Label-free MS/MS analyses of the dinoflagellate Lingulodinium identifies rhythmic proteins facilitating adaptation to a diurnal LD cycle.

Protein levels were assessed in the dinoflagellate Lingulodinium polyedra over the course of a diurnal cycle using a label-free LC-MS/MS approach. Roughly 1700 proteins were quantitated in a triplicate dataset over a daily period, and 13 were found to show significant rhythmic changes. Included among the proteins found to be most abundant at night were the two bioluminescence proteins, luciferase and luciferin binding protein, as well as a proliferating cell nuclear protein involved in the nightly DNA replication.

Exploring dinoflagellate biology with high-throughput proteomics.

Dinoflagellates are notorious for their ability to form the harmful algal blooms known as "red tides," yet the mechanisms underlying bloom formation remain poorly understood. Despite recent advances in nucleic acid sequencing, which have generated transcriptomes from a wide range of species exposed to a variety of different conditions, measuring changes in RNA levels have not generally produced great insight into dinoflagellate cell biology or environmental physiology, nor do we have a thorough grasp on the molecular events underpinning bloom formation. Not only is the transcriptomic response of dinoflagellates to environmental change generally muted, but there is a markedly low degree of congruency between mRNA expression and protein expression in dinoflagellates.

Refining Transcriptome Gene Catalogs by MS-Validation of Expressed Proteins.

Protein sequence identification by tandem mass spectroscopy (LC-MS/MS) identifies thousands of protein sequences even in complex mixtures, and provides valuable insight into the biological functions of different cells. For non-model organisms, transcriptomes are generally used to allow peptide identification, an important addition to their use as a gene catalog allowing the potential metabolic activities of cells to be determined. We used LC-MS/MS data to identify which of the six possible reading frames in the transcriptome was actually used by the cell to make protein, and asked whether this would have an impact on downstream analyses using the dataset.

Comparative proteomic studies of a Scrippsiella acuminata bloom with its laboratory-grown culture using a N-metabolic labeling approach.

Comparative proteomic analysis was carried out using cells isolated from a natural bloom of Scrippsiella acuminata (formerly Scrippsiella trochoidea) in the early bloom (EB) and late bloom (LB) stages as well as with laboratory-grown cultures of cells isolated from the bloom in early growth (EG) and late growth (LG) stages. For quantitative proteomics, LG cells were grown for 20 generations in the presence of N as a reference (i.e.

Mercury species of sediment and fish in freshwater fish ponds around the Pearl River Delta, PR China: human health risk assessment.

This study investigated total mercury (THg) and methylmercury (MeHg) concentrations in five species of freshwater fish and their associated fish pond sediments collected from 18 freshwater fish ponds around the Pearl River Delta (PRD). The concentrations of THg and MeHg in fish pond surface sediments were 33.1-386 ng g(-1) dry wt and 0.

Application of fluorescence difference gel electrophoresis technology in searching for protein biomarkers in chick myopia.

The lens-induced myopia (LIM) in response to concave lens (negative lens) is a well established animal model for studying myopia development. However, the exact visual and neurochemical signaling mechanisms involving myopic eye growth are yet to be elucidated. The feasibility of applying a novel two-dimensional fluorescence difference gel electrophoresis technique for global protein profilings and a search for differential protein expressions in LIM were explored in the present study.

The time effect of pressure on tissue viability: investigation using an experimental rat model.

An experimental rat model was used to investigate the time-pressure effect on tissue viability. External loading equivalent to 13.3 kPa (100 mm Hg) of pressure was applied to the greater trochanter and tibialis area of Sprague-Dawley rats using pneumatic indentors for duration of 6 hrs each day for 1 to 4 days.

Effects of prolonged surface pressure on the skin blood flowmotions in anaesthetized rats--an assessment by spectral analysis of laser Doppler flowmetry signals.

The objective of this study is to assess the effect of prolonged surface compression on the skin blood flowmotion in rats using spectral analysis based on wavelets transform of the periodic oscillations of the cutaneous laser Doppler flowmetry (LDF) signal. An external pressure of 13.3 kPa (100 mmHg) was applied to the trochanter area and the distal lateral tibia of Sprague-Dawley rats via two specifically designed pneumatic indentors.

A chick retinal proteome database and differential retinal protein expressions during early ocular development.

Proteomics approach as a research tool has gained popularity in a growing number of basic and clinical researches. However, proteomic research has yet to gain significant momentum in eye research. Hence, we decided to build a retinal proteome database using postnatal retinal tissue from chick, a commonly used animal model in eye research.

Electro-acupuncture potentiates the disulphide-reducing activities of thioredoxin system by increasing thioredoxin expression in ischemia-reperfused rat brains.

Reactive oxygen species can directly affect the conformation and activity of sulfhydryl-containing proteins by oxidation of their thiol moiety. During the process of ischemia-reperfusion, the thioredoxin (Trx) system (consisting of thioredoxin reductase (TR), Trx and NADPH) prevents susceptible proteins from this oxidative modification. Oxidative damage is one of the most damaging stress in ischemia.

Effectiveness of multiple pre-ischemia electro-acupuncture on attenuating lipid peroxidation induced by cerebral ischemia in adult rats.

Free radicals induced by cerebral ischemia-reperfusion injury can trigger lipid peroxidation, leading to the production of malondialdehyde (MDA) and 4-hydroxy-2(E)-nonenal (4-HNE). Post-ischemia electroacupuncture (EA) therapy was able to reduce extent of lipid peroxidation. However, the effect of pre-ischemic EA therapy has not been reported.

Conformational changes in the reaction of pyridoxal kinase.

To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.

Electroacupuncture reduces the extent of lipid peroxidation by increasing superoxide dismutase and glutathione peroxidase activities in ischemic-reperfused rat brains.

Reactive oxygen species can be scavenged by superoxide dismutase (SOD) and glutathione peroxidase (GPx). During ischemia-reperfusion, the normal functioning of these antioxidant enzymes may be insufficient for the prevention of oxidant-induced peroxidation of membrane lipids and hence cerebral infarction. We therefore investigated whether electroacupuncture (EA) treatment at Fengchi points in post-ischemic rats could increase the antioxidant enzyme activities and thereby reduce the extent of lipid peroxidation.

Evaluation of leachate recirculation on nitrous oxide production in the Likang Landfill, China.

Landfill leachate recirculation is efficient in reducing the leachate quantity handled by a leachate treatment plant. However, after land application of leachate, nitrification and denitrification of the ammoniacal N becomes possible and the greenhouse gas nitrous oxide (N2O) is produced. Lack of information on the effects of leachate recirculation on N2O production led to a field study being conducted in the Likang Landfill (Guangzhou, China) where leachate recirculation had been practiced for 8 yr.

Treatment of experimentally induced transient cerebral ischemia with low energy laser inhibits nitric oxide synthase activity and up-regulates the expression of transforming growth factor-beta 1.

Background And Objectives: Nitric oxide (NO) has been shown to be neurotoxic while transforming growth factor-beta 1 (TGF-beta1) is neuroprotective in the stroke model. The present study investigates the effects of low energy laser on nitric oxide synthase (NOS) and TGF-beta1 activities after cerebral ischemia and reperfusion injury.

Study Design/materials And Methods: Cerebral ischemia was induced for 1 hour in male adult Sprague-Dawley (S.

Cloning and characterization of Arabidopsis thaliana pyridoxal kinase.

Pyridoxal kinase (PK; EC 2.7.1.

Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.

The three-dimensional structures of brain pyridoxal kinase and its complex with the nucleotide ATP have been elucidated in the dimeric form at 2.1 and 2.6 A, respectively.

Study of substrate-enzyme interaction between immobilized pyridoxamine and recombinant porcine pyridoxal kinase using surface plasmon resonance biosensor.

Pyridoxal kinase (PK) is an important enzyme involved in bioactivation of vitamin B(6). Binding of PK with its substrate is the prerequisite step for the subsequent catalytic phosphorylation of the substrate. In the present study, a surface plasmon resonance biosensor (BIAcore) was employed to characterize the binding interaction between wild-type porcine PK and an immobilized substrate, pyridoxamine.