Biology subjects

Galli, P.

Publications and source records attributed to Galli, P..

6 recordsLinked to original sources

bioRxiv2026

Unlocking Targeted Underwater Delivery of Coral Probiotics

The rapid global decline of coral reefs has intensified the need for innovative conservation strategies, including microbial therapies to enhance coral health and resilience. A major limitation, however, is the lack of effective delivery systems for administering Beneficial Microorganisms for Corals (BMCs). In this study, we present natural, biodegradable systems for the underwater delivery of probiotic bacteria to corals. Three customized alginate-based delivery formats (beads, hydrogels, and filaments) were developed and loaded with the probiotic Pseudoalteromonas peptidolytica. The materials were loaded with the bacterium at an average concentration of 10^(4) CFU/g of dry polymer and engineered to sink underwater while keeping their structural integrity over time. In vitro assays showed controlled release kinetics, with encapsulated probiotics remaining viable and capable of replication. In vivo experiments compared syringe-based inoculation with the application of alginate beads, hydrogels, and filaments to corals. Microbiome analyses performed before and after inoculation confirmed successful probiotic colonization following deployment of the alginate-based delivery systems. Relative abundance of the probiotic genus Pseudoalteromonas increased markedly in treated corals, reaching 11.5 % after 48 h with alginate beads, 12.7 % after 48 h with hydrogels, and 12.6 % after 24 h with filaments. Furthermore, the degradation mechanisms of the three delivery systems were investigated. As the first biomaterial-based underwater delivery systems specifically engineered for coral probiotics, these alginate-based materials provide a promising foundation for advancing microbial therapies in both controlled aquaria and natural reef environments.

bioengineering↗

bioRxiv2025

Mapping the latent CRBN-molecular glue degrader interactome

Molecular glue degraders (MGDs) are a transformative modality in drug discovery. MGDs that work in concert with the E3 ligase CRL4CRBN can degrade a range of substrates through tailored MGDs. To explore CRL4CRBN reprogrammability, we tested whether reported CRBN-MGD substrates are part of a network of latent CRBN interactors, detectable with generic CRBN-MGDs. Leveraging highly parallel interaction measurement (GluePCA) between CRL4CRBN and human zinc-fingers (ZFs), we identified [~]210 ZFs bound to CRBN-pomalidomide, where top binders are already reported as degraded by dedicated MGDs. To map latent CRBN-MGDs interactions proteome-wide, and thus define the immediately accessible CRBN target space, we combined AI-derived protein surface queries (MaSIF-mimicry) with GluePCA. This pipeline identified 6 known and 43 novel CRBN-pomalidomide binders, thereby providing privileged starting points for MGD development. We expect this binding-focused, highly parallel workflow to be readily applicable to other MGD/E3 ligase systems, extending the target landscape of this emerging drug class.

molecular biology↗

bioRxiv2023

Surface-sourced eDNA to track deep-diver cetaceans: the study case of Cuvier's beaked whale (Ziphius cavirostris) at Caprera Canyon and surrounding areas (Western Mediterranean Sea)

Among cetaceans, the Cuviers beaked whale is considered an extreme diver, very challenging to be studied with standard monitoring methods due to its elusive behaviour and a preference for deep offshore waters. These limitations seem to be mitigated by the use of new molecular methodologies capable of intercepting small traces of DNA left in the environment (eDNA) by marine organisms. Moreover, the collection of water from the superficial layer of the sea represents a perfect case study for the targeting of marine mammals, as the constraints imposed by their nature implies periodic and frequent surfacing. Therefore, we designed and tested a taxon-specific primer set to infer the Cuviers beaked whale presence, with the aims of 1) examining the effectiveness of the eDNA technique to detect the presence of deep-diving cetacean in open waters, using the Cuviers beaked whale as case study; 2) providing data on the spatiotemporal occurrence of this species within the Canyon of Caprera; and 3) assessing the species occurrence in central northern Mediterranean Sea based on molecular traces. Results from this study demonstrated that collection of superficial waters is a valid approach to monitor deep-diving cetacean species, without the need for complementary visual survey monitoring. Specifically, this study provides evidence of the regular presence of the Cuviers beaked whale in the Canyon of Caprera, with a preference for bathymetry in the range of 700-1000 m. This study also showed a potential inshore movement of this species during fall, which is possibly related to migration of its cephalopod prey or a shift in prey preferences. Overall, the data presented here are particularly relevant in the optic of proposing the Caprera Canyon as an Important Marine Mammal Area (IMMA) in the Mediterranean Sea. At a wider level, this study also showed that the stronger positive signals were recorded in sampling stations located on submarine canyon systems, demonstrating the importance of these areas as elective habitats for the Cuviers beaked whale, thus the pivotal priority to their conservation.

ecology↗

bioRxiv2021

Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity

Marine environmental DNA (eDNA) is an important tool for biodiversity research and monitoring but challenges remain in scaling surveys over large spatial areas, and increasing the frequency of sampling in remote locations at reasonable cost. Here we demonstrate the feasibility of sampling from commercial vessels (Mediterranean ferries) while underway, as a strategy to facilitate replicable, systematic marine eDNA surveys in locations that would normally be challenging and expensive for researchers to access. Sixteen eDNA samples were collected from 4 fixed sampling stations, and in response to 4 cetacean sightings, across three cruises undertaken along the 300 km ferry route between Livorno (Tuscany) and Golfo Aranci (Sardinia) in the Ligurian/Tyrrhenian Seas, June-July 2018. Using 12SrDNA and 16SrDNA metabarcoding markers, we recovered diverse marine vertebrate Molecular Operational Taxonomic Units (MOTUs) from teleost fish, elasmobranchs, and cetaceans. We detected sample heterogeneity consistent with previously known variation in species occurrences, including putative species spawning peaks associated with specific sea surface temperature ranges, and increased night time abundance of bathypelagic species known to undertake diel migrations through the water column. We suggest commercial vessel based marine eDNA sampling using the global shipping network has potential to facilitate broad-scale biodiversity monitoring in the worlds oceans.

molecular biology↗

bioRxiv2021

Newly developed ad hoc molecular assays shows how eDNA can witness and anticipate the monk seal recolonization of central Mediterranean

The monk seal Monachus monachus is the most endangered pinniped worldwide and the only one found in the Mediterranean, where its distribution and abundance have suffered a drastic decline in the last few decades. Data on its status are scattered due to both its rarity and evasiveness, and records are biased towards occasional, mostly coastal, encounters. Nowadays molecular techniques allow us to detect and quantify minute amounts of DNA traces released in the environment (eDNA) by any organism. We present three qPCR-assays targeting the monk seal mitogenome. The assays were soundly tested on an extensive and diversified sample set (n=73), including positive controls from Madeira breeding population collected during the peak of abundance, and two opportunistic Mediterranean eDNA-sample collections (offshore/coastal) from on-going projects. Monk seal DNA was detected in 47.2% and 66.7% of the samples collected in the Tyrrhenian from a ferry platform (2018-2019) and in the Pelagie archipelago -Strait of Sicily- (2020) respectively, anticipating (up to 2 year) visual observations occurred subsequently in proximity of the sampled areas. In the Tyrrhenian, detection occurrence increased between 2018 and 2019. Monk seal DNA recoveries were commoner in night-time ferry-samples, suggesting nocturnal predatory activity in pelagic waters. The proposed technique provides a non-invasive and yet highly-sensitive tool for defining the monk seal actual distribution and home range, its recovery rate and pinpoint coastal/offshore localities where prioritizing conservation, research, citizen science and education initiatives.

molecular biology↗

bioRxiv2019

Novel Universal Primers For Metabarcoding eDNA Surveys Of Marine Mammals And Other Marine Vertebrates

Metabarcoding studies using environmental DNA (eDNA) and high throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals have received less attention. Similarly, there have been few attempts to identify potentially universal barcode loci which may be informative across multiple marine vertebrate Orders. Here we describe the design and validation of four new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. In silico validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.

ecology↗