Variations, seasonal shifts and ambient conditions affecting airborne microorganisms and particles at a southeastern Mediterranean site.

Airborne particles are known climate drivers whilst the impact of microorganisms is investigated with increasing interest. The particle number size distribution (0.012-10 µm), PM10 concentrations, bacterial communities and cultivable microorganisms (bacteria and fungi) were measured simultaneously throughout a yearly campaign at a suburban location at the city of Chania (Greece). Most of the bacteria identified belonged to Proteobacteria, Actinobacteriota, Cyanobacteria, and Firmicutes, with Sphingomonas having a dominant partition at the genus level. Statistically lower concentrations of all microorganisms and bacterial species richness during the warm season due to the direct impact of temperature and solar radiation suggested notable seasonality. On the other hand, statistically significant higher concentrations of particles <0.1 µm during the cold season was attributed to indirect seasonality with enrichment due to heating emissions. Analysis of wind direction data demonstrated that a land prevailing origin of air resulted in statistically higher microorganism concentrations, bacterial species richness and diversity, indicating the continental environment as a dominant contributor in shaping airborne microbial load (compared to a marine air origin). Likewise, statistically higher concentration of particles <0.1 µm were measured during a land prevailing air origin as a direct result of nanoparticle enrichment from anthropogenic activities. Long-range transport of both particles and biological components was evidenced by the increased concentrations of cultivable microorganisms (with a distinct contribution at sizes >1 µm), supermicron particles and bacterial species richness during Sahara dust events. Factorial analysis of the impact of 7 environmental parameters on bacterial communities profile has identified temperature, solar radiation, wind origin and Sahara dust as strong contributors. Increased correlations between airborne microorganisms and coarser particles (0.5-10 µm) suggested resuspension, especially during stronger winds and moderate ambient humidity, whereas, increased relative humidity during stagnant conditions acted as inhibitor for suspension.

Airborne particles and microorganisms in a dental clinic: Variability of indoor concentrations, impact of dental procedures, and personal exposure during everyday practice.

This study presents for the first time comprehensive measurements of the particle number size distribution (10 nm to 10 µm) together with next-generation sequencing analysis of airborne bacteria inside a dental clinic. A substantial enrichment of the indoor environment with new particles in all size classes was identified by both activities to background and indoor/outdoor (I/O) ratios. Grinding and drilling were the principal dental activities to produce new particles in the air, closely followed by polishing. Illumina MiSeq sequencing of 16S rRNA of bioaerosol collected indoors revealed the presence of 86 bacterial genera, 26 of them previously characterized as potential human pathogens. Bacterial species richness and concentration determined both by qPCR, and culture-dependent analysis were significantly higher in the treatment room. Bacterial load of the treatment room impacted in the nearby waiting room where no dental procedures took place. I/O ratio of bacterial concentration in the treatment room followed the fluctuation of I/O ratio of airborne particles in the biology-relevant size classes of 1-2.5, 2.5-5, and 5-10 µm. Exposure analysis revealed increased inhaled number of particles and microorganisms during dental procedures. These findings provide a detailed insight on airborne particles of both biotic and abiotic origin in a dental clinic.

Nuclear and Wolbachia-based multimarker approach for the rapid and accurate identification of tsetse species.

BACKGROUND: Tsetse flies (Diptera: Glossinidae) are solely responsible for the transmission of African trypanosomes, causative agents of sleeping sickness in humans and nagana in livestock. Due to the lack of efficient vaccines and the emergence of drug resistance, vector control approaches such as the sterile insect technique (SIT), remain the most effective way to control disease. SIT is a species-specific approach and therefore requires accurate identification of natural pest populations at the species level. However, the presence of morphologically similar species (species complexes and sub-species) in tsetse flies challenges the successful implementation of SIT-based population control. RESULTS: In this study, we evaluate different molecular tools that can be applied for the delimitation of different Glossina species using tsetse samples derived from laboratory colonies, natural populations and museum specimens. The use of mitochondrial markers, nuclear markers (including internal transcribed spacer 1 (ITS1) and different microsatellites), and bacterial symbiotic markers (Wolbachia infection status) in combination with relatively inexpensive techniques such as PCR, agarose gel electrophoresis, and to some extent sequencing provided a rapid, cost effective, and accurate identification of several tsetse species. CONCLUSIONS: The effectiveness of SIT benefits from the fine resolution of species limits in nature. The present study supports the quick identification of large samples using simple and cost effective universalized protocols, which can be easily applied by countries/laboratories with limited resources and expertise.

Different laboratory populations similar bacterial profile? The case of Glossina palpalis gambiensis.

BACKGROUND: Microbiota plays an important role in the biology, ecology and evolution of insects including tsetse flies. The bacterial profile of 3 Glossina palpalis gambiensis laboratory colonies was examined using 16S rRNA gene amplicon sequencing to evaluate the dynamics of the bacterial diversity within and between each G. p. gambiensis colony. RESULTS: The three G. p. gambiensis laboratory colonies displayed similar bacterial diversity indices and OTU distribution. Larval guts displayed a higher diversity when compared with the gastrointestinal tract of adults while no statistically significant differences were observed between testes and ovaries. Wigglesworthia and Sodalis were the most dominant taxa. In more detail, the gastrointestinal tract of adults was more enriched by Wigglesworthia while Sodalis were prominent in gonads. Interestingly, in larval guts a balanced co-existence between Wigglesworthia and Sodalis was observed. Sequences assigned to Wolbachia, Propionibacterium, and Providencia were also detected but to a much lesser degree. Clustering analysis indicated that the bacterial profile in G. p. gambiensis exhibits tissue tropism, hence distinguishing the gut bacterial profile from that present in reproductive organs. CONCLUSIONS: Our results indicated that age, gender and the origin of the laboratory colonies did not significantly influence the formation of the bacterial profile, once these populations were kept under the same rearing conditions. Within the laboratory populations a tissue tropism was observed between the gut and gonadal bacterial profile.

Combined GWAS and 'guilt by association'-based prioritization analysis identifies functional candidate genes for body size in sheep.

BACKGROUND: Body size in sheep is an important indicator of productivity, growth and health as well as of environmental adaptation. It is a composite quantitative trait that has been studied with high-throughput genomic methods, i.e. genome-wide association studies (GWAS) in various mammalian species. Several genomic markers have been associated with body size traits and genes have been identified as causative candidates in humans, dog and cattle. A limited number of related GWAS have been performed in various sheep breeds and have identified genomic regions and candidate genes that partly account for body size variability. Here, we conducted a GWAS in Frizarta dairy sheep with phenotypic data from 10 body size measurements and genotypic data (from Illumina ovineSNP50 BeadChip) for 459 ewes. RESULTS: The 10 body size measurements were subjected to principal component analysis and three independent principal components (PC) were constructed, interpretable as width, height and length dimensions, respectively. The GWAS performed for each PC identified 11 significant SNPs, at the chromosome level, one on each of the chromosomes 3, 8, 9, 10, 11, 12, 19, 20, 23 and two on chromosome 25. Nine out of the 11 SNPs were located on previously identified quantitative trait loci for sheep meat, production or reproduction. One hundred and ninety-seven positional candidate genes within a 1-Mb distance from each significant SNP were found. A guilt-by-association-based (GBA) prioritization analysis (PA) was performed to identify the most plausible functional candidate genes. GBA-based PA identified 39 genes that were significantly associated with gene networks relevant to body size traits. Prioritized genes were identified in the vicinity of all significant SNPs except for those on chromosomes 10 and 12. The top five ranking genes were TP53, BMPR1A, PIK3R5, RPL26 and PRKDC. CONCLUSIONS: The results of this GWAS provide evidence for 39 causative candidate genes across nine chromosomal regions for body size traits, some of which are novel and some are previously identified candidates from other studies (e.g. TP53, NTN1 and ZNF521). GBA-based PA has proved to be a useful tool to identify genes with increased biological relevance but it is subjected to certain limitations.

Wolbachia prophage DNA adenine methyltransferase genes in different Drosophila-Wolbachia associations.

Wolbachia is an obligatory intracellular bacterium which often manipulates the reproduction of its insect and isopod hosts. In contrast, Wolbachia is an essential symbiont in filarial nematodes. Lately, Wolbachia has been implicated in genomic imprinting of host DNA through cytosine methylation. The importance of DNA methylation in cell fate and biology calls for in depth studying of putative methylation-related genes. We present a molecular and phylogenetic analysis of a putative DNA adenine methyltransferase encoded by a prophage in the Wolbachia genome. Two slightly different copies of the gene, met1 and met2, exhibit a different distribution over various Wolbachia strains. The met2 gene is present in the majority of strains, in wAu, however, it contains a frameshift caused by a 2 bp deletion. Phylogenetic analysis of the met2 DNA sequences suggests a long association of the gene with the Wolbachia host strains. In addition, our analysis provides evidence for previously unnoticed multiple infections, the detection of which is critical for the molecular elucidation of modification and/or rescue mechanism of cytoplasmic incompatibility.

Wolbachia: more than just a bug in insects genitals.

Research on the intracellular bacterial symbiont Wolbachia has grown on many levels, providing interesting insights on various aspects of the microbe's biology. Although data from fully sequenced genomes of different Wolbachia strains and from experimental studies of host-microbe interactions continue to arise, most of the molecular mechanisms employed by Wolbachia to manipulate the host cytoplasmic machinery and to ensure vertical transmission are yet to be discovered. Apart from the well-established role of Wolbachia in triggering reproductive alterations, a new fascinating aspect is emerging, related to the ecological benefits that the symbiont provides to the host. The mutualistic relationship of Wolbachia strains with disease vectors remains among the top research priorities with new insights having an impact on putative anti-filarial strategies.

Identification of differentially expressed proteins in senescent human embryonic fibroblasts.

Normal human fibroblasts undergo a limited number of divisions in culture, a process known as replicative senescence (RS). Although several senescence-specific genes have been identified, analysis at the level of protein expression can provide additional insights into the mechanisms that regulate RS. We have performed a proteomic comparison between young and replicative senescent human embryonic WI-38 fibroblasts and we have identified 13 proteins, which are differentially expressed in senescent cells. Some of the identified proteins are components of the cellular cytoskeleton, while others are implicated in key cellular functions including metabolism and energy production, Ca(2+) signalling, nucleo-cytoplasmic trafficking and telomerase activity regulation. In summary, our analysis contributes to the list of senescence-associated proteins by identifying new biomarkers and provides novel information on functional protein networks that are perturbed during replicative senescence of human fibroblast cultures.

Identification of growth factor-regulated proteins using 2D electrophoresis and mass spectrometry.

Proteomic technology has recently emerged as a powerful tool for detecting both qualitative and quantitative changes of proteins that occur upon activation of complex signaling pathways. In the present study, comparison of the protein profile of platelet-derived growth factor (PDGF), epidermal growth factor (EGF) and nerve growth factor (NGF)-stimulated and unstimulated cells with two-dimensional electrophoresis followed by mass spectrometric analysis led to the identification of a number of proteins, several of which had not been previously shown to be regulated by receptor-tyrosine kinases. Using subcellular fractionation, our approach was able to identify not only changes due to altered gene transcription, but also due to intracellular protein translocation or modification. One of the proteins that was identified among other PDGF-regulated molecules was prohibitin, a potential tumour suppressor previously implicated in cell cycle regulation and protection of mitochondrial proteins from degradation. Further analysis confirmed that mitochondria-associated prohibitin translocates to an insoluble perinuclear compartment. This study demonstrates the utility of proteomic strategies in identifying potential growth factor-regulated effectors.