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PubMed1986

High mutation rate of a spleen necrosis virus-based retrovirus vector.

Spleen necrosis virus (SNV) is an avian retrovirus that efficiently infects some mammalian cells (e.g., dog and rat cells). We constructed an SNV-based vector, which contains less than 1 kilobase (kb) of the retrovirus sequence, and a number of derivatives containing selectable markers. We obtained high-titer virus stocks, over 10(6) transforming units per ml, with a vector whose genomic RNA consists of 1,850 bases (full-length SNV RNA is 7.7 kb). We also studied two vectors that both carry two genes which should be expressed from a single promoter, one gene from unspliced mRNA and the other gene from spliced mRNA. In one vector, both genes were efficiently expressed as expected. However, in the other vector, expression of the gene 3' to the splice acceptor was inhibited. When we selected for expression of the 3' gene is this latter case, we found that the resistant cells contained mutant proviruses in which the 3' gene could be expressed. Furthermore, we found that mutations were generated during a single round of virus replication (provirus to provirus) at a rate of approximately 0.5% mutations per cycle.

Animals↗

PubMed2003

Diffuse endothelial dysfunction is common to ANCA associated systemic vasculitis and polyarteritis nodosa.

BACKGROUND: Excess cardiovascular mortality complicates systemic rheumatic disease, suggesting an accelerated atheromatous process, which it has been proposed relates to the vascular inflammation common in such diseases. Impaired endothelium dependent vasodilatation is an early marker of atheromatous disease. It has previously been shown that such endothelial cell dysfunction (ECD) occurring in the brachial artery can complicate primary systemic necrotising vasculitis (SNV). OBJECTIVE: To determine if ECD occurs in a wider spectrum of primary SNV, if it is restricted to the major arteries, and whether vasculitis subgroup, ANCA status, or renal involvement influenced the endothelial responses. METHODS: Fifty four patients attending the Birmingham vasculitis clinic, including patients with a range of ANCA and non-ANCA associated primary vasculitides, and a group of age matched controls were recruited. The length of patient follow up and disease activity was variable. Disease activity, damage scores, and cardiovascular risk factors were recorded before assessment of flow mediated brachial artery vasodilatation by high resolution ultrasound. Dermal microvascular responses to acetylcholine were also measured in 32 patients and 21 controls by laser Doppler flowmetry. RESULTS: ECD was demonstrated in all primary SNV subgroups of patients with ANCA associated vasculitis and in polyarteritis nodosa, compared with controls. Significant impairment occurred in both vascular beds, regardless of vessel size targeted in the inflammatory vasculitis, ANCA association and titre, or renal involvement. CONCLUSIONS: Diffuse endothelial dysfunction, a predictor of atherosclerotic disease, is found extensively in primary systemic vasculitis. Involvement of different vascular beds is independent of target vessel size or ANCA association, and is unrelated to local disease expression. It is suggested that this results from a systemic response that may be a consequence of primary vasculitis, but is distinct from the local inflammatory vasculitic process.

Adult↗

PubMed2004

Cloning and characterization of deer mouse (Peromyscus maniculatus) cytokine and chemokine cDNAs.

BACKGROUND: Sin Nombre virus (SNV) establishes a persistent infection in the deer mouse, Peromyscus maniculatus. A strong antibody response occurs in response to SNV infection, but the role of the innate immune response is unclear. To address this issue, we have initiated an effort to identify and characterize deer mouse cytokine and chemokine genes. Such cytokines and chemokines are involved in various aspects of immunity, including the transition from innate to adaptive responses, type I and type II responses, recruitment of leukocytes to sites of infection, and production of mature cells from bone marrow progenitors. RESULTS: We established a colony of SNV antibody-negative deer mice and cloned 11 cytokine and chemokine partial cDNA sequences using directed PCR. Most of the deer mouse sequences were highly conserved with orthologous sequences from other rodent species and functional domains were identified in each putative polypeptide. CONCLUSIONS: The availability of these sequences will allow the examination of the role of these cytokines in deer mouse responses to infection with Sin Nombre virus.

Amino Acid Sequence↗

PubMed2004

Generation of competent bone marrow-derived antigen presenting cells from the deer mouse (Peromyscus maniculatus).

BACKGROUND: Human infections with Sin Nombre virus (SNV) and related New World hantaviruses often lead to hantavirus cardiopulmonary syndrome (HCPS), a sometimes fatal illness. Lungs of patients who die from HCPS exhibit cytokine-producing mononuclear infiltrates and pronounced pulmonary inflammation. Deer mice (Peromyscus maniculatus) are the principal natural hosts of SNV, in which the virus establishes life-long persistence without conspicuous pathology. Little is known about the mechanisms SNV employs to evade the immune response of deer mice, and experimental examination of this question has been difficult because of a lack of methodologies for examining such responses during infection. One such deficiency is our inability to characterize T cell responses because susceptible syngeneic deer mice are not available. RESULTS: To solve this problem, we have developed an in vitro method of expanding and generating competent antigen presenting cells (APC) from deer mouse bone marrow using commercially-available house mouse (Mus musculus) granulocyte-macrophage colony stimulating factor. These cells are capable of processing and presenting soluble protein to antigen-specific autologous helper T cells in vitro. Inclusion of antigen-specific deer mouse antibody augments T cell stimulation, presumably through Fc receptor-mediated endocytosis. CONCLUSIONS: The use of these APC has allowed us to dramatically expand deer mouse helper T cells in culture and should permit extensive characterization of T cell epitopes. Considering the evolutionary divergence between deer mice and house mice, it is probable that this method will be useful to other investigators using unconventional models of rodent-borne diseases.

Animals↗

PubMed2006

Profiling helper T cell subset gene expression in deer mice.

BACKGROUND: Deer mice (Peromyscus maniculatus) are the most common mammals in North America and are reservoirs for several zoonotic agents, including Sin Nombre virus (SNV), the principal etiologic agent of hantavirus cardiopulmonary syndrome (HCPS) in North America. Unlike human HCPS patients, SNV-infected deer mice show no overt pathological symptoms, despite the presence of virus in the lungs. A neutralizing IgG antibody response occurs, but the virus establishes a persistent infection. Limitations of detailed analysis of deer mouse immune responses to SNV are the lack of reagents and methods for evaluating such responses. RESULTS: We developed real-time PCR-based detection assays for several immune-related transcription factor and cytokine genes from deer mice that permit the profiling of CD4+ helper T cells, including markers of Th1 cells (T-bet, STAT4, IFNgamma, TNF, LT), Th2 cells (GATA-3, STAT6, IL-4, IL-5) and regulatory T cells (Fox-p3, IL-10, TGFbeta1). These assays compare the expression of in vitro antigen-stimulated and unstimulated T cells from individual deer mice. CONCLUSION: We developed molecular methods for profiling immune gene expression in deer mice, including a multiplexed real-time PCR assay for assessing expression of several cytokine and transcription factor genes. These assays should be useful for characterizing the immune responses of experimentally- and naturally-infected deer mice.

Animals↗

PubMed2026

Molecular residual disease assessment in colorectal and bladder cancer by somatic structural variant analysis of cell-free DNA whole-genome sequencing data.

BACKGROUND: Whole-genome sequencing (WGS)-based methods for circulating tumor DNA (ctDNA) detection typically rely on tumor-informed identification of somatic single nucleotide variants (SNVs). Somatic structural variants (SVs) are another type of cancer-specific genomic alteration, which owing to their larger genomic footprint and unique breakpoint junctions, are easier to distinguish from sequencing noise than SNVs. They are, however, rarely used for ctDNA detection because of (1) artifacts from WGS procedures that SV callers may falsely interpret as genuine SVs. This makes it difficult to establish high-confidence SV catalogos from short-read tumor WGS and can cause false-positive ctDNA detections. (2) Lack of robust strategies to quantify SV-supporting reads in plasma WGS. To address these barriers and enable integration of SV biomarkers into WGS-based ctDNA detection, we present a bioinformatic framework for algorithmic curation of somatic SV calls from fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tumors, coupled with a novel approach for sensitive, accurate mapping and quantification of SV breakpoint-supporting reads in plasma WGS. METHODS: Tumor, normal and plasma WGS data from 144 patients with stage III colorectal cancer was used to establish the bioinformatic framework. This included ~30x WGS data from 1564 serially collected plasma samples. The framework was validated using tumor/normal/plasma WGS data from 32 patients with muscle-invasive bladder cancer. SV-based ctDNA detection was benchmarked against previously published SNV-based ctDNA results for the same samples. RESULTS: After curation of SV calls and quantification in plasma WGS, our SV-based approach enabled robust ctDNA detection with overall specificity exceeding 99% in plasma samples. Furthermore, we observed strong concordance (Pearson’s r > 0.93, p < 2.2 × 10− 16) between ctDNA-positive samples identified by our SV-based method and previous SNV-based analyses, validating the reliability of our approach. Finally, we demonstrated application of the method in an independent bladder cancer cohort, highlighting its generalizability and potential clinical use. CONCLUSIONS: We provide a bioinformatic framework that establishes somatic SVs as ultra-specific biomarkers for WGS-based, tumor-informed ctDNA detection. The approach delivers specific detection even when the SV catalogos are established from FFPE samples. The SV framework can stand alone or enhance SNV-based analysis pipelines.

Humans↗

PubMed2026

Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.

BACKGROUND: The gut microbiome possesses substantial genetic diversity that supports microbial adaptation, but the genomic variation patterns across its prokaryotic and viral populations remain incompletely characterized. RESULTS: Through integrated metagenomic and metatranscriptomic analysis of ten indigenous chicken breeds from China, we recovered 1527 representative prokaryotic MAGs, 37,555 representative DNA viral contigs, and 1867 representative RNA viral contigs (primarily comprising Bacillota/Bacteroidota, Uroviricota, and Lenarviricota/Pisuviricota, respectively). By integrating complementary short-read and long-read metagenomics with metatranscriptomics, we identified structural variants (SVs) and single-nucleotide variants (SNVs) in these cross-kingdom genomes. Positive SV-SNV density correlations occurred consistently across all microbial groups, indicating coordinated mutational processes. DNA viruses exhibited the highest variant prevalence (86.9% SNVs, 47.7% SVs), with temperate phages accumulating significantly more variants than virulent phages. Functionally, prokaryotic variants accumulated in carbohydrate metabolism and amino acid metabolism, while viral variants demonstrated broad metabolic hijacking. Horizontal gene transfer (HGT) was characterized by a strong virus-associated signature (69.40% of 536 events) and marked by an asymmetric pattern, with phage-to-bacteria (P-to-B) flow alone constituting 37.50% of all events. Random forest analysis revealed a strong bidirectional predictive relationship between SV and SNV densities across prokaryotic, DNA viral, and RNA viral populations, suggesting coupled genomic instability. Niche breadth emerged as a major driver of SNVs across kingdoms and was positively correlated with variant density. In prokaryotes, HGT events significantly shaped variant patterns. For viruses, genomic GC content was an important factor and consistently showed a negative correlation with SNV density in both DNA and RNA viruses. CONCLUSIONS: These findings demonstrate that coordinated mutational processes and kingdom-specific intrinsic factors drive genomic variation, with viruses serving as key genetic exchange vectors in chicken gut ecosystems. Video Abstract.

Animals↗

PubMed2004

Sensory neuropathy in vasculitis: a clinical, pathologic, and electrophysiologic study.

BACKGROUND: Vasculitis is not usually considered as a cause of symmetric sensory neuropathy. OBJECTIVE AND METHODS: To present the clinical, pathologic, and electrophysiologic features of 17 (16%) cases of sensory neuropathy in vasculitis (SNV) among 106 cases with histologically proven vasculitic neuropathy that were collected over the last 30 years. RESULTS: In 41% of cases, SNV was found as systemic vasculitic neuropathy in association with primary vasculitic disease. The most common clinical presentation was symmetric polyneuropathy, seen in 53% of cases. The most common nerve conduction pattern was diffuse neuropathy pattern of axonal degeneration. Sural nerve biopsy was diagnostic in 88% of cases. In two cases, muscle biopsy was necessary for the definite diagnosis of vasculitis. Non-systemic SNV is usually benign. Of 11 patients followed for longer than 2 years, none developed motor weakness due to neuropathy. CONCLUSION: Sensory neuropathy, regardless of symmetry, can be due to vasculitis.

Adult↗

PubMed2003

From vasoactive intestinal peptide (VIP) through activity-dependent neuroprotective protein (ADNP) to NAP: a view of neuroprotection and cell division.

Accelerated neuronal death brings about cognitive as well as motor and other dysfunctions. A major neuropeptide, vasoactive intestinal peptide (VIP), has been shown to be neuroprotective. However, VIP-based drug design is hampered by the instability of the peptide and its limited bioavailability. Two independent approaches were thus taken to exploit VIP as a lead drug candidate: (1) Potent neuroprotective lipophilic analogs of VIP were synthesized, e.g. [stearyl-norleucine-17] VIP (SNV); and (2) potent neuroprotective peptide derivatives were identified that mimic the activity of VIP-responsive neuroprotective glial proteins. VIP provides neuronal defense by inducing the synthesis and secretion of neuroprotective proteins from astrocytes; activity-dependent neuroprotective protein (ADNP) was discovered as such glial cell mediator of VIP- and SNV-induced neuroprotection. In subsequent studies, an eight-amino-acid peptide, NAP, was identified as the smallest active element of ADNP exhibiting potent neuroprotective activities. This paper summarizes the biological effects of SNV and NAP and further reports advances in NAP studies toward clinical development. An original finding described here shows that NAP, while protecting neurons, demonstrated no apparent effect on cell division in a multiplicity of cell lines, strengthening the notion that NAP is a specific neuroprotective drug candidate.

Animals↗

PubMed2003

Reticuloendotheliosis viruses and derived vectors for human gene therapy.

The reticuloendotheliosis viruses (REV) spleen necrosis virus (SNV) and reticuloendotheliosis virus strain-A (REV-A) are amphotropic retroviruses which infect a large variety of cells of avian and some mammalian species. They normally do not infect primate or rodent cells. However, they efficiently infect and integrate their genome into that of human cells when they are pseudotyped with the envelope protein of other mammalian retroviruses or the G protein of vesicular stomatitis virus (VSV) or rabies viruses (RV). Moreover, SNV-derived retroviral vectors, which display single chain antibodies or other targeting ligands on the viral surface enable cell-type-specific gene delivery into various human cells. My laboratory has developed genetically engineered REV vectors, which are capable of infecting non-dividing cells such as quiescent human T-cells, primary monocyte-derived macrophages, and mature neurons. Thus, REV-derived vectors appear to be very interesting candidates for the further development of vectors for human gene therapy. This article reviews the replication of REVs and vectors derived from REV-A and SNV for gene transfer into human cells.

Animals↗

PubMedDate not supplied

Genetic diversity and distribution of Peromyscus-borne hantaviruses in North America.

The 1993 outbreak of hantavirus pulmonary syndrome (HPS) in the southwestern United States was associated with Sin Nombre virus, a rodent-borne hantavirus; The virus' primary reservoir is the deer mouse (Peromyscus maniculatus). Hantavirus-infected rodents were identified in various regions of North America. An extensive nucleotide sequence database of an 139 bp fragment amplified from virus M genomic segments was generated. Phylogenetic analysis confirmed that SNV-like hantaviruses are widely distributed in Peromyscus species rodents throughout North America. Classic SNV is the major cause of HPS in North America, but other Peromyscine-borne hantaviruses, e.g., New York and Monongahela viruses, are also associated with HPS cases. Although genetically diverse, SNV-like viruses have slowly coevolved with their rodent hosts. We show that the genetic relationships of hantaviruses in the Americas are complex, most likely as a result of the rapid radiation and speciation of New World sigmodontine rodents and occasional virus-host switching events.

Animals↗

PubMedDate not supplied

Remote sensing and geographic information systems: charting Sin Nombre virus infections in deer mice.

We tested environmental data from remote sensing and geographic information system maps as indicators of Sin Nombre virus (SNV) infections in deer mouse (Peromyscus maniculatus) populations in the Walker River Basin, Nevada and California. We determined by serologic testing the presence of SNV infections in deer mice from 144 field sites. We used remote sensing and geographic information systems data to characterize the vegetation type and density, elevation, slope, and hydrologic features of each site. The data retroactively predicted infection status of deer mice with up to 80% accuracy. If models of SNV temporal dynamics can be integrated with baseline spatial models, human risk for infection may be assessed with reasonable accuracy.

Animals↗

PubMed2004

Neutralizing antibodies and Sin Nombre virus RNA after recovery from hantavirus cardiopulmonary syndrome.

Patients who later have a mild course of hantavirus cardiopulmonary syndrome (HCPS) are more likely to exhibit a high titer of neutralizing antibodies against Sin Nombre virus (SNV), the etiologic agent of HCPS, at the time of hospital admission. Because administering plasma from patients who have recovered from HCPS to those in the early stages of disease may be an advantageous form of passive immunotherapy, we examined the neutralizing antibody titers of 21 patients who had recovered from SNV infection. Even 1,000 days after admission to the hospital, 6 of 10 patients had titers of 800 or higher, with one sample retaining a titer of 3,200 after more than 1,400 days. None of the convalescent-phase serum samples contained detectable viral RNA. These results confirm that patients retain high titers of neutralizing antibodies long after recovery from SNV infection.

Adolescent↗

PubMed2000

[Hantavirus pulmonary syndrome in southern Argentina].

Andes virus was identified in 1995 as the etiologic agent of Hantavirus Pulmonary Syndrome (HPS) in Southern Argentina. We describe herein the main clinical characteristics of 25 HPS confirmed cases acquired in this area between 1993 and September 1999. The mean age was 34 years (range 11-70), with 72% males. Clinical characteristics were similar to those previously reported for Sin Nombre virus (SNV) cases. However, in this group of patients we also observed conjuntival injection in 10/25 (42%), facial flushing in 8/25 (33%), pharyngeal congestion in 7/25 (29%) and petechiae in 3/25 (12%). On the other hand, BUN was increased in 83% of cases (mean 0.77 g/l range 0.31-2.01). Mean serum creatinine concentration was 26.8 mg/l (range: 8.1-110 mg/l) with serum creatinine being higher than 20 mg/l in 8/15 patients (53%). Urinalysis was abnormal in 12/12 cases and was characterized by presence of proteins, red blood cells and granular casts. Aminotransferases were increased in 90% of cases with levels 5-10 times over normal values in 50% of cases. Serum creatine kinase concentration was elevated in 11/14 cases. Two patients required hemodialysis. Case fatality rate was 44% (11/25) and 10 of these cases died among the first 10 days of illness. Mononuclear myocarditis was observed in two cases, a finding that has not been reported for SNV cases. During the 1996 HPS outbreak in Southern Argentina due to Andes virus, there were epidemiological and molecular evidences of person-to-person transmission, a feature not previously shown for other members of the hantavirus genus. These data would also be indicative of some distinctive clinical characteristics of HPS caused by Andes virus, with more frequent renal involvement than in SNV cases.

Adolescent↗

PubMedDate not supplied

A serological survey of rural dogs and cats on the southwestern Canadian prairie for zoonotic pathogens.

A survey for antibodies against agents of plague, tularemia, and Rocky Mountain spotted fever (RMSF), and against Sin Nombre hantavirus (SNV), Bartonella henselae and B. clarridgeiae was conducted in the summer of 1995 using serum from rural dogs and cats living in the vicinity of four public parks in southeastern Alberta and southwestern Saskatchewan. Antibodies to all pathogens were detected in all survey areas. Overall prevalence rates were 0.075 for Yersinia pestis, 0.089 for Francisella tularensis, 0.025 for Rickettsia rickettsii (dogs only), and 0.029, 0.178 and 0.186 for SNV, B. henselae and B. clarridgeiae, respectively (cats only). This serological survey of rural dogs and cats was more sensitive and efficient than previous surveys based on collection and culture of rodents and ectoparasites. All six pathogens appear endemic to the region. Surveillance for plague, tularemia, RMSF and SNV, and management of associated public risks should be done in endemic regions.

Animals↗

PubMed1992

Effect of electric charged molecules on Sindbis virus hemagglutination and hemolysis.

The role of electrostatic interactions in the attachment and fusion at acidic pH of Sindbis virus (SNV) with goose erythrocytes was studied, investigating the effect of several anionic and cationic polyelectrolytes on SNV hemagglutination and hemolysis. In order to establish the target of active drugs, the compounds were incubated either with the virus particles or with the erythrocytes. Dextran sulfate was the only compound able to inhibit the attachment of SNV to the erythrocytes. Fusion of virus with red cells was reduced dose-dependently by the polyanions dextran sulfate, mucin and polygalacturonic acid. On the contrary two polycations, polylysine and polybrene, enhanced viral hemolytic activity. However the effect of polyions is not exclusively related to the electric charge since ineffective molecules were found in both classes of compounds.

Animals↗

PubMed1995

Prognostic factors in systemic necrotizing vasculitis of the polyarteritis nodosa group--a review of 45 cases.

OBJECTIVE: To evaluate the prognostic importance for mortality of age, fever, hypertension, and involvement of renal, cardiac, neural, pulmonary, gastrointestinal and cutaneous systems as well as elevated transaminases, thrombocytosis, leukocytosis, anemia, smoking status, comorbid diseases and disease severity, in 45 patients with systemic necrotizing vasculitis (SNV) identified by histological, radiological, and clinical criteria. METHODS: Kaplan-Meier nonparametric survival functions and Cox proportional hazards regression models were used. RESULTS: Twenty-four deaths were observed during the 5 year mean followup period. Five year survival was 58%. Comorbidity and severity of involvement were not predictive of mortality. Multivariable survival analysis showed that cardiac or renal involvement was associated with a relative risk of dying of 2.91 (95% CI: 1.25, 6.77). Elevated serum transaminase demonstrated a trend to having a protective effect [relative risk of 0.14 (95% CI: 0.02, 1.07)]. No other variable was an independent predictor of fatality. No cohort effect could be documented following the introduction of cytotoxic drugs in the treatment of SNV. CONCLUSION: SNV remains associated with a high mortality due largely to renal or cardiac involvement.

Adult↗

PubMed1998

[The effects of aging on the volume of human vestibular nuclei].

Elderly persons often have balance disorders, with dizziness that sometimes leads to falls. Changes in the peripheral vestibular system with age, with loss of the hair cells and neurons of Scarpa's nucleus, have been studied for years. However, the changes in the vestibular nuclear complex with age have not been examined. We studied paraffin-embedded brainstems from nine persons of different ages in order to analyze possible changes with age. No abnormalities were observed in the volume or length of the vestibular nuclei, except for a decrease in both dimensions in the superior vestibular nucleus (SNV). All the main vestibular nuclei showed an increase in lipofuscin content with age that seemed to be less marked in the SNV. The low lipofuscin concentration in the SNV could be related with the conservation of vestibular reflexes, the center of which seems to be the SVN, in elderly persons.

Adult↗