Genome sequences of actinobacteriophages JorRay, Blocker23, Nibbles, and OlgasClover.

JorRay, Blocker23, Nibbles, and OlgasClover are actinobacteriophages belonging to clusters G1, B2, CT, and DJ, respectively. JorRay and Blocker23 were identified in host bacterium Mycobacterium smegmatis mc2155. Nibbles and OlgasClover were identified in host bacterium Gordonia rubripertincta NRRL B-16540.

Genome Sequences of Gordonia rubripertincta Bacteriophages AnarQue and Figliar.

AnarQue and Figliar are bacteriophages identified from the host bacterium Gordonia rubripertincta NRRL B-16540. AnarQue is circularly permuted and has a length of 61,822 bp; it is assigned to cluster DR. Figliar has a 3' sticky overhang and a length of 61,147 bp; it is assigned to cluster DJ.

Genome Sequences of Gordonia Bacteriophages Jodelie19, BlingBling, and Burnsey.

Jodelie19, BlingBling, and Burnsey are bacteriophages identified using host bacteria of the genus Gordonia Jodelie19 is a lytic phage found in Gordonia rubripertincta NRRL B-16540. The temperate phage BlingBling and lytic phage Burnsey were both isolated using the host bacterium Gordonia terrae 3612.

Genome Sequences of Gordonia rubripertincta Bacteriophages Jellybones and NHagos.

Jellybones and NHagos are bacteriophages that were identified in the host bacterium Gordonia rubripertincta NRRL B-16540. Jellybones has a direct terminal repeat and was assigned to the CS2 subcluster with a length of 77,514 bp. NHagos is circularly permuted and was assigned to the DR cluster with a length of 59,580 bp.

Trace Elements in Gluten-free Pastas and Flours from Markets Located in the Las Vegas, Nevada Area.

The popularity of gluten-free foods has been increasing across the United States and abroad. A significant reason for this trend involves marketing efforts targeted towards individuals seeking to avoid the consequences of celiac disease or a perceived gluten intolerance. Many gluten-free food products originate in regions of the world where irrigation with metal-contaminated waters is common. Calcium, Fe, Mg, Ti and Zn were detected at various levels across all foods products. Cadmium was detected in 96.8% of U.S. and 54.5% of Asian gluten-free foods with gluten containing foods above reported averages (216 µg kg-1 Cd); as was Co (140µg kg-1) in 48.4 % of U.S., 72.7% of Asian gluten-free foods, and 40% of the gluten containing foods; Cr was in 54.8% of the U.S., 72.5% of Asian gluten-free foods, and 100% of gluten containing food products; while Ca, Fe, Mg, Ti and Zn were greater than 10,000 µg kg-1 with Ba, Cd, Co, Mo, and Ni above reported averages. Finally, trace metals were more commonly detected in the gluten containing foods overall. It was found that trace elements were more commonly found in the gluten containing products; however, none of the higher than expected levels pose a significant health risk to consumers.

Genome rearrangements detected by SNP microarrays in individuals with intellectual disability referred with possible Williams syndrome.

BACKGROUND: Intellectual disability (ID) affects 2-3% of the population and may occur with or without multiple congenital anomalies (MCA) or other medical conditions. Established genetic syndromes and visible chromosome abnormalities account for a substantial percentage of ID diagnoses, although for approximately 50% the molecular etiology is unknown. Individuals with features suggestive of various syndromes but lacking their associated genetic anomalies pose a formidable clinical challenge. With the advent of microarray techniques, submicroscopic genome alterations not associated with known syndromes are emerging as a significant cause of ID and MCA. METHODOLOGY/PRINCIPAL FINDINGS: High-density SNP microarrays were used to determine genome wide copy number in 42 individuals: 7 with confirmed alterations in the WS region but atypical clinical phenotypes, 31 with ID and/or MCA, and 4 controls. One individual from the first group had the most telomeric gene in the WS critical region deleted along with 2 Mb of flanking sequence. A second person had the classic WS deletion and a rearrangement on chromosome 5p within the Cri du Chat syndrome (OMIM:123450) region. Six individuals from the ID/MCA group had large rearrangements (3 deletions, 3 duplications), one of whom had a large inversion associated with a deletion that was not detected by the SNP arrays. CONCLUSIONS/SIGNIFICANCE: Combining SNP microarray analyses and qPCR allowed us to clone and sequence 21 deletion breakpoints in individuals with atypical deletions in the WS region and/or ID or MCA. Comparison of these breakpoints to databases of genomic variation revealed that 52% occurred in regions harboring structural variants in the general population. For two probands the genomic alterations were flanked by segmental duplications, which frequently mediate recurrent genome rearrangements; these may represent new genomic disorders. While SNP arrays and related technologies can identify potentially pathogenic deletions and duplications, obtaining sequence information from the breakpoints frequently provides additional information.

Inversion of the Williams syndrome region is a common polymorphism found more frequently in parents of children with Williams syndrome.

Williams syndrome (WS) is a multisystem disorder caused by deletion of about 1.55 Mb of DNA (including 26 genes) on chromosome 7q11.23, a region predisposed to recombination due to its genomic structure. Deletion of the Williams syndrome chromosome region (WSCR) occurs sporadically. To better define chance for familial recurrence and to investigate the prevalence of genomic rearrangements of the region, 257 children with WS and their parents were studied. We determined deletion size in probands by metaphase FISH, parent-of-origin of the deleted chromosome by molecular genetic methods, and inversion status of the WSCR in both parents by interphase FISH. The frequency of WSCR inversion in the transmitting parent group was 24.9%. In contrast, the rate of inversion in the non-transmitting parent group (a reasonable estimate of the rate in the general population) was 5.8%. There were no significant gender differences with respect to parent-of-origin for the deleted chromosome or the incidence of the inversion polymorphism. There was no difference in the rate of spontaneous abortion for mothers heterozygous for the WSCR inversion relative to mothers without the inversion. We calculate that for a parent heterozygous for a WSCR inversion, the chance to have a child with WS is about 1 in 1,750, in contrast to the 1 in 9,500 chance for a parent without an inversion.

BAC-FISH refutes report of an 8p22-8p23.1 inversion or duplication in 8 patients with Kabuki syndrome.

BACKGROUND: Kabuki syndrome is a multiple congenital anomaly/mental retardation syndrome. The syndrome is characterized by varying degrees of mental retardation, postnatal growth retardation, distinct facial characteristics resembling the Kabuki actor's make-up, cleft or high-arched palate, brachydactyly, scoliosis, and persistence of finger pads. The multiple organ involvement suggests that this is a contiguous gene syndrome but no chromosomal anomalies have been isolated as an etiology. Recent studies have focused on possible duplications in the 8p22-8p23.1 region but no consensus has been reached. METHODS: We used bacterial artificial chromosome-fluorescent in-situ hybridization (BAC-FISH) and G-band analysis to study eight patients with Kabuki syndrome. RESULTS: Metaphase analysis revealed no deletions or duplications with any of the BAC probes. Interphase studies of the Kabuki patients yielded no evidence of inversions when using three-color FISH across the region. These results agree with other research groups' findings but disagree with the findings of Milunsky and Huang. CONCLUSION: It seems likely that Kabuki syndrome is not a contiguous gene syndrome of the 8p region studied.

GTF2I hemizygosity implicated in mental retardation in Williams syndrome: genotype-phenotype analysis of five families with deletions in the Williams syndrome region.

Most individuals with Williams syndrome (WS) have a 1.6 Mb deletion in chromosome 7q11.23 that encompasses the elastin (ELN) gene, while most families with autosomal dominant supravalvar aortic stenosis (SVAS) have point mutations in ELN. The overlap of the clinical phenotypes of the two conditions (cardiovascular disease and connective tissue abnormalities such as hernias) is due to the effect of haploinsufficiency of ELN. SVAS families often have affected individuals with some WS facial features, most commonly in infancy, suggesting that ELN plays a role in WS facial gestalt as well. To find other genes contributing to the WS phenotype, we studied five families with SVAS who have small deletions in the WS region. None of the families had mental retardation, but affected family members had the Williams Syndrome Cognitive Profile (WSCP). All families shared a deletion of LIMK1, which encodes a protein strongly expressed in the brain, supporting the hypothesis that LIMK1 hemizygosity contributes to impairment in visuospatial constructive cognition. While the deletions from the families nearly spanned the WS region, none had a deletion of FKBP6 or GTF2I, suggesting that the mental retardation seen in WS is associated with deletion of either the centromeric and/or telomeric portions of the region. Comparison of these five families with reports of other individuals with partial deletions of the WS region most strongly implicates GTF2I in the mental retardation of WS.