In this study, we investigate the effect of nucleotide content on the conductivity of plasmid len... more In this study, we investigate the effect of nucleotide content on the conductivity of plasmid length DNA molecular wires covalently bound to high aspect-ratio gold electrodes. The DNA wires were all between 2.20-2.35μm in length (>6000bp), and contained either 39%, 53%, or 64% GC base-pairs. We compared the current-voltage (I-V) and frequency-impedance characteristics of the DNA wires with varying GC content, and observed statistically significantly higher conductivity in DNA wires containing higher GC content in both AC and DC measurement methods. Additionally, we noted that the conductivity decreased as a function of time for all DNA wires, with the impedance at 100Hz nearly doubling over a period of seven days. All readings were taken in humidity and temperature controlled environments on DNA wires suspended above an insulative substrate, thus minimizing the effect of experimental and environmental factors as well as potential for nonlinear alternate DNA confirmations. While other groups have studied the effect of GC content on the conductivity of nano-scale DNA molecules (<50bp), we were able to demonstrate that nucleotide content can affect the conductivity of micron length DNA wires at scales that may be required during the fabrication of DNA-based electronics. Furthermore, our results provide further evidence that many of the charge transfer theories developed from experiments using nano-scale DNA molecules may still be applicable for DNA wires at the micro-scale.
AIDS Research and Human Retroviruses, Aug 20, 2002
The HIV-1 epidemic in South Africa is largely due to subtype C viruses, which preferentially use ... more The HIV-1 epidemic in South Africa is largely due to subtype C viruses, which preferentially use CCR5 as a coreceptor for infection. We describe full-length genome sequences of two CXCR4-utilizing HIV-1 subtype C viruses and two intersubtype recombinants from South Africa. Three of the viruses (99ZACM4, 99ZACM9, and 99ZASW7) were isolated in 1999 from AIDS patients in Johannesburg, and a fourth virus (98ZADu178) was isolated in Durban in 1998 from an asymptomatic female sex worker. Isolates 99ZASW7 and 99ZACM9 from Johannesburg were subtype C throughout the genome, 99ZASW7 used the CXCR4 coreceptor, and 99ZACM9 used both CCR5 and CXCR4. Isolate 98ZADu178 from Durban was a novel recombinant between subsubtype A2 and subtype C. The third isolate from Johannesburg, 99ZACM4, was a complex, novel recombinant with multiple breakpoints and contained segments of subtypes A, C, D, G, and K. These results establish the presence of intersubtype recombinants in South Africa, indicating that ongoing surveillance for other subtypes and recombinants is necessary.
HIV-1 is capable of mimicking the ligand of integrin α(4)β(7) by displaying a tripeptide mimotope... more HIV-1 is capable of mimicking the ligand of integrin α(4)β(7) by displaying a tripeptide mimotope on the V2 region. Through this mimicry HIV can bind the α(4)β(7) integrin and get carried through the lymphocyte proliferation signaling pathway, cell-to-cell adhesion and can migrate to gut-associated lymphoid tissues. The same tripeptide motif was suggested to be the epicenter of neutralization in laboratory strains of HIV-1. In this study, we compared the α(4)β(7) binding sites of two HIV-1 subtypes prevalent in China and found that the tripeptide binding domain of α(4)β(7) was more diverse in subtype B' strains than in CRF07_BC.
<p>A. For each amplicons, the sequencing was carried out with primers other than those used... more <p>A. For each amplicons, the sequencing was carried out with primers other than those used for full-genome amplification. The linear sequencing template (black line), the PCR primers are shown at both ends of the amplicons. Bleu lines (amplicons 671F-892R), green lines (amplicons 6838F-6972R), red lines (amplicons 6838F-7076R) represent the sequenced regions attached to the corresponding sequencing primers. Numbers included in primer IDs represent the position relative to HPV_SD2 genome. B. Alignment of sequences generated by Sanger method along the HPV_SD2 generated by 454 sequencing. Bars in blue, green and red correspond to sequences shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058404#pone-0058404-g006" target="_blank">Figure 6A</a>. The newly generated sequences covered 4,622 nucleotides representing 63.3% of the total HPV_SD2 genome. C. Comparison of the sequences generated by Sanger method and HPV_SD2 contig generated by 454 sequencing. Size of each Sanger sequence and percentage identity are shown.</p
<p>The tree was visualized with the Interactive Tree of Life (iTOL) <a href="http:/... more <p>The tree was visualized with the Interactive Tree of Life (iTOL) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058404#pone.0058404-Letunic1" target="_blank">[32]</a>. Bootstrap values with at least 50%, 75% or 100% (100 re-samplings) are indicated. Note, another HPV_SD1 from this study was added in this analysis clustered with reference HPV_49.</p
<b>Copyright information:</b>Taken from "Curation of complex, context-dependent ... more <b>Copyright information:</b>Taken from "Curation of complex, context-dependent immunological data"BMC Bioinformatics 2006;7():341-341.Published online 12 Jul 2006PMCID:PMC1534061.
<b>Copyright information:</b>Taken from "Curation of complex, context-dependent ... more <b>Copyright information:</b>Taken from "Curation of complex, context-dependent immunological data"BMC Bioinformatics 2006;7():341-341.Published online 12 Jul 2006PMCID:PMC1534061.b. References related to epitopes derived from NIAID Category A–C pathogens.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Li... more This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Heterosexual transmission accounts for the majority of human immunodeficiency virus–1 (HIV-1) inf... more Heterosexual transmission accounts for the majority of human immunodeficiency virus–1 (HIV-1) infections worldwide, yet the viral properties that determine transmission fitness or outgrowth have not been elucidated. Here we show, for eight heterosexual transmission pairs, that recipient viruses were monophyletic, encoding compact, glycan-restricted envelope glycoproteins. These viruses were also uniquely sensitive to neutralization by antibody from the transmitting partner. Thus, the exposure of neutralizing epitopes, which are lost in chronic infection because of immune escape, appears to be favored in the newly infected host. This reveals characteristics of the envelope glycoprotein that influence HIV-1 transmission and may have implications for vaccine design.
In this study, we investigate the effect of nucleotide content on the conductivity of plasmid len... more In this study, we investigate the effect of nucleotide content on the conductivity of plasmid length DNA molecular wires covalently bound to high aspect-ratio gold electrodes. The DNA wires were all between 2.20-2.35μm in length (&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;6000bp), and contained either 39%, 53%, or 64% GC base-pairs. We compared the current-voltage (I-V) and frequency-impedance characteristics of the DNA wires with varying GC content, and observed statistically significantly higher conductivity in DNA wires containing higher GC content in both AC and DC measurement methods. Additionally, we noted that the conductivity decreased as a function of time for all DNA wires, with the impedance at 100Hz nearly doubling over a period of seven days. All readings were taken in humidity and temperature controlled environments on DNA wires suspended above an insulative substrate, thus minimizing the effect of experimental and environmental factors as well as potential for nonlinear alternate DNA confirmations. While other groups have studied the effect of GC content on the conductivity of nano-scale DNA molecules (&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;50bp), we were able to demonstrate that nucleotide content can affect the conductivity of micron length DNA wires at scales that may be required during the fabrication of DNA-based electronics. Furthermore, our results provide further evidence that many of the charge transfer theories developed from experiments using nano-scale DNA molecules may still be applicable for DNA wires at the micro-scale.
AIDS Research and Human Retroviruses, Aug 20, 2002
The HIV-1 epidemic in South Africa is largely due to subtype C viruses, which preferentially use ... more The HIV-1 epidemic in South Africa is largely due to subtype C viruses, which preferentially use CCR5 as a coreceptor for infection. We describe full-length genome sequences of two CXCR4-utilizing HIV-1 subtype C viruses and two intersubtype recombinants from South Africa. Three of the viruses (99ZACM4, 99ZACM9, and 99ZASW7) were isolated in 1999 from AIDS patients in Johannesburg, and a fourth virus (98ZADu178) was isolated in Durban in 1998 from an asymptomatic female sex worker. Isolates 99ZASW7 and 99ZACM9 from Johannesburg were subtype C throughout the genome, 99ZASW7 used the CXCR4 coreceptor, and 99ZACM9 used both CCR5 and CXCR4. Isolate 98ZADu178 from Durban was a novel recombinant between subsubtype A2 and subtype C. The third isolate from Johannesburg, 99ZACM4, was a complex, novel recombinant with multiple breakpoints and contained segments of subtypes A, C, D, G, and K. These results establish the presence of intersubtype recombinants in South Africa, indicating that ongoing surveillance for other subtypes and recombinants is necessary.
HIV-1 is capable of mimicking the ligand of integrin α(4)β(7) by displaying a tripeptide mimotope... more HIV-1 is capable of mimicking the ligand of integrin α(4)β(7) by displaying a tripeptide mimotope on the V2 region. Through this mimicry HIV can bind the α(4)β(7) integrin and get carried through the lymphocyte proliferation signaling pathway, cell-to-cell adhesion and can migrate to gut-associated lymphoid tissues. The same tripeptide motif was suggested to be the epicenter of neutralization in laboratory strains of HIV-1. In this study, we compared the α(4)β(7) binding sites of two HIV-1 subtypes prevalent in China and found that the tripeptide binding domain of α(4)β(7) was more diverse in subtype B&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; strains than in CRF07_BC.
<p>A. For each amplicons, the sequencing was carried out with primers other than those used... more <p>A. For each amplicons, the sequencing was carried out with primers other than those used for full-genome amplification. The linear sequencing template (black line), the PCR primers are shown at both ends of the amplicons. Bleu lines (amplicons 671F-892R), green lines (amplicons 6838F-6972R), red lines (amplicons 6838F-7076R) represent the sequenced regions attached to the corresponding sequencing primers. Numbers included in primer IDs represent the position relative to HPV_SD2 genome. B. Alignment of sequences generated by Sanger method along the HPV_SD2 generated by 454 sequencing. Bars in blue, green and red correspond to sequences shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058404#pone-0058404-g006" target="_blank">Figure 6A</a>. The newly generated sequences covered 4,622 nucleotides representing 63.3% of the total HPV_SD2 genome. C. Comparison of the sequences generated by Sanger method and HPV_SD2 contig generated by 454 sequencing. Size of each Sanger sequence and percentage identity are shown.</p
<p>The tree was visualized with the Interactive Tree of Life (iTOL) <a href="http:/... more <p>The tree was visualized with the Interactive Tree of Life (iTOL) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058404#pone.0058404-Letunic1" target="_blank">[32]</a>. Bootstrap values with at least 50%, 75% or 100% (100 re-samplings) are indicated. Note, another HPV_SD1 from this study was added in this analysis clustered with reference HPV_49.</p
<b>Copyright information:</b>Taken from "Curation of complex, context-dependent ... more <b>Copyright information:</b>Taken from "Curation of complex, context-dependent immunological data"BMC Bioinformatics 2006;7():341-341.Published online 12 Jul 2006PMCID:PMC1534061.
<b>Copyright information:</b>Taken from "Curation of complex, context-dependent ... more <b>Copyright information:</b>Taken from "Curation of complex, context-dependent immunological data"BMC Bioinformatics 2006;7():341-341.Published online 12 Jul 2006PMCID:PMC1534061.b. References related to epitopes derived from NIAID Category A–C pathogens.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Li... more This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Heterosexual transmission accounts for the majority of human immunodeficiency virus–1 (HIV-1) inf... more Heterosexual transmission accounts for the majority of human immunodeficiency virus–1 (HIV-1) infections worldwide, yet the viral properties that determine transmission fitness or outgrowth have not been elucidated. Here we show, for eight heterosexual transmission pairs, that recipient viruses were monophyletic, encoding compact, glycan-restricted envelope glycoproteins. These viruses were also uniquely sensitive to neutralization by antibody from the transmitting partner. Thus, the exposure of neutralizing epitopes, which are lost in chronic infection because of immune escape, appears to be favored in the newly infected host. This reveals characteristics of the envelope glycoprotein that influence HIV-1 transmission and may have implications for vaccine design.
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