Contacts between DNA gyrase and its binding site on DNA: features of symmetry and asymmetry revealed by protection from nucleases

DNA gyrase supercoils DNA by passing one DNA segment through another by means of a reversible double-strand break at specific DNA sites. We determined the nucleotide sequence of two highly preferred gyrase binding sites and analyzed the grip of gyrase on the DNA by using protection from nuclease attack. The DNA-breakage site of gyrase was centered in about 50 base pairs (bp) of DNA that was completely protected from DNase I and flanked by DNA regions cut at average intervals of 9.9 bases. The same pattern of protection from DNase I was observed with topoisomerase II', an enzyme that shares structural homology with gyrase. The gyrase site of DNA breakage was off-center in the 140 bp of DNA protected from exonuclease III digestion. ATP or inhibitors of gyrase had little specific effect on DNase I protection. On addition of a nonhydrolyzable analogue of ATP, previously stable barriers to exonuclease III were invaded and new barriers appeared. We discuss a detailed model uniting these results with previous data on gyrase structure and mechanism.

DNA polymerase II, the probable homolog of mammalian DNA polymerase epsilon, replicates chromosomal DNA in the yeast Saccharomyces cerevisiae

Two temperature-sensitive DNA polymerase II mutants (pol2-9 and pol2-18) of the yeast Saccharomyces cerevisiae were isolated by the plasmid shuffling method. DNA polymerase II activity partially purified from both mutants was thermolabile, while DNA polymerase I and III activities remained thermotolerant. At the restrictive temperature, the pol2 mutants were defective in chromosomal DNA replication and exhibited the dumbbell terminal morphology typical of DNA replication mutants. The POL2 transcript accumulated periodically during the cell cycle, peaking at the G1/S boundary in the same manner as the transcripts of more than 10 other DNA replication genes. These results indicate that DNA polymerase II participates in nuclear DNA replication. The similarities in structure and activities between the DNA polymerases of yeast and mammals make it likely that mammalian DNA polymerase epsilon too is required for chromosomal DNA replication.

Elderly women in northern New England exhibit seasonal changes in bone mineral density and calciotropic hormones

A seasonal component to bone loss has been reported in some postmenopausal women. We hypothesized that elderly women in northern New England would be at high risk for bone loss during winter because of their age, diet and lack of sunlight. Eighteen elderly but healthy women (mean age 77 years) started a 2-year observational study in a remote area of northwestern Maine (Greenville: 45.5 degrees N latitude). Fifteen women completed the study. Bone mineral density of the spine (L-BMD) and hip (F-BMD) and biochemical markers of bone turnover were measured biannually. In vitro photo-conversion of provitamin D3 to previtamin D3 was determined in the winter and spring. Initial calcium and vitamin D intake averaged 700 +/- 72 mg/day and 6.2 +/- 1.2 micrograms/day, respectively. During the first year L-BMD dropped 4.2% (P = 0.002) while F-BMD dropped 2.4% (P = 0.09), primarily because of steep declines during the fall and winter (August to February: L-BMD: 3.6%, P = 0.001; F-BMD: 3.0%, P = 0.04). In that 6-month period, serum 25 hydroxyvitamin D (25(OH)D) fell 13 +/- 6% (P = 0.06) and PTH rose 27 +/- 11% (P = 0.01). Additionally, there was no detectable in vitro conversion of provitamin D to previtamin D over 8 h of one sunny winter day. In the summer, PTH and 25(OH)D reverted to basal levels and significant in vitro photoconversion of provitamin D to previtamin D was detected. In the 2nd year of the study, vitamin D consumption increased (+2.0 +/- 1.2 micrograms/day, P = 0.03 vs. baseline), L-BMD increased slightly (+1.8%, P = 0.05) and F-BMD did not change (+0.5%, P = NS). Again, changes in BMD and vitamin D were seasonal: L-BMD and F-BMD were constant during fall and winter but both sites showed increases during summer (L-BMD: +1.7%, P = 0.04, F-BMD: +1.6%, P = 0.25). In the second winter, serum 25(OH)D fell nearly 20% and PTH rose 17%. Increased dietary consumption of vitamin D was positively correlated with changes in F-BMD at 18 months (r = 0.61, P = 0.02) and resulted in slightly greater serum 25(OH)D concentrations during the second winter than the first. The difference in serum 25(OH)D between the first and second winter was the strongest predictor of lumbar bone accretion during the second year of the study (r = 0.59, P = 0.04). In this 24-month observational study, significant seasonal changes in BMD, 25(OH)D and PTH were reported.(ABSTRACT TRUNCATED AT 250 WORDS)

The role of kreisler in segmentation during hindbrain development

The mouse kreisler gene is expressed in rhombomeres (r) 5 and 6 during neural development and kreisler mutants have patterning defects in the hindbrain that are not fully understood. Here we analyzed this phenotype with a combination of genetic, molecular, and cellular marking techniques. Using Hox/lacZ transgenic mice as reporter lines and by analyzing Eph/ephrin expression, we have found that while r5 fails to form in these mice, r6 is present. This shows that kreisler has an early role in the formation of r5. We also observed patterning defects in r3 and r4 that are outside the normal domain of kreisler expression. In both heterozygous and homozygous kreisler embryos some r5 markers are induced in r3, suggesting that there is a partial change in r3 identity that is not dependent upon the loss of r5. To investigate the cellular character of r6 in kreisler embryos we performed heterotopic grafting experiments in the mouse hindbrain to monitor its mixing properties. Control experiments revealed that cells from even- or odd-numbered segments only mixed freely with themselves, but not with cells of opposite character. Transposition of cells from the r6 territory of kreisler mutants reveals that they adopt mature r6 characteristics, as they freely mix only with cells from even-numbered rhombomeres. Analysis of Phox2b expression shows that some aspects of later neurogenesis in r6 are altered, which may be associated with the additional roles of kreisler in regulating segmental identity. Together these results suggest that the formation of r6 has not been affected in kreisler mutants. This analysis has revealed phenotypic and mechanistic differences between kreisler and its zebrafish equivalent valentino. While valentino is believed to subdivide preexisting segmental units, in the mouse kreisler specifies a particular segment. The formation of r6 independent of r5 argues against a role of kreisler in prorhombomeric segmentation of the mouse hindbrain. We conclude that the mouse kreisler gene regulates multiple steps in segmental patterning involving both the formation of segments and their A-P identity.

Cloning DPB3, the gene encoding the third subunit of DNA polymerase II of Saccharomyces cerevisiae

DNA polymerase II purified from Saccharomyces cerevisiae contains polypeptides with apparent molecular masses of greater than 200, 80, 34, 30 and 29 kDa, the two largest of which (subunits A and B) are encoded by the essential genes POL2 and DPB2. By probing a lambda gt11 expression library of yeast DNA with antiserum against DNA polymerase II, we isolated a single gene, DPB3, that encodes both the 34- and 30-kDa polypeptides (subunit C and C'). The nucleotide sequence of DPB3 contained an open reading frame encoding a 23-kDa protein, significantly smaller than the observed molecular masses, 34- or 30-kDa, which might represent post-translationally modified forms of the DPB3 product. The predicted amino acid sequence contained a possible NTP-binding motif and a glutamate-rich region. NTP-binding motif and a glutamate-rich region. A dpb3 deletion mutant (dpb3 delta) was viable and yielded a DNA polymerase II lacking the 34- and 30-kDa polypeptides. dpb3 delta strains exhibited an increased spontaneous mutation rate, suggesting that the DPB3 product is required to maintain fidelity of chromosomal replication. Since a fifth, 29-kDa polypeptide was present in DNA polymerase II preparations from wild-type cell extracts throughout purification, the subunit composition appears to be A, B, C (or C and C') and D. The 5' nontranscribed region of DPB3 contained the MulI-related sequence ACGCGA, while the 0.9-kb DPB3 transcript accumulated periodically during the cell cycle and peaked at the G1/S boundary. The level of DPB3 transcript thus appears to be under the same cell cycle control as those of POL2, DPB2 and other DNA replication genes. DPB3 was mapped to chromosome II, 30 cM distal to his7.

Leishmania donovani chagasi: new clinical variant of cutaneous leishmaniasis in Honduras

During surveillance for endemic visceral leishmaniasis on an island off the Pacific coast of Honduras, an unusual form of cutaneous leishmaniasis was encountered. By clinical and laboratory criteria, 17 cases were identified over 5 months; children aged 4 to 15 years were primarily affected. Lesions were generally few in number, small, always papular, and non-ulcerative, even when present for several years. Patients with skin lesions seemed otherwise healthy and were well nourished. Montenegro skin tests with Leishmania mexicana and L major antigens were positive in 10 of 17 patients tested, and lesions from 9 patients were positive by culture. Since the summer of 1988, cases of atypical cutaneous leishmaniasis continue to occur on the island (8) as well as on the mainland of southern Honduras (23). A total of 9 parasite isolates from skin lesions, 4 from bone marrow of patients with kala-azar, and 2 from sandflies were identified as L donovani chagasi and were indistinguishable from one another by isoenzyme analysis.

Osteonecrosis of the jaw (ONJ): diagnosis and management in 2015

Osteonecrosis of the jaw (ONJ) has been associated with the use of aminobisphosphonates and denosumab. The vast majority (>90%) of cases occur in the oncology patient population receiving high doses of intravenous bisphosphonates or subcutaneous denosumab. The incidence of ONJ in the osteoporosis patient population is very low and is estimated at 1-90 per 100,000 patient-years of exposure. In the oncology patient population the incidence appears to be related to dose and duration of exposure, and prevalence has been estimated to be as high as 18.6%. A number of risk factors in addition to antiresorptive therapy have been identified. These include the presence of periodontal disease, oral surgical procedures with extractions or implants, radiation therapy, chemotherapy, diabetes, glucocorticoid use, and smoking. Antiangiogenic agents appear to contribute to the risk of ONJ, however, data at this time are limited and further evidence is required prior to confirming a causal relationship. ONJ may be prevented with optimization of oral hygiene, the use of oral antimicrobial mouth rinses, as well as systemic antibiotic therapy. Individuals not responding to conservative management or in the advanced stages of ONJ may be considered for surgery, as data over the past several years have demonstrated surgical success in this patient population. Case reports have indicated that teriparatide may enhance healing. A number of experimental therapies are being evaluated and include the use of bone marrow stem cell intralesional transplantation, local application of platelet-derived growth factor, hyperbaric oxygen, tissue grafting, and low-level laser therapy. This paper summarizes the current research as well as the international consensus on the diagnosis and management of ONJ.

Survival factors in replantation and revascularization of the amputated thumb--10 years experience

An unabridged series of 73 thumb amputations subjected to replantation or revascularization surgery in the years 1971 to 1980 has been examined in detail as a combined prospective and retrospective study to determine the factors playing a role in survival and failure. The causes of failure and complications are demonstrated. The overall failure rate was 27%. The factors influencing the outcome were: the injury--mechanical type and degree of amputation; the patient--age and amputation level; and the surgeon--frequency of utilization of vein grafts. The highest failure was seen in the complete amputation with avulsion/diffuse crush injury group (63%). Incomplete amputations had the lowest failure rate, particularly if the injury type was guillotine/local crush and at a level proximal to the metacarpophalangeal joint. Patients aged 11 to 20 years had a low failure rate (18%) whereas children under 5 years had a high failure rate (40%). Arterial thrombosis was the most frequent complication and cause of failure. The surgeon could modify the result by frequent use of vein grafts for arterial reconstruction and by reoperation for thrombotic complication. Five thumbs failed to revascularize at the primary operation and were removed at this primary operation.

Quality of life of community-residing persons with dementia based on self-rated and caregiver-rated measures

PURPOSE

To identify correlates of self-rated and caregiver-rated quality of life (QOL) in community-residing persons with dementia (PWD) for intervention development.

METHODS

Cross-sectional data of 254 PWD and their caregivers participating in a clinical trial were derived from in-home assessments. Self-rated QOL was measured with the Quality of Life-Alzheimer Disease (QOL-AD) scale, and caregiver-rated QOL was measured using the QOL-AD and Alzheimer Disease-Related Quality of Life (ADRQL) scales. Multivariate modeling identified correlates of the PWD' QOL.

RESULTS

Self-rated QOL was related significantly to participant race, unmet needs, depression, and total medications. Caregiver-rated QOL-AD scores were significantly associated with participant function, unmet needs, depression, and health problems and with caregiver burden and self-rated health. Significant correlates of ADRQL scores included neuropsychiatric symptom severity, functional and cognitive impairment, and caregiver burden and depression.

CONCLUSIONS

Correlates of QOL in community-residing PWD depend on who rates the PWD's QOL and which measure is used. Addressing health problems, medication use, and dementia-related unmet needs, reducing functional dependency, and treating neuropsychiatric symptoms in PWD, while reducing caregiver burden and depression, may maximize QOL in those with dementia.

Oxidative stress mediates synthesis of cytosolic phospholipase A2 after UVB injury

UVB irradiation has previously been shown to significantly increase phospholipase activity and prostaglandin synthesis. Because UVB irradiation is a potent oxidative stress, the role of active oxygen species in regulating UV-induced cPLA2 synthesis and phosphorylation was examined. In the present study, irradiation produced a 3-fold increase in synthesis within 6 h following irradiation. Phosphorylation of cPLA2 was also increased to a similar extent. UVB-induced synthesis and phosphorylation of cPLA2 could be inhibited by pretreatment with the antioxidants 2,2,5,7,8-pentamethyl-6-hydroxychromane (50 microM) or N-acetylcysteine (10 mM). Treatment of unirradiated cultures with the potent oxidant tert-butyl hydroperoxide (500 microM) also increased cPLA2 synthesis and phosphorylation, suggesting that oxidative injury is an important regulator of cPLA2 synthesis. Increased synthesis of cPLA2 correlated well with increased [3H]arachidonic acid release, PGE2 synthesis and lipid peroxidation in epidermis after oxidant or UVB treatment. The results indicate that UVB-induced upregulation of cPLA2 synthesis is mediated by UVB-induced formation of free radicals.

Shame, guilt, and depression in men and women in recovery from addiction

Men and women in recovery from addiction were compared on levels of depression and self-conscious affect including proneness to shame, guilt, externalization, detachment, and pride. The sample consisted of 130 subjects (88 men and 42 women; mean age 33.04), 90 of whom were active participants in a 12-step recovery program, and 40 of whom were in a residential treatment community. Subjects completed The Beck Depression Inventory and The Test of Self-Conscious Affect. Significant differences between the sexes were found for proneness to shame, detachment, and depression. Women were significantly higher on shame and depression; men were significantly higher on detachment. The subjects were compared to subjects who were not chemically dependent. It was found that these recovering drug-addicted subjects scored significantly higher in proneness to shame and externalization and significantly lower on proneness to guilt. Treatment implications of proneness to shame in the drug-addicted population, and particularly in women, are discussed. The use of confrontational drug treatment strategies may be contraindicated.

In vitro and transgenic analysis of a human HOXD4 retinoid-responsive enhancer

Expression of vertebrate Hox genes is regulated by retinoids in cell culture and in early embryonic development. We have identified a 185-bp retinoid-responsive transcriptional enhancer 5′ of the human HOXD4 gene, which regulates inducibility of the gene in embryonal carcinoma cells through a pattern of DNA-protein interaction on at least two distinct elements. One of these elements contains a direct repeat mediating ligand-dependent interaction with retinoic acid receptors, and is necessary though not sufficient for the enhancer function. The HOXD4 enhancer directs expression of a lacZ reporter gene in the neural tube of transgenic mouse embryos in a time-regulated and regionally restricted fashion, reproducing part of the anterior neuroectodermal expression pattern of the endogenous Hoxd-4 gene. Administration of retinoic acid to developing embryos causes alterations in the spatial restriction of the transgene expression domain, indicating that the HOXD4 enhancer is also a retinoid-responsive element in vivo. The timing of the retinoic acid response differs from that seen with more 3′ Hox genes, in that it occurs much later. This shows that the temporal window of competence in the ability to respond to retinoic acid differs between Hox genes and can be linked to specific enhancers. Mutations in the direct repeat or in a second element in the enhancer affect both retinoid response in culture and developmental regulation in embryos, suggesting that co-operative interactions between different factors mediate the enhancer activity. These data provide further support for a role of endogenous retinoids in regulation and spatial restriction of Hox gene expression in the central nervous system.

HOXD4 and regulation of the group 4 paralog genes

From an evolutionary perspective, it is important to understand the degree of conservation of cis-regulatory mechanisms between paralogous Hox genes. In this study, we have used transgenic analysis of the human HOXD4 locus to identify one neural and two mesodermal 3′ enhancers that are capable of mediating the proper anterior limits of expression in the hindbrain and paraxial mesoderm (somites), respectively. In addition to directing expression in the central nervous system (CNS) up to the correct rhombomere 6/7 boundary in the hindbrain, the neural enhancer also mediates a three rhombomere anterior shift from this boundary in response to retinoic acid (RA), mimicking the endogenous Hoxd4 response. We have extended the transgenic analysis to Hoxa4 identifying mesodermal, neural and retinoid responsive components in the 3′ flanking region of that gene, which reflect aspects of endogenous Hoxa4 expression. Comparative analysis of the retinoid responses of Hoxd4, Hoxa4 and Hoxb4 reveals that, while they can be rapidly induced by RA, there is a window of competence for this response, which is different to that of more 3′ Hox genes. Mesodermal regulation involves multiple regions with overlapping or related activity and is complex, but with respect to neural regulation and response to RA, Hoxb4 and Hoxd4 appear to be more closely related to each other than Hoxa4. These results illustrate that much of the general positioning of 5′ and 3′ flanking regulatory regions has been conserved between three of the group 4 paralogs during vertebrate evolution, which most likely reflects the original positioning of regulatory regions in the ancestral Hox complex.

Problems associated with nursing staff shortage: an analysis of the first 3600 incident reports submitted to the Australian Incident Monitoring Study (AIMS-ICU)

Although many studies have attempted to define appropriate nursing staff levels, allocation and patient dependency, minimal data is available on the effect of nursing staff shortage (NSS) on quality of care provided in intensive care. This study aimed to identify incidents associated with staff shortage as reported to the Australian Incident Monitoring Study-ICU (AIMS-ICU) project and to assess their estimated effect on patient outcome. A search of narrative keywords and contributing factors identified 89 nursing staff shortage incidents (NSS-INCIDENTS) and 373 incidents involving nursing staff shortage contributing factors (NSS-CF). NSS resulted from inappropriate rostering for current patient load (81%) and inability to respond to increased unit activity (19%). Most frequent associated incidents included problems with: drug administration/documentation (47), patient supervision (20), set-up of ventilators/equipment (16), and accidental extubation (14). Undesirable patient outcomes included: major physiological change (22%), patient/relative dissatisfaction (12%), and physical injury (3%). This study suggests that inadequate staffing results in incidents and compromised patient safety.

Guilt, shame, and depression in clients in recovery from addiction

Men and women in recovery from addiction were compared on levels of depression, guilt, and shame. The measurement of guilt included subscales of Survivor Guilt, Separation Guilt, Omnipotent Responsibility Guilt, Trait Guilt, State Guilt, and Adaptive Guilt. The sample included 75 men and 33 women in treatment in a residential treatment community. It was found that women were significantly higher than men in depression. The recovering subjects were compared to nonaddicted subjects and established norms, and it was found that the recovering people were higher on depression, shame, and the subscales of maladaptive guilt. Both men and women in recovery were significantly lower than norms in adaptive guilt.

Treating asthma with omega-3 fatty acids: where is the evidence? A systematic review

Background

Considerable interest exists in the potential therapeutic value of dietary supplementation with the omega-3 fatty acids. Given the interplay between pro-inflammatory omega-6 fatty acids, and the less pro-inflammatory omega-3 fatty acids, it has been thought that the latter could play a key role in treating or preventing asthma. The purpose was to systematically review the scientific-medical literature in order to identify, appraise, and synthesize the evidence for possible treatment effects of omega-3 fatty acids in asthma.

Methods

Medline, Premedline, Embase, Cochrane Central Register of Controlled Trials, CAB Health, and, Dissertation Abstracts were searched to April 2003. We included randomized controlled trials (RCT's) of subjects of any age that used any foods or extracts containing omega-3 fatty acids as treatment or prevention for asthma. Data included all asthma related outcomes, potential covariates, characteristics of the study, design, population, intervention/exposure, comparators, and co interventions.

Results

Ten RCT's were found pertinent to the present report.

Conclusion

Given the largely inconsistent picture within and across respiratory outcomes, it is impossible to determine whether or not omega-3 fatty acids are an efficacious adjuvant or monotherapy for children or adults. Based on this systematic review we recommend a large randomized controlled study of the effects of high-dose encapsulated omega-3 fatty acids on ventilatory and inflammatory measures of asthma controlling diet and other asthma risk factors. This review was limited because Meta-analysis was considered inappropriate due to missing data; poorly or heterogeneously defined populations, interventions, intervention-comparator combinations, and outcomes. In addition, small sample sizes made it impossible to meaningfully assess the impact on clinical outcomes of co-variables. Last, few significant effects were found.

Identification of community-residing individuals with dementia and their unmet needs for care

BACKGROUND

Innovative approaches to the widespread delivery of evidence-based dementia care are needed. The aims of this study were to determine whether a telephone screening method could efficiently identify individuals in the community in need of care for dementia and to develop a multidimensional needs assessment tool for identifying the type and frequency of unmet needs related to memory disorders in the home setting.

METHODS

This was a cross-sectional evaluation of 292 community-residing individuals aged 70 and older in Maryland. Participants were given a brief cognitive telephone screen. A subsample (n=43) received a comprehensive in-home assessment for dementia and dementia-related needs. Cognitive, functional, behavioral, and clinical factors were assessed. The Johns Hopkins Dementia Care Needs Assessment (JHDCNA) was used to identify unmet needs related to dementia.

RESULTS

Telephone screening for the sample took 350 h, and 27% screened positive for dementia. Virtually all participants with dementia who received an in-home assessment had at least one unmet need, with the most frequent unmet needs being for a dementia workup, general medical care, environmental safety, assistance with ADL impairments, and access to meaningful activities. Caregivers, when present, also had a number of unmet needs, with the most common being caregiver education about dementia, knowledge of community resources, and caregiver mental health care.

CONCLUSIONS

Effective and efficient means for identifying community-residing individuals with dementia are needed so that dementia care interventions can be provided to address unmet care needs of patients and their caregivers.

Suspected skin malignancy: a comparison of diagnoses of family practitioners and dermatologists in 493 patients

BACKGROUND

In the Irish health system, dermatology patients present to their family practitioner for diagnosis and treatment, and are referred to a dermatologist for a second opinion where diagnosis is in doubt or when there has been therapeutic failure. The level of expertise in dermatology amongst family practitioners varies considerably.

AIM

To compare the diagnoses of general practitioners and dermatologists over a selected period in patients with a possible diagnosis of skin cancer.

METHODS

Four hundred and ninety-three patients were seen by one of two dermatologists over a 1-year period at a rapid referral clinic for patients suspected by their family practitioners of having unstable or possibly malignant skin lesions; 213 of these patients had a diagnosis made on clinical examination by the dermatologist, while 264 had diagnostic or therapeutic biopsies performed; 16 patients defaulted on surgery.

RESULTS

The diagnoses of the family practitioners agreed with the diagnoses of the dermatologists on patients diagnosed clinically in 54% of cases. Thirty-eight patients had histologically proven skin malignancy. These were diagnosed accurately by the referring family practitioner in 22% of patients, while the dermatologists made the correct diagnosis prior to biopsy in 87%.

CONCLUSIONS

In over 50% of cases diagnosed clinically, the dermatologist and family practitioner agreed. Histologically proven skin cancers were diagnosed accurately in only 22% of cases by family practitioners, compared to 87% of cases by dermatologists. Specific areas of diagnostic difficulty for family practitioners include benign pigmented actinic and seborrheic keratoses, squamous cell carcinoma, and melanoma. Postgraduate education for family practitioners should be directed towards these areas of deficiency. Dermatologists had difficulty distinguishing pigmented actinic keratoses from melanoma.