Showing papers by "Universidade Federal de Viçosa published in 2020"

Global Organization and Proposed Megataxonomy of the Virus World

Abstract: Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.

Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020).

Abstract: This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020 The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes

The New Scope of Virus Taxonomy: Partitioning the Virosphere Into 15 Hierarchical Ranks

Abstract: Virus taxonomy emerged as a discipline in the middle of the twentieth century. Traditionally, classification by virus taxonomists has been focussed on the grouping of relatively closely related viruses. However, during the past few years, the International Committee on Taxonomy of Viruses (ICTV) has recognized that the taxonomy it develops can be usefully extended to include the basal evolutionary relationships among distantly related viruses. Consequently, the ICTV has changed its Code to allow a 15-rank classification hierarchy that closely aligns with the Linnaean taxonomic system and may accommodate the entire spectrum of genetic divergence in the virosphere. The current taxonomies of three human pathogens, Ebola virus, severe acute respiratory syndrome coronavirus and herpes simplex virus 1 are used to illustrate the impact of the expanded rank structure. This new rank hierarchy of virus taxonomy will stimulate further research on virus origins and evolution, and vice versa, and could promote crosstalk with the taxonomies of cellular organisms.

A mathematical model for the spatiotemporal epidemic spreading of COVID19

Abstract: An outbreak of a novel coronavirus, named SARS-CoV-2, that provokes the COVID-19 disease, was first reported in Hubei, mainland China on 31 December 2019. As of 20 March 2020, cases have been reported in 166 countries/regions, including cases of human-to-human transmission around the world. The proportions of this epidemics is probably one of the largest challenges faced by our interconnected modern societies. According to the current epidemiological reports, the large basic reproduction number, R_0 ~ 2.3, number of secondary cases produced by an infected individual in a population of susceptible individuals, as well as an asymptomatic period (up to 14 days) in which infectious individuals are undetectable without further analysis, pave the way for a major crisis of the national health capacity systems. Recent scientific reports have pointed out that the detected cases of COVID19 at young ages is strikingly short and that lethality is concentrated at large ages. Here we adapt a Microscopic Markov Chain Approach (MMCA) metapopulation mobility model to capture the spread of COVID-19. We propose a model that stratifies the population by ages, and account for the different incidences of the disease at each strata. The model is used to predict the incidence of the epidemics in a spatial population through time, permitting investigation of control measures. The model is applied to the current epidemic in Spain, using the estimates of the epidemiological parameters and the mobility and demographic census data of the national institute of statistics (INE). The results indicate that the peak of incidence will happen in the first half of April 2020 in absence of mobility restrictions. These results can be refined with improved estimates of epidemiological parameters, and can be adapted to precise mobility restrictions at the level of municipalities. The current estimates largely compromises the Spanish health capacity system, in particular that for intensive care units, from the end of March. However, the model allows for the scrutiny of containment measures that can be used for health authorities to forecast with accuracy their impact in prevalence of COVID--19. Here we show by testing different epidemic containment scenarios that we urge to enforce total lockdown to avoid a massive collapse of the Spanish national health system.

Modeling the Spatiotemporal Epidemic Spreading of COVID-19 and the Impact of Mobility and Social Distancing Interventions

Abstract: On 31 December, 2019, an outbreak of a novel coronavirus, SARS-CoV-2, that causes the COVID-19 disease, was first reported in Hubei, mainland China This epidemics' health threat is probably one of the biggest challenges faced by our interconnected modern societies According to the epidemiological reports, the large basic reproduction number R-0 similar to 3 0, together with a huge fraction of asymptomatic infections, paved the way for a major crisis of the national health capacity systems Here, we develop an age-stratified mobility-based metapopulation model that encapsulates the main particularities of the spreading of COVID-19 regarding (i) its transmission among individuals, (ii) the specificities of certain demographic groups with respect to the impact of COVID-19, and (iii) the human mobility patterns inside and among regions The full dynamics of the epidemic is formalized in terms of a microscopic Markov chain approach that incorporates the former elements and the possibility of implementing containment measures based on social distancing and confinement With this model, we study the evolution of the effective reproduction number R(t), the key epidemiological parameter to track the evolution of the transmissibility and the effects of containment measures, as it quantifies the number of secondary infections generated by an infected individual The suppression of the epidemic is directly related to this value and is attained when R < 1 We find an analytical expression connecting R with nonpharmacological interventions, and its phase diagram is presented We apply this model at the municipality level in Spain, successfully forecasting the observed incidence and the number of fatalities in the country at each of its regions The expression for R should assist policymakers to evaluate the epidemics' response to actions, such as enforcing or relaxing confinement and social distancing

A Survey on Load Transportation Using Multirotor UAVs

Abstract: Load transportation by quadrotors and similar aircrafts is a topic of great interest to the robotics community nowadays, most likely due to logistic gains for deliveries of commercial cargo. Aiming at being the first reading for novice researchers and graduate students, this survey highlights meaningful research works of several groups worldwide, considering two basic approaches, namely grasped and cable-suspended load transportation. Different control techniques and maneuver strategies are analyzed, and their benefits and drawbacks are discussed. Moreover, experimental validation was a key aspect to the highlighted works, thus, links to the videos showing the experimental results are provided for each work.

Laser-Induced Graphene Electrochemical Immunosensors for Rapid and Label-Free Monitoring of Salmonella enterica in Chicken Broth

Abstract: Food-borne illnesses are a growing concern for the food industry and consumers, with millions of cases reported every year. Consequently, there is a critical need to develop rapid, sensitive, and inexpensive techniques for pathogen detection in order to mitigate this problem. However, current pathogen detection strategies mainly include time-consuming laboratory methods and highly trained personnel. Electrochemical in-field biosensors offer a rapid, low-cost alternative to laboratory techniques, but the electrodes used in these biosensors require expensive nanomaterials to increase their sensitivity, such as noble metals (e.g., platinum, gold) or carbon nanomaterials (e.g., carbon nanotubes, or graphene). Herein, we report the fabrication of a highly sensitive and label-free laser-induced graphene (LIG) electrode that is subsequently functionalized with antibodies to electrochemically quantify the food-borne pathogen Salmonella enterica serovar Typhimurium. The LIG electrodes were produced by laser induction on the polyimide film in ambient conditions and, hence, circumvent the need for high-temperature, vacuum environment, and metal seed catalysts commonly associated with graphene-based electrodes fabricated via chemical vapor deposition processes. After functionalization with Salmonella antibodies, the LIG biosensors were able to detect live Salmonella in chicken broth across a wide linear range (25 to 105 CFU mL-1) and with a low detection limit (13 ± 7 CFU mL-1; n = 3, mean ± standard deviation). These results were acquired with an average response time of 22 min without the need for sample preconcentration or redox labeling techniques. Moreover, these LIG immunosensors displayed high selectivity as demonstrated by nonsignificant response to other bacteria strains. These results demonstrate how LIG-based electrodes can be used for electrochemical immunosensing in general and, more specifically, could be used as a viable option for rapid and low-cost pathogen detection in food processing facilities before contaminated foods reach the consumer.

From visual estimates to fully automated sensor-based measurements of plant disease severity: status and challenges for improving accuracy

Abstract: The severity of plant diseases, traditionally the proportion of the plant tissue exhibiting symptoms, is a key quantitative variable to know for many diseases and is prone to error. Good quality disease severity data should be accurate (close to the true value). Earliest quantification of disease severity was by visual estimates. Sensor-based image analysis including visible spectrum and hyperspectral and multispectral sensors are established technologies that promise to substitute, or complement visual ratings. Indeed, these technologies have measured disease severity accurately under controlled conditions but are yet to demonstrate their full potential for accurate measurement under field conditions. Sensor technology is advancing rapidly, and artificial intelligence may help overcome issues for automating severity measurement under hyper-variable field conditions. The adoption of appropriate scales, training, instruction and aids (standard area diagrams) has contributed to improved accuracy of visual estimates. The apogee of accuracy for visual estimation is likely being approached, and any remaining increases in accuracy are likely to be small. Due to automation and rapidity, sensor-based measurement offers potential advantages compared with visual estimates, but the latter will remain important for years to come. Mobile, automated sensor-based systems will become increasingly common in controlled conditions and, eventually, in the field for measuring plant disease severity for the purpose of research and decision making.

New Guinea has the world’s richest island flora

Abstract: New Guinea is the world’s largest tropical island and has fascinated naturalists for centuries1,2. Home to some of the best-preserved ecosystems on the planet3 and to intact ecological gradients—from mangroves to tropical alpine grasslands—that are unmatched in the Asia-Pacific region4,5, it is a globally recognized centre of biological and cultural diversity6,7. So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea. Here we present the first, to our knowledge, expert-verified checklist of the vascular plants of mainland New Guinea and surrounding islands. Our publicly available checklist includes 13,634 species (68% endemic), 1,742 genera and 264 families—suggesting that New Guinea is the most floristically diverse island in the world. Expert knowledge is essential for building checklists in the digital era: reliance on online taxonomic resources alone would have inflated species counts by 22%. Species discovery shows no sign of levelling off, and we discuss steps to accelerate botanical research in the ‘Last Unknown’8. A catalogue of the vascular flora of New Guinea indicates that this island is the most floristically diverse in the world, and that 68% of the species identified are endemic to New Guinea.

Cressdnaviricota: a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes.

Abstract: Eukaryotic single-stranded (ss) DNA viruses are classified into ten families (Table 1) but many remain 38 unclassified (1, 2).….

Thresholds of freshwater biodiversity in response to riparian vegetation loss in the Neotropical region

Abstract: Protecting riparian vegetation around streams is vital in reducing the detrimental effects of environmental change on freshwater ecosystems and in maintaining aquatic biodiversity. Thus, identifying ecological thresholds is useful for defining regulatory limits and for guiding the management of riparian zones towards the conservation of freshwater biota. Using nationwide data on fish and invertebrates occurring in small Brazilian streams, we estimated thresholds of native vegetation loss in which there are abrupt changes in the occurrence and abundance of freshwater bioindicators and tested whether there are congruent responses among different biomes, biological groups and riparian buffer sizes. Mean thresholds of native vegetation cover loss varied widely among biomes, buffer sizes and biological groups: ranging from 0.5% to 77.4% for fish, from 2.9% to 37.0% for aquatic invertebrates and from 3.8% to 43.2% for a subset of aquatic invertebrates. Confidence intervals for thresholds were wide, but the minimum values of these intervals were lower for the smaller riparian buffers (50 and 100 m) than larger ones (200 and 500 m), indicating that land use should be kept away from the streams. Also, thresholds occurred at a lower percentage of riparian vegetation loss in the smaller buffers, and were critically lower for invertebrates: reducing only 6.5% of native vegetation cover within a 50-m riparian buffer is enough to cross thresholds for invertebrates. Synthesis and applications. The high variability in biodiversity responses to loss of native riparian vegetation suggests caution in the use of a single riparian width for conservation actions or policy definitions nationwide. The most sensitive bioindicators can be used as early warning signals of abrupt changes in freshwater biodiversity. In practice, maintaining at least 50-m wide riparian reserves on each side of streams would be more effective to protect freshwater biodiversity in Brazil. However, incentives and conservation strategies to protect even wider riparian reserves (~100 m) and also taking into consideration the regional context will promote a greater benefit. This information should be used to set conservation goals and to create complementary mechanisms and policies to protect wider riparian reserves than those currently required by the federal law.

Potential use of ceramic waste as precursor in the geopolymerization reaction for the production of ceramic roof tiles

Abstract: The red ceramic industry is responsible for generating high amounts of solid wastes around the world from manufacture process failures, such as ineffective firing and issues related to the products transportation. Besides the necessity of clean alternatives to discard the solid wastes, the civil construction industry has been demanding the development of better technological properties new materials. One an example of those new materials is the geopolymeric materials, characterized by the gain of mechanical strength at early ages, high fire resistance, low water absorption and refractoriness. All these characteristics imply that geopolymers are suitable for civil construction applications. The characterization of clay bricks waste, named chamotte, and its use as an alternative precursor to produce geopolymeric materials, such as roof tiles for buildings are the aims of this present work. The chemical characterization, particle size distribution, X-ray diffraction, specific mass, pozzolanic activity index (PAI) and scanning electron microscopy (SEM) were performed, in addition to the technological tests carried out on the geopolymer specimens, such as flexural strength, water absorption, linear shrinkage and apparent porosity. The chemical and mineralogical analysis proved that the waste is rich in silica and alumina, which are fundamental compounds for the geopolymers synthesis. The chamotte also has fine particles and high pozzolanic reactivity. Thus, this waste has great potential to be used as a raw material for obtaining of ceramic roof tiles by means of geopolymeric reactions.

Down Regulation and Loss of Auxin Response Factor 4 Function Using CRISPR/Cas9 Alters Plant Growth, Stomatal Function and Improves Tomato Tolerance to Salinity and Osmotic Stress.

Abstract: Auxin controls multiple aspects of plant growth and development. However, its role in stress responses remains poorly understood. Auxin acts on the transcriptional regulation of target genes, mainly through Auxin Response Factors (ARF). This study focuses on the involvement of SlARF4 in tomato tolerance to salinity and osmotic stress. Using a reverse genetic approach, we found that the antisense down-regulation of SlARF4 promotes root development and density, increases soluble sugars content and maintains chlorophyll content at high levels under stress conditions. Furthermore, ARF4-as displayed higher tolerance to salt and osmotic stress through reduced stomatal conductance coupled with increased leaf relative water content and Abscisic acid (ABA) content under normal and stressful conditions. This increase in ABA content was correlated with the activation of ABA biosynthesis genes and the repression of ABA catabolism genes. Cu/ZnSOD and mdhar genes were up-regulated in ARF4-as plants which can result in a better tolerance to salt and osmotic stress. A CRISPR/Cas9 induced SlARF4 mutant showed similar growth and stomatal responses as ARF4-as plants, which suggest that arf4-cr can tolerate salt and osmotic stresses. Our data support the involvement of ARF4 as a key factor in tomato tolerance to salt and osmotic stresses and confirm the use of CRISPR technology as an efficient tool for functional reverse genetics studies.

Rethinking biorational insecticides for pest management: unintended effects and consequences.

Abstract: Biorational insecticides are composed of natural products, including animals, plants, microbes, and minerals, or are their derivates. The use of biorational products for the management of insect pests has grown intensively in recent years, which has increased their popularity and share on the insecticide global market. Much of these recent increases in the use of biorational insecticides has been derived from the generalized perception that conventional insecticides have undesirable ecological and human health impacts. However, the idea of simply replacing synthetic compounds with biorational insecticides without considering their potential unintended effects can mislead their use and reduce the market life of such pest management tools. A systematic literature survey encompassing over 15 000 scientific manuscripts published between 1945 and 2019 reinforces the bias of focusing on studying the targeted effects while overlooking the potential detrimental effects of biorational products on human health and the environment (e.g. death and negative sublethal effects on pollinators and beneficial arthropods such as parasitoids and predators). Thus, the risks associated with biorational compounds (e.g. control failures, the evolution of resistance, shift in dominance, and outbreaks of secondary or primary pests) need to be revisited and the outcomes of such inquiry could be decisive for their future use in pest management programs. The shortcomings of regulatory processes, knowledge gaps, and the outlook for the use of the biorational products in pest management are discussed. © 2020 Society of Chemical Industry.

(In)Segurança alimentar no contexto da pandemia por SARS-CoV-2.

Abstract: Como tentativa de frear a propagacao do virus, a Organizacao Mundial da Saude (OMS) e as principais autarquias de saude no Brasil divulgaram como cuidados: higienizar as maos, cobrir a boca com o antebraco ou lenco descartavel ao tossir e espirrar, evitar aglomeracoes e manter-se em isolamento domiciliar, por ate 14 dias, em caso de sintomas da doenca 4. Tambem e incentivada a manutencao das pessoas em ambientes bem ventilados 5 e que as empresas e instituicoes publicas considerem a realizacao de trabalho remoto (home office), reunioes virtuais e cancelamento de viagens.

Secondary forest fragments offer important carbon and biodiversity cobenefits.

Abstract: Tropical forests store large amounts of carbon and high biodiversity, but are being degraded at alarming rates. The emerging global Forest and Landscape Restoration (FLR) agenda seeks to limit global climate change by removing carbon dioxide from the atmosphere through the growth of trees. In doing so, it may also protect biodiversity as a free co‐benefit, which is vital given the massive shortfall in funding for biodiversity conservation. We investigated whether natural forest regeneration on abandoned pastureland offers such co‐benefits, focusing for the first time on the recovery of taxonomic, phylogenetic and functional diversity of trees, including the recovery of threatened and endemic species richness, within isolated secondary forest fragments. We focused on the globally threatened Brazilian Atlantic Forest, where commitments have been made to restore one million hectares under FLR. Three decades after land abandonment, regenerating forests had recovered ~20% (72 Mg/ha−1) of the above‐ground carbon stocks of a primary forest, with cattle pasture containing just 3% of stocks relative to primary forests. Over this period, secondary forest recovered ~76% of taxonomic, 84% of phylogenetic and 96% of functional diversity found within primary forests. In addition, secondary forests had on average recovered 65% of threatened and ~30% of endemic species richness of primary Atlantic forest. Finally, we find positive relationships between carbon stock and tree diversity recovery. Our results emphasize that secondary forest fragments offer co‐benefits under FLR and other carbon‐based payments for ecosystem service schemes (e.g. carbon enhancements under REDD +). They also indicate that even isolated patches of secondary forest could help to mitigate climate change and the biodiversity extinction crisis by recovering species of high conservation concern and improving landscape connectivity.

Food consumption by degree of processing and cardiometabolic risk: a systematic review.

Abstract: Processed and ultra-processed foods (UPF) consumption has been associated with development of noncommunicable chronic diseases (NCD). This systematic review aims to summarise and discuss evidence of the relationship between food consumption according to degree of food processing and cardiometabolic risk. Data search was conducted in databases as PubMed, Bireme and Science Direct until July 2018. Studies have shown a positive association of UPF consumption with excess body weight, hypertension, dyslipidemia and metabolic syndrome features. However, disparities found in the studies analysed regarding dietary assessment, confounding factors and differences in food classifications makes comparisons between studies difficult. In conclusion, current evidences indicate the need to monitor UPF intake in global population. However, more studies are necessary to interpret better these associations with similar methodologies used in the studies. As well as longitudinal analyses can help to improve comparisons between outcomes and establish cause-effect relationship between UPF intake and cardiometabolic risk.

Assessing current and future trends of climate extremes across Brazil based on reanalyses and earth system model projections

Abstract: Brazil experiences extreme weather and climate events that cause numerous economic and social losses, and according to climate change projections, these events will increase in intensity and frequency over this century.This study adds to the body of research on Brazil’s climate change by analyzing the historical patterns and projected changes in temperature and precipitation extremes across Brazil using the World Climate Research Program’s Expert Team on Climate Change Detection and Indices framework. This novel approach analyzes climate extreme events over the past four decades (1980–2016) using multiple gridded observation and reanalysis datasets. Furthermore, future changes in climate extremes are analyzed from 20 downscaled Earth System Models (ESMs) at high horizontal resolution (0.25° of latitude/longitude), under two representative concentration pathway scenarios (RCP4.5 and RCP8.5). Projected changes in the extreme indices are analyzed over mid-twenty-first century (2046–2065) and end-of-twenty-first century (2081–2100) relative to the reference period 1986–2005. Results show consistent warming patterns with increasing (decreasing) trends in warm (cold) extremes in the historical datasets. A similar but more intense warm pattern is projected in the mid and end of the twenty-first century. For precipitation indices, observations show an increase in consecutive dry days and a reduction of consecutive wet days over almost all Brazil. The frequency and intensity of extremely wet days over Brazil are expected to increase according to future scenarios. Designing effective adaptation and mitigation measures in response to changes in climate extremes events depends on this improved understanding of how conditions have and are likely to change in the future at regional scales.