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Background/aim Serine/threonine kinase B-Raf proto-oncogene (BRAF) mutant colon cancer has a poor prognosis and there is an absence of targeted treatments for this subtype. Here, we investigated the effects of inhibition of casein kinase 2 (CK2) on the inhibitory effects of BRAF and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) inhibition in BRAF-mutant colon cancer cells. Materials and methods Colon cancer cell lines with mutations in components of the mitogen-activated protein kinase (MAPK) and PI3K signalling pathway were used. Cell viability was determined after exposure to single agent and combinations of erlotinib (EGFR inhibitor), dabrafenib (MEK inhibitor), GDC0941 (PI3K inhibitor) and CX4945 (CK2 inhibitor). Western blots were used to examine MAPK and AKT serine/threonine kinase (AKT) pathway activation. Results Addition of CX4945 to dabrafenib did not enhance the antiproliferative effects of single-agent dabrafenib. Use of GDC0941 alone was highly effective in controlling growth of both BRAF-mutant and wild-type cells and this effect was enhanced by CK2 inhibition. Conclusion Inhibition of the PI3K/AKT pathway is central to regulating growth of colon cancer cells and this can be enhanced by CK2 inhibition.

The inclusion of grain sorghum in diets for broiler chickens is quite common; however, under Australian conditions, the utilisation of starch/energy by birds offered sorghum-based diets appears inadequate. Various factors inherent in sorghum, including kafirin, phenolic compounds and phytate, may limit energy utilisation. The recent quantification of kafirin, the dominant protein fraction in sorghum, has allowed its nutritional significance to be assessed. This is important as indirect evidence suggests that kafirin concentrations in local sorghums are increasing as an unintended consequence of breeding programs. Presently, Australian sorghums do not contain condensed tannin but, from analyses and assessments of other polyphenolic compounds and phenolic acids, “non-tannin” phenols appear to be negative influences. Anecdotally, white sorghums are considered to be superior to red varieties thus the fact that polyphenolic pigments are responsible for the “redness” of sorghum assumes relevance. Inclusions of sulphite reducing agents in broiler diets have generated promising responses but seem dependent on sorghum properties. Preliminary studies have shown the possibilities of using rapid visco-analyser (RVA) starch pasting profiles, promatest protein solubilities and grain textures to indicate sorghum quality and further studies are required to confirm these hypotheses. These assessments may indicate which sorghums will best respond to reducing agents such as sodium metabisulphite. Finally, the usually modest responses of broilers to exogenous feed enzyme inclusions in sorghum-based are considered in this review.

The Liverpool Plains is a fertile agricultural region in New South Wales, Australia. Two sorghums from the 2009 Liverpool Plains harvest, sorghums #3 and #5, were extensively characterised which included concentrations of kafirin and phenolic compounds plus rapid visco-analysis (RVA) starch pasting profiles. Diets based on these two sorghums were formulated to be iso-nitrogenous and iso-energetic and were offered to male Ross 308 broiler chicks from 7 to 28 days post--hatch as either intact pellets or reground mash following steam-pelleting at conditioning temperatures of either 65 or 97°C. Thus the feeding study consisted of a 2 × 2 × 2 factorial array of dietary treatments: two sorghum varieties, two feed forms and two conditioning temperatures. Each of the eight treatments was replicated six times with six birds per replicate cage. Assessed parameters included growth performance, nutrient utilisation, apparent starch and protein (N) digestibility coefficients and disappearance rates from the distal jejunum and distal ileum. Intact pellets supported higher (P < 0.001) feed intakes and weight gains by 9.83 and 9.08%, respectively, than reground mash diets. Feed conversion ratios of broilers offered diets steam-conditioned at 97°C were 2.46% inferior (P < 0.001) in comparison to 65°C diets and both apparent metabolizable energy (AME) and N-corrected AME (AMEn) were compromised. Broilers offered sorghum #3-based diets significantly (P < 0.001) outperformed their sorghum #5 counterparts in terms of weight gain by 3.75% (1,334 versus 1,223 g/bird), FCR by 4.81% (1.524 versus 1.601), AME by 1.06 MJ (13.61 versus 12.55 MJ/kg), ME:GE ratio (ME:GE) by 4.81% (0.806 versus 0.769) and AMEn by 1.03 MJ (12.38 versus 11.35 MJ/kg). The inferiority of sorghum #5 appeared to be associated with higher concentrations of kafirin (61.5 versus 50.7 g/kg) and conjugated phenolic acids, including ferulic acid (31.1 versus 25.6 µg/g). There were no significant differences in jejunal and ileal starch and protein (N) digestibility coefficients between the two sorghums. However, starch to protein (N) disappearance rate ratios from the distal jejunum were significantly (P < 0.001) correlated with ME:GE and AME. The multiple linear regression equations indicated that energy utilisation was enhanced by coupling rapidly digestible protein with slowly digestible starch, which suggests that bilateral bioavailability of starch and protein is pivotal to efficient energy utilisation. Keywords: Broiler chickens, Ferulic acid, Kafirin, Protein, Sorghum, Starch

Substantial reductions in yield caused by drought stress can occur when parts of the root system experience water deficit even though other parts have sufficient access to soil water. To identify proteins associated to drought signaling, rice (Oryza sativa L. cv. IR64.) plants were transplanted into plastic pots with an internal wall dividing each pot into two equal compartments, allowing for equal distribution of soil and the root system between these compartments. The following treatments were applied: either both compartments were watered daily ("wet" roots), or water was withheld from both compartments ("dry" roots), or water was withheld from only one of the two compartments in each pot ("wet" and "dry" roots). The substantial differences in physiological parameters of different growth conditions were accompanied by differential changes in protein abundances. Label-free quantitative shotgun proteomics have resulted in identification of 1383 reproducible proteins across all three conditions. Differentially expressed proteins were categorized within 17 functional groups. The patterns observed were interesting in that in some categories such as protein metabolism and oxidation-reduction, substantial numbers of proteins were most abundant when leaves were receiving signals from "wet" and "dry" roots. In yet other categories such as transport, several key transporters were surprisingly abundant in leaves supported by partially or completely droughted root systems, especially plasma membrane and vacuolar transporters. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soils. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. These results suggest that drought signals are complex interactions and not simply the additive effect of water supply to the roots.

Low root temperature causes a decrease in water uptake, which leads to mineral and nutrient deficiencies with potentially decreased root and shoot growth. Differential temperature effects in plants have been studied extensively, however, the effect of root chilling on the global protein expression in shoots has not been explored. In this study, we imposed chilling temperatures on roots of rice plants while maintaining shoots at optimum atmospheric temperature. Shoot materials (growing zones and leaves) were harvested at five points over a time course of four days, including a two-day recovery period. Proteins were quantified by tandem mass tags and triple stage MS, using a method developed to overcome ratio compression in isobaric-labelled quantitation. Over 3000 proteins in each of the tissues were quantified by multiple peptides. Proteins significantly differentially expressed as compared with the control included abscisic acid-responsive and drought-associated proteins. The data also contained evidence of a possible induction of a sugar signalling pathway.

Grape thaumatin-like (TL) proteins and chitinases play roles in plant-pathogen interactions and can cause protein haze in white wine unless removed prior to bottling. A two-step method is described that highly purified hundreds of milligrams of TL proteins and chitinases from two juices by strong cation exchange (SCX) and hydrophobic interaction chromatography (HIC). The method was fast and separated isoforms of TL proteins and chitinases from within the same juice, in most cases to >97% purity. The isolated proteins were identified by peptide nanoLC-MS/MS and crystallized using a high-throughput screening method. Crystals from three protein fractions produced high-resolution X-ray crystallography data.

The aim of this project was to investigate the molecular mechanisms of shade-avoidance response in tomato ( Solanum lycopersicum) plants. Plants were grown in direct sunlight in ambient temperature and in an adjacent environment under shade cloth. Leaves were harvested, and protein expression differences were investigated using two-dimensional differential in-gel electrophoresis and nanoflow high-performance liquid chromatography-tandem mass spectrometry. Striking differences in plant physiology and protein expression were observed. Plants grown in the shade grew very tall but bore almost no fruit and displayed a dramatic reduction in the accumulation of Rubisco and a number of other metabolic enzymes. We have identified, quantified, and classified 59 protein features found to be up- or down-regulated as part of a shade-avoidance response in S. lycopersicum and correlated these with phenotypic data. A large group of proteins related to metabolism and respiration were greatly reduced in accumulation in shade-grown plants, and there was also evidence of significant proteolysis occurring. Four stress-related proteins appear to be constitutively expressed as a result of heat acclimation, while three distinct stress-related proteins appear to accumulate as part of the shade-avoidance response. The identification and functional classification of all 59 differentially accumulating proteins is presented and discussed.

In this chapter we describe the workflow used in our laboratory to analyze rice leaf samples using label-free shotgun proteomics based on SDS-PAGE fractionation of proteins. Rice proteomics has benefitted substantially from successful execution of shotgun proteomics techniques. We describe steps on how to proceed starting from rice protein extraction, SDS-PAGE, in-gel protein digestion with trypsin, nanoLC-MS/MS, and database searching using the GPM. Data from these experiments can be used for spectral counting, where simultaneous quantitation of several thousand proteins can be obtained.

In this chapter we describe the workflow used in our laboratory to analyze rice leaf samples using label-free shotgun proteomics based on SDS-PAGE fractionation of proteins. Rice proteomics has benefitted substantially from successful execution of shotgun proteomics techniques. We describe steps on how to proceed starting from rice protein extraction, SDS-PAGE, in-gel protein digestion with trypsin, nanoLC-MS/MS, and database searching using the GPM. Data from these experiments can be used for spectral counting, where simultaneous quantitation of several thousand proteins can be obtained.

In this chapter we describe the workflow used in our laboratory for label-free quantitative shotgun proteomics based on spectral counting. The main tools used are a series of R modules known collectively as the Scrappy program. We describe how to go from peptide to spectrum matching in a shotgun proteomics experiment using the XTandem algorithm, to simultaneous quantification of up to thousands of proteins, using normalized spectral abundance factors. The outputs of the software are described in detail, with illustrative examples provided for some of the graphical images generated. While it is not strictly within the scope of this chapter, some consideration is given to how best to extract meaningful biological information from quantitative shotgun proteomics data outputs.

In this chapter we describe the workflow used in our laboratory for label-free quantitative shotgun proteomics based on spectral counting. The main tools used are a series of R modules known collectively as the Scrappy program. We describe how to go from peptide to spectrum matching in a shotgun proteomics experiment using the XTandem algorithm, to simultaneous quantification of up to thousands of proteins, using normalized spectral abundance factors. The outputs of the software are described in detail, with illustrative examples provided for some of the graphical images generated. While it is not strictly within the scope of this chapter, some consideration is given to how best to extract meaningful biological information from quantitative shotgun proteomics data outputs.

Grape chitinase was found to be the primary cause of heat-induced haze formation in white wines. Chitinase was the dominant protein in a haze induced by treating Sauvignon blanc wine at 30 °C for 22 h. In artificial wines and real wines, chitinase concentration was directly correlated to the turbidity of heat-induced haze formation (50 °C for 3 h). Sulfate was confirmed to have a role in haze formation, likely by converting soluble aggregates into larger visible haze particles. Thaumatin-like protein was detected in the insoluble fraction by SDS-PAGE analysis but had no measurable impact on turbidity. Differential scanning calorimetry demonstrated that the complex mixture of molecules in wine plays a role in thermal instability of wine proteins and contributes additional complexity to the wine haze phenomenon.

Rice is susceptible to cold stress and with a future of climatic instability we will be unable to produce enough rice to satisfy increasing demand. A thorough understanding of the molecular responses to thermal stress is imperative for engineering cultivars, which have greater resistance to low temperature stress. In this study we investigated the proteomic response of rice seedlings to 48, 72 and 96 h of cold stress at 12-14°C. The use of both label-free and iTRAQ approaches in the analysis of global protein expression enabled us to assess the complementarity of the two techniques for use in plant proteomics. The approaches yielded a similar biological response to cold stress despite a disparity in proteins identified. The label-free approach identified 236 cold-responsive proteins compared to 85 in iTRAQ results, with only 24 proteins in common. Functional analysis revealed differential expression of proteins involved in transport, photosynthesis, generation of precursor metabolites and energy; and, more specifically, histones and vitamin B biosynthetic proteins were observed to be affected by cold stress.

In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label-free quantitation. Limitations of label-free approaches are considered, label-free approaches are compared with labelling techniques, and forward-looking applications for label-free quantitative data are presented. We conclude that label-free quantitative proteomics is a reliable, versatile, and cost-effective alternative to labelled quantitation.