Role of size, alio-/multi-valency and non-stoichiometry in the synthesis of phase-pure high entropy oxide (Co,Cu,Mg,Na,Ni,Zn)O.

A nanocrystalline high entropy oxide with near-equimolar composition consisting of 5 transition metal cations and one alkali cation (Co,Cu,Mg,Na,Ni,Zn)O was synthesised by a reverse co-precipitation (RCP) process and characterised by standard methods of X-ray diffraction (for crystallite size and phases), electron microscopy (for particle morphology and size distribution) and Fourier transform infra-red spectroscopy (for bond identification and bond lengths). Charge compensation in the lattice by the formation of Co3+ and/or Ni3+ (in order to offset the +1 oxidation state of Na) and the creation of oxygen vacancies was quantified from X-ray photoelectron spectroscopy and Raman spectroscopy and further studied using vibrating sample magnetometry (VSM). The influence of different transition metals in being able to accommodate the larger and aliovalent sodium ion in a single phase-pure rocksalt lattice was investigated and the criteria for element selection in such multicomponent systems for single-phase formation examined. Presence of multivalency/non-stoichiometry to accommodate a different-sized cation and maintaining electroneutrality were identified as the critical criteria for single-phase formation in multicomponent systems and further confirmed through synthesis of various lower combination systems (by systematic removal of one transition metal cation) and by addition of bivalent Ca as well as cations of higher valencies. These criteria would aid in designing the compositions of high entropy oxides with aliovalent substitutions.

MSR1 repeats modulate gene expression and affect risk of breast and prostate cancer.

Background: MSR1 repeats are a 36-38 bp minisatellite element that have recently been implicated in the regulation of gene expression, through copy number variation (CNV). Patients and methods: Bioinformatic and experimental methods were used to assess the distribution of MSR1 across the genome, evaluate the regulatory potential of such elements and explore the role of MSR1 elements in cancer, particularly non-familial breast cancer and prostate cancer. Results: MSR1s are predominately located at chromosome 19 and are functionally enriched in regulatory regions of the genome, particularly regions implicated in short-range regulatory activities (H3K27ac, H3K4me1 and H3K4me3). MSR1-regulated genes were found to have specific molecular roles, such as serine-protease activity (P = 4.80 × 10-7) and ion channel activity (P = 2.7 × 10-4). The kallikrein locus was found to contain a large number of MSR1 clusters, and at least six of these showed CNV. An MSR1 cluster was identified within KLK14, with 9 and 11 copies being normal variants. A significant association with the 9-copy allele and non-familial breast cancer was found in two independent populations (P = 0.004; P = 0.03). In the white British population, the minor allele conferred an increased risk of 1.21-3.51 times for all non-familial disease, or 1.7-5.3 times in early-onset disease. The 9-copy allele was also found to be associated with increased risk of prostate cancer in an independent population (odds ratio = 1.27-1.56; P =0.009). Conclusions: MSR1 repeats act as molecular switches that modulate gene expression. It is likely that CNV of MSR1 will affect risk of development of various forms of cancer, including that of breast and prostate. The MSR1 cluster at KLK14 represents the strongest risk factor identified to date in non-familial breast cancer and a significant risk factor for prostate cancer. Analysis of MSR1 genotype will allow development of precise stratification of disease risk and provide a novel target for therapeutic agents.

Variant haploinsufficiency and phenotypic non-penetrance in PRPF31-associated retinitis pigmentosa.

Retinitis pigmentosa (RP) is a genetically heterogenous group of inherited disorders, characterized by death of the retinal photoreceptor cells, leading to progressive visual impairment. One form of RP is caused by mutations in the ubiquitously expressed splicing factor, PRPF31, this form being known as RP11. An intriguing feature of RP11 is the presence of non-penetrance, which has been observed in the majority of PRPF31 mutation-carrying families. In contrast to variable expressivity, which is highly pervasive, true non-penetrance is a very rare phenomenon in Mendelian disorders. In this article, the molecular mechanisms underlying phenotypic non-penetrance in RP11 are explored. It is an elegant example of how our understanding of monogenic disorders has evolved from studying only the disease gene, to considering a mutation on the genetic background of the individual - the logical evolution in this genomic era.

The effects of composting approaches on the emissions of anthropogenic volatile organic compounds: A comparison between vermicomposting and general aerobic composting.

Emission patterns of 13 VOCs were investigated in three types of vermicomposting systems (Eisenia fetida, Metaphire posthuma, and Lampito mauritii) in reference to a traditional aerobic composting system by feeding the systems with mixtures of three materials (coal ash (CA), municipal solid waste (MSW), and cow dung (CD)). On an average, the emission rates of aromatic VOCs (benzene, toluene, xylenes, and styrene) were two to three times higher than all other groups (aldehyde, ketones, esters, and alcohols) from all three types of feeding mixtures. However, the emission rates of aromatic VOCs were generally reduced over time in both aerobic composting and vermicomposting systems. Such reduction in the emission rates was most prominent from Eisenia-treated CD + MSW (1:1), Lampito-treated CD + CA (1:1), and Metaphire-treated CD. The results clearly indicated that the increase in humified organic C fractions (humic acid and fulvic acid) and the microbial biomass present during the biocomposting processes greatly reduced the emissions of VOCs. Hence, the study recommends that vermicomposting of coal ash and municipal solid waste in combination with cow dung in 1:1 ratio is an environmentally gainful proposition.

Diverse clinical phenotypes associated with a nonsense mutation in FAM161A.

PURPOSE: Mutations in the FAM161A gene have been reported in association with autosomal recessive retinitis pigmentosa (arRP) in several ethnic populations. This study aimed to assess the prevalence of FAM161A-related retinopathy in a British cohort and to characterise the phenotype associated with mutations in this gene. METHODS: The FAM161A coding region and intron-exon boundaries were screened by Sanger sequencing in 120 retinitis pigmentosa (RP) patients (with likely autosomal recessive inheritance) in whom mutations in other known major RP genes have been ruled out by commercially available testing. Homozygosity mapping was performed in one consanguineous family, and high-throughput sequencing of candidate genes was performed to identify disease-associated changes. Clinical assessment of affected individuals included perimetry testing, fundus autofluorescence imaging, and optical coherence tomography. RESULTS: Two patients of British origin with a homozygous mutation in FAM161A (c.1309A>T, p.Arg437*) were identified by Sanger sequencing. Homozygosity mapping and subsequent high-throughput sequencing analysis identified a further family of Pakistani origin with the same genotype. Clinical examination of affected members of these families revealed that this mutation was associated with a diverse clinical phenotype, ranging from mild disease with preservation of central acuity to severe visual impairment. CONCLUSIONS: Homozygosity for the c.1309A>T, p.Arg437* variant in FAM161A is a relatively common cause of arRP. The mutation occurs in diverse ethnic populations, associated with typical retinitis pigmentosa with disease onset usually in the second or third decade of life.

HMG20A is required for SNAI1-mediated epithelial to mesenchymal transition.

HMG20A is a high mobility group (HMG) domain containing protein homologous to HMG20B, a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Here, we show that HMG20A can replace HMG20B and, therefore, they are mutually exclusive subunits of the complex. Both proteins interact through a coiled-coil domain with BHC80, another subunit of the LSD1-CoREST complex. To investigate the functional differences between the two proteins, we performed transcriptomic analysis of HMG20A- and HMG20B-depleted cells. Analysis of the misregulated genes in HMG20A-knockdown cells evidenced a high proportion of genes related to the epithelial-to-mesenchymal transition (EMT) process. EMT occurs during embryonic development or during the course of malignant cancer progression and consists in the dynamic and reversible transitions between epithelial and mesenchymal phenotypes. We show that HMG20A together with LSD1 are required for SNAI1-dependent repression of epithelial genes and for (transforming growth factor ß) TGF-ß-triggered EMT. Importantly, HMG20A-depleted cells displayed reduced binding of LSD1 to epithelial gene promoters and increased methylation of lysine 4 of histone H3, suggesting a role of HMG20A in recruiting or in stabilizing the complex at the chromatin. SNAI1 and the TGF-ß-related transcription factor SMAD4 were found to be associated with the LSD1-CoREST complex containing HMG20A. Furthermore, we show that HMG20A-depleted cells displayed reduced motility and invasion activity. Finally, we show that expression of HMG20A correlates positively with mesenchymal markers and negatively with epithelial markers in human tumor samples. Taken together, our data demonstrate that HMG20A is essential for the mesenchymal phenotype.

Vermicomposting of Tea Factory Coal Ash: metal accumulation and metallothionein response in Eisenia fetida (Savigny) and Lampito mauritii (Kinberg).

Earthworms can accumulate heavy metals in their intestines to a great extent. Impact of feed materials and duration of metal exposure on natural activity of earthworms are rather unclear; this investigation therefore addresses the impact of metal rich Tea Factory Coal Ash (TFCA) on reproduction, composting and metal accumulation ability of Eisenia fetida and Lampito mauritii. Earthworm count and cocoon production increased significantly during vermicomposting. pH of the vermicomposted mixtures shifted toward neutrality, total organic C decreased substantially and total N enhanced significantly compared to composting. High heavy metal (Mn, Zn, Cu, As) accumulation was recorded in the intestine of both the earthworm species. Moreover, gradual increase in the metal-inducible metallothionein concentration indicated the causal mechanism of metal accumulation in these species. TFCA+cow dung (CD) (1:1) were most favorable feed mixture for E. fetida and TFCA+CD (1:2) were good for L. mauritii in regard to metal accumulation and compost quality.

Efficacy of bioconversion of paper mill bamboo sludge and lime waste by composting and vermiconversion technologies.

Paper mill bamboo sludge (PMBS) and Paper mill lime waste (PMLW) are extensively produced as solid wastes in paper mills. Untreated PMBS and PMLW contain substantial amount of heavy metals (Zn, Pb, Ni, Cd, Cr) in soluble forms. Efficiency of vermiconversion and aerobic composting with these wastes is reported here. Adopted bioconversion systems enhanced the availability of some essential nutrients (N, P, K and Zn) in various combinations of cow dung (CD) with PMBS and PMLW. Colonization of nitrogen fixing bacteria and phosphate solubilizing bacteria considerably intensified under the vermiconversion system. Moreover, significant metal detoxification occurred due to vermiconversion. Various combinations of bioconverted PMBS and PMLW were applied to tissue cultured bamboo (Bambusa tulda) and chilli (Capsicum annum). Accelerated nutrient uptake coupled with improved soil quality resulted in significant production of chilli. Furthermore, vermiconverted PMBS+CD (1:1) and PMLW+CD (1:3) confirmed as potential enriching substrate for tissue cultured bamboo.

Occurrence & antibiogram of Salmonella Typhi & S. Paratyphi A isolated from Rourkela, Orissa.

BACKGROUND & OBJECTIVES: Almost round-the-year occurrence of Salmonella Typhi and Salmonella Paratyphi A has been noticed in Rourkela since last 13 and five years respectively. The incidence of infection along with the antibiogram of these two serotypes in this area were carried out. METHODS: The study was carried out at Ispat General Hospital, Rourkela, India, between January 2005 and December 2008 with 5340 blood samples collected from patients with suspected enteric fever and pyrexia of unknown origin. Isolation, identification and antibiogram of the causative organisms were performed according to standard bacteriological procedures. RESULTS: A total of 298 Salmonella isolates showed an overall per cent positivity of 5.58. Multidrug resistance was found in 11.96 per cent and 15.62 per cent isolates of S. Typhi and S. Paratyphi A respectively. Less than 2 per cent isolates of Salmonella showed resistance to ciprofloxacin. A resistance of 3.0 to 6.25 per cent against third generation cephalosporins was observed among the salmonella isolates. INTERPRETATION & CONCLUSION: A round-the-year occurrence of Salmonella spp. in Rourkela might have been due to the presence of a considerable number of carriers in the locality, poor sanitation in nearby slum areas, and inadequate and contaminated community water supply at times. Higher degree of susceptibility among S. Typhi isolates against various antibiotics was encouraging, but increasing trend of resistance observed among S. Paratyphi A isolates was a matter of concern.

Effect of gas flow rates on the anatase-rutile transformation temperature of nanocrystalline TiO2 synthesised by chemical vapour synthesis.

Of the three crystallographic allotropes of nanocrystalline titania (rutile, anatase and brookite), anatase exhibits the greatest potential for a variety of applications, especially in the area of catalysis and sensors. However, with rutile being thermodynamically the most stable phase, anatase tends to transform into rutile on heating to temperatures in the range of 500 degrees C to 700 degrees C. Efforts made to stabilize the anatase phase at higher temperatures by doping with metal oxides suffer from the problems of having a large amorphous content on synthesis as well as the formation of secondary impurity phases on doping. Recent studies have suggested that the as-synthesised phase composition, crystallite size, initial surface area and processing conditions greatly influence the anatase to rutile transformation temperature. In this study nanocrystalline titania was synthesised in the anatase form bya chemical vapour synthesis (CVS) method using titanium tetra iso-propoxide (TTIP) as a precursor under varying flow rates of oxygen and helium. The anatase to rutile transformation was studied using high temperature X-ray diffraction (HTXRD) and simultaneous thermogravimetric analysis (STA), followed by transmission electron microscopy (TEM). It was demonstrated that the anatase-rutile transformation temperatures were dependent on the oxygen to helium flow rate ratio during CVS and the results are presented and discussed.

Optimization of laccase mediated biodegradation of 2,4-dichlorophenol using genetic algorithm.

The present investigation focuses on the development of an effective strategy to determine the optimum environmental conditions leading to the maximum rate of biodegradation of 2,4-DCP by coupling response surface methodology (RSM) with a developed genetic algorithm (GA) thereby ensuring minimum contact time. RSM is utilized to create an efficient analytical model for biodegradation of 2,4-DCP in terms of environmental parameters: pH, temperature, enzyme activity and time of incubation. For this purpose, a number of degradation experiments based on statistical three-level Box Behnken design methods were carried out. An effective response surface (RS) model is developed by carrying out experiments designed using the Box Behnken method. The RS model thus developed is further interfaced with the GA to optimize the degradation conditions for optimum degradation with minimum contact time. The GA increases the biodegradation conditions to >99% within a time period of 8h within the given range of experimental conditions. The conditions obtained from GA were verified experimentally.

Laccase mediated biodegradation of 2,4-dichlorophenol using response surface methodology.

The effects of different environmental parameters, i.e., pH, temperature, time and enzyme concentration on the biodegradation of 2,4-dichlorophenol (2,4-DCP) in aqueous phase was evaluated with laccase from Pleurotus sp. using response surface methodology (RSM) in the present investigation. The Box-Behnken design of experiments was used to construct second order response surfaces with the investigated parameters. It was observed that the maximum degradation efficiency of approximately 98% was achieved at pH 6, temperature of 40 degrees C, time 9h and an enzyme concentration of 8 IU ml(-1). The adequacy of the model was confirmed by the coefficient of multiple regression, R(2) and adjusted R(2) which were adjudged to be 87.9% and 73.6%, respectively indicating a reasonably good model for practical implementation. Despite the fact that many successful attempts have been taken in the past for biodegradation of 2,4-DCP using whole cells, the present study emphasizes the fastest biodegradation of 2,4-DCP, a potent xenobiotic compound.

Linkage validation of RP25 Using the 10K genechip array and further refinement of the locus by new linked families.

Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of retinal dystrophies, characterised by rod photoreceptor cell degeneration with autosomal recessive RP (arRP) as the commonest form worldwide. To date, a total of 26 loci have been reported for arRP, each having a prevalence of 1-5%, except for the RP25 locus which was identified as the genetic cause of 14% of arRP cases in Spain. In order to validate the original linkage of RP25, we undertook a total genome scan using the 10K GeneChip mapping array on three of the previously linked families. The data obtained supported the initial findings of linkage. Additionally, linkage analysis in 18 newly ascertained arRP families was performed using microsatellite markers spanning the chromosome 6p12.1-q15 interval. Five out of the 18 families showed suggestive evidence of linkage to RP25, hence supporting the high prevalence of this locus in the Spanish population. Furthermore, the finding of a crossover in one of these families is likely to have refined the disease interval from the original 16 cM to only a 2.67 cM region between D6S257 and D6S1557.

Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

A large scale bioinformatics and molecular analysis of a 34 Mb interval on chromosome 6q12 was undertaken as part of our ongoing study to identify the gene responsible for an autosomal recessive retinitis pigmentosa (arRP) locus, RP25. Extensive bioinformatics analysis indicated in excess of 110 genes within the region and we also noted unfinished sequence on chromosome 6q in the Human Genome Database, between 58 and 61.2 Mb. Forty three genes within the RP25 interval were considered as good candidates for mutation screening. Direct sequence analysis of the selected genes in 7 Spanish families with arRP revealed a total of 244 sequence variants, of which 67 were novel but none were pathogenic. This, together with previous reports, excludes 60 genes within the interval ( approximately 55%) as disease causing for RP. To investigate if copy number variation (CNV) exists within RP25, a comparative genomic hybridization (CGH) analysis was performed on a consanguineous family. A clone from the tiling path array, chr6tp-19C7, spanning approximately 100-Kb was found to be deleted in all affected members of the family, leading to a major refinement of the interval. This will eventually have a significant impact on cloning of the RP25 gene.

Sequencing of the CHST6 gene in Czech macular corneal dystrophy patients supports the evidence of a founder mutation.

AIMS: To characterise the role of the carbohydrate sulfotransferase gene (CHST6) in macular corneal dystrophy (MCD) in Czech patients. METHODS: The coding region of the CHST6 gene was directly sequenced in 10 affected and five unaffected members from eight apparently unrelated MCD families. The type of MCD was determined by enzyme-linked immunosorbent assay of antigenic keratan sulfate (KS) in serum and by immunohistochemical staining of corneas with monoclonal anti-KS antibody. RESULTS: The following changes in the coding sequence of the CHST6 gene were observed; homozygous mutation of c.1A>T (p.M1?); homozygous mutation c.599T>G (p.L200R); compound heterozygosity for c.599T>G and c.614G>A (p.R205Q); compound heterozygosity for c.494G>A (p.C165Y) and c.599T>G; heterozygous c.599T>G mutation and no other change in the coding sequence. One proband exhibited no changes. The pathogenic mutation c.599T>G (p.L200R) was in allelic association with the c.484C>G (p.R162G) polymorphism. Nine patients from seven families were of MCD type I including the subtype IA. CONCLUSION: Four different CHST6 missense mutations, of which p.C165Y is novel, were identified. Allelic association of the c.[484C>G; 599T>G] in six probands out of eight, as well as occurrence of this particular allele in a heterozygous state in one healthy control individual, supports a common founder effect for MCD in the Czech Republic.

Genetic analysis of FAM46A in Spanish families with autosomal recessive retinitis pigmentosa: characterisation of novel VNTRs.

Retinitis pigmentosa (RP) is a group of retinal dystrophies characterised primarily by rod photoreceptor cell degeneration. Exhibiting great clinical and genetic heterogeneity, RP be inherited as an autosomal dominant (ad) and recessive (ar), X-linked (xl) and digenic disorder. RP25, a locus for arRP, was mapped to chromosome 6p12.1-q14.1 where several retinal dystrophy loci are located. A gene expressed in the retina, FAM46A, mapped within the RP25 locus, and computational data revealed its involvement in retinal signalling pathways. Therefore, we chose to perform molecular evaluation of this gene as a good candidate in arRP families linked to the RP25 interval. A comprehensive bioinformatic and retinal tissue expression characterisation of FAM46A was performed, together with mutation screening of seven RP25 families. Herein we present 4 novel sequence variants, of which one is a novel deletion within a low complexity region close to the initiation codon of FAM46A. Furthermore, we have characterised for the first time a coding tandem variation in the Caucasian population. This study reports on bioinformatic and moleculardata for the FAM46A gene that may give a wider insight into the putative function of this gene and its pathologic relevance to RP25 and other retinal diseases mapping within the 6q chromosomal interval.