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PubMed2006

JAK2(V617F): Prevalence in a large Chinese hospital population.

Recently, the JAK2(V617F) mutation was found in patients with myeloproliferative disorders (MPDs), including most with polycythemia vera (PV). The mutant JAK2 has increased kinase activity, and it was shown to be pathogenic in mouse models. Herein, we analyzed blood samples randomly collected from a clinical laboratory. Surprisingly, as many as 37 samples from a total of 3935 were found positive for the JAK2 mutation. However, only one of these samples had blood test results indicative for probable PV, but several had nonhematologic diseases. On average, samples with the mutation had normal red cell counts but significantly higher white blood cell and platelet counts, although most were within the normal range. The data suggest that the JAK2(V617F) mutation is apparently much more common than MPDs. Its occurrence may be a prelude to full blood cell abnormalities and other diseases, but it cannot by itself diagnose MPDs.

Adult↗

PubMed2000

Cell senescence and human aging: where's the link?

Normal human cells will not divide forever in culture. After a defined number of passages, every culture enters a viable non-dividing state termed senescence. This led to the proposal that the progressive accumulation of senescent cells contributes to (but does not exclusively cause) the aging process. Data now suggest that cell senescence, like apoptosis, occurs as an anti-cancer mechanism. In vivo, extremely low rates of division occur over very long periods of time. Thus, by the end of its lifespan, an organism has performed a surprisingly large amount of cell turnover. In a normal culture the fraction of senescent cells increases smoothly with proliferation in vitro. This process can be accurately modelled by the progressive loss of telomeric sequence (proposed as a counting mechanism for senescence). Telomere length is usually maintained by the enzyme telomerase (repressed in many human tissues). Re-introduction of telomerase prevents the onset of senescence. However, data suggest that a separate telomere-independent pathway exists. Evidence that this pathway is present in humans is now emerging.

Aging↗

PubMed2005

Disruption of murine Tenr results in teratospermia and male infertility.

Gametes rely heavily on posttranscriptional control for their differentiation. Translational control, alternative splicing, and alternative processing of the 3' end of mRNAs are all common during spermatogenesis. Tenr, which encodes a highly conserved 72-kDa protein, is expressed solely in germ cells of the testis from the mid-pachytene stage until the elongating spermatid stage. TENR contains a double-stranded RNA binding domain, is localized to the nucleus, and is phylogenetically related to a family of adenosine deaminases involved in RNA editing. We show here that targeted mutation of the Tenr gene causes male sterility. Tenr mutant males have a reduced sperm count, and Tenr-/- sperm show a decrease in motility and an increase in malformed heads. Despite their sterility, some epididymal sperm from Tenr mutants have normal morphology. The ability of Tenr mutant sperm to fertilize zona pellucida-free oocytes and to bind to, but not fertilize, zona pellucida-intact oocytes suggests that the normal-appearing sperm are not able to penetrate the zona pellucida. These data suggest that TENR plays an essential function in spermatid morphogenesis.

Amino Acid Sequence↗

PubMed2003

Prevalence and clinical implications of insertions in the HIV-1 p6Gag N-terminal region in drug-naive individuals initiating antiretroviral therapy.

We assessed the prevalence and clinical impact of insertions within the HIV-1 p6Gag proline-rich (PTAP) region on initial antiretroviral therapy response in 461 HIV-infected, drug-naive individuals initiating therapy in British Columbia, Canada between June 1996 and August 1998. HIV p6Gag insertions were detected by nested RT-PCR of extracted patient plasma followed by direct DNA sequencing. Insertions were observed in 70 of 423 successfully genotyped samples (16.5%). HIV p6Gag insertions were significantly associated with a lower baseline CD4 cell count (P<<0.05) and the presence of basic amino acids at key positions in the HIV envelope V3 loop linked to a syncytium-inducing phenotype (P<<0.05). After adjusting for baseline factors, no effect of HIV p6Gag insertions was observed on time to virological success (pVL < or = 500 copies/ml), virological failure (subsequent confirmed pVL > or = 500 copies/ml) or immunological failure (confirmed CD4 count below baseline), as evaluated by Kaplan-Meier methods and Cox proportional hazard regression (P>0.1). The data suggest that HIV p6Gag insertions are not exclusively related to drug resistance and may not influence response to antiretroviral therapy, but may be linked to sequence variations in the HIV envelope.

Adult↗

PubMed2005

[Analysis of genetic polymorphism in randomized donor's HPA 1-16 antigens and establishment of typed platelet donor data bank].

To study the genetic polymorphism of HPA 1-16 platelet antigen alleles among unrelated volunteer donors and establish a typed platelet donor panel in Handan, typing was perfomed by polymerase chain reaction using sequence-specific primers (SSP-PCR); 148 random unrelated blood donors in Handan were genotyped for each of the HPA 1-16 antigen. The gene frequencies were analyzed and the genetype frequencies were determined by direct counting, and these data were compared with HPA distribution among various population by the chi-square test. The results indicated that HPA-1a, 2a, 4a-14a, 16a genes were found among the 16 HPAs in every sample tested. Monomorphic HPA-4a, 7a-14a, 16a were found in the samples. For HPA-1, 2, 5 and 6, a/a homozygosity was predominant with frequencies of 0.9595, 0.8108, 0.9865, 0.9797, respectively, and none of HPA b/b was found in the samples. HPA-1b, 2b, 5b, 6b were rarely found among subjects. HPA-15 had the greatest heterozygosity with a gene frequency of 0.2230, 0.5270, 0.2500 for HPA15a/15a, HPA15a/15b, HPA15b/15b, respectively. HPA-3 showed the second greatest heterozygosity with a gene frequency of 0.3851, 0.5135, 0.1014 for HPA3a/3a, HPA3a/3b, HPA3b/3b, respectively. HPA genotype frequencies showed a good fit to Hardy-Weinberg equilibrium. HPA1-5 gene frequencies for Chinese people in Handan were consistent with those of Chinese people in Shijiazhuang (P > 0.05). Among the HPA1-13, -15, the frequencies of HPA-1, -2, -6 for Chinese people in Handan differed appreciably from those for Chinese people in Taiwan (P < 0.05), others were similar to those of Chinese people in Taiwan. Among the HPA 1 - 8, a similarity was noted between Chinese people in Handan and Koreans (P > 0.05), except for HPA-3. Frequencies of HPA-1, -2, -5 significantly were differed from those in African Americans, as compared with HPA 1-5 (P < 0.05). Comparison of gene frequencies from HPA-1 and -5 showed significant differences between Chinese people in Handan and people in UK (P < 0.05). It is concluded that HPA-2, -3, -5, -15 of people in Western region of China have polymorphism, incompatible frequency of HPA antigen distribution is higher, which inevitably results in the increase of immunologic exposure, therefore attention must be paid to the importance of HPA-2, -3, -5, -15 in clinical disorders. This study for the first time completely analyses HPA1-16 gene frequencies in China, and provides data for establishing a typed platelet donor panel in Handan, China.

Antigens, Human Platelet↗

PubMed1990

DNA hybridization evidence of hominoid phylogeny: a reanalysis of the data.

Sibley and Ahlquist (1984, 1987) presented the results of a study of 514 DNA-DNA hybrids among the hominoids and Old World monkeys (Cercopithecidae). They concluded that the branching order of the living hominoid lineages, from oldest to most recent, was gibbons, orangutan, gorilla, chimpanzees, and human. Thus, a chimpanzee-human clade was indicated, rather than the chimpanzee-gorilla clade usually suggested from morphological evidence. The positions of the gibbon and orangutan branches in the phylogeny are supported by substantial evidence, but whether the chimpanzee lineage branched most recently from the human lineage or from the gorilla lineage remains controversial. The conclusions of Sibley and Ahlquist (1984, 1987) have been supported by several independent studies cited by Sibley and Ahlquist (1987), plus the DNA sequence data of Hayasaka et al. (1988), Miyamoto et al. (1988), Goodman et al. (1989, 1990), and the DNA-DNA hybridization data of Caccone and Powell (1989). The laboratory and data analysis methods have been criticized by Marks et al. (1988) and Sarich et al. (1989). In response to these critics, and for our own interests, we present a reanalysis of the Sibley and Ahlquist data, including a description of the corrections applied to the "raw counts." The validity of the laboratory methods is supported by the congruence of tree topology and delta values with those of Caccone and Powell (1989), although their tetraethylammonium chloride technique differs from the hydroxyapatite method in several respects. The utility of the T50H distance measure is indicated by its congruence with percent sequence divergence at least to delta T50H 30, as noted by Goodman et al. (1990). The Sibley and Ahlquist uncorrected data indicate that Pan is genetically closer to Homo than to Gorilla, but that Gorilla may be genetically closer to Pan than to Homo. Melting curves are presented for the pertinent experiments, plus one that includes representatives of most of the groups of living primates.

Animals↗

PubMed1993

Ratio of variance to mean of action potential counts for an auditory nerve fiber model with second-order refractory behavior.

Sequences of interval times were generated with the first- and second-order interval probability dependence proposed by Gaumond et al. [J. Neurophysiol. 48, 856-873 (1982)] to characterize cochlear nerve fiber spontaneous action potential (AP) sequences. The ratio F(T) of the variance to the mean of the count of APs in bins of T s was computed for the simulated sequences, and compared to the corresponding measure for cochlear nerve fiber data presented by Lowen and Teich [J. Acoust. Soc. Am. 92, 803-806 (1992)]. The simulations were generally consistent with the data in the range 15 < T < 100 ms.

Cochlea↗

PubMed1997

Analysis of protein domain families in Caenorhabditis elegans.

The Caenorhabditis elegans genome sequencing project has completed over half of this nematode's 100-Mb genome. Proteins predicted in the finished sequence have been compiled and released in the data-base Wormpep. Presented here is a comprehensive analysis of protein domain families in Wormpep 11, which comprises 7299 proteins. The relative abundance of common protein domain families was counted by comparing all Wormpep proteins to the Pfam collection of protein families, which is based on recognition by hidden Markov models. This analysis also identified a number of previously unannotated domains. To investigate new apparently nematode-specific protein families, Wormpep was clustered into domain families on the basis of sequence similarity using the Domainer program. The largest clusters that lacked clear homology to proteins outside Nematoda were analyzed in further detail, after which some could be assigned a putative function. We compared all proteins in Wormpep 11 to proteins in the human, Saccharomyces cerevisiae, and Haemophilus influenzae genomes. Among the results are the estimation that over two-thirds of the currently known human proteins are likely to have a homologue in the whole C. elegans genome and that a significant number of proteins are well conserved between C. elegans and H. influenzae, that are not found in S. cerevisiae.

Amino Acid Sequence↗

PubMed2006

Maximum likelihood inference of imprinting and allele-specific expression from EST data.

MOTIVATION: In a diploid organism the proportion of transcripts that are produced from the two parental alleles can differ substantially due, for example to epigenetic modification that causes complete or partial silencing of one parental allele or to cis acting polymorphisms that affect transcriptional regulation. Counts of SNP alleles derived from EST sequences have been used to identify both novel candidates for genomic imprinting as well as examples of genes with allelic differences in expression. RESULTS: We have developed a set of statistical models in a maximum likelihood framework that can make highly efficient use of public transcript data to identify genes with unequal representation of alternative alleles in cDNA libraries. We modelled both imprinting and allele-specific expression and applied the models to a large dataset of SNPs mapped to EST sequences. Using simulations, matched closely to real data, we demonstrate significantly improved performance over existing methods that have been applied to the same data. We further validated the power of this approach to detect imprinting using a set of known imprinted genes and inferred a set of candidate imprinted genes, several of which are in close proximity to known imprinted genes. We report evidence that there are undiscovered imprinted genes in known imprinted regions. Overall, more than half of the genes for which the most data are available show some evidence of allele-specific expression. AVAILABILITY: Software is available from the authors on request.

Alleles↗

PubMed1995

Changes in the viral mRNA expression pattern correlate with a rapid rate of CD4+ T-cell number decline in human immunodeficiency virus type 1-infected individuals.

The rate of disease progression varies considerably among human immunodeficiency virus type 1 (HIV-1)-infected individuals. Several cross-sectional studies have shown an association between the stage of HIV-1 disease and the viral burden or the relative levels of viral gene expression. To study the extent of HIV-1 transcription and replication and its correlations with disease progression, we quantified serial, longitudinal samples of blood cells from 10 HIV-1-infected individuals with markedly different rates of CD4+ T-cell number decline following seroconversion. After normalization for the input nucleic acid content, multiply spliced viral mRNA and unspliced viral RNA were quantified by competitive reverse transcription-PCR using oligonucleotide primers which flank the major tat/rev/nef splice junction and span an internal region of the gag open reading frame, respectively. Coamplification of internal cRNA template controls was used to normalize for variation in the efficiency of reverse transcription and in vitro enzymatic amplification. Similarly, proviral DNA was also quantified by competitive PCR performed within the linear range of amplification. Viral RNA was detected in the blood cells of each individual from all time points regardless of the rate of CD4+ T-cell decline. Unspliced genomic viral RNA rapidly increased in the blood cells from HIV-1-infected individuals who had a precipitously declining CD4+ T-cell number. In contrast, both unspliced and multiply spliced viral mRNAs remained relatively stable in the blood cells from HIV-1-infected individuals who have had a relatively benign clinical course. These data demonstrate that the extent of viral transcription and replication correlates with the rate of CD4+ T-cell number decline and that quantifying intracellular viral RNA is of potential prognostic value.

Base Sequence↗

PubMed2026

Non-structural maintenance of chromosome condensin I complex subunit H knockdown suppresses malignant progression of esophageal squamous cell carcinoma via the Wnt/β-catenin signaling pathway.

BACKGROUND: Esophageal squamous cell carcinoma (ESCC) remains a major cause of cancer-related mortality, and effective therapeutic targets are still limited. Non-structural maintenance of chromosome condensin I complex subunit H (NCAPH) has been implicated in tumorigenesis; however, its clinical relevance, functional roles, and underlying mechanisms in ESCC are not fully defined. We aimed to characterize the expression pattern, prognostic value, biological functions, and mechanistic basis of NCAPH in ESCC. METHODS: Public datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to evaluate NCAPH expression and clinical associations. Single-cell RNA sequencing (scRNA-seq) data were used to map cell-type-specific distribution of NCAPH in tumor and adjacent tissues. NCAPH was silenced in KYSE150 and KYSE510 cells using lentiviral short hairpin RNAs (shRNAs), followed by Cell Counting Kit-8 (CCK-8), colony formation, wound-healing, and Transwell migration/invasion assays. A nude mouse xenograft model was established to assess the effect of NCAPH knockdown in vivo. RNA sequencing (RNA-seq), quantitative polymerase chain reaction (qPCR), western blotting, and enzyme-linked immunosorbent assay (ELISA) were performed to explore potential mechanisms. RESULTS: NCAPH was consistently upregulated in ESCC across multiple cohorts and was associated with unfavorable clinicopathological features and poorer survival. Functional assays demonstrated that NCAPH knockdown significantly inhibited ESCC cell proliferation, migration, invasion, and clonogenic growth. In vivo, NCAPH silencing suppressed xenograft tumor growth. Mechanistically, transcriptomic profiling and molecular validation indicated attenuation of Wnt/β-catenin signaling following NCAPH depletion, accompanied by reduced β-catenin and downstream targets. CONCLUSIONS: NCAPH promotes malignant progression of ESCC, at least in part through activation of the Wnt/β-catenin pathway, and may serve as a potential biomarker and therapeutic target.

Esophageal squamous cell carcinoma (ESCC)↗

PubMed1996

Multifractals, encoded walks and the ergodicity of protein sequences.

A variety of statistical methods have been developed to explore correlations in protein and nucleic acid sequences. Such correlations have important implications for the evolution and stability of these macromolecules. Recently, a number of fractal analyses of sequence data have been developed. These analyses have considerable appeal as they are extremely sensitive to long range correlations and to hierarchical structures. One such analysis decodes sequence information into a random walk and the statistics of the resulting random walk is investigated. Anomalous scaling of such walks has been interpreted as indicative of a fractal structure. Alternatively, a generalized box counting analysis of decoded sequences can be used to establish multifractal properties. In this work, the connection between these two seemingly disparate approaches is established. This connection is exploited to investigate correlations in protein sequences. An ensemble consisting of a comprehensive data set of representative protein sequences is analyzed to establish the ergodicity of protein sequences. The implications of this ergodicity for information theoretical approaches to protein structure prediction is explored.

Amino Acid Sequence↗

PubMed1999

Antibody to human endogenous retrovirus peptide in urine of human immunodeficiency virus type 1-positive patients.

Human endogenous retrovirus (HERV)-like sequences are normal inherited elements that constitute several hundredths of the human genome. The expression of genes located within these elements can occur as a consequence of several different events, including persistent inflammation or genotoxic events. Antibodies to endogenous retroviral gene products have been found in a number of infectious, chronic, and malignant diseases, suggesting a role in disease initiation and progression. We studied human immunodeficiency virus type 1 (HIV-1)-infected patients for evidence of urine antibody to a HERV peptide and investigated correlates with clinical and laboratory parameters. Forty-three HIV-1-infected patients in documented asymptomatic, symptomatic, or AIDS stages of disease and 21 age- and gender-matched, uninfected controls were tested for antibody to HERV-related peptide 4.1. Urine specimens were examined in a blinded fashion with the Calypte Biomedical Corp. experimental enzyme immunoassay for antibody to peptide 4.1. Results were compared with demographic data, medical history, clinical state of disease, and results of other laboratory tests. Thirty-six percent of the asymptomatic (Centers for Disease Control and Prevention [CDC] category A) and 81.3% of both the symptomatic (CDC category B) and AIDS (CDC category C) patients were positive for antibody to HERV-related peptide 4.1. None of the controls were positive. In this study, antibodies to HERV-related peptide 4.1 were found more frequently in patients with advanced stages (categories B and C) of HIV-1 disease than in those patients with an earlier stage (category A) of HIV disease. In HIV patients, severe immunosuppression, defined as having had at least one opportunistic infection, correlated with the expression of antibody to a HERV-related peptide.

Adult↗

PubMed2004

Selecting factors predictive of heterogeneity in multivariate event time data.

In multivariate survival analysis, investigators are often interested in testing for heterogeneity among clusters, both overall and within specific classes. We represent different hypotheses about the heterogeneity structure using a sequence of gamma frailty models, ranging from a null model with no random effects to a full model having random effects for each class. Following a Bayesian approach, we define prior distributions for the frailty variances consisting of mixtures of point masses at zero and inverse-gamma densities. Since frailties with zero variance effectively drop out of the model, this prior allocates probability to each model in the sequence, including the overall null hypothesis of homogeneity. Using a counting process formulation, the conditional posterior distributions of the frailties and proportional hazards regression coefficients have simple forms. Posterior computation proceeds via a data augmentation Gibbs sampling algorithm, a single run of which can be used to obtain model-averaged estimates of the population parameters and posterior model probabilities for testing hypotheses about the heterogeneity structure. The methods are illustrated using data from a lung cancer trial.

Algorithms↗

PubMed1995

Quantitative determination of DNA-binding parameters for the human estrogen receptor in a solid-phase, nonseparation assay.

Binding of transcription factors to specific sequences of DNA has been studied for more than a decade and has become a very productive field of research. This paper describes the application of the recently developed technique of scintillating microtitration plates in the study of protein-DNA interactions. A DNA sequence containing the classical consensus estrogen response element derived from the 5' upstream regulatory region of the frog vitellogenin gene was immobilized to scintillating microtitration plates. Equilibrium binding studies and kinetic studies were performed with [3H] estradiol labeled human estrogen receptor. The observed equilibrium dissociation constant (Kd) was 2.0 +/- 0.3 nM and the observed Hill coefficient of 2.0 indicated a positive cooperativity. Two association rate constants were observed, one slower of 0.3 x 10(6) M-1 min-1 for lower concentrations of estrogen receptor and one faster of 6.3 x 10(6) M-1 min-1 for higher concentrations. The dissociation rate was 0.005 min-1. The technique described has a potential in basic research concerning characterization of DNA binding. It is also well suited to applied research as a tool in high-throughput screening of compound libraries in the search of agents inhibiting transcription factor binding to DNA.

Animals↗

PubMed2004

Features of bacterial cellulose synthesis in a mutant generated by disruption of the diguanylate cyclase 1 gene of Acetobacter xylinum BPR 2001.

The diguanylate cyclase 1 (DGC1) (dgc1) gene in Acetobacter xylinum BPR 2001--a bacterial cellulose (BC) producer--was cloned and sequenced, and a DGC1 gene-disrupted mutant, strain DD, was constructed. The production and structural characteristics of the BC formed by DD were compared with those of the parental strain BPR 2001. BC production by DD was almost the same as that by BPR 2001 in static cultivation and in shake flask cultivation. However, in a jar fermentor DD produced about 36% more BC than the parental strain. DD produced suspended particle materials that cannot aggregate owing to their random structural characteristics in static cultivation; more uniformly dispersed BC pellicles and smaller BC pellets are produced on average in a jar fermentor, as reflected by the higher BC production by DD than by the parental strain in a jar fermentor. Micrographs of BC produced by DD revealed that the width of cellulose ribbons assemblies decreased as a result of differences in the ultrastructure and mechanism of formation of BC between the two strains. These results reveal that disruption of the dgc1 gene, which catalyzes synthesis of c-di-GMP (an effector of BC synthase), is not fatal for BC synthesis, although it affects BC structure.

Cellulose↗

PubMed1999

Low prevalence of the immunoglobulin-A-binding beta antigen of the C protein among Streptococcus agalactiae isolates causing neonatal sepsis.

Streptococcus agalactiae (Group B streptococcus, GBS) is the most important pathogen causing neonatal sepsis. The role of bacterial proteins contributing to pathogenicity in GBS infections has not yet been clearly determined, but the C protein complex has been suggested to be involved in both virulence and protective immunity. The aim of this study was to assess the prevalence of GBS strains bearing the gene encoding for the beta antigen of the C protein among clinical isolates from 68 neonates with sepsis, 45 newborns colonized without clinical signs of infection, and 50 isolates from pregnant women. The prevalence of the beta antigen gene in all three groups was low (24% vs. 19% vs. 22%) [corrected], and the differences between groups were not statistically significant. Clinical characteristics and cytokine plasma levels did not differ between septic patients with beta antigen-positive and -negative strains. The beta-antigen gene was not found among serotype III isolates, which accounted for roughly half of all the strains isolated. Thus, polymerase chain reaction (PCR) analysis based on the beta antigen gene seems not helpful for distinguishing invasive from colonizing GBS strains. A vaccine based on peptide antigens from the beta antigen of the C protein would most probably not provide protection against the majority of GBS isolates. When analyzing the PCR products of the C protein beta antigen gene by DNA sequencing, a genetic heterogeneity was observed, revealing small repetitive genetic elements within the amplified fragment, an observation that should be studied further.

Antigens, Bacterial↗

PubMed1995

Human papillomavirus infection in human immunodeficiency virus-seropositive women.

OBJECTIVE: To compare the prevalence of human papillomavirus (HPV) infections in women who are seropositive and seronegative for human immunodeficiency virus (HIV), and to determine if associations between HPV and cervical disease are altered in HIV-seropositive women. METHODS: In this cross-sectional study, 344 HIV-seropositive and 325 HIV-seronegative women underwent colposcopy and HPV DNA testing. RESULTS: Human immunodeficiency virus-seropositive women were more likely than HIV-seronegative women to have HPV DNA of any type detected (60 versus 36%, P < .001). Infections with HPV type 16 (27 versus 17%, P < .05), type 18 (24 versus 9%, P < .05), and more than one type of HPV (51 versus 26%, P < .05) were also more common in HIV-positive women. Although both latent HPV infection and HPV infections associated with cervical intraepithelial neoplasia (CIN) were more prevalent in the HIV-seropositive group, the ratio between these two types of infections was altered markedly in the HIV-seropositive women. Human immunodeficiency virus-seropositive women who were HPV-infected were significantly more likely to have CIN than were HPV-infected HIV-seronegative women, an increase observed at all levels of immunosuppression. Analysis of specific HPV types associated with latent HPV infection and CIN indicated that HIV seropositivity only minimally alters the known associations between specific types of HPV and cervical disease. CONCLUSION: Human papillomavirus infections are more common among HIV-seropositive women at all levels of immunosuppression. However, relationships between HIV and HPV are complex and cannot be explained completely by an increased susceptibility to new HPV infections in the immunosuppressed patient.

Adult↗