Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: a novel tool for the identification and differentiation of humans

In traditional approaches, mitochondrial DNA (mtDNA) variation is exploited for forensic identity testing by sequencing the two hypervariable regions of the human mtDNA control region. To reduce time and labor, single nucleotide polymorphism (SNP) assays are being sought to possibly replace sequencing. However, most SNP assays capture only a portion of the total variation within the desired regions, require a priori knowledge of the position of the SNP in the genome, and are generally not quantitative. Furthermore, with mtDNA, the clustering of SNPs complicates the design of SNP extension primers or hybridization probes. This article describes an automated electrospray ionization mass spectrometry method that can detect a number of clustered SNPs within an amplicon without a priori knowledge of specific SNP positions and can do so quantitatively. With this technique, the base composition of a PCR amplicon, less than 140 nucleotides in length, can be calculated. The difference in base composition between two samples indicates the presence of an SNP. Therefore, no post-PCR analytical construct needs to be developed to assess variation within a fragment. Of the 2754 different mtDNA sequences in the public forensic mtDNA database, nearly 90% could be resolved by the assay. The mass spectrometer is well suited to characterize and quantitate heteroplasmic samples or those containing mixtures. This makes possible the interpretation of mtDNA mixtures (as well as mixtures when assaying other SNPs). This assay can be expanded to assess genetic variation in the coding region of the mtDNA genome and can be automated to facilitate analysis of a large number of samples such as those encountered after a mass disaster.     

Peroxisome proliferator activated receptor alpha regulates a male-specific cytochrome P450 in mouse liver

We set out to find if the strain-specific, male-specific hepatic expression of Cyp4a protein in mouse was due to expression of Cyp4a12 and to understand the genetic basis for reported differences in expression. 12-Lauric acid hydroxylase (LAH) activity was found to show higher levels in male ddY, but not C57Bl/6, mouse liver microsomes. The expression of Cyp4a12 mRNA was studied using RNAase protection assays in male and female liver and kidney of nine mouse strains. Cyp4a12 was found to be highly expressed in male liver and kidney, but at much lower levels in female liver and kidney, in all strains studied. Western blotting with an antibody specific for Cyp4a12 confirmed that Cyp4a12 was expressed in a male specific fashion in C57Bl/6 mouse liver. RNAase protection analysis for Cyp4a10 and 14 in ddY mice revealed that neither of these genes showed male-specific expression. To further investigate genetic factors that control male-specific Cyp4a12 expression, PPARalpha+/+ and -/- mice were studied, showing that total P450 and 12-LAH activity was male-specific in +/+, but not -/- mice. RNAase protection assays were used to confirm that Cyp4a12 was lower in -/- mice. However, the male-specific Slp and MUP-1 genes retained hepatic male-specific levels of expression in +/+ and -/- mice, showing that the decrease in Cyp4a12 was not a general effect on male-specific expression. Thus, PPARalpha has a specific effect on constitutive expression of Cyp4a12.     

Cytochrome P450 Cyp4x1 is a major P450 protein in mouse brain

A novel cytochrome P450, CYP4x1, was identified in EST databases on the basis of similarity to a conserved region in the C-helix of the CYP4A family. The human and mouse CYP4x1 cDNAs were cloned and found to encode putative cytochrome P450 proteins. Molecular modelling of CYP4x1 predicted an unusual substrate binding channel for the CYP4 family. Expression of human CYP4x1 was detected in brain by EST analysis, and in aorta by northern blotting. The mouse cDNA was used to demonstrate that the Cyp4x RNA was expressed principally in brain, and at much lower levels in liver; hepatic levels of the Cyp4x1 RNA were not affected by treatment with the inducing agents phenobarbital, dioxin, dexamethasone or ciprofibrate, nor were the levels affected in PPARalpha-/- mice. A specific antibody for Cyp4x1 was developed, and shown to detect Cyp4x1 in brain; quantitation of the Cyp4x1 protein in brain demonstrated approximately 10 ng of Cyp4x1 protein.mg(-1) microsomal protein, showing that Cyp4x1 is a major brain P450. Immunohistochemical localization of the Cyp4x1 protein in brain showed specific staining of neurons, choroids epithelial cells and vascular endothelial cells. These data suggest an important role for Cyp4x1 in the brain.     

Decorin antagonizes Met receptor activity and down-regulates {beta}-catenin and Myc levels

A theme emerging during the past few years is that members of the small leucine-rich proteoglycan gene family affect cell growth by interacting with multiple receptor tyrosine kinases (RTKs), mostly by a physical down-regulation of the receptors, thereby depriving tumor cells of pro-survival signals. Decorin binds and down-regulates several RTKs, including Met, the receptor for hepatocyte growth factor. Here we demonstrate that decorin blocks several biological activities mediated by the Met signaling axis, including cell scatter, evasion, and migration. These effects were mediated by a profound down-regulation of noncanonical β-catenin levels. In addition, Myc, a downstream target of β-catenin, was markedly down-regulated by decorin, whereas phosphorylation of Myc at threonine 58 was markedly induced. The latter is known to destabilize Myc and target it for proteasomal degradation. We also discovered that systemic delivery of decorin using three distinct tumor xenograft models caused down-regulation of Met and a concurrent suppression of β-catenin and Myc levels. We found that decorin protein core labeled with the near infrared dye IR800 specifically targeted the tumor cells expressing Met. Even 68-h post-injection, decorin was found to reside within the tumor xenografts with little or no binding to other tissues. Collectively, our results indicate a role for a secreted proteoglycan in suppressing the expression of key oncogenic factors required for tumor progression.     

Low O2 avoidance is associated with physiological perturbation but not exhaustion in the snapper (Pagrus auratus: Sparidae)

It is already known that the New Zealand snapper (Pagrus auratus, Sparidae) does not avoid hypoxia until reaching an oxygen partial pressure (PO(2)) of 3.1±1.2 kPa at 18 °C. Avoidance at this level of PO(2) and temperature is below the critical oxygen partial pressure of the species (P(crit)=5.8±0.6 kPa, 43.5±4.5 mmHg) and is therefore expected to result in major physiological stress. Results from the current study showed that avoidance was associated with numerous physiological perturbations, including a significant endocrine response, haematological changes, osmoregulatory disturbance and metabolic adjustments in the heart, liver and muscle. Snapper clearly experienced physiological stress at the point of avoidance but they were not however in a state of physiological exhaustion since some fuel reserves were still available. In addition to avoidance, snapper also showed a subtle reduction in swimming speed - this energy-saving response may have helped snapper minimise the physiological challenge of low O(2) residence. It is therefore concluded that snapper can reside in water below their P(crit) threshold for brief periods of time and, without any evidence of physiological exhaustion at the point of avoidance, fish should recover quickly once normoxia is selected. Lastly, with signs of anaerobic metabolism in cardiac tissue at the point of avoidance, we tentatively suggest that snapper may leave hypoxia to protect heart function.     

Peak power, force, and velocity during jump squats in professional rugby players

Training at the optimal load for peak power output (PPO) has been proposed as a method for enhancing power output, although others argue that the force, velocity, and PPO are of interest across the full range of loads. The aim of this study was to examine the influence of load on PPO, peak barbell velocity (BV), and peak vertical ground reaction force (VGRF) during the jump squat (JS) in a group of professional rugby players. Eleven male professional rugby players (age, 26 ± 3 years; height, 1.83 ± 6.12 m; mass, 97.3 ± 11.6 kg) performed loaded JS at loads of 20-100% of 1 repetition maximum (1RM) JS. A force plate and linear position transducer, with a mechanical braking unit, were used to measure PPO, VGRF, and BV. Load had very large significant effects on PPO (p < 0.001, partial η2 = 0.915); peak VGRF (p < 0.001, partial η2 = 0.854); and peak BV (p < 0.001, partial η2 = 0.973). The PPO and peak BV were the highest at 20% 1RM, though PPO was not significantly greater than that at 30% 1RM. The peak VGRF was significantly greater at 1RM than all other loads, with no significant difference between 20 and 60% 1RM. In resistance trained professional rugby players, the optimal load for eliciting PPO during the loaded JS in the range measured occurs at 20% 1RM JS, with decreases in PPO and BV, and increases in VGRF, as the load is increased, although greater PPO likely occurs without any additional load.     

CNS SIRT3 Expression Is Altered by Reactive Oxygen Species and in Alzheimer’s Disease

Progressive mitochondrial dysfunction contributes to neuronal degeneration in age-mediated disease. An essential regulator of mitochondrial function is the deacetylase, sirtuin 3 (SIRT3). Here we investigate a role for CNS Sirt3 in mitochondrial responses to reactive oxygen species (ROS)- and Alzheimer’s disease (AD)-mediated stress. Pharmacological augmentation of mitochondrial ROS increases Sirt3 expression in primary hippocampal culture with SIRT3 over-expression being neuroprotective. Furthermore, Sirt3 expression mirrors spatiotemporal deposition of β-amyloid in an AD mouse model and is also upregulated in AD patient temporal neocortex. Thus, our data suggest a role for SIRT3 in mechanisms sensing and tackling ROS- and AD-mediated mitochondrial stress.