Analysis of plasma proteins using 2D gels and novel fluorescent probes: in search of blood based biomarkers for Alzheimer's disease.

Background: The Australian Imaging and Biomarker Lifestyle (AIBL) study of aging is designed to aid the discovery of biomarkers. The current study aimed to discover differentially expressed plasma proteins that could yield a blood-based screening tool for Alzheimer's disease.

Methods: The concentration of proteins in plasma covers a vast range of 12 orders of magnitude.

Proteomic comparison of near-isogenic barley (Hordeum vulgare L.) germplasm differing in the allelic state of a major senescence QTL identifies numerous proteins involved in plant pathogen defense.

Senescence is the last developmental phase of plant tissues, organs and, in the case of monocarpic senescence, entire plants. In monocarpic crops such as barley, it leads to massive remobilization of nitrogen and other nutrients to developing seeds. To further investigate this process, a proteomic comparison of flag leaves of near-isogenic late- and early-senescing barley germplasm was performed.

Selective trapping of SNO-BSA and GSNO by benzenesulfinic acid sodium salt: mechanistic study of thiosulphonate formation and feasibility as a protein -nitrosothiol detection strategy.

The conversion of -nitrosothiols to thiosulphonates by reaction with the sodium salt of benzenesulfinic acid (PhSONa) has been examined in detail with the exemplary substrates -nitrosoglutathione (GSNO) and -nitrosylated bovine serum albumin (SNO-BSA). The reaction stoichiometry (2:1, PhSONa:RSNO) and the rate law (first order in both PhSONa and RSNO) have been determined under mild acidic conditions (pH 4.0).

Expanding the paradigm of thiol redox in the thermophilic root of life.

Background: The current paradigm of intracellular redox chemistry maintains that cells establish a reducing environment maintained by a pool of small molecule and protein thiol to protect against oxidative damage. This strategy is conserved in mesophilic organisms from all domains of life, but has been confounded in thermophilic organisms where evidence suggests that intracellular proteins have abundant disulfides.

Methods: Chemical labeling and 2-dimensional gel electrophoresis were used to capture disulfide bonding in the proteome of the model thermophile Sulfolobus solfataricus.

Aggregatibacter actinomycetemcomitans biofilm killing by a targeted ciprofloxacin prodrug.

A pH-sensitive ciprofloxacin prodrug was synthesized and targeted against biofilms of the periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa). The dose required to reduce the viability of a mature biofilm of Aa by ~80% was in the range of ng cm(-2) of colonized area (mean biofilm density 2.33 × 10(9) cells cm(-2)).

Enhanced sensitivity employing zwitterionic and pI balancing dyes (Z-CyDyes) optimized for 2D-gel electrophoresis based on side chain modifications of CyDye fluorophores. New tools for use in proteomics and diagnostics.

The CyDye family of fluorescent dyes is currently the overwhelming choice for applications in proteomic analysis, using two-dimensional difference gel electrophoresis (2D-DIGE). Protein labeling with CyDyes is hampered by protein precipitation and gel smearing when used above minimal labeling. The solubility of labeled protein may be improved by introducing water solubilizing groups on the dye such as cysteic acids.

Global analysis of viral infection in an archaeal model system.

The origin and evolutionary relationship of viruses is poorly understood. This makes archaeal virus-host systems of particular interest because the hosts generally root near the base of phylogenetic trees, while some of the viruses have clear structural similarities to those that infect prokaryotic and eukaryotic cells. Despite the advantageous position for use in evolutionary studies, little is known about archaeal viruses or how they interact with their hosts, compared to viruses of bacteria and eukaryotes.