Activity of Uridine Diphosphate N-Acetylglucosamine-4-Epimerase During Spherulation of Physarum polycephalum

The specific activity of uridine diphosphate N-acetylglucosamine-4-epimerase increases during spherulation of Physarum polycephalum, a process that involves the synthesis of galactosamine walls. This increase is prevented by the addition of cycloheximide.     

Mass isolation and culture of sea urchin micromeres

Summary A procedure is described for large-scale isolation of micromeres from 16-cell stage sea urchin embryos. One to two grams of >99% pure, viable micromeres (2.3 to 4.6 × 10⁸ cells) are routinely isolated in a single preparation. In culture, these cells uniformly proceed through their normal development, in synchrony with micromeres in whole embryos, ultimately differentiating typical larval skeletal structures. The attributes of this procedure are: (a) the very early time of isolation of the cells, directly after the division that establishes the cell line; (b) the large yield of cells; (c) the purity of the preparation of cell; and (d) their synchronous development in culture through skeletogenesis. The procedure greatly aids in making sea urchin micromeres a favorable material for molecular analysis of development. This work was supported in part by the following grants from the National Institutes of Health: Grant HL-10312 to A.H.W., Grant GM-20784 to Helen R. Whiteley, Grant ES-02190 to N. Karle Mottet, M.D., and Training Grants ES-07032 and HD-00266.     

Protists have divergent effects on bacterial diversity along a productivity gradient

Productivity and predation are thought to be crucial drivers of bacterial diversity. We tested how the productivity–diversity of a natural bacterial community is modified by the presence of protist predators with different feeding preferences. In the absence of predators, there was a unimodal relationship between bacterial diversity and productivity. We found that three protist species (Bodo, Spumella and Cyclidium) had widely divergent effects on bacterial diversity across the productivity gradient. Bodo and Cyclidium had little effect on the shape of the productivity–diversity gradient, while Spumella flattened the relationship. We explain these results in terms of the feeding preferences of these predators.     

Molecular chaperones stimulate the functional expression of the cocaine-sensitive serotonin transporter.

The serotonin transporter (SERT) is an N-glycosylated integral membrane protein that is predicted to contain 12 transmembrane regions. SERT is the major binding site in the brain for antidepressant drugs, and it also binds amphetamines and cocaine. The ability of various molecular chaperones to interact with a tagged version of SERT (Myc-SERT) was investigated using the baculovirus expression system. Overexpression of Myc-SERT using the baculovirus system led to substantial quantities of inactive transporter, together with small amounts of fully active and, therefore, correctly folded molecules. The high levels of inactive Myc-SERT probably arose because folding was rate-limiting due, perhaps, to insufficient molecular chaperones. Therefore, Myc-SERT was co-expressed with the endoplasmic reticulum (ER) molecular chaperones calnexin, calreticulin and immunoglobulin heavy chain binding protein (BiP), and the foldase, ERp57. The expression of functional Myc-SERT, as determined by an inhibitor binding assay, was enhanced nearly 3-fold by co-expressing calnexin, and to a lesser degree on co-expression of calreticulin and BiP. Co-expression of ERp57 did not increase the functional expression of Myc-SERT. A physical interaction between Myc-SERT-calnexin and Myc-SERT-calreticulin was demonstrated by co-immunoprecipitation. These associations were inhibited in vivo by deoxynojirimycin, an inhibitor of N-glycan precusor trimming that is known to prevent the calnexin/calreticulin-N-glycan interaction. Functional expression of the unglycosylated SERT mutant, SERT-QQ, was also increased on co-expression of calnexin, suggesting that the interaction between calnexin and SERT is not entirely dictated by the N-glycan. SERT is the first member of the neurotransmitter transporter family whose folding has been shown to be assisted by the molecular chaperones calnexin, calreticulin, and BiP.     

Anti-Peptide Monoclonal Antibodies Generated for Immuno-Multiple Reaction Monitoring-Mass Spectrometry Assays Have a High Probability of Supporting Western blot and ELISA

Immunoaffinity enrichment of peptides coupled to targeted, multiple reaction monitoring-mass spectrometry (immuno-MRM) has recently been developed for quantitative analysis of peptide and protein expression. As part of this technology, antibodies are generated to short, linear, tryptic peptides that are well-suited for detection by mass spectrometry. Despite its favorable analytical performance, a major obstacle to widespread adoption of immuno-MRM is a lack of validated affinity reagents because commercial antibody suppliers are reluctant to commit resources to producing anti-peptide antibodies for immuno-MRM while the market is much larger for conventional technologies, especially Western blotting and ELISA. Part of this reluctance has been the concern that affinity reagents generated to short, linear, tryptic peptide sequences may not perform well in traditional assays that detect full-length proteins. In this study, we test the feasibility and success rates of generating immuno-MRM monoclonal antibodies (mAbs) (targeting tryptic peptide antigens) that are also compatible with conventional, protein-based immuno-affinity technologies. We generated 40 novel, peptide immuno-MRM assays and determined that the cross-over success rates for using immuno-MRM monoclonals for Western blotting is 58% and for ELISA is 43%, which compare favorably to cross-over success rates amongst conventional immunoassay technologies. These success rates could most likely be increased if conventional and immuno-MRM antigen design strategies were combined, and we suggest a workflow for such a comprehensive approach. Additionally, the 40 novel immuno-MRM assays underwent fit-for-purpose analytical validation, and all mAbs and assays have been made available as a resource to the community via the Clinical Proteomic Tumor Analysis Consortium''s (CPTAC) Antibody (http://antibodies.cancer.gov) and Assay Portals (http://assays.cancer.gov), respectively. This study also represents the first determination of the success rate (92%) for generating mAbs for immuno-MRM using a recombinant B cell cloning approach, which is considerably faster than the traditional hybridoma approach.The ability to measure specific proteins of interest is critical to the basic sciences and clinical research. To this end, immunoaffinity-based assays such as Western blotting, immunohistochemistry, and ELISAs have been in use for decades, but have several shortcomings including difficulty in multiplexing, a lack of standardization, and a semi-quantitative nature (e.g. Western blotting and immunohistochemistry) (1). Recently, there has been tremendous growth in using the sensitive, specific, multiplexable, and quantitative technology, multiple reaction monitoring-mass spectrometry, to measure tryptic peptides as stoichiometric surrogates for the detection of proteins from complex samples (2–7). The sensitivity of targeted multiple reaction monitoring (MRM)¹ is enhanced 10³–10⁴-fold by coupling it upstream with immunoaffinity enrichment of tryptic peptides in a peptide immuno-MRM assay (8–14). Advantages of immuno-MRM include high specificity, multiplexability (15, 16), and standardization, enabling high inter-laboratory reproducibility (17).The extent to which antibodies generated for immuno-MRM could support widely-used conventional immunoassay formats has not been investigated. This question is important because a lack of validated affinity reagents is a major obstacle to widespread implementation of immuno-MRM, which has considerable analytical advantages over traditional methods. Because the market for immuno-MRM is at present small relative to that for widely adopted conventional immunoassay formats (e.g. Western blotting and ELISA), commercial antibody suppliers are not incentivized to develop content specifically for immuno-MRM assays. Thus, we reasoned that if antibodies could be generated that are capable of supporting both conventional technologies as well as the emerging MRM platform, this might spark commercial interest by increasing the value of the antibodies, ultimately providing reagents to foster widespread implementation of immuno-MRM.Antigens used for antibody generation in conventional assays typically consist of either purified proteins, protein segments of 100–150 amino acids, or synthetic peptide sequences (18, 19). Antigenic prediction algorithms are often used to identify regions of target proteins that are most likely to be exposed on the surface of the protein and, thus, accessible for antibody binding. In contrast, proteotypic peptide antigens are selected for development of antibodies for immuno-MRM based on their uniqueness in the genome and their robust detectability by mass spectrometry, without regard to protein structure (because the protein will be proteolyzed during the assay). Because some widely used conventional immunoassay formats (e.g. Western blotting and indirect ELISA) detect proteins in their denatured form, it was reasonable to ask whether antibodies raised against short, linear, tryptic peptides would also work in these alternative formats.Here, we develop, characterize, and make publicly available 40 novel immuno-MRM assays and the associated monoclonals, and report the success rate of generating recombinant monoclonal antibodies (mAbs) that work in immuno-MRM assays. Furthermore, we determine the cross-over success rates of applying the mAbs in Western blotting and indirect ELISA assays.     

Old trees contribute bio-available nitrogen through canopy bryophytes

Symbiotic cyanobacteria??bryophyte associations on the forest floor are shown to contribute significantly to stand-level nitrogen budgets through the process of biological nitrogen fixation (BNF), but few studies have considered the role of canopy bryophytes. Given the high biomass of epiphytic bryophytes in many tree species of the North American temperate rain forest, we suggest that canopy bryophytes may contribute substantially to stand-level N dynamics. We confirm the presence of cyanobacteria and measure rates of BNF at three heights (0, 15 and 30 m) in Sitka spruce trees across three watershed estuaries of Clayoquot Sound, British Columbia, Canada. This study is the first to report BNF by cyanobacteria associated with epiphytic and forest floor bryophytes in the coastal temperate rain forest of North America. Cyanobacteria density was significantly greater in epiphytic bryophytes compared to mosses on the forest floor, and rates of BNF were highest at 30 m in the canopy. The majority of total stand-level BNF (0.76 kg N · ha^-1 · yr^-1) occurs in the canopy, rather than on the forest floor (0.26 kg N · ha^-1 · yr^-1). We suggest that BNF by cyanobacterial-bryophyte associations in the canopy of coastal temperate rain forests is a unique source of ecosystem N, which is dependent on large, old trees with high epiphytic bryophyte biomass.     

BACKGROUND MATCHING AND COLOR-CHANGE PLASTICITY IN COLONIZING FRESHWATER SCULPIN POPULATIONS FOLLOWING RAPID DEGLACIATION

Anthropogenic-induced change is forcing organisms to shift their distributions and colonize novel habitats at an increasing rate, which leads to complex interactions among evolutionary processes. Coastrange sculpin ( Cottus aleuticus ) have colonized recently deglaciated streams of Glacier Bay in Alaska within the last 220 years. We examined divergence among populations in background matching coloration and tested the hypothesis that observed variation is due to morphological color plasticity. To examine how color-change plasticity has interacted with other evolutionary processes, we also determined the influence of colonization on neutral genetic diversity. We observed clinal variation in substrate-matching fish color along the chronological continuum of streams. Microsatellites provided little evidence of genetic subdivision among sculpin populations. Fish color was significantly correlated to substrate color, but was not correlated to neutral population genetic structure. Furthermore, a laboratory experiment revealed that morphological color plasticity could explain much, but not all, of the observed fish color divergence. Our study demonstrates that sculpin in Glacier Bay have colonized and adapted to recently deglaciated habitat and suggests that color change plasticity has aided in this process. This research, therefore, highlights the important role phenotypic plasticity may play in the adaptation of species to rapid climate change.