Abundance and Genetic Diversity of nifH Gene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of Sao Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies.

Comparison of wing geometry data and genetic data for assessing the population structure of Aedes aegypti

Aedes aegypti is the most important vector of dengue viruses in tropical and subtropical regions. Because vaccines are still under development, dengue prevention depends primarily on vector control. Population genetics is a common approach in research involving Ae. aegypti. In the context of medical entomology, wing morphometric analysis has been proposed as a strong and low-cost complementary tool for investigating population structure. Therefore, we comparatively evaluated the genetic and phenotypic variability of population samples of Ae. aegypti from four sampling sites in the metropolitan area of Sao Paulo city, Brazil. The distances between the sites ranged from 7.1 to 50 km. This area, where knowledge on the population genetics of this mosquito is incipient, was chosen due to the thousands of dengue cases registered yearly. The analysed loci were polymorphic, and they revealed population structure (global F-ST = 0.062; p < 0.05) and low levels of gene flow (Nm = 0.47) between the four locations. Principal component and discriminant analyses of wing shape variables (18 landmarks) demonstrated that wing polymorphisms were only slightly more common between populations than within populations. Whereas microsatellites allowed for geographic differentiation, wing geometry failed to distinguish the samples. These data suggest that microevolution in this species may affect genetic and morphological characters to different degrees. In this case, wing shape was not validated as a marker for assessing population structure. According to the interpretation of a previous report, the wing shape of Ae. aegypti does not vary significantly because it is stabilised by selective pressure. (C) 2011 Elsevier B.V. All rights reserved.

Expanding the Clinical and Genetic Spectrum of Human CD40L Deficiency: The Occurrence of Paracoccidioidomycosis and Other Unusual Infections in Brazilian Patients

CD40 ligand (CD40L) deficiency or X-linked hyper-IgM syndrome (X-HIGM) is a well-described primary immunodeficiency in which Pneumocystis jiroveci pneumonia is a common clinical feature. We have identified an unusual high incidence of fungal infections and other not yet described infections in a cohort of 11 X-HIGM patients from nine unrelated Brazilian families. Among these, we describe the first case of paracoccidioidomycosis (PCM) in X-HIGM. The molecular genetic analysis of CD40L was performed by gene sequencing and evaluation of CD40L protein expression. Nine of these 11 patients (82%) had fungal infections. These included fungal species common to CD40L deficiency (P. jiroveci and Candida albicans) as well as Paracoccidioides brasiliensis. One patient presented with PCM at age 11 years and is now doing well at 18 years of age. Additionally, one patient presented with a simultaneous infection with Klebsiella and Acinetobacter, and one with condyloma caused by human papilloma virus. Molecular analysis revealed four previously described CD40L mutations, two novel missense mutations (c.433 T>G and c.476 G>C) resulting in the absence of CD40L protein expression by activated CD4(+) cells and one novel insertion (c.484_485insAA) within the TNFH domain leading to a frame shift and premature stop codon. These observations demonstrated that the susceptibility to fungal infections in X-HIGM extends beyond those typically associated with X-HIGM (P. jiroveci and C. albicans) and that these patients need to be monitored for those pathogens.

Morphological and genetic variability in Hippolyte obliquimanus dana, 1852 (Decapoda, Caridea, Hippolytidae) from Brazil and the caribbean sea

Hippolyte obliquimanus is a marine shrimp reported from the Caribbean Sea and Brazil. The literature provides indications for morphological variation between populations from those regions and the species has a troubled taxonomic history. The aims of this study were to analyse morphological and genetic variation in the populations of H. obliquimanus from Brazil and the Caribbean Sea and to verify if those might support separation of H. obliquimanus into two or more species. This hypothesis was tested with the analysis of morphological and genetic data (mitochondrial gene 16S and the barcode region Cytochrome Oxidase I). The material analysed was obtained from samples and from loans of zoological collections. The rostrum as well as pereiopods 3, 4, and 5 were the adult morphological characters that showed variation, but this occurred in samples from both regions, Brazil and the Caribbean Sea. The sequences of the 16S gene were identical among all specimens analysed. There was, however, variation among the sequences of the barcoding gene COI (<2.0%); this divergence separated the specimens into two groups (Brazil versus the Caribbean) and these groups did not share haplotypes. In conclusion, specimens from the regions analysed showed both morphological and genetic variation, but these did not support the separation of H. obliquimanus into two or more species.

Non-inflammatory destructive periodontal disease: a clinical, microbiological, immunological and genetic investigation

Periodontitis comprises a group of multifactorial diseases in which periodontopathogens accumulate in dental plaque and trigger host chronic inflammatory and immune responses against periodontal structures, which are determinant to the disease outcome. Although unusual cases of non-inflammatory destructive periodontal disease (NIDPD) are described, their pathogenesis remains unknown. A unique NIDPD case was investigated by clinical, microbiological, immunological and genetic tools. The patient, a non-smoking dental surgeon with excessive oral hygiene practice, presented a generalized bone resorption and tooth mobility, but not gingival inflammation or occlusion problems. No hematological, immunological or endocrine alterations were found. No periodontopathogens (A. actinomycetemcomitans, P. gingivalis, F. nucleatum and T. denticola) or viruses (HCMV, EBV-1 and HSV-1) were detected, along with levels of IL-1 beta and TNF-alpha in GCF compatible with healthy tissues. Conversely ALP, ACP and RANKL GCF levels were similar to diseased periodontal sites. Genetic investigation demonstrated that the patient carried some SNPs, as well HLA-DR4 (*0404) and HLA-B27 alleles, considered risk factors for bone loss. Then, a less vigorous and diminished frequency of toothbrushing was recommended to the patient, resulting in the arrest of alveolar bone loss, associated with the return of ALP, ACP and RANKL in GCF to normality levels. In conclusion, the unusual case presented here is compatible with the previous description of NIDPD, and the results that a possible combination of excessive force and frequency of mechanical stimulation with a potentially bone loss prone genotype could result in the alveolar bone loss seen in NIDPD.

Successful Improvement of Frequency and Symptoms of Premature Complexes after Oral Magnesium Administration

Background: Premature ventricular and supraventricular complexes (PVC and PsVC) are frequent and often symptomatic. The magnesium (Mg) ion plays a role in the physiology of cell membranes and cardiac rhythm. Objective: We evaluated whether the administration of Mg Pidolate (MgP) in patients with PVC and PsVC is superior to placebo (P) in improving symptoms and arrhythmia frequency. Methods: Randomized double-blind study with 60 consecutive symptomatic patients with more than 240 PVC or PsVC/h on 24-hour Holter monitoring who were selected to receive placebo or MgP. To evaluate symptom improvement, a categorical and a specific questionnaire for symptoms related to PVC and PsVC was made. Improvement in premature complex density (PCD) per hour was considered significant if percentage reduction was >= 70% after treatment. The dose of MgP was 3.0 g/day for 30 days, equivalent to 260mg of Mg element. None of the patients had structural heart disease or renal failure. Results: Of the 60 patients, 33 were female (55%). Ages ranged from 16 to 70 years old. In the MgP group, 76.6% of patients had a PCD reduction >70%, 10% of them >50% and only 13.4% <50%. In the P group, 40% showed slight improvement, <30%, in the premature complexes frequency (p < 0.001). Symptom improvement was achieved in 93.3% of patients in the MgP group, compared with only 16.7% in the P group (p < 0.001). Conclusion: Oral Mg supplementation decreases PCD, resulting in symptom improvement. (Arq Bras Cardiol 2012;98(6):480-487)

Mechanism of colonization in the Mediterranean-sea. Asperarca nodulosa: morphological and genetic analysis

Il mar Mediterraneo è un bacino acquifero peculiare per la recente colonizzazione di specie aliene, per l’evento geologico legato alla Crisi di salinità del Messiniano e per l’ampio range di salinità. L’individuazione dei meccanismi di colonizzazione si è incentrata sullo studio morfologico, istologico e molecolare delle specie Asperarca nodulosa ed Anadara demiri (Arcidae-Bivalvia-Mollusca). La ricerca si è basata sulla caratterizzazione morfologica, con utilizzo del microscopio elettronico a scansione, al fine di individuare il tipo di sviluppo larvale. Successivamente i dati rilevati al S.E.M. sono stati supportati dall’indagine istologica che ha evidenziato la presenza di gonadi a sessi distinti e la non incubazione larvale. L’ulteriore analisi filogenetica ha permesso di evidenziare la netta suddivisione tra le tre popolazioni studiate, indagine effettuata tramite marcatori arbitrari (RAPDs) e nucleari specifici (ITS). I risultati ottenuti trovano supporto da quanto noto su base morfologica. I dati, nel complesso, mostrano una perdita delle capacità di diffusione della specie tramite sviluppo larvale plantotrofico a favore di quello lecitotrofico o diretto; tale tesi è ulteriormente supportata dai dati molecolari che mostrano una netta separazione delle popolazioni prese in esame ed un conseguente isolamento tra individui appartenenti a zone di profondità del Mediterraneo (sub-bacini abissali). La ricerca ha, inoltre,esaminato i meccanismi di introduzione attuali nel bacino acquifero che è soggetto ad una nuova invasione da parte specie aliene dovuta all’apertura del canale di Suez. L’analisi si è focalizzata sullo studio per l’ individuazione dell’origine della specie aliena A. demiri , di presunta derivazione Indo-Pacifica, ma rivelatasi, nei dati preliminari, di origine Atlantica.

Intrinsic ordering, combinatorial numbers and reliability engineering

[EN]A new algorithm for evaluating the top event probability of large fault trees (FTs) is presented. This algorithm does not require any previous qualitative analysis of the FT. Indeed, its efficiency is independent of the FT logic, and it only depends on the number n of basic system components and on their failure probabilities. Our method provides exact lower and upper bounds on the top event probability by using new properties of the intrinsic order relation between binary strings. The intrinsic order enables one to select binary n-tuples with large occurrence probabilities without necessity to evaluate them. This drastically reduces the complexity of the problem from exponential (2n binary n-tuples) to linear (n Boolean variables)...

Phylogeny and genetic diversity of Italian species of hares (genus Lepus)

In this study we have analysed the genetic variability in ca. 700 samples belonging to six species of genus Lepus using maternal and biparental molecular markers (mitochondrial DNA, microsatellites, Single Nucleotide Polimorphisms). We aimed to reconstruct the phylogenetic relationships of species of hares living in Europe, and assess the occurrence of hybridization between the European hare Lepus europaeus and the Italian hare Lepus corsicanus. Results showed a deep genetic differentiation and absence of hybridization between L. corsicanus and L. europaeus, confirming that they are distinct and distantly related biological species. In contrast, we showed small genetic distances and a close phylogenetic relationship between the Italian hare and Cantabrian hare L. castroviejoi, which suggest a deeper evaluation of their taxonomic status. Populations of L. corsicanus are geographically differentiated. In particular, the peninsular and Sicilian populations of Italian hares are sharply genetically distinct, which calls for avoiding any translocation between Italy and Sicily. Information on genetic variability and population structure is being used to implement the Italian Action Plan for L. corsicanus.

Study of variability and genetic structure of European populations of Myotis emarginatus and Myotis capaccinii (Chiroptera, Vespertilionidae)

The Geoffroy’s bat Myotis emarginatus is mainly present in southern, south-eastern and central Europe (Červerný, 1999) and is often recorded from northern Spain (Quetglas, 2002; Flaquer et al., 2004). It has demonstrated the species’ preference for forest. Myotis capaccinii, confined to the Mediterranean (Guille´n, 1999), is classified as ‘vulnerable’ on a global scale (Hutson, Mickleburgh & Racey, 2001). In general, the species preferred calm waters bordered by well-developed riparian vegetation and large (> 5 m) inter-bank distances (Biscardi et al. 2007). In this study we present the first results about population genetic structure of these two species of genus Myotis. We used two methods of sampling: invasive and non-invasive techniques. A total of 323 invasive samples and a total of 107 non-invasive samples were collected and analyzed. For Myotis emarginatus we have individuated for the first time a set of 7 microsatellites, which can work on this species, started from a set developed on Myotis myotis (Castella et al. 2000). We developed also a method for analysis of non-invasive samples, that given a good percentage of positive analyzed samples. The results have highlighted for the species Myotis emarginatus the presence on the European territory of two big groups, discovered by using the microsatellites tracers. On this species, 33 haplotypes of Dloop have been identified, some of them are presented only in some colonies. We identified respectively 33 haplotypes of Dloop and 10 of cytB for Myotis emarginatus and 25 of dloop and 15 of cytB for Myotis capaccinii. Myotis emarginatus’ results, both microsatellites and mtDNA, show that there is a strong genetic flow between different colonies across Europe. The results achieved on Myotis capaccinii are very interesting, in this case either for the microsatellites or the mitochondrial DNA sequences, and it has been highlighted a big difference between different colonies.

Functional and Genetic characterization of new genomic islands from an E. coli strain associated with neonatal meningitis.

Enterobacteriaceae genomes evolve through mutations, rearrangements and horizontal gene transfer (HGT). The latter evolutionary pathway works through the acquisition DNA (GEI) modules of foreign origin that enhances fitness of the host to a given environment. The genome of E. coli IHE3034, a strain isolated from a case of neonatal meningitis, has recently been sequenced and its subsequent sequence analysis has predicted 18 possible GEIs, of which: 8 have not been previously described, 5 fully meet the pathogenic island definition and at least 10 that seem to be of prophagic origin. In order to study the GEI distribution of our reference strain, we screened for the presence 18 GEIs a panel of 132 strains, representative of E. coli diversity. Also, using an inverse nested PCR approach we identified 9 GEI that can form an extrachromosomal circular intermediate (CI) and their respective attachment sites (att). Further, we set up a qPCR approach that allowed us to determine the excision rates of 5 genomic islands in different growth conditions. Four islands, specific for strains appertaining to the sequence type complex 95 (STC95), have been deleted in order to assess their function in a Dictyostelium discoideum grazing assays. Overall, the distribution data presented here indicate that 16 IHE3034 GEIs are more associated to the STC95 strains. Also the functional and genetic characterization has uncovered that GEI 13, 17 and 19 are involved in the resistance to phagocitation by Dictyostelium d thus suggesting a possible role in the adaptation of the pathogen during certain stages of infection.

Possibilities for the healthy and nutritional improvement of confectionery and sweet products.

The overall objective of this PhD was to investigate the possibility to increase the nutritional value of confectionary products by the use of natural ingredients with healthy functions. The first part of the thesis focused on the possible substitution of the most characteristic component of confectionary products, i.e. refined sugar. Many natural whole sweetening alternatives are available, though not widely used; the use of molasses, the byproduct of sugar beet and cane production, still rich in healthy components as minerals and phytochemicals is hereby discussed; after having verified molasses effectiveness in oxidative stress counteraction on liver cultured cells, the higher antioxidant capacity of a sweet food prepared with molasses instead of refined sugar was confirmed. A second step of the project dealt with another main ingredient of various sweet products, namely wheat. Particularly, the exploitation of soft and durum wheat byproducts could be another sustainable strategy to improve the healthy value of confectionery. The isolation of oligosaccharides with bioactive functions form different fractions of the wheat milling stream was studied and the new ingredients were shown to have a high dietary fiber and antioxidants content. As valid alternative, product developers should consider the appealing and healthy addition of ancient grains flour to sweet baked goods. The possibility of substituting the modern whole durum wheat with the ancient Kamut® khorasan was considered, and the antioxidant and anti-inflammatory effects of these grains were evaluated and compared both in vitro and in vivo on rats. Finally, since high consumption of confectionery is a risk factor for obesity, a possible strategy for the counteraction of this disease was investigated. The ability of three bioactives in inhibiting adipocytes differentiation was investigated. In fact, theoretically, compounds able to influence adipogenesis could be used in the formulation of functional sweet products and contribute to prevent obesity.