Biology subjects

Nunes, D.

Publications and source records attributed to Nunes, D..

4 recordsLinked to original sources

bioRxiv2025

Loss of Vitellogenin Receptor Function Results in Yolk Depletion, Virome Expansion and Reduced Bacterial Load Within the Oocytes of Rhodnius prolixus

The vitellogenin receptor (VgR) mediates yolk protein uptake during oogenesis and is essential for embryogenesis in oviparous species. Here we characterize the single Rhodnius prolixus VgR isoform and uncover an unexpected role in microbial regulation within the reproductive system. The receptor displays a conserved LDLR-like structure and is highly expressed in early oocytes. RNAi-mediated VgR silencing caused defective yolk granule biogenesis, leading to the accumulation of the main yolk protein precursors, Vg and RHBP, in the hemolymph, yet oviposition and fertilization proceeded normally. The resulting eggs were yolk-depleted and non-viable. Remarkably, VgR knockdown reduced bacterial 16S rRNA levels in oocytes while promoting the expansion of several members of the core virome, a phenotype not reproduced by Vg silencing. Neither purified Vg nor changes in immune (defensin) or RNA interference pathways explained the microbial shifts. These findings indicate that VgR governs not only yolk endocytosis but also the trafficking of microbial components into developing oocytes. We propose that VgR contributes to the linking of yolk endocytic dynamics and microbial homeostasis, influencing the balance of microbial components within developing oocytes. This connection broadens the functional scope of the VgR and provides new insight into how vertical transmission processes are shaped in this major Chagas disease vector. Author summaryEgg-laying animals must load their eggs with enough nutrients to support early development. In insects, this process depends on a receptor that brings yolk proteins into the growing egg. Here, we studied this receptor in Rhodnius prolixus, a major vector of Chagas disease, and uncovered an unexpected link between yolk uptake and the microorganisms that enter the egg. When we blocked the receptor, females continued to produce and lay eggs, but these eggs failed to accumulate yolk and could not support embryonic development. Strikingly, the absence of the receptor also shifted the microbial community inside the oocyte: bacterial levels dropped, while several viruses expanded. These changes did not result from differences in yolk proteins, immune activation, or direct antimicrobial effects, indicating that the receptor itself influences microbial entry or persistence in the egg. Our findings reveal that this yolk receptor plays a dual role, providing nutrients and shaping the microbial community that is passed from mother to offspring. This work highlights an unrecognized layer of interaction between reproduction and microbial transmission in an important disease vector, offering new perspectives for understanding and potentially disrupting vertical transmission pathways.

cell biology↗

bioRxiv2023

Variability and Bias in Microbiome Metagenomic Sequencing: an Interlaboratory Study Comparing Experimental Protocols

BackgroundSeveral studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5x human stool samples and 2x mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. ResultsA total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. ConclusionThis study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.

microbiology↗

bioRxiv2018

APOBEC-mediated DNA alterations: a possible new mechanism of carcinogenesis in EBV-positive gastric cancer

Mechanisms of viral oncogenesis are diverse and include the off-target activity of enzymes expressed by the infected cells, which evolved to target viral genomes for controlling their infection. Among these enzymes, the single-strand DNA editing capability of APOBECs represent a well-conserved viral infection response that can also cause untoward mutations in host DNA. Here we show, after evaluating somatic single-nucleotide variations and transcriptome data in 240 gastric cancer samples, a positive correlation between APOBEC3s mRNA-expression and the APOBEC-mutation signature, both increased in EBV+ tumors. The correlation was reinforced by the observation of APOBEC-mutations preferentially occuring in transcriptionally-active loci. The EBV-infection and APOBEC3 mutation-signature axis was confirmed in a validation cohort of 112 gastric cancer patients. Our findings suggest that APOBEC3 upregulation in EBV+ cancer may boost the mutation load, providing further clues to the mechanisms of EBV-induced gastric carcinogenesis. After further validation, this EBV-APOBEC axis may prove to be a secondary driving force in the mutational evolution of EBV+ gastric tumors, whose consequences in terms of prognosis and treatment implications should be vetted.

cancer biology↗

bioRxiv2018

Similarity and strength of glomerular odor representations define neural metric of sniff-invariant discrimination time

The olfactory environment is first represented by glomerular activity patterns in the olfactory bulb. It remained unclear, how these activity patterns intersect with sampling behavior to account for the time required to discriminate odors. Using different classes of volatile stimuli, we investigated glomerular activity patterns and sniffing behavior during olfactory decision-making. Mice discriminated monomolecular odorants and binary mixtures on a fast time scale and learned to increase their breathing frequency at a fixed latency after trial initiation, independent of odor identity. Relative to the increase in breathing frequency, monomolecular odorants were discriminated within 10-40 ms while binary mixtures required an additional 60-70 ms. Intrinsic imaging of odor-evoked glomerular activity maps in anesthetized and awake mice revealed that the Euclidean distance between glomerular patterns elicited by different odors, a measure of similarity and activation strength, was anti-correlated with discrimination time. Therefore, the similarity of glomerular patterns and their activation strengths, rather than sampling behavior, define the extent of neuronal processing required for odor discrimination, establishing a neural metric to predict olfactory discrimination time.

neuroscience↗