Biology subjects

Virgilio, M.

Publications and source records attributed to Virgilio, M..

4 recordsLinked to original sources

bioRxiv2023

Diversity and abundance of pestiferous fruit flies (Diptera: Tephritidae) infesting cucurbit crops in Morogoro, eastern-central Tanzania

Fruit flies represent a significant threat to cucurbit production. They inflict about 30% to 100% losses on cucurbit crops. The aim of this study was to characterize the community of fruit flies infesting cucurbit crops in Morogoro, Tanzania. We investigate the diversity and abundance of fruit fly species infesting cucumber, watermelon, and squash across the two agroecological zones of the Morogoro using three attractants (Cue Lure, Zingerone and Biolure). The attractants were deployed for 16 weeks from June to November 2020. In total, 12017 fruit fly specimens were collected. Of these, 77.23% were collected from the mountainous and the remaining 22.77% from the plateau zone. All specimens belonged to the genera Dacus, Zeugodacus and Bactrocera. Zeugodacus cucurbitae was the most abundant species (77.6%) while the remaining species constituted 22.4%. The mountainous zone harboured a significantly higher number of fruit fly species than the plateau zone. The abundance of fruit flies was significantly influenced by altitudes and seasons. The study characterized the community of fruit flies in Morogoro and confirms the prevalence of Z. cucurbitae, D. bivittatus and D. punctatifrons as prominent species in this region. Therefore, management programs should focus on containing these species regardless of the agroecological zones and seasons.

ecology↗

bioRxiv2023

Host use preference of fruit flies (Diptera: Tephritidae) among selected cucurbitaceous vegetables in Morogoro, Eastern-Central Tanzania

Fruit flies (Diptera, Tephritidae) represent a major threat to cucurbit production in Tanzania. They cause huge economic losses on cucurbit crops. Information on the infestation and yield loss caused by fruit flies on cucurbit crops is vital in designing a sound fruit fly management program. We identified the fruit fly species attacking cucurbit crops (Cucurbitales: Cucurbitaceae): cucumber (Cucumis sativus L.), watermelon (Citrullus lanatus [Thunb.] Matsum. & Nakai) and squash (Cucurbita moschata D.) in the Morogoro region and quantified their incidence and infestation per crop species. A weekly sampling of ten fruits per crop was repeated twice per plot for each zone for five consecutive weeks between March and October 2020. The number of fruit flies emerging from the collected fruits was quantified and infestation per crop species was determined. We observed significant differences in infestation between cucurbit species, across zones and seasons. Squash showed the highest infestation of Zeugodacus cucurbitae (Coquillet) in both zones followed by watermelon. Watermelon was highly infested by Dacus vertebratus (Bigot) in the plateau zone followed by squash. Squash showed the highest infestation of Dacus ciliatus Loew in the plateau zone followed by watermelon. Cucumber had the lowest infestation for all fruit fly species.

ecology↗

bioRxiv2021

Single-cell multi-omic velocity infers dynamic and decoupled gene regulation

Single-cell multi-omic datasets, in which multiple molecular modalities are profiled within the same cell, provide a unique opportunity to discover the relationships between cellular epigenomic and transcriptomic changes. To realize this potential, we developed MultiVelo, a mechanistic model of gene expression that extends the RNA velocity framework to incorporate epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of chromatin accessibility and gene expression from single-cell data, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes. Incorporating chromatin accessibility data significantly improves the accuracy of cell fate prediction compared to velocity estimates from RNA only. Fitting MultiVelo on single-cell multi-omic datasets from brain, skin, and blood cells reveals two distinct classes of genes distinguished by whether chromatin closes before or after transcription ceases. Our model also identifies four types of cell states-two states in which epigenome and transcriptome are coupled and two distinct decoupled states. The parameters inferred by MultiVelo quantify the length of time for which genes occupy each of the four states, ranking genes by the degree of coupling between transcriptome and epigenome. Finally, we identify time lags between transcription factor expression and binding site accessibility and between disease-associated SNP accessibility and expression of the linked genes. We provide an open-source Python implementation of MultiVelo on PyPI and GitHub (https://github.com/welch-lab/MultiVelo).

bioinformatics↗

bioRxiv2019

Mannose receptor is a restriction factor of HIV in macrophages and is counteracted by the accessory protein Vpr

HIV-1 Vpr is necessary to support HIV infection and spread in macrophages. Evolutionary conservation of Vpr suggests an important yet poorly understood role for macrophages in HIV pathogenesis. Vpr counteracts a previously unknown macrophage-specific restriction factor that targets and reduces the expression of HIV Env. Here, we report that the macrophage mannose receptor (MR), is the restriction factor targeting Env in primary human monocyte-derived macrophages. Vpr acts synergistically with HIV Nef to target distinct stages of the MR biosynthetic pathway and dramatically reduce MR expression. Silencing MR or deleting mannose residues on Env rescues Env expression in HIV-1-infected macrophages lacking Vpr. However, we also show that disrupting interactions between Env and MR reduces initial infection of macrophages by cell-free virus. Together these results reveal a Vpr-Nef-Env axis that hijacks a macrophage mannose-MR response system to facilitate infection while evading MRs normal role, which is to trap and destroy mannose-expressing pathogens.

immunology↗