approach effectively overrides default telencephalic fate in cerebral organoids and induces stable cerebellar identities. Cerebellar organoids derived from both human and mouse ESCs exhibit species-specific size differences at comparable developmental stages and show robust induction of cerebellar master regulators and progenitor cell types. This model provides a powerful tool for investigating the mechanisms underlying cerebellar development in the context of both evolution and disease.
Dosage compensation and sexual conflict in female heterogametic methylomes
Authors: Tangili Marianthi , Sudyka Joanna , Furni Fabricio , Palsbøll Per , Verhulst Simon
Published: October 2024

DNA methylation (DNAm) suppresses gene expression and contributes to dosage compensation in mammals but whether DNAm plays a similar role in female ZW chromosome heterogametic species remains unresolved. We assessed chromosome-level DNAm using whole genome bisulphite sequencing in two avian species, zebra finches and jackdaws. Dosage compensation by DNAm would result in higher and more variable DNAm level in males relative to females on the Z chromosome. However, we found that the level of DNAm and its variance on the Z chromosome was lower in males. Moreover, male Z chromosome-based gene promoters were more frequently hypomethylated compared to females, indicating absence of upregulation on a gene-by-gene basis across the female Z chromosome. We suggest our findings reveal mitigation of an intra-genomic sexual conflict, with females suppressing expression of Z chromosome-based genes that benefit male but not female fitness. W was the most methylated chromosome, but hypermethylation on the W chromosome was mostly confined to intergenic regions, presumably resulting in the downregulation of transposable elements known to comprise a large part of the W chromosome. Thus, DNAm is involved in the development of sex-dependent phenotypes, but dosage compensation is achieved through other mechanisms.
Ixodes ricinusnymphs prefer blood withBorreliainfection and low corticosteroid concentration
Authors: Vanroy Tosca , Catfolis Bram , Verbrugghe Elin , Verheyen Kris , Lens Luc , Strubbe Diederik , Pasmans Frank , Martel An , Croubels Siska , Cherlet Marc , Baeten Lander
Published: October 2024

Ticks play a significant role in the transmission of various pathogens, impacting both human and animal health. Understanding the factors influencing tick feeding preferences is crucial for mitigating the risk of tick-borne diseases. This study investigates the blood preference ofIxodes ricinusnymphs, focusing on host species, stress hormone levels (glucocorticoids), and the presence ofBorrelia burgdorferibacteria. Three series ofin vitroexperiments were conducted. The setup involved placing individual blood drops (15 μl) on filter paper over a 37°C plate. Ticks were placed in the center, and their movements were tracked for two minutes to record preferences. The first experiment evaluated the tick's preference for blood from different hosts (mouse, bird, sheep). The second experiment explored the role of stress hormones by assessing the ticks' response to blood with varying levels of supplemented cortisol and corticosterone (0, 10, 100 and 1000 ng/ml). The third experiment examined the potential influence ofBorreliainfection, combined with elevated stress hormone levels, on blood preference. Our results show thatI. ricinusnymphs show a significant preference for blood without added glucocorticoids and, in mice, blood withBorreliainfection. No clear preference for a specific host species was observed. These findings provide valuable insights into the complex interactions between ticks, blood characteristics, andBorreliainfection status, highlighting the potential importance of host physiological state in tick host selection. Future studies should explore the mechanisms behind these preferences, which could lead to the development of new methods to control the spread of tick-borne diseases.
Divergence and parallelism in two tropical drosophilids simultaneously invading a desert environment
Authors: El-Sabrout Ahmed M. , Moreno Céline , Temperville Mélody , Ferreira Erina A. , Ogereau David , Hassani Issa Mze , Bastide Héloïse , Abou-Youssef Amira Y. , Yassin Amir
Published: October 2024

Invasive species have once been called a ‘grand experiment in evolution’ but natural replicates of such experiments are often scarce. In particular, whether the rapid adaptation to the new environment involves genetic predisposition in the ancestral range or mainly occurs via post-introductory selection on a genetically variable propagule remains unknown. Here, we investigate the parallel adaptation of two drosophilid species of the genusZaprionus,Z. indianus(the African fig fly) andZ. tuberculatus, to contrasting agrarian and desert environments following their introduction in Egypt during the last four decades. Field collection unraveled distinct spatial distribution of the two species. Population genomics analyses showed correlated differentiation levels at orthologous genes before and after introduction in both species. Nonetheless, phenotypic analyses revealed distinct fruit preference and desiccation resistance between both species as well as between introduced and nativeZ. tuberculatuspopulations. Hence, despite signals of genomic parallelism, ecological divergence between the two species likely facilitates their co-existence in the introduced regions. Our results provide a significant step towards understanding the mechanisms underlying the simultaneous invasive success of both species, which have also recently invaded the Americas and Europe, and of which one at least is a notorious pest.
Unlearning Virus Knowledge Toward Safe and Responsible Mutation Effect Predictions
Authors: Li Mingchen , Zhou Bingxin , Tan Yang , Hong Liang
Published: October 2024

Abstract

Pre-trained deep protein models have become essential tools in fields such as biomedical research, enzyme engineering, and therapeutics due to their ability to predict and optimize protein properties effectively. However, the diverse and broad training data used to enhance the generalizability of these models may also inadvertently introduce ethical risks and pose biosafety concerns, such as the enhancement of harmful viral properties like transmissibility or drug resistance. To address this issue, we introduce a novel approach using knowledge unlearning to selectively remove virus-related knowledge while retaining other useful capabilities. We propose a learning scheme, PROEDIT, for editing a pre-trained protein language model toward safe and responsible mutation effect prediction. Extensive validation on open benchmarks demonstrates that PROEDIT significantly reduces the model’s ability to enhance the properties of virus mutants without compromising its performance on non-virus proteins. As the first thorough exploration of safety issues in deep learning solutions for protein engineering, this study provides a foundational step toward ethical and responsible AI in biology.
Traction force generation in motile malaria parasites is modulated by thePlasmodiumadhesin TLP
Authors: Ripp Johanna , Probst Dimitri , Singer Mirko , Schwarz Ulrich S. , Frischknecht Friedrich
Published: October 2024

Plasmodiumsporozoites are the highly polarized and motile forms of the malaria parasite that are transmitted by mosquitoes to the vertebrate hosts. Sporozoites use myosin molecular motors to generate retrograde flow of actin filaments. These are linked to plasma-membrane spanning adhesins, which in turn bind to the extracellular environment, resulting in forward directed gliding motility. The gliding motility machine of sporozoites leads to high speeds in the range of micrometer per second, which are essential for efficient migration in the skin. Yet, it is not clear how the individual parts of the machinery work together to generate force during migration. Sporozoites are elongated and curved cells and move on circular tracksin vitro. Sporozoites lacking the adhesin thrombospondin related anonymous protein (TRAP) like protein, TLP, can still migrate in the skin, but at a lower level. TLP lacking sporozoites generate a lower force on the dorsal (non-substrate facing) surface as measured by laser tweezers. Here we use traction force microscopy to investigate motile sporozoites and the forces they produce during migration on their ventral surface. Both wild type andtlp(-)sporozoites show distinct foci of force generation, buttlp(-)sporozoites generating overall lower forces. Our findings demonstrate that TLP is an important element of the force-generating machinery during sporozoite gliding motility.
OpenExo: An Open-Source Modular Exoskeleton to Augment Human Function
Authors: Williams Jack R. , Cuddeback Chance F. , Fang Shanpu , Colley Daniel , Enlow Noah , Cox Payton , Pridham Paul , Lerner Zachary F.
Published: October 2024

While the field of wearable robotic exoskeletons is rapidly expanding, there are several barriers to entry that discourage many from pursuing research in this area, ultimately hindering growth. Chief among these are the lengthy and costly development time to get an exoskeleton from conception to implementation and the necessity for a broad set of expertise. Additionally, many exoskeletons are designed for a specific utility (e.g., ankle plantarflexor assistance) and are confined to the laboratory environment, limiting the flexibility of the designed system to adapt to answer new questions and explore new domains. To address these barriers, we present OpenExo, an open-source modular untethered exoskeleton framework that provides access to all aspects of the design process including (1) software, (2) electronics, (3) hardware, and (4) control schemes. To demonstrate the utility of this exoskeleton framework, we performed benchtop and experimental validation testing with the system across multiple configurations including (1) hip-only incline assistance, (2) ankle-only indoor and outdoor assistance, (3) hip-and-ankle load-carriage assistance, and (4) elbow-only weightlifting assistance. All aspects of the software architecture, electrical components, hip and Bowden-cable transmission designs, and control schemes are freely available for other researchers to access, use, and modify when looking to address research questions in the field of wearable exoskeletons. Our hope is that OpenExo will rapidly accelerate the development and testing of new exoskeleton designs and control schemes, while simultaneously encouraging others, including those who would have been turned away from entering the field, to explore new and unique research questions.

One-Sentence Summary

We present an open-source, open-hardware exoskeleton to aid in accelerating the growth of robotic exoskeleton research.
An engineered chromatin protein with enhanced preferential binding of H3K27me3 over H3K9me3
Authors: Franklin Kierra A. , Priode J. Harrison , Steppe Paige , Haynes Karmella A.
Published: October 2024

The human genome is organized within the nucleus as chromatin, which is largely comprised of histone proteins that assemble on DNA into nucleosome complexes. Histone post-translational modifications (PTMs) are dynamic chromatin features that signal distinct gene expression states and modulate important cellular functions like cell differentiation. Histone binding domains (HBDs) from chromatin reader-effector proteins are being used as new tools to target and track histone PTMs in living cells. HBDs bind histones through multi-contact interactions that may confer more specificity than antibodies, but are hard to study because of their weaker affinityin vitro. To explore the large HBD design space, we developed the “Cell-Free Histone-Binding Immunoassay” (CHIA) where interactions between cell-free-expressed HBD proteins and immobilized biotinylated histone peptides are measured in an ELISA-style assay. We showed that the number of functional CBX8 polycomb chromodomains (PCD) in a fusion protein scales with H3K27me3 binding. We tackled the challenge of engineering a high affinity HBD that distinguishes H3 A-A-R-K27me3-S from a similar region on the same histone, T-A-R-K9me3-S. Previously reported K33E and Q9D CBX7 PCD variants bound with high affinity to H3K27me3, and bound as strongly with H3K9me3. In contrast, the K33E substitution enhanced CBX8 PCD binding to K27me3 with minimal K9me3 binding. To determine if the CBX8 hydrophobic clasp (V10 and L49) supports K27me3 specificity we tested hydrophobic substitutions, and observed increased affinity and strong specificity for H3K27me3. These results will enable more robust sensing of H3K27me3 for applications such as histone PTM-detection, and cell engineering.
Seasonal contact and migration structure mass epidemics and inform outbreak preparedness in bottlenose dolphins
Authors: Collier Melissa , Urian Kim , Theisen Sarah , Jacoby Ann-Marie , Wilkin Sarah , Patterson Eric M. , Wallen Megan M. , Colizza Vittoria , Mann Janet , Bansal Shweta
Published: October 2024

Infectious respiratory diseases have detrimental impacts across wildlife taxa, particularly in marine species. Despite this vulnerability, we lack information on the complex spatial and contact structures of marine populations which reduces our ability to understand disease spread and our preparedness for epidemic response. We leveraged a collated dataset to establish the first data-driven epidemiological model on a cetacean species, the Tamanend’s bottlenose dolphin (Tursiops erebennus), whose populations are periodically impacted by deadly respiratory disease in the northwest Atlantic. We found their spatial distribution and contact is heterogeneous along the coastline and varies by ecotype, which explains differences in infection burdens observed in past outbreaks. We also determined that outbreaks beginning in northern parts of their habitat during migratory seasons have the highest epidemic risk and that dolphins in North Carolina estuaries would be the best sentinels for disease surveillance. Our mathematical model provides a generalizable, non-invasive tool that takes advantage of routinely collected marine mammal data to mechanistically understand disease transmission and inform disease surveillance tactics for marine sentinels. Our findings highlight the heterogeneities that play a crucial role in shaping the impacts of infectious diseases in wildlife, and how a data-driven understanding of these mechanisms can enhance epidemic preparedness.
Convergent transcriptomic and genomic adaptation in xeric rodents
Authors: Domitille Chalopin , Carine Rey , Jeremy Ganofsky , Juliana Blin , Pascale Chevret , Marion Mouginot , Bastien Boussau , Sophie Pantalacci , Marie Sémon
Published: October 2024

Repeated adaptations rely in part on convergent genetic changes. The extent of convergent changes at the genomic scale is debated and may depend on the interplay between different factors. Rodents have repeatedly adapted to life in arid conditions, notably with altered renal morphology and physiology. This occurred at different time periods, allowing us to test the importance of time in convergent genomic evolution. We analyzed kidney transcriptomes from 34 species to quantify and characterize convergent evolution at the level of gene expression, tissue composition, and coding sequences. We found that several genes showed convergent expression changes, some of which also carried convergent changes in their coding sequence. We then subdivided these data to test the influence of evolutionary history. First, within the subfamily Murinae, we found more convergent gene expression, reflecting convergent changes in cell proportions. Second, we compared data for recent (within genera) and ancient (between genera) adaptations, and observed more convergent changes in the latter. Our study shows that adaptation to xeric environments in rodents involves repeated changes in tissue composition, gene expression and coding sequences, and that the degree of convergent evolution increases with both the age of the adaptations and species relatedness.
Genome-widein vivodynamics of cohesin-mediated loop extrusion and its role in transcription activation
Authors: Popay Tessa M. , Pant Ami , Munting Femke , Black Morgan E. , Haghani Nicholas , Dixon Jesse R.
Published: October 2024

The organization of the genome in three-dimensional space is highly dynamic, yet how these dynamics are regulated and the role they play in genome function is poorly understood. Here, we utilized acute depletion of NIPBL to characterize the role of cohesin-mediated loop extrusionin vivo. Using this approach, we found that many chromatin loops are rapidly diminished upon loss of NIBPL, consistent with recent single locus imaging studies showing that chromatin loops are transient. However, we also identified cohesin-dependent chromatin loops that are associated with distinct chromatin states and may be “long-lived”, given that they require NIPBL for their establishment upon mitotic exit, but are persistent when NIPBL is depleted from interphase cells. In addition to the reformation of 3D genome structures, mitotic exit coincides with widespread transcriptional activation. We found that NIPBL is essential for establishing the expression of lineage-defining genes during the M-G1 transition but has diminished impact on the steady-state maintenance of their expression. At genes sensitive to its depletion, NIPBL supports a unique local genome organization defined by greater spatial proximity to nearby super-enhancers and weaker transcription start site insulation of genomic contacts. Overall, we show that NIPBL-mediated loop extrusion is critical to genome organization and transcription regulationin vivo.
Reference-free variant calling with local graph construction with ska lo (SKA)
Authors: Derelle Romain , Madon Kieran , Hellewell Joel , Rodríguez-Bouza Víctor , Arinaminpathy Nimalan , Lalvani Ajit , Croucher Nicholas J. , Harris Simon R. , Lees John A. , Chindelevitch Leonid
Published: October 2024

The study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant calling methods from whole-genome sequencing data rely on reference-based alignment, which can introduce biases and require significant computational resources. Alignment-free and reference-free approaches offer an alternative by leveraging k-mer-based methods, but existing implementations often suffer from sensitivity limitations, particularly in high mutation density genomic regions. Here, we present ska lo, a graph-based algorithm that aims to identify variants between pathogen whole-genome sequencing data by traversing a coloured De Bruijn graph and building variant groups (ie, sets of variant combinations). Through in-silico benchmarking and real-world dataset analyses, we demonstrate that ska lo achieves high sensitivity in SNP calls while also enabling the detection of insertions and deletions, as well as SNP positioning on a reference genome for recombination analyses. These findings highlight ska lo as a simple, fast and effective tool for pathogen genomic epidemiology, extending the range of reference-free variant calling approaches. ska lo is freely available as part of the SKA program (https://github.com/bacpop/ska.rust).
Cryo-EM structures of G4-stalled CMG reveal inchworm mechanism of DNA translocation
Authors: Batra Sahil , Allwein Benjamin , Kumar Charanya , Devbhandari Sujan , Bruning Jan-Gert , Bahng Soon , Lee Chong , Marians Kenneth J. , Hite Richard K. , Remus Dirk
Published: October 2024

DNA G-quadruplexes (G4s) are non-B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we have characterized fork collisions with preformed G4s in the parental DNA using fully reconstituted yeast and human replisomes. We demonstrate that a single G4 in the leading strand template is sufficient to stall replisomes by blocking the CMG helicase. An ensemble of high-resolution cryo-EM structures of stalled yeast and human CMG complexes reveals that the G4 is fully folded and lodged inside the CMG central channel. The stalled CMG is conformationally constrained and arrests in the transition between translocation states. Unexpectedly, our analysis suggests that CMG employs an unprecedented inchworm mechanism to translocate on DNA. These findings illuminate the eukaryotic replication fork mechanism under both normal and perturbed conditions.
Autophosphorylation of the oncogenic protein TEL-ABL confers resistance to the allosteric ABL inhibitor asciminib
Authors: Muratcioglu Serena , Eide Christopher A. , Gorday Kent , Sumpena Emily , Zuo Wenqi , Groves Jay T. , Druker Brian J. , Kuriyan John
Published: October 2024

Chromosomal translocations that fuse the ABL1 gene to BCR and TEL cause human leukemias. Oligomerization and the loss of an inhibitory myristoylation modification lead to unregulated kinase activity of the BCR-ABL and TEL-ABL fusion proteins. ATP-competitive ABL inhibitors, such as imatinib and ponatinib, are effective against both fusion proteins. We discovered that asciminib, an allosteric inhibitor of BCR-ABL that binds to the myristoyl binding site in the ABL kinase domain, is >2000-fold less potent against TEL-ABL than BCR-ABL in cell-growth assays. This is surprising because the ABL components of the two fusion proteins, including the asciminib binding sites, have identical sequence. We deleted a short helical segment in the ABL kinase domain that closes over asciminib when it is bound. This deletion results in asciminib resistance in BCR-ABL, but has no effect on TEL-ABL, suggesting that the native autoinhibitory mechanism that asciminib engages in BCR-ABL is disrupted in TEL-ABL. We show, using mammalian cell expression and single-molecule microscopy, that BCR-ABL is mainly dimeric while TEL-ABL forms higher-order oligomers. Oligomerization can promote trans-autophosphorylation of ABL, and we find that a regulatory phosphorylation site in the SH3 domain of ABL (Tyr 89) is highly phosphorylated in TEL-ABL. This phosphorylation is expected to disassemble the autoinhibited conformation of ABL, thereby preventing asciminib binding. We show that TEL-ABL is intrinsically susceptible to inhibition by asciminib, but that increased phosphorylation results in resistance. Our results demonstrate that different ABL fusion proteins can have dramatically different responses to allosteric inhibitors due to differential phosphorylation.

One Sentence Summary

When TEL-ABL is phosphorylated, it is insensitive to asciminib. However, when TEL-ABL is dephosphorylated by a phosphatase, asciminib sensitivity is restored.
Soil depth determines the microbial communities inSorghum bicolorfields
Authors: Murray Emily R. , Minich Jeremiah J. , Saxton Jocelyn , de Gracia Marie , Eck Nathaniel , Allsing Nicholas , Kitony Justine , Patel-Jhawar Kavi , Allen Eric E. , Michael Todd P. , Shakoor Nadia
Published: October 2024

Sorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a unique and stratified soil microbiome that plays a crucial role in plant health, growth, and carbon storage. Microbiome studies on agricultural soils, particularly fields growingS. bicolor, have been mostly limited to surface soils (<30 cm). Here we investigated the abiotic factors of soil properties, field location, depth, and the biotic factors of sorghum type across 38 genotypes on the soil microbiome. Utilizing 16S rRNA gene amplicon sequencing, our analysis reveals significant changes in microbial composition and decreasing diversity at increasing soil depths withinS. bicolorregardless of genotype or fields. Notably, specific microbial families, such as Thermogemmatisporaceae and an unclassified family within the ABS-6 order, were enriched in deeper soil layers beyond 30 cm. Additionally, microbial richness and diversity declined with depth, reaching a minimum at the 60 - 90 cm layer, with layers beyond 90 cm increasing in alpha diversity. These findings highlight the importance of soil depth in agricultural soil microbiome studies.
Tunable Low-Rate Genomic Recombination with Cre-lox inE. coli: A Versatile Tool for Synthetic Biology and Environmental Sensing
Authors: Garabello Elisa , Yoon Hyun , Reid Matthew C. , Giometto Andrea
Published: October 2024

A variety of synthetic biology applications, from environmental sensing to bioproduction, would benefit from the ability to induce genomic alterations at low, tunable rates. Site-specific recombinases can be used to perform a variety of targeted DNA modifications such as excisions, inversions, and integrations. Their specificity and efficiency are offset by leaky expression and challenges in engineering a dynamic range of recombination rates. Here, we developed a tightly regulated, titratable Cre recombinase system that is tailored to achieve low recombination rates inEscherichia coli. As a proof-of-concept application of this design, we developed a whole-cell recombination-based arsenic biosensor, with detection sensitivity comparable to traditional wet chemical methods. Furthermore, our biosensor allows decoupling exposure from measurement, which could benefit assays in more complex, realistic settings. This system enables targeted genetic recombination events at experimentally tunable rates with application in ecological, environmental and cell physiology research, and beyond.

Abstract Figure
Advancing Adoptive Cell Therapy: Optimized Expansion of Adaptive NK Cells for Solid Tumors
Authors: Almazán Nerea Martín , Román Sara , Sun Yizhe , Bräutigam Lars , Pantalone Mattia Russel , Stragliotto Giuseppe , Gultekin Okan , Saheli Sahar , Lehti Kaisa , Nauclér Cecilia Söderberg , Sarhan Dhifaf
Published: October 2024

Background

Immune therapies are emerging as a critical component of cancer treatment, capable of delivering durable and potentially curative responses. While CAR-T cell therapy has proven effective for hematological malignancies, it faces challenges in treating solid tumors due to tumor antigen heterogeneity, an immunosuppressive tumor microenvironment, and physical barriers hindering CAR-T cell infiltration. NK cells, particularly adaptive NK (aNK) cells, offer a promising alternative due to their ability to recognize and kill tumor cells without prior sensitization and their resistance to immunosuppressive environments.

Purpose

The study investigates the role of cytokines, specifically IL-21 and IL-15, in enhancing aNK cell expansion and activation using peripheral blood mononuclear cells (PBMCs) from healthy donors and tumor-infiltrating lymphocytes (TILs) from glioblastoma (GBM) patients.

Methods

Buffy coats and GBM TILs were collected from Karolinska Hospital. NK cells were isolated and expanded in vitro with IL-15 and IL-21 cytokines and feeder cells (K562 and K562E). Furthermore, tumor lysate was added in the cultures to boost memory responses in aNK cells. NK cell functionality, cytotoxicity, and phenotyping was assessed using flow cytometry and statistical analysis (t-test and two-way ANOVA) used to validate the results. Further animal model was used to validate the cytotoxicity capacities of these cells against GBM tumors using a zebrafish model.

Results

IL-21 drives the expansion of aNK better than IL-15 controls, data shown in PBMCs and TILs derived from GBM patients and IPLA OVCA patients. Additionally, the use of tumor lysate as a booster for restimulation further amplifies the cytotoxic capacity of aNK cells against autologous tumors. The zebrafish model validates this method, by decreasing the tumor size in zebrafish animals after 3 days of injection.

Conclusion

The results demonstrate that IL-21 is essential for the specific expansion of aNK cells, enhancing their aggressiveness towards tumor cells. Additionally, tumor lysate significantly increases the cytotoxic efficacy of aNK cells upon restimulation with the same tumor cells. These findings suggest that IL-21 plays a crucial role in the specific expansion and activation of aNK cells, enhancing their aggressiveness towards tumor cells.

By optimizing the expansion protocol, this method aims to advance the clinical application of aNK cells in immunotherapies for solid tumors, offering a potential solution to the limitations faced by current CAR-T therapies.
Coordinate post-transcriptional regulation by microRNAs and RNA binding proteins is critical for early embryonic cell fate decisions
Authors: Sangokoya Carolyn , Blelloch Robert
Published: October 2024

Abstract/Summary

Post-transcriptional control by RNA binding proteins (RBPs) and microRNAs play central roles in mRNA stability and translation (1). However, little is known about how RBPs and microRNAs coordinate in developmental time to regulate cell fate. Here, we show that coordinate RBP and microRNA control of a single transcript, Profilin 2 (Pfn2), is essential for differentiation of embryonic stem cells (ESCs) into the primary germ layer lineages. The Pfn2 3’untranslated region has a binding site for Iron Regulatory Proteins and a nearby binding site for ESC enriched microRNAs (2,3). Deletion of this microRNA site leads to increased PFN2 and reduced FGF signaling during pluripotency transition prior to germ layer formation (4). In contrast, deletion of the iron response element leads to decreased PFN2 and a Wnt signaling defect, reduced nuclear beta-catenin, and a subsequent block in mesendodermal lineages during early germ layer formation. The choreographed microRNA-IRE axis of control on the Pfn2 transcript is essential for two key signal transduction steps during ESC differentiation.
Machine learning sparse reaction-diffusion models from stochastic dynamics and spatiotemporal patterns
Authors: Abubaker-Sharif Bedri , Devreotes Peter N. , Iglesias Pablo A.
Published: October 2024

In recent years, live-cell imaging has generated detailed spatiotemporal datasets of biochemical networks within cells. These networks often exhibit characteristics of spatially-distributed excitable systems, with propagating waves of signaling activity that govern processes such as cell migration, division, and other essential physiological functions. Traditionally, these reaction-diffusion systems have been modeled using stochastic partial differential equations incorporating spatial Langevin-type dynamics. Although these knowledge-based models have provided valuable insights, they are typically not directly inferred from experimental data. In this study, we introduce and apply two data-driven methodologies for learning the structure and parameters of spatial Langevin equation (SLE) models: 1) Kramers-Moyal regression, an adaptation of an established approach to fit microscale stochastic dynamics, and 2) wave features optimization, a novel approach to match macroscale spatiotemporal patterns. Unlike black-box neural network models that predict system behavior but provide no mechanistic insight, this approach estimates nonlinear model equations that directly relate to system structure and dynamics. As a proof-of-concept, we focus on simulation datasets derived from two stochastic reaction-diffusion models: one based on the FitzHugh-Nagumo equations (FHN model) and another on a biochemically adapted version of the FHN equations (FR model). Our results demonstrate that optimizing stochastic dynamics and wave patterns enables the accurate estimation of SLE model structure and parameters directly from 1D and 2D spatial data. With sparsity enforcement, we also identify novel sparse reaction-diffusion models for excitable systems. We show that this approach effectively approximates system behavior even when working with datasets similar to experimental conditions, with low temporal resolution and unobserved molecular components. By leveraging machine learning techniques for robust estimation of excitable reaction-diffusion models from spatiotemporal data, this work enhances our ability to model and understand the complex systems that regulate cell behavior.
Red sandstone surface microbiota: functional convergence despite taxonomic divergence under dispersal limitation and hetero selection
Authors: Wang Bowen , Zhu Chengshuai , Wang Xin , Yang Tianyu , Zhang Bingjian , Hu Yulan
Published: October 2024

Understanding the role of microbiota on stone surfaces is essential for developing effective grottoes conservation strategies. However, ecological feature of microbial communities on stone surfaces remains underexplored. In this study, we explored diversity, ecological feature, and functional profiles of microbial communities on the red sandstone surface of the Leshan Giant Buddha from microbial ecology perspective. The results show that Proteobacteria, Actinobacteria, and Cyanobacteria are the dominant prokaryotic phyla, and Ascomycota is the most dominant eukaryotic phylum. Interestingly, despite taxonomic divergence, the functional profiles of different types of the microbial communities remain convergent across all samples. As indicated by the ecological modelling, the interplay of dispersal limitation and hetero selection might have contributed to such species divergence, while selective pressure from the harsh environment on the stone surface promoted functional convergence. The assembly of visually distinct microbial communities is linked to a narrower ecological niche, higher proportion of habitat specialists, elevated complexity, and increased resilience of the prokaryotic network to disturbances. Microbial-mediated ammonium assimilation and nitrogen mineralization might be the two prominent processes that contribute to stone biodeterioration. This study deepens our understanding of microbial community assembly mechanism on stone cultural heritage surfaces and functional potentials, which provides microbial ecological insights for the conservation of these cultural treasures.
Decoding Collagen's Thermally Induced Unfolding and Refolding Pathways
Authors: Al-Shaer Alaa , Forde Nancy R
Published: October 2024

Collagen has been evolutionarily selected as the preferred building block of extracellular structures. Despite inherent thermal instability of individual proteins at body temperature, collagen manages to assemble into higher-order structures that provide mechanical support to tissues. Sequence features that enhance collagen stability have been deduced largely from studies of collagen-mimetic peptides, as the large sizes of collagens have precluded high-resolution studies of their structure. Thus, there is a need for new methods to analyze the structure and mechanics of native collagen proteins. In this study, we used AFM imaging to investigate the temperature response of collagen types I, III and particularly IV. We observed a time-dependent loss of folded structures upon exposure to body temperature, with structural destabilization along the collagenous domain reflected by a shorter overall contour length. We characterized the sequence-dependent bending stiffness profile of collagen IV as a function of temperature and identified a putative initiation site for thermally induced unfolding. Interchain disulfide bonds in collagen IV were shown to enhance thermal stability and serve as the primary nucleation sites for in vitro refolding. In contrast to the canonical C-to-N terminal folding direction, we found an interchain cystine knot to enable folding in the opposite direction. Multiple sequence alignments revealed that this cystine knot is evolutionarily conserved across metazoan phyla, highlighting its significance in the stabilization of early collagen IV structures. Our findings provide mechanistic insights into the unfolding and refolding pathway of collagen IV, providing valuable insight into how its heterogeneous sequence influences stability and mechanics.
Starch granule initiation doesn’t require a starch synthase 4 isoform inChlamydomonas reinhardtii
Authors: Courseaux Adeline , Deschamps Philippe , Dauvillée David
Published: October 2024

The initiation of starch granule synthesis remains a relatively poorly understood phenomenon. Recent advances enabled the establishment of a model explaining the synthesis of new starch granules inArabidopsis thaliana. These characterizations revealed the involvement of both a specific starch synthase isoform (SS4) and of several non-enzymatic proteins in this process.

In this work, we investigated whether the initiation of starch synthesis in the green microalgaChlamydomonas reinhardtiiinvolves the same machinery as those uncovered in the plant model. Our extensive phylogenetic analysis revealed that most of the key players that were identified in higher plants are not found in microalgae suggesting that a different pathway is taking place. We showed that restoration of ADP-glucose synthesis in a mutant strain devoid of any endogenous primers allowed normal starch synthesis, revealing the existence of an initiation mechanism in Chlamydomonas. Our biochemical characterizations revealed that starch synthase isoform 3 possesses the intrinsic capacity to initiate polysaccharide synthesisin vitroand could be one of the functions involved in starch initiation. Our work suggests that the initiation of starch synthesis in Chlamydomonas involves a different pathway to that described in Arabidopsis and that further efforts will be required to identify the proteins involved in this process.
Kinetic theory of vacuum pair production in uniform electric fields revisited
Authors: Aleksandrov I. A. , Kudlis A. , Klochai A. I.
Published: October 2024

We investigate the phenomenon of electron-positron pair production from vacuum in the presence of a uniform time-dependent electric field of arbitrary polarization. Taking into account the interaction with the external classical background in a nonperturbative manner, we quantize the electron-positron field and derive a system of ten quantum kinetic equations (QKEs) showing that the previously-used QKEs are incorrect once the external field rotates in space. We employ then the Wigner-function formalism of the field quantization and establish a direct connection between the Dirac-Heisenberg-Wigner (DHW) approach to investigating the vacuum pair-production process and the QKEs. We provide a self-contained description of the two theoretical frameworks rigorously proving their equivalence and present an exact one-to-one correspondence between the kinetic functions involved within the two techniques. Special focus is placed on the analysis of the spin effects in the final particle distributions.

Published by the American Physical Society
2024
Shaping sustainable tourism: how minimalism and citizenship behavior influence tourists’ proenvironmental behavior
Authors: Rasheed A.K. Fazeen , Balakrishnan Janarthanan
Published: October 2024

Purpose

This study aims to examine the roles of minimalist and citizenship behaviors in influencing sustainable tourism practices. It further examined the role of moral credit as a mediating factor in these relationships. Additionally, this research scrutinizes the moderating effects of age and gender on these behavioral influences.

Design/methodology/approach

This study used a descriptive, quantitative and cross-sectional design to examine the data of 451 tourists visiting three destinations in India. The proposed conceptual model was evaluated through partial least squares structural equation Modeling, and the impact of the control variables was examined via PLS-Multi Group Analysis.

Findings

The results confirmed that minimalist and citizenship behaviors significantly influence pro-environmental actions. Moral credit has emerged as a pivotal bridge between these behaviors and sustainable tourism practices, underscoring its mediating role. Additionally, the analysis revealed that age and gender substantially moderated these relationships, highlighting the demographic-specific dynamics.

Originality/value

This study provides novel insights into how behaviors such as minimalism and citizenship contribute to sustainable travel practices. The identification of moral credit as a key mediator, along with the demographic nuances of age and gender, offers unique perspectives on sustainable consumer behavior dynamics within tourism. These findings provide valuable directions for stakeholders in sustainable tourism and policymakers aiming to cultivate positive consumer behaviors and advance the sustainability of the sector.
The use of investigation management documents in rape and serious sexual offence cases
Authors: Gekoski Anna
Published: October 2024

Purpose

In the context of rising reports of rape, set against falling convictions, it has been argued that rape has been de facto decriminalised in England and Wales. This paper aims to explore how police and prosecutors investigating rape and serious sexual offences (RASSO) use and perceive investigation management documents (IMDs), and how high-quality IMDs may lead to better justice outcomes. IMDs must be started by police at the beginning of an investigation and should document: what an officer is/is not doing and why; what the reasonable lines of enquiry are and their outcomes; and what has translated to evidence and supports charge, disclosure or unused material. The document is shared with the crown prosecution service at the point a charging decision is sought.

Design/methodology/approach

Semi-structured interviews were conducted with 32 police officers and five crown prosecutors across five areas in Year 2 of Operation Soteria Bluestone, a project that aimed to improve how police investigate rape. These interviews were analysed using the qualitative method of thematic analysis.

Findings

Three main themes were identified relating to timeliness, understanding, and quality of IMDs. It was found that IMDs are not always started at the beginning of RASSO investigations or even at all. Officers also lacked understanding around the purpose of IMDs, often seeing them as duplications of other case files. Finally, prosecutors and police concurred that the quality of IMDs are generally poor and lacking in critical reflection.

Originality/value

To the best of the author’s knowledge, this is the first academic paper to consider the use of IMDs by police and prosecutors in RASSO investigations. As such, it is both a unique contribution to the field and also provides a platform for future research. Understanding how police officers can produce the highest quality IMDs, in a timely fashion, is of paramount importance given the wider societal context of increasing reports of rape alongside low charge rates. Implications for training are considered.
Optimization of paddle trajectory for fin-wheel underwater robot
Authors: Liao Jianbin , Liu Xinxin , Xu Shengzui , Liu Liangyu , Li Yunxiang , Wang Wei , Zhang Zhiqiang
Published: October 2024

Purpose

The purpose of this paper is to investigate the oscillating trajectory of the paddle of a fin-wheel underwater robot to enhance its propulsion efficiency in water. This robot can be used for underwater detection and military operations.

Design/methodology/approach

By studying the propulsion mode of underwater fin-based robots, it is found that such robots periodically generate a large reverse thrust during the swing process, resulting in low propulsion efficiency. Therefore, according to the propulsion characteristics of the oscillating paddle in the underwater environment, the hydrodynamic model and physical constraints of the oscillating paddle are established. Then, the oscillating gait trajectory of the paddle is optimized by the trajectory optimization method. The performance of the optimized trajectory was tested in the simulation environment and the actual underwater environment.

Findings

The prototype of the robot was built and tested in a small swimming pool. The research results confirm that the propulsion efficiency of the optimized trajectory is higher than that of the traditional trajectory under the condition of the same amplitude and period. Specifically, the maximum speed of the robot can reach 0.24 m/s when using the optimized trajectory, which is about 50% higher than that before optimization.

Originality/value

The optimized trajectory with the generated impulse as the optimization target is applied to the paddle oscillation, which can improve the thrust impulse generated by the fin-wheel underwater robot during underwater motion, thereby greatly improving the underwater propulsion efficiency and moving speed.
A comprehensive study on the effects of printing parameters on the mechanical properties of PLA
Authors: Turan Mehmet Kivanc , Sabirli Muhammet Üsame , Bakirci Altug , Kartal Emirhan , Karpat Fatih
Published: October 2024

Purpose

This study aims to investigate the effects of five different printing parameters, namely, printing speed (PS), printing temperature/nozzle temperature/extrusion temperature, heated-bed temperature, raster angle (RA) and layer height (LT), on mechanical properties.

Design/methodology/approach

American Society for Testing and Materials (ASTM) standards were used for the specimen design. Then, the Taguchi method was used for the design of the experiment and an L16 orthogonal array was preferred. Tensile, Shore D and surface roughness tests were conducted on polylactic acid test specimens. The test results were analyzed using the signal-to-noise ratio and analysis of variance (ANOVA).

Findings

As a result of the study, it was seen that RA is the most important parameter for the tensile strength, PS is for the hardness and LT is for the surface roughness. According to the ANOVA results, the effects of the RA, PS and LT on the maximum tensile strength, hardness and surface roughness were 41.59%, 69.51% and 44.6%, respectively.

Originality/value

To the best of the authors’ knowledge, this study is one of the most comprehensive parameter optimization studies for additive manufacturing in the literature because it includes five different printing parameters and three mechanical test procedures.