ChromClust: A semi-supervised chromatin clustering toolkit for mining histone modifications interplay.

Mining patterns of histone modifications interplay from epigenomic profiles are one of the leading research areas these days. Various methods based on clustering approaches and hidden Markov models have been presented so far with some limitations. Here we present ChromClust, a semi-supervised clustering tool for mining commonly occurring histone modifications at various locations of the genome. Applying our method to 11 chromatin marks in nine human cell types recovered 11 clusters based on distinct chromatin signatures mapping to various elements of the genome. Our approach is efficient in respect to time and space usage along with the added facility of maintaining database at the backend. It outperforms the existing methods with respect to mining patterns in a semi-supervised fashion mapping to various functional elements of the genome. It will aid in future by saving the resources of time and space along with efficiently retrieving the hidden interplay of histone combinations.

A novel recessive mutation in the gene ELOVL4 causes a neuro-ichthyotic disorder with variable expressivity.

BACKGROUND: A rare neuro-ichthyotic disorder characterized by ichthyosis, spastic quadriplegia and intellectual disability and caused by recessive mutations in ELOVL4, encoding elongase-4 protein has recently been described. The objective of the study was to search for sequence variants in the gene ELOVL4 in three affected individuals of a consanguineous Pakistani family exhibiting features of neuro-ichthyotic disorder. METHODS: Linkage in the family was searched by genotyping microsatellite markers linked to the gene ELOVL4, mapped at chromosome 6p14.1. Exons and splice junction sites of the gene ELOVL4 were polymerase chain reaction amplified and sequenced in an automated DNA sequencer. RESULTS: DNA sequence analysis revealed a novel homozygous nonsense mutation (c.78C > G; p.Tyr26*). CONCLUSIONS: Our report further confirms the recently described ELOVL4-related neuro-ichthyosis and shows that the neurological phenotype can be absent in some individuals.

Bioactive phenolics from Seriphidium stenocephalum.

Chromatographic separation of the ethyl acetate soluble part of the methanolic extract from Seriphidium stenocephalum yielded three new compounds: stenocepflavone (1), stenocepflavan (2), and stenocephol (3), together with cirsimaritin (4), 5,7,5'-trihydroxy-3',4',6-trimethoxyflavone (5), 5,6,7,5'-tetrahydroxy-4'-methoxyflavone (6), and axillaroside (7). All isolates were characterized with the help of spectroscopic data including 1D, 2D NMR, and high resolution mass spectrometry and/or in comparison with the related compounds in literature. All compounds were tested for in vitro enzyme inhibitory activities against acetylcholinesterase, butyrylcholinesterase, and lipoxygenase. Compounds 1 and 4-7 exhibited significant activity against all the tested enzymes, whereas compounds 2 and 3 were found inactive.

Novel homozygous mutations in the genes ARL6 and BBS10 underlying Bardet-Biedl syndrome.

Bardet-Biedl syndrome (BBS) is an autosomal recessive disorder resulting from structural and functional defects in numerous organs. Frequent manifestations reported in the syndrome include obesity, renal dysplasia, cognitive impairment, postaxial polydactyly, pigmentary retinal degeneration and hypogonadism. To date, 17 genes causing BBS have been identified. Two of these BBS1 and BBS10 are the most frequently mutated genes. The present report describes two consanguineous families (A, B) with clinical manifestations of BBS. Linkage in the family A was established to ARL6 on chromosome 3q11.2, while family B showed linkage to BBS10 on chromosome 12q21.2. Sequence analysis revealed a novel homozygous missense mutation (c.281T>C, p.Ile94Thr) in the gene ARL6 in family A and a nonsense mutation (c.1075C>T, p.Gln359*) in the gene BBS10 in family B. Mutations identified in the present study extend the body of evidence implicating the genes ARL6 and BBS10 in causing Bardet-Biedl syndrome.

A novel chondroectodermal dysplasia mapped to chromosome 2q24.1-q31.1.

Chondroectodermal dysplasias are genetically heterogeneous group of disorders involving defects in one or more ectodermal appendages (hair, nail, teeth and sweat glands) in association with anomalies of the cartilage. In the present study a novel form of chondroectodermal dysplasia, segregating in an autosomal recessive pattern in a Pakistani family, was investigated. The clinical features including proportionate short stature, osteopenia with fracturing and breaking of bones, hypodontia, hypertrophic and convex shaped nails, night blindness, watering eyes and infection of ears were observed in affected individuals of the family. Genetic linkage study mapped the novel autosomal recessive form of chondroectodermal dysplasia on human chromosome 2q24.1-q31.1. Linkage to the region was established by scanning human genome using Human Mapping 250K Nsp array. Linkage interval for chondroectodermal dysplasia on human chromosome 2q24.1-q31.1 spans 13.76 cM, which corresponds to 15.72 Mb according to the sequence-based physical map (Build 36.2). The maximum multipoint LOD score of 3.37 was obtained with several markers along the disease interval. Sequence analysis of three candidate genes (TANK, ITGB6, TBR1) located in the candidate interval did not discover potentially causal variants.