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  • ItemDissertação de mestrado
    Indicadores de estresse por déficit hídrico em plantas de laranjeira e relações com florescimento
    (Universidade Estadual Paulista (Unesp), 2023-08-02) Zanata, Renan Moisés Paneghini; Cazetta, Jairo Osvaldo
    A citricultura é uma atividade agrícola de notável importância econômica e social no Brasil e no mundo. O florescimento da laranjeira é um evento fisiológico de singular importância, sendo ponto de partida para uma nova colheita, de modo que obtê-lo de forma vigorosa faz-se indispensável para o alcance de boas produtividades. Este processo é determinado por diversos fatores atuando em conjunto, sendo o déficit hídrico decisório no centro-norte do Estado de São Paulo. Há carência de informações para predizer o momento de interromper o estresse, fazendo uso de irrigação. O presente trabalho objetivou quantificar alguns atributos fisiológicos das plantas de laranjeira mediante estresse por déficit hídrico e relacionar estes parâmetros com manejo da irrigação e florescimento. O ensaio constou de 5 tratamentos e 4 repetições, com delineamento em blocos casualizados, sendo os tratamentos caracterizados por diferentes momentos de interrupção do estresse hídrico, realizado em pomar em idade de produção, localizado em Pitangueiras - SP. Foram mensurados diversos parâmetros, como teor de amido em folhas e ramos, teor de clorofila total, liberação de eletrólitos e índices NDVI, entre junho e outubro de 2021. Durante o período avaliado, os teores de amido variaram entre os tratamentos e no tempo (p<0,05). Outros atributos variaram no tempo, mas não entre os tratamentos. O NDVI esboçou correlação negativa com o número de flores de laranjeira, ao passo que liberação de eletrólitos e concentração de amido nos ramos apresentaram correlação positiva, porém mais baixa, de forma que estes três parâmetros, nessa ordem, podem ser considerados bons indicativos do momento de interromper o estresse obtendo como resposta quantidade de flores uniforme e viável. Houve diferença na quantidade de frutos, mas teor de suco, acidez total titulável e teor de sólidos solúveis foram semelhantes (p>0,05) em todos os tratamentos testados.
  • ItemArtigo
    Proteome profiling of vascular sap regarding Eucalyptus grandis, Eucalyptus urophylla, and Eucalyptus camaldulensis
    (2023-01-01) da Silva, Felipe Alexsander Rodrigues [UNESP]; Balbuena, Tiago Santana [UNESP]; Universidade Estadual Paulista (UNESP)
    The plant vascular system is a key element for long-distance communication. Understanding its composition may provide valuable information on how plants grow and develop themselves. In this study, a quantitative proteome dataset of the vascular sap proteome of three commercially important Eucalyptus species was shown. Protein extraction was carried out using a pressure bomb, whereas only in silico predicted extracellular proteins were considered as part of the sap proteome. A total of 132 different proteins were identified in all three Eucalyptus species and the most abundant proteome subset within all three species was comprised of proteins involved in the carbohydrate metabolic process, proteolysis, components of membrane, and defense response. The sap proteome of the species E. grandis and E. urophylla revealed the highest similarities. Functional classification indicated that the sap proteome of E. grandis and E. urophylla are mostly comprised of proteins involved in defense response and proteolysis; whereas no prominent functional class was observed for the E. camaldulensis species. Quantitative comparison highlighted characteristic sap proteins in each of the Eucalyptus species. The results that could be found in this study can be used as a reference for the proteome sap analysis of Eucalyptus plants grown under different conditions.
  • ItemArtigo
    Proteomics research in forest trees: A 2012-2022 update
    (2023-01-01) Castillejo, María Angeles; Pascual, Jesús; Jorrín-Novo, Jesus V.; Balbuena, Tiago Santana [UNESP]; University of Cordoba; University of Oviedo; Universidade Estadual Paulista (UNESP)
    This review is a compilation of proteomic studies on forest tree species published in the last decade (2012-2022), mostly focused on the most investigated species, including Eucalyptus, Pinus, and Quercus. Improvements in equipment, platforms, and methods in addition to the increasing availability of genomic data have favored the biological knowledge of these species at the molecular, organismal, and community levels. Integration of proteomics with physiological, biochemical and other large-scale omics in the direction of the Systems Biology, will provide a comprehensive understanding of different biological processes, from growth and development to responses to biotic and abiotic stresses. As main issue we envisage that proteomics in long-living plants will thrive light on the plant responses and resilience to global climate change, contributing to climate mitigation strategies and molecular breeding programs. Proteomics not only will provide a molecular knowledge of the mechanisms of resilience to either biotic or abiotic stresses, but also will allow the identification on key gene products and its interaction. Proteomics research has also a translational character being applied to the characterization of the variability and biodiversity, as well as to wood and non-wood derived products, traceability, allergen and bioactive peptides identification, among others. Even thought, the full potential of proteomics is far from being fully exploited in forest tree research, with PTMs and interactomics being reserved to plant model systems. The most outstanding achievements in forest tree proteomics in the last decade as well as prospects are discussed.
  • ItemArtigo
    Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population
    (2023-01-01) Cheng, Lin; Li, Mengge; Wang, Yachao; Han, Qunwei; Hao, Yanlin; Qiao, Zhen; Zhang, Wei; Qiu, Lin; Gong, Andong; Zhang, Zhihan; Li, Tao; Luo, Shanshan; Tang, Linshuang; Liu, Daliang; Yin, Hao; Lu, Song; Balbuena, Tiago Santana [UNESP]; Zhao, Yiyong; Xinyang Normal University; Beijing Forestry University; Xinyang Forestry Bureau; Northeast Forestry University; Guizhou University; Universidade Estadual Paulista (UNESP)
    As one of the world’s top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.
  • ItemArtigo
    Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups
    (2023-02-01) Serna-García, Marta [UNESP]; Fonseca, Larissa Fernanda Simielli [UNESP]; Panadero Romero, Joaquin Javier; Carretero Asuncion, Julian; dos Santos Silva, Danielly Beraldo [UNESP]; Salatta, Bruna Maria [UNESP]; Frezarim, Gabriela Bonfá [UNESP]; Mercadante, Maria Eugênia Zerlotti; Bonilha, Sarah Figueiredo Martins; Ferro, Jesus Aparecido [UNESP]; De Albuquerque, Lucia Galvão [UNESP]; Universidade Estadual Paulista (UNESP); Igenomix S.L.; University of Valencia; National Council for Scientific and Technological Development (CNPq); Institute of Animal Science
    The identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls. The RNA-seq of the samples from their liver tissues was performed using an Illumina HiSeq 2000. In genetic group 2 (G2), 20 samples of liver tissue of Nellore bulls divergent for RFI (LRFI, n = 10 versus HRFI, n = 10) were selected from 83 animals. The raw data of the G2 were chosen from the ENA repository. A total of 1811 DEGs were found for the G1 and 2054 for the G2 (p-value ≤ 0.05). We detected 88 common genes in both genetic groups, of which 33 were involved in the immune response and in blocking oxidative stress. In addition, seven (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, and ABCF3) possible gene biomarkers were identified through a receiver operating characteristic analysis (ROC) considering an AUC > 0.70. The B2M gene was overexpressed in the LRFI group. This gene regulates the lipid metabolism protein turnover and inhibits cell death. We also found non-coding RNAs in both groups. MIR25 was up-regulated and SNORD16 was down-regulated in the LRFI for G1. For G2, up-regulated RNase_MRP and SCARNA10 were found. We highlight MIR25 as being able to act by blocking cytotoxicity and oxidative stress and RMRP as a blocker of mitochondrial damage. The biological pathways associated with RFI of the liver in Nellore cattle in the two genetic groups were for energy metabolism, protein turnover, redox homeostasis and the immune response. The common transcripts, biomarkers and metabolic pathways found in the two genetic groups make this unprecedented work even more relevant, since the results are valid for different herds raised in different ways. The results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the liver tissue transcriptome of Nellore cattle.
  • ItemArtigo
    Effect of spacing and cutting on pigeon pea development under subtropical conditions
    (2023-01-01) Azevedo, Gláucia Santos Dias; Cazetta, Jairo Osvaldo [UNESP]; Meireles, Rubens de Oliveira; Instituto Federal do Pará; Universidade Estadual Paulista (UNESP)
    Depending on the purpose of its cultivation, pigeon pea can be grown under different spacings and cuts, since it quickly resprouts. This study aimed to assess the pigeon pea growth, forage production and quality, considering two spacings and one cut. A field experiment using a completely randomized design, with three treatments [1.0 × 0.2 m spacing (between rows and plants, respectively), without cuts; 0.5 × 0.1 m, without cuts; and 0.5 × 0.1 m, with cut at 90 days after emergence (DAE)], was carried out. The spacings did not affect the plant height. The 0.5 × 0.1 m spacing showed an individual plant growth worse, but a forage yield (kg ha-1) higher than the 1.0 × 0.2 m treatment, from 120 to 180 DAE. The 0.5 × 0.1 m spacing was more advantageous than the 1.0 × 0.2 m, with the highest forage yield obtained by harvesting at 150 DAE. It is better to harvest the forage at 90 DAE and harvest it again at 180 DAE than maintaining a continuous plant growth and harvest it at 180 DAE. In each sampling date, there was no difference for stem and leaf crude protein and starch content as a function of the treatments. The forage harvested from 90 to 180 DAE showed similar crude protein and starch contents. So, for this period, the forage quality is not a limiting factor for establishing the harvest time.
  • ItemArtigo
    Nickel reduces blossom-end rot even under calcium deficiency conditions evidence from physiological responses of the NI - CA interaction
    (2023-01-01) Macedo, Fernando Giovannetti; de Melo, Wanderley José [UNESP]; Cecílio Filho, Arthur Bernardes [UNESP]; Santos, Elcio Ferreira; Cruz, Renata Beatriz; Belloti, Mariana; Science and Technology of Mato Grosso do Sul; Universidade Estadual Paulista (UNESP); Brazil University; Universidade de São Paulo (USP)
    The isolated study of calcium (Ca) as a cause of blossom-end rot (BER), has not demonstrated advances in the knowledge of this physiological disorder. Recent studies have shown that the Ni-Ca interaction can increase tomato yield and reduce the incidence of BER. Thus, this work aimed to evaluate the effect of nickel (Ni) and Ca interaction on the physiology of tomato plants focusing on nutrient balance, gas exchange and activity of urease and glyoxalase I and II enzymes. Tomato plants were grown in pots with substrate. A random design was used in a 2 x 4 factorial scheme. Two Ca doses (sufficient Ca - Ca S = 0.35; and deficient Ca - Ca D = 0.70 g kg−1) and four Ni doses (0.0, 0.5, 1.0 and 2.0 mg dm−3) was used. The activity of the glyoxalases I and II were used as an indicator of a stress condition. In plants grown under Ca S, the Ni application showed an increase in leaf content of nitrogen, phosphorus, Ca, iron, zinc, boron, copper and Ni, as well the gas exchange enhanced. The urease activity increased as a function of the Ni doses increase. Plants grown with Ca S and Ni doses of 0.5 and 1.0 mg dm−3 showed the lowest glyoxalase activities. The use of Ni at the mentioned doses should be considered in tomato fertilization programs focused on BER reduction.
  • ItemArtigo
    Effects of edible coatings on the quality and storage of early harvested guava
    (2022-10-01) Formiga, Anderson S. [UNESP]; Pereira, Emmanuel M. [UNESP]; Junior, José S. Pinzetta [UNESP]; Costa, Franciscleudo B.; Mattiuz, Ben-Hur [UNESP]; Universidade Estadual Paulista (UNESP); Federal University of Campina Grande (UFCG)
    Guava is a world-renowned fruit of climacteric nature. It is characterized as a perishable fruit and has a short post-harvest shelf life when stored at room temperature. The objective of this work is to study the effects of coatings on the physiology and shelf life of 'Pedro Sato' guavas harvested early. For this, the effect of edible coatings based on hydroxypropyl methylcellulose (HPMC) and beeswax (BW) applied to guavas harvested green and stored for eight days at 22 °C was evaluated. Guavas were coated with HPMC+10% BW; HPMC+20% BW; HPMC+40% BW and Control-uncoated. The coatings reduced the respiration rate, inhibited ethylene synthesis and slowed the ripening process. The main benefits were the reduction in mass loss, maintenance of green color and firmness retention. The treatment with HPMC+20% BW presented the best results in maintaining the quality of the fruits, reducing the activity of the PG enzyme and delaying the ripening of 'Pedro Sato' guavas without promoting the activity of the ADH enzyme and consequently the fermentation of the fruits. fruits. The fruits treated with HPMC+20% CA showed a gain in shelf life of at least six days and despite being harvested green, no disorder affected the ripening process and its quality.
  • ItemArtigo
    Effects of Starch Overload and Cecal Buffering on Fecal Microbiota of Horses
    (2022-12-01) Bustamante, Caio C. [UNESP]; de Paula, Vanessa B. [UNESP]; Rabelo, Isabela P. [UNESP]; Fernandes, Camila C. [UNESP]; Kishi, Luciano T. [UNESP]; Canola, Paulo A. [UNESP]; Lemos, Eliana Gertrudes de M. [UNESP]; Valadão, Carlos Augusto A. [UNESP]; Universidade Estadual Paulista (UNESP)
    Starch overload in horses causes gastrointestinal and metabolic disorders that are associated with microbiota changes. Therefore, we identified the fecal microbiota and hypothesized that intracecal injection of alkaline solution (buffer; Mg(OH)2 + Al(OH)3) could stabilize these microbiota and clinical changes in horses submitted to corn starch overload. Ten crossbred horses (females and geldings) were allocated to group I (water–saline and starch–buffer treatments) and group II (water–buffer and starch–saline treatments). Clinical signs, gross analysis of the feces, and fecal microbiota were evaluated through 72 h (T0; T8; T12; T24; T48; T72). Corn starch or water were administrated by nasogastric tube at T0, and the buffer injected into the cecum at T8 in starch–buffer and water–buffer treatments. Starch overload reduced the richness (p < 0.001) and diversity (p = 0.001) of the fecal microbiota. However, the starch–buffer treatment showed greater increase in amylolytic bacteria (Bifidobacterium 0.0% to 5.6%; Lactobacillus 0.1% to 7.4%; p < 0.05) and decrease in fibrolytic bacteria (Lachnospiraceae 10.2% to 5.0%; Ruminococcaceae 11.7% to 4.2%; p < 0.05) than starch–saline treatment. Additionally, animals that received starch–buffer treatment showed more signs of abdominal discomfort and lameness associated with dysbiosis (amylolytic r > 0.5; fribolytic r < 0.1; p < 0.05), showing that cecal infusion of buffer did not prevent, but intensified intestinal disturbances and the risk of laminitis.
  • ItemArtigo
    Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination
    (2023-02-01) Araujo, Ademir Sergio Ferreira; Miranda, Ana Roberta Lima; Pereira, Arthur Prudêncio de Araujo; de Melo, Wanderley José [UNESP]; Melo, Vania Maria Maciel; Ventura, Sabrina Hermelindo; Brito Junior, Eudemio Sousa; de Medeiros, Erika Valente; Araujo, Fabio Fernando; Mendes, Lucas William; Universidade Federal Do Piaui; Instituto Federal de Educacao Tecnologica Do Maranhao; Universidade Federal Do Ceara; Universidade Estadual Paulista (UNESP); UFAPE; Universidade Do Oeste Paulista; Universidade de São Paulo (USP)
    Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg−1 Cr) and Cr-contaminated soils (∼250 mg kg−1 Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.
  • ItemArtigo
    Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae
    (2022-11-03) Cheng, Lin; Han, Qunwei; Chen, Fei; Li, Mengge; Balbuena, Tiago Santana [UNESP]; Zhao, Yiyong; Xinyang Normal University; Hainan University; Universidade Estadual Paulista (UNESP); Fudan University; Guizhou University
    Hybridization is common and considered as an important evolutionary force to increase intraspecific genetic diversity. Detecting hybridization events is crucial for understanding the evolutionary history of species and further improving molecular breeding. The studies on identifying hybridization events through the phylogenomic approach are still limited. We proposed the conception and method of identifying allopolyploidy events by phylogenomics. The reconciliation and summary of nuclear multi-labeled gene family trees were adopted to untangle hybridization events from next-generation data in our novel phylogenomic approach. Given horticulturalists’ relatively clear cultivated crossbreeding history, the water lily family is a suitable case for examining recent allopolyploidy events. Here, we reconstructed and confirmed the well-resolved nuclear phylogeny for the Nymphaeales family in the context of geological time as a framework for identifying hybridization signals. We successfully identified two possible allopolyploidy events with the parental lineages for the hybrids in the family Nymphaeaceae based on summarization from multi-labeled gene family trees of Nymphaeales. The lineages where species Nymphaea colorata and Nymphaea caerulea are located may be the progenitors of horticultural cultivated species Nymphaea ‘midnight’ and Nymphaea ‘Woods blue goddess’. The proposed hybridization hypothesis is also supported by horticultural breeding records. Our methodology can be widely applied to identify hybridization events and theoretically facilitate the genome breeding design of hybrid plants.
  • ItemArtigo
    Comparative genomics study of Staphylococcus aureus isolated from cattle and humans reveals virulence patterns exclusively associated with bovine clinical mastitis strains
    (2022-11-07) Rodrigues, Romário Alves [UNESP]; Pizauro, Lucas José Luduverio [UNESP]; Varani, Alessandro de Mello [UNESP]; de Almeida, Camila Chioda [UNESP]; Silva, Saura Rodrigues [UNESP]; Cardozo, Marita Vedovelli; MacInnes, Janet I.; Kropinski, Andrew M.; Melo, Poliana de Castro; Ávila, Fernando Antonio [UNESP]; Universidade Estadual Paulista (UNESP); Santa Cruz State University; Minas Gerais State University; University of Guelph
    Staphylococcus aureus causes nosocomial and intramammary infections in humans and cattle, respectively. A large number of virulence factors are thought to play important roles in the pathogenesis of this bacterium. Currently, genome-wide and data-analysis studies are being used to better understand its epidemiology. In this study, we conducted a genome wide comparison and phylogenomic analyses of S. aureus to find specific virulence patterns associated with clinical and subclinical mastitis strains in cattle and compare them with those of human origin. The presence/absence of key virulence factors such as adhesin, biofilm, antimicrobial resistance, and toxin genes, as well as the phylogeny and sequence type of the isolates were evaluated. A total of 248 genomes (27 clinical mastitis, 43 subclinical mastitis, 21 milk, 53 skin-related abscesses, 49 skin infections, and 55 pus from cellulitis) isolated from 32 countries were evaluated. We found that the cflA, fnbA, ebpS, spa, sdrC, coa, emp, vWF, atl, sasH, sasA, and sasF adhesion genes, as well as the aur, hglA, hglB, and hglC toxin genes were highly associated in clinical mastitis strains. The strains had diverse genetic origins (72 protein A and 48 sequence types with ST97, ST8 and ST152 being frequent in isolates from clinical mastitis, abscess, and skin infection, respectively). Further, our phylogenomic analyses suggested that zoonotic and/or zooanthroponotic transmission may have occurred. These findings contribute to a better understanding of S. aureus epidemiology and the relationships between adhesion mechanisms, biofilm formation, antimicrobial resistance, and toxins and could aid in the development of improved vaccines and strain genotyping methods.
  • ItemArtigo
    Charcoal fine residues used as biochar in heavy clayey soil improve carrot production
    (2022-01-01) de Mendonça, Ademir Ribeiro [UNESP]; Cazetta, Jairo Osvaldo [UNESP]; Gonçalves, Paula Wellen Barbosa [UNESP]; Universidade Estadual Paulista (UNESP)
    Carrot plants do not develop well in clayey soils. In its turn, the charcoal fine (CF), which is a residue composed of porous particles, has the potential to be mixed in the soil to reduce its density. However, there is no evidence that the application of CF improves carrot production in clayey soil. Thus, an experiment in pots was designed, consisting of 16 treatments composed of the combination of 5 sizes of CF particles (1-2 mm, 2-4 mm, 4-8 mm, 8-16 mm, 16-32 mm) with 3 volumetric rates of CF (25%, 50% and 75%, plus a control (soil alone), aiming to verify which situation promotes the better plant growth and production. It was observed that mixing CF into the soil decreases substrate density and increases substrate water retention. The results of this research also revealed that the highest yield (fresh and dry weight) of carrots was achieved with CF mixed with the soil at a rate of 50%, using a CF particle size of 2-4 mm. The greatest length and diameter of carrots were obtained with a dose of CF of around 45%. CF-containing substrates delayed initial plant growth up to 45 DAE, but increased plant development after 75 DAE and improved plant performance and carrot yield measured at the harvest time (90 DAE).
  • ItemArtigo
    Dynamics of the role of LacMeta laccase in the complete degradation and detoxification of malachite green
    (2023-05-01) Lima, Natália Sarmanho Monteiro [UNESP]; Gomes-Pepe, Elisângela Soares [UNESP]; Kock, Flavio Vinicius Crizostomo; Colnago, Luiz Alberto; de Macedo Lemos, Eliana Gertrudes [UNESP]; Universidade Estadual Paulista (UNESP); Institute for Research in Bioenergy (IPBEN); Universidade Federal de São Carlos (UFSCar); Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
    Laccases highlight for xenobiotic bioremediation, as well as application in the fine chemical, textile, biofuel and food industries. In a previous work, we described the preliminary characterization of laccase LacMeta, a promising enzyme for the bioremediation of dyes, able to decolorization malachite green (MG), trypan blue, methylene blue. Here we demonstrate that LacMeta is indeed suitable for the complete degradation and detoxification of MG dye, not just for its discoloration, since some works show false positives due to the formation of colorless intermediates such as leucomalachite. The optimal pH and temperature parameters of LacMeta were 5.0 and 50 °C, respectively (MG as substrate). LacMeta was tolerant of up to 10 mmol L− 1 EDTA (82%) and up to 5% (V/V) acetone (91%) and methanol (71%), while SDS promoted severe inhibition. For ions, a high tolerance to cobalt, zinc, manganese, and calcium (10 mmol L− 1) was also observed (> 90%). Even under high-salinity conditions (1 mol L− 1 NaCl), the residual bleaching activity of the dye remained at 61%. Furthermore, the bleaching product of MG did not inhibit the germination of sorghum and tomato seeds and was inert to the vegetative structures of the germinated seedlings. Additionally, this treatment effectively reduced the cytotoxic effect of the dye on microorganisms (Escherichia coli and Azospirillum brasilense), which can be explained by H-NMR spectral analysis results since LacMeta completely degraded the peak signals corresponding to the aromatic rings in the dye, demonstrating extreme efficiency in the bioremediation of the xenobiotic at high concentrations (50 mg L− 1).
  • ItemArtigo
    Genome-wide analysis of the chromatin sites targeted by HEX 70a storage protein in the honeybee brain and fat body
    (2023-06-01) Martins, Juliana R.; Pinheiro, Daniel G. [UNESP]; Ahmed, Amy C. C.; Giuliatti, Silvana; Mizzen, Craig A.; Bitondi, Márcia M. G.; Faculdade de Medicina de Ribeirão Preto; Universidade Estadual Paulista (UNESP); Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Ciências e Letras de Ribeirão Preto
    Hexamerins, the proteins massively stored in the larval haemolymph of insects, are gradually used throughout metamorphosis as a source of raw material and energy for the development of adult tissues. Such behaviour defined hexamerins as storage proteins. Immunofluorescence experiments coupled with confocal microscopy show a hexamerin, HEX 70a, in the nucleus of the brain and fat body cells from honeybee workers, an unexpected localization for a storage protein. HEX 70a colocalizes with fibrillarin, a nucleolar-specific protein and H3 histone, thus suggesting a potential role as a chromatin-binding protein. This was investigated through chromatin immunoprecipitation and high-throughput DNA sequencing (ChIP-seq). The significant HEX 70a-DNA binding sites were mainly localized at the intergenic, promoter and intronic regions. HEX 70a targeted DNA stretches mapped to the genomic regions encompassing genes with relevant functional attributes. Several HEX 70a targeted genes were associated with H3K27ac or/and H3K27me3, known as active and repressive histone marks. Brain and fat body tissues shared a fraction of the HEX 70 targeted genes, and tissue-specific targets were also detected. The presence of overrepresented DNA motifs in the binding sites is consistent with specific HEX 70a-chromatin association. In addition, a search for HEX 70a targets in RNA-seq public libraries of fat bodies from nurses and foragers revealed differentially expressed targets displaying hex 70a-correlated developmental expression, thus supporting a regulatory activity for HEX 70a. Our results support the premise that HEX 70a is a moonlighting protein that binds chromatin and has roles in the brain and fat body cell nuclei, apart from its canonical role as a storage protein.
  • ItemArtigo
    The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae)
    (2023-04-01) Silva, Saura R. [UNESP]; Miranda, Vitor F.O. [UNESP]; Michael, Todd P.; Płachno, Bartosz J.; Matos, Ramon G. [UNESP]; Adamec, Lubomir; Pond, Sergei L.K.; Lucaci, Alexander G.; Pinheiro, Daniel G. [UNESP]; Varani, Alessandro M. [UNESP]; Universidade Estadual Paulista (UNESP); The Salk Institute for Biological Studies; Jagiellonian University in Kraków; Institute of Botany CAS; Temple University
    Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts’ nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.
  • ItemCapítulo de livro
    Influence of Long-Term Soil Application of Sewage Sludge Rich in Phosphorus on Heavy Metals Bioavailability to Plants
    (2018-01-01) de Melo, Wanderley José [UNESP]; Peruca de Melo, Gabriel Maurício; de Melo, Valéria Peruca; Universidade Estadual Paulista (UNESP); Universidade Camilo Castelo Branco
    Sewage sludge presents risk to the environment and to human health, and therefore its correct disposal is a problem to be solved as quickly as possible. Its use in agriculture as a fertilizer or soil amendment has drawn the attention of producers because sewage sludge contains large concentrations of organic matter and plant nutrients such as nitrogen (N), phosphorus (P), zinc (Zn), and others. However, along with these welcome components, sewage sludge also contains in its composition potentially toxic trace elements and organic substances that are hazardous. Considering the benets and the risks of applying sewage sludge in agriculture, it is important to know the composition of the residue to be used, the soil properties where it will be used, and the climatic conditions. These factors are important because the trace elements available to plants will also move down the soil prole and contaminate underground water. It is important to prevent the entering of trace elements in the human food chain.
  • ItemArtigo
    The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew
    (2022-10-18) Varani, Alessandro M. [UNESP]; Silva, Saura R. [UNESP]; Lopes, Simone; Barbosa, Jose Beethoven Figueiredo; Oliveira, Danilo; Corrêa, Maria Alice; Moraes, Ana Paula; Miranda, Vitor F.O. [UNESP]; Prosdocimi, Francisco; Universidade Estadual Paulista (UNESP); State University of Paraíba (UEPB); Federal University of Roraima (UFRR); Universidade Federal do Rio de Janeiro (UFRJ); Universidade Federal do ABC (UFABC)
    Psychotria viridis (Rubioideae: Rubiaceae), popularly known as chacrona, is commonly found as a shrub in the Amazon region and is well-known to produce psychoactive compounds, such as the N,N-dimethyltryptamine (DMT). Together with the liana Banisteropsis caapi, P. viridis is one of the main components of the Amerindian traditional, entheogenic beverage known as ayahuasca. In this work, we assembled and annotated the organellar genomes (ptDNA and mtDNA), presenting the first genomics resources for this species. The P. viridis ptDNA exhibits 154,106 bp, encoding all known ptDNA gene repertoire found in angiosperms. The Psychotria genus is a complex paraphyletic group, and according to phylogenomic analyses, P. viridis is nested in the Psychotrieae clade. Comparative ptDNA analyses indicate that most Rubiaceae plastomes present conserved ptDNA structures, often showing slight differences at the junction sites of the major four regions (LSC-IR-SSC). For the mitochondrion, assembly graph-based analysis supports a complex mtDNA organization, presenting at least two alternative and circular mitogenomes structures exhibiting two main repeats spanning 24 kb and 749 bp that may symmetrically isomerize the mitogenome into variable arrangements and isoforms. The circular mtDNA sequences (615,370 and 570,344 bp) encode almost all plant mitochondrial genes (except for the ccmC, rps7, rps10, rps14, rps19, rpl2 and rpl16 that appears as pseudogenes, and the absent genes sdh3, rps2, rsp4, rsp8, rps11, rpl6, and rpl10), showing slight variations related to exclusive regions, ptDNA integration, and relics of previous events of LTR-RT integration. The detection of two mitogenomes haplotypes is evidence of heteroplasmy as observed by the complex organization of the mitochondrial genome using graph-based analysis. Taken together, these results elicit the primary insights into the genome biology and evolutionary history of Psychotria viridis and may be used to aid strategies for conservation of this sacred, entheogenic species.
  • ItemArtigo
    Iron biofortification in quinoa: Effect of iron application methods on nutritional quality, anti-nutrient composition, and grain productivity
    (2023-03-15) Lata-Tenesaca, Luis Felipe [UNESP]; de Mello Prado, Renato [UNESP]; Ajila-Celi, Gabriela Eugenia [UNESP]; da Silva, Dalila Lopes; Junior, José Sidnaldo Pinzetta [UNESP]; Mattiuz, Ben-Hur [UNESP]; Universidade Federal de Viçosa (UFV); Universidade Estadual Paulista (UNESP); Universidade de São Paulo (USP)
    Biofortification of iron (Fe) in quinoa (Chenopodium quinoa) grains should have benefits for human health and food security. However, effects of this approach on productivity, as well as Fe content and grain quality remain unknown. Thus, a greenhouse experiment was conducted to determine the impacts of different methods of Fe delivery in a hydroponic system, root application (90 µmol/L), foliar spraying (9 mmol/L), combined root and foliar application, and control (no Fe). Foliar Fe application in four applications at vegetative and reproductive stages stood out from root application in promoting quinoa growth and productivity, perhaps because of greater accumulation of Fe in the plants, leading to increased photosynthetic pigments and electron transport. Foliar application of Fe also improved grain quality, as it was associated with higher Fe contents, ascorbic acid (AsA), total proteins, and manganese (Mn). In addition, there was a decrease in antinutritional compounds and phosphorus (P) in grains. Foliar Fe application can be an efficient agronomic practice to obtain Fe-biofortified quinoa grains and was associated with improved physiological responses and productivity.
  • ItemArtigo
    Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins
    (2022-01-01) Rodrigues Blanco, Iago; José Luduverio Pizauro, Lucas [UNESP]; Victor dos Anjos Almeida, João [UNESP]; Miguel Nóbrega Mendonça, Carlos; de Mello Varani, Alessandro [UNESP]; Pinheiro de Souza Oliveira, Ricardo; Universidade de São Paulo (USP); Universidade Estadual Paulista (UNESP)
    Bacteriocins are antimicrobial peptides produced by different species of bacteria, especially the Gram-positive lactic acid bacteria (LAB). Pediococcus pentosaceus is widely applied in the industry and stands out as Bacteriocin-Like Inhibitory Substances (BLIS) producer known to inhibit pathogens commonly considered a concern in the food industries. This study aimed to perform in silico comparisons of P. pentosaceus genomes available in the public GenBank database focusing on their pediocin-like bacteriocins repertoire. The pan-genome analysis evidenced a temporal signal in the pattern of gene gain and loss, supporting the hypothesis that the complete genetic repertoire of this group of bacteria is still uncovered. Thirteen bacteriocin genes from Class II and III were predicted in the accessory genome. Four pediocin-like bacteriocins (54% of the detected bacteriocin repertoire) and their accompanying immunity genes are highlighted; penocin A, coagulin A, pediocin PA-1, and plantaricin 423. Additionally, in silico, modeling of the pediocin-like bacteriocins revealed different configurations of the helix motif compared to other physically determined pediocin-like structures. Comparative and phylogenomic analyses support the hypothesis that a dynamic mechanism of bacteriocin acquisition and purging is not dependent on the bacterial isolation source origin. Synteny analysis revealed that while coagulin A, pediocin PA-1, and Plantaricin 423 loci are associated with insertion sequences mainly from the IS30 family and are likely of plasmid origin, penocin A lies in a conserved chromosomal locus. The results presented here provide insights into the unique pediocin-like bacteriocin peptide fold, genomic diversity, and the evolution of the bacteriocin genetic repertoire of P. pentosaceus, shedding new insights into the role of these biomolecules for application in inhibiting bacterial pathogens, and suggesting that prospecting and sequencing new strains is still an alternative to mining for new probiotic compounds.