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Biomedical subjects

A Muhammad

Publications and source records attributed to A Muhammad.

13 recordsLinked to original sources
PubMed2003

KDBI: Kinetic Data of Bio-molecular Interactions database.

Understanding of cellular processes and underlying molecular events requires knowledge about different aspects of molecular interactions, networks of molecules and pathways in addition to the sequence, structure and function of individual molecules involved. Databases of interacting molecules, pathways and related chemical reaction equations have been developed. The kinetic data for these interactions, which is important for mechanistic investigation, quantitative study and simulation of cellular processes and events, is not provided in the existing databases. We introduce a new database of Kinetic Data of Bio-molecular Interactions (KDBI) aimed at providing experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature. KDBI contains information about binding or reaction event, participating molecules (name, synonyms, molecular formula, classification, SWISS-PROT AC or CAS number), binding or reaction equation, kinetic data and related references. The kinetic data is in terms of one or a combination of the following quantities as given in the literature of a particular event: association/dissociation or on/off rate constant, first/second/third/. order rate constant, equilibrium rate constant, catalytic rate constant, equilibrium association/dissociation constant, inhibition constant and binding affinity constant. Each entry can be retrieved through protein or nucleic acid or ligand name, SWISS-PROT AC number, ligand CAS number and full-text search of a binding or reaction event. KDBI currently contains 8273 entries of biomolecular binding or reaction events involving 1380 proteins, 143 nucleic acids and 1395 small molecules. Hyperlinks are provided for accessing references in Medline and available 3D structures in PDB and NDB. This database can be accessed at http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp.

DNA↗
PubMed2003

Persistent organic pollutants in little egret eggs from selected wetlands in Pakistan.

The main goal of the present work has been to study the use of egret eggs to assess environmental pollution by POPs (HCB, HCHs, cyclodienes, DDTs and PCBs) in three Pakistani wetlands that are presumed to be affected by different types of pollution. Taunsa Barrage, affected mainly by agricultural pollutants; Karachi Harbor because of the supposed exposure to industrial activity-related POPs; and Haleji Lake as a relatively pristine area because of its location in a stony desert. Taunsa Barrage and Haleji Lake are wetlands of international importance according to the Ramsar Convention, while the Karachi Harbor is of interest because of the large human population living there. Eggs of the white ( Egretta garzetta garzetta) and dark ( Egretta garzetta gularis) morphs of Little Egrets were used as monitoring tools. Concentrations were also determined in several prey in this species' diet and in the sediments collected in their foraging areas. Differences in egg pollutant content among the three localities were significant for all the compounds. Overall, the eggs from Haleji Lake and Karachi showed, respectively, the lowest and highest percentages of detection and organochlorine concentrations. Biomagnification from sediments to prey and then to eggs has been documented in the three areas studied and is accompanied by higher percentages of detection of different compounds through the compartments. Differences in the biomagnification factor among the areas were small, even when differences in pollutant concentrations were high, suggesting that eggs are reliable indicators of POPs in the environment. The values found were generally lower than those reported for the eggs of large herons from North America or the Mediterranean basin, and are about the same order of magnitude that those of other medium-sized egrets from other parts of the world.

Animals↗
PubMed2003

Egrets as monitors of trace-metal contamination in wetlands of Pakistan.

Environments in Pakistan are subject to increasing pollution, but previous studies were very scanty. During 1999 and 2000, we assessed trace element contamination at three wetlands, Karachi Harbour (with presumed industrial-urban pollution), Taunsa Barrage (agricultural pollution), and Haleji Lake (relatively unpolluted), using as indicators the eggs and the feathers of colonial waterbirds, particularly Little Egrets, their prey, and the sediments collected within their foraging areas. The concentrations of As, Cd, Cr, Pb, Hg, Mn, Se, and Zn were generally within the normal background level, and mostly below the threshold that may affect bird survival or reproduction. However, somewhat high concentrations were found in fish from Karachi, for Pb that was at levels that may harm fish reproduction, and for Hg that was at limit concentration for human consumption. Alarming concentrations were found for Cr and Se in sediments from Karachi, that were above the critical levels for contaminated soil, and Se in eggs, that may affect egret reproduction. The differences among the three wetlands were less marked than hypothesized. The egret species within the same area differed in the concentration of certain elements in their eggs, possibly because females may have foraged in different habitats before breeding, whereas no interspecies difference was found in chick feathers, presumably because their food had been collected in similar habitats around the colony. High bioaccumulation from sediments to organic samples occurred for Hg, while Cd, Se, and Zn exhibited low accumulation; for all these elements, feathers of predatory birds such as the egrets are the best indicators of environmental contamination. On the other hand, As and Cr did not bioaccumulate, and the sediments, or the organisms low in the food chain, like fish or crustaceans, are better indicators of their presence in the environment than predatory birds.

Animals↗
PubMed1999

Separation and characterization of proteins from green and etiolated shoots of rice (Oryza sativa L.): towards a rice proteome.

Proteins extracted from green and etiolated shoots of rice were separated by two-dimensional polyacrylamide gel electrophoresis and relative molecular weights and isoelectric points were determined. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane and 85 proteins were analyzed by a gas-phase protein sequencer. The N-terminal amino acid sequences of 21 out of 85 proteins were determined in this manner. N-terminal regions of the remaining proteins could not be sequenced. The internal amino acid sequences of proteins were determined by sequence analysis of peptides obtained by the Cleveland peptide mapping method and compared with those of known plant and animal protein sequences to understand the nature of the proteins. Green shoots revealed the presence of photosynthetic proteins as expected; however, as etiolated shoots were not photosynthetic, only precursors of the photosynthetic proteins were identified. Interestingly, the presence of L-ascorbate peroxidase only in etiolated shoots suggests a cellular protectant function for this antioxidant enzyme in the etiolating shoots. Using this experimental approach, we could identify the major proteins involved in growth regulation in photosynthetic green shoots as well as in etiolating rice seedlings.

Ascorbate Peroxidases↗
PubMed1987

Comparison of echocardiographic methods for assessment of left ventricular shortening and wall stress.

M-mode echocardiographic measurement of left ventricular fractional shortening and meridional wall stress has been used extensively alone and in combination to describe left ventricular systolic function. To determine whether the improved dimensional information afforded by two-dimensional echocardiography might result in shortening and stress calculations yielding a different view of left ventricular function, we compared two-dimensional and M-mode echocardiograms in 69 subjects (19 normal, 13 with aortic stenosis, 22 with aortic regurgitation and 15 with congestive cardiomyopathy). Fractional shortening was greater with M-mode than with two-dimensional echocardiography in all subjects, especially in those with cardiomyopathy (p less than 0.05). In aortic stenosis, two-dimensional shortening, at 24 +/- 5%, was reduced (p less than 0.05 versus normal), but M-mode shortening, at 34 +/- 5%, was not. M-mode estimates of meridional stress were higher than two-dimensional values, again especially in cardiomyopathy. Two-dimensional echocardiography enabled determination of long- and short-axis ratios, circumferential stress and the ratio of circumferential to meridional stresses. Circumferential stress was elevated in aortic stenosis at 302 +/- 65 X 10(3) dynes/cm2, suggesting afterload excess as the cause for the observed reduction in two-dimensional shortening. The more spherical cardiomyopathic hearts had a meridional to circumferential stress ratio closer to 1, such that use of meridional stress alone would overestimate effective afterload. It is concluded that M-mode and two-dimensional echocardiographic analyses of left ventricular shortening and stress produce different results. Two-dimensional echocardiographic methods may enhance the assessment of ventricular function, especially in patients with aortic stenosis and cardiomyopathy.

Adult↗
PubMed1987

Experimental congestive heart failure produced by rapid ventricular pacing in the dog: cardiac effects.

Chronic rapid ventricular pacing in the dog reportedly produces a useful preparation of low-output heart failure. However, little information is available regarding cardiac changes in this preparation. Accordingly, we evaluated the effects of both short-term (3 weeks) and prolonged (2 months) rapid ventricular pacing on cardiac hemodynamics, mass, and chamber size. The effects of short-term pacing on left ventricular wall thickening, blood flow, and metabolism were also examined. Compared with 16 control dogs, dogs paced for either 3 weeks (n = 8) or 2 months (n = 13) exhibited reduced cardiac outputs (control 130 +/- 20 ml/min/kg, 3 week pacing 112 +/- 19 ml/min/kg, 2 month pacing 116 +/- 14 ml/min/kg) and elevated pulmonary wedge pressures (control 10 +/- 3 mm Hg, 3 week pacing 26 +/- 5 mm Hg, 2 month pacing 26 +/- 8 mm Hg) and right atrial pressures (control 4 +/- 1 mm Hg, 3 week pacing 13 +/- 3 mm Hg, 2 month pacing 9 +/- 3 mm Hg) (all p less than .01 vs control). At the postmortem examination, both groups of paced dogs also exhibited increased left ventricular volumes (control 13 +/- 6 ml, 3 week pacing 27 +/- 6 ml, 2 month pacing 26 +/- 8 ml), right ventricular volumes (control 13 +/- 5 ml, 3 week pacing 27 +/- 9, 2 month pacing 24 +/- 7 ml), and right ventricular mass (control 27 +/- 5 g, 3 week pacing 32 +/- 6 g, 2 month pacing 34 +/- 6 g) (all p less than .03 vs control) but had normal left ventricular mass. Three weeks of pacing also decreased percent left ventricular shortening (34 +/- 6% to 17 +/- 7%) associated with a disproportionate deterioration of posterior wall thickening (58 +/- 16% to 17 +/- 18%) (both p less than .01), as assessed by echocardiography. This left ventricular dysfunction was associated with no change in myocardial lactate extraction (prepacing 40 +/- 10%, 3 week pacing 36 +/- 10%), myocardial arteriovenous O2 difference, or myocardial histology, suggesting that it was not due to myocardial ischemia. These data indicate that rapid ventricular pacing in the dog produces a useful experimental preparation of low-output heart failure characterized by biventricular pump dysfunction, biventricular cardiac dilation, and nonischemic impairment of left ventricular contractility.

Animals↗
PubMed1986

Intraoperative assessment of left ventricular heterogeneity.

To evaluate regional differences in thickness and systolic function of human myocardium perfused by angiographically normal coronary arteries in valvular and ischemic heart disease, we performed intraoperative epicardial M-mode mapping of ventriculographically normal wall regions (perfused by normal coronary arteries) in 22 subjects undergoing either coronary bypass surgery for stenoses in other vessels (n = 15) or mitral (n = 5) and/or aortic valve replacement (n = 4). In patients in whom both anterior and inferior walls were ventriculographically normal and normally perfused (n = 6), comparison of the two walls showed the anterior wall to be thicker at both end diastole and end systole, but there was no difference in the percentage of systolic thickening. Analysis of myocardium along the long axis revealed apical sites to be thinner than basal sites at both end diastole and end systole. Percentage of systolic thickening was also increased at apical sites. In patients in whom only the anterior wall was normal, a similar decrease in anterior wall thickness was noted at the apex. Thus systematic regional heterogeneity along both the left ventricular major and minor axes is found in the chronically diseased human heart as it is in the normal heart. Assessment of myocardial structure and function and of the effects of therapeutic interventions must take this heterogeneity into account.

Coronary Artery Bypass↗
PubMed1985

Relative wall thickness analysis by two-dimensional echocardiography.

M-mode echocardiographic relative wall thickness (RWT) has been used extensively as an index of left ventricular hypertrophy. To determine whether the more extensive tomographic sampling and enhanced spatial orientation provided by two-dimensional echocardiography (2DE) might improve the value of RWT analysis, we compared 2DE and M-mode RWT in 69 subjects (19 normals, 13 with aortic stenosis, 22 with aortic regurgitation, and 15 with congestive cardiomyopathy). M-mode results correlated relatively weakly with 2DE RWT (r = 0.62 at end diastole; r = 0.81 at end systole). End-systolic M-mode values were larger than 2DE results, while end-diastolic M-mode values were generally smaller than 2DE results (both p less than 0.001). Thus, in congestive cardiomyopathy M-mode RWT was larger than 2DE end-diastolic results and therefore failed to distinguish between cardiomyopathy, aortic regurgitation, and normals. We conclude that M-mode and 2DE analysis of RWT yield disparate results. Moreover, 2DE may enhance the value of RWT in the assessment of left ventricular hypertrophy due to volume overload and cardiomyopathy.

Adolescent↗
PubMed1981

Two dimensional echographic imaging of the left ventricle: comparison of mechanical and phased array systems in vitro.

To determine the reliability of two dimensional echographic images of the left ventricle with different two dimensional echographic instruments, two dimensional echographic images of the left ventricle were compared in vitro using two phased array and two mechanical systems to image 22 short axis slices of the three postmortem human hearts (one with infarction, one with left ventricular aneurysm, one with mitral regurgitation). Total left ventricular area and left ventricular cavity area were determined with planimetry and myocardial area was derived by subtraction. Comparison of total, myocardial and cavity areas with calibrated photographs of each slice showed excellent correlations for each echographic system (r = 0.93 to 0.97 for total area; 0.90 to 0.94 for cavity area; 0.89 to 0.95 for myocardial area). For total left ventricular area, the ratio of echographic to photographic image size was close to unity (0.95 to 1.08) for one mechanical and two phased array systems, but significantly lower for mechanical system 2 (0.71, p less than 0.001). For myocardial area the echographic/photographic ratio was also close to unity (0.96 to 1.15) for two phase array systems and mechanical system 1 but significantly lower for mechanical system 2 (0.77, p less than 0.005). In contrast, all systems underestimated left ventricular cavity area with lower, more variable echographic/photographic ratios (0.48 to 0.78), with mechanical system 2 again giving significantly lower values (p less than 0.02) than the other systems. Underestimation of left ventricular cavity area appears to result from inaccurate endocardial display. We conclude that accurate left ventricular image quantitation is possible with either phased array or mechanical systems if each variable studied is calibrated against an independent reference standard and echographic results are corrected by the resultant regression equation.

Echocardiography↗
PubMedDate not supplied

Initial characterization of an antineoplastic, polysaccharide-rich extract of Mycobacterium bovis BCG, Tice substrain.

A purified hot-water extract from Mycobacterium bovis (BCG vaccine) has been found to have significant antitumor activity against a murine sarcoma in vivo, but not in vitro, suggesting that the active compound is behaving as an immunostimulant. The material, termed PS1, has an average molecular weight of 22.4 kDa, is freely soluble in water, but has low solubility in acetone or ethanol, and is remarkably heat-stable, as is the parent BCG vaccine in terms of high-dose antitumor activity. PS1 contains at least 50% carbohydrate, consisting mainly of glucose, galactose and mannose, and about 10% lipid that may correspond to phosphatidylinositol. It shares chemical and biological properties with an arabinomannan isolated from M. tuberculosis, but it contains only trace quantities of lipoarabinomannan (LAM). Crossed immunoelectrophoresis indicated that PS1 contains the mycobacterial antigen 89, but only a single, non-migrating precipitin arc appeared on immunoelectrophoresis against a standard anti-BCG serum. PS1 appears to be non-toxic in mice up to a dose of 5 mg/kg, while as little as 70 micrograms/kg is sufficient to inhibit tumor formation significantly.

Animals↗