Semi-industrial ultrasound-assisted extraction of grape-seed proteins.

BACKGROUND: To manage industrial waste in accordance with the circular bioeconomy concept it is sometimes necessary to handle grape seeds, an abundant by-product of the wine-making process. This study presents a process based on ultrasound technology for the extraction of grape-seed proteins, due to their nutritional and techno-functional properties. The protein content of extracts obtained under silent and lab-scale conditions was compared with that obtained under semi-industrial ultrasound conditions, and the chemical composition (carbohydrates, total phenols, and lipids) and the elemental profiles of the final, up-scaled downstream extracts were characterized. RESULTS: This work found that the maximum amount of protein in the final product was 378.31 g.kg-1 of the extract. Chemical characterization revealed that each 1 kg of extract had an average content of 326.19 g gallic acid equivalent as total phenols, 162.57 g glucose equivalent as carbohydrates, and 382.76 g of lipophilic compounds. Furthermore, when the extract was checked for hazardous elements, none were found in levels that could be considered a risk for human health. CONCLUSION: The proposed semi-industrial strategy has the potential to contribute greatly to the valorization of grape seeds through the preparation of a protein-rich extract that can be used as an alternative to synthetic wine stabilizers and for the development of novel food and nutraceutical products. © 2024 Society of Chemical Industry.

ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy.

SUMMARY: ITSoneWB (ITSone WorkBench) is a Galaxy-based bioinformatic environment where comprehensive and high-quality reference data are connected with established pipelines and new tools in an automated and easy-to-use service targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing. AVAILABILITY AND IMPLEMENTATION: ITSoneWB has been deployed on the INFN-Bari ReCaS cloud facility and is freely available on the web at http://itsonewb.cloud.ba.infn.it/galaxy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data.

High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the 'interactome sequencing' approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains ('domainome') or epitopes ('epitome') from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https://InteractomeSeq.ba.itb.cnr.it/.

Mechanochemical Applications of Reactive Extrusion from Organic Synthesis to Catalytic and Active Materials.

In the past, the use of mechanochemical methods in organic synthesis was reported as somewhat of a curiosity. However, perceptions have changed over the last two decades, and this technology is now being appreciated as a greener and more efficient synthetic method. The qualified "offer" of ball mills that make use of different set-ups, materials, and dimensions has allowed this technology to mature. Nevertheless, the intrinsic batch nature of mechanochemical methods hinders industrial scale-ups. New studies have found, in reactive extrusion, a powerful technique with which to activate chemical reactions with mechanical forces in a continuous flow. This new environmentally friendly mechanochemical synthetic method may be able to miniaturize production plants with outstanding process intensifications by removing organic solvents and working in a flow mode. Compared to conventional processes, reactive extrusions display high simplicity, safety, and cleanliness, which can be exploited in a variety of applications. This paper presents perspective examples in the better-known areas of reactive extrusions, including oxidation reactions, polymer processing, and biomass conversion. This work should stimulate further developments, as it highlights the versatility of reactive extrusion and the huge potential of solid-phase flow chemistry.

Green Deep Eutectic Solvents for Microwave-Assisted Biomass Delignification and Valorisation.

Aiming to fulfil the sustainability criteria of future biorefineries, a novel biomass pretreatment combining natural deep eutectic solvents (NaDESs) and microwave (MW) technology was developed. Results showed that NaDESs have a high potential as green solvents for lignin fractionation/recovery and sugar release in the following enzymatic hydrolysis. A new class of lignin derived NaDESs (LigDESs) was also investigated, showing promising effects in wheat straw delignification. MW irradiation enabled a fast pretreatment under mild condition (120 °C, 30 min). To better understand the interaction of MW with these green solvents, the dielectric properties of NaDESs were investigated. Furthermore, a NaDES using the lignin recovered from biomass pretreatment as hydrogen bond donor was prepared, thus paving the way for a "closed-loop" biorefinery process.

Combined microRNA and mRNA expression analysis in pediatric multiple sclerosis: an integrated approach to uncover novel pathogenic mechanisms of the disease.

Multiple sclerosis (MS) is a complex disease of the CNS that usually affects young adults, although 3-5% of cases are diagnosed in childhood and adolescence (hence called pediatric MS, PedMS). Genetic predisposition, among other factors, seems to contribute to the risk of the onset, in pediatric as in adult ages, but few studies have investigated the genetic 'environmentally naïve' load of PedMS. The main goal of this study was to identify circulating markers (miRNAs), target genes (mRNAs) and functional pathways associated with PedMS; we also verified the impact of miRNAs on clinical features, i.e. disability and cognitive performances. The investigation was performed in 19 PedMS and 20 pediatric controls (PCs) using a High-Throughput Next-generation Sequencing (HT-NGS) approach followed by an integrated bioinformatics/biostatistics analysis. Twelve miRNAs were significantly upregulated (let-7a-5p, let-7b-5p, miR-25-3p, miR-125a-5p, miR-942-5p, miR-221-3p, miR-652-3p, miR-182-5p, miR-185-5p, miR-181a-5p, miR-320a, miR-99b-5p) and 1 miRNA was downregulated (miR-148b-3p) in PedMS compared with PCs. The interactions between the significant miRNAs and their targets uncovered predicted genes (i.e. TNFSF13B, TLR2, BACH2, KLF4) related to immunological functions, as well as genes involved in autophagy-related processes (i.e. ATG16L1, SORT1, LAMP2) and ATPase activity (i.e. ABCA1, GPX3). No significant molecular profiles were associated with any PedMS demographic/clinical features. Both miRNAs and mRNA expressions predicted the phenotypes (PedMS-PC) with an accuracy of 92% and 91%, respectively. In our view, this original strategy of contemporary miRNA/mRNA analysis may help to shed light in the genetic background of the disease, suggesting further molecular investigations in novel pathogenic mechanisms.

ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive.

WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes.

The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria. RNA-sequencing or microarray-based gene expression data are provided as input, along with gene annotations. The user can select genomic annotations from an internal database including 2780 bacterial strains, or provide custom genomic annotations. The analysis produces as output the lists of positionally related genes showing a coordinated trend of differential expression. Graphical representations, including a circular plot of the analyzed chromosome, allow intuitive browsing of the results. The analysis procedure is based on our previously published R-package PREDA. The release of this tool is timely and relevant for the scientific community, as WoPPER will fill an existing gap in prokaryotic gene expression data analysis and visualization tools. WoPPER is open to all users and can be reached at the following URL: https://WoPPER.ba.itb.cnr.it.

A fuzzy method for RNA-Seq differential expression analysis in presence of multireads.

BACKGROUND: When the reads obtained from high-throughput RNA sequencing are mapped against a reference database, a significant proportion of them - known as multireads - can map to more than one reference sequence. These multireads originate from gene duplications, repetitive regions or overlapping genes. Removing the multireads from the mapping results, in RNA-Seq analyses, causes an underestimation of the read counts, while estimating the real read count can lead to false positives during the detection of differentially expressed sequences. RESULTS: We present an innovative approach to deal with multireads and evaluate differential expression events, entirely based on fuzzy set theory. Since multireads cause uncertainty in the estimation of read counts during gene expression computation, they can also influence the reliability of differential expression analysis results, by producing false positives. Our method manages the uncertainty in gene expression estimation by defining the fuzzy read counts and evaluates the possibility of a gene to be differentially expressed with three fuzzy concepts: over-expression, same-expression and under-expression. The output of the method is a list of differentially expressed genes enriched with information about the uncertainty of the results due to the multiread presence. We have tested the method on RNA-Seq data designed for case-control studies and we have compared the obtained results with other existing tools for read count estimation and differential expression analysis. CONCLUSIONS: The management of multireads with the use of fuzzy sets allows to obtain a list of differential expression events which takes in account the uncertainty in the results caused by the presence of multireads. Such additional information can be used by the biologists when they have to select the most relevant differential expression events to validate with laboratory assays. Our method can be used to compute reliable differential expression events and to highlight possible false positives in the lists of differentially expressed genes computed with other tools.

Microwave-Assisted γ-Valerolactone Production for Biomass Lignin Extraction: A Cascade Protocol.

The general need to slow the depletion of fossil resources and reduce carbon footprints has led to tremendous effort being invested in creating "greener" industrial processes and developing alternative means to produce fuels and synthesize platform chemicals. This work aims to design a microwave-assisted cascade process for a full biomass valorisation cycle. GVL (γ-valerolactone), a renewable green solvent, has been used in aqueous acidic solution to achieve complete biomass lignin extraction. After lignin precipitation, the levulinic acid (LA)-rich organic fraction was hydrogenated, which regenerated the starting solvent for further biomass delignification. This process does not requires a purification step because GVL plays the dual role of solvent and product, while the reagent (LA) is a product of biomass delignification. In summary, this bio-refinery approach to lignin extraction is a cascade protocol in which the solvent loss is integrated into the conversion cycle, leading to simplified methods for biomass valorisation.

Reference databases for taxonomic assignment in metagenomics.

Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.

Long-term culture of patient-derived mammary organoids in non-biogenic electrospun scaffolds for identifying metalloprotein and motor protein activities in aging and senescence.

We recently identified TMEM230 as a master regulator of the endomembrane system of cells. TMEM230 expression is necessary for promoting motor protein dependent intracellular trafficking of metalloproteins for cellular energy production in mitochondria. TMEM230 is also required for transport and secretion of metalloproteinases for autophagy and phagosome dependent clearance of misfolded proteins, defective RNAs and damaged cells, activities that decline with aging. This suggests that aberrant levels of TMEM230 may contribute to aging and regain of proper levels may have therapeutic applications. The components of the endomembrane system include the Golgi complex, other membrane bound organelles, and secreted vesicles and factors. Secreted cellular components modulate immune response and tissue regeneration in aging. Upregulation of intracellular packaging, trafficking and secretion of endosome components while necessary for tissue homeostasis and normal wound healing, also promote secretion of pro-inflammatory and pro-senescence factors. We recently determined that TMEM230 is co-regulated with trafficked cargo of the endomembrane system, including lysosome factors such as RNASET2. Normal tissue regeneration (in aging), repair (following injury) and aberrant destructive tissue remodeling (in cancer or autoimmunity) likely are regulated by TMEM230 activities of the endomembrane system, mitochondria and autophagosomes. The role of TMEM230 in aging is supported by its ability to regulate the pro-inflammatory secretome and senescence-associated secretory phenotype in tissue cells of patients with advanced age and chronic disease. Identifying secreted factors regulated by TMEM230 in young patients and patients of advanced age will facilitate identification of aging associated targets that aberrantly promote, inhibit or reverse aging. Ex situ culture of patient derived cells for identifying secreted factors in tissue regeneration and aging provides opportunities in developing therapeutic and personalized medicine strategies. Identification and validation of human secreted factors in tissue regeneration requires long-term stabile scaffold culture conditions that are different from those previously reported for cell lines used as cell models for aging. We describe a 3 dimensional (3D) platform utilizing non-biogenic and non-labile poly ε-caprolactone scaffolds that supports maintenance of long-term continuous cultures of human stem cells, in vitro generated 3D organoids and patient derived tissue. Combined with animal component free culture media, non-biogenic scaffolds are suitable for proteomic and glycobiological analyses to identify human factors in aging. Applications of electrospun nanofiber technologies in 3D cell culture allow for ex situ screening and the development of patient personalized therapeutic strategies and predicting their effectiveness in mitigating or promoting aging.

Industrial Multiple-Effect Fractional Condensation under Vacuum for the Recovery of Hop Terpene Fractions in Water.

The inflorescences of Humulus lupulus L. are the most valuable ingredient in the brewing industry. Only female cones are used as their bitterness and aroma, much associated with beer, are granted by the production of resins and essential oils, respectively. The traditional brewing process for the extraction of the organic volatiles in hops is called dry hopping. It consists of extended maceration at low temperature after the fermentation phase. New extraction technologies can improve extraction rates and product quality while saving time and money. This article proves that multiple-effect fractional condensation under a vacuum is suitable for flavouring applications and especially for performing dry hopping without contamination risks and reductions in hop amounts. This technique leads to the recovery of aqueous aromatic fractions that are very rich in hop sesquiterpenes and monoterpenes. These suspensions are extremely stable when stored at 5-8 °C and avoid degradation even after several months. This feature is crucial for the marketing of non-alcoholic beverages, where the dilution of essential oils is otherwise problematic.

CeO2 Frustrated Lewis Pairs Improving CO2 and CH3OH Conversion to Monomethylcarbonate.

Frustrated Lewis pairs (FLPs), discovered in the last few decades for homogeneous catalysts and in the last few years also for heterogeneous catalysts, are stimulating the scientific community's interest for their potential in small-molecule activation. Nevertheless, how an FLP activates stable molecules such as CO2 is still undefined. Through a careful spectroscopic study, we here report the formation of FLPs over a highly defective CeO2 sample prepared by microwave-assisted synthesis. Carbon dioxide activation over FLP is shown to occur through a bidentate carbonate bridging the FLP and implying a Ce3+-to-CO2 charge transfer, thus enhancing its activation. Carbon dioxide reaction with methanol to form monomethylcarbonate is here employed to demonstrate active roles of FLP and, eventually, to propose a reaction mechanism clarifying the role of Ce3+ and oxygen vacancies.

Unlocking the Bioactive Potential of Pomegranate Peels: A Green Extraction Approach.

Pomegranate (Punica granatum L.) is well known for its high content of bioactives, including polyphenols, flavonoids, and tannins, which have been shown to exhibit a wide range of biological activities, such as antioxidant, antimicrobial, and anticancer effects. It is worth noting that the majority of these molecules are found in the peels, which are usually disposed of after processing, causing a significant amount of waste, amounting to more than 3.6 million t/y. This work investigates microwave-assisted extraction (MAE) in water for the recovery of antioxidants from pomegranate peels (PP), including the optimisation of temperature and extraction times. The total phenolic, anthocyanin, flavonoid, and tannin contents of the recovered extracts were determined, as well as their antioxidant activities, which were found to be 356.35 mgGAE/gExtr, 303.97 µgCy3G/gExtr, 37.28 mgQE/gExtr, 56.48 mgGAE/gExtr, and 5.72 mmolTE/gExtr, respectively (according to the adopted reference). All results were compared with those obtained using a conventional protocol. In addition, the potential for water recycling by means of downstream nanofiltration in optimised MAE was investigated, leading to overall water reuse of approx. 75%. Power consumption (20.92 W/mgGAE) and common green metrics, Reaction Mass Efficiency (RME), E-Factor, and the Process Mass Intensiti/efficiency (PMI, PME), were considered in evaluating the proposed PP valorisation strategy. Finally, the biological activities of the main products were assessed. The antimicrobial properties of the PP extracts against three Gram-positive and three Gram-negative bacteria and their antiproliferative activity towards human cancer cells were tested. S. aureus bacteria was the most susceptible to the PP extracts. All tested products displayed antiproliferative activity against HeLa cells when higher concentrations were tested, with D-PP/NF (obtained from dried PP and sequential nanofiltration) being the most effective. This result was also confirmed via clonogenic analysis, which generally indicated the possible anti-cancer activity of pomegranate peel extracts obtained using this green approach.

CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data.

Flow cytometry (FCM) can investigate dozens of parameters from millions of cells and hundreds of specimens in a short time and at a reasonable cost, but the amount of data that is generated is considerable. Computational approaches are useful to identify novel subpopulations and molecular biomarkers, but generally require deep expertize in bioinformatics and the use of different platforms. To overcome these limitations, we introduce CRUSTY, an interactive, user-friendly webtool incorporating the most popular algorithms for FCM data analysis, and capable of visualizing graphical and tabular results and automatically generating publication-quality figures within minutes. CRUSTY also hosts an interactive interface for the exploration of results in real time. Thus, CRUSTY enables a large number of users to mine complex datasets and reduce the time required for data exploration and interpretation. CRUSTY is accessible at https://crusty.humanitas.it/ .

Batch and Flow Green Microwave-Assisted Catalytic Conversion Of Levulinic Acid to Pyrrolidones.

This paper reports a new sustainable protocol for the microwave-assisted catalytic conversion of levulinic acid into N-substituted pyrrolidones over tailor-made mono (Pd, Au) or bimetallic (PdAu) catalysts supported on either highly mesoporous silica (HMS) or titania-doped HMS, exploiting the advantages of dielectric heating. MW-assisted reductive aminations of levulinic acid with several amines were first optimized in batch mode under hydrogen pressure (5 bar) in solvent-free conditions. Good-to-excellent yields were recorded at 150 °C in 90 min over the PdTiHMS and PdAuTiHMS, that proved recyclable and almost completely stable after six reaction cycles. Aiming to scale-up this protocol, a MW-assisted flow reactor was used in combination with different green solvents. Cyclopentyl methyl ether (CPME) provided a 99 % yield of N-(4-methoxyphenyl) pyrrolidin-2-one at 150 °C over PdTiHMS. The described MW-assisted flow synthesis proves to be a safe procedure suitable for further industrial applications, while averting the use of toxic organic solvents.

Food-Waste Valorisation: Synergistic Effects of Enabling Technologies and Eutectic Solvents on the Recovery of Bioactives from Violet Potato Peels.

The recovery of valuable bioactive compounds from the main underutilised by-products of the food industry is one of the greatest challenges to be addressed in circular economy. Potato peels are the largest waste generated during potato processing. However, they could be a potential source of valuable bioactive compounds, such as polyphenols, that can be reused as natural antioxidants. Currently, environmentally benign enabling technologies and new types of non-toxic organic solvents for the extraction of bioactive compounds may dramatically improve the sustainability of these processes. This paper focuses on the potential inherent in the valorisation of violet potato peels (VPPs) by recovering antioxidants using natural deep eutectic solvents (NaDES) under ultrasound (US)- and microwave (MW)-assisted extraction. Both the enabling technologies provided performances that were superior to those of conventional extractions in terms of antioxidant activity determined by the DPPH· (2,2-diphenyl-1-picrylhydrazyl) assay. In particular, the most promising approach using NaDES is proven to be the acoustic cavitation with a Trolox eq. of 1874.0 mmolTE/gExtr (40 °C, 500 W, 30 min), vs. the 510.1 mmolTE/gExtr of hydroalcoholic extraction (80 °C, 4 h). The shelf-life of both hydroalcoholic and NaDES-VPPs extracts have been assessed over a period of 24 months, and found that NaDES granted a 5.6-fold shelf-life extension. Finally, the antiproliferative activity of both hydroalcoholic and NaDES-VPPs extracts was evaluated in vitro using the MTS assay on human tumour Caco-2 cells and normal human keratinocyte cells (HaCaT). In particular, NaDES-VPPs extracts exhibited a significantly more pronounced antiproliferative activity compared to the ethanolic extracts without a noteworthy difference between effects on the two cell lines.

Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models.

Long non-coding RNAs (lncRNAs) have emerged as key regulators of cellular senescence by transcriptionally and post-transcriptionally modulating the expression of many important genes involved in senescence-associated pathways and processes. Among the different lncRNAs associated to senescence, Senescence Associated Long Non-coding RNA (SALNR) was found to be down-regulated in different cellular models of senescence. Since its release in 2015, SALNR has not been annotated in any database or public repository, and no other experimental data have been published. The SALNR sequence is located on the long arm of chromosome 10, at band 10q23.33, and it overlaps the 3' end of the HELLS gene. This investigation helped to unravel the mystery of the existence of SALNR by analyzing publicly available short- and long-read RNA sequencing data sets and RT-PCR analysis in human tissues and cell lines. Additionally, the expression of HELLS has been studied in cellular models of replicative senescence, both in silico and in vitro. Our findings, while not supporting the actual existence of SALNR as an independent transcript in the analyzed experimental models, demonstrate the expression of a predicted HELLS isoform entirely covering the SALNR genomic region. Furthermore, we observed a strong down-regulation of HELLS in senescent cells versus proliferating cells, supporting its role in the senescence and aging process.

GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity Database.

BACKGROUND: In the scientific biodiversity community, it is increasingly perceived the need to build a bridge between molecular and traditional biodiversity studies. We believe that the information technology could have a preeminent role in integrating the information generated by these studies with the large amount of molecular data we can find in bioinformatics public databases. This work is primarily aimed at building a bioinformatic infrastructure for the integration of public and private biodiversity data through the development of GIDL, an Intelligent Data Loader coupled with the Molecular Biodiversity Database. The system presented here organizes in an ontological way and locally stores the sequence and annotation data contained in the GenBank primary database. METHODS: The GIDL architecture consists of a relational database and of an intelligent data loader software. The relational database schema is designed to manage biodiversity information (Molecular Biodiversity Database) and it is organized in four areas: MolecularData, Experiment, Collection and Taxonomy. The MolecularData area is inspired to an established standard in Generic Model Organism Databases, the Chado relational schema. The peculiarity of Chado, and also its strength, is the adoption of an ontological schema which makes use of the Sequence Ontology. The Intelligent Data Loader (IDL) component of GIDL is an Extract, Transform and Load software able to parse data, to discover hidden information in the GenBank entries and to populate the Molecular Biodiversity Database. The IDL is composed by three main modules: the Parser, able to parse GenBank flat files; the Reasoner, which automatically builds CLIPS facts mapping the biological knowledge expressed by the Sequence Ontology; the DBFiller, which translates the CLIPS facts into ordered SQL statements used to populate the database. In GIDL Semantic Web technologies have been adopted due to their advantages in data representation, integration and processing. RESULTS AND CONCLUSIONS: Entries coming from Virus (814,122), Plant (1,365,360) and Invertebrate (959,065) divisions of GenBank rel.180 have been loaded in the Molecular Biodiversity Database by GIDL. Our system, combining the Sequence Ontology and the Chado schema, allows a more powerful query expressiveness compared with the most commonly used sequence retrieval systems like Entrez or SRS.