Miracle-dz/UniFAR-FTUs huggingface dataset:
Title: β Cell microRNAs Function as Molecular Hubs of Type 1 Diabetes Pathogenesis and as Biomarkers of Diabetes Risk

MicroRNAs (miRNAs) are small non-coding RNAs that play a crucial role in modulating gene expression and are enriched in cell-derived extracellular vesicles (EVs). We investigated whether miRNAs from human islets and islet-derived EVs could provide insight into β cell stress pathways activated during type 1 diabetes (T1D) evolution, therefore serving as potential disease biomarkers. We treated human islets from 10 cadaveric donors with IL-1β and IFN-γ to model T1D ex vivo. MicroRNAs were isolated from islets and islet-derived EVs, and small RNA sequencing was performed. We found 20 and 14 differentially expressed (DE) miRNAs in cytokine-versus control-treated islets and EVs, respectively. Interestingly, the miRNAs found in EVs were mostly different from those found in islets. Only two miRNAs, miR-155-5p and miR-146a-5p, were upregulated in both islets and EVs, suggesting selective sorting of miRNAs into EVs. We used machine learning algorithms to rank DE EV-associated miRNAs, and developed custom label-free Localized Surface Plasmon Resonance-based biosensors to measure top ranked EVs in human plasma. Results from this analysis revealed that miR-155, miR-146, miR-30c, and miR-802 were upregulated and miR-124-3p was downregulated in plasma-derived EVs from children with recent-onset T1D. In addition, miR-146 and miR-30c were upregulated in plasma-derived EVs of autoantibody positive (AAb+) children compared to matched non-diabetic controls, while miR-124 was downregulated in both T1D and AAb+ groups. Furthermore, single-molecule fluorescence in situ hybridization confirmed increased expression of the most highly upregulated islet miRNA, miR-155, in pancreatic sections from organ donors with AAb+ and T1D. One Sentence Summary miRNA expression patterns in human pancreatic islets and EVs change under inflammatory conditions and can be leveraged to inform biomarkers strategies for T1D.
Convergence, plasticity, and tissue residence of regulatory T cell response via TCR repertoire prism

Suppressive function of regulatory T cells (Treg) is dependent on signaling of their antigen receptors triggered by cognate self, dietary or microbial antigens in the form of peptide-MHC class II complexes. However, it remains largely unknown whether distinct or shared repertoires of Treg TCRs are mobilized in response to different challenges in the same tissue or the same challenge in different tissues. Here we used a fixed TCRβ chain FoxP3-GFP mouse model to analyze conventional (eCD4) and regulatory (eTreg) effector TCRα repertoires in response to six distinct antigenic challenges to the lung and skin. This model showed highly “digital” repertoire behavior, allowing for easy-to-track challenge-specific TCRα CDR3 clusters. For both studied subsets, we observed challenge-specific clonal expansion yielding homologous TCRα clusters within and across animals and exposure sites, which were also reflected in the draining lymph nodes but not systemically. Some clusters were shared across cancer challenges, suggesting response to common tumor-associated antigens. For most challenges, eCD4 and eTreg clonal response did not overlap, indicating the distinct origin of the two cell subsets. At the same time, we observed such overlap at the sites of certain tumor challenges. The overlaps included dominant responding TCRα motif and characteristic iNKT TCRα, suggesting the tumor-induced eCD4-eTreg plasticity. Additionally, our TCRα repertoire analysis demonstrated that distinct antigenic specificities are characteristic for eTreg cells residing in particular lymphatic tissues, regardless of the challenge, revealing the homing-specific, antigen-specific resident Treg populations. Altogether, our study highlights both challenge-specific and tissue-specific responses of Treg cells associated with distinct clonal expansions. Graphical abstract
The activity of engrailed imaginal disc enhancers is modulated epigenetically by chromatin and autoregulation

engrailed (en) encodes a homeodomain transcription factor crucial for the proper development of Drosophila embryos and adults. Like many developmental transcription factors, en expression is regulated by many enhancers, some of overlapping function, that drive expression in spatially and temporally restricted patterns. The en embryonic enhancers are located in discrete DNA fragments that can function correctly in small reporter transgenes. In contrast, the en imaginal disc enhancers (IDEs) do not function correctly in small reporter transgenes. En is expressed in the posterior compartment of wing imaginal disks; small IDE-reporter transgenes are expressed in the anterior compartment, the opposite of what is expected. Our data show that the En protein binds to en IDEs, and we suggest that En directly represses IDE function. We identified two en IDEs, ‘O’ and ‘S’. Deletion of either of these IDEs from a 79kb HA-en rescue transgene (HAen79) caused a loss-of-function en phenotype when the HAen79 transgene was the sole source of En. In contrast, flies with a deletion of the same IDEs from the endogenous en gene had no phenotype, suggesting a resiliency not seen in the HAen79 rescue transgene. Inserting a gypsy insulator in HAen79 between en regulatory DNA and flanking sequences strengthened the activity of HAen79, giving better function in both the ON and OFF transcriptional states. Altogether our data show that the en IDEs stimulate expression in the entire imaginal disc, and that the ON/OFF state is set by epigenetic regulators. Further, the endogenous locus imparts a stability to en function not seen even in a large transgene, reflecting the importance of both positive and negative epigenetic influences that act over relatively large distances in chromatin. Author Summary Genes that control development are often used at different times and places in a developing embryo. Transcription of these important genes must be tightly regulated; therefore, these genes often have large arrays of regulatory DNA. In Drosophila, discrete fragments of DNA (enhancers) can be identified that turn genes on in patterns in the early embryo. In cells where the genes are transcriptionally ON, there are active modifications on chromatin, setting later enhancers in a transcription-permission environment. In cells where the genes are OFF, repressive chromatin marks keep later enhancers inactive. In this paper we studied two late enhancers of the Drosophila en gene. We show that the correct activity of these enhancers is dependent on being next to other, earlier acting en enhancers. Our data also show that En can repress its own expression, likely directly by acting on these late enhancers. The chromatin-regulated activity of these en late enhancers is similar to what was described for a late enhancer of another Drosophila developmental gene, Ubx. We suggest that this mode of regulation is likely to be important for many late-acting developmental enhancers in many different organisms.
Comparative analysis of PDZ-binding motifs in the diacylglycerol kinase family

Diacylglycerol kinases (DGKs) control local and temporal amounts of diacylglycerol (DAG) and phosphatidic acid (PA) by converting DAG to PA through phosphorylation in cells. Certain DGK enzymes possess C-terminal sequences that encode potential PDZ-binding motifs (PBMs), which could be involved in their recruitment into supramolecular signaling complexes. In this study, we used two different interactomic approaches, quantitative native holdup (nHU) and qualitative affinity purification (AP), both coupled to mass spectrometry (MS) to investigate the PDZ partners associated with the potential PBMs of DGKs. Complementing these results with site-specific affinity interactomic data measured on isolated PDZ domain fragments and PBM motifs, as well as evolutionary conservation analysis of the PBMs of DGKs, we explored functional differences within different DGK groups. All our results indicate that putative PBM sequences of type II enzymes are likely to be nonfunctional. In contrast, type IV enzymes possess highly promiscuous PBMs that interact with a set of PDZ proteins with very similar affinity interactomes. The combination of various interactomic assays and evolutionary analyses provides a useful strategy for identifying functional domains and motifs within diverse enzyme families.
Common molecular signatures between coronavirus infection and Alzheimer’s disease reveal targets for drug development

Cognitive decline has been reported as a common consequence of COVID-19, and studies have suggested a link between COVID-19 infection and Alzheimer’s disease (AD). However, the molecular mechanisms underlying this association remain unclear. To shed light on this link, we conducted an integrated genomic analysis using a novel Robust Rank Aggregation method to identify common transcriptional signatures of the frontal cortex, a critical area for cognitive function, between individuals with AD and COVID-19. We then performed various analyses, including the KEGG pathway, GO ontology, protein-protein interaction, hub gene, gene-miRNA, and gene-transcription factor interaction analyses to identify molecular components of biological pathways that are associated with AD in the brain also show similar changes in severe COVID-19. Our findings revealed the molecular mechanisms underpinning the association between COVID-19 infection and AD development and identified several genes, miRNAs, and TFs that may be targeted for therapeutic purposes. However, further research is needed to investigate the diagnostic and therapeutic applications of these findings.
Pneumatically Controlled Non-Equibiaxial Cell Stretching Device with Live-cell Imaging

Objective Adherent cell behavior is influenced by a complex interplay of factors, including chemical and mechanical signals. In vitro experiments that mimic the mechanical environment experienced by cells in vivo are crucial for understanding cellular behavior and the progression of disease. In this study, we developed and validated a low-cost pneumatically-controlled cell stretcher with independent control of strain in two directions of a membrane, enabling unequal biaxial stretching and realtime microscopy during actuation. Methods The stretching was achieved by two independent pneumatic channels controlled by electrical signals. We used finite element simulations to compute the membrane’s strain field and particle tracking algorithms based on image processing techniques to validate the strain fields and measure the cell orientation and morphology. Results The device can supply uniaxial, equibiaxial, and unequal biaxial stretching up to 15% strain in each direction at a frequency of 1Hz, with a strain measurement error of less than 1%. Through live cell imaging, we determined that distinct stretching patterns elicited differing responses and alterations in cell orientation and morphology, particularly in terms of cell length and area. Conclusion The device successfully provides a large, uniform, and variable strain field for cell experiments, while also enabling real-time, live cell imaging. Significance This scalable, low-cost platform provides mechanical stimulation to cell cultures by independently controlling strains in two directions. This could contribute to a deeper understanding of cellular response to biorealistic strains and could be useful for future in vitro drug testing platforms.
Predicting cued and oddball visual search performance from neural representational similarity

Capacity limitations in visual tasks can be observed when the number of task-related objects increases. An influential idea is that such capacity limitations are determined by competition at the neural level: two objects that are encoded by shared neural populations interfere more in behavior (e.g., visual search) than two objects encoded by separate neural populations. However, the neural representational similarity of objects varies across brain regions and across time, raising the question of where and when competition determines task performance. Furthermore, it is unclear whether the association between neural representational similarity and task performance is common or unique across tasks. Here, we used neural representational similarity derived from fMRI, MEG, and deep neural networks (DNN) to predict performance on two visual search tasks involving the same objects and requiring the same responses but differing in instructions: cued visual search and oddball visual search. Separate groups of human participants (both sexes) viewed the individual objects in neuroimaging experiments to establish the neural representational similarity between those objects. Results showed that performance on both search tasks could be predicted by neural representational similarity throughout the visual system (fMRI), from 80 msec after onset (MEG), and in all DNN layers. Stepwise regression analysis, however, revealed task-specific associations, with unique variability in oddball search performance predicted by early/posterior neural similarity, and unique variability in cued search task performance predicted by late/anterior neural similarity. These results reveal that capacity limitations in superficially similar visual search tasks may reflect competition at different stages of visual processing. Significance Statement Visual search for target objects is slowed down by the presence of distractors, but not all distractors are equally distracting – the more similar a distractor is to the target, the more it slows down search. Here, we used fMRI, MEG, and a deep neural network to reveal where, when, and how neural similarity between targets and distractors predicts visual search performance across two search tasks: oddball visual search (locating the different-looking object) and cued visual search (locating the cued object). Results also revealed brain regions, time points, and feature levels that predicted task-unique performance. These results provide a neural basis for similarity theories of visual search and show that this neural basis differs across visual search tasks.
Disentangling the cascading effects of Grapevine Red Blotch Virus infection on vine physiology

Grapevine Red Blotch Virus is a major grapevine pathogen and is associated with reduced carbon assimilation and delayed berry ripening in Vitis vinifera L. Recent work suggests that the virus alters leaf carbon metabolism prior to emergence of visible symptoms. Therefore, diurnal and seasonal measurements were conducted to quantify changes in leaf carbon balance and to elucidate the chronology of symptom progression in leaves and fruit. Healthy and infected vines were assayed in a commercial vineyard during which leaf water relations, photosynthesis, and nonstructural carbohydrates were measured. Additionally, sugar and anthocyanin accumulation in the fruit were monitored at the end of the season to characterize the impact of the virus on ripening. Virus infection significantly reduced carbon assimilation pre- and postveraison, but the impact was more pronounced postveraison and during the afternoon when vine water status was the lowest. Similarly, virus infection significantly increased leaf starch concentration pre- and postveraison, but increased leaf starch in infected vines was detected two weeks prior to veraison. Virus infection had the greatest impact on obstructing leaf carbon export postveraison, especially during the afternoon. The virus had no impact on chlorophyll fluorescence, indicating there was no sustained photosystem impairment and suggesting that changes in chlorophyll fluorescence were a transient response to reduced carbon assimilation and export. This study provides evidence that reduced carbon export constitutes a feedback inhibition response to accumulation of leaf starch prior to the appearance of visible symptoms or impacts to ripening, which may aid earlier detection of the virus.
Analysis of follow-up data in large biobank cohorts: a review of methodology

Survival analysis in clinical trials has been extensively researched, but its applicability to large omics-based biobanks requires further investigation. This study addresses two important issues in time-to-event data analysis in biobank settings. First, there is the need to pay attention to left-truncation of some outcomes that would prevent individuals joining the biobank, if the event of interest occurs before possible recruitment time. To avoid biases due to left-truncation, it has been suggested to use age as time scale in the analysis, whereas an individual is considered at risk only after recruitment to the biobank. Second, one needs to address the computational burden due to relative slowness of the conventional algorithm to maximize the partial likelihood function for the Cox model. This study examines the impact of the choice of timescale on the bias and power, while varying effect size and censoring rate in the range realistically seen in a typical biobank setting. Moreover, the study explores a computationally fast two-step martingale residual (MR) based approach for Cox modeling in high-dimensional omics data. The findings indicate that the choice of timescale has minimal impact on accuracy for small hazard ratios (HR), but for larger HRs, accounting for left-truncation is crucial to reduce bias. When maximizing power for association discovery, using participant age as the time scale (whereas individual is considered to be at risk immediately after birth) yields the highest power. The two-step MR approach is recommended for genome-wide association studies due to acceptable precision and retained power for small effect sizes. However, for predictions and polygenic risk score calculations, effect sizes should be recalculated using the conventional Cox proportional hazards model while accounting for left-truncation. The conclusions are based on simulations and illustrated with survival data from the Estonian Biobank cohort.
Prolonged exposure to hypergravity increases number and size of cells and enhances lignin deposition in the stem of Arabidopsis thaliana (L.) Heynh

We have performed a lab-based hypergravity cultivation experiment using a centrifuge equipped with a lighting system and examined long-term effects of hypergravity on the development of the main axis (stem) of the Arabidopsis (Arabidopsis thaliana (L.) Heynh. ) primary inflorescence. Plants grown under 1 × g (gravitational acceleration on Earth) conditions for 20-23 days and having the first visible flower bud were exposed to hypergravity at 8 × g for 10 days. We analyzed the effect of prolonged hypergravity conditions on growth, lignin deposition, and tissue anatomy of the main axis. As a result, the length of the main axis decreased and cross-sectional area, dry mass per unit length, cell number, lignin content of the main axis significantly increased under hypergravity. Lignin content in the rosette leaves also increased when they were exposed to hypergravity during their development. Except for interfascicular fibers, cross-sectional areas of the tissues composing the internode significantly increased under hypergravity in most type of the tissues in the basal part than the apical part of the main axis, indicating that the effect of hypergravity is more pronounced in the basal part than the apical part. The number of cells in fascicular cambium and xylem significantly increased under hypergravity both in the apical and basal internodes of the main axis, indicating a possibility that hypergravity stimulates procambium activity to produce xylem element more than phloem element. The main axis was suggested to be strengthened through changes in its morphological characteristics as well as lignin deposition under prolonged hypergravity conditions.
Plasticity of the proteasome-targeting signal Fat10 enhances substrate degradation

The proteasome controls levels of most cellular proteins, and its activity is regulated under stress, quiescence, and inflammation. However, factors determining the proteasomal degradation activity remain poorly understood. Proteasome substrates are conjugated with small proteins (tags) like ubiquitin and Fat10 to target them to the proteasome. It is unclear if the structural plasticity of proteasome-targeting tags influences substrate degradation. The tag Fat10 is activated during inflammation, and ambiguously, Fat10 and its substrates undergo rapid proteasomal degradation. We report that the rapid degradation of Fat10 substrates depends on its structural plasticity. While the ubiquitin tag is recycled at the proteasome, Fat10 is degraded with the substrate, and the mechanical unfolding kinetics of Fat10 regulates substrate degradation. Our studies reveal that long-range salt bridges are absent in the Fat10 structure, creating a plastic protein with partially unstructured regions suitable for proteasome engagement. Such a malleable structure also provides low resistance to mechanical unfolding and expedites proteasomal degradation. We also uncovered that the Fat10 plasticity destabilizes substrates significantly and creates partially unstructured regions in the substrate to enhance degradation. NMR-relaxation-derived order parameters and temperature dependence of chemical shifts identify the Fat10-induced partially unstructured regions in the substrate. They correlated excellently to the regions where Fat10 contacts the substrate, suggesting that the tag-substrate collision destabilizes the substrate. These results highlight a strong dependence of proteasomal degradation on the structural plasticity and thermodynamic properties of the proteasome-targeting tag.
Building alternative splicing and evolution-aware sequence-structure maps for protein repeats

Alternative splicing of repeats in proteins provides a mechanism for rewiring and fine-tuning protein interaction networks. In this work, we developed a robust and versatile method, ASPRING, to identify alternatively spliced protein repeats from gene annotations. ASPRING leverages evolutionary meaningful alternative splicing-aware hierarchical graphs to provide maps between protein repeats sequences and 3D structures. We re-think the definition of repeats by explicitly accounting for transcript diversity across several genes/species. Using a stringent sequence-based similarity criterion, we detected over 5,000 evolutionary conserved repeats by screening virtually all human protein-coding genes and their orthologs across a dozen species. Through a joint analysis of their sequences and structures, we extracted specificity-determining sequence signatures and assessed their implication in experimentally resolved and modelled protein interactions. Our findings demonstrate the widespread alternative usage of protein repeats in modulating protein interactions and open avenues for targeting repeat-mediated interactions. Highlights Robust detection of alternatively used repeated protein regions in evolution The approach relies on sequence similarity and identifies conserved signatures Mapping of the repeats onto protein isoform 3D models predicted by AlphaFold 5 000 repeats detected over the human coding fraction, about one third disordered Assessment of the structural coverage of their interactions with protein partners