Draft genome sequence of Enterococcus faecium SP15, a potential probiotic strain isolated from spring water.

OBJECTIVES: Enterococci are Gram-positive lactic acid bacteria and common inhabitants of the gastrointestinal tract of mammals, including humans. They are also widely distributed in diverse environments such as soil, water, vegetables and food. Enterococcus faecium is able to produce antimicrobial compounds (enterocins) and thus can act as a probiotic. E. faecium SP15 is a newly identified enterocin-producing strain from spring water that has been subjected to genome sequence analysis to provide understanding of its antimicrobial and probiotic properties. DATA DESCRIPTION: The draft genome of E. faecium SP15 comprises of 2,783,033 bp with a G+C content of 38.08%. Five genetic loci predicted to specify enterocin production were identified, but no virulence factors could be detected and only two potential antibiotic resistance genes were noted.

Confirmation of the Role of DHX38 in the Etiology of Early-Onset Retinitis Pigmentosa.

Purpose: Retinitis pigmentosa (RP) is a genetically heterogeneous trait with autosomal-recessive (ar) inheritance underlying 50% of genetic disease cases. Sixty-one arRP genes have been identified, and recently, DHX38 has been reported as a potential candidate gene for arRP with only a single family reported with a variant of unknown significance. We identified a missense variant in DHX38 that co-segregates with the arRP phenotype in two Pakistani families confirming the involvement of DHX38 in the etiology of early-onset RP. Methods: Exome sequencing was performed using two DNA samples from affected members of Pakistani families (MA88 and MA157) with early onset arRP. Sanger sequencing of DNA samples from all family members confirmed the segregation of candidate variant within both families. Results: A novel missense DHX38 variant c.971G>A; p.(Arg324Gln) was identified which segregates with the arRP phenotype and yielded a logarithm of the odds (LOD) score of 5.0 and 4.3 for families MA88 and MA157, respectively. This variant is predicted to be conserved and deleterious by several bioinformatics tools. Conclusions: We identified a second deleterious DHX38 variant that segregates with arRP in two families, providing additional evidence that DHX38 is involved in RP etiology. DHX38 encodes for pre-mRNA splicing factor PRP16, which is important in catalyzing pre-mRNA splicing.

Novel missense and 3'-UTR splice site variants in LHFPL5 cause autosomal recessive nonsyndromic hearing impairment.

LHFPL5, the gene for DFNB67, underlies autosomal recessive nonsyndromic hearing impairment. We identified seven Pakistani families that mapped to 6p21.31, which includes the LHFPL5 gene. Sanger sequencing of LHFPL5 using DNA samples from hearing impaired and unaffected members of these seven families identified four variants. Among the identified variants, two were novel: one missense c.452 G > T (p.Gly151Val) and one splice site variant (c.*16 + 1 G > A) were each identified in two families. Two known variants: c.250delC (p.Leu84*) and c.380 A > G (p.Tyr127Cys) were also observed in two families and a single family, respectively. Nucleotides c.452G and c.*16 + 1G and amino-acid residue p.Gly151 are under strong evolutionary conservation. In silico bioinformatics analyses predicted these variants to be damaging. The splice site variant (c.*16 + 1 G > A) is predicted to affect pre-mRNA splicing and a loss of the 5' donor splice site in the 3'-untranslated region (3'-UTR). Further analysis supports the activation of a cryptic splice site approximately 357-bp downstream, leading to an extended 3'-UTR with additional regulatory motifs. In conclusion, we identified two novel variants in LHFPL5, including a unique 3'-UTR splice site variant that is predicted to impact pre-mRNA splicing and regulation through an extended 3'-UTR.

Novel sequence variants in the LIPH and LPAR6 genes underlies autosomal recessive woolly hair/hypotrichosis in consanguineous families.

Autosomal-recessive woolly hair/hypotrichosis (ARWH/H) is a rare genetic disorder of hair caused by variants in the LIPH and LPAR6 genes. The disease is characterized by congenital tightly curled hair leading to sparse hair later in life. In the present report genetic characterization of three consanguineous families of Pakistani origin, displaying clinical features of ARWH/H, was performed. Haplotype and DNA sequence analysis of the LIPH gene revealed a novel homozygous nonsense variant (c.688C > T; p.Gln230*) in family A. In two other families, B and C, sequence analysis of the LPAR6 gene revealed a novel homozygous frameshift variant (c.68_69dupGCAT; p.Phe24Hisfs*29) and a previously reported missense variant (c.188A > T; p.Asp63Val), respectively. Taken together, our findings will expand the spectrum of variants reported in the LIPH and LPAR6 genes.

Biallelic truncating mutations in FMN2, encoding the actin-regulatory protein Formin 2, cause nonsyndromic autosomal-recessive intellectual disability.

Dendritic spines represent the major site of neuronal activity in the brain; they serve as the receiving point for neurotransmitters and undergo rapid activity-dependent morphological changes that correlate with learning and memory. Using a combination of homozygosity mapping and next-generation sequencing in two consanguineous families affected by nonsyndromic autosomal-recessive intellectual disability, we identified truncating mutations in formin 2 (FMN2), encoding a protein that belongs to the formin family of actin cytoskeleton nucleation factors and is highly expressed in the maturing brain. We found that FMN2 localizes to punctae along dendrites and that germline inactivation of mouse Fmn2 resulted in animals with decreased spine density; such mice were previously demonstrated to have a conditioned fear-learning defect. Furthermore, patient neural cells derived from induced pluripotent stem cells showed correlated decreased synaptic density. Thus, FMN2 mutations link intellectual disability either directly or indirectly to the regulation of actin-mediated synaptic spine density.

Synthesis, Structural Characterization, and Evaluation of the Biological Properties of Heteroleptic Palladium(II) Complexes.

Five heteroleptic palladium(II) complexes of the general formula Pd(PR3)(tu)Cl2, where PR3 = triphenylphosphine (1), diphenyl-o-tolylphosphine (2), diphenyl-p-tolylphosphine (3), diphenyl-t-butylphosphine (4), and diphenyl-o-methoxyphenylphosphine (5), and tu = 1,3-bis(2-methoxyphenyl) thiourea. They all have been synthesized and characterized by various spectroscopic techniques (elemental analysis, FTIR, and (1)H NMR and the ligand 1,3-bis(2-methoxyphenyl) thiourea was synthesized by single crystal X-ray diffraction technique). The synthesized compounds were screened for their antibacterial activity against four strains of bacteria (Escherichia coli, Shigella flexneri, Staphylococcus aureus, and Bacillus subtilis). The antitumor potential was evaluated in terms of activity against brine shrimp eggs and DNA interaction. The mixed ligand complexes have exhibited moderate antibacterial activity and promising antitumor potential.

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.

Ranging and foraging of Himalayan grey langurs (Semnopithecus ajax) in Machiara National Park, Pakistan.

Grey langurs (Semnopithecus spp.) occupy a variety of habitats, ranging from lowland forests and semi-desert to alpine forests. Little is known about their foraging and ranging in alpine forests, which appear to contain less food than lowland forests. We conducted a 1-year study of Himalayan grey langurs (Semnopithecus ajax) in Machiara National Park, Pakistan, where they occur at relatively high altitudes (range 2000-4733 m). We followed three groups of different sizes and compositions and examined the effects of ecological and social factors on ranging and feeding. The home-range sizes of a small bisexual group (SBG), a large bisexual group (LBG), and an all-male group (AMG) were 2.35 ± 0.92 (mean ± SD; average of four seasons), 3.28 ± 0.55, and 3.52 ± 1.00 km(2), respectively, and were largest in winter for all groups. The daily path lengths of the SBG, LBG, and AMG were 1.23 ± 0.28 (mean ± SD; average of four seasons), 1.75 ± 0.34, and 1.84 ± 0.70 km, respectively; that of the LBG was longer in winter, while that of the AMG was shorter in summer. Both the home-range size and daily path length of the AMG were larger than those of the other groups, even after partialling out the effect of group size differences. The mean altitude used by the langurs and the proportion of animals seen feeding did not differ among seasons or group types. As the mean temperature increased, the altitude used by langurs significantly increased for the SBG and LBG, but not for the AMG. On the other hand, as the temperature increased, the home-range sizes significantly decreased for the SBG and AMG, but not for the LBG. Rainfall did not show any correlation with ranging or feeding in any of the groups. Our results suggested that grey langurs in Machiara National Park employ a high-cost, high-return foraging strategy in winter, and that the ranging of the AMG also reflects its reproductive strategy.

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.

A novel splice site mutation in gene C2orf37 underlying Woodhouse-Sakati syndrome (WSS) in a consanguineous family of Pakistani origin.

Woodhouse-Sakati Syndrome (WSS) is a rare autosomal recessive multisystemic disorder that is marked by hypogonadism, alopecia, intellectual disability, deafness, diabetes mellitus and progressive extrapyramidal defects. Mutations in the gene C2orf37 are the cause of Woodhouse-Sakati syndrome. In the present study, a four-generation consanguineous family with clinical manifestations of WSS was ascertained from a remote region of Pakistan. Linkage in the family was tested using microsatellite markers linked to several genes involved in producing WSS related phenotypes. Linkage in the family was established to the gene C2orf37, mapped on chromosome 2q22.3-2q35. DNA sequence analysis revealed a novel splice site mutation involving a homozygous G→A transition in the splice donor site of intron 3 (c.321+1G>A) of C2orf37. This study presents a first report of Woodhouse-Sakati syndrome identified in Pakistani population.

Genetic analysis of four Pakistani families with achromatopsia and a novel S4 motif mutation of CNGA3.

BACKGROUND: To identify the causative variants of achromatopsia (ACHM) in four Pakistani families presenting autosomal recessive ACHM. METHODS: Four families (50, 55, 70 and 74) exhibiting features of achromatopsia were subjected to homozygosity mapping with STS markers flanking known ACHM loci. Mutation screening was done for two of the families linked to CNGA3 and CNGB3 by direct sequencing of the coding regions and exon-intron boundaries of genes to find the pathogenic variant. RESULTS: Homozygosity mapping showed co-segregation of CNGA3 in family 50 and CNGB3 in family 74. Sequencing of coding regions of CNGA3 in family 50 revealed a novel missense mutation, c.827A>G, in exon 7, which results in p.N276S substitution. N276S is located in the S4 motif of the CNGA3 protein and is conserved in all channel proteins. Bioinformatics analysis showed that the N276S substitution altered the channel conformation by shifting the helix. No pathogenic variation was identified in any affected members of family 74 in the coding sequence of CNGB3. The other two families, 55 and 70, were not linked to any known ACHM loci, indicating further heterogeneity of the ACHM phenotype. CONCLUSIONS: We describe a novel S4 motif mutation of CNGA3 in a Pakistani family.

Ectodermal dysplasia-cutaneous syndactyly syndrome maps to chromosome 7p21.1-p14.3.

Ectodermal dysplasia syndromes are genetically heterogeneous group of disorders involving one or more of the classical ectodermal appendages (hair, nail, teeth, sweat glands) in association with anomalies of other organs or systems. In the present study a novel form of ectodermal dysplasia syndrome, ectodermal dysplasia cutaneous syndactyly (EDCS), segregating in an autosomal recessive pattern in a Pakistani family was investigated. The clinical features of the affected individuals included large prominent ear pinnae, tooth enamel hypoplasia, hypoplastic nails, bilateral partial cutaneous syndactyly, hypotrichosis, palmoplantar keratoderma and hyperhidrosis. Through genetic linkage study, EDCS syndrome was mapped on human chromosome 7p21.1-p14.3 flanked by markers D7S488 and D7S817. A maximum two-point LOD score of 2.94 (theta = 0.00) was obtained at marker D7S2496 while a maximum multipoint LOD score of 3.07 was obtained with several markers along the disease-interval. This interval spans 19.80-cM, which corresponds to 13.74-Mbp according to the sequence-based physical map (Build 36.1). Sequence analysis of 27 candidate genes, located in the candidate interval, did not reveal any functional sequence variant.

Novel protein-truncating mutations in the ASPM gene in families with autosomal recessive primary microcephaly.

Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder that causes reduction in brain size. Individuals affected with the disorder show a small but architecturally normal cerebral cortex and are associated with mental retardation of mild-to severe form. MCPH is genetically heterogeneous with six loci, and four genes have been identified so far. Homozygous mutations in the ASPM gene, located at MCPH5 locus on chromosome 1q31, are the most common cause of MCPH particularly in the Pakistani population. In the present study, we have ascertained ten Pakistani and one Kashmiri family with primary microcephaly. We screened for potential mutations of the ASPM gene in seven consanguineous families (six Pakistani and one Kashmiri) linked to MCPH5 locus. Two previously reported (8508delGA, W1326X) and four novel sequence variants (Y1712X, I1717X, Y3353X, R3244X) were detected and all were predicted to be protein truncating. The degree of mental retardation in the affected individuals of the seven families varied from mild to moderate, and was not dependent on the location of mutations in the ASPM gene.