Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> and <Emphasis Type="Italic">Arabidopsis lyrata</Emphasis>

Background  

There has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because orthology is difficult to establish. Orthology is even more problematic for intergenic regions of plant nuclear genomes, because plant genomes generally harbor a wealth of repetitive DNA. In theory orthologous intergenic data is valuable for studying rate variation because nucleotide substitutions in these regions should be under little selective constraint compared to coding regions. As a result, evolutionary rates in intergenic regions may more accurately reflect genomic features, like recombination and GC content, that contribute to nucleotide substitution.     

Disparate Postnatal Ontogenies Do Not Add to the Shape Disparity of Infants

Integrating studies of ontogeny with analyses of disparity can reveal important and surprising insights into the origins of disparity and why it varies among groups. One such potentially surprising insight is that disparity could be constant over ontogeny even though species differ in both rates and timings of development and in their ontogenetic changes in shape. Several studies of both primates and rodents have concluded that disparity is generated prenatally although some have concluded that it arises postnatally. However, neither constancy nor an ontogenetic increase in disparity has been ever been rigorously documented for either primates or rodents. For a small sample of rodents, we show that species differ in their postnatal ontogenies but infants are neither more nor less disparate than adults and the major dimensions of disparity distinguishing the main clades also do not change. The constancy in both the level of disparity and its main dimensions does not result primarily from the subtlety of postnatal differences. Those differences are indeed subtle but the disparity in directions of ontogenetic shape change is nonetheless sufficient to increase shape disparity significantly. Disparity does not increase postnatally primarily because ontogenies are not strictly linear; disparity generated postnatally counteracts that produced earlier. What limits the progressive accumulation of disparity is the curvature of ontogenetic trajectories, a curvature presumably due to ontogenetic changes in the spatial distribution of rates of bone deposition and resorption.     

The Effects of Elevated Specific Conductivity on the Chronic Toxicity of Mining Influenced Streams Using Ceriodaphnia dubia

Salinization of freshwater ecosystems as a result of human activities has markedly increased in recent years. Much attention is currently directed at evaluating the effects of increased salinity on freshwater biota. In the Central Appalachian region of the eastern United States, specific conductance from alkaline discharges associated with mountain top mining practices has been implicated in macroinvertebrate community declines in streams receiving coal mining discharges. Whole effluent toxicity testing of receiving stream water was used to test the hypothesis that mine discharges are toxic to laboratory test organisms and further, that toxicity is related to ionic concentrations as indicated by conductivity. Chronic toxicity testing using Ceriodaphnia dubia was conducted by contract laboratories at 72 sites with a total of 129 tests over a 3.5 year period. The database was evaluated to determine the ionic composition of mine effluent dominated streams and whether discharge constituents were related to toxicity in C. dubia. As expected, sulfate was found to be the dominant anion in streams receiving mining discharges with bicarbonate variable and sometimes a substantial component of the dissolved solids. Overall, the temporal variability in conductance was low at each site which would indicate fairly stable water quality conditions. Results of the toxicity tests show no relationship between conductance and survival of C. dubia in the mining influenced streams with the traditional toxicity test endpoints. However, consideration of the entire dataset revealed a significant inverse relationship between conductivity and neonate production. While conductivity explained very little of the high variability in the offspring production (r² = 0.1304), the average numbers of offspring were consistently less than 20 neonates at the highest conductivities.     

Contrasting two methods for determining trace metal partitioning in oxidized lake sediments

A simultaneous (SIM) sediment extraction procedure for low carbonate sediments, which partitions sediment-bound trace metals (Fe, Mn, Zn, Cu, and Cd) into easily reducible (associated with Mn oxides), reducible (associated with Fe oxides) and alkaline extracted (bound to organic) metal is presented. The SIM method was compared to the sequential (SEQ) extraction procedure of Tessier et al. (1979). Both methods showed good agreement for the partitioning of Zn and Cd among the easily reducible, reducible and organic components of sediment. Both methods also showed the same general distribution of Mn, Fe and Cu among the three sediment components, however concentrations of metals recovered by the two methods differed; less Mn and Fe and more Cu was recovered from sediments by the SEQ vs. the SIM procedure. Less recovery of Mn is in part attributed to the loss of this metal in the `in between' reagent rinses required in the SEQ procedure. Greater recovery of Cu by the SEQ vs. the SIM method may be due to the pretreatment of sediment with strong reducing agents prior to the step used for liberating organically bound metals. Advantages of a SIM over the SEQ include rapid sample processing time (i.e. the treatment of 40 samples per day vs. 40 samples in three days), plus minimal sample manipulation. Hence, for partitioning metals into easily reducible, reducible and organic sediment components in sediments low in carbonate, we recommend the use of a SIM extraction over that of a SEQ procedure.     

Regulation of organelle transport: Lessons from color change in fish

Organelles transported along microtubules are normally moved to precise locations within cells. For example, synaptic vesiceles are transported to the neruronal synapse, the Golgi apparatus is generally found in a perinuclear location, and the membranes of the endoplasmic reticulum are actively extended to the cell periphery. The correct positioning of these organelles depends on microtubules and microtubule motors. Melanophores provide an extreme example of organized organelle transport. These cells are specialized to transport pigment granules, which are coordinately moved towards or away from the cell center, and result in the cell appearing alternately light or dark. Melanophores have proved to be an ideal system for studying the mechanisms by which the cell controls the direction of its organelle transport. Pigment granule dispersion (the movement away from the cell center) requires protein phosphorylation, while pigment aggregation (the movement towards the cell center) requires protein dephosphorylation. The target of this phosphorylation and dephosphorylation event is a protein that interacts with the microtubule motor protein, kinesin. Thus, the direction of organelle transport along microtubules may be regulated by controlling the activity of a microtubule motor.     

Large-scale expansion of feeder-free mouse embryonic stem cells serially passaged in stirred suspension bioreactors at low inoculation densities directly from cryopreservation

Embryonic stem cells (ESCs) have almost unlimited proliferation capacity in vitro and can retain the ability to contribute to all cell lineages, making them an ideal platform material for cell-based therapies. ESCs are traditionally cultured in static flasks on a feeder layer of murine embryonic fibroblast cells. Although sufficient to generate cells for research purposes, this approach is impractical to achieve large quantities for clinical applications. In this study, we have developed protocols that address a variety of challenges that currently bottleneck clinical translation of ESCs expanded in stirred suspension bioreactors. We demonstrated that mouse ESCs (mESCs) cryopreserved in the absence of feeder cells could be thawed directly into stirred suspension bioreactors at extremely low inoculation densities (100 cells/ml). These cells sustained proliferative capacity through multiple passages and various reactor sizes and geometries, producing clinically relevant numbers (10⁹ cells) and maintaining pluripotency phenotypic and functional properties. Passages were completed in stirred suspension bioreactors of increasing scale, under defined batch conditions which greatly improved resource efficiency. Output mESCs were analyzed for pluripotency marker expression (SSEA-1, SOX-2, and Nanog) through flow cytometry, and spontaneous differentiation and teratoma analysis was used to demonstrate functional maintenance of pluripotency.     

Adhesion of anaerobic microorganisms to solid surfaces and the effect of sequential attachment on adhesion characteristics

The attachment of three anaerobic microorganisms, Desulfomonile tiedjei, Syntrophomonas wolfei, and Desulfovibrio sp. strain G11, was investigated to determine if the presence of one species could influence the adhesion of another species to glass surfaces. The results indicated that the numbers and distribution of attached cells of one species could be influenced considerably by the presence of another species and the order in which the test species were exposed to the surface. D. tiedjei was found to detach readily from surfaces when it was not the primary colonizer. The attachment of Desulfovibrio G11 as the primary colonizer appeared to be stabilized by exposure to another test species. Under certain experimental conditions the test organisms formed close associations with each other on the surfaces. These findings demonstrate that the characteristics of anaerobic community biofilms can be determined by both the adhesion characteristics of the individual species and the interactions among those microorganisms.