The assessment of leading traits in the taxonomy of the Bacillus cereus group

Bacillus cereus sensu lato strains (B. cereus group) are widely distributed in nature and have received interest for decades due to their importance in insect pest management, food production and their positive and negative repercussions in human health. Consideration of practical uses such as virulence, physiology, morphology, or ill-defined features have been applied to describe and classify species of the group. However, current comparative studies have exposed inconsistencies between evolutionary relatedness and biological significance among genomospecies of the B. cereus group. Here, the combined analyses of core-based phylogeny and all versus all Average Nucleotide Identity values based on 2116 strains were conducted to update the genomospecies circumscriptions within B. cereus group. These analyses suggested the existence of 57 genomospecies, 37 of which are novel, thus indicating that the taxonomic identities of more than 39% of the analyzed strains should be revised or updated. In addition, we found that whole-genome in silico analyses were suitable to differentiate genomospecies such as B. anthracis, B. cereus and B. thuringiensis. The prevalence of toxin and virulence factors coding genes in each of the genomospecies of the B. cereus group was also examined, using phylogeny-aware methods at wide-genome scale. Remarkably, Cry and emetic toxins, commonly assumed to be associated with B. thuringiensis and emetic B. paranthracis, respectively, did not show a positive correlation with those genomospecies. On the other hand, anthrax-like toxin and capsule-biosynthesis coding genes were positively correlated with B. anthracis genomospecies, despite not being present in all strains, and with presumably non-pathogenic genomospecies. Hence, despite these features have been so far considered relevant for industrial or medical classification of related species of the B. cereus group, they were inappropriate for their circumscription. In this study, genomospecies of the group were accurately affiliated and representative strains defined, generating a rational framework that will allow comparative analysis in epidemiological or ecological studies. Based on this classification the role of specific markers such as Type VII secretion system, cytolysin, bacillolysin, and siderophores such as petrobactin were pointed out for further analysis.Fil: Torres Manno, Mariano Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Repizo, Guillermo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Magni, Christian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Dunlap, Christopher A.. United States Department of Agriculture; Estados UnidosFil: Espariz, Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentin

Genetic and phenotypic features defining industrial relevant Lactococcus lactis, L. cremoris and L. lactis biovar. diacetylactis strains

Lactococcus lactis strains constitute one of the most important starter cultures for cheese production. In this study, a genome-wide analysis was performed including 68 available genomes of L. lactis group strains showing the existence of two species (L. lactis and L. cremoris) and two biovars (L. lactis biovar. diacetylactis and L. cremoris biovar. lactis). The proposed classification scheme revealed coherency among phenotypic (through in silico and in vivo bacterial function profiling), phylogenomic (through maximum likelihood trees) and genomic (using overall genome sequence-based parameters) approaches. Strain biodiversity for the industrial biovar. diacetylactis was also analyzed, finding they are formed by at least three variants with the CC1 clonal complex as the only one distributed worldwide. These findings and methodologies will help improve the selection of L. lactis group strains for industrial use as well as facilitate the interpretation of previous or future research studies on this diverse group of bacteria.Fil: Torres Manno, Mariano Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Zuljan, Federico Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Alarcon, Sergio Hugo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Química Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario; ArgentinaFil: Esteban, Luis. Universidad Nacional de Rosario; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Blancato, Victor Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Espariz, Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Magni, Christian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentin

Antagonism of Bacillus safensis strain against phytopathogenic bacteria

Citrus canker caused by Xanthomonas citri subsp. citri (Xcc), is a bacterial disease which affects all the citrics. One alternative to manage it is the use of antagonist bacteria. The aim of this work was to investigate the antagonist activity of Bacillus safensis (S9) against Xcc. The activity was tested by diffusion assays. Xcc and S9 were grown overnight in Luria Bertani (LB) and potato dextrose (PD) medium, respectively, with continuous agitation at 28°C and then, were diluted to a concentration of 108 CFU/mL. Petri dishes were covered with 15 mL of LB-agar containing 100 μL of the Xcc dilution. Once the medium was solidified, 4 μL drops of S9 were inoculated 3 times in each Petri dish, and the experiment was made by triplicate. After 48 hours of incubation at 28°C, the inhibition zone was measured, and the average inhibition area was calculated as IA = average area of the inhibition zone - average area of the colony. A significant inhibition area of 5.18 cm2 was obtained (one-sample t- test, p<0.05). At the same time, diffusion assays with the supernatant were made to prove its inhibitory ability. Petri dishes were prepared as described above. The supernatant was obtained by centrifugation of the S9 culture grown in PD medium, and then by bacteria filtration. Three filter paper discs embedded with the supernatant were placed per Petri dish, by triplicate. The inhibition zone was measured after 48 hours and calculated the IA. A significant inhibition area of 2.29 cm2 was obtained (one-sample t-test, p<0.05). Besides, a study at genomic level comparing S9 with ten Bacillus strains was made. Different clusters of secondary metabolite synthesis pathways were detected, three common with B. velezensis strains (surfactin, basilicin and bacilibactin). These strains were tested as inhibitors of Xcc and they did not show inhibition (Bacillus sp and B. megaterium) or showed less inhibition (B. velezensis). The difference might be on the expression level of the clusters. These results suggest the potential use of S9 as a canker control agent and further studies will be necessary to identify the Xcc- inhibitor metabolite.Fil: Olivella, Laura. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Ciencias Agropecuarias del Litoral. - Universidad Nacional del Litoral. Instituto de Ciencias Agropecuarias del Litoral.; ArgentinaFil: Gaido, Jimena Daiana. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Ciencias Agropecuarias del Litoral. - Universidad Nacional del Litoral. Instituto de Ciencias Agropecuarias del Litoral.; ArgentinaFil: Torres Manno, Mariano Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Química Orgánica; ArgentinaFil: Petitti, Tomás Denis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Espariz, Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Daurelio, Lucas Damian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaLVII Annual Meeting of the Argentine Society for Biochemistry and Molecular Biology Research; XVI Annual Meeting of the Argentinean Society for General MicrobiologyBuenos AiresArgentinaSociedad Argentina de Bioquímica y Biología MolecularSociedad Argentina de Microbiología Genera

A population-based cohort approach to assess excess mortality due to the spread of COVID-19 in Italy, January-May 2020

Aims: To assess the impact of the COVID-19 pandemic on all-cause mortality in Italy during the first wave of the epidemic, taking into consideration the geographical heterogeneity of the spread of COVID-19. Methods: This study is a retrospective, population-based cohort study using national statistics throughout Italy. Survival analysis was applied to data aggregated by day of death, age groups, sex, and Italian administrative units (107 provinces). We applied Cox models to estimate the relative hazards (RH) of excess mortality, comparing all-cause deaths in 2020 with the expected deaths from all causes in the same time period. The RH of excess deaths was estimated in areas with a high, moderate, and low spread of COVID-19. We reported the estimate also restricting the analysis to the period of March-April 2020 (first peak of the epidemic). Results: The study population consisted of 57,204,501 individuals living in Italy as of January 1, 2020. The number of excess deaths was 36,445, which accounts for 13.4% of excess mortalities from all causes during January-May 2020 (i.e., RH = 1.134; 95% confidence interval (CI): 1.129-1.140). In the macro-area with a relatively higher spread of COVID-19 (i.e., incidence rate, IR): 450-1,610 cases per 100,000 residents), the RH of excess deaths was 1.375 (95% CI: 1.364-1.386). In the area with a relatively moderate spread of COVID-19 (i.e., IR: 150-449 cases) it was 1.049 (95% CI: 1.038-1.060). In the area with a relatively lower spread of COVID-19 (i.e., IR: 30-149 cases), it was 0.967 (95% CI: 0.959-0.976). Between March and April (peak months of the first wave of the epidemic in Italy), we estimated an excess mortality from all causes of 43.5%. The RH of all-cause mortality for increments of 500 cases per 100,000 residents was 1.352 (95% CI: 1.346-1.359), corresponding to an increase of about 35%. Conclusions: Our analysis, making use of a population-based cohort model, estimated all-cause excess mortality in Italy taking account of both time period and of COVID-19 geographical spread. The study highlights the importance of a temporal/geographic framework in analyzing the risk of COVID-19-epidemy related mortality

A new clinical score for cranial CT in ED non-trauma patients: Definition and first validation.

Introduction:Well recognized guidelines are available for the use of cranial computed tomography (CCT) in traumatic patients,while no definitely accepted standards exists to for CCT in patientswithout history of head injury. The aimof this study is to propose an easy clinical score to stratify the need of CCT inemergency department (ED) patients with suspect non-traumatic intracranial pathology. Methods: We retrospectively evaluated patients presenting to the ED for neurological deficit, postural instability, acute headache, alteredmental status, seizures, confusion, dizziness, vertigo, syncope, and pre-syncope.Webuild a score for positive CCT prediction by using a logistic regression model on clinical factors significant at univariate analysis. The score was validated on a population of prospectively observed patients. Results: We reviewed clinical data of 1156 patients; positivity of CCT was 15.2%. Persistent neurological deficit, new onset acute headache, seizures and/or altered state of consciousness, and transient neurological disorders were independent predictors of positive CCT. We observed 508 patients in a validation prospective cohort; CCT was positive in 11.3%. Our score performed well in validation population with a ROC AUC of 0.787 (CI 95% 0.748\u20130.822). Avoiding CT in score 0 patients would have saved 82 (16.2%) exams. No patients with score 0 had a positive CCT findings; score sensitivity was 100.0 (CI 95% 93.7\u2013100.0). Conclusions: A score for risk stratification of patients with suspect of intra-cranial pathology could reduce CT request in ED, avoiding a significant number of CCT while minimizing the risk of missing positive results

Occupational Toluene Exposure Induces Cytochrome P450 2E1 mRNA Expression in Peripheral Lymphocytes

Print workers are exposed to organic solvents, of which the systemic toxicant toluene is a main component. Toluene induces expression of cytochrome P450 2E1 (CYP2E1), an enzyme involved in its own metabolism and that of other protoxicants, including some procarcinogens. Therefore, we investigated the association between toluene exposure and the CYP2E1 response, as assessed by mRNA content in peripheral lymphocytes or the 6-hydroxychlorzoxazone (6OH-CHZ)/chlorzoxazone (CHZ) quotient (known as CHZ metabolic ratio) in plasma, and the role of genotype (5′-flanking region RsaI/PstI polymorphic sites) in 97 male print workers. The geometric mean (GM) of toluene concentration in the air was 52.80 ppm (10–760 ppm); 54% of the study participants were exposed to toluene concentrations that exceeded the maximum permissible exposure level (MPEL). The GM of urinary hippuric acid at the end of a work shift (0.041 g/g creatinine) was elevated relative to that before the shift (0.027 g/g creatinine; p < 0.05). The GM of the CHZ metabolic ratio was 0.33 (0–9.3), with 40% of the subjects having ratios below the GM. However, the average CYP2E1 mRNA level in peripheral lymphocytes was 1.07 (0.30–3.08), and CYP2E1 mRNA levels within subjects correlated with the toluene exposure ratio (environmental toluene concentration:urinary hippuric acid concentration) (p = 0.014). Genotype did not alter the association between the toluene exposure ratio and mRNA content. In summary, with further validation, CYP2E1 mRNA content in peripheral lymphocytes could be a sensitive and noninvasive biomarker for the continuous monitoring of toluene effects in exposed persons

The Sicilian Grid Infrastructure for High Performance Computing

The conjugation of High Performance Computing (HPC) and Grid paradigm with applications based on commercial software is one among the major challenges of today e-Infrastructures. Several research communities from either industry or academia need to run high parallel applications based on licensed software over hundreds of CPU cores; a satisfactory fulfillment of such requests is one of the keys for the penetration of this computing paradigm into the industry world and sustainability of Grid infrastructures. This problem has been tackled in the context of the PI2S2 project that created a regional e-Infrastructure in Sicily, the first in Italy over a regional area. Present article will describe the features added in order to integrate an HPC facility into the PI2S2 Grid infrastructure, the adoption of the InifiniBand low-latency net connection, the gLite middleware extended to support MPI/MPI2 jobs, the newly developed license server and the specific scheduling policy adopted. Moreover, it will show the results of some relevant use cases belonging to Computer Fluid-Dynamics (Fluent, OpenFOAM), Chemistry (GAMESS), Astro-Physics (Flash) and Bio-Informatics (ClustalW))

The Sicilian Grid Infrastructure for High Performance Computing

The conjugation of High Performance Computing (HPC) and Grid paradigm with applications based on commercial software is one among the major challenges of today e-Infrastructures. Several research communities from either industry or academia need to run high parallel applications based on licensed software over hundreds of CPU cores; a satisfactory fulfillment of such requests is one of the keys for the penetration of this computing paradigm into the industry world and sustainability of Grid infrastructures. This problem has been tackled in the context of the PI2S2 project that created a regional e-Infrastructure in Sicily, the first in Italy over a regional area. Present paper will describe the features added in order to integrate an HPC facility into the PI2S2 Grid infrastructure, the adoption of the InifiniBand low-latency net connection, the gLite middleware extended to support MPI/MPI2 jobs, the newly developed license server and the specific scheduling policy adopted. Moreover, it will show the results of some relevant use cases belonging to Computer Fluid-Dynamics (Fluent, OpenFOAM), Chemistry (GAMESS), Astro-Physics (Flash) and Bio-Informatics (ClustalW))

Gene Therapy for Leber's Congenital Amaurosis is Safe and Effective Through 1.5 Years After Vector Administration

The safety and efficacy of gene therapy for inherited retinal diseases is being tested in humans affected with Leber's congenital amaurosis (LCA), an autosomal recessive blinding disease. Three independent studies have provided evidence that the subretinal administration of adeno-associated viral (AAV) vectors encoding RPE65 in patients affected with LCA2 due to mutations in the RPE65 gene, is safe and, in some cases, results in efficacy. We evaluated the long-term safety and efficacy (global effects on retinal/visual function) resulting from subretinal administration of AAV2-hRPE65v2. Both the safety and the efficacy noted at early timepoints persist through at least 1.5 years after injection in the three LCA2 patients enrolled in the low dose cohort of our trial. A transient rise in neutralizing antibodies to AAV capsid was observed but there was no humoral response to RPE65 protein. The persistence of functional amelioration suggests that AAV-mediated gene transfer to the human retina does not elicit immunological responses which cause significant loss of transduced cells. The persistence of physiologic effect supports the possibility that gene therapy may influence LCA2 disease progression. The safety of the intervention and the stability of the improvement in visual and retinal function in these subjects support the use of AAV-mediated gene augmentation therapy for treatment of inherited retinal diseases