The maize α-zein promoter can be utilized as a strong inducer of cellulase enzyme expression in maize kernels

Transgenic Research - Expression of recombinant proteins in plants is a technology for producing vaccines, pharmaceuticals and industrial enzymes. For the past several years, we have produced...     

Single-dose murine monoclonal antibody ricin A chain immunotoxin in the treatment of metastatic melanoma: a phase I trial.

To determine the maximally tolerated dose of a ricin A chain-conjugated antimelanoma antibody (XomaZyme-Mel), 20 patients with metastatic melanoma were treated with escalating doses of the murine immunotoxin given as single intravenous infusion over 30 minutes. The starting dose was 0.6 mg/kg and was escalated in five groups to a maximum of 1.6 mg/kg. The maximally tolerated dose was 1.25 mg/kg as three of six patients treated at 1.6 mg/kg developed unacceptable toxicity. The dose-limiting toxicity consisted of profound fatigue, myalgias, and arthralgias. These occurred within 4 days and resolved in 7 to 10 days. Other non-dose-limiting toxicities encountered consisted of hypoalbuminemia, weight gain, peripheral edema, mild hypotension, and flu-like syndrome; the severity of these was also dose related. In addition, two allergic reactions occurred, one severe. There was one durable complete response of 12+ months' duration and one brief mixed response lasting 3 months. We conclude that the maximum tolerated single dose of XomaZyme-Mel is 1.25 mg/kg. Phase I studies evaluating 1.25 mg/kg given in multiple doses at 2- to 4-week intervals and phase II studies to determine the response rate of a single 1.25 mg/kg dose are warranted.     

A Genetic Polymorphism in Coumarin 7-Hydroxylation: Sequence of the Human CYP2A Gnes and Identification of Variant CYP2A6 Alleles

A group of human cytochrome P450 genes encompassing the CYP2A, CYP2B, and CYP2F subfamilies were cloned and assembled into a 350-kb contig localized on the long arm of chromosome 19. Three complete CYP2A genes—CYP2A6, CYP2A7, and CYP2A13—plus two pseudogenes truncated after exon 5, were identified and sequenced. A variant CYP2A6 allele that differed from the corresponding CYP2A6 and CYP2A7 cDNAs previously sequenced was found and was designated CYP2A6ν2. Sequence differences in the CYP2A6ν2 gene are restricted to regions encompassing exons 3, 6, and 8, which bear sequence relatedness with the corresponding exons of the CYP2A7 gene, located downstream and centromeric of CYP2A6ν2, suggesting recent gene-conversion events. The sequencing of all the CYP2A genes allowed the design of a PCR diagnostic test for the normal CYP2A6 allele, the CYP2A6ν2 allele, and a variant—designated CYP2A6ν1—that encodes an enzyme with a single inactivating amino acid change. These variant alleles were found in individuals who were deficient in their ability to metabolize the CYP2A6 probe drug coumarin. The allelic frequencies of CYP2A6ν1 and CYP2A6ν2 differed significantly between Caucasian, Asian, and African-American populations. These studies establish the existence of a new cytochrome P450 genetic polymorphism.     

The path to next generation biofuels: successes and challenges in the era of synthetic biology

Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels.     

Understanding osmotic stress tolerance in leaves and nodules of two <Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> cultivars with contrasting drought tolerance

Drought and salinity are environmental constraints that affect crop yields worldwide. In nature, both stresses are multifaceted problems that are usually associated with other adverse circumstances which limit plant performance such as water shortage and nutrient deficits. In order to assess common features of both stresses, the effects of mannitol-induced osmotic stress were monitored using two Phaseolus vulgaris cultivars, Cv. ‘Flamingo’ (tolerant) and Cv. ‘Coco Blanc’ (sensitive) which differed in their drought and salinity tolerance. Growth, water relations, organic and inorganic compound accumulation and soluble protein contents were measured in leaves and nodules of these N₂-fixing plants. The aim of the present study was to check whether osmotic stress tolerance is associated with accumulation of some of these compounds either in leaves, nodules or both organs. At the whole-plant level, Cv. ‘Flamingo’ showed a better maintenance of plant biomass and shoot water status. At the cell level, this was related to a better osmotic adjustment ability both in leaves and nodules and also to a better adjustment of the cell wall elasticity. At the metabolic level, the contrasting accumulation of the different amino acids in nodules of each cultivar suggested that amino acids pathways can be regulated to different degrees under stress conditions. At the metabolic level, it seems that symbiosis in the sink organ (the nodule) plays a crucial role in conferring drought and salinity tolerance in the common bean.     

Pinus taeda forest growth predictions in the 21st century vary with site mean annual temperature and site quality

Climate projections from 20 downscaled global climate models (GCMs) were used with the 3‐PG model to predict the future productivity and water use of planted loblolly pine (Pinus taeda) growing across the southeastern United States. Predictions were made using Representative Concentration Pathways (RCP) 4.5 and 8.5. These represent scenarios in which total radiative forcing stabilizes before 2100 (RCP 4.5) or continues increasing throughout the century (RCP 8.5). Thirty‐six sites evenly distributed across the native range of the species were used in the analysis. These sites represent a range in current mean annual temperature (14.9–21.6°C) and precipitation (1,120–1,680 mm/year). The site index of each site, which is a measure of growth potential, was varied to represent different levels of management. The 3‐PG model predicted that aboveground biomass growth and net primary productivity will increase by 10%–40% in many parts of the region in the future. At cooler sites, the relative growth increase was greater than at warmer sites. By running the model with the baseline [CO₂] or the anticipated elevated [CO₂], the effect of CO₂ on growth was separated from that of other climate factors. The growth increase at warmer sites was due almost entirely to elevated [CO₂]. The growth increase at cooler sites was due to a combination of elevated [CO₂] and increased air temperature. Low site index stands had a greater relative increase in growth under the climate change scenarios than those with a high site index. Water use increased in proportion to increases in leaf area and productivity but precipitation was still adequate, based on the downscaled GCM climate projections. We conclude that an increase in productivity can be expected for a large majority of the planted loblolly pine stands in the southeastern United States during this century.     

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells

Proteomics strategies based on nanoflow (nano-) LC-MS/MS allow the identification of hundreds to thousands of proteins in complex mixtures. When combined with protein isotopic labeling, quantitative comparison of the proteome from different samples can be achieved using these approaches. However, bioinformatics analysis of the data remains a bottleneck in large scale quantitative proteomics studies. Here we present a new software named Mascot File Parsing and Quantification (MFPaQ) that easily processes the results of the Mascot search engine and performs protein quantification in the case of isotopic labeling experiments using either the ICAT or SILAC (stable isotope labeling with amino acids in cell culture) method. This new tool provides a convenient interface to retrieve Mascot protein lists; sort them according to Mascot scoring or to user-defined criteria based on the number, the score, and the rank of identified peptides; and to validate the results. Moreover the software extracts quantitative data from raw files obtained by nano-LC-MS/MS, calculates peptide ratios, and generates a non-redundant list of proteins identified in a multisearch experiment with their calculated averaged and normalized ratio. Here we apply this software to the proteomics analysis of membrane proteins from primary human endothelial cells (ECs), a cell type involved in many physiological and pathological processes including chronic inflammatory diseases such as rheumatoid arthritis. We analyzed the EC membrane proteome and set up methods for quantitative analysis of this proteome by ICAT labeling. EC microsomal proteins were fractionated and analyzed by nano-LC-MS/MS, and database searches were performed with Mascot. Data validation and clustering of proteins were performed with MFPaQ, which allowed identification of more than 600 unique proteins. The software was also successfully used in a quantitative differential proteomics analysis of the EC membrane proteome after stimulation with a combination of proinflammatory mediators (tumor necrosis factor-alpha, interferon-gamma, and lymphotoxin alpha/beta) that resulted in the identification of a full spectrum of EC membrane proteins regulated by inflammation.     

Pax7 identifies neural crest, chromatophore lineages and pigment stem cells during zebrafish development

Using immunostaining during early zebrafish embryogenesis, we report that the cranial and trunk neural crest expresses the paired box protein Pax7, thus revealing a novel neural crest marker in zebrafish. In the head, we show that Pax7 is broadly expressed in the cranial crest cells, which indicates that duplication of the paralogous group Pax3/7 at the origin of vertebrates included the conserved expression of Pax7 in the head neural crest of all of the vertebrates species studied so far. In the trunk, Pax7 recognizes both premigratory and migratory neural crest cells. Notably, we observed the expression of Pax7 during the development of melanophore, xanthophore and iridophore precursor cells. In contrast to the case of melanocyte precursors in birds, Pax7 showed overlapping expression with early melanin pigment. Finally, during the larva to adult transition, we show that pigment stem cells recapitulate the expression of Pax7.