Autotoxic potential of cucurbit crops

Soil sickness is often observed in cucurbit crops such as Citrullus lanatus, Cucumis melo and Cucumis sativus, but not in cucurbit crops such as Cucurbita moschata, Lagenaria leucantha and Luffa cylindrica. Results showed that root aqueous extracts of Citrullus lanatus, Cucumis melo and Cucumis sativus were autotoxic, but those of Cucurbita moschata, Momordica charantia and Luffa cylindrica were less autotoxic to the radicle elongation of respective species. Plant growth of Citrullus lanatus, Cucumis melo and Cucumis sativus were greatly inhibited by autotoxic substances released from powered root tissue at a rate of 1 g per seedling. Root exudates of Citrullus lanatus, Cucumis melo and Cucumis sativus were autotoxic to radicle elongation and seedling growth of respective species. However, root exudates of Citrullus lanatus did not inhibit radicle elongation of Cucurbita ficifolia, which is commonly used as rootstock for the grafting of Citrullus lanatus, Cucumis melo and Cucumis sativus to decrease soil-borne diseases in commercial production. It seems possible to overcome autotoxicity in cucurbit crops by grafting on Cucurbita ficifolia. This revised version was published online in June 2006 with corrections to the Cover Date.     

Differential ConA-enriched urinary proteome in rat experimental glomerular diseases

Glomerular diseases are leading causes of end-stage renal diseases worldwide. They are considered to be consequences of injury primarily to the three types of glomerular cells. Differential diagnosis typically relies on invasive biopsy findings. We expected that injuries of different glomerular cells would cause different changes in urinary proteome. The goal of this study was to identify differential urinary proteins distinguishing between injuries of different glomerular cells before significant histopathologic changes. Adriamycin nephropathy and Thy1.1 glomerulonephritis were employed as models with different primary impaired cells. ConA-enriched urinary glycoproteome on day3 were profiled by gel-free shotgun tandem mass spectrometry, and compared with self-healthy controls to identify differential urinary proteins for each model. By comparing the changes of the differential proteins between these two models, we identified 39 proteins with different directions of changes, which may potentially be useful in differentiation; and 7 proteins with the same direction of changes, which may be potential indicators of early renal damage. These differential proteins were of several origins: plasma proteins, proteins with urine or kidney specificity, proteins without tissue-specificity (mainly inflammatory mediators) etc. Our results may help better understand the effects of injuries of different glomerular cells at the initial stage, and lead to the discovery of novel early diagnostic markers for human focal segmental glomerulosclerosis (FSGS) and mesangioproliferative glomerulonephritis (MsPGN) which have the same primary impaired cells with adriamycin nephropathy and Thy1.1 glomerulonephritis, respectively.     

Predicting protein fold types by the general form of Chou's pseudo amino acid composition: approached from optimal feature extractions

Identification on protein folding types is always based on the 27-class folds dataset, which was provided by Ding & Dubchak in 2001. But with the avalanche of protein sequences, fold data is also expanding, so it will be the inevitable trend to improve the existing dataset and expand more folding types. In this paper, we construct a multi-class protein fold dataset, which contains 3,457 protein chains with sequence identity below 35% and could be classified into 76 fold types. It was 4 times larger than Ding & Dubchak's dataset. Furthermore, our work proposes a novel approach of support vector machine based on optimal features. By combining motif frequency, low-frequency power spectral density, amino acid composition, the predicted secondary structure and the values of auto-correlation function as feature parameters set, the method adopts criterion of the maximum correlation and the minimum redundancy to filter these features and obtain a 95-dimensions optimal feature subset. Based on the ensemble classification strategy, with 95-dimensions optimal feature as input parameters of support vector machine, we identify the 76-class protein folds and overall accuracy measures up to 44.92% by independent test. In addition, this method has been further used to identify upgraded 27-class protein folds, overall accuracy achieves 66.56%. At last, we also test our method on Ding & Dubchak's 27-class folds dataset and obtained better identification results than most of the previous reported results.     

The neurotoxicity of iron,copper and cobalt in Parkinson’s disease through ROS-mediated mechanisms

Parkinson’s disease (PD) is the second most common neurodegenerative disease with gradual loss of dopaminergic neurons. Despite extensive research in the past decades, the etiology of PD remains elusive. Nevertheless, multiple lines of evidence suggest that oxidative stress is one of the common causes in the pathogenesis of PD. It has also been suggested that heavy metal-associated oxidative stress may be implicated in the etiology and pathogenesis of PD. Here we review the roles of redox metals, including iron, copper and cobalt, in PD. Iron is a highly reactive element and deregulation of iron homeostasis is accompanied by concomitant oxidation processes in PD. Copper is a key metal in cell division process, and it has been shown to have an important role in neurodegenerative diseases such as PD. Cobalt induces the generation of reactive oxygen species (ROS) and DNA damage in brain tissues.     

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding

Background

More than 7000 papers related to “protein refolding” have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource – “REFOLDdb” that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest.

Results

We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17^th, 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/.

Conclusion

REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

     

Large-scale identification of proteins in human salivary proteome by liquid chromatography/mass spectrometry and two-dimensional gel electrophoresis-mass spectrometry

Human saliva contains a large number of proteins and peptides (salivary proteome) that help maintain homeostasis in the oral cavity. Global analysis of human salivary proteome is important for understanding oral health and disease pathogenesis. In this study, large-scale identification of salivary proteins was demonstrated by using shotgun proteomics and two-dimensinal gel electrophoresis-mass spectrometry (2-DE-MS). For the shotgun approach, whole saliva proteins were prefractionated according to molecular weight. The smallest fraction, presumably containing salivary peptides, was directly separated by capillary liquid chromatography (LC). However, the large protein fractions were digested into peptides for subsequent LC separation. Separated peptides were analyzed by on-line electrospray tandem mass spectrometry (MS/MS) using a quadrupole-time of flight mass spectrometer, and the obtained spectra were automatically processed to search human protein sequence database for protein identification. Additionally, 2-DE was used to map out the proteins in whole saliva. Protein spots 105 in number were excised and in-gel digested; and the resulting peptide fragments were measured by matrix-assisted laser desorption/ionization-mass spectrometry and sequenced by LC-MS/MS for protein identification. In total, we cataloged 309 proteins from human whole saliva by using these two proteomic approaches.     

阿片类物质在中枢神经系统的免疫调控作用

内源及外源性阿片具有调节神经元与胶质细胞的功能,这些调节具有保护或损伤脑功能的双重作用。吗啡具有促进受病毒复制及继发感染的作用。另一方面,阿片受体中的ｋａｐｐａ受体可能具有保护神经元的作用。更深层次的研究应是了解阿片通过什么机制作用在胶质细胞和神经元上,藉此以促进研制出具有明显疗效的新药。     

Evaluation of Finnish Diabetes Risk Score in Screening Undiagnosed Diabetes and Prediabetes among U.S. Adults by Gender and Race: NHANES 1999-2010

Objective

To evaluate the performance of Finnish Diabetes Risk Score (FINDRISC) in detecting undiagnosed diabetes and prediabetes among U.S. adults by gender and race.

Methods

This cross-sectional analysis included participants (aged ≥20 years) from the National Health and Nutrition Examination Survey (NHANES) 1999–2010. Sensitivity, specificity, area under the receiver operating characteristic (ROC) curve and the optimal cutoff points for identifying undiagnosed diabetes and prediabetes were calculated for FINDRISC by gender and race/ethnicity.

Results

Among the 20,633 adults (≥20 years), 49.8% were women and 53.0% were non-Hispanic White. The prevalence of undiagnosed diabetes and prediabetes was 4.1% and 35.6%, respectively. FINDRISC was positively associated with the prevalence of diabetes (OR = 1.48 for 1 unit increase, p<0.001) and prediabetes (OR = 1.15 for 1 unit increase, p<0.001). The area under ROC for detecting undiagnosed diabetes was 0.75 for total population, 0.74 for men and 0.78 for women (p = 0.04); 0.76 for White, 0.76 for Black and 0.72 for Hispanics (p = 0.03 for White vs. Hispanics). The area under ROC for detecting prediabetes was 0.67 for total population, 0.66 for men and 0.70 for women (p<0.001); 0.68 for White, 0.67 for Black and 0.65 for Hispanics (p<0.001 for White vs. Hispanics). The optimal cutoff point was 10 (sensitivity = 0.75) for men and 12 (sensitivity = 0.72) for women for detecting undiagnosed diabetes; 9 (sensitivity = 0.61) for men and 10 (sensitivity = 0.69) for women for detecting prediabetes.

Conclusions

FINDRISC is a simple and non-invasive screening tool to identify individuals at high risk for diabetes in the U.S. adults.     

Alterations in cell membrane properties caused by perfluorinated compounds

The recent detection of perfluorinated compounds (PFCs) in wildlife from even remote locations has spurred interest in the environmental occurrence and effects of these chemicals. While the global distribution of PFCs is increasingly understood, there is still little information available on their effects on wildlife. The amphiphillic nature of PFCs suggests that their effects could be primarily on cell membranes. In this study we measured the effects of PFCs on membrane fluidity and mitochondrial membrane potential using flow cytometry and effects on membrane permeability using cell bioassay procedures (H4IIE, MCF-7, PLHC-1). Of the PFCs tested, only perfluorooctane sulfonic acid (PFOS) increased the permeability of cell membranes to the hydrophobic ligands used. Three PFCs were tested in the membrane fluidity assay: PFOS, perfluorohexane sulfonic acid (PFHS), and perfluorobutane sulfonic acid (PFBS). PFOS increased membrane fluidity in fish leukocytes in a dose-dependent fashion, while PFHS and PFBS had no effect in the concentration range tested. The lowest effective concentrations for the membrane fluidity effects of PFOS were 5-15 mg/l. Effects on mitochondrial membrane potential occurred in the same concentration range as effects on membrane fluidity. This suggests that PFOS effects membrane properties at concentrations below those associated with other adverse effects.     

EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences

Background  

Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in bioinformatics for improving the prediction accuracy by exploiting the synergetic prediction capability of multiple algorithms.