Sampling properties of DNA sequence data in phylogenetic analysis

We inferred phylogenetic trees from individual genes and random samples of nucleotides from the mitochondrial genomes of 10 vertebrates and compared the results to those obtained by analyzing the whole genomes. Individual genes are poor samples in that they infrequently lead to the whole-genome tree. A large number of nucleotide sites is needed to exactly determine the whole-genome tree. A relatively small number of sites, however, often results in a tree close to the whole-genome tree. We found that blocks of contiguous sites were less likely to lead to the whole-genome tree than samples composed of sites drawn individually from throughout the genome. Samples of contiguous sites are not representative of the entire genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies.      

Target cell susceptibility to lysis by human natural killer cells is augmented by alpha(1,3)-galactosyltransferase and reduced by alpha(1, 2)-fucosyltransferase

Susceptibility of porcine endothelial cells to human natural killer (NK) cell lysis was found to reflect surface expression of ligands containing Gal alpha(1,3)Gal beta(1,4)GlcNAc [corrected], the principal antigen on porcine endothelium recognized by xenoreactive human antibodies. Genetically modifying expression of this epitope on porcine endothelium by transfection with the alpha(1,2)-fucosyltransferase gene reduced susceptibility to human NK lysis. These results indicate that surface carbohydrate remodeling profoundly affects target cell susceptibility to NK lysis, and suggest that successful transgenic strategies to limit xenograft rejection by NK cells and xenoreactive antibodies will need to incorporate carbohydrate remodeling.     

Some observations on the effect of Daflon (micronized purified flavonoid fraction of Rutaceae aurantiae) in bancroftian filarial lymphoedema

BACKGROUND: Morbidity management is a core component of the global programme for the elimination of lymphatic filariasis. In a double-blind clinical trial, the tolerability and efficacy of Daflon (500 mg) + DEC (25 mg) or DEC (25 mg) alone, twice daily for 90 days, was studied in 26 patients with bancroftian filarial lymphoedema. RESULTS: None of the patients in either drug group reported any adverse reaction throughout the treatment period (90 days). Haematological and biochemical parameters were within normal limits and there was no significant difference between the pre-treatment (day 0) and post-treatment (day 90) values. The group receiving Daflon showed significant reduction in oedema volume from day 90 (140.6 PlusMinus; 18.8 ml) to day 360 (71.8 PlusMinus; 20.7 ml) compared to the pre-treatment (day 0, 198.4 PlusMinus; 16.5 ml) value. This accounted for a 63.8% reduction in oedema volume by day 360 (considering the pre-treatment (day 0) as 100%). In the DEC group, the changes in oedema volume (between day 1 and day 360) were not significant when compared to the pre-treatment (day 0) value. The percentage reduction at day 360 was only 9%, which was not significant (P > 0.05). CONCLUSION: This study has shown that Daflon (500 mg, twice a day for 90 days) is both safe and efficacious in reducing oedema volume in bancroftian filarial lymphoedema. Further clinical trials are essential for strengthening the evidence base on the role of this drug in the morbidity management of lymphatic filariasis.     

Historical Invasion Records Can Be Misleading: Genetic Evidence for Multiple Introductions of Invasive Raccoons (Procyon lotor) in Germany

Biological invasions provide excellent study systems to understand evolutionary, genetic and ecological processes during range expansions. There is strong evidence for positive effects of high propagule pressure and the associated higher genetic diversity on invasion success, but some species have become invasive despite small founder numbers. The raccoon (Procyon lotor) is often considered as a typical example for such a successful invasion resulting from a small number of founders. The species’ largest non-native population in Germany is commonly assumed to stem from a small number of founders and two separate founding events in the 1930s and 1940s. In the present study we analyzed 407 raccoons at 20 microsatellite loci sampled from the invasive range in Western Europe to test if these assumptions are correct. Contrary to the expectations, different genetic clustering methods detected evidence for at least four independent introduction events that gave rise to genetically differentiated subpopulations. Further smaller clusters were either artifacts or resulted from founder events at the range margin and recent release of captive individuals. We also found genetic evidence for on-going introductions of individuals. Furthermore a novel randomization process was used to determine the potential range of founder population size that would suffice to capture all the alleles present in a cluster. Our results falsify the assumption that this species has become widespread and abundant despite being genetically depauperate and show that historical records of species introductions may be misleading.     

Genetic structure inside a declining red oak community in old-growth forest

Problems with oak regeneration have been documented in the last 50 years at numerous sites in the Midwestern United States. We applied nuclear microsatellites to examine the demographic and fine-scale spatial genetic structure of red oaks in two old-growth stands in Indiana. Oaks in one stand have declined in numbers over the past several decades whereas oaks in the other, smaller stand have increased. Large amounts of genetic variation were maintained within stands, and there was slight but significant differentiation among stands. There was significant but weak isolation by distance genetic structure within the large stand, likely reflecting family structure. No significant differences exist in allele frequencies or in levels of genetic diversity between cohorts that remain well represented within each stand, even between medium-sized adults and those antedating European settlement of the area. However, a virtual absence of smaller size classes in the forest interior of the large stand represents the early stages of a genetic bottleneck in what had been the core habitat of this stand. Whether future generations of this old-growth stand will retain the present genetic character depends on the oaks regenerating at the forest margins, absent any major changes in disturbance regimes. Similar demographic and genetic dynamics are likely occurring in a large number of remnant oak forests across the Midwest.     

Social environment affects juvenile dispersal in great tits (Parus major)

1.?Habitat selection can affect individual fitness, and therefore, individuals are expected to assess habitat quality of potential breeding sites before settlement. 2.?We investigated the role of social environment on juvenile dispersal behaviour in the great tit (Parus major). Two main contradictory hypotheses can be formulated regarding social effects on juvenile dispersal as follows: (i) High fledgling density and sex ratio may enhance the intensity of local (kin) competition and, therefore, reduce individual survival chance, enhance emigration and reduce settlement ('repulsion' hypothesis) (ii) Alternatively, high fledgling density and sex ratio may signal high-quality habitat or lead to aggregation and thus increase individual survival chance, reduce emigration and enhance settlement ('attraction' hypothesis). 3.?To disentangle positive from negative effects of high density and male-biased sex ratio on dispersal, we manipulated the social composition of the fledgling population in 12 semi-isolated nest-box areas (plots) via a change of fledgling density (low/high) as well as fledgling sex ratio (female-biased/balanced/male-biased) across 3?years. We then tested whether experimental variation in male and female fledgling densities affected variation in local survival, emigration and settlement of juveniles, and whether social effects on survival and dispersal support the 'repulsion' or 'attraction' hypothesis. 4.?We found no experimental effects on local survival and emigration probabilities. However, consistent with the 'attraction' hypothesis, settlement was significantly and positively affected by local experimental sex ratio in each of the study years: both male and female juveniles avoided female-biased plots and settled more in plots that were balanced and male-biased the previous year. 5.?Our study provides unprecedented experimental evidence that local sex ratio plays a causal role in habitat selection. We suggest that settlers avoid female-biased plots because a high proportion of females may reflect the absence or the low quality of local resources in the habitat. Alternatively, male territory acquisition may be facilitated by a high local density of 'candidate' males, and therefore, juveniles were less successful in settling in female-biased plots.     

Data,Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing

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Highlights

• •In-depth proteomes of 4 SARS-CoV-2 cell line models (Vero E6, Calu-3, Caco-2, A549).
• •Proteomic evidence for thousands of Chlorocebus sabaeus proteins.
• •Proteomic response of Vero E6 cells to SARS-CoV-2 infection.
• •Synthetic peptides, spectral libraries, and targeted assays for SARS-CoV-2 proteins.