Association of mutation and hypermethylation of p21 gene with susceptibility to breast cancer: a study from north India

p21 gene located at chromosome 6p21.2 is a possible tumour suppressor gene involved in the pathogenesis of breast cancer. Both genetic and epigenetic alterations in p21 have been implicated in breast carcinoma. In the present study, our main aim was to study the impact of these two kinds of alterations of p21 gene in Indian female breast cancer patients. A total of 150 female breast cancer patients of north India were screened by PCR-SSCP followed by direct sequencing and methylation specific PCR. Mutational screening of p21 gene revealed significant amount of mutations [32.66 % (49/150)] in exon 2, whereas p21 promoter was found hypermethylated in 42 of 150 (28 %) breast cancer patients in our population. The intriguing feature of the study was the G>T transition (GAG>TAG) at codon 107 and the A>C transition (AGC>CGC) at codon 146 possibly rendering p21 completely ineffective in its anti- proliferative activity. Our results suggest a significant association between the mutational and hypermethylation profile of p21 gene. Therefore, we show for the first time that the significant association of p21 mutation and hypermethylation leads to the complete inactivation of p21 gene in Indian female breast cancer patients. Complete silencing of the p21 gene seems to be the result not only of genetic alterations but also of epigenetic modification.     

Tricyclic HIV integrase inhibitors: potent and orally bioavailable C5-aza analogs

A series of C5-aza tricyclic HIV integrase inhibitors was prepared. A highly potent and orally bioavailable compound (compound 9) was identified and selected for development.     

Green Space Functionality Along an Urban Gradient in Karachi,Pakistan: A Socio-Ecological Study

An important component of urban green space functionality is the way in which such spaces are perceived and used by urban residents. Use is affected by many factors including the nature and dynamics of urban morphology at the city and neighbourhood scale. This paper demonstrates a method for conducting analyses of green space socio-ecological functionality and presents the results of its application to Karachi, Pakistan. The paper explores the use of the results of an urban gradient analysis for site selection and presents the results of an associated survey of functions using three case study green spaces. The results show that, although urban dwellers in the city use green spaces infrequently, when they do it tends to be for long periods of time and for a range of purposes. Levels of overcrowding at the more accessible sites indicate the value that urban dwellers place on these resources, and their importance to the city as a whole. The results of this study provide evidence for the need to protect green spaces from the competing demands associated with increasing urbanisation, especially if the wider goal of urban sustainability is to be achieved.     

NMR spectroscopy-based metabolomic study of serum in sulfur mustard exposed patients with lung disease

Sulfur mustard (SM) is a vesication chemical warfare agent for which there is currently no antidote. Despite years of research, there is no common consensus about the pathophysiological basis of chronic pulmonary disease caused by this chemical warfare agent. In this study, we combined chemometric techniques with nuclear magnetic resonance (NMR) spectroscopy to explore the metabolic profile of sera from SM-exposed patients. A total of 29 serum samples obtained from 17 SM-injured patients, and 12 healthy controls were analyzed by Random Forest. Increased concentrations of seven amino acids, glycerol, dimethylamine, ketone bodies, lactate, acetate, citrulline and creatine together with the decreased very low-density lipoproteins (VLDL) levels were observed in patients compared with control subjects. Our study reveals the metabolic profile of sera from SM-injured patients and indicates that NMR-based methods can distinguish these patients from healthy controls.     

Molecular Epidemiology of Influenza A(H1N1)pdm09 Viruses from Pakistan in 2009-2010

Background

In early 2009, a novel influenza A(H1N1) virus that emerged in Mexico and United States rapidly disseminated worldwide. The spread of this virus caused considerable morbidity with over 18000 recorded deaths. The new virus was found to be a reassortant containing gene segments from human, avian and swine influenza viruses.

Methods/Results

The first case of human infection with A(H1N1)pdm09 in Pakistan was detected on 18^th June 2009. Since then, 262 laboratory-confirmed cases have been detected during various outbreaks with 29 deaths (as of 31^st August 2010). The peak of the epidemic was observed in December with over 51% of total respiratory cases positive for influenza. Representative isolates from Pakistan viruses were sequenced and analyzed antigenically. Sequence analysis of genes coding for surface glycoproteins HA and NA showed high degree of high levels of sequence identity with corresponding genes of regional viruses circulating South East Asia. All tested viruses were sensitive to Oseltamivir in the Neuraminidase Inhibition assays.

Conclusions

Influenza A(H1N1)pdm09 viruses from Pakistan form a homogenous group of viruses. Their HA genes belong to clade 7 and show antigenic profile similar to the vaccine strain A/California/07/2009. These isolates do not show any amino acid changes indicative of high pathogenicity and virulence. It is imperative to continue monitoring of these viruses for identification of potential variants of high virulence or drug resistance.     

A quantitative electron microscope autoradiographic study on I-human choriogonadotropin internalization in bovine luteal slices

Very few silver grains were seen on the cell surface and none intracellularly after incubation for 2 h at 4 °C. However, numerous grains were seen in various subcellular organelles when the tissues were incubated for 2 h at 22 ° or 38 °C. The grain distribution was qualitatively similar, but quantitatively, there were fewer grains at 22 ° than at 38 °C. Co-incubation of ¹²⁵I-hCG with excess unlabelled hCG resulted in the virtual disappearance of silver grains from all the subcellular organelles. Excess unlabelled human luteinizing hormone (but not follicle-stimulating hormone or prolactin) inhibited the appearance of silver grains in luteal tissue. There were no silver grains in bovine liver slices incubated with ¹²⁵I-hCG.The plasma membrane-associated grains progressively decreased, while intracellular organelle-associated grains increased with time at 38 °C. There were no grains in nuclei at 5 min, but they appeared at 10 min and increased until 120 min. After correction for radiation spread by three-step mask analysis, smooth endoplasmic reticulum and mitochondria did not contain any grains. The grain density was the highest in Golgi, followed by lysosomes, rough endoplasmic reticulum, nuclei, and plasma membranes after incubation for 2 h at 38 °C. Thus, the electron microscope autoradiography approach confirmed our biochemical data in the preceding paper (Chegini et al., Exp cell res 151 (1984) 466 [5]) on time, temperature dependency and specificity of ¹²⁵I-hCG internalization, association of internalized hormone with a variety of intracellular organelles, and the highest uptake in Golgi.     

The attachments of the lateral and medial ends of the extensor retinaculum of the human wrist

The attachments of the lateral and medial ends of the extensor retinaculum of the human wrist were observed in 52 human upper limbs (from 26 cadavers) by dissection. In all the specimens used in this study, the lateral end of the retinaculum was found to be attached to the distal part of the anterior border of the radius and its medial end was attached to the styloid process of the ulna, the pisiform and the triquetrum.     

Identification of potential inter-domain disulfides in three higher plant mitochondrial citrate synthases: Paradoxical differences in redox-sensitivity as compared with the animal enzyme

The mitochondrial citrate synthases (EC 4.1.3.7) of pummelo, potato and Arabidopsis are activated in crude extracts by dithiothreitol treatment and/or inactivated by the strong oxidizing agent diamide. Surprisingly, homology modeling reveals a potential disulfide involving two cysteine residues which are also present in the redox-insensitive model enzyme, pig heart citrate synthase. Energy minimization calculations suggest that differences in the charge distribution enhance disulfide bond formation in the plant mitochondrial citrate synthase and inhibit disulfide bond formation in the mammalian enzyme.     

Androgen receptor affinity chromatography: synthesis and properties of 17 alpha-epoxypropyl-dihydrotestosterone Sepharose

We have prepared a new affinity chromatography reagent, 17 alpha-epoxypropyl-dihydrotestosterone linked to Thiopropyl-Sepharose, with potential for use in purification of androgen receptor and other specific androgen binding proteins. The linkage is stable, and the ligand has reasonably high affinity for the receptor. Starting with 5 alpha-androstane-3 beta-ol-17-one, we synthesized in two steps 17 alpha-allyl-dihydrotestosterone, which was then oxidized to 17 alpha-epoxypropyl-DHT yielding 2 diastereomers in about a 4:1 ratio. The 17 alpha-allyl-DHT had about 50% of DHT's affinity for rat uterine androgen receptor, while the affinity of the major epoxide isomer was 9% and that of the minor isomer was 4%. Reaction of the epoxides with Thiopropyl-Sepharose-6B gave about 7 mumol of covalently bound DHT per ml of beads. These beads took up 83% of the androgen receptor from a rat uterine cytosol in a preliminary study, which more than equalled the performance of identically prepared estradiol beads successfully used for estrogen receptor purification. The use of the new DHT beads in purifications of the androgen receptor and other binding proteins is now being explored by other laboratories.     

Expression of <Emphasis Type=Italic>rol</Emphasis> genes in transgenic soybean (<Emphasis Type=Italic>Glycine max</Emphasis> L.) leads to changes in plant phenotype,leaf morphology,and flowering time

Soybean (Glycine max L.) cultivar NARC-4 was transformed with constructs carrying rolA, rolB, or rolC genes, each under the control of the Cauliflower Mosaic Virus 70S promoter. Cotyledonary nodes of soybean seeds were infected with Agrobacterium tumefaciens strain LBA4404 carrying one of the three rol genes, along with nptII in the plasmid pLBR. The efficiency of the transformation varied slightly among the three constructs, with frequencies of 6, 7, and 5% for the rolA, rolB, and rolC genes, respectively, being observed. Southern blot analysis confirmed the integration of rol genes in the soybean genome with varying numbers of copies of the transgene. All transformed plants showed enhanced rooting, but the number of adventitious roots was higher for transformants carrying the rolB transgene. rolA and rolC transformants showed dwarf phenotypes, clustered branching, and variations in leaf morphology. Furthermore, these plants flowered within a short period of time and produced lower numbers of flowers. rolB transformants showed variations in phenotype, including dwarf to semi-dwarf and shrubby growth, abnormal stem growth, short internodes, variations in leaf morphology, and greenish to yellowish-green colored leaves. These plants also flowered early, but dwarf plants produced low numbers of flowers, while shrubby plants produced high numbers of flowers, but these were mostly infertile.