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Biomedical subjects

T F Smith

Publications and source records attributed to T F Smith.

At least 253 records · Page 14Linked to original sources
PubMed1984

Analysis of Pneumocystis carinii cysts with a fluorescence-activated cell sorter.

Human sera from Pneumocystis carinii-infected patients and specific rabbit antisera have antibodies against the cyst form of the organism. Lung tissue concentrations from cortisone-treated C3H/HeN mice and six open lung biopsy-positive patients were centrifuged and suspended, and immunofluorescent staining was done. We utilized the fluorescence-activated cell sorter to analyze and sort P. carinii cysts from lung homogenates into a morphologically distinct population. A quantitative basis was used for the definition of the cyst population by displaying the frequency of cells as a function of parameter (fluorescence intensity and light scatter) expression. In 14 of 15 histogram analyses, P. carinii-infected homogenates were differentiated from normal- and bacterial-control homogenates. The parameter range of light scatter (size) was 2 to 8 micron, and the fluorescence intensity was greater than a threshold based on the histogram profile.

Animals↗
PubMed1983

Statistical characterization of nucleic acid sequence functional domains.

It has long been recognized that various genome classes were distinguishable on the basis of base composition and nearest neighbor frequencies. In addition Grantham et al. (8) have recently presented evidence that these distinctions are preserved at the level of codon usage. As discussed in this report it is now clear that these and related statistics can uniquely characterize the various functional domains of the genome. In particular peptide coding, intervening segments, structural RNA coding and mitochondrial domains of the vertebrate genome are uniquely characterizable. The statistical measures not only reflect understood functional differences among these domains but suggest others. The ability of these simple statistics of nucleic acid sequences to reflect so much of the encoded complex pattern information and/or effects of selective constraints is somewhat surprising. Here, we investigated the statistical measures most distinctive of the various domains and then linked them to our current understandings in so far as possible.

Animals↗
PubMed1983

Regulatory pattern identification in nucleic acid sequences.

In addition to the sequence homologies and statistical patterns identified among numerous genetic sequences, there are subtler classes of patterns for which most current computer search methods offer very limited utility. This class includes various presumptive eukaryotic regulatory sites. A critique of the often employed consensus and local homology methods suggests the need for new tools. In particular, such new methods should use the positional and structural data now becoming available on exactly what it is that is recognized in the DNA sequence by sequence-specific binding proteins.

Animals↗
PubMed1983

Mapping the order of DNA restriction fragments.

A straightforward method was designed for mapping the order of DNA restriction fragments obtained by a double and two single digestions, without the necessity of using a computer or a radioactive label. All possible solutions compatible with a pre-set level of error in the determination of sequence lengths are obtained. The primary assumptions are given, and the appropriate modifications of the algorithm are presented as a function of any assumptions one is unable (or unwilling) to make. Use of the method in connection with end-labeled fragments is also described.

Chromosome Mapping↗
PubMed1983

Optimal sequence alignments.

Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment between a set of codons for the chicken alpha- and beta-hemoglobin sequence when it is in fact discoverable by a more general treatment of gaps. Fundamental reasons for this are discussed.

Journal Article↗
PubMed1983

Comparison of growth of Mycoplasma pneumoniae on modified New York City and Hayflick media.

Modified New York City medium was compared to Hayflick solid medium without methylene blue, using 23 stock strains of Mycoplasma pneumoniae. Time to recovery was the same for both media, never longer than 24 hours. Sensitivity, as measured by colony counts, was significantly greater with Hayflick medium. Modified New York City medium may not be more rapid than Hayflick medium and may not offer significant advantages over the latter.

Culture Media↗
PubMed1983

Detection of chlamydial cervicitis by Papanicolaou stained smears and culture.

The ability of the cervical Papanicolaou (Pap) smear to detect cervicitis associated with Chlamydia trachomatis was investigated. Cultures and cervical cytology samples were obtained from 487 women seen at the Mayo Clinic Department of Obstetrics and Gynecology and at the Sexually Transmitted Disease clinic of the Olmsted County Health Department. Adequate pap smears contained endocervical or metaplastic cells. Thirty-seven patients had positive Chlamydia cultures; of these, 14 were cytologically suggestive of Chlamydia, 10 were negative but satisfactory, and 13 were unsatisfactory. Of the 450 patients with negative cultures, 21 had cytologic findings suggesting infection. Thus, of 35 cases suggestive cytologically, 14 (40%) were confirmed by culture. Of the 21 false-positive cytologies, eight were in postpartum women. Because of problems with specificity and inadequate smears, cervical cytology specimens should not replace culture as a means of detection, but can identify women who should be cultured for C. trachomatis.

Cells, Cultured↗
PubMed1983

Evaluation of calcium alginate-tipped aluminum swabs transported in Culturettes containing ampules of 2-sucrose phosphate medium for recovery of Chlamydia trachomatis.

Two calcium alginate-tipped wire swab specimens were obtained from 94 men and 106 women attending a sexually transmitted disease clinic. One swab was extracted thoroughly in 2-sucrose phosphate (2SP) immediately after obtaining the specimen. The second swab was returned to the Culturette cylinder (Marion Scientific, Kansas City, MO), and the ampule containing 2SP was crushed to moisten the swab during transport to the laboratory. After receipt in the laboratory, the swab was removed from the Culturette and extracted into 2 mL of 2SP. Both specimens then were cultured for the presence of Chlamydia trachomatis in McCoy's cells. C. trachomatis was recovered from 22 of 94 men (23.4%); 16 isolates came from both the Culturette swabs and vials. Six isolates were recovered exclusively from vials. Of 106 women, 13 (12.3%) were positive for C. trachomatis. In five instances, both vials and swabs yielded C. trachomatis; the organism was recovered eight times from vials but not swabs. The 2SP transport system for the 200 specimens was superior to the Culturettes for the recovery of C. trachomatis (P less than 0.01). Based on our results, swab specimens taken for laboratory diagnosis of C. trachomatis should be extracted immediately after collection in a vial containing 2SP. In addition, experiments comparing swab fibers indicated that there was a trend indicating higher inclusion counts with rayon-tipped swabs, compared with those containing calcium alginate. Because of possible toxicity of substances in calcium alginate fibers for several organisms causing sexually transmitted disease, rayon-tipped swabs or swabs of other composition should be used.

Alginates↗
PubMed1982

Hierarchical analysis of influenza A hemagglutinin gene sequences.

Five recently sequenced hemagglutinin genes from Influenza A virus strains are studied for similarities in a hierarchical fashion. The sequences are compared for similarity, first on the level of sequence homology, and then on several progressively more general levels. Though the HA1 subsequences contain regions where homology drops to that of a Monte Carlo generated reference value, subsequent tests reveal great similarity due to constraints on the level of amino acid sequence. Other tests detect statistically significant differences between subtypes due to constraints acting below the level of amino acid sequence, such as the 2 degrees structure of the viral RNA, or involving translation of the mRNA. The general applicability of the hierarchical approach to sequence analysis is discussed.

Base Sequence↗
PubMed1982

Between history and physics.

Biology has traditionally occupied a middle ground between the determinism of classical physics and the uncertainties of history. These issues are analyzed with respect to statistical laws which are applied to the prebiotic domain and strategy laws which characterize evolutionary biology. The differences in approach between biology and physics are discussed in detail. The origin of life is discussed in the context of physical chemical laws. A scenario for biogenesis is presented in terms of known molecular hardware. Evolutionary biology is then examined with respect to the kinds of laws that are possible in a domain where thermal fluctuations (mutations) have macroscopic effects. Game theory is employed to demonstrate the kinds of theory appropriate to this historical domain. The transition point between physics and history is the origin and development of the code. This is discussed and it is concluded that we are not yet able to assign the code to either the deterministic domain or to the arena of history.

Animals↗
PubMed1982

Prevalence of antibody to Chlamydia in renal transplant recipients and other population groups.

The serologic response to Chlamydia was determined with three sequential serum specimens from 25 renal transplant recipients (RTR) and from 25 blood donors who were matched for age and sex with the study group. Antibodies to Chlamydia were also measured in serum specimens from several other populations. The geometric mean titers (GMT) were significantly higher (P less than 0.05) for infants with pneumonia (1:6927) and women attending a sexually transmitted disease (STD) clinic (1:35) compared with pregnant women (1:25), normal infants, less than 23 weeks of age (1:11), and RTR (1:13). Titer increases of greater than or equal to fourfold were detected in 4 of 25 (16%) RTR, but could not be correlated with clinical pneumonia. Because of the high background prevalence (20% in RTR, 80% in STD patients), combined with low GMT of chlamydial antibody in these groups, the serologic diagnosis of respiratory tract infections in immunosuppressed adults required serial serum specimens.

Adult↗
PubMed1982

Acridine orange staining of Pneumocystis carinii.

Acridine orange was used to stain smears of mouse lung which contained cyst and trophozoite forms of Pneumocystis carinii. Trophozoite forms stained yellow to orange; however, cyst forms did not stain. Acridine orange is a rapid and sensitive method for demonstrating trophozoites of P. carinii in mouse lung tissue.

Acridine Orange↗