Agavin induces beneficial microbes in the shrimp microbiota under farming conditions.

Prebiotics and probiotics have shown a number of beneficial impacts preventing diseases in cultured shrimps. Complex soluble carbohydrates are considered ideal for fostering microbiota biodiversity by fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPS). Here we evaluated the growth performance and microbiota composition of the white shrimp Litopenaeus vannamei after dietary intervention using agavin as a FODMAP prebiotic under farming conditions.

Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome.

Changes in the human gut microbiome are associated with obesity and metabolic syndrome, but the role of the gut virome in both diseases remains largely unknown. We characterized the gut dsDNA virome of 28 school-aged children with healthy normal-weight (NW, n = 10), obesity (O, n = 10), and obesity with metabolic syndrome (OMS, n = 8), using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. The virome classification confirmed the bacteriophages' dominance, mainly composed of Caudovirales.

Whole-genome of Mexican-crAssphage isolated from the human gut microbiome.

Objectives: crAssphage is a newly found phage described as the most abundant virus in the human gut microbiome. The majority of the crAssphage proteins are unknown in sequences databases, and its pathogenicity and epidemiology in humans are yet unclear. Hence, being one of the most abundant phages in the human gut microbiome more investigation at the genomic level is necessary to improve our understanding, especially in the Latin American population.

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data.

Background: In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample.

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions.

Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene.

Secretome Prediction of Two Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets.

The Excreted/Secreted (ES) proteins play important roles during invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48).

Genetic engineering of the phosphocarrier protein NPr of the Escherichia coli phosphotransferase system selectively improves sugar uptake activity.

The Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system (PTS) in prokaryotes mediates the uptake and phosphorylation of its numerous substrates through a phosphoryl transfer chain where a phosphoryl transfer protein, HPr, transfers its phosphoryl group to any of several sugar-specific Enzyme IIA proteins in preparation for sugar transport. A phosphoryl transfer protein of the PTS, NPr, homologous to HPr, functions to regulate nitrogen metabolism and shows virtually no enzymatic cross-reactivity with HPr. Here we describe the genetic engineering of a "chimeric" HPr/NPr protein, termed CPr14 because 14 amino acid residues of the interface were replaced.

Exploring the Structure-Function Loop Adaptability of a (β/α)(8)-Barrel Enzyme through Loop Swapping and Hinge Variability.

Evolution of proteins involves sequence changes that are frequently localized at loop regions, revealing their important role in natural evolution. However, the development of strategies to understand and imitate such events constitutes a challenge to design novel enzymes in the laboratory. In this study, we show how to adapt loop swapping as semiautonomous units of functional groups in an enzyme with the (β/α)(8)-barrel and how this functional adaptation can be measured in vivo.

Protein design through systematic catalytic loop exchange in the (beta/alpha)8 fold.

Protein engineering by directed evolution has proven effective in achieving various functional modifications, but the well-established protocols for the introduction of variability, typically limited to random point mutations, seriously restrict the scope of the approach. In an attempt to overcome this limitation, we sought to explore variant libraries with richer diversity at regions recognized as functionally important through an exchange of natural components, thus combining design with combinatorial diversity. With this approach, we expected to maintain interactions important for protein stability while directing the introduction of variability to areas important for catalysis.

Generation of variability by in vivo recombination of halves of a (beta/alpha)8 barrel protein.

Similar to what has been achieved with nucleic acids, directed evolution of proteins would be greatly facilitated by the availability of large libraries and efficient selection methods. So far, host cell transformation efficiency has been a bottleneck, practically limiting libraries to sizes less than 10(9). One way to circumvent this problem has been implemented with antibody systems, where contribution to the binding site is provided by two different polypeptides (light and heavy chains).