The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins

Plasma, the soluble component of the human blood, is believed to harbor thousands of distinct proteins, which originate from a variety of cells and tissues through either active secretion or leakage from blood cells or tissues. The dynamic range of plasma protein concentrations comprises at least nine orders of magnitude. Proteins involved in coagulation, immune defense, small molecule transport, and protease inhibition, many of them present in high abundance in this body fluid, have been functionally characterized and associated with disease processes. For example, protein sequence mutations in coagulation factors cause various serious disease states. Diagnosing and monitoring such diseases in blood plasma of affected individuals has typically been conducted by use of enzyme-linked immunosorbent assays, which using a specific antibody quantitatively measure only the affected protein in the tested plasma samples. The discovery of protein biomarkers in plasma for diseases with no known correlations to genetic mutations is challenging. It requires a highly parallel display and quantitation strategy for proteins. We fractionated blood serum proteins prior to display on two-dimensional electrophoresis (2-DE) gels using immunoaffinity chromatography to remove the most abundant serum proteins, followed by sequential anion-exchange and size-exclusion chromatography. Serum proteins from 74 fractions were displayed on 2-DE gels. This approach succeeded in resolving approximately 3700 distinct protein spots, many of them post-translationally modified variants of plasma proteins. About 1800 distinct serum protein spots were identified by mass spectrometry. They collapsed into 325 distinct proteins, after sequence homology and similarity searches were carried out to eliminate redundant protein annotations. Although a relatively insensitive dye, Coomassie Brilliant Blue G-250, was used to visualize protein spots, several proteins known to be present in serum in < 10 ng/mL concentrations were identified such as interleukin-6, cathepsins, and peptide hormones. Considering that our strategy allows highly parallel protein quantitation on 2-DE gels, it holds promise to accelerate the discovery of novel serum protein biomarkers.     

High-throughput proteomic analysis of human infiltrating ductal carcinoma of the breast

Large-scale proteomics will play a critical role in the rapid display, identification and validation of new protein targets, and elucidation of the underlying molecular events that are associated with disease development, progression and severity. However, because the proteome of most organisms are significantly more complex than the genome, the comprehensive analysis of protein expression changes will require an analytical effort beyond the capacity of standard laboratory equipment. We describe the first high-throughput proteomic analysis of human breast infiltrating ductal carcinoma (IDCA) using OCT (optimal cutting temperature) embedded biopsies, two-dimensional difference gel electrophoresis (2-D DIGE) technology and a fully automated spot handling workstation. Total proteins from four breast IDCAs (Stage I, IIA, IIB and IIIA) were individually compared to protein from non-neoplastic tissue obtained from a female donor with no personal or family history of breast cancer. We detected differences in protein abundance that ranged from 14.8% in stage I IDCA versus normal, to 30.6% in stage IIB IDCA versus normal. A total of 524 proteins that showed > or = three-fold difference in abundance between IDCA and normal tissue were picked, processed and identified by mass spectrometry. Out of the proteins picked, approximately 80% were unambiguously assigned identities by matrix-assisted laser desorbtion/ionization-time of flight mass spectrometry or liquid chromatography-tandem mass spectrometry in the first pass. Bioinformatics tools were also used to mine databases to determine if the identified proteins are involved in important pathways and/or interact with other proteins. Gelsolin, vinculin, lumican, alpha-1-antitrypsin, heat shock protein-60, cytokeratin-18, transferrin, enolase-1 and beta-actin, showed differential abundance between IDCA and normal tissue, but the trend was not consistent in all samples. Out of the proteins with database hits, only heat shock protein-70 (more abundant) and peroxiredoxin-2 (less abundant) displayed the same trend in all the IDCAs examined. This preliminary study demonstrates quantitative and qualitative differences in protein abundance between breast IDCAs and reveals 2-D DIGE portraits that may be a reflection of the histological and pathological status of breast IDCA.     

Novel approaches for regulating gas supply to plant systems <Emphasis Type="Italic">in vitro</Emphasis>: Application and benefits of artificial gas carriers

Summary The composition of the gaseous environment within tissue culture vessels is a critical factor in determining in vitro plant growth and morphogenic responsiveness. Consequently, the provision of an adequate and sustainable oxygen supply for cultured plant cells (including isolated protoplasts), tissues and organs is a crucial prerequisite for optimization and regulation of such cultural responses. During the past decade, research has focused on improving growth and development using artificial gas carriers based on inert perfluorocarbon (PFC) liquids and hemoglobin (Hb) solution. Supplementation of culture media with such artificial oxygen carriers has demonstrated beneficial effects of increased and sustainable cellular mitotic division and subsequent biomass production in a diverse range of plant species, during both short- and longer-term culture. Studies have targeted systems where oxygen availability is actually or potentially a major growth-limiting factor. Undoubtedly, gas carrier-facilitated improvements in regulating the supply of respiratory gases to cultured cells, tissues and organs will have increasingly important biotechnological and practical implications in the context of plant micropropagation, somatic hybridization, transgenic plant production, and secondary product biosynthesis.     

A new identity for MLK3 as an NIMA-related,cell cycle-regulated kinase that is localized near centrosomes and influences microtubule organization

Although conserved counterparts for most proteins involved in the G(2)/M transition of the cell cycle have been found in all eukaryotes, a notable exception is the essential but functionally enigmatic fungal kinase NIMA. While a number of vertebrate kinases have been identified with catalytic domain homology to NIMA, none of these resemble NIMA within its extensive noncatalytic region, a region critical for NIMA function in Aspergillus nidulans. We used a bioinformatics approach to search for proteins with homology to the noncatalytic region of NIMA and identified mixed lineage kinase 3 (MLK3). MLK3 has been proposed to serve as a component in MAP kinase cascades, particularly those resulting in the activation of the c-Jun N-terminal kinase (JNK). Here we describe the first in-depth study of endogenous MLK3 and report that, like NIMA, MLK3 phosphorylation and activity are enhanced during G(2)/M, whereas JNK remains inactive. Coincident with the G(2)/M transition, a period marked by dramatic reorganization of the cytoplasmic microtubule network, endogenous MLK3 transiently disperses away from the centrosome and centrosomal-proximal sites where it is localized during interphase. Furthermore, when overexpressed, MLK3, like NIMA, localizes to the centrosomal region, induces profound disruption of cytoplasmic microtubules and a nuclear distortion phenotype that differs from mitotic chromosome condensation. Cellular depletion of MLK3 protein using siRNA technology results in an increased sensitivity to the microtubule-stabilizing agent taxol. Our studies suggest a new role for MLK3, separable from its function in the JNK pathway, that may contribute to promoting microtubule instability, a hallmark of M phase entry.     

Induction of cyclooxygenase 2 by Escherichia coli but not Helicobacter pylori lipopolysaccharide in gastric epithelial cells in vitro

Background. Cyclooxygenase 2 (COX‐2) is an inducible enzyme that plays a key role in the synthesis of prostaglandins in response to inflammatory stimuli. It is expressed in the gastric mucosa as part of the response to infection with Helicobacter pylori. The specific interaction between H. pylori and the gastric epithelium that results in COX‐2 expression has not been identified. Methods. In order to investigate the hypothesis that lipopolysaccharide (LPS) from H. pylori plays a role in the induction of cyclooxygenase 2 in the stomach, gastric cell lines MKN‐7 and MKN‐45 were incubated with LPS from either H. pylori NCTC 11637 or Escherichia coli 055:B5. Incubation of cells with live H. pylori NCTC 11637 was also carried out as a positive control. Cells were then analysed for COX‐2 protein and mRNA and prostaglandin E2 synthesis. Results. Cyclooxygenase 2 protein and mRNA expression was induced by E. coli LPS and live H. pylori, but not by H. pylori LPS. Prostaglandin E₂ synthesis increased in a dose‐dependent manner in both cell lines with E. coli but not H. pylori LPS. Conclusions. H. pylori LPS is of low biological activity when compared with E. coli LPS in its ability to induce the expression of cyclooxygenase 2 and synthesis of prostaglandin E₂. This may provide one mechanism by which H. pylori minimizes the inflammatory response in the gastric mucosa, allowing chronic infection.     

The mbk-2 kinase is required for inactivation of MEI-1/katanin in the one-cell Caenorhabditis elegans embryo

The Caenorhabditis elegans early embryo is widely used to study the regulation of microtubule-related processes. In a screen for mutants affecting the first cell division, we isolated a temperature-sensitive mutation affecting pronuclear migration and spindle positioning, phenotypes typically linked to microtubule or centrosome defects. In the mutant, microtubules are shorter and chromosome segregation is impaired, while centrosome organization appears normal. The mutation corresponds to a strong loss of function in mbk-2, a conserved serine/threonine kinase. The microtubule-related defects are due to the postmeiotic persistence of MEI-1, a homologue of the microtubule-severing protein katanin. In addition, P-granule distribution is abnormal in mbk-2 mutants, consistent with genetic evidence that mbk-2 has other functions and with the requirement of mbk-2 activity at the one-cell stage. We propose that mbk-2 potentiates the degradation of MEI-1 and other proteins, possibly via direct phosphorylation.     

Can animals recall the past and plan for the future?

According to the 'mental time travel hypothesis' animals, unlike humans, cannot mentally travel backwards in time to recollect specific past events (episodic memory) or forwards to anticipate future needs (future planning). Until recently, there was little evidence in animals for either ability. Experiments on memory in food-caching birds, however, question this assumption by showing that western scrub-jays form integrated, flexible, trial-unique memories of what they hid, where and when. Moreover, these birds can adjust their caching behaviour in anticipation of future needs. We suggest that some animals have elements of both episodic-like memory and future planning.     

Release characteristics of novel pH-sensitive p(HEMA-DMAEMA) hydrogels containing 3-(trimethoxy-silyl) propyl methacrylate

An amphiphilic hydrogel of poly(2-hydroxyethyl methacrylate) cross-linked with tetraethyleneglycol diacrylate (TEGDA) was synthesized to contain the hydrophobic monomer 3-(trimethoxy-silyl) propyl methacrylate (PMA) and the pH-responsive, hydrophilic monomer N',N'-dimethylaminoethyl methacrylate (DMAEMA). The gels were separately loaded with two biomolecular probes, insulin and protamine, via both physical entrapment and equilibrium imbibition methods. The release profiles for these biomolecular probes, possessing similar MW (5.7 and 4-6 kDa, respectively) but different pI's (5.3 and 10.0, respectively), were investigated with respect to variation in the pH of the bathing medium as well as the DMAEMA content, and the cross-link density of the hydrogel. Gels exhibited classical Fickian diffusion release profiles. For a typical gel composition 66:15:10:09 mol % (HEMA:DMAEMA:PMA:TEGDA), as the pH of the release media decreased from 7.3 to 4.0, the rate of release of both biomolecular probes increased. When loaded via entrapment, the insulin release rate increased ca. 4-fold (1.0-3.7 x 10(-7) cm(2) s(-1)), whereas that of protamine increased 10-fold (0.3-3.3 x 10(-7) cm(2) s(-1)). When loaded by imbibition, the insulin diffusion coefficient increased 2-fold (3.8-7.2 x 10(-7) cm(2) s(-1)), whereas that of protamine increased 3-fold (1.9-5.5 x 10(-7) cm(2) s(-1)). The reduction of pH, through its protonation of the gel network, has a more dramatic influence on protamine release, the result of its higher pI (10.0) compared to that of insulin (5.3). As the DMAEMA content of the hydrogel was increased from 0 to 20 mol %, the diffusion coefficient of protamine increased by ca. 7-fold (1.7-12.2 x 10(-7) cm(2) s(-1)), whereas that of insulin increased only ca. 2-fold (1.7-4.0 x 10(-7) cm(2) s(-1)). This differential release confirms the role of internal protonation in effecting the greater release of the protonated drug molecule. Increasing the TEGDA content from 3 to 15 mol % reduced the diffusion coefficient ca. 3-fold for insulin (1.6-0.5 x 10(-7) cm(2) s(-1)) and 5-fold for protamine (4.0-0.8 x 10(-7) cm(2) s(-1)). The final D(ip) at 15 mol % TEGDA suggests that the smaller mesh size offsets any differential release that arises from protonation. The presence of PMA in the hydrogel formulation, which contributes additional cross-links by reason of the formation of siloxane macromers, did not change the usually observed Fickian diffusion mechanism.