Biomedical subjects

A Mazumder

Publications and source records attributed to A Mazumder.

At least 19 recordsLinked to original sources

PubMed2006

The use and performance of BioSand filters in the Artibonite Valley of Haiti: a field study of 107 households.

INTRODUCTION: Approximately one billion people world-wide lack access to adequate amounts of safe water. Most are in developing countries, especially in rapidly expanding urban fringes, poor rural areas, and indigenous communities. METHODS: In February and March 2005, a field study of 107 households was conducted to evaluate the use and performance of the Manz BioSand filter in the Artibonite Valley of Haiti. Approximately 2000 filters had been installed in this area over the preceding 5 years by the staff in Community Development at Hospital Albert Schweitzer, Deschappelle, Haiti. Interviews, observations, and water samplings were carried-out by two teams of Haitian enumerators, each consisting of a nurse and a filter technician. Water analyses were performed by Haitian lab technicians using the membrane filtration method to determine Escherichia coli counts. The enumerators and the lab technicians completed a 2 week training program before beginning the study; they worked under the direct supervision of the primary investigator. Laboratory quality was monitored by running 10% blank and 10% duplicate samples. RESULTS: The households contained an average of 5.4 persons. Filters had been in use for an average of 2.5 years, and participants were generally satisfied with their filter's performance. Shallow, hand-dug wells provided the only source of water for 61% of the households, with 26% using water piped from springs or deep wells, and 13% having access to both. Only 3% had plumbing in their homes. Source water from shallow wells contained an average of 234 E. coli cfu/100 mL. Piped sources averaged 195 E. coli cfu/100 mL. Of the source water samples 26% contained 0-10 E. coli cfu/100 mL. Of the filtered water samples 97% contained 0-10 E. coli cfu/100 mL (80% with 0 cfu/100 mL, and 17% with 1-10 cfu/100 mL). Overall bacterial removal efficiency for the filters was calculated to be 98.5%. Turbidity decreased from an average of 6.2 NTU in source water samples to 0.9 NTU in the filtered water. None of the households treated the water after filtering; 91% used the filtered water only for drinking. No problems related to filter construction were observed; 13% were found to have significantly decreased flow rates (all restored by cleaning the filter). Recontamination was found to occur, with only 3% of the samples from the filters' spouts containing >10 E. coli cfu/100 mL and 22% of the stored filtered water samples at point-of-use containing >10 cfu/100 mL. CONCLUSION: The Manz BioSand filters are an attractive option for supplying water treatment to family units in rural areas of poorly developed countries.

Developing Countries↗

PubMed2006

Purification and characterization of a novel caffeine oxidase from Alcaligenes species.

Alcaligenes species CF8 isolated from surface water of a lake produced a novel serine type metallo-caffeine oxidase. The optimal medium for caffeine oxidase production by this strain was (w/v) NaNO(3), 0.4%; KH(2)PO(4), 0.15%; Na(2)HPO(4), 0.05%; FeCl(3).6H(2)O, 0.0005%; CaCl(2).2H(2)O, 0.001%; MgSO(4).7H(2)O, 0.02%; glucose, 0.2%; caffeine, 0.05%, pH 7.5. The enzyme was purified to 63-fold by using ammonium sulfate precipitation, dialysis, ion exchange (diethylaminoethyl-cellulose) and gel filtration (Sephadex G-100) chromatographic techniques. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the purified caffeine oxidase was monomeric with a molecular mass of 65 kDa. The purified caffeine oxidase with a half-life of 20 min at 50 degrees C had maximal activity at pH 7.5 and 35 degrees C. The purified caffeine oxidase had strict substrate specificity towards caffeine (K(m) 8.94 microM and V(max) 47.62 U mg protein(-1)) and was not able to oxidize xanthine and hypoxanthine. The enzyme activity was not inhibited by para-chloromercuribenzoic acid, iodoacetamide, n-methylmaleimide, salicylic acid and sodium arsenite indicating the enzyme did not belong to xanthine oxidase family. The enzyme was not affected by Ca(+2), Mg(+2) and Na(+), but was completely inhibited by Co(+2), Cu(+2) and Mn(+2) at 1mM level. The novel caffeine oxidase isolated here from Alcaligenes species CF8 may be useful in biotechnological processes including waste treatment and biosensor development.

Alcaligenes↗

PubMed2004

Origins and implications of drinking water odours in lakes and reservoirs of British Columbia, Canada.

The relationship between commonly measured limnological parameters and odours was examined in 16 reservoirs and lakes used as sources for drinking water and three reference lakes. Odour analysis was conducted using flavour profile analysis (FPA) and, on select lakes, gas chromatography ion-trap mass spectrometry (GC-ITMS) for target compounds. Total phosphorus (TP) was the best single predictor of FPA intensity and multiple regression models accounted for 37-39% of intensity variance in the epilimnion and metalimnion, respectively. Earthy odours were more prevalent in reservoirs and lakes with higher TP, whereas decomposing vegetation and green vegetation+grassy odours almost exclusively occurred when TP was lower (<13 microg P/L). Only geosmin was identified with GC-ITMS, and it was found to occur in lakes and reservoirs of higher trophic status (e.g. more algal biomass). Infrequent episodic events in the Greater Victoria's principal reservoir (e.g. algal blooms) have previously been linked with taste and odour problems in their tap water. However, analysis of odours under the conditions of this study (i.e. no strong odour episodes in the source reservoir) suggest that typical odours prevalent in tap water originating from Sooke Lake Reservoir are derived from treatment processes or the distribution system, not directly from the reservoir. This study demonstrates the utility of employing relatively simple and established methods to better understand management issues of a drinking water system.

British Columbia↗

PubMed2004

Foraminifers as indicators of marine pollution: a culture experiment with Rosalina leei.

In order to develop a viable foraminiferal proxy for heavy metal pollutants, juvenile specimens of Rosalina leei were subjected to different mercury concentrations (0-180 ng/l). Initially considerable growth was observed in specimens kept in saline water having a mercury concentration up to 100 ng/l. But with the gradual increase in concentration of mercury the growth rate started decreasing. Total growth achieved was significantly lower in case of specimens kept at relatively higher mercury concentrations then those maintained in normal saline water. The most significant result of this experiment was the addition of abnormal chambers in the specimens kept at higher mercury concentration. Later the specimens kept at highest concentration (180 ng/l) were subjected to progressively increasing concentration of mercury to see the further effects and it was found that the specimens were still living at as high a mercury concentration as 260 ng/l although there was no growth.

Cell Culture Techniques↗

PubMed2001

Biological purging of breast cancer cells using an attenuated replication-competent herpes simplex virus in human hematopoietic stem cell transplantation.

Autologous hematopoietic stem cell transplantation after myelosuppressive chemotherapy is used for the treatment of high-risk breast cancer and other solid tumors. However, contamination of the autologous graft with tumor cells may adversely affect outcomes. Human hematopoietic bone marrow cells are resistant to herpes simplex virus type 1 (HSV-1) replication, whereas human breast cancer cells are sensitive to HSV-1 cytotoxicity. Therefore, we examined the utility of G207, a safe replication-competent multimutated HSV-1 vector, as a biological purging agent for breast cancer in the setting of stem cell transplantation. G207 infection of human bone marrow cells had no effect on the proportion or clonogenic capacity of CD34+ cells but did enhance the proliferation of bone marrow cells in culture and the proportion of CD14+ and CD38+ cells. On the other hand, G207 at a multiplicity of infection of 0.1 was able to purge bone marrow of contaminating human breast cancer cells. Because G207 also stimulates the proliferation of human hematopoietic cells, it overcomes a limitation of other purging methods that result in delayed reconstitution of hematopoiesis. The efficient infection of human bone marrow cells in the absence of detected toxicity suggests that HSV vectors may also prove useful for gene therapy to hematopoietic progenitor cells.

Bone Marrow Cells↗

PubMed2001

The immunomodulatory effects of gentamicin, imipenem, piperacillin and amphotericin B on LAK effector function in vitro.

An understanding of the immunomodulating effects of anti-microbial regimens on recombinant interleukin-2 (rIL-2) induced peripheral leukocyte function, i.e. lymphokine-activated killer (LAK)-cell efficacy, would be clinically useful in the selection of commonly employed bone marrow transplantation (BMT) antibiotics to avoid post-transplant complications and optimize anti-microbial, anti-viral, anti-tumor therapies. In this report we evaluated the modulatory effects of a number of antibiotics used in BMT on LAK-cell cytotoxicities, in vitro. Our data showed that, even at serum trough titer, amphotericin B was significantly (P < or =0.05) immunostimulatory, whereas gentamicin, imipenem, and piperacillin, individually, were significantly (P < or =0.05) immunosuppressive. Statistical analysis detected no modulation due to aztreonam, amikacin, cotrimoxazole, or ceftazidime, or any of the six cephalosporins tested at molar equivalent concentration. We conclude that certain antibiotics may be more suitable for infection prone BMT hosts.

Adjuvants, Immunologic↗

PubMed2001

Effects of nutrient loading and planktivory on the accumulation of organochlorine pesticides in aquatic food chains.

The effects of nutrients and planktivory on the accumulation of hydrophobic organic contaminants (HOCs) in aquatic food chains were investigated in large lake enclosures. Food-chain compositions in the enclosures were manipulated by additions of planktivorous fish (+F), nutrients (+N), both nutrients and fish (+NF), or received no additions (-NF). The treatments resulted in higher plankton but lower zooplankton biomass in the +NF enclosures than in the other enclosures. Once enclosure communities were established, a suite of organochlorine pesticides (alpha-hexachlorocyclohexane, methoxychlor, heptachlor, cis- and trans-chlordane, cis- and trans-nonachlor, and mirex) was added to all enclosures in amounts sufficient to obtain initial concentrations in the epilimnion of approximately 15 ng/L. Dissipation of HOCs from the water and accumulation in phytoplankton, zooplankton, and fish were monitored for four months. The HOC concentrations in plankton did not differ significantly across treatments. However, on a total-mass basis, greater amounts of HOCs were sorbed to phytoplankton in the +NF enclosures (20%) than in the three other sets of enclosures. Concentrations in zooplankton of some HOCs differed significantly between treatments as a function of nutrient loading. Chlordane and nonachlor concentrations were greater in zooplankton from enclosures with no fish (+N, -NF) than in those from enclosures with fish (+F, +NF). The HOC residues in fish were highest in low-nutrient enclosures. The results demonstrate that fish predation and nutrient loading can modify the size-related processes of HOC partitioning and affect its accumulation in the aquatic food chain.

Animals↗

PubMed2000

Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping.

BACKGROUND: Genetic diversity can help explain disease susceptibility and differential drug response. The most common type of variant is the single nucleotide polymorphism (SNP). We present a low-cost, high throughput assay for SNP genotyping. METHODS: The assay uses oligonucleotide probes covalently attached to fluorescently encoded microspheres. These probes are hybridized directly to fluorescently labeled polymerase chain reaction (PCR) products and the results are analyzed in a standard flow cytometer. RESULTS: The genotypes determined with our assay are in good agreement with those determined by TaqMan. The range of G/C content for oligonucleotide probes was 23.5-65% in the 17 bases surrounding the SNP. Further optimization of probe length and target concentration is shown to dramatically enhance the assay performance for certain SNPs. Using microspheres which have unique fluorescent signatures, we performed a 32-plex assay where we simultaneously determined the genotypes of eight different polymorphic genes. CONCLUSIONS: We demonstrate, for the first time, the feasibility of multiplexed genotyping with suspension arrays using direct hybridization analyses. Our approach enables probes to be removed from or added to an array, enhancing flexibility over conventional chips. The ability to multiplex both the PCR preparation and the hybridization should enhance the throughput, cost, and speed of the assay.

Artifacts↗

PubMed2000

Hydroxychloroquine for the treatment of chronic graft-versus-host disease.

Chronic graft-versus-host disease (GVHD) is a major complication of allogeneic bone marrow transplantation. Both the disease and the medications used to treat it are associated with significant morbidity and mortality. The manifestations of chronic GVHD often resemble those of autoimmune disorders. Hydroxychloroquine (HCQ) is a 4-aminoquinoline antimalarial drug used for the treatment of autoimmune diseases. HCQ interferes with antigen processing and presentation, cytokine production, and cytotoxicity and is synergistic with cyclosporine and tacrolimus in vitro. Forty patients with steroid-resistant or steroid-dependent chronic GVHD were enrolled in a phase 2 trial of HCQ 800 mg (12 mg/kg) per day. Three complete responses and 14 partial responses were seen in 32 evaluable patients (53% response rate). All responders tolerated a >50% reduction in their steroid dose while receiving HCQ. Clinical response occurred at a median of 8 weeks (range, 4 to 24 weeks). No hematologic, hepatic, renal, or retinal toxicity was associated with HCQ. In light of its mechanisms of action, clinical activity for GVHD, and low toxicity profile, HCQ may be useful in a multiagent approach for the treatment of extensive chronic GVHD.

Adolescent↗

PubMed1999

Improvement of gene transduction efficiency in T lymphocytes using retroviral vectors.

Successful gene transfer into T lymphocytes would provide a useful therapeutic modality for the treatment of various diseases and a valuable way to study T cell functions. Currently, most protocols involving gene transfer into T lymphocytes utilize amphotropic retroviral vectors. However, transduction efficiency using these vectors is relatively low because of the high proportion of resting cells, the concentration-dependent growth manner of T lymphocytes, and the low titer of retroviral vectors. In this article we define conditions that provide high levels of transduction by using IL-2 prestimulation and LipofectAMINE for both mouse and human T lymphocytes. We compared the effects of IL-2 prestimulation on transduction efficiencies at different time points and achieved maximum transfer levels at 72 hr after the incubation. By combining the best prestimulation time and cationic lipids-LipofectAMINE at a dose of 0.8 microM, the transduction efficiencies were increased to 45-75% (62.3 +/- 4.3%) in human T lymphocytes and to 21-33% (27 +/- 1.42%) in murine T lymphocytes as determine by FDG staining and X-Gal visualization, compared with 5% with conventional methods. These results indicate that transduction efficiencies in T lymphocytes can be significantly improved by a prolonged preincubation with IL-2 and by the addition of LipofectAMINE.

Animals↗

PubMed1999

Paclitaxel vs cyclophosphamide in peripheral blood stem cell mobilization: comparative studies in a murine model.

Paclitaxel is a promising drug for the treatment of breast and ovarian cancer. It also may play a role in mobilization of peripheral blood stem cells (PBSC), as an alternative to cyclophosphamide (Cy). We investigated the PBSC-mobilizing potential of paclitaxel compared to Cy in a murine model. C57B1/6 mice were primed with intraperitoneal injections of Cy (200 mg/kg) or paclitaxel (60 mg/kg) and were sacrificed 4, 6, 8, or 10 days later. Spleens were harvested and processed to obtain low-density mononuclear cells that were used as PBSC. The number of hematopoietic progenitors (CFU-C) on day 4 was significantly higher in the paclitaxel group when compared to mice receiving Cy (72.0 +/- 1.8 vs 9.8 +/- 2.8, p < 0.001). By day 6, CFU-C became significantly higher in the Cy-treated group compared to the paclitaxel-treated group (195.6 +/- 31.9 vs 95.8 +/- 20.7, p < 0.05) and this trend was maintained. However, the total number of CFU-C recovered per spleen was greater in the paclitaxel-treated group (1.27 x 10(5) +/- 0.53 x 10(5) vs 1.06 x 10(5) +/- 0.36 x 10(5), NS). In contrast to paclitaxel, mobilization with Cy was associated with marked perturbation in the proportion of lymphoid cell subsets in the PBSC population along with functional impairment of lymphocytes. After 24 hours of in vitro IL-2 activation, the cytotoxic effector cell function of the Cy-mobilized PBSC population was lower than that of paclitaxel-mobilized cells when tested against three tumor cell lines (B16, melanoma; C1498, AML; and Yak-1, lymphoma). These results indicate that paclitaxel is an efficient mobilizer of PBSC, leading to early (day 4 to 6) mobilization of PBSC when compared to Cy (day 6 to 8). In addition, paclitaxel was associated with less perturbation of phenotypic and functional characteristics of cells contained within the mobilized PBSC population.

Animals↗

PubMed1999

Immunotherapy with interleukin-2 and alpha-interferon after IL-2-activated hematopoietic stem cell transplantation for breast cancer.

We previously demonstrated findings suggestive of autologous GVHD in patients receiving IL-2-activated peripheral blood stem cells (PBSC) with IL-2 after transplantation. A pilot study was designed to test tolerability, feasibility and frequency of autologous GVHD and engraftment using IL-2 and alpha-IFN post-transplantation. After cyclophosphamide (6 g/m2) and carboplatin (1800 mg/m2), patients with high-risk stage II or III breast cancer received chemotherapy and rhG-CSF mobilized autologous PBSC that had been cultured in IL-2 for 24 h. Subcutaneous administration of IL-2 began on day 0 at 6 x 10(5) IU/m2/day for 5 of 7 days each week and continued for 4 weeks. Once engraftment occurred, alpha-IFN was initiated at a dose of 1 x 10(6)/m2/day subcutaneously for 30 days. Thirty-four consecutive patients with stage II (n=20), IIIA (n=6) and IIIB (n=8) disease were treated. All patients were without evidence of disease at the time of transplantation. The average time required for the ANC to reach 500/mm3 was 10 days (range: 8-11 days) and for platelets to reach 20000/mm3 was 10.7 days (range: 6-21 days). Forty-seven percent of patients (n=16) completed the full course of immunotherapy; the remaining patients received attenuated doses due to patient's request (n=6), development of temperature >38 degrees C (n=3), development of neutropenia (n=3), serious infection (n=1) and miscellaneous reasons (n=5). Four patients experienced transient moderate toxicities (level 3) including elevated liver function tests, nausea, rash and capillary leak syndrome. Pathological findings suggestive of skin GVHD developed in 43% of patients (12/28 patients) when skin biopsies were evaluated in a blinded fashion. At 13 months post-transplant (median; range: 5-24 months), 28 patients (82%) remain disease-free. These results demonstrate the feasibility and toxicity of this regimen along with pathological findings compatible with autologous GVHD of the skin.

Adult↗

PubMed1999

Differential effects of IL-2 incubation on hematopoietic potential of autologous bone marrow and mobilized PBSC from patients with hematologic malignancies.

Culturing of hematopoietic progenitor cells for 24 h with IL-2 generates cytotoxic effector cells that mediate in vitro and possibly in vivo antitumor activity. We examined the effect of IL-2 incubation on progenitor cells from 24 patients with hematologic malignancies using paired autologous bone marrow (ABM) and PBSC to determine differences in hematopoietic potential. Cells were cryopreserved and stored in liquid nitrogen until conditioning therapy was completed. After thawing, cells were incubated with IL-2 for 24 h at 37 degrees C. Paired samples of ABM and PBSC from the same patient were analyzed for nucleated and mononuclear cell number, CD34 antigen expression, and colony-forming unit (CFU) activity before and after IL-2 incubation. There was a significant decrease in the average number of mononuclear cells (MNC) (x10(8)/kg) (<0.001) and CD34+ cells (x10(6)/kg) (0.006) from both ABM and PBSC after 24 h IL-2 culture (ABM MNC: 0.6+/-0.1 vs. 0.4+/-0.0, p = <0.001; PBSC MNC: 4.4+/-0.5 vs. 3.7+/-0.4, p = 0.03; ABM CD34+: 2.4+/-0.5 vs. 1.3+/-0.3, p = <0.001; PBSC CD34+: 6.6+/-1.8 vs. 5.0+/-1.2, p = 0.05). However, whereas ABM CFU/10(5) MNC plated (269.3+/-47.2 vs. 385.6+/-70.6) were significantly increased (p = 0.005), there was no change in PBSC CFU (271.0+/-47.2 vs. 257.3+/-48.5). The mean plating efficiency (%) of ABM CD34+ cells was markedly increased after IL-2 incubation (10.1+/-3.3 vs. 19.0+/-7.2, p = 0.04), although it was lower than that of PBSC CD34+ cells, which did not change significantly in culture (29.4+/-5.5 vs. 36.0+/-6.5). Additional work is in progress to determine the cause and significance of the enhanced plating efficiency of the ABM progenitor cells.

Adult↗

PubMed1999

A pilot trial of GM-CSF and MDX-H210 in patients with erbB-2-positive advanced malignancies.

MDX-H210 is a chemically, cross-linked, half-humanized bispecific antibody composed of F(ab') fragment from monoclonal antibody (mAb) H22 that binds to the high-affinity receptor Fc gamma RI and F(ab') of mAb 520C9 that recognizes the erbB-2 (HER2/neu) oncoprotein. In a previous trial, the murine bispecific, MDX-210 at a dose of 7 mg/m2, was well tolerated and activated monocytes and macrophages in vivo in doses as low as 0.35 mg/m2. In our multidose trial, granulocyte-macrophage colony-stimulating factor, which increases and activates potential effector cells, was given on days 1-4 at 250 micrograms/m2 s.c. and MDX-H210 was given on day 4 weekly for 4 consecutive weeks. Thirteen patients were treated at dose levels of 1, 3.5, 7, 10, 15, and 20 mg/m2 without dose-limiting toxicity. Fever, chills, and rigors occurred during and up to 2 h postinfusion and correlated with the time to peak levels of tumor necrosis factor-alpha (median 88.2 pg/ml; range 15.6-887 pg/ml) and interleukin-6 (median 371 pg/ml; range 175-2,149 pg/ml). By the fourth consecutive week of treatment the side effects and cytokine levels decreased significantly. Human antibispecific antibody (HABA) levels were increased by 200- to 500-fold above pretreatment levels in 5 of 11 evaluable patients after 3 weeks of treatment. The monocyte and granulocyte population increased on days 4 and 11 (median 44%; range 18-68% and 42%; 19-71%), respectively, for monocytes and (60%; 43-75% and 74%; 54-82%) on days 4 and 11 for granulocytes. There was a significant decrease in the monocyte populations immediately after MDX-H210 administration (median decrease 73%; range 42-94%) and (52%; 12-72%) on days 4 and 11, respectively. Ten patients completed 4 weeks of treatment. One patient had a 48% reduction in an index lesions and six patients had stable disease at the time of evaluation. Three patients progressed before the fourth week. The therapy was generally well tolerated with toxicity, primarily, limited to the days of treatment.

Adenocarcinoma↗

PubMed1999

Analysis and characterization of hematopoietic progenitor cells from fetal bone marrow, adult bone marrow, peripheral blood, and cord blood.

Hematopoietic stem cell transplantation has been increasingly used to replace a defective hematopoietic system and to treat various genetic defects as well as malignant diseases. However, the limitations of conventional bone marrow transplantation have stimulated an intense interest in exploring the use of alternative sources of hematopoietic stem cells, including peripheral blood mononuclear cells (PBMC) and cord blood (CB). A major investigative effort of our laboratory has been focused on evaluating fetal bone marrow (FBM) for transplantation. The current study compares and characterizes the functional and phenotypic characteristics of FBM, CB, adult bone marrow (ABM), and PBMC by clonogenicity assays, immunogenicity, and the quantification of progenitor cells. There was a striking difference in the proportion of CD34+ cells in FBM, ABM, PBMC, and CB (24.6%, 2.1%, 0.5%, and 2.0%, respectively). The clonogenic potential, as measured by colony forming unit in culture (CFU-C) assay, was significantly higher in FBM when compared with ABM, PBMC, and CB (202.5, 73.5, 40.8, and 65.5 colonies/10(5) cells, respectively). There was a significant decrease in proliferative responsiveness in mixed lymphocyte reaction (MLR) assay of FBM and CB compared with ABM and PBMC. These observations indicate that each source of hematopoietic stem cells has different intrinsic properties closely correlated with ontogenetic age that is a vital determinant for phenotypic characteristics, lineage commitments, immunogenicity, and proliferative potentials.

Adult↗

PubMed1998

A high throughput method to investigate oligodeoxyribonucleotide hybridization kinetics and thermodynamics.

We describe a high throughput microtiter-based assay to measure binding of oligodeoxyribonucleotides to nucleic acid targets. The assay utilizes oligodeoxyribonucleotide probes labeled with a highly chemiluminescent acridinium ester (AE). Reaction of AE with sodium sulfite renders it non-chemiluminescent. When an AE-labeled probe hybridizes to a target nucleic acid AE is protected from reaction with sodium sulfite and thus remains chemiluminescent. In contrast, unhybridized probe readily reacts with sodium sulfite and is rendered non-chemiluminescent. Hybridization of an AE-labeled probe to a target nucleic acid can therefore be detected without physical separation of unhybridized probe by treatment of the hybridization reaction with sodium sulfite and measurement of the remaining chemiluminescence. Using this method we measured hybridization rate constants and thermodynamic affinities of oligodeoxyribonucleotide probes binding to simple synthetic targets as well as large complex biological targets. The kinetic and thermodynamic parameters were measured with a high degree of accuracy and were in excellent agreement with values measured by other established techniques.

Base Sequence↗

PubMed1998

Technology for microarray analysis of gene expression.

The past year has demonstrated the versatility of microarrays for the analysis of whole model-organism genomes and has seen the development of chips to measure the expression of 40,000 human genes. Microarray technology has also become considerably more robust and sensitive. Technology enhancements include the use of noncontact printing methods, improved 2-color sample preparation, and statistically based software for data analysis.

Biotechnology↗

PubMed1998

Highly potent synthetic polyamides, bisdistamycins, and lexitropsins as inhibitors of human immunodeficiency virus type 1 integrase.

Alignment of the available human immunodeficiency virus type 1 (HIV-1) viral DNA termini [U5 and U3 long terminal repeats (LTRs)] shows a high degree of conservation and the presence of a stretch of five or six consecutive adenine and thymine (AT) sequences approximately 10 nucleotides away from each LTR end. A series of AT-selective minor-groove binders, including distamycin and bisdistamycins, bisnetropsins, novel lexitropsins, and the classic monomeric DNA binders Hoechst 33258, 4'-diamino-2-phenylindole, pentamidine, berenil, spermine, and spermidine, were tested for their inhibitory activities against HIV-1 integrase (IN). Although netropsin, distamycin, and all other monomeric DNA binders showed weak activities in the range of 50-200 microM, some of the polyamides, bisdistamycins, and lexitropsins were remarkably active at nanomolar concentrations. Bisdistamycins were 200 times less potent when the conserved AAAAT stretch present in the U5 LTR was replaced with GGGGG, consistent with the preferred binding of these drugs to AT sequences. DNase I footprinting of the U5 LTR further demonstrated the selectivity of these bisdistamycins for the conserved AT sequence. The tested compounds were more potent in Mg+2 than in Mn+2 and inhibited IN50-212 deletion mutant in disintegration assays and the formation of IN/DNA complexes. The lexitropsins also were active against HIV-2 IN. Some of the synthetic polyamides exhibited significant antiviral activity. Taken together, these data suggest that selective targeting of the U5 and U3 ends of the HIV-1 LTRs can inhibit IN function. Polyamides might represent new leads for the development of antiviral agents against acquired immune deficiency syndrome.

Anti-HIV Agents↗