Stem-loop structures in prokaryotic genomes

BACKGROUND: Prediction of secondary structures in the expressed sequences of bacterial genomes allows to investigate spontaneous folding of the corresponding RNA. This is particularly relevant in untranslated mRNA regions, where base pairing is less affected by interactions with the translation machinery. Relatively large stem-loops significantly contribute to the formation of more complex secondary structures, often important for the activity of sequence elements controlling gene expression. RESULTS: Systematic analysis of the distribution of stem-loop structures (SLSs) in 40 wholly-sequenced bacterial genomes is presented. SLSs were searched as stems measuring at least 12 bp, bordering loops 5 to 100 nt in length. G-U pairing in the stems was allowed. SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and composition. The large majority of SLSs fall within protein-coding regions but enrichment of specific, non random, SLS sub-populations of higher stability was observed within the intergenic regions of the chromosomes of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs. Some intergenic SLS regions are members of novel repeated sequence families. CONCLUSION: In depth analysis of SLS features and distribution in 40 different bacterial genomes showed the presence of non random populations of such structures in all species. Many of these structures are plausibly transcribed, and might be involved in the control of transcription termination, or might serve as RNA elements which can enhance either the stability or the turnover of cotranscribed mRNAs. Three previously undescribed families of repeated sequences were found in Yersiniae, Bordetellae and Enterococci

Quality, integrity and utility of COVID-19 science: opportunities for public health researchers

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Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity

BACKGROUND: Protein kinases are a well defined family of proteins, characterized by the presence of a common kinase catalytic domain and playing a significant role in many important cellular processes, such as proliferation, maintenance of cell shape, apoptosys. In many members of the family, additional non-kinase domains contribute further specialization, resulting in subcellular localization, protein binding and regulation of activity, among others. About 500 genes encode members of the kinase family in the human genome, and although many of them represent well known genes, a larger number of genes code for proteins of more recent identification, or for unknown proteins identified as kinase only after computational studies. RESULTS: A systematic in silico study performed on the human genome, led to the identification of 5 genes, on chromosome 1, 11, 13, 15 and 16 respectively, and 1 pseudogene on chromosome X; some of these genes are reported as kinases from NCBI but are absent in other databases, such as KinBase. Comparative analysis of 483 gene regions and subsequent computational analysis, aimed at identifying unannotated exons, indicates that a large number of kinase may code for alternately spliced forms or be incorrectly annotated. An InterProScan automated analysis was perfomed to study domain distribution and combination in the various families. At the same time, other structural features were also added to the annotation process, including the putative presence of transmembrane alpha helices, and the cystein propensity to participate into a disulfide bridge. CONCLUSION: The predicted human kinome was extended by identifiying both additional genes and potential splice variants, resulting in a varied panorama where functionality may be searched at the gene and protein level. Structural analysis of kinase proteins domains as defined in multiple sources together with transmembrane alpha helices and signal peptide prediction provides hints to function assignment. The results of the human kinome analysis are collected in the KinWeb database, available for browsing and searching over the internet, where all results from the comparative analysis and the gene structure annotation are made available, alongside the domain information. Kinases may be searched by domain combinations and the relative genes may be viewed in a graphic browser at various level of magnification up to gene organization on the full chromosome set

DG-CST (Disease Gene Conserved Sequence Tags), a database of human�mouse conserved elements associated to disease genes

The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better elucidate the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human–mouse conserved genomic sequences that are localized within or in the vicinity of human disease-related genes. CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp. The database contains CST data relative to over 1088 genes responsible for monogenetic human genetic diseases or involved in the susceptibility to multifactorial/polygenic diseases. DG-CST is accessible via the internet at http://dgcst.ceinge.unina.it/ and may be searched using both simple and complex queries. A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts

DG-CST (Disease Gene Conserved Sequence Tags), a database of human–mouse conserved elements associated to disease genes

The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better elucidate the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human–mouse conserved genomic sequences that are localized within or in the vicinity of human disease-related genes. CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp. The database contains CST data relative to over 1088 genes responsible for monogenetic human genetic diseases or involved in the susceptibility to multifactorial/polygenic diseases. DG-CST is accessible via the internet at http://dgcst.ceinge.unina.it/ and may be searched using both simple and complex queries. A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts

Microbiological quality of surface waters of Rome and it’s County from 1890 to 2010: a systematic review of Roman Hygiene School

Research on the quality of surface waters has been erformed in Italy during the development of large urban areas, and in Rome this has been the duty of the Istituto di Igiene of the Sapienza University since 1890. Using MedLine - along with traditional consultation of papers printed before 1968 - we identified 100 articles published in the period from 1890-2010. Thirty of them met the inclusion criteria (to have been written by researchers of Roman universities and to contain microbiological information about the surface waters of Rome). The majority of papers identified (46.6%) were published during the Sixties and Seventies, and 30% in the twenty years that followed (1980-1999). The most frequent microbiological descriptors were “Total coliforms” and “Streptococci”. The body of waters most frequently investigated were the river Tiber and the coastal waters around Fiumicino, where the Tiber flows into the Tyrrhenian sea. The quality of surface waters has always been of central interest to the researchers of the Roman School of Hygiene. The excellent quality of past research, and the renovated interest of International Organizations and of the European Union, should encourage public health researchers to persist in this strategic field of investigation which has strong interconnections with the protection of individual well-being and community health, as well as with environmental preservation

Glial cell line-derived neurotrophic factor induces proliferative inhibition of NT2/D1 cells through RET-mediated up-regulation of the cyclin-dependent kinase inhibitor p27kip 1

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Temporal pattern of microbial indicators of ready-to-eat rocket salads during shelf life

 Introduction. From 2001-2009 there have been numerous community alerts and notifications about the rocket salad produced in Italy and distributed in Europe. Our study describes the evolution of the microbial quality of ready to eat rocket salad during shelf life among three different Italian producers.Material and methods. Total Mesophilic Count (TMC) and Escherichia coli (EC) count were measured in 248 samples. We used Wilcoxon test to compare the median values of TMC and EC counts and Kruskal Wallis test to compare the producers. Results. The TMC and EC values differed among producers at the stages of raw material and in the finished product (Kruskall Wallis test, p < 0.05). The evolution of bacterial charges had significant differences among producers at expiration date (Wilcoxon test, p < 0.05). More than half of the samples (54.8%) exceed reference standard for TMC after 48 h from packaging.Conclusion. Differences among producers may linked to the different minimal processing technologies adopted after harvesting.