bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial programming of fibroblasts promotes resolution of tissue inflammation through immune cell exclusion
Authors: Reis Nisa Patricia , Mahony Christopher , Hackland Annie , Clay Elizabeth , Chin Paulynn , Marsh Lucy-Jayne , Bolton Chrissy , Kemble Samuel , Smith Charlotte G , Neag Georgiana , Singh Ruchir , Turner Jason D , Filer Andrew , Raza Karim , Richard Jean-Baptiste , Midwood Kim S , Buckley Christopher D , Wei Kevin , McGettrick Helen M , Coles Mark , Croft Adam P
Published: September 2024

The role of fibroblasts in determining tissue topography and immune cell organisation within chronically inflamed tissues is poorly understood. Herein, we use multi-omic spatial analysis to define the cellular zonation pattern of the synovium in patients with inflammatory arthritis, identifying discrete tissue niches underpinned by spatially programmed subsets of synovial fibroblasts. We observe that perivascular fibroblasts switch on distinct matrix programs in response to cytokine signalling from neighbouring cells, forming adapted tissue niches that either permit or restrict immune cell trafficking. Specifically, IFN-gamma responsive fibroblasts form a pathogenic lymphocyte-permissive niche that supports the persistence of leukocytes in the tissue, whilst TGF-beta responsive, matrix-synthesising fibroblasts comprise a reparative niche, composed of a collagen-rich barrier around blood vessels that restricts leukocyte migration and promotes resolution of tissue inflammation. Augmentation of such endogenous pathways to promote resolution of inflammation may offer therapeutically tractable approaches for restoration of tissue homeostasis.
Spatiotemporal dynamics and assembly process differ in fungal communities across contiguous habitats in tropical forests
Authors: Lin Chieh-Ping , Lin Yu-Fei , Liu Yu-Ching , Lu Mei-Yeh Jade , Ke Huei-Mien , Tsai Isheng Jason
Published: September 2024

Background

The variation in fungal community composition within a single habitat space has been extensively studied in forest ecosystems. However, the spatial and temporal distribution of fungi across contiguous habitats, particularly at a local scale and in tropical regions, remains underexplored. In this study, we examined the fungal community composition across multiple habitats proximal to each other over two seasons in seven Fagaceae species in Taiwanese broadleaf forests. We tested how local spatial scale and habitat influence community assembly.

Results

Using a metabarcoding approach, we sequenced ITS3/ITS4 amplicons from 864 samples collected from four distinct habitats—leaves, twigs, litter, and soil. We identified 11,600 fungal amplicon sequence variants (ASVs), with community composition differing significantly between habitats proximal to each other. Phyllosphere (leaves and twigs) fungi exhibited higher diversity compared to soil. Habitat type and long-term precipitation emerged as the most influential factors driving fungal diversity and composition, with a clear distance-decay relationship observed in leaf and twig but not in soil. Random forest analysis accurately classified habitats based on ASVs’ relative abundances, with strong predictors were mostly endemic ASVs prevalent in soil. Misclassified samples were due to secondary contact of fungi between adjacent habitats. Co-occurrence network analysis revealed more complex and deterministic networks in leaf and twig habitats, while soil was driven by stochastic processes and contained most endemic ASVs. ACladosporiumsp. emerged as a keystone species, maintaining network stability across forests.

Conclusion

This study reveals how local spatial variation and habitat shape distinct fungal communities in tropical forests, with deterministic processes dominating in some habitats and stochasticity playing a key role in others. We show local fungal taxa were strong habitat predictors and drivers of community cohesion. These findings highlight the importance of studying coexisting habitats to gain a deeper understanding of fungal biogeography and ecosystem function.
Exploring the Flexible Penalization of Bayesian Survival Analysis Using Beta Process Prior for Baseline Hazard
Authors: Dauda Kazeem A. , Adeniyi Ebenezer J. , Lamidi Rasheed K. , Wahab Olalekan T.
Published: September 2024

High-dimensional data has significantly captured the interest of many researchers, particularly in the context of variable selection. However, when dealing with time-to-event data in survival analysis, where censoring is a key consideration, progress in addressing this complex problem has remained somewhat limited. More-over, in microarray research, it is common to identify groupings of genes involved in the same biological pathways. These gene groupings frequently collaborate and operate as a unified entity. Therefore, this study is motivated to adopt the idea of a Penalized semi-parametric Bayesian Cox (PSBC) model through elastic-net and group lasso penalty functions (PSBC-EN-G and PSBC-GL-G) to incorporate the grouping structure of the covariates (genes) and optimally perform variable selection. The proposed methods assign a beta prior process to the cumulative baseline hazard function (PSBC-EN-B and PSBC-GL-B), instead of the gamma prior process used in existing methods (PSBC-EN-G and PSBC-GL-G). Three real-life datasets and simulation scenarios were considered to compare and validate the efficiency of the modified methods with existing techniques, using Bayesian Information Criteria (BIC). The results of the simulated studies provided empirical evidence that the proposed methods performed better than the existing methods across a wide range of data scenarios. Similarly, the results of the real-life study showed that the proposed methods revealed a substantial improvement over the existing techniques in terms of feature selection and grouping behavior.
Machine learning-optimized targeted detection of alternative splicing
Authors: Yang Kevin , Islas Nathaniel , Jewell San , Jha Anupama , Radens Caleb M. , Pleiss Jeffrey A. , Lynch Kristen W. , Barash Yoseph , Choi Peter S.
Published: September 2024

RNA-sequencing (RNA-seq) is widely adopted for transcriptome analysis but has inherent biases which hinder the comprehensive detection and quantification of alternative splicing. To address this, we present an efficient targeted RNA-seq method that greatly enriches for splicing-informative junction-spanning reads. Local Splicing Variation sequencing (LSV-seq) utilizes multiplexed reverse transcription from highly scalable pools of primers anchored near splicing events of interest. Primers are designed using Optimal Prime, a novel machine learning algorithm trained on the performance of thousands of primer sequences. In experimental benchmarks, LSV-seq achieves high on-target capture rates and concordance with RNA-seq, while requiring significantly lower sequencing depth. Leveraging deep learning splicing code predictions, we used LSV-seq to target events with low coverage in GTEx RNA-seq data and newly discover hundreds of tissue-specific splicing events. Our results demonstrate the ability of LSV-seq to quantify splicing of events of interest at high-throughput and with exceptional sensitivity.
Effect of heterozygous deletions on phenotypic changes and dosage compensation inArabidopsis thaliana
Authors: Ikoma Takuya , Nishijima Ryo , Ikeda Miho , Ishii Kotaro , Nagalla Asanga Deshappriya , Abe Tomoko , Kazama Yusuke
Published: September 2024

Heterozygous deletions, which include a large number of genes, are often caused by the induction of mutations. The induction of gene dosage compensation should be considered when assessing the effects of heterozygous deletions on phenotypic changes. This mechanism is known to balance the expression levels of genes with different copy numbers in sex chromosomes, but it is also known to operate in autosomes. In the present study, 12Arabidopsis thalianaBC1mutants with heterozygous deletions were produced by crossing wild-type Col-0 plants with mutants induced by heavy ion beams. The sizes of the deletions ranged from 50.9 kb to 2.03 Mb, and the number of deleted genes ranged from 8 to 92. Nine of the 12 BC1mutants showed phenotypic changes in fresh weight 14 days after cultivation or during the flowering period. RNA-sequencing (RNA-seq) analyses of 14-day-old leaves, 40-day-old leaves, and flower buds showed that dosage compensation did not occur in any stage or tissue tested. These results indicate that heterozygous deletions cause phenotypic changes owing to the absence of dosage compensation.

Article Summary

In this study, we examined the impact of heterozygous deletions inArabidopsis thaliana. By crossing wild-type Col-0 plants with mutants induced by heavy ion beams, we created 12 BC1 mutants, each having heterozygous deletions. The deletions ranged from 50.9 kb to 2.03 Mb, affecting 8 to 92 genes. Nine mutants showed changes in fresh weight or flowering time. RNA-seq analyses of leaves and flower buds revealed no gene dosage compensation. Our findings indicate that phenotypic changes result from the lack of dosage compensation in heterozygous deletions.
Sample size considerations for species co-occurrence models
Authors: Cowans Amber , Bigata Albert Bonet , Sutherland Chris
Published: September 2024

The multi-species occupancy model of Rotaet al. (2016) is widely applied for inferences about interactions in the occurrence of different species, but convergence and estimation issues under realistic sample sizes are common. We conducted a simulation study to evaluate the ability to recover co-occurrence estimates using standard and penalised likelihood under varying sample size and interaction scenarios while increasing model complexity in two dimensions: the number of interacting species and the number of covariates. We demonstrate that the ability to quantify interactions in species occupancy using these models is highly sensitive to sample size and interaction strength. Even in the simplest scenario, there is high bias and low coverage in natural parameters (used for inference) for sample sizes below 400 sites. Strong co-occurrence is detected consistently above 400 sites, but weak co-occurrence is never consistently detected even with 3000 sites. We demonstrate that mean predictive ability is less affected by sample size and complexity, with low bias in derived probabilities at 100 sites. We caution the use of these models for inference in small datasets or when co-occurrence is expected to be weak, but show they are suitable to detect strong co-occurrence in larger datasets and generate predictions of site occupancy states.
Tau P301S Transgenic Mice Develop Gait and Eye Movement Impairments That Mimic Progressive Supranuclear Palsy
Authors: Creed Rose B. , Harris Scott C. , Sridhar Sadhana , du Lac Sascha , Zee David S. , Dunn Felice A. , Bouvier Guy , Nelson Alexandra B.
Published: September 2024

Progressive supranuclear palsy (PSP) is a neurodegenerative disorder with an estimated prevalence of 5-7 people in 100,000. Clinically characterized by impairments in gait, balance, and eye movements, as well as aggregated Tau pathology, PSP leads to death in approximately 5-8 years. No disease-modifying treatments are currently available. The contribution of Tau pathology to the symptoms of patients with PSP is poorly understood, in part due to lack of a rodent model that recapitulates characteristic aspects of PSP. Here, we assessed the hTau.P301S mouse for key clinical features of PSP, finding progressive impairments in balance and gait coordination. Additionally, we found impairments in fast vertical eye movements, one of the most distinctive features of PSP. Across animals, we found that Tau pathology in motor control regions correlated with motor deficits. These findings highlight the utility of the hP301S mouse in modeling key aspects of PSP.
Application and Significance of SIRVB Model in Analyzing COVID-19 Dynamics
Authors: Ariyaratne Pavithra , Ramasinghe Lumbini P. , Ayyash Johathan S. , Kelley Tyler M. , Plant-Collins Terry A. , Shinkle Logan W. , Zuercher Aoife M. , Chen Jixin
Published: September 2024

In the summer of 2024, COVID-19 positive cases spiked in many countries, but it is no longer a deadly pandemic thanks to global herd immunity to the SARS-CoV-2 viruses. In our physical chemistry lab in spring 2024, students practice kinetic models, SIR (Susceptible, Infected, and Recovered) and SIRV (Susceptible, Infected, Recovered, Vaccinated) using COVID-19 positive cases and vaccination data from World Health Organization (WHO). In this report, we further introduce virus breakthrough to the existing model updating it the SIRVB (Susceptible, Infectious, Recovered, Vaccinated, Breakthrough) model. We believe this is the simplest model possible to explain the COVID-19 kinetics in all countries in the past four years. Parameters obtained from such practice correlate with many indices of different countries. These models and parameters have significant value to researchers and policymakers in predicting the stages of future outbreaks of infectious diseases.

TOC
Emergence to dominance: Estimating time to dominance of SARS-CoV-2 variants using nonlinear statistical models
Authors: Awasthi Srishti , Dehkharghani Maryam Zolfaghari , Fudolig Miguel
Published: September 2024

Background/Objective

Relative proportion of cases in a multi-strain pandemic like the COVID-19 pandemic provides insight on how fast a newly emergent variant dominates the infected population. However, the behavior of relative proportion of emerging variants is an understudied field. We investigated the emerging behavior of dominant COVID-19 variants using nonlinear statistical methods and calculated the time to dominance of each variant.

Method

We used a phenomenological approach to model national- and regional-level variant share data from the national genomic surveillance system provided by the Centers for Disease Control and Prevention to determine the best model to describe the emergence of two recent dominant variants of the SARS-CoV-2 virus: XBB.1.5 and JN.1. The proportions were modeled using logistic, Weibull, and generalized additive models. Model performance was evaluated using the Akaike Information Criteria (AIC) and the root mean square error (RMSE).

Findings

The Weibull model performed the worst out of all three approaches. The generalized additive model approach slightly outperformed the logistic model based on fit statistics, but lacked in interpretability compared to the logistic model. These models were then used to estimate the time elapsed from emergence to dominance in the infected population, denoted by the time to dominance (TTD). All three models yielded similar TTD estimates. The XBB.1.5 variant was found to dominate the population faster compared to the JN.1 variant, especially in HHS Region 2 (New York) where the XBB.1.5 was believed to emerge. This research expounds on how emerging viral strains transition to dominance, informing public health interventions against future emergent COVID-19 variants and other infectious diseases.
Do pyrethroid insecticides influence sex ratios in agile frogs (Rana dalmatina)?
Authors: Balogh Emese , Hócza Szabolcs , Ujhegyi Nikolett , Kásler Andrea , Holly Dóra , Herczeg Dávid , Ujszegi János , Gál Zoltán , Hoffmann Orsolya I. , Bókony Veronika , Mikó Zsanett
Published: September 2024

Environmental pollutants have the potential to alter sex ratios in wildlife through sex-biased mortality. Furthermore, endocrine disruptors may cause sex reversal during early ontogeny in ectothermic vertebrates, resulting in a phenotypic sex that is not concordant with the genotypic sex encoded by the sex chromosomes. Despite the wide-ranging implications of these sex-ratio biasing effects, they are rarely studied in ecotoxicology, especially in a way that allows for disentangling the two mechanisms. We investigated these effects of two synthetic pyrethroids, deltamethrin and etofenprox, that are commonly used insecticides and have been linked to adverse effects on fish and amphibian biodiversity. We assessed the effects of environmentally relevant concentrations of these two pyrethroids on phenotypic sex ratio, sex-dependent mortality, and sex reversal in agile frogs (Rana dalmatina). Tadpoles from field-collected eggs were reared in mesocosm until metamorphosis by adding 0.03 or 0.3 μg/L of deltamethrin or etofenprox three times to the water. We observed no effect in three of the four treatment groups. However, in the lower-concentration etofenprox treatment, phenotypic sex ratio was male-biased two months post-metamorphosis, and genotypic sexing revealed that this was due to female-biased mortality during metamorphosis and not to sex reversal. Although the estimation certainty of these effects was somewhat limited, they highlight that not all sex-ratio distorting effects are caused by sex reversal. Therefore, ecotoxicological studies aiming to understand the endocrine distruptor effects of environmental contaminants should strive to separate the effects on sex determination and sex-dependent mortality.
Effects of Inosine-5’-Monophosphate Dehydrogenase (IMPDH/GuaB) Inhibitors onBorrelia burgdorferiGrowth in Standard and Modified Culture Conditions
Authors: Siegel Eric L. , Rich Connor , Saravanan Sanchana , Pearson Patrick , Xu Guang , Rich Stephen M.
Published: September 2024

Borrelia burgdorferi’s Inosine-5’-Monophosphate dehydrogenase (IMPDH, GuaB) is a potential therapeutic target. GuaB is not needed forB. burgdorferisurvival and replication in standard growth media, therefore our ability to test novel drugs against the whole organism is limited to tests using mammalian hosts. Modifications to standard culture conditions that can induce borreliastatic effects of GuaB inhibitors will enhance our ability to evaluate these inhibitors. This study aimed to evaluate basic modifications to standard growth media that can achieve this objective. Effects of GuaB inhibitors (mycophenolic acid, 6-Chloropurine) were compared in standard Barbour-Stoenner-Kelly-II (BSK-II) medium with BSK-II modified to 60% concentration rabbit serum, usingB. burgdorferi5A1. Effects were also evaluated with another BSK-II modification with the direct supplementation of hypoxanthine, adenine, and nicotinamide (75 μM each). In standard BSK-II, neither mycophenolic acid nor 6-Chloropurine riboside affectedB. burgdorferigrowth. An ANOVA showed significant, dose-dependent interactions between culture condition and treatment considering modified growth conditions (F = 4.471, P = 0.001). Mycophenolic acid at 250 μM reduced replication by 48 and 50% (P < 0.001 each). 6-Chloropurine riboside was more effective in both conditions at 250 μM, reducing growth by 64 and 65% (P < 0.001 each). Effects of GuaB inhibitors were shown against whole organismBorrelia burgdorferifor the first time. Modification of BSK-II medium with physiologically relevant levels of mammalian serum supports replication and induces GuaB inhibitor-mediated suppression of replication. Effects of 6-Chloropurine riboside were demonstrated for the first time, indicating that B. burgdorferi can salvage and phosphorylate these analogue purine derivatives. These molecules can be manipulated to better inhibit replication. Optimisation will allow the assessment of novel Borrelia-specific IMPDH inhibitor molecules in culture for Lyme disease interventions.

Highlights

Effects of IMPDH inhibitors are shown against whole organismBorrelia burgdorferifor the first time.

Modification of BSK-II medium with physiologically relevant levels of mammalian serum supports replication and induces IMPDH inhibitor-mediated suppression of replication.

Effects of 6-Chloropurine riboside are demonstrated for the first time, indicating thatB. burgdorferican salvage and phosphorylate these analogue purine derivatives. These molecules can be manipulated to better inhibit replication.

Optimisation of modified BSK-II will allow the assessment of novelBorrelia-specific IMPDH inhibitor molecules in culture for Lyme disease interventions.
Neuroinvasive and neurovirulent potential of SARS-CoV-2 in the acute and post-acute phase of intranasally inoculated ferrets
Authors: Benavides Feline F. W. , Kroeze Edwin J. B. Veldhuis , Leijten Lonneke , Schmitz Katharina S. , van Run Peter , Kuiken Thijs , de Vries Rory D. , Bauer Lisa , van Riel Debby
Published: September 2024

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) can cause systemic disease, including neurological complications, even after mild respiratory disease. Previous studies have shown that SARS-CoV-2 infection can induce neurovirulence through microglial activation in the brains of patients and experimentally inoculated animals, which are models representative for moderate to severe respiratory disease. Here, we aimed to investigate the neuroinvasive and neurovirulent potential of SARS-CoV-2 in intranasally inoculated ferrets, a model for subclinical to mild respiratory disease. The presence of viral RNA, histological lesions, virus-infected cells, and the number and surface area of microglia and astrocytes were investigated. Viral RNA was detected in various respiratory tissue samples by qPCR at 7 days post inoculation (dpi). Virus antigen was detected in the nasal turbinates of ferrets sacrificed at 7 dpi and was associated with inflammation. Viral RNA was detected in the brains of ferrets sacrificed 7 dpi, butin situhybridization nor immunohistochemistry did not verify evidence of infection. Histopathological analysis of the brains showed no evidence for an influx of inflammatory cells. Despite this, we observed an increased number of Alzheimer type II astrocytes in the hindbrains of SARS-CoV-2 inoculated ferrets. Additionally, we detected an increased microglial activation in the olfactory bulb and hippocampus, and a decrease in the astrocytic activation status in the white matter and hippocampus of SARS-CoV-2 inoculated ferrets. In conclusion, although showed that SARS-CoV-2 has limited neuroinvasive potential in this model for subclinical to mild respiratory disease, there is evidence for neurovirulent potential. This study highlights the value of this ferret model to study the neuropathogenecity of SARS-CoV-2 and reveals that a mild SARS-CoV-2 infection can affect both microglia and astrocytes in different parts of the brain.
Postmortem findings of free-ranging North American beavers (Castor canadensis) reveal potential threats to California freshwater ecosystems
Authors: Gonzales-Viera Omar A. , Woods Leslie W. , Mete Aslı , Fritz Heather , Armien Anibal G. , Lantz Emma , Gomez-Puerta Luis A. , Famini Daniel , Sherman Jaime , Rudd Jaime L. , Camp Lauren E. , Shapiro Karen , Clifford Deana L.
Published: September 2024

North American beavers (Castor canadensis) are semi-aquatic rodents recognized as keystone species that increase the diversity of freshwater ecosystems. This study aimed to characterize the mortality and pathological findings of free-ranging beavers in California and, based on these results, establish the potential threats to freshwater ecosystems. This study included eighteen beavers submitted for postmortem examination between 2008 and 2024 at the California Animal Health and Food Safety Laboratory, UC Davis. Gross and microscopic examination, bacteriological, parasitological, immunohistochemical, and molecular techniques were used as tools to diagnose the cause of death/reason for euthanasia and comorbidities in the beavers. Encephalitis caused by the larva migrans ofBaylisascarisspp. was the most prevalent (9/18) cause of mortality/reason for euthanasia followed by bacterial infections in 6 individuals. In these 6 animals, bacterial bronchopneumonia was diagnosed in two (Staphylococcus aureusand a mix of gram-negative and -positive bacterial infection) andListeria monocytogenesencephalitis, bacterial myofascitis (Aeromonas bestiarumandPasteurella multocida), bacterial encephalitis (Acinetobacter towneri), and tularemia (Francisella tularensis) were diagnosed in one beaver each. Three animals died or were euthanized due to non-infectious causes including motor vehicle trauma, squamous cell carcinoma, and capture cardiomyopathy. Endoparasitism was the main comorbidity including granulomatous hepatitis by a suspected capillarid species, cerebral toxoplasmosis, Giardia infection, gastric nematodiasis, and cecal trematodiasis. In California, beavers are exposed to various pathogens that represent threats to humans, domestic animals, and wildlife. Since the interspecies transmission of these pathogens occurs in rivers, streams, lakes, and ponds, we suggest that studying beaver health can reflect freshwater ecosystem health. This study also indicates that the translocation of beavers into new areas without consideration and/or mitigation represents a potential risk for pathogen introduction.
Tailoring a CRISPR/Cas-based Epigenome Editor for Programmable Chromatin Acylation and Decreased Cytotoxicity
Authors: Goell Jacob H , Li Jing , Mahata Barun , Ma Alex J , Kim Sunghwan , Shah Spencer , Shah Shriya , Contreras Maria , Misra Suchir , Reed Daniel , Bedford Guy C , Escobar Mario , Hilton Isaac B
Published: September 2024

Engineering histone acylation states can inform mechanistic epigenetics and catalyze therapeutic epigenome editing opportunities. Here, we developed engineered lysine acyltransferases that enable the programmable deposition of acetylation and longer-chain acylations. We show that targeting an engineered lysine crotonyltransferase results in weak levels of endogenous enhancer activation yet retains potency when targeted to promoters. We further identify a single mutation within the catalytic core of human p300 that preserves enzymatic activity while substantially reducing cytotoxicity, enabling improved viral delivery. We leveraged these capabilities to perform single-cell CRISPR activation screening and map enhancers to the genes they regulate in situ. We also discover acylation-specific interactions and find that recruitment of p300, regardless of catalytic activity, to prime editing sites can improve editing efficiency. These new programmable epigenome editing tools and insights expand our ability to understand the mechanistic role of lysine acylation in epigenetic and cellular processes and perform functional genomic screens.
Cell Contractile Forces Drive Spatiotemporal Morphing in 4D Bioprinted Living Constructs
Authors: Cleveland David S , Gasvoda Kaelyn L. , Ding Aixiang , Alsberg Eben
Published: September 2024

Current 4D materials typically rely on external stimuli such as heat or light to accomplish changes in shape, limiting the biocompatibility of these materials. Here, a composite bioink consisting of oxidized and methacrylated alginate (OMA), methacrylated gelatin (GelMA), and gelatin microspheres is developed to accomplish free-standing 4D bioprinting of cell-laden structures driven by an internal stimulus: cell-contractile forces (CCF). 4D changes in shape are directed by forming bilayer constructs consisting of one cell-free and one cell-laden layer. Human mesenchymal stem cells (hMSCs) are encapsulated to demonstrate the ability to simultaneously induce changes in shape and chondrogenic differentiation. Finally, the capability to pattern each layer of the printed constructs is exhibited to obtain complex geometric changes, including bending around two separate, non-parallel axes. Bioprinting of such 4D constructs mediated by CCF empowers the formation of more complex constructs, contributing to a greater degree ofin vitrobiomimicry of biological 4D phenomena.
Sequestration of dead-end undecaprenyl phosphate-linked oligosaccharide intermediate
Authors: Hong Yaoqin , Reeves Peter R.
Published: September 2024

In the predominant Wzx/Wzy-dependent bacterial surface polysaccharide biosynthetic pathway, synthesis is divided between the cytoplasmic and periplasmic faces of the membrane. Initially, an oligosaccharide composed of 3-8 sugars is synthesized on a membrane-embedded lipid carrier, Und-P, within the cytoplasmic face of the membrane. This Und-P-linked oligosaccharide is then translocated to the periplasmic face by the Wzx flippase, where it is polymerized into a repeat-unit polysaccharide. Structural alterations to the repeating oligosaccharide significantly reduce polysaccharide yield and lead to cell death or morphological abnormalities. These effects are attributed to the substrate recognition function of the Wzx flippase, which we postulated to act as a gatekeeper to ensure only complete substrates are translocated to the periplasmic face. Here, we labelledSalmonella entericaserovar Typhimurium Group B1 with [14C] D-galactose. Our results showed that strains unable to synthesize the full O-antigen repeat unit accumulate significantly higher levels of Und-P-linked material (∼10-fold). Importantly, this sequestration is alleviated by mild membrane disruption which opens the cytosolic face Und-PP-linked material to O-antigen ligation that supports the accumulation to occur at the cytosolic face of the membrane.
Importance of higher-order epistasis in large protein sequence-function relationships
Authors: Sethi Palash , Zhou Juannan
Published: September 2024

Epistasis complicates our understanding of protein sequence-function relationships and impedes our ability to build accurate predictive models for novel genotypes. Although pairwise epistasis has been extensively studied in proteins, the significance of higher-order epistasis for protein sequence-function relationships remains contentious, largely due to challenges in fitting higher-order epistatatic interactions for full-length proteins. Here, we introduce a novel transformer-based approach. The key feature of our method is that we can adjust the order of interactions fit by the model by changing the number of attention layers while also accounting for any global nonlinearity induced by the experimental conditions. This allows us to test if inclusion of higher-order interactions leads to enhanced model performance. Applying our method to 10 large protein sequence-function datasets, we found that the importance of higher-order epistasis differs substantially between proteins, accounting for up to 60% of the total variance attributed to epistasis. We also found that including higher-order epistasis is particularly important for generalizing locally sampled fitness data to distant regions of sequence space and for modeling an additional multipeak fitness landscape derived from combining mutagenesis data from 4 orthologous green fluorescencent proteins. Our findings suggest that higher-order epistasis often does play an important role in protein sequence-function relationships, and thus should be properly incorporated during protein engineering and evolutionary data analysis.
Beyond Static Brain Atlases: AI-Powered Open Databasing and Dynamic Mining of Brain-Wide Neuron Morphometry
Authors: Jiang Shengdian , Wang Lijun , Yun Zhixi , Chen Hanbo , Yao Jianhua , Peng Hanchuan
Published: September 2024

We introduce NeuroXiv (neuroxiv.org), a large-scale, AI-powered database that provides detailed 3D morphologies of individual neurons mapped to a standard brain atlas, designed to support a wide array of dynamic, interactive neuroscience applications. NeuroXiv offers a comprehensive collection of 175,149 atlas-oriented reconstructed morphologies of individual neurons derived from more than 518 mouse brains, classified into 292 distinct types and mapped into the Common Coordinate Framework Version 3 (CCFv3). Different from conventional static brain atlases that are often limited to data-browsing, NeuroXiv allows interactive analyses as well as uploading and databasing custom neuron morphologies, which are mapped to the brain atlas for objective comparisons. Powered by a cutting-edge AI engine (AIPOM), NeuroXiv enables dynamic, user-specific analysis and data mining. We specifically developed a mixture-of-experts algorithm to harness the capabilities of multiple large language models. We also developed a client program to achieve more than 10 times better performance compared to a typical server-side setup. We demonstrate NeuroXiv’s scalability, efficiency, flexibility, openness, and robustness through various applications.
Joint Modeling of Cellular Heterogeneity and Condition Effects with scPCA in Single-Cell RNA-Seq
Authors: Vöhringer Harald , Dietrich Sascha
Published: September 2024

Single-cell RNA sequencing (scRNA-seq) in multi-condition experiments enables the systematic assessment of treatment effects. Analyzing scRNA-seq data relies on linear dimensionality reduction (DR) methods like principal component analysis (PCA). These methods decompose high-dimensional gene expression profiles into tractable factor representations and prototypical gene expression patterns (components), facilitating the study of cell type variation. However, integrating study covariates within linear DR frameworks remains a challenging task. We present scPCA, a flexible DR framework that jointly models cellular heterogeneity and conditioning variables, allowing it to recover an integrated factor representation and reveal transcriptional changes across conditions and components of the decomposition. We show that scPCA extracts an interpretable latent representation by analyzing unstimulated and IFN-beta-treated PBMCs, and showcase that the model may be employed to effectively address batch effects. We examine age-related changes in rodent lung cell populations, uncovering a previously unreported surge inCcl5expression in T cells. We illustrate how scPCA may be employed to identify coordinated transcriptional changes across multiple time-points in depolarized visual cortex neurons. Finally, we show that scPCA elucidates transcriptional shifts in CRISPR-Cas9 chordin knockout zebrafish fish single-cell data despite large difference cell abundance across conditions. Since scPCA introduces a general approach to account for conditioning variables in high-dimensional data, it may also be applicable to datasets other than scRNA-seq.
Constructing a Mouse Brain Atlas of Dendritic Microenvironments Helps Discover Hidden Associations Between Anatomical Layout, Projection Targets and Transcriptomic Profiles of Neurons
Authors: Liu Yufeng , Zhao Sujun , Yun Zhixi , Xiong Feng , Peng Hanchuan
Published: September 2024

Digital brain atlases have become essential anatomical references for understanding the spatial and functional organization of brains. For mice, typical resources include the Allen Reference Atlas, the Allen Common Coordinate Framework (CCF), and their variants, like CCFv3. However, previous whole-brain atlases were constructed based on limited neuronal features, such as cell body (soma) density or average maps from collections of registered brain images, without considering the spatial organization of neuronal arbors. This study introduces a microenvironment representation that incorporates the morphological features of neighboring neurons to better quantify brain modularity. We generated a large dataset containing dendrites from 101,136 neurons across 111 mouse brains, covering 91% of non-ventricular, non-fiber-tract CCF regions, and constructed a multidimensional microenvironment feature map of the whole brain. Our findings reveal that the spatial organization of these microenvironments outperforms the CCFv3 and a state-of-the-art spatial transcriptomic cell atlas by providing complementary subregions within established regions, nearly doubling the total number of brain regions compared to CCFv3. In this way, our atlas enables the identification of previously unobserved neuron groupings or “subtypes”. Our results also demonstrate that this microenvironment atlas enhances local spatial homogeneity while maintaining spatial differentiation within established CCF brain regions. For example, we found that the microenvironments of hippocampal neurons are correlated with axonal projection targets and improve the specificity of projection mapping, which implies the potential characterization of long-range axonal projections of mammalian neurons based on only local dendritic organization. The sub-parcellation of the caudoputamen (CP) aligns well with previous studies on projections, connectivity, and transcriptomics, revealing diverse input and output wiring patterns among CP subregions.
Population dynamics of fruit flies (Diptera: Tephritidae) in a semirural area under subtropical monsoon climate of Bangladesh
Authors: Momen Mahfuza , Hossain Md. Aftab , Seheli Kajla , Hossain Md. Forhad , Bari Md. Abdul
Published: September 2024

Fruit flies belonging to Tephritidae family are highly destructive agricultural pests, posing a significant threat to various fruits and vegetables grown in Bangladesh. A comprehensive year-round survey was conducted at Atomic Energy Research Establishment (AERE) campus located in the central region of Bangladesh. Three types of male lures (methyl eugenol, cue-lure and zingerone) were used to detect and assess the diversity of pest fruit fly species. A total of seventeen species of Tephritidae fruit flies were detected in this survey. TheBactrocera carambolaefruit fly has been discovered for the first time in our survey area, indicating spread of its range towards the north-west region from its previous detection sites (Chattogram and Sylhet Divisions) in Bangladesh. Among the detected pest species, we identified six abundant species:Bactrocera dorsalis, Zeugodacus cucurbitae, Zeugodacus tau, Bactrocera rubigina, Bactrocera zonata, andDacus longicornis. The most abundant species was the polyphagous fruit pestB. dorsalis, comprising 76.83% of all captured flies. The speciesZ. cucurbitaewas the second most abundant, representing 13.82% of the total trapped flies. The fitted curve to survey data using Gaussian mixture model revealed the existence of overlapped subgroups in the population ofB. dorsalisandZ. cucurbitae. In addition, our statistical analysis of the six abundant Tephritidae fruit fly species revealed correlation of population dynamics with several factors including temperature, rainfall, humidity, photoperiod, and fruiting time of host plant species in the selected area.
An initial genome editing toolset forCaldimonasthermodepolymerans, the first model of thermophilic polyhydroxyalkanoates producer
Authors: Grybchuk-Ieremenko Anastasiia , Lipovská Kristýna , Kouřilová Xenie , Obruča Stanislav , Dvořák Pavel
Published: September 2024

The limited number of well-characterized model bacteria cannot address all the challenges in a circular bioeconomy. Therefore, there is a growing demand for new production strains with enhanced resistance to extreme conditions, versatile metabolic capabilities, and the ability to utilize cost-effective renewable resources while efficiently generating attractive biobased products. Particular thermophilic microorganisms fulfill these requirements. Non-virulent Gram-negativeCaldimonas thermodepolymeransDSM15344 is one such attractive thermophile that efficiently converts a spectrum of plant biomass sugars into high quantities of polyhydroxyalkanoates (PHA) - a fully biodegradable substitutes for synthetic plastics. However, to enhance its biotechnological potential, the bacterium needs to be “domesticated”. In this study we established effective homologous recombination and transposon-based genome editing systems forC. thermodepolymerans. By optimizing the electroporation protocol and refining counterselection methods, we achieved significant improvements in genetic manipulation and constructed the AI01 chassis strain with improved transformation efficiency and a ΔphaCmutant that will be used to study the importance of PHA synthesis inCaldimonas. The advances described herein highlight the need for tailored approaches when working with thermophilic bacteria and provide a springboard for further genetic and metabolic engineering ofC. thermodepolymerans, which can be considered the first model of thermophilic PHA producer.
TDRD3 functions as a selective autophagy receptor with dual roles in autophagy and modulation of stress granule stability
Authors: Deater Matthew , Lloyd Richard E.
Published: September 2024

Tudor Domain Containing 3 (TDRD3) is a methylarginine-reader protein that functions as a scaffold in the nucleus facilitating transcription, however TDRD3 is also recruited to stress granules (SGs) during the Integrated Stress Response (ISR) although its function therein remains largely unknown. We previously showed that TDRD3 is a novel antiviral restriction factor that is cleaved by virus 2A protease, and plays complex modulatory roles in both interferon and inflammatory signaling during stress and enterovirus infections. Here we have found that TDRD3 contains structural motifs similar to known selective autophagy receptors such as p62/SQSTM1, sharing ubiquitin associated domains (UBA) and LC3 interacting regions (LIR) that anchor cargo destined for autophagosomes to activated LC3 protein coating autophagosome membranes. This is of interest since enteroviruses hijack autophagy machinery to facilitate formation of viral replication factories, virus assembly and egress from the infected cell. Here we explored possible roles of TDRD3 in autophagy, hypothesizing that TDRD3 may function as a specialized selective autophagy receptor. We found that KO of TDRD3 in HeLa cells significantly reduces starvation induced autophagy, while its reintroduction restores it in a dose-dependent manner. Autophagy receptors are degraded during autophagy and expression levels decrease during this time. We found that TDRD3 levels decrease to the same extent as the autophagy receptor p62/SQSTM1 during autophagy, indicating autophagy-targeted turnover in that role. Knockout of TDRD3 or G3BP1 did not make significant changes in overall cell localization of LC3B or p62/SQSTM1, but did result in greater concentration of Lamp2 phagosome marker for phagosomes and phagolysosomes. To test the potential roles of TDRD3 in autophagic processes, we created a series of deletion mutants of TDRD3 lacking either UBA domain or the various LIR motifs that are predicted to interact with LC3B. Microscopic examination of starved cells expressing these variants of TDRD3 showed ΔLIR-TDRD3 had defects in colocalization with LC3B or Lamp2. Further, super resolution microscopy revealed ring structures with TDRD3 interfacing with p62/SQSTM1. In examination of arsenite induced stress granules we found recruitment of TDRD3 variants disrupted normally tight SG condensation, altered the decay rate of SGs upon release from stress and the kinetics of SG formation. We found evidence that the LIR3 motif on TDRD3 is involved in TDRD3 interaction with LC3B in coIP experiments, colocalization studies, and that this motif plays a key role in TDRD3 recruitment to SGs and SG resolution. Overall, these data support a functional role of TDRD3 in selective autophagy in a mode similar to p62/SQSTM1, with specific roles in SG stability and turnover. Enterovirus cleavage of TDRD3 likely affects both antiviral and autophagic responses that the virus controls for replication.
Distinct Neural Representations of Hunger and Thirst in Neonatal Mice before the Emergence of Food- and Water-seeking Behaviors
Authors: Wang David C. , Wu Yunming , Mehaffy Conor , Espinoza-Campomanes Leslie A. , Santos-Valencia Fernando , Franks Kevin M. , Luo Liqun
Published: September 2024

Hunger and thirst are two fundamental drives for maintaining homeostasis and elicit distinct food- and water-seeking behaviors essential for survival. For neonatal mammals, however, both hunger and thirst are sated by consuming milk from their mother. While distinct neural circuits underlying hunger and thirst drives in the adult brain have been characterized, it is unclear when these distinctions emerge in neonates and what processes may affect their development. Here we show that hypothalamic hunger and thirst regions already exhibit specific responses to starvation and dehydration well before a neonatal mouse can seek food and water separately. At this early age, hunger neurons drive feeding behaviors more than do thirst neurons.In vivoNeuropixels recordings in dehydrated and starved neonatal mice revealed that maternal presentation leads to a relative increase in activity which is suppressed by feeding on short timescales, particularly in hypothalamic and thalamic neurons. Changes in activity become more heterogeneous on longer timescales. Lastly, within neonatal regions that respond to both hunger and thirst, subpopulations of neurons respond distinctly to one or the other need. Combining food and water into a liquid diet throughout the animal’s life does not alter the distinct representations of hunger and thirst in the adult brain. Thus, neural representations of hunger and thirst in mice become distinct before food- and water-seeking behaviors mature and are robust to environmental changes in food and water sources.
Leg compliance is required to explain the ground reaction force patterns and speed ranges in different gaits
Authors: Safa Ali Tehrani , Biswas Tirthabir , Ramakrishnan Arun , Bhandawat Vikas
Published: September 2024

Two simple models, vaulting over stiff legs and rebounding over compliant legs, are employed to describe the mechanics of legged locomotion. It is agreed that compliant legs are necessary for describing running and that legs are compliant while walking. Despite this agreement, stiff legs continue to be employed to model walking. Here, we show that leg compliance is necessary to model walking and, in the process, identify the principles that underpin two important features of legged locomotion: First, at the same speed, step length, and stance duration, multiple gaits that differ in the number of leg contraction cycles are possible. Among them, humans and other animals choose a gait with M-shaped vertical ground reaction forces because it is energetically favored. Second, the transition from walking to running occurs because of the inability to redirect the vertical component of the velocity during the double stance phase. Additionally, we also examine the limits of double spring-loaded pendulum (DSLIP) as a quantitative model for locomotion, and conclude that DSLIP is limited as a model for walking. However, insights gleaned from the analytical treatment of DSLIP are general and will inform the construction of more accurate models of walking.