Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization

Tuberculosis is a chronic infectious disease that is transmitted by cough-propelled droplets that carry the etiologic bacterium, Mycobacterium tuberculosis. Although currently available drugs kill most isolates of M. tuberculosis, strains resistant to each of these have emerged, and multiply resistant strains are increasingly widespread. The growing problem of drug resistance combined with a global incidence of seven million new cases per year underscore the urgent need for new antituberculosis therapies. The recent publication of the complete sequence of the M. tuberculosis genome has made possible, for the first time, a comprehensive genomic approach to the biology of this organism and to the drug discovery process. We used a DNA microarray containing 97% of the ORFs predicted from this sequence to monitor changes in M. tuberculosis gene expression in response to the antituberculous drug isoniazid. Here we show that isoniazid induced several genes that encode proteins physiologically relevant to the drug's mode of action, including an operonic cluster of five genes encoding type II fatty acid synthase enzymes and fbpC, which encodes trehalose dimycolyl transferase. Other genes, not apparently within directly affected biosynthetic pathways, also were induced. These genes, efpA, fadE23, fadE24, and ahpC, likely mediate processes that are linked to the toxic consequences of the drug. Insights gained from this approach may define new drug targets and suggest new methods for identifying compounds that inhibit those targets.

Bronchopulmonary segmental lavage with Surfaxin (KL(4)-surfactant) for acute respiratory distress syndrome

We performed a trial to assess the safety and tolerability of sequential bronchopulmonary segmental lavage with a dilute synthetic surfactant (Surfaxin) in 12 adults with ARDS. Patients received one of three dosing regimens in which aliquots of Surfaxin were administered via a wedged bronchoscope to each of the 19 bronchopulmonary segments. Suctioning was performed 10-30 s after instillation of individual aliquots. Group 1 patients (n = 3) received one 30-ml aliquot of a 2.5-mg/ml concentration of Surfaxin in each segment, followed by a second 30-ml aliquot with a 10-mg/ml concentration. Group 2 patients (n = 4) received two 30-ml aliquots of the 2.5-mg/ml concentration followed by a third lavage with the 10-mg/ml concentration. Group 3 patients (n = 5) received therapy identical to that received by patients in Group 2 and were eligible for repeat dosing 6 to 24 h later. All patients tolerated the procedure. There were no serious adverse experiences ascribed to either the procedure or the surfactant. In the 96 h after treatment initiation, FI(O(2)) decreased from 0.80 to 0.52 and PEEP decreased from 10.3 to 7.6 cm H(2)O. Bronchoscopic "cleansing" of the lungs with dilute Surfaxin may offer a safe and feasible approach to improving outcomes in patients with ARDS. Wiswell TE, Smith RM, Katz LB, Mastroianni L, Wong DY, Willms D, Heard S, Wilson M, Hite RD, Anzueto A, Revak SD, Cochrane CG. Bronchopulmonary segmental lavage with Surfaxin (KL(4)-surfactant) for acute respiratory distress syndrome.

Patient with a 22q11.2 deletion with no overlap of the minimal DiGeorge syndrome critical region (MDGCR)

The apparent lack of genotype/phenotype correlation in patients with the DiGeorge anomaly and velocardiofacial syndrome (DGA/VCFS; the "22q11 deletion syndrome") indicates a complex genetic condition. Most cases, whatever the phenotype, have a 1.5-3 Mb chromosomal deletion that includes the minimal DiGeorge critical region (MDGCR). Another potential critical region on 22q11 has been suggested based on two patients with distal deletions outside the MDGCR. We report on a patient with a VCFS phenotype who has a deletion, mapped by short tandem repeat polymorphic loci and fluorescence in situ hybridization analysis, distal to and not overlapping the MDGCR. This patient is deleted for several genes, including the T-box 1 gene (TBX1; a transcription regulator expressed early in embryogenesis) and catechol-O-methyltransferase (COMT; involved in neurotransmitter metabolism). We discuss the role these two genes may play in the clinical phenotype of the patient.

Relationship of amniotic fluid markers of intra-amniotic infection with histopathology in cases of preterm labor with intact membranes

OBJECTIVE

To evaluate the correlation of amniotic fluid (AF) markers (AFMs) of intra-amniotic infection with histopathologic findings in cases of preterm labor with intact membranes, between 22 and 36 weeks' gestation.

STUDY DESIGN

We reviewed the charts of patients admitted in preterm labor with intact membranes between January 1993 and December 1996. Those having amniocentesis were identified, and AFMs were compared with histopathology in patients who delivered within 48 hours of the amniocentesis. The AFMs evaluated were glucose, polymorphonuclear leukocytes, Gram stain, and culture. All placentae were reviewed by a single pathologist blinded to the AF findings. Histologic evidence of acute inflammation was defined by findings of both subchorial intervillositis and marginating choriodeciduitis. The sensitivities, specificities, and positive and negative predictive values of the various AFMs were calculated.

RESULTS

Of 556 women with intact membranes presenting in preterm labor, 181 (32.6%) had amniocentesis and 88 delivered within 48 hours of the amniocentesis. Histopathologic chorioamnionitis was seen in 53 patients (60.2%). The findings (with their sensitivity, specificity, and positive and negative predictive values) were: polymorphonuclear leukocytes at > 10/high-power field (22.6%, 97.2%, 92.3%, and 46.1%), positive Gram stain (26.4%, 94.6%, 87.5%, and 47.3%), culture (28.3%, 92.1%, 83.3%, and 47.9%), and glucose of < 15 mg/dl (28.3%, 94.6%, 88.2%, and 47.9%), respectively. Using a receiver-operator characteristic curve for different level of AF glucose, a glucose level of < 20 mg/dl was the most sensitive AF predictor of histologic chorioamnionitis.

CONCLUSION

Histopathologic evidence of chorioamnionitis was present in 60.2% of cases of preterm births due to preterm labor in women who at our institution were offered and accepted amniocentesis and subsequently delivered within 48 hours. AFMs may be useful predictors of histologic chorioamnionitis. The most efficient AFM for chorioamnionitis in this group of patients was glucose at < 20 mg/dl.

A cardiovascular risk factor reduction clinic

OBJECTIVE

To describe a cohort of patients referred to a cardiovascular risk factor reduction unit (CRFRU).

DESIGN

Prospective cohort study.

SETTING

Out-patients referred to a specialty clinic in a tertiary care hospital.

PATIENTS

Seven hundred and four consecutive male and female patients with one or more cardiovascular risk factors, of whom 388 were reassessed after one year.

INTERVENTIONS

Standard risk factors were measured in all participants. The probability of coronary artery disease (CAD) was assessed according to the Framingham equation and results were compared with data from the Saskatchewan Heart Health Survey for the general population of Saskatchewan. Patients received dietary and fitness advice, as well as drug therapy when indicated. For follow-up studies, the change in probability of CAD and selected variables after one year were measured.

MAIN RESULTS

Patients referred to the CRFRU were at considerably higher risk for CAD than the general population. One hundred and sixty-eight of 235 men and 77 of 153 women seen in follow-up had a reduced risk score. Those who improved had a favourable change in systolic blood pressure and in their lipid profile, as well as greater weight loss.

CONCLUSIONS

A CRFRU is feasible and appears to reduce risk in a considerable proportion of patients.

The use of chloromethyl-X-rosamine (Mitotracker red) to measure loss of mitochondrial membrane potential in apoptotic cells is incompatible with cell fixation

BACKGROUND

A recent report by Macho et al. (Cytometry 25: 333-340, 1996) described the use of chloromethyl-X-rosamine (CMX-Ros) as a fixable probe for detection of loss of mitochondrial membrane potential (psi(mit)), an early event in many models of apoptosis. However, this previous report lacked a description of any direct comparisons between pre- and post-fixation analyses of normal and apoptotic cells stained with CMX-Ros.

METHODS

Using a variety of cell types, we investigated the effect of paraformaldehyde fixation on cellular retention of CMX-Ros and the implications of this for the subsequent analysis of changes in psi(mit) in cells undergoing apoptosis.

RESULTS

We found that following fixation, the resolution between normal cells with polarized mitochondria and apoptotic cells with depolarized mitochondria is reduced to the extent that accurate discrimination between the cell types is no longer possible.

CONCLUSIONS

Overall, our results are consistent with CMX-Ros being a valid probe for psi(mit) in intact cells but only when the cells are stained and analyzed immediately. Thus, our results suggest that the proposed applications for CMX-Ros in multiple parameter analysis of fixed cells are inappropriate and will lead to spurious results.

Transfer of a conjugative transposon, Tn5397 in a model oral biofilm

A tetracycline resistance profile was established from a microcosm dental plaque in a constant depth film fermenter. The fermenter was inoculated with a Bacillus subtilis strain which contained the conjugative transposon, Tn5397, which confers tetracycline resistance upon its host. After 6 hour and 24 hour the tetracycline resistance profile of the biofilm was redetermined and a tetracycline resistant Streptococcus species was isolated. A molecular analysis of this strain confirmed that Tn5397 was present in the genomic DNA of the isolate. These data represent the first report, to our knowledge, of intergeneric transfer of a conjugative transposon in a mixed species biofilm and demonstrates the ability of conjugative transposons to disseminate antibiotic resistance genes in a mixed species environment.

Antimicrobial susceptibility and composition of microcosm dental plaques supplemented with sucrose

The aims of this study were to evaluate the effects of repeated chlorhexidine gluconate (CHG) pulsing on the viability and bacterial composition of microcosm dental plaques derived from human saliva. The biofilms were grown on bovine enamel discs in a constant-depth film fermentor fed with an artificial saliva which was supplemented thrice daily with sucrose. The microcosm plaques had total viable anaerobic counts of 5 x 10(8) CFU per mm2 and consisted of 12% Actinomyces spp., 85% streptococci, and 0.2% Veillonella spp. When pulsed twice daily with 0.2% CHG, there was an immediate 1.3-log10 reduction in the total viable (anaerobic) count. However, as pulsing continued, the viable counts recovered, and after 4 days, the anaerobic count reached its pre-CHG-pulsing level, although the bacterial composition of the biofilms had changed. The results of this study show that twice-daily pulsing with 0.2% CHG over a 4-day period was ineffective at reducing the total anaerobic viable count of the biofilms but did alter their bacterial composition.

Dominant inheritance of cleft palate with minor abnormalities of hands and feet: a new syndrome?

We report a family in which four members of three generations are affected by median cleft palate. The proband and her mother have additional features including bilateral single transverse palmar creases, broad great toes and hypoplastic fifth toenails. Dominant isolated cleft palate has rarely been reported, and there are no previous reports of dominant cleft palate with these associated features. We believe that this represents a previously unreported syndrome, which needs to be considered when assessing recurrence risk for cleft palate.

Using benchmarking practices for the learning resource center

Structured ongoing and systematic evaluation is required to ensure up-to-date resources and continuous quality improvement plans to meet the learning needs of the diverse student population and the complex needs of patients. Using benchmarking to achieve evaluation goals in the learning resource center has great merit as schools of nursing respond to consumer demand for improvement, rapid changes resulting from changing patient needs, and the technology explosion.

Structure-activity analysis of the effects of lysophosphatidic acid on platelet aggregation

Lysophosphatidic acid (1-acyl-sn-glycero-3-phosphate or LPA) is a phospholipid mediator displaying numerous and widespread biological activities and thought to act via G-protein-coupled receptors. Here we have studied the effects on human platelets of a number of LPA analogues, including two enantiomers of both N-palmitoyl-(L)-serine-3-phosphate ((L) and (D)NAPS for N-acyl-phosphoserine) and 2-(R)-N-palmitoyl-norleucinol-1-phosphate ((R) and (S)PNPA), cyclic analogues of 1-acyl-sn-glycero-3-phosphate (cPA) and of 1-O-hexadecyl-sn-glycero-3-phosphate (cAGP), sphingosine-1-phosphate (SPP), as well as two palmitoyl derivatives of dioxazaphosphocanes bearing either a P-H or a P-OH bond (DOXP-H and DOXP-OH, respectively). Nine of these compounds induced platelet aggregation with the following order of potency: SPP < cAGP < DOXP-OH < (L)NAPS = (D)NAPS < (R)PNPA = (S)PNPA < LPA < AGP, EC50 varying between 9.8 nM and 8.3 microM. Two of these compounds (SPP and cAGP) appeared as weak agonists inducing platelet aggregation to only 33% and 41%, respectively, of the maximal response attained with LPA and other analogues. In cross-desensitization experiments, all of these compounds specifically inhibited LPA-induced aggregation, suggesting that they were all acting on the same receptor(s). In contrast, cPA and DOXP-H did not trigger platelet aggregation but instead specifically inhibited the effects of LPA in a concentration-dependent manner. The inhibitory action of cPA did not vary with the acyl chain length or the presence of a double bond and did not involve an increase in cAMP. These data thus confirm the lack of stereospecificity of platelet LPA receptor(s). In addition, since the order of potency of some analogues is different from that described in other cells, our results suggest that platelets contain (a) pharmacologically distinct receptor(s) whose molecular identity still remains to be established. Finally, this unique series of compounds might be used for further characterization of other endogenous or recombinant LPA receptors.

Differences in uniquantal amplitude between sites reduce uniquantal variance when few release sites are active

In many types of central neurons, the coefficient of variation (CV) of stimulus-evoked uniquantal events inferred from quantal analysis is small, frequently less than 20%. In contrast, spontaneous putative uniquantal events (minis) from the same neurons are much more variable in amplitude, having a CV of roughly 50% or more. One explanation for this discrepancy is that, if the variance in mini amplitude were generated by differences between release sites, the small number of sites activated during stimulation would sometimes fortuitously have similar quantal amplitudes. Only in these fortuitous cases where uniquantal variance is small could quantal peaks be resolved, and therefore the uniquantal CV seen in the subset of cells where quantal analysis can be performed would systematically be much smaller than predicted by the mini distribution. We have explored this possibility by Monte Carlo simulation assuming all variance in mini amplitude to be due to intersite differences in uniquantal amplitude. We find that when a small number of release sites are activated under these conditions, there is a reduction in the expected uniquantal variance. However, the expected uniquantal CV is highly variable from one experiment to the next, and low uniquantal CVs are not expected to be seen often enough to account for the high frequency with which quantal peaks with a uniquantal CV < 20% are observed experimentally. We conclude that variance in mini amplitude between release sites cannot account for the small uniquantal CV seen in quantal analysis of many central synapses.

A 15-month evaluation of the effects of repeated subgingival minocycline in chronic adult periodontitis

BACKGROUND

A double-blind, randomized, parallel, comparative study was designed to evaluate the long-term safety and efficacy of subgingivally administered minocycline ointment versus a vehicle control.

METHODS

One hundred four patients (104) with moderate to severe adult periodontitis (34 to 64 years of age; mean 46 years) were enrolled in the study. Following scaling and root planing, patients were randomized to receive either 2% minocycline ointment or a matched vehicle control. Study medication was administered directly into the periodontal pocket with a specially designed, graduated, disposable applicator at baseline; week 2; and at months 1, 3, 6, 9, and 12. Scaling and root planing was repeated at months 6 and 12. Standard clinical variables (including probing depth and attachment level) were evaluated at baseline and at months 1, 3, 6, 9, 12, and 15. Microbiological sampling using DNA probes was done at baseline; at week 2; and at months 1, 3, 6, 9, 12, and 15.

RESULTS

Both treatment groups showed significant and clinically relevant reductions in the numbers of each of the 7 microorganisms measured during the entire 15-month study period. When differences were detected, sites treated with minocycline ointment always produced statistically significantly greater reductions than sites which received the vehicle control. For initial pockets > or =5 mm, a mean reduction in probing depth of 1.9 mm was seen in the test sites, versus 1.2 mm in the control sites. Sites with a baseline probing depth > or =7 mm and bleeding index >2 showed an average of 2.5 mm reduction with minocycline versus 1.5 mm with the vehicle. Gains in attachment (0.9 mm and 1.1 mm) were observed in minocycline-treated sites, with baseline probing depth > or =5 mm and > or =7 mm, respectively, compared with 0.5 mm and 0.7 mm gain at control sites. Subgingival administration of minocycline ointment was well tolerated.

CONCLUSIONS

Overall, the results demonstrate that repeated subgingival administration of minocycline ointment in the treatment of adult periodontitis is safe and leads to significant adjunctive improvement after subgingival instrumentation in both clinical and microbiologic variables over a 15-month period.

Entomopathogenic nematodes to control black vine weevil (Coleoptera: Curculionidae) on strawberry

We investigated the potential of heterorhabditid nematodes to control larvae of the black vine weevil, Otiorhynchus sulcatus (F.), in 2 field experiments in commercial strawberry plantings. In both experiments, nematodes were applied directly onto the straw mulch, or onto the soil after temporary removal of the mulch. Heterorhabditis marelatus Lui & Berry (Rhabditida: Heterorhabditidae) reduced numbers of weevil larvae and the percentage of plants infested in both experiments, irrespective of straw removal. In the 1st field experiment, a sponge-packed H. marelatus formulation produced lower numbers of O. sulcatus larvae per strawberry plant (mean O. sulcatus larvae per plant = 0.7) and proportion of infested plants (42%) compared with a vermiculite formulation (mean O. sulcatus larvae per plant = 1.8, proportion infested plants 67%) and an untreated control (mean O. sulcatus larvae per plant = 1.9, proportion infested plants 75%). In the first 2 wk after application, more H. marelatus were found in soil samples collected from plots treated with sponge-packed nematodes, than from plots treated with vermiculite-formulated nematodes. In the 2nd field experiment, sponge-packed formulations of H. bacteriophora Poinar (Rhabditida: Heterorhabditidae) and H. marelatus were tested. H. marelatus caused a reduction in both numbers of weevil larvae (mean O. sulcatus larvae per plant = 0.1) and proportion of infested plants (9%) but H. bacteriophora did not (mean O. sulcatus larvae per plant = 0.45, proportion infested plants 34%). More H. bacteriophora were recovered from soil samples than H. marelatus during the first 7 d of this experiment. However, laboratory studies revealed no difference in the persistence of these 2 nematodes in sand.

Organization of the genes encoding the human proteasome activators PA28alpha and beta

Two proteasome activators PA28alpha and beta, which have been implicated in antigen processing for loading class I MHC molecules, are synthesized in response to Ifn-gamma. The human genes encoding these activators (PSME1 and PSME2, respectively) were analyzed by sequencing. Each gene comprised 11 exons, consistent with gene duplication during vertebrate evolution. The intron/exon organization of both genes was highly conserved, the major difference being the absence of the exon encoding the lysine and glutamic acid-rich 'KEKE' motif in PA28beta. Two other genes of relevance to the immune system were located close to those for PA28 at 14q11.2 including ISGF3G, a protein involved in transcription after IFNalpha signalling. These sequences were also characterized.

Endoscopic ultrasound guided fine needle aspiration biopsy: a large single centre experience

BACKGROUND

Endoscopic ultrasound guided fine needle aspiration biopsy (EUS-FNA) is a recent innovation in the evaluation of gastrointestinal and pulmonary malignancies.

AIMS

To review the experience with EUS-FNA of a large single centre.

METHODS

333 consecutive patients underwent EUS-FNA. Follow up data were available on 327 lesions in 317 patients, including 160 lymph nodes, 144 pancreatic lesions, 15 extraintestinal masses, and eight intramural tumours.

RESULTS

A primary diagnosis of malignancy was obtained by EUS-FNA in 62% of patients with clinically suspicious lesions. The overall accuracy of EUS-FNA for the diagnosis of malignancy was 86%, with sensitivity of 84% and specificity of 96%. With respect to lesion types, the sensitivity, specificity, and accuracy were 85%, 100%, and 89% for lymph nodes; 82%, 100%, and 85% for pancreatic lesions; 88%, 100%, and 90% for perirectal masses; and 50%, 25%, and 38% for intramural lesions, respectively. Compared with size and sonographic criteria, EUS-FNA in the evaluation of lymph nodes provided superior accuracy and specificity, without compromising sensitivity. Inadequate specimens were obtained from only six patients, including 3/5 with stromal tumors. Only one complication occurred.

CONCLUSIONS

EUS-FNA is safe and can readily obtain tissue specimens adequate for cytopathological diagnoses. Compared with size and sonographic criteria, it is a superior modality for the detection of nodal metastases. While providing accurate diagnosis of pancreatic and perirectal malignancies, results suggest the technique is less useful for intramural lesions.

The neuron-specific K-Cl cotransporter, KCC2. Antibody development and initial characterization of the protein

The neuron-specific K-Cl cotransporter (KCC2) is hypothesized to function as an active Cl- extrusion pathway important in postsynaptic inhibition mediated by ligand-gated anion channels, like gamma-aminobutyric acid type A (GABAA) and glycine receptors. To understand better the functional role of KCC2 in the nervous system, we developed polyclonal antibodies to a KCC2 fusion protein and used these antibodies to characterize and localize KCC2 in the rat cerebellum. The antibodies specifically recognized the KCC2 protein which is an approximately 140-kDa glycoprotein detectable only within the central nervous system. The KCC2 protein displayed a robust and punctate distribution in primary cultured retinal amacrine cells known to form exclusively GABAAergic synapses in culture. In immunolocalization studies, KCC2 was absent from axons and glia but was highly expressed at neuronal somata and dendrites, indicating a specific postsynaptic distribution of the protein. In the granule cell layer, KCC2 exhibited a distinct colocalization with the beta2/beta3-subunits of the GABAA receptor at the plasma membrane of granule cell somata and at cerebellar glomeruli. KCC2 lightly labeled the plasma membrane of Purkinje cell somata. Within the molecular layer, KCC2 exhibited a distinctly punctate distribution along dendrites, indicating it may be highly localized at inhibitory synapses along these processes. The distinct postsynaptic localization of KCC2 and its colocalization with GABAA receptor in the cerebellum are consistent with the putative role of KCC2 in neuronal Cl- extrusion and postsynaptic inhibition.

The Philadelphia story: the 22q11.2 deletion: report on 250 patients

A submicroscopic deletion of chromosome 22q11.2 has been identified in the majority of patients with the DiGeorge, velocardiofacial, and conotruncal anomaly face syndromes, and in some patients with the Opitz G/BBB and Cayler cardiofacial syndromes. We have been involved in the analysis of DiGeorge syndrome and related diagnoses since 1982 and have evaluated a large number of patients with the deletion. We describe our cohort of 250 patients whose clinical findings help to define the extremely variable phenotype associated with the 22q11.2 deletion and may assist clinicians in providing genetic counseling and guidelines for clinical management based on these findings.

Germline mutations in the extracellular domains of the 55 kDa TNF receptor, TNFR1, define a family of dominantly inherited autoinflammatory syndromes

Autosomal dominant periodic fever syndromes are characterized by unexplained episodes of fever and severe localized inflammation. In seven affected families, we found six different missense mutations of the 55 kDa tumor necrosis factor receptor (TNFR1), five of which disrupt conserved extracellular disulfide bonds. Soluble plasma TNFR1 levels in patients were approximately half normal. Leukocytes bearing a C52F mutation showed increased membrane TNFR1 and reduced receptor cleavage following stimulation. We propose that the autoinflammatory phenotype results from impaired downregulation of membrane TNFR1 and diminished shedding of potentially antagonistic soluble receptor. TNFR1-associated periodic syndromes (TRAPS) establish an important class of mutations in TNF receptors. Detailed analysis of one such mutation suggests impaired cytokine receptor clearance as a novel mechanism of disease.

Exposure to violence and posttraumatic stress symptomatology among abortion clinic workers

The intent of this study was to examine the relationship between exposure to abortion clinic violence, either as a victim or witness, and the reporting of posttraumatic stress disorder (PTSD) symptoms among clinic employees. Semi-structured interviews with 71 clinic workers from eight abortion clinics in a Southeastern state were used for analyses. Findings showed that as victims, clinic workers experienced moderate forms of violence and witnessed greater variety and numbers of violent acts. Twenty-one percent of the sampled workers reported symptoms similar to the syndrome described in the DSM-IIIR/DSM-IV classification for PTSD. A multivariate analysis showed that even when controlling for significant life circumstances and stressors outside the clinic setting, witnessing violence was a significant predictor of PTSD symptomatology.