J. Ojwang - Academia.edu (original) (raw)
Papers by J. Ojwang
Emerging infectious diseases, Jun 1, 2017
In September 2014, a single fatal case of Marburg virus was identified in a healthcare worker in ... more In September 2014, a single fatal case of Marburg virus was identified in a healthcare worker in Kampala, Uganda. The source of infection was not identified, and no secondary cases were identified. We describe the rapid identification, laboratory diagnosis, and case investigation of the third Marburg virus outbreak in Uganda.
Cancer research, 2000
Both Bcl-xL and Bcl-2, antiapoptotic members of the Bcl family, are found in prostate cancer cell... more Both Bcl-xL and Bcl-2, antiapoptotic members of the Bcl family, are found in prostate cancer cell lines. Although these proteins may have similar antiapoptotic functions, it is not clear to what extent each serves as an antiapoptotic effector in prostate cancer cells. We engineered LNCaP and PC-3 cells to overexpress Bcl-xL protein and demonstrated that this desensitized them to the effects of cytotoxic chemotherapy. We then used two "antisense" strategies to down-regulate Bcl-xL protein expression in the parental lines. The first strategy used CS-propynylated phosphorothioate-phosphodiester oligonucleotides and co-down-regulated both Bcl-xL and Bcl-2; the second strategy used isosequential "gap-mer" phosphorothioate oligonucleotides containing 2'-O-methyl oligoribonucleotides at the 3' and 5' termini. In this case, only Bcl-xL protein expression was affected. The most active oligonucleotides of both types decreased the level of Bcl-xL protein express...
Antiviral chemistry & chemotherapy, 1998
The synthesis and in vitro antiviral activity of certain hydroxyalkoxymethyl, hydroxyalkyl, hydro... more The synthesis and in vitro antiviral activity of certain hydroxyalkoxymethyl, hydroxyalkyl, hydroxyalkenyl and phosphonoalkenyl derivatives of the guanine congener 5-aminothiazolo[4,5-d]pyrimidine-2,7(3H,6H)-dione are reported. The compounds of this study were selected for their structural similarity to acyclonucleosides with known anti-herpesvirus activity. 5-Amino-3-[(Z)-4-hydroxy-2-buten-1-yl]thiazolo[4,5-d]pyrimidine-2, 7(3H,6H)- dione was the only member of the series to display significant in vitro activity against human cytomegalovirus (HCMV); however, this compound did not inhibit other herpesviruses, human immunodeficiency virus type 1 or murine cytomegalovirus. It was found to have a cytotoxicity profile similar to that of ganciclovir (DHPG). The antiviral effect was found to be sensitive to the initial viral input and the time of addition during the virus replication cycle. Significantly, the compound was found to have equal anti-HCMV activity, against standard virus stra...
Antimicrobial agents and chemotherapy, 1998
The objective of the proposed study was to determine the distribution in plasma lipoprotein of fr... more The objective of the proposed study was to determine the distribution in plasma lipoprotein of free all-trans retinoic acid (ATRA) and liposomal ATRA (Atragen; composed of dimyristoyl phosphatidylcholine and soybean oil) following incubation in human, rat, and dog plasma. When ATRA and Atragen at concentrations of 1, 5, 10, and 25 micrograms/ml were incubated in human and rat plasma for 5, 60, and 180 min, the majority of the tretinoin was recovered in the lipoprotein-deficient plasma fraction. However, when ATRA and Afragen were incubated in dog plasma, the majority of the tretinoin (> 40%) was recovered in the high-density lipoprotein (HDL) fraction. No differences in the plasma distribution between ATRA and Atragen were found. These data suggest that a significant percentage of tretinoin associates with plasma lipoproteins (primarily the HDL fraction) upon incubation in human, dog, and rat plasma. Differences between the lipoprotein lipid and protein profiles in human plasma a...
Journal of acquired immune deficiency syndromes, 1994
Oligonucleotide compounds composed of only deoxyguanosine and deoxythymidine were able to signifi... more Oligonucleotide compounds composed of only deoxyguanosine and deoxythymidine were able to significantly inhibit human immunodeficiency virus type -1 (HIV-1)-induced syncytium formation and virus production (as measured by p24 core antigen expression) in an acute infection assay system. The oligonucleotides did not share any homology with or possess any complementary (antisense) sequence motifs to the HIV-1 genome. The guanosine/thymidine-containing oligonucleotides (GTOs) that showed this anti-HIV activity contained natural phosphodiester (PD) linkages (backbones) between the nucleosides. One of the PD oligonucleotide sequence motifs tested was capable of inhibiting HIV-1-induced syncytium formation and p24 production with a median effective dose in culture (ED50) in the submicromolar range. In addition, oligonucleotides tested were able to significantly suppress HIV-1 p24 levels > or = 7 days after removal of the drug from the infected cell culture medium. The growth inhibition ...
We perform first-principles linear response computations within LDA+U and GGA+U to systematically... more We perform first-principles linear response computations within LDA+U and GGA+U to systematically investigate the pressure dependence of magnetic exchange interactions for archetypal transition metal oxides (TMOs): MnO, FeO, CoO, and NiO. We obtain the Neel temperatures (TN) using Monte Carlo simulations. We find that the magnitude of the next nearest neighbor coupling constant, J2, which dominates TN, increases with increasing
Argon is a common pressure-transmitting medium in diamond anvil cell (DAC) experiments, and is of... more Argon is a common pressure-transmitting medium in diamond anvil cell (DAC) experiments, and is often used as thermal insulation in the laser heated DAC. A more thorough understanding of the thermal properties of argon under extreme conditions is essential for measuring ...
We are using a variety of methods, including density functional theory, dynamical mean field theo... more We are using a variety of methods, including density functional theory, dynamical mean field theory, and quantum Monte Carlo, to better understand the behavior of FeO in particular, and ferrous iron and other transition metal oxides in general, under compression. We have computed the spin-wave dispersion and effective Heisenberg couplings for FeO under compression, and find that the J2 (second
Proceedings of the National Academy of Sciences, 2009
This article contains supporting information online at www.pnas.org/cgi/content/full/ 0901181106/... more This article contains supporting information online at www.pnas.org/cgi/content/full/ 0901181106/DCSupplemental.
Proceedings of the National Academy of Sciences, 1993
Ribozymes have enormous potential as antiviral agents. We have previously reported that a hairpin... more Ribozymes have enormous potential as antiviral agents. We have previously reported that a hairpin ribozyme expressed under the control of the 3-actin promoter that cleaves human Immunodeficiency virus type 1 (HIV-1)
Antisense and Nucleic Acid Drug Development, 1997
Tumor necrosis factor-alpha (TNF-alpha) is a highly pleiotropic cytokine produced mainly by activ... more Tumor necrosis factor-alpha (TNF-alpha) is a highly pleiotropic cytokine produced mainly by activated macrophages. This cytokine has been found to mediate the growth of certain tumors, the replication of HIV-1, septic shock, cachexia, graft-versus-host disease, and autoimmune diseases. The binding of TNF-alpha to the p55 tumor necrosis factor receptor type I (TNFRI) is considered one of the initial steps responsible for the multiple physiologic effects mediated by TNF-alpha. The role of TNF-alpha as an inflammatory mediator through TNFRI makes both of these genes attractive targets for intervention in both acute and chronic inflammatory diseases. We have designed antisense oligodeoxynucleotides (ODNs) containing chemically modified purine and pyrimidine bases that specifically inhibit TNFRI expression and functions. These ODNs were designed to hybridize to the 3'-polyadenylation signal region of the TNFRI gene. In cell-based assays, gene-specific antisense inhibition occurred in a dose-dependent fashion at submicromolar concentrations in the presence of cellular uptake enhancing agents. Within ODN sets with a common pattern of stabilizing backbone substitution, the inhibition of the gene expression is found to be correlated with the affinity of the ODNs for their cognate mRNA target sites, providing direct evidence for an antisense mechanism of action. In addition, events triggered by the binding of TNF-alpha to TNFRI, such as the production of IL-6 and IL-8, were significantly reduced by treatment of cells with the anti-TNFRI ODN. Therefore, antisense ODNs can be used to control biologic processes mediated by TNF-alpha and may be useful as therapeutic agents to treat conditions resulting from overproduction of TNF-alpha.
Molecular Pharmacology, 1997
Oligonucleotides that can form a highly stable intramolecular four-stranded DNA structure contain... more Oligonucleotides that can form a highly stable intramolecular four-stranded DNA structure containing two stacked guanosine-quartets (G-quartets) have been reported to inhibit the replication of the human immunodeficiency virus type 1 (HIV-1) in cell culture. Two possible mechanisms for the observed antiviral activity have been proposed: interference with virus adsorption to the cell and/or inhibition of HIV-1 integrase. We investigated the molecular interaction of G-quartet-containing oligonucleotides with HIV-1 integrase in comparison with random oligonucleotides and dextran sulfate. The prototypical G-quartet-containing oligonucleotide, T30177 (Zintevir), inhibited the overall integration reaction with an IC50 value of 80 nM. A random oligonucleotide was 10-fold less potent, but dextran sulfate was more potent, with an IC50 value of 7 nM. We developed novel kinetic assays to dissect the overall integration reaction in three steps: the formation of the initial stable complex (ISC), the 3'-processing reaction, and the DNA strand-transfer step. We then analyzed the kinetics of the ISC formation and 3'-processing. The rate constant determined for the conversion of ISC into the cleaved product was 0.08 +/- 0.01 min-1. T30177 did not inhibit 3'-processing or DNA strand transfer, whereas dextran sulfate inhibited DNA strand transfer to some extent. Binding studies using surface plasmon resonance technology revealed that both T30177 and dextran sulfate were capable of preventing the binding of integrase to specific DNA. We propose a model in which the interaction of HIV-1 integrase with G-quartets results in the inhibition of the formation of the ISC between integrase and substrate DNA. Finally, we selected for an HIV-1 strain that was resistant to T30177 in cell culture. DNA sequence analysis revealed mutations in the envelope glycoprotein gp120 but not in the integrase gene. Although gp120 seems to be the main target for the antiviral activity in cell culture of G-quartets, the study of their specific inhibition of HIV-1 integrase may lead to the development of effective integrase inhibitors.
Journal of Biological Chemistry, 1995
An oligonucleotide (I100-15) composed of only deoxyguanosine and thymidine was able to inhibit hu... more An oligonucleotide (I100-15) composed of only deoxyguanosine and thymidine was able to inhibit human immunodeficiency virus type-1 (HIV-1) in culture assay systems. I100-15 did not block virus entry into cells but did reduce viral-specific transcripts. As assessed by NMR and polyacrylamide gel methods, I100-15 appears to form a structure in which two stacked guanosine tetrads are connected by three two-base long loops. Structure/activity experiments indicated that formation of intramolecular guanosine tetrads was necessary to achieve maximum antiviral activity. The single deoxyguanosine nucleotide present in each loop was found to be extremely important for the overall antiviral activity. The toxicity of I100-15 was determined to be well above the 50% effective dose (ED50) in culture which yielded a high therapeutic index (> 100). The addition of a cholesterol moiety to the 3' terminus of I100-15 (I100-23) reduced the ED50 value to less than 50 nM (from 0.12 microM for I100-15) and increased the duration of viral suppression to greater than 21 days (versus 7-10 days for I100-15) after removal of the drug from infected cell cultures. The favorable therapeutic index of such molecules coupled with the prolonged suppression of HIV-1, suggest that such compounds further warrant investigation as potential therapeutic agents.
Journal of Applied Physics, 2013
ABSTRACT We present calculations of the thermal conductivity of fcc Argon at high pressures (pres... more ABSTRACT We present calculations of the thermal conductivity of fcc Argon at high pressures (pressure range is 10–150 GPa, temperatures range is 400–1200 K) from first principles in the framework of density functional theory and solution of the Boltzmann Transport Equation. Local density approximation (LDA) and generalized gradient approximation (GGA) produce similar thermal conductivities, with differences accounted by the known overbinding and underbinding of the LDA and GGA, correspondingly. Thermal conductivities at all considered pressures and temperatures are found to be consistent with the results of previous molecular dynamics simulations based on classical 2-body potentials. However, they are not consistent with recent experimental findings. Possible reasons for this disagreement are discussed. In addition, in light of our calculations, we critically examine analytically tractable approximations for thermal conductivity as applied to solid argon.
Human Molecular Genetics, 2009
Genes and Immunity, 2011
§ On behalf of the BIOLUPUS Network. The members of the network are listed in the acknowledgement... more § On behalf of the BIOLUPUS Network. The members of the network are listed in the acknowledgements. § § On behalf of the GENLES collaboration. The members of this collaboration are listed in the acknowledgements.
Genes and Immunity, 2009
In our previous study, we utilized a Bayesian design to probe the association of ~1,000 genes (~1... more In our previous study, we utilized a Bayesian design to probe the association of ~1,000 genes (~10,000 SNPs) with SLE on a moderate number of trios of parents and children with SLE. Two genes associated with SLE with a multitest corrected False Discovery Rate (FDR) of <0.05. were identified, and a number of noteworthy genes with FDR of <0.8 were also found, pointing out a future direction for the study. In the present report, using a large population of controls and adultor -childhood onset SLE cases, we have extended the previous investigation to explore the SLE association of ten of these noteworthy genes (109 SNPs). We have found that seven of these genes exhibit significant (FDR < 0.05) association with SLE, both confirming some genes that have previously been found to be associated with SLE (PTPN22 and IRF5) and novel findings of genes (KLRG1, IL-16, PTPRT, TLR8 and CASP10) which have not been previously reported. The results signify that the two-step candidate pathway design is an efficient way to study the genetic foundations of complex diseases. Furthermore, the novel genes identified in this study point to new directions in both the diagnosis and the eventual treatment of this debilitating disease.
Antimicrobial Agents and Chemotherapy, 1995
T30177, an oligonucleotide composed of only deoxyguanosine and thymidine, is 17 nucleotides in le... more T30177, an oligonucleotide composed of only deoxyguanosine and thymidine, is 17 nucleotides in length and contains single phosphorothioate internucleoside linkages at its 5 and 3 ends for stability. This oligonucleotide does not share significant primary sequence homology with or possess any complementary (antisense) sequence motifs to the human immunodeficiency virus type 1 (HIV-1) genome. T30177 inhibited replication of multiple laboratory strains of HIV-1 in human T-cell lines, peripheral blood lymphocytes, and macrophages. T30177 was also found to be capable of inhibiting multiple clinical isolates of HIV-1 and preventing the cytopathic effect of HIV-1 in primary CD4 ؉ T lymphocytes. In assays with human peripheral blood lymphocytes there was no observable toxicity associated with T30177 at the highest concentration tested (100 M), while the median inhibitory concentration was determined to be in the range of 0.1 to 1.0 M for the clinical isolates tested, resulting in a high therapeutic index for this drug. In temporal studies, the kinetics of addition of T30177 to infected cell cultures indicated that, like the known viral adsorption blocking agents dextran sulfate and Chicago sky blue, T30177 needed to be added to cells during or very soon after viral infection. However, analysis of nucleic acids extracted at 12 h postinfection from cells treated with T30177 at the time of virus infection established the presence of unintegrated viral cDNA, including circular proviral DNA, in the treated cells. In vitro analysis of viral enzymes revealed that T30177 was a potent inhibitor of HIV-1 integrase, reducing enzymatic activity by 50% at concentrations in the range of 0.050 to 0.09 M. T30177 was also able to inhibit viral reverse transcriptase activity; however, the 50% inhibitory value obtained was in the range of 1 to 10 M, depending on the template used in the enzymatic assay. No observable inhibition of viral protease was detected at the highest concentration of T30177 used (10 M). In experiments in which T30177 was removed from infected cell cultures at 4 days post-HIV-1 infection, total suppression of virus production was observed for more than 27 days.
Raman scattering measurements and x-ray diffraction of ammonia have been made under simultaneous ... more Raman scattering measurements and x-ray diffraction of ammonia have been made under simultaneous conditions of high temperature and high static pressure in the laser heated diamond anvil cell. The experimental results on phase transitions with pressure increase at room temperature are found to be in accord with previous studies [1]. Pressure was increased up to 52 GPa and temperature ramped up to 2000 K. On increasing temperature at high pressure, strong changes in the ammonia Raman spectra are observed, which could be associated with melting. On melting, ammonia undergoes partial decomposition into nitrogen and hydrogen. We also observed the appearance of new N-H stretch bands at high temperatures which may be related to the formation of new bonds. When quenched back to room temperature the starting phase of solid ammonia is recovered. The shift in frequencies of the vibron bands of nitrogen with pressure shows that it is phase segregated from ammonia.
Emerging infectious diseases, 2017
In September 2014, a single fatal case of Marburg virus was identified in a healthcare worker in ... more In September 2014, a single fatal case of Marburg virus was identified in a healthcare worker in Kampala, Uganda. The source of infection was not identified, and no secondary cases were identified. We describe the rapid identification, laboratory diagnosis, and case investigation of the third Marburg virus outbreak in Uganda.
Emerging infectious diseases, Jun 1, 2017
In September 2014, a single fatal case of Marburg virus was identified in a healthcare worker in ... more In September 2014, a single fatal case of Marburg virus was identified in a healthcare worker in Kampala, Uganda. The source of infection was not identified, and no secondary cases were identified. We describe the rapid identification, laboratory diagnosis, and case investigation of the third Marburg virus outbreak in Uganda.
Cancer research, 2000
Both Bcl-xL and Bcl-2, antiapoptotic members of the Bcl family, are found in prostate cancer cell... more Both Bcl-xL and Bcl-2, antiapoptotic members of the Bcl family, are found in prostate cancer cell lines. Although these proteins may have similar antiapoptotic functions, it is not clear to what extent each serves as an antiapoptotic effector in prostate cancer cells. We engineered LNCaP and PC-3 cells to overexpress Bcl-xL protein and demonstrated that this desensitized them to the effects of cytotoxic chemotherapy. We then used two "antisense" strategies to down-regulate Bcl-xL protein expression in the parental lines. The first strategy used CS-propynylated phosphorothioate-phosphodiester oligonucleotides and co-down-regulated both Bcl-xL and Bcl-2; the second strategy used isosequential "gap-mer" phosphorothioate oligonucleotides containing 2'-O-methyl oligoribonucleotides at the 3' and 5' termini. In this case, only Bcl-xL protein expression was affected. The most active oligonucleotides of both types decreased the level of Bcl-xL protein express...
Antiviral chemistry & chemotherapy, 1998
The synthesis and in vitro antiviral activity of certain hydroxyalkoxymethyl, hydroxyalkyl, hydro... more The synthesis and in vitro antiviral activity of certain hydroxyalkoxymethyl, hydroxyalkyl, hydroxyalkenyl and phosphonoalkenyl derivatives of the guanine congener 5-aminothiazolo[4,5-d]pyrimidine-2,7(3H,6H)-dione are reported. The compounds of this study were selected for their structural similarity to acyclonucleosides with known anti-herpesvirus activity. 5-Amino-3-[(Z)-4-hydroxy-2-buten-1-yl]thiazolo[4,5-d]pyrimidine-2, 7(3H,6H)- dione was the only member of the series to display significant in vitro activity against human cytomegalovirus (HCMV); however, this compound did not inhibit other herpesviruses, human immunodeficiency virus type 1 or murine cytomegalovirus. It was found to have a cytotoxicity profile similar to that of ganciclovir (DHPG). The antiviral effect was found to be sensitive to the initial viral input and the time of addition during the virus replication cycle. Significantly, the compound was found to have equal anti-HCMV activity, against standard virus stra...
Antimicrobial agents and chemotherapy, 1998
The objective of the proposed study was to determine the distribution in plasma lipoprotein of fr... more The objective of the proposed study was to determine the distribution in plasma lipoprotein of free all-trans retinoic acid (ATRA) and liposomal ATRA (Atragen; composed of dimyristoyl phosphatidylcholine and soybean oil) following incubation in human, rat, and dog plasma. When ATRA and Atragen at concentrations of 1, 5, 10, and 25 micrograms/ml were incubated in human and rat plasma for 5, 60, and 180 min, the majority of the tretinoin was recovered in the lipoprotein-deficient plasma fraction. However, when ATRA and Afragen were incubated in dog plasma, the majority of the tretinoin (> 40%) was recovered in the high-density lipoprotein (HDL) fraction. No differences in the plasma distribution between ATRA and Atragen were found. These data suggest that a significant percentage of tretinoin associates with plasma lipoproteins (primarily the HDL fraction) upon incubation in human, dog, and rat plasma. Differences between the lipoprotein lipid and protein profiles in human plasma a...
Journal of acquired immune deficiency syndromes, 1994
Oligonucleotide compounds composed of only deoxyguanosine and deoxythymidine were able to signifi... more Oligonucleotide compounds composed of only deoxyguanosine and deoxythymidine were able to significantly inhibit human immunodeficiency virus type -1 (HIV-1)-induced syncytium formation and virus production (as measured by p24 core antigen expression) in an acute infection assay system. The oligonucleotides did not share any homology with or possess any complementary (antisense) sequence motifs to the HIV-1 genome. The guanosine/thymidine-containing oligonucleotides (GTOs) that showed this anti-HIV activity contained natural phosphodiester (PD) linkages (backbones) between the nucleosides. One of the PD oligonucleotide sequence motifs tested was capable of inhibiting HIV-1-induced syncytium formation and p24 production with a median effective dose in culture (ED50) in the submicromolar range. In addition, oligonucleotides tested were able to significantly suppress HIV-1 p24 levels > or = 7 days after removal of the drug from the infected cell culture medium. The growth inhibition ...
We perform first-principles linear response computations within LDA+U and GGA+U to systematically... more We perform first-principles linear response computations within LDA+U and GGA+U to systematically investigate the pressure dependence of magnetic exchange interactions for archetypal transition metal oxides (TMOs): MnO, FeO, CoO, and NiO. We obtain the Neel temperatures (TN) using Monte Carlo simulations. We find that the magnitude of the next nearest neighbor coupling constant, J2, which dominates TN, increases with increasing
Argon is a common pressure-transmitting medium in diamond anvil cell (DAC) experiments, and is of... more Argon is a common pressure-transmitting medium in diamond anvil cell (DAC) experiments, and is often used as thermal insulation in the laser heated DAC. A more thorough understanding of the thermal properties of argon under extreme conditions is essential for measuring ...
We are using a variety of methods, including density functional theory, dynamical mean field theo... more We are using a variety of methods, including density functional theory, dynamical mean field theory, and quantum Monte Carlo, to better understand the behavior of FeO in particular, and ferrous iron and other transition metal oxides in general, under compression. We have computed the spin-wave dispersion and effective Heisenberg couplings for FeO under compression, and find that the J2 (second
Proceedings of the National Academy of Sciences, 2009
This article contains supporting information online at www.pnas.org/cgi/content/full/ 0901181106/... more This article contains supporting information online at www.pnas.org/cgi/content/full/ 0901181106/DCSupplemental.
Proceedings of the National Academy of Sciences, 1993
Ribozymes have enormous potential as antiviral agents. We have previously reported that a hairpin... more Ribozymes have enormous potential as antiviral agents. We have previously reported that a hairpin ribozyme expressed under the control of the 3-actin promoter that cleaves human Immunodeficiency virus type 1 (HIV-1)
Antisense and Nucleic Acid Drug Development, 1997
Tumor necrosis factor-alpha (TNF-alpha) is a highly pleiotropic cytokine produced mainly by activ... more Tumor necrosis factor-alpha (TNF-alpha) is a highly pleiotropic cytokine produced mainly by activated macrophages. This cytokine has been found to mediate the growth of certain tumors, the replication of HIV-1, septic shock, cachexia, graft-versus-host disease, and autoimmune diseases. The binding of TNF-alpha to the p55 tumor necrosis factor receptor type I (TNFRI) is considered one of the initial steps responsible for the multiple physiologic effects mediated by TNF-alpha. The role of TNF-alpha as an inflammatory mediator through TNFRI makes both of these genes attractive targets for intervention in both acute and chronic inflammatory diseases. We have designed antisense oligodeoxynucleotides (ODNs) containing chemically modified purine and pyrimidine bases that specifically inhibit TNFRI expression and functions. These ODNs were designed to hybridize to the 3'-polyadenylation signal region of the TNFRI gene. In cell-based assays, gene-specific antisense inhibition occurred in a dose-dependent fashion at submicromolar concentrations in the presence of cellular uptake enhancing agents. Within ODN sets with a common pattern of stabilizing backbone substitution, the inhibition of the gene expression is found to be correlated with the affinity of the ODNs for their cognate mRNA target sites, providing direct evidence for an antisense mechanism of action. In addition, events triggered by the binding of TNF-alpha to TNFRI, such as the production of IL-6 and IL-8, were significantly reduced by treatment of cells with the anti-TNFRI ODN. Therefore, antisense ODNs can be used to control biologic processes mediated by TNF-alpha and may be useful as therapeutic agents to treat conditions resulting from overproduction of TNF-alpha.
Molecular Pharmacology, 1997
Oligonucleotides that can form a highly stable intramolecular four-stranded DNA structure contain... more Oligonucleotides that can form a highly stable intramolecular four-stranded DNA structure containing two stacked guanosine-quartets (G-quartets) have been reported to inhibit the replication of the human immunodeficiency virus type 1 (HIV-1) in cell culture. Two possible mechanisms for the observed antiviral activity have been proposed: interference with virus adsorption to the cell and/or inhibition of HIV-1 integrase. We investigated the molecular interaction of G-quartet-containing oligonucleotides with HIV-1 integrase in comparison with random oligonucleotides and dextran sulfate. The prototypical G-quartet-containing oligonucleotide, T30177 (Zintevir), inhibited the overall integration reaction with an IC50 value of 80 nM. A random oligonucleotide was 10-fold less potent, but dextran sulfate was more potent, with an IC50 value of 7 nM. We developed novel kinetic assays to dissect the overall integration reaction in three steps: the formation of the initial stable complex (ISC), the 3&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-processing reaction, and the DNA strand-transfer step. We then analyzed the kinetics of the ISC formation and 3&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-processing. The rate constant determined for the conversion of ISC into the cleaved product was 0.08 +/- 0.01 min-1. T30177 did not inhibit 3&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-processing or DNA strand transfer, whereas dextran sulfate inhibited DNA strand transfer to some extent. Binding studies using surface plasmon resonance technology revealed that both T30177 and dextran sulfate were capable of preventing the binding of integrase to specific DNA. We propose a model in which the interaction of HIV-1 integrase with G-quartets results in the inhibition of the formation of the ISC between integrase and substrate DNA. Finally, we selected for an HIV-1 strain that was resistant to T30177 in cell culture. DNA sequence analysis revealed mutations in the envelope glycoprotein gp120 but not in the integrase gene. Although gp120 seems to be the main target for the antiviral activity in cell culture of G-quartets, the study of their specific inhibition of HIV-1 integrase may lead to the development of effective integrase inhibitors.
Journal of Biological Chemistry, 1995
An oligonucleotide (I100-15) composed of only deoxyguanosine and thymidine was able to inhibit hu... more An oligonucleotide (I100-15) composed of only deoxyguanosine and thymidine was able to inhibit human immunodeficiency virus type-1 (HIV-1) in culture assay systems. I100-15 did not block virus entry into cells but did reduce viral-specific transcripts. As assessed by NMR and polyacrylamide gel methods, I100-15 appears to form a structure in which two stacked guanosine tetrads are connected by three two-base long loops. Structure/activity experiments indicated that formation of intramolecular guanosine tetrads was necessary to achieve maximum antiviral activity. The single deoxyguanosine nucleotide present in each loop was found to be extremely important for the overall antiviral activity. The toxicity of I100-15 was determined to be well above the 50% effective dose (ED50) in culture which yielded a high therapeutic index (> 100). The addition of a cholesterol moiety to the 3' terminus of I100-15 (I100-23) reduced the ED50 value to less than 50 nM (from 0.12 microM for I100-15) and increased the duration of viral suppression to greater than 21 days (versus 7-10 days for I100-15) after removal of the drug from infected cell cultures. The favorable therapeutic index of such molecules coupled with the prolonged suppression of HIV-1, suggest that such compounds further warrant investigation as potential therapeutic agents.
Journal of Applied Physics, 2013
ABSTRACT We present calculations of the thermal conductivity of fcc Argon at high pressures (pres... more ABSTRACT We present calculations of the thermal conductivity of fcc Argon at high pressures (pressure range is 10–150 GPa, temperatures range is 400–1200 K) from first principles in the framework of density functional theory and solution of the Boltzmann Transport Equation. Local density approximation (LDA) and generalized gradient approximation (GGA) produce similar thermal conductivities, with differences accounted by the known overbinding and underbinding of the LDA and GGA, correspondingly. Thermal conductivities at all considered pressures and temperatures are found to be consistent with the results of previous molecular dynamics simulations based on classical 2-body potentials. However, they are not consistent with recent experimental findings. Possible reasons for this disagreement are discussed. In addition, in light of our calculations, we critically examine analytically tractable approximations for thermal conductivity as applied to solid argon.
Human Molecular Genetics, 2009
Genes and Immunity, 2011
§ On behalf of the BIOLUPUS Network. The members of the network are listed in the acknowledgement... more § On behalf of the BIOLUPUS Network. The members of the network are listed in the acknowledgements. § § On behalf of the GENLES collaboration. The members of this collaboration are listed in the acknowledgements.
Genes and Immunity, 2009
In our previous study, we utilized a Bayesian design to probe the association of ~1,000 genes (~1... more In our previous study, we utilized a Bayesian design to probe the association of ~1,000 genes (~10,000 SNPs) with SLE on a moderate number of trios of parents and children with SLE. Two genes associated with SLE with a multitest corrected False Discovery Rate (FDR) of <0.05. were identified, and a number of noteworthy genes with FDR of <0.8 were also found, pointing out a future direction for the study. In the present report, using a large population of controls and adultor -childhood onset SLE cases, we have extended the previous investigation to explore the SLE association of ten of these noteworthy genes (109 SNPs). We have found that seven of these genes exhibit significant (FDR < 0.05) association with SLE, both confirming some genes that have previously been found to be associated with SLE (PTPN22 and IRF5) and novel findings of genes (KLRG1, IL-16, PTPRT, TLR8 and CASP10) which have not been previously reported. The results signify that the two-step candidate pathway design is an efficient way to study the genetic foundations of complex diseases. Furthermore, the novel genes identified in this study point to new directions in both the diagnosis and the eventual treatment of this debilitating disease.
Antimicrobial Agents and Chemotherapy, 1995
T30177, an oligonucleotide composed of only deoxyguanosine and thymidine, is 17 nucleotides in le... more T30177, an oligonucleotide composed of only deoxyguanosine and thymidine, is 17 nucleotides in length and contains single phosphorothioate internucleoside linkages at its 5 and 3 ends for stability. This oligonucleotide does not share significant primary sequence homology with or possess any complementary (antisense) sequence motifs to the human immunodeficiency virus type 1 (HIV-1) genome. T30177 inhibited replication of multiple laboratory strains of HIV-1 in human T-cell lines, peripheral blood lymphocytes, and macrophages. T30177 was also found to be capable of inhibiting multiple clinical isolates of HIV-1 and preventing the cytopathic effect of HIV-1 in primary CD4 ؉ T lymphocytes. In assays with human peripheral blood lymphocytes there was no observable toxicity associated with T30177 at the highest concentration tested (100 M), while the median inhibitory concentration was determined to be in the range of 0.1 to 1.0 M for the clinical isolates tested, resulting in a high therapeutic index for this drug. In temporal studies, the kinetics of addition of T30177 to infected cell cultures indicated that, like the known viral adsorption blocking agents dextran sulfate and Chicago sky blue, T30177 needed to be added to cells during or very soon after viral infection. However, analysis of nucleic acids extracted at 12 h postinfection from cells treated with T30177 at the time of virus infection established the presence of unintegrated viral cDNA, including circular proviral DNA, in the treated cells. In vitro analysis of viral enzymes revealed that T30177 was a potent inhibitor of HIV-1 integrase, reducing enzymatic activity by 50% at concentrations in the range of 0.050 to 0.09 M. T30177 was also able to inhibit viral reverse transcriptase activity; however, the 50% inhibitory value obtained was in the range of 1 to 10 M, depending on the template used in the enzymatic assay. No observable inhibition of viral protease was detected at the highest concentration of T30177 used (10 M). In experiments in which T30177 was removed from infected cell cultures at 4 days post-HIV-1 infection, total suppression of virus production was observed for more than 27 days.
Raman scattering measurements and x-ray diffraction of ammonia have been made under simultaneous ... more Raman scattering measurements and x-ray diffraction of ammonia have been made under simultaneous conditions of high temperature and high static pressure in the laser heated diamond anvil cell. The experimental results on phase transitions with pressure increase at room temperature are found to be in accord with previous studies [1]. Pressure was increased up to 52 GPa and temperature ramped up to 2000 K. On increasing temperature at high pressure, strong changes in the ammonia Raman spectra are observed, which could be associated with melting. On melting, ammonia undergoes partial decomposition into nitrogen and hydrogen. We also observed the appearance of new N-H stretch bands at high temperatures which may be related to the formation of new bonds. When quenched back to room temperature the starting phase of solid ammonia is recovered. The shift in frequencies of the vibron bands of nitrogen with pressure shows that it is phase segregated from ammonia.
Emerging infectious diseases, 2017
In September 2014, a single fatal case of Marburg virus was identified in a healthcare worker in ... more In September 2014, a single fatal case of Marburg virus was identified in a healthcare worker in Kampala, Uganda. The source of infection was not identified, and no secondary cases were identified. We describe the rapid identification, laboratory diagnosis, and case investigation of the third Marburg virus outbreak in Uganda.