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Alok Srivastava

Publications and source records attributed to Alok Srivastava.

At least 19 recordsLinked to original sources
PubMed2006

Severe suppression of Frzb/sFRP3 transcription in osteogenic sarcoma.

Deciphering the molecular basis of cancer is critical for developing novel diagnostic and therapeutic strategies. To better understand the early molecular events involving osteogenic sarcoma (OGS), we have initiated a program to identify potential tumor suppressor genes. Expression profiling of total RNA from ten normal bone cell lines and eleven OGS-derived cell lines by microarray showed 135-fold lower expression of FRZB/sFRP3 mRNA in OGS cells compared to bone cells; this down-regulation of Frzb/sFRP3 mRNA expression was found to be serum-independent. Subsequently, fourteen OGS biopsy specimens showed nine-fold down-regulation of Frzb/sFRP3 mRNA expression compared to expression in eight normal bone specimens as determined by microarray. FRZB /sFRP3 protein level was also found to be at a very low level in 4/4 OGS cell lines examined. Quantitation by RT-PCR indicated approximately 70% and approximately 90% loss of Frzb/sFRP3 mRNA expression in OGS biopsy specimens and OGS-derived cell lines respectively, compared to expression in bone (p<0.0001). Hybridization experiments of a cDNA microarray containing paired normal and tumor specimens from nineteen different organs did not show any significant difference in the level of Frzb/sFRP3 mRNA expression between the normal and the corresponding tumor tissues. Exogenous expression of FRZB/sFRP3 mRNA in two OGS-derived cell lines lacking endogenous expression of the mRNA produced abundant mRNA from the exogenous gene, eliminating degradation as a possibility for very low level of FRZB/sFRP3 mRNA in OGS specimens. Results from PCR-based experiments suggest that the FRZB/sFRP3 gene is not deleted in OGS cell lines, however, karyotyping shows gross abnormalities involving chromosome 2 (location of the FRZB gene) in five of twelve OGS-derived cell lines. Together, these data suggest a tumor-suppressive potential for FRZB/sFRP3 in OGS.

Adaptor Proteins, Signal Transducing↗
PubMed2006

High WT1 expression is associated with very poor survival of patients with osteogenic sarcoma metastasis.

PURPOSE: Although metastasis is the primary determinant of poor survival of patients with osteogenic sarcoma, some patients live much longer than others, indicating metastatic heterogeneity underlying survival outcome. The purpose of the investigation was to identify genes underlying survival outcome of patients with osteogenic sarcoma metastasis. EXPERIMENTAL DESIGN: We have used microarray to first compare mRNA expression between normal bone and osteogenic sarcoma specimens, identified genes overexpressed in osteogenic sarcoma, and compared expression of the selected gene between a poorly metastatic (SAOS) and two highly metastatic cell lines (LM8 and 143B). Finally, expression of the selected gene was assessed by immunostaining of osteogenic sarcoma samples with known survival outcome. RESULTS: Microarray analysis revealed 5.3-fold more expression of WT1 mRNA in osteogenic sarcoma compared with normal bone and >2-fold overexpression in 143B and LM8 cells compared with SAOS. Furthermore, WT1 mRNA was absent in normal bone (10 of 10) by reverse transcription-PCR but present in osteogenic sarcoma-derived cell lines (5 of 8). One hundred percent (42 of 42) of low-grade osteogenic sarcoma specimens expressed no WT1 as determined by immunostaining; however, 24% (12 of 49) of the high-grade specimens showed intense staining. Mean survival of patients with high-grade metastatic osteogenic sarcoma but low WT1 staining (27 of 37) was 96.5 +/- 129.3 months, whereas mean survival of patients with high-grade metastatic osteogenic sarcoma having intense staining (10 of 37) was 18.3 +/- 12.3 months (P > 0.0143). All splice variants of WT1 mRNA, including a hitherto unknown variant (lacking exons 4 and 5), were found to be expressed in osteogenic sarcoma. CONCLUSION: WT1 seems to be associated with very poor survival of patients with osteogenic sarcoma metastasis.

Base Sequence↗
PubMed2006

Numerical model for DNA loading in microdevices: stacking and autogating effects.

Many electrophoresis-based DNA sequencing and genotyping microdevices rely on field-driven effects to load and preconcentrate the sample. A quantitative model is developed for a broad class of electrophoresis-based microfabricated sample injectors. Quantitative predictions of DNA preconcentration are compared with experimental data and are shown to qualitatively reproduce the detailed time-evolving sample distribution in the injector. The model provides practical guidance on device and protocol design, in order to optimize this critical aspect of microfluidic devices.

DNA↗
PubMed2006

Molecular diversity of Glanzmann thrombasthenia in southern India: new insights into mRNA splicing and structure-function correlations of alphaIIbbeta3 integrin (ITGA2B, ITGB3).

The molecular basis of Glanzmann thrombasthenia (GT) was studied in 40 families from southern India. Of 23 identified mutations (13 in the alphaIIb (ITGA2B) gene and 10 in the beta3 (ITGB3) gene), 20 were novel and three were described previously. Three mutations in the beta3 gene-p.Leu143Trp (Leu117Trp), p.Tyr307Stop (Tyr281Stop), and p.Arg119Gln (Arg93Gln)-were detected in 12, three, and two families, respectively, with definite founder effects observed for the first two mutations. Alternative splicing was predicted in silico for the normal variant and a missense variant of the beta3 gene, and for 10/11 frameshift or nonsense mutations in alphaIIb or beta3. The prediction was confirmed experimentally for a c.2898_2902dupCCCCT mutation in exon 28 of the alphaIIb gene that induced exon skipping. Seven out of nine missense mutations substituted highly conserved amino acids buried in the proteins' cores, predicting structural abnormalities. Among these, a beta3 substitution, p.Cys39Gly (Cys13Gly) was found to cause intracellular degradation of the beta3 subunit, in contrast to previous findings that mutations at Cys435, the partner of Cys13 in a disulfide bond, cause constitutive activation of alphaIIbbeta3. The two patients with a beta3 Arg93Gln mutation had normal clot retraction, consistent with a recent finding that this substitution is associated with normal surface expression of alphaIIbbeta3. In conclusion, this study demonstrates that a variety of mutations account for GT in southern Indian patients, provides new insights into mRNA splicing, and highlights the role of specific amino acids in structure-function correlations of alphaIIbbeta3.

Alternative Splicing↗
PubMed2006

Expression of a novel alternatively spliced UCP-2 transcript in osteogenic sarcoma.

BACKGROUND: Development of chemoresistance is common in patients with osteogenic sarcoma (OGS); however, the underlying mechanism is largely unknown. Many anticancer drugs exert their therapeutic action by generating reactive oxygen radicals, which might be countered by the cancer cell through induction of uncoupling protein 2 (UCP-2). UCP-2 has been shown to be able to protect tumor cells from the cytotoxic actions of chemotherapeutic drugs. Because OGS is seldom completely cured by current chemotherapy regimens, we hypothesized that increased expression of UCP-2 underlies this phenomenon. The primary initial interest of our research was to evaluate the level of UCP-2 mRNA in OGS. METHODS: The level of UCP-2 mRNA was determined by reverse transcriptase polymerase chain reaction (RT-PCR) comparing expression in normal-bone-derived specimens and OGS-derived specimens. Semiquantification of mRNA expression was achieved by radioactive RT-PCR. Nucleotide sequencing was performed using automated instruments. RESULTS: Interestingly, we failed to observe induction of UCP-2 mRNA in OGS tumor specimens and OGS-derived primary cell lines compared to the expression level in normal bone. However, we found expression of a hitherto unknown UCP-2 transcript in eight of eight OGS-derived and one EWS-derived cell lines and in nine of ten OGS biopsy specimens but in only one of six normal bone-derived specimens. Thus, tumor samples express both types (normal and the novel one) of UCP-2 mRNAs, whereas normal bone expresses only the wild-type form. Further experiments identified the novel mRNA species as an alternatively spliced UCP-2 transcript (termed UCP-2as). UCP-2as has a 22-nucleotide insertion from the 3' end of intron 3 that introduces an early stop codon in exon 4, which theoretically can produce a protein 79 amino acids long. CONCLUSIONS: We have identified a hitherto unknown UCP-2 transcript. Expression of the novel transcript appears to be OGS-specific, implying a function advantageous to the tumor.

Bone Neoplasms↗
PubMed2006

Functional assessment of arthropathy--an international perspective.

Treatment of hemophilia aims to minimize structural damage to joints and maximize patients' functional independence and quality of life. From an orthopedic perspective, treatment efficacy can be judged by quantifying the extent of musculoskeletal damage. Joint scores--both clinical and radiologic--have traditionally been measured in patients with hemophilia. However, such scores may lack the sensitivity to detect early changes in the hemophilic joint, and this has prompted the development of more sensitive measures. In addition, scores based on the status of individual joints do not consider the impact of arthropathy on overall musculoskeletal function. It would prove valuable to understand the implications of small differences in clinical/radiologic scores in terms of overall musculoskeletal function and patients' quality of life. The development of functional scores such as the Functional Independence Score for Haemophilia (FISH) and the Haemophilia Activities List (HAL), along with the quality-of-life (QoL) measurement tools, have helped to provide a more comprehensive assessment of health in hemophilia. Such improved understanding should assist with the development of contextually relevant guidelines for the management of hemophilia.

Adolescent↗
PubMed2006

Infections in children undergoing allogeneic bone marrow transplantation in India.

We studied the clinical profile of infections among 221 pediatric patients who underwent 230 allogeneic transplants between 1986 and June 2004. All patients developed febrile neutropenia. There were 283 documented infections, which included bacterial (36.9%), viral (45.7%), fungal (11.1%) and other infections (6.3%) including tuberculosis. Bacterial and fungal infections were more common in the first 30 days following BMT, while viral infections were more common >30 days after BMT. Bacterial pathogens were predominantly gram-negative organisms (72.7%), when compared with gram-positive organisms (27.3%). Common gram-negative organisms included NFGNB, Pseudomonas, Escherichia coli and Klebsiella while coagulase negative Staphylococci was the main gram-positive organism. Bacteremia (61.2%) was the main source positive cultures and was mainly because of gram-negative organisms (81%), predominantly NFGNB and Pseudomonas. Exactly 103/221(43.7%) transplants had 128 documented viral infections commonly because of Cytomegalovirus, Herpes group of viruses and transfusion related hepatitis. Thirty of 221 (13.5%) of transplants had 30 documented fungal infections with the majority being because of aspergillus (90%). Tuberculosis was seen in 1.7% of transplants while catheter infections were seen in 21 patients (9.1%). Infection related mortality was seen in 12% predominantly because of CMV or fungal infections. A sub group analysis (pre-1998 vs. post-1998) revealed higher incidences of gram-negative infections, bacteremia and bacterial infection related mortality in the pre-1998 era when compared with the recent times. The profile and mortality of infections in this series from India is not significantly different from reports from the West.

Adolescent↗
PubMed2006

Mutations in coagulation factor XIII A gene in eight unrelated Indians. Five novel mutations identified by a novel PCR-CSGE approach.

Factor XIII deficiency is a rare autosomal (1:2,000,000) recessive disorder of blood coagulation usually attributed to mutations in the coagulation factor XIII (FXIII) A gene. We have studied the molecular basis of FXIII deficiency in eight unrelated South Indian patients. Their diagnosis was based on clinical history, normal plasma clotting times and increased solubility of fibrin clot in 5 mol/l urea. Genomic DNA was screened for FXIII A gene defects by a novel PCR and CSGE strategy. Mutations were identified in all these patients. Five of these were novel mutations occurring in four patients. These included a novel c.210T > G transversion in homozygosity in exon 3 predicting a Tyr69X in the beta-sandwich domain in one patient. Another patient was compound heterozygote for a novel c.791C > T transition predicting a Ser263Phe in the core domain and a novel c.2045-1G > A transition at the acceptor splice junction of intron 14. Two novel frame shifts were also identified in two patients in a homozygous condition. One of them resulted from a single base 'G' duplication (c.892_895dupG) at codons Ser290/Ala291fs affecting the core domain and the other was due to a single base 'A' duplication (c.1642_1644dupA) and at codonTyr547fs affecting barrel-1 domain. The remaining four patients had the previously reported Arg260His, Ser413Leu, and Val414Phe (n = 2) missense mutations in the core domain. The novel mutations identified were considered to be disease causative by studying the nature of mutation, the degree of conservation of the mutated aminoacid among transglutaminases of different species and by molecular modeling. Apart from describing a significant number of novel mutations, this report is the first study from Southern India to describe FXIII A gene mutations.

Adolescent↗
PubMed2005

Single-agent arsenic trioxide in the treatment of newly diagnosed acute promyelocytic leukemia: durable remissions with minimal toxicity.

Arsenic trioxide, as a single agent, has proven efficacy in inducing molecular remission in patients with acute promyelocytic leukemia (APL). There is limited long-term outcome data with single-agent As2O3 in the management of newly diagnosed cases of APL. Between January 1998 to December 2004, 72 newly diagnosed cases of APL were treated with a regimen of single-agent As2O3 at our center. Complete hematologic remission was achieved in 86.1%. At a median follow-up of 25 months (range: 8-92 months), the 3-year Kaplan-Meier estimate of EFS, DFS, and OS was 74.87% +/- 5.6%, 87.21% +/- 4.93%, and 86.11% +/- 4.08%, respectively. Patients presenting with a white blood cell (WBC) count lower than 5 x 10(9)/L and a platelet count higher than 20 x 10(9)/L at diagnosis (n = 22 [30.6%]) have an excellent prognosis with this regimen (EFS, OS, and DFS of 100%). The toxicity profile, in the majority, was mild and reversible. After remission induction, this regimen was administered on an outpatient basis. Single-agent As2O3, as used in this series, in the management of newly diagnosed cases of APL, is associated with responses comparable with conventional chemotherapy regimens. Additionally, this regimen has minimal toxicity and can be administered on an outpatient basis after remission induction.

Adolescent↗
PubMed2005

Numerical simulation of DNA sample preconcentration in microdevice electrophoresis.

A numerical model is presented for the accurate and efficient prediction of preconcentration and transport of DNA during sample introduction and injection in microcapillary electrophoresis. The model incorporates conservation laws for the different buffer ions, salt ions, and DNA sample, coupled through a Gaussian electric field to account for the field modifications that cause electromigration. The accuracy and efficiency required to capture the physics associated with such a complex transient problem are realized by the use of the finite element-flux corrected transport (FE-FCT) algorithm in two dimensions. The model has been employed for the prediction of DNA sample preconcentration and transport during electrophoresis in a double-T injector microdevice. To test its validity, the numerical results have been compared with the corresponding experimental data under similar conditions, and excellent agreement has been found. Finally, detailed results from a simulation of DNA sample preconcentration in electrophoretic microdevices are presented using as parameters the electric field strength and the other species concentrations. The effect of the Tris concentration on sample stacking is also investigated. These results demonstrate the great potential offered by the model for future optimization of such microchip devices with respect to significantly enhanced speed and resolution of sample separation.

Computer Simulation↗
PubMed2005

Comparative evaluation of two two-dimensional gel electrophoresis image analysis software applications using synovial fluids from patients with joint disease.

The proteomic composition of synovial fluid (SF) may hold clues to understanding the molecular basis of arthritis. However, the highly viscous nature and proteomic complexity of SF present a challenge when analyzing results obtained by two-dimensional gel electrophoresis (2D-GE). Several software applications are available for analyzing 2D-GE images. Despite inherent strengths and weaknesses, no comparison between these applications has been reported using SF or any human fluid specimens. We evaluated two common software packages--PDQuest and Progenesis Workstation--for spot detection, matching, and quantitation of 2D-GE images of SF from four patients with arthritic disease. Initially, whole 2D-gel images were analyzed for spot detection, which suggested that PDQuest is more consistent than Progenesis; however, PDQuest appeared to require more user intervention than Progenesis. Subsequently, two small areas (spots well resolved and spots not well resolved) were selected from each gel image, which were analyzed by the software for spot detection, matching, volume, and resolution. These analyses suggest that both tools can quantify well-resolved spots relatively consistently when compared with manual spot detection (the "gold standard"). The "3D viewer" option offered by both tools enables correct spot identification and matching. The strengths and weaknesses of these computer tools can provide guidance in the choice of a particular workstation for identifying biomarkers of arthritis.

Adult↗
PubMed2005

An overview of an indoor radon study carried out in dwellings in India and Bangladesh during the last decade using solid state nuclear track detectors.

This paper reports on radon concentrations in dwellings from fifty different locations of India. The incorporated data were obtained using the passive solid state nuclear track detector technique. The estimated geometric mean value for India is 67.1 Bq m(-3). Chuadanga in Bangladesh had the lowest observed indoor radon concentration of 27.3 Bq m(-3) and Una in the northern part of India had the highest concentration of 281.5 Bq m(-3). This paper discusses the national geometrical mean value in terms of the national geometric mean values of other countries and also in terms of the geological influence. The estimated indoor radon levels are compared with the indoor radon levels as recommended by the International Commission on Radiation Protection (ICRP). It was observed that there are several locations in India where dwellings have higher indoor radon levels than the ICRP recommended value and requires some sort of intervention from regulating authorities. The mean value for indoor radon level given in the report of UNSCEAR 2000 for India needs to be revised.

Air Pollution, Indoor↗
PubMed2005

von Willebrand disease in the developing world.

von Willebrand disease (VWD) is considered to be the most common inherited bleeding disorder. Data on its epidemiology and impact in developing countries are limited. The biologic heterogeneity and variable presentation of VWD make diagnosis difficult. Although there is no accurate estimate of the prevalence of VWD in developing countries, available data suggest that the proportion of diagnosed cases is lower than the expected number, often accounting for only 6% to 13% of patients with hereditary bleeding disorders. Although accurate subtyping is often not possible, the number with severe disease tends to be much higher, particularly in those parts of the world where consanguinity is common. Agents used to treat patients with VWD range from plasma to purified factor concentrates. Desmopressin (DDAVP) is commonly used. Preliminary data on molecular genetics suggests that there are significant population differences. There is inadequate awareness of this condition and lack of support for these patients from the health care system in many developing countries. Concerted efforts are needed at the scientific and social levels to improve this situation.

Africa↗
PubMed2005

Hemophilia treatment in developing countries: products and protocols.

The most important aspect of management of hemophilia is to provide adequate replacement of safe clotting factor concentrates to prevent or treat bleeding episodes. There has been considerable progress in many countries in the developing world with regard to this aspect of care. However, very little data are available in the literature on the types of products being used for factor replacement and the doses being administered for control or treatment of bleeding in different countries. These data are important to document because only then can data from different centers be compared. This article provides data from seven countries: Korea, Malaysia, Thailand, Venezuela, Argentina, Iran, and India. It shows that there is wide variability not only in the types of products used (plasma to recombinant factor concentrates) but also in the doses administered (minimal to very high) for similar indications. Prospective documentation of data on musculoskeletal outcome at these centers and correlation with dose of factor replacement could help identify different models of care. Comparing such data and collating the experience in different countries could be useful for optimizing care and establishing cost-effective models. The combined experience in the developing world in providing hemophilia services should be used to define standards of care that are practical and to set achievable goals.

Developing Countries↗
PubMed2005

Surgery for hemophilia in developing countries.

Surgical interventions in patients with hemophilia (PWH) in the developing world are difficult in the setting of limited availability of factor concentrates. Although the adequacy of international guidelines for factor concentrate prophylaxis for PWH undergoing surgery has been established, frequently it is not practical in the developing world. These recommendations were not established based on large clinical trials and fail to define the safe lower limit of factor concentrate prophylaxis for surgery. The need to define these lower limits is essential in the developing world so that the limited resources may be used optimally for the cohort of PWH. There are limited data from the developing world with regard to PWH undergoing surgical procedures. In this article, we outline experience from our institution, a tertiary referral center for hemophilia care in India. We trace the basis on which our current factor concentrate prophylaxis regimen (which is lower than that recommended internationally) was established. In our experience our low-dose protocols are effective, reduce factor consumption by one third, and are not associated with a significantly increased risk of delayed hemorrhage. We hope that this experience will form a framework on which guidelines can be established for developing countries.

Blood Coagulation Factors↗
PubMed2005

Epidemiology of von Willebrand disease in developing countries.

There is limited information on von Willebrand disease (vWD) in developing countries. A questionnaire survey in 1998 showed that overall, less than one third of the expected number of patients with vWD in the population had been detected. Among those registered, the proportion with the severe form of the disease was relatively higher, forming up to 50% of the total, particularly in those countries with high prevalence of consanguineous marriages. Diagnosis was based on von Willebrand factor antigen (vWF:Ag) assays, vWF ristocetin cofactor (vWF:Rco) activity, and ristocetin-induced platelet aggregation (RIPA) at the reporting centers, but vWF multimer analysis was not widely available. Responsiveness to desmopressin acetate (DDAVP), which could be very significant clinically, was not often assessed. An attempt was made to assess accuracy of reporting of the prevalence of vWD by conducting a second survey aimed at normalizing the reported numbers with that of severe hemophilia A in a defined population on the presumption that the latter is less likely to be missed. These data showed that in most countries, the ratio of patients with vWD to severe hemophilia varied between 0.1 to 0.6 with a mean of approximately 0.4, as opposed to an expected ratio of approximately 1 (based on population-based data from Italy), confirming the underdiagnosis of vWD even within the same health-care system. A system for collecting more extensive and detailed data on vWD from developing countries (where 80% of the world's population lives) is required. Efforts are needed to develop national registries and make at least basic services for diagnosis and treatment widely available.

Delivery of Health Care↗
PubMed2005

Hyperbilirubinemia in homozygous HbE disease is associated with the UGT1A1 gene polymorphism.

Homozygous HbE [beta26(B8)Glu-->Lys] is a clinically mild disorder with no significant symptoms. However, we have frequently noted hyperbilirubinemia among patients with homozygous HbE in the Indian population, with jaundice being the major complaint at presentation. A study of the UGT1A1 gene polymorphism shows that the variant TA7 in the promoter region of the UGT1A1 gene is associated with hyperbilirubinemia in homozygous HbE patients.

Female↗