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Article ; Online: Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions

Marina Püpke Marone / Maria Fernanda Zaneli Campanari / Fabio Trigo Raya / Gonçalo Amarante Guimarães Pereira / Marcelo Falsarella Carazzolle

PeerJ, Vol 10, p e

2022 Volume 13252

Abstract: Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. ... ...

Abstract	Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting point to the study of the potential uses of agaves’ ...
Keywords	Agave ; Microbiome ; Transcriptome ; Root ; Drought resistance ; Fungal communities ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Time for Chocolate

Paulo José Pereira Lima Teixeira / Daniela Paula de Toledo Thomazella / Gonçalo Amarante Guimarães Pereira

PLoS Pathogens, Vol 11, Iss 10, p e

Current Understanding and New Perspectives on Cacao Witches' Broom Disease Research.

2015 Volume 1005130

Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2015-10-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Static microplate fermentation and automated growth analysis approaches identified a highly-aldehyde resistant Saccharomyces cerevisiae strain

de Mello, Fellipe da Silveira Bezerra / Alessandro Luis Venega Coradini / Gleidson Silva Teixeira / Gonçalo Amarante Guimarães Pereira / Marcelo Falsarella Carazzolle / Pedro Augusto Galvão Tizei

Biomass and bioenergy. 2019 Jan., v. 120

2019

Abstract: The need to replace fossil fuels has motivated research to develop alternative technologies for renewable energy production. For second generation ethanol, this includes the high-throughput screening and selection of yeast strains resistant to inhibitory ...

Abstract	The need to replace fossil fuels has motivated research to develop alternative technologies for renewable energy production. For second generation ethanol, this includes the high-throughput screening and selection of yeast strains resistant to inhibitory byproducts of biomass pretreatment. In this work, we evaluated the use of static growth in 96-well microplates as a fermentative assay for Saccharomyces cerevisiae high-throughput screening, together with robust OD measurement correlations that overcome the low absorbance limit found in conventional plate spectrophotometers. This resulted in a method of yeast cultivation in microplates that requires no agitation and results in accurate kinetic parameters that can be used for the screening of S. cerevisiae. In order to automate calculation of these physiological parameters, we created OCHT®, an open-source high-throughput phenotype profiling software for processing, analyzing and visualizing S. cerevisiae growth data. Together, the cultivation standardization and data analysis toolbox allowed the evaluation and comparison of four S. cerevisiae strains in media containing aldehydes growth inhibitors, typically found in hydrolysates produced from sugarcane biomass. We identified FMY001 (SA1-derived) as a tolerant strain at high concentrations of HMF, furfural and vanillin. The individual analysis of segregants derived from FMY001 demonstrated their potential application in emerging biotechnological processes and gave us preliminary insights about the genetic mechanisms related to its high HMF concentration tolerance.
Keywords	absorbance ; agitation ; automation ; biomass ; byproducts ; computer software ; ethanol ; fermentation ; fossil fuels ; furfural ; growth inhibitors ; hydrolysates ; hydroxymethylfurfural ; phenotype ; renewable energy sources ; Saccharomyces cerevisiae ; screening ; spectrophotometers ; sugarcane ; vanillin ; yeasts
Language	English
Dates of publication	2019-01
Size	p. 49-58.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1090121-8
ISSN	0961-9534
ISSN	0961-9534
DOI	10.1016/j.biombioe.2018.10.019
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Author Correction

Thais Sibioni Berti Bastos / André Guilherme Portela de Paula / Rebeca Bosso dos Santos Luz / Anali M. B. Garnique / Marco A. A. Belo / Silas Fernandes Eto / Dayanne Carla Fernandes / Fausto Klabund Ferraris / Leticia Gomes de Pontes / Tábata Takahashi França / Leonardo José Gil Barcellos / Flavio P. Veras / Pamela Bermejo / Giovanna Guidelli / Carla Maneira / Fellipe da Silveira Bezerra de Mello / Gleidson Teixeira / Gonçalo Amarante Guimarães Pereira / Bianca H. Ventura Fernandes /

Paulo R. S. Sanches / Helyson Lucas Bezerra Braz / Roberta Jeane Bezerra Jorge / Guilherme Malafaia / Eduardo M. Cilli / Danilo da Silva Olivier / Marcos Serrou do Amaral / Renata J. Medeiros / Antonio Condino-Neto / Luciani R. Carvalho / Glaucia M. Machado-Santelli / Ives Charlie-Silva / Jorge Galindo-Villegas / Tárcio Teodoro Braga

Scientific Reports, Vol 13, Iss 1, Pp 1-

A novel insight on SARS-CoV-2 S-derived fragments in the control of the host immunity

2023 Volume 2

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A novel insight on SARS-CoV-2 S-derived fragments in the control of the host immunity

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 15

Abstract: Abstract Despite all efforts to combat the pandemic of COVID-19, we are still living with high numbers of infected persons, an overburdened health care system, and the lack of an effective and definitive treatment. Understanding the pathophysiology of ... ...

Abstract	Abstract Despite all efforts to combat the pandemic of COVID-19, we are still living with high numbers of infected persons, an overburdened health care system, and the lack of an effective and definitive treatment. Understanding the pathophysiology of the disease is crucial for the development of new technologies and therapies for the best clinical management of patients. Since the manipulation of the whole virus requires a structure with an adequate level of biosafety, the development of alternative technologies, such as the synthesis of peptides from viral proteins, is a possible solution to circumvent this problem. In addition, the use and validation of animal models is of extreme importance to screen new drugs and to compress the organism's response to the disease. Peptides derived from recombinant S protein from SARS-CoV-2 were synthesized and validated by in silico, in vitro and in vivo methodologies. Macrophages and neutrophils were challenged with the peptides and the production of inflammatory mediators and activation profile were evaluated. These peptides were also inoculated into the swim bladder of transgenic zebrafish larvae at 6 days post fertilization (dpf) to mimic the inflammatory process triggered by the virus, which was evaluated by confocal microscopy. In addition, toxicity and oxidative stress assays were also developed. In silico and molecular dynamics assays revealed that the peptides bind to the ACE2 receptor stably and interact with receptors and adhesion molecules, such as MHC and TCR, from humans and zebrafish. Macrophages stimulated with one of the peptides showed increased production of NO, TNF-α and CXCL2. Inoculation of the peptides in zebrafish larvae triggered an inflammatory process marked by macrophage recruitment and increased mortality, as well as histopathological changes, similarly to what is observed in individuals with COVID-19. The use of peptides is a valuable alternative for the study of host immune response in the context of COVID-19. The use of zebrafish as an animal ...
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Conversion of an inactive xylose isomerase into a functional enzyme by co-expression of GroEL-GroES chaperonins in Saccharomyces cerevisiae

Temer, Beatriz / Cidnei Marschalk / Gonçalo Amarante Guimarães Pereira / Juliana José / Juliana Pimentel Galhardo / Leandro Vieira dos Santos / Marcelo Falsarella Carazzolle / Pedro Henrique Mello Magalhães / Thamy Lívia Ribeiro Corrêa / Victor Augusti Negri

BMC biotechnology. 2017 Dec., v. 17, no. 1

2017

Abstract: BACKGROUND: Second-generation ethanol production is a clean bioenergy source with potential to mitigate fossil fuel emissions. The engineering of Saccharomyces cerevisiae for xylose utilization is an essential step towards the production of this biofuel. ...

Abstract	BACKGROUND: Second-generation ethanol production is a clean bioenergy source with potential to mitigate fossil fuel emissions. The engineering of Saccharomyces cerevisiae for xylose utilization is an essential step towards the production of this biofuel. Though xylose isomerase (XI) is the key enzyme for xylose conversion, almost half of the XI genes are not functional when expressed in S. cerevisiae. To date, protein misfolding is the most plausible hypothesis to explain this phenomenon. RESULTS: This study demonstrated that XI from the bacterium Propionibacterium acidipropionici becomes functional in S. cerevisiae when co-expressed with GroEL-GroES chaperonin complex from Escherichia coli. The developed strain BTY34, harboring the chaperonin complex, is able to efficiently convert xylose to ethanol with a yield of 0.44 g ethanol/g xylose. Furthermore, the BTY34 strain presents a xylose consumption rate similar to those observed for strains carrying the widely used XI from the fungus Orpinomyces sp. In addition, the tetrameric XI structure from P. acidipropionici showed an elevated number of hydrophobic amino acid residues on the surface of protein when compared to XI commonly expressed in S. cerevisiae. CONCLUSIONS: Based on our results, we elaborate an extensive discussion concerning the uncertainties that surround heterologous expression of xylose isomerases in S. cerevisiae. Probably, a correct folding promoted by GroEL-GroES could solve some issues regarding a limited or absent XI activity in S. cerevisiae. The strains developed in this work have promising industrial characteristics, and the designed strategy could be an interesting approach to overcome the non-functionality of bacterial protein expression in yeasts.
Keywords	amino acids ; bacteria ; bacterial proteins ; biofuels ; chaperonins ; emissions ; engineering ; Escherichia coli ; ethanol ; ethanol production ; fossil fuels ; genes ; heterologous gene expression ; hydrophobicity ; Propionibacterium acidipropionici ; protein folding ; protein synthesis ; Saccharomyces cerevisiae ; uncertainty ; xylose ; xylose isomerase ; yeasts
Language	English
Dates of publication	2017-12
Size	p. 71.
Publishing place	BioMed Central
Document type	Article
ISSN	1472-6750
DOI	10.1186/s12896-017-0389-7
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance

Ramon Oliveira Vidal / Leandro Costa do Nascimento / Jorge Maurício Costa Mondego / Gonçalo Amarante Guimarães Pereira / Marcelo Falsarella Carazzolle

Genetics and Molecular Biology, Vol 35, Iss 1, Pp 331-

2012 Volume 334

Abstract: The legume Glycine max (soybean) plays an important economic role in the international commodities market, with a world production of almost 260 million tons for the 2009/2010 harvest. The increase in drought events in the last decade has caused ... ...

Abstract	The legume Glycine max (soybean) plays an important economic role in the international commodities market, with a world production of almost 260 million tons for the 2009/2010 harvest. The increase in drought events in the last decade has caused production losses in recent harvests. This fact compels us to understand the drought tolerance mechanisms in soybean, taking into account its variability among commercial and developing cultivars. In order to identify single nucleotide polymorphisms (SNPs) in genes up-regulated during drought stress, we evaluated suppression subtractive libraries (SSH) from two contrasting cultivars upon water deprivation: sensitive (BR 16) and tolerant (Embrapa 48). A total of 2,222 soybean genes were up-regulated in both cultivars. Our method identified more than 6,000 SNPs in tolerant and sensitive Brazilian cultivars in those drought stress related genes. Among these SNPs, 165 (in 127 genes) are positioned at soybean chromosome ends, including transcription factors (MYB, WRKY) related to tolerance to abiotic stress.
Keywords	single nucleotide polymorphisms ; deep sequencing ; drought resistance ; Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	580
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Sociedade Brasileira de Genética
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A web-based bioinformatics interface applied to the GENOSOJA project

Leandro Costa do Nascimento / Gustavo Gilson Lacerda Costa / Eliseu Binneck / Gonçalo Amarante Guimarães Pereira / Marcelo Falsarella Carazzolle

Genetics and Molecular Biology, Vol 35, Iss 1, Pp 203-

databases and pipelines

2012 Volume 211

Abstract: The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic ... ...

Abstract	The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive cDNA libraries), as well as web interfaces to access information about soybean gene annotation and expression.
Keywords	bioinformatics ; database ; gene expression ; soybean ; Genosoja ; Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	004
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Sociedade Brasileira de Genética
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis.

Suzana Tiemi Ivamoto / Osvaldo Reis / Douglas Silva Domingues / Tiago Benedito Dos Santos / Fernanda Freitas de Oliveira / David Pot / Thierry Leroy / Luiz Gonzaga Esteves Vieira / Marcelo Falsarella Carazzolle / Gonçalo Amarante Guimarães Pereira / Luiz Filipe Protasio Pereira

PLoS ONE, Vol 12, Iss 1, p e

2017 Volume 0169595

Abstract: Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are ...

Abstract	Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs). These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we identified ~24,000 putative target sites for microRNAs (miRNAs) and 134 putative transcriptionally active transposable elements (TE) sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: IIS--Integrated Interactome System

Marcelo Falsarella Carazzolle / Lucas Miguel de Carvalho / Hugo Henrique Slepicka / Ramon Oliveira Vidal / Gonçalo Amarante Guimarães Pereira / Jörg Kobarg / Gabriela Vaz Meirelles

PLoS ONE, Vol 9, Iss 6, p e

a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools.

2014 Volume 100385

Abstract: High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic ... ...

Abstract	High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted.We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web.We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it ...
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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