Spruce proteome DB: a resource for conifer proteomics research

Proteomics research is hampered in many organisms due to a lack of an appropriate reference genome sequence that can be used in the interpretation of tandem mass spectrometry data for the identification of proteins. Public DNA sequence repositories have grown to considerable size and can, in most cases, serve to provide at least partial interpretation of a large-scale proteomics dataset. However, when species-specific sequences or sequences from a closely related species are available, a boutique sequence database can provide considerable increases in specificity, confidence, and completeness of protein identification. Here, we describe the development of a protein database from a large-scale expressed sequence tag and full-length complementary DNA sequencing project in the economically and ecologically important spruce (Picea) genus.     

The larval legacy: cascading effects of recruit phenotype on post‐recruitment interactions

For organisms with complex life‐cycles, the abundance of individuals in a given stage is driven by the quantity of individuals in the previous stage. The successful recruitment of juveniles to adult populations is, however, the product of both recruit quantity and quality. Previous studies on recruit quality have revealed that better quality individuals have higher growth and survival, yet few studies have considered how recruit quality and quantity interact. In a sessile marine invertebrate, we experimentally tested whether the larval food environment causes variation in recruit quality and affects post‐metamorphic performance. We found that larvae that were fed higher concentrations of phytoplankton had higher survivorship, but that this higher survivorship meant recruit density was higher in this treatment, intensified intraspecific competition and lowered post‐metamorphic growth. Our results highlight the complex repercussions that the presence of phenotypic links among life‐history stages can have for population dynamics and the interdependence of pre‐and post‐recruitment processes in shaping populations. Overall, we suggest that pre‐recruitment events can shape the post‐recruitment environment independently of recruit number.     

Glycosylation site-targeted PEGylation of glucose oxidase retains native enzymatic activity

Targeted PEGylation of glucose oxidase at its glycosylation sites was investigated to determine the effect on enzymatic activity, as well as the bioconjugate's potential in an optical biosensing assay. Methoxy-poly(ethylene glycol)-hydrazide (4.5 kDa) was covalently coupled to periodate-oxidized glycosylation sites of glucose oxidase from Aspergillus niger. The bioconjugate was characterized using gel electrophoresis, liquid chromatography, mass spectrometry, and dynamic light scattering. Gel electrophoresis data showed that the PEGylation protocol resulted in a drastic increase (ca. 100 kDa) in the apparent molecular mass of the protein subunit, with complete conversion to the bioconjugate; liquid chromatography data corroborated this large increase in molecular size. Mass spectrometry data proved that the extent of PEGylation was six poly(ethylene glycol) chains per glucose oxidase dimer. Dynamic light scattering data indicated the absence of higher-order oligomers in the PEGylated GOx sample. To assess stability, enzymatic activity assays were performed in triplicate at multiple time points over the course of 29 days in the absence of glucose, as well as before and after exposure to 5% w/v glucose for 24 h. At a confidence level of 95%, the bioconjugate's performance was statistically equivalent to native glucose oxidase in terms of activity retention over the 29 day time period, as well as following the 24 h glucose exposure. Finally, the bioconjugate was entrapped within a poly(2-hydroxyethyl methacrylate) hydrogel containing an oxygen-sensitive phosphor, and the construct was shown to respond approximately linearly with a 220 ± 73% signal change (n = 4, 95% confidence interval) over the physiologically-relevant glucose range (i.e., 0–400 mg/dL); to our knowledge, this represents the first demonstration of PEGylated glucose oxidase incorporated into an optical biosensing assay.     

Modification of genital kidney nephrons for sperm transport in a plethodontid salamander,Eurycea longicauda

Salamanders possess kidneys with two distinct regions: a caudal pelvic portion and cranial genital portion. Nephrons of the pelvic region are responsible for urine formation and transport. Nephrons of the genital region transport sperm from testes to Wolffian ducts; however, nephrons of the genital region possess all the same functional regions found in pelvic kidney nephrons that are involved with urine formation and transport (renal corpuscles, proximal tubules, distal tubules, and collecting ducts). Morphological similarities between pelvic and genital regions stimulated past researchers to hypothesize that nephrons of genital kidneys possess dual function; that is, sperm transport and urine formation/transport. Considering size of glomeruli is directly related to the total amount of blood plasma filtered into the Bowman's space, we tested the hypothesis that nephrons of genital kidneys have reduced urine formation function by comparing glomerular size between nephrons of pelvic and genital kidney regions in Eurycea longicauda with general histological techniques. Light microscopy analysis revealed that glomeruli of pelvic kidneys were significantly larger than those measured from genital kidneys. Transmission electron microscopy analysis also revealed modifications in genital kidney nephrons when compared to pelvic kidney nephrons that suggested a decrease in urine formation function in genital kidneys. Such modifications included a decrease in basal and lateral plasma membrane folding in genital kidney proximal and distal tubules compared to that of pelvic kidney proximal and distal tubules. Genital kidney proximal tubules were also ciliated, which was not observed in pelvic kidney proximal tubules. In conclusion, although structurally similar at the histological level, it appears that nephrons of genital kidneys have decreased urine formation function based on glomerular size comparison and nephron ultrastructure.     

Mate Choice for Genetic Benefits: Time to Put the Pieces Together

It is thought that mate choice allows individuals to obtain genetic benefits for their offspring, and although many studies have found some support for this hypothesis, several critical questions remain unresolved. One main problem is that empirical studies on mate choice and genetic benefits have been rather piecemeal. Some studies (1) aimed to test how mate choice affects offspring fitness, but have not examined whether the benefits are because of genetic effects. Other studies tested whether mate choice provides (2) additive or (3) non-additive genetic benefits and only a few studies (4) considered these genetic effects together. Finally, some studies (5) examined whether the potential benefits that might be gained from mate choice are due to additive genetic effects vs. non-additive effects, and although they found evidence for both, they did not examine whether mate choice is relevant. Furthermore, previous studies have usually not controlled for non-genetic sources of variation in offspring fitness. Thus, there remain gaping holes in our understanding, and it is the connections among the research approaches that now need more attention. We suggest that studies are needed that measure non-genetic effects, the potential benefits from both additive and non-additive genetic effects, and also determine whether mate choice exploits these potential benefits. Such integrative studies are necessary to put the pieces together and clarify the role of genetic benefits in the evolution of mate choice.