Microbacterium suwonense sp. nov., isolated from cow dung

An actinomycete strain, designated M1T8B9^T, was isolated from cow dung in Suwon, Republic of Korea. The isolate was a Gram-positive, nonmotile, and non-spore-forming bacterium. Phylogenetic evaluation based on 16S rRNA gene sequence similarity showed that this isolate belongs to the genus Microbacterium, with its closest neighbors being Microbacterium soli DCY17^T (98.2%) and Microbacterium esteraromaticum DSM 8609^T (98.0%). The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, and one unknown glycolipid. Strain M1T8B9^T contained the major fatty acids C_15:0 anteiso, C_16:0 iso, C _17:0 anteiso, and C_15:0 iso, and the cell-wall peptidoglycan was of type B2β. According to DNA-DNA hybridization studies, strain M1T8B9^T showed 42% and 26% relatedness with M. soli DCY17^T and M. esteraromaticum DSM 8609^T, respectively. On the basis of the data presented, strain M1T8B9^T is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium suwonense sp. nov. is proposed. The type strain is M1T8B9^T (=KACC 14058^T =NBRC 106310^T).     

Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field

A bacterial strain, designated GR24-5^T, was isolated from soil cultivated with Korean ginseng. Cells were Gram-negative, strictly aerobic, catalase- and oxidase-positive, non-spore-forming motile rods. Based on the 16S rRNA gene sequence, strain GR24-5^T could be assigned to the family Alcaligenaceae. Strain GR24-5^T showed the highest sequence similarities with Parapusillimonas granuli Ch07^T (97.1%), Pusillimonas noertemannii BN9^T (96.9%), Pigmentiphaga kullae DSM 13608^T (96.5%), and Castellaniella defragrans 54Pin^T (96.3%). Strain GR24-5^T demonstrated a low DNA-DNA relatedness (23%) with P. granuli Ch07^T. The major respiratory quinone is ubiquinone 8 (Q-8) and the major fatty acids are C_16:0, C_17:0 cyclo, and summed feature 1 (C_14:0 3-OH/iso-C_16:1 I/C_12:0 aide). Putrescine, spermidine, and 2-hydroxyputrescine are the major polyamines. The major polar lipids are phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, di-phosphatidylglycerol, and an unknown aminophospholipid. Polar lipid patterns of strain GR24-5^T were unique in having a large amount of phosphatidylmethylethanolamine. Based on phylogenetic analysis and physiological and biochemical characteristics, strain GR245^T represents a novel genus and species, for which the name Paralcaligenes ureilyticus gen. nov., sp. nov. is proposed. The type strain of P. aralcaligenes ureilyticus is GR24-5^T (=KACC 13888 =DSM 24591^T).     

Metabolite profiles and the risk of developing diabetes

Emerging technologies allow the high-throughput profiling of metabolic status from a blood specimen (metabolomics). We investigated whether metabolite profiles could predict the development of diabetes. Among 2,422 normoglycemic individuals followed for 12 years, 201 developed diabetes. Amino acids, amines and other polar metabolites were profiled in baseline specimens by liquid chromatography-tandem mass spectrometry (LC-MS). Cases and controls were matched for age, body mass index and fasting glucose. Five branched-chain and aromatic amino acids had highly significant associations with future diabetes: isoleucine, leucine, valine, tyrosine and phenylalanine. A combination of three amino acids predicted future diabetes (with a more than fivefold higher risk for individuals in top quartile). The results were replicated in an independent, prospective cohort. These findings underscore the potential key role of amino acid metabolism early in the pathogenesis of diabetes and suggest that amino acid profiles could aid in diabetes risk assessment.     

Cyclophilin D deficiency protects against acetaminophen-induced oxidant stress and liver injury

Acetaminophen (APAP) hepatotoxicity is the main cause of acute liver failure in humans. Although mitochondrial oxidant stress and induction of the mitochondrial permeability transition (MPT) have been implicated in APAP-induced hepatotoxicity, the link between these events is unclear. To investigate this, this study evaluated APAP hepatotoxicity in mice deficient of cyclophilin D, a protein component of the MPT. Treatment of wild type mice with APAP resulted in focal centrilobular necrosis, nuclear DNA fragmentation and formation of reactive oxygen (elevated glutathione disulphide levels) and peroxynitrite (nitrotyrosine immunostaining) in the liver. CypD-deficient (Ppif(-/-)) mice were completely protected against APAP-induced liver injury and DNA fragmentation. Oxidant stress and peroxynitrite formation were blunted but not eliminated in CypD-deficient mice. Thus, mitochondrial oxidative stress and induction of the MPT are critical events in APAP hepatotoxicity in vivo and at least part of the APAP-induced oxidant stress and peroxynitrite formation occurs downstream of the MPT.     

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

Background

Sorghum (Sorghum bicolor) is globally produced as a source of food, feed, fiber and fuel. Grain and sweet sorghums differ in a number of important traits, including stem sugar and juice accumulation, plant height as well as grain and biomass production. The first whole genome sequence of a grain sorghum is available, but additional genome sequences are required to study genome-wide and intraspecific variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C₄ crop.

Results

We resequenced two sweet and one grain sorghum inbred lines, and identified a set of nearly 1,500 genes differentiating sweet and grain sorghum. These genes fall into ten major metabolic pathways involved in sugar and starch metabolisms, lignin and coumarin biosynthesis, nucleic acid metabolism, stress responses and DNA damage repair. In addition, we uncovered 1,057,018 SNPs, 99,948 indels of 1 to 10 bp in length and 16,487 presence/absence variations as well as 17,111 copy number variations. The majority of the large-effect SNPs, indels and presence/absence variations resided in the genes containing leucine rich repeats, PPR repeats and disease resistance R genes possessing diverse biological functions or under diversifying selection, but were absent in genes that are essential for life.

Conclusions

This is a first report of the identification of genome-wide patterns of genetic variation in sorghum. High-density SNP and indel markers reported here will be a valuable resource for future gene-phenotype studies and the molecular breeding of this important crop and related species.     

Biomechanical signals and the C-type natriuretic peptide counteract catabolic activities induced by IL-1β in chondrocyte/agarose constructs

Introduction  

The present study examined the effect of C-type natriuretic peptide (CNP) on the anabolic and catabolic activities in chondrocyte/agarose constructs subjected to dynamic compression.     

Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation

Determining the forces that conserve amino acid positions in proteins across species is a fundamental pursuit of molecular evolution. Evolutionary conservation is driven by either a protein's function or its thermodynamic stability. Highly conserved histone proteins offer a platform to evaluate these driving forces. While the conservation of histone H3 and H4 "tail" domains and surface residues are driven by functional importance, the driving force behind the conservation of buried histone residues has not been examined. Using a computational approach, we determined the thermodynamically preferred amino acids at each buried position in H3 and H4. In agreement with what is normally observed in proteins, we find a significant correlation between thermodynamic stability and evolutionary conservation in the buried residues in H4. In striking contrast, we find that thermodynamic stability of buried H3 residues does not correlate with evolutionary conservation. Given that these H3 residues are not post-translationally modified and only regulate H3-H3 and H3-H4 stabilizing interactions, our data imply an unknown function responsible for driving conservation of these buried H3 residues.     

Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links

The differences in efficacy and molecular mechanisms of platinum anti-cancer drugs cisplatin (CP) and oxaliplatin (OX) are thought to be partially due to the differences in the DNA conformations of the CP and OX adducts that form on adjacent guanines on DNA, which in turn influence the binding of damage-recognition proteins that control downstream effects of the adducts. Here we report a comprehensive comparison of the structural distortion of DNA caused by CP and OX adducts in the TGGT sequence context using nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations. When compared to our previous studies in other sequence contexts, these structural studies help us understand the effect of the sequence context on the conformation of Pt-GG DNA adducts. We find that both the sequence context and the type of Pt-GG DNA adduct (CP vs. OX) play an important role in the conformation and the conformational dynamics of Pt-DNA adducts, possibly explaining their influence on the ability of many damage-recognition proteins to bind to Pt-DNA adducts.