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1.  Structural studies of haemoglobin from pisces species shortfin mako shark (Isurus oxyrinchus) at 1.9 Å resolution 
Journal of Synchrotron Radiation  2013;20(Pt 6):843-847.
Shortfin mako shark haemoglobin adopts an unliganded deoxy T state conformation, which is shown from the quaternary structural features, interface interactions and heme binding sites of different subunits of haemoglobin with high-resolution X-ray data.
Haemoglobin (Hb) is a tetrameric iron-containing protein that carries oxygen from the lungs to tissues and carbon dioxide from tissues back to the lungs. Pisces are the advanced aquatic vertebrates capable of surviving at wide depth ranges. The shortfin mako shark (SMS) is the pelagic, largest, fastest and most sophisticated species of the shark kingdom with well developed eyes. Mostly the pisces species are cold blooded in nature. Distinctly, the SMSs are warm-blooded animals with an advanced circulatory system. SMSs are capable of maintaining elevated muscle temperatures up to 33 K above the ambient water temperatures at a depth of 150–500 m. SMSs have a diverged air-breathing mechanism compared with other vertebrates. The haemoglobin molecule consists of four polypeptide chains, namely two α chains, each with 140 amino acids and two β chains each having 136 amino acids. The SMS Hb was found to crystallize in monoclinic space group P21 using the hanging-drop vapour-diffusion method at room temperature. The crystal packing parameters for the SMS Hb structure contain one whole biological molecule in the asymmetric unit with a solvent content of 47%. The SMS Hb quaternary structural features interface–interface interactions and heme binding sites are discussed with different state Hbs and the results reveal that SMS Hb adopts an unliganded deoxy T state conformation.
doi:10.1107/S0909049513021572
PMCID: PMC3795541  PMID: 24121325
haemoglobin; shark; monoclinic; oxygen transport; crystal structure; heme; tetramer
2.  Influence of limonin on Wnt signalling molecule in HepG2 cell lines 
Objective:
The role of limonin as potent anti carcinogenic, apoptosis and chemotherapeutic agents has been supported by limited studies.
Materials and Methods:
In this study, limonin is identified as a potent anti proliferative agent against human hepatoma HepG2 cells based on the cell viability study, LDH leakage assay. Induction of apoptosis in HepG2 cells by limonin was evidenced by western blot analysis of Bax, Cyclin D1, Caspase 3 and Caspase9.
Results:
Since Wnt signalling is involved in the initiation and sustaining of hepatocellular carcinoma we studied differential expression of LRP5, LRP6 and DKK wnt players.
Conclusion:
Limonin found to down regulate these players which forms a rationale for further investigation on effect on limonin in cancer therapy.
doi:10.4103/0976-9668.107276
PMCID: PMC3633262  PMID: 23633848
Apoptosis; caspases; hepatocellular carcinoma; limonin; Wnt; β-catenin
3.  Agreement between Heidelberg Retina Tomograph-I and -II in detecting glaucomatous changes using topographic change analysis 
Eye  2010;25(1):31-42.
Purpose
To evaluate the suitability of including both Heidelberg Retina Tomograph-I (HRT-I) and HRT-II examinations in the same longitudinal series for HRT topographic change analysis (TCA) and to evaluate parabolic error correction (PEC) to improve the agreement between HRT-I and HRT-II examinations.
Methods
A total of 66 eyes from the University of California San Diego Diagnostic Innovations in Glaucoma Study with baseline HRT-I and HRT-II examinations obtained on the same day and ≥3 HRT-II follow-up examinations were included. Two TCA analyses, HRT-I examination at baseline (HRT-I–mixed series) and HRT-II examination at baseline (HRT-II–only series) were compared. Agreement between the HRT-I–mixed and HRT-II–only series were estimated using Bland–Altman plots. Agreement was assessed: (1) using the current HRT software settings (PEC applied only to HRT-II–only series), and (2) modified HRT settings (PEC also applied to HRT-I–mixed series).
Results
With current HRT software settings, the HRT-I–mixed series significantly overestimated change locations (ie, red pixels) compared with the HRT-II–only series as indicated by statistically significant proportional biases in the Bland–Altman analysis. By applying PEC to HRT-I–mixed series there were no statistically significant biases in the TCA parameter estimates compared with the HRT-II–only series.
Conclusion
In some eyes, HRT-I and HRT-II baseline examinations are not interchangeable in TCA analysis without parabolic error correction. HRT-I–mixed series detected more changes characteristic of glaucoma when there were only minimal changes in the HRT-II–only series. Our results suggest that in the majority of cases, with PEC, HRT-I examinations may be included in a longitudinal series containing HRT-II examinations.
doi:10.1038/eye.2010.124
PMCID: PMC3144652  PMID: 20885428
glaucoma; progression; optic disk topography; topographic change analysis; agreement; parabolic error correction
4.  Purification, crystallization and preliminary crystallographic study of haemoglobin from camel (Camelus dromedarius): a high oxygen-affinity lowland species 
Haemoglobin from Camelus dromedarius provides an interesting case study of adaptation to life in deserts at extremely high temperatures. An ambition to unravel the integrated structural and functional aspects of the casual survival of this animal at high temperatures led the authors to specifically work on this problem. This work reports the preliminary crystallographic study of camel haemoglobin.
Haemoglobin is a prototypical allosteric protein that is mainly involved in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs in an intrinsically coordinated manner to maintain the viability of cells. Haemoglobin from Camelus dromedarius provides an interesting case study of adaptation to life in deserts at extremely high temperatures. An ambition to unravel the integrated structural and functional aspects of the casual survival of this animal at high temperatures led us to specifically work on this problem. The present work reports the preliminary crystallographic study of camel haemo­globin. Camel blood was collected and the haemoglobin was purified by anion-exchange chromatography and crystallized using the hanging-drop vapour-diffusion method under buffered high salt concentration using PEG 3350 as a precipitant. Intensity data were collected using a MAR 345 dtb image-plate detector system. Camel haemo­globin crystallized in the monoclinic space group P21, with one whole biological molecule (α2β2) in the asymmetric unit and unit-cell parameters a = 52.759, b = 116.782, c = 52.807 Å, β = 120.07°.
doi:10.1107/S1744309109024154
PMCID: PMC2720330  PMID: 19652336
haemoglobin; Camelus dromedarius; oxygen affinity
5.  Purification, crystallization and preliminary crystallographic study of low oxygen-affinity haemoglobin from cat (Felis silvestris catus) in two different crystal forms 
Preliminary studies were carried out to purify and crystallize the sample from cat (Felis silvestris catus), a low oxygen-affinity haemoglobin in different crystal forms.
Haemoglobin is a metalloprotein which plays a major role in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs. The present work reports the preliminary crystallographic study of low oxygen-affinity haemoglobin from cat in different crystal forms. Cat blood was collected, purified by anion-exchange chromatography and crystallized in two different conditions by the hanging-drop vapour-diffusion method under unbuffered low-salt and buffered high-salt concentrations using PEG 3350 as a precipitant. Intensity data were collected using MAR345 and MAR345dtb image-plate detector systems. Cat haemoglobin crystallizes in monoclinic and orthorhombic crystal forms with one and two whole biological molecules (α2β2), respectively, in the asymmetric unit.
doi:10.1107/S1744309109004503
PMCID: PMC2650469  PMID: 19255493
haemoglobin; low oxygen affinity
6.  Purification, crystallization and preliminary X-ray diffraction studies on avian haemoglobin from pigeon (Columba livia) 
Crystallization of pigeon haemoglobin at low pH (5.5) and high ionic concentration (1 M) using the hanging-drop vapour-diffusion method is reported.
Haemoglobin is a physiologically significant metalloprotein that is involved in the exchange of gases for sustaining life. The respiratory system of birds is unique and complex compared with that of mammals. Many investigations of avian haemoglobins have revealed the presence of inositol pentaphosphate (IP5), a principal allosteric effector that is involved in regulation of their function. Structural investigations of avian haemoglobins are presently not adequate to explain their function. Efforts have been made in this direction in order to understand the oxygen-binding affinity involved in adapting to hypoxia in avian haemoglobins. Fresh whole blood was collected from pigeon (Columba livia) and purified using a DEAE cellulose anion-exchange chromatographic column. Crystallization of pigeon haemoglobin was accomplished using the hanging-drop vapour-diffusion method using PEG 3350 as a precipitant in 50 mM sodium acetate buffer pH 5.5 with 1 M NaCl. Data collection was carried out using a MAR345 image-plate detector system. The crystals diffracted to 2 Å resolution. Pigeon haemoglobin crystallizes in a triclinic space group, with two whole biological molecules in the asymmetric unit and with unit-cell parameters a = 55.005, b = 65.528, c = 104.370 Å, α = 78.742, β = 89.819, γ = 65.320°.
doi:10.1107/S1744309108038505
PMCID: PMC2635874  PMID: 19194000
allosteric effectors; oxygen affinity; triclinic; avian haemoglobins
7.  Inhibitory effects of Indigofera aspalathoides on 20-methylcholanthrene-induced chemical carcinogenesis in rats 
Background:
The anticancer and antioxidant effects of the aqueous extract of Indigofera aspalathoides on 20-methylcholanthrene (20-MCA) induced fibrosarcoma were investigated in male albino rats.
Materials and Methods:
The rats were divided into four different groups, each group consisting of six animals. Group I animals were served as normal control, Group II animals were fibrosarcoma-bearing animals after the incubation period, Group III animals were fibrosarcoma-bearing animals, treated with aqueous extract of I. aspalathoides intraperitoneally at a dose of 250 mg/kg b.w. for 30 days and Group IV animals were administered with the aqueous extract of I. aspalathoides alone, at a dose of 250 mg/kg b.w. for 30 days, served as drug control animals. After the experimental period, all the rats were weighed and killed by cervical decapitation. The serum was separated from the blood for analysis. The weights of the liver and the kidneys were noted. The fibrosarcoma was proved by pathological examinations. The liver and kidney tissues were excised and then homogenized in an ice-cold buffer. These tissues were used for biochemical analysis.
Results:
The activities of antioxidant enzymes, e.g. catalase (CAT), glutathione peroxidase (GPx) and superoxide dismutase (SOD), in blood serum, liver, and kidney of control and experimental animals, respectively, have been reported.
Conclusion:
The present observations suggested that the aqueous extract of I. aspalathoides treatment enhanced the recovery from 20-MCA-induced fibrosarcoma due to its antioxidants and antineoplastic properties.
doi:10.4103/1477-3163.75458
PMCID: PMC3030762  PMID: 21297921
Antioxidant enzymes; chemoprevention; fibrosarcoma; Indigofera aspalathoides; 20-MCA
8.  Crystallization of sheep (Ovis aries) and goat (Capra hircus) haemoglobins under unbuffered low-salt conditions 
The haemoglobins from low oxygen affinity species, sheep and goat are crystallized under unbuffered low-salt conditions to explore the possibility of obtaining new crystal forms.
Haemoglobin is a tetrameric protein that plays a vital role in the transport of oxygen from the lungs to the tissues and of carbon dioxide back to the lungs. Even though a large amount of work has already been performed in this area, the study of the haemoglobin structures of avian and mammalian species is rather incomplete. Efforts are being made to understand the salient features of the species mentioned above. Here, whole blood plasma was collected from sheep and goat and purified by anion-exchange chromatography; the haemoglobins were crystallized by the hanging-drop vapour-diffusion method under unbuffered low-salt conditions using PEG 3350 as a precipitant. Data collection was carried out using a MAR345 image-plate detector system. Sheep haemoglobin crystallizes in the orthorhombic space group P212121 with one whole biological molecule (α2β2) in the asymmetric unit, with unit-cell parameters a = 60.231, b = 70.695, c = 131.479 Å. In contrast, goat haemoglobin crystallizes in the triclinic system with two biological molecules (α2β2) in the unit cell. The unit-cell parameters are a = 53.103, b = 69.382, c = 96.098 Å, α = 110.867, β = 91.133, γ = 109.437°.
doi:10.1107/S1744309107044296
PMCID: PMC2339733  PMID: 17909297
haemoglobin
9.  Multi-area visuotopic map complexes in macaque striate and extra-striate cortex 
Vision research  2006;46(20):3336-3359.
We propose that a simple, closed-form mathematical expression—the Wedge–Dipole mapping—provides a concise approximation to the full-field, two-dimensional topographic structure of macaque V1, V2, and V3. A single map function, which we term a map complex, acts as a simultaneous descriptor of all three areas. Quantitative estimation of the Wedge–Dipole parameters is provided via 2DG data of central-field V1 topography and a publicly available data set of full-field macaque V1 and V2 topography. Good quantitative agreement is obtained between the data and the model presented here. The increasing importance of fMRI-based brain imaging motivates the development of more sophisticated two-dimensional models of cortical visuotopy, in contrast to the one-dimensional approximations that have been in common use. One reason is that topography has traditionally supplied an important aspect of “ground truth,” or validation, for brain imaging, suggesting that further development of high-resolution fMRI will be facilitated by this data analysis. In addition, several important insights into the nature of cortical topography follow from this work. The presence of anisotropy in cortical magnification factor is shown to follow mathematically from the shared boundary conditions at the V1–V2 and V2–V3 borders, and therefore may not causally follow from the existence of columnar systems in these areas, as is widely assumed. An application of the Wedge–Dipole model to localizing aspects of visual processing to specific cortical areas—extending previous work in correlating V1 cortical magnification factor to retinal anatomy or visual psychophysics data—is briefly discussed.
doi:10.1016/j.visres.2006.03.006
PMCID: PMC2248457  PMID: 16831455
Visual cortex; Retinotopic; Quasiconformal mapping; Topographic modeling; Topographic map complex
10.  A PRELIMINARY STANDARD FOR ‘SURADARULEPA CHURNA’- AN AYURVEDIC PREPARATION 
Ancient Science of Life  1989;8(3-4):293-297.
SURADARU LEPA CHURNA’-A Compound drug formulation in Ayurvedic system of medicine was analysed. The proximate chemical analysis, the microscopic method of identifying their ingredients, flourescese study and thin layer chromatographic studies of the drug have been reported in this paper.
PMCID: PMC3336721  PMID: 22557664
11.  NAGAKESARA – A COMPARATIVE PHARMACOGNOSY 
Ancient Science of Life  1986;5(4):263-268.
Dried floral buds of Mesua ferrea Linn, dried fruits of Dillenia pentagyna Roxb and dried fruiting inflorescence of Cinnamomum wightii Meissn are used as Nagakesara in different regions of India. This elaborate study presents to the pharmacognosy of these three different drugs of Nagakesara.
PMCID: PMC3331473  PMID: 22557537
12.  A PRELIMINARY STANDARD FOR NILAAVARAI CURNAM - A SIDDHA PREPARATION 
Ancient Science of Life  1983;3(2):67-71.
Nilavarai Curnam, a compound drug formulation in Siddha System of Medicine was analysed. The Microscopic methods of identifying their ingredients, Chemical analysis, Fluorescence, and Thin Layer Chromatographic studies of the drug have been reported here.
PMCID: PMC3331551  PMID: 22557382
13.  THE PHARMACOGNOSY OF NATTU ATIVIDAYAM – THE CORMS OF CRYPTOCORYNE SPIRALIS FISCH 
Ancient Science of Life  1982;1(4):200-205.
The pharmacognosy of Nattu Attivdayam the corms of Cryptocoryne spiralis Fisch – its macroscopical, microscopical and chemical studies – is reported
PMCID: PMC3336695  PMID: 22556490

Results 1-14 (14)