Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes.

Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.

Comparison of two point-of-care respiratory panels for the detection of influenza A/B virus.

BACKGROUND: Rapid and accurate diagnostics of patients with suspected seasonal influenza or pathogens of the upper respiratory tract is crucial. Fast detection is important especially for influenza A/B virus, so that isolation measures should be taken to prevent the spread of the virus. METHODS: We compared the performance of two syndromic testing methodologies (QIAstat-Dx RP, BioFire RP2plus) against the Alere™ i as the comparator method. Totally, 97 swab samples were included from patients with symptoms of acute respiratory infection admitted in the hospitals of the wider region of Crete, Greece. RESULTS: The Positive Percent Agreement (PPA) of the BioFire RP2plus was 100% (95% CI 87.66%-100%), while the Negative Percent Agreement (NPA) was estimated at 91.3% (95% CI 82.03%-96.74%). This method produced no invalid results. For QIAstat-Dx RP the PPA was 89.29% (95% CI 71.77%-97.73%), while the NPA was 91.3% (95% CI 82.03%-96.74%, 63/69). The BioFire RP2plus managed to determine the subtype in more samples than the QIAstat-Dx RP. CONCLUSIONS: Both panels can be valuable tools for clinicians, since they both display high sensitivity and specificity. We report a slightly better performance for BioFire RP2plus, since it produced no invalid results.

Rapid identification of SARS-CoV-2 variants: Validation of the simplexa SARS-CoV-2 variant direct assay.

The circulation of certain SARS-CoV-2 variants may have a great impact on the epidemiological status of a geographical area; therefore, it is important that their presence is monitored. Currently, the gold standard method used to identify newly emerged variants is sequencing of either genes or whole genomes. However, since this method is relatively expensive and has a long turnaround time, other rapid strategies should also be employed. The current study aimed to evaluate the performance of the Simplexa® SARS-CoV-2 Variants Direct assay, which is a RT-PCR that determines the variant present in a nasopharyngeal swab sample in approximately two hours. Totally, 527 positive samples for SARS-CoV-2 were analyzed from January until December 2022 and next-generation sequencing (NGS) was used as the reference method. The assay showed high sensitivity, ranging from 94.12 % to 100 %, depending on the variant. The assay also showed high specificity, reaching 100 % for Delta and BA.1 variants, and 99.74 % and 98.67 % for BA.2 and BA.4/BA.5 variants, respectively. Moreover, the assay was able to identify the correct variant category in the presence of any subvariant in the sample. We conclude that the assay can be used to facilitate faster monitoring of circulating SARS-CoV-2 variants, however sequencing cannot be completely replaced, since new variants always emerge, and constant updates are needed, so that the user is able to interpret the melting curve patterns.

Evaluation of STANDARDTM M10 SARS-CoV-2 assay as a diagnostic tool for SARS-CoV-2 in nasopharyngeal or oropharyngeal swab samples.

The SARS-CoV-2 pandemic led to an urgent need for rapid diagnostic testing in order to inform timely patients' management. This study aimed to assess the performance of the STANDARD™ M10 SARS-CoV-2 assay as a diagnostic tool for COVID-19. A total of 400 nasopharyngeal or oropharyngeal swabs were tested against a reference real-time RT-PCR, including 200 positive samples spanning the full range of observed Ct values. The sensitivity of the STANDARD™ M10 SARS-CoV-2 assay was 98.00% (95% CI 94.96% to 99.45%, 196/200), while the specificity was also estimated at 97.50% (95% CI 94.26% to 99.18%, 195/200). The assay proved highly efficient for the detection of SARS-CoV-2, even in samples with low viral load (Ct>25), presenting lower Ct values compared to the reference method. We concluded that the STANDARD™ M10 SARS-CoV-2 assay has a similar performance compared to the reference method and other molecular point-of-care assays and can be a valuable tool for rapid and accurate diagnosis.

NUMTs Can Imitate Biparental Transmission of mtDNA-A Case in Drosophila melanogaster.

mtDNA sequences can be incorporated into the nuclear genome and produce nuclear mitochondrial fragments (NUMTs), which resemble mtDNA in their sequence but are transmitted biparentally, like the nuclear genome. NUMTs can be mistaken as real mtDNA and may lead to the erroneous impression that mtDNA is biparentally transmitted. Here, we report a case of mtDNA heteroplasmy in a Drosophila melanogaster DGRP line, in which the one haplotype was biparentally transmitted in an autosomal manner. Given the sequence identity of this haplotype with the mtDNA, the crossing experiments led to uncertainty about whether heteroplasmy was real or an artifact due to a NUMT. More specific experiments revealed that there is a large NUMT insertion in the X chromosome of a specific DGRP line, imitating biparental inheritance of mtDNA. Our result suggests that studies on mtDNA heteroplasmy and on mtDNA inheritance should first exclude the possibility of NUMT interference in their data.

mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences.

Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects of heteroplasmy regarding its origin and its significance on mtDNA function and evolution, which has been progressively recognized in the last several years. Heteroplasmic organisms commonly occur through somatic mutations during an individual's lifetime. They also occur due to leakage of paternal mtDNA, which rarely happens during fertilization. Alternatively, heteroplasmy can be potentially inherited maternally if an egg is already heteroplasmic. Recent advances in sequencing techniques have increased the ability to detect and quantify heteroplasmy and have revealed that mitochondrial DNA copies in the nucleus (NUMTs) can imitate true heteroplasmy. Heteroplasmy can have significant evolutionary consequences on the survival of mtDNA from the accumulation of deleterious mutations and for its coevolution with the nuclear genome. Particularly in humans, heteroplasmy plays an important role in the emergence of mitochondrial diseases and determines the success of the mitochondrial replacement therapy, a recent method that has been developed to cure mitochondrial diseases.

Paternal leakage of mitochondrial DNA and maternal inheritance of heteroplasmy in Drosophila hybrids.

Mitochondrial DNA (mtDNA) is maternally transmitted in animals and therefore, individuals are expected to have a single mtDNA haplotype (homoplasmy). Yet, heteroplasmic individuals have been observed in a large number of animal species. Heteroplasmy may emerge as a result of somatic mtDNA mutations, paternal leakage during fertilization or be inherited from a heteroplasmic mother. Understanding the causes of heteroplasmy could shed light into the evolution of mtDNA inheritance. In this study we examined heteroplasmy in progeny from heterospecific crosses of Drosophila for two consecutive generations. We studied the generation of heteroplasmy from paternal leakage and the maternal transmission of heteroplasmy. Our data reveal non-random patterns in the emergence and transmission of heteroplasmy and suggest that heteroplasmy depends on the family of origin.

Searching for doubly uniparental inheritance of mtDNA in the apple snail Pomacea diffusa.

Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) is an exceptional mode of mtDNA transmission, restricted so far to the class of bivalves. We searched for DUI outside bivalves using the apple snail Pomacea diffusa. It was an appropriate candidate to search for DUI for three reasons; it belongs to gastropods, which is the closest sister group to bivalves, it is gonochoristic and it has a strong sex bias in the progeny of different female individuals. These phenomena (gonochorism and sex-biased progeny) are also found in species with DUI. We searched for heteroplasmy in males and for high sequence divergence among mtDNA sequences obtained from male and female gonads. All sequences examined were identical. These data suggest that the mtDNA in P. diffusa is maternally transmitted and DUI remains an exclusive characteristic of bivalves.