Background: Drosophila suzukii is a worldwide invasive species with serious economic impacts. Herein, we are presenting the first project of sequencing and assembling the whole genomes of two lines of D. suzukii derived from Romanian local populations using exclusively Oxford Nanopore Technologies data. Methods: We implemented both MinION and Flongle flow-cells and tested the impact of various basecalling models and assembly strategies on the quality of the sought-after representative genome assemblies. Results: We demonstrate that the sup-basecalling model significantly improved the read quality and that adding a relatively small collection of reads had a significant positive impact over the assembly quality. The novel dScaff bioinformatics prototype tool allowed us to perform sequence-level quality tests, as well as to represent assembly selections and display both the contig redundancy and the repeats-enriched genomic sub-sequences. Moreover, we used dScaff to propose a minimal assembly variant corresponding to one of our lines, GB-ls-coga4, which assured a basic linear coverage of the genome and exhibited quality parameters comparable with those particular to the current reference genome assembly. Conclusions: The study presents the first sequencing and assembly of a D. suzukii line in Romania and argues the efficiency of long-read sequencing strategies.

Gene expression assays that are based on quantitative real-time PCR (qRT-PCR) method are still very popular, therefore, we developed qDATA, a modern open-source R based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a straightforward specific data input consisting in Ct values and a few other mandatory fields specifying the experimental and control groups, as well as the target and house-keeping genes. Afterwards, it automatically performs descriptive statistics, normality and statistical testing on 2 ^-ΔCt (or ΔCt) and 2 ^-ΔΔCt terms calculated with Livak’s method. Each computation is indicated in dedicated tabs that display their output consisting in dynamic data tables and publishing quality graphs. We also detail a qRT-PCR data analysis framework that depends on performing exhaustive ΔCt calculations within discrete biological replicates (BRs). The Livak formula is used for the complete sets of available data. These prerequisites arguably lead to an improved data analysis and statistical relevance. In order to maximize the relevance of the results we recommend using at least three BRs and three technical replicates. The efficiency of our computing approach was tested with qDATA using input Ct values corresponding to immune related gene expression evaluated in experimental infection of Drosophila melanogaster and summer versus winter Apis mellifera workers, respectively. Our results reveal that our working strategy is very reliable and highlight the efficacy and performance of qDATA application.

Drosophila melanogaster (the fruit fly) is a valuable experimental platform for modeling host–pathogen interactions. It is also commonly used to define innate immunity pathways and to understand the mechanisms of both host tolerance to commensal microbiota and response to pathogenic agents. Herein, we investigate how the host response to bacterial infection is mirrored in the expression of genes of Imd and Toll pathways when D. melanogaster strains with different γCOP genetic backgrounds are infected with Pseudomonas aeruginosa ATCC 27853. Using microarray technology, we have interrogated the whole-body transcriptome of infected versus uninfected fruit fly males with three specific genotypes, namely wild-type Oregon, γCOP^S057302/TM6B and γCOP^14a/γCOP^14a. While the expression of genes pertaining to Imd and Toll is not significantly modulated by P. aeruginosa infection in Oregon males, many of the components of these cascades are up- or downregulated in both infected and uninfected γCOP^S057302/TM6B and γCOP^14a/γCOP^14a males. Thus, our results suggest that a γCOP genetic background modulates the gene expression profiles of Imd and Toll cascades involved in the innate immune response of D. melanogaster, inducing the occurrence of immunological dysfunctions in γCOP mutants.

Drosophila melanogaster has been at the forefront of genetic studies and biochemical modeling for over a century. Yet, the functions of many genes are still unknown, mainly because no phenotypic data are available. Herein, we present the first evidence data regarding the particular molecular and other quantifiable phenotypes, such as viability and anatomical anomalies, induced by a novel P{lacW} insertional mutant allele of the CG18135 gene. So far, the CG18135 functions have only been theorized based on electronic annotation and presumptive associations inferred upon high-throughput proteomics or RNA sequencing experiments. The descendants of individuals harboring the CG18135^{P{lacW}CG18135} allele were scored in order to assess mutant embryonic, larval, and pupal viability versus Canton Special (CantonS). Our results revealed that the homozygous CG18135^{P{lacW}CG18135}/CG18135^{P{lacW}CG18135} genotype determines significant lethality both at the inception of the larval stage and during pupal development. The very few imago escapers that either breach or fully exit the puparium exhibit specific eye depigmentation, wing abnormal unfolding, strong locomotor impairment with apparent spasmodic leg movements, and their maximum lifespan is shorter than 2 days. Using the quantitative real-time PCR (qRT-PCR) method, we found that CG18135 is upregulated in male flies, but an unexpected gene upregulation was also detected in heterozygous mutants compared to wild-type flies, probably because of regulatory perturbations induced by the P{lacW} transposon. Our work provides the first phenotypic evidence for the essential role of CG18135, a scenario in accordance with the putative role of this gene in carbohydrate-binding processes.

Rapid evolution of long-read sequencing technologies requires accurate, fast and user-friendly genome assembly and scaffolding tools. In this article we present Digital Scaffolding (dScaff), a bioinformatics tool that performs scaffolding of de novo genome assemblies based on reference scaffolds or chromosomes. dScaff makes use of a series of bash and R scripts in order to create a minimal complete scaffold from a genome assembly, with future features to be implemented. Herein, we demonstrate the functionality of dScaff on a novel genome assembly pertaining to a recently sequenced local strain of Drosophila suzukii .

Multidrug resistance (MDR) is a major global health challenge, necessitating alternative or adjuvant strategies such as lactoferrin (Lf) and probiotics. Opportunistic bacteria are key drivers of healthcare-associated infections (HAIs) due to their ability to form biofilms and cause persistent infections. Lf, a glycoprotein present in mammalian milk and secretions, exhibits antimicrobial properties as part of innate immunity. Similarly, probiotics—primarily lactic acid bacteria (LAB)—influence pathogen growth and adhesion. This study evaluated the antimicrobial and anti-biofilm effects of purified bovine Lf (bLf) versus commercial Lf, alone and combined with LAB-derived supernatants, against several opportunistic strains. Using qualitative and quantitative methods, we assessed the antimicrobial, anti-adherence, and immunomodulatory activities of bLf (Sigma-Aldrich), commercial Lf (Jarrow Formulas), and LAB supernatants. High-purity bLf demonstrated superior antimicrobial and antibiofilm effects compared to supplement-derived Lf. Furthermore, commercial Lf, combined with LAB metabolites, effectively inhibited biofilm formation, reduced inflammation, and prevented bacterial adhesion to eukaryotic cells. These findings support the potential use of lactoferrin, alone or in synergy with probiotics, as adjuvants or prophylactic agents, particularly for immunocompromised patients, to limit bacterial adherence and prevent chronic infections.