Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Background  

In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner.     

High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection

HIV-1 mutations, which reduce or abolish CTL responses against virus-infected cells, are frequently selected in acute and chronic HIV infection. Among population HIV-1 sequences, immune selection is evident as human leukocyte antigen (HLA) allele-associated substitutions of amino acids within or near CD8 T-cell epitopes. In these cases, the non-adapted epitope is susceptible to immune recognition until an escape mutation renders the epitope less immunogenic. However, several population-based studies have independently identified HLA-associated viral changes, which lead to the formation of a new T-cell epitope, suggesting that the immune responses that these variants or 'neo-epitopes' elicit provide an evolutionary advantage to the virus rather than the host. Here, we examined the functional characteristics of eight CD8 T-cell responses that result from viral adaptation in 125 HLA-genotyped individuals with chronic HIV-1 infection. Neo-epitopes included well-characterized immunodominant epitopes restricted by common HLA alleles, and in most cases the T-cell responses against the neo-epitope showed significantly greater functional avidity and higher IFNγ production than T cells for non-adapted epitopes, but were not more cytotoxic. Neo-epitope formation and emergence of cognate T-cell response coincident with a rise in viral load was then observed in vivo in an acutely infected individual. These findings show that HIV-1 adaptation not only abrogates the immune recognition of early targeted epitopes, but may also increase immune recognition to other epitopes, which elicit immunodominant but non-protective T-cell responses. These data have implications for immunodominance associated with polyvalent vaccines based on the diversity of chronic HIV-1 sequences.     

Streptomyces nodosus host strains optimized for polyene glycosylation engineering

The AmphDI glycosyltransferase transfers a mycosaminyl sugar residue from GDP onto 8-deoxyamphoteronolide B, the aglycone of the antifungal amphotericin B. In this study the amphDI gene was inactivated in Streptomyces nodosus strains lacking the AmphN cytochrome P450. The new mutants produced 8-deoxy-16-methyl-16-descarboxyl amphoteronolides in high yield. These strains and aglycones should prove valuable for in vivo and in vitro glycosylation engineering.     

The immunoregulatory role of CD4⁺ FoxP3⁺ CD25⁻ regulatory T cells in lungs of mice infected with Bordetella pertussis

The identification of regulatory T (Treg) cells was originally based on CD25 expression; however, CD25 is also expressed by activated effector T cells. FoxP3 is a more definitive marker of Treg cells, and CD4(+) FoxP3(+) CD25(+) T cells are considered the dominant natural Treg (nTreg) population. It has been suggested that certain CD4(+) FoxP3(+) Treg cells do not express CD25. In this study, we used a murine model of respiratory infection with Bordetella pertussis to examine the role of Treg cells in protective immunity in the lung. We first demonstrated that CD4(+) FoxP3(+) CD25(-) cells are the dominant Treg population in the lung, gut and liver. Pre-activated lung CD4(+) FoxP3(+) CD25(-) cells suppressed CD4(+) effector T cells in vitro, which was partly mediated by IL-10 and not dependent on cell contact. Furthermore, CD4(+) FoxP3(+) CD25(-) IL-10(+) T cells were found in the lungs of mice at the peak of infection with B. pertussis. The rate of bacterial clearance was not affected by depletion of CD25(+) cells or in IL-10-deficient (IL-10(-/-) ) mice, but was compromised in CD25-depleted IL-10(-/-) mice. Our findings suggest that IL-10-producing CD4(+) FoxP3(+) CD25(-) T cells represent an important regulatory cell in the lung.     

The value of muscular and skeletal scores in the live animal and carcass classification scores as indicators of carcass composition in cattle

The objective was to determine the relationship of muscular and skeletal scores taken on the live animal and carcass conformation and fat scores with carcass composition and value. Bulls (n = 48) and heifers (n = 37) of 0.75 to 1.0 late-maturing breed genotypes slaughtered at 16 and 20 months of age, respectively, were used. At 8 months of age (weaning) and immediately pre-slaughter, visual muscular scores were recorded for each animal and additionally skeletal scores were recorded pre-slaughter. Carcass weight, kidney and channel fat weight, carcass conformation and fat scores, fat depth over the longissimus dorsi muscle at the 12th (bulls) or 10th (heifers) rib and carcass length were recorded post-slaughter. Each carcass was subsequently dissected into meat, fat and bone using a commercial dissection procedure. Muscular scores taken pre-slaughter showed positive correlations with killing-out rate (r ≈ 0.65), carcass meat proportion (r ≈ 0.60), value (r ≈ 0.55) and conformation score (r ≈ 0.70), and negative correlations with carcass bone (r ≈ -0.60) and fat (r ≈ -0.4) proportions. Corresponding correlations with muscular scores at weaning were lower. Correlations of skeletal scores taken pre-slaughter, carcass length and carcass weight with killing-out rate and the various carcass traits were mainly not significant. Carcass fat depth and kidney and channel fat weight were negatively correlated with carcass meat proportion and value, and positively correlated with fat proportion. Correlations of carcass conformation score were positive (r = 0.50 to 0.68) with killing-out rate, carcass meat proportion and carcass value and negative with bone (r ≈ -0.56) and fat (r ≈ -0.40) proportions. Corresponding correlations with carcass fat score were mainly negative except for carcass fat proportion (r ≈ 0.79). A one-unit (scale 1 to 15) increase in carcass conformation score increased carcass meat proportion by 8.9 and 8.1 g/kg, decreased fat proportion by 4.0 and 2.9 g/kg and decreased bone proportion by 4.9 and 5.2 g/kg in bulls and heifers, respectively. Corresponding values per unit increase in carcass fat score were -11.9 and -9.7 g/kg, 12.4 and 9.9 g/kg, and -0.5 and -0.2 g/kg. Carcass conformation and fat scores explained 0.70 and 0.55 of the total variation in meat yield for bulls and heifers, respectively. It is concluded that live animal muscular scores, and carcass conformation and fat scores, are useful indicators of carcass meat proportion and value.     

Blood parasites in owls with conservation implications for the Spotted Owl (Strix occidentalis)

The three subspecies of Spotted Owl (Northern, Strix occidentalis caurina; California, S. o. occidentalis; and Mexican, S. o. lucida) are all threatened by habitat loss and range expansion of the Barred Owl (S. varia). An unaddressed threat is whether Barred Owls could be a source of novel strains of disease such as avian malaria (Plasmodium spp.) or other blood parasites potentially harmful for Spotted Owls. Although Barred Owls commonly harbor Plasmodium infections, these parasites have not been documented in the Spotted Owl. We screened 111 Spotted Owls, 44 Barred Owls, and 387 owls of nine other species for haemosporidian parasites (Leucocytozoon, Plasmodium, and Haemoproteus spp.). California Spotted Owls had the greatest number of simultaneous multi-species infections (44%). Additionally, sequencing results revealed that the Northern and California Spotted Owl subspecies together had the highest number of Leucocytozoon parasite lineages (n = 17) and unique lineages (n = 12). This high level of sequence diversity is significant because only one Leucocytozoon species (L. danilewskyi) has been accepted as valid among all owls, suggesting that L. danilewskyi is a cryptic species. Furthermore, a Plasmodium parasite was documented in a Northern Spotted Owl for the first time. West Coast Barred Owls had a lower prevalence of infection (15%) when compared to sympatric Spotted Owls (S. o. caurina 52%, S. o. occidentalis 79%) and Barred Owls from the historic range (61%). Consequently, Barred Owls on the West Coast may have a competitive advantage over the potentially immune compromised Spotted Owls.     

Population dynamics, biomass and productivity of Limapontia depressa (Gastropoda, Opisthobranchia) at Bull Island, Dublin, Ireland

Limapontia depressa was present in the saltmarsh pools at Bull Island, Dublin from October to June each year. Numbers peaked in December, with a secondary peak in April, and the maximum density recorded was just under 23000 indiv m^–2. The strong population seasonal cycle was not linked to salinity or chlorophyll-a cycles but did coincide with the drying of the pools. Average production (P) was 233 kJ m^–2 y^–1, with a P:B ratio of just 2:1, which is rather low for such a small animal and may be a function of the low growth rate. These conclusions must be treated with caution due to uncertainty over recruitment mechanisms. Gamete output (G) was calculated at a maximum of 28.6 kJ m^–2 y^–1. This is a higher secondary production than previously reported for saltmarsh herbivores, and may be an important link into the wider estuarine trophic system and a vital food resource for small waders. The low G:P ratio suggests that not all semelparous species necessarily adopt an r-strategy of 'reproductive recklessness'.     

A study on in vitro glycation processes by matrix-assisted laser desorption ionization mass spectrometry

The number of glucose molecules condensed on glycated bovine serum albumin have been easily determined by means of matrix-assisted laser desorption/ionization mass spectrometry. Measurements were carried out on samples from incubation of the proteins with glucose at different concentrations (0.02 M, 0.2 M, 2 M and 5 M). A clear increase in molecular mass of BSA with respect to incubation time is detected. In contrast to what is observed with fluorescence, the plots of molecular mass increase vs. incubation time show tha occurrence of a steady state, corresponding to the complete saturation of all the protein sites against glucose. Comparison of fluorescence and molecular mass data reveals that some further reactions, different from condensation, must take place, which could be in principle either intramolecular or originated by reactivity of modified condensed gluocse moieties vs. free glucose.