Saccharomycopsis praedatoria sp. nov., a predacious yeast isolated from soil and rotten wood in an Amazonian rainforest biome.

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589T. The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

A genome-wide atlas of human cell morphology.

A key challenge of the modern genomics era is developing data-driven representations of gene function. Here, we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-scale genotype-phenotype maps comprising >20,000 single-gene CRISPR-Cas9-based knockout experiments in >30 million cells. Our optical pooled cell profiling approach (PERISCOPE) combines a de-stainable high-dimensional phenotyping panel (based on Cell Painting1,2) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This approach provides high-dimensional phenotypic profiles of individual cells, while simultaneously enabling interrogation of subcellular processes. Our atlas reconstructs known pathways and protein-protein interaction networks, identifies culture media-specific responses to gene knockout, and clusters thousands of human genes by phenotypic similarity. Using this atlas, we identify the poorly-characterized disease-associated transmembrane protein TMEM251/LYSET as a Golgi-resident protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes, showing the power of these representations. In sum, our atlas and screening technology represent a rich and accessible resource for connecting genes to cellular functions at scale.

Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review.

A set of diseases caused by fungi and oomycetes are responsible for large losses in annual world cocoa production. Managing the impact caused by these diseases is very complex because a common solution has yet to be found for different pathogens. In this context, the systematic knowledge of Theobroma cacao L. pathogens' molecular characteristics may help researchers understand the possibilities and limitations of cocoa disease management strategies. This work systematically organized and summarized the main findings of omics studies of T. cacao eukaryotic pathogens, focusing on the plant-pathogen interaction and production dynamics. Using the PRISMA protocol and a semiautomated process, we selected papers from the Scopus and Web of Science databases and collected data from the selected papers. From the initial 3169 studies, 149 were selected. The first author's affiliations were mostly from two countries, Brazil (55%) and the USA (22%). The most frequent genera were Moniliophthora (105 studies), Phytophthora (59 studies) and Ceratocystis (13 studies). The systematic review database includes papers reporting the whole-genome sequence from six cocoa pathogens and evidence of some necrosis-inducing-like proteins, which are common in T. cacao pathogen genomes. This review contributes to the knowledge about T. cacao diseases, providing an integrated discussion of T. cacao pathogens' molecular characteristics, common mechanisms of pathogenicity and how this knowledge is produced worldwide.

Salivary protein candidates for biomarkers of oral disorders in people with a crack cocaine use disorder.

The use of cocaine and its main derivative, crack, can cause some systemic effects that may lead to the development of some oral disorders. To assess the oral health of people with a crack cocaine use disorder and identify salivary protein candidates for biomarkers of oral disorders. A total of 40 volunteers hospitalized for rehabilitation for crack cocaine addiction were enrolled; nine were randomly selected for proteomic analysis. Intraoral examination, report of DMFT, gingival and plaque index, xerostomia, and non-stimulated saliva collection were performed. A list of proteins identified was generated from the UniProt database and manually revised. The mean age (n=40) was 32 (±8.88; 18-51) years; the mean DMFT index was 16±7.70; the mean plaque and gingival index were 2.07±0.65 and 2.12±0.64, respectively; and 20 (50%) volunteers reported xerostomia. We identified 305 salivary proteins (n=9), of which 23 were classified as candidate for biomarkers associated with 14 oral disorders. The highest number of candidates for biomarkers was associated with carcinoma of head and neck (n=7) and nasopharyngeal carcinoma (n=7), followed by periodontitis (n=6). People with a crack cocaine use disorder had an increased risk of dental caries and gingival inflammation; less than half had oral mucosal alterations, and half experienced xerostomia. As possible biomarkers for 14 oral disorders, 23 salivary proteins were identified. Oral cancer and periodontal disease were the most often associated disorders with biomarkers.

A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes.

Recent large-scale genomic association studies found evidence for a genetic link between increased risk of type 2 diabetes and decreased risk for adiposity-related traits, reminiscent of metabolically obese normal weight (MONW) association signatures. However, the target genes and cellular mechanisms driving such MONW associations remain to be identified. Here, we systematically identify the cellular programmes of one of the top-scoring MONW risk loci, the 2q24.3 risk locus, in subcutaneous adipocytes. We identify a causal genetic variant, rs6712203, an intronic single-nucleotide polymorphism in the COBLL1 gene, which changes the conserved transcription factor motif of POU domain, class 2, transcription factor 2, and leads to differential COBLL1 gene expression by altering the enhancer activity at the locus in subcutaneous adipocytes. We then establish the cellular programme under the genetic control of the 2q24.3 MONW risk locus and the effector gene COBLL1, which is characterized by impaired actin cytoskeleton remodelling in differentiating subcutaneous adipocytes and subsequent failure of these cells to accumulate lipids and develop into metabolically active and insulin-sensitive adipocytes. Finally, we show that perturbations of the effector gene Cobll1 in a mouse model result in organismal phenotypes matching the MONW association signature, including decreased subcutaneous body fat mass and body weight along with impaired glucose tolerance. Taken together, our results provide a mechanistic link between the genetic risk for insulin resistance and low adiposity, providing a potential therapeutic hypothesis and a framework for future identification of causal relationships between genome associations and cellular programmes in other disorders.

The Whole Genome of Colletes collaris (Hymenoptera: Colletidae): An Important Step in Comparative Genomics of Cellophane Bees.

Gaining knowledge on bees is of the utmost importance due to the paramount role that they play in angiosperm pollination. Herein, we provide the first genome assembly of Colletes collaris, a pan-Eurasian cellophane bee. We sequenced 50.53 Gbp of long-read data plus 57.36 Gbp of short-read data in Oxford Nanopore Technologies and Illumina platforms, respectively. The genome assembly consisted of 374.75 Mbp distributed across 374 contigs, with L50 and N50 of 9 and 8.96 Mbp, respectively. We predicted the genome to comprise 20,399 protein-coding genes, 467,947 repeats, and 4,315 non-coding RNA genes. The transcriptome and mitochondrial genome of the species were also assembled. Gene family analysis with 15 insect species identified 14,417 families, 9,517 of them found in C. collaris. A dated phylogenomic analysis revealed high numbers of orthogroups experiencing rapid evolution within Colletes.

The Effect of Magneto-Priming on the Physiological Quality of Soybean Seeds.

Microwaves have been applied to the drying of seeds of several species due to their maintenance of the quality of the seeds and reduction of time and costs. However, few is known about the effect of microwaves on the increase of the physiological quality of soybean seeds and especially their effects on longevity. Therefore, the use of microwaves as magneto-priming in soybean seeds was the object of study in this work. For this purpose, two soybean cultivars were selected and submitted to the ultra-high frequency (UHF) microwave exposure of 2.45 GHz, in the wavelength of 11 cm, and power of 0.2 W/g, for 15 min. The results showed that this condition of exposure to the microwave brought benefits in both cultivars after treatment. Incremental improvements were observed in the germinability indexes, the seedling length, the water absorption by the seeds, the fresh mass, dry mass, and longevity. The genes related to seed germination and longevity showed superior expression (HSFA3, HSP21, HSP17.6b, EXP, ABI3) with magneto-priming treatment. The data found ensure the use of the technique as a viable option for pre-treatment as magneto-priming in soybean seeds in order to improve seed quality.

Unique ligand and kinase-independent roles of the insulin receptor in regulation of cell cycle, senescence and apoptosis.

Insulin acts through the insulin receptor (IR) tyrosine kinase to exert its classical metabolic and mitogenic actions. Here, using receptors with either short or long deletion of the ß-subunit or mutation of the kinase active site (K1030R), we have uncovered a second, previously unrecognized IR signaling pathway that is intracellular domain-dependent, but ligand and tyrosine kinase-independent (LYK-I). These LYK-I actions of the IR are linked to changes in phosphorylation of a network of proteins involved in the regulation of extracellular matrix organization, cell cycle, ATM signaling and cellular senescence; and result in upregulation of expression of multiple extracellular matrix-related genes and proteins, down-regulation of immune/interferon-related genes and proteins, and increased sensitivity to apoptosis. Thus, in addition to classical ligand and tyrosine kinase-dependent (LYK-D) signaling, the IR regulates a second, ligand and tyrosine kinase-independent (LYK-I) pathway, which regulates the cellular machinery involved in senescence, matrix interaction and response to extrinsic challenges.

Salivary protein candidates for biomarkers of oral disorders in people with a crack cocaine use disorder

Abstract The use of cocaine and its main derivative, crack, can cause some systemic effects that may lead to the development of some oral disorders. Objective To assess the oral health of people with a crack cocaine use disorder and identify salivary protein candidates for biomarkers of oral disorders. Methodology A total of 40 volunteers hospitalized for rehabilitation for crack cocaine addiction were enrolled; nine were randomly selected for proteomic analysis. Intraoral examination, report of DMFT, gingival and plaque index, xerostomia, and non-stimulated saliva collection were performed. A list of proteins identified was generated from the UniProt database and manually revised. Results The mean age (n=40) was 32 (±8.88; 18-51) years; the mean DMFT index was 16±7.70; the mean plaque and gingival index were 2.07±0.65 and 2.12±0.64, respectively; and 20 (50%) volunteers reported xerostomia. We identified 305 salivary proteins (n=9), of which 23 were classified as candidate for biomarkers associated with 14 oral disorders. The highest number of candidates for biomarkers was associated with carcinoma of head and neck (n=7) and nasopharyngeal carcinoma (n=7), followed by periodontitis (n=6). Conclusions People with a crack cocaine use disorder had an increased risk of dental caries and gingival inflammation; less than half had oral mucosal alterations, and half experienced xerostomia. As possible biomarkers for 14 oral disorders, 23 salivary proteins were identified. Oral cancer and periodontal disease were the most often associated disorders with biomarkers.

Quality of cowpea seeds: A food security strategy in the tropical environment.

What is the relation between seed quality and food security? Here we built a summary diagram that links the development stages of the seeds with their potential of providing grain yield. This idea was tested using cowpea as a model crop, grown in a tropical environment. Initially, seed quality attributes such as water content, dry weight, germination, vigor, and longevity were characterized during seed development. With this, we were able to elucidate at which point the late maturation phase and the acquisition of seed with superior physiological quality starts. From these data, the proposed summary diagram highlighted the seed quality as a technological basis for generating a more productive plant community. It also showed that only seeds with a high-quality profile have a better chance to establishment in an increasingly challenging agricultural environment. Overall, we bring the concept that cowpea seeds with superior quality besides being the essential input for tropical agriculture is also a strategy that can contribute food security.

Liming enhances longevity of wheat seeds produced in acid soils.

The environment where plants grow, such as acidic soils, interferes with the nutrient concentration and physiological quality of seeds. This hypothesis was tested using wheat seeds as a model crop, grown in a tropical soil with and without lime application for twelve years. Here we show that lime provides remarkable enhancements in soil chemistry and seed composition, without altering the seed's germination and vigor. Also, it favors the production of seeds with additional molecular mechanisms that extend their longevity. Our results indicate that the application of lime mitigates acidity in tropical soils and ensures the production of seeds with enhanced chemical composition and longer life span.

Apolipoprotein C3 and circulating mediators of preadipocyte proliferation in states of lipodystrophy.

Adipogenesis is a complex process controlled by intrinsic and extrinsic factors that regulate preadipocyte proliferation, adipogenic capacity and maturation of metabolic function. Here we show that insulin and IGF-1 receptors are essential for mature adipocyte survival and that deletion of both IR and IGF1R specifically in fat using a tamoxifen inducible-AdipoQ-Cre (Ai-DKO) leads to rapid and severe loss of adipocytes in all depots, associated with a metabolic syndrome characterized by hypertriglyceridemia, hyperglycemia, hyperinsulinemia, fatty liver, and pancreatic beta cell proliferation. In this model, this pathological phenotype reverses over a few weeks, in large part, due to preadipocyte proliferation and adipose tissue regeneration. Incubation of preadipocytes with serum from the Ai-DKO mice in vitro stimulates cell proliferation, and this effect can be mimicked by conditioned media from liver slices of Ai-DKO mice, but not by media of cultured Ai-DKO adipocytes, indicating a hepatic origin of the growth factor. Proteomic analysis of serum reveals apolipoprotein C3 (APOC3), a protein secreted by liver, as one of the most upregulated proteins in the Ai-DKO mice. In vitro, purified and delipidated APOC3 stimulates preadipocyte proliferation, however, knockdown of hepatic APOC3 in vivo in Ai-DKO mice is not sufficient to block adipose regeneration. Thus, lipodystrophy is associated with presence of increased preadipocyte-stimulating growth factors in serum. Our study indicates that APOC3 is one contributing factor to preadipocyte proliferation, however, other still-unidentified circulating growth factors are also likely present in Ai-DKO mice. Identification of these factors may provide a new approach to regulation of adipose mass in health and disease.

A Reliable Method to Recognize Soybean Seed Maturation Stages Based on Autofluorescence-Spectral Imaging Combined With Machine Learning Algorithms.

In recent years, technological innovations have allowed significant advances in the diagnosis of seed quality. Seeds with superior physiological quality are those with the highest level of physiological maturity and the integration of rapid and precise methods to separate them contributes to better performance in the field. Autofluorescence-spectral imaging is an innovative technique based on fluorescence signals from fluorophores present in seed tissues, which have biological implications for seed quality. Thus, through this technique, it would be possible to classify seeds in different maturation stages. To test this, we produced plants of a commercial cultivar (MG/BR 46 "Conquista") and collected the seeds at five reproductive (R) stages: R7.1 (beginning of maturity), R7.2 (mass maturity), R7.3 (seed disconnected from the mother plant), R8 (harvest point), and R9 (final maturity). Autofluorescence signals were extracted from images captured at different excitation/emission combinations. In parallel, we investigated physical parameters, germination, vigor and the dynamics of pigments in seeds from different maturation stages. To verify the accuracy in predicting the seed maturation stages based on autofluorescence-spectral imaging, we created machine learning models based on three algorithms: (i) random forest, (ii) neural network, and (iii) support vector machine. Here, we reported the unprecedented use of the autofluorescence-spectral technique to classify the maturation stages of soybean seeds, especially using the excitation/emission combination of chlorophyll a (660/700 nm) and b (405/600 nm). Taken together, the machine learning algorithms showed high performance segmenting the different stages of seed maturation. In summary, our results demonstrated that the maturation stages of soybean seeds have their autofluorescence-spectral identity in the wavelengths of chlorophylls, which allows the use of this technique as a marker of seed maturity and superior physiological quality.

Dietary Protein Modulates the Efficacy of Taurine Supplementation on Adaptive Islet Function and Morphology in Obesity.

Adaptation of islet ß-cell mass and function under limiting or excess nutrient availability is critical for maintenance of glucose homeostasis. Taurine regulates islet function of obese mice in normal and low dietary protein conditions, but whether this involves remodeling of the endocrine pancreas architecture is not well understood. Here, we carried functional and morphometric evaluation of the endocrine pancreas of normal and protein-restricted mice fed a high-fat diet (HFD) and investigated the role of taurine supplementation. Weaned mice were placed in a normal (C) or a low-protein diet (R) for 6 weeks, followed by HFD for 8 weeks (CH and RH). Half of HFD groups received 5% taurine supplementation since weaning (CHT and RHT) until the end of the experiment. Isolated islets from both CH and RH groups showed increased insulin release in association with increased pancreas weight and independently of changes in islet or ß-cell area. In normal protein CHT mice, taurine supplementation prevented obesity-induced insulin hypersecretion and promoted increased islet and ß-cell areas in association with increased protein expression of the proliferation marker, PCNA. On a low-protein background, taurine effects on islet function and morphology were blunted, but it prevented obesity-induced DNA fragmentation. In summary, taurine regulates islet function and morphology to improve the adaptive response to diet-induced obesity, but these effects are dependent on adequate dietary protein levels.

An Approach Using Emerging Optical Technologies and Artificial Intelligence Brings New Markers to Evaluate Peanut Seed Quality.

Seeds of high physiological quality are defined by their superior germination capacity and uniform seedling establishment. Here, it was investigated whether multispectral images combined with machine learning models can efficiently categorize the quality of peanut seedlots. The seed quality from seven lots was assessed traditionally (seed weight, water content, germination, and vigor) and by multispectral images (area, length, width, brightness, chlorophyll fluorescence, anthocyanin, and reflectance: 365 to 970 nm). Seedlings from the seeds of each lot were evaluated for their photosynthetic capacity (fluorescence and chlorophyll index, F0, Fm, and Fv/Fm) and stress indices (anthocyanin and NDVI). Artificial intelligence features (QDA method) applied to the data extracted from the seed images categorized lots with high and low quality. Higher levels of anthocyanin were found in the leaves of seedlings from low quality seeds. Therefore, this information is promising since the initial behavior of the seedlings reflected the quality of the seeds. The existence of new markers that effectively screen peanut seed quality was confirmed. The combination of physical properties (area, length, width, and coat brightness), pigments (chlorophyll fluorescence and anthocyanin), and light reflectance (660, 690, and 780 nm), is highly efficient to identify peanut seedlots with superior quality (98% accuracy).

Transcripts Expressed during Germination Sensu Stricto Are Associated with Vigor in Soybean Seeds.

The rapid and uniform establishment of crop plants in the field underpins food security through uniform mechanical crop harvesting. In order to achieve this, seeds with greater vigor should be used. Vigor is a component of physiological quality related to seed resilience. Despite this importance, there is little knowledge of the association between events at the molecular level and seed vigor. In this study, we investigated the relationship between gene expression during germination and seed vigor in soybean. The expression level of twenty genes related to growth at the beginning of the germination process was correlated with vigor. In this paper, vigor was evaluated by different tests. Then we reported the identification of the genes Expansin-like A1, Xyloglucan endotransglucosylase/hydrolase 22, 65-kDa microtubule-associated protein, Xyloglucan endotransglucosylase/hydrolase 2, N-glycosylase/DNA lyase OGG1 and Cellulose synthase A catalytic subunit 2, which are expressed during germination, that correlated with several vigor tests commonly used in routine analysis of soybean seed quality. The identification of these transcripts provides tools to study vigor in soybean seeds at the molecular level.

Oral conditions and salivary analysis in HIV-uninfected subjects using preexposure prophylaxis

Background: New prevention strategies have been advocated to control the progression of HIV/AIDS, such as preexposure prophylaxis (PrEP). The aim of this study is to evaluate the potential changes in the oral and salivary conditions of HIV-uninfected subjects using PrEP. Material and Methods: Subjects were evaluated before beginning the medication (T0), at the first follow-up (T1), and at the second follow-up (T2). Xerostomia, presence of untreated cavitated caries, oral hygiene habits, taste, gingival and plaque index, stimulated salivary flow rate (SSFR), and salivary concentrations of calcium, glucose, urea, and total proteins were evaluated. Data obtained were analyzed using statistical tests (p<0.05). Results: Forty-seven participants (41 men; 6 women) were evaluated at T0. Thirty (28 men; 2 women) and 17 men were reassessed at T1 and T2, respectively. There was no difference between the SSFR and oral and salivary conditions between T0, T1, and T2 (p>0.05), except for the salivary calcium concentration, that increased at T2 compared to T1 (p=0.02). There was significant difference between taste and xerostomia at T1 (p=0.017), and the need to drink to swallow at T2 (p=0.015). There was significant correlation between the reported amount of saliva and taste (p=0.039, r=-0.378) at T1. Conclusions: The prolonged use of PrEP seems to be associated with reports of dry mouth and worsening of taste, possibly associated with increased salivary calcium concentration.(AU)

The potential impact of vegetarian diet on the oral mucosa: A preliminary cytopathological study.

BACKGROUND/PURPOSE: Actually, many individuals have opted for the vegetarian diet. The objective of this study was to evaluate the impact of the vegetarian diet on the oral epithelium through cytopathology. METHODS: Oral smears of the tongue and buccal mucosa of 60 adult subjects (30 vegetarians and 30 controls) were collected. Smears were analyzed morphologically and for three morphometric variables: nucleus area (NA), cytoplasm area (CA) and nucleus/cytoplasm ratio. RESULTS: Vegetarians were classified as ovolactovegetarian (53.3%), vegans (30%) and strict vegetarians (16.7%). The NA and CA of the epithelial cells of vegetarian individuals were smaller when compared to controls both in the region of the buccal mucosa and tongue. However, there was no statistically significant difference according to the Student's t-test. For the NA/CA ratio, cells in the oral mucosa region were larger for vegetarians compared to controls. For the tongue, both groups had the same value and the Mann-Whitney U test confirmed that there is no difference between the groups for this cytomorphometric variable. RESULTS: Vegan individuals had a smaller (but not larger) area of CA when compared to controls for the tongue (vegan = 2604.2 ± 179.2 versus control = 3256.7 ± 463.8 p = 0.013). Most smears showed normal epithelial cells and some individuals had changes of an inflammatory nature, mainly in the tongue. CONCLUSION: Despite the small sample size, the results of this study raise the hypothesis that the vegetarian diet (especially the vegan diet) can compromise the thickness of the oral epithelium of the tongue.

Effect of nighttime light exposure on glucose metabolism in protein-restricted mice.

Disruption of biological rhythms due to exposure to artificial light at night (ALAN) has emerged as a new risk factor for metabolic diseases. However, the effects of ALAN exposure on energy metabolism with concomitant misalignment in the circadian system caused by nutritional imbalance remain largely unexplored. Here, we evaluate whether a low-protein (LP) diet could enhance the effects induced by exposure to ALAN on the energy metabolism and consequently predispose to metabolic disorders. Male C57BL6/J mice were weaned on a normal protein (NP) or a LP diet and housed on 12 h light:12 h darkness (LD) cycle. After 6 weeks, mice maintained on their respective diets were subdivided into normal light/darkness cycle (NP/LD; LP/LD) or exposed to ALAN (NP/LL; LP/LL) for 8 weeks. We observed that exposure to ALAN concomitant to LP diet disrupts the behavioral rhythms, without shifting the timing of food intake. Furthermore, exposure to ALAN leads to increased body and fat pad weights, higher levels of fast and fed glycemia and glucose intolerance independent of the diet consumed. Importantly, the effects of ALAN on circadian regulation of insulin sensitivity were diet-dependent with LP/LL mice showing insulin resistance in an opposite time of day than NP/LL. At the molecular level, exposure to ALAN concurrent with LP diet increased the expression of phosphoenolpyruvate carboxykinase 1 in both periods analyzed and inverted the pattern of fibroblast growth factor 21 (Fgf21) expression in the liver. Our data suggest that dietary protein restriction modulates the effects induced by nighttime light exposure on glucose metabolism, which could be partially related with the dysregulation of hepatic Fgf21 expression.