Degradation activity of fungal communities on avocado peel (Persea americana Mill.) in a solid-state process: mycobiota successions and trophic guild shifts.

To explore the capability of soil mycobiota to degrade avocado peel waste and identify relevant successions and trophic guild shifts, fungal communities from three environments with different land uses were evaluated in a solid-state process. Soil samples used as inoculum were collected from a pristine mature tropical forest, a traditionally managed Mayan land, and an intensively managed monospecific avocado plantation. Soil-substrate mixes were evaluated for 52 weeks to evaluate organic matter decay and the carbon-to-nitrogen ratio. Amplicon-based high-throughput sequencing from internally transcribed spacer (ITS) analysis revealed significant differences in fungal communities widely dominated by Fusarium sp. and Clonostachys sp.; however, less represented taxa showed relevant shifts concomitantly with organic matter content drops. Trophic guild assignment revealed different behaviors in fungal communities between treatments over the 52 weeks, suggesting distinct preconditioning of fungal communities in these environments. Overall, the results lead to the identification of promising degradation moments and inoculum sources for further consortia enrichment or bioprospecting efforts.

Data mining of metagenomes to find novel enzymes: a non-computationally intensive method.

Currently, there is a need of non-computationally-intensive bioinformatics tools to cope with the increase of large datasets produced by Next Generation Sequencing technologies. We present a simple and robust bioinformatics pipeline to search for novel enzymes in metagenomic sequences. The strategy is based on pattern searching using as reference conserved motifs coded as regular expressions. As a case study, we applied this scheme to search for novel proteases S8A in a publicly available metagenome. Briefly, (1) the metagenome was assembled and translated into amino acids; (2) patterns were matched using regular expressions; (3) retrieved sequences were annotated; and (4) diversity analyses were conducted. Following this pipeline, we were able to identify nine sequences containing an S8 catalytic triad, starting from a metagenome containing 9,921,136 Illumina reads. Identity of these nine sequences was confirmed by BLASTp against databases at NCBI and MEROPS. Identities ranged from 62 to 89% to their respective nearest ortholog, which belonged to phyla Proteobacteria, Actinobacteria, Planctomycetes, Bacterioidetes, and Cyanobacteria, consistent with the most abundant phyla reported for this metagenome. All these results support the idea that they all are novel S8 sequences and strongly suggest that our methodology is robust and suitable to detect novel enzymes.

Fungal Screening on Olive Oil for Extracellular Triacylglycerol Lipases: Selection of a Trichoderma harzianum Strain and Genome Wide Search for the Genes.

A lipolytic screening with fungal strains isolated from lignocellulosic waste collected in banana plantation dumps was carried out. A Trichoderma harzianum strain (B13-1) showed good extracellular lipolytic activity (205 UmL-1). Subsequently, functional screening of the lipolytic activity on Rhodamine B enriched with olive oil as the only carbon source was performed. The successful growth of the strain allows us to suggest that a true lipase is responsible for the lipolytic activity in the B13-1 strain. In order to identify the gene(s) encoding the protein responsible for the lipolytic activity, in silico identification and characterization of triacylglycerol lipases from T. harzianum is reported for the first time. A survey in the genome of this fungus retrieved 50 lipases; however, bioinformatic analyses and putative functional descriptions in different databases allowed us to choose seven lipases as candidates. Suitability of the bioinformatic screening to select the candidates was confirmed by reverse transcription polymerase chain reaction (RT-PCR). The gene codifying 526309 was expressed when the fungus grew in a medium with olive oil as carbon source. This protein shares homology with commercial lipases, making it a candidate for further applications. The success in identifying a lipase gene inducible with olive oil and the suitability of the functional screening and bioinformatic survey carried out herein, support the premise that the strategy can be used in other microorganisms with sequenced genomes to search for true lipases, or other enzymes belonging to large protein families.

A randomized placebo-controlled phase II study of a Pseudomonas vaccine in ventilated ICU patients.

BACKGROUND: Currently, no vaccine against Pseudomonas is available. IC43 is a new, recombinant, protein (OprF/I)-based vaccine against the opportunistic pathogen, Pseudomonas aeruginosa, a major cause of serious hospital-acquired infections. IC43 has proven immunogenicity and tolerability in healthy volunteers, patients with burns, and patients with chronic lung diseases. In order to assess the immunogenicity and safety of IC43 in patients who are most at risk of acquiring Pseudomonas infections, it was evaluated in mechanically ventilated ICU patients. METHODS: We conducted a randomized, placebo-controlled, partially blinded study in mechanically ventilated ICU patients. The immunogenicity of IC43 at day 14 was determined as the primary endpoint, and safety, efficacy against P. aeruginosa infections, and all-cause mortality were evaluated as secondary endpoints. Vaccinations (100 µg or 200 µg IC43 with adjuvant, or 100 µg IC43 without adjuvant, or placebo) were given twice in a 7-day interval and patients were followed up for 90 days. RESULTS: Higher OprF/I IgG antibody titers were seen at day 14 for all IC43 groups versus placebo (P < 0.0001). Seroconversion (≥4-fold increase in OprF/I IgG titer from days 0 to 14) was highest with 100 µg IC43 without adjuvant (80.6%). There were no significant differences in P. aeruginosa infection rates, with a low rate of invasive infections (pneumonia or bacteremia) in the IC43 groups (11.2-14.0%). Serious adverse events (SAEs) considered possibly related to therapy were reported by 2 patients (1.9%) in the group of 100 µg IC43 with adjuvant. Both SAEs resolved and no deaths were related to study treatment. Local tolerability symptoms were mild and rare (<5% of patients), a low rate of treatment-related treatment-emergent adverse events (3.1-10.6%) was observed in the IC43 groups. CONCLUSION: This phase II study has shown that IC43 vaccination of ventilated ICU patients produced a significant immunogenic effect. P. aeruginosa infection rates did not differ significantly between groups. In the absence of any difference in immune response following administration of 100 µg IC43 without adjuvant compared with 200 µg IC43 with adjuvant, the 100 µg dose without adjuvant was considered for further testing of its possible benefit of improved outcomes. There were no safety or mortality concerns. TRIAL REGISTRATION: ClinicalTrials.gov, NCT00876252 . Registered on 3 April 2009.

Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water.

Metagenomics is a culture-independent technology that allows access to novel and potentially useful genetic resources from a wide range of unknown microorganisms. In this study, a fosmid metagenomic library of tropical underground water was constructed, and clones were functionally screened for extracellular proteolytic activity. One of the positive clones, containing a 41,614-bp insert, had two genes with 60% and 68% identity respectively with a peptidase S8 of Chitinimonas koreensis. When these genes were individually sub-cloned, in both cases their sub-clones showed proteolytic phenotype, confirming that they both encode functional proteases. These genes -named PrAY5 and PrAY6- are next to each other. They are similar in size (1845bp and 1824bp respectively) and share 66.5% identity. An extensive in silico characterization showed that their ORFs encode complex zymogens having a signal peptide at their 5' end, followed by a pro-peptide, a catalytic region, and a PPC domain at their 3' end. Their translated sequences were classified as peptidases S8A by sequence comparisons against the non-redundant database and corroborated by Pfam and MEROPS. Phylogenetic analysis of the catalytic region showed that they encode novel proteases that clustered with the sub-family S8_13, which according to the CDD database at NCBI, is an uncharacterized subfamily. They clustered in a clade different from the other three proteases S8 found so far by functional metagenomics, and also different from proteases S8 found in sequenced environmental samples, thereby expanding the range of potentially useful proteases that have been identified by metagenomics. I-TASSER modeling corroborated that they may be subtilases, thus possibly they participate in the hydrolysis of proteins with broad specificity for peptide bonds, and have a preference for a large uncharged residue in P1.

Evolución histórica y logros de la gerencia sectorial de producción del Instituto Nacional de Higiene Rafael Rangel / Historical evolution and achievements of the sector's production management of the Instituto Nacional de Higiene Rafael Rangel

La Gerencia Sectorial de Producción elabora vacunas bacterianas y virales de uso humano y veterinario, para satisfacer necesidades específicas de nuestra población. Igualmente responde a los requerimientos del resto de las áreas técnicas de la institución, a las que provee de insumos, reactivos químicos y biológicos como cultivos celulares y animales de experimentación, entre otros. También presta servicios con fines diagnósticos, productivos, de control e investigación. Un ejemplo relevante de proyección de la Gerencia Sectorial de Producción, y del Instituto, lo constituye la nueva Planta de Vacunas, instalación de alta tecnología que representa un contundente aporte para consolidar la autosuficiencia nacional en la producción de tan importantes rubros para la salud.

The Sectorial Productión Management produces bacterial and viral vaccines for human and veterinary use to satisfy specific needs of our population. It also responds, to the requirements of the rest of the technical units of the Institute, to whom it provides with chemical and biological reagents like cellular cultures and laboratory animals, among others. It also carry out activities for diag nostic purposes, production, control and research. An excellent example of projection of The Sectorial Productión Management and the Institute constitutes the new Vaccine Plant, installation of high technology that will allow to consolidate the national self-sufficiency in the production of such important headings for the health.

La importancia de declarar un conflicto de intereses en las revistas médicas / The relevance of declaring an interest conflict in medical journals

Medical journals are often at risk of difussinng research articles, reviews, position articles, editorials or letters ubose message has been influenced by a conflict of interest. The readers may then be induced to accept conclusions and recommendations based on bisaaed protocols or an unwarranted interpretation of the results. Financial support or professional links witb pharmaceutical companies or other supporting agencies are the most common sources of conflict of interests, often difficult to detect. Similarly, reviews of manuscripts can be biassed by personal relationsbips (good or bad) between reviewers and autbors, by academic competition or intellectual passion, becoming otber sources of conflict of interest. Even uben a potential conflict of interest exists, it may not necessarily bave influenced the manuscript or its review but in order to defend the transparency of the editorial process, from submission to publication, authors, reviewers and editors sbould declare any conflict of interest they may have and allou others to decide whether the action has been biassed or not. In the present issue of Revista Médica de Chile, and updated text of the Instructions to Authors establishes that all autbors should sign a statement of habing or not a conflict of interest, clarifying which aspects of the work might have been affected by it

Actualización de los criterios de autoría en las publicaciones biomédicas / Update in authorship criteria in biomedical articles

In the year 2000, a previous Editorial in this journal reviewed the criteria for authorship as defined by experienced authors and editors, discussed in selected references from the biomedical literature. An emphasis was given to the definition of authorship stated in the available 1997 version of the "Uniform Requirements for Manuscripts Submitted to Biomedical Journals". After that Editorial was published, an updated version of the "Uniform Requirements" established important changes in their criteria; eg. Participation of each author in the work should permit them to take public responsibility for "appropiate portions of the content"; and acquisition of data was added as an acceptable alternative in the first requisite for authorship. These and other changes should be difussed to prospective authors, particularly in multicentric studies usually leading to multiauthorship. This new Editorial and a translation into Spanish of the authorship criteria contained in an updated (2001) version of the "Uniform Requirements" are included in this issue of Revista Médica de Chile with the purpose of stimulating authors and readers to think in their implications

Vibrio vulnificus: una causa infrecuente de shock séptico / Septic shock caused by vibrio vulnificus: report of 1 case

Vibrio vulnificus is a lactose positive Gram negative rod that lives in warm seas and can infect wounds and produce sepsis. Its infection is acquired after eating oysters or other filtering marine organisms. We report a 53 years old diabetic male who started with fever after a voyage to Central America. He was admitted febrile, hipotense, dehydrated and polypneic. Painful erythematous lesions and lumps were observed in his upper and lower limbs. After 72 hours of evolution, the lesions became violaceous, with crepitating vesicles full of hemorrhagic exudate. He developed a renal failure and a disseminated intravascular coagulation. Blood cultures demonstrated the presence of Vibrio vulnificus and the patient died 68 hours after admission

Estudio de la cinética de citoquinas en sepsis grave y su relación con mortalidad y score de disfunción orgánica / Cytokine kinetics in severe sepsis: its relationship with mortality and organic dysfunction

Background: The Infectious Systemic Inflammatory Response syndrome and multiple organic dysfunction have common physiopathological mechanisms. Multiple organic dysfunction can be assessed using severity scores. Aim: To relate cytokine kinetics with a multiple organic dysfunction score during sepsis. Material and methods : Tumor necrosis factor a (TNFa) and interleukin 6 (IL6) kinetics were studied in 25 patients with severe sepsis with less than 48 h of evolution and interleukin 1ß (ILß) kinetics was studied in 13 patients. Measurements were made at 0, 12, 24 and 48 hours after admission to the study, using an ELISA technique. These parameters were correlated with the Marshall multiple organic dysfunction score and survival. Results: Mean age of study subjects was 70 years, the APACHE II score was 16.9ñ6 and the Marshall score was 6.8ñ3.6. Sepsis was of pulmonary origin in 56 percent of patients and intra abdominal in 32 percent. Mortality was 36 percent. TNFa increased during the study period (24.1 pg/ml initially and 37.8 pg/ml at 24 hours, with a slight posterior reduction, p<0.02). These levels had no association with mortality or organic dysfunction. IL6 remained elevated during the first hours and had a tendency to decrease thereafter. Deceased patients had higher values than survivors (306 pg/ml and 55.4 pg/ml respectively, p=0.011). Its values were tightly correlated with Marshall score, with the number of failing organs, with the presence of shock and with probability of dying during hospitalization. IL1ß remained low and was not associated with clinical parameters. Conclusions: There is a tight correlation between the elevation of IL6 and the severity of the Systemic Inflammatory Response and mortality in these patients with sepsis

El Comité Asesor Internacional / The International Advisory Committee

The Editors of Revista Médica de Chile are taking steps aimed to improve the "visibility" of this journal and to stimulate local and foreign authors to submit better original articles, appealing to a broader and international readership. Until now, the journal's editorial policy has been to stress its educational role, focused in Chilean readers and authors. In the recent years, an increasing number of research articles is being received, including manuscripts from North America, Europe and other Latinamerican countries. This is explainable, in part, by the fact that this journal is indexed in MEDLINE, ISI (Current Contents/Clinical Medicine) and several other major databases. The Revista is also one of the oldest medical journals in the world, published since 1872. In this issue of the Revista we welcome the new members of an "International Advisory Committee", with prominent physicians, scientists and teachers from the U.S.A. and Europe. They accepted to advise the Editors in their task, to submit review articles, state-of-the-art or position papers on topics of their own interest, and to help in the assessment of some manuscripts. We thank them warmly for their enthusiastic response to our invitation

Necrólisis epidérmica tóxica: terapia en UCI con inmunoglobulinas intravenosas en un caso / Toxic epidermal necrolysis: report of 1 case treated with intravenous immunoglobulins

We report a 27 years old homosexual male with AIDS that was admitted to the ICU dehydrated, with fever and severe malaise. He had irregular bullae, an extensive purpuric exanthema and a zone of epidermic detachment in the right arm. A toxic epidermal necrolysis was diagnosed and therapy with i.v. immunoglobulins was started. After four days of treatment, bullous lesions disappeared and the extension of exanthema decreased. Toxic epidermal necrolysis is a potentially fatal disease and the use of intravenous immunoglobulins for this condition has been reported as successful

La autoría en los manuscritos publicados en revistas biomédicas / Authorship in manuscripts published in biomedical journals

Multiauthorship shows an increasing trend in biomedical and other scientific journals. A main concern for editors, reviewers and readers is to find out whether all individuals enlisted as authors actually fulfill criteria for authorship as defined in the document "Uniform Requirements for Manuscripts Submitted to Biomedical Journals". Revista MÄdica de Chile is addressing this relevant topic with a combined strategy: (1) A retrospective analysis of the manuscripts published in the recent decades in the Revista will quantify and illustrate the local trend in multiauthorship; (2) A "Statement of accountability": signed by all authors in manuscripts submitted to the Revista, is in use since 1997; and (3) A new form of this "Statement of accountability" requests all authors to identify their personal involvement in the work represented by the manuscript. This information will be available to every person participating in the editorial assessment of the manuscript (editors and external reviewers) but during a trial period of six months authors will be allowed to object the publication of this data, stating the reasons for this objection. After six months the editors will evaluate the information collected and the self-declared role of every author enlisted. The terms "Authors" and "Main author" will continue being used to designate participants because "contributor" (replacement alternative proposed by Rennie et al., currently in use by several leading general medical journals) has a different main meaning in Spanish than in English and it might have a negative effect

Artículos de investigación / Research articles

Since 1973, Revista Médica de Chile has classified biomedical and clinical prospective research papers in a Section named Research Articles, while purely clinical and retrospective studies were classified into another Section, named Clinical Experiences. This distinction seems no longer necessary, because both types of manuscripts are subjected to a uniform external peer-review system and their intrinsic quality is not a distinctive feature. Furthermore, the name of Sections where similar papers are classified by the major general clinical medicine journals is clearly non-uniform. Therefore, Research Articles and Clinical Experiences will from now on be included into a single Section: Research Articles