OCTAL: Optimal Completion of gene trees in polynomial time

Background

For a combination of reasons (including data generation protocols, approaches to taxon and gene sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they do not contain all of the species of interest. As incomplete gene trees can impact downstream analyses, accurate completion of gene trees is desirable.

Results

We introduce the Optimal Tree Completion problem, a general optimization problem that involves completing an unrooted binary tree (i.e., adding missing leaves) so as to minimize its distance from a reference tree on a superset of the leaves. We present OCTAL, an algorithm that finds an optimal solution to this problem when the distance between trees is defined using the Robinson–Foulds (RF) distance, and we prove that OCTAL runs in \(O(n^2)\) time, where n is the total number of species. We report on a simulation study in which gene trees can differ from the species tree due to incomplete lineage sorting, and estimated gene trees are completed using OCTAL with a reference tree based on a species tree estimated from the multi-locus dataset. OCTAL produces completed gene trees that are closer to the true gene trees than an existing heuristic approach in ASTRAL-II, but the accuracy of a completed gene tree computed by OCTAL depends on how topologically similar the reference tree (typically an estimated species tree) is to the true gene tree.

Conclusions

OCTAL is a useful technique for adding missing taxa to incomplete gene trees and provides good accuracy under a wide range of model conditions. However, results show that OCTAL’s accuracy can be reduced when incomplete lineage sorting is high, as the reference tree can be far from the true gene tree. Hence, this study suggests that OCTAL would benefit from using other types of reference trees instead of species trees when there are large topological distances between true gene trees and species trees.

     

A multiplatform strategy for the discovery of conventional monoclonal antibodies that inhibit the voltage-gated potassium channel Kv1.3

Identifying monoclonal antibodies that block human voltage-gated ion channels (VGICs) is a challenging endeavor exacerbated by difficulties in producing recombinant ion channel proteins in amounts that support drug discovery programs. We have developed a general strategy to address this challenge by combining high-level expression of recombinant VGICs in Tetrahymena thermophila with immunization of phylogenetically diverse species and unique screening tools that allow deep-mining for antibodies that could potentially bind functionally important regions of the protein. Using this approach, we targeted human Kv1.3, a voltage-gated potassium channel widely recognized as a therapeutic target for the treatment of a variety of T-cell mediated autoimmune diseases. Recombinant Kv1.3 was used to generate and recover 69 full-length anti-Kv1.3 mAbs from immunized chickens and llamas, of which 10 were able to inhibit Kv1.3 current. Select antibodies were shown to be potent (IC₅₀<10 nM) and specific for Kv1.3 over related Kv1 family members, hERG and hNav1.5.     

Distribution of parvalbumin isotypes in adult snook and their potential applications as species-specific biomarkers

The highly stable Ca²⁺ binding protein, parvalbumin, is prevalent in fish white muscle tissue. The properties of this protein make it a promising antigen for use as a specific biomarker for fish identification. Parvalbumin was purified from white muscle of an adult common snook Centropomus undecimalis using ammonium sulfate precipitation, size-exclusion chromatography (SEC) and anion-exchange HPLC. Parvalbumins were characterized by the presence of an 11-kDa band following gradient-SDS gel electrophoresis and by their immunoreactivity against mouse anti-parvalbumin antibodies. Anion-exchange chromatography of the parvalbumin fraction separated from the SEC column yielded nine fractions. Subsequent analysis of these fractions by isoelectric focusing gel electrophoresis led to a total of seven parvalbumin isotypes, which may lend themselves as biomarkers in fish identification. The presence of these seven parvalbumin isotypes was confirmed independently by reversed-phase HPLC. A dilution endpoint immunoassay was developed for C. undecimalis parvalbumin using a monoclonal antibody directed against its highly conserved calcium binding site. The utility of parvalbumin isotype distribution and specific monoclonal antibodies against fish parvalbumin in species identification is discussed.     

Lymphocyte norepinephrine and epinephrine as indices of long-term changes in sympathoadrenal activity in human subjects

Researchers propose that long-term changes in sympathoadrenal activity during space flight can be evaluated by lymphocyte norepinephrine measurements in the early post-flight period. The metabolism of thrombocyte and lymphocyte catecholamines is explored to support the hypothesis.     

Physiological (antioxidant) responses of estuarine fishes to variability in dissolved oxygen

Cycles of dissolved oxygen (DO) in estuaries can range from anoxia to various levels of supersaturation (200–300%) over short time periods. Aerobic metabolism causes formation of damaging reactive oxygen species (ROS), a process exacerbated by high or low DO. Fish can generate physiological defenses (e.g. antioxidant enzymes) against ROS, however, there are little data tying this to environmental conditions. We investigated physiological defenses generated by estuarine fishes in response to high DO and various DO cycles. We hypothesized that chemical defenses and/or oxidative damage are related to patterns of DO supersaturation. Specific activities of antioxidants in fish tissues should be positively correlated with increasing levels of DO, if high DO levels are physiologically stressful. We caged common benthic fishes (longjaw mudsucker, Gillichthysmirabilis, and staghorn sculpin, Leptocottusarmatus, in CA and spot, Leiostomusxanthurus and pinfish, Lagodonrhomboides, in NC) during summer 1998 in two estuarine sites in southern North Carolina and two in central California. At each site a water quality meter measured bottom DO, salinity, temperature, depth, pH and turbidity at 30 min intervals throughout the study. These sites exhibited a wide variety of dissolved oxygen patterns. After 2 weeks in the cages, fish gills and livers were analyzed for antioxidant enzymes (glutathione peroxidase, catalase and superoxide dismutase) and the metabolite glutathione. All fish exhibited antioxidant enzyme activity. There was a significant site-dependent effect on all enzyme activities at the NC sites, with the most activity at the site with the highest DO cycling and the most DO supersaturation. There was a trend towards higher enzyme activities under high DO levels at the CA sites.     

Flow cytometry and sorting of meiotic prophase cells of female rabbits

We present a new, flow cytometric method by which cells in various stages of the meiotic prophase can be quantitated and sorted in partly enriched fractions. Ovarian cells of 3-16-day-old rabbits were mechanically dispersed and fixed in ethanol and aldehydes. The cell suspension was stained with the DNA fluorochrome mithramycin and analysed and sorted in a FACS IV cell sorter according to the fluorescence and forward light scatter distribution. Cells sorted onto slides were stained with haematoxylin and eosin and differentially counted in the microscope. In the diploid fraction, preleptotene cells were more fluorescent than somatic cells. Leptotene cells were found throughout the S fraction and the tetraploid fraction. Zygotene and pachytene cells caused a major peak in the tetraploid region with 10-25% more fluorescence than somatic cells. Cells in diplotene had 5-15% more fluorescence than somatic cells. Mitotic cells were 20-40% more fluorescent than somatic cells and scattered the light more intensely than did meiotic cells with the same fluorescence.     

Effect on Young Swine of Consumption of Rations Containing Corn Invaded by Fusarium roseum

Both male and female pigs given a ration containing corn invaded by Fusarium roseum, in amounts sufficient to provide 500 to 600 ppm of F-2, for the first 64 days of the test and which for another 60 days were given a commercial pig ration were much lower in weight than the controls which were given a commercial pig ration throughout. In relation to the weight of the animals, in the pigs receiving the ration containing F-2, the weight of the uterine horn of the gilts was much greater and the weight of the testes of the males was much less than the weight of the same organs of the controls.