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QUANTITATIVE APPROACH TO THE STUDY OF BACTERIAL SPECIES.

Liston, J. (University of Washington, Seattle), W. Wiebe, and R. R. Colwell. Quantitative approach to the study of bacterial species. J. Bacteriol. 85:1061-1070. 1963.-The stability of strains of various species of gram-negative, rod-shaped bacteria was investigated by subculturing each strain through ten different media, testing the substrains so produced through a standard series of tests, and analyzing the resulting data by electronic computer. Strain stability was shown to be high [similarity coefficient (S) >/= 80%], and some evidence was obtained for species stability (S >/= 75%). The limits of variability for a species were studied by use of Pseudomonas aeruginosa; 33 P. aeruginosa strains (from the American Type Culture Collection) were tested and found to share a high level of similarity. An analysis was made of the distribution of positive characters among the strains, and the group was found to have a mean total of 35 characters (out of a possible 78 which were coded and included in the computer analyses) with a range of 33 to 39 positive characters in individual organisms. The frequency of occurrence of each positive character and the probability of mutual occurrence of pairs of positive characters were calculated. By use of the quantitative and qualitative data so obtained, a hypothetical Median Organism for the P. aeruginosa group was derived. The species may then be defined as consisting of all strains which show an S relationship of 75% or more with the Median Organism. The general applicability of this concept is discussed.

Aeromonas↗

Use of lung transplantation survival models to refine patient selection in cystic fibrosis.

Lung transplantation in cystic fibrosis may improve survival for patients with low 5-year predicted survival. Identifying characteristics that affect post-transplantation survival may improve patient selection and survival benefit. Using Cystic Fibrosis Foundation Patient Registry and United Network for Organ Sharing data, we identified 845 lung transplant recipients from 1991-2001, and 12,826 control patients from 1997. We used Cox proportional hazards models to identify variables that influence post-transplantation survival. To estimate the survival benefit of transplantation for patients affected by identified variables, we compared Kaplan-Meier survival curves of transplanted and control patients stratified by 5-year predicted survival. Post-transplantation survival improved annually. Youth, Burkholderia cepacia, and cystic fibrosis-related arthropathy increased the post-transplantation hazard of death. Compared with control subjects, transplanted adults with a 5-year predicted survival of less than 50% without B. cepacia or arthropathy have improved survival. Transplanted adults with B. cepacia, arthropathy, or a 5-year predicted survival of greater than 50% have decreased survival. Transplantation never improves survivorship for pediatric patients. Patients with arthropathy, B. cepacia infection, or younger age derive no aggregate survival benefit and must appraise carefully the high risk of decreased post-transplantation survival. Adult patients with low 5-year predicted survival without B. cepacia infection should receive priority for lung transplantation.

Adult↗

Neural sensitization model for multiple chemical sensitivity: overview of theory and empirical evidence.

This paper summarizes theory and evidence for a neural sensitization model of hyperresponsivity to low-level chemical exposures in multiple chemical sensitivity (MCS). MCS is a chronic polysymptomatic condition in which patients report illness from low levels of many different, structurally unrelated environmental chemicals (chemical intolerance, CI). Neural sensitization is the progressive host amplification of a response over time from repeated, intermittent exposures to a stimulus. Drugs, chemicals, endogenous mediators, and exogenous stressors can all initiate sensitization and can exhibit cross-sensitization between different classes of stimuli. The properties of sensitization overlap much of the clinical phenomenology of MCS. Animal studies have demonstrated sensitization to toluene, formaldehyde, and certain pesticides, as well as cross-sensitization, e.g., formaldehyde and cocaine. Controlled human studies in persons with self-reported CI have shown heightened sensitizability in the laboratory to nonspecific experimental factors and to specific chemical exposures. Useful outcome measures include spectral electroencephalography, blood pressure, heart rate, and plasma beta-endorphin. Findings implicate, in part, dopaminergic mesolimbic pathways and limbic structures. A convergence of evidence suggests that persons with MCS or with low-level CI may share some characteristics with individuals genetically vulnerable to substance abuse: (a) elevated family histories of alcohol or drug problems; (b) heightened capacity for sensitization of autonomic variables in the laboratory; (c) increased amounts of electroencephalographic alpha activity at rest and under challenge conditions over time. Sensitization is compatible with other models for MCS as well. The neural sensitization model provides a direction for further systematic human and animal research on the physiological bases of MCS and CI.

Autonomic Nervous System↗

Preparation of name and address data for record linkage using hidden Markov models.

BACKGROUND: Record linkage refers to the process of joining records that relate to the same entity or event in one or more data collections. In the absence of a shared, unique key, record linkage involves the comparison of ensembles of partially-identifying, non-unique data items between pairs of records. Data items with variable formats, such as names and addresses, need to be transformed and normalised in order to validly carry out these comparisons. Traditionally, deterministic rule-based data processing systems have been used to carry out this pre-processing, which is commonly referred to as "standardisation". This paper describes an alternative approach to standardisation, using a combination of lexicon-based tokenisation and probabilistic hidden Markov models (HMMs). METHODS: HMMs were trained to standardise typical Australian name and address data drawn from a range of health data collections. The accuracy of the results was compared to that produced by rule-based systems. RESULTS: Training of HMMs was found to be quick and did not require any specialised skills. For addresses, HMMs produced equal or better standardisation accuracy than a widely-used rule-based system. However, accuracy was worse when used with simpler name data. Possible reasons for this poorer performance are discussed. CONCLUSION: Lexicon-based tokenisation and HMMs provide a viable and effort-effective alternative to rule-based systems for pre-processing more complex variably formatted data such as addresses. Further work is required to improve the performance of this approach with simpler data such as names. Software which implements the methods described in this paper is freely available under an open source license for other researchers to use and improve.

Data Collection↗

Genetic variation of the MHC DQB locus in the finless porpoise (Neophocaena phocaenoides).

The Major Histocompatibility Complex (MHC) is a large multigene coding for glycoproteins that play a key role in the initiation of immune responses in vertebrates. The exon 2 region of the MHC DQB locus was analyzed using 160 finless porpoises from 5 populations in Japanese waters. The 5 populations were based on a previous mitochondrial DNA control region analysis, which showed distinct geographical separation. Eight DQB alleles were detected, and the geographical distribution of the alleles indicated that most of them are shared among the populations. Heterozygosity of the DQB alleles in each population ranged from 0.55 to 0.78, and for all 5 populations was 0.78. Low MHC variability is not a common feature in marine mammals, but the finless porpoise populations inhabiting coastal waters had a relatively high MHC heterozygosity. Balancing selection in the MHC DQB alleles of the finless porpoise was indicated by the higher rate of nonsynonymous than synonymous substitutions for PBR; however, an excess of hetrozygotes compared to expectation was not observed. This suggests that the MHC DQB locus in the finless porpoise may have been under balancing selection for a long evolutionary time period, and is influenced by genetic drift beyond the effect of balancing selection for short time periods in small local populations.

Alleles↗

Psoriatic arthritis joint fluids are characterized by CD8 and CD4 T cell clonal expansions appear antigen driven.

The CD8 alphabetaT cell receptor repertoire in joint fluid of individuals with active psoriatic arthritis contained an average of 32 major oligoclonal expansions in many variable genes of the TCR beta chain (BV) families, as shown by beta-chain CDR3 length analysis. Interestingly, a small number of oligoclonal expansions were shared between simultaneous samples of joint fluid and blood; however, most expansions found in joint fluid were not identifiable in blood emphasizing the immunologic specificity of the clonal events for the inflamed joint at a given point of time. The CD4 T cell joint fluid repertoire contained fewer and smaller oligoclonal expansions also largely restricted to the joint, suggesting that CD4 T cells participate perhaps by interacting cognitively to generate the CD8 clones. The inferred amino acid sequence of a single CD8 oligoclonal expansion revealed that they usually are composed of one or a few structurally related clones at the amino acid sequence level with beta-chains that encode identical or highly homologous CDR3 motifs. These were not shared among patients. Moreover, several clones that encoded the same amino acid sequence were found to be structurally distinct at the nucleotide level, strongly implying clonal selection and expansion is operating at the level of specific TCR-peptide interactions. The findings support a model of psoriatic arthritis inflammation involving extensive and selective Ag, likely autoantigen, driven intra-articular CD4, and CD8 T cell clonal expansions.

Amino Acid Sequence↗

[Prevalence of hepatitis C virus among HIV-infected patients in Area 2 of Madrid].

INTRODUCTION: The evolution of HIV infection, a rapid and fatal illness not long time ago, has become a chronic disease due to the implementation of new antiretroviral treatment. Therefore it is essential to focus on the management of concurrent illnesses such as chronic hepatitis C infection, specially as they share common routes of transmission. METHODS: A cross sectional survey was done to determine the prevalence of HIV and HCV coinfection, measuring different HIV and HCV variables among 651 HIV infected patients of a health area in Madrid. RESULTS: 500 patients (76.8%) were male and 151 female (23%). HCV serology was performed in all the patients and resulted positive in 45.7% (298) most of them drug users (84.8%). The CD4 cell count was lower in patients HIV-HCV coinfected compared to those HCV negative (p < 0.001). CONCLUSION: This study shows a high prevalence of HIV-HCV coinfection, mainly due to parenteral transmission. We emphasize the low percentage of coinfected patients treated with interferon and ribavirine which probably will increase in the future.

Adult↗

Prophylactic Oophorectomy: Reducing the U.S. Death Rate from Epithelial Ovarian Cancer. A Continuing Debate.

If instead of the title "Prophylactic Oophorectomy: Reducing the U.S. Death Rate from Epithelial Ovarian Cancer," the title were "Drug X Reducing the U.S. Death Rate from Epithelial Ovarian Cancer," there would be great media and medical attention worldwide to such a report. Correctly so. Regrettably, there probably is no new Drug X in the foreseeable future that will significantly reduce the death rate from ovarian cancer, be it Taxol&reg;, taxotere, topotecan, gemcitabine, or liposomal doxorubicin-although each may result in significant responses and some prolongation of median survival. Epithelial ovarian cancer is a much more complex disease than anyone envisioned, when it was believed that extensive debulking surgery and the newest cytotoxic chemotherapy would radically reduce the death rate from ovarian cancer in the United States. Over 20 years after the first patient was treated with cisplatin for epithelial ovarian cancer, the annual death rate from ovarian cancer continued to increase. Just in the past decade, the number of women in the United States dying from ovarian cancer has increased 18% (Fig. 1) [1]. Although ovarian cancer is estimated to account for 26,700 cases and 14,800 deaths in 1996, it is a low-prevalence disease in comparison with breast cancer, which in 1996 is estimated to account for 185,700 cases and 44,560 deaths. Inexplicably, similar to breast cancer, the lifetime risk for ovarian cancer in the United States continues to increase. The most recent Surveillance, Epidemiology and End Results (SEER) calculations of lifetime risk for ovarian cancer are that 1 in 55 women will develop ovarian cancer over their lifetime, or 1.8%, up from the 1970 figures of 1 in 70, or 1.4% [2]. The 1.8% baseline lifetime risk for the general population is used to estimate the lifetime risk of known ovarian cancer risk factors (Table 1). Even utilizing what are now believed to be two of the most effective cytotoxic drugs against stage III and IV epithelial ovarian cancer, Taxol&reg; and cisplatin, researchers reported that this resulted in an increase in the median disease-free survival of only five months, as compared with those women allocated to receive cisplatin and cyclophosphamide (median disease-free survival of 18 and 12.9 months, respectively), felt then to be the standard therapy [3]. Patients treated with Taxol&reg; and cisplatin survived a median of 14 months longer than those treated with cisplatin and cyclophosphamide. These results may improve in women whose cancers were optimally debulked to </=1 cm residual disease, since the current study included only women with residual cancer greater than 1 cm. Given these sobering statistics, the public health issue is whether prophylactic oophorectomy for two select groups of women may be one measure in reducing the mortality from ovarian cancer in the United States. The two groups of women are: A) women age 40 or older who undergo hysterectomy for non-cancerous uterine conditions and B) those with a family history of ovarian cancer. PROPHYLACTIC OOPHORECTOMY AT THE TIME OF HYSTERECTOMY IN WOMEN AGE 40 OR OLDER: Concerning the first group of women, researchers from the University of Miami reported that 4.5%-14.1% of women develop ovarian cancer after prior hysterectomy for non-ovarian conditions (Table 2) [4-9]. Utilizing their University of Miami experience and the three other similar series in the literature, they were able to determine the number of ovarian cancer patients who had previously undergone hysterectomy at age 40 or older for non-cancerous uterine conditions. Of the 2,632 ovarian cancer cases, they predicted that 5.2% (138) of the ovarian cancers could have been prevented if prophylactic oophorectomy were performed in women 40 years or older at the time of hysterectomy for benign disease. Confirming these results is a recent survey of the American College of Surgeons which reported that of 12,316 cases of ovarian cancer studied, 18.2% of these women had had a previous hysterectomy for benign disease with ovarian preservation, 57.4% of which were performed in women over the age of 40 [10]. Prophylactic oophorectomy in such cases has not been a uniformly accepted practice because it has been assumed that preserved ovaries continue to function normally and thus delay both the onset of osteoporosis and menopause with its effect on the cardiovascular system. However, as many as 30% of women have postmenopausal symptoms within 24 months of hysterectomy with preservation of the ovaries [11]. In addition, in an important cross-sectional study of bone density of premenopausal women who had undergone hysterectomy with ovarian conservation compared with a matched group which had not had hysterectomy, investigators reported that bone density in the hysterectomy group was significantly reduced [12]. They concluded that premenopausal women who had undergone hysterectomy with ovarian preservation will have a significantly low bone density, somewhat negating the value of ovarian preservation. Women age 40 or over who undergo prophylactic oophorectomy at the time of hysterectomy for benign uterine conditions can be started immediately on hormone replacement therapy, thus helping to prevent loss of bone density and the onset of osteoporosis. PROPHYLACTIC OOPHORECTOMY IN WOMEN WITH A FAMILY HISTORY OF OVARIAN CANCER: Since familial (also known as site-specific or hereditary) ovarian cancer is considered to be an autosomal dominant inheritance with variable penetrance, sisters and daughters of families with a history of familial ovarian cancer (two or more first-degree relatives [mother, sister, daughter-who share one-half of one's genes]) may have as high as a 50% chance of inheriting the deleterious gene. Easton has estimated that for women with a BRCA1 mutation, the lifetime risk for developing ovarian cancer by age 70 is 63% [13]. The lifetime risk for BRCA2 mutations has not yet been calculated [14]. We have included women with two or more first-degree or a first- and second-degree relative with epithelial ovarian cancer as having a history of familial ovarian cancer. However, the Breast Cancer Linkage Consortium stated that "families with three or more cases of ovarian cancer are generally considered to be examples of hereditary ovarian cancer" [15]. In 1982, we first recommended prophylactic oophorectomy in women with a history of familial ovarian cancer. This definition included any woman with two or more first-degree or first- and second-degree relatives with epithelial ovarian cancer [16]. Because of what appeared to be an apparent increase in frequency of familial ovarian cancer in the 1970s, the Familial Ovarian Cancer Registry was formed in 1981 to further evaluate familial ovarian cancer syndrome. The Registry, renamed the Gilda Radner Familial Ovarian Cancer Registry in 1989 in memory of the late comedienne after her death from ovarian cancer, has registered as of June 1996, 1,376 families with ovarian cancer. A report on the first 1,000 families was recently published [17]. Previously, it was estimated that 5%-10% of all ovarian cancers are hereditary. However, scientists from the University of Pennsylvania believed the estimate of ovarian cancer cases that are hereditary may be as high as 20%, based on their recent report of germline BRCA2 mutations in women with ovarian cancer but without a family history of ovarian cancer [18]. In the CASH study, researchers compared 493 women with ovarian cancer to 2,465 matched controls [19]. The relative risk for ovarian cancer for any first-degree relative was 3.6, resulting in a lifetime risk of 6.5% (Table 1). However, if the mother was the first-degree relative with ovarian cancer, the relative risk was 4.3 and the lifetime risk was 7.5%. Although the latter risk is almost four times that of the general population, it is currently not recommended that women with only one first-degree relative with ovarian cancer undergo prophylactic oophorectomy. This recommendation would also be applicable to women with a strong family history of breast cancer but only one case of ovarian cancer in their family and to hereditary non-polyposis colorectal cancer (Lynch Syndrome II) if there were only one case of ovarian cancer. However, if a first-degree relative in a family with only one case of ovarian cancer carries the same BRCA1 or BRCA2 mutation as the germline mutation in the patient with ovarian cancer, prophylactic oophorectomy would be indicated. Using complex segregation analysis in evaluating the observed number of cases of ovarian cancer as compared with the expected number of cases during the same time period in England and Wales, researchers from the Ovarian Cancer Screening Clinic at Kings College Hospital in the United Kingdom studied 391 ovarian cancer family pedigrees [20]. The overall risk for any first-degree relative (8.1%) was almost exactly the same as that of the CASH study (Table 1). However, if the mother developed ovarian cancer before the age of 45, the relative risk was 14.2 with a calculated lifetime risk of 25%. This young age is consistent with an inherited cancer even with only one first-degree relative. If this study can be confirmed by other researchers, then prophylactic oophorectomy in women who have one first-degree relative who developed ovarian cancer before the age of 45 would indeed be indicated. As previously stated, we have used the definition of familial ovarian cancer as any family with two or more first-degree (mother, sister, daughter) or first- and second-degree relatives (grandmother, aunt) with epithelial ovarian cancer, and, further, that these women are candidates for prophylactic oophorectomy after age 35 if they have completed their family and desire the surgery. In contrast, the Breast Cancer Linkage Consortium studying inherited ovarian and breast cancer stated that "families with three or more cases of ovarian cancer are generally considered to be examples of hereditary ovarian cancer, and families with a total of five or more breast or ovarian cancers in first- or second-degree relatives qualify" [15]. In a study by one member of the Breast Cancer Consortium of hereditary or familial ovarian cancer in southern Ontario, Canada, the author stated that "our distinction between hereditary and familial ovarian cancer is arbitrary. We have included families with three ovarian cancers or five or more cases of ovarian cancer or breast cancer in the hereditary group" [21]. The U.S. NIH Consensus Conference on Ovarian Cancer in its 1990 report did not define site-specific ovarian cancer in its statement that "less than 0.5% of women are at a significant risk (for the development of ovarian cancer) because of three hereditary ovarian cancer syndromes: (1) breast/ovarian cancer syndrome; (2) site-specific ovarian cancer; and (3) hereditary non-polyposis colorectal cancer (Lynch Syndrome II), colorectal, endometrial, GI, kidney, and ovarian cancer" [22]. With the "arbitrary" definition of site-specific ovarian cancer by the Breast Cancer Consortium and the absence of a definition by the NIH Consensus Conference on Ovarian Cancer, we continue to define familial or site-specific ovarian cancer as two or more first-degree or first- and second-degree relatives with ovarian cancer. As seen in Table 3, it can be very difficult to assess the risk of familial ovarian cancer. PRIMARY PERITONEAL CARCINOMA AFTER PROPHYLACTIC OOPHORECTOMY FOR A FAMILY HISTORY OF OVARIAN CANCER: In 1982, scientists from the National Cancer Institute reported that three women with a familial history of ovarian cancer developed widespread adenocarcinoma "indistinguishable histopathologically from ovarian cancer" 1, 5, and 11 years after undergoing prophylactic oophorectomy [23]. These three cases were from 16 families in which 28 women had undergone prophylactic oophorectomy. This important report brought into question the value of prophylactic oophorectomy for women in such families. To study this problem utilizing members of the Gilda Radner Familial Ovarian Cancer Registry, we evaluated the women in the Registry from its initiation in 1981 through July 1992 [24]. At that time, the Registry had registered 931 families totaling 2,221 cases of familial ovarian cancer. Of the 324 women who had undergone prophylactic oophorectomy, 103 had two or more first-degree relatives, 166 had a first- and a second-degree or more relative, 41 had two or more second-degree relatives, and 14 had other relatives with ovarian cancer. Six, or 1.8%, of these 324 women developed primary peritoneal carcinoma indistinguishable from ovarian cancer 1, 2, 5, 13, 15, and 27 years after prophylactic oophorectomy. Of these six women, whose ages ranged from 43 to 75, five had two or more first-degree relatives with ovarian cancer and the sixth had three second-degree relatives with ovarian cancer (Figure 2). The Registry was able to confirm primary peritoneal carcinoma similar to ovarian adenocarcinoma and previously normal ovaries in all six cases. To date, there have been 12 cases of primary peritoneal carcinoma after prophylactic oophorectomy for a family history of ovarian cancer (Table 4). However, there have also been five cases of stage IA ovarian cancer diagnosed in women undergoing prophylactic oophorectomy for a family history of ovarian cancer. Although prophylactic oophorectomy will provide 100% protection against the development of ovarian cancer, it is clear that a very small fraction of such women will subsequently develop primary peritoneal carcinoma. Whether the inherited BRCA1 and BRCA2 mutations that result in familial ovarian cancer also cause primary peritoneal carcinoma is as yet unknown. All such women are followed closely post prophylactic oophorectomy by physical examination and CA125 blood testing. In conclusion, it is posited that prophylactic oophorectomy in women with a history of familial ovarian cancer who have completed their family by age 35 and desire prophylactic oophorectomy and in women age 40 or older who undergo hysterectomy for benign uterine conditions may result in a significant decrease in the death rate from ovarian cancer - a disease in search of a highly sensitive screening test(s) and improved therapy.

Journal Article↗

Sequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus.

N1-methylation of G748 within 23S ribosomal RNA results in resistance to the macrolide tylosin in Streptomyces. In contrast, the Escherichia coli mutant lacking N1-methylation of G745 exhibits increased resistance to viomycin, in addition to severe defects of growth characteristics. Both methylated guanines are located in hairpin 35, in domain II of prokaryotic 23S rRNA. G748 and G745 are modified by related S-adenosylmethionine-dependent methyltransferases (MTases), TlrB and RrmA respectively. Earlier sequence comparisons allowed identification of the AdoMet-binding site, however the catalytic site and the target-recognition region of these enzymes could not be delineated unambiguously. In this work, we carried out sequence-to-structure threading of the rRNA:m1G MTase family against the database of known structures to Identify those "missing regions". Our analysis confirms the earlier prediction of the AdoMet-binding site, but suggests a different location of the putative catalytic center than was previously postulated. We predict that RrmA and TlrB possess two regions that may be responsible for specific interactions with their target nucleic acid sequences: a putative Zn-finger domain in the N-terminus and the variable domain close to the C-terminus, which indicates that 23S rRNA MTases exhibit the primary structural organization distinct from other nucleic acid MTases, despite sharing the common catalytic domain.

Amino Acid Sequence↗

Using predicted disease outcome to provide differentiated treatment of early rheumatoid arthritis.

OBJECTIVE: To determine the usefulness of a prediction model for making treatment decisions in early rheumatoid arthritis (RA). METHODS: In 152 patients with early RA, progression of radiological damage during the first year [Sharp-van der Heijde (SH) score > 0] was assessed and used to define actual disease outcome. Available variables at baseline were entered in a multivariate regression analysis with progression score as dependent variable. This model was used to predict disease outcome in every patient. Using the standard deviations of the predicted disease outcome, patients were divided into 3 groups: (1) severe disease: high probability (> or = 0.8) for progression > 0, (2) mild disease: high probability (> or =0.8) for progression < or = 0, and (3) not classified: no high probability for either option. It was determined how many patients could be classified by using this model. RESULTS: One hundred nine patients (71.7%) showed joint damage progression during the first year. Baseline variables available were: age, sex, duration of symptoms, duration of morning stiffness, patient's global assessment of disease activity, Health Assessment Questionnaire score, swollen and painful joint count, bilateral compression pain in metatarsophalangeals, rheumatoid factor positivity, erythrocyte sedimentation rate, shared epitope positivity, SH-score, and the presence of erosions. The R2 value (approximately variation explained) of the prediction model was 0.36. By using this model 46.3% of patients could be classified as having severe disease, 0% as having mild disease, and 53.7% could not be classified. CONCLUSION: To be able to make treatment decisions in early RA based on predicted disease outcome, a better prediction of disease outcome is needed, making the search for better prognostic variables urgent.

Aged↗

Antigenic variation among group A streptococcal M proteins. Nucleotide sequence of the serotype 5 M protein gene and its relationship with genes encoding types 6 and 24 M proteins.

The 1479-base pair (bp) nucleotide sequence of the serotype 5 M protein gene (smp5) from Streptococcus pyogenes contains three distinct types of tandemly repeated sequences, designated A, B, and C. Repeat A (21 bp x 6, in the 5'-half of smp5), shares no homology with the types 6 or 24 M protein genes (Hollingshead, S. K., Fischetti, V. A., and Scott, J. R. (1986) J. Biol. Chem. 261, 1677-1686; Mouw, A. R., Beachey, E. H., and Burdett, V. (1988) J. Bacteriol., in press). Repeat B (75 bp x 3.6, in the center of smp5) is also present in the M6, but not in the M24 gene. Repeat C (105 bp x 2.7, just distal to the B repeats) shares homology with repeats in both the M6 and M24 genes. All three genes share extensive homology in their 3'-halves and in 5' sequences encoding the N-terminal signal peptides, but between these two regions there are highly variable sequences that are responsible for antigenic diversity. These relationships suggest that both intergenic and intragenic recombination has occurred during the evolution of distinct M protein serotypes. All three M proteins contain conserved hydrophobic and proline-rich sequences at their C-terminal ends, suggestive of a membrane anchor and a peptidoglycan spanning region.

Amino Acid Sequence↗

[A study of interstitial pneumonia associated with collagen vascular disease--comparison with the data of idiopathic pulmonary fibrosis].

To clarify the pathogenesis of idiopathic interstitial pneumonia (IIP), we compared the data of interstitial pneumonia (IP) associated with collagen vascular disease (CVD) with those of idiopathic pulmonary fibrosis (IPF). These disorders are found to have similar clinical, radiographic, and morphological findings, and lung function. However, the in vitro behavior of fibroblasts from CVD-IP and IPF, and the detection of soluble ICAM-1 were different. Further, in the T cell receptor repertoire, the predominance of different genes was found in bronchoalveolar lavage cells from CVD and IPF. These differences could partly explain the variability of IP pattern seen in CVD. In summary, our results indicate the possibility that CVD-IF and IPF result from different mechanisms although they share the same spectrum of pulmonary changes.

Collagen Diseases↗

Body composition and blood pressure in children based on age, race, and sex.

We evaluated 675 nine- and twelve-year-old children for body composition and circulatory differences based on age, race, and sex. The specific variables measured included height, weight, triceps and subscapula skinfolds, body mass index, percentage fat, fat-free weight, and systolic, diastolic, and mean arterial blood pressures. A 2 x 2 x 2 factorial multiple analysis of variance (MANOVA) test of significance showed body composition and blood pressure differences (P < .01) for race, age, and sex. The univariate test of the specific variables within the factors showed that black children had higher fat-free weights and lower fat levels but higher blood pressure values (P < .05) than white children. Boys had lower fat levels than girls, and the older children had higher values on the body composition variables but not on blood pressure. Zero order correlations between body composition and blood pressure ranged from 0.14 to 0.55; systolic blood pressure and body weight shared the highest correlation. These data show that, although black children have less body fat than white children, they are heavier and have higher blood pressure. We hypothesize that some aspect of fat-free body weight may contribute to hypertension in black individuals.

Age Factors↗

Children's sensitivity to syllables, onsets, rimes, and phonemes.

It has been argued that children's performance on phonological awareness tasks varies with the linguistic level that is tapped by the task. For example, tasks that involve syllables are thought to be easier than tasks that involve lower-level linguistic units, and tasks that tap the level of onsets are thought to be easier than tasks that require access to single phonemes. In previous research, however, the linguistic status of a unit has often been confounded with its size. Five experiments were carried out in an attempt to disentangle these variables and so to provide a better test of the linguistic status hypothesis. In the first study, preschoolers and kindergartners more readily judged that two stimuli shared a beginning sound when that sound was an onset on its own than when it was part of a cluster onset. In two additional experiments, there was an advantage for syllables over rimes in kindergarten and first-grade children when the shared units occurred in the middle syllables of trisyllabic stimuli. The superiority for syllables was largely masked in two other studies in which the stimuli that shared a unit rhymed. This latter result suggests that children's familiarity with rhyme can override the syllable advantage. Overall, the results support the linguistic status hypothesis by indicating that effects of linguistic level on phonological sensitivity cannot always be reduced to effects of unit size.

Child↗

CDR3 sequence motifs shared by oligoclonal rheumatoid arthritis synovial T cells. Evidence for an antigen-driven response.

T lymphocytes reactive with as yet undefined joint-localized foreign or autoantigens may be important in the pathogenesis of RA. Molecular studies demonstrating skewed T cell antigen receptor (TCR) variable gene usage and selective expansion of particular T cell clones within the synovial compartment support this view. Based on our recent study documenting selective expansion of V beta 17+ T cells in RA, we have pursued the identification of T cells relevant to the disease process, in an informative patient, by combining molecular analysis of freshly explanted RA synovial tissue V beta 17 TCR transcripts with in vitro expansion of V beta 17+ synovial tissue T cell clones. Peripheral blood V beta 17 cDNA transcripts proved heterogeneous. In contrast, two closely related sequences, not found in the peripheral blood, dominated synovial tissue V beta 17 transcripts, suggesting selective localization and oligoclonal expansion at the site of pathology. CD4+, V beta 17+ synovial tissue-derived T cell clones, isolated and grown in vitro, were found to express TCR beta chain transcripts homologous to the dominant V beta 17 synovial tissue sequences. One clone shares with a dominant synovial tissue sequence a conserved cluster of 4/5 amino acids (IGQ-N) in the highly diverse antigen binding CDR3 region, suggesting that the T cells from which these transcripts derive may recognize the same antigen. These findings have permitted a complete characterization of the alpha/beta TCR expressed by putatively pathogenic T cell clones in RA. Functional analysis suggests that the conserved CDR3 sequence may confer specificity for, or restriction by, the MHC class II antigen, DR4.

Aged↗

Identification of MART-1-specific T-cell receptors: T cells utilizing distinct T-cell receptor variable and joining regions recognize the same tumor epitope.

Tumor-specific cytotoxic T lymphocytes (CTLs) can mediate tumor regression in patients with metastatic melanoma and play a central role in the immune response to cancer. The recent identification of shared melanoma antigens has raised the possibility of a limited melanoma-specific T-cell receptor (TCR) repertoire, but subsequent studies have been controversial and difficult to interpret without knowing which tumor-associated antigens (TAAs) are being recognized by specific TCRs. However, the recent cloning of several melanoma TAAs now allows for the identification of the specifically recognized TAA and its epitope. We evaluated the TCR of two clonal CD8+ CTL lines, A42 and 1E2, from two HLA-A2+ patients with metastatic melanoma. Both CTL lines were MART-1 specific, and both demonstrate reactivity to the same epitope when presented in an HLA-A2.1 context. The TCR genes of the two clones were sequenced. All of the productively rearranged A42 TCR beta chain genes were V beta 7/D beta 2.1/J beta 2.7/C beta 2; the TCR alpha chain genes were V alpha 21/J alpha 42/C alpha. The 1E2 TCR beta chain genes were V beta 3/D beta 1.1/J beta 1.1/C beta 1, and TCR alpha chains were V alpha 25/J alpha 54/C alpha. This study is the first report of TCR sequences specific for a melanoma epitope. These TCR clones may be useful for the development of more effective immunotherapies and in studies of the mechanism of T-cell recognition of tumor antigen. They also provide direct evidence that the immune system can provide more than one TCR capable of recognizing a TAA epitope.

Antigens, Neoplasm↗

Mesiodistal tooth crown dimensions of the primary dentition: a worldwide survey.

This analysis reports on a spatial-temporal survey of published studies of primary tooth crown dimensions in humans (80 samples). Mesiodistal data are analyzed for the 10 tooth crown dimensions. The purpose was to evaluate the numerous case reports (descriptive analyses of single samples) in the literature in order to assess patterning of variation 1) in tooth size, 2) among tooth types, 3) across sexes, 4) with space (historical affinity), and 5) with time. Sexual dimorphism is low in the primary dentition, averaging 2% across all 10 tooth types. All size distributions of the samples are positively skewed because of megadont native Australians. Europeans, who are most frequently represented in the literature, have the smallest tooth crowns of any continental grouping assessed. The method by Darroch Mosimann ([1985] Biometrika 72:241-252) of reducing size effects was used, basically standardizing the data variable-wise, and then ordinating groups on their factor scores. Principal components analysis produced just two canonical axes: overall size (68%) and a front-back (i1-i2-c vs. m1-m2) polarity (11%), based on the intergroup (not ontogenetic) covariance matrix. This second component discriminates between groups with relatively large anterior teeth (Europeans) and those where relatively more tooth substance is apportioned to the molars (Africans and Asians). Size differences predominate over shape between sexes from the same groups. Europeans have small teeth with comparatively large anterior dimensions. Asian and sub-Saharan African samples share features of average crown size but large cheek teeth. Indian and European samples show considerable overlap on both canonical axes, with average size overall but comparatively large anterior teeth. The few Amerindian samples are too variable to characterize. Based on comparisons of archaeological and living samples, tooth size reductions are documented here for Europe, India, and the Near East compared to tooth sizes of Neolithic and Mesolithic samples. The temporal changes parallel those documented elsewhere for the permanent dentition. The biological and anthropological relevance of these distributions is discussed.

Dentition↗

Data withholding in genetics and the other life sciences: prevalences and predictors.

PURPOSE: To better understand the variety and prevalence of data withholding in genetics and the other life sciences and to explore factors associated with these behaviors. METHOD: In 2000, a sample of 2,893 geneticists and other life scientists (OLS) at the 100 most research-intensive universities in the United States were surveyed concerning data withholding and sharing. The instrument was developed and pretested in 1999. The two primary outcome measures were withholding in verbal exchanges with colleagues about unpublished research (verbal withholding) and withholding as part of the publishing process (publishing withholding). The independent variables related to the personal characteristics, research characteristics of faculty, and previous experience with data withholding. RESULTS: A total of 1,849 faculty responded (64%): 1,240 geneticists and 600 OLS. Forty-four percent of geneticists and 32% of OLS reported participating in any one of 13 forms of data withholding in the three previous years. Publishing withholding (geneticists 35%, OLS 25%) was more frequent than verbal withholding (geneticists 23%, OLS 12%). In multivariate analyses, male gender, participation in relationships with industry, mentors' discouraging data sharing, receipt of formal instruction in data sharing, and negative past experience with sharing were significantly associated with either verbal or publishing withholding among either geneticists or OLS. CONCLUSIONS: Data withholding is common in biomedical science, takes multiple forms, is influenced by a variety of characteristics of investigators and their training, and varies by field of science. Encouraging openness during the formative experiences of young investigators may be critical to increased data sharing, but the effects of formal training do not appear straightforward.

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