Women, Co-occurring Disorders, and Violence Study: evaluation design and study population.

The Women, Co-occurring Disorders, and Violence Study (WCDVS) was a multi-site cooperative study to evaluate new service models for women with co-occurring mental health and substance use disorders and a history of physical and/or sexual abuse. Despite common features in the service interventions and evaluation procedures, diversity across the nine sites plus differences introduced by non-random assignment led to numerous methodological challenges. This article describes the design, measurement, and analysis decisions behind the WCDVS and lays the foundation for understanding participant-level outcomes and service costs. This article also describes the study population, as recruited and following attrition at the 6-month follow-up, in order to address the threat of selection bias to inferences drawn from this multi-site study.

Speech processing strategy preferences among 55 European CLARION cochlear implant users.

This multicentre study investigates the preference and performance of a group of 55 adult CLARION cochlear implant users with the choice of simultaneous analogue stimulation (SAS) and continuous interleaved sampler (CIS) strategies during the first 3 months of implant use. Subjects were programmed with both strategies and instructed to use each of the two strategies in daily life to ascertain preference. Subjects were tested in both strategies with open-set sentence materials, auditory alone, at 2, 6 and 12 weeks after the initial programming session. Questionnaires were completed with preference ratings being recorded for the two strategies: 25% of subjects preferred SAS and 75% CIS. Subjects performed better in their strategy of choice. Preferences were set very early on in the process and did not change. Factors influencing preference are discussed. Offering the choice of fundamentally different strategies improves both individual and group performance.

In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions between 5'- and 3'-terminal regions that influence RNA structure.

Viral replicases of many positive-strand RNA viruses are membrane-bound complexes of cellular and viral proteins that include viral RNA-dependent RNA polymerase (RdRP). The in vitro RdRP assay system that utilizes cytoplasmic extracts from dengue viral-infected cells and exogenous RNA templates was developed to understand the mechanism of viral replication in vivo. Our results indicated that in vitro RNA synthesis at the 3'-untranslated region (UTR) required the presence of the 5'-terminal region (TR) and the two cyclization (CYC) motifs suggesting a functional interaction between the TRs. In this study, using a psoralen-UV cross-linking method and an in vitro RdRP assay, we analyzed structural determinants for physical and functional interactions. Exogenous RNA templates that were used in the assays contained deletion mutations in the 5'-TR and substitution mutations in the 3'-stem-loop structure including those that would disrupt the predicted pseudoknot structure. Our results indicate that there is physical interaction between the 5'-TR and 3'-UTR that requires only the CYC motifs. RNA synthesis at the 3'-UTR, however, requires long range interactions involving the 5'-UTR, CYC motifs, and the 3'-stem-loop region that includes the tertiary pseudoknot structure.

Points to consider in the development of a surrogate for efficacy of novel Japanese encephalitis virus vaccines.

Although an effective killed virus vaccine to prevent illness due to Japanese encephalitis virus (JEV) infection exists, many authorities recognize that a safe, effective live JEV vaccine is desirable in order to reduce the cost and the number of doses of vaccine required per immunization. A large-scale clinical efficacy trail for such a vaccine would be both unethical and impractical. Therefore, a surrogate for the efficacy of JE vaccines should be established. Detection of virus-neutralizing antibodies in sera of vaccinees could constitute such a surrogate for efficacy. Field studies of vaccinees in endemic areas and studies done in mice already exist to support this concept. Also, titers of virus-neutralizing antibodies are already accepted as a surrogate for the efficacy of yellow fever virus vaccines and for the efficacy of other viral vaccines as well. In developing a correlation between N antibody titers and protection from JEV infection, standard procedures must be validated and adopted for both measuring N antibodies and for testing in animals. A novel live virus vaccine could be tested in the mouse and/or the monkey model of JEV infection to establish a correlation between virus-neutralizing antibodies elicited by the vaccines and protection from encephalitis. In addition, sera of subjects receiving the novel live JEV vaccine in early clinical trials could be passively transferred to mice or monkeys in order to establish the protective immunogenicity of the vaccine in humans. A monkey model for JEV infection was recently established by scientists at WRAIR in the US. From this group, pools of JEV of known infectivity for Rhesus macaques may be obtained for testing of immunity elicited by live JE vaccine virus.

Identification of specific nucleotide sequences within the conserved 3'-SL in the dengue type 2 virus genome required for replication.

The flavivirus genome is a positive-stranded approximately 11-kb RNA including 5' and 3' noncoding regions (NCR) of approximately 100 and 400 to 600 nucleotides (nt), respectively. The 3' NCR contains adjacent, thermodynamically stable, conserved short and long stem-and-loop structures (the 3'-SL), formed by the 3'-terminal approximately 100 nt. The nucleotide sequences within the 3'-SL are not well conserved among species. We examined the requirement for the 3'-SL in the context of dengue virus type 2 (DEN2) replication by mutagenesis of an infectious cDNA copy of a DEN2 genome. Genomic full-length RNA was transcribed in vitro and used to transfect monkey kidney cells. A substitution mutation, in which the 3'-terminal 93 nt constituting the wild-type (wt) DEN2 3'-SL sequence were replaced by the 96-nt sequence of the West Nile virus (WN) 3'-SL, was sublethal for virus replication. An analysis of the growth phenotypes of additional mutant viruses derived from RNAs containing DEN2-WN chimeric 3'-SL structures suggested that the wt DEN2 nucleotide sequence forming the bottom half of the long stem and loop in the 3'-SL was required for viability. One 7-bp substitution mutation in this domain resulted in a mutant virus that grew well in monkey kidney cells but was severely restricted in cultured mosquito cells. In contrast, transpositions of and/or substitutions in the wt DEN2 nucleotide sequence in the top half of the long stem and in the short stem and loop were relatively well tolerated, provided the stem-loop secondary structure was conserved.

A conserved internal hydrophobic domain mediates the stable membrane integration of the dengue virus capsid protein.

The mature flavivirus capsid protein (virion C) is commonly thought to be free in the cytoplasm of infected cells and to form a nucleocapsid-like complex with genomic RNA in mature virus particles. There is little sequence conservation among flavivirus virion C proteins, but they are similar in size (e.g., 99 amino acids [aa] for the dengue-4 [DEN4] C) and in bearing a net positive charge. In addition, we noted that C contained a conserved internal hydrophobic segment (spanning aa 45-65 in the DEN4 C). Results of in vivo expression and in vitro translation of wt and mutant forms of the DEN4 virion C demonstrated that the conserved internal hydrophobic segment in the DEN C functioned as a membrane anchor domain. Signal peptide function of this segment was also suggested by its requirement for the entry of C into membranes. Virion C was integrated in membranes in a "hairpin" conformation; positively charged segments amino- and carboxy-terminal to the hydrophobic signal-anchor segment were accessible to protease digestion in the "cytoplasm." The net positive charge in the amino-terminal extramembraneous portion of C (aa 1-44) was one determinant of the hairpin membrane orientation; a conserved positively charged residue within the hydrophobic segment (Arg-54 in the DEN4 C) was not.

Evidence that flavivirus NS1-NS2A cleavage is mediated by a membrane-bound host protease in the endoplasmic reticulum.

Previous deletion mutagenesis studies have shown that the flavivirus NS1-NS2A clevage requires the eight C-terminal residues of NS1, constituting the cleavage recognition sequence, and sequences in NS2A far downstream of the cleavage site. We now demonstrate that replacement of all of NS1 upstream of the cleavage recognition sequence with prM sequences still allows cleavage in vivo. Thus, other than the eight C-terminal residues, NS1 is dispensable for NS1-NS2A cleavage. However, deletion of the N-terminal signal sequence abrogated cleavage, suggesting that entry into the exocytic pathway is required. Cleavage in vivo was not blocked by brefeldin A, and cleavage could occur in vitro in the presence of dog pancreas microsomes, indicating that NS1-NS2A cleavage occurs in the endoplasmic reticulum. Four in-frame deletions in NS2A were cleavage defective in vitro, as were two mutants in which NS4A-NS4B sequences were substituted for NS2A, suggesting that most of NS2A is required. A series of substitution mutants were constructed in which all Asp, Cys, Glu, His, and Ser residues in NS2A were collectively replaced; all standard proteases require at least one of these residues in their active sites. No single mutant was cleavage defective, suggesting that NS2A is not a protease. Fractionation of the microsomes indicated that the lumenal contents were not required for NS1-NS2A cleavage. It seems most likely that NS1-NS2A cleavage is effected by a host membrane-bound endoplasmic reticulum-resident protease, quite possibly signalase, and that NS2A is required to present the cleavage recognition sequence in the correct conformation to the host enzyme for cleavage.

Correlation between detection of plasminogen cross-reactive antibodies and hemorrhage in dengue virus infection.

Although dengue fever (DF) is usually self-limited, some patients experience severe and prolonged illness characterized by capillary leakage, which may progress to hypovolemic shock (dengue hemorrhagic fever/dengue shock syndrome; DHF/DSS) with hemorrhage of unknown etiology. Development of antibodies potentially cross-reactive to plasminogen has been reported in a high percentage of Thai patients with DF and DHF/DSS. Correlation between detection of plasminogen cross-reactive antibodies and hemorrhage was evaluated in 88 Tahitian children with dengue virus type 3 infection who presented with (n = 59) or without (n = 29) hemorrhage. Plasminogen cross-reactive antibodies were found in acute and convalescent sera of 33 and 11 children, respectively (56% vs. 31%, P < .05), and closely paralleled antibodies to the cross-reactive site in dengue virus E protein. Antibodies were more frequent in children with secondary than primary infections (60% vs. 32%, P < .05). Plasminogen cross-reactive antibodies did not correlate with occurrence of DHF/DSS or thrombocytopenia. These results are consistent with the possibility that plasminogen cross-reactive antibodies play a role in the etiology of hemorrhage in dengue virus infection.

Processing of flavivirus structural glycoproteins: stable membrane insertion of premembrane requires the envelope signal peptide.

The flavivirus structural proteins capsid (C), premembrane (prM), and envelope (E) are cleaved in that order from the N-terminus of the polyprotein by the ER intralumenal enzyme signal peptidase. The prM-E and E-NS1 junctions contain hydrophobic domains with both transmembrane and signal function. These domains reside at the C-termini of prM and E, respectively, after cleavage. We studied the functions of the 37-amino-acid C-terminus of the dengue virus type 4 (DEN4) prM (amino acids 243-279 of the DEN4 polyprotein) in the processing of prM and E. Hydrophobicity in this domain is interrupted by a conserved Arg residue (Arg-264) within a short amphipathic segment. Hydrophobic amino acids upstream from Arg-264 (aa 243-263) were presumed to constitute the membrane anchor for prM (the "tm" segment). Previous results had suggested that sequences downstream from Arg-264 (aa 265-279) constitute the E signal peptide. RNA transcripts prepared from wild-type (wt) and deletion-mutant DEN4 cDNAs encoding the prM signal peptide, prM, E, and the N-terminus of the nonstructural glycoprotein, NS1, were translated in rabbit reticulocyte lysate in the presence of microsomes. Processing of wt prM and E in vitro appeared to mimic processing occurring during flavivirus infection. Analysis of mutants confirmed the localization of the E signal peptide within residues 265 to 279. However, deletions within either the E signal peptide or the tm segment resulted in a defect in both membrane insertion of prM and cleavage of the prM-E junction. Membrane anchoring of prM appeared to be a two-step process requiring function of both the tm segment and the E signal peptide, and fully efficient prM-E cleavage was also dependent upon the integrity of both hydrophobic domains. We propose a model for the processing of the flavivirus structural glycoproteins based on these results.

Development of cross-reactive antibodies to plasminogen during the immune response to dengue virus infection.

The four serotypes of dengue virus (a mosquito-borne flavivirus) cause an acute febrile illness (dengue fever) or a more prolonged illness with plasma leakage resulting in hypovolemia (dengue hemorrhagic fever). Hemorrhage may accompany either. Epidemiologic data suggest a role for dengue antibodies in pathogenesis. Computer analysis revealed a 20-residue region of similarity in amino acid sequence between the dengue type 4 envelope glycoprotein (E) and a family of clotting factors, including plasminogen, the prime mediator of fibrinolysis. By use of synthetic peptides in ELISA, E antibodies that potentially bind plasminogen were detected in 75% of 40 Thai patients acutely infected with dengue virus type 1, 2, 3, or 4. Plasminogen cross-reactivity of dengue antibodies was shown to be specific for the related sites in E and plasminogen. The dengue E sequence with similarity to plasminogen is largely conserved within the currently known flavivirus E sequences. However, 15 Thai patients hospitalized for illness caused by Japanese encephalitis virus (a flavivirus not associated with hemorrhage) did not develop plasminogen-cross-reactive antibodies, and this finding correlated with failure of Japanese encephalitis virus antibodies to bind to the plasminogen-cross-reactive site in E.

In vitro processing of dengue virus structural proteins: cleavage of the pre-membrane protein.

Processing of dengue virus structural proteins was assessed in vitro. RNA transcripts for cell-free translation were prepared from cloned DNA (dengue virus type 4, strain 814669 genome) encoding capsid, pre-membrane (prM), and the first 23 amino acids of envelope (E). Processing of a 33-kilodalton precursor polypeptide encoded by wild-type RNA transcripts occurred only in the presence of added microsomal membranes. Under these conditions, cleavage at the capsid-prM and prM-E sites and glycosylation of prM occurred in association with translocation. Amino acid sequence analysis confirmed that translation initiated at the predicted N terminus of the capsid and that capsid-prM cleavage occurred at the predicted site for the action of signal peptidase following a candidate signal sequence (hydrophobic residues 100 to 113) in the dengue virus precursor. Mutations were introduced into the dengue virus DNA template by site-directed mutagenesis, altering nucleotide sequences encoding the capsid and the candidate signal for prM. The phenotypes of the mutants were deduced by analysis of the products of cell-free translation of the respective RNA transcripts. The resulting observations confirmed that cleavage at the capsid-prM and prM-E sites is effected entirely by signal peptidase and that the candidate signal is required for translocation.

Mice immunized with recombinant vaccinia virus expressing dengue 4 virus structural proteins with or without nonstructural protein NS1 are protected against fatal dengue virus encephalitis.

We have constructed vaccinia virus recombinants expressing dengue virus proteins from cloned DNA for use in experimental immunoprophylaxis. A recombinant virus containing a 4.0-kilobase DNA sequence that codes for three structural proteins, capsid (C), premembrane (pre-M), and envelope (E), and for nonstructural proteins NS1 and NS2a produced authentic pre-M, E, and NS1 in infected CV-1 cells. Mice immunized with this recombinant were protected against an intracerebral injection of 100 50% lethal doses of dengue 4 virus. A recombinant containing only genes C, pre-M, and E also induced solid resistance to challenge. Deletion of the putative C-terminal hydrophobic anchor of the E glycoprotein did not result in secretion of E from recombinant-virus-infected cells. Recombinants expressing only the E protein preceded by its own predicted N-terminal hydrophobic signal or by the signal of influenza A virus hemagglutinin or by the N-terminal 71 amino acids of the G glycoprotein of respiratory syncytial virus produced glycosylated E protein products of expected molecular sizes. These vaccinia virus recombinants also protected mice.

The nucleotide sequence of dengue type 4 virus: analysis of genes coding for nonstructural proteins.

We recently cloned a full-length DNA copy of the dengue type 4 virus genome. Analysis of the 5' terminal nucleotide sequence suggested that the three-virion structural proteins are synthesized by proteolytic cleavage of a polyprotein precursor which is encoded in one open reading frame. We now present the remaining sequence of the dengue type 4 virus genome which codes for the nonstructural proteins. The entire genome, which is 10,644 nucleotides in length, contains one long open reading frame which codes for a single large polyprotein 3386 amino acids in length. Alignment of the dengue nonstructural protein sequence with that of other flaviviruses, including yellow fever and West Nile viruses, revealed that significant homology exists throughout the entire nonstructural region of the dengue genome and this allowed tentative assignment of individual nonstructural proteins in the following order: NS1, NS2a, NS2b, NS3, NS4a, NS4b, and NS5-COOH. Processing of the nonstructural proteins appears to involve two types of proteolytic cleavage: the first occurs after a long hydrophobic signal sequence and the second occurs at a junction between two basic amino acids and a small polar amino acid. A notable exception is the cleavage at the N-terminus of the dengue NS3 which may take place at the junction between Gln-Arg and Ser. Comparative analysis suggests that dengue NS3 and NS5 may be involved in enzymatic activities related to viral replication and/or transcription. Putative nonstructural proteins NS2a, NS2b, NS4a, and NS4b are extremely hydrophobic, suggesting that these proteins are most likely associated with cellular membranes.

Cloning full-length dengue type 4 viral DNA sequences: analysis of genes coding for structural proteins.

DNA sequences (approximately 11,000 nucleotides) representing the full-length genome of the dengue virus type 4 were cloned. The sequence of the first 2,429 nucleotides at the 5' terminus which includes the coding region for the structural proteins is presented. The virion structural proteins are encoded in one long open reading frame specifying a polyprotein precursor which is apparently proteolytically cleaved by a mechanism resembling that proposed for expression of structural proteins of other flaviviruses such as yellow fever (YF) and West Nile (WN) viruses. The N terminus for each of the dengue virus structural proteins was tentatively assigned by homology alignment to the corresponding sequence of YF or WN virus. Comparison of sequence homology of structural proteins suggests that dengue virus is more closely related to WN virus than to YF virus or Murray Valley encephalitis virus. Finally, analysis of the extreme 5'- and 3'-terminal nucleotides of the dengue virus genome revealed sequences that may be involved in transcription, replication, and packaging of viral RNA.

Glycosylation and surface expression of the influenza virus neuraminidase requires the N-terminal hydrophobic region.

A full-length double-stranded DNA copy of an influenza A virus N2 neuraminidase (NA) gene was cloned into the late region of pSV2330, a hybrid expression vector that includes pBR322 plasmid DNA sequences and the simian virus 40 early region and simian virus 40 late region promoters, splice sequences, and transcription termination sites. The protein encoded by the cloned wild-type NA gene was shown to be present in the cytoplasm of fixed cells and at the surface of "live" or unfixed cells by indirect immunofluorescence with N2 monoclonal antibodies. Immunoprecipitation and sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of [35S]methionine-labeled proteins from wild-type vector-infected cells with heterospecific N2 antibody showed that the product of the cloned NA DNA comigrated with glycosylated NA from influenza virus-infected cells, remained associated with internal membranes of cells fractionated into membrane and cytoplasmic fractions, and could form an immunoprecipitable dimer. NA enzymatic activity was detectable after simian virus 40 lysis of vector-infected cells. These properties of the product of the cloned wild-type gene were compared with those of the polypeptides produced by three deletion mutant NA DNAs that were also cloned into the late region of the pSV2330 vector. These mutants lacked 7 (dlk), 21 (dlI), or all 23 amino acids (dlZ) of the amino (N)-terminal variable hydrophobic region that anchors the mature wild-type NA tetrameric structure in the infected cell or influenza viral membrane. Comparison of the phenotypes of these mutants showed that this region in the NA molecule also includes sequences that control translocation of the nascent polypeptide into membrane organelles for glycosylation.

Influenza virus hemagglutinin containing an altered hydrophobic carboxy terminus accumulates intracellularly.

The influenza virus hemagglutinin (HA) glycoprotein synthesized from cloned DNA in a simian virus 40 vector is expressed on the surface of infected primate cells. Previously, it has been demonstrated that mutant HAs lacking the hydrophobic carboxy terminus fail to anchor on the cell surface and therefore are secreted extracellularly. During analysis of additional HA deletion mutants derived from an HA-simian virus 40 recombinant, we found a mutant with an altered hydrophobic carboxy terminus that exhibited another phenotype. This deletion mutant, dl-12, produced HA that was neither secreted nor expressed on the infected cell surface. The mutant HA was similar to the wild-type HA in apparent molecular weight and extent of glycosylation as assayed by endoglycosidase H sensitivity. The mutant HA localized near the perinuclear region of infected cells as indicated by an indirect immunofluorescence assay. Sequence analysis showed that a 5-base-pair deletion had occurred before the region encoding the hydrophobic carboxy terminus. Nevertheless, the physicochemical properties of the wild-type HA carboxy terminus were maintained in that the truncated HA carboxy terminus consisted of predominantly hydrophobic amino acids followed by several charged amino acids residues. This similarity in the carboxy terminus between the wild-type and mutant HAs may be responsible for the functional similarities observed. In spite of these similarities, the mutant HA failed to mature at the surface. These results suggest that the maturation of the mutant HA is blocked during a late stage in the transit to the cell surface.

Cell surface expression of the influenza virus hemagglutinin requires the hydrophobic carboxy-terminal sequences.

We investigated the requirements of the carboxyterminal sequence for surface expression of the influenza viral hemagglutinin (HA). Deletions in the cloned hemagglutinin gene were introduced at locations upstream from and spanning into the region that codes for the hydrophobic carboxyl terminus. Primate cells infected with recombinants of the deleted HA gene and an SV40 vector were negative for surface immunofluorescence and failed to adsorb erythrocytes. Polypeptide analysis showed that the mutant hemagglutinins lacking the normal hydrophobic carboxy-terminal sequences were secreted into the medium. These data provide evidence that these sequences of the influenza hemagglutinin are responsible for accumulation at the cell surface. During infection with each deletion mutant, a truncated HA polypeptide was found intracellularly. Both intracellular and extracellular HAs were glycosylated, since a third species representing the unglycosylated mutant hemagglutinin was detected in the presence of tunicamycin. Interestingly, the secreted and intracellular mutant HA polypeptides differ from the surface HA in their sensitivity to endoglycosidase H, indicating that an alteration of glycosylation has occurred.

Production and level of genetic stability of an influenza A virus temperature-sensitive mutant containing two genes with ts mutations.

Temperature-sensitive (ts) reassortant vaccine strains derived from the A/Udorn/72 ts-1A2 donor virus were not sufficiently stable genetically in humans. We therefore sought to produce a new, more stable donor virus. We had previously identified a stable ts virus with a ts P3 gene and in the current study identified another relatively stable single-lesion ts virus with a ts mutation in the NP gene. A new ts reassortant virus was constructed by mating these two single mutants and by isolating three reassortant progeny, clones 20, 53, and 55, that contained both a ts P3 and a ts NP gene. These reassortant progeny possessed a 37 to 38 degrees C shutoff temperature and were as restricted in their replication in hamster lungs as the A/Udorn/72 ts-1A2 virus. All isolates from the lungs and nasal turbinates of hamsters were temperature sensitive. An in vitro stress test was used to determine whether the new ts P3 ts NP reassortant virus would undergo loss of its ts phenotype after replication at semipermissive temperature. Clone 20 and 55 reassortants underwent progressive loss of their ts phenotype in vitro, although at a rate slightly less than that of the A/Udorn/72 ts-1A2 virus. The level of genetic stability after replication in vivo was assessed in cyclophosphamide-treated hamsters in which virus replication continued for up to 15 days. Again, both the A/Udorn/72 ts-1A2 and the new ts P3 ts NP reassortant clone 55 manifested a progressive loss of temperature sensitivity after 7 days of replication. Clone 55 virus lost temperature sensitivity significantly less rapidly than the A/Udorn/72 ts-1A2 virus. These results indicated that, although the new ts P3 ts NP reassortant virus was more stable than the A/Udorn/72 ts-1A2 virus, it nevertheless underwent progressive loss of temperature sensitivity after replication in vitro and in vivo. Therefore, it does not appear to be a satisfactory donor virus. This experience plus that gained earlier with other ts mutants of influenza A virus suggest that influenza A virus mutants that rely solely upon their ts phenotype for attenuation are unlikely to exhibit the phenotypic stability required of a vaccine virus. Other genetic techniques are needed to produce more stable influenza A virus strains.