Atypical mitochondrial DNA from the deep-sea scallop Placopecten magellanicus

The mitochondrial DNA of most metazoan animals is highly conserved in size, averaging about 17 kilobase paris (kbp). The mitochondrial DNA from the deep-sea scallop Placopecten magellanicus, in contrast, has been found to be approximately 34 kbp long. It is also highly variable in size from individual to individual and is unusual in the extent of its size variation. Mitochondrial DNAs from individuals collected at the same site differ by as much as 7 kbp. The size variation is due largely to differences in the number of copies of a tandemly repeated 1.2-kbp element.

Novel transcribed regions in the human genome

We have used genomic tiling arrays to identify transcribed regions throughout the human genome. Analysis of the mapping results of RNA isolated from five cell/tissue types, NB4 cells, NB4 cells treated with retinoic acid (RA), NB4 cells treated with 12-O-tetradecanoylphorbol-13 acetate (TPA), neutrophils, and placenta, throughout the ENCODE region reveals a large number of novel transcribed regions. Interestingly, neutrophils exhibit a great deal of novel expression in several intronic regions. Comparison of the hybridization results of NB4 cells treated with different stimuli relative to untreated cells reveals that many new regions are expressed upon cell differentiation. One such region is the Hox locus, which contains a large number of novel regions expressed in a number of cell types. Analysis of the trinucleotide composition of the novel transcribed regions reveals that it is similar to that of known exons. These results suggest that many of the novel transcribed regions may have a functional role.

Relation of nursing activities to increases in intracranial pressure

Increased intracranial pressure (ICP), a frequent finding in head trauma and other cerebral pathology, poses a serious threat to patients' prognosis and recovery. While considerable attention has been given to medical therapies used in reducing ICP, only recently has nursing looked at the effect care specific activities may have. In this descriptive and observational study of nine patients with cranial pathology and a Richmond bolt for measuring ICP, findings confirmed that nursing activities and environmental factors are associated with pressure increases. Respiratory care activities (mean 12.7 mmHg) and repositioning (mean 12.6 mmHg) resulted in the highest increases while lesser increases were associated with doing neuro-assessments (mean 7.2 mmHg) and spontaneous movements (mean 7.9 mmHg) of the patient. When the conversation was directed to the patient, the pressure increased in 33 of the 86 observations (mean 8.6 mmHg), in 21 of the 35 conversations about the patient, the mean pressure increase was 9.03 mmHg. Because many activities occurred simultaneously, it was difficult to derive the extent of elevation associated with a specific activity. Findings from this study and studies by other nurse researchers suggest actions nurses can use to minimize pressure increases. Many areas for further study exist.

Microcyntm: a novel super-oxidized water with neutral pH and disinfectant activity

A new super-oxidized water (SOW) product, Microcyn, was tested for in vitro antimicrobial and antiviral activities. The effectiveness of this neutral-pH SOW at killing Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Salmonella typhi and Candida albicans in pure culture was evaluated. One millilitre (approximately 10(8)colony-forming units/mL) of each micro-organism was subjected to 9 mL Microcyn or sterile water at room temperature for 30s. Under these conditions, a log(10) reduction factor of 8 in the level of all pathogens occurred in the treatment samples. In addition, results of tests with three batches of Microcyn exposed to Bacillus atrophaeus spores for 5 min demonstrated complete inactivation of the spores within 2-3 min (log(10) reduction factor >4). The effectiveness of Microcyn in reducing human immunodeficiency virus-1 (HIV-1) on hard surfaces (glass) was also evaluated in compliance with Environmental Protection Agency requirements for virucidal claims. After exposure of the tested surfaces to Microcyn for 5 min without agitation, there was a log(10) reduction factor >3 in the viral load as measured by both cytopathic effect and antigen p24 of HIV-1 production in MT-2 cultures. Microcyn activity against adenoviral vector type 5 was also analysed under simulated laboratory in-use conditions with viral suspensions. In order to increase the sensitivity of the test, the fluorescent light emitted by AdGFP-infected cells was measured with the use of a flow cytometer. A log(10) reduction factor >3 in the viral load was achieved after a 5-min exposure to Microcyn under these strict conditions. These results show that Microcyn exerts a wide antimicrobial spectrum with major advantages over acidic SOWs, including neutral pH, lower free active chlorine (51-85 ppm) and long shelf life (1 year).

Selection of polarized growth sites in yeast

The budding yeast Saccharomyces cerevisiae responds to intracellular and extracellular cues to direct cell growth. Genetic analysis has revealed many components that participate in this process and has provided insight into the mechanisms by which these proteins function. Several of these components, such as the septins, pheromone receptors and GTPase proteins, have homologues in multicellular eukaryotes, suggesting that many aspects of polarized cell growth may be conserved throughout evolution. This review discusses our current understanding of the molecular mechanisms of growth-site selection during the different stages of the yeast life cycle.

Comparison of office visit and nurse advice hotline data for syndromic surveillance--Baltimore-Washington, D.C., metropolitan area, 2002

INTRODUCTION

Kaiser Permanente of the Mid-Atlantic States (KPMAS) is collaborating with the Electronic Surveillance System for Early Notification of Community-Based Epidemics II (ESSENCE II) program to understand how managed-care data can be effectively used for syndromic surveillance.

OBJECTIVES

This study examined whether KPMAS nurse advice hotline data would be able to predict the syndrome diagnoses made during subsequent KPMAS office visits.

METHODS

All nurse advice hotline calls during 2002 that were linked to an outpatient office visit were identified. By using International Classification of Diseases, Ninth Revision (ICD-9) codes, outpatient visits were categorized into seven ESSENCE II syndrome groups (coma, gastrointestinal, respiratory, neurologic, hemorrhagic, infectious dermatologic, and fever). Nurse advice hotline calls were categorized into ESSENCE II syndrome groups on the basis of the advice guidelines assigned. For each syndrome group, the sensitivity, specificity, and positive predictive value of hotline calls were calculated by using office visits as a diagnostic standard. For matching syndrome call-visit pairs, the lag (i.e., the number of hours that elapsed between the date and time the patient spoke to an advice nurse and the date and time the patient made an office visit) was calculated.

RESULTS

Of all syndrome groups, the sensitivity of hotline calls for respiratory syndrome was highest (74.7%), followed by hotline calls for gastrointestinal syndrome (72.0%). The specificity of all nurse advice syndrome groups ranged from 88.9% to 99.9%. The mean lag between hotline calls and office visits ranged from 8.3 to 50 hours, depending on the syndrome group.

CONCLUSIONS

The timeliness of hotline data capture compared with office visit data capture, as well as the sensitivity and specificity of hotline calls for detecting respiratory and gastrointestinal syndromes, indicate that KPMAS nurse advice hotline data can be used to predict KPMAS syndromic outpatient office visits.

Issues in complementary therapies: how we got to where we are

Consumer interest in and use of complementary/alternative therapies has increased exponentially in the past decades. Although many of the over 1800 therapies have not been used in the delivery of nursing care, a number of these therapies have a long tradition of use in nursing. Additionally, nurses have conducted research on selected complementary therapies. Nursing is in an excellent position to be a leader in integrating these therapies into the Western biomedical health model and in continuing the research that will provide a better scientific base for the use of complementary therapies.

A filamentous growth response mediated by the yeast mating pathway

Haploid cells of the budding yeast Saccharomyces cerevisiae respond to mating pheromones by arresting their cell-division cycle in G1 and differentiating into a cell type capable of locating and fusing with mating partners. Yeast cells undergo chemotactic cell surface growth when pheromones are present above a threshold level for morphogenesis; however, the morphogenetic responses of cells to levels of pheromone below this threshold have not been systematically explored. Here we show that MATa haploid cells exposed to low levels of the alpha-factor mating pheromone undergo a novel cellular response: cells modulate their division patterns and cell shape, forming colonies composed of filamentous chains of cells. Time-lapse analysis of filament formation shows that its dynamics are distinct from that of pseudohyphal growth; during pheromone-induced filament formation, daughter cells are delayed relative to mother cells with respect to the timing of bud emergence. Filament formation requires the RSR1(BUD1), BUD8, SLK1/BCK1, and SPA2 genes and many elements of the STE11/STE7 MAP kinase pathway; this response is also independent of FAR1, a gene involved in orienting cell polarization during the mating response. We suggest that mating yeast cells undergo a complex response to low levels of pheromone that may enhance the ability of cells to search for mating partners through the modification of cell shape and alteration of cell-division patterns.

Phosphorylation of gamma-tubulin regulates microtubule organization in budding yeast

gamma-Tubulin is essential for microtubule nucleation in yeast and other organisms; whether this protein is regulated in vivo has not been explored. We show that the budding yeast gamma-tubulin (Tub4p) is phosphorylated in vivo. Hyperphosphorylated Tub4p isoforms are restricted to G1. A conserved tyrosine near the carboxy terminus (Tyr445) is required for phosphorylation in vivo. A point mutation, Tyr445 to Asp, causes cells to arrest prior to anaphase. The frequency of new microtubules appearing in the SPB region and the number of microtubules are increased in tub4-Y445D cells, suggesting this mutation promotes microtubule assembly. These data suggest that modification of gamma-tubulin is important for controlling microtubule number, thereby influencing microtubule organization and function during the yeast cell cycle.

Global analysis of protein activities using proteome chips

To facilitate studies of the yeast proteome, we cloned 5800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. We identified many new calmodulin- and phospholipid-interacting proteins; a common potential binding motif was identified for many of the calmodulin-binding proteins. Thus, microarrays of an entire eukaryotic proteome can be prepared and screened for diverse biochemical activities. The microarrays can also be used to screen protein-drug interactions and to detect posttranslational modifications.

Facilitators and barriers to elders' practice of t'ai chi. A mind-body, low-intensity exercise

Research has documented the positive effects that t'ai chi has on the well-being of elders. However, the reasons that elders practice t'ai chi have not been explored. The purpose of this study was to describe the facilitators and barriers to t'ai chi practice in elderly populations. Taiwanese community-dwelling elders (40 of whom practiced t'ai chi and 40 who did not) aged 65 and older, matched on age and gender, were interviewed. Results showed that encouragement from others was the most important factor for elders to practice t'ai chi, whereas positive health outcomes were the reason they continued to practice it. Most of the non-t'ai chi group participants had never thought about practicing t'ai chi because they felt they were too weak to practice. Because t'ai chi can be helpful in promoting the well-being of elders, it is essential for health care professionals to overcome the barriers to its uses in elderly populations.

A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae

A genome-wide screen of 4168 homozygous diploid yeast deletion strains has been performed to identify nonessential genes that participate in the bipolar budding pattern. By examining bud scar patterns representing the sites of previous cell divisions, 127 mutants representing three different phenotypes were found: unipolar, axial-like, and random. From this screen, 11 functional classes of known genes were identified, including those involved in actin-cytoskeleton organization, general bud site selection, cell polarity, vesicular transport, cell wall synthesis, protein modification, transcription, nuclear function, translation, and other functions. Four characterized genes that were not known previously to participate in bud site selection were also found to be important for the haploid axial budding pattern. In addition to known genes, we found 22 novel genes (20 are designated BUD13-BUD32) important for bud site selection. Deletion of one resulted in unipolar budding exclusively from the proximal pole, suggesting that this gene plays an important role in diploid distal budding. Mutations in 20 other novel BUD genes produced a random budding phenotype and one produced an axial-like budding defect. Several of the novel Bud proteins were fused to green fluorescence protein; two proteins were found to localize to sites of polarized cell growth (i.e., the bud tip in small budded cells and the neck in cells undergoing cytokinesis), similar to that postulated for the bipolar signals and proteins that target cell division site tags to their proper location in the cell. Four others localized to the nucleus, suggesting that they play a role in gene expression. The bipolar distal marker Bud8 was localized in a number of mutants; many showed an altered Bud8-green fluorescence protein localization pattern. Through the genome-wide identification and analysis of different mutants involved in bipolar bud site selection, an integrated pathway for this process is presented in which proximal and distal bud site selection tags are synthesized and localized at their appropriate poles, thereby directing growth at those sites. Genome-wide screens of defined collections of mutants hold significant promise for dissecting many biological processes in yeast.

Clinical use of tai chi in elderly populations

Tai chi, a type of low-intensity exercise, has received growing attention in both eastern and western cultures, especially its use with the most rapidly increasing segment of the population-elders. Previous research findings further supported the idea that tai chi is appropriate for elderly populations and helps promote their well-being. In this article, the beneficial effects of tai chi for elders are summarized, resources to increase awareness about the exercise are provided, and ways to promote tai chi in elderly populations are suggested.

Stress, loneliness, and depression in Taiwanese rural community-dwelling elders

This study examined the stressors and stress levels, loneliness, and depression experienced by Taiwanese rural elders and determine if differences in the level of stress were associated with specific person-environmental characteristics. The relationship between stress and depression was also explored. A total of 201 older rural community residents participated in the study. Findings showed that rural elders experienced a number of stressors related to health and family issues. Differences in the degree of stressfulness of individuals differed by gender, educational level, living arrangement, and socioeconomic status (SES). Findings in this study also showed that there was a high association among stress level, depressive symptoms, and mood status. The findings of this study will assist community health policy-makers in determining the need for health-related services for rural elders experiencing these problems.

Genome-wide transposon mutagenesis in yeast

This unit provides comprehensive protocols for the use of insertional libraries generated by shuttle mutagenesis. From the basic protocol, a small aliquot of insertional library DNA may be used to mutagenize yeast, producing strains containing a single transposon insertion within a transcribed and translated region of the genome. This transposon-mutagenized bank of yeast strains may be screened for any desired mutant phenotype. Alternatively, since the transposon contains a reporter gene lacking its start codon and promoter, transposon-tagged strains may also be screened for specific patterns of gene expression. Strains of interest may be characterized by vectorette PCR (protocol provided) in order to locate the precise genomic site of transposon insertion within each mutant. A method by which Cre/lox recombination may be used to reduce the transposon in yeast to a small insertion element encoding an epitope tag is described. This tag serves as a tool by which transposon-mutagenized gene products may be analyzed further (e.g., localized to a discrete subcellular site).

Facilitators and barriers to adherence with home monitoring using electronic spirometry

Adherence with prescribed therapies is a key factor in maintaining health in persons with chronic illnesses. The purpose of this descriptive study (which is one segment of a larger study being conducted to develop decision rules for early detection of infection or rejection in posttransplant patients) is to explore facilitators and barriers to adherence with home monitoring. Use of latent analysis revealed that the facilitators to adherence were health promotion, commitment to research, and following advice. Barriers to adherence were poor health status, laziness, and time conflict. Health professionals can use this information to plan strategies to promote adherence to home monitoring.

Emerging technologies in yeast genomics

The genomic revolution is undeniable: in the past year alone, the term 'genomics' was found in nearly 500 research articles, and at least 6 journals are devoted solely to genomic biology. More than just a buzzword, molecular biology has genuinely embraced genomics (the systematic, large-scale study of genomes and their functions). With its facile genetics, the budding yeast Saccharomyces cerevisiae has emerged as an important model organism in the development of many current genomic methodologies. These techniques have greatly influenced the manner in which biology is studied in yeast and in other organisms. In this review, we summarize the most promising technologies in yeast genomics.

The Cbk1p pathway is important for polarized cell growth and cell separation in Saccharomyces cerevisiae

During the early stages of budding, cell wall remodeling and polarized secretion are concentrated at the bud tip (apical growth). The CBK1 gene, encoding a putative serine/threonine protein kinase, was identified in a screen designed to isolate mutations that affect apical growth. Analysis of cbk1Delta cells reveals that Cbk1p is required for efficient apical growth, proper mating projection morphology, bipolar bud site selection in diploid cells, and cell separation. Epitope-tagged Cbk1p localizes to both sides of the bud neck in late anaphase, just prior to cell separation. CBK1 and another gene, HYM1, were previously identified in a screen for genes involved in transcriptional repression and proposed to function in the same pathway. Deletion of HYM1 causes phenotypes similar to those observed in cbk1Delta cells and disrupts the bud neck localization of Cbk1p. Whole-genome transcriptional analysis of cbk1Delta suggests that the kinase regulates the expression of a number of genes with cell wall-related functions, including two genes required for efficient cell separation: the chitinase-encoding gene CTS1 and the glucanase-encoding gene SCW11. The Ace2p transcription factor is required for expression of CTS1 and has been shown to physically interact with Cbk1p. Analysis of ace2Delta cells reveals that Ace2p is required for cell separation but not for polarized growth. Our results suggest that Cbk1p and Hym1p function to regulate two distinct cell morphogenesis pathways: an ACE2-independent pathway that is required for efficient apical growth and mating projection formation and an ACE2-dependent pathway that is required for efficient cell separation following cytokinesis. Cbk1p is most closely related to the Neurospora crassa Cot-1; Schizosaccharomyces pombe Orb6; Caenorhabditis elegans, Drosophila, and human Ndr; and Drosophila and mammalian WARTS/LATS kinases. Many Cbk1-related kinases have been shown to regulate cellular morphology.

Underestimation of mortality following lung volume reduction surgery resulting from incomplete follow-up

STUDY OBJECTIVES

Incomplete follow-up can bias interpretation of data that are collected in longitudinal studies. We noted that many patients failed to return for follow-up in a study of effect of lung volume reduction surgery (LVRS) on quality of life (QOL). Accordingly, we designed this investigation to determine the reasons patients dropped out, and to assess differences between those who continued in the study (attendees) and those who did not (nonattendees).

DESIGN

Telephone survey.

SUBJECTS

Patients with advanced emphysema who had undergone LVRS and had previously agreed to participate in a longitudinal QOL study.

RESULTS

No differences were found with regard to age, gender, preoperative pulmonary function, or oxygen use between attendees and nonattendees. Long-term mortality in nonattendees (27%) was considerably greater than that seen in attendees (3%, p < 0.05). Distance from the hospital, financial burden, and living out of the region were the most common reasons cited by surviving nonattendees for their failure to return for follow-up.

CONCLUSIONS

Studies reporting the long-term mortality after LVRS can be biased in the direction of underestimating the true value if they are compromised by incomplete follow-up.

A glider swing intervention for people with dementia

The soothing, repetitive movement of rocking and swinging is well known to anyone who has enjoyed a porch swing or rocking chair. Positive effects of rocking have been reported. However, investigations on its effect in people with dementia are limited. The purposes of this quasi-experimental, repeated-measures design study were to measure the effects of a glider swing on emotions, relaxation, and aggressive behaviors in a group of nursing home residents with dementia (n = 30). Data were obtained during a 5-day baseline phase, a 10-day intervention phase, and a 5-day posttreatment phase. Subjects were placed on the glider for 20 minutes each day during the intervention phase. The results of the study indicate that the glider intervention significantly improved emotions and relaxation. The most noted changes were found after 10 minutes of swinging. However, no differences were found in aggressive behaviors.

Probe-guided surgery for colorectal cancer

Anti-CEA-scintigraphy turned out to be very reliable in detecting primary and recurrent colorectal cancer, its overall accuracy being more than 90%. The intraoperative application of this technology should provide similar results when focussing at extrahepatic tumor deposits, for example in lymph nodes, thus allowing accurate staging of the underlying disease. To test this hypothesis we launched the following feasibility study the results of which are compared to those reported in the recent literature. We investigated 20 patients, six with rectum and 14 with colon cancer. 24 hours before surgery they were intravenously given 1 ml of a fab'-fragment-antibody to CEA, labeled with 25 mCi of 99mTc (CEA-Scan). During surgery the radioactivity in lymph glands regional to the tumors was measured and compared to the much lower activity in healthy nodes. For this we used a scintillation probe (C-Trak, Care Wise, Inc., Morgan Hill, CA). All lymph nodes of interest were then excised and submitted to frozen section pathology. In 7 out of 20 cases scintimetry led to an up-staging of the disease. In addition we found metastatic spread to lymph nodes that were basically not regional to the primary tumor (retroperitoneum, renal hilum etc.). Scintimetry can precisely identify even very small tumor deposits. So it leads to accurate staging while surgery is still ongoing. In a further step the concept of sentinel node diagnosis, which is right now being clinically evaluated, may some day be applied in colorectal surgical oncology.

Large-scale mutagenesis: yeast genetics in the genome era

The completion of the DNA sequence of the budding yeast Saccharomyces cerevisiae resulted in the identification of a large number of genes. However, the function of most of these genes is not known. One of the best ways to determine gene function is to carry out mutational and phenotypic analysis. In recent years, several approaches have been developed for the mutational analysis of yeast genes on a large scale. These include transposon-based insertional mutagenesis, and systematic deletions using PCR-based approaches. These projects have produced collections of yeast strains and plasmid alleles that can be screened using novel approaches. Analysis of these collections by the scientific community promises to reveal a great deal of biological information about this organism.

Protein arrays and microarrays

In the past, studies of protein activities have focused on studying a single protein at a time, which is often time-consuming and expensive. Recently, with the sequencing of entire genomes, large-scale proteome analysis has begun. Arrays of proteins have been used for the determination of subcellular localization, analysis of protein-protein interactions and biochemical analysis of protein function. New protein-microarray technologies have been introduced that enable the high-throughput analysis of protein activities. These have the potential to revolutionize the analysis of entire proteomes.

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

Proteins interact with genomic DNA to bring the genome to life; and these interactions also define many functional features of the genome. SBF and MBF are sequence-specific transcription factors that activate gene expression during the G1/S transition of the cell cycle in yeast. SBF is a heterodimer of Swi4 and Swi6, and MBF is a heterodimer of Mbpl and Swi6 (refs 1, 3). The related Swi4 and Mbp1 proteins are the DNA-binding components of the respective factors, and Swi6 mayhave a regulatory function. A small number of SBF and MBF target genes have been identified. Here we define the genomic binding sites of the SBF and MBF transcription factors in vivo, by using DNA microarrays. In addition to the previously characterized targets, we have identified about 200 new putative targets. Our results support the hypothesis that SBF activated genes are predominantly involved in budding, and in membrane and cell-wall biosynthesis, whereas DNA replication and repair are the dominant functions among MBF activated genes. The functional specialization of these factors may provide a mechanism for independent regulation of distinct molecular processes that normally occur in synchrony during the mitotic cell cycle.

A metadata framework for interoperating heterogeneous genome data using XML

The rapid advances in the Human Genome Project and genomic technologies have produced massive amounts of data populated in a large number of network-accessible databases. These technological advances and the associated data can have a great impact on biomedicine and healthcare. To answer many of the biologically or medically important questions, researchers often need to integrate data from a number of independent but related genome databases. One common practice is to download data sets (text files) from various genome Web sites and process them by some local programs. One main problem with this approach is that these programs are written on a case-by-case basis because the data sets involved are heterogeneous in structure. To address this problem, we define metadata that maps these heterogeneously structured files into a common eXtensible Markup Language (XML) structure to facilitate data interoperation. We illustrate this approach by interoperating two sets of essential yeast genes that are stored in two yeast genome databases (MIPS and YPD).