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Liquid biopsies are an integral part of the diagnosis of cancer. Here, we have extended previous validation studies of a new targeted NGS panel to include the detection of copy number amplifications (CNAs), fusions, and exon skipping variants. Detection of these gene classes included specimens from clinical and healthy donors and cell lines (fusions: ROS1, EML4-ALK, NTRK1; exon skipping: MET exon 14; CNAs: HER2, CDK6, EGFR, MYC, and MET). The limit of detection (LOD) for fusion/skipping was 42 copies (QC threshold was three copies) and was verified using three additional fusion/skipping variants. LOD for CNAs was 1.40-fold-change (QC threshold = 1.15-fold change) and was verified with three additional CNAs. In repeatability and intermediate precision (within lab) studies, all fusion/skipping variants were detected in all runs and all days of testing (n = 18/18; 100%); average CV for repeatability was 20.5% (range 8.7–34.8%), and for intermediate precision it was 20.8% (range 15.7–30.5%). For CNAs, 28/29 (96.6%) copy gains were detected. For CNAs, the average CV was 1.85% (range 0% to 5.49%) for repeatability and 6.59% (range 1.65% to 9.22%) for intermediate precision. The test panel meets the criteria for being highly sensitive and specific and extends its utility for the serial detection of clinically relevant variants in cancer.

TMS1 (target of methylation-induced silencing) is a CpG island-associated gene that functions in the regulation of apoptosis and encodes a caspase recruitment domain, a recently described motif found in apoptotic signaling molecules. Recent evidence suggests that silencing of genes in the apoptotic pathway contribute to human carcinogenesis. We examined the DNA methylation status of the TMS1 promoter in lung and breast tumor tissues, tumor cell lines and nonmalignant tissues by methylation-specific polymerase chain reaction (MSP) and its mRNA expression by reverse transcription PCR. Aberrant methylation of TMS1 was present in 70% (40 of 57) of small cell lung cancer (SCLC) cell lines and 41% (13 of 32) of SCLC tumor tissues, 48% (29 of 61) of non small cell lung cancer (NSCLC) cell lines and 40% (28 of 70) of NSCLC tumor tissues and 46% (12 of 26) of breast cancer cell lines and 32% (20 of 63) of breast tumor tissues. Methylation was absent in the peripheral blood lymphocytes and buccal epithelium from healthy volunteers, as well as in nonmalignant lung tissues and was rare in nonmalignant breast tissues 7% (2 of 30). DNA methylation was confirmed by sequence analysis and the methylation status correlated inversely with TMS1 RNA expression in 18 cell lines tested. RNA expression was restored by treatment with the demethylating agent 5-aza-2'-deoxycytidine, in 4 of 4 methylated cell lines that lacked the TMS1 transcript. Our results suggest that methylation of TMS1 may play a role in the pathogenesis of small cell and non small lung and breast cancers. © 2003 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

A gram-negative, aerobic, obligatory halophilic, curved-to-spiral rod-shaped, uni- or bi-polar flagellated motile bacterium 139Z-12(T) was isolated from water samples collected from Southern Ocean surrounding Antarctica as part of the Indo-German iron fertilization experiment "LOHAFEX." The bacterium was positive for catalase, oxidase, and gelatinase, with C18:1ω7c (20.1 %), C16:0 (7.3 %), C16:1ω7c (28.9 %), and C12:0 (19.0 %) as the predominant fatty acids, phosphatidylglycerol, and phosphatidylethanolamine as major lipids and Q-10 as the major respiratory quinone. DNA G + C content (mol%) of strain 139Z-12(T) was 53.0. Both BLAST and EzTaxon identified strain 139Z-12(T) as affiliated species of the genus Thalassospira with 16S rRNA gene sequence similarities ranging from 97.9 to 99.9 %. Based on above characteristics, strain 139Z-12(T) was assigned to the genus Thalassospira. Since strain 139Z-12(T) shared a DNA-DNA similarity of <70.0 % with members of the genus Thalassospira, 139Z-12(T) was identified as a novel species of the genus and named as Thalassospira lohafexi sp. nov. In addition to this, strain 139Z-12(T), based on REP-PCR, delineated at a similarity coefficient of <0.67 from other species of the genus Thalassospira and also exhibited a MLSA distance of <95.5 %, a value less than the interspecies distance determined previously for the genus Thalassospira, further supporting the species status. In addition, species rank was further confirmed by other polyphasic characteristics. The type strain of Thalassospira lohafexi sp. nov. is 139Z-12(T) (KCTC 32347(T) = LMG 27449(T) = MCC 2233(T) = NBRC 110402(T)).

We report the 4.36-Mb genome of Cryobacterium roopkundensis strain RuGl7, isolated from a soil sample collected in the periphery of Roopkund Lake, Himalayas, India. The draft genome consists of 4,356,863 bp, 4,048 protein-coding sequences, and 50 RNAs, with 65.3% G+C DNA content., (Copyright © 2014 Sathyanarayana Reddy et al.)

We report the 4.5-Mbp genome sequences of Sphingobacterium antarcticum 4BY, a psychrophilic bacterium isolated from the soils of Schirmacher Oasis, Antarctica. The draft genome of S. antarcticum strain 4BY consists of 4,566,318 bp with 40.4% G+C content, 4,234 protein coding genes, and 52 RNAs., (Copyright © 2014 Sreenivas et al.)

The 4.3-Mb genome of Lutibaculum baratangense strain AMV1(T), isolated from a soil sample collected from a mud volcano in Andamans, India, is reported. The draft genome of strain Lutibaculum baratangense AMV1(T) consists of 4,300,776 bp with a G+C content of 66.93 mol% and 4,198 predicted coding regions, including 56 RNAs., (Copyright © 2014 Singh et al.)

A rare case of gastric duplication cyst of tongue is reported.

A 29-year-old man presented with symptoms suggestive of acute pancreatitis of 3 day's duration. No definite aetiology was identifiable at admission. The patient had been receiving corticosteroids for the preceding 1 month, after the evacuation of a traumatic subdural haematoma. During the hospital stay, he developed a macular skin rash, which evolved over a period of 48 hours to a papulovesicular rash typical of varicella infection. Liver function tests were suggestive of anicteric hepatitis. Acyclovir therapy was instituted. However, the patient succumbed to an episode ventricular arrhythmia of sudden onset, possibly due to varicella myocarditis. A high index of suspicion for varicella infection in immunocompromised patients presenting with acute pancreatitis is necessary for early diagnosis. The rash may at times be atypical and may rarely appear after the onset of pancreatitis. Whenever any rash develops in the setting of pancreatitis of unknown aetiology, rapid diagnostic tests should be undertaken to establish the diagnosis and start appropriate therapy.

Background: Alterations in surface-active material may contribute to the pathogenesis of idiopathic pulmonary fibrosis both by increasing the elastic recoil due to surface forces and by promoting alveolar collapse. This study intends to evaluate the surfactant protein-A levels in bronchoalveolar lavage in patients of idiopathic pulmonary fibrosis., Material and Methods: Ten patients of idiopathic pulmonary fibrosis (IPF) of either sex were taken up for estimation of surfactant protein-A (SP-A) levels in bronchoalveolar lavage. The final diagnosis of IPF was based on histopathology and high resolution CT. Ten controls were taken out of which five patients were histopathologically proven cases of sarcoidosis and five patients with normal chest X-ray and CT scan. History, physical examination and routine investigations were done to rule out any concomitant illness., Results: Age range of patients varied from 37-65 years (mean +/- SD of 50.65 +/- 9.05) and controls 30-62 years (42.50 +/- 9.95). Fiberoptic bronchoscopy and bronchoalveolar lavage was carried out and fluid aspirated was studied for surfactant protein-A. The level of surfactant protein-A recovered was lower in patients with idiopathic pulmonary fibrosis in comparison to control group p < 0.01 (1.86 +/- 1.26 and 5.76 +/- 2.0 microg/ml respectively). The levels of surfactant protein-A also revealed that the level decreased with derangement of pulmonary function., Conclusions: The study thus showed that the level of surfactant protein A is reduced in patients with idiopathic pulmonary fibrosis. It is likely that they have a significant role in pathogenesis of idiopathic pulmonary fibrosis and its progression. Surfactant-A may have important therapeutic implications. Further studies are required for a definite answer.

Idiopathic pulmonary fibrosis is a chronic inflammatory disorder of unknown aetiology with a number of inflammatory cells playing a role in its pathogenesis. In this study, we have attempted to find out the possible role of nitric oxide in its pathogenesis by way of measuring the nitrite and nitrate levels in the bronchoalveolar lavage fluid. Ten patients of histologically proved idiopathic pulmonary fibrosis and 10 controls (5 with normal chest skiagrams and 5 with sarcoidosis) were included in the study Bronchoalveolar lavage was carried out in these cases. The levels of nitrates and nitrites were increased in cases of idiopathic pulmonary fibrosis (0.77+/- 0.36 and 8.93 +/- 2.63 nmol/mg of protein) compared to those in controls (0.38 +/- 0.06 and 3.80 +/- 1.11, respectively for sarcoidosis patients); (0.39 +/- 0.13 and 6.56 +/- 1.61 for subjects with normal chest skiagrams). These differences were statistically significant (p < 0.05 to 0.01). These findings suggest a possible role of nitric oxide in the pathogenesis of idiopathic pulmonary fibrosis.