Miracle-dz/UniFAR-FTUs huggingface dataset:
Rats spontaneously perceive global motion direction of drifting plaids

Computing global motion direction of extended visual objects is a hallmark of primate high-level vision. Although neurons selective for global motion have also been found in mouse visual cortex, we still do not know whether rodents can combine multiple motion signals into global, integrated percepts. Here, we trained two groups of rats to discriminate motion direction of either gratings or plaids (i.e., superpositions of two gratings) and we tested whether these visual patterns were able to prime rat perception consistently with an integrated representation of plaid direction. We found that, depending on the identity of the training stimuli, rats displayed either a shared representation of gratings and plaids based on global motion, or a non-shared one. As shown by computational modeling, these findings are consistent with the existence of a population of pattern-like cells, playing a functional role similar to that demonstrated in primates.
Comparison study of sixteen differential abundance methods using two large Parkinson disease gut microbiome datasets

Background When studying the relationship between the microbiome and a disease, a common question asked is what individual microbes are differentially abundant between a disease and healthy state. Numerous differential abundance (DA) testing methods exist and range from standard statistical tests to methods specifically designed for microbiome data. Comparison studies of DA testing methods have been performed, but none were performed on microbiome datasets collected for the study of real, complex disease. Due to this, we performed DA testing of microbial genera using 16 DA methods in two large, uniformly collected gut microbiome datasets on Parkinson disease (PD), and compared their results. Results Pairwise concordances between methods ranged from 46%-99% similarity. Average pairwise concordance per dataset was 76%, and dropped to 62% when taking replication of signals across datasets into account. Certain methods consistently resulted in above average concordances (e.g. Kruskal-Wallis, ALDEx2, GLM with centered-log-ratio transform), while others consistently resulted in lower than average concordances (e.g. edgeR, fitZIG). Overall, ∼80% of genera tested were detected as differentially abundant by at least one method in each dataset. Requiring associations to replicate across datasets reduced significant signals by almost half. Further requirement of signals to be replicated by the majority of methods (≥8) yielded 19 associations. Only one genus (Agathobacter) was replicated by all methods. Use of hierarchical clustering revealed three groups of DA signatures that were (1) replicated by the majority of methods and included genera previously associated with PD, (2) replicated by few or no methods, and (3) replicated by a subset of methods and included rarer genera, all enriched in PD. Conclusions Differential abundance tests yielded varied results. Using one method on one dataset may find true associations, but may also detect non-reproducible signals, adding to inconsistency in the literature. To help lower false positives, one might analyze data with two or more DA methods to gauge concordance, and use a built-in replication dataset to show reproducibility. This study corroborated previously reported taxa-associations in PD, and revealed a potential new group of rarer taxa whose abundance is significantly elevated in PD, and might be worth pursuing in future investigations.
Asymmetric Contraction of Adherens Junctions arises through RhoA and E-cadherin feedback

Tissue morphogenesis often arises from the culmination of discrete changes in cell-cell junction behaviors, namely ratcheted junction contractions that lead to collective cellular rearrangements. Mechanochemical signaling in the form of RhoA underlies these ratcheted contractions, which occur asymmetrically as one highly motile vertex contracts toward a relatively less motile tricellular vertex. The underlying mechanisms driving asymmetric vertex movement remains unknown. Here, we use optogenetically controlled RhoA in model epithelia together with biophysical modeling to uncover the mechanism lending to asymmetric vertex motion. We find that both local and global RhoA activation leads to increases in junctional tension, thereby facilitating vertex motion. RhoA activation occurs in discrete regions along the junction and is skewed towards the less-motile vertex. At these less-motile vertices, E-cadherin acts as an opposing factor to limit vertex motion through increased frictional drag. Surprisingly, we uncover a feedback loop between RhoA and E-cadherin, as regional optogenetic activation of specified junctional zones pools E-cadherin to the location of RhoA activation. Incorporating this circuit into a mathematical model, we find that a positive feedback between RhoA-mediated tension and E-cadherin-induced frictional drag on tricellular vertices recapitulates experimental data. As such, the location of RhoA determines which vertex is under high tension, pooling E-cadherin and increasing the frictional load at the tricellular vertex to limit its motion. This feedback drives a tension-dependent intercellular “clutch” at tricellular vertices which stabilizes vertex motion upon tensional load.
Cascading indirect genetic effects in a clonal vertebrate

Understanding how individual differences among organisms arise and how their effects propagate through groups of interacting individuals are fundamental questions in biology.Individual differences can arise from genetically-based variation in the conspecifics with which an individual interacts, and these effects might then be propagated to other individuals. Using a clonal species, the Amazon molly (Poecilia formosa), we test the hypothesis that such indirect genetic effects (IGE) propagate beyond individuals that experience them firsthand. We tested this hypothesis by exposing genetically identical Amazon mollies to social partners of different genotypes, and then moving these individuals to new social groups in which they were the only member to have experienced the IGE. We found that genetically different social environments induced different levels of aggression experienced by the focal animals, and that these genetically-based social effects carried over into new social groups to influence the behavior of individuals that did not directly experience the previous social environments. Our data reveal that IGE can cascade beyond the individuals that directly experience them to influence phenotypes even when there is no genetically-based variation present within interacting groups. Theoretical and empirical expansion of the quantitative genetic framework developed for IGE to include cascading and other types of carry-over effects will improve understanding of social behavior and its evolution.
EVALUATION OF ACUTE AND SUB ACUTE TOXICITIES OF LEAF EXTRACT OF CAESALPINIA BONDUCELLA (L.) FLEM

The acute and sub acute toxicity studies of ethyl acetate extract of Caesalpinia bonducella leaves in albino mice were investigated. Various doses of eth yl acetate leaf extract from 800 to 2000 mg/kg body weight were administered orally to the test groups of mice, while distilled water was given to the con trol group to evaluate the toxicity in mice after ingest ion of the extract for one day (acute model) and fo r 15 days (sub acute model). The behavioral response profile of the treated mice was also evaluated along with o ther parameters such as, body weight, absolute and relat ive weight of various organs. Biochemical, hematol ogical and histopathological parameters were analyzed in o rder to study the time-dependent effect and correla tion of the extract. The results indicated that LD 50 of the extract is higher than 2000 mg/kg and no ch anges were observed in any behavioral parameters in mice. Body weight of mice increased along with the time in su b acute model. The biochemical (total protein, DNA, RNA, alkaline phosphatase, acid phosphatase, cholest erol, and carbohydrate) and hematological parameters (tot al RBC and WBC) and histopathological studies of liver, heart, lung and kidney indicated either no or less alteration in the treated group. However, a slight change in liver cellular architecture with hydropic changes i n the epithelium, congested sinusoids and dilation of central vein was observed in liver of test animal.
Functional Characterization of Ovine Dorsal Root Ganglion Neurons Reveal Peripheral Sensitization after Osteochondral Defect

Abstract Knee joint trauma can cause an osteochondral defect (OD), a risk factor for osteoarthritis (OA) and cause of debilitating pain in patients. Rodent OD models are less translatable because of their smaller joint size and open growth plate. This study proposes sheep as a translationally relevant model to understand the neuronal basis of OD pain. A unilateral 6-mm deep OD was induced in adult female sheep. Two to six weeks after operation, lumbar dorsal root ganglia (DRG) neurons were collected from the contralateral (Ctrl) and OD side of operated sheep. Functional assessment of neuronal excitability and activity of the pain-related ion channels transient receptor potential vanilloid receptor 1 (TRPV1) and P2X3 was conducted using electrophysiology and Ca2+ imaging. Immunohistochemistry was used to verify expression of pain-related proteins. We observed that an increased proportion of OD DRG neurons (sheep, N = 3; Ctrl neurons, n = 15, OD neurons, n = 16) showed spontaneous electrical excitability (Ctrl: 20.33 ± 4.5%; OD: 50 ± 10%; p = 0.009, unpaired t test) and an increased proportion fired a greater number of spikes above baseline in response to application of a TRPV1 agonist (capsaicin) application (Ctrl: 40%; OD: 75%; p = 0.04, χ2 test). Capsaicin also produced Ca2+ influx in an increased proportion of isolated OD DRG neurons (Ctrl: 25%; OD: 44%; p = 0.001, χ2 test). Neither protein expression, nor functionality of the P2X3 ion channel were altered in OD neurons. Overall, we provide evidence of increased excitability of DRG neurons (an important neural correlate of pain) and TRPV1 function in an OD sheep model. Our data show that functional assessment of sheep DRG neurons can provide important insights into the neural basis of OD pain and thus potentially prevent its progression into arthritic pain.
Defining kinetic roles of transcriptional activators in the early Drosophila embryo

Most animal transcription factors are categorized as activators or repressors without specifying their mechanisms of action. Defining their specific roles is critical for deciphering the logic of transcriptional regulation and predicting the function of regulatory sequences. Here, we define the kinetic roles of three activating transcription factors in the Drosophila embryo—Zelda, Bicoid and Stat92E—by introducing their binding sites into the even skipped stripe 2 enhancer and measuring transcriptional output with live imaging. We find that these transcription factors act on different subsets of kinetic parameters, and these subsets can change over the course of nuclear cycle (NC) 14. These transcription factors all increase the fraction of active nuclei. Zelda dramatically shortens the time interval between the start of NC 14 and initial activation, and Stat92E increases the duration of active transcription intervals throughout NC 14. Zelda also decreases the time intervals between instances of active transcription early in NC 14, while Stat92E does so later. Different transcription factors therefore play distinct kinetic roles in activating transcription; this has consequences for understanding both regulatory DNA sequences as well as the biochemical function of transcription factors.
Myo-inositol Oxygenase Overexpression Rescues Vitamin C Deficient Arabidopsis (vtc) Mutants

Biosynthesis of l-ascorbate (AsA) in plants is carried out by a complex metabolic network, which involves d-mannose/l-galactose, d-galacturonate, l-gulose, and myo-inositol as main precursors. Arabidopsis lines over-expressing enzymes in the myo-inositol pathway have elevated AsA, accumulate more biomass of both aerial and root tissues, and are tolerant to abiotic stresses as shown by manual and digital phenotyping. We crossed myo-inositol oxygenase (MIOX4) over-expressers with two low-vitamin C mutants (vtc1-1 and vtc2-1) encoding enzymes involved in d-mannose/l-galactose route. The purpose of developing these crosses was to test MIOX4’s ability to restore the low AsA phenotype in mutants, and to assess the contribution of individual biosynthetic pathways to abiotic stress tolerance. We used a powerful high-throughput phenotyping platform for detailed phenotypic characterization of the Arabidopsis crosses with visible, fluorescence, near-infrared and infrared sensors. We combined digital phenotyping with photosynthetic parameters and soil water potential measurements. Our results show that MIOX4 is able to restore the AsA content of the mutants and the restored lines (vtc+MIOX4) show high AsA, enhanced growth rate, accumulate more biomass, and display healthier chlorophyll fluorescence and water content profiles compared to controls. Highlights Constitutive expression of a myo-inositol oxygenase restored vitamin C deficient (vtc mutants). The restored lines have elevated ascorbate content and are tolerant to abiotic stresses. Under normal and abiotic stress conditions, the restored lines have enhanced biomass and increased water retention.
Termination of DNA replication at Tus-ter barriers results in under-replication of template DNA

The complete and accurate duplication of genomic information is vital to maintain genome stability in all domains of life. In Escherichia coli, replication termination, the final stage of the duplication process, is confined to the ‘replication fork trap’ region by multiple unidirectional fork barriers formed by the binding of Tus protein to genomic ter sites. Termination typically occurs away from Tus-ter complexes, but they become part of the fork fusion process when a delay to one replisome allows the second to travel more than halfway around the chromosome. In this instance, replisome progression is blocked at the non-permissive interface of Tus-ter and termination occurs when a converging replisome meets the non-permissive interface. To investigate the consequences of replication fork fusion at Tus-ter complexes, we established a plasmid-based replication system where we could mimic the termination process at Tus-ter in vitro. We developed a termination mapping assay to measure leading strand replication fork progression and demonstrate that the DNA template is under-replicated by 15-24 bases when replication forks fuse at Tus-ter complexes. This gap could not be closed by the inclusion of lagging strand processing enzymes as well as several helicases that promote DNA replication. Our results indicate that accurate fork fusion at Tus-ter barriers requires further enzymatic processing, highlighting large gaps that still exist in our understanding of the final stages of chromosome duplication and the evolutionary advantage of having a replication fork trap.
A new murine Rpl5 (uL18) mutation provides a unique model of variably penetrant Diamond-Blackfan anemia

Ribosome dysfunction is implicated in multiple abnormal developmental and disease states in humans. Heterozygous germline mutations in genes encoding ribosomal proteins (RPs) are found in the majority of individuals with Diamond Blackfan anemia (DBA) while somatic mutations have been implicated in a variety of cancers and other disorders. Ribosomal protein-deficient animal models show variable phenotypes and penetrance, similar to human DBA patients. The spontaneous anemia remission observed in some DBA patients occurs via unknown mechanism(s) and has not been previously described in animal models. Here we characterized a novel ENU mouse mutant (Skax23m1Jus) with growth and skeletal defects, cardiac malformations and increased mortality. Following genetic mapping and whole exome sequencing, we identified an intronic Rpl5 mutation, which segregated with all affected mice. This mutation was associated with decreased ribosome generation, consistent with Rpl5 haploinsufficiency. Rpl5Skax23-Jus mutant animals had a profound delay in erythroid maturation and increased mortality at embryonic day E12.5, which improved by E14.5. Surviving mutant animals had a macrocytic anemia at birth as well as evidence of ventricular septal defect (VSD). Surviving adult and aged mice exhibited no hematopoietic defect or VSD. We propose that this novel Rpl5Skax23-Jus mutant mouse will be useful to study the factors influencing the variable penetrance and anemia remission that are observed in DBA.
Condensation of the Drosophila Nerve Cord is Oscillatory and depends on Coordinated Mechanical Interactions

During development, organs must form with precise shapes and sizes. Organ morphology is not always obtained through growth; a classic counterexample is condensation of the nervous system during Drosophila embryogenesis. The mechanics underlying such condensation remain poorly understood. Here, we combine in toto live-imaging, biophysical and genetic perturbations, and atomic force microscopy to characterize the condensation of the Drosophila ventral nerve cord (VNC) during embryonic development at both subcellular and tissue scales. This analysis reveals that condensation is not a unidirectional continuous process, but instead occurs through oscillatory contractions alternating from anterior and posterior ends. The VNC mechanical properties spatially and temporally vary during its condensation, and forces along its longitudinal axis are spatially heterogeneous, with larger ones exerted between neuromeres. We demonstrate that the process of VNC condensation is dependent on the coordinated mechanical activities of neurons and glia. Finally, we show that these outcomes are consistent with a viscoelastic model of condensation, which incorporates time delays due to the different time scales on which the mechanical processes act, and effective frictional interactions. In summary, we have defined the complex and progressive mechanics driving VNC condensation, providing insights into how a highly viscous tissue can autonomously change shape and size.
Visualization of SARS-CoV-2 Infection Scenes by ‘Zero-Shot’ Enhancements of Electron Microscopy Images

Electron microscopy (EM) recordings of infected tissues serve to diagnose a disease, and they can contribute to our understanding of infection processes. Consequently, a large number of EM images of the interaction of SARS-CoV-2 viruses with cells have been made available by numerous labs. However, due to EM recording techniques at high resolution, images of infection scenes are very noisy and they appear two dimensional (‘flat’). Current research consequently aims (A) at methods that can remove noise, and (B) at techniques that allow for recovering a 3D impression of the virus or its parts. Here we discuss a novel method which can recover a spatial impression of a whole infection scene at high resolution. In contrast to previous approaches which aim at the reconstruction of single spike proteins or a single virus, the here used method can be applied to a single noisy EM image of an infection scene. As one example image, we show a high resolution image of SARS-CoV-2 viruses in Vero cell cultures (Fig. 1). The method we use is based on probabilistic machine learning algorithms which can operate in a ‘zero-shot’ setting, i.e., in a setting when just one noisy image (and no large and clean image corpus) is available. The probabilistic method we apply can estimate non-noisy images by inferring first order statistics (pixel means) across image patches using a previously learned probabilistic image representation. Estimating higher order statistics and appropriately chosen probabilistic models then allow for the generation of images that enhance details and give a spatial impression of a full nanoscopic scene.
IFNγ and iNOS-Mediated Alterations in the Bone Marrow and Thymus and Its Impact on Mycobacterium avium-Induced Thymic Atrophy

Disseminated infection with the high virulence strain of Mycobacterium avium 25291 lead to progressive thymic atrophy. We previously uncovered that M. avium-induced thymic atrophy is due to increased levels of glucocorticoids synergizing with nitric oxide (NO) produced by interferon gamma (IFNγ) activated macrophages. Where and how these mediators are playing, was yet to be understood. We hypothesized that IFNγ and NO might be affecting bone marrow (BM) T cell precursors and/or T cell differentiation in the thymus. We show that M. avium infection causes a reduction on the percentage of lymphoid-primed multipotent progenitors (LMPP) and common lymphoid progenitors (CLP). Additionally, BM precursors from infected mice are unable to reconstitute thymi of RAGKO mice in an IFNγ-dependent way. Thymi from infected mice presents a NO-dependent inflammation. When transplanted under the kidney capsule of non-infected mice, thymic stroma from infected mice is unable to sustain T cell differentiation. Finally, we observed increased thymocyte death via apoptosis after infection, independent of both IFNγ and iNOS, and a decrease on activated caspase-3 positive thymocytes, that was not observed in the absence of iNOS expression. Together our data suggests that M. avium-induced thymic atrophy results from a combination of impairments, mediated by IFNγ and NO, affecting different steps of T cell differentiation from T cell precursor cells in the BM to the thymic stroma and thymocytes.