Norah Torrez-Martinez

Chronic neurodegenerative disease associated with HTLV-II infection

Although human T-cell leukemia virus (HTLV) type I is known to cause a number of diseases, there has been no convincing evidence of pathological changes after infection with the related virus, HTLV-II. We have found an endemic focus of HTLV-II infection among members of an American Indian population in New Mexico, USA. We set out to determine the pathological consequences of HTLV-II infection in this population and identified two sisters (aged 59 and 46 years) with a disease superficially resembling the myeloneuropathy induced by HTLV-I. These women had a syndrome similar to the olivopontocerebellar atrophy variant of multiple system atrophy, and HTLV-II infection was confirmed by western blot and the polymerase chain reaction. Thus, HTLV-II may, like HTLV-I, cause a progressive neurodegenerative disease.

Genotyping of Human Papillomavirus in Liquid Cytology Cervical Specimens by the PGMY Line Blot Assay and the SPF10 Line Probe Assay

ABSTRACT A comparison of two PCR-based human papillomavirus (HPV) DNA detection and genotyping systems (PGMY LBA and SPF10 LiPA) was conducted in two laboratories. Both systems are based on broad-spectrum PCR for the detection of HPV DNA, followed by reverse hybridization with type-specific probes. A total of 400 selected cervical scrape specimens in PreservCyt solution (55% normal cytology, 18% atypical squamous cells of unknown significance, 14.8% low-grade squamous intraepithelial lesions [SIL], and 12.5% high-grade SIL) were tested for the presence of HPV DNA. In this selected group of specimens, the overall agreement between the two methods for the detection of any HPV DNA was high (κ = 0.859). When the 20 common HPV genotypes identified by both methods were considered (HPV types 6, 11, 16, 18, 31, 33, 35, 39, 40, 42, 45, 51, 52, 53, 54, 56, 58, 59, 66, and 68), compatible genotype-specific results were observed in 96.5% of the samples, even when multiple HPV genotypes were present. However, for some specific HPV genotypes, there were significant differences in HPV detection by the two methods. PGMY LBA detected more HPV type 42 (P = 0.002), HPV type 56 (P = 0.039), and HPV type 59 (P < 0.001), whereas SPF10 LiPA detected more HPV type 31 (P < 0.001) and HPV type 52 (P = 0.031). For the remaining genotypes, including HPV types 16 and 18, the results obtained by the two methods were not significantly different. In general, both genotyping methods are highly suitable for clinical and epidemiological studies.

Sequence analysis of the long control region of human papillomavirus type 16 variants and functional consequences for P97 promoter activity.

Genital human papillomaviruses (HPV) are considered to be one of the main risk factors for the development of cervical cancer. The P97 promoter at the E6-proximal end of the long control region (LCR) regulates the transcription of viral genes, especially the oncogenes E6 and E7. The LCR contains binding sites of several viral and cellular transcription factors, which either activate or repress the P97 promoter. Intratype variants of HPV-16 belong to six geographically clustered phylogenetic groups distributed all over the world. These variants exhibit differences in E6 protein activities and in tumour progression in vivo. Seven HPV-16 variants were investigated by sequencing the entire LCR (nt 7060-124) and by comparing the transcriptional activities of their P97 promoters. Previously unknown nucleotide variations were identified in all LCRs investigated. In luciferase assays, 3.3- and 2.8-fold increases in P97 promoter activity were detected in the Asian American c and North American 1 variants when compared with the European reference clone. The African variants 1a and 2a exhibited P97 promoter activities comparable to the European reference clone. After recombining different LCR fragments, the region responsible for enhanced transcription in the Asian American c and North American 1 variants could be attributed to the E6-proximal end of the LCR (nt 7619-124).

Isla Vista virus: a genetically novel hantavirus of the California vole Microtus californicus.

Prospect Hill virus (PH) was isolated from a meadow vole (Microtus pennsylvanicus) in 1982, and much of its genome has been sequenced. Hantaviruses of other New World microtine rodents have not been genetically characterized. We show that another Microtus species (the California vole M. californicus) from the United States is host to a genetically distinct PH-like hantavirus, Isla Vista virus (ILV). The nucleocapsid protein of ILV differs from that of PH by 11.1% and a portion of the G2 glycoprotein differs from that of PH by 19.6%. ILV antibodies were identified in five of 33 specimens of M. californicus collected in 1975 and 1994-1995. Enzymatic amplification studies showed that 1975 and 1994-1995 ILV genomes were highly similar. Secondary infection of Peromyscus californicus was identified in Santa Barbara County, California. A long-standing enzootic of a genetically distinct hantavirus lineage is present in California voles.

Dominant glycoprotein epitope of four corners hantavirus is conserved across a wide geographical area

A newly identified hantavirus, tentatively called Four Corners virus (FCV), was found to be the aetiological agent of a 1993 outbreak of hantavirus pulmonary syndrome (HPS) in the southwestern United States. Immunodominant epitopes of 43 and 31 amino acids were identified in the nucleocapsid protein and G1 glycoprotein, respectively. The G1 genes of different hantaviruses are highly divergent, suggesting that geographically diverse FCVs might fail to cross-react owing to antigenic drift. We now show that the immunodominant epitope of G1 is conserved among 18 FCVs from a broad geographical area, despite extensive nucleotide sequence heterogeneity. Antibodies from all 45 HPS patients, separated by more than 3000 km were shown to be reactive with the dominant G1 epitope. Evidence for limited cross-reactivity between the G1 antigen of a novel hantavirus of the cotton rat and that of FCV is presented.

RELATIONSHIP OF ECOLOGICAL VARIABLES TO SIN NOMBRE VIRUS ANTIBODY SEROPREVALENCE IN POPULATIONS OF DEER MICE

Abstract Because recent studies have not demonstrated a strong relationship between rodent density and Sin Nombre virus (SNV) seroprevalence, there is speculation that seroprevalence may be related to other factors, including habitat quality and food availability. We evaluated densities of deer mice (Peromyscus maniculatus), plant cover and biomass, and terrestrial arthropod biomass at 2 sites in the southwestern United States to identify factors that may affect the seroprevalence rate of SNV within a rodent population. Seroprevalence differed significantly between years. Although interaction of deer-mouse density, plant cover and biomass, and arthropod biomass was not a strong predictor of seroprevalence (R2 = 0.64, P = 0.04), we observed a significant contribution to a repeated-measures model by deer-mouse density (P = 0.02). Our data suggest that as rodent density increases, so does the seroprevalence rate within that population. Although not significantly correlated, we observed the lowest levels of arthropod biomass when seroprevalence was highest. Based on our results, evaluating changes in habitat quality and incorporating measurement of local ecological variables with studies of fluctuations in rodent density may aid in predicting human outbreaks of hantavirus disease.

Dual primer emulsion PCR for next- generation DNA sequencing.

We have developed a highly sensitive single-molecule clonal amplification method called dual primer emulsion PCR (DPePCR) for next-generation DNA sequencing. The approach is similar in concept to standard emulsion PCR; however, in DPePCR both primers are attached to the beads, therefore following PCR amplification, both strands of the PCR products are attached to the beads. The ends of each strand can be freed for analysis by restriction digestion of the bridged PCR fragments, which allows efficient paired-end sequencing of fragment libraries.

High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp. MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio Technologies

ABSTRACT Here, we report the high-quality draft genome sequence of actinobacterium Kibdelosporangium sp. MJ126-NF4, producer of the type II polyketide azicemicins, obtained using Illumina and PacBio sequencing technologies. The 11.75-Mbp genome contains >11,000 genes and 22 polyketide and nonribosomal peptide natural product gene clusters.

Genomic analysis of Saccharomyces cerevisiae isolates that grow optimally with glucose as the sole carbon source

A population of Saccharomyces cerevisiae was cultured for approximately 450 generations in the presence of high glucose to select for genetic variants that grew optimally under these conditions. Using the parental strain BY4741 as the starting population, an evolved culture was obtained after aerobic growth in a high glucose medium for approximately 450 generations. After the evolution period, three single colony isolates were selected for analysis. Next‐generation Ion Torrent sequencing was used to evaluate genetic changes. Greater than 100 deletion/insertion changes were found with approximately half of these effecting genes. Additionally, over 180 SNPs were identified with more than one‐quarter of these resulting in a nonsynonymous mutation. Affymetrix DNA microarrays and RNseq analysis were used to determine differences in gene expression in the evolved strains compared to the parental strain. It was established that approximately 900 genes demonstrated significantly altered expression in the evolved strains relative to the parental strain. Many of these genes showed similar alterations in their expression in all three evolved strains. Interestingly, genes with altered expression in the three evolved strains included genes with a role in oxidative metabolism. Overall these results are consistent with the physiological observations of optimal growth with glucose as the carbon source. Namely, the decreased ethanol production suggest that the underlying metabolism switched from fermentation to respiration during the selection for optimal growth on glucose.