Phylogeny of parasitic parabasalia and free-living relatives inferred from conventional markers vs. Rpb1, a single-copy gene

Background

Parabasalia are single-celled eukaryotes (protists) that are mainly comprised of endosymbionts of termites and wood roaches, intestinal commensals, human or veterinary parasites, and free-living species. Phylogenetic comparisons of parabasalids are typically based upon morphological characters and 18S ribosomal RNA gene sequence data (rDNA), while biochemical or molecular studies of parabasalids are limited to a few axenically cultivable parasites. These previous analyses and other studies based on PCR amplification of duplicated protein-coding genes are unable to fully resolve the evolutionary relationships of parabasalids. As a result, genetic studies of Parabasalia lag behind other organisms.

Principal Findings

Comparing parabasalid EF1α, α-tubulin, enolase and MDH protein-coding genes with information from the Trichomonas vaginalis genome reveals difficulty in resolving the history of species or isolates apart from duplicated genes. A conserved single-copy gene encodes the largest subunit of RNA polymerase II (Rpb1) in T. vaginalis and other eukaryotes. Here we directly sequenced Rpb1 degenerate PCR products from 10 parabasalid genera, including several T. vaginalis isolates and avian isolates, and compared these data by phylogenetic analyses. Rpb1 genes from parabasalids, diplomonads, Parabodo, Diplonema and Percolomonas were all intronless, unlike intron-rich homologs in Naegleria, Jakoba and Malawimonas.

Conclusions/Significance

The phylogeny of Rpb1 from parasitic and free-living parabasalids, and conserved Rpb1 insertions, support Trichomonadea, Tritrichomonadea, and Hypotrichomonadea as monophyletic groups. These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data. The Rpb1 phylogenetic tree also resolves species- and isolate-level relationships. These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia.     

Test of the principle of initial value in rat genetic models of exercise capacity

An inverse relationship between initial level of physical capacity and the magnitude of response to training is termed the principle of initial value. We tested the operation of this principle under experimental conditions of minimal genetic and environmental variation. Inbred rat strains previously identified as genetic models of low [Copenhagen (COP)] and high [Dark Agouti (DA)] intrinsic (untrained) exercise capacity were trained for 8 wk on a treadmill using two disparate protocols: 1) a relative mode where each rat exercised daily according to its initial capacity, and 2) an absolute mode where both strains received the same amount of training independent of initial capacity. Response to exercise was the change in running capacity as estimated by meters run to exhaustion before and after training. When trained with the relative mode, COP rats gained 88 m (+21%; NS) whereas DA rats increased distance run by 228 m (+36%; P < 0.001). When each strain trained with the same absolute amount of training, the COP strain showed essentially no change (-6 m, -2%) and the DA strain gained 325 m (+49%; P < 0.009). Differences in response to exercise between the COP and DA could not be explained by body mass differences, oxidative enzyme activity (citrate synthase or ATP), or spontaneous behavioral activity. Our data demonstrate that genetic factors causative of high response to exercise are not uniquely associated with genetic factors for low intrinsic capacity and thus are not in accord with the principle of initial value.     

Coincidence detection in phosphoinositide signaling

Phosphoinositide lipids function as both signaling molecules and as compartment-specific localization signals for phosphoinositide-binding proteins. In recent years, both phosphoinositides and phosphoinositide-binding proteins have been reported to display a restricted, rather than a uniform, distribution across intracellular membranes. Here, we examine recent data documenting the restricted distribution of both phosphoinositides and phosphoinositide-binding proteins and examine how phosphoinositide-binding proteins might engage multiple binding partners to achieve these restricted localizations, effectively acting as detectors of coincident localization signals.     

Phytoplankton and zooplankton as indicators of water quality in Discovery Bay,Jamaica

Several investigations exist which use planktonic communities as indicators of water quality in Jamaican and Caribbean Bays, however, few are conducted before there are obvious effects of eutrophication. Therefore, most of our ‘baseline’ data are for bays already severely affected by pollution. This study was conducted to assess water quality in Discovery Bay, Jamaica, before there were severe signs of eutrophication. The bay was monitored over a 12-month period (October 1995–September 1996) using 10 stations. Physicochemical data indicated a well mixed upper 5 m of water column, below which discontinuities in temperature/salinity profiles indicated the influence of colder, more saline waters associated with deep offshore currents. Physicochemical variables were within the range for oligotrophic systems with a tendency towards mesotrophic in localized areas close to the shoreline. Signs of anthropogenic stress were associated with the eastern, southwestern and western sections of the bay. Of the over 120 species of phytoplankton found in the waters of Discovery Bay, most were neritic/oceanic and diatoms dominated while 11 were found to be potentially harmful species. While these harmful species occurred at all stations they occurred most frequently at stations on the eastern side of the bay. About 107 zooplankton species were identified, 52 of which were copepods. The species also represented a mix of neritic and oceanic taxa and mean abundances for the area ranged from 1077 m⁻³ at the mouth of the bay to 3794 m⁻³ close to the south shore (station 6). Generally stations closest to shore had greater zooplankton abundances than centrally located bay stations and stations close to oceanic influence. Acartia tonsa and Lucifer faxoni showed greatest densities at shoreline areas of the bay while Oithona plumifera, Undinula vulgaris and Temora stylifera were important at stations closest to oceanic influences. These species were thus considered as indicators of these different areas within the bay. From physicochemical data and the planktonic assemblage, Discovery Bay cannot be considered polluted, it is still more accurately classified as generally pristine with mesotrophic zones in the eastern and southeastern sections of the bay. These data therefore provide a real baseline of conditions for similar tropical coastal embayments.     

Sorting nexins--unifying trends and new perspectives

The sorting nexins (SNXs) are a family of PX domain-containing proteins found in yeast and mammalian cells that have been proposed to regulate intracellular trafficking. Mammalian SNXs have been suggested to function variously in pro-degradative sorting, internalization, endosomal recycling, or simply in endosomal sorting. In yeast, the defining function for these proteins is a regulation of cargo retrieval. Here we examine recent data on the SNX family of proteins and attempt to draw out unifying themes between the work performed in yeast and mammalian systems.     

Photobiomodulation directly benefits primary neurons functionally inactivated by toxins: role of cytochrome c oxidase

Far red and near infrared (NIR) light promotes wound healing, but the mechanism is poorly understood. Our previous studies using 670 nm light-emitting diode (LED) arrays suggest that cytochrome c oxidase, a photoacceptor in the NIR range, plays an important role in therapeutic photobiomodulation. If this is true, then an irreversible inhibitor of cytochrome c oxidase, potassium cyanide (KCN), should compete with LED and reduce its beneficial effects. This hypothesis was tested on primary cultured neurons. LED treatment partially restored enzyme activity blocked by 10-100 microm KCN. It significantly reduced neuronal cell death induced by 300 microm KCN from 83.6 to 43.5%. However, at 1-100 mm KCN, the protective effects of LED decreased, and neuronal deaths increased. LED significantly restored neuronal ATP content only at 10 microm KCN but not at higher concentrations of KCN tested. Pretreatment with LED enhanced efficacy of LED during exposure to 10 or 100 microm KCN but did not restore enzyme activity to control levels. In contrast, LED was able to completely reverse the detrimental effect of tetrodotoxin, which only indirectly down-regulated enzyme levels. Among the wavelengths tested (670, 728, 770, 830, and 880 nm), the most effective ones (830 nm, 670 nm) paralleled the NIR absorption spectrum of oxidized cytochrome c oxidase, whereas the least effective wavelength, 728 nm, did not. The results are consistent with our hypothesis that the mechanism of photobiomodulation involves the up-regulation of cytochrome c oxidase, leading to increased energy metabolism in neurons functionally inactivated by toxins.