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DNA base composition, nature of intracellular DNA, morphology, and classification of bacteriophages infecting Micrococcus luteus.

Ten bacteriophages infecting Micrococcus luteus have been characterized. All phages contain double-stranded DNA, of 64.3--73.5 mol% guanine plus cytosine (GC). The DNA of phage N7 has the highest GC content reported for any bacterial virus. No unusual bases have been found. The intracellular replicating DNAs of six phages are covalently closed circular molecules. All 10 phages have isometric, probably icosahedral, heads and long, flexible, noncontractile tails and can be sorted into two morphological groups based on size and presence or absence of a collar. Host-range studies indicate six host-range groups.

Bacteriophages↗

Low prevalence of latently Epstein-Barr virus-infected cells in chronic gastritis.

The association of Epstein-Barr virus (EBV) with a proportion of gastric carcinomas is well established. The role of EBV in conditions predisposing to carcinoma such as chronic gastritis has remained undefined, however. We used in situ hybridization with radioactive and nonradioactive single-stranded RNA probes specific for the EBV small latent nuclear transcripts, EBER1 and EBER2, to analyze biopsy specimens from 242 patients with mild to severe chronic gastritis of Sydney classification types A, B, and C. A small number of EBV infected lymphocytes was detected in only nine cases, even in biopsies investigated with radioactive probes. Labeling of epithelial or stromal cells was not observed. The paucity of latently EBV-infected cells in chronic gastritis biopsies differs from the previously reported higher prevalence of virus carrying cells in inflammatory conditions at other sites of the gastrointestinal tract. These findings argue against a direct involvement of EBV in the pathogenesis of chronic gastritis. The low prevalence of EBV-positive cells suggests that local factors do not favor the entry and retention of circulating EBV-infected lymphocytes in gastric mucosa. Moreover, our findings indicate that EBV infection of gastric epithelial cells is not an early event in gastric carcinogenesis.

Adolescent↗

AIDS-related lymphoma in Brazil. Histopathology, immunophenotype, and association with Epstein-Barr virus.

The occurrence of malignant lymphoma is an increasingly important cause of morbidity and mortality in AIDS patients. The incidence of AIDS-related lymphoma in some developing countries such as Brazil is increasing as the survival of HIV infection has improved. Although there is a clear association between several types of immunodeficiency-related lymphomas and Epstein-Barr virus (EBV), the association of EBV infection in AIDS-related lymphoma in Brazil, where the incidence of AIDS is high, is unknown. Formalin-fixed, paraffin-embedded tissue from 24 cases of AIDS-related lymphoma in Brazil were analyzed for morphologic classification, immunophenotype, and EBV association using in situ hybridization studies with an EBV-EBER1 biotinylated probe. Twenty cases of AIDS-related lymphoma were classified as non-Hodgkin's lymphoma and four cases were Hodgkin's disease. Eleven non-Hodgkin's lymphomas were classified as diffuse large cell type, five cases were small non-cleaved cell, Burkitt-type, and four cases were large cell immunoblastic non-Hodgkin's lymphoma. Eighteen cases were of B-cell phenotype; one was a T-cell lymphoma, and one was classified as null. Epstein-Barr virus (EBV) was demonstrated in the majority of tumor cells of 11 of 20 (55%) of the cases non-Hodgkin's lymphomas and in 3 of 4 (75%) cases of Hodgkin's disease. AIDS-related lymphomas in Brazil are usually of large cell/immunoblastic type, but Hodgkin's disease is also seen. Both non-Hodgkin's lymphoma and Hodgkin's disease are often associated with EBV infection. The non-Hodgkin's lymphoma is predominantly of B-cell phenotype.

Adult↗

Genetic diversity and evolution of hepatitis C virus--15 years on.

In the 15 years since the discovery of hepatitis C virus (HCV), much has been learned about its role as a major causative agent of human liver disease and its ability to persist in the face of host-cell defences and the immune system. This review describes what is known about the diversity of HCV, the current classification of HCV genotypes within the family Flaviviridae and how this genetic diversity contributes to its pathogenesis. On one hand, diversification of HCV has been constrained by its intimate adaptation to its host. Despite the >30 % nucleotide sequence divergence between genotypes, HCV variants nevertheless remain remarkably similar in their transmission dynamics, persistence and disease development. Nowhere is this more evident than in the evolutionary conservation of numerous evasion methods to counteract the cell's innate antiviral defence pathways; this series of highly complex virus-host interactions may represent key components in establishing its 'ecological niche' in the human liver. On the other hand, the mutability and large population size of HCV enables it to respond very rapidly to new selection pressures, manifested by immune-driven changes in T- and B-cell epitopes that are encountered on transmission between individuals with different antigen-recognition repertoires. If human immunodeficiency virus type 1 is a precedent, future therapies that target virus protease or polymerase enzymes may also select very rapidly for antiviral-resistant mutants. These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses.

Biological Evolution↗

Crystal structures of Nipah and Hendra virus fusion core proteins.

The Nipah and Hendra viruses are highly pathogenic paramyxoviruses that recently emerged from flying foxes to cause serious disease outbreaks in humans and livestock in Australia, Malaysia, Singapore and Bangladesh. Their unique genetic constitution, high virulence and wide host range set them apart from other paramyxoviruses. These characteristics have led to their classification into the new genus Henpavirus within the family Paramyxoviridae and to their designation as Biosafety Level 4 pathogens. The fusion protein, an enveloped glycoprotein essential for viral entry, belongs to the family of class I fusion proteins and is characterized by the presence of two heptad repeat (HR) regions, HR1 and HR2. These two regions associate to form a fusion-active hairpin conformation that juxtaposes the viral and cellular membranes to facilitate membrane fusion and enable subsequent viral entry. The Hendra and Nipah virus fusion core proteins were crystallized and their structures determined to 2.2 A resolution. The Nipah and Hendra fusion core structures are six-helix bundles with three HR2 helices packed against the hydrophobic grooves on the surface of a central coiled coil formed by three parallel HR1 helices in an oblique antiparallel manner. Because of the high level of conservation in core regions, it is proposed that the Nipah and Hendra virus fusion cores can provide a model for membrane fusion in all paramyxoviruses. The relatively deep grooves on the surface of the central coiled coil represent a good target site for drug discovery strategies aimed at inhibiting viral entry by blocking hairpin formation.

Amino Acid Sequence↗

Spontaneous short-range silencing of a GFP transgene in Nicotiana benthamiana is possibly mediated by small quantities of siRNA that do not trigger systemic silencing.

A green fluorescent protein (GFP) transgene under the control of the 35S cauliflower mosaic virus (CaMV) promoter was introduced by Agrobacterium-mediated transformation into Nicotiana benthamiana to generate fourteen transgenic lines. Homozygous lines that contained one or two copies of the transgene showed great variation of GFP expression under ultraviolet (UV) light, which allowed classification into three types of transgenic plants. Plants from more than half of the transgenic lines underwent systemic RNA silencing and produced short interfering RNA (siRNA) as young seedlings, while plants of the remaining lines developed, in a spontaneous manner, defined GFP-silenced zones on their leaves, mostly in the form of circular spots that expanded to about 4-7 mm in size. In some of the latter lines, the GFP-silenced spots remained stable, but no systemic silencing occurred. Here we characterize this phenomenon, which we term spontaneous short-range silencing (SSRS). Biochemical analysis of silenced spot tissue did not reveal detectable levels of siRNA. However, agro-infiltration with the suppressor proteins P19 of cymbidium ring spot virus (CymRSV), HC-Pro of tobacco etch virus (TEV), and crosses to a P19 transgenic line, nevertheless suggests that low concentrations of siRNA may have a functional role in the locally silenced zone. We propose that small alterations in the steady-state concentration of siRNAs and their cognate mRNA are decisive with regard to whether silencing remains local or spreads in a systemic manner.

Gene Expression Regulation, Plant↗

[Prolonged clinical remission of cholangitis in early human immunodeficiency virus infection after surgical biliary derivation].

During the acquired immunodeficiency syndrome, most cases of cholangitis develop at an advanced stage of disease. We report a case of cholangitis in a 47-year-old homosexual man, stage IIa according to Center of Disease Control classification. An isolated jaundice was the first manifestation of the disease. The number of CD4 was 380/microL. Ultrasonography and endoscopic retrograde cholangiography showed a 7 cm stenosis of the common bile duct, and cystic duct stenosis, with associated intra-hepatic biliary duct dilatation. No infectious agent was found. Cholecystectomy and hepaticojejunostomy were performed. Pathological examination of liver biopsy and a sample of the resected common bile duct was consistent with sclerosing cholangitis. The postoperative course was uneventful. During a three year follow-up period, the patient was disease free but he suddenly died of uncontrolled bleeding from duodenal ulcer. In HIV-infected patients, surgical treatment can be performed in case of symptomatic long stenosis of the common bile duct.

Biliary Tract Surgical Procedures↗

E pluribus unum: The riddle of focal segmental glomerulosclerosis.

A recent consensus conference proposed a new classification for focal segmental glomerulosclerosis (FSGS). Five patterns have been defined: FSGS not otherwise specified, perihilar variant, cellular variant, tip variant, and collapsing variant. In light of the multiplicity of classification schemes in use, the promise of a rational and uniform scheme for FSGS pathology is most welcome. This approach has worked extremely well for the classification of lupus nephritis. It does not necessarily mean, however, that this new classification scheme will help to select treatment protocols according to histopathologic subsets of FSGS. In fact, one renal biopsy examination may show multiple variants and this classification, despite many merits, still lumps categories that should be split and splits categories that should be lumped together. It has become clear that despite its histologic diversity FSGS begins as a podocyte disease that progresses from a cellular to a scar lesion. Recent years have brought about astonishing insight into the complex molecular array of proteins forming the slit diaphragm between podocyte foot processes, a narrow space essential for restricting glomerular permeability to albumin. Concentrating on the podocyte rather than on the glomerular tuft is helpful for abolishing the classic distinction between primary versus secondary forms of FSGS, a distinction that crumbles away with each new evidence of genetic, ischemic, or viral etiologies of FSGS, despite similar lesions. In fact, recent studies focusing on the podocyte changes that occur in various subsets of FSGS have unraveled the striking phenomena of podocyte dedifferentiation and transdifferentiation along with differential expression of cyclin-dependent kinase inhibitors. Interestingly, the latter showed that expression of cyclin-dependent kinase inhibitors p21 and proliferation marker Ki-67 are the same in cellular FSGS, collapsing glomerulopathy, and human immunodeficiency virus-associated FSGS. Taken together these findings lead to a reassuring unitary interpretation of the pluralistic appearance of FSGS by histopathology. Clearly, further studies of the podocyte will lead to improved understanding of FSGS and to improved classification schemes that are grounded in molecular understanding of glomerular injury and that will guide the clinician in the choice of treatment and prognosis.

Animals↗

[Verrucous carcinoma and carcinoma cuniculatum--forms of squamous cell carcinoma?].

The morphology of verrucous carcinoma (Ackerman tumor) and carcinoma cuniculatum is described and the problems of diagnosis and classification are discussed on the basis of the relevant literature. Both lesions are closely related aggressive proliferations of squamous epithelium of the skin and mucous membranes. Verrucous carcinoma exhibits an exophytic as well as endophytic growth pattern on a broad front; dissociated invasive growth, however, is usually absent. Carcinoma cuniculatum is similar; however, conspicuous deep duct-like formations and keratin-filled sinuses are formed. Clinically, these tumors appear to be malignant. Histological evaluation often results in the tumors being underestimated and a false diagnosis of a benign papillomatous lesion or pseudoepitheliomatous hyperplasia being made. The necessity is stressed of a thorough histological investigation of the tumors in multiple sections and of a search for dissociated invasive growth. It is suggested that cases without this feature should not be termed carcinoma but should rather be given a more descriptive diagnosis such as verrucous hyperplasia or proliferation. Cases with clear invasive growth should be classified as papillary squamous cell carcinomas (grade I). A detailed characterization should be given in addition. Although both tumors show features of viral lesions, it has so far not been possible to demonstrate viruses by electron microscopy or structural antigens of human papilloma viruses (HPV). Both clinical picture and histology must be taken into consideration when diagnosing these two tumors ("clinicopathologic entity"). Close cooperation between the clinician and the pathologist is desirable for individual assessment of these lesions as regards classification and therapy.

Carcinoma, Papillary↗

Apoptosis in lymphocytic leukemias and lymphomas.

Most current classifications of lymphoid neoplasms define the tumors based on the cell of origin, phenotype, genetic abnormalities, and clinical features. Here it is proposed that human lymphocytic tumors can be categorized based on the propensity and capacity of the tumor cells to undergo apoptosis. The first category is defined by malignant cells that are resistant to apoptosis due to expression of anti-apoptotic factors such as bcl-2 and cellular inhibitors of apoptosis (IAPs). These tumors would include CLL and follicular lymphomas, as well as some malignancies in which the tumor cells are infected by viruses that co-opt cell survival pathways, such as human T-cell leukemia/lymphoma virus (HTLV)-1. The second category, in which the malignant cells are apoptosis-prone, would include tumors arising in the context of impaired cytotoxic T-cell function. These neoplasms would include some human immunodeficiency virus (HIV)-related lymphomas such as Burkitt's lymphoma, and post-transplantation lymphomas. The third category would include neoplasms of intermediate sensitivity to apoptosis, some of which are associated with infection such as mucosa-associated lymphoid tissue (MALT) lymphomas of the stomach. Although this classification is tentative, it should evolve in parallel with our understanding of pathogenic mechanisms in lymphoid neoplasia, and provides a novel framework with which to consider the appropriateness of specific therapeutic strategies. Distinctions among lymphocytic tumors in terms of the likelihood of response to therapies such as antisense to bcl-2 related proteins, inhibitors of NF-kappa B activity, and new approaches aimed at bolstering the host's immune response, would cross standard classifications based on the T or B-cell origin of the tumor cells.

Apoptosis↗

Elevated alpha-tumor necrosis factor levels in spinal fluid from HIV-1-infected patients with central nervous system involvement.

To assess the role of alpha-tumor necrosis factor in the pathogenesis of central nervous system involvement during human immunodeficiency virus type 1 infection, we recorded clinical data and measured alpha-tumor necrosis factor levels in serum and cerebrospinal fluid samples from 45 patients infected with human immunodeficiency virus type 1, classified as group II/III (10), group IV A (5), group IV B (10), and group IV C-1 (20) of the Centers for Disease Control acquired immunodeficiency syndrome classification system and 42 controls. Alpha-tumor necrosis factor was above the limit of detection in only 3 of 15 sera and 3 of 15 cerebrospinal fluid samples from patients in group II/III and group IV A, whereas it was detected in 17 of 30 sera (p less than 0.05) and 22 of 30 cerebrospinal fluid (p less than 0.0002) samples from clinically more advanced patients (group IV B and group IV C-1). Alpha-tumor necrosis factor mean values were 21.5 pg/ml in sera and 50.0 pg/ml in cerebrospinal fluid from group IV B patients and 30.4 pg/ml in sera and 24 pg/ml in cerebrospinal fluid from group IV C-1 patients.(ABSTRACT TRUNCATED AT 250 WORDS)

AIDS Dementia Complex↗

Improved cell typing by charge-state deconvolution of matrix-assisted laser desorption/ionization mass spectra.

Robust, specific, and rapid identification of toxic strains of bacteria and viruses, to guide the mitigation of their adverse health effects and optimum implementation of other response actions, remains a major analytical challenge. This need has driven the development of methods for classification of microorganisms using mass spectrometry, particularly matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), that allows high-throughput analyses with minimum sample preparation. We describe a novel approach to cell typing based on pattern recognition of MALDI mass spectra, which involves charge-state deconvolution in conjunction with a new correlation analysis procedure. The method is applicable to both prokaryotic and eukaryotic cells. Charge-state deconvolution improves the quantitative reproducibility of spectra because multiply charged ions resulting from the same biomarker attaching a different number of protons are recognized and their abundances are combined. This allows a clearer distinction of bacterial strains or of cancerous and normal liver cells. Improved class distinction provided by charge-state deconvolution was demonstrated by cluster spacing on canonical variate score charts and by correlation analyses. Deconvolution may enhance detection of early disease state or therapy progress markers in various tissues analyzed by MALDI-MS.

Algorithms↗

Nucleotide sequences of the VP4 and VP7 genes of a Chinese lamb rotavirus: evidence for a new P type in a G10 type virus.

The VP7 and VP4 genes of a group A rotavirus (Lp14) isolated from a lamb with diarrhea in Qinhai province, China, in 1981 were reverse transcribed, amplified by PCR, cloned, and sequenced. The virus was found to possess a VP7 gene, classifying it as a G10 type, and a VP4 gene which showed only limited homology with any other known VP4 gene, suggesting its classification as a new P type and providing further evidence for the vast diversity of group A rotaviruses.

Amino Acid Sequence↗

Primary genetic characterization of HIV-1 isolates from WHO-sponsored vaccine evaluation sites by the RNase-A mismatch method.

We have analyzed by the RNase-A mismatch method 35 isolates from four WHO-sponsored vaccine evaluation sites as a secondary laboratory of the WHO Network for HIV Isolation and Characterization. The application of an estimator for the establishment of genetic distances based on the RNase-A digestion patterns in combination with the phylogenetic analysis has allowed us to construct a tree with five well defined groups of viruses. Because the clustering with known reference strains, samples from Brazil could be grouped as subtype B and the majority of those from Thailand were subtype E. Some of the samples from Uganda were classified as subtype D. Isolates from Rwanda and some from Uganda were identified as subtype A viruses. These results coincide with data obtained by heteroduplex mobility assay and nucleotide sequencing in env regions. The RNase-A mismatch method combined with phylogenetic analysis permitted the primary genetic classification of 33 of 35 samples from the WHO Network.

AIDS Vaccines↗

Detection of hepatitis C infection by polymerase chain reaction among hemodialysis patients.

One hundred forty-five patients on regular hemodialysis (HD) at our institution were evaluated for the presence of hepatitis C virus (HCV) infection. Forty-three patients (29%) were found to have detectable antibodies to HCV using second-generation enzyme-linked immunosorbent and recombinant immunoblot assays. Forty positive patients (anti-HCV+) and 10 negative patients (anti-HCV-) were tested for direct detection of the HCV genome by the polymerase chain reaction (PCR). Twenty-one anti-HCV+ patients (52%) had detectable RNA HCV in plasma (PCR+). No anti-HCV- patient had viremia. In addition, we compared the 43 anti-HCV+ patients with the 102 anti-HCV- patients for duration of HD, history of blood transfusion, serologic markers of hepatitis B virus, and acute and chronic liver disease. On retrospective univariate analysis, statistically significant associations with anti-HCV+ were duration of HD (P = 0.0001), blood transfusions (P = 0.0005), co-infection with hepatitis B virus (P = 0.01), and acute and chronic liver disease (P = 0.06 and 0.01, respectively). Three significant variables (duration of HD, chronic hepatitis, and blood transfusions) of the multivariate analysis permit the classification of 65% of anti-HCV+ patients and 81% of anti-HCV- patients. In the anti-HCV+ group, when the same parameters were compared in PCR+ or PCR- patients, no statistical difference appeared. These results reveal that 52% of anti-HCV+ HD patients have HCV infection. The clinical consequences of HCV infection in that population are not characterized since no difference has been documented between PCR+ and PCR- results.

Adolescent↗

Molecular biology of Hendra and Nipah viruses.

The structure and genetic organization of Hendra and Nipah viruses places them in the subfamily Paramyxovirinae. However, low homology with other subfamily members and several novel biological and molecular features such as genome length and F(0 )cleavage site suggest classification in a new genus within the Paramyxovirinae.

Amino Acid Sequence↗

Prevalence of Sjögren's-like syndrome in a cohort of HIV-1-positive patients: descriptive pathology and immunopathology.

The aims of the study were (a) to investigate the prevalence of Sjögren's-like syndrome (SLS) in an unselected population of HIV-1-positive patients and (b) to describe the pathology and immunopathology of the labial minor salivary gland biopsy. Seventy-seven HIV-1-positive patients were asked to answer the validated questionnaire of the European preliminary criteria for the classification of Sjögren's syndrome on oral and ocular sicca symptoms. Twenty-six patients gave one positive answer to both ocular and oral symptoms, and of these 14 (hepatitis C virus negative) consented to participate in the study (patients group). Ten age- and sex-matched HIV-1-positive patients with a negative questionnaire constituted the control group. Patients and controls had: (a) Schirmer's test and slit-lamp examination after Rose Bengal staining; (b) parotid gland scanning with technetium; (c) detection of autoantibodies in sera to Ro/SSA and La/SSB; (d) labial salivary gland biopsy (patients group only). The control group gave negative parotid gland scanning and only one gave a positive Rose Bengal staining test. In the patients group, parotid gland enlargement was manifested by three patients and only one gave positive Rose Bengal staining test. Six out of the 14 patients had biopsies identical with Sjögren's syndrome and five of these gave positive parotid gland scanning. In the biopsies of four other patients, mucoid degeneration of the stroma was found. Immunopathology revealed that the predominant cells were T cells with the CD8 phenotype. None of the patient and control sera had autoantibodies to Ro/SSA and La/SSB, whereas all patients had hypergammaglobulinaemia. The overall prevalence of possible SLS in a mixed population of HIV(+) patients (88.3% men and 11.7% women) was 7.79% which is >2.5 times higher than that observed in normal Greek adult females.

Adult↗

An exploratory analysis of survival with AIDS using a nonparametric tree-structured approach.

We illustrate an analysis with classification and regression trees applied to survival data. Through this application, we provide a description of the opportunistic diseases and sociodemographic factors that contribute to survival among people with human immunodeficiency virus disease. The analyses are based on 43,795 cases reported to the Centers for Disease Control between January 1, 1984, and December 31, 1987. We used vital status as of December 31, 1989, to estimate mortality rates. We identified Kaposi's sarcoma and opportunistic diseases causing central nervous system damage (cryptococcosis, primary lymphoma of the brain, cytomegalovirus disease, and progressive multifocal leukoencephalopathy) as important predictors of death. In addition, advanced age at diagnosis (50+), race (white/other), and history of illicit drug use were found to be important determinants. Estimates of the cumulative probability of survival for subgroups of individuals defined by the tree structure illustrate the effect of these determinants on mortality. For the purpose of comparison, two proportional hazards models were also fit to the data using factors identified in the tree structure as the determinants of interest. This application illustrates the utility and limitations of both this new technique and proportional hazards models for epidemiologic research.

Acquired Immunodeficiency Syndrome↗