Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

Foraminifera have one of the best known fossil records among the unicellular eukaryotes. However, the origin and phylogenetic relationships of the extant foraminiferal lineages are poorly understood. To test the current paleontological hypotheses on evolution of foraminifera, we sequenced about 1,000 base pairs from the 3' end of the small subunit rRNA gene (SSU rDNA) in 22 species representing all major taxonomic groups. Phylogenies were derived using neighbor- joining, maximum-parsimony, and maximum-likelihood methods. All analyses confirm the monophyletic origin of foraminifera. Evolutionary relationships within foraminifera inferred from rDNA sequences, however, depend on the method of tree building and on the choice of analyzed sites. In particular, the position of planktonic foraminifera shows important variations. We have shown that these changes result from the extremely high rate of rDNA evolution in this group. By comparing the number of substitutions with the divergence times inferred from the fossil record, we have estimated that the rate of rDNA evolution in planktonic foraminifera is 50 to 100 times faster than in some benthic foraminifera. The use of the maximum-likelihood method and limitation of analyzed sites to the most conserved parts of the SSU rRNA molecule render molecular and paleontological data generally congruent.      

Successful immunotherapy with matrix metalloproteinase-derived peptides in adjuvant arthritis depends on the timing of peptide administration

We have recently found that matrix metalloproteinases (MMPs) are targets for T-cell and B-cell reactivity in experimental arthritis. In the present article, we investigate whether modulation of MMP-specific T-cell responses could influence the course of adjuvant arthritis (AA). Lewis rats were treated nasally with MMP peptides prior to or after AA induction. Administration of the MMP-10 or the MMP-16 peptide prior to AA induction reduced the arthritic symptoms. In contrast, administration of the MMP-10 peptide after AA induction aggravated the arthritic symptoms. The present study shows the possible usefulness of MMP peptides for immunotherapy. However, a clear understanding of proper timing of peptide administration is crucial for the development of such therapies.     

Trimethyloxonium modification of single batrachotoxin-activated sodium channels in planar bilayers. Changes in unit conductance and in block by saxitoxin and calcium

Single batrachotoxin-activated sodium channels from rat brain were modified by trimethyloxonium (TMO) after incorporation in planar lipid bilayers. TMO modification eliminated saxitoxin (STX) sensitivity, reduced the single channel conductance by 37%, and reduced calcium block of inward sodium currents. These effects always occurred concomitantly, in an all-or-none fashion. Calcium and STX protected sodium channels from TMO modification with potencies similar to their affinities for block. Calcium inhibited STX binding to rat brain membrane vesicles and relieved toxin block of channels in bilayers, apparently by competing with STX for the toxin binding site. These results suggest that toxins, permeant cations, and blocking cations can interact with a common site on the sodium channel near the extracellular surface. It is likely that permeant cations transiently bind to this superficial site, as the first of several steps in passing inward through the channel.     

DNA Is Taken Up by Root Hairs and Pollen,and Stimulates Root and Pollen Tube Growth

Phosphorus (P) enters roots as inorganic phosphate (P_i) derived from organic and inorganic P compounds in the soil. Nucleic acids can support plant growth as the sole source of P in axenic culture but are thought to be converted into P_i by plant-derived nucleases and phosphatases prior to uptake. Here, we show that a nuclease-resistant analog of DNA is taken up by plant cells. Fluorescently labeled S-DNA of 25 bp, which is protected against enzymatic breakdown by its phosphorothioate backbone, was taken up and detected in root cells including root hairs and pollen tubes. These results indicate that current views of plant P acquisition may have to be revised to include uptake of DNA into cells. We further show that addition of DNA to P_i-containing growth medium enhanced the growth of lateral roots and root hairs even though plants were P replete and had similar biomass as plants supplied with P_i only. Exogenously supplied DNA increased length growth of pollen tubes, which were studied because they have similar elongated and polarized growth as root hairs. Our results indicate that DNA is not only taken up and used as a P source by plants, but ironically and independent of P_i supply, DNA also induces morphological changes in roots similar to those observed with P limitation. This study provides, to our knowledge, first evidence that exogenous DNA could act nonspecifically as signaling molecules for root development.Phosphorus (P) is an essential macronutrient that limits plant growth in many situations due to a low availability in soils (for review, see Schachtman et al., 1998; Raghothama, 1999; Vance et al., 2003; Lambers et al., 2008). P enters plant roots as orthophosphates (P_i) via active transport across the plasma membrane (Smith et al., 2003; Park et al., 2007; Xu et al., 2007). Concentrations of P_i in soil solution are generally very low (<10 μm; Bieleski, 1973) and plants have evolved root specializations to access P from inorganic and organic sources (Raghothama, 1999; Hinsinger, 2001; López-Bucio et al., 2003; Vance et al., 2003; Lambers et al., 2008). Roots exude enzymes and chemicals to mobilize P directly from soil compounds or indirectly via enhanced activity of soil microbes, and form symbioses with P-mobilizing mycorrhizal fungi (Schachtman et al., 1998; Raghothama, 1999; Bucher, 2007).However, similar to other nutrients, notably nitrogen, research on P nutrition of plants has focused on inorganic sources although organic P (P_org) in soil can account for 40% to 80% of the total P pool of mineral and organic soils, respectively (Bower, 1945; Raghothama, 1999; Vance et al., 2003). P_org compounds in soils are derived from plant residues, soil biota, and from synthesis by soil microbes (Jencks et al., 1964). Soil P_org is composed primarily of phospholipids, nucleic acids, and phytin (Dyer and Wrenshall, 1941). Phytic acid (inositol hexaphosphate) and its salts phytate, account for a large proportion of the P_org pool of soils (Anderson, 1980). Nucleic acids (RNA, DNA) represent approximately 1% to 2% of the soil P_org pool (Dalal, 1977). It can be released from prokaryotic and eukaryotic cells after death and protected against nuclease degradation by its adsorption on soil colloids and sand particles (Pietramellara et al., 2009).Although P_org can be a substantial constituent of the soil P pool, its contribution to the P nutrition of plants is poorly understood. P_org can be converted to P_i via root-exuded enzymes (Tarafdar and Claassen, 1988; Marschner, 1995; Vance et al., 2003). Secretion of nucleolytic enzymes and breakdown of nucleic acid were considered the reason for the observed growth of axenic Arabidopsis (Arabidopsis thaliana) and wheat (Triticum aestivum) on nucleic acid substrates as the sole P source (Chen et al., 2000; Richardson et al., 2000).Whether plants take up intact DNA has not been reported. We recently showed that roots take up protein, possibly via endocytosis (Paungfoo-Lonhienne et al., 2008). We hypothesized that roots may take up DNA by a similar process and grew Arabidopsis in the presence of phosphorothioate oligonucleotides (S-DNA) labeled with Cy3-fluorescent dye. S-DNA has a sulfur backbone and cannot be digested by plant nucleases, allowing tracking DNA of known size into cells (Spitzer and Eckstein, 1988). We examined if S-DNA of 25 nucleotides in length enters root hairs and pollen tubes as both types of cells are strongly elongated and have similar polarized growth (Schiefelbein et al., 1993; Hepler et al., 2001). We also assessed if addition of DNA to the growth medium affects the morphology of roots and pollen tubes. Here, we present evidence that plants take up DNA and demonstrate that the presence of DNA in the growth medium enhances lateral branching of roots, and the length of root hairs and pollen tubes, irrespective of P_i supply.     

Genome-wide association genetics of an adaptive trait in lodgepole pine

Pine cones that remain closed and retain seeds until fire causes the cones to open (cone serotiny) represent a key adaptive trait in a variety of pine species. In lodgepole pine, there is substantial geographical variation in serotiny across the Rocky Mountain region. This variation in serotiny has evolved as a result of geographically divergent selection, with consequences that extend to forest communities and ecosystems. An understanding of the genetic architecture of this trait is of interest owing to the wide-reaching ecological consequences of serotiny and also because of the repeated evolution of the trait across the genus. Here, we present and utilize an inexpensive and time-effective method for generating population genomic data. The method uses restriction enzymes and PCR amplification to generate a library of fragments that can be sequenced with a high level of multiplexing. We obtained data for more than 95,000 single nucleotide polymorphisms across 98 serotinous and nonserotinous lodgepole pines from three populations. We used a Bayesian generalized linear model (GLM) to test for an association between genotypic variation at these loci and serotiny. The probability of serotiny varied by genotype at 11 loci, and the association between genotype and serotiny at these loci was consistent in each of the three populations of pines. Genetic variation across these 11 loci explained 50% of the phenotypic variation in serotiny. Our results provide a first genome-wide association map of serotiny in pines and demonstrate an inexpensive and efficient method for generating population genomic data.     

Portable light transmission measuring system for preserved corneas

Background  

The authors have developed a small portable device for the objective measurement of the transparency of corneas stored in preservative medium, for use by eye banks in evaluation prior to transplantation.     

Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.     

Soybean genomic survey: BAC-end sequences near RFLP and SSR markers.

We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs (bacterial artificial chromosomes) from two soybean BAC libraries. The libraries were prepared from two genotypes, each digested with a different restriction enzyme. The BACs identified by each marker were grouped into contigs. We have obtained BAC- end sequence from BACs within each contig. The sequences were analyzed by the University of Minnesota Center for Computational Genomics and Bioinformatics using BLAST algorithms to search nucleotide and protein databases. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was due to a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs that was offset in part, however, by a somewhat larger proportion of RFLP-identified significant hits with similarity to experimentally defined genes and soybean ESTs (expressed sequence tags). These genes represented a wide range of metabolic functions. In these analyses, only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC-end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. This map-based approach to genome sampling provides a means of assaying soybean genome structure and organization.