Selected cachaça yeast strains share a genomic profile related to traits relevant to industrial fermentation processes.

The isolation and selection of yeast strains to improve the quality of the cachaça-Brazilian Spirit-have been studied in our research group. Our strategy considers Saccharomyces cerevisiae as the predominant species involved in sugarcane juice fermentation and the presence of different stressors (osmolarity, temperature, ethanol content, and competition with other microorganisms). It also considers producing balanced concentrations of volatile compounds (higher alcohols and acetate and/or ethyl esters), flocculation capacity, and ethanol production. Since the genetic bases behind these traits of interest are not fully established, the whole genome sequencing of 11 different Saccharomyces cerevisiae strains isolated and selected from different places was analyzed to identify the presence of a specific genetic variation common to cachaça yeast strains. We have identified 20,128 single-nucleotide variants shared by all genomes. Of these shared variants, 37 were new variants (being six missenses), and 4,451 were identified as missenses. We performed a detailed functional annotation (using enrichment analysis, protein-protein interaction network analysis, and database and in-depth literature searches) of these new and missense variants. Many genes carrying these variations were involved in the phenotypes of flocculation, tolerance to fermentative stresses, and production of volatile compounds and ethanol. These results demonstrate the existence of a genetic profile shared by the 11 strains under study that could be associated with the applied selective strategy. Thus, this study points out genes and variants that may be used as molecular markers for selecting strains well suited to the fermentation process, including genetic improvement by genome editing, ultimately producing high-quality beverages and adding value.IMPORTANCEThis work demonstrates the existence of new genetic markers related to different phenotypes used to select yeast strains and mutations in genes directly involved in producing flavoring compounds and ethanol, and others related to flocculation and stress resistance.

Bacterial volatile organic compounds induce adverse ultrastructural changes and DNA damage to the sugarcane pathogenic fungus Thielaviopsis ethacetica.

Due to an increasing demand for sustainable agricultural practices, the adoption of microbial volatile organic compounds (VOCs) as antagonists against phytopathogens has emerged as an eco-friendly alternative to the use of agrochemicals. Here, we identified three Pseudomonas strains that were able to inhibit, in vitro, up to 80% of mycelial growth of the phytopathogenic fungus Thielaviopsis ethacetica, the causal agent of pineapple sett rot disease in sugarcane. Using GC/MS, we found that these bacteria produced 62 different VOCs, and further functional validation revealed compounds with high antagonistic activity to T. ethacetica. Transcriptomic analysis of the fungal response to VOCs indicated that these metabolites downregulated genes related to fungal central metabolism, such as those involved in carbohydrate metabolism. Interestingly, genes related to the DNA damage response were upregulated, and micro-FTIR analysis corroborated our hypothesis that VOCs triggered DNA damage. Electron microscopy analysis showed critical morphological changes in mycelia treated with VOCs. Altogether, these results indicated that VOCs hampered fungal growth and could lead to cell death. This study represents the first demonstration of the molecular mechanisms involved in the antagonism of sugarcane phytopathogens by VOCs and reinforces that VOCs can be a sustainable alternative for use in phytopathogen biocontrol.

Root nitrate uptake in sugarcane (Saccharum spp.) is modulated by transcriptional and presumably posttranscriptional regulation of the NRT2.1/NRT3.1 transport system.

KEY MESSAGE: Nitrate uptake in sugarcane roots is regulated at the transcriptional and posttranscriptional levels based on the physiological status of the plant and is likely a determinant mechanism for discrimination against nitrate. Sugarcane (Saccharum spp.) is one of the most suitable energy crops for biofuel feedstock, but the reduced recovery of nitrogen (N) fertilizer by sugarcane roots increases the crop carbon footprint. The low nitrogen use efficiency (NUE) of sugarcane has been associated with the significantly low nitrate uptake, which limits the utilization of the large amount of nitrate available in agricultural soils. To understand the regulation of nitrate uptake in sugarcane roots, we identified the major canonical nitrate transporter genes (NRTs-NITRATE TRANSPORTERS) and then determined their expression profiles in roots under contrasting N conditions. Correlation of gene expression with 15N-nitrate uptake revealed that under N deprivation or inorganic N (ammonium or nitrate) supply in N-sufficient roots, the regulation of ScNRT2.1 and ScNRT3.1 expression is the predominant mechanism for the modulation of the activity of the nitrate high-affinity transport system. Conversely, in N-deficient roots, the induction of ScNRT2.1 and ScNRT3.1 transcription is not correlated with the marked repression of nitrate uptake in response to nitrate resupply or high N provision, which suggested the existence of a posttranscriptional regulatory mechanism. Our findings suggested that high-affinity nitrate uptake is regulated at the transcriptional and presumably at the posttranscriptional levels based on the physiological N status and that the regulation of NRT2.1 and NRT3.1 activity is likely a determinant mechanism for the discrimination against nitrate uptake observed in sugarcane roots, which contributes to the low NUE in this crop species.

The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence.

Aspergillus fumigatus is an opportunistic fungal pathogen that secretes an array of immune-modulatory molecules, including secondary metabolites (SMs), which contribute to enhancing fungal fitness and growth within the mammalian host. Gliotoxin (GT) is a SM that interferes with the function and recruitment of innate immune cells, which are essential for eliminating A. fumigatus during invasive infections. We identified a C6 Zn cluster-type transcription factor (TF), subsequently named RglT, important for A. fumigatus oxidative stress resistance, GT biosynthesis and self-protection. RglT regulates the expression of several gli genes of the GT biosynthetic gene cluster, including the oxidoreductase-encoding gene gliT, by directly binding to their respective promoter regions. Subsequently, RglT was shown to be important for virulence in a chemotherapeutic murine model of invasive pulmonary aspergillosis (IPA). Homologues of RglT and GliT are present in eurotiomycete and sordariomycete fungi, including the non-GT-producing fungus A. nidulans, where a conservation of function was described. Phylogenetically informed model testing led to an evolutionary scenario in which the GliT-based resistance mechanism is ancestral and RglT-mediated regulation of GliT occurred subsequently. In conclusion, this work describes the function of a previously uncharacterised TF in oxidative stress resistance, GT biosynthesis and self-protection in both GT-producing and non-producing Aspergillus species.

The experience of teaching introductory programming skills to bioscientists in Brazil.

Computational biology has gained traction as an independent scientific discipline over the last years in South America. However, there is still a growing need for bioscientists, from different backgrounds, with different levels, to acquire programming skills, which could reduce the time from data to insights and bridge communication between life scientists and computer scientists. Python is a programming language extensively used in bioinformatics and data science, which is particularly suitable for beginners. Here, we describe the conception, organization, and implementation of the Brazilian Python Workshop for Biological Data. This workshop has been organized by graduate and undergraduate students and supported, mostly in administrative matters, by experienced faculty members since 2017. The workshop was conceived for teaching bioscientists, mainly students in Brazil, on how to program in a biological context. The goal of this article was to share our experience with the 2020 edition of the workshop in its virtual format due to the Coronavirus Disease 2019 (COVID-19) pandemic and to compare and contrast this year's experience with the previous in-person editions. We described a hands-on and live coding workshop model for teaching introductory Python programming. We also highlighted the adaptations made from in-person to online format in 2020, the participants' assessment of learning progression, and general workshop management. Lastly, we provided a summary and reflections from our personal experiences from the workshops of the last 4 years. Our takeaways included the benefits of the learning from learners' feedback (LLF) that allowed us to improve the workshop in real time, in the short, and likely in the long term. We concluded that the Brazilian Python Workshop for Biological Data is a highly effective workshop model for teaching a programming language that allows bioscientists to go beyond an initial exploration of programming skills for data analysis in the medium to long term.

Weighted Iterative CD-Spline for Mitigating Occlusion Effects on Building Boundary Regularization Using Airborne LiDAR Data.

Building occlusions usually decreases the accuracy of boundary regularization. Thus, it is essential that modeling methods address this problem, aiming to minimize its effects. In this context, we propose a weighted iterative changeable degree spline (WICDS) approach. The idea is to use a weight function for initial building boundary points, assigning a lower weight to the points in the occlusion region. As a contribution, the proposed method allows the minimization of errors caused by the occlusions, resulting in a more accurate contour modeling. The conducted experiments are performed using both simulated and real data. In general, the results indicate the potential of the WICDS approach to model a building boundary with occlusions, including curved boundary segments. In terms of Fscore and PoLiS, the proposed approach presents values around 99% and 0.19 m, respectively. Compared with the previous iterative changeable degree spline (ICDS), the WICDS resulted in an improvement of around 6.5% for completeness, 4% for Fscore, and 0.24 m for the PoLiS metric.

Outdoor Community Ambulation Interventions to Improve Physical and Mental Health in Older Adults: A Systematic Review and Meta-Analysis.

Limited community ambulation, defined as independent mobility outside the home, predicts adverse outcomes in older adults. We performed a systematic review and meta-analysis to examine outdoor community ambulation intervention effectiveness in older adults. We searched six databases until October 2021. Studies with an evaluative research objective, older adult population, and outdoor community ambulation interventions were eligible. After reviewing 23,172 records, five studies were included. The meta-analysis found no significant difference in walking endurance and depression outcomes between outdoor community ambulation and comparison interventions. For outcomes not suitable for meta-analysis, studies showed no significant difference in walking activity, anxiety, and general and health-related quality of life, and possible improvements in gait speed and lower extremity function and strength. Most evidence was of low to very low certainty. Considering the limited evidence base, the design, implementation, and evaluation of outdoor community ambulation interventions in older adults should be prioritized in primary research.

Knowledge management in the classroom using Mendeley technology.

Research in higher education institutions is present in all courses, and academic instruction in research methodology is vital, with educational technologies being an essential component of this process. With the Covid-19 pandemic, there were changes in teaching, learning, and in performing scientific research in undergraduate courses. Among the technologies, the Mendeley reference management tool has become increasingly helpful in these contexts. Therefore, this manuscript is an account of workshop experiences for the use of the Mendeley tool in the teaching of Research Methodology and Scientific Methodology offered in the distance education modality in undergraduate courses at the Universidade do Contestado, Brazil. After basic instruction on Mendeley, students participating in the workshops were guided to apply the tool using Bardin's content analysis technique. This technique is usually laborious and seldom involved in literature reviews by undergraduate students; Mendeley technology makes it more accessible. From experiences with the 2020 and 2021 workshops, during the COVID-19 pandemic, it is suggested that the content analysis method combined with the Mendeley technology can help students present better literature reviews, especially for final graduation projects such as course completion monographs.

Reduction in Pain Inhibitory Modulation and Cognitive-Behavioral Changes in Patients With Chronic Low Back Pain: A Case-Control Study.

BACKGROUND: Recent studies indicate that the assessment of conditioned pain modulation (CPM) responses and emotional factors can provide important information regarding chronification mechanisms, choices for more efficient therapeutic strategies, and clinical variables supporting a therapeutic prognosis. AIMS: To investigate the impact of nonspecific chronic low back pain (NSCLBP) on CPM and psychosocial factors in individuals with NSCLBP compared with healthy controls. DESIGN: Case-control study. METHODS: Eighteen patients with NSCLBP and 18 healthy controls were recruited for this study. Pain intensity and affective-emotional aspects of pain, functional disability, kinesiophobia, depression, anxiety, and catastrophizing pain were obtained using a questionnaire. A CPM protocol was established to assess the functioning of the descending inhibitory system, with a cold pressor test as a conditioning stimulus and pressure pain threshold as a test stimulus. The maximal isometric strength of the trunk extensors also was evaluated. RESULTS: Healthy participants demonstrated a greater CPM response than those with NSCLBP. Patients with NSCLBP exhibited significantly lower pressure pain threshold than healthy subjects. Moreover, patients with NSCLBP presented with a considerable exacerbation of cognitive-behavioral changes. NSCLBP patients showed diminished maximal isometric strength of the trunk extensor compared to healthy subjects. CONCLUSIONS: The endogenous pain inhibition system is reduced in patients with NSCLBP, with significant cognitive-behavioral changes indicated by high levels of anxiety and moderate pain intensity. SETTING: Clinical School of Physical Therapy of the Federal University of Delta of Parnaíba, Piauí - Brazil. PARTICIPANTS/SUBJECTS: 36 subjects with and without NSCLBP.

Medical education in Brazil.

This paper aims to describe and analyze medical education in Brazil, a history of over 200 years. As in most European countries and influenced by the Flexner Report, an undergraduate medical course in Brazil takes 6 years. Recently, medical education research has been advocating a shift from a teacher-centered and hospital-based approach to student-centered and community-based education. Nevertheless, a huge variation exists among Brazilian medical schools. The physicians' supply program known as "More Physicians" has strongly impacted the number of medical schools in Brazil, which is growing rapidly. Professors of medicine from several institutions and other stakeholders have alerted authorities to the risks of operating so many schools without adequate time to prepare teachers, clinician-educators, curricula, and sufficient pedagogical structure to ensure quality medical education. The possibility of an imminent catastrophe in medical education has united stakeholders in pursuit of a guarantee of quality maintenance. This effort has resulted in the creation of an independent accreditation system approved by the World Federation of Medical Education. The study of the unbalanced relationship between stakeholders in medical education in Brazil until now has provided valuable information concerning the importance of having their roles and limits clear. It is possible that these findings might be replicable around the world.

ploidyNGS: visually exploring ploidy with Next Generation Sequencing data.

SUMMARY: ploidyNGS is a model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data. We tested ploidyNGS using both simulated and real NGS data of the model yeast Saccharomyces cerevisiae. ploidyNGS allows the identification of the ploidy level of a newly sequenced genome in a visual way. AVAILABILITY AND IMPLEMENTATION: ploidyNGS is available under the GNU General Public License (GPL) at https://github.com/diriano/ploidyNGS. ploidyNGS is implemented in Python and R. CONTACT: diriano@gmail.com.

Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei.

BACKGROUND: Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source. RESULTS: Particular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated. CONCLUSIONS: This is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement.

Learning HMMs for nucleotide sequences from amino acid alignments.

Profile hidden Markov models (profile HMMs) are known to efficiently predict whether an amino acid (AA) sequence belongs to a specific protein family. Profile HMMs can also be used to search for protein domains in genome sequences. In this case, HMMs are typically learned from AA sequences and then used to search on the six-frame translation of nucleotide (NT) sequences. However, this approach demands additional processing of the original data and search results. Here, we propose an alternative and more direct method which converts an AA alignment into an NT one, after which an NT-based HMM is trained to be applied directly on a genome.

Van der Waals stacks of few-layer h-AlN with graphene: an ab initio study of structural, interaction and electronic properties.

Graphite-like hexagonal AlN (h-AlN) multilayers have been experimentally manifested and theoretically modeled. The development of any functional electronics applications of h-AlN would most certainly require its integration with other layered materials, particularly graphene. Here, by employing vdW-corrected density functional theory calculations, we investigate structure, interaction energy, and electronic properties of van der Waals stacking sequences of few-layer h-AlN with graphene. We find that the presence of a template such as graphene induces enough interlayer charge separation in h-AlN, favoring a graphite-like stacking formation. We also find that the interface dipole, calculated per unit cell of the stacks, tends to increase with the number of stacked layers of h-AlN and graphene.

Models for Allee effect based on physical principles.

We propose some models of single species with Allee effect based on physical principles. A method is used to obtain the expression for the per capita growth rate (a macroscopic information) starting from the characteristics of interactions between the individuals (a microscopic information). We assume that the agents in a model of a single species interact according to the distance between them. Moreover these agents must (i) cooperate with their nearest neighbors, (ii) compete with neighbors at an intermediate distance, and (iii) being indifferent to those who are far away. Using these assumptions and based on fundamental physical principles, we find what appears to be a new way of establishing models of single species with Allee effect.

Pseudozyma brasiliensis sp. nov., a xylanolytic, ustilaginomycetous yeast species isolated from an insect pest of sugarcane roots.

A novel ustilaginomycetous yeast isolated from the intestinal tract of an insect pest of sugarcane roots in Ribeirão Preto, São Paulo State, Brazil, represents a novel species of the genus Pseudozyma based on molecular analyses of the D1/D2 rDNA large subunit and the internal transcribed spacer (ITS1+ITS2) regions. The name Pseudozyma brasiliensis sp. nov. is proposed for this species, with GHG001(T) ( = CBS 13268(T) = UFMG-CM-Y307(T)) as the type strain. P. brasiliensis sp. nov. is a sister species of Pseudozyma vetiver, originally isolated from leaves of vetiver grass and sugarcane in Thailand. P. brasiliensis sp. nov. is able to grow well with xylan as the sole carbon source and produces high levels of an endo-1,4-xylanase that has a higher specific activity in comparison with other eukaryotic xylanases. This enzyme has a variety of industrial applications, indicating the great biotechnological potential of P. brasiliensis.

Density Functional Theory-Fed Phase Field Model for Semiconductor Nanostructures: The Case of Self-Induced Core-Shell InAlN Nanorods.

The self-induced formation of core-shell InAlN nanorods (NRs) is addressed at the mesoscopic scale by density functional theory (DFT)-resulting parameters to develop phase field modeling (PFM). Accounting for the structural, bonding, and electronic features of immiscible semiconductor systems at the nanometer scale, we advance DFT-based procedures for computation of the parameters necessary for PFM simulation runs, namely, interfacial energies and diffusion coefficients. The developed DFT procedures conform to experimental self-induced InAlN NRs' concerning phase-separation, core/shell interface, morphology, and composition. Finally, we infer the prospects for the transferability of the coupled DFT-PFM simulation approach to a wider range of nanostructured semiconductor materials.

Evaluations of virtual exercise programmes for adults with mobility limitations: a scoping review protocol incorporating an equity lens to inform the development of strategies to optimise participation of under-represented groups.

INTRODUCTION: For individuals with mobility limitations, virtual exercise programmes can address the challenges of in-person participation in community exercise programmes. A synthesis of studies of virtual exercise programmes targeting mobility limitations provided outside of conventional rehabilitation services and strategies used to optimise equitable access and inclusivity in these programmes is lacking. We aim to characterise evaluations of virtual exercise programmes for adults with mobility limitations, and the nature of and extent to which equity, diversity and inclusion considerations are integrated in the research process. METHODS AND ANALYSIS: A scoping review following a six-stage methodological framework, including a consultation exercise, is proposed. A comprehensive strategy will be used to search Medline, Embase, PEDro, CINAHL and Scopus to identify peer-reviewed studies evaluating virtual exercise programmes for adults with mobility limitations living in the community. Three trained reviewers will select studies independently. Data (eg, study methodology, programme structure and content, participant characteristics) will be extracted using a standardised form, and collated and summarised using quantitative and qualitative methods. The PROGRESS-Plus and International Classification of Functioning, Disability and Health frameworks will be used to classify participant characteristics and study outcomes, respectively. During the consultation exercise, key knowledge users, including exercise participants, programme providers and coordinators, and members of community organisations for persons living with disabilities and under-represented groups, will be asked to provide insights regarding the applicability of review findings. A directed content analysis of data from the consultation exercise will be performed. ETHICS AND DISSEMINATION: The research ethics board at the University of Toronto approved the consultation exercise. Findings will be disseminated through peer-reviewed publications and conference presentations. Findings will enhance understanding of current research evaluating virtual exercise programmes and inform future research and strategies for promoting equitable access and outcomes for individuals with mobility limitations. REGISTRATION DETAILS: https://doi.org/10.17605/OSF.IO/X5JMA.