A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

We have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches

Hyperimmune anti-HBs plasma as alternative to commercial immunoglobulins for prevention of HBV recurrence after liver transplantation

BACKGROUND: Hepatitis B immune globulins (HBIG) in combination with nucleos(t)ide analogues (NA) are effectively used for the prevention of hepatitis B virus (HBV) recurrence after liver transplantation (LT). However, associated treatment costs for HBIG are exceedingly high. METHODS: Fresh frozen plasma obtained from blood donors with high anti-HBs levels (hyperimmune plasma, HIP) containing at least 4,500 IU anti-HBs was used as alternative treatment for HBV recurrence prophylaxis post-LT. RESULTS: Twenty-one HBV-related LT recipients received HIP starting at transplantation, followed by long-term combination treatment with NA. Mean follow-up time was 4.5 years (range 0.5-12.6) and each patient received on average 8.2 HIP per year (range 5.8-11.4). Anti-HBs terminal elimination kinetic after HIP administration was 20.6 days (range 13.8-30.9), which is comparable to values reported for commercial HBIG products. All 21 patients remained free of HBV recurrence during follow-up and no transfusion-transmitted infection or other serious complication was observed. Seven patients developed reversible mild transfusion reactions. The cost for one HIP unit was USD 140; average yearly HBIG treatment cost was USD 1,148 per patient, as compared to USD 25,000-100,000 for treatment with commercial HBIG. CONCLUSION: The results of this study suggest that the use of HIP may be a useful and economical approach for the prevention of HBV recurrence post-LT if used in combination with NA. Additional prospective controlled studies in larger populations are needed to confirm these results

La radiación sale a la comunidad : Prevención de los efectos sobre los seres humanos de la radiación

En gran cantidad de centros de Atención Primaria, consultorios de atención médica y Odontológica y salas sanitarias, se trabaja con equipos radiográficos, que utilizan radiaciones ionizantes. La radioprotección es un tema poco abordado en proyectos de extensión universitaria y salud pública, todos los pacientes conocen lo que es una radiografía pero la mayoría desconoce que se utilizan radiaciones ionizantes las cuales son acumulativas durante toda la vida del ser humano y que las cuales pueden causar posibles efectos perjudiciales sino se utilizan las medidas de radioprotección. La radiación ionizante es un tipo de energía liberada por los átomos en forma de ondas electromagnéticas (rayos X) o partículas. Debido a la desinformación y por demanda de un sector de la comunidad, vimos la importancia de ejecutar desde la FOLP (Facultad de Odontología de La Plata) este proyecto en dos lugares puntuales de Lisandro Olmos y Berisso. Allí se llevarán a cabo actividades de difusión y concientización sobre esta problemática para lo cual se crearán grupos de trabajo multi e interdisciplinarios. Para esto se realizarán charlas informativas, talleres y proyección de material didáctico con la finalidad de generar interés respecto a radioprotección. Por tal motivo, en contexto de pandemia, revisamos nuestro rol de agentes promotores de salud, viendo necesario además de tratar la problemática de radioprotección, se abordarán todas las acciones y medidas preventivas sobre Covid 19. De esta manera, reformulamos, redirigimos y ajustamos nuestro proyecto original a fin de contribuir a las necesidades actuales en relación a la salud integral de la sociedad y la relevancia que conlleva la prevención. Esta temática es de suma importancia en la actualidad, pero no siendo ajenos a la situación sanitaria que atravesamos, traspasamos la barrera de la radioprotección para involucrarnos en lo que nos ocurre como sociedad. Se llevarán a cabo actividades de concientización y difusión sobre radioprotección y Covid 19 para lo cual se crearán grupos de trabajo multi e interdisciplinarios. Y se realizarán reuniones informativas, talleres y proyección de material didáctico por vía virtual.Facultad de Odontologí

La radiación sale a la comunidad : Parte 2

Todos los pacientes conocen lo que es una radiografía pero la mayoría desconoce que se utilizan radiaciones ionizantes las cuales son acumulativas durante toda la vida del ser humano y que las cuales pueden causar posibles efectos perjudiciales sino se utilizan las medidas de radioprotección. La radiación ionizante es un tipo de energía liberada por los átomos en forma de ondas electromagnéticas (rayos X) o partículas. El fenómeno de la radiación es la propagación de energía en forma de ondas electromagnéticas o partículas subatómicas a través del vacío o de un medio material. Existen las ionizantes y no ionizantes. Siendo las ionizantes las que producen los efectos biológicos de los que se debe proteger a cada uno de los integrantes de la comunidad. La radiación puede afectar el funcionamiento de células, tejidos, órganos y producir efectos como dermatitis, alteraciones de la formula sanguínea, caída del cabello, quemaduras, carcinomas, mutaciones y hasta la muerte del individuo. Creemos necesaria la difusión y conc ientización en la comunidad para que se conozcan los posibles riesgos de las radiaciones y poder prevenirlas. Se debe tener en cuenta que las dosis recibidas con los estudios radiográficos si se cumplen las normas de radioprotección no implican la absorción de dosis altas de radiación. La comunidad está expuesta además a estudios radiográficos médicos. Teniendo en cuenta que en la actualidad ya se está estudiando la probabilidad de aparición de alteraciones con dosis bajas de radiación y como consecuencia a través de su participación exija el cumplimiento de las normas de radioprotección y actúen como multiplicadores de salud. Los límites de dosis actualmente en vigor, están referidos a un periodo de tiempo de un año oficial y diferencian entre trabajadores expuestos, personas en formación o estudiantes y miembros del público. También están establecidos límites y medidas de protección especial para determinados casos, como mujeres embarazadas y en período de lactancia y exposiciones especialmente autorizadas. Es de suma importancia que los integrantes de la comunidad y los operadores conozcan la existencia de principios básicos de radioprotección, que actúan como barreras reduciendo la exposición a la radiación para evitar la aparición de alteraciones. En este trabajo de investigación se vincula con la docencia y la extensión, ya que en la carrera de grado de Odontología los alumnos realizan sus prácticas en los centros operativos de Atención Primaria pertenecientes a la Facultad de Odontología de la UNLP, prestando atención en salud bucal y brindando de esta manera un servicio a la Sociedad. Al desarrollar una actividad clínica (ya que en los centros se brinda atención odontológica), tanto los alumnos como los pacientes están en contacto con radiaciones por lo que se hace esencial trabajar sobre los cuidados en radioprotección.Facultad de Odontologí

ASEtrap: A biological method for speeding up the exploration of spliceomes

Alternative splicing (AS) of pre-messenger RNA is a major mechanism for generating protein diversity from a limited number of genes in higher eukaryotes, and it constitutes a central mode of genetic regulation. Thus, efficient methods are needed to systematically identify new AS events at a genomic scale across different tissues, stages of development, and physiological or pathological conditions in order to better understand gene expression. To fulfill this goal, we have designed the ASEtrap, which is a cloning procedure for producing AS libraries that is based on a single-stranded trap consisting of an ssDNA-binding protein. In this paper, we have applied our approach to the construction of an AS library and a Control library from human placenta. By analyzing 9226 and 9999 sequences of the AS and Control libraries, respectively, we show that internal AS events (events that can be identified by the sole resources provided by either the AS or the Control library) and the discovery rate of new AS events measured at early stages of sequencing were nine to 10 times higher in the former than in the latter. Moreover, by performing a search for new AS events within a group of 162 known drug target genes, we identified six new events in six genes, and we observed that they all were discovered exclusively through the AS library. Thus, it appears that ASEtrap has the potential to greatly facilitate the determination of the total complement of splice variants expressed in human, as well as other organisms

Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach

Expansive knowledge of bacterial metabolism has been gained from genome sequencing output, but the high proportion of genes lacking a proper functional annotation in a given genome still impedes the accurate prediction of the metabolism of a cell. To access to a more global view of the functioning of the soil bacterium Acinetobacter baylyi ADP1, we adopted a multi ‘omics’ approach. Application of RNA-seq transcriptomics and LC/MS-based metabolomics, along with the systematic phenotyping of the complete collection of single-gene deletion mutants of A. baylyi ADP1 made possible to interrogate on the metabolic perturbations encountered by the bacterium upon a biotic change. Shifting the sole carbon source from succinate to quinate elicited in the cell not only a specific transcriptional response, necessary to catabolize the new carbon source, but also a major reorganization of the transcription pattern. Here, the expression of more than 12 % of the total number of genes was affected, most of them being of unknown function. These perturbations were ultimately reflected in the metabolome, in which the concentration of about 50 % of the LC/MS-detected metabolites was impacted. And the differential regulation of many genes of unknown function is probably related to the synthesis of the numerous unidentified compounds that were present exclusively in quinate-grown cells. Together, these data suggest that A. baylyi ADP1 metabolism involves unsuspected enzymatic reactions that await discovery. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-014-0662-x) contains supplementary material, which is available to authorized users

Whole Genome Sequence Comparisons and “Full-Length” cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation

To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides evidence that the gene catalog of Arabidopsis is not yet complete, and that a number of these annotations require re-examination. To improve the Arabidopsis genome annotation further, we used a novel “full-length” enriched cDNA collection prepared from several tissues. An additional 1931 genes were covered by new “full-length” cDNA sequences, raising the number of annotated genes with a corresponding “full-length” cDNA sequence to about 14,000. Detailed comparisons between these “full-length” cDNA sequences and annotated genes show that this resource is very helpful in determining the correct structure of genes, in particular, those not yet supported by “full-length” cDNAs. In addition, a total of 326 genomic regions not included previously in the Arabidopsis genome annotation were detected by this cDNA resource, providing clues for new gene discovery. Because, as expected, the two data sets only partially overlap, their combination produces very useful information for improving the Arabidopsis genome annotation

A Tribute to Disorder in the Genome of the Bloom- Forming Freshwater Cyanobacterium Microcystis aeruginosa

International audienceMicrocystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including threenew putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments