Background: The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity.

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BackgroundAnthocyanin pigments aid in reproduction and provide ultraviolet protection to land plants. We have examined the phylogenetic relationships among the five primary enzymes responsible for producing anthocyanin pigment in its three major forms. Dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), Flavonoid 3’glucosyltransferase (F3GT), flavonoid 3’hydroxylase (F3’H), and flavonoid 3’5’ hydroxylase (F3’5’H) are responsible for the final steps in anthocyanin pigment production.ResultsWe were interested in how conserved the anthocyanin pathway genes may be among land plants, and evolutionarily how far back into the plant lineage anthocyanin production may be traced. The DFR, ANS, F3GT, and F3’H genes date back 450 million years to the first land plants. Mosses, spike mosses, and ferns express these four products, although there is no evidence of sequence orthologues for these genes in algae. Additionally, F3’5’H is not evident in organisms that predated gymnosperms.ConclusionOur findings support the hypothesis that “blue” anthocyanin pigments did not evolve until 300-350 mya along with the gymnosperms, although the “red” anthocyanin pigments may be as ancient as the mosses (~450 mya).Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-55-10) contains supplementary material, which is available to authorized users.

This study investigates how the ILR1-like indole acetic acid (IAA) amidohydrolase family of genes has functionally evolved in the monocotyledonous species wheat (Triticum aestivum). An ortholog for the Arabidopsis IAR3 auxin amidohydrolase gene has been isolated from wheat (TaIAR3). The TaIAR3 protein hydrolyzes negligible levels of IAA-Ala and no other IAA amino acid conjugates tested, unlike its ortholog IAR3. Instead, TaIAR3 has low specificity for the ester conjugates IAA-Glc and IAAmyoinositol and high specificity for the conjugates of indole-3-butyric acid (IBA-Ala and IBA-Gly) and indole-3-propionic-acid (IPA-Ala) so far tested. TaIAR3 did not convert the methyl esters of the IBA conjugates with Ala and Gly. IBA and IBA conjugates were detected in wheat seedlings by gas chromatography-mass spectrometry, where the conjugate of IBA with Ala may serve as a natural substrate for this enzyme. Endogenous IPA and IPA conjugates were not detected in the seedlings. Additionally, crude protein extracts of wheat seedlings possess auxin amidohydrolase activity. Temporal expression studies of TaIAR3 indicate that the transcript is initially expressed at day 1 after germination. Expression decreases through days 2, 5, 10, 15, and 20. Spatial expression studies found similar levels of expression throughout all wheat tissues examined.In vascular plants, auxins, primarily indole-3-acetic acid (IAA), regulate gene expression, cell division, and cell elongation and differentiation in plant tissue. Auxins also affect vascularization, phototropism, geotropism, fruit development, flower development, and apical dominance (Davies, 1995). While IAA in low concentrations stimulates growth and development, higher concentrations can be toxic to the plant (Bandurski et al., 1995). Therefore, tight control of IAA concentration is necessary for proper plant development.IAA is stored in conjugated forms that are mostly considered to be inactive. Two main types of conjugated molecules have been studied: the amide-linked IAA forms bound to one or more amino acids and the ester-linked forms primarily bound to a sugar(s). These two types of conjugates appear to be found at varying concentrations in the diverse tissues of angiosperms (Domagalski et al., 1987). On average, 95% of all IAA in a plant is conjugated into these storage forms (Cohen and Bandurski, 1982;Bandurski et al., 1995;Campanella et al., 1996;Walz et al., 2002).There have been a variety of amide conjugates found in the plants studied to date. IAA-Asp has been identified as a natural conjugate in Scots pine (Pinus sylvestris; Andersson and Sandberg, 1982) and, together with IAA-Glu, in cucumber (Sonner and Purves, 1985) and soybean (Cohen, 1982). IAA-Ala has been detected in Picea abies Karst (Ö stin et al., 1992). Additionally, IAA-Ala, IAA-Asp, IAA-Leu, and IAA-Glu have been detected in Arabidopsis L. Heynh (Tam et al., 2000;Kowalczyk and Sandberg, 2001), although recent data suggest that IAA peptides may account for the majority of amide conjugates in this and other plant ...

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Within Barnegat Bay, New Jersey, Zostera marina populations have declined by 62% over the last 20 years, and restoration efforts have met with mixed success. We have completed a microsatellite-based genetic investigation of eight populations of Z. marina within Barnegat Bay to determine whether the genetic stock origins of the plants used in management projects may affect restoration success. Additionally, we assessed the genetic diversity of Z. marina in Barnegat Bay to better understand its population structure. Clonal diversity ranged from 0.70 to 0.95 for the populations studied. Individually, Barnegat Bay populations are not genetically diverse, and there is also little divergence among populations. The Atlantic populations had mean Hobs values (0.20-0.34) that were far lower than the Hexp values (0.69-0.83). Also, the F IS values in all of the eastern populations indicate a surfeit of homozygotes over heterozygotes, suggesting a low degree of outcrossing in the Barnegat Bay populations. Six of the ten populations studied (Ham Island, Manahawkin Bay, Shelter Island, Marsh Elder, Harvey Cedar Sedge, and Long Island) show evidence of historical bottlenecks. Mean estimated F ST values would suggest that most alleles are undergoing moderate genetic differentiation, with values that range from 0.06 to 0.13. Oyster Creek and Sedge Island demonstrate the largest estimated effective population sizes and may be the most appropriate populations for use in future eelgrass restoration projects.

The ILR1-like family of hydrolase genes was initially isolated in Arabidopsis thaliana and is thought to help regulate levels of free indole-3-acetic-acid.We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve orthologous genes. The relationships among these sequences were assessed employing phylogenomic analyses to examine molecular evolution and phylogeny. The members of the ILR1-like family analysed were ILL1, ILL2, ILL3, ILL6, ILR1 and IAR3. Present evidence suggests that IAR3 has undergone the least evolution and is most conserved. This conclusion is based on IAR3 having the largest number of total interspecific orthologues, orthologous species and unique orthologues. Although less conserved than IAR3, DNA and protein sequence analyses of ILL1 and ILR1 suggest high conservation. Based on this conservation, IAR3, ILL1 and ILR1 may have had major roles in the physiological evolution of ‘higher’ plants. ILL3 is least conserved, with the fewest orthologous species and orthologues. The monocotyledonous orthologues for most family-members examined have evolved into two separate molecular clades from dicotyledons, indicating active evolutionary change. The monocotyledon clades are: (a) those possessing a putative endoplasmic reticulum localizing signal; and (b) those that are putative cytoplasmic hydrolases. IAR3, ILL1 and ILL6 are all highly orthologous to a gene in the gymnosperm Pinus taeda, indicating an ancient enzymatic activity. No orthologues could be detected in Chlamydomonas, moss and fern databases.

The roles of conductivity and structure in the reversibility, rate capability, capacity and capacity retention of nickel oxide anodes for lithium-ion batteries were investigated.Conductivity was controlled by the systematic addition of non-intercalating carbon. The NiO nanostructure was controlled through four different preparation procedures. Overall, the topperforming electrodes were made from tetrahedral-shaped particles with a broad particle size distribution that were derived from a simple direct calcination of nickel nitrate salt. Capacity values >700 mAh/g after 100 cycles at 1C were observed, and a rate capability >400 mAh/g at 5C was achieved for electrodes with 40% carbon added. The addition of carbon universally improved anode performance by influencing the charge transferability, as evidenced by SEI peak shifts and reduced resistances seen via EIS. Reversibility was greatly enhanced by the impartation of conductivity which enabled otherwise inactive anode particles to maintain activity after many cycles. This work suggests that improved conductivity, as opposed to the conventional opinion regarding nanostructure, is the key to creating high performance anodes for next generation lithium-ion batteries.