Understanding watershed‐scale variation in juvenile salmonid survival and growth can provide insights into factors influencing demographics and can help target restoration and mitigation efforts for ...imperiled fish populations. We assessed growth, movement, and apparent overwinter survival of individually tagged juvenile coho salmon Oncorhynchus kisutch in a coastal Oregon watershed from June 2002 to June 2003 and related growth and survival parameters to stream characteristics. Fall body size of juvenile coho salmon was a good predictor of smolt size and survival, but smolt size was also influenced by overwintering location. This was due to strong spatial patterns in winter growth rates associated with residency and movement into a small intermittent tributary. Though nearly dry in midsummer, this stream supported high densities of spawning coho salmon in the fall, and juveniles rearing there exhibited relatively high growth rates and emigrated as larger smolts. Improved winter growth and survival of juvenile coho salmon utilizing tributary habitats underscore the importance of maintaining connectivity between seasonal habitats and providing a diversity of sheltering and foraging opportunities, particularly where main‐stem habitats have been simplified by human land uses.
The genome of the sheep visna lentivirus contains an open reading frame, Q, which has a coding potential of 230 amino acid residues. This paper reports the identification and the subcellular ...localization of the Q ORF-encoded protein detected in lysates of visna virus-infected sheep choroid plexus cells. Sera from sheep either experimentally or naturally infected with visna virus reacted with the bacterially synthesized Q protein indicating that the in vivo expressed Q product is immunogenic. Antibodies raised against a synthetic N-terminal peptide, reacted with either the bacterial Q or the in vitro translated Q protein as well as with the Q protein expressed during cellular infection. This 29 kDa protein is detectable late in the lytic viral cycle, i.e., 72 hr postinfection, and this expression correlates with the late transcription of its 4.8-kb mRNA. These results provide evidence for the first time that the Q ORF is a late gene of visna virus and that the Q protein is located in the cytosol compartment, without evidence of accumulation at the cell membrane, or in cell-free virion particles.
The lentivirus caprine arthritis-encephalitis virus (CAEV) is closely related by nucleotide sequence homology to visna virus and other sheep lentiviruses and shows less similarity to the other animal ...and human lentiviruses. The genomic organization of CAEV is very similar to that of visna virus and the South African ovine maedi visna virus (SA-OMVV) as well as to those of other primate lentiviruses. The CAEV genome includes the small open reading frames (ORF) between pol and env which are the hallmarks of the lentivirus genomes. The most striking difference in the organization of CAEV is in the env gene. The Env polyproteins of visna virus and the related SA-OMVV contain 20 amino acids between the translational start and the signal peptide not present in CAEV. In addition to nucleotide sequence analysis, the transcriptional products of CAEV were determined by Northern analysis. The viral mRNA present in cells transfected with the infectious clone reveal a pattern characteristic of the mRNAs observed in other lentivirus infections. The putative tat ORF of CAEV could be identified by genomic location and amino acid homology to the visna virus tat gene. However, the CAEV rev gene could not be identified in a similar fashion. Thus, to determine the location of the rev ORF cDNA clones were obtained by PCR amplification of the mRNA from infected cells. To determine if a Rev response element was contained in the CAEV genome, secondary structural analysis of the viral RNA was performed. A stable stem loop structure which is similar in location, stability, and configuration to that determined for the Rev response element of HIV was found.
We have determined the sequence of the human immunodeficiency virus type 1 (HIV-1) vif genes from a cohort of 42 long-term nonprogressors (LTNP) and compared these sequences to those of 8 late ...progressors. The coding potential of the vif open reading frame directly derived by nested PCR from uncultured peripheral blood mononuclear cell DNA was conserved in all 50 individuals. The nucleotide distances between vif sequences were not significantly different between LTNP and late progressors, indicating similar selections of viruses within both types of long-term HIV-1-infected subjects. However, a statistically significant correlation between an amino acid signature at position 132 of Vif and the viral load was found within LTNP. Namely, amino acid Ser was associated with low viral load and amino acid Arg with high viral load. This signature was also observed when LTNP with low viral load were compared to progressors. The Ser132 signature was introduced in place of Arg132 present in the HIV-1 YU-2 Vif prototype into chimeric viruses to assess the impact of Vif signature on the virus. While the replication properties in the SupT1 cell line were unmodified, the mutagenized virus revealed a fivefold decreased replication in activated PBMC, suggesting a possible role of this Vif signature for viral production in vivo.
Soon after infection of ovine cell cultures, visna virus expression is first indicated by the accumulation of two multi-spliced transcripts of 1.2 and 1.6 kb that at present we have renamed 1.4 and ...1.7 kb according to their exact length. The early 1.4-kb mRNA encodes for a protein which increases the level of transcripts directed from visna virus long terminal repeat (trans-activation). This trans-activating protein was previously called VEP1 and at present is renamed as the product of the rev gene according to significant amino acid sequence homologies between this protein and the rev gene products of simian immunodeficiency virus and human immunodeficiency virus type 2. In this study, the 1.7-kb mRNA was cloned, sequenced, and in vitro translated. It is 1491 nucleotides long, contains two short open reading frames, (orfs), tat (previously orf S) and rev which is the bipartite trans-acting gene specific for the early 1.4-kb mRNA. The tat gene of visna virus encodes for a protein of 11 kDa which in transient expression assays has a positive transacting effect on transcription as the rev gene product does.
The mechanisms of HIV-triggered immunodeficiency were examined by determining the segregation of R5 and X4 HIV-1 variants into memory T cell subsets expressing differentially a homing receptor, ...CD62L-selectin, in human lymphoid tissue.
Subpopulations of CD3 and intracellular p24 gag-positive cells in human lymphoid tissue infected ex vivo with X4 HIV-1 variant NL4-3 and R5 HIV-1 variant AD8 were analysed for expression of the T cell memory markers CD45RO and CD45RA, the T cell homing receptor for lymphoid tissue CD62L, and the HIV-1 coreceptors CCR5 and CXCR4.
Memory CD4 T cells were the predominant targets for productive infection of lymphoid tissue ex vivo with both R5 and X4 HIV-1. R5 HIV-1 predominantly infected CD62L-negative memory T cells, which selectively express CCR5. In contrast, X4 HIV-1 variants predominantly infected CD62L+ memory T cells, although CXCR4 coreceptor was equally expressed by memory T cells of both CD62L-positive and CD62L-negative subsets. A high proportion of X4 HIV-1, but not of R5 HIV-1, productively infected T cells, displayed a CD45RA+CD45RO+ phenotype.
The selective expression of the CCR5 coreceptor by CD62L-negative terminally differentiated memory T cells correlates with the preferential productive infection of these cells with the R5 HIV-1 variant. The predominance of X4 HIV-1 variants in less-differentiated memory T cells may be related to their recent activation state, as suggested by the coexpression of both CD45RA and CD45RO molecules on their surface. Differential homing of CD62L-positive and CD62L-negative cells suggests different routes of dissemination of X4 and R5 viruses.
Visna lentivirus persists in sheep under a restricted form. Following induction events not yet defined at the molecular level, visna virus is activated to replicate productively through a short lytic ...cycle, the usual expression of visna virus in tissue culture. In an attempt to understand the relationship between latency and lytic replication, we characterized the transcripts of visna virus during its lytic growth by Northern blotting and S1 mapping analyses. The viral transcription pattern is relatively complex with a sequential expression in two steps: (i) an early (24 hr postinfection) expression of two multispliced mRNAs of 1.6 and 1.2 kb, which contain sequences from the 5' end of the genome, sequences from the central part of the genome from the 3' end of pol to the 5' end of env, and 3'-terminal sequences, and (ii) a late (72 hr postinfection) expression of both small mRNAs plus that of four large mRNAs of 9.4, 4.8, 4.3, and 3.7 kb. Except for the 9.4-kb RNA which is the genomic transcript, the three other large transcripts arise by a single splicing event joining 5'-terminal sequences to sequences located at positions 3' to the pol gene. This two-step expression of early and late genes of visna virus represents a novel important feature of the replicative cycle of lentiviruses.
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