Survival and Transcriptomic Response of Clinically relevant pathogens on Surfaces in Relation to Probiotic and Traditional Cleaning Strategies

Prolonged survival of clinically relevant pathogens on inanimate surfaces represents a major concern in healthcare facilities. Contaminated surfaces can serve as reservoirs of potential pathogens and greatly hinder the prevention of healthcare-associated infections. Probiotic cleaning using environmental microorganisms to promote inter-species competition has been proposed as an alternative to traditional chemical-based cleaning using antimicrobials. Probiotic cleaning seeks to take advantage of ecological principles such as competitive exclusion and utilize benign microorganisms to inhibit viable pathogens on indoor surfaces. However, limited mechanistic study has yielded direct evidence that enables the scientific community to understand the stress response, or microbe-microbe interactions between healthcare-associated pathogens and probiotic bacteria. Therefore, to bridge this knowledge gap, we combined transcriptomics and traditional microbiology techniques to investigate the differential impact of chemical-based and probiotic surface cleaners on the survival of Acinetobacter baumannii and Klebsiella pneumoniae, two clinically important pathogens. Although probiotic Bacillus included in a commercialized All-Purpose Probiotic Cleaner persisted on surfaces for an extended period of time, surfaces contaminated with A. baumannii cleaned using chemical-based detergent with and without probiotic Bacillus showed no statistical difference in the viable colony forming units (CFUs) of A. baumannii. Similarly, for Klebsiella pneumoniae, there were negligible statistical differences in CFUs between probiotic and detergent cleaning scenarios. The transcriptome of A. baumannii with and without probiotic addition shared a high degree of similarity in overall gene expression, while the transcriptome of K. pneumoniae with and without probiotic addition differed in overall gene expression. Together, these results highlight the need to fully understand the underlying biological and ecological mechanisms for different pathogens and practical implications of probiotic indoor cleaning.

Metabolic Processes Are Differentially Regulated During Wild-Type and Attenuated Dengue Virus Infection in Aedes aegypti

Successful completion of the dengue virus (DENV) life cycle in its mosquito vectors is important for efficient human–mosquito–human cycle of transmission, but the virus–mosquito interactions that underpin this critical event are poorly defined. To understand the virus–host interactions that determine viral infection by Aedes aegypti, the principal DENV vector, the authors compared transcriptomic changes in the head/thorax of the mosquito after intrathoracic infection with the wild-type DENV2 16681 strain and its attenuated derivative, PDK53. Using high-throughput RNA-sequencing, the authors identified 1,629 differentially expressed genes (DEGs) during 16681 infection, compared with only 22 DEGs identified during PDK53 infection, indicating that 16681 infection triggers a more robust host transcriptomic response compared with PDK53 infection. The authors further found that 16681 infection, but not PDK53 infection, altered metabolism in these heads/thoraces. Altogether, our findings reveal differential regulation of metabolic processes during wild-type and attenuated DENV infection, and suggest the need for future work to study the role of metabolic processes in determining DENV infection and replication in its mosquito vectors.

Sperm exposure to accessory gland secretions alters the transcriptomic response of the endometrium in cattle

In a recent study from our group, mating to intact, but not vasectomised, bulls modified the endometrial transcriptome, suggesting an important role of sperm in the modulation of the uterine environment in this species. However, it is not clear whether these changes are driven by intrinsic sperm factors, or by factors of accessory gland (AG) origin that bind to sperm at ejaculation. Thus, the aim of the present study was to determine whether ejaculated sperm, which are suspended in the secretions of the AGs, elicit a different endometrial transcriptomic response than epididymal sperm, which have never been exposed to AG factors. To this end, bovine endometrial explants collected from heifers in oestrus were incubated alone (control), or with epididymal or ejaculated sperm. RNA-sequencing revealed 1912 differentially expressed genes (DEGs) between in endometrial explants exposed to epididymal sperm compared with control explants, whereas 115 DEGs genes detected between endometrial explants exposed to ejaculated sperm in comparison to control explants. In both cases, the top pathways associated with these genes included T cell regulation and NF-KB and IL17 signalling. To confirm whether AG factors were directly responsible for the dampening of the endometrial response elicited by ejaculated sperm, endometrial explants were incubated with epididymal sperm previously exposed, or not, to seminal plasma (SP). Exposure to SP abrogated the downregulation of SQSTM1 by epididymal sperm, and partially inhibited the upregulation of MYL4 and CHRM3 and downregulation of SCRIB. These data indicate that factors of AG origin modulate the interaction between sperm and the endometrium in cattle.

The onset of whole-body regeneration in Botryllus schlosseri: morphological and molecular characterization

Colonial tunicates are the only chordates that regularly regenerate a fully functional whole body as part of their asexual life cycle, starting from specific epithelia and/or mesenchymal cells. In addition, in some species, whole-body regeneration (WBR) can also be triggered by extensive injuries, which deplete most of their tissues and organs and leave behind only small fragments of their body. In this manuscript, we characterized the onset of WBR in Botryllus schlosseri, one colonial tunicate long used as a laboratory model. We first analyzed the transcriptomic response to a WBR-triggering injury. Then, through morphological characterization, in vivo observations via time-lapse, vital dyes, and cell transplant assays, we started to reconstruct the dynamics of the cells triggering regeneration, highlighting an interplay between mesenchymal and epithelial cells. The dynamics described here suggest that WBR in B. schlosseri is initiated by extravascular tissue fragments derived from the injured individuals rather than particular populations of blood-borne cells, as has been described in closely related species. The morphological and molecular datasets here reported provide the background for future mechanistic studies of the WBR ontogenesis in B. schlosseri and allow to compare it with other regenerative processes occurring in other tunicate species and possibly independently evolved.

Purine Auxotrophic Starvation Evokes Phenotype Similar to Stationary Phase Cells in Budding Yeast

Purine auxotrophy is an abundant trait among eukaryotic parasites and a typical marker for many budding yeast strains. Supplementation with an additional purine source (such as adenine) is necessary to cultivate these strains. If not supplied in adequate amounts, purine starvation sets in. We explored purine starvation effects in a model organism, a budding yeast Saccharomyces cerevisiae ade8 knockout, at the level of cellular morphology, central carbon metabolism, and global transcriptome. We observed that purine-starved cells stopped their cycle in G1/G0 state and accumulated trehalose, and the intracellular concentration of AXP decreased, but adenylate charge remained stable. Cells became tolerant to severe environmental stresses. Intracellular RNA concentration decreased, and massive downregulation of ribosomal biosynthesis genes occurred. We proved that the expression of new proteins during purine starvation is critical for cells to attain stress tolerance phenotype Msn2/4p targets are upregulated in purine-starved cells when compared to cells cultivated in purine-rich media. The overall transcriptomic response to purine starvation resembles that of stationary phase cells. Our results demonstrate that the induction of a strong stress resistance phenotype in budding yeast can be caused not only by natural starvation, but also starvation for metabolic intermediates, such as purines.

TimesVector-Web: A Web Service for Analysing Time Course Transcriptome Data with Multiple Conditions

From time course gene expression data, we may identify genes that modulate in a certain pattern across time. Such patterns are advantageous to investigate the transcriptomic response to a certain condition. Especially, it is of interest to compare two or more conditions to detect gene expression patterns that significantly differ between them. Time course analysis can become difficult using traditional differentially expressed gene (DEG) analysis methods since they are based on pair-wise sample comparison instead of a series of time points. Most importantly, the related tools are mostly available as local Software, requiring technical expertise. Here, we present TimesVector-web, which is an easy to use web service for analysing time course gene expression data with multiple conditions. The web-service was developed to (1) alleviate the burden for analyzing multi-class time course data and (2) provide downstream analysis on the results for biological interpretation including TF, miRNA target, gene ontology and pathway analysis. TimesVector-web was validated using three case studies that use both microarray and RNA-seq time course data and showed that the results captured important biological findings from the original studies.

Differential Transcriptomic Response of Rainbow Trout to Infection with Two Strains of IPNV

The IPN virus (IPNV) causes a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into seven genogroups, of which two are present in Chile, genogroups 1 and 5. This study aimed to compare the transcriptomic response of rainbow trout fry challenged with two Chilean isolates of IPNV, RTTX (genogroup 1), and ALKA (genogroup 5). Tissue samples from challenged individuals and controls were taken at 1, 7, and 20 days post-challenge and analyzed by RNA-Seq. The results revealed that infection with RTTX elicited a greater modulation of the trout transcriptome compared to ALKA infection, generating a greater number of highly differentially expressed genes in relation to the control fish. Gene Ontology enrichment indicated that functions related to the inflammatory and immune responses were modulated in fish challenged with both isolates throughout the trial, but with different regulation patterns. On day 1 post challenge, these functions were activated in those challenged with ALKA, but suppressed in RTTX-challenged fish. These results suggest that rainbow trout exhibit a differential transcriptomic response to infection with the two genetically distinct IPNV isolates, especially at early times post-infection.