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Biomedical subjects

D J Mazur

Publications and source records attributed to D J Mazur.

At least 19 recordsLinked to original sources
PubMed2001

Excision of 3' termini by the Trex1 and TREX2 3'-->5' exonucleases. Characterization of the recombinant proteins.

The excision of nucleotides from DNA 3' termini is an important step in DNA replication, repair, and recombination pathways to generate correctly base paired termini for subsequent processing. The mammalian TREX1 and TREX2 proteins contain potent 3'-->5' exonucleases capable of functioning in this capacity. To study the activities of these exonucleases we have developed strategies to express and purify the recombinant mouse Trex1 and human TREX2 proteins in Escherichia coli in quantities sufficient for biochemical characterization. The Trex1 and TREX2 proteins are homodimers that exhibit robust 3' excision activities with very similar preferred reaction conditions and preferences for specific DNA substrates. In a steady-state kinetic analysis, oligonucleotide substrates were used to measure 3' nucleotide excision by Trex1 and TREX2. The Michaelis constants derived from these data indicate similar apparent kcat values of 22 s(-1) for Trex1 and 16 s(-1) for TREX2 using single-stranded oligonucleotides. The apparent KM values of 19 nm for Trex1 and 190 nm for TREX2 suggest relatively high affinities for DNA for both Trex1 and TREX2. An exonuclease competition assay was designed using heparin as a nonsubstrate inhibitor with a series of partial duplex DNAs to delineate the substrate structure preferences for 3' nucleotide excision by Trex1 and TREX2. The catalytic properties of the TREX proteins suggest roles for these enzymes in the 3' end-trimming processes necessary for producing correctly base paired 3' termini.

Animals↗
PubMed2001

Structure and expression of the TREX1 and TREX2 3' --> 5' exonuclease genes.

The TREX1 and TREX2 genes encode mammalian 3'-->5' exonucleases. Expression of the TREX genes in human cells was investigated using a reverse transcription-polymerase chain reaction strategy. Our results show that TREX1 and TREX2 are expressed in all tissues tested, providing direct evidence for the expression of these genes in human cells. Potential transcription start sites are identified for the TREX genes using rapid amplification of cDNA ends to recover the 5'-flanking regions of the TREX transcripts. The 5'-flanking sequences indicate transcription initiation from consensus putative promoters identified -140 and -650 base pairs upstream of the TREX1 open reading frame (ORF) and -623 and -753 base pairs upstream of the TREX2 ORF. Novel TREX1 and TREX2 cDNAs are identified that contain protein-coding sequences generated from exons positioned in genomic DNA up to 18 kilobases 5' to the TREX1 ORF and up to 25 kilobases 5' to the TREX2 ORF. These novel cDNAs and sequences in the GenBank data base indicate that transcripts containing the TREX1 and TREX2 ORFs are produced using a variety of mechanisms that include alternate promoter usage, alternative splicing, and varied sites for 3' cleavage and polyadenylation. These initial studies have revealed previously unrecognized complexities in the structure and expression of the TREX1 and TREX2 genes.

Amino Acid Sequence↗
PubMed1999

Identification and expression of the TREX1 and TREX2 cDNA sequences encoding mammalian 3'-->5' exonucleases.

The 3'-->5' exonucleases catalyze the excision of nucleoside monophosphates from the 3' termini of DNA. We have identified the cDNA sequences encoding two 3'-->5' exonucleases (TREX1 and TREX2) from mammalian cells. The TREX1 and TREX2 proteins are 304 and 236 amino acids in length, respectively. Analysis of the TREX1 and TREX2 sequences identifies three conserved motifs that likely generate the exonuclease active site in these enzymes. The specific amino acids in these three conserved motifs suggest that these mammalian exonucleases are most closely related to the proofreading exonucleases of the bacterial replicative DNA polymerases and the RNase T enzymes. Expression of TREX1 and TREX2 in Escherichia coli demonstrates that these recombinant proteins are active 3'-->5' exonucleases. The recombinant TREX1 protein was purified, and exonuclease activity was measured using single-stranded, partial duplex, and mispaired oligonucleotide DNA substrates. The greatest activity of the TREX1 protein was detected using a partial duplex DNA containing five mispaired nucleotides at the 3' terminus. No activity was detected using single-stranded RNA or an RNA-DNA partial duplex. Identification of the TREX1 and TREX2 cDNA sequences provides the genetic tools to investigate the physiological roles of these exonucleases in mammalian DNA replication, repair, and recombination pathways.

Amino Acid Sequence↗
PubMed1999

Exonucleases and the incorporation of aranucleotides into DNA.

The polymerization of nucleotide analogs into DNA is a common strategy used to inhibit DNA synthesis in rapidly dividing tumor cells and viruses. The mammalian DNA polymerases catalyze the insertion of the arabinofuranosyl analogs of dNTPs (aranucleotides) into DNA efficiently, but elongate from the 3' aranucleotides poorly. Slow elongation provides an opportunity for exonucleases to remove aranucleotides. The exonuclease activity associated with DNA polymerase delta removes araCMP from 3' termini with the same efficiency that it removes a paired 3' deoxycytosine suggesting that the proofreading exonucleases associated with DNA polymerases might remove aranucleotides inefficiently. A separate 30 kDa exonuclease has been purified from mammalian cells that removes araCMP from 3' termini. The activity of this enzyme in the cell could remove aranucleotides from 3' termini of DNA and decrease the efficacy of the analogs. Inhibition analysis of the purified exonuclease shows that this enzyme is inhibited by thioinosine monophosphate (TIMP) with a Ki = 17 microM. When high TIMP levels are generated in HL-60 cells, incorporation of araC in DNA is increased about 16-fold relative to total DNA synthesis. This increased araC in DNA is likely a result of exonuclease inhibition in the cell. Thus, exonucleases in cells might play an important role in removing aranucleotides inserted by DNA polymerases.

Animals↗
PubMed1997

Patients' preferences for risk disclosure and role in decision making for invasive medical procedures.

OBJECTIVE: To assess the level of involvement patients want in decision making related to the acceptance or rejection of an invasive medical intervention and whether their preference for decision making is related to their preference for qualitative (verbal) or quantitative (numeric) information about the risks of the procedure. SETTING: A university-based Department of Veterans Affairs Medical Center. DESIGN: Cross-sectional study using structured interviews of consecutive patients seen for continuity care visits in a general medicine clinic. PATIENTS: Four hundred and sixty-seven consecutive patients with a mean age of 65.2 years (SD 10.70 years, range 31-88 years) and with a mean of 12.6 years (SD 2.96 years, range 0-24 years) of formal education. MEASUREMENTS AND MAIN RESULTS: In the context of an invasive diagnostic or therapeutic intervention, patients were asked whether they preferred patient-based, physician-based, or shared patient-physician decision making. Patients were asked to give the ratio of patient-to-physician decision making they preferred, and whether they preferred discussions using words, numbers, or both. Of 467 subjects, 318 (68%) preferred shared decision making; 100 (21.4%) preferred physician-based decision making; and 49 (10.5%) preferred patient-based decision making. In terms of risk disclosure, 436 (93.4%) preferred that their physician disclose risk information to them. Of these 436 patients, 42.7% preferred disclosure of information about the probability of adverse outcomes using qualitative (verbal) expressions of probability; 35.7% preferred disclosure in terms of quantitative (numeric) expressions of probability; and 9.8% preferred disclosure in both qualitative and quantitative terms. Younger patients (odds ratio [OR] 0.96; confidence interval [CI] 0.93, 0.99), patients who had at least one stroke (OR 3.03; CI 1.03, 8.90), and patients who preferred to discuss risk information with their physicians in terms of numbers (OR 2.39; CI 1.40, 4.06) tended to prefer patient-based or shared decision making. CONCLUSIONS: Male veterans consistently preferred shared patient-physician decision making in the context of invasive medical interventions.

Adult↗
PubMed1997

How older patient preferences are influenced by consideration of future health outcomes.

OBJECTIVE: To determine patients' willingness to accept intubation and ventilatory support (IVS) when the best outcome available is a state involving both cognitive and physical/behavioral deficits. DESIGN: Structured interviews with patients seen consecutively in a continuity care general medicine clinic. SETTING: A university-based Department of Veterans Affairs Medical Center. SUBJECTS: A total of 113 patients (mean age = 67.3 years, age range 42-89; mean level of formal education = 12.6 years, range 2-24). MEASUREMENTS: Patients were asked to consider whether they would permit their physicians to intubate them and put them on ventilatory support when the best outcome to be expected was one of three future health care states, presented in the following order: State 1, where their mental and physical state of recovery would be exactly like their current mental and physical states at the time of their visit to the general medicine clinic (the patient's current baseline mental and physical functioning); State 2, involving cognitive compromise; State 3, involving both cognitive and physical/behavioral compromise. RESULTS: One patient refused IVS on State 1; 20.4% (23/113) of patients refused IVS on State 2; 23.0% (26/113) refused IVS on State 3; and 49.6% (56/113) reported they would accept IVS resulting in all three states. Six of 113 patients (5.3%) reported they would leave the decision up to their physician beginning with State 1 and continuing through State 3. One patient reported that he would leave the decision (State 1 through State 3) up to his wife. A reported history of stroke is related to patients' expressed dislike of IVS that would leave them with residual deficits. CONCLUSION: The results suggest that a substantial number of our older male veteran population would prefer intubation and ventilatory support if presented with a situation in which the best outcome that a physician could offer them was cognitive, physical, and behavioral dysfunction. These results also indicate that those patients who have had a stroke seem to be less inclined to accept IVS in more severe outcomes states.

Adult↗
PubMed1996

Patients' willingness to accept life-sustaining treatment when the expected outcome is a diminished mental health state: an exploratory study.

OBJECTIVE: To assess patients' willingness to accept life-sustaining treatment when the expected outcome is a diminished mental health state. DESIGN: Structured interviews with a consecutive series of patients. SETTING: A university-based Department of Veterans Affairs Medical Center. PATIENTS: One hundred four male patients (mean age = 65.4 years; range 37-82) seen consecutively in a general medicine clinic. MEASUREMENTS: We assessed the acceptability of temporary ventilatory support of a hypothetical case of severe pneumonia. Patients were asked to consider mental health states involving minor cognitive deficits that varied only in their expected frequency and duration. RESULTS: All patients except one were willing to accept temporary life support in the management of severe pneumonia. Of these 103 patients, 76 patients specified the number of days they would allow themselves to be continued on intubation and ventilatory support. The length of time varied from 1 day to 2 years and was longer when patients reported having had a stroke of reported being in fair of poor health. Fifty patients were willing to accept all diminished mental health states, including the most severe state (F). Patients who reported having been in a medical intensive care unit were more likely to accept intubation in the most severe state (F). CONCLUSIONS: In the case of "severe pneumonia", about half of our older male veterans reported a willingness to accept intubation and ventilatory support even if it resulted in persistent cognitive disability. These results suggest that experience in a medical intensive care unit with the ventilators and experience with strokes may make patients more tolerant of treatments that may result in impaired cognitive function.

Adult↗
PubMed1996

How older patients' treatment preferences are influenced by disclosures about therapeutic uncertainty: surgery versus expectant management for localized prostate cancer.

OBJECTIVES: There is an ongoing debate about the proper management of localized prostate cancer in older men. We assessed whether older patients differ in their willingness to accept surgery versus expectant management for a hypothetical early stage, low grade, clinically localized prostate carcinoma, and whether patients' current levels or past history of urologic dysfunction (difficulties initiating urination, failing to empty the bladder, urinary dribbling, getting up at night to urinate, and frequency of sexual activity) influence their decisions. We assessed patients' willingness to choose surgery over expectant management by varying the expected survival benefit in years (ESBs-em) of surgery over expectant management. DESIGN: Structured interviews with a consecutive series of male patients. SETTING: A university-based Department of Veterans Affairs Medical Center. PATIENTS: One hundred forty-eight patients seen consecutively in General Medicine Clinic at the Department of Veterans Affairs Medical Center in Portland, Oregon, were enrolled in the study. Mean age of the patients was 66.3 years (SD = 10.3, range = 30-85); mean level of formal education was 12.6 years (SD = 2.7, range = 6-22). MEASUREMENTS: Patients were asked whether they would accept surgery or expectant management in one of 11 treatment comparisons. We varied the ESBs-em in 1-year increments from 0 years to 10 years. As described to patients, surgery carried a mortality risk at the time of treatment of 1 to 2%. Once any patient indicated a willingness to accept surgery at any of the treatment comparisons or if any patient reported preferring expectant management across all treatment comparisons, the elicitation procedure was stopped. All patients were asked to complete a urological and sexual functioning questionnaire to determine the presence of coexisting urological dysfunction and level of sexual activity both at present and in the past. RESULTS: Of the 148 patients enrolled in the study, 43.2% (64/148) preferred surgery with a zero expected life benefit over expectant management (ESBs-em = 0) and a 1 to 2% chance of dying within 1 month of surgery; 24.3% (36/148) rejected surgery as the expected life benefit of surgery was increased (0 < ESBs-em < or = 10 years); 26.4% (39/148) preferred expectant management even when there was a 10-year expected life benefit of surgery; 4.7% (7/148) preferred that their physician make the decision for them; and 1.4% (2/148) of patients reported that they preferred radiation therapy, an option that was not offered to them explicitly. Our results suggest that older patients are more likely to report a preference for expectant management (OR = 1.07). Further, our results suggest that patients who report current urinary dribbling (OR = 9.03) are much more likely to prefer expectant management but that this preference decreases with the amount of time they have had this problem. Similarly, we find that patients who have difficulty with starting urination are much more likely to prefer surgery (OR = 0.13), and this preference is also mediated by the number of years they have experienced this problem. Treatment choice was not associated with formal education, present health status, or the other urological symptoms we assessed. CONCLUSION: Our study in an older male veteran population showed preferences for a variety of options in prostate cancer. Although the majority of men preferred surgery, a significant number preferred expectant management. Our results show that preferences reflect patients' experiences with physical problems associated with disease and that these experiences need to be explored and considered by patients and their providers when making treatment decisions.

Adult↗
PubMed1996

Five-year survival curves: how much data are enough for patient-physician decision making in general surgery?

OBJECTIVE: To find out whether patients' preferences for a particular type of treatment are changed by the way in which the information is presented (point estimates-year 0 and year 5 data points-or two five-year survival curves). DESIGN: Prospective study. SETTING: University-based Department of Veterans Affairs Medical Center, USA. SUBJECTS: 236 Consecutive patients seen in a general medical outpatient clinic. INTERVENTIONS: Patients were asked to choose between two treatments, one with a 10% immediate mortality and 37% five-year survival (treatment A) and one with no immediate mortality and 22% five-year survival (treatment B). They were randomised to be given the survival data either as point estimates or as two five-year survival curves. MAIN OUTCOME MEASURES: Number of patients who chose each treatment. RESULTS: The mean age was 67 years (range 40-84) and mean duration of education was 13 years (range 0-22). Significantly fewer patients chose the treatment with better immediate survival when they were given the data as survival curves (47/140, 34% compared with 93/140, 66% p < 0.0001) than when they were given data as point estimates (57/96, 59%, compared with 39/96, 41%). CONCLUSION: Patients are significantly more likely to make different decisions when given more data (in the form of five-year survival curves which show short, medium, and long term results) than when they are presented with only point estimates.

Adult↗
PubMed1995

Older patients' willingness to trade off urologic adverse outcomes for a better chance at five-year survival in the clinical setting of prostate cancer.

OBJECTIVE: To assess whether patients report a willingness to trade-off urologic adverse outcomes--urinary incontinence and total impotence--for a better chance of 5-year survival in the clinical setting of prostate cancer; and, if so, whether patients' current levels of symptoms of urinary incontinence, impotence, and frequency of sexual activity influence their decisions. DESIGN: Structured interviews with a convenience sample of male patients. SETTING: A university-based Department of Veterans Affairs Medical Center. PATIENTS: One hundred sixty-three patients seen consecutively in General Medical Clinic at the Department of Veterans Affairs Medical Center in Portland, Oregon, were enrolled in the study. Mean age of the patients was 65.2 years (SD = 10.6, range - 35-84); mean level of formal education completed was 13 years (SD = 2.7, range = 5-19). MEASUREMENTS: In a hypothetical clinical setting of prostate cancer, patients were offered a choice of two procedures--Treatment A (surgery: worse short-term, better long-term survival) and Treatment B (radiation therapy: better short-term, worse long-term survival)--with varying benefit/risk trade-offs in time. Patients were presented with pairs of treatment curves that were developed from research data on survival for surgery versus radiation therapy for stage II prostate cancer confined to the prostate gland. Treatments were not identified to control for labeling effects. Patients were asked their willingness to accept a chance of immediate mortality for better 5-year survival in one of four treatment curve comparisons. Of those who accepted the net beneficial procedure, we then inquired as to whether urologic complications--urinary incontinence and wearing an appliance to collect urine or total impotence--altered the acceptability of that treatment. RESULTS: Ninety-four percent (153/163) of patients were willing to choose Treatment A (worse short-term, better long-term survival) on one of the four scenarios; the remainder (10/163) were unwilling to take Treatment A (worse short-term, better long-term survival) on any of the four scenarios. Sixty-two percent (95/153) of patients were willing to accept a 100% chance of urinary incontinence; 83% (127/153) were willing to accept a 100% chance of impotence (chi-square = 16.8 with 1 df, P = .0001). CONCLUSIONS: Our results in an older male veteran population suggest than many patients are more concerned with long-term survival in the clinical setting of prostate cancer than with short-term treatment risks. In addition, patients are more willing to accept an impotence outcome than a urinary incontinence outcome, but this result was not related to patients' reported frequency of sexual activity.

Adult↗
PubMed1994

Patients' interpretations of verbal expressions of probability: implications for securing informed consent to medical interventions.

Physicians often use verbal expressions of probability to characterize their uncertainty about outcomes and the risks or side effects of proposed therapies. However, there is an extensive literature that documents the inherent vagueness of such expressions. Because of the potential importance of probability terms to physician-patient communication and decision-making, we asked patients to tell us the odds they thought applicable to the term "rare," as used by their physician to discuss the likelihood of an adverse outcome from surgery. Patients were randomly assigned to one of three outcome groups: death, severe heart attack, or severe pneumonia. Demographic data were elicited from each subject, as were indicators of present health status, medical history for certain diseases and surgery, and life expectancy. Linear regression and ANOVA analyses of the responses indicate that patient age, education level, perceived health status, and recency of experience with disease and medical care influence patients' numeric interpretations. We discuss the implications of these results.

Adult↗
PubMed1994

How age, outcome severity, and scale influence general medicine clinic patients' interpretations of verbal probability terms.

OBJECTIVE: To assess whether the type of scale used (scaling effects) and the severity of outcome (outcome severity) influence patients' numerical interpretations of verbal probability expressions. DESIGN: Cross-sectional survey of patients in a general medicine clinic. SETTING: A university-based Department of Veterans Affairs Medical Center. PARTICIPANTS: 210 patients seen consecutively in a general medicine clinic. MEASUREMENTS AND RESULTS: The patients were randomized to scale and health outcome (complications of surgery). Two scales (a long form and a short form) were used to expressly allow patients to choose probabilities less than 1%. The long form had a lower bound of "< 1 out of 1,000,000"; the short form had a lower bound of "< 1 out of 1,000." Two complications were used: "death from anesthesia" and "severe pneumonia." In the context of being told that their surgeon believed that the chance the complication would occur was "rare," patients were asked to give the numerical estimate of that chance. The values elicited on both scales were significantly different for the two outcomes, with the "rare" risk of death from anesthesia being characterized as less likely than the "rare" risk of severe pneumonia (F = 5.24, p = 0.023). Linear regression and three-factor analysis of variance showed significant differences in the probabilities elicited for scale, outcome, and age, with older patients generally responding with higher probabilities than did younger patients. CONCLUSIONS: These findings suggest that the severity of the associated outcome and the scale used to elicit patients' numerical estimates of verbal probability expressions influence patients' quantitative interpretations of the verbal probability statement; and older patients respond with higher probabilities of negative outcomes than do younger patients. Future studies must continue to explore whether verbal probability expressions are adequate for communicating medical risk to patients or whether patients should be provided with numerical estimates of frequency.

Adult↗
PubMed1993

Patient preferences: survival vs quality-of-life considerations.

OBJECTIVE: To assess whether patients can weigh risk comparisons involving mortality and quality of life in an understandable manner based on their willingness to accept risks of complications. DESIGN: Cross-sectional survey of patients. SETTING: University-based Department of Veterans Affairs Medical Center. PARTICIPANTS: 230 men patients seen in a general medicine clinic. MEASUREMENTS: Two survival graphs were used. Each graph contained survival curves for two alternative unidentified treatments for an unidentified medical condition. Graph 2 contained one curve that had a life expectancy that was 14% higher than the life expectancy of the corresponding curve in graph 1. Respondents were randomly assigned one of the two graphs and were asked to indicate which treatment they preferred and what risk of a change in their quality of life (urinary incontinence or importance) they were willing to accept to achieve longer survival. Patients were also asked whether they had a history of urinary incontinence or impotence. RESULTS AND CONCLUSIONS: Patients tended to be unwilling to accept worse quality of life to achieve increased survival over time. For both curve comparisons, significantly more (p < 0.01) patients accepted a treatment associated with higher mortality to avoid a 100% chance of incontinence than to avoid a 100% chance of impotence. Of the 75% (172/230) of patients reporting willingness to accept risk of either urinary incontinence or total impotence or both, 62% reported having at least some symptoms related to urinary incontinence or impotence. Of the 58 patients not willing to accept the complication risks, only 11% reported a history of urinary incontinence or impotence. The results show that patients are able to make distinctions about severity of morbidity, men are less willing to accept the risk of urinary incontinence than that of total impotence, and men patients who are symptomatic with urinary incontinence or impotence are more willing to accept the risks of treatment than are asymptomatic patients.

Aged↗
PubMed1993

How the manner of presentation of data influences older patients in determining their treatment preferences.

OBJECTIVE: To assess how the manner of presentation of graphic data to older patients influences their treatment preferences. DESIGN: Cross-sectional structured interviews with patients. SETTING: A university-based Department of Veterans Affairs Medical Center. PATIENTS: One hundred sixty-six consecutive patients (mean age = 64.8 years, range of ages 29-82) seen in a Department of Veterans Affairs general medicine clinic. MEASUREMENTS: Five pairs of 5-year survival curves were presented to patients. Each pair was composed of two survival curves for alternative unidentified treatments for an unidentified medical condition. Curve A (LT = better long-term, worse short-term survival) was fixed throughout all curve pairs. Curve B (ST = better short-term, worse long-term survival) changed in each curve pair, showing incrementally better chances of short-term survival across the five curve pairs. Patients were randomly assigned to view the curve pairs in forward (increasing short-term survival) or backward (decreasing short-term survival) order. RESULTS: Order is a significant predictor of patients' initial preferences for the short-term survival curve (P = 0.0004) as well as their willingness to shift preferences during presentation of the five curve pairs. Patients > or = 65 were more likely to initially choose the ST curve in forward order presentation than patients < 65. More educated patients generally were less likely to prefer the ST curve under both elicitation orders. CONCLUSIONS: The data indicate that the method of eliciting patients' preferences strongly influenced their expressed preferences, and that these preferences may have predictable relationships with demographic characteristics such as age.

Adult↗
PubMed1992

Disruptive medical patients. Forensically informed decision making.

Patients who disrupt medical care create problems for physicians. The risks are not entirely clinical. Although these patients may compromise sound clinical judgment, some are also litigious and express their dissatisfaction in legal or other forums. It then becomes necessary for treating physicians to be aware of the legal and ethical boundaries of their patient care responsibilities. Some disruptive patients are treated by setting limits, which is usually affirmed by health care agreements. A hospital review board may advise clinicians on these agreements and on the management of disruptive patients. If termination of the physician-patient relationship is considered, physicians must follow proper protocol. We examine these forensic considerations and place them in the context of malpractice. Communication, consultation, and documentation are the key elements in reducing liability.

Adult↗