Characteristics of a cholera phage.
The basic physical, chemical and physiological properties of a group II cholera phage belonging to Mukerjee's classification has been described.
Adsorption↗
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Prime time for Bacillus megaterium.
It is evident that B. megaterium is an intriguing organism because of its biochemical versatility, its wide distribution ecologically, its ability to undergo sporulation, and its usefulness as an industrial production strain and expression host. With the progress in genetics and the availability of molecular tools such as new transposons, vectors and efficient transformation, an understanding of some of the organization and regulation of many genes is increasing rapidly. Such recent discoveries as the ability of oxetanocin to combat some medically significant, recalcitrant viruses further demonstrates that there is much to be learned and much to benefit from continued study of B. megaterium.
Bacillus megaterium↗
[Physicochemical characteristics of cyanophages and their components].
The paper presents the results of the study on the physicochemical properties of DNA, polypeptide composition of proteins, as well as features of quaternary structure of virions of cyanophages LPP-IA, LPP-3, LPP-3A, A-1, A-2, and N-2 lysing filamentous and heterocyst cyanobacteria. Such characteristics may be used as hierarchially important signs in compiling the classificational scheme of cyanophages.
Chemical Phenomena↗
HCV and HGV in B-cell non-Hodgkin's lymphoma.
BACKGROUND/AIMS: A causative role of hepatitis C virus infection (HCV) has been discussed in the pathogenesis of mixed cryoglobulinaemia and in B-cell non-Hodgkin's lymphoma. No data are available concerning the newly discovered hepatitis G virus (HGV) and extrahepatic manifestations such as haematological malignancies. But, HCV and HGV most probably belong to the same family of Flavivirus. Consequently, we looked for the prevalence of HCV, HGV and cryoglobulins in patients with B-cell non-Hodgkin's lymphoma. METHODS: Serum samples from 69 patients with non-Hodgkin's lymphoma were studied. Diagnosis of non-Hodgkin's lymphoma was established according to the Kiel classification. Active HCV- and HGV infections were investigated using polymerase chain reaction for detection of viral RNA. Cryoglobulins were detected from serum and monoclonal immunoglobulin components were analysed with immunofixation electrophoresis. In addition, we assessed the clinical course of HCV- and HGV-infected patients under chemotherapy. RESULTS: Three of 69 (4.3%) patients with B-cell non-Hodgkin's lymphoma were HCV-infected and nine non-Hodgkin's lymphoma patients (13.0%) were positive for hepatitis G virus RNA. All HGV infected patients were suffering from low-grade non-Hodgkin's lymphoma. No HGV-infected patient was co-infected by HCV and neither HCV- nor HGV-infected patients showed clinical signs of chronic liver disease before, during or after chemotherapy. Serum samples from all patients were devoid of cryoglobulins. CONCLUSIONS: HCV seems to have no significance for the pathogenesis of non-Hodgkin's lymphoma in Germany. The increased prevalence of hepatitis G (16.3%) in patients with low-grade non-Hodgkin's lymphoma could suggest a pathological consequence of HGV infection outside of the liver. Evidence of clinically relevant hepatic disease in HGV infected patients was not obtained. Further, chemotherapy does not seem to affect the subsequent clinical course of HGV infection.
Adult↗
AIDS-related Kaposi's sarcoma: prospective validation of the AIDS Clinical Trials Group staging classification. AIDS Clinical Trials Group Oncology Committee.
PURPOSE: To prospectively validate the AIDS Clinical Trials Group (ACTG) staging classification for AIDS-associated Kaposi's sarcoma (KS). PATIENTS AND METHODS: Two hundred ninety-four consecutive patients enrolled in eight ACTG therapeutic trials for AIDS-associated KS were staged prospectively according to tumor extent (T), severity of immunosuppression (I), and other systemic human immunodeficiency virus type 1 (HIV-1)-associated illness (S) and were observed for survival. Patients were classified as good risk (subscript 0) or poor risk (subscript 1) for each variable according to published ACTG criteria. Univariate and multivariate analyses were used to evaluate the associations between TIS variables and survival; additional analyses were conducted to improve the predictive value of the staging system. RESULTS: Survival was significantly shorter for patients in the poor-risk category for each of the TIS variables. Respective median survivals for patients in the good- and poor-risk categories were 27 and 15 months for T (P < .001); 40 and 13 months for I (P < .001) when I0 included CD4 counts > or = 200/microL and 22 and 16 months for S (P = .04). Multivariate analysis indicated that severity of immunosuppression gave the most predictive information but also showed that T provided significant additional predictive information in patients whose immune function was least impaired. Refined Cox models using a CD4 count of 150/microL rather than 200/microL to distinguish I0 and I1 yielded a simplified model with better fit to the observed data. CONCLUSION: The ACTG TIS classification predicts survival in patients with AIDS-associated KS; CD4 count and tumor stage provide the most predictive information. However, a lower CD4 count than the one originally proposed provides better discrimination between prognostic groups.
Acquired Immunodeficiency Syndrome↗
Autoantibodies against the human asialoglycoprotein receptor: effects of therapy in autoimmune and virus-induced chronic active hepatitis.
The hepatic asialoglycoprotein receptor (ASGPR) was recently identified as a target antigen for both humoral and cellular immune response in inflammatory liver diseases. Thereby anti-ASGPR autoantibodies directed against human substrate were closely associated with autoimmune chronic active hepatitis. The present study compares the occurrence, titer and immunoglobulin classification of anti-human(h-)-ASGPR antibodies in 23 patients with newly diagnosed autoimmune chronic hepatitis before and after initiation of immunosuppressive therapy to 22 patients with autoimmune hepatitis in remission. Additionally, 1-year follow-up examinations of 42 patients with HBsAg-positive chronic hepatitis and of 32 patients with chronic hepatitis C receiving recombinant interferon-alpha were included. Nineteen of 23 patients with newly diagnosed and 9/22 with autoimmune hepatitis in remission, 5/42 with untreated chronic hepatitis B and 5/32 patients with chronic hepatitis C exhibited anti-h-ASGPR at the beginning of the study. In autoimmune hepatitis anti-h-ASGPR were found in higher titers (median > 1:1000) than in viral hepatitis (maximum 1:400). After initiation of immunosuppressive therapy in autoimmune hepatitis anti-h-ASGPR decreased sharply. Eight of 19 patients eliminated anti-h-ASGPR within 18 months in contrast to 11 patients with persistent anti-h-ASGPR titer over 18 months and longer. Anti-h-ASGPR with maximum titer of 1:600 were detected in 5 patients with chronic hepatitis B (transiently in 4/5 patients) and in 2 patients with chronic hepatitis C during interferon-alpha. Anti-h-ASGPR were from immunoglobulin classes IgG and IgM in cases with untreated autoimmune hepatitis and chronic hepatitis B and C exhibiting mainly IgG2-subclass in autoimmune and IgG4 in viral hepatitis.(ABSTRACT TRUNCATED AT 250 WORDS)
Adolescent↗
Human immunodeficiency virus type 1 subtype F reverse transcriptase sequence and drug susceptibility.
We sequenced and phylogenetically analyzed the reverse transcriptase (RT) regions of the pol genes of 14 human immunodeficiency virus type 1 (HIV-1) isolates from Romanian patients, which were classified as subtype F on the basis of env gene structure. The RT sequences showed that the strains clustered phylogenetically and were equidistant from other HIV-1 subtypes as shown by the neighbor-joining and maximum-likelihood methods, allowing us to define HIV-1 subtype F according to the pol classification. The subtype F RT sequences differed from reported group M RT sequences by 10.94% (for nucleotides) and 7.6% (for amino acids). Phenotypic analysis of subtype F susceptibility to three classes of antiretroviral compounds showed an increase in the 50% inhibitory concentration of the tetrahydroimidazo[4,5,1-jk] [1,4]-benzodiazepin-2-(1H)-one and -thione (TIBO) derivate R82913 for one strain which was naturally resistant to this compound. This first report of subtype F pol sequences confirms the perfect correlation between the phylogenetic positions determined by env and pol analyses and suggests that virus variability might influence the efficacy of antiretroviral treatments. This finding warrants a global evaluation of the phenotypic and genotypic susceptibility of HIV-1 subtypes to antiretroviral drugs.
Adult↗
Alphaviral gene transfer in neurobiology.
Semliki Forest virus (SFV), Sindbis virus (SIN), and Venezuelan equine encephalitis virus are simple, enveloped plus-strand RNA viruses belonging to the Alphavirus genus of the Togaviridae family. They have been developed into expression vectors that infect a wide host cell range and cause rapid and high-level transgene expression. Their easy and fast generation, classification into biosafety levels 1 and 2, and preferential transduction of neurons in cell and tissue cultures makes them an increasingly used gene transfer system. This review summarizes the alphaviral replication and expression, the replicon system, and its application in neurobiology. Alphaviral vectors can introduce multiple transgenes into host cells, and mutants with low or absent cytotoxicity and increased or decreased transgene expression levels are available. Temperature-dependent mutants permit to control the host cell specificity as well as the on- and offset of gene expression. These features, together with the transduction characteristics revealed in a direct comparison of alphaviral and other viral vectors in hippocampal slice cultures, make SFV and SIN vectors a powerful tool for neurobiological studies.
Alphavirus↗
Systemic vasculitic syndromes.
The current lack of knowledge about the factors underlying both the etiopathogenesis and extent of the clinical expression of necrotizing vasculitis is illustrated by recent articles. "Benign" vasculitis may present as localized disease in skin, gut, or even muscle; but on long-term follow-up, systemic involvement frequently occurs. Exciting studies on the occurrence of viruses such as hepatitis C in vasculitis compound these problems, because they are associated with multiple syndromes and the mechanism underlying their relationship to vasculitis remains to be elucidated. Further subdivision of antineutrophil cytoplasmic antibodies may aid in classification, but currently, their association with disease activity and extent obscures that role. Age is also less useful, because Kawasaki syndrome may occur rarely in adults and polyarteritis nodosa was reported in a large series of children. Differentiation is important because of the various responses to therapy. The first controlled study of cyclophosphamide as therapy for necrotizing vasculitis confirms its early benefit but, interestingly, shows no difference in 10-year survival rates. The addition of plasma exchange is of benefit only in the small number of patients with severe renal involvement who are dialysis-dependent at onset.
Humans↗
Prognostic indicators for the development of AIDS in HIV antibody positive haemophiliac patients: results of a three-year longitudinal study.
In February 1986, 40 out of 75 adult patients with haemophilia A attending St. James's University Hospital were human immunodeficiency virus (HIV) antibody positive. Over a three-year period these patients were prospectively studied with regard to possible prognostic indicators for the development of the acquired immune deficiency syndrome (AIDS). Using the Centres for Disease Control (CDC) classification of HIV infection, 17 patients (42.5%) developed group 4 disease during this time, giving an actuarial three-year progression rate of 44%, and 5 patients (12.5%) died. The following parameters measured at recruitment were found independently to predict progression to AIDS: a serum beta 2-m level of greater than 3.5 mg/l, (chi 2 = 15.95, P less than 0.001), a serum IgA level of greater than 4.5 milligram(s) (chi 2 = 6.08, P less than 0.02) and p24 antigenaemia (chi 2 = 5.7, P less than 0.05). The actuarial three-year progression rate in those patients abnormal by two or more of these parameters was 100% (n = 7), compared to only 7% in patients who were normal by all three values (n = 15). CD4+ lymphocyte counts and CD4+:CD8+ ratios were significantly lower in HIV positive compared with HIV negative patients (P less than 0.01), but did not predict the development of AIDS.
Acquired Immunodeficiency Syndrome↗
Classification of human heterophile antibodies.
A classification of heterophile antibodies is proposed, which is based on interactions with guinea pig kidney homogenate. The major groups of antibodies combining with guinea pig kidney encompass Hanganutziu-Deicher antibodies, Forssman antibodies, and antibodies to Newcastle disease virus. Antibodies which fail to combine with guinea pig kidney are primarily those of Paul-Bunnell variety.
Animals↗
Early detection of neurophysiological abnormalities in infection by human immunodeficiency virus.
The human immunodeficiency virus causes serious, progressive and irreversible deterioration of the immunocompetence system and of the nervous system, so neurological pathology in infected patients is frequent (30-40%), affecting both the central and the peripheral nervous systems. There are different clinical and laboratory indicators of bad prognosis, considering the important neurotropism of the virus. This study attempts to evaluate which neurophysiological parameters are altered during the initial phases of infection by HIV. A total of 46 individuals were studied, 30 seronegative and 16 seropositive in stage A of the CDC-93 classification. Motor and sensory conduction studies were carried out on all of them on the upper and lower extremities, as well as visual, somatosensory and auditory evoked potentials and endogenous potentials, mainly P300. The analysis of the neurophysiological parameters evaluated in our series, showed alterations of the conduction velocity of the sural nerve, latency of N1 of the SSEP of median and posterior tibial nerves and P300 in the initial phases of the infection even in the absence of clinical symptomatology.
Adult↗
Progress in protein structural class prediction and its impact to bioinformatics and proteomics.
The structural class is an important attribute used to characterize the overall folding type of a protein or its domain. Since the concept of protein structural class was developed about 3 decades ago based on a visual inspection of polypeptide chain topologies in a dataset of only 31 gloular proteins, the number of structure-known proteins has been increased rapidly. For example, as of 12-July-2005, the entries deposited into RCSB PDB Protein Data Bank for proteins, peptides, and viruses whose 3-dimensional structures were determined by X-ray and NMR techniques have been increased to 28,920. To properly cover more and more structure-known proteins, some modification and expansion from the original structural classification scheme have been developed. Meanwhile, many different approaches have been proposed for predicting the structural class of proteins. In this review, the new classification schemes are briefly introduced. The attention is focused on the progress in structural class prediction and its impact in stimulating the development of identifying the other attributes of proteins. It is interesting to point out that the development of the latter has actually in turn greatly enriched the power of the former. Also, some promising approaches for the further development of protein structural class prediction are also addressed.
Computational Biology↗
[HIV (human immunodeficiency virus) and HIV-associated diseases].
The discovery of the Human Immunodeficiency Virus (HIV), the characterization of its molecular biology and the development of serologic methods for detecting antibodies have led to a better understanding of HIV-associated clinical syndromes. Recently, the Centre of Disease Control has proposed a classification of HIV-related conditions. This classification forms the basis for this review. It is completed by remarks on antiviral and immunomodulating drugs and its effects on HIV. Difficulties in development of vaccines are discussed.
AIDS Serodiagnosis↗
Hepatitis C virus (HCV) core serotypes in chronic HCV infection.
Recently, two distinct hepatitis C virus (HCV) serologic types have been identified on the basis of amino acid variations in the core region. The two serologic types can readily discriminate between genotypes I-II-V (serotype 1) and III-IV (serotype 2), according to the Okamoto classification. We compared HCV core serotyping with genotyping with sera from 363 anti-HCV-positive patients (309 HCV RNA positive by PCR) using a synthetic core peptide-based enzyme immunoassay and PCR amplification of core region sequences with type-specific primers, respectively. Serologic responses to HCV serotypes were successfully identified in 164 (45%) patients, of whom 153 were viremic. Eighty-nine patients had evidence of exposure to serotype 1: 8 of these were infected with genotype I, 50 were infected with genotype II, 2 were infected with genotype III, 7 were infected with genotype V, 13 had infections with mixed genotypes, 3 were infected with an indeterminate genotype, and 6 were nonviremic. Seventy-four patients had been exposed to serotype 2: 64 were infected with genotype III, 3 were infected with mixed genotypes, 2 were infected with an indeterminate genotype, and 5 were nonviremic. The serum of one patient, infected with genotype III, showed reactivity to both serotypes. Comparative evaluation of HCV core region serotyping and genotyping with sera from 294 viremic patients infected with a known HCV genotype showed a remarkable concordance between HCV core region genotyping and serotyping, with only 2 apparently discordant serum samples (both from patients with genotype III infection) of 148 (1.4%) successfully serotyped samples. Serotype 1 infection was more frequently observed in patients with overt chronic liver disease and accounted for all successfully serotyped samples from intravenous drug abusers. In contrast, serotype 2 was more prevalent in subjects with biochemically silent HCV infection (alanine aminotransferase, < 45 U/liter), in agreement with previous findings at the molecular level. HCV core serologic typing is a simple, inexpensive, and highly reproducible assay that can be applied to more than 50% of viremic HCV antibody carriers prior to the use of more sophisticated molecular typing techniques. Moreover, it may be helpful in tracking transmissions routes, particularly for incorrectly stored samples in which the RNA has degraded or for subjects who have cleared the virus and therefore have only antibodies remaining to testify to a remote infection. The lack of recognition of the core sequence from residues 67 to 81, which contains a minor B-cell epitope used to detect type-specific immunoreactivity, may explain the negative serologic findings for half of the patients.
Adolescent↗
Specificity of satellite activation by tobacco necrosis virus correlates with nucleic acid hybridization pattern between helper virus isolates.
Tobacco necrosis virus (TNV) comprises over 20 different isolates which are usually classified on the basis of serological cross-reactivity of their virus particles or specific activation of satellite virus strains (STNV-1, -2, and -C). We have studied the relationships between five TNV isolates, TNV-A, -G, -CN, -D, and -AC36 which exhibit considerable differences in symptom formation on Phaseolus vulgaris. It is shown that, like TNV-A, TNV-G and -CN support the multiplication of STNV-1 and -2. The ability to activate STNV-1 and -2 is not completely correlated with the virulence of the TNV isolates on Phaseolus as TNV-CN infects Phaseolus very inefficiently. The RNAs of all STNV-1 and -2 supporting TNV isolates were detectable by Northern blot analysis using RNA probes derived from TNV-A, whereas the RNAs of the STNV-C activating isolates (TNV-D and -AC36) were only detected with a TNV-D-derived RNA probe. This indicates that the classification of the TNV isolates on the basis of satellite activation is representative of the evolutionary relationships between the isolates.
Base Sequence↗
Detection of respiratory syncytial virus by reverse transcription-PCR and hybridization with a DNA enzyme immunoassay.
Nasal aspirates from 238 infants hospitalized with acute respiratory infections during the winter of 1994 and 1995 were tested for respiratory syncytial virus (RSV) by immunofluorescence assay (IFA) and the viral isolation technique (VIT) and by two PCR and hybridization methods: reverse transcription PCR 1 (RT-PCR1), which amplifies the RNAs of all RSV strains, and RT-PCR-2, which allows subgroup classification of RSV. RT-PCR-1 and RT-PCR-2 detected viral sequences in 56.7% (135 of 238) and 48.3% (115 of 238) of the samples, respectively, while only 80 (33.6%) samples were found to be positive by IFA and VIT. Of the PCR-positive specimens, 57 were missed by these routine techniques in RT-PCR-1 and 45 were missed in RT-PCR-2. Although the RSV-PCR-1 and RSV-PCR-2 techniques amplified two different sequences of the RSV genome, they gave similar results for 218 (91.6%) nasal aspirates. Compared with conventional methods, the sensitivity, specificity, and agreement were 97.5, 63.9, and 75.2%, respectively, for RT-PCR-1 and 89.7, 71.9, and 77.7%, respectively, for RT-PCR-2, and for these two RT-PCR assays, the positive predictive value (PPV) and the index of agreement (kappa) were comparable and moderate, respectively: PPV was 57.8% and kappa was 0.52 in RT-PCR-1, and PPV was 60.9% and kappa was 0.54 in RT-PCR-2. However, there was a perfect correlation between the two RT-PCRs, with a PPV of 100% and an excellent index of agreement (kappa = 0.88). Therefore, most RT-PCR results were really true positive, and VIT and IFA, which missed some of them, appeared to be less sensitive.
Base Sequence↗
T lymphocyte subset changes in human immunodeficiency virus infection.
The absolute number of CD4+ and CD8+ T cells was determined by an immunomagnetic technique directly in the blood of 75 healthy controls and 223 HIV-infected individuals. The HIV-seropositive individuals were also classified clinically according to the system recommended by the Centers for Disease Control (CDC), and the CDC classification was correlated with the patients' T cell subset counts. Compared to the control group, the HIV-infected individuals demonstrated an early and sustained increase in the number of CD8+ T cells with median values of CDC groups II, III, and IV C2 twice that observed in the control group. Patients with AIDS had CD8+ T cell counts comparable to those of the control group. The HIV-infected individuals showed a decrease in the number of CD4+ T cells correlating with clinical deterioration of the disease. T cell subset counts significantly distinguished the group of healthy seropositive individuals from those with HIV-related disease, and the group of patients with AIDS from those with other HIV-related opportunistic infections.
Acquired Immunodeficiency Syndrome↗