The evolutionary analysis of the Tnt1 retrotransposon in Nicotiana species reveals the high variability of its regulatory sequences

We studied the evolution of the tobacco Tnt1 retrotransposon by analyzing Tnt1 partial sequences containing both coding domains and U3 regulatory sequences obtained from a number of Nicotiana species. We detected three different subfamilies of Tnt1 elements, Tnt1A, Tnt1B, and Tnt1C, that differ completely in their U3 regions but share conserved flanking coding and LTR regions. U3 divergence between the three subfamilies is found in the region that contains the regulatory sequences that control the expression of the well-characterized Tnt1-94 element. This suggests that expression of the three Tnt1 subfamilies might be differently regulated. The three Tnt1 subfamilies were present in the Nicotiana genome at the time of species divergence, but have evolved independently since then in the different genomes. Each Tnt1 subfamily seems to have conserved its ability to transpose in a limited and different number of Nicotiana species. Our results illustrate the high variability of Tnt1 regulatory sequences. We propose that this high sequence variability could allow these elements to evolve regulatory mechanisms in order to optimize their coexistence with their host genome.      

Quantitative, standardized assays for determining the concentrations of bovine lactoperoxidase, human salivary peroxidase, and human myeloperoxidase

Because of the important biological functions of peroxidases, there is growing interest in the measurement of their concentrations in various secretions. At present, there is no standard method which allows for comparisons in reported activities. This report describes procedures which can be used to measure peroxidase enzyme concentrations by commonly employed assays. Regression equations have been determined which can be used to calculate concentrations of bovine lactoperoxidase (LPO), human salivary peroxidase (SPO), and human myeloperoxidase (MPO) from activities measured with the following donors: pyrogallol, guaiacol, 2,2'-azinobis(3-ethylbenzylthiazoline-6-sulfonic acid), and thiocyanate (SCN-). The peroxidation rates of these donors depend upon the concentrations of hydrogen peroxide (H2O2) used in the individual assays and thus, for accurate, reproducible results, these concentrations must be carefully controlled. The SCN- normally present in human saliva will reduce observed reaction rates by simple competition kinetics in the ABTS, guaiacol and pyrogallol assays and will increase the rates observed when Cl- is used as a donor in NBS assay for MPO. Therefore, SCN- must be removed from saliva samples prior to peroxidase activity determination by all assays except the thionitrobenzoic acid (NBS) assay. LPO cannot be used as a standard for either SPO or MPO because the specific activities of LPO, SPO, and MPO are significantly different.     

Survival rate,blood feeding habits and sibling species composition of Aedes simpsoni complex: Implications for arbovirus transmission risk in East Africa

Aedes simpsoni complex has a wide distribution in Africa and comprises at least three described sub-species including the yellow fever virus (YFV) vector Ae. bromeliae. To date, the distribution and relative contributions of the sub-species and/or subpopulations including bionomic characteristics in relation to YF transmission dynamics remain poorly studied. In this study conducted in two areas with divergent ecosystems: peri-urban (coastal Rabai) and rural (Rift Valley Kerio Valley) in Kenya, survival rate was estimated by parity in Ae. simpsoni s.l. mosquitoes sampled using CO₂-baited BG Sentinel traps. We then applied PCR targeting the nuclear internal transcribed spacer 2 (ITS2), region followed by sequencing and phylogenetic analytics to identify the sibling species in the Ae. simpsoni complex among parous and blood fed cohorts. Our results show that Ae. bromeliae was the most dominant sub-species in both areas, exhibiting high survival rates, human blood-feeding, and potentially, high vectorial capacity for pathogen transmission. We document for the first time the presence of Ae. lilii in Kenya and potentially yet-to-be described species in the complex displaying human feeding tendencies. We also infer a wide host feeding range on rodents, reptile, and domestic livestock besides humans especially for Ae. bromeliae. This feeding trend could likely expose humans to various zoonotic pathogens. Taken together, we highlight the utility of genotype-based analyses to generate precision surveillance data of vector populations for enhanced disease risk prediction and to guide cost-effective interventions (e.g. YF vaccinations).     

A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data

Drosophila melanogaster belongs to a closely related group of eight species collectively known as the melanogaster subgroup; all are native to sub-Saharan Africa and islands off the east coast of Africa. The phylogenetic relationships of most species in this subgroup have been well documented; however, the three most closely related species, D. simulans, D. sechellia, and D. mauritiana, have remained problematic from a phylogenetic standpoint as no data set has unambiguously resolved them. We present new DNA sequence data on the nullo and Serendipity-alpha genes and combine them with all available nuclear DNA sequence data; the total data encompass 12 genes and the ITS of rDNA. A methodological problem arose because nine of the genes had information on intraspecific polymorphisms in at least one species. We explored the effect of inclusion/exclusion of polymorphic sites and found that it had very little effect on phylogenetic inferences, due largely to the fact that 82% of polymorphisms are autapomorphies (unique to one species). We have also reanalyzed our previous DNA-DNA hybridization data with a bootstrap procedure. The combined sequence data set and the DNA-DNA hybridization data strongly support the sister status of the two island species, D. sechellia and D. mauritiana. This at least partially resolves what had been a paradox of parallel evolution in these two species.      

Autoantibodies directed to novel components of the PM/Scl complex, the human exosome

The autoantigenic polymyositis/scleroderma (PM/Scl) complex was recently shown to be the human homologue of the yeast exosome, which is an RNA-processing complex. Our aim was to assess whether, in addition to targeting the known autoantigens PM/Scl-100 and PM/Scl-75, autoantibodies also target recently identified components of the PM/Scl complex. The prevalence of autoantibodies directed to six novel human exosome components (hRrp4p, hRrp40p, hRrp41p, hRrp42p, hRrp46p, hCsl4p) was determined in sera from patients with idiopathic inflammatory myopathy (n = 48), scleroderma (n = 11), or the PM/Scl overlap syndrome (n = 10). The sera were analyzed by enzyme-linked immunosorbent assays and western blotting using the affinity-purified recombinant proteins. Our results show that each human exosome component is recognized by autoantibodies. The hRrp4p and hRrp42p components were most frequently targeted. The presence of autoantibodies directed to the novel components of the human exosome was correlated with the presence of the anti-PM/Scl-100 autoantibody in the sera of patients with idiopathic inflammatory myopathy (IIM), as was previously found for the anti-PM/Scl-75 autoantibody. Other clear associations between autoantibody activities were not found. These results further support the conception that the autoimmune response may initially be directed to PM/Scl-100, whereas intermolecular epitope spreading may have caused the autoantibody response directed to the associated components.     

A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE)

Background  

The embryonic definitive endoderm (DE) gives rise to organs of the gastrointestinal and respiratory tract including the liver, pancreas and epithelia of the lung and colon. Understanding how DE progenitor cells generate these tissues is critical to understanding the cause of visceral organ disorders and cancers, and will ultimately lead to novel therapies including tissue and organ regeneration. However, investigation into the molecular mechanisms of DE differentiation has been hindered by the lack of early DE-specific markers.     

Sequencing the genome of the Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis>)

The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids.     

Removing celiac disease-related gluten proteins from bread wheat while retaining technological properties: a study with Chinese Spring deletion lines

Background  

Gluten proteins can induce celiac disease (CD) in genetically susceptible individuals. In CD patients gluten-derived peptides are presented to the immune system, which leads to a CD4⁺ T-cell mediated immune response and inflammation of the small intestine. However, not all gluten proteins contain T-cell stimulatory epitopes. Gluten proteins are encoded by multigene loci present on chromosomes 1 and 6 of the three different genomes of hexaploid bread wheat (Triticum aestivum) (AABBDD).