Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol

Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.     

Oestrogènes et reproduction masculine

The role of estrogen on male reproductive function has become clearer in the last decade. During these years the study of the effect of testosterone, estrogen or an aromatase inhibitor in hypogonadal men provided a first evidence of the effects of estrogens in the regulation of gonadotropin secretion. At the same time, the development of a line of transgenic male mice lacking estrogen receptor α, estrogen receptor β or aromatase gene provided further evidence about the role of estrogens not only in the regulation of gonadotropin secretion, but also on the effects of estrogens on testicular function and development. A confirmation of these actions of estrogens came from the observation of naturally occurring mutations of the estrogen receptor and of the aromatase gene in human males. Based on these data it has been demonstrated that estrogens are major regulators of gonadotropin secretion acting both at pituitary and hypotalamic level. The presence in the human reproductive structures of estrogen receptor α, estrogen receptor β and the aromatase enzyme indicates the existence of receptor α, estrogen receptor β or aromatase estrogen actions at this level. Anyway, the precise role of estrogens in testicular development and function and on the regulation of human spermatogenesis has not yet been precisely clarified.     

Intensification of agriculture in southwestern Germany between the Bronze Age and Medieval period,based on archaeobotanical data from Baden-Württemberg

Vegetation History and Archaeobotany - A system of farming with an alternation of land use between being cultivated or left fallow as grassland (Feldgraswirtschaft) developed in southwestern...     

Discovery of 17 conserved structural RNAs in fungi

Many non-coding RNAs with known functions are structurally conserved: their intramolecular secondary and tertiary interactions are maintained across evolutionary time. Consequently, the presence of conserved structure in multiple sequence alignments can be used to identify candidate functional non-coding RNAs. Here, we present a bioinformatics method that couples iterative homology search with covariation analysis to assess whether a genomic region has evidence of conserved RNA structure. We used this method to examine all unannotated regions of five well-studied fungal genomes (Saccharomyces cerevisiae, Candida albicans, Neurospora crassa, Aspergillus fumigatus, and Schizosaccharomyces pombe). We identified 17 novel structurally conserved non-coding RNA candidates, which include four H/ACA box small nucleolar RNAs, four intergenic RNAs and nine RNA structures located within the introns and untranslated regions (UTRs) of mRNAs. For the two structures in the 3′ UTRs of the metabolic genes GLY1 and MET13, we performed experiments that provide evidence against them being eukaryotic riboswitches.     

Complete cysteine-scanning mutagenesis of the Salmonella typhimurium melibiose permease

The melibiose permease of Salmonella typhimurium (MelB_St) catalyzes the stoichiometric symport of galactopyranoside with a cation (H⁺, Li⁺, or Na⁺) and is a prototype for Na⁺-coupled major facilitator superfamily (MFS) transporters presenting from bacteria to mammals. X-ray crystal structures of MelB_St have revealed the molecular recognition mechanism for sugar binding; however, understanding of the cation site and symport mechanism is still vague. To further investigate the transport mechanism and conformational dynamics of MelB_St, we generated a complete single-Cys library containing 476 unique mutants by placing a Cys at each position on a functional Cys-less background. Surprisingly, 105 mutants (22%) exhibit poor transport activities (<15% of Cys-less transport), although the expression levels of most mutants were comparable to that of the control. The affected positions are distributed throughout the protein. Helices I and X and transmembrane residues Asp and Tyr are most affected by cysteine replacement, while helix IX, the cytoplasmic middle-loop, and C-terminal tail are least affected. Single-Cys replacements at the major sugar-binding positions (K18, D19, D124, W128, R149, and W342) or at positions important for cation binding (D55, N58, D59, and T121) abolished the Na⁺-coupled active transport, as expected. We mapped 50 loss-of-function mutants outside of these substrate-binding sites that suffered from defects in protein expression/stability or conformational dynamics. This complete Cys-scanning mutagenesis study indicates that MelB_St is highly susceptible to single-Cys mutations, and this library will be a useful tool for further structural and functional studies to gain insights into the cation-coupled symport mechanism for Na⁺-coupled MFS transporters.     

CRISPR/Cas9-mediated gfp gene inactivation in Arabidopsis suspension cells

Molecular Biology Reports - Targeted genome editing using CRISPR/Cas9 is a promising technology successfully verified in various plant species; however, it has hardly been used in plant cell...     

Studies of lipopolysaccharides from Yersinia pseudotuberculosis subtypes VA and VB

Lipopolysaccharides (LPS) from various strains of Yersinia pseudotuberculosis type V have been isolated and characterised. Differences in sugar composition and serological activity of LPS from various strains within the same subtype of Y. pseudotuberculosis have been revealed.     

Patch dynamics of the Mediterranean seagrass Posidonia oceanica: Implications for recolonisation process

Patch dynamics of the Mediterranean slow-growing seagrass Posidonia oceanica was studied in two shallow sites (3–10 m) of the Balearic Archipelago (Spain) through repeated censuses (1–2 year⁻¹). In the sheltered site of Es Port Bay (Cabrera Island), initial patch density (October 2001) was low: 0.05 patches m⁻², and the patch size (number of shoots) distribution was bimodal: most of the patches had less than 6 shoots or between 20 and 50 shoots. Mean patch recruitment in Es Port Bay (0.006 ± 0.002 patches m⁻² year⁻¹) exceeded mean patch loss (0.001 ± 0.001 patches m⁻² year⁻¹), yielding positive net patch recruitment (0.004 ± 0.003 patches m⁻² year⁻¹) and a slightly increased patch density 3 years later (July 2004, 0.06 patches m⁻²). In the exposed site of S’Estanyol, the initial patch density was higher (1.38 patches m⁻², August 2003), and patch size frequency decreased exponentially with size. Patch recruitment (0.26 patches m⁻² year⁻¹) and loss (0.24 patches m⁻² year⁻¹) were high, yielding a slightly increased patch density in the area 1 year later (October 2004, 1.40 patches m⁻²). Most recruited patches consisted of rooting vegetative fragments of 1–2 shoots. Seedling recruitment was observed in Summer 2004 at both sites. Episodic, seedling recruitment comprised 30% and 25% of total patch recruitment in Es Port Bay and S’Estanyol, respectively. Patch survival increased with patch size and no direct removal was observed among patches of 5 shoots or more. Most patches grew along the study, shifting patch distribution towards larger sizes. Within the size range studied (1–150 shoots), absolute shoot recruitment (shoots year⁻¹) increased linearly with patch size (R² = 0.64, p < 4 × 10⁻⁵, N = 125), while specific shoot recruitment was constant (about 0.25 ± 0.05 year⁻¹), although its variance was large for small patches. Given the slow growth rate and the high survival of patches with 5 or more shoots, even the low patch recruitment rates reported here could play a significant role in the colonisation process of P. oceanica.