Brazilian Microbiome Project: Revealing the Unexplored Microbial Diversity—Challenges and Prospects

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world’s macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world’s catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.     

Isolation of three new ent-labdane diterpenes from Dodonaea viscosa Jacquin (Sapindaceae): Preliminary evaluation of antiherpes activity

Investigation of the crude ethanolic extract obtained from the aerial parts of Dodonaea viscosa led to the isolation of three new ent-labdane diterpenes (1–3). The structures were established on the basis of their ESI–MS, UV, IR and NMR spectral data. The crude extract, fractions and compounds were evaluated for in vitro antiviral activity against Herpes Simplex Virus type 1 (HSV-1). The crude extract showed promising antiherpes activity expressed by a selectivity index of 6.2.     

Proteomic Identification of Differentially Altered Proteins During Regeneration from Nodular Cluster Cultures in Vriesea reitzii (Bromeliaceae)

Tissue culture techniques have been employed for bromeliad mass propagation by means of the morphogenetic route of nodular cluster cultures (NC), which exhibit high regenerative potential. This study aimed to identify proteins differentially altered during the regeneration of shoots from NC in the bromeliad Vriesea reitzii. Proteomic analysis was performed by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. Image analysis from NC, microshoots and shoots resulted in the detection of 345, 482, and 209 protein spots, respectively. Proteins related to the stress response (catalase, probable l-ascorbate peroxidase 3 and heat shock protein 81-1) and amino acid metabolism (glutamine synthetase, 4-hydroxy-tetrahydrodipicolinate reductase 1, serine hydroxymethyltransferase 1 and 14-3-3-like protein GF14-F) and other proteins (elongation factor Ts, probable signal peptidase complex subunit 2, calcium-dependent protein kinase 23, and ubiquitin-like protein-NEDD8-like protein RUB3) exhibited increased abundance in the early stages of development. On the other hand, proteins related to carbohydrate metabolism (ribulose bisphosphate carboxylase/oxygenase activase, ribulose bisphosphate carboxylase, and phosphoglycerate kinase 1) and ATP synthesis (ATP synthase subunit alpha and ATP synthase subunit beta) exhibited increased abundance in later stages. Changes in proteins related to cellular metabolic processes, the assembly of the photosynthetic mechanism, the response to medium stress and the dynamics of the cell cytoskeleton contribute to a high regenerative potential, which characterizes NC. To our knowledge, this is the first proteomic analysis performed during the regeneration process from NC in bromeliads. This study may provide important insights into proteins and cellular events involved in the micropropagation of this group of plants.

     

Risk factors for antimony treatment failure in American Cutaneous Leishmaniasis in Northwestern-Argentina

Background. To date, there is no specific literature available on the determinants for therapeutic failure (TF) with meglumine antimoniate (MA) in Northwestern-Argentina. This study aimed to identify epidemiological, clinical, and treatment-related factors that could be involved in TF. Methodology/Principal Findings. We performed a case-control study. Cases were represented by patients who showed TF after administration of the first course of MA treatment, whereas, controls were determined as patients who evolved towards healing after the first MA cycle received. Crude Odds Ratios and their corresponding 90% confidence intervals (CI) were calculated, and risk factors were then tested by multivariate analysis using logistic binary regression. Three hundred and eighty-four patients with a presumptive diagnosis of ACL were recruited, and 153 with a positive diagnosis were selected. We included in the study 71 patients, who underwent specific treatment with MA, presented complete data on response to treatment, and had a minimum post-treatment follow-up of 6 months in cutaneous leishmaniasis, and 12 months in mucosal leishmaniasis. Of these, 34 (47.9%) presented TF. In the initial analysis, TF was significantly associated with the geographical area of disease acquisition (p = 0.036), the presence of mucosal lesions (p = 0.042), the presence of concomitant skin and mucosal lesions (p = 0.002), and lesion age ≥ 6 months (p = 0.018). Risk factors influencing TF in the final multivariate model included the geographical area where the disease was acquired (adjusted Odd Ratio 8.062; 95% CI 1.914–33.959; p = 0.004), and lesion age ≥ 6 months (adjusted Odd Ratio 10.037; 95% CI 1.383–72.843; p = 0.023). Conclusions/Significance. The results of the present study suggest the existence of some risk factors linked to TF in Northwestern-Argentina, which deserve further investigation. Herein we recorded a high percentage of TF and we described clinical and epidemiological characteristics associated with TF that could be taken into account improving the clinical management of patients.     

mRNA secondary structure optimization using a correlated stem–loop prediction

Secondary structure of messenger RNA plays an important role in the bio-synthesis of proteins. Its negative impact on translation can reduce the yield of protein by slowing or blocking the initiation and movement of ribosomes along the mRNA, becoming a major factor in the regulation of gene expression. Several algorithms can predict the formation of secondary structures by calculating the minimum free energy of RNA sequences, or perform the inverse process of obtaining an RNA sequence for a given structure. However, there is still no approach to redesign an mRNA to achieve minimal secondary structure without affecting the amino acid sequence. Here we present the first strategy to optimize mRNA secondary structures, to increase (or decrease) the minimum free energy of a nucleotide sequence, without changing its resulting polypeptide, in a time-efficient manner, through a simplistic approximation to hairpin formation. Our data show that this approach can efficiently increase the minimum free energy by >40%, strongly reducing the strength of secondary structures. Applications of this technique range from multi-objective optimization of genes by controlling minimum free energy together with CAI and other gene expression variables, to optimization of secondary structures at the genomic level.     

Early Antenatal Care: Does It Make a Difference to Outcomes of Pregnancy Associated with Syphilis? A Systematic Review and Meta-Analysis

Objective

Despite an increase in the proportion of women who access antenatal care, mother-to-child transmission of syphilis continues to be a consequence of undiagnosed, untreated, or inadequately treated maternal syphilis. We reviewed evidence on the optimal timing of antenatal interventions to prevent mother-to-child transmission of syphilis and its associated adverse outcomes.

Design

Systematic review and meta-analysis of published literature. English-language articles were included if they (1) reported the gestational age at which the mother was screened or tested for syphilis; (2) reported on pregnancy outcome. No publication date limits were set.

Results

We identified a total of 1,199 publications, of which 84 were selected for further review and five were included. All showed a lower prevalence of any adverse outcome among women who received an intervention (to include screening and treatment) in the first and second trimesters of pregnancy compared to the third trimester. The overall odds ratio for any adverse outcome was 2.24 (95% CI 1.28, 3.93). All sub-analyses by type of outcome presented important heterogeneity between studies, except for those studies reporting an infected infant (odds ratio 2.92, 95% CI 0.66, 12.87; I² = 48.2%, p = 0.165).

Conclusions

Our review has shown that the timing of antenatal care interventions makes a significant difference in the risk of having an adverse outcome due to syphilis. Women who sought care in the first two trimesters of their pregnancy, and received the appropriate intervention, were more likely to have a healthy infant, compared to women screened and treated in the third trimester. Encouraging ALL pregnant women to seek care in the first two trimesters of their pregnancy should be a priority for health programmes. For interventions to be effective within these health programmes, health systems and community engagement programmes need to be strengthened to enable pregnant women to seek antenatal care early.     

Nucleotide sequence of a DRw10 beta chain cDNA clone. Identity of the third D region with that of the DRw53 allele of the beta 2 locus and as the probable site encoding a polymorphic MHC class II epitope

The nucleotide and inferred amino acid sequence of a DRw10 beta chain was obtained from cDNA clones isolated from a DR1, DRw10 heterozygous cell line. The sequence of this beta chain gene was distinctive, differing from those of all other defined DR types. The DRw10 beta chain gene was shown by transfection experiments to encode a polymorphic epitope recognized by mAb 109d6 that is also encoded by the DRw53 beta 2 chain gene. Comparison of the nucleotide sequence of both genes revealed that their third D regions (amino acids 67 to 73) were identical. This suggested first that the 109d6 epitope could be encoded by residues of this region, and second, that a putative gene conversion event transferred this sequence along with the information encoding the 109d6 epitope from a donor gene such as DRw53 beta 2. The sequence of the DRw10 beta chain gene was observed to be identical to that of clone pII beta 4 derived from the non-DR3 haplotype in the Raji cell line, which was also demonstrated to express the determinant recognized by antibody 109d6, suggesting that the typing of this cell line is HLA-DR3/DRw10. No evidence was found for the existence of a DR beta 2 chain gene product encoded by the DRw10 haplotype. The DRw10 haplotype was of particular interest because it was present along with a DR1 haplotype in the propositus who had rheumatoid arthritis, and was shared by the DR4-positive son of the propositus, who also had rheumatoid arthritis. This raised the possibility that the DRw10 haplotype, and most probably one or more specific conformations encoded by the DR beta chain, are involved in the definition of the disease susceptibility phenotype.     

Modifier gene study of meconium ileus in cystic fibrosis: statistical considerations and gene mapping results

Cystic fibrosis (CF) is a monogenic disease due to mutations in the CFTR gene. Yet, variability in CF disease presentation is presumed to be affected by modifier genes, such as those recently demonstrated for the pulmonary aspect. Here, we conduct a modifier gene study for meconium ileus (MI), an intestinal obstruction that occurs in 16–20% of CF newborns, providing linkage and association results from large family and case–control samples. Linkage analysis of modifier traits is different than linkage analysis of primary traits on which a sample was ascertained. Here, we articulate a source of confounding unique to modifier gene studies and provide an example of how one might overcome the confounding in the context of linkage studies. Our linkage analysis provided evidence of a MI locus on chromosome 12p13.3, which was segregating in up to 80% of MI families with at least one affected offspring (HLOD = 2.9). Fine mapping of the 12p13.3 region in a large case–control sample of pancreatic insufficient Canadian CF patients with and without MI pointed to the involvement of ADIPOR2 in MI (p = 0.002). This marker was substantially out of Hardy–Weinberg equilibrium in the cases only, and provided evidence of a cohort effect. The association with rs9300298 in the ADIPOR2 gene at the 12p13.3 locus was replicated in an independent sample of CF families. A protective locus, using the phenotype of no-MI, mapped to 4q13.3 (HLOD = 3.19), with substantial heterogeneity. A candidate gene in the region, SLC4A4, provided preliminary evidence of association (p = 0.002), warranting further follow-up studies. Our linkage approach was used to direct our fine-mapping studies, which uncovered two potential modifier genes worthy of follow-up.