bluuebunny/crossref_metadata_2025 huggingface dataset:
Incidence and Trends in Ischemic Stroke and Mortality in Patients with and Without Type 2 Diabetes in Taiwan 2000-2018
Authors: Yen Fu-Shun , Wei James Cheng-Chung , Hsu Tzu-Ju , Shih Ying-Hsiu , Yeh Yun Kai , Hsu Chih-Cheng , Hwu Chii-Min
Published: December 2023

BACKGROUND

Stroke has a significant impact on life expectancy, comparable to that of cardiovascular disease in Asia. We conducted this longitudinal study to examine the incidence of ischemic stroke and 30-day mortality among persons with and without type 2 diabetes (T2D). We also compared outcomes between those over and under 60 years and between men and women.

METHODS

We enrolled participants from the 2000 to 2018 National Health Insurance Research Database in Taiwan. Cox proportional-hazard models were used to examine the outcomes.

RESULTS

The incidence of in-hospital ischemic stroke in patients with and without T2D had significant reductions of 64.42% and 55.63%, respectively. The relative risk of stroke associated with diabetes remained significantly higher (2.01 to 2.33 times) than non-diabetes. The relative risk of stroke in patients under 60 with T2D was 2.56 to 4.36 times higher than in those without T2D. Between 2000 and 2018, there was a significant 83.24% and 88.55% reduction in the risk of 30-day mortality after stroke in patients with and without T2D. There was no significant increase in the risk of 30-day mortality in people with diabetes compared to those without diabetes. However, the relative risk of death from stroke in patients under 60 years with diabetes was 1.63 to 2.49 times higher than in those without diabetes.

CONCLUSIONS

This nationwide cohort study showed that the incidence of in-hospital ischemic stroke and 30-day mortality in patients with and without T2D exhibited a significant decreasing trend from 2000 to 2018. Patients with T2D had about twice the relative risk of ischemic stroke compared to those without T2D.
Multipair phase-modulated temporal interference electrical stimulation combined with fMRI
Authors: Savvateev Iurii , Missey Florian , Beliaeva Valeriia , Markicevic Marija , Kindler Diana , Razansky Daniel , Jirsa Viktor , Williamson Adam , Polania Rafael , Zerbi Valerio
Published: December 2023

Temporal Interference Stimulation (TI) is a novel brain stimulation technique that aims to integrate the depth characteristic of conventional deep brain stimulation protocols with the non-invasive nature of transcranial electric stimulation. Recent publications in both mice and humans demonstrate that subcortical areas including hippocampus and striatum can be targeted using TI. However, whereas TI stimulation is set to be focused on a specific region of interest, other off-target areas may still be stimulated, including cortical structures. This is a major concern as off-target stimulation carries the risk of modulating unwanted brain structures and circuits. In the present study, we focused on the prefrontal cortex (PFC) in mice and developed a computational modelling approach to identify the best electrode locations for targeting PFC. Usingin-vivoelectrophysiological recordings and functional magnetic resonance imaging (fMRI) combined with TI, we confirmed the presence of induced TI fields and hemodynamic responses in the PFC but also identified off-target stimulated sites. To minimize the occurrence of off-target effects, we propose a new configuration with three electrode pairs, one of which has an active phase shift of 180 degrees in relation to the other two TI-inducing pairs. The use of this phase-canceling field allowed us to improve the focality of TI by reducing off-target stimulations without significantly affecting the TI field in the target area. The proposed design effectively addresses one of TI’s most critical shortcomings and opens new avenues for applications.
Phylogenomics recovers multiple origins of portable case-making in caddisflies (Insecta: Trichoptera), the world’s most common underwater architects
Authors: Frandsen Paul B. , Holzenthal Ralph W. , Espeland Marianne , Breinholt Jesse , Thomas Jessica A. , Simon Sabrina , Kawahara Akito Y. , Plotkin David , Hotaling Scott , Li Yiyuan , Nelson C. Riley , Niehuis Oliver , Mayer Christoph , Podsiadlowski Lars , Donath Alex , Misof Bernhard , Lemmon Emily Moriarty , Lemmon Alan , Morse John C. , Pauls Steffen , Zhou Xin
Published: December 2023

Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16,000 described species. They play an outsized role in freshwater ecology and environmental engineering in streams, rivers, and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programs. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case-making, have been unanswered due to the lack of a well-resolved phylogenetic tree. To shed light on these questions in Trichoptera, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 206 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with a set of 33 carefully selected fossils. The first caddisflies originated in the Permian and the major suborders began to diversify in the Triassic. Ancestral state reconstruction and diversification analysis revealed that portable case-making evolved in three separate lineages and shifts in diversification occurred in concert with key evolutionary innovations other than case-making.
A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence
Authors: Ivankovic Mario , Brand Jeremias N. , Pandolfini Luca , Brown Tom , Pippel Martin , Rozanski Andrei , Schubert Til , Grohme Markus A. , Winkler Sylke , Robledillo Laura , Zhang Meng , Codino Azzurra , Gustincich Stefano , Vila-Farré Miquel , Zhang Shu , Papantonis Argyris , Marques André , Rink Jochen C.
Published: December 2023

The planarianSchmidtea mediterraneacan regenerate its entire body from small tissue fragments and is studied as regeneration model species. The assembly and functional analysis of planarian genomes has proven challenging due its high A/T content (70% A/T), repetitive nature, and limited transferability of routine laboratory protocols due to their divergent biochemistry. Only few and often fragmented genome assemblies are currently available, and open challenges include the provision of well-annotated chromosome-scale reference assemblies of the model species and other planarians for a comparative genome evolution perspective. Here we report a haplotype-phased, chromosome-scale genome assembly and high-quality gene annotations of the sexual S2 strain ofS. mediterraneaand provide putative regulatory region annotations via optimized ATAC-seq and ChIP-seq protocols. To additionally leverage sequence conservation for regulatory element annotations, we generated chromosome-scale genome assemblies and chromatin accessibility data for the three closest relatives ofS. mediterranea:S. polychroa,S. nova, andS. lugubris. We find substantial divergence in protein-coding sequences and regulatory regions, yet reveal remarkable conservation in ChIP-mark bearing open chromatin regions identified as promoters and enhancers inS. mediterranea. The resulting high-confidence set of evolutionary conserved enhancers and promoters provides a valuable resource for the analysis of gene regulatory circuits and their evolution within the taxon. In addition, our four chromosome-scale genome assemblies provide a first comparative perspective on planarian genome evolution. Our analyses reveal frequent retrotransposon-associated chromosomal inversions and inter-chromosomal translocations that lead to a degradation of synteny across the genus. Interestingly, we further find independent and near-complete losses of the ancestral metazoan synteny acrossSchmidteaand two other flatworm groups, indicating that platyhelminth genomes largely evolve without syntenic constraints. Our work provides valuable genome resources for the planarian research community and sets a foundation for the comparative genomics of planarians. We reveal a contrast between the fast structural evolution of planarian genomes and the conservation of their regulatory elements, suggesting a unique genome evolution in flatworms where gene positioning may not be essential.
Comparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota
Authors: Kanungo Slipa , Bonilla-Rosso Germán , Sarton-Lohéac Garance , Kuffer Marianne , Hilty Markus , Geiser Thomas , Engel Philipp , Das Sudip
Published: December 2023

Streptococci are one of the predominant and the most diverse genus in the human lung. Previously, we isolated human distal lung Streptococci from bronchoalvolear lavage fluid (BALF) as part of the human Lung Microbiota culture Collection (LuMiCol). Here, we performed whole genome sequencing, comparative phylogenomics and phenotypic characterization of six Streptococcal isolates representing the phylogenetic diversity of the genus in distal human lung. Here, we report five new species and one new subspecies including phylogenetic intermediates of commonly found Streptococci not limited to human lung. Pangenome analysis reveals gene content, evolutionary relationships, and metabolic functions shedding light on contribution of these Streptococci to lung microbial metabolism. Antimicrobial resistance gene analysis followed by MIC determination revealed macrolide, lincosamide and tetracycline resistance in lung Streptococci. We show the presence of capsular genes in lung streptococci both matching to the prototypical capsular genes (cps) and unique genes. Interestingly, the newStreptococcusisolate sp. nov. P2E5, genetically identical to the most prevalentStreptococcusin the human distal lung was revealed to be a phylogenetic intermediate between theS. mitisgroup andS. pneumoniae.It also harbors the pneumolysin (ply) gene and was found to have the serotype 21E. Finally, core genome phylogeny reveals that lung Streptococci the are evolutionary distinct from oral Streptococcal isolates in expanded Human Oral Microbiome Database (eHOMD). Hence, these findings we reveal new phylogenetically distinct Streptococcal species from the human distal lung microbiota and its genetic diversity and metabolism to understand the microbial ecology of human lung.

Importance

A healthy human distal lung harbour characteristic microbial communities mostly composed of oropharyngeal taxa, which are facultative or obligative anaerobes despite lung being the medium of oxygen intake. However, little is known about the genetic and functional diversity of these bacteria owing to the lack of resources including availability of primary lung isolate from human samples. Therefore, we have established a large bacterial collection that covers all major phyla by cultivating human bronchoalveolar lavage fluid (BALF) under various conditions.Streptococcusis the most prevalent and diverse genera in the human lung microbiota. Using genetic and biochemical approaches, we studied six diverse lung isolates from our collection representing the actual Streptococcal diversity and identify these as new species and subspecies. We hypothesize that learning about the phylogenetic genetic diversity, preferred metabolism and molecular structures of these Streptococci will provide with new insights on the understudied microbial ecosystem of the human lung.
Antibody-mediated depletion of select T cell subsets in blood and tissue of nonhuman primates
Authors: Sutton Matthew S. , Bucsan Allison N. , Lehman Chelsea C. , Kamath Megha , Pokkali Supriya , Magnani Diogo M. , Seder Robert , Darrah Patricia A. , Roederer Mario
Published: December 2023

Understanding the immunological control of pathogens requires a detailed evaluation of the mechanistic contributions of individual cell types within the immune system. While knockout mouse models that lack certain cell types have been used to help define the role of those cells, the biological and physiological characteristics of mice do not necessarily recapitulate that of a human. To overcome some of these differences, studies often look towards nonhuman primates (NHPs) due to their close phylogenetic relationship to humans.

To evaluate the immunological role of select cell types, the NHP model provides distinct advantages since NHP more closely mirror the disease manifestations and immunological characteristics of humans. However, many of the experimental manipulations routinely used in mice (e.g., gene knock-out) cannot be used with the NHP model. As an alternative, thein vivoinfusion of monoclonal antibodies that target surface proteins on specific cells to either functionally inhibit or deplete cells can be a useful tool. Such depleting antibodies have been used in NHP studies to address immunological mechanisms of action. In these studies, the extent of depletion has generally been reported for blood, but not thoroughly assessed in tissues.

Here, we evaluated four depleting regimens that primarily target T cells in NHP: anti-CD4, anti-CD8α, anti-CD8β, and immunotoxin-conjugated anti-CD3. We evaluated these treatments in healthy unvaccinated and IV BCG-vaccinated NHP to measure the extent that vaccine-elicited T cells – which may be activated, increased in number, or resident in specific tissues – are depleted compared to resting populations in unvaccinated NHPs. We report quantitative measurements ofin vivodepletion at multiple tissue sites providing insight into the range of cell types depleted by a given mAb. While we found substantial depletion of target cell types in blood and tissue of many animals, residual cells remained, often residing within tissue. Notably, we find that animal-to-animal variation is substantial and consequently studies that use these reagents should be powered accordingly.
Suppression of piriform cortex alters brain-wide dynamics and alleviates seizures in temporal lobe epilepsy
Authors: Zhang Huiqi , Chiu Arthur , Jiang Hehai , Choi Harry M. C. , Huang Zhuo , Lau Chunyue Geoffrey
Published: December 2023

Temporal lobe epilepsy (TLE) is a pathological state that involves altered excitation-inhibition (E-I) in the brain and exhibits recurrent seizures. Many circuit studies of TLE have focused on the hippocampus. Anterior piriform cortex (APC) is also a limbic area closely associated with TLE, but is understudied. In the APC, parvalbumin-expressing (PV+) interneurons provide strong inhibition and help maintain E-I balance. However, whether APCPVneurons play a causal role in TLE is unclear.

We used the systemic pilocarpine and intrahippocampal kainic acid (KA) mouse models, which showed pathological changes and spontaneous recurrent seizures (SRSs) akin to those observed in patients with TLE. Whole-cell patch clamp recording and immunohistochemistry were used to examine inhibitory synaptic transmission in the pilocarpine model. Then, using chemogenetics and multi-site local field potential (LFP) recording, we manipulated APCPVneurons at different periods, before applying convulsant, during status epilepticus (SE) and in chronic epileptic phase, and examined the efficacy of APCPVneuronal activation on seizures. For chronic period experiments, KA-injected mice underwent four-site longitudinal LFP recordings. We quantified SRSs based on the frequency and duration of epileptic discharges (> 2 Hz, 10 seconds). For the underlying functional network dynamics, we analyzed the power of each recording site and functional connectivity of each pair of regions in four epileptic states, preictal, ictal, postictal and interictal.

In the pilocarpine model, we found impaired synaptic inhibition and loss of PV synapses in the APC. APCPVneuronal pre-activation decreased seizure susceptibility and mortality, but could not stop an ongoing SE. In the chronic KA model, activation of APCPVneurons reduced the frequency and duration of SRSs in the hippocampus. Interestingly, APCPVneuronal activation altered the brain-wide dynamics of seizure network and afforded differential modulation based on epileptic states, brain regions and frequency bands.

Our work demonstrates the causal role of APCPVin TLE and provides detailed functional characterization of mechanisms underlying the effectiveness of APCPVactivation. We reveal how a cortical microcircuit can alter neural activity in multiple brain regions and exert antiepileptic benefits. These findings strengthen the idea that large-scale connections from APC play a key role in maintaining the E-I balance of the entire seizure network and thus provide the basis for future circuit-based therapies.
Piezo1-induced durotaxis of pancreatic stellate cells depends on TRPC1 and TRPV4 channels
Authors: Budde Ilka , Schlichting André , Ing David , Schimmelpfennig Sandra , Kuntze Anna , Fels Benedikt , Romac Joelle M-J , Swain Sandip M , Liddle Rodger A , Stevens Angela , Schwab Albrecht , Pethő Zoltán
Published: December 2023

Pancreatic stellate cells (PSCs) are primarily responsible for producing the stiff tumor tissue in pancreatic ductal adenocarcinoma (PDAC). Thereby, PSCs generate a stiffness gradient between the healthy pancreas and the tumor. This gradient induces durotaxis, a form of directional cell migration driven by differential stiffness. The molecular sensors behind durotaxis are still unclear. To investigate the role of mechanosensitive ion channels in PSC durotaxis, we established a two-dimensional stiffness gradient mimicking PDAC. Using pharmacological and genetic methods, we investigated the role of the ion channels Piezo1, TRPC1, and TRPV4 in PSC durotaxis. We found that PSC migration towards a stiffer substrate is diminished by altering Piezo1 activity. Moreover, disrupting TRPC1 along with TRPV4 abolishes PSC durotaxis even when Piezo1 is functional. Hence, PSC durotaxis is optimal with an intermediary level of mechanosensitive channel activity, which we simulated using a numerically discretized mathematical model. Our findings suggest that mechanosensitive ion channels, particularly Piezo1, detect the mechanical microenvironment to guide PSC migration.

Cells move towards regions with higher stiffness in a process called durotaxis. This study shows that ion channels Piezo1, TRPV4, and TRPC1 are crucial sensors in pancreatic stellate cells. They act together to orchestrate durotaxis of pancreatic stellate cells which may be relevant in pancreatic cancer.
EryDB: a transcriptomic profile database for erythropoiesis and erythroid-related diseases
Authors: Zheng Guangmin , Wu Song , Zhang Zhaojun , Xin Zijuan , Zhang Lijuan , Zhao Siqi , Wu Jing , Liu Yanxia , Li Meng , Ruan Xiuyan , Bao Yiming , Qu Hongzhu , Fang Xiangdong
Published: December 2023

Erythropoiesis is a finely regulated and complex process that involves multiple transformations from hematopoietic stem cells to mature red blood cells at hematopoietic sites from the embryonic to the adult stages. Investigations into its molecular mechanisms have generated a wealth of expression data, including bulk and single-cell RNA sequencing data. A comprehensively integrated and well-curated erythropoiesis-specific database will greatly facilitate the mining of gene expression data and enable large-scale research of erythropoiesis and erythroid related diseases. Here, we present EryDB, an open-access and comprehensive database dedicated to the collection, integration, analysis, and visualization of transcriptomic data for erythropoiesis and erythroid-related diseases. Currently, the database includes expertly curated quality-assured data of 3,803 samples and 1,187,119 single cells derived from 107 public studies of three species (Homo sapiens,Mus musculus, andDanio rerio), nine tissue types, and five diseases. EryDB provides users with the ability to not only browse the molecular features of erythropoiesis between tissues and species, but also perform computational analyses of single-cell and bulk RNA sequencing data, thus serving as a convenient platform for customized queries and analyses. EryDB v1.0 is freely accessible athttps://ngdc.cncb.ac.cn/EryDB/home.
An Immunological Synapse Formation Between T Regulatory Cells and Cancer-Associated Fibroblasts Promotes Tumor Development
Authors: Varveri Athina , Papadopoulou Miranta , Papadovasilakis Zacharias , Compeer Ewoud B. , Legaki Aigli-Ioanna , Delis Anastasios , Damaskou Vasileia , Boon Louis , Papadogiorgaki Sevasti , Samiotaki Martina , Foukas Periklis G. , Hatzioannou Aikaterini , Alissafi Themis , Dustin Michael L. , Verginis Panayotis
Published: December 2023

Cancer-associated fibroblasts (CAFs) have emerged as a dominant non-hematopoietic cell population in the tumor microenvironment, serving diverse functions in tumor progression, invasion, matrix remodeling and resistance to therapy; yet, the precise mechanisms via which CAFs imprint on the anti-tumor immunity remain poorly understood. Extensive molecular characterization revealed an increased heterogeneity in the CAF compartment and proposed an interaction between CAFs and tumor-infiltrating immune cells, which may shape tumor immune evasion. Herein, we describe a synapse formation between α-SMA+CAFs and regulatory T cells (Tregs) in the TME. Foxp3+Tregs were localized close to α-SMA+CAFs in diverse types of tumor models as well as biopsies from melanoma and colorectal cancer patients. Notably, phenotypically tolerogenic α-SMA+CAFs demonstrated the ability to phagocytose and process tumor antigens, instructing Treg movement arrest, activation and proliferation, in an antigen-specific manner. Of interest, α-SMA+CAFs were characterized by the presence of double-membrane structures, resembling autophagosomes, in their cytoplasm, while analysis of single-cell transcriptomic data pointed autophagy and antigen processing/presentation pathways to be enriched in α-SMA-expressing CAF clusters. In a mechanistic view, conditional knockout of the autophagy pathway in α-SMA+CAFs promoted an inflammatory re-programming of CAFs, reduced Treg infiltration, attenuated tumor development, and potentiated the efficacy of immune checkpoint inhibitor immunotherapy. Overall, our findings reveal an immunosuppressive mechanism operating in the TME, which entails the formation of synapses between α-SMA+CAFs and Tregs in an autophagy-dependent fashion and raises the potential for the development of CAF-targeted therapies in cancer.

One Sentence Summary

α-SMA+Cancer Associated Fibroblasts process and present tumor antigens via autophagy to form immunological synapses with Foxp3+T regulatory cells in the tumor microenvironment, promoting tumor development.
Biodistribution of DNA-origami nanostructures in live zebrafish embryos with single-cell resolution
Authors: Kolonelou Christina , Bräutigam Lars , Edwards Steven , Engström Enya , Dias José M. , Spratt Joel , Karampelias Christos , Wennmalm Stefan , Brismar Hjalmar , Andersson Olov , Teixeira Ana I.
Published: December 2023

DNA origami-based nanotechnology is a versatile tool for exploring fundamental biological questions and holds significant promise for future biomedical applications. However, the development of DNA origami-based therapeutic agents is hindered by the challenge of translatingin vitroperformance into effective applicationsin vivo. Here, we exploit the optical transparency of the embryonic zebrafish to track intravenously injected, fluorescently labelled wireframe DNA origami nanostructures. Our approach integrated long-term, high-resolution imaging of transgenic live embryos with single-cell RNA sequencing, to elucidate the biodistribution of DNA nanostructures over time, up to 3 days post-injection (dpi). Notably, we observed rapid accumulation of nanostructures in the caudal hematopoietic tissue (CHT), akin to the fetal liver in mammals. We tested the effects of coating the nanostructures with an oligolysine PEG copolymer (K-PEG), a widely used strategy to enhance their stability. The K-PEG coating mitigated the accumulation rate in CHT, enabling higher percentages of the nanostructures to engage with other tissues. Additionally, our findings highlighted the pivotal role of scavenger endothelial cells in DNA origami clearance, with K-PEG offering sustained protection for the nanostructures at the CHT. Furthermore, by monitoring DNA origami in a transgenic zebrafish line designed for targeted macrophage ablation, we found that macrophages contribute to nanostructure clearance at later time points. This study introduces a framework for the analyses of the biodistribution and clearance of DNA origami nanostructures in vivo with single cell resolution and establishes a foundation for the investigation of DNA origami-based nanomedicines in animal models.
Sex-Specific DNA-Replication In The Early Mammalian Embryo
Authors: Halliwell Jason Alexander , Martin-Gonzalez Javier , Hashim Adnan , Dahl John Arne , Hoffmann Eva Ran , Lerdrup Mads
Published: December 2023

The timing of mammalian DNA replication is crucial for minimizing errors and is influenced locally by genome usage and chromatin states. However, our understanding of replication timing in the unique environment that exists in newly formed mammalian embryos is limited. Here, we performed genome-wide investigations of replication timing in mouse zygotes and 2-cell embryos. We discovered that zygotes lack a conventional replication timing, but a program emerged in 2-cell embryos. Notably, this program differs from embryonic stem cells and shows asynchrony between the parental genomes. We observed late replication of maternal pericentromeric regions and DNA associated with the nuclear lamina in each parental genome, whereas unexpected early replication occurred in regions with histone marks deposited by Polycomb Repressive Complexes on the maternal chromatin. This atypical and asynchronous replication of the two parental genomes may advance our understanding of replication stress in early human embryos and trigger strategies to reduce errors and aneuploidies.
Dissecting the Complexities of Learning With Infinite Hidden Markov Models
Authors: Bruijns Sebastian A. ,   International Brain Laboratory, Bougrova Kcénia , Laranjeira Inês C. , Lau Petrina Y. P. , Meijer Guido T. , Miska Nathaniel J. , Noel Jean-Paul , Pan-Vazquez Alejandro , Roth Noam , Socha Karolina Z. , Urai Anne E. , Dayan Peter
Published: December 2023

Learning to exploit the contingencies of a complex experiment is not an easy task for animals. Individuals learn in an idiosyncratic manner, revising their approaches multiple times as they are shaped, or shape themselves, and potentially end up with different strategies. Their long-run learning curves are therefore a tantalizing target for the sort of individualized quantitative characterizations that sophisticated modelling can provide. However, any such model requires a flexible and extensible structure which can capture radically new behaviours as well as slow changes in existing ones. To this end, we suggest a dynamic input-output infinite hidden semi-Markov model, whose latent states are associated with specific components of behaviour. This model includes an infinite number of potential states and so has the capacity to describe substantially new behaviours by unearthing extra states; while dynamics in the model allow it to capture more modest adaptations to existing behaviours. We individually fit the model to data collected from more than 100 mice as they learned a contrast detection task over tens of sessions and around fifteen thousand trials each. Despite large individual differences, we found that most animals progressed through three major stages of learning, the transitions between which were marked by distinct additions to task understanding. We furthermore showed that marked changes in behaviour are much more likely to occur at the very beginning of sessions, i.e. after a period of rest, and that response biases in earlier stages are not predictive of biases later on in this task.
Rapid Prediction of Lipid Interaction Sites on Pleckstrin Homology Domains Using Deep Graph Neural Networks and Molecular Dynamics Simulations
Authors: Le Huray Kyle I.P. , Sobott Frank , Wang He , Kalli Antreas C.
Published: December 2023

Interactions between membrane proteins and specific lipid molecules play a major role in cellular biology, but characterizing these interactions can be challenging due to the complexity and physicochemical properties of membranes. Molecular dynamics (MD) simulations allow researchers to predict protein-lipid interaction sites and generate testable models. MD simulations are however computationally expensive and require specialist expertise. In this study, we demonstrate that graph neural networks trained on coarse-grained MD simulation data can predict phosphoinositide lipid interaction sites on Pleckstrin Homology (PH) domain structures, a large family of membrane binding domains. The predictions are comparable to the results of simulations and require only seconds to compute. Comparison with experimental data shows that the model can predict known phosphoinositide interaction sites and can be used to form hypotheses for PH domains for which there is no experimental data. This model is a next generation tool for predicting protein-lipid interactions of PH domains and offers a basis for further development of models applicable to other membrane protein classes.
Internal representation of future interactions in rats
Authors: Dvorakova T , Lobellova V , Manubens-Coda P , Sanchez-Jimenez A , Villacorta-Atienza JA , Stuchlik A , Levcik D
Published: December 2023

Animals and humans receive the most critical information from parts of the environment that are immediately inaccessible, possibly only visually explored, and highly dynamic. The brain must effectively process potential interactions between elements in such an environment to make appropriate decisions in critical situations. We trained male Long-Evans rats to discriminate static and dynamic visuospatial stimuli displayed on an inaccessible computer screen. We demonstrated that the rats learned to discriminate dynamic visuospatial stimuli faster, with greater accuracy and shorter reaction time than complementary static stimuli. Furthermore, we provide behavioral evidence indicating that rats internally represent dynamic environments as static maps that capture meaningful future interactions. These observations highlight the ecological importance of dynamic stimuli in the outside world and support previous findings in humans that internal static representations can encapsulate relevant spatiotemporal information of dynamic environments. Such a mechanism would allow animals and humans to process complex time-changing situations neatly.
Genomic analysis ofAncylistes closterii, an enigmatic alga parasitic fungus in the arthropod-associated Entomophthoromycotina
Authors: Seto K , James TY
Published: December 2023

Recent advances in fungal genome sequencing have dramatically altered our understanding of the phylogeny and evolution of Fungi. However, there are still many poorly studied obligate parasitic or symbiotic fungi for which we lack any genomic information or knowledge of where they fit in the fungal phylogeny.Ancylistes,an endoparasite of desmid green algae, is such an understudied fungal genus. This genus has been taxonomically placed in the group of arthropod pathogens and saprobes, Entomophthoromycotina in Zoopagomycota. Understanding the phylogenetic position ofAncylistesprovides insights into the nutritional evolution of Zoopagomycota, which is primarily composed of animal-associated fungi. In this study, we found and cultivatedAncylistes closteriiwith its hostClosteriumsp. and sequenced its genome to investigate its phylogenetic position and evolution. Phylogenetic analyses using rDNA and genome-scale datasets showed thatA. closteriiwas sister to other Entomophthoromycotina fungi, confirming the taxonomic position ofAncylistes. Despite the ecological distinctiveness betweenAncylistesand other Entomophthoromycotina fungi, our comparative genomic analyses revealed many shared traits of these fungi such as lineage-specific subtilases and hybrid histidine kinases.Ancylistesalso possessed unique genes among Zoopagomycota fungi, such as plant cell wall degrading enzymes which could be important for infection of algae.

Significance

Improved taxon sampling is important for inferring a robust phylogeny of Fungi. However, there are still poorly studied obligate parasitic taxa whose DNA sequencing is challenging, especially in Zoopagomycota, one of the early diverging lineages of Fungi. This study focused on a long-neglected algal parasite,Ancylistes closterii, which belongs to the arthropod-associated group, Entomophthoromycotina. We rediscoveredA. closteriiand established a dual culture of fungus and its host alga, which enabled the first molecular analysis of this enigmatic parasite. Our results provide new insights into the nutritional evolution of primarily animal-associated Zoopagomycota.
Optimization of chondroitin production inE. coliusing genome scale models
Authors: Couto Márcia R. , Rodrigues Joana L. , Braga Adelaide , Dias Oscar , Rodrigues Lígia
Published: December 2023

Chondroitin is a natural occurring glycosaminoglycan with applications as a nutraceutical and pharmaceutical ingredient and can be extracted from animal tissues. Microbial chondroitin-like polysaccharides emerged as a safer and more sustainable alternative source. However, chondroitin titers using either natural or recombinant microorganisms are still far from meeting the increasing demand. The use of genome-scale models and computational predictions can assist the design of microbial cell factories with possible improved titers of these value-added compounds. Genome-scale models have been used to predict genetic modifications inEscherichia coliengineered strains that would potentially lead to improved chondroitin production. Additionally, using synthetic biology approaches, a pathway for producing chondroitin has been designed and engineered inE. coli. Afterwards, the most promising mutants identified based on bioinformatics predictions were constructed and evaluated for chondroitin production in flask fermentation. This resulted in the production of 118 mg/L of extracellular chondroitin by overexpressing both superoxide dismutase (sodA) and a lytic murein transglycosylase (mltB). Then, batch and fed-batch fermentations at bioreactor scale were also evaluated, in which the mutant overexpressingmltBled to an extracellular chondroitin production of 427 mg/L and 535 mg/L, respectively. The computational approach herein described identified several potential novel targets for improved chondroitin biosynthesis, which may ultimately lead to a more efficient production of this glycosaminoglycan.
A diverse proteome is present and enzymatically active in metabolite extracts
Authors: House Rachel (Rae) J. , Soper-Hopper Molly T. , Vincent Michael P. , Ellis Abigail E. , Capan Colt D. , Madaj Zachary B. , Wolfrum Emily , Isaguirre Christine N. , Castello Carlos D. , Johnson Amy B. , Galvis Martha L. Escobar , Williams Kelsey S. , Lee Hyoungjoo , Sheldon Ryan D.
Published: December 2023

Metabolomics, a foundational tool in metabolism research, relies on the accurate transmittal of biochemical profiles underlying biological phenotypes. Over the years, workflows used in metabolomics have been assumed to remove enzymes to preserve metabolite levels during processing. Here, we uncover a diverse landscape of over 1,000 proteins, strongly enriched for metabolic enzymes, within metabolite extracts generated using common extraction workflows. Moreover, by combining in-extract stable isotope additions and enzyme inhibitors, we demonstrate transaminase activity, which is preventable by protein removal by 3 kDa filtration. We extend these findings to untargeted metabolomics, revealing that both post-extraction formation of glutamate dipeptide and depletion of total glutathione can also be prevented by removing proteins. Finally, we present a simple yet novel workflow that integrates passive filtration for protein removal of crude metabolite extracts as a superior method for broad-coverage metabolomics. Our findings have broad-reaching experimental implications across all fields that use metabolomics and molecular metabolism, especially cancer, immunology, and diabetes research.
Genome size and ploidy of the German species ofVeronicaL. (Plantaginaceae)
Authors: Albach Dirk C. , Daubert Mareike
Published: December 2023

Chromosome numbers and genome size estimates provide essential information for the differentiation of plant species. Especially, closely related species that are morphologically difficult to distinguish are often easily distinguishable by genome size. Flow cytometry has facilitated in recent years the detection of such differentiation at the genomic level. It further helped understand the distribution of ploidy levels within species. The genusVeronicaincludes 37 species in Germany including some taxonomically challenging species groups and some species with intraspecific variation in ploidy. We, here, present 36 new genome size estimates and 44 estimates of ploidy, six and seven, respectively, from Germany, for these 37 species. Estimates ofV. aphylla, V. alpina, V. fruticans, andV. fruticulosaare first estimates for the species. These estimates provide an important basis for future studies on the genus. Some examples are discussed in more details, such as the distribution of ploidy levels inV. longifoliaandV. chamaedrysin Germany or the importance to study ploidy levels inV. satureiifoliaand relatives in southwestern Germany.
Optimising age-specific insulin signalling to slow down reproductive ageing increases fitness in different environments
Authors: Sultanova Zahida , Shen Aykut , Hencel Katarzyna , Carlsson Hanne , Crighton Zoe , Clifton Daniel , Akay Alper , Maklakov Alexei A.
Published: December 2023

The developmental theory of ageing proposes that age-specific decline in the force of natural selection results in suboptimal levels of gene expression in adulthood, leading to functional senescence. This theory explicitly predicts that optimising gene expression in adulthood can ameliorate functional senescence and improve fitness. Reduced insulin/IGF-1 signalling (rIIS) extends the reproductive lifespan ofCaenorhabditis elegansat the cost of reduced reproduction. Here, we show that adulthood-only rIIS improves late-life reproduction without any detrimental effects on other life-history traits in both benign and stressful conditions. Remarkably, we show that rIIS additively extends late-life reproduction and lifespan when animals are exposed to a fluctuating food environment – intermittent fasting (IF) – resulting in reduced food intake in early adulthood. Full factorial genome-wide RNA-Seq across the life course demonstrated that IF and rIIS modulate the age-specific expression of pro-longevity genes. IF, rIIS and combined IF + rIIS treatment downregulated genes involved in peptide metabolism in early life and differentially regulated immunity genes in later life. Importantly, combined IF + rIIS treatment uniquely regulated a large cluster of genes in mid-life that are associated with immune response. These results suggest that optimising gene expression in adulthood can decelerate reproductive ageing and increase fitness.
Genomic resources forMacadamia tetraphyllaand an examination of its historic use as a crop resource in Hawaii
Authors: Bartlett Bjarne , Cho Alyssa , Laspisa Daniel , Gore Michael A. , Kantar Michael
Published: December 2023

Macadamia tetraphyllais a wild relative of the economically valuable cropMacadamia integrifolia. Genomic knowledge of crop wild relatives is central to determining their possible role in breeding programs to mitigate biotic and abiotic stress in the future. The goal of this project was to develop a genomic resource for macadamia agriculture in Hawai‘i through constructing a transcriptome ofM. tetraphyllaand testing for hybridity in University of Hawai‘i at Mānoa breeding material. The transcriptome assembly ofM. tetraphyllarevealed large differences in gene expression attributable to tissue type. Advanced breeding lines (HI862 and HI879) appear to be hybridized with the crop wild relativeM. tetraphylla. Additionally, a putativeM. tetraphyllatree sampled from a remnant orchard planting at the Waimānalo research station on Oahu did not match anecdotal accounts of the orchard as it appeared to be of hybrid ancestry.
Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis
Authors: Sun Nawei , Teyssier Noam , Wang Belinda , Drake Sam , Seyler Meghan , Zaltsman Yefim , Everitt Amanda , Teerikorpi Nia , Willsey Helen Rankin , Goodarzi Hani , Tian Ruilin , Kampmann Martin , Willsey A. Jeremy
Published: December 2023

Recent studies have identified over one hundred high-confidence (hc) autism spectrum disorder (ASD) genes. Systems biological and functional analyses on smaller subsets of these genes have consistently implicated excitatory neurogenesis. However, the extent to which the broader set of hcASD genes are involved in this process has not been explored systematically nor have the biological pathways underlying this convergence been identified. Here, we leveraged CROP-Seq to repress 87 hcASD genes in a humanin vitromodel of cortical neurogenesis. We identified 17 hcASD genes whose repression significantly alters developmental trajectory and results in a common cellular state characterized by disruptions in proliferation, differentiation, cell cycle, microtubule biology, and RNA-binding proteins (RBPs). We also characterized over 3,000 differentially expressed genes, 286 of which had expression profiles correlated with changes in developmental trajectory. Overall, we uncovered transcriptional disruptions downstream of hcASD gene perturbations, correlated these disruptions with distinct differentiation phenotypes, and reinforced neurogenesis, microtubule biology, and RBPs as convergent points of disruption in ASD.
Microsecond Molecular Dynamics Simulations and Markov State Models of Mutation-Induced Allosteric Mechanisms for the Light-Oxygen-Voltage 2 Protein : Revealing Structural Basis of Signal Transmission Induced by Photoactivation of the Light Protein State
Authors: Xiao Sian , Ibrahim Mayar Tarek , Verkhivker Gennady M. , Zoltowski Brian D. , Tao Peng
Published: December 2023

Avena Sativa phototropin 1 Light-oxygen-voltage 2 domain (AsLOV2) is the model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change is initiated by the unfolding of the N-terminal helix in the dark state followed by the unfolding of the C-terminal helix. The light state is defined by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets have been identified as crucial components for mediating allosteric signal transmission between the two termini. In this study, we combined microsecond all-atm molecular dynamics simulations and Markov state modeling of conformational states to quantify molecular basis of mutation-induced allostery in the AsLOV2 protein. Through a combination of computational investigations, we determine that the Hβ and Iβ strands are the most critical structural elements involved in the allosteric mechanism. To elucidate the role of these β-sheets, we introduced 13 distinct mutations (F490L, N492A, L493A, F494L, H495L, L496F, Q497A, R500A, F509L, Q513A, L514A, D515V, and T517V) and conducted comprehensive simulation analysis. The results highlighted the role of two hydrogen bond Asn482-Leu453 and Gln479-Val520 in the observed distinct behaviors of L493A, L496F, Q497A, and D515V mutants. The comprehensive atomistic-level analysis of the conformational landscapes revealed the critical functional role of β-sheet segments in the transmission of the allosteric signal upon the photoactivation of the light state.
Comparison of gastric inflammation and metaplasia induced byHelicobacter pyloriorHelicobacter feliscolonization in mice
Authors: Druffner Sara R. , Venkateshwaraprabu Shrinidhi , Khadka Stuti , Duncan Benjamin C. , Morris Maeve T. , Sen-Kilic Emel , Damron Fredrick H. , Liechti George W. , Busada Jonathan T.
Published: December 2023

Background

Gastric cancer is the fifth most diagnosed cancer in the world. Infection by the bacteriaHelicobacter pylori(HP) is associated with approximately 75% of gastric cancer cases. HP infection induces chronic gastric inflammation, damaging the stomach and fostering carcinogenesis. Most mechanistic studies onHelicobacter-induced gastric cancer initiation are performed in mice and utilize either mouse-adapted strains of HP or the natural mouse pathogenHelicobacter felis(HF). Each of these infection models is associated with strengths and weaknesses. Here, we identified the differences in immunogenicity and gastric pathological changes associated with HP and HF infection in mice.

Material and Methods

PMSS1 HP strain or with the CS1 HF strain were co-cultured with mouse peritoneal macrophages to assess their immunostimulatory effects. C57BL/6J mice were infected with HP or HF, and gastric inflammation, atrophy, and metaplasia development were assessed 2 months post-infection.

Results

HP and HF induced similar cytokine production from cultured mouse peritoneal macrophages. HP-infected mice caused modest inflammation within both the gastric corpus and antrum and did not induce significant atrophy within the gastric corpus. In contrast, HF induced significant inflammation throughout the gastric corpus and antrum. Moreover, HF infection was associated with significant atrophy of the chief and parietal cell compartments and induced expression of pyloric metaplasia markers.

Conclusions

HP is poorly immunogenic compared to HF. HF induces dramatic CD4+ T cell activation, which is associated with increased gastric cancer risk in humans. Thus, HP studies in mice are better suited for studies on colonization, while HF is more strongly suited for pathogenesis and cancer initiation studies.