Miracle-dz/UniFAR-FTUs huggingface dataset:
Drosophila VCP/p97 Mediates Dynein-Dependent Retrograde Mitochondrial Motility in Axons

Valosin-containing protein (VCP), also called p97, is an evolutionarily conserved and ubiquitously expressed ATPase with diverse cellular functions. Dominant mutations in VCP are found in a late-onset multisystem degenerative proteinopathy. The neurological manifestations of the disorder include frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). In these patients, long motor neuron axons could be particularly susceptible to defects in axonal transport. However, whether VCP has a physiological function in maintaining axonal transport and whether this role is impaired by disease-causing mutations remains elusive. Here, by employing live-imaging methods in Drosophila larval axons and performing genetic interaction experiments, we discover that VCP regulates the axonal transport of mitochondria. Downregulation of VCP enhances the retrograde transport of mitochondria and reduces the density of mitochondria in larval axons. This unidirectional motility phenotype is rescued by removing one copy of the retrograde motor dynein heavy chain (DHC), or elevating Miro which facilitates anterograde mitochondrial movement by interacting with the anterograde motor kinesin heavy chain (KHC). Importantly, Miro upregulation also significantly improves ATP production of VCP mutant larvae. We investigate human VCP pathogenic mutations in our fly system. We find that expressing these mutations affects mitochondrial transport in the same way as knocking down VCP. Our results reveal a new role of VCP in mediating axonal mitochondrial transport, and provide evidence implicating impaired mitochondrial motility in the pathophysiology of VCP-relevant neurodegenerative diseases.
Genotypic and Phenotypic Characterization of Fecal Staphylococcus epidermidis Isolates Suggests Plasticity to Adapt to Different Human Body Sites

Staphylococcus epidermidis is a commensal species that has been increasingly identified as a nosocomial agent. Despite the interest, little is known about the ability of S. epidermidis isolates to adapt to different ecological niches through comparisons at genotype or phenotype levels. One niche where S. epidermidis has been reported is the human gut. Here, we present three S. epidermidis strains isolated from feces and show that they are not phylogenetically distinct from S. epidermidis isolated from other human body sites. Both gut and skin strains harbored multiple genes associated with biofilm formation and showed similar levels of biofilm formation on abiotic surfaces. High-throughput physiological tests using the BIOLOG technology showed no major metabolic differences between isolates from stool, skin, or cheese, while an isolate from bovine mastitis showed more phenotypic variation. Gut and skin isolates showed the ability to metabolize glycine-conjugated bile acids and to grow in the presence of bile, but the gut isolates exhibited faster anaerobic growth compared to isolates of skin origin.
Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.
Functional Identification and Structural Analysis of a New Lipoate Protein Ligase in Mycoplasma hyopneumoniae

Mycoplasma hyopneumoniae (M. hyopneumoniae) is the causative agent of pandemic pneumonia among pigs, namely, swine enzootic pneumonia. Although M. hyopneumoniae was first identified in 1965, little is known regarding its metabolic pathways, which might play a pivotal role during disease pathogenesis. Lipoate is an essential cofactor for enzymes important for central metabolism. However, the lipoate metabolism pathway in M. hyopneumoniae is definitely unclear. Here, we identified a novel gene, lpl, encoding a lipoate protein ligase in the genome of M. hyopneumoniae (Mhp-Lpl). This gene contains 1,032 base pairs and encodes a protein of 343 amino acids, which is between 7.5 and 36.09% identical to lipoate protein ligases (Lpls) of other species. Similar to its homologs in other species, Mhp-Lpl catalyzes the ATP-dependent activation of lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of M. hyopneumoniae GcvH (Mhp H) in vitro. Enzymatic and mutagenesis analysis indicate that residue K56 within the SKT sequence of Mhp H protein is the lipoyl moiety acceptor site. The three-dimensional structure showed typical lipoate protein ligase folding, with a large N-terminal domain and a small C-terminal domain. The large N-terminal domain is responsible for the full enzymatic activity of Mhp-Lpl. The identification and characterization of Mhp-Lpl will be beneficial to our understanding of M. hyopneumoniae metabolism. Summary Lipoic acid is an essential cofactor for the activation of some enzyme complexes involved in key metabolic processes. Lipoate protein ligases (Lpls) are responsible for the metabolism of lipoic acid. To date, little is known regarding the Lpls in M. hyopneumoniae. In this study, we identified a lipoate protein ligase of M. hyopneumoniae. We further analyzed the function, overall structure and ligand-binding site of this protein. The lipoate acceptor site on M. hyopneumoniae GcvH was also identified. Together, these findings reveal that Lpl exists in M. hyopneumoniae and will provide a basis for further exploration of the pathway of lipoic acid metabolism in M. hyopneumoniae.
Caring for Family Members With Alzheimer’s and Burnout Syndrome: Impairment of the Health of Housewives

Being a housewife may already be a psychosocial risk factor leading to chronic stress and burnout, and this may be aggravated when the housewife must also become the caregiver of a family member with Alzheimer’s. The burnout syndrome and how it can affect general health and the presence of emotional disorders were studied in housewives who were family caregivers of an Alzheimer’s patient. The sample selected was made up of 193 housewives, 96 of whom were also caregivers for a family member with Alzheimer’s. Sociodemographic measures used were the Maslach Burnout Inventory and The General Health Questionnaire. Burnout was found in a significant percentage of participants. Emotional exhaustion, effect on general health, and presence of emotional disorders were higher in caregivers. Emotional exhaustion, general health, and anxiety were more influential, while depersonalization affected the appearance of depressive symptoms more. Being a caregiver and emotional exhaustion appeared to be the best predictors of emotional disorders. It was confirmed that emotional exhaustion influenced appearance of anxiety and depression equally in both groups. In the case of caregivers, an exhaustion-illness spiral was produced. In this group, emotional exhaustion seemed to become more severe as a consequence of the presence of chronic illnesses, and possibly influence the number of hours spent on care and having children living at home. Future research should analyze in greater depth and in a larger sample, the role of these variables and widen the focus of attention to personal variables that could be acting as protective factors and could be subject to intervention. The discussion concludes with some actions that should be included in prevention programs for the groups studied.
Examining the Role of DNA Methylation in Transcriptomic Plasticity of Early Stage Sea Urchins: Developmental and Maternal Effects in a Kelp Forest Herbivore

Gene expression plasticity can confer physiological plasticity in response to the environment. However, whether epigenetic marks contribute to the dynamics of gene expression is still not well described in most marine invertebrates. Here, we explored the extent and molecular basis of intra- and intergenerational plasticity in the purple sea urchin, Strongylocentrotus purpuratus, by examining relationships between changes in DNA methylation, transcription, and embryo spicule length. Adult urchins were conditioned in the lab for 4 months to treatments that represent upwelling (∼1200 μatm pCO2, 13°C) and non-upwelling conditions (∼500 μatm pCO2, 17°C). Embryos spawned from conditioned adults were reared in either the same adult treatment or the reciprocal condition. Maternal conditioning resulted in significantly differentially methylated CpG sites and differential gene expression in embryos, despite no evidence of maternal effects on embryo spicule length. In contrast, conditions experienced during development resulted in significant differences in embryo spicule length. Intragenerational plasticity in spicule length was strongly correlated to transcriptomic plasticity, despite low levels of intragenerational plasticity in CpG methylation. We find plasticity in DNA methylation and gene expression in response to different maternal environments and these changes have similarities across broad functional groups of genes; yet exhibit little overlap on a gene-by-gene basis. Our results suggest that different forms of environmentally induced plasticity are observable across different time scales and that DNA methylation dynamics may be uncoupled from fast transcriptional responses to the environment and whole organism traits. Overall, this study illuminates the extent to which environmental differences can induce both intra- and intergenerational phenotypic plasticity in a common kelp forest herbivore.
Intrastriatal Administration of Exosome-Associated Pathological Alpha-Synuclein Is Not Sufficient by Itself to Cause Pathology Transmission

α-Synuclein (α-syn) has been genetically and biochemically linked to the pathogenesis of Parkinson’s disease (PD). There is accumulating evidence that misfolded α-syn species spread between cells in a prion-like manner and seed the aggregation of endogenous protein in the recipient cells. Exosomes have been proposed to mediate the transfer of misfolded α-syn and thus facilitate disease transmission, although the pathological mechanism remains elusive. Here, we investigated the seeding capacity of exosome-associated α-syn, in vivo. Disease-associated α-syn was present in exosome fractions isolated from transgenic A53T mouse brain. However, following intrastriatal injection of such exosomes in wild-type (wt) mice, we were not able to detect any accumulation of endogenous α-syn. In addition, recombinant fibrillar α-syn, when loaded to isolated brain exosomes, induced minor pathological α-syn brain accumulation at 7 months post injection. These data suggest that exosomes neutralize the effect of toxic α-syn species and raise additional questions on their paracrine modulatory role in disease transmission.
Genetic variation in an ephemeral mudflat species: The role of the soil seed bank and dispersal in river and secondary anthropogenic habitats

Abstract Many ephemeral mudflat species, which rely on a soil seed bank to build up the next generation, are endangered in their natural habitat due to the widespread regulation of rivers. The aim of the present study was to elucidate the role of the soil seed bank and dispersal for the maintenance of genetic diversity in populations of near‐natural river habitats and anthropogenic habitats created by traditional fish farming practices using Cyperus fuscus as a model. Using microsatellite markers, we found no difference in genetic diversity levels between soil seed bank and above‐ground population and only moderate differentiation between the two fractions. One possible interpretation is the difference in short‐term selection during germination under specific conditions (glasshouse versus field) resulting in an ecological filtering of genotypes out of the reservoir in the soil. River populations harbored significantly more genetic diversity than populations from the anthropogenic pond types. We suggest that altered levels and patterns of dispersal together with stronger selection pressures and historical bottlenecks in anthropogenic habitats are responsible for the observed reduction in genetic diversity. Dispersal is also supposed to largely prohibit genetic structure across Europe, although there is a gradient in private allelic richness from southern Europe (high values) to northern, especially north‐western, Europe (low values), which probably relates to postglacial expansion out of southern and/or eastern refugia.
From the Soft to the Hard: Changes in Microchemistry During Cell Wall Maturation of Walnut Shells

The walnut shell is a hard and protective layer that provides an essential barrier between the seed and its environment. The shell is based on only one unit cell type: the polylobate sclerenchyma cell. For a better understanding of the interlocked walnut shell tissue, we investigate the structural and compositional changes during the development of the shell from the soft to the hard state. Structural changes at the macro level are explored by X-ray tomography and on the cell and cell wall level various microscopic techniques are applied. Walnut shell development takes place beneath the outer green husk, which protects and delivers components during the development of the walnut. The cells toward this outer green husk have the thickest and most lignified cell walls. With maturation secondary cell wall thickening takes place and the amount of all cell wall components (cellulose, hemicelluloses and especially lignin) is increased as revealed by FTIR microscopy. Focusing on the cell wall level, Raman imaging showed that lignin is deposited first into the pectin network between the cells and cell corners, at the very beginning of secondary cell wall formation. Furthermore, Raman imaging of fluorescence visualized numerous pits as a network of channels, connecting all the interlocked polylobate walnut shells. In the final mature stage, fluorescence increased throughout the cell wall and a fluorescent layer was detected toward the lumen in the inner part. This accumulation of aromatic components is reminiscent of heartwood formation of trees and is suggested to improve protection properties of the mature walnut shell. Understanding the walnut shell and its development will inspire biomimetic material design and packaging concepts, but is also important for waste valorization, considering that walnuts are the most widespread tree nuts in the world.
Short-Duration Beta-Alanine Supplementation Did Not Prevent the Detrimental Effects of an Intense Preparatory Period on Exercise Capacity in Top-Level Female Footballers

Purpose: High-intensity activity is an important aspect of football performance during competitive match play. The aim of this study was to investigate the effect of beta-alanine supplementation throughout a short-duration intense football-specific training period prior to an international competition on measures of high-intensity running performance. Methods: Twenty-four elite international U20 female footballers (age 18 ± 1 y, height 1.67 ± 0.07 m, body mass 62.7 ± 7.4 kg) volunteered to perform the YoYo Intermittent Recovery Test Level 1 (YoYo IR1), the Running Anaerobic Sprint Test (RAST) and a 20-m maximal sprint test on two separate occasions, separated by 3 weeks of training and supplementation. Participants were randomly assigned to receive either 6.4 g·day−1 sustained-release beta-alanine (BA, N = 12) or an equivalent dose of maltodextrin (placebo, PL, N = 12) throughout a 3-week standardized training camp. Results: There was a main effect of group (P = 0.05) and time (P = 0.004) on YoYo IR1; overall values were lower in PL and distance covered was lower post- vs. pre-supplementation. There was no group × time interaction (P = 0.07). There was an effect of sprint number for RAST, but no further main effects and there were no effect for the 20-m sprint. Conclusions: Top-level female footballers involved in this intense 3-week training period prior to a competition worsened their high-intensity intermittent exercise capacity, and this negative result was not attenuated by a short-duration BA supplementation protocol throughout the same period. Further work is necessary to elucidate whether adapted training protocols and BA dosing regimens could lead to better results.
Coronavirus Pandemic (SARS-COV-2): Pre-Exercise Screening Questionnaire (PESQ) for Telepresential Exercise

The coronavirus pandemic (SARS-COV2) began in 2019 in Wuhan, Hubei Province, China (1). At the present moment, there is an exponential increase in both the number of people infected and the number of people dead. On the 31st of March, more than 30,000 people were reported to have died from COVID-19 (1). In fact, the World Health Organization (WHO) (1) announced on the 30th of January, 2020, that COVID-19 is a public health emergency of international interest, and, more recently, on March 11th, 2020, the WHO classified it as a pandemic (1). The pandemic process of infectious diseases occurs in three stages: (a) imported cases, (b) local transmission, and (c) sustained community transmission. In an attempt to contain the speed of dissemination of the new virus between and within territories, the WHO (2020) adopted several health measures, based both on the evolution of the disease and the analysis of cases that occurred between countries in Asia and Europe. Such measures have so far ranged from social isolation, surveillance of cases coming from epidemic areas, and increasing public awareness to infection control in health facilities (2). Among the health facilities that are very crowded and that can be a space of virus transmission, the gymnasium, and sports facilities stand out. Thus, in an attempt to reduce the scenarios of high virus transmission in Brazil, the Ministry of Health announced, on March 13th, guidelines to avoid the spread of the coronavirus, such as choosing to exercise outdoors instead of taking gymnastics classes in enclosed spaces (3). This article has aimed to discuss the need for screening for the practice of physical exercise and to present The Pre-Exercise Screening Questionnaire (PESQ) (Table 1) for screening and identify people that are in a suitable place to start exercising during the COVID-19 pandemic.
Apoplastic Hydrogen Peroxide in the Growth Zone of the Maize Primary Root. Increased Levels Differentially Modulate Root Elongation Under Well-Watered and Water-Stressed Conditions

Reactive oxygen species (ROS) can act as signaling molecules involved in the acclimation of plants to various abiotic and biotic stresses. However, it is not clear how the generalized increases in ROS and downstream signaling events that occur in response to stressful conditions are coordinated to modify plant growth and development. Previous studies of maize (Zea mays L.) primary root growth under water deficit stress showed that cell elongation is maintained in the apical region of the growth zone but progressively inhibited further from the apex, and that the rate of cell production is also decreased. It was observed that apoplastic ROS, particularly hydrogen peroxide (H2O2), increased specifically in the apical region of the growth zone under water stress, resulting at least partly from increased oxalate oxidase activity in this region. To assess the function of the increase in apoplastic H2O2 in root growth regulation, transgenic maize lines constitutively expressing a wheat oxalate oxidase were utilized in combination with kinematic growth analysis to examine effects of increased apoplastic H2O2 on the spatial pattern of cell elongation and on cell production in well-watered and water-stressed roots. Effects of H2O2 removal (via scavenger pretreatment) specifically from the apical region of the growth zone were also assessed. The results show that apoplastic H2O2 positively modulates cell production and root elongation under well-watered conditions, whereas the normal increase in apoplastic H2O2 in water-stressed roots is causally related to down-regulation of cell production and root growth inhibition. The effects on cell production were accompanied by changes in spatial profiles of cell elongation and in the length of the growth zone. However, effects on overall cell elongation, as reflected in final cell lengths, were minor. These results reveal a fundamental role of apoplastic H2O2 in regulating cell production and root elongation in both well-watered and water-stressed conditions.
Development of a Digital RT-PCR Method for Absolute Quantification of Bluetongue Virus in Field Samples

Bluetongue (BT) is a major Office International des Epizooties (OIE)-listed disease of wild and domestic ruminants caused by several serotypes of Bluetongue virus (BTV), a virus with a segmented dsRNA genome belonging to the family Reoviridae, genus Orbivirus. BTV is transmitted through the bites of Culicoides midges. The aim of this study was to develop a new method for quantification of BTV Seg-10 by droplet digital RT-PCR (RTdd-PCR), using nucleic acids purified from complex matrices such as blood, tissues, and midges, that notoriously contain strong PCR inhibitors. First, RTdd-PCR was optimized by using RNAs purified from serially 10-fold dilutions of a BTV-1 isolate (105.43TCID50/ml up to 10−0.57 TCID50/ml) and from the same dilutions spiked into fresh ovine EDTA-blood and spleen homogenate. The method showed a good degree of linearity (R2 ≥ 0.995). The limit of detection (LoD) and the limit of quantification (LoQ) established were 10−0.67TCID50/ml (0.72 copies/μl) and 100.03TCID50/ml (3.05 copies/μl) of BTV-1, respectively. Second, the newly developed test was compared, using the same set of biological samples, to the quantitative RT-PCR (RT-qPCR) detecting Seg-10 assay widely used for the molecular diagnosis of BTV from field samples. Results showed a difference mean of 0.30 log between the two assays with these samples (p < 0.05). Anyway, the analysis of correlation demonstrated that both assays provided similar measurements with a very close agreement between the systems.