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Heterodera glycines, the soybean cyst nematode, and Macrophomina phaseolina, causal agent of charcoal rot, are economically important soybean pathogens. The impact and effect of these pathogens on soybean yield in coinfested fields in the Midwest production region is not known. Both pathogens are soilborne, with spatially aggregated distribution and effects. Spatial regression analysis, therefore, is an appropriate method to account for the spatial dependency in either the dependent variable or regression error term from data produced in fields naturally infested with H. glycines and M. phaseolina. The objectives of this study were twofold: to evaluate the combined effect of H. glycines and M. phaseolina on soybean yield in naturally infested commercial fields with ordinary least squares and spatial regression models; and to evaluate, under environmentally controlled conditions, the combined effect of H. glycines and M. phaseolina through nematode reproduction and plant tissue fungal colonization. Six trials were conducted in fields naturally infested with H. glycines and M. phaseolina in Ohio. Systematic-grid sampling was used to determine the population densities of H. glycines and M. phaseolina, and soybean yield estimates. Though not used in any statistical analysis, M. phaseolina colony forming units from plant tissue, charcoal rot severity, and H. glycines type were also recorded and summarized. In two greenhouse experiments, treatments consisted of H. glycines alone, M. phaseolina alone, and coinfestation of soybean with both pathogens. Moran's I test indicated that the yield from five fields was spatially correlated (P < 0.05) and aggregated. In these fields, to account for spatial dependence, spatial regression models were fitted to the data. Spatial regression analyses revealed a significant interaction effect between H. glycines and M. phaseolina on soybean yield for fields with high initial population densities of both pathogens. In the greenhouse experiments, H. glycines reproduction was significantly (P < 0.05) reduced in the presence of M. phaseolina; however, soybean tissue fungal colonization was not affected by the presence of H. glycines. The direct mechanisms by which H. glycines and M. phaseolina interact were not demonstrated in this study. Future studies must be conducted in the field and greenhouse to better understand this interaction effect.

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The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H(+) in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly (13)C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and (13)C(18)O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm(-1) for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

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This preliminary report sought to provide insight into the genetic diversity of human immunodeficiency virus drug resistance (HIVDR) in Jamaica. This was done by investigating the genetic diversity associated with drug resistance in pregnant women living with HIV attending antenatal clinics in Kingston, Jamaica. Blood samples were collected and viral RNA were extracted and analysed. The protease and reverse transcriptase (Pro-RT) genes were amplified using the nested polymerase chain reaction (PCR) method. Polymerase chain reaction amplicons were obtained for nine of 16 patients (56%), of which five (55%) were antiretroviral (ARV) drug naïve and four (45%) were treatment experienced. Three minor protease resistant-conferring mutations (A71AT, A71V, A71T) and five mutations conferring high to low-level resistance (K219EK, T69S, K103S, G190A and K103N) were detected in the RT region. More than 50% of the resistance mutations found were detected in ARV drug naïve individuals, implying that viruses are being transmitted with the ARV resistance. These preliminary results will inform the health practitioners of the level of drug resistance that is being transmitted as well as strengthen the need to initiate a national baseline survey on HIVDR in Jamaica.

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Urea/water is an archetypical "biological" mixture and is especially well-known for its relevance to protein thermodynamics as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea's influence on water structure. On the basis of a variety of methods and of definitions of the water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral toward water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs the water structure. Both this work and experiments by Rezus and Bakker, however, show that water's rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules.

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The aim of this study was to assess HIV prevalence and associated risk behaviours among international truck drivers (TDs) in Azerbaijan. The subjects signed consent and completed a questionnaire. Blood was tested using two rapid HIV tests: Determine and OraQuick. Genotyping was performed on 13 positives. Overall, 3763 TDs from 21 countries were enrolled. Fifty-eight (1.54%) were HIV-positive. Highest prevalence was among Russians (2.88%), Ukrainians (1.66%) and Azerbaijani (1.09%). On univariate analysis, highest prevalence (60%) was among injecting drug users (IDUs) compared with 0.4% among non-IDUs (P < 0.001). The prevalence in men who had sex with men (MSM) (42.9%) was high (P

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The objective of this cross-sectional study was to assess prevalence and correlates of self-treatment of sexually transmitted diseases (STD) among female sex workers (FSW) in Tashkent, Uzbekistan. Enrolled FSW completed a self-administered questionnaire, HIV serologic testing and optional pelvic examination. STD diagnosis was based on physical examination and/or microscopic findings. Of 448 women, 337 (75.0%) accepted examination; of these, 316 (93.8%) received at least one STD-related diagnosis. Nearly half (45.4%) reported prior STD self-treatment, which was associated with HIV infection (age-adjusted odds ratio [AOR] = 3.20, 95% confidence interval [CI] = 1.45-7.53) and condom knowledge (AOR = 2.10, 95% CI = 1.16-3.80). For those with history of STD, immediate resumption of sex work before completing treatment was common (87.0%). STD self-treatment is common among FSW in Tashkent, particularly women with HIV infection. Confidential venues for STD care and condom utilization programmes targeted to FSW and their clients are needed to prevent STD in this setting.

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HIV prevalence is increasing among high-risk populations in the Mexican-U.S. border cities of Tijuana and Ciudad Juarez. In 2005, the molecular epidemiology of HIV-1 was studied among injecting drug users (IDU) and female sex workers (FSW) in these cities, which are corridors for over two-thirds of the migrant flow between Mexico and the United States. Eleven samples (eight IDU and three FSW) were successfully amplified, sequenced, and analyzed. The results revealed that all 11 samples were subtype B. There was no phylogenetic clustering or separation of the strains between IDU and FSW or between Tijuana and Ciudad Juarez nor was the Mexican strain phylogenetically distinct from other subtype B strains. Two of three drug naive FSWs had low-level HIV-1 resistance mutations. This community-based study demonstrated that HIV-positive IDUs and FSWs in Ciudad Juarez and Tijuana were predominantly infected with subtype B. Further prevalence studies on HIV-1 resistance mutations among FSWs in these border cities are warranted.

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The objective of this paper is to describe prevalence and correlates of sexual risk behaviors among injection drug users (IDUs) in Tashkent, Uzbekistan. Participants in this cross-sectional study completed a questionnaire detailing sociodemographic, medical and drug and sexual risk behaviors and HIV antibody testing. Of 701 IDUs surveyed, only 20.5% reported consistent condom use, which was more likely for women. Prior sexually-transmitted infection (STI) diagnosis was reported by 36.2% of participants and was associated with early (

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OBJECTIVE: Assessment of HIV prevalence and associated risk behaviours among female commercial sex workers (FCSW) across major cities in South America. METHODS: Seroepidemiological, cross sectional studies of 13 600 FCSW were conducted in nine countries of South America during the years 1999-2002. Participants were recruited in brothels, massage parlours, hotels, and streets where anonymous questionnaires and blood samples were collected. HIV infection was determined by enzyme linked immunosorbent assay (ELISA) screening and western blot confirmatory tests. RESULTS: The overall HIV seroprevalence was 1.2% (range 0.0%-4.5%). The highest HIV seroprevalences were reported in Argentina (4.5%) and Paraguay (2.6%); no HIV infected FCSW were detected in Venezuela and Chile. Consistent predictors of HIV seropositivity were: (1) a previous history of sexually transmitted infections (STI, AORs = 3.8-8.3), and (2) 10 years or more in commercial sex work (AORs = 2.2-24.8). In addition, multiple (> or =3) sexual contacts (AOR = 5.0), sex with foreigners (AOR = 6.9), use of illegal drugs (AOR = 3.2), and marijuana use (AOR = 8.2) were associated with HIV seropositivity in Southern Cone countries. CONCLUSIONS: Consistently low HIV seroprevalences were detected among FCSW in South America, particularly in the Andean region. Predictors of HIV infection across the continent were STI and length of commercial sex work; however, use of illegal drugs, especially marijuana, and sexual contacts with foreigners were also found to be associated risk factors in the Southern Cone region. Interventions for the control of HIV and other STI need to be region and country specific; drug use appears to have an ever increasing role in the spread of HIV among heterosexually active populations.

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The population distribution of alleles of the classical HLA class I loci in Cameroon has not been well studied but is of particular interest given the AIDS and malarial epidemics afflicting this population. We investigated the genetic diversity of HLA-A, HLA-B and HLA-C alleles in remote populations of Cameroon. Subjects from seven small, isolated, indigenous populations (N = 274) in the rainforest of southern Cameroon were typed for HLA-A, HLA-B and HLA-C alleles using a polymerase chain reaction/sequence-specific oligonucleotide probe assay and sequence analysis. Multiple alleles of the HLA-A (N = 28), HLA-B (N = 41) and HLA-C (N = 21) loci were identified, of which A*2301[allele frequency (AF) = 12.8%], B*5802 (AF = 10.9%) and Cw*0401 (AF = 16.6%) were the most frequent individual alleles and A*02 (AF = 19.0%), B*58 (AF = 15.9%) and Cw*07 (AF = 22.4%) the most common serologically defined groups of alleles. Twenty-six (28.9%) alleles with a frequency of less than 1% (AF < 1%), 39 (43%) with a frequency of 2.0-15.0% (AF = 2.0-15.0%), three globally uncommon alleles [A*2612 (AF = 2.0%), B*4016 (AF = 0.7%) and B*4407 (AF = 1.4%)], and the A*2612-Cw*0701/06/18-B*4407 haplotype (haplotype frequency = 1.3%) were also identified. Heterozygosity values of 0.89, 0.92 and 0.89 were determined for HLA-A, HLA-B and HLA-C, respectively. The extensive allelic and haplotypic diversity observed in this population may have resulted from varied natural selective pressures on the population, as well as intermingling of peoples from multiple origins. Thus, from an anthropologic perspective, these data highlight the challenges in T-cell-based vaccine development, the identification of allogeneic transplant donors and the understanding of infectious disease patterns in different populations.

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We examined the genetic makeup of 221 HIV-1 strains from Chilean persons living with HIV/AIDS by HMA and DNA sequencing of the env gene: 143 cases were infected by sexual contact with an already-infected partner, 76 were infected by mother-to-child transmission, and 2 were transfusion related. We found env HIV-1 subtype B in 202 cases (91.4%) and subtype F in 19 cases (8.6%). Subtype B strains were found throughout the country whereas subtype F viruses were predominantly found in cases from the metropolitan/central to the northern regions of Chile (p < 0.01). Chilean F subtypes clustered in two different groups: viruses from the central region clustered with F subtypes from Argentina, Uruguay, and Brazil, and viruses from the northern region, which independently segregated from other South American and European F strains. All of the 59 men having sex with men (MSM) were infected with B subtype strains whereas 7 (9.2%) and 12 (15.8%), respectively, of heterosexually infected females and children were infected with F subtype strains (p < 0.01). It appears that F subtype strains have been introduced into Chile by separate heterosexual transmission events from other nearby countries in the Southern Cone whereas B subtype strains have continued to persist predominantly among MSM.

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HIV subtypes B, F, and BF recombinants have been previously reported in South America. This report describes the presence of HIV-1 subtype C infection in the countries of Argentina, Uruguay, and Paraguay dating back to at least 1999. Surveillance for uncommon non-B/non-F subtype viruses circulating in South America has been conducted in samples obtained from nine countries. Peripheral blood mononuclear cells (PBMC), dried filter paper (FP), and fresh blood (FB) samples were collected from HIV-positive patients from Ecuador, Colombia, Venezuela, Peru, Chile, Bolivia, Argentina, Uruguay, and Paraguay. From a total of 2962 HIV seropositive samples examined during a 9-year period (1995-2003), only 11 (0.4%) were found to be infected with non-B/non-F HIV variants. Eight of these 11 strains were determined to be subtype C by heteroduplex mobility assay (HMA). Five of these 8 strains were further characterized by sequencing and phylogenetic analysis of the protease (Pro) and reverse transcriptase (RT) region of the genome and two were sequenced full length. One of the strains was found to be a unique BC recombinant. The spread of a third subtype of HIV, subtype C, should raise the question of its potential future role in the HIV epidemic in this region.

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OBJECTIVES: Sex among men constitutes an important route of transmission for HIV type 1 (HIV-1) in Latin America. Seeking better understanding of risk behaviours in this region, we determined the seroprevalence, potential risk factors, and geographic distribution of HIV-1 among groups of men who have sex with men (MSM). METHODS: Seroepidemiological, cross sectional studies of 13,847 MSM were conducted in seven countries of South America during the years 1999-2002. Volunteers were recruited in city venues and streets where anonymous questionnaires and blood samples were obtained. HIV-1 infection was determined by enzyme linked immunosorbent assay (ELISA) screening and western blot (WB) confirmatory tests. RESULTS: HIV-1 seroprevalence varied widely (overall 12.3%, range 11.0%-20.6%). The highest HIV-1 seroprevalence was noted in Bolivia (20.6%) and the lowest in Peru (11.0%). Predictors of HIV-1 infection varied among countries; however, a history of previous sexually transmitted disease (STD) was associated with a consistent increased risk (ORs=1.9-2.9, AORs=1.8-2.7). Multiple weekly sexual contacts was found to represent a secondary risk factor in Ecuador, Peru, and Argentina (ORs=1.6-2.9, AORs=1.6-3.1), whereas use of drugs such as cocaine was found to increase risk in Bolivia, Uruguay, and Paraguay (ORs=2.5-6.5, AORs=2.6-6.1). CONCLUSION: The results of this study illustrate an elevated HIV-1 seroprevalence among MSM participants from Andean countries. A previous STD history and multiple partners predicted HIV-1 infection in the seven countries of South America. In Southern Cone countries, HIV-1 infection was also associated with use of illegal drugs such as cocaine.

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With the objective of monitoring the distribution of HIV-1 subtypes and circulating recombinant forms (CRFs)in South America, population-based surveillance studies were performed in seven countries. Peripheral blood mononuclear cell, filter paper, fresh blood, and cocultivation samples were collected from HIV-positive patients from Colombia, Ecuador, Peru, Bolivia, Chile, Argentina, and Uruguay, during a 7-year period(1995-2001). DNA was prepared and HIV envelope subtypes were determined by heteroduplex mobility as-say and DNA sequencing from 1289 HIV-positive samples. While subtypes B and F were the most commonly observed subtypes, two CRF02_AG strains were detected, in Ecuador. This is the first report of the existence of this CRF in South America.

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Two different BC recombinant HIV-1 strains have arisen and begun to circulate among intravenous drug users in China. The recombinants are mostly subtype C with a few small subtype B segments. Additional full-genome sequences of the two recombinants, termed CRF07_BC and CRFO&_BC, are now available for analysis. Four CRF07_BC strains, including c54, 97CNU01, 98CN009, and a new strain CNGL-179, described here, and four CRF08_BC strains, including 97CNGX-6, 97CNGX-7, 97CNGX-9, and 98CN006, were compared for their recombination breakpoints by bootscanning and software for fine mapping of recombinants. The four CRF07_BC strains shared an identical recombination structure and the four CRF08_BC strains shared an identical, but different, recombination structure. The two CRFs share five precise subtype B/C boundaries, although although other segments differ between them, suggesting that they shared a common ancestor, itself a BC recombinant that separately "back-crossed" onto different subtype C strains. Both CRFs are broadly distributed from north to south in western China and have maintained low interpatient diversity.

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The molecular epidemiology of HIV-1 in Argentina is more complex than was previously appreciated. One circulating recombinant form, CRF12_BF, and many related BF recombinant forms predominate in the capital city, Buenos Aires. This study of HIV-1 subtypes acquired perinatally between 1984 and 2000 has permitted, for the first time, a reconstruction of the history of BF recombination in Argentina. Sequencing of a partial genome region from the beginning of vpu to the beginning of env(gp120), which spans a breakpoint common in most contemporary Argentine BF recombinants, enabled samples to be rapidly screened. Among 23 children born between 1984 and 2000, 15 including 1 child born in 1986, harbored a BF recombinant. Thirteen of the 15 recombinants shared a common breakpoint at the 5' end of env(gp120). Full genome sequencing of two viruses, from 1986 and 1987, respectively, revealed them to be genetically related but not identical to CRF12_BF. Both contained more subtype B sequence than did CRF12_BF. BF recombinants related to CRF12_BF have been in circulation in Buenos Aires since 1986 and continue to predominate in perinatal transmissions.

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OBJECTIVE: To describe the genetic diversity of HIV-1 in South America by full genome sequencing and analysis. METHODS: Purified peripheral blood mononuclear cell DNA from HIV-infected individuals in Argentina, Uruguay and Bolivia was used to amplify full HIV-1 genomes. These were sequenced using the ABI 3100 automated sequencer and phylogenetically analysed. RESULTS: Twenty-one HIV-1 strains from three South American countries, 17 of which were pre-screened by envelope heteroduplex mobility assay (HMA), were studied. Ten out of 10 HMA subtype F and four out of seven HMA subtype B strains were actually BF recombinants upon full genome analysis. Two BF recombinants from Argentina and two from Uruguay had the same structure, representing a new circulating recombinant form termed CRF12_BF(ARMA159). Twelve other BF recombinants had structures related to CRF12 but with additional segments of subtype B; each was unique. BF recombinants were temporally and geographically widespread, found as early as 1986-1987 in vertically infected Argentinian children and in Argentina, Uruguay, and Bolivia.

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We analyzed the genetic diversity of HIV-1 strains circulating in the Czech Republic. Phylogenetic analysis of the env and gag gene sequence fragments from 39 isolates revealed that the majority of these strains (32 of 39, 82%) were of subtype B; other genetic subtypes identified were A, C, F, and recombinant circulating form CRF01_AE. The isolates that did not cluster with subtype B originated almost exclusively from a heterosexual route of transmission. The molecular epidemiological data are suggestive of multiple entry of HIV-1 infection into the Czech Republic and show that the genetic pattern of the HIV-1 strains circulating in this country corresponds to that found in other European countries.

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The genetic diversity of group M HIV-1 is highest in west central Africa. Blood samples from four locations in Cameroon were collected to determine the molecular epidemiology of HIV-1. The C2-V5 region of envelope was sequenced from 39 of the 40 samples collected, and 7 samples were sequenced across the genome. All strains belonged to group M of HIV-1. The circulating recombinant form CRF02 AG (IbNG) was the most common strain (22/39, 56%). Two of these were confirmed by full genome analysis. Four samples (4/39, 10%) clustered with the sub-subtype F2 and one of these was confirmed by full genome sequencing. Recombinant forms, each different but containing subtype A, accounted for the next most common form (7/39, 18%). Among these recombinants, those combining subtypes A and G were the most common (4/7, 57%). Also found were 3 subtype A, 2 subtype G, and 1 subtype B strain. Many recombination break points were shared between IbNG and the other AG recombinants, though none of these other AG recombinants included IbNG as a parent. This suggests that there was an ancestral AG recombinant that gave rise to CRF02 AG (IbNG), the successful circulating recombinant form, and to others that were less successful and are now rare.

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