1,099 research outputs found
A specific mechanism based on alternative 5’UTRs controls the VDAC1 translation in D. melanogaster
No full textDifferent aubergine alleles confirm the specificity of different RNAi pathways in Drosophila melanogaster
No full textThe crystal-Stellate system is one of the best-known examples of heterochromatin-euchromatin interaction. The components of this system are homologous repetitive sequences clustered in three regions: 12E1 and h27 on the X and h11 on the Y. The symptom of a disrupted crystal-Stellate interaction is the presence of crystals in the spermatocytes of males lacking the crystal region. Stellate silencing is based on the RNAi process. Many modifiers of this system have been isolated and many of these are involved in RNAi. One of these modifiers is aubergine(sting); this is a "gain of function" allele in somatic tissues. Here we report the different behavior of two aubergine alleles with respect to the RNAi pathway: aub(sting) and a "loss of function" heteroallelic combination aub(HN)/aub(QC42). An increased amount of Aub interferes with the correct functioning of the somatic yellow hairpin RNAi, whereas the Aub reduction does not. We also demonstrate the different behavior of these alleles on the I transposon silencing in ovaries. Intriguingly, neither of these aubergine alleles silence the Stellate locus. We can conclude that the crystal-Stellate system reveals different RNAi pathways even though much still remains to be done to completely explain the molecular bases of the crystal-Stellate interaction
The Role of HSP90 in Preserving the Integrity of Genomes Against Transposons Is Evolutionarily Conserved
No full textThe HSP90 protein is a molecular chaperone intensively studied for its role in numerous cellular processes both under physiological and stress conditions. This protein acts on a wide range of substrates with a well-established role in cancer and neurological disorders. In this review, we focused on the involvement of HSP90 in the silencing of transposable elements and in the genomic integrity maintenance. The common feature of transposable elements is the potential jumping in new genomic positions, causing chromosome structure rearrangements, gene mutations, and influencing gene expression levels. The role of HSP90 in the control of these elements is evolutionarily conserved and opens new perspectives in the HSP90-related mechanisms underlying human disorders. Here, we discuss the hypothesis that its role in the piRNA pathway regulating transposons may be implicated in the onset of neurological diseases
How many Non-Indigenous Species occurring in the Mediterranean Sea can actually be identified through environmental DNA? A gap analysis of NIS DNA barcodes in the reference libraries
No full textThe Mediterranean Sea is known for hosting a high diversity of species, with more than 17,000 reported marine species, one fifth which are endemic. Moreover, the number of non-indigenous species (NIS) in the Mediterranean Sea is recently reported to be increasing. The monitoring and the distribution of NIS is a key requirement for the conservation and management of the ecosystems, as also foreseen by the regulation (EU) No 1143/2014 of the European Parliament and of the Council of 22 October 2014 on the prevention and management of the introduction and spread of invasive alien species. A promising innovative approach for the identification of species and biodiversity is the use of molecular tools (DNA barcoding and metabarcoding). Combined with environmental DNA (eDNA) extracted from environmental samples like water or sediment, traces of species can be identified. Currently, the main limitation in the use of molecular tools (DNA barcoding and metabarcoding, eDNA) for species identification is the incompleteness of the DNA barcode reference databases. We assessed the extent of gaps in DNA barcode reference libraries, using the most updated inventory of 666 confirmed alien species occurring in the Mediterranean Sea. Also, the availability of primers for the amplification process was investigated. 32.58% of these species lack DNA barcodes in the reference libraries. Also, 70% of the retrieved NIS in the DNA barcode libraries lack the public availability of the primers used for the amplification process.The results of this study allow us to direct scientific efforts towards specific taxonomic groups in order to complete the NIS DNA barcode reference libraries and enable effective application of eDNA in investigations of the occurrence and the distribution of NIS in the Mediterranean Sea, and in the first sighting of still unknown NIS
Environmental DNA as Early Warning for Alien Species in Mediterranean Coastal Lagoons: Implications for Conservation and Management
No full textNon-indigenous species (NIS) introduction notoriously threatens the Mediterranean Sea. In addition, Mediterranean coastal lagoons play a crucial role as nurseries for marine species, which new NIS arrivals can threaten. Therefore, monitoring and early warning of NIS presence is essential in preserving biodiversity. An innovative technique for rapid and accurate species identification and biodiversity screening is the application of environmental DNA (eDNA) metabarcoding. In this research, different Penaeidae (Arthropoda, Crustacea, Decapoda) NIS specimens were collected from a Mediterranean coastal lagoon after an early warning about a potentially invasive NIS arising from next-generation sequencing data. DNA barcoding of the DNA extracted from tissue samples and amplified with specifically designed primer pairs led to the recognition of Penaeus aztecus in this NATURA 2000 protected ecosystem for the first time. DNA barcoding from DNA isolated from the water where the living specimens were stored further validated the possibility of identifying P. aztecus starting from eDNA. This approach demonstrated the validity of environmental DNA analysis in the early screening of potentially invasive NIS presence in Mediterranean protected areas and ecosystems. This work describes an applicative example of the efficacy in improving the biomonitoring of lagoon ecosystems using molecular tools and it represents a guideline for the validation of eDNA metabarcoding data for the presence of potentially invasive species
Isolation of Two Bacterial Species from Argan Soil in Morocco Associated with Polyhydroxybutyrate (PHB) Accumulation: Current Potential and Future Prospects for the Bio-Based Polymer Production
No full textThe environmental issues caused by the impacts of synthetic plastics use and derived wastes are arising the attention to bio-based plastics, natural polymers produced from renewable resources, including agricultural, industrial, and domestic wastes. Bio-based plastics represent a potential alternative to petroleum-based materials, due to the insufficient availability of fossil resources in the future and the affordable low cost of renewable ones that might be consumed for the biopolymer synthesis. Among the polyhydroxyalkanoates (PHA), the polyhydroxybutyrate (PHB) biopolymer has been synthesized and characterized with great interest due to its wide range of industrial applications. Currently, a wide number of bacterial species from soil, activated sludge, wastewater, industrial wastes, and compost have been identified as PHB producers. This work has the purpose of isolating and characterizing PHB-producing bacteria from the agricultural soil samples of Argania spinosa in the south region of Morocco where the plant species is endemic and preserved. During this research, four heat-resistant bacterial strains have been isolated. Among them, two species have been identified as endospore forming bacteria following the Schaffer-Fulton staining method with Malachite green and the Methylene blue method. Black intracellular granules have been appreciated in microscopy at 100× for both strains after staining with Sudan black B. The morphological and biochemical analyses of the isolates, including sugar fermentation and antibiotic susceptibility tests, preliminarily identified the strains 1B and 2D1 belonging to the genus Serratia and Proteus, respectivel
Assessing benthic macroinvertebrate communities’ spatial heterogeneity in Mediterranean transitional waters through eDNA metabarcoding
No full textTransitional waters are important habitats both for biodiversity and ecological functions, providing valuable natural resources and relevant ecosystem services. However, they are highly susceptible to climate changes and anthropogenic pressures responsible for biodiversity losses and require specific biomonitoring programs. Benthic macroinvertebrates are suitable as ecological indicators of transitional waters, being affected by biological, chemical, and physical conditions of the ecosystems about their life cycles and space-use behaviour. The advent of high-throughput sequencing technologies has allowed biodiversity investigations, at the molecular level, in multiple ecosystems and for different ecological guilds. Benthic macroinvertebrate communities’ composition has been investigated, at the molecular level, mainly through DNA extracted from sediments in marine and riverine ecosystems. In this work, benthic macroinvertebrate communities are explored through eDNA metabarcoding from water samples in a Mediterranean transitional water ecosystem. This research highlighted the validity of eDNA metabarcoding as an efficient tool for the assessment of benthic macroinvertebrate community structure in transitional waters, unveiling the spatial heterogeneity of benthic macroinvertebrate communities correlated to the measured environmental gradients. The results suggest that peculiar features of transitional water ecosystems, such as shallow waters and limited currents, facilitate the assessment of benthic macroinvertebrate communities through environmental DNA analysis from surface water samples, opening for more rapid and accurate monitoring programs for these valuable ecosystems
PHB Produced by Bacteria Present in the Argan Field Soil: A New Perspective for the Synthesis of the Bio-Based Polymer
No full textGap analysis for DNA barcodes of aquatic macroinvertebrate species in the Southeast of Italy
No full textDNA metabarcoding for the identification of species and ecosystem biomonitoring is a promising innovative approach. The applicability of this tool is at first dependent on the coverage of the DNA sequence reference libraries. We performed a gap analysis of available DNA barcodes in the international databases using the aquatic macroinvertebrate species checklist of the Apulia region in southeast Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups in particular at local/regional level. The DNA-barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more extensive use of the DNA metabarcoding. We also highlighted the opportunity to develop combinations of primers useful at the regional level. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Aquatina di Frigole” in the Apulia region) which are richer in humic substances than other aquatic environments and in which DNA metabarcoding remains under explored
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