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1.  Evaluation of Cover Crops with Potential for Use in Anaerobic Soil Disinfestation (ASD) for Susceptibility to Three Species of Meloidogyne 
Journal of Nematology  2013;45(4):272-278.
Several cover crops with potential for use in tropical and subtropical regions were assessed for susceptibility to three common species of root-knot nematode, Meloidogyne arenaria, M. incognita, and M. javanica. Crops were selected based on potential use as organic amendments in anaerobic soil disinfestation (ASD) applications. Nematode juvenile (J2) numbers in soil and roots, egg production, and host plant root galling were evaluated on arugula (Eruca sativa, cv. Nemat), cowpea (Vigna unguiculata, cv. Iron & Clay), jack bean (Canavalia ensiformis, cv. Comum), two commercial mixtures of Indian mustard and white mustard (Brassica juncea & Sinapis alba, mixtures Caliente 61 and Caliente 99), pearl millet (Pennisetum glaucum, cv. Tifleaf III), sorghum-sudangrass hybrid (Sorghum bicolor × S. bicolor var. sudanense, cv. Sugar Grazer II), and three cultivars of sunflower (Helianthus annuus, cvs. 545A, Nusun 660CL, and Nusun 5672). Tomato (Solanum lycopersicum, cv. Rutgers) was included in all trials as a susceptible host to all three nematode species. The majority of cover crops tested were less susceptible than tomato to M. arenaria, with the exception of jack bean. Sunflower cv. Nusun 5672 had fewer M. arenaria J2 isolated from roots than the other sunflower cultivars, less galling than tomato, and fewer eggs than tomato and sunflower cv. 545A. Several cover crops did not support high populations of M. incognita in roots or exhibit significant galling, although high numbers of M. incognita J2 were isolated from the soil. Arugula, cowpea, and mustard mixture Caliente 99 did not support M. incognita in soil or roots. Jack bean and all three cultivars of sunflower were highly susceptible to M. javanica, and all sunflower cultivars had high numbers of eggs isolated from roots. Sunflower, jack bean, and both mustard mixtures exhibited significant galling in response to M. javanica. Arugula, cowpea, and sorghum-sudangrass consistently had low numbers of all three Meloidogyne species associated with roots and are good selections for use in ASD for root-knot nematode control. The remainder of crops tested had significant levels of galling, J2, and eggs associated with roots, which varied among the Meloidogyne species tested.
PMCID: PMC3873904  PMID: 24379486
Anaerobic soil disinfestation; ASD; Brassica juncea & Sinapis alba; Canavalia ensiformis; cover crops; cowpea; Eruca sativa; Helianthus annuus; jack bean; management; Meloidogyne arenaria; M. incognita; M. javanica; mustard; pearl millet; Pennisetum glaucum; root-knot nematodes; sorghum-sudangrass; sunflower; Vigna unguiculata
2.  Herpes simplex virus 2 serostatus and viral loads of HIV-1 in blood and semen as risk factors for HIV transmission among men who have sex with men 
AIDS (London, England)  2008;22(13):1667-1671.
Objective
Human immunodeficiency virus type 1 blood plasma viral load is correlated with the sexual transmission of HIV, although transmission from men involves virus from semen instead of blood. We quantified HIV-1 RNA in the blood and semen of men who did or did not transmit HIV to their sex partners. We compared the relationships of HIV-1 transmission risk with blood plasma viral load, seminal plasma viral load, herpes simplex virus 2 serostatus and other factors.
Design
A case–control study.
Methods
Participants were men evaluated for primary HIV infection and their recent male sex partners. They were interviewed, and clinical specimens were collected. Epidemiologic and phylogenetic linkages were determined by history and molecular techniques. Couples were grouped on the basis of transmission after exposure. Fisher’s exact test and Wilcoxon tests were used for comparisons between groups. Multivariable logistic regressions were fit to identify independent predictors of transmission.
Results
HIV-transmitting partners (n=15) had a higher median seminal plasma viral load (P<0.015) and median blood plasma viral load (P<0.001) than nontransmitting partners (n=32). Herpes simplex virus 2 serostatus was associated with transmission only when the HIV-infected source partner was herpes simplex virus 2 seropositive and the HIV-exposed partner was not (odds ratio 16, P<0.03). Adjusting for other factors, HIV transmission was significantly associated with blood plasma viral load (odds ratio 13.4, P<0.02) but not seminal plasma viral load (odds ratio 0.69, P=not significant).
Conclusion
Blood and seminal plasma viral load were both associated with human immunodeficiency virus type 1 transmission, but blood plasma viral load was the stronger predictor in this cohort. Herpes simplex virus 2 coinfection was associated with the risk of transmission but not acquisition of human immunodeficiency virus type 1.
doi:10.1097/QAD.0b013e32830bfed8
PMCID: PMC2653089  PMID: 18670228
herpes simplex virus 2; HIV; men who have sex with men; seminal viral load; transmission
4.  The Origins of Sexually Transmitted HIV Among Men Who Have Sex with Men 
Science translational medicine  2010;2(18):18re1.
Although it is known that most HIV-1 infections worldwide result from exposure to virus in semen, it has not yet been established whether transmitted strains originate as RNA virions in seminal plasma or as integrated proviral DNA in infected seminal leukocytes. We present phylogenetic evidence that among six transmitting pairs of men who have sex with men, blood plasma virus in the recipient is consistently more closely related to the seminal plasma virus in the source. All sequences were subtype B, and the env C2V3 of transmitted variants tended to have higher mean isoelectric points, contain potential N-linked glycosylation sites, and favor CCR5 co-receptor usage. A statistically robust phylogenetically corrected analysis did not detect genetic signatures reliably associated with transmission, but further investigation of larger samples of transmitting pairs holds promise for determining which structural and genetic features of viral genomes are associated with transmission.
doi:10.1126/scitranslmed.3000447
PMCID: PMC2945226  PMID: 20371483
5.  Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure 
AIDS (London, England)  2010;24(3):411-416.
Background
Most of our knowledge about how antiretrovirals and host immune responses influence the HIV-1 protease gene is derived from studies of subtype B virus. We investigated the effect of protease resistance-associated mutations (PRAMs) and population-based HLA haplotype frequencies on polymorphisms found in CRF01_AE pro.
Methods
We used all CRF01_AE protease sequences retrieved from the LANL database and obtained regional HLA frequencies from the dbMHC database. Polymorphisms and major PRAMs in the sequences were identified using the Stanford Resistance Database, and we performed phylogenetic and selection analyses using HyPhy. HLA binding affinities were estimated using the Immune Epitope Database and Analysis.
Results
Overall, 99% of CRF01_AE sequences had at least 1 polymorphism and 10% had at least 1 major PRAM. Three polymorphisms (L10 V, K20RMI and I62 V) were associated with the presence of a major PRAM (P < 0.05). Compared to the subtype B consensus, six additional polymorphisms (I13 V, E35D, M36I, R41K, H69K, L89M) were identified in the CRF01_AE consensus; all but L89M were located within epitopes recognized by HLA class I alleles. Of the predominant HLA haplotypes in the Asian regions of CRF01_AE origin, 80% were positively associated with the observed polymorphisms, and estimated HLA binding affinity was estimated to decrease 19–40 fold with the observed polymorphisms at positions 35, 36 and 41.
Conclusion
Polymorphisms in CRF01_AE protease gene were common, and polymorphisms at residues 10, 20 and 62 most likely represent selection by use of protease inhibitors, whereas R41K and H69K were more likely attributable to recognition of epitopes by the HLA haplotypes of the host population.
doi:10.1097/QAD.0b013e3283350eef
PMCID: PMC2913588  PMID: 20009919
CRF01_AE; HIV; HLA; polymorphisms; protease; resistance
6.  The Efficiency of Single Genome Amplification and Sequencing is Improved by Quantitation and Use of a Bioinformatics Tool 
Journal of virological methods  2009;162(1-2):280-283.
Typically, population-based sequencing of HIV does not detect minority variants present at levels below 20-30%. Single genome amplification (SGA) and sequencing improves detection, but it requires many PCRs to find the optimal terminal dilution to use. A novel method for guiding the selection of a terminal dilution was developed and compared to standard methods. A quantitative real-time PCR (qRT-PCR) protocol was developed. HIV RNA was extracted, reverse transcribed, and quantitated. A bioinformatics web-based application was created for calculating the optimal concentration of cDNA to use based on results of a trial PCR using the dilution suggested by the qRT-PCR results. This method was compared to the standard. Using the standard protocol, the mean number of PCRs giving an average of 30 (26-34, SD=3) SGA per sample was 245 (218-266, SD=20) after an average of 8 trial dilutions. Using this method, 135 PCRs (135-135, SD=0) produced 30 (27-30, SD=1) SGA using exactly two dilutions. This new method reduced turnaround time from 8 to 2 days.
Standard methods of SGA sequencing can be costly and both time- and labor-intensive. By choosing a terminal dilution concentration with the proposed method, the number of PCRs required is decreased and efficiency improved.
doi:10.1016/j.jviromet.2009.08.002
PMCID: PMC2761514  PMID: 19698751
Single Genome Amplification; quantitative real-time PCR; population-based sequencing; single genome sequencing; minority variant detection
7.  Active Methamphetamine Use is Associated with Transmitted Drug Resis-tance to Non-Nucleoside Reverse Transcriptase Inhibitors in Individuals with HIV Infection of Unknown Duration 
The Open AIDS Journal  2007;1:5-10.
Background:
Frequent methamphetamine use among recently HIV infected individuals is associated with transmitted drug resistance (TDR) to non-nucleoside reverse transcriptase inhibitors (NNRTI); however, the reversion time of TDR to drug susceptible HIV may exceed 3 years. We assessed whether recreational substance use is associated with detectable TDR among individuals newly diagnosed with HIV infection of unknown duration.
Design:
Cross-sectional analysis.
Methods:
Subjects were enrolled at the University California, San Diego Early Intervention Program. Demographic, clinical and substance use data were collected using structured interviews. Genotypic resistance testing was performed using GeneSeq™, Monogram Biosciences. We analyzed the association between substance use and TDR using bivariate analyses and the corresponding transmission networks using phylogenetic models.
Results:
Between April 2004 and July 2006, 115 individuals with genotype data were enrolled. The prevalence of alcohol, marijuana and methamphetamine use were 98%, 71% and 64% respectively. Only active methamphetamine use in the 30 days prior to HIV diagnosis was independently associated with TDR to NNRTI (OR: 6.6; p=0.002).
Conclusion:
Despite not knowing the duration of their HIV infection, individuals reporting active methamphetamine use in the 30 days prior to HIV diagnosis are at an increased risk of having HIV strains that are resistant to NNRTI.
doi:10.2174/1874613600701010005
PMCID: PMC2556194  PMID: 18923691
HIV; NNRTI; transmitted drug resistance; methamphetamine.

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