Transcriptional analysis of the recA gene of Streptococcus thermophilus

BACKGROUND: RecA is a highly conserved prokaryotic protein that not only plays several important roles connected to DNA metabolism but also affects the cell response to various stress conditions. While RecA is highly conserved, the mechanism of transcriptional regulation of its structural gene is less conserved. In Escherichia coli the LexA protein acts as a recA repressor and is able, in response to DNA damage, of RecA-promoted self-cleavage, thus allowing recA transcription. The LexA paradigm, although confirmed in a wide number of cases, is not universally valid. In some cases LexA does not control recA transcription while in other RecA-containing bacteria a LexA homologue is not present. RESULTS: We have studied the recA transcriptional regulation in S. thermophilus, a bacterium that does not contain a LexA homologue. We have characterized the promoter region of the gene and observed that its expression is strongly induced by DNA damage. The analysis of deletion mutants and of translational gene fusions showed that a DNA region of 83 base pairs, containg the recA promoter and the transcriptional start site, is sufficient to ensure normal expression of the gene. Unlike LexA of E. coli, the factor controlling recA expression in S. thermophilus acts in a RecA-independent way since recA induction was observed in a strain carrying a recA null mutation. CONCLUSION: In S. thermophilus, as in many other bacteria,recA expression is strongly induced by DNA damage, however, in this organism expression of the gene is controlled by a factor different from those well characterized in other bacteria. A small DNA region extending from 62 base pairs upstream of the recA transcriptional start site to 21 base pairs downstream of it carries all the information needed for normal regulation of the S. thermophilus recA gene

Global transcriptome analysis of the heat shock response of Bifidobacterium longum

Bifidobacteria are natural inhabitants of the human gastrointestinal tract and have been widely used as functional foods in different products. During industrial processing, bacterial cells undergo several stresses that can limit large-scale production and stability of the final product. To better understand the stress-response mechanisms of bifidobacteria, microarrays were used to obtain a global transcriptome profile of Bifidobacterium longum NCC2705 exposed to a heat shock treatment at 50°C for 3, 7 and 12 min. Gene expression data highlighted a profound modification of gene expression, with 46% of the genes being altered. This analysis revealed a slow-down of Bi. longum general metabolic activity during stress with a simultaneous activation of the classical heat shock stimulon. Moreover, the expression of several genes with unknown function was highly induced under stress conditions. Three of these were conserved in other bacteria species where they were also previously shown to be induced by high temperature, suggesting their widespread role in the heat stress response. Finally, the implication of the trans-translation machinery in the response of Bi. longum cells to heat shock was suggested by the induction of the gene encoding the tmRNA-associated small protein B (SmpB) with concomitant high constitutive expression of the tmRNA gen

Point Mutation I261M Affects the Dynamics of BVDV and its Interaction with Benzimidazole Antiviral 227G

Bovine viral diarrhea virus (BVDV) is a Pestivirus of the Flaviviridae family and represents a major viral pathogen in cattle and other ruminants. Infection with BVDV can result in a wide assortment of disease manifestations including resorption, mummification, or abortion of the dead fetus. Recently the point mutation I261M on the thumb domain was shown to confer resistance to BDVD against 227G and other benzimidazole compounds. Here we investigated the role of this mutation by using a multidisciplinary protocol, not involving free energy calculations on structures of the mutated complex which are taken a priori similar to those of the wild one. Namely, we firstly performed MD simulations on the wild and mutated BVDV RdRp proteins in aqueous solution. Then, we selected representative equilibrium conformations by performing a cluster analysis, and ran docking calculations of 277G on representative of the 5 most populated clusters of each protein. Finally, we performed MD simulation on selected complexes as to assess structural and dynamical differences between wild and mutated 227G-protein adducts. Interestingly, the mutation affects the structure and the dynamics of the protein, particularly in the region of binding of the ligand, and this results in a different binding site of 227G with respect to the wild protein. Moreover, while 227G closes the entrance to the RNA strand in the case of the wild protein, a gate and a channel leading to the catalytic site are still present in the mutated complex. These results could offer a possible molecular explanation of the resistance mechanism by mutation I261M

Synthesis, cytotoxicity and antiviral evaluation of new series of imidazo[4,5-g]quinoline and pyrido[2,3-g]quinoxalinone derivatives

Linear aromatic N-tricyclic compounds with promising antiviral activity and minimal cytotoxicity were prepared and analyzed in the last years. Specifically, the pyrido[2,3-g]quinoxalinone nucleus was found endowed with high potency against several pathogenic RNA viruses as etiological agents of important veterinary and human pathologies. Following our research program on new antiviral agents we have designed, synthesized and assayed new series of imidazo[4,5-g]quinoline and pyrido[2,3-g]quinoxalinone derivatives. Lead compounds 1-4 were further modified to enhance their antiviral activity and reduce their cytotoxicity. Thus, different substituents were introduced on N atom at position 1 or the O atom at position 2 of the leads; contextually, several groups were inserted on the nitrogen atom at position 7 of diaminoquinoline intermediates. Title compounds were tested in cell-based assays for cytotoxicity and antiviral activity against RNA virus families containing single-stranded (either positive-sense (ssRNA+) or negative-sense (ssRNA-)), and double-stranded genomes (dsRNA), and against two representatives of DNA virus families. Some derivatives emerged as potential leads for further development as antiviral agents against some viruses of public health significance, such as RSV, Reo, BVDV and HCV. Particularly, compounds 4, 11b, 11c, 13c, 15a, 18 and 21 resulted active against BVDV at concentrations ranging from 1.3 to 5\ua0\u3bcM. Compound 21 was also evaluated for its activity on the BVDV RdRp. Compound 4 was also tested as potential anti-HCV compound in a subgenomic replication assay. Molecular simulation results provided a molecular rationale for the anti-BVDV activity of these compounds

Starquakes in millisecond pulsars and gravitational waves emission

So far, only transient Gravitational waves (GWs) produced by catastrophic events of extra-galactic origin have been detected. However, it is generally believed that there should be also continuous sources of GWs within our galaxy, such as accreting neutron stars (NSs). In fact, in accreting NSs, centrifugal forces can be so strong to break the neutron star crust (causing a starquake), thus producing a quadrupole moment responsible for the continuous emission of GWs. At equilibrium, the angular momentum gained by accretion and lost via GWs emission should balance each other, stopping the stellar spin-up. We hereinafter investigate the above physical picture within the framework of a Newtonian model describing compressible, non-magnetized, and self-gravitating NSs. In particular, we calculate the rotational frequency need to break the stellar crust of an accreting pulsar and we estimate the upper limit for the ellipticity due to this event. Depending on the equation of state (EoS) and on the mass of the star, we calculated that the starquake-induced ellipticity ranges from $10^{-9}$ to $10^{-5}$. The corresponding equilibrium frequency that we find is in good agreement with observations and, for all the scenarios, it is below the observational limit frequency of $716.36$ Hz. Finally, we also discuss possible observational constraints on the ellipticity upper limit of accreting pulsars.Comment: 12 pages, 9 figure

A Comparison of Different Topic Modeling Methods through a Real Case Study of Italian Customer Care

The paper deals with the analysis of conversation transcriptions between customers and agents in a call center of a customer care service. The objective is to support the analysis of text transcription of human-to-human conversations, to obtain reports on customer problems and complaints, and on the way an agent has solved them. The aim is to provide customer care service with a high level of efficiency and user satisfaction. To this aim, topic modeling is considered since it facilitates insightful analysis from large documents and datasets, such as a summarization of the main topics and topic characteristics. This paper presents a performance comparison of four topic modeling algorithms: (i) Latent Dirichlet Allocation (LDA); (ii) Non-negative Matrix Factorization (NMF); (iii) Neural-ProdLDA (Neural LDA) and Contextualized Topic Models (CTM). The comparison study is based on a database containing real conversation transcriptions in Italian Natural Language. Experimental results and different topic evaluation metrics are analyzed in this paper to determine the most suitable model for the case study. The gained knowledge can be exploited by practitioners to identify the optimal strategy and to perform and evaluate topic modeling on Italian natural language transcriptions of human-to-human conversations. This work can be an asset for grounding applications of topic modeling and can be inspiring for similar case studies in the domain of customer care quality