Biology subjects

Melo, F. L.

Publications and source records attributed to Melo, F. L..

6 recordsLinked to original sources

bioRxiv2025

In silico description of a new Amalgavirus in the Cannabis sativa transcriptome

Cannabis sativa has a variety of industrial interest products, such as phytocannabinoids, terpenoids, phenylpropanoids, acyl sugars, and fibers. Several described pathogens, including viral species, will impact the current green cannabis revolution. The recent sequencing of its genome and transcriptome, allowing the optimization and understanding of the production of the metabolite, are a relevant tool for viruses presence analyzing. Using the cannabis transcriptome and Data mining analysis, we describe the first amalgavirus infecting Cannabis, the Cannabis sativa amalgavirus 1 (CSA1). The plant amalgaviruses has nine species infecting relevant crops. Like the other genus members, this cannabis virus has approximately 3.5 kb with two partially overlapping putative open reading frames with the characteristic +1 programmed ribosomal frameshifting. Mainly detected in the male plant, the CSA1 mapped reads were present in the flower and leaf tissues. Nevertheless, the possible impacts of viral replication on host metabolism and the production of secondary compounds are unknown.

bioinformatics↗

bioRxiv2024

Development of Int-Plex@ binary memory switch system: plant genome modulation driven by large serine-integrases.

The comprehension of virus-host interactions has allowed numerous advances in developing biotechnological methodologies for plant genome editions, constituting a promising path for plant genetic engineering. Among these advancements, phage- encoded large serine-integrases have emerged as noteworthy tools to modulate plant metabolic pathways by inserting, excising, or inverting DNA stretches in a reversible and specific way. The present work shows the foundation of the Int-Plex@ (INTegrase PLant EXpression) binary memory switch system, which consists of the application of four distinct orthogonal prophage large serine-integrases (Int) (BxB1, phiC31, Int13, and Int9) as an input trigger mechanism for the inversion or excision of genomic DNA. The memory genetic switch is divided into the excision module and the inversion module. The excision module is activated by BxB1 or phiC31 enzymes (input). In this case, the DNA sequence flanked by its attachment sites is excised from the genome (output). The inversion module is activated by Int9 or Int13 (input). The inverted mgf gene sequence is flipped to its functional coding sequence, and the switch output is mGFP. Moreover, prokaryotic-based cell-free in vitro transcription-translation reactions (TxTl) were used as a fast platform for testing Ints attB/P in tandem site activity. Furthermore different plasmid delivery strategies for plant cell Int heterologous expression were tested: leaf tissue agroinfiltration of Agrobacterium tumefaciens transformed with binary plasmids and a biolistic system. After each treatment, the edited genomic DNA sequences were amplified and verified by Sanger and Nanopore sequencing. Despite the challenges of using Ints, the potential benefits are significant and deserve deeper exploration and development. The Int-Plex@ binary genome memory switch system can be applied to produce genetic circuits combined with omics tools and sgRNAs to engineer and modulate plant metabolic pathways temporally and reversibly.

synthetic biology↗

bioRxiv2021

Real-time genomic surveillance during the 2021 re-emergence of the yellow fever virus in Rio Grande do Sul State, Brazil

The yellow fever virus (YFV) re-emergence in Rio Grande do Sul, Brazil, raised big concerns and led the state to declare a Public Health Emergency of State Importance. Here, we generated near-complete genomes from the ongoing outbreak in Southern Brazil, aiming to better understand the phylogenetic aspects and also spatio-temporal dynamics of the virus. Our findings highlight the path and dispersion in Rio Grande do Sul and that YFV was reintroduced from Sao Paulo to the Rio Grande do Sul state through Parana and Santa Catarina states, at the end of 2020.

genomics↗

bioRxiv2021

Detection of potential new SARS-CoV-2 Gamma-related lineage in Tocantins shows the spread and ongoing evolution of P.1 in Brazil

After more than a year of the pandemic situation of COVID-19, the United Kingdom (UK), South Africa, and Brazil became the epicenter of new lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Variants of Concern (VOCs) were identified through a continuous genomic surveillance global effort, the B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and P.1 (Gamma) harboring a constellation set of mutations. This research aims to: (i) report the predominance of the Gamma (P.1) lineage presenting the epidemiological situation of the SARS-CoV-2 genomic surveillance at the state of Tocantins, and (ii) describe the emergence of possible new mutations and viral variants with the potential new lineage (P1-related) represented by 8 genomes from the Tocantins harboring the mutation L106F in ORF3a. At the moment, 6,687 SARS-CoV-2 genomes from GISAID carry this mutation. The whole-genome sequencing has an important role in understanding the evolution and genomic diversity of SARS-CoV-2, thus, the continuous monitoring will help in the control measures and restrictions imposed by the secretary of health of the state to prevent the spread of variants.

genomics↗

bioRxiv2020

Heterogeneity in the response of different subtypes of Drosophila melanogaster enteroendocrine cells to viral infections

Single cell RNA sequencing (scRNA-seq) offers the possibility to monitor both host and pathogens transcriptomes at the cellular level. Here, public scRNA-seq data from Drosophila melanogaster have been used to compare the differences in replication strategy and cellular response between two viruses, Thika virus (TV) and D. melanogaster Nora virus (DMelNV) in enteroendocrine cells (EEs). TV and DMelNV exhibited different patterns of replication and for TV, accumulation varied according to cell subtype. Cells infected with TV underwent down-regulation of genes that represent bottlenecks in the fruit fly interactome, while cells infected with DMelNV went through a down-expression of translation-related genes that represent both hubs and bottlenecks in the host interactome. In contrast, flies infected with DMelNV show only a systemic level down-regulation of bottleneck genes. Here, we use scRNA-seq to highlight the differences and commonalities between cellular response to TV and DMelNV and between cellular and systemic response to DMelNV.

systems biology↗

bioRxiv2018

Genome-wide diversity in temporal and regional populations of the betabaculovirus Erinnyis ello granulovirus (ErelGV)

BackgroundErinnyis ello granulovirus (ErelGV) is a betabaculovirus infecting caterpillars of the sphingid moth E. ello ello (cassava hornworm), an important pest of cassava crops (Manihot esculenta). In this study, the genome of seven field isolates of the virus ErelGV were deep sequenced and their inter-and intrapopulational sequence diversity were analyzed.\n\nResultsNo events of gene gain/loss or translocations were observed, and indels were mainly found within highly repetitive regions (direct repeats, drs). A naturally occurring isolate from Northern Brazil (Acre State, an Amazonian region) has shown to be the most diverse population, with a unique pattern of polymorphisms. Overall, non-synonymous substitutions were found all over the seven genomes, with no specific gathering of mutations on hotspot regions. Independently of their sizes, some ORFs have shown higher levels of non-synonymous changes than others. Non-core genes of known functions and structural genes were among the most diverse ones; and as expected, core genes were the least variable genes. We observed remarkable differences on diversity of paralogous genes, as in multiple copies of p10, fgf, and pep. Another important contrast on sequence diversity was found on genes encoding complex subunits and/or involved in the same biological processes, as late expression factors (lefs) and per os infectivity factors (pifs). Interestingly, several polymorphisms in coding regions lie on sequences encoding specific protein domains.\n\nConclusionsBy comparing and integrating information about inter-and intrapopulational diversity of viral isolates, we provide a detailed description on how evolution operates on field isolates of a betabaculovirus. Our results revealed that 35-41% of the SNPs of ErelGV lead to amino acid changes (non-synonymous substitutions). Some genes, especially non-core genes of unknown functions, tend to accumulate more mutations, while core genes evolve slowly and are more conserved. Additional studies would be necessary to understand the actual effects of such gene variations on viral infection and fitness.

genomics↗