A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing,the Case of the Mitochondrial Genome

The advent of massive parallel sequencing (MPS) has revolutionized the field of human molecular genetics, including the diagnostic study of mitochondrial (mt) DNA dysfunction. The analysis of the complete mitochondrial genome using MPS platforms is now common and will soon outrun conventional sequencing. However, the development of a robust and reliable protocol is rather challenging. A previous pilot study for the re-sequencing of human mtDNA revealed an uneven coverage, affecting predominantly part of the plus strand. In an attempt to address this problem, we undertook a comparative study of standard and modified protocols for the Ion Torrent PGM system. We could not improve strand representation by altering the recommended shearing methodology of the standard workflow or omitting the DNA polymerase amplification step from the library construction process. However, we were able to associate coverage bias of the plus strand with a specific sequence motif. Additionally, we compared coverage and variant calling across technologies. The same samples were also sequenced on a MiSeq device which showed that coverage and heteroplasmic variant calling were much improved.     

Genetic mark–recapture population estimation in black bears and issues of scale

Abundance estimates for black bears (Ursus americanus) are important for effective management. Recently, DNA technology has resulted in widespread use of noninvasive, genetic capture–mark–recapture (CMR) approaches to estimate populations. Few studies have compared the genetic CMR methods to other estimation methods. We used genetic CMR to estimate the bear population at 2 study sites in northern New Hampshire (Pittsburg and Milan) in 2 consecutive years. We compared these estimates to those derived from traditional methods used by the New Hampshire Fish and Game Department (NHFG) using hunter harvest and mortality data. Density estimates produced with genetic CMR methods were similar both years and were comparable to those derived from traditional methods. In 2006, the estimated number of bears in Pittsburg was 79 (95% CI = 60–98) corresponding to a density of 15–24 (95% CI) bears/100 km²; the 2007 estimate was 83 (95% CI = 67–99; density = 16–24 bears/100 km²). In 2006, the estimated number of bears in Milan was 95 (95% CI = 74–117; density = 16–25 bears/100 km²); the 2007 estimate was 96 (95% CI = 77–114; density = 17–25 bears/100 km²). We found that genetic CMR methods were able to identify demographic variation at a local scale, including a strongly skewed sex ratio (2 M:1 F) in the Milan population. Genetic CMR is a useful tool for wildlife managers to monitor populations of local concern, where abundance or demographic characteristics may deviate from regional estimates. Future monitoring of the Milan population with genetic CMR is recommended to determine if the sex ratio bias continues, possibly warranting a change in local harvest regimes. © 2011 The Wildlife Society.     

Characterization of complex III deficiency and liver dysfunction in GRACILE syndrome caused by a BCS1L mutation

A homozygous mutation in the complex III chaperone BCS1L causes GRACILE syndrome (intrauterine growth restriction, aminoaciduria, cholestasis, hepatic iron overload, lactacidosis). In control and patient fibroblasts we localized BCS1L in inner mitochondrial membranes. In patient liver, kidney, and heart BCS1L and Rieske protein levels, as well as the amount and activity of complex III, were decreased. Major histopathology was found in kidney and liver with cirrhosis and iron deposition, but of iron-related proteins only ferritin levels were high. In placenta from a GRACILE fetus, the ferrooxidases ceruloplasmin and hephaestin were upregulated suggesting association between iron overload and placental dysfunction.     

2D proteome analysis initiates new Insights on the Salmonella Typhimurium LuxS protein

Background  

Quorum sensing is a term describing a bacterial communication system mediated by the production and recognition of small signaling molecules. The LuxS enzyme, catalyzing the synthesis of AI-2, is conserved in a wide diversity of bacteria. AI-2 has therefore been suggested as an interspecies quorum sensing signal. To investigate the role of endogenous AI-2 in protein expression of the Gram-negative pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), we performed a 2D-DIGE proteomics experiment comparing total protein extract of wildtype S. Typhimurium with that of a luxS mutant, unable to produce AI-2.     

The effect of temperature on lipid-n-alkane interactions in lipid bilayers

The relationship between age-related alterations in the lipid composition of cultured rat-heart fibroblasts and several biochemical and biophysical parameters was investigated. Aged (14-15-day-old) cultures displayed higher mole ratios of sphingomyelin to phosphatidylcholine, as well as elevated cholesterol levels. A concomitant increase was observed in the total protein content of the cells and in the Vmax values of both membranal and cytoplasmic marker enzymes. Fluorescence photobleaching recovery was employed to study the lateral mobility of the lipid probe NBD-phosphatidylethanolamine and of membrane glycoproteins that bind succinylated concanavalin A. The mobile fractions of both probes were higher in aged cultures, while the lateral diffusion coefficients were lower. To further demonstrate the dependence of the above parameters on the cellular lipid composition, we have manipulated the lipid composition of old cultures by treatments with liposomes (small unilamellar vesicles) of specific compositions. Treatments which reversed the lipid composition towards that of young (5-6-day-old) cultures caused a concomitant reversal of the measured biochemical and biophysical parameters to the values observed in young cultures. These findings suggest that alterations in the organization and mobility of cell membrane constituents are involved in mediating changes in cellular functions. In view of our previous findings on cultures of rat-heart myocytes (Yechiel, E., Barenholz, Y. and Henis, Y.I. (1985) J. Biol. Chem. 260, 9132-9136), it appears that the modulation of cellular properties through the membrane lipid composition may be a general phenomenon in many cell types.     

Kinetic Evidence for Unique Regulation of GLUT4 Trafficking by Insulin and AMP-activated Protein Kinase Activators in L6 Myotubes

In L6 myotubes, redistribution of a hemagglutinin (HA) epitope-tagged GLUT4 (HA-GLUT4) to the cell surface occurs rapidly in response to insulin stimulation and AMP-activated protein kinase (AMPK) activation. We have examined whether these separate signaling pathways have a convergent mechanism that leads to GLUT4 mobilization and to changes in GLUT4 recycling. HA antibody uptake on GLUT4 in the basal steady state reached a final equilibrium level that was only 81% of the insulin-stimulated level. AMPK activators (5-aminoimidazole-4-carboxyamide ribonucleoside (AICAR) and A-769662) led to a similar level of antibody uptake to that found in insulin-stimulated cells. However, the combined responses to insulin stimulation and AMPK activation led to an antibody uptake level of ∼20% above the insulin level. Increases in antibody uptake due to insulin, but not AICAR or A-769662, treatment were reduced by both wortmannin and Akt inhibitor. The GLUT4 internalization rate constant in the basal steady state was very rapid (0.43 min⁻¹) and was decreased during the steady-state responses to insulin (0.18 min⁻¹), AICAR (0.16 min⁻¹), and A-769662 (0.24 min⁻¹). This study has revealed a nonconvergent mobilization of GLUT4 in response to activation of Akt and AMPK signaling. Furthermore, GLUT4 trafficking in L6 muscle cells is very reliant on regulated endocytosis for control of cell surface GLUT4 levels.