High throughput parallel analysis of hundreds of patient samples for more than 100 mutations in multiple disease genes

As more mutations are identified in genes of known sequence, there is a crucial need in the areas of medical genetics and genome analysis for rapid, accurate and cost-effective methods of mutation detection. We have developed a multiplex allele-specific diagnostic assay (MASDA) for analysis of large numbers of samples (> 500) simultaneously for a large number of known mutations (> 100) in a single assay. MASDA utilizes oligonucleotide hybridization to interrogate DNA sequences. Multiplex DNA samples are immobilized on a solid support and a single hybridization is performed with a pool of allele-specific oligonucleotide (ASO) probes. Any probes complementary to specific mutations present in a given sample are in effect affinity purified from the pool by the target DNA. Sequence-specific band patterns (fingerprints), generated by chemical or enzymatic sequencing of the bound ASO(s), easily identify the specific mutation(s). Using this design, in a single diagnostic assay, we tested samples for 66 cystic fibrosis (CF) mutations, 14 beta-thalassemia mutations, two sickle cell anemia (SCA) mutations, three Tay-Sachs mutations, eight Gaucher mutations, four mutations in Canavan disease, four mutations in Fanconi anemia, and five mutations in BRCA1. Each mutation was correctly identified. Finally, in a blinded study of 106 of these mutations in > 500 patients, all mutations were properly identified. There were no false positives or false negatives. The MASDA assay is capable of detecting point mutations as well as small insertion or deletion mutations. This technology is amenable to automation and is suitable for immediate utilization for high-throughput genetic diagnostics in clinical and research laboratories.      

Design, fabrication, and characterization of a tissue-equivalent phantom for optical elastography

We suitably adapt the design of a tissue-equivalent phantom used for photoacoustic imaging to construct phantoms for optical elastography. The elastography phantom we consider should have optical properties such as scattering coefficient, scattering anisotropy factor, and refractive index; mechanical properties such as storage and loss modulus; and acoustic properties such as ultrasound velocity, attenuation coefficient, and acoustic impedance to match healthy and diseased tissues. The phantom is made of poly (vinyl alcohol) (PVA) and its mechanical, optical, and acoustic properties are tailored by physical cross-linking effected through subjecting a suitable mix of PVA stock and water to a number of freeze-thaw cycles and by varying the degree of hydrolysis in the PVA stock. The optical, mechanical, and acoustic properties of the samples prepared are measured by employing different techniques. The measured variations in the values of optical scattering coefficient, scattering anisotropy factor, and refractive index and storage modulus are found to be comparable to those in normal and diseased breast tissues. The acoustic properties such as sound speed, acoustic attenuation coefficient, and density are found to be close to the average values reported in the literature for normal breast tissue.     

Primary adenocarcinoma (intestinal type) of nasal septum--a case report

Primary nasal septal adenocarcinoma is a rare lesion. A sporadic case of septal adenocarcinoma in a 22 years old male is being described along with review of literature.     

Electrophoretic analysis of Salmonella typhi and other bacteria

A comparative study involving SDS-PAGE of Salmonella typhi and other Bacteria was conducted. Protoplasmic antigens of Salmonella typhi. Salmonella paratyphi A, Salmonella typhimurium, Proteus sp, Klebsiellas sp. Pseudomonas aeruginosa, Shigella flexneri, Staphylococcus aureus were separated and compared on SDS-PAGE followed by checking of their cross reactivity by gel diffusion using antisera raised against whole cell and lysates of Salmonella typhi. Lines of identity between Salmonella typhi, Salmonella paratyphi A and Salmonella typhimurium were observed. No lines of identity were seen among Salmonella typhi, Pseudomonas aeruginosa and Sfaphylococcus aureus.     

Mouse homologues of the human AZF candidate gene RBM are expressed in spermatogonia and spermatids, and map to a Y chromosome deletion interval associated with a high incidence of sperm abnormalities

An RNA-binding motif (RBM) gene family has been identified on the human Y chromosome that maps to the same deletion interval as the 'azoospermia factor' (AZF). We have identified the homologous gene family (Rbm) on the mouse Y with a view to investigating the proposal that this gene family plays a role in spermatogenesis. At least 25 and probably >50 copies of Rbm are present on the mouse Y chromosome short arm located between Sry and the centromere. As in the human, a role in spermatogenesis is indicated by a germ cell-specific pattern of expression in the testis, but there are distinct differences in the pattern of expression between the two species. Mice carrying the deletion Yd1, that maps to the proximal Y short arm, are female due to a position effect resulting in non-expression of Sry ; sex-reversing such mice with an Sry transgene produces males with a high incidence of abnormal sperm, making this the third deletion interval on the mouse Y that affects some aspect of spermatogenesis. Most of the copies of Rbm map to this deletion interval, and the Yd1males have markedly reduced Rbm expression, suggesting that RBM deficiency may be responsible for, or contribute to, the abnormal sperm development. In man, deletion of the functional copies of RBM is associated with meiotic arrest rather than sperm anomalies; however, the different effects of deletion are consistent with the differences in expression between the two species.      

Histopathological and ultrastructural alterations of induced Yersinia enterocolitica infection in mice

Yersinia enterocolitica is an enteric bacterium and infections by this organism are mostly foodborne. It has been implicated to cause enterocolitis, terminal ilitis. diarrhoea, mesenteric lymphadenitis and arthritis in man. Due to paucity of information regarding histopathological and specially ultrastructural alterations in tissues affected, this study was planned with mice as the experimental model. Nine pathogenic Y.enterocoliticaisolates were used to infect 80 albino mice by oral and intraperitoneal route. Pathological alterations were studied by light and electron microscopy. Histopathological examination of intestines showed severe edema, purulent enteritis, goblet cell hyperplasia infiltration of mononuclear cells, thickening of mucosa and necrosis of the tips of villi. Liver showed congestion, hepatocellular degeneration and necrosis, atrophy of hepatocytes and microabcesses. The lungs revealed congestion, edema, haemorrhage and purulent ronchopneumonia, while kidneys showed mild necrotic changes and bacterial emboli in glomeruli. Ultrastructural changes were indicative of mitochondrial degeneration and their loss in kidneys, membranous degeneration with formation of myelin figures in lungs and disorganization, disruption and bleb formation of microvilli in intestines. Y.enterocolitica caused significant histopathological and ultrastructural alterations in experimentally infected mice. Variation in pathogenicity of different strains of Y.enterocolitica was also observed.