Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?

The genus Pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. The relationship of the Pseudomonas genus to Azotobacter vinelandii is examined using three genomic sequence-based methods. First, using 16S rRNA trees, it is shown that A. vinelandii groups within the Pseudomonas close to Pseudomonas aeruginosa. Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster. Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms. Third, exhaustive BLAST comparisons demonstrate that the fraction of shared genes between A. vinelandii and Pseudomonas genomes is similar to that of Pseudomonas species with each other. The results of these different methods point to a high similarity between A. vinelandii and the Pseudomonas genus, suggesting that Azotobacter might actually be a Pseudomonas

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies

Characteristics of Different Systems for the Solar Drying of Crops

Solar dryers are used to enable the preservation of agricultural crops, food processing industries for dehydration of fruits and vegetables, fish and meat drying, dairy industries for production of milk powder, seasoning of wood and timber, textile industries for drying of textile materials. The fundamental concepts and contexts of their use to dry crops is discussed in the chapter. It is shown that solar drying is the outcome of complex interactions particular between the intensity and duration of solar energy, the prevailing ambient relative humidity and temperature, the characteristics of the particular crop and its pre-preparation and the design and operation of the solar dryer

A new era for understanding amyloid structures and disease

The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention

Development of an enzyme-linked immunosorbent assay for quantification of Salmonella enteritidis-specific antibodies in egg yolk

The present study aims at developing an indirect ELISA to quantify yolk antibodies specific to all surface proteins of the invasive Salmonella Enteritidis (SE), which acquired the 1.8, 14.1, and ~ 50 Kb plasmids. An ELISA checkerboard was used in four different experiments to account for the different parameters included in the preliminary ELISA procedure, and consequently to maximize the difference in Optical Density (OD) values between control positive and negative yolk samples. The first experiment aimed at studying the impact of 5% Bovine Serum Albumin (BSA) dissolved in distilled water as a blocking reagent on a 28 µg/well SE antigen-coated plate, while applying the positive and negative control yolk samples to different concentrations of Phosphate-Buffered Saline (PBS).Conjugate application was maintained constant at a dilution of 1:500 in PBS. The second experiment was similar to the first one, but the positive and negative control yolk samples were diluted in PBS-Tween 20, and the conjugate dilution was changed to 1:1500 in PBS-Tween 20. In the third experiment, the conjugate was diluted at 1:1500 in 5% BSA/PBS-Tween 20 diluent or PBS-Tween 20 diluent with no 5% BSA. The objective of the fourth experiment was to study the impact of four different concentrations of SE-coated antigen levels (28µg/well, 56µg/well, 84µg/well, and 112µg/well), while fixing the blocking step with 5% BSA in distilled water, and the conjugate dilution set at 1:1000 in 5% BSA/PBSTween 20, and fixing the control yolk samples dilution at 1% in PBS-Tween 20. This last experimental procedure allowed the highest difference in mean absorbance OD values of the positive control minus the negative control samples, which was equivalent to 0.381. In addition, the final protocol for this ELISA was applied on individual egg yolk samples of two groups of chicken layers: one challenged in the esophagus at 11 days with 5.4 x 10(10) CFU/ml/bird of SE, and the second group was not challenged. The mean OD values of the egg yolk of antibodies specific against SE of the two groups were significantly different (0.8578 versus 0.5250; p<0.05), which indicates the possible application of the developed ELISA for screening SE infection by examining egg yolks produced by commercial layers