On-chip identification and interaction analysis of gel-resolved proteins using a diamond-like carbon-coated plate

We developed a novel protein chip made of a diamond-like, carbon-coated stainless steel plate (DLC plate), the surface of which is chemically modified with N-hydroxysuccinimide ester. To produce a high-density protein chip using the DLC plate, proteins separated by SDS gel electrophoresis or two-dimensional electrophoresis were electroblotted onto the DLC plate and immobilized covalently. A high blotting efficiency (25-70%) for transferring proteins from the gels onto the DLC plates was achieved by improvement of the electrophoresis device and electroblotting techniques. With the use of the DLC plate, we developed novel techniques to identify proteins immobilized on the chip and to detect protein-protein interactions on the chip by mass spectrometric analysis. We also developed a technique to identify post-translationally modified proteins, such as glycoproteins, on the protein chip.     

Effects of different nitrogen rich substrates and their combination to the yield performance of oyster mushroom (<Emphasis Type="Italic">Pleurotus ostreatus</Emphasis>)

This study was conducted to assess the effect of nitrogen (N) variations from lignocellulosic substrates of empty fruit bunch (EFB), palm oil frond (POF), palm oil trunks (POT), A.mangium bark (AB) and Cogongrass (IC), and combinations among them using biological supplements (POF and POT) for suitability as a substrate of P. ostreatus. Three different sets of substrates were evaluated in response to different parameters of P. ostreatus including spawn running, primordial initiation, fruit body yield and biological efficiency (BE). The supplementation of POT and POF generally revealed significant differences on the crop performance of P. ostreatus compared to the un-supplemented substrate. POT demonstrated reduced production time, while POF was the best supplement to promote fresh weight and BE. The most rapid spawn running took place within 18.6 ± 0.9 days, while the primordial initiation was observed within 23.2 ± 0.5 days in the combination of IC + POT. The most suitable substrate for higher mushroom weight and BE was IC + POF (19.6 ± 1.3 g; 70.5 ± 5.5%). In addition, the interval between primordial formations was found to be fastest in the un-supplemented EFB and the combination of EFB + POF, which supported a shortened production time. Therefore, IC and EFB appeared to be the better alternative materials for growing P. ostreatus, either with or without any supplementation.     

The COP1 ortholog PPS regulates the juvenile-adult and vegetative-reproductive phase changes in rice

Because plant reproductive development occurs only in adult plants, the juvenile-to-adult phase change is an indispensable part of the plant life cycle. We identified two allelic mutants, peter pan syndrome-1 (pps-1) and pps-2, that prolong the juvenile phase in rice (Oryza sativa) and showed that rice PPS is an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC1. The pps-1 mutant exhibits delayed expression of miR156 and miR172 and the suppression of GA biosynthetic genes, reducing the GA(3) content in this mutant. In spite of its prolonged juvenile phase, the pps-1 mutant flowers early, and this is associated with derepression of RAP1B expression in pps-1 plants independently of the Hd1-Hd3a/RFT1 photoperiodic pathway. PPS is strongly expressed in the fourth and fifth leaves, suggesting that it regulates the onset of the adult phase downstream of MORI1 and upstream of miR156 and miR172. Its ability to regulate the vegetative phase change and the time of flowering suggests that rice PPS acquired novel functions during the evolution of rice/monocots.     

Functional and genetic survey of all known single-nucleotide polymorphisms within the human deoxyribonuclease I gene in wide-ranging ethnic groups

The single-nucleotide polymorphisms (SNPs) in the human DNase I gene (DNASE1) might be involved in susceptibility to some common diseases; however, only limited population data are available. Further, the effects of these SNPs on in vivo DNase I activity remain unknown. The genotype and haplotype of all the SNPs in DNASE1 were determined in 3 ethnic groups including 14 populations using newly developed methods. Together with our previous data on the nonsynonymous SNPs, two major haplotypes based on the five exonic SNPs were identified; genetic diversity in the Asian population was low. Among 10 SNPs, other than exonic SNPs in the gene, only 3 were polymorphic among all the populations. Haplotype distribution, based on all the polymorphic SNPs, was clarified to be generally varied in an ethnic-dependent manner. Thus, the genetic aspects of DNASE1 with regard to all the SNPs in wide-ranging ethnic groups could be first demonstrated. Further, there was no correlation of all the polymorphic SNPs other than nonsynonymous ones with serum DNase I activity levels. Polymorphic SNPs other than the exonic SNPs might not be directly related to common diseases through alterations in in vivo levels of the activity.     

PIWI-interacting small RNAs: the vanguard of genome defence

PIWI-interacting RNAs (piRNAs) are a distinct class of small non-coding RNAs that form the piRNA-induced silencing complex (piRISC) in the germ line of many animal species. The piRISC protects the integrity of the genome from invasion by 'genomic parasites'--transposable elements--by silencing them. Owing to their limited expression in gonads and their sequence diversity, piRNAs have been the most mysterious class of small non-coding RNAs regulating RNA silencing. Now, much progress is being made into our understanding of their biogenesis and molecular functions, including the specific subcellular compartmentalization of the piRNA pathway in granular cytoplasmic bodies.     

Plasma L-cystine/L-glutamate imbalance increases tumor necrosis factor-alpha from CD14+ circulating monocytes in patients with advanced cirrhosis

Background and Aims

The innate immune cells can not normally respond to the pathogen in patients with decompensated cirrhosis. Previous studies reported that antigen-presenting cells take up L-Cystine (L-Cys) and secrete substantial amounts of L-Glutamate (L-Glu) via the transport system Xc- (4F2hc+xCT), and that this exchange influences the immune responses. The aim of this study is to investigate the influence of the plasma L-Cys/L-Glu imbalance observed in patients with advanced cirrhosis on the function of circulating monocytes.

Methods

We used a serum-free culture medium consistent with the average concentrations of plasma amino acids from patients with advanced cirrhosis (ACM), and examined the function of CD14+ monocytes or THP-1 under ACM that contained 0–300 nmol/mL L-Cys with LPS. In patients with advanced cirrhosis, we actually determined the TNF-alpha and xCT mRNA of monocytes, and evaluated the correlation between the plasma L-Cys/L-Glu ratio and TNF-alpha.

Results

The addition of L-Cys significantly increased the production of TNF alpha from monocytes under ACM. Monocytes with LPS and THP-1 expressed xCT and a high level of extracellular L-Cys enhanced L-Cys/L-Glu antiport, and the intracellular GSH/GSSG ratio was decreased. The L-Cys transport was inhibited by excess L-Glu. In patients with advanced cirrhosis (n = 19), the TNF-alpha and xCT mRNA of monocytes were increased according to the Child-Pugh grade. The TNF-alpha mRNA of monocytes was significantly higher in the high L-Cys/L-Glu ratio group than in the low ratio group, and the plasma TNF-alpha was significantly correlated with the L-Cys/L-Glu ratio.

Conclusions

A plasma L-Cys/L-Glu imbalance, which appears in patients with advanced cirrhosis, increased the TNF-alpha from circulating monocytes via increasing the intracellular oxidative stress. These results may reflect the immune abnormality that appears in patients with decompensated cirrhosis.     

Neuronal representations of stimuli in the mouth: the primate insular taste cortex, orbitofrontal cortex and amygdala

The responses of 3687 neurons in the macaque primary taste cortex in the insula/frontal operculum, orbitofrontal cortex (OFC) and amygdala to oral sensory stimuli reveals principles of representation in these areas. Information about the taste, texture of what is in the mouth (viscosity, fat texture and grittiness, which reflect somatosensory inputs), temperature and capsaicin is represented in all three areas. In the primary taste cortex, taste and viscosity are more likely to activate different neurons, with more convergence onto single neurons particularly in the OFC and amygdala. The different responses of different OFC neurons to different combinations of these oral sensory stimuli potentially provides a basis for different behavioral responses. Consistently, the mean correlations between the representations of the different stimuli provided by the population of OFC neurons were lower (0.71) than for the insula (0.81) and amygdala (0.89). Further, the encoding was more sparse in the OFC (0.67) than in the insula (0.74) and amygdala (0.79). The insular neurons did not respond to olfactory and visual stimuli, with convergence occurring in the OFC and amygdala. Human psychophysics showed that the sensory spaces revealed by multidimensional scaling were similar to those provided by the neurons.