Identification of a recurrent insertion mutation in the LDLR gene in a Pakistani family with autosomal dominant hypercholesterolemia

Familial Hypercholesterolemia (FH) results in elevated levels of blood lipids including total cholesterol (TC) and low density lipoprotein cholesterol (LDL-C) with normal triglycerides (TG). This disease is one of the major contributors towards an early onset of coronary heart disease (CHD). The aim of the present study was to identify the genes responsible for causing FH in Pakistani population, for this purpose a large consanguineous FH family was selected for genetic analysis. Serum lipid levels, including TC, TG, LDL-C and high density lipoprotein cholesterol (HDL-C), were determined in patients and healthy controls. In order to find the causative mutation in this family, direct sequencing of the low density lipoprotein receptor (LDLR) gene was performed. In addition the part of the Apolipoprotein-B (APOB) gene containing the mutations R3500Q and R3500W was also sequenced. Affected individuals of the family were found to have raised TC and LDL-C levels. Sequencing revealed an insertion mutation (c.2416_2417InsG) in exon 17 of the LDLR gene in all the affected individuals of the family. Common FH causing APOB mutations were not present in this family. Heterozygous individuals had TC levels ranging from ~300–500 mg/dl and the only homozygous individual with typical xanthomas had TC levels exceeding 900 mg/dl. This is the first report of a known LDLR gene mutation causing FH in the Pakistani population. Despite a large heterogeneity of LDLR mutations there are still some common mutations which are responsible for FH throughout the world.     

Comparison of five methods for determination of total plasma protein concentration

Quantitation of exact total protein content is often a key step and is common to many applications in general biochemistry research and routine clinical laboratory practice. Before embarking on any type of protein analysis, particularly comparative techniques, it is important to accurately quantitate the amount of protein in the sample. In order to assess the quality of total protein estimation results, five methods were tested and were applied to the same pooled plasma sample. For this aim, Bradford (Coomassie Brilliant Blue), Lowry (Folin-Ciocalteau), Biüret, Pesce and Strande (Ponceau-S/TCA), and modified method of Schaffner-Weismann (Amido Black 10B) were used. The last two methods employ simultaneous precipitation of proteins with the acid containing dye solutions followed by dissolution of precipitate in a NaOH solution. It is shown that each assay has advantages and disadvantages relative to sensitivity, ease of performance, acceptance in literature, accuracy and reproducibility/coefficient of variation. All of the methods tested show a CV % < 6. Besides pooled plasma, a known concentration of human serum albumin was also analyzed and discussed by means of standardization of plasma total protein content.     

Analysis of citrate accumulation during peach fruit development via a model approach

Based on the citrate model of Lobit and colleagues and measured data, a new model, which is able to reproduce the variation over time of citrate concentration in two peach cultivars, has been proposed. As in the original one, the new model calculates the rate of citrate synthesis or degradation as the product of a 'synthesis potential' and an 'efficiency level'. While in the old model the 'efficiency level' was a simple linear function of temperature and respiration, in the new one its relationship with respiration is accounted for by a coefficient that decreases throughout fruit development. The differences in model parameters between the two cultivars were investigated: late-maturing cv. Suncrest had significantly lower citrate synthesis potential than mid-maturing cv. Fidelia. The responses of citrate concentration to model parameters, temperature, fruit respiration, and growth curves were studied. The most important parameter in the new model, k(4,2), represented the date when the relationship between respiration and 'efficiency level' changed from positive to negative. Raising mean temperature increased the citrate concentration at the beginning and decreased it near maturity for cv. Suncrest, while citrate concentration increased throughout fruit development and more strongly for cv. Fidelia. An increase in the mesocarp dry weight increased both fruit respiration and citrate concentration at the beginning of fruit development, while near maturity it increased fruit respiration but decreased citrate concentration. The model was also able to reproduce the effect of assimilate supply (leaf:fruit ratio). Further potential uses of the model were discussed.     

Towards a virtual fruit focusing on quality: modelling features and potential uses

The fruit is a hierarchically organized organ composed of cells from different tissues. Its quality, defined by traits such as fruit size and composition, is the result of a complex chain of biological processes. These processes involve exchanges (transpiration, respiration, photosynthesis, phloem and xylem fluxes, and ethylene emission) between the fruit and its environment (atmosphere or plant), tissue differentiation, and cell functioning (division, endoreduplication, expansion, metabolic transformations, and vacuolar storage). In order to progress in our understanding of quality development, it is necessary to analyse the fruit as a system, in which processes interact. In this case, a process-based modelling approach is particularly powerful. Such a modelling approach is proposed to develop a future 'virtual fruit' model. The value of a virtual fruit for agronomists and geneticists is also discussed.     

Large scale genotype-phenotype correlation analysis based on phylogenetic trees

We provide two methods for identifying changes in genotype that are correlated with changes in a phenotype implied by phylogenetic trees. The first method, VENN, works when the number of branches over which the change occurred are modest. VENN looks for genetic changes that are completely penetrant with phenotype changes on a tree. The second method, CCTSWEEP, allows for a partial matching between changes in phenotypes and genotypes and provides a score for each change using Maddison's concentrated changes test. The mutations that are highly correlated with phenotypic change can be ranked by score. We use these methods to find SNPs correlated with resistance to Bacillus anthracis in inbred mouse strains. Our findings are consistent with the current biological literature, and also suggest potential novel candidate genes.     

Aerobic training increases the expression of adiponectin receptor genes in the peripheral blood mononuclear cells of young men

Little is known about the effect of exercise training on the expression of adiponectin receptor genes in peripheral blood mononuclear cells (PBMCs). In this study, we investigated the effects of aerobic training on the expression of AdipoR1 and AidpoR2 mRNAs in PBMCs, whole body insulin sensitivity, and circulating adiponectins in men. Thirty young men were randomly assigned to either a control (n=15) or an exercise (n=15) group. Subjects assigned to the exercise group underwent a 12-week jogging and/or running programme on a motor-driven treadmill at an intensity of 60%-75% of the age-based maximum heart rate with duration of 40 minutes per session and a frequency of 5 days per week. Two-way mixed ANOVA with repeated measures was used to test any significant time-by-group interaction effects for the measured variables at p=0.05. We found significant time-by-group interaction effects for waist circumference (p=0.001), VO_2max (p<0.001), fasting insulin (p=0.016), homeostasis model assessment for insulin resistance (HOMA-IR) (p=0.010), area under the curve (AUC) for insulin response during the 75-g oral glucose tolerance test (p=0.002), high-molecular weight (HMW) adiponectin (p=0.016), and the PBMC mRNA levels of AdipoR1 (p<0.001) and AdipoR2 (p=0.001). The exercise group had significantly increased mRNA levels of AdipoR1 and AdipoR2 in PBMCs, along with increased whole body insulin sensitivity and HMW adiponectin, decreased waist circumference, and increased VO_2max compared with the control group. In summary, the current findings suggest that exercise training modulates the expression of AdipoR1 and AdipoR2 mRNAs in PBMCs, implying that manipulation of the expression of these genes could be a potential surrogate for lifestyle intervention-mediated improvements of whole body insulin sensitivity and glucose homeostasis.     

Intracellular adaptor molecules and AR signalling in the tumour microenvironment

Androgen deprivation therapy is the mainstay for treating advanced prostate cancer. A better understanding in the complexity of the androgen receptor (AR) signalling pathway has highlighted that this form of treatment is not sufficient. Since Huggins and Hodges made their crucial observations on the benefits of castration for prostate cancer, significant progress has been achieved in understanding the importance of the cross-talk between the hormone signalling pathway and the kinase signalling network. We now know that preventing androgen production or ligand binding to the AR does not necessarily mark the end of the road for prostate tumour growth. Emerging evidence suggests that there exists a complex set of compensatory mechanisms which allows growth factors to push the transformed cells into a ‘survival adaptation mode’ within the tumour microenvironment. An increase in autocrine and paracrine cascades of growth factor are the most commonly reported events to correlate with progression of androgen-dependent disease to a disseminated androgen independent state. The mechanism of how growth factors can sustain AR activation when cells are deprived of androgens is unknown. This is due to the lack of information about the critical factors linking the intracellular signalling molecules associated with the downstream AR signalling events triggered by growth factors. The aim of this mini review is to highlight a potentially new insight into how intracellular adaptor molecules activated by growth factors may influence and act as a molecular switch to allow the continuation of AR activity in the presence of therapeutic anti-androgens following chemical or surgical castration.     

Evidences of lateral gene transfer between archaea and pathogenic bacteria

Acquisition of new genetic material through horizontal gene transfer has been shown to be an important feature in the evolution of many pathogenic bacteria. Changes in the genetic repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens. However, horizontal gene transfer across the domains i.e. archaea and bacteria is not so common. In this context, we explore events of horizontal gene transfer between archaea and bacteria. In order to determine whether the acquisition of archaeal genes by lateral gene transfer is an important feature in the evolutionary history of the pathogenic bacteria, we have developed a scheme of stepwise eliminations that identifies archaeal-like genes in various bacterial genomes. We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism’s biology and may play a role in pathogenesis.     

An Investigation of the Soil Property Changes and Heavy Metal Accumulation in Relation to Long-term Wastewater Irrigation in the Semi-arid Region of Iran

Concentrations and spatial distribution of Zn, Cu, Cd, and Pb along two landscapes including a wastewater-irrigated area and a control area were determined to assess the impact of long-term wastewater irrigation and landscape properties on heavy metal contamination. Some disturbed and undisturbed soil samples were taken from soil trenches and soil cores, located on three main landscape positions (upper slope, midslope, and lower slope) in northwestern Iran. The investigation showed that the mean concentration of the heavy metals followed the order Zn > Cu > Pb > Cd in the wastewater-irrigated soil and Pb > Zn > Cu > Cd in the control soils. On average, compared to similar positions in the control region, the wastewater-irrigated regions contained 3.0 (midslope) to 4.9 (lower slope), 2.7 (midslope) to 4.6 (lower slope), 3.3 (upper slope) to 4.1 (lower slope), and 1.7 (upper slope) to 2.6 (lower slope) times higher amounts of Zn, Cu, Cd, and Pb, respectively. Significant positive relationships (P < 0.05) were recorded between the heavy metals concentration with <0.002 mm particle-size fraction and organic matter content, the fractions linked to runoff and soil erosion. It is believed that the two soil fractions play a crucial role in the distribution of the metals along the wastewater-irrigated landscape. Despite the significant increase of heavy metals (P < 0.05) in the wastewater-irrigated soils compared with control soils, the concentration of all evaluated metals was below the maximum accepted limits (Zn < 300 mg/kg, Cu < 100 mg/kg, Cd < 5 mg/kg, and Pb < 100 mg/kg), and grouped as “not-enriched” to “moderately-enriched” categories regarding the topsoil enrichment index. Overall, the lower slope was shown to be more contaminated with the heavy metals compared to the other positions.     

Au-Catalyzed Silicon Nanoneedles Synthesized from Pure Silane Gas at Various RF Powers on Silicon Substrate by VHF-PECVD

Silicon nanonowires (SiNWs) were synthesized with approximately 100 nm/min by very-high-frequency plasma-enhanced chemical vapor deposition method via a vapor–liquid–solid mechanism. Pure silane gas was deposited on Au-coated silicon substrates at various radio frequency (RF) powers varied from 5 to 20 W, keeping other deposition parameters constant. Synthesized SiNWs were needle-like shape with an ultra-sharp tip diameter of about 10 nm and a length about 3 μm, which differs from the standard cylindrical nanowire produced by similar techniques. Furthermore, it was shown that the average length of nanoneedles augmented with the increase of RF power. High-resolution transition electron microscopy displayed that the nanowires were composed of a crystalline Si core with an amorphous oxide shell. Raman spectroscopy also revealed the presence of crystalline Si in the grown Si nanoneedles.