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Spears PA, Devine P, Finestone S. Abstract P4-18-03: Measuring what is important to patients in clinical trials: Hearing the patient's voice. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p4-18-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Patients who participate in clinical trials are important to clinical research and contribute to the advancement of medical discoveries. However, typical clinical trials do not always capture information that is important to patients: how they feel, function and survive. The only way to accurately measure how a patient feels or functions is to ask them. This can be done through the administration of health related questionnaires that are filled out by the patient without interpretation from anyone else; these are referred to as Patient Reported Outcomes (PROs). Although, PRO assessments have been used in clinical trials for the past 30 years through the collection of global quality of life (QOL) and later health related QOL (HR-QOL) measurements, the information has been too broad and has not been precise enough to use in drug approvals, descriptive drug label information or to inform other patients.
There is an effort to change the paradigm of PRO assessment to measure the information most relevant to patients in clinical trials. This includes measuring treatment toxicity, symptom burden and physical function. This is relevant information that other patients want to know about a specific treatment for a specific disease to help them in their treatment decision making. The voice of the patient is critical to assess these items, through PRO measurements. In order to ensure that PRO questionnaires are filled out during a clinical trial, there are ways to make them more acceptable to patients by involving patients in their development (what questions are asked/how many questions are asked/when they are given to patients/how they are given to patients). Patients can inform study teams on the acceptability, understandability and relevance of the questions being asked. Patients can be a key contributor to clinical trial development by identifying the questions that are most important to them and the best way to ask these questions during a clinical trial.
Patient advocacy and educational organizations like Cancer Information & Support Network (CISN) are advocating for changes in PRO collection in clinical trials. Based on information collected from many survivors, caregivers and advocates, a patient-centric clinical trial development model will be proposed. The model includes the involvement of patients as key stakeholders early in clinical trial development to incorporate PROs into clinical trials that are acceptable for patients to complete and the outcomes are meaningful and matter to future patients.
Citation Format: Spears PA, Devine P, Finestone S. Measuring what is important to patients in clinical trials: Hearing the patient's voice [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-18-03.
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Affiliation(s)
- PA Spears
- Cancer Information & Support Network, Auburn, CA
| | - P Devine
- Cancer Information & Support Network, Auburn, CA
| | - S Finestone
- Cancer Information & Support Network, Auburn, CA
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Spears PA, Devine P, Finestone S, Carbine N. Abstract P5-10-02: Clinical trials: "A holistic approach". Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p5-10-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Goal:
New and improved treatments depend on the completion of successful clinical trials. Our goal is to impact all aspects of the clinical trial process to enhance accrual and outcomes.
1) To provide patient focused feedback at the design phase of clinical trials
2) To increase health literacy about clinical trials at both the national and community level
3) To provide decision aids for individual trials
4) To provide patient focused staff communication trainings
Strategy: CISN principals are currently working with the following groups
National Clinical Trial Network
Academic Medical Centers: UCSF and Mayo
Industry: Genentech, Pfizer, Novartis, and Lilly
Nonprofit Organizations: AACR, Faster Cures, Susan G. Komen, SOCRA
CISN principals are working within the NCTN to accomplish strategies one and two. The goal is to branch out to more community venues in the future. A 2001 study by Lara et. al. reported that the consent process with its legalistic and confusing forms is itself a barrier to patient participation with 49% of eligible patients declining enrollment. We address these concerns by accomplishing strategies 3 and 4 above.
Action Taken
CISN is introducing the medical community to an array of issues affecting patients considering participation in clinical trials. They are also developing patient-centered, study specific, educational materials included as part of the informed consent process. These interventions may enhance patient literacy, improve patient satisfaction and advance public trust in the research enterprise, leading to responsible increased accrual and retention. Additionally, CISN has worked as a contractor for several biotech companies to develop patient educational materials for several studies.
Work done at the Clinical Trial Summit documented that 67% of professionals consenting patients have less than 6 hours of psychosocial training. To address that issue, CISN developed a training program for those professionals who administer consent. Two PhD psychologists where brought onboard as consultants to assist in the development of the training. To date CISN has conducted many trainings for various groups and will soon submit grants to partner with other organizations to translate the materials into Spanish and work with patient navigators to further ensure proper training in all communities.
Outcome
Interest in our methods and materials continues to grow. CISN was identified by Faster Cures as having "best practice" methods in the area of informed consent. We work closely with academic, government, other non-profits and industry researchers to help foster public awareness about the importance of medical research to daily life. CISN addresses these issues and presents various strategies that might be applied to NCI network group and industry trials so as to bridge the research gap, move research forward, and adopt the best course to serve the needs of the community, researchers and patients.
Citation Format: Spears PA, Devine P, Finestone S, Carbine N. Clinical trials: "A holistic approach". [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-10-02.
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Affiliation(s)
- PA Spears
- Cancer Information & Support Network (CISN), Auburn, CA
| | - P Devine
- Cancer Information & Support Network (CISN), Auburn, CA
| | - S Finestone
- Cancer Information & Support Network (CISN), Auburn, CA
| | - N Carbine
- Cancer Information & Support Network (CISN), Auburn, CA
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Petersen JA, Gauthier MA, Piault E, DeBusk KPA, Buzaglo JS, Eng-Wong J, Glazer JR, Green MC, Johnson JM, Spears PA, Evans CJ. Abstract P1-10-20: Importance of the patient voice in drug development: Early-stage breast cancer and measurement gaps concerning the treatment experience. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p1-10-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Most early-stage breast cancer (EBC) patients (pts) do not experience signs or symptoms of disease; approximately 90% of women diagnosed in breast screening are asymptomatic in the US (Ryerson et al. 2015). Rather, side effects of cancer therapy have the greatest impact and can be burdensome to pts on and after treatment. Bother and impact have not been thoroughly assessed from the patient perspective in trials. Qualitative research with 56 pts undergoing or completing (after 3 and within 24 mos of) systemic treatment were conducted to assess the need for EBC-focused patient-reported outcome (PRO) measures.
Methods: Semi-structured interviews were conducted to better understand the treatment experience; the interview guide was developed in consultation with breast cancer advocates who were former pts. The interview sample was determined to capture findings across EBC therapies (HER2-targeted [HER2], hormone/endocrine [H/E], and/or chemotherapy [CT]). Treatment experience, including treatment-related symptoms and treatment impact (e.g. on activities of daily living, emotional aspects) were discussed in each 90-minute session. Pts rated level of bother of symptoms and impacts on an 11-point scale. Disease stage, treatment received, surgery, and other health information was collected from medical charts. Qualitative analysis was conducted with ATLAS.ti software. Symptom data was reviewed to appropriately analyze therapy subgroups.
Results: Stage Ia (17.9%), Ib (14.3%), IIa (32.1%), IIb (25.0%), or IIIa (7.1%) pts that received adjuvant (75%) or neoadjuvant (25%) therapy participated; 106 unique treatment-related symptoms were reported. Symptoms most frequently reported included hair loss (86.7%), change in taste (73.3%), and tiredness/fatigue (71.1%) on CT (n=45); tiredness/fatigue (34.8%), runny nose (26.1%), and watery eyes (21.7%) on HER2 (n=23); and hot flashes (50.0%), joint pain (37.5%), and weight gain (20.1%) on H/E (n=24). The most common symptoms reported after therapy completion included memory loss (63.6%), symptoms of neuropathy (numbness, tingling, and pain in fingers, 63.6%), and tiredness/fatigue (45.5%) (n=11). CT symptoms rated by ≥ 25% of pts that were most bothersome included tiredness/fatigue (x -=8.2, n=18**), hair loss (x -=8.2, n=32**), and memory loss (x -=7.7, n=15**). HER2 and H/E ratings of bother were less frequent. EBC treatment was associated with significant impact on pts' lives; categories described are below:
Impact category Average bother rating* (n**)Concerns with treatment9.5 (2)Physical/functional7.7 (36)Work or school7.5 (37)Sleep7.5 (21)Daily tasks and activities7.4 (95)Emotional7.4 (62)Sexual behavior7.1 (22)Cognitive function6.8 (6)Social6.7 (54)Appearance6.5 (32)* Rating on 11-pt scale; 0=none to 10=extremely bothersome ** n=number of patients rating the level of bother
Conclusion: Treatment-related symptoms and associated degree of bother differed by treatment group. Pts' descriptions of treatment impact provided additional insight into the burden of EBC. EBC-specific PROs included in trials that gain pts' perspective on experience with treatment would further inform pts and may also inform therapy choice.
Citation Format: Petersen JA, Gauthier MA, Piault E, DeBusk KPA, Buzaglo JS, Eng-Wong J, Glazer JR, Green MC, Johnson JM, Spears PA, Evans CJ. Importance of the patient voice in drug development: Early-stage breast cancer and measurement gaps concerning the treatment experience. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-10-20.
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Affiliation(s)
- JA Petersen
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - MA Gauthier
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - E Piault
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - KPA DeBusk
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - JS Buzaglo
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - J Eng-Wong
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - JR Glazer
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - MC Green
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - JM Johnson
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - PA Spears
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
| | - CJ Evans
- Genentech, Inc., South San Francisco, CA; Endpoint Outcomes, Boston, MA; Cancer Support Community, Washington, DC; Young Survival Coalition, NY, NY; Komen Advocates in Science, St. Louis, MO; Komen Advocates in Science, Raleigh, NC
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Harris SL, Spears PA, Havell EA, Hamrick TS, Horton JR, Orndorff PE. Characterization of Escherichia coli type 1 pilus mutants with altered binding specificities. J Bacteriol 2001; 183:4099-102. [PMID: 11395476 PMCID: PMC95295 DOI: 10.1128/jb.183.13.4099-4102.2001] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR mutagenesis and a unique enrichment scheme were used to obtain two mutants, each with a single lesion in fimH, the chromosomal gene that encodes the adhesin protein (FimH) of Escherichia coli type 1 pili. These mutants were noteworthy in part because both were altered in the normal range of cell types bound by FimH. One mutation altered an amino acid at a site previously shown to be involved in temperature-dependent binding, and the other altered an amino acid lining the predicted FimH binding pocket.
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Affiliation(s)
- S L Harris
- Department of Microbiology, Pathology, and Parasitology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27606, USA
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Hamrick TS, Harris SL, Spears PA, Havell EA, Horton JR, Russell PW, Orndorff PE. Genetic characterization of Escherichia coli type 1 pilus adhesin mutants and identification of a novel binding phenotype. J Bacteriol 2000; 182:4012-21. [PMID: 10869080 PMCID: PMC94587 DOI: 10.1128/jb.182.14.4012-4021.2000] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five Escherichia coli type 1 pilus mutants that had point mutations in fimH, the gene encoding the type 1 pilus adhesin FimH, were characterized. FimH is a minor component of type 1 pili that is required for the pili to bind and agglutinate guinea pig erythrocytes in a mannose-inhibitable manner. Point mutations were located by DNA sequencing and deletion mapping. All mutations mapped within the signal sequence or in the first 28% of the predicted mature protein. All mutations were missense mutations except for one, a frameshift lesion that was predicted to cause the loss of approximately 60% of the mature FimH protein. Bacterial agglutination tests with polyclonal antiserum raised to a LacZ-FimH fusion protein failed to confirm that parental amounts of FimH cross-reacting material were expressed in four of the five mutants. The remaining mutant, a temperature-sensitive (ts) fimH mutant that agglutinated guinea pig erythrocytes after growth at 31 degrees C but not at 42 degrees C, reacted with antiserum at both temperatures in a manner similar to the parent. Consequently, this mutant was chosen for further study. Temperature shift experiments revealed that new FimH biosynthesis was required for the phenotypic change. Guinea pig erythrocyte and mouse macrophage binding experiments using the ts mutant grown at the restrictive and permissive temperatures revealed that whereas erythrocyte binding was reduced to a level comparable to that of a fimH insertion mutant at the restrictive temperature, mouse peritoneal macrophages were bound with parental efficiency at both the permissive and restrictive temperatures. Also, macrophage binding by the ts mutant was insensitive to mannose inhibition after growth at 42 degrees C but sensitive after growth at 31 degrees C. The ts mutant thus binds macrophages with one receptor specificity at 31 degrees C and another at 42 degrees C.
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Affiliation(s)
- T S Hamrick
- Department of Microbiology, Pathology and Parasitology, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA
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Abstract
We isolated two insertion mutants of Bordetella avium that exhibited a peculiar clumped-growth phenotype and found them to be attenuated in turkey tracheal colonization. The mutants contained transposon insertions in homologues of the wlbA and wlbL genes of Bordetella pertussis. The wlb genetic locus of B. pertussis has been previously described as containing 12 genes involved in lipopolysaccharide (LPS) biosynthesis. Polyacrylamide gel analysis of LPS from B. avium wlbA and wlbL insertion mutants confirmed an alteration in the LPS profile. Subsequent cloning and complementation of the wlbA and wlbL mutants in trans with a recombinant plasmid containing the homologous wlb locus from B. avium eliminated the clumped-growth phenotype and restored the LPS profile to that of wild-type B. avium. Also, a parental level of tracheal colonization was restored to both mutants by the recombinant plasmid. Interestingly, complementation of the wlbA and wlbL mutants with a recombinant plasmid containing the heterologous wlb locus from B. pertussis, B. bronchiseptica, or Bordetella parapertussis eliminated the clumped-growth phenotype and resulted in a change in the LPS profile, although not to that of wild-type B. avium. The mutants also acquired resistance to a newly identified B. avium-specific bacteriophage, Ba1. Complementation of both wlbA and wlbL mutants with the homologous wlb locus of B. avium, but not the heterologous B. pertussis locus, restored sensitivity to Ba1. Complementation of the wlbL mutant, but not the wlbA mutant, with the heterologous wlb locus of Bordetella bronchiseptica or B. parapertussis restored partial sensitivity to Ba1. Comparisons of the LPS profile and phage sensitivity of the mutants upon complementation by wlb loci from the heterologous species and by B. avium suggested that phage sensitivity required the presence of O-antigen. At the mechanistic level, both mutants showed a dramatic decrease in serum resistance and a decrease in binding to turkey tracheal rings in vitro. In the case of serum resistance, complementation of both mutants with the homologous wlb locus of B. avium restored serum resistance to wild-type levels. However, in the case of epithelial cell binding, only complementation of the wlbA mutant completely restored binding to wild-type levels (binding was only partially restored in the wlbL mutant). This is the first characterization of LPS mutants of B. avium at the genetic level and the first report of virulence changes by both in vivo and in vitro measurements.
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Affiliation(s)
- P A Spears
- Department of Microbiology, Pathology, and Parasitology, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA.
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Ryan JR, Levine JF, Apperson CS, Lubke L, Wirtz RA, Spears PA, Orndorff PE. An experimental chain of infection reveals that distinct Borrelia burgdorferi populations are selected in arthropod and mammalian hosts. Mol Microbiol 1998; 30:365-79. [PMID: 9791181 DOI: 10.1046/j.1365-2958.1998.01071.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The prokaryotic, spirochaetal microorganism Borrelia burgdorferi is the causative agent of Lyme disease, an arthropod-borne disease of a variety of vertebrates and the most prevalent arthropod-borne disease of humans in the United States. In order to understand better the normal life cycle of B. burgdorferi, an experimental chain of infection was devised that involved multiple sequential arthropod and mammalian passages. By examining populations of B. burgdorferi emerging from different points in this infectious chain, we demonstrate that selection of B. burgdorferi populations peculiar to arthropod or vertebrate hosts is a property of at least one of the two ecologically distinct strains we examined. Distinct B. burgdorferi populations were identified using an antigenic profile, defined by a set of monoclonal antibodies to eight B. burgdorferi antigens, and a plasmid profile, defined by the naturally occurring plasmids in the starting clonal populations. These two profiles constituted the phenotypical signature of the population. In the strain exhibiting selection in the different hosts, transition from one host to another produced a striking series of alternating phenotypical signatures down the chain of infection. At the molecular level, the alternating signatures were manifested as a reciprocal relationship between the expression of certain antigenic forms of outer surface protein (Osp) B and OspC. In the case of OspC, the antigenic changes could be correlated to the presence of one of two distinctly different alleles of the ospC gene in a full-length and presumably transcriptionally active state. In the case of OspB, two alleles were again identified. However, their differences were minor and their relationship to OspB antigenic variation more complicated. In addition to the reciprocating changes in the antigenic profile, a reciprocating change in the size (probably the multimeric state) of a 9.0 kbp supercoiled plasmid was also noted. Selection of distinct populations in the tick may be responsible for the microorganism's ability to infect a wide range of vertebrate hosts efficiently, in that the tick might provide selective pressure for the elimination of the population selected in the previous host.
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Affiliation(s)
- J R Ryan
- Department of Entomology, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC 27606, USA
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Milla MA, Spears PA, Pearson RE, Walker GT. Use of the restriction enzyme AvaI and exo- Bst polymerase in strand displacement amplification. Biotechniques 1998; 24:392-6. [PMID: 9526646 DOI: 10.2144/98243bm12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- M A Milla
- Becton Dickinson Research Center, Research Triangle Park, NC, USA
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Spears PA, Linn CP, Woodard DL, Walker GT. Simultaneous strand displacement amplification and fluorescence polarization detection of Chlamydia trachomatis DNA. Anal Biochem 1997; 247:130-7. [PMID: 9126382 DOI: 10.1006/abio.1997.2043] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Strand displacement amplification (SDA) is an isothermal DNA amplification technology that uses a restriction enzyme and polymerase. We have developed a target-specific method which allows simultaneous SDA and detection in a homogeneous format. This is accomplished by including a detector oligodeoxynucleotide labeled with 5-(4,6-dichlorotriazin-2-yl)amino fluorescein in the SDA reaction. Fluorescence polarization is used to monitor hybridization of the detector probe to the amplification product as it rises in concentration during SDA. We have demonstrated real-time SDA detection for the cryptic plasmid of Chlamydia trachomatis with high sensitivity in only 30 min.
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Affiliation(s)
- P A Spears
- Becton Dickinson Research Center, Research Triangle Park, North Carolina 27709, USA
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Spargo CA, Fraiser MS, Van Cleve M, Wright DJ, Nycz CM, Spears PA, Walker GT. Detection of M. tuberculosis DNA using thermophilic strand displacement amplification. Mol Cell Probes 1996; 10:247-56. [PMID: 8865173 DOI: 10.1006/mcpr.1996.0034] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Strand Displacement Amplification (SDA) is an isothermal, in vitro method of amplifying DNA that is based upon the combined action of a DNA polymerase and restriction enzyme. Previously, a form of SDA was developed which utilizes the exonuclease deficient Klenow fragment of E. coli polymerase I (exo Klenow) and the restriction enzyme HincII to achieve 10(8)-fold amplification in 2 h at 37 degrees C (Walker, G.T., 1993, PCR Methods and Applications 3; 1-6). A new thermophilic form of SDA is reported here which uses a restriction endonuclease from Bacillus stearothermophilus (BsoBI) and a 5'-->3' exonuclease deficient polymerase from Bacillus caldotenax (exo Bca). SDA was used to amplify DNA from Mycobacterium tuberculosis. An amplification factor of 10(10)-fold was achieved after 15 min of SDA at 60 degrees C. The new thermophilic system is much more specific than the previous mesophilic system as evidenced by a dramatic decrease in background amplification products. Thermophilic SDA was also optimized with dUTP substituted for TTP to enable amplicon decontamination using uracil-DNA glycosylase.
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Affiliation(s)
- C A Spargo
- Department of Molecular Biology, Becton Dickinson Research Center, Research Triangle Park, NC 27709, USA
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Abstract
We isolated and determined the nucleotide sequence of the 70K gene from nine mycobacteria and from two related non-mycobacteria with the goal of obtaining a region of requisite specificity to serve as a mycobacterial genus-specific probe. Two different primer sets were then designed to amplify the 70K gene using strand displacement amplification. Using one of the primer sets, 10 different mycobacteria were readily detected with sensitivities of 100 molecules DNA, and with only cross-reactivity to two non-mycobacteria. The other set of primers that were tested amplified the same set of mycobacteria, but exhibited no crossreactivity with non-mycobacterial DNAs. By employing one of the primer sets, we were able to successfully amplify with high sensitivity three different target DNA sequences comprised of the 70K mycobacterial genus target, an IS 6110 (M. tuberculosis complex) target, and an internal amplification control using SDA. These results demonstrate the potential of the 70K gene to serve as a mycobacterial genus-specific probe, and demonstrate the first multiplex amplification by SDA of three DNA targets.
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Affiliation(s)
- M C Little
- Becton Dickinson Research Center, Research Triangle Park, NC 27709-2016
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Walker GT, Nadeau JG, Spears PA, Schram JL, Nycz CM, Shank DD. Multiplex strand displacement amplification (SDA) and detection of DNA sequences from Mycobacterium tuberculosis and other mycobacteria. Nucleic Acids Res 1994; 22:2670-7. [PMID: 8041630 PMCID: PMC308226 DOI: 10.1093/nar/22.13.2670] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Strand Displacement Amplification (SDA) is an isothermal, in vitro method of amplifying a DNA target sequence prior to detection [Walker et al (1992) Nucleic Acids Res., 20, 1691-1693]. Here we describe a multiplex form of SDA that allows two target sequences and an internal amplification control to be co-amplified by a single pair of primers after common priming sequences are spontaneously appended to the ends of target fragments. Multiplex SDA operates at a single temperature, under the same simple protocol previously developed for single-target SDA. We applied multiplex SDA to co-amplification of a target sequence (IS6110) that is specific to members of the Mycobacterium tuberculosis-complex and a target (16S ribosomal gene) that is common to most clinically relevant species of mycobacteria. Both targets are amplified 10(8)-fold during a 2 hour, single temperature incubation. The relative sensitivity of the system was evaluated across a number of clinically relevant mycobacteria and checked for crossreactivity against organisms that are closely related to mycobacteria.
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Affiliation(s)
- G T Walker
- Becton Dickinson Research Center, Research Triangle Park, NC 27709-2016
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Spears P. PPOs and homecare providers: a perfect partnership. AAPPO J 1991; 1:41-5. [PMID: 10149644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Nasim FH, Spears PA, Hoffmann HM, Kuo HC, Grabowski PJ. A Sequential splicing mechanism promotes selection of an optimal exon by repositioning a downstream 5' splice site in preprotachykinin pre-mRNA. Genes Dev 1990; 4:1172-84. [PMID: 2210374 DOI: 10.1101/gad.4.7.1172] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To explore the structural basis of alternative splicing, we have analyzed the splicing of pre-mRNAs containing an optional exon, E4, from the preprotachykinin gene. This gene encodes substance P and related tachykinin peptides by alternative splicing of a common pre-mRNA. We have shown that alternative splicing of preprotachykinin pre-mRNA occurs by preferential skipping of optional E4. The competing mechanism that incorporates E4 into the final spliced RNA is constrained by an initial block to splicing of the immediate upstream intervening sequence (IVS), IVS3. This block is relieved by sequential splicing, in which the immediate downstream IVS4 is removed first. The structural change resulting from the first splicing event is directly responsible for activation of IVS3 splicing. This structural rearrangement replaces IVS4 sequences with E5 and its adjacent IVS5 sequences. To determine how this structural change promoted IVS3 splicing, we asked what structural change(s) would restore activity of IVS3 splicing-defective mutants. The most significant effect was observed by a 2-nucleotide substitution that converted the 5' splice site of E4 to an exact consensus match, GUAAGU. Exon 5 sequences alone were found not to promote splicing when present in one or multiple copies. However, when a 15-nucleotide segment of IVS5 containing GUAAGU was inserted into a splicing-defective mutant just downstream of the hybrid exon segment E4E5, splicing activity was recovered. Curiously, the 72-nucleotide L2 exon of adenovirus, without its associated 5' splice site, activates splicing when juxtaposed to E4. Models for the activation of splicing by an RNA structural change are discussed.
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Affiliation(s)
- F H Nasim
- Section of Biochemistry, Brown University, Providence, Rhode Island 02912
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Spears P. Indian health service: can it meet the needs of Native American clients? Okla Nurse 1989; 34:10. [PMID: 2628807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
Mutants of Vibrio cholerae defective in intestinal colonization have been constructed. Characterization of these mutants has led to the identification of a gene cluster involved in the assembly of a pilus colonization factor called TCP. The tcp operon has been cloned and strains of V. cholerae have been constructed that overproduce this pilus and the B subunit of cholera toxin. Together these studies may contribute to the eventual construction of efficient live and killed, oral cholera vaccines.
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Affiliation(s)
- R Taylor
- Department of Microbiology and Immunology, University of Tennessee, Memphis 38163
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Berne M, Gustavsson B, Almersjö O, Spears P, Sundström E. Inhibition of thymidylate synthase after administration of doxifluridine in a transplantable colon carcinoma in the rat. Cancer Invest 1988; 6:377-83. [PMID: 2972339 DOI: 10.3109/07357908809080065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Parameters for inhibition of thymidylate synthase (TS) in a DMH-induced transplantable rat colon carcinoma were studied after intraperitoneal administration of bolus doxifluridine (5'-dFUR) 200 mg/kg. Levels of 5'-dFUR, 5-fluorouracil (5-FU), fluorouridinediphosphate (FUDP), and fluorouridinetriphosphate (FUTP) were determined by use of high-performance liquid chromatography. Micromethods for analysis of 5-fluoro-2'-deoxyuridylate (FdUMP) and TS were used to study the in vivo intracellular pharmacokinetics of TS inhibition. Peak values of 5'-dFUR and 5-FU were found at 30 min and showed exponential declines with values close to zero at 5 hr. Substantial levels of FUDP and FUTP were found throughout the 24 h observation time. Peak FdUMP levels were modest compared to those observed after equimolar administration of 5-FU, but FdUMP persisted in amounts well above available binding sites on TS for the 24 h observation time. Reduction of free TS enzyme to undetectable levels (less than 0.05 pmol/g) lasted for 4 h, and at 24 h, there was still almost 70% enzyme inhibition. The total amount of TS (TStot) defined as free [3H]FdUMP-titrable enzyme (TSf) plus TS bound to FdUMP in a ternary complex (TSb) increased as a result of 5'-dFUR bolus injection from 15 to 50 pmol/g during the 24 hr observation time. We conclude from these data that 5'-dFUR is converted to 5-FU and subsequently to FdUMP, and the results suggest that 5'-dFUR exerts its cytotoxic effects through inhibition of TS and incorporation into RNA.
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Affiliation(s)
- M Berne
- Department of Surgery, Ostra Sjukhuset University of Gothenburg, Sweden
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Spears PA, Schauer D, Orndorff PE. Metastable regulation of type 1 piliation in Escherichia coli and isolation and characterization of a phenotypically stable mutant. J Bacteriol 1986; 168:179-85. [PMID: 3019997 PMCID: PMC213435 DOI: 10.1128/jb.168.1.179-185.1986] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Type 1 piliation in Escherichia coli exhibits phase variation due to the inversion of a small, ca. 300-base-pair, element that regulates pilA (fimA), the gene that encodes the structural subunit of pili (Abraham et al., Proc. Natl. Acad. Sci. USA 82:5724-5727, 1985). We have used the inversion as an assay to characterize a stably piliated mutant. The mutant strain did not exhibit the pilA ON and pilA OFF colonial variants characteristic of the wild type; rather, every clone produced a level of pilA expression intermediate between ON and OFF wild-type populations. The mutant phenotype was conferred by a lesion at a previously undescribed locus between hemA and trpA, which we have termed pilG. Examination of the pilA promoter region in four pilG mutant populations indicated that the phenotypic stability conferred by the pilG mutation was not due to an inability to carry out the inversion. Rather, all pilG mutant populations consisted of approximately equal mixtures of ON and OFF individuals. We suggest that pilG mutants may undergo such rapid switching of the pilA promoter that populations exhibit an intermediate level of pilA expression and phenotypic stability.
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Keith BR, Maurer L, Spears PA, Orndorff PE. Receptor-binding function of type 1 pili effects bladder colonization by a clinical isolate of Escherichia coli. Infect Immun 1986; 53:693-6. [PMID: 2875030 PMCID: PMC260849 DOI: 10.1128/iai.53.3.693-696.1986] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The role of type 1 pili in promoting bladder colonization was examined by constructing two mutant strains of a clinical Escherichia coli isolate. One mutant was isogenic to the parental strain save for a lesion in a gene required for pilus receptor binding; the other mutant was isogenic save for a lesion in the gene encoding the pilus structural subunit. Using mixed infections of the parental and mutant strains in an ascending rat cystitis model, we found that type 1-piliated mutants that lacked the receptor-binding function were as ineffective in bladder colonization as were mutants lacking the entire organelle.
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Abstract
Type 1 piliation in Escherichia coli is subject to metastable regulation at the transcriptional level (B. I. Eisenstein, Science 214:337-339, 1981). However, the genes controlling in this fashion are not known. We present evidence that the pilA gene, encoding the structural subunit of type 1 pili, is subject to metastable transcriptional regulation. A pilA'-lacZ fusion, constructed in vitro on a recombinant plasmid, was used in conjunction with a recBC sbcB mutant of E. coli K-12 to introduce the fusion into the chromosomal region encoding Pil. This fusion was found to be subject to metastable transcriptional control. The rate of switching from the Lac+ to the Lac- phenotype was 4 X 10(-4) per cell per generation and 6.2 X 10(-4) in the opposite direction. A ca. 10-fold difference in beta-galactosidase activity was observed between phenotypically "ON" (Lac+) and "OFF" (Lac-) populations. P1 transduction experiments showed that the element determining the ON or OFF phenotype was tightly linked to pilA. In addition to the metastable regulation of pilA, a second type of transcriptional regulation was effected by the product of a gene, hyp, adjacent to pilA. By using a recombinant plasmid containing just a pilA'-lacZ fusion and the putative pilA promoter, we found that a lesion in hyp conferred a beta-galactosidase activity about fivefold higher than that of a strain possessing the parental hyp gene. Mutants constructed to have a pilA'-lacZ fusion and a hyp::Tn5-132 mutation in the chromosome exhibited a frequency of switching from Lac+ to Lac- and vice versa indistinguishable from that of the parental strain. However, in the ON mode, hyp::Tn5-132 mutants showed a twofold-higher beta-galactosidase activity. Thus, hyp does not appear to affect metastable variation but does affect the level of transcription of the pilA gene in the ON (transcribed) mode.
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Cotter TG, Spears P, Henson PM. A monoclonal antibody inhibiting human neutrophil chemotaxis and degranulation. The Journal of Immunology 1981. [DOI: 10.4049/jimmunol.127.4.1355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
The hybridoma technique of Kohler and Milstein was used to raise a monoclonal antibody against human neutrophils it has been found to inhibit neutrophil chemotaxis and degranulation. The antibody has been termed NCD 1. Incubation of 12 micrograms of NCD 1 with neutrophils (2 X 10(6)), followed by incubation with cytochalasin B and stimulation with either C5a, fMet-Leu-Phe, or soluble aggregated immunoglobulin, resulted in the inhibition of lysosomal enzyme release. The inhibition was not cytochalasin B dependent, since lysosomal enzyme release induced by opsonized zymosan or opsonized sheep erythrocytes was also inhibited, even in the absence of cytochalasin B. NCD 1 had no affect on enzyme release induced by the calcium ionophore A23138 or by phorbol myristate acetate. The antibody also inhibited neutrophil chemotaxis to zymosan-activated plasma and fMet-Leu-Phe. By contrast, superoxide production stimulated by phorbol myristate acetate, opsonized zymosan, or fMet-Leu-Phe was not affected by NCD 1. Similarly, uptake of 51Cr-labeled opsonized sheep erythrocytes into neutrophils was resistant to the effects of the antibody. NCD 1 Fab fragments did not inhibit lysosomal enzyme release or chemotaxis, althugh binding to the neutrophil surface was demonstrated by immunofluorescence. NCD 1 F(ab')2 fragments behaved analogously to the whole antibody. Binding of both fMet-Leu-[3H]Phe or 125I-soluble aggregated immunoglobulin to the cells was not inhibited by the antibody, which implied that NCD 1 was inhibiting some post-ligand binding event.
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Cotter TG, Spears P, Henson PM. A monoclonal antibody inhibiting human neutrophil chemotaxis and degranulation. J Immunol 1981; 127:1355-60. [PMID: 6268706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The hybridoma technique of Kohler and Milstein was used to raise a monoclonal antibody against human neutrophils it has been found to inhibit neutrophil chemotaxis and degranulation. The antibody has been termed NCD 1. Incubation of 12 micrograms of NCD 1 with neutrophils (2 X 10(6)), followed by incubation with cytochalasin B and stimulation with either C5a, fMet-Leu-Phe, or soluble aggregated immunoglobulin, resulted in the inhibition of lysosomal enzyme release. The inhibition was not cytochalasin B dependent, since lysosomal enzyme release induced by opsonized zymosan or opsonized sheep erythrocytes was also inhibited, even in the absence of cytochalasin B. NCD 1 had no affect on enzyme release induced by the calcium ionophore A23138 or by phorbol myristate acetate. The antibody also inhibited neutrophil chemotaxis to zymosan-activated plasma and fMet-Leu-Phe. By contrast, superoxide production stimulated by phorbol myristate acetate, opsonized zymosan, or fMet-Leu-Phe was not affected by NCD 1. Similarly, uptake of 51Cr-labeled opsonized sheep erythrocytes into neutrophils was resistant to the effects of the antibody. NCD 1 Fab fragments did not inhibit lysosomal enzyme release or chemotaxis, althugh binding to the neutrophil surface was demonstrated by immunofluorescence. NCD 1 F(ab')2 fragments behaved analogously to the whole antibody. Binding of both fMet-Leu-[3H]Phe or 125I-soluble aggregated immunoglobulin to the cells was not inhibited by the antibody, which implied that NCD 1 was inhibiting some post-ligand binding event.
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Abstract
The growth characteristics of Chlamydia psittaci serotypes 1 and 2 (ovine and bovine origin) were studed in mouse L cells. Formation of inclusions and yield of infectious progeny for serotype 1 were maximal when host cells were treated with cycloheximide and the pH in the cell culture medium was 7.2-7.4. The number of cells that contained inclusions and the infectivity yield for serotype 2 were maximal when the pH was 6.6-7.0. Treatments with diethylaminoethyl dextran and cycloheximide increased inclusion formation in serotype 2 but decreased the yield per infected cell. For both serotypes, centrifugation of the chlamydiae onto monolayers infected 50-1,200 times the number of cells infected with use of stationary adsorption. An enumeration method for L-cell infectious units was developed that gave higher titers than the chicken embryo 50% lethal dose after yolk sac inoculation.
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Spears P, Storz J. Changes in the ultrastructure of Chlamydia psittaci produced by treatment of the host cell with DEAE-dextran and cycloheximide. J Ultrastruct Res 1979; 67:152-60. [PMID: 469985 DOI: 10.1016/s0022-5320(79)80004-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Spears P, Storz J. Biotyping of Chlamydia psittaci based on inclusion morphology and response to diethylaminoethyl-dextran and cycloheximide. Infect Immun 1979; 24:224-32. [PMID: 457272 PMCID: PMC414287 DOI: 10.1128/iai.24.1.224-232.1979] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Strains of Chlamydia psittaci from cattle, sheep, pigs, mice, guinea pigs, rabbits, cats, and parrots were subdivided based on their biological characteristics. Chlamydiae grown in the yolk sac of chicken embryos were used to infect L cell monolayers. The host cells were infected without further treatment or treated with diethylaminoethyl-dextran, cycloheximide, or both. The following criteria were used for biotyping the strains: the morphology of the inclusions and time after infection at which they appeared, the effect of chlamydial multiplication on the host cell cytoskeleton, and the change in the number of cells infected in response to diethylaminoethyl-dextran and cycloheximide. These properties were determined for 29 strains of C. psittaci. Based on the results, the strains were placed into eight biotypes.
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Bowen RA, Spears P, Stotz J, Deidel GE. Mechanisms of infertility in genital tract infections due to Chlamydia psittaci transmitted through contaminated semen. J Infect Dis 1978; 138:95-8. [PMID: 681792 DOI: 10.1093/infdis/138.1.95] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Ten heifers inseminated with semen artificially contaminated with Chlamydia psittaci were not pregnant 40 days later, whereas five of 10 control heifers inseminated with the same semen mixed with control diluent became pregnant. Normal embryos were recovered two and one-half or three days after insemination of another group of animals with semen containing C. psittaci, a finding indicating that fertilization failure was not responsible for the infertility. Uterine biopsy samples taken from two heifers in this group contained scattered Chlamydia-infected cells that were detected by immunofluorescence in the subepithelial tissues of the uterine horns. This finding suggests that the infertility may result from an alteration in the uterine environment caused by multiplication of C. psittaci.
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