Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleo-cytoplasmic shuttling of splicing factor SRSF1 is required for development and cilia function

Shuttling RNA-binding proteins coordinate nuclear and cytoplasmic steps of gene expression. The SR family proteins regulate RNA splicing in the nucleus and a subset of them, including SRSF1, shuttles between the nucleus and cytoplasm affecting post-splicing processes. However, the physiological significance of this remains unclear. Here, we used genome editing to knock-in a nuclear retention signal (NRS) in Srsf1 to create a mouse model harboring an SRSF1 protein that is retained exclusively in the nucleus. Srsf1NRS/NRS mutants displayed small body size, hydrocephalus and immotile sperm, all traits associated with ciliary defects. We observed reduced translation of a subset of mRNAs and decreased abundance of proteins involved in multiciliogenesis, with disruption of ciliary ultrastructure and motility in cells derived from this mouse model. These results demonstrate that SRSF1 shuttling is used to reprogram gene expression networks in the context of high cellular demands, as observed here, during motile ciliogenesis.
Proximity proteomics reveal EPH tyrosine kinase receptors’ regulation of cell polarity and identify Par3 scaffold protein as a novel effector of EPH signaling

The EPH family is the largest among receptor tyrosine kinases (RTKs) in humans. In contrast to other RTKs, EPH receptors (EPHRs) cognate ligands, ephrins, are tethered to the cell surface. This results in EPHRs-ephrin signaling being mainly involved in short-range cell-cell communication events that regulate cell adhesion, migration and tissue boundary formation. Although EPHRs functions have been broadly studied, the molecular mechanisms by which they mediate these processes are far from being understood. To address this question, we sought to identify new downstream effector proteins for EPHRs and to determine their requirement for EPHR-regulated functions. To unravel EPHR-associated signaling complexes under native conditions, we applied a mass spectrometry-based approach, namely BioID proximity labeling. We obtained a composite proximity network from EPHA4, -B2, -B3 and -B4 receptors that comprises 395 proteins, most of which were not previously linked to EPH signaling. A gene ontology and pathway term analysis of the candidates common to at least three EPHR proximity networks highlighted cell polarity as a process not previously linked with EPH signaling. We found that EPHA1 and EPHB4 expression is restricted to the basal and lateral membrane domains in polarized Caco-2 3D spheroidal cell cultures. We further discovered that their depletion impairs spheroids morphogenesis. In parallel, we examined the contribution of a number of candidates, selected from EPHR proximity networks, via loss-of-function in an EPHR-dependent cell segregation assay. We showed that depletion of the signaling scaffold Par3 blocks cell sorting. We also delineated a signalling complex involving C-terminal SRC kinase (CSK), whose recruitment to Par3 complexes is dependent on EPHR signals. Our work sheds light on EPHR signaling networks and provides a better understanding of the mechanisms by which EPHRs signal at the membrane to contribute to the establishment of cellular phenotypes.
Soil characteristics constrain the response of bacterial and fungal communities and hydrocarbon degradation genes to phenanthrene soil contamination and phytoremediation with poplars

Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhance natural microbial degradation in soils. However, little is known about how this initial microbiota influences the rhizodegradation outcome in a context of different soil microbiotas. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this hypothesis, we planted (P) or not (NP) balsam poplars (Populus balsamifera) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg-1 of phenanthrene (PHE). The DNA from the rhizosphere of the P and the bulk soil of the NP pots was extracted and the bacterial genes encoding for the 16S rRNA, the PAH ring-hydroxylating dioxygenase alpha subunits (PAH-RHDα) of gram-positive (GP) and gram-negative (GN) bacteria, and the fungal ITS region were sequenced to characterize the microbial communities. and the abundance of the PAH-RHDα genes were also quantified by real-time quantitative PCR. Plant presence had a significant effect on PHE degradation only in the forest soil, whereas both NP and P agricultural soils degraded the same amount of PHE. Bacterial communities were principally affected by the soil type, and upon contamination the dominant PAH degrading community was similarly constrained by soil type. Our results highlight the crucial importance of soil microbial and physicochemical characteristics in the outcome of rhizoremediation.
No evidence for cross-contextual consistency in spatial learning and behavioural flexibility in a passerine

Although the evolution of cognitive differences among species has long been of interest in ecology, whether natural selection acts on cognitive processes within populations has only begun to receive similar attention. One of the key challenges is to understand how consistently cognitive traits within any one domain are expressed over time and across different contexts, as this has direct implications for the way in which selection might act on this variation. Animal studies typically measure a cognitive domain using only one task in one context, and assume that this captures the likely expression of that domain in different contexts. This deficit is not surprising because, from an ecologist’s perspective, cognitive tasks are notoriously laborious to employ, and for design reasons most tasks can only be deployed in a specific context. Thus our knowledge of whether individual differences in cognitive abilities are consistent across contexts is limited. Using a wild population of great tits (Parus major) we characterised consistency of two cognitive abilities, each in two different contexts: 1) spatial learning at two different spatial scales, and 2) behavioural flexibility as both performance in a detour reaching task and reversal learning in a spatial task. We found no evidence of a correlation between the two spatial learning speeds, or between the two measures of behavioural flexibility. This suggests that cognitive performance is highly plastic and sensitive to differences across tasks, or that variants of these well-known tasks may tap into different combinations of both cognitive and non-cognitive mechanisms, or that they simply do not adequately measure each putative cognitive domain. Our results highlight the challenges of developing standardised cognitive assays to explain natural behaviour and to understand the selective consequences of that variation.
Visualizing Borrelia burgdorferi infection using a small molecule imaging probe

In vivo diagnostic imaging of bacterial infections is currently reliant on targeting their metabolic pathways, an ineffective method to identify microbial species with low metabolic activity. Here we establish HS-198 as a small molecule-fluorescent conjugate that selectively targets the highly conserved bacterial protein, HtpG (High temperature protein G), within B. burgdorferi, the bacteria responsible for Lyme Disease. We describe the use of HS-198 to target morphologic forms of B. burgdorferi in both the logarithmic growth phase and the metabolically dormant stationary phase. Furthermore, in a murine infection model, systemically injected HS-198 identified B. burgdorferi as revealed by imaging in post necropsy tissue sections. These findings demonstrate how small molecule probes directed at conserved bacterial protein targets can function to identify the microbe using non-invasive imaging and potentially as scaffolds to deliver antimicrobial agents to the pathogen.
Conserved cysteines in titin sustain the mechanical function of cardiomyocytes

The protein titin determines cardiomyocyte contraction and truncating variants in the titin gene (TTN) are the most common cause of dilated cardiomyopathy (DCM). Different to truncations, missense variants in TTN are currently classified as variants of uncertain significance due to their high frequency in the population and the absence of functional annotation. Here, we report the regulatory role of conserved, mechanically active titin cysteines, which, contrary to current views, we uncover to be reversibly oxidized in basal conditions leading to isoform- and force-dependent modulation of titin stiffness and dynamics. Building on our functional studies, we demonstrate that missense mutations targeting a conserved titin cysteine alter myocyte contractile function and cause DCM in humans. Our findings have a direct impact on genetic counselling in clinical practice. One sentence summary Mutations targeting cysteines key to the mechanoredox control of titin cause human dilated cardiomyopathy
Exploratory polarization facilitates mating partner selection in Saccharomyces cerevisiae

Yeast decode pheromone gradients to locate mating partners, providing a model for chemotropism. How yeast polarize toward a single partner in crowded environments is unclear. Initially, cells often polarize in unproductive directions, but then they relocate the polarity site until two partners’ polarity sites align, whereupon the cells “commit” to each other by stabilizing polarity to promote fusion. Here we address the role of the early mobile polarity sites. We found that commitment by either partner failed if just one partner was defective in generating, orienting, or stabilizing its mobile polarity sites. Mobile polarity sites were enriched for pheromone receptors and G proteins, and we suggest that such sites engage in an exploratory search of the local pheromone landscape, stabilizing only when they detect elevated pheromone levels. Mobile polarity sites were also enriched for pheromone secretion factors, and simulations suggest that only focal secretion at polarity sites would produce high pheromone concentrations at the partner’s polarity site, triggering commitment.
An evolutionarily acquired microRNA shapes development of mammalian cortical projections

Significance The mammalian central nervous system contains unique projections from the cerebral cortex thought to underpin complex motor and cognitive skills, including the corticospinal tract and corpus callosum. The neurons giving rise to these projections—corticospinal and callosal projection neurons—develop from the same progenitors, but acquire strikingly different fates. The broad evolutionary conservation of known genes controlling cortical projection neuron fates raises the question of how the more narrowly conserved corticospinal and callosal projections evolved. We identify a microRNA cluster selectively expressed by corticospinal projection neurons and exclusive to placental mammals. One of these microRNAs promotes corticospinal fate via regulation of the callosal gene LMO4, suggesting a mechanism whereby microRNA regulation during development promotes evolution of neuronal diversity. The corticospinal tract is unique to mammals and the corpus callosum is unique to placental mammals (eutherians). The emergence of these structures is thought to underpin the evolutionary acquisition of complex motor and cognitive skills. Corticospinal motor neurons (CSMN) and callosal projection neurons (CPN) are the archetypal projection neurons of the corticospinal tract and corpus callosum, respectively. Although a number of conserved transcriptional regulators of CSMN and CPN development have been identified in vertebrates, none are unique to mammals and most are coexpressed across multiple projection neuron subtypes. Here, we discover 17 CSMN-enriched microRNAs (miRNAs), 15 of which map to a single genomic cluster that is exclusive to eutherians. One of these, miR-409-3p, promotes CSMN subtype identity in part via repression of LMO4, a key transcriptional regulator of CPN development. In vivo, miR-409-3p is sufficient to convert deep-layer CPN into CSMN. This is a demonstration of an evolutionarily acquired miRNA in eutherians that refines cortical projection neuron subtype development. Our findings implicate miRNAs in the eutherians’ increase in neuronal subtype and projection diversity, the anatomic underpinnings of their complex behavior.
Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – A cross-sectional study

Background Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. We estimate the seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar. Methods 2906 persons >18 years of age selected from hospital visitors across District Srinagar participated in the study. We tested samples for the presence of SARS-CoV-2 specific IgG antibodies using a chemiluminescent microparticle immunoassay-based serologic test. Results Age- and gender-standardized seroprevalence was 3.6% (95% CI 2.9% to 4.3%). Age 30-69 years, a recent history of symptoms of an influenza-like-illness, and a history of being placed under quarantine were significantly related to higher odds of the presence of SARS-CoV-2 specific IgG antibodies. The estimated number of SARS-CoV-2 infections during the two weeks preceding the study, adjusted for test performance, was 32602 with an estimated (median) infection-to-known-case ratio of 46 (95% CI 36 to 57). Conclusions The seroprevalence of SARS-CoV-2 specific IgG antibodies is low in the District. A large proportion of the population is still susceptible to the infection. A sizeable number of infections remain undetected, and a substantial proportion of people with symptoms compatible with COVID-19 are not tested.
Forward genetics in Wolbachia: Regulation of Wolbachia proliferation by the amplification and deletion of an addictive genomic island

Wolbachia is one of the most prevalent bacterial endosymbionts, infecting approximately 40% of terrestrial arthropod species. Wolbachia is often a reproductive parasite but can also provide fitness benefits to its host, as for example protection against viral pathogens. This protective effect is currently being applied to fight arboviruses transmission by releasing Wolbachia-transinfected mosquitoes. Titre regulation is a crucial aspect of Wolbachia biology. Higher titres can lead to stronger phenotypes and fidelity of transmission but can have a cost to the host. Since Wolbachia is maternally transmitted, its fitness depends on host fitness, and, therefore, its cost to the host needs to be controlled. Understanding this and other aspects of Wolbachia biology has been hampered by the lack of genetic tools. Here we developed a new forward genetic screen to identify Wolbachia over-proliferative mutant variants. We characterized in detail two of these new mutants, wMelPop2 and wMelOctoless, and show that the amplification or loss of the Octomom genomic region causes their over-proliferation. These results confirm previous data and expand on the complex role of this genomic region in the control of Wolbachia proliferation. Both new mutants shorten the host lifespan and increase antiviral protection. Moreover, we show that Wolbachia proliferation rate in Drosophila melanogaster depends on the interaction between Octomom copy number, the host developmental stage, and temperature. Our analysis also suggests that the life shortening phenotype and antiviral protection of Wolbachia are dependent on related, but different, properties of the endosymbiont; the rate of proliferation and the titres at time of infection, respectively. Altogether, we demonstrate the feasibility of a novel and unbiased experimental approach to study Wolbachia biology, which can be further adapted to characterize other genetically intractable bacterial endosymbionts.
Taxonomic Status of Roe Deer in Northeastern China Based on Mitochondrial DNA Sequences

Roe deer play an important ecological role as a main food resource for large carnivores and is an important game species. They are distributed widely across northeastern and northwestern regions of China. However,the taxonomic status of Chinese roe deer is still in dispute because there have been no genetic analyses of the phylogenetic relationship of Chinese roe deer to other populations. Mitochondrial DNA (mtDNA) is a highly sensitive marker suitable for studies of closely related taxa or populations because it is maternally inherited and has a relatively rapid rate of change . We utilized PCR technique and DNA sequencing to analyze portions of mtDNA Cyt b gene (415 bp) and parts of the mtDNA control region sequence(764 bp) to assess the taxonomic status of roe deer in northeastern China. Specimen collections were made from Wanda Mountains (46°15′N, 133°16′E), Lesser Khinghan Mountains (47°10′N, 128°54′E), Great Khinghan Mountains (52°10′N, 123°15′E), Sanjiang Wetland Nature Reserve (46°30′N,133°15′E), and Jilin Xianghai Wetland Nature Reserve (45°40′N, 122°20′E). We compared results of our sequencing to those derived from European and Siberian roe deer (from GenBank) to assess their phylogenetic relationship. The average divergence of Cyt b gene and the control region sequence between roe deer from northeastern China and Europe was 4.12% and 4.89% respectively, indicating sufficient variation to consider them separate species. However, divergence between northeastern Chinese and Siberian roe deer was only 1.61% (Cyt b) and 2.44% (control region). Considering similarities in body size and antler characteristics, we believe roe deer of northeastern China and Siberia should be regarded as a single species, distinct from European roe deer. We propose that the scientific name of roe deer in northeastern China should be changed to Capreolus pygargus from Capreolus capreolus. Assuming the cytochrome b gene diverged at a rate of 0.02 nucleotide distance/million years, we infer that roe deer from northeastern China diverged from the European species about 2 million years ago, while divergence with Siberian roe deer was only about 800 thousand years ago. Additional specimens from other localities in China are needed for further research of the taxonomic status of roe deer in China.
The deacylase SIRT5 supports melanoma viability by regulating chromatin dynamics

Cutaneous melanoma remains the most lethal skin cancer, and ranks third among all malignancies in terms of years of life lost. Despite the advent of immune checkpoint and targeted therapies, only roughly half of patients with advanced melanoma achieve a durable remission. SIRT5 is a member of the sirtuin family of protein deacylases that regulate metabolism and other biological processes. Germline Sirt5 deficiency is associated with mild phenotypes in mice. Here we show that SIRT5 is required for proliferation and survival across all cutaneous melanoma genotypes tested, as well as uveal melanoma, a genetically distinct melanoma subtype that arises in the eye, and is incurable once metastatic. Likewise, SIRT5 is required for efficient tumor formation by melanoma xenografts, and in an autochthonous mouse Braf;Pten-driven melanoma model. Via metabolite and transcriptomic analyses, we find that SIRT5 is required to maintain histone acetylation and methylation levels in melanoma cells, thereby promoting proper gene expression. SIRT5-dependent genes notably include MITF, a key lineage-specific survival oncogene in melanoma, and the c-MYC proto-oncogene. SIRT5 may represent a novel, druggable genotype-independent addiction in melanoma.
Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics

Serving a robust platform for reverse genetics enabling the in vivo study of gene functions primarily in enterobacteriaceae, recombineering -or recombination-mediated genetic engineering-represents a powerful and relative straightforward genetic engineering tool. Catalyzed by components of bacteriophage-encoded homologous recombination systems and only requiring short ∼40–50 base homologies, the targeted and precise introduction of modifications (e.g., deletions, knockouts, insertions and point mutations) into the chromosome and other episomal replicons is empowered. Furthermore, by its ability to make use of both double- and single-stranded linear DNA editing substrates (e.g., PCR products or oligonucleotides, respectively), lengthy subcloning of specific DNA sequences is circumvented. Further, the more recent implementation of CRISPR-associated endonucleases has allowed for more efficient screening of successful recombinants by the selective purging of non-edited cells, as well as the creation of markerless and scarless mutants. In this review we discuss various recombineering strategies to promote different types of gene modifications, how they are best applied, and their possible pitfalls.
Communication Development and Verification for Python-Based Machine Learning Models for Real-Time Hybrid Simulation

Hybrid simulation (HS) combines analytical modeling with experimental testing to provide a better understanding of both structural elements and entire systems while keeping cost-effective solutions. However, extending real-time HS (RTHS) to bigger problems becomes challenging when the analytical models get more complex. On the other hand, using machine learning (ML) techniques in solving engineering problems across different disciplines keeps evolving and likewise is a promising resource for structural engineering. The main goal of this study is to explore the validity of ML models for conducting RTHS and specifically introduce and validate the necessary communication schemes to achieve this goal. A preliminary study with a simplified linear regression ML model that can be readily implemented in Simulink is presented first to introduce the idea of using metamodels as analytical substructures. However, for ML, commonly used platforms for RTHS such as Simulink and MATLAB have limited capacity when compared to Python for instance. Thus, the main focus of this study was to introduce Python-based advanced ML models for RTHS analytical substructures. Deep long short-term memory networks in Python were considered for advanced metamodeling for RTHS tests. The performance of Python can be enhanced by running the models using high-performance computers, which was also considered in this study. Several RTHS tests were successfully conducted at the University of Nevada, Reno, with Python-based ML algorithms that were run from both local PC and a cluster. The tests were validated through comparisons with the pure analytical solutions obtained from finite element models. The study also explored the idea of embedding the delay compensators within the ML model for RTHS.