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Biology subjects

Ruggiero, M.

Publications and source records attributed to Ruggiero, M..

4 recordsLinked to original sources

Passive Acoustic Monitoring within the Northwest Forest Plan Area: 2023 Annual Report

Here we document progress in implementing large-scale passive acoustic monitoring across the Northwest Forest Plan area to track population trends of northern spotted owls (Strix occidentalis caurina), barred owls (S. varia), marbled murrelets (Brachyramphus marmoratus), and a broad array of forest-adapted wildlife. In 2023, we deployed 4,012 autonomous recording units across 1,009 randomly selected 5-km{superscript 2} hexagons, generating nearly 2.2 million hours of recordings, representing approximately 1 petabyte of acoustic data. These data were processed with PNW-Cnet v5, the latest version of our convolutional neural network model, trained on 135 sound classes representing over 80 species and environmental sounds. Model performance demonstrated high precision for focal species and many additional taxa, substantially reducing manual review effort while enabling broad-scale biodiversity assessments. Results confirmed northern spotted owl detections in all 20% sample areas, with occupancy varying geographically and declining notably in the Tyee study area. Barred owls were widely detected, with the highest prevalence in Oregon and Washington and comparatively lower occupancy in California. Marbled murrelets were consistently detected in coastal areas, particularly the Olympic Peninsula and Oregon Coast Range. Beyond these focal species, PAM and PNW-Cnet generated robust datasets for a wide range of birds, mammals, and disturbance indicators, underscoring the value of random-site, multi-species monitoring. The 2023 field season marked the first full implementation of the 2% + 20% NWFP sampling design, expanding monitoring coverage while strengthening collaborations with federal and state partners. These efforts provide the foundation for long-term, cost-effective wildlife monitoring and inform conservation strategies in dynamic forest ecosystems.

ecology↗

Experimental evidence for the role of natural radioactivity in influencing viability of commensal microorganisms

The role of natural radioactivity in influencing viability of commensal microorganisms, with particular reference to those pertaining to the human microbiota, has not been investigated in detail. The results of experiments culturing a diversified array of microorganims - probiotics - in naturally radioactive mineral water or deuterium-depleted water are here described. Culturing microorganisms in naturally radioactive mineral water yielded one order of magnitude more live microbial cells in comparison with culturing in deuterium-depleted water. Based on these experimental results, a method for co-culturing prebiotic microorganisms (cyanobacteria) that are extremely resistant to the harmful effects of radiations, together with the probiotics mentioned above, is described. The goal of this co-culture in naturally radioactive mineral water is to transfer the information from the radiation-resistant microorganisms to the probiotics whose viability is enhanced by natural radioactivity. Expression of DNA repair genes in cyanobacteria is induced by co-culturing in a medium of carbonated mineral water naturally containing the radioactive isotopes 228U and 226Ra. The culture medium, in addition to naturally radioactive water, contains silica from vegetal origin to enhance horizontal gene transfer. Finally, it is described the transfer of resistance to the harmful effects of radiations to human cells through a Lactococcus phage-encoded protein, ORF252, that is the evolutionary precursor of human proteins involved in DNA repair and cancer protection.

microbiology↗

Significance of hydrophobic and charged sequence similarities in sodium-bile acid cotransporter and vitamin D-binding protein macrophage activating factor

Sodium-bile acid cotransporter, also denominated sodium-taurocholate cotransporting polypeptide (NTCP) is an integral membrane protein with multiple hydrophobic transmembrane domains. The third extracellular domain of NTCP presents a stretch of nine aminoacids (KGIVISLVL) that is characterized by pronounced hydrophobicity and serves as receptor for a protein, preS1, showing the hydrophobic epta-peptide sequence NPLGFFP. Vitamin D-binding protein macrophage activating factor (DBP-MAF) is a multifunctional protein that is characterized by two hydrophobic regions able to bind fatty acids and vitamin D, respectively. Here we demonstrate that NTCP and DBP-MAF show significant sequence similarities as far as hydrophobic stretches of aminoacids are concerned. Alignment of the sequence of seven aminoacids preceding the 157-KGIVISLVL-165 stretch of NTCP shows four aminoacids that are identical to those of the corresponding sequence of DBP-MAF, and two that are conserved substitutions. In addition, in the sequence of DBP-MAF that is aligned with the sequence YKGIVISLVL of NTCP, there are two contiguous negatively charged aminoacids (ED) and, in the preceding epta-peptide sequence, there are three negatively charged aminoacids (D-ED), whereas in the corresponding sequence of NTCP there are only two (D--D) that are not contiguous. This concentration of negatively charged aminoacids may be involved in binding of protein inserts characterized by high density of positively charges residues. The alternating hydrophobic and electrostatic interactions described in this paper may help elucidating the biological roles of these proteins as far as protein-protein interactions are concerned.

bioinformatics↗

Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames

Bacteriophages (phages), Earths most numerous biological entities, are natural constituents of alimentary matrices; in this study we describe the characterization of phage populations in a product obtained by fermentation of bovine milk and colostrum. Such characterizations were achieved using a microarray consisting of a chip covered in short DNA sequences that are specific to certain target organisms for a total of approximately 12,000 species. The only viruses evidenced by the array belonged to Siphoviridae, the largest phage family that targets bacteria and archea. The array yielded 27 iterations corresponding to a unique target. We discuss the putative role of some open reading frames of these phages in conferring health-supporting properties with particular reference to cells signaling and neurological development. We also describe the in vitro interaction of this fermented product with alpha-N-acetylgalactosaminidase, an enzyme whose activity in serum is elevated in neurodevelopmental disorders.

microbiology↗