Analysis of acetic acid bacteria by different culture-independent techniques in a controlled superficial acetification

Three molecular techniques [denaturing gradient gel electrophoresis (DGGE-PCR), restriction fragment length polymorphism of the 16S rRNA gene amplicon (RFLP-PCR 16S rRNA) and real-time PCR (RT-PCR) with SybrGreen and with specific TaqMan-Minor Groove Binder (MGB) probes] were used to identify and monitor acetic acid bacteria (AAB) species during a controlled acetification. This process was initiated by seeding a starter culture comprising a mixture of one strain each of Acetobacter pasteurianus, Gluconacetobacter europaeus and Gluconacetobacter hansenii. Analysis at the species level indicated that the population of A. pasteurianus increased quickly, subsequently acquiring a dominant position, whereas the other two species gradually disappeared. All three methods confirmed this result. When the total AAB population was estimated, the results obtained based on summing the three species by TaqMan-MGB RT-PCR, total AAB RT-PCR and the direct microscopic count method were similar. Using TaqMan-MGB RT-PCR we were able to detect species with populations 3 log units lower than that of the major species and which could not be detected by other methods.     

Community diversity outweighs effect of warming on plant colonization

Abiotic environmental change, local species extinctions and colonization of new species often co‐occur. Whether species colonization is driven by changes in abiotic conditions or reduced biotic resistance will affect community functional composition and ecosystem management. We use a grassland experiment to disentangle effects of climate warming and community diversity on plant species colonization. Community diversity had dramatic impacts on the biomass, richness and traits of plant colonists. Three times as many species colonized the monocultures than the high diversity 17 species communities (~30 vs. 10 species), and colonists collectively produced 10 times as much biomass in the monocultures than the high diversity communities (~30 vs. 3 g/m²). Colonists with resource‐acquisitive strategies (high specific leaf area, light seeds, short heights) accrued more biomass in low diversity communities, whereas species with conservative strategies accrued most biomass in high diversity communities. Communities with higher biomass of resident C4 grasses were more resistant to colonization by legume, nonlegume forb and C3 grass colonists, but not by C4 grass colonists. Compared with effects of diversity, 6 years of 3°C‐above‐ambient temperatures had little impact on plant colonization. Warmed subplots had ~3 fewer colonist species than ambient subplots and selected for heavier seeded colonists. They also showed diversity‐dependent changes in biomass of C3 grass colonists, which decreased under low diversity and increased under high diversity. Our findings suggest that species colonization is more strongly affected by biotic resistance from residents than 3°C of climate warming. If these results were extended to invasive species management, preserving community diversity should help limit plant invasion, even under climate warming.     

Resistance Mutations and CTL Epitopes in Archived HIV-1 DNA of Patients on Antiviral Treatment: Toward a New Concept of Vaccine

Eleven patients responding successfully to first-line antiretroviral therapy (ART) were investigated for proviral drug resistance mutations (DRMs) in RT by ultra-deep pyrosequencing (UDPS). After molecular typing of the class I alleles A and B, the CTL epitopes in the Gag, Nef and Pol regions of the provirus were sequenced and compared to the reference HXB2 HIV-1 epitopes. They were then matched with the HLA alleles with determination of theoretical affinity (TA). For 3 patients, the results could be compared with an RNA sample of the circulating virus at initiation of therapy. Five out of 11 patients exhibited DRMs by UDPS. The issue is whether a therapeutic switch is relevant in these patients by taking into account the identity of the archived resistance mutations. When the archived CTL epitopes were determined on the basis of the HLA alleles, different patterns were observed. Some epitopes were identical to those reported for the reference with the same TA, while others were mutated with a decrease in TA. In 2 cases, an epitope was observed as a combination of subpopulations at entry and was retrieved as a single population with lower TA at success. With regard to immunological stimulation and given the variability of the archived CTL epitopes, we propose a new concept of curative vaccine based on identification of HIV-1 CTL epitopes after prior sequencing of proviral DNA and matching with HLA class I alleles.     

Secondary metabolites of soil <Emphasis Type="Italic">Bacillus</Emphasis> spp.

Bacillus species produce secondary metabolites that are the object of natural product chemistry studies. The wide structural variability of these compounds has attracted the curiosity of chemists and their biological activities have inspired the pharmaceutical industry to search for lead structures in microbial extracts. Screening of microbial extracts reveals the large structural diversity of natural compounds with broad biological activities, such as antimicrobial, antiviral, immunosuppressive, and antitumor activities, that enable the bacterium to survive in its natural environment. These findings widen the potential industrial importance of Bacillus spp., particularly of B. thuringiensis, beyond insecticidal usage and may help explain the role of Bacillus spp. in the soil ecosystem.     

Anatomical location of LPA1 activation and LPA phospholipid precursors in rodent and human brain

Lysophosphatidic acid (LPA) is a signaling molecule that binds to six known G protein‐coupled receptors: LPA₁–LPA₆. LPA evokes several responses in the CNS, including cortical development and folding, growth of the axonal cone and its retraction process. Those cell processes involve survival, migration, adhesion proliferation, differentiation, and myelination. The anatomical localization of LPA₁ is incompletely understood, particularly with regard to LPA binding. Therefore, we have used functional [³⁵S]GTPγS autoradiography to verify the anatomical distribution of LPA₁ binding sites in adult rodent and human brain. The greatest activity was observed in myelinated areas of the white matter such as corpus callosum, internal capsule and cerebellum. MaLPA₁‐null mice (a variant of LPA₁‐null) lack [³⁵S]GTPγS basal binding in white matter areas, where the LPA₁ receptor is expressed at high levels, suggesting a relevant role of the activity of this receptor in the most myelinated brain areas. In addition, phospholipid precursors of LPA were localized by MALDI‐IMS in both rodent and human brain slices identifying numerous species of phosphatides and phosphatidylcholines. Both phosphatides and phosphatidylcholines species represent potential LPA precursors. The anatomical distribution of these precursors in rodent and human brain may indicate a metabolic relationship between LPA and LPA₁ receptors.

     

Egb 761 in the postgenomic era: new tools from molecular biology for the study of complex products such as Ginkgo biloba extract.

The decoding of the human genome has completely changed our views on medicine. Beyond sequencing, tools of the postgenomic era may lead to a better understanding of various therapies, especially those with a complex effect on numerous cellular components and functions. The development of high-density oligonucleotide microarrays led to pioneer studies on the multiple gene expression effects exhibited by Ginkgo biloba extract EGb 761, changing traditional pharmacology and medicine concepts. Instead of studying a simple gene or protein, a global investigation of all genes or proteins at once can give insights of the complexity of biological systems.     

Genetic manipulation in <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> for strain improvement

Bacillus thuringiensis (Bt) has been used as a biopesticide in agriculture, forestry and mosquito control because of its advantages of specific toxicity against target insects, lack of polluting residues and safety to non-target organisms. The insecticidal properties of this bacterium are due to insecticidal proteins produced during sporulation. Despite these ecological benefits, the use of Bt biopesticides has lagged behind the synthetic chemicals. Genetic improvement of Bt natural strains, in particular Bt recombination, offers a promising means of improving efficacy and cost-effectiveness of Bt-based bioinsecticide products to develop new biotechnological applications.     

Polymorphisms in the Apolipoprotein L1 gene and their effects on blood lipid and glucose levels in middle age males

Apolipoprotein L1 in plasma is associated with high-density lipoprotein. Novel APOL1 polymorphisms are investigated along with the association of two common haplotypes (Lysl66Glu, Ile244Met, Lys271Arg) with circulating lipid and glucose levels. Although the amino acid substitutions occur in the amphipathic alpha helices region involved in lipid binding, these substitutions were found not to independently account for variability in circulating lipid and glucose levels in 149 middle age males.