Practical application of genomic selection in a doubled-haploid winter wheat breeding program

Crop improvement is a long-term, expensive institutional endeavor. Genomic selection (GS), which uses single nucleotide polymorphism (SNP) information to estimate genomic breeding values, has proven efficient to increasing genetic gain by accelerating the breeding process in animal breeding programs. As for crop improvement, with few exceptions, GS applicability remains in the evaluation of algorithm performance. In this study, we examined factors related to GS applicability in line development stage for grain yield using a hard red winter wheat (Triticum aestivum L.) doubled-haploid population. The performance of GS was evaluated in two consecutive years to predict grain yield. In general, the semi-parametric reproducing kernel Hilbert space prediction algorithm outperformed parametric genomic best linear unbiased prediction. For both parametric and semi-parametric algorithms, an upward bias in predictability was apparent in within-year cross-validation, suggesting the prerequisite of cross-year validation for a more reliable prediction. Adjusting the training population’s phenotype for genotype by environment effect had a positive impact on GS model’s predictive ability. Possibly due to marker redundancy, a selected subset of SNPs at an absolute pairwise correlation coefficient threshold value of 0.4 produced comparable results and reduced the computational burden of considering the full SNP set. Finally, in the context of an ongoing breeding and selection effort, the present study has provided a measure of confidence based on the deviation of line selection from GS results, supporting the implementation of GS in wheat variety development.     

1,3,4-Trisubstituted pyrrolidine CCR5 receptor antagonists. Part 4: synthesis of N-1 acidic functionality affording analogues with enhanced antiviral activity against HIV

A series of alpha-(pyrrolidin-1-yl)acetic acids is presented as selective and potent antivirals against HIV. Several of the pyrrolidine zwitterions demonstrated reasonable in vitro properties, enhanced antiviral activities and improved pharmacokinetic profiles over pyrrolidine 1.     

Polymeric Microspheres as Protein Transduction Reagents

Discovering the function of an unknown protein, particularly one with neither structural nor functional correlates, is a daunting task. Interaction analyses determine binding partners, whereas DNA transfection, either transient or stable, leads to intracellular expression, though not necessarily at physiologically relevant levels. In theory, direct intracellular protein delivery (protein transduction) provides a conceptually simpler alternative, but in practice the approach is problematic. Domains such as HIV TAT protein are valuable, but their effectiveness is protein specific. Similarly, the delivery of intact proteins via endocytic pathways (e.g. using liposomes) is problematic for functional analysis because of the potential for protein degradation in the endosomes/lysosomes. Consequently, recent reports that microspheres can deliver bio-cargoes into cells via a non-endocytic, energy-independent pathway offer an exciting and promising alternative for in vitro delivery of functional protein. In order for such promise to be fully exploited, microspheres are required that (i) are stably linked to proteins, (ii) can deliver those proteins with good efficiency, (iii) release functional protein once inside the cells, and (iv) permit concomitant tracking. Herein, we report the application of microspheres to successfully address all of these criteria simultaneously, for the first time. After cellular uptake, protein release was autocatalyzed by the reducing cytoplasmic environment. Outside of cells, the covalent microsphere–protein linkage was stable for ≥90 h at 37 °C. Using conservative methods of estimation, 74.3% ± 5.6% of cells were shown to take up these microspheres after 24 h of incubation, with the whole process of delivery and intracellular protein release occurring within 36 h. Intended for in vitro functional protein research, this approach will enable study of the consequences of protein delivery at physiologically relevant levels, without recourse to nucleic acids, and offers a useful alternative to commercial protein transfection reagents such as Chariot™. We also provide clear immunostaining evidence to resolve residual controversy surrounding FACS-based assessment of microsphere uptake.Many proteomic techniques can be used to build a picture of a protein with unknown function, but eventually the individual protein''s activity must be studied. Traditional transfection of encoding DNA permits intracellular expression, but often at uncontrolled, nonphysiological levels. Moreover, DNA transfection can neither deliver protein–inhibitor complexes nor readily deliver multiple proteins in a single experiment and thus exploit knowledge from proteomic protein–protein interaction analyses. In contrast, a truly generic protein transduction reagent could theoretically address all possibilities. We believe that polymeric microspheres could fulfill this role, and we have recently synthesized and characterized dual-functionalized, bio-compatible microspheres that permit intracellular tracking (1). Herein, we now report the development of those microspheres into a protein transduction reagent that can carry protein stably, deliver it efficiently to cells, release the protein in the cytoplasm, and concurrently permit fluorescent imaging of transduced cells.Phagocytosis of microspheres was first observed over 30 years ago (2). Perhaps more unexpectedly, uptake of polystyrene microspheres has recently been reported in many other, nonphagocytic cell types, some of which are traditionally considered to be resistant to DNA transfection and/or protein transduction. For example, microspheres are taken up readily by primary immune cells (3), embryonic stem cells (4), human neural stem cells (5), differentiating mouse neural stem cells (5), and several nonphagocytic cell lines (3, 6, 7). In all instances, the reported efficiency of cellular uptake is high, with “beadfection” of up to 90% of cells being typical (4, 5, 8). No additional reagents aside from the microspheres themselves are required in order to promote cellular uptake, and critically, no toxicity has been observed in any of the cell types beadfected, including HEK293T and L929 cells 2 days after beadfection (8), E14g2a embryonic stem cells 3 days after beadfection (4), and mouse and human neural stem cells 30 days after beadfection (5). In the latter case, the microspheres did not have any deleterious effect on the differentiation of human neural stem cells 30 days after beadfection (5).The mechanism of microsphere entry is also nontoxic, and compelling evidence has been published recently that polystyrene-based microspheres (from 0.2 μm to as large as 2 μm) enter cells via a non-endocytosis, energy-independent mechanism (8). Although unusual, such a mechanism is consistent with claims for the commercial reagent Chariot™ (9). Interestingly, a non-endocytic, energy-independent mechanism has also been reported for the entry of rhenium cluster/polymer hybrid particles into HeLa cells (10). Failure of the microspheres to be endocytosed, at least via a clathrin-dependent mechanism, is perhaps to be predicted, as their diameter considerably exceeds that of clathrin-coated vesicles (typically 100 nm). Bradley and co-workers (8) propose that the entry mechanism for polystyrene-based microspheres is one of passive diffusion in which the microsphere interacts with the membrane, anchors, and, after membrane reorganization, enters the cell, resulting in direct cytoplasmic localization.For functional analysis following transduction, the avoidance of endocytosis or phagocytosis is particularly relevant, as endocytosed particles are destined for endosomes and then, normally, for the lysosomes. The lowered pH of the endosome and, more seriously, the acidic and hydrolytic environment of the lysosome risk disruption of the protein structure and/or function. In contrast, for vaccine delivery (where liposomes can be employed), such exposure is advantageous because protein breakdown forms an essential part of antigen presentation. The potential for protein breakdown in endosomes is also irrelevant for the delivery of protein/peptide drugs such as insulin (for which microencapsulation has proven effective for long-term controlled drug release (11, 12)), as these drugs typically function in the extracellular environment, often exerting their effects by binding to membrane-bound receptors. Thus, although vehicles such as liposomes and nanoparticles are employed both extensively and successfully as drug and vaccine delivery vectors in vivo (13–16), they are far from ideal for studying the biological effect of a delivered protein in vitro. Colloidal particles are also endocytosed (17), and therefore these delivery vehicles may present similar disadvantages.Traditionally, protein transduction domains such as HIV TAT (18–20) or other cell-penetrating peptides (21–23) are used to deliver proteins to cells. Whereas positively charged peptides such as TAT are thought to enter the cells via macropinocytosis (reviewed in Ref. 24), a recent publication suggests that at least some cell-penetrating peptide/bio-cargo complexes (siRNA) are endocytosed (25). Here, although the cargoes avoid the lysosomes, acidification of the endosome is required for endosomal escape of the delivered cargo, and indeed, acidification appears to be a recurring requirement for endosomal escape of biomolecular cargoes using cell-penetrating peptides (reviewed in Ref. 24). Consequently, cell-penetrating peptides are unlikely to become generic tools for functional protein delivery.In contrast, the recent demonstrations that polystyrene microspheres can carry a variety of molecular cargoes with them into the cytoplasm (4, 5, 7, 26, 27) make them particularly exciting as potential vectors for delivering functional proteins and/or protein complexes. β-Galactosidase retains its activity when delivered via this route (7), confirming the potential of microspheres to act as generic protein-delivery vehicles. However, delivered proteins have to date remained tethered to the microspheres, and thus existing studies are limited to proteins that are active in the cytoplasm and, critically, retain their activity when immobilized on polystyrene. For the broad-based study of protein function, the subsequent release of the delivered protein within the cell is desirable.An ideal technology would deliver any protein to any cell type and release that protein in the cell, where it could undertake its normal activity. Here we report the first example of such a microsphere-based approach. Protein is delivered on microspheres and then released in the cell by the reducing cytoplasmic environment. This release is mediated by a linker that attaches the protein stably and covalently to the microspheres in vitro but intracellularly is cleaved over a period of hours. It has already been shown that microspheres are taken up with high efficiency by a range of cell types and can carry a variety of cargoes. Because the chemistry of the linker described herein is amenable to linkage with any molecule containing a free amine moiety, the technology provides a new generic platform for in vitro, cell-based delivery of individual proteins, protein complexes, protein mixtures, or other amino-functionalized molecules.     

Use of monetary wetland value estimates by EPA Clean Water Act Section 404 regulators

U.S. Environmental Protection Agency wetland regulators appear to use monetary estimates of the societal value of wetlands relatively infrequently in Section 404 permit review, enforcement, and compensatory mitigation-related activities. While 52 % of surveyed EPA regulators had used such estimates at least once, only 3 % reported using them frequently. Forty-eight percent said they never used them. Survey respondents indicated that their use of such estimates is inhibited by a lack of relevant information, uncertainty about the scientific validity of estimates, and concerns about the scientific and legal defensibility of estimate use. Respondents said they would be more apt to use estimates in regulatory activities if they perceived agency approval for such use and had access to training and best practices. The barriers and inducements EPA regulators cited largely accord with the literature on the science-policy divide and with the argument that regulatory use of valuation estimates may be inappropriate because research in this arena is not sufficiently advanced.     

Membrane progesterone receptor expression in mammalian tissues: A review of regulation and physiological implications

The recent discovery of a novel, membrane localized progestin receptor (mPR) unrelated to the classical progesterone receptor (PR) in fishes and its subsequent identification in mammals suggests a potential mediator of non-traditional progestin actions, particularly in tissues where PR is absent. While early studies on mPR focused on final oocyte maturation in fishes, more current studies have examined mPRs in multiple mammalian systems in both reproductive and non-reproductive tissues as well as in diseased tissues. Here we review the current data on mPR in mammalian systems including male and female reproductive tracts, liver, neuroendocrine tissues, the immune system and breast and ovarian cancer. We also provide new data demonstrating mPR expression in the RAW 264.7 immune cell line and bone marrow-derived macrophages as well as mPR expression and downstream gene regulation in ovarian cancer cells.     

Production of pea lectin in Escherichia coli

In order to explore the molecular basis for the glycopeptide specificity of legume lectins, we have developed an experimental system in which specific amino acid alterations can be introduced into the carbohydrate binding site of pea lectin. This system is based on the production of pea lectin in Escherichia coli. The plasmid coding for the lectin was constructed from two lectin cDNA sequences isolated from Pisum sativum seeds (Higgins, T. J. V., Chandler, P. M., Zurawski, G., Button, S. C., and Spencer, D. (1983) J. Biol. Chem. 258, 9544-9549) and an expression vector based on the gene for the outer membrane lipoprotein of E. coli (Nakamura, K., and Inouye, M. (1982) EMBO J. 1, 771-775). The lectin is produced as a single polypeptide chain and forms insoluble aggregates in E. coli cells (2-5 mg/liter). Functional lectin is recovered by solubilization of the aggregates in guanidinium hydrochloride, renaturation in the presence of MnCl2 and CaCl2, and affinity purification on Sephadex. This procedure yields a homogeneous 28,000-dalton protein. Comparison of the recombinant lectin with natural pea lectin in an inhibition of hemagglutination assay demonstrated that there is no detectable difference in the carbohydrate binding properties of the two lectins.