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Embryonal histone H1 subtypes of the sea urchin Strongylocentrotus purpuratus: purification, characterization, and immunological comparison with H1 subtypes of the adult.

The four H1 subtypes utilized during embryonic development of Strongylocentrotus purpuratus were purified. Their amino acid compositions and immunological reactivities show that they have different primary structures. Antisera against them were used to identify the H1 subtypes present in adult tissues. These experiments revealed that adult tissues do not contain detectable levels of the two H1 subtypes expressed in the earliest embryonic stages (H1 cs and H1 alpha) but do contain the two subtypes expressed from the blastula stage on (H1 beta and H1 gamma). In addition, all adult tissues examined contain H1 lambda, a subtype of unusually low apparent molecular weight, which is not found in the embryo prior to the feeding larval stage and is not closely related immunologically to any of the embryonal H1 subtypes.

Animals↗

Identification of human immunodeficiency virus type 1 subtypes B and F B/F recombinant and dual infection with these subtypes in Argentina.

DNA sequences encoding the third variable region (V3) of human immunodeficiency virus type-1 (HIV-1) envelope glycoprotein gp120 were obtained from 18 infected individuals residing in different regions of Argentina. Proviral DNA representing the env V3 region was obtained by PCR from uncultured peripheral blood mononuclear cells (PBMC) and genetic heterogeneity was examined by phylogenetic analysis. Sequences representing the gag p17 region were also obtained for a subset of these samples. Moreover, 1 sample that it was not possible to classify according to initial phylogenetic analysis was further analysed by molecular cloning of both V3 and p17 regions. Phylogenetic analysis according to different methodologies were performed comparing obtained sequences with a set of reference sequences representing previously characterized HIV-1 subtypes. The recombinant identification program (RIP) was used to study the presence of possible recombinant sequences. Phylogenetic analysis demonstrated that viruses representing both subtypes B and F are circulating among HIV-1 infected individuals in Argentina. In addition, RIP analysis showed that an initially unclassified sequence exhibited similarities to subtypes B and F in different fragments of the V3 region. Separate phylogenetic analysis of each of these fragments revealed divergent clustering, suggesting that this sequence harbours a point of recombination within the V3 loop. Interestingly, we also identified a dually infected individual with viruses belonging to subtypes B and F, as demonstrated by molecular cloning analysis of the env V3 and the gag p17 regions. Taken together, our study shows that both subtypes B and F are circulating in different regions of Argentina. Moreover, the data presented here show that dual infections with subtypes B and F can occur, and consequently B/F recombinant sequences are arising in the region.

Adult↗

Use of missing-data methods to correct bias and improve precision in case-control studies in which cases are subtyped but subtype information is incomplete.

Histologic and genetic markers can sometimes make it possible to refine a disease into subtypes. In a case-control study, an attempt to subcategorize a disease in this way can be important to elucidating its etiology if the subtypes tend to result from distinct causal pathways. Using subtyped case outcomes, one can carry out either a case-case analysis to investigate etiologic heterogeneity or do polytomous logistic regression to estimate odds ratios specific to subtypes. Unfortunately, especially when such an analysis is undertaken after the study has been completed, it may be compromised by the unavailability of tissue specimens, resulting in missing subtype data for many enrolled cases. The authors propose that one can more fully use the available data, including that provided by cases with missing subtype, by using the expectation-maximization algorithm to estimate risk parameters. For illustration, they apply the method to a study of non-Hodgkin's lymphoma in the midwestern United States. The simulations then demonstrate that, under assumptions likely to hold in many settings, the approach eliminates bias that would arise if unclassified cases were ignored and also improves the precision of estimation. Under the same assumptions, empirical confidence interval coverage is consistent with the nominal 95%.

Algorithms↗

Molecular epidemiology of HIV-1 infection in the Philippines, 1985 to 1997: transmission of subtypes B and E and potential emergence of subtypes C and F.

The molecular epidemiology of HIV-1 infection in the Philippines from 1985 to 1997 was investigated following subtyping of 54 (33 women, 21 men) prospectively collected clinical specimens using the heteroduplex mobility assay (HMA). In contrast with other Asian countries, subtype B accounted for most (70%) of the infections in the population studied, among female commercial sex workers (CSWs, 18 of 28), overseas contract workers (OCWs, 7 of 10), and men who have sex with men (MSM, 8 of 10). However, although viral specimens from HIV-seropositive persons diagnosed before 1993 (n = 16) were all of subtype B, diagnoses in more recent years (1993-present, n = 38) indicate the existence of subtypes E (29%), F (8%), and C (5%) in the population. Since its estimated introduction in the early 1990s, subtype E has accounted for 60% of the infections among female CSWs diagnosed after 1992 (n = 15). This genotype distribution shift occurred in parallel with a shift in transmission focus from the U.S. military bases to the the Philippine national capital region. So far, both events appear to have had no significant effect on the stability of HIV-1 transmission in the country. The recent identification of non-B subtypes in the Philippines may present novel insights on the dynamics of HIV-1 transmission in a high-risk but low-HIV prevalence setting in Asia.

Adult↗

An alpha4beta4 nicotinic receptor subtype is present in chick retina: identification, characterization and pharmacological comparison with the transfected alpha4beta4 and alpha6beta4 subtypes.

Retina from 1-day-old chicks is a valuable tissue model for studying neuronal nicotinic receptors because it expresses a large number of the developmentally regulated high affinity [(3)H]epibatidine labeled nicotinic receptors. Most of these receptors contain the beta4 subunit associated with different alpha subunits. Using a sequential immunodepletion procedure with anti-alpha6, anti-beta3, anti-beta2, and anti-beta4 antibodies, we purified an alpha4beta4 nicotinic receptor subtype that accounts for approximately 20 to 25% of the high affinity [(3)H]epibatidine labeled receptors present in retina at that developmental time. Immunoprecipitation and Western blotting experiments confirmed that the purified subtype contains only the alpha4 and beta4 subunits. This receptor binds a number of agonists and the antagonist dihydro-beta-erythroidine with nanomolar affinity, whereas it has micromolar affinity for the alpha-conotoxin MII and methyllycaconitine toxins and other nicotinic antagonists. Comparison of the pharmacological profile of this purified native subtype with that of the same subtype transiently expressed in human BOSC23 cells showed that they have very similar rank orders and absolute Ki values for several nicotinic drugs. Finally, because chick retina expresses an alpha6beta4-containing subtype with a high affinity for the alpha-conotoxin MII, we used native and transfected alpha4beta4 and alpha6beta4 subtypes to investigate the relative contributions of the alpha and beta subunits to this binding, and found that the alpha6 subunit determines the high affinity for this toxin.

Animals↗

Plasma RNA viral load in human immunodeficiency virus type 2 subtype A and subtype B infections.

Human immunodeficiency virus type 2 (HIV-2) is much less pathogenic than HIV-1, and HIV-2 infection is associated with plasma viral loads significantly lower than those found in HIV-1 infection. We have developed a real-time quantitative PCR method for measuring the HIV-2 RNA load that covers the range of genetic diversity of HIV-2 isolates and that detects extremely low viral loads. Samples from 49 patients were studied. Proviral DNA was first detected and quantified. The strains that were detected were then genotyped: 21 patients were infected with HIV-2 subtype A and 15 patients were infected with HIV-2 subtype B; 1 patient was infected with a highly divergent strain. Env PCR failed for the remaining 12 patients, so subtypes could not be determined. For viral RNA quantification, a stock of HIV-2 strain NIHZ, which was counted by electron microscopy, was used as the standard. Several primer sets targeting the highly conserved gag region were evaluated. Various primer combinations failed to amplify subtype B strains. With the final primer pair selected, which detected both subtype A and subtype B strains, the sensitivity of the assay was 100% at a viral load of 250 copies/ml and 66% at a viral load of 125 copies/ml. We found a correlation between the CD4(+)-cell count, the clinical stage, and the plasma HIV-2 RNA level. The median plasma HIV-2 RNA value for the 33 asymptomatic patients was 2.14 log(10), whereas it was 3.1 log(10) for the 16 patients with AIDS (P < 0.01). Proviral DNA was detectable in 18 symptom-free patients with high CD4(+)-cell counts, in whom viral RNA was undetectable.

Base Sequence↗

Novel hepatitis B virus genotype a subtyping assay that distinguishes subtype Aa from Ae and its application in epidemiological studies.

The eight genotypes of hepatitis B virus (HBV) have different geographical distributions, virological characteristics, and clinical manifestations. A unique subtype of HBV genotype A (HBV/A) was reported in sub-Saharan Africa, raising the possibility that patients infected with this subtype (HBV/Aa ["a" for African and Asian]) may have different clinical outcomes than other HBV/A isolates (HBV/Ae ["e" for European]). Comparison between 30 HBV/Aa and 30 HBV/Ae isolates indicated that almost all HBV/Ae isolates had G at nucleotide (nt) 1809 and C at nt 1812, whereas HBV/Aa isolates had T1809/T1812. Taking advantage of these two single nucleotide polymorphisms (SNPs), a novel subtype-specific PCR assay in the X/precore/core region was developed. This assay was combined with a restriction fragment length polymorphism assay using BglII in a different region (nt 1984 to 1989), which has a SNP distinguishing HBV/Aa from HBV/Ae, resulting in 100% specificity for the combined assay. Application of the subtyping assay using sera from 109 paid donors in the United States indicated significantly different distributions of HBV/A subtypes among races; African-Americans, Caucasians, and Hispanics had HBV/Ae, whereas Asians had mainly HBV/Aa, suggesting that the HBV/Aa isolates may have been imported by recent immigration from Asia. In conclusion, the specificity and sensitivity of the combined subtyping assay were confirmed, and its usefulness was demonstrated in a practical context.

Adolescent↗

Studies of molecular pharmacophore/receptor models for GABAA/benzodiazepine receptor subtypes: binding affinities of substituted beta-carbolines at recombinant alpha x beta 3 gamma 2 subtypes and quantitative structure-activity relationship studies via a comparative molecular field analysis.

Binding affinities of a series of 44 beta-carbolines with various substituents at the 3-, 4-, 6- and 7-positions are reported at 5 distinct recombinant GABAA/benzodiazepine receptor (BzR) subtypes [alpha x beta 3 gamma 2 (x = 1-3, 5, 6)]. Many of these ligands displayed better selectivity for the alpha 1 containing GABAA isoform. The most selective BCCT 2 and SPH 195 (17) displayed potent affinity (Ki = 0.72 and 7.2 nM for the alpha 1 beta 3 gamma 2 receptor subtype, respectively) and an overall selectivity of 20 and 23 fold, respectively, for the alpha 1 beta 3 gamma 2 receptor subtype. These are the most selective ligands in vitro for the alpha 1 containing GABAA/Bz receptor isoform reported to date to our knowledge. QSAR studies of these ligands for each receptor subtype have been carried out via a Comparative Molecular Field Analysis (CoMFA) and an included volume analysis. Geometries and charge distributions of these ligands have been optimized using ab initio methods (J. Med. Chem., 1992, 35, 4001-4010). Active conformations of flexible 3-alkoxylated beta-carbolines have been examined via a CoMFA approach. QSAR studies via CoMFA support the previous hypothesis that beta-carbolines with different intrinsic activities may follow an alternative alignment rule when they bind into the pharmacophore/receptor site of the BzR. Examination of binding affinities of beta-carbolines by this modeling strategy has established some of the differences, in particular, topologic differences between the lipophilic pockets in the alpha 1 beta 3 gamma 2, alpha 2 beta 3 gamma 2, alpha 3 beta 3 gamma 2, alpha 5 beta 3 gamma 2 and alpha 6 beta 3 gamma 2 subtypes as well as some of the similarities among the pharmacophore/receptor models of these five distinct GABAA/Bz receptor subtypes.

Binding Sites↗

Pharmacological characteristics of alpha 2-adrenergic receptors: comparison of pharmacologically defined subtypes with subtypes identified by molecular cloning.

On the basis of extensive radioligand data and more limited functional data, three pharmacological subtypes of alpha 2-adrenergic receptors have been identified. More recently, three human genes or cDNAs for alpha 2-adrenergic receptors have been identified by molecular cloning. The relationship, however, among the pharmacologically defined subtypes and those identified by molecular cloning has not been clear. In order to resolve this issue, we have compared the pharmacological characteristics of the receptors identified by molecular cloning and expressed in COS-7 cells with the characteristics of the pharmacologically defined receptors in their respective prototypic tissue or cell line. The affinities (Ki values) of 12 subtype-selective alpha 2-adrenergic antagonists were determined for the alpha 2 receptor in the six preparations, by radioligand binding. Correlation analyses of the pKi values indicate that the alpha 2A subtype, as defined in the HT29 cell line, the alpha 2B receptor of the neonatal rat lung, and the alpha 2C subtype, as defined in an oppossum kidney cell line, correspond to the cloned human alpha 2-C10, alpha 2-C2, and alpha 2-C4 receptor subtypes, respectively.

Adrenergic alpha-Antagonists↗

Fine needle aspiration cytodiagnosis of Hodgkin's disease and its subtypes. II. Subtyping by differential cell counts.

Differential cell counts were performed on fine needle aspiration (FNA) smears from 96 cytologically diagnosed and subsequently biopsy-proven cases of Hodgkin's disease (HD). Reed-Sternberg cells and Hodgkin cells showed a definitely increasing trend in three major HD subtypes (as diagnosed on the smears): lymphocytic predominance (LP), mixed cellularity (MC) and lymphocytic depletion (LD). Lymphocytes, on the other hand, showed a decreasing trend between these subtypes. The differences in the percentages of Hodgkin cells, Reed-Sternberg cells and lymphocytes were highly significant (P less than .001). No trends (increasing or decreasing) were observed in the smear content of other reactive components (non-neoplastic histiocytes, eosinophils, plasma cells and neutrophils). In 88.0% to 95.0% of the cytologically diagnosed cases of LP, MC and LD subtypes, the percentages of Hodgkin cells plus Reed-Sternberg cells fell within a distinct range: less than 1.5% for LP, greater than or equal to 1.5% to less than 7.5% for MC and greater than or equal to 7.5% for LD. Analysis of the data based on histopathologic subtyping of the cases showed similar significant trends in the proportions of Hodgkin cells, Reed-Sternberg cells and lymphocytes, with 70.0% to 80.0% of the LP, MC and LD subtype cases within these ranges. These results demonstrate the validity of the subjective subtyping of HD on FNA smears in most cases.

Adult↗

Pituitary cell line GH3 expresses two somatostatin receptor subtypes that inhibit adenylyl cyclase: functional expression of rat somatostatin receptor subtypes 1 and 2 in human embryonic kidney 293 cells.

Using a polymerase chain reaction approach, we have studied the expression of somatostatin receptor (SSTR) subtypes in the GH3 rat pituitary cell line, a well established in vitro model for the cellular effects of somatostatin. We found that the previously identified SSTR1 and SSTR2 are the major subtypes expressed in this cell line. No other SSTR subtype was detected by our analysis. Northern blots confirmed that both subtypes, but not SSTR3, are expressed in GH3 cells. We studied the functional expression of both SSTR subtypes by transfection of their cDNAs into human embryonic kidney 293 cells. We found that somatostatin inhibited cAMP accumulation in human embryonic kidney 293 cells only when cells were transfected with either SSTR1 or SSTR2. This inhibition was blocked by treatment of the transfected cells with pertussis toxin, demonstrating that it is mediated by G proteins sensitive to this toxin. In addition, we provide pharmacological evidence that the endogenous SSTR2 subtype mediates inhibition of cAMP accumulation in intact GH3 cells. Our results contradict previous reports that concluded thsat neither SSTR1 nor SSTR2 is involved in inhibition of adenylyl cyclase. The reasons for this apparent contradiction are discussed. We conclude that both SSTR1 and SSTR2 are capable of coupling to pertussis toxin-sensitive G proteins to inhibit adenylyl cyclase.

Adenylate Cyclase Toxin↗

Fractionation of human H1 subtypes and characterization of a subtype-specific antibody exhibiting non-uniform nuclear staining.

Four histone H1 subtypes and H1(0) were fractionated from human placental nuclei and purified to homogeneity by a combination of Bio-Rex 70 chromatography and reverse-phase high-performance liquid chromatography (RP-HPLC). Polyclonal antibodies were generated in rabbits against one of these subtypes designated H1-3. Antibodies reacted only against this subtype in enzyme-linked immunosorbent assays and Western assays; subtype specificity was documented further by Western blotting of cell and nuclear extracts. They crossreacted with monkey H1, but not with H1 from other vertebrates tested. The epitope(s) recognized were mapped by immunoblotting against peptides prepared by cleavage with N-bromosuccinimide (NBS) and alpha-chymotrypsin; it includes the variant amino-terminal tail of the protein as well as a portion of the globular domain. The antibody stains mitotic chromosomes weakly but uniformly and, unlike antibodies that recognize total H1 which show uniform nuclear staining after indirect immunofluorescence localization, anti-H1-3 exhibits preferential labelling of the nuclear periphery. This non-uniform staining suggests compartmentalization of this subtype which may have functional significance with respect to differential chromatin condensation.

Amino Acid Sequence↗

Evidence for native NMDA receptor subtype pharmacology as revealed by differential effects on the NMDA-evoked release of striatal neuromodulators: eliprodil, ifenprodil and other native NMDA receptor subtype selective compounds.

NMDA increases the release of [14C]acetylcholine and [3H]spermidine or of [14C]GABA and [3H]dopamine from rat striatal slices. The pharmacology of these responses suggests that release of dopamine and GABA, acetylcholine, and spermidine is mediated, respectively, by three distinct NMDA receptor subtypes. IC50 values of compounds for the inhibition of dopamine and GABA release were closely matched, suggesting mediation by the same subtype. This receptor was generally more sensitive to all NMDA antagonists tested relative to that controlling acetylcholine or spermidine release (channel blockers, glycine antagonists, competitive antagonists and polyamine antagonists). The receptors controlling acetylcholine and spermidine release were characterised by lower antagonist sensitivity in general, and that controlling spermidine release was further defined by a marked insensitivity to ifenprodil, eliprodil, magnesium, dextromethorphan, dextrorphan, memantine, desipramine and polyamine spider toxins. In binding studies in which the displacement of 2 nM [3H]MK801 was studied in membranes prepared from a number of brain regions (in the presence of saturating concentrations of glutamate, glycine and spermidine) small regional differences in IC50 values were observed for a number of channel blockers, but no compound generated biphasic displacement curves that would allow masking of a particular subtype and it was not possible to detect binding components that were insensitive to memantine, dextrorphan dextromethorphan or desipramine. Ifenprodil produced biphasic displacement curves in the 1-day-old rat cortex and midbrain (with IC50 values of approximately 2 and 70 microM) and both ifenprodil and eliprodil displaced a small proportion (18%) of [3H]MK-801 with high affinity in the adult rat spinal cord. Displacement of [3H]MK801 by these compounds in all other adult brain regions (cortex, striatum, hippocampus, thalamus, pons, medulla, cerebellum) was monophasic and of low affinity. In general the subtype selectivity suggested by the release studies was not mirrored in the binding experiments, probably because of excessive heterogeneity of sites in the membrane preparations and to the subtype selectivity of [3H]MK801 itself.

Animals↗

Identification of diagnostic subtypes of chronic pelvic pain and how subtypes differ in health status and trauma history.

OBJECTIVE: Our primary aim was to identify subtypes of chronic pelvic pain and to compare the cases of women with the identified subtypes on health status and trauma history. We hypothesized that women with diffuse abdominal/pelvic pain would have greater health impairment and report more lifetime trauma than women with vulvovaginal pain or cyclic pain. STUDY DESIGN: We collected questionnaire data on 289 consecutive women patients from a university chronic pelvic pain clinic. From patient records, 1 gynecologist identified chronic pelvic pain subtypes on the basis of reported symptoms and the localization of pain during examination. We used analysis of covariance with pairwise contrasts. RESULTS: Seven diagnostic subtypes were identified. Patients with diffuse abdominal/pelvic pain had more trauma and worse mental and physical health status compared with patients with vulvovaginal pain and cyclic pain. Those patients with abdominal/pelvic pain also had poorer health than patients with neuropathic and fibroid pain. Endometriosis was unrelated to health status. CONCLUSION: There is immense need for further research to define subtypes of chronic pelvic pain.

Adolescent↗

Detection of Molluscum contagiosum virus (MCV) subtype I as a single dominant virus subtype in Molluscum lesions from a Turkish population.

BACKGROUND: Molluscum contagiosum has a worldwide occurrence and its primary mode of transmission is via direct human contact including sexual means. The aim of the study was to implement a polymerase chain reaction-based assay for detection and subtyping of Molluscum contagiosum virus (MCV) in skin lesions diagnosed with molluscum contagiosum in a large regional teaching hospital in Turkey. METHODS: For this purpose, a total of 61 patients were included in the study. Randomly selected single lesion from each patient was used to extract DNA material and a specific PCR reaction amplifying 393-bp- and 575-bp-long regions from MCV genome was used in the detection. Subtyping was carried out by digestion of the amplified 575-bp product with restriction endonuclease enzyme BamHI. Both amplified and restriction enzyme digested products visualized on agarose gel electrophoresis. RESULTS: All 61 molluscum cases (100%) included in the study contained MCV genetic material as demonstrated by the presence of 393- and 575-bp-long PCR amplified products. Restriction enzyme BamHI digestion of the 575-bp-long amplicon indicated that the infecting subtype in all the cases (100%) was MCV subtype I. CONCLUSIONS: Results of this study demonstrate that subtype I is the only infecting strain dominant in our region. Because the only consecutive molluscum patients admitted to our hospital were included in the study, our data do not rule out the possibility that other genotypes might be present in the Turkish population. However, it is not unreasonable to conclude that similar trends exist in the rest of the country. Results also show that a molecular-based diagnostic assay would be feasible in cases where diagnosis was deemed necessary.

Adolescent↗

Two subtypes (subgenotypes) of hepatitis B virus genotype C: A novel subtyping assay based on restriction fragment length polymorphism.

Recently hepatitis B virus genotype C (HBV/C) has been classified into geographically typical two subtypes (subgenotypes); HBV/C1 in Southeast Asia (Cs) and HBV/C2 in East Asia (Ce). Our aim is to develop a rapid subtyping assay and to examine the virological features of these two subtypes. Based on 171 HBV/C strains retrieved from the database, 17 single nucleotides polymorphisms (SNPs) were found between two subtypes. Taking advantage of five SNPs in non-overlapping polymerase region, a restriction fragment length polymporphism method with three endonucleases was newly developed for distinguishing between HBV/Cs and HBV/Ce. The method was applied to 49 HBV/C carriers from Japan and Hong Kong. The 24 in Hong Kong were classified into HBV/Cs, and the 25 in Japan were HBV/Ce, confirmed by sequencing. Some specific mutations were detected in the encapsidation signal; precore stop mutation (A1896), accompanied by a C-to-T substitution at nt 1858, was found in HBV/Ce strains, and another precore mutation (A1898), accompanied by a C-to-T mutation at nt 1856, was found in HBV/Cs. Especially, two closely linked mutations (A1896 and A1899) in HBV/Ce could stabilize the epsilon loop structure more efficiently and influece viral replication. Hence, these virological differences between the two subtypes might influence clinical features.

Journal Article↗

Epstein-Barr virus is associated with all histological subtypes of Hodgkin lymphoma in Vietnamese children with special emphasis on the entity of lymphocyte predominance subtype.

Early acquisition of Epstein-Barr virus (EBV) infection is prevalent in developing countries. We studied infectious mononucleosis (IM) and the subtypes of Hodgkin lymphoma (HL) with the status of EBV infection in Vietnamese children. Among the 46 cases of HL, the male-to-female ratio was 38:8, and the mean age at presentation was 6.6 years. Similar to the subtype distribution in developed countries, cases were classified as nodular sclerosis (NSHL) subtype in 56.5% (n = 26), mixed cellularity (MCHL) in 23.9% (n = 11), lymphocyte-rich classic (LRCHL) in 8.7% (n = 4), lymphocyte depletion (LDHL) subtype in 4.4% (n = 2), and nodular lymphocyte predominance (NLPHL) subtype in 6.5% (n = 3). However, in situ hybridization for EBV-encoded RNA revealed that the tumor cells were positive in 93.2% (41/44) of cases, including all 3 cases of nodular lymphocyte predominance HL. Expression of CD20 on Reed-Sternberg cells could be demonstrated in 17% (7/42) of classic HL. The high incidence of EBV in these cases of HL was correlated with an earlier mean age of presentation of primary EBV infection (ie, IM), at 5.3 years, in this patient population, compared with an average of 15 to 19 years reported in developed countries. This study demonstrates that in an area with an earlier mean age of onset of EBV infection, nearly all cases of pediatric HL, including all histological patterns, may be related to EBV infection. The association of NLPHL with EBV is unusual, and the literature is reviewed and discussed.

Adolescent↗