Spectrum of MECP2 gene mutations in a cohort of Indian patients with Rett syndrome: Report of two novel mutations

Rett syndrome (RTT) is an X-linked neurodevelopmental disorder, primarily affecting females and characterized by developmental regression, epilepsy, stereotypical hand movements, and motor abnormalities. Its prevalence is about 1 in 10,000 female births. Rett syndrome is caused by mutations within methyl CpG-binding protein 2 (MECP2) gene. Over 270 individual nucleotide changes which cause pathogenic mutations have been reported. However, eight most commonly occurring missense and nonsense mutations account for almost 70% of all patients. We screened 90 individuals with Rett syndrome phenotype. A total of 19 different MECP2 mutations and polymorphisms were identified in 27 patients. Of the 19 mutations, we identified 7 (37%) frameshift, 6 (31%) nonsense, 14 (74%) missense mutations and one duplication (5%). The most frequent pathogenic changes were: missense p.T158M (11%), p.R133C (7.4%), and p.R306C (7.4%) and nonsense p.R168X (11%), p.R255X (7.4%) mutations. We have identified two novel mutations namely p.385-388delPLPP present in atypical patients and p.Glu290AlafsX38 present in a classical patient of Rett syndrome. Sequence homology for p.385-388delPLPP mutation revealed that these 4 amino acids were conserved across mammalian species. This indicated the importance of these 4 amino acids in structure and function of the protein. A novel variant p.T479T has also been identified in a patient with atypical Rett syndrome.     

Effect of gibberellin biosynthesis inhibitors on shoot regeneration from hypocotyl explants of Albizzia julibrissin

Summary Hypocotyl explants of Albizzia julibrissin were placed on Gamborg's B5 medium supplemented with various levels of paclobutrazol, uniconazole, prohexadione calcium, or GA₃. Callus formation was evident within one week after placement of the explants on the culture media. Green nodule-like structures protruded from the distal end of the explants within 10 days and developed into shoots within a month. These shoots readily formed adventitious roots when placed on fresh culture medium. All three of the gibberellin biosynthesis inhibitors increased shoot formation compared to the control. The number of shoots per explants was increased 107, 79, and 168% by 0.3–0.4 μM paclobutrazol, uniconazole, and prohexadione calcium, respectively. In contrast to the gibberellin biosynthesis inhibitors, GA₃ decreased shoot formation. These results indicate that modification of gibberellin status can have a strong impact on the number of shoots formed.     

Biomimetic sensor for certain catecholamines employing copper(II) complex and silver nanoparticle modified glassy carbon paste electrode

A dimeric Cu(II) complex [Cu(μ(2)-hep)(hep-H)](2)·2ClO(4) (1) containing bidentate (hep-H=2-(2-hydroxyethyl)pyridine) ligand was synthesized and characterized by single crystal X-ray diffraction studies. Each Cu-ion in 1 is in a distorted square pyramidal geometry. Further 1 along with silver nanoparticles (SNPs) have been used as modifier in the construction of a biomimetic sensor (1-SNP-GCPE) for determining certain catecholamines viz., dopamine (DA), levodopa (l-Dopa), epinephrine (EP) and norepinephrine (NE) using cyclic voltammetry, chronocoulometry, electrochemical impedance spectroscopy and adsorptive stripping square wave voltammetry (AdSSWV). Finally, the catalytic properties of the sensor were characterized by chronoamperometry. Employing AdSSWV, the calibration curves showed linear response ranging between 10(-6) and 10(-9)M for all the four analytes with detection limits (S/N=3) of 8.52×10(-10)M, 2.41×10(-9)M, 3.96×10(-10)M and 3.54×10(-10)M for DA, l-Dopa, EP and NE respectively. The lifetime of the biomimetic sensor was 3 months at room temperature. The prepared modified electrode shows several advantages such as simple preparation method, high sensitivity, high stability, ease of preparation and regeneration of the electrode surface by simple polishing along with excellent reproducibility. The method has been applied for the selective and precise analysis of DA, l-Dopa, EP and NE in pharmaceutical formulations, urine and blood serum samples.     

Gas chromatographic method using nitrogen–phosphorus detection for the measurement of tramadol and its O-desmethyl metabolite in plasma and brain tissue of mice and rats

A method that allows the measurement of plasma and brain levels of the centrally-acting analgesic tramadol and its major metabolite (O-desmethyl tramadol) in mice and rats was developed using gas chromatography equipped with nitrogen–phosphorus detection (GC–NPD). Plasma samples were extracted with methyl tert.-butyl ether (MTBE) and were injected directly into the GC system. Brain tissue homogenates were precipitated with methanol, the resulting supernatant was dried then acidified with hydrochloric acid. The aqueous solution was washed with MTBE twice, alkalinized, and extracted with MTBE. The MTBE layer was dried, reconstituted and injected into the GC system. The GC assay used a DB-1 capillary column with an oven temperature ramp (135 to 179°C at 4°C/min). Dextromethorphan was used as the internal standard. The calibration curves for tramadol and O-desmethyl tramadol in plasma and brain tissue were linear in the range of 10 to 10 000 ng/ml (plasma) and ng/g (brain). Assay accuracy and precision of back calculated standards were within ±15%.     

Compromised Spindle Assembly Checkpoint due to Altered Expression of Ubch10 and Cdc20 in Human Papillomavirus Type 16 E6- and E7-Expressing Keratinocytes

Cells expressing human papillomavirus type 16 (HPV-16) E6 and E7 proteins exhibit deregulation of G₂/M genes, allowing bypass of DNA damage arrest signals. Normally, cells with DNA damage that override the G₂ damage checkpoint would precociously enter mitosis and ultimately face mitotic catastrophe and apoptotic cell death. However, E6/E7-expressing cells (E6/E7 cells) have the ability to enter and exit mitosis in the presence of DNA damage and continue with the next round of the cell cycle. Little is known about the mechanism that allows these cells to gain entry into and exit from mitosis. Here, we show that in the presence of DNA damage, E6/E7 cells have elevated levels of cyclin B, which would allow entry into mitosis. Also, as required for exit from mitosis, cyclin B is degraded in these cells, permitting initiation of the next round of DNA synthesis and cell cycle progression. Proteasomal degradation of cyclin B by anaphase-promoting complex/cyclosome (APC/C) is, in part, due to elevated levels of the E2-conjugating enzyme, Ubch10, and the substrate recognition protein, Cdc20, of APC/C. Also, in E6/E7 cells with DNA damage, while Cdc20 is complexed with BubR1, indicating an active checkpoint, it is also present in complexes free of BubR1, presumably allowing APC/C activity and slippage through the checkpoint.Failure to activate cell cycle checkpoints in the presence of any DNA damage leads to genomic instability, polyploidy, and subsequently, aneuploidy, which is a hallmark of many cancers (26). Human papillomaviruses (HPVs) which cause various epithelial cancers, produce two proteins, E6 and E7, whose expression allows bypass or overriding of normal DNA damage and spindle checkpoint signals, primarily through inactivation of p53 and retinoblastoma family members, respectively (11, 16, 17). Our laboratory and others have previously shown that bypass of these arrest signals due to the presence of the viral genes gives rise to a significant population of cells that are polyploid (13, 16, 24, 32). Polyploid and aneuploid cells predominantly arise due to defects in the spindle assembly checkpoint (SAC) during mitosis. While we have some understanding of the mechanisms that lead to bypass of DNA damage arrest signals at the G₂/M stage of the cell cycle, it is not clear how the E6/E7-expressing cells with DNA damage and abnormal chromosomes are allowed to (i) to enter into mitosis and (ii) exit out of mitosis to initiate the next round of replication. Progression through mitosis is regulated by the ubiquitin-dependent degradation machinery, consisting of the anaphase-promoting complex/cyclosome (APC/C), a multisubunit ubiquitin ligase. The activity of APC/C is dependent on the substrate-specifying proteins Cdc20 in metaphase and Cdh1 in telophase (25, 37). In normal cells, spindle checkpoint proteins Mad2 and BubR1 serve to inhibit APC/C until all the chromosomes are aligned correctly on the mitotic spindle by binding Cdc20 and preventing it from activating APC/C (5, 21, 31). In the event of DNA damage and/or unattached kinetochores, the SAC will arrest cells before exit from mitosis by inhibiting activation of APC/C. As a consequence of APC/C inhibition, cyclin B is not degraded, thus preventing cells from mitotic exit (6). Work by Chen''s group (11) has shown that E6- and E7-expressing cells (also referred to here as E6/E7 cells) adapt to an active SAC and are capable of mitotic slippage. So, what is the mechanism that underlies mitotic slippage in E6/E7 cells and allows them to enter the next round of cell cycle? Recent work by van Ree et al. (34) has shown that overexpression of E2 ubiquitin-conjugating enzyme Ubch10 leads to uncontrolled APC/C activity and degradation of cyclin B even in the presence of an active mitotic checkpoint, leading to mitotic slippage. In this report, we show that primary human foreskin keratinocytes (HFKs) expressing E6/E7 have high levels of cyclin B, which allows entry into mitosis in the presence of DNA damage. We show that these cells successfully exit mitosis by, in part, indirect activation of APC/C through upregulation of the E2-conjugating protein, Ubch10, and the substrate-specific component of APC/C, Cdc20, leading to the required degradation of cyclin B. In addition, Cdc20 is detected in different complexes; one includes the protein BubR1, indicating an active checkpoint, while other complexes are free of BubR1 and are thus free to activate APC/C. Upregulation of cyclin B and Ubch10 as well as Cdc20 is primarily through E6 and its ability to target p53 degradation, although inhibition of the pRb family members by E7 may also play a part.     

A text mining approach to detect mentions of protein glycosylation in biomedical text

Protein Glycosylation is an important post translational event that plays a pivotal role in protein folding and protein is trafficking. We describe a dictionary based and a rule based approach to mine ‘mentions‘ of protein glycosylation in text. The dictionary based approach relies on a set of manually curated dictionaries specially constructed to address this task. Abstracts are then screened for the ‘mentions‘ of words from these dictionaries which are further scored followed by classification on the basis of a threshold. The rule based approaches also relies on the words in the dictionary to arrive at the features which are used for classification. The performance of the system using both the approaches has been evaluated using a manually curated corpus of 3133 abstracts. The evaluation suggests that the performance of the Rule based approach supersedes that of the Dictionary based approach.