Haemochromatosis and HLA--H

The recently identified can didate gene, HLA-H, for haemochromatosis (HH) by Feder et al. generated considerable scientific interest coupled with a degree of uncertainty about the likely involvement of this gene in this common iron metabolism disorder, Feder et al. found a single point mutation resulting in an amino acid substitution (C282Y) that was homozygous in 148 (83%) of their patients, heterozygous in 9 patients (5%) but completely absent in 21 patients (12%). They proposed that the lack of a causative mutation in HLA-H in 12% of their patients was because these cases were not linked to chromosome 6p. A significant weakness in this argument is that all familial studies of the disorder so far have concluded that HH is due to a single major HLA-linked gene5-7. The ultimate test for a candidate gene is the clear segregation of a mutation with the disorder in all patients. Thus, some of the uncertainty surrounding the role of HLA-H in HH may be resolved by the identification of complete concordance of the C282Y mutation (or some other mutation) in HLA H with disease status in HH families. One potential problem in the design of such an experimental analysis is that a number of studies have shown the presence of a predominant ancestral haplotype in all HH populations examined: Australian, French, Italian, UK and US Thus in the analysis of a putative causative mutation, it is important to include families with...

Maximum loadability achievement in SWER networks using optimal sizing and locating of batteries

This paper presents an optimisation algorithm to maximize the loadability of single wire earth return (SWER) by minimizing the cost of batteries and regulators considering the voltage constraints and thermal limits. This algorithm, that finds the optimum location of batteries and regulators, uses hybrid discrete particle swarm optimization and mutation (DPSO + Mutation). The simulation results on realistic highly loaded SWER network show the effectiveness of using battery to improve the loadability of SWER network in a cost-effective way. In this case, while only 61% of peak load can be supplied without violating the constraints by existing network, the loadability of the network is increased to peak load by utilizing two battery sites which are located optimally. That is, in a SWER system like the studied one, each installed kVA of batteries, optimally located, supports a loadability increase as 2 kVA.

A modified particle swarm optimization for correlated phenomena

The wide applicability of correlation analysis inspired the development of this paper. In this paper, a new correlated modified particle swarm optimization (COM-PSO) is developed. The Correlation Adjustment algorithm is proposed to recover the correlation between the considered variables of all particles at each of iterations. It is shown that the best solution, the mean and standard deviation of the solutions over the multiple runs as well as the convergence speed were improved when the correlation between the variables was increased. However, for some rotated benchmark function, the contrary results are obtained. Moreover, the best solution, the mean and standard deviation of the solutions are improved when the number of correlated variables of the benchmark functions is increased. The results of simulations and convergence performance are compared with the original PSO. The improvement of results, the convergence speed, and the ability to simulate the correlated phenomena by the proposed COM-PSO are discussed by the experimental results.

An efficient hybrid evolutionary optimization algorithm based on PSO and SA for clustering

The K-means algorithm is one of the most popular techniques in clustering. Nevertheless, the performance of the K-means algorithm depends highly on initial cluster centers and converges to local minima. This paper proposes a hybrid evolutionary programming based clustering algorithm, called PSO-SA, by combining particle swarm optimization (PSO) and simulated annealing (SA). The basic idea is to search around the global solution by SA and to increase the information exchange among particles using a mutation operator to escape local optima. Three datasets, Iris, Wisconsin Breast Cancer, and Ripley’s Glass, have been considered to show the effectiveness of the proposed clustering algorithm in providing optimal clusters. The simulation results show that the PSO-SA clustering algorithm not only has a better response but also converges more quickly than the K-means, PSO, and SA algorithms.

Distribution harmonic state estimation based on a modified PSO considering parameters uncertainty

This paper presents a new algorithm based on a Modified Particle Swarm Optimization (MPSO) to estimate the harmonic state variables in a distribution networks. The proposed algorithm performs the estimation for both amplitude and phase of each injection harmonic currents by minimizing the error between the measured values from Phasor Measurement Units (PMUs) and the values computed from the estimated parameters during the estimation process. The proposed algorithm can take into account the uncertainty of the harmonic pseudo measurement and the tolerance in the line impedances of the network as well as the uncertainty of the Distributed Generators (DGs) such as Wind Turbines (WTs). The main features of the proposed MPSO algorithm are usage of a primary and secondary PSO loop and applying the mutation function. The simulation results on 34-bus IEEE radial and a 70-bus realistic radial test networks are presented. The results demonstrate that the speed and the accuracy of the proposed Distribution Harmonic State Estimation (DHSE) algorithm are very excellent compared to the algorithms such as Weight Least Square (WLS), Genetic Algorithm (GA), original PSO, and Honey Bees Mating Optimization (HBMO).

Distribution harmonic state estimation based on a hybrid PSO and SA algorithm considering parameters uncertainty

This paper presents a new algorithm based on a Hybrid Particle Swarm Optimization (PSO) and Simulated Annealing (SA) called PSO-SA to estimate harmonic state variables in distribution networks. The proposed algorithm performs estimation for both amplitude and phase of each harmonic currents injection by minimizing the error between the measured values from Phasor Measurement Units (PMUs) and the values computed from the estimated parameters during the estimation process. The proposed algorithm can take into account the uncertainty of the harmonic pseudo measurement and the tolerance in the line impedances of the network as well as uncertainty of the Distributed Generators (DGs) such as Wind Turbines (WT). The main feature of proposed PSO-SA algorithm is to reach quickly around the global optimum by PSO with enabling a mutation function and then to find that optimum by SA searching algorithm. Simulation results on IEEE 34 bus radial and a realistic 70-bus radial test networks are presented to demonstrate the speed and accuracy of proposed Distribution Harmonic State Estimation (DHSE) algorithm is extremely effective and efficient in comparison with the conventional algorithms such as Weight Least Square (WLS), Genetic Algorithm (GA), original PSO and Honey Bees Mating Optimization (HBMO) algorithm.

Distribution state estimation based on particle swarm and doubly loop mutant optimization (DLM-PSO)

This paper presents a novel algorithm based on particle swarm optimization (PSO) to estimate the states of electric distribution networks. In order to improve the performance, accuracy, convergence speed, and eliminate the stagnation effect of original PSO, a secondary PSO loop and mutation algorithm as well as stretching function is proposed. For accounting uncertainties of loads in distribution networks, pseudo-measurements is modeled as loads with the realistic errors. Simulation results on 6-bus radial and 34-bus IEEE test distribution networks show that the distribution state estimation based on proposed DLM-PSO presents lower estimation error and standard deviation in comparison with algorithms such as WLS, GA, HBMO, and original PSO.

The reduced expression of the HADH2 protein causes X-linked mental retardation, choreoathetosis, and abnormal behavior

Recently, we defined a new syndromic form of X-linked mental retardation in a 4-generation family with a unique clinical phenotype characterized by mild mental retardation, choreoathetosis, and abnormal behavior (MRXS10). Linkage analysis in this family revealed a candidate region of 13.4 Mb between markers DXS1201 and DXS991 on Xp11; therefore, mutation analysis was performed by direct sequencing in most of the 135 annotated genes located in the region. The gene (HADH2) encoding L-3-hydroxyacyl-CoA dehydrogenase II displayed a sequence alteration (c.574 C-->A; p.R192R) in all patients and carrier females that was absent in unaffected male family members and could not be found in 2,500 control X chromosomes, including in those of 500 healthy males. The silent C-->A substitution is located in exon 5 and was shown by western blot to reduce the amount of HADH2 protein by 60%-70% in the patient. Quantitative in vivo and in vitro expression studies revealed a ratio of splicing transcript amounts different from those normally seen in controls. Apparently, the reduced expression of the wild-type fragment, which results in the decreased protein expression, rather than the increased amount of aberrant splicing fragments of the HADH2 gene, is pathogenic. Our data therefore strongly suggest that reduced expression of the HADH2 protein causes MRXS10, a phenotype different from that caused by 2-methyl-3-hydroxybutyryl-CoA dehydrogenase deficiency, which is a neurodegenerative disorder caused by missense mutations in this multifunctional protein.

Integrin αvβ3 mediates upregulation of epidermal growth-factor receptor expression and activity in human ovarian cancer cells

Upon overexpression of integrin αvβ3 and its engagement by vitronectin, we previously showed enhanced adhesion, proliferation, and motility of human ovarian cancer cells. By studying differential expression of genes possibly related to these tumor biological events, we identified the epidermal growth-factor receptor (EGF-R) to be under control of αvβ3 expression levels. Thus in the present study we characterized αvβ3-dependent changes of EGF-R and found significant upregulation of its expression and activity which was reflected by prominent changes of EGF-R promoter activity. Upon disruption of DNA-binding motifs for the transcription factors p53, ETF, the repressor ETR, p50, and c-rel, respectively, we sought to identify DNA elements contributing to αvβ3-mediated EGF-R promoter induction. Both, the p53- and ETF-mutant, while exhibiting considerably lower EGF-R promoter activity than the wild type promoter, retained inducibility by αvβ3. Mutation of the repressor motif ETR, as expected, enhanced EGF-R promoter activity with a further moderate increase upon αvβ3 elevation. The p50-mutant displayed EGF-R promoter activity almost comparable to that of the wild type promoter with no impairment of induction by αvβ3. However, the activity of an EGF-R promoter mutant displaying a disrupted c-rel-binding motif did not only prominently decline, but, moreover, was not longer responsive to enhanced αvβ3, involving this DNA element in αvβ3-dependent EGF-R upregulation. Moreover, αvβ3 did not only increase the EGF-R but, moreover, also led to obvious co-clustering on the cancer cell surface. By studying αvβ3/EGF-R-effects on the focal adhesion kinase (FAK) and the mitogen activated protein kinases (MAPK) p44/42 (erk−1/erk−2), having important functions in synergistic crosstalk between integrins and growth-factor receptors, we found for both significant enhancement of expression and activity upon αvβ3/VN interaction and cell stimulation by EGF. Upregulation of the EGF-R by integrin αvβ3, both receptor molecules with a well-defined role as targets for cancer treatment, might represent an additional mechanism to adapt synergistic receptor signaling and crosstalk in response to an altered tumor cell microenvironment during ovarian cancer progression.

Epidemiology of Clostridium difficile infection (CDI) in Queensland, Australia

Background: International epidemic clones (ribotypes 027 and 078) of Clostridium difficile have been associated with death, toxic megacolon and other adverse outcomes in North America and Europe. In 2010, the first local transmission of an epidemic strain (027) of C. difficile was reported in the state of Victoria, Australia, but no cases of infection with this strain were reported in the state of Queensland. In 2012, a prevalence study was undertaken in all public and selected private hospitals to examine the epidemiology of CDI and determine the prevalence of epidemic C. difficile strains in Queensland. Methods: Enhanced surveillance was undertaken on all hospital identified CDI cases aged over 2 years between 10 April and 15 June 2012. Where available, patient samples were cultured and isolates of C. difficile ribotyped. The toxin profile of each isolate was determined by PCR. Results: In total, 168 cases of CDI were identified during the study period. A majority (58.3%) of cases had onset of symptoms in hospital. Of the 62 patients with community onset of symptoms, most (74%) had a hospital admission in the previous 3 months. Only 4 of 168 patients had onset of symptoms within a residential care facility. Thirteen out of the 168 (7.7%) patients included in the study had severe disease (ICU admission and/or death within 30 days of onset). Overall 136/168 (81%) of cases had been prescribed antibiotics in the last month. Of concern was the emergence of a novel ribotype (244) which has recently been described in other parts of Australia and is genetically related to ribotype 027. Seven patients were infected with C. difficile ribotype 244 (8% of 83 samples ribotyped), including one patient requiring ICU admission and one patient who died. Ribotype 244 was tcdA, tcdB and CDT positive and contained a tcdC mutation at position 117. Conclusion: Ongoing surveillance is required to determine the origin and epidemiology of C. difficile ribotype 244 infections in Australia.

Characterization of ENU-induced mutations in red blood cell structural proteins

Murine models with modified gene function as a result of N-ethyl-N-nitrosourea (ENU) mutagenesis have been used to study phenotypes resulting from genetic change. This study investigated genetic factors associated with red blood cell (RBC) physiology and structural integrity that may impact on blood component storage and transfusion outcome. Forward and reverse genetic approaches were employed with pedigrees of ENU-treated mice using a homozygous recessive breeding strategy. In a “forward genetic” approach, pedigree selection was based upon identification of an altered phenotype followed by exome sequencing to identify a causative mutation. In a second strategy, a “reverse genetic” approach based on selection of pedigrees with mutations in genes of interest was utilised and, following breeding to homozygosity, phenotype assessed. Thirty-three pedigrees were screened by the forward genetic approach. One pedigree demonstrated reticulocytosis, microcytic anaemia and thrombocytosis. Exome sequencing revealed a novel single nucleotide variation (SNV) in Ank1 encoding the RBC structural protein ankyrin-1 and the pedigree was designated Ank1EX34. The reticulocytosis and microcytic anaemia observed in the Ank1EX34 pedigree were similar to clinical features of hereditary spherocytosis in humans. For the reverse genetic approach three pedigrees with different point mutations in Spnb1 encoding RBC protein spectrin-1β, and one pedigree with a mutation in Epb4.1, encoding band 4.1 were selected for study. When bred to homozygosity two of the spectrin-1β pedigrees (a, b) demonstrated increased RBC count, haemoglobin (Hb) and haematocrit (HCT). The third Spnb1 mutation (spectrin-1β c) and mutation in Epb4.1 (band 4.1) did not significantly affect the haematological phenotype, despite these two mutations having a PolyPhen score predicting the mutation may be damaging. Exome sequencing allows rapid identification of causative mutations and development of databases of mutations predicted to be disruptive. These tools require further refinement but provide new approaches to the study of genetically defined changes that may impact on blood component storage and transfusion outcome.

Mendel, 150 years on

Mendel's paper 'Versuche über Pflanzen-Hybriden' is the best known in a series of studies published in the late 18th and 19th centuries that built our understanding of the mechanism of inheritance. Mendel investigated the segregation of seven gene characters of pea (Pisum sativum), of which four have been identified. Here, we review what is known about the molecular nature of these genes, which encode enzymes (R and Le), a biochemical regulator (I) and a transcription factor (A). The mutations are: a transposon insertion (r), an amino acid insertion (i), a splice variant (a) and a missense mutation (le-1). The nature of the three remaining uncharacterized characters (green versus yellow pods, inflated versus constricted pods, and axial versus terminal flowers) is discussed.

UNIFOLIATA regulates leaf and flower morphogenesis in pea

Background The vegetative phenotype of the pea mutant unifoliata (uni) is a simplification of the wild-type compound leaf to a single leaflet. Mutant uni plants are also self-sterile and the flowers resemble known floral meristem and organ identity mutants. In Antirrhinum and Arabidopsis, mutations in the floral meristem identity gene FLORICAULA/LEAFY (FLO/LFY) affect flower development alone, whereas the tobacco FLO/LFY homologue, NFL, is expressed in vegetative tissues, suggesting that NFL specifies determinacy in the progenitor cells for both flowers and leaves. In this paper, we characterised the pea homologue of FLO/LFY. Results The pea cDNA homologue of FLO/LFY, PEAFLO, mapped to the uni locus in recombinant-inbred mapping populations and markers based on PEAFLO cosegregated with uni in segregating sibling populations. The characterisation of two spontaneous uni mutant alleles, one containing a deletion and the other a point mutation in the PEAFLO coding sequences, predicted that PEAFLO corresponds to UNI and that the mutant vegetative phenotype was conferred by the defective PEAFLO gene. Conclusions The uni mutant demonstrates that there are shared regulatory processes in the morphogenesis of leaves and flowers and that floral meristem identity genes have an extended role in plant development. Pleiotropic regulatory genes such as UNI support the hypothesis that leaves and flowers derive from a common ancestral sporophyll-like structure. The regulation of indeterminacy during leaf and flower morphogenesis by UNI may reflect a primitive function for the gene in the pre-angiosperm era.

High and low mammographic density human breast tissues maintain histological differential in murine tissue engineering chambers

Mammographic density (MD) is the area of breast tissue that appears radiologically white on mammography. Although high MD is a strong risk factor for breast cancer, independent of BRCA1/2 mutation status, the molecular basis of high MD and its associated breast cancer risk is poorly understood. MD studies will benefit from an animal model, where hormonal, gene and drug perturbations on MD can be measured in a preclinical context. High and low MD tissues were selectively sampled by stereotactic biopsy from operative specimens of high-risk women undergoing prophylactic mastectomy. The high and low MD tissues were transferred into separate vascularised biochambers in the groins of SCID mice. Chamber material was harvested after 6 weeks for histological analyses and immunohistochemistry for cytokeratins, vimentin and a human-specific mitochondrial antigen. Within-individual analysis was performed in replicate mice, eliminating confounding by age, body mass index and process-related factors, and comparisons were made to the parental human tissue. Maintenance of differential MD post-propagation was assessed radiographically. Immunohistochemical staining confirmed the preservation of human glandular and stromal components in the murine biochambers, with maintenance of radiographic MD differential. Propagated high MD regions had higher stromal (p = 0.0002) and lower adipose (p = 0.0006) composition, reflecting the findings in the original human breast tissue, although glands appeared small and non-complex in both high and low MD groups. No significant differences were observed in glandular area (p = 0.4) or count (p = 0.4) between high and low MD biochamber tissues. Human mammary glandular and stromal tissues were viably maintained in murine biochambers, with preservation of differential radiographic density and histological features. Our study provides a murine model for future studies into the biomolecular basis of MD as a risk factor for breast cancer.

MT1-MMP-dependent and -independent regulation of gelatinase A activation in long-term, ascorbate-treated fibroblast cultures: Regulation by fibrillar collagen

Human skin fibroblasts were cultured long-term in the presence of ascorbic acid to allow formation of a three-dimensional collagen matrix, and the effects of this on activation of secreted matrix metalloproteinase-2 (MMP-2) were examined. Accumulation of collagen over time correlated with increased levels of both mature MMP-2 and cell-associated membrane type 1-MMP (MT1-MMP), and subsequently increased mRNA levels for MT1-MMP, providing temporal resolution of the "nontranscriptional" and "transcriptional" effects of collagen on MT-1MMP functionality. MMP-2 activation by these cultures was blocked by inhibitors of prolyl-4-hydroxylase, or when fibroblasts derived from the collagen α1(I) gene-deficient Mov-13 mouse were used. MMP-2 activation by the Mov-13 fibroblasts was rescued by transfection of a full-length α1(I) collagen cDNA, and to our surprise, also by transfection with an α1(I) collagen cDNA carrying a mutation at the C-proteinase cleavage, which almost abrogated fibrillogenesis. Although studies with ascorbate-cultured MT1-MMP-/- fibroblasts showed that MT1-MMP played a significant role in the collagen-induced MMP-2 activation, a residual MT1-MMP-independent activation of MMP-2 was seen which resembled the level of MMP-2 activation persisting when wild-type fibroblasts were cultured in the presence of both ascorbic acid and MMP inhibitors. We were also unable to block this residual activation with inhibitors specific for serinyl, aspartyl, or cysteinyl enzymes.