Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.

Histidine kinases and response regulator proteins in two-component signaling systems

Phosphotransfer-mediated signaling pathways allow cells to sense and respond to environmental stimuli. Autophosphorylating histidine protein kinases provide phosphoryl groups for response regulator proteins which, in turn, function as molecular switches that control diverse effector activities. Structural studies of proteins involved in two-component signaling systems have revealed a modular architecture with versatile conserved domains that are readily adapted to the specific needs of individual systems.

alpha-Synuclein gene haplotypes are associated with Parkinson's disease

We report haplotype analysis of the alpha-synuclein gene in Parkinson's disease (PD), extending earlier reports of an association with a polymorphism within the gene promoter. This analysis showed significant differences in haplotypes between PD cases and controls. Our analyses demonstrate that genetic variability in the alpha-synuclein gene is a risk factor for the development of PD. These genetic findings are analogous to the tau haplotype over-represented in progressive supranuclear palsy and further extend the similarity in the etiologies and pathogeneses of the synucleinopathies and tauopathies.

Structure of the Mg(2+)-bound form of CheY and mechanism of phosphoryl transfer in bacterial chemotaxis

The response regulator protein of bacterial chemotaxis, CheY, is representative of a large family of signal transduction proteins that function as phosphorylation-activated switches to regulate the activities of associated effector domains. These regulators catalyze the metal ion-dependent phosphoryl transfer and dephosphorylation reactions that control the effector activities. The crystal structures of Salmonella typhimurium CheY with and without Mg2+ bound at the active site have been determined and refined at 1.8-A resolution. While the overall structures of metal-bound and metal-free CheY are similar, significant rearrangements occur within the active site involving the three most highly conserved residues of the response regulator family. Conservation of the cluster of carboxylate side chains at the active site of response regulator domains can be rationalized in terms of their role in coordinating the catalytically essential divalent metal ion. The Mg2+ coordination geometry provides insights to the mechanism of phosphoryl transfer.

Characterization of human HtrA2, a novel serine protease involved in the mammalian cellular stress response

Human HtrA2 is a novel member of the HtrA serine protease family and shows extensive homology to the Escherichia coli HtrA genes that are essential for bacterial survival at high temperatures. HumHtrA2 is also homologous to human HtrA1, also known as L56/HtrA, which is differentially expressed in human osteoarthritic cartilage and after SV40 transformation of human fibroblasts. HumHtrA2 is upregulated in mammalian cells in response to stress induced by both heat shock and tunicamycin treatment. Biochemical characterization of humHtrA2 shows it to be predominantly a nuclear protease which undergoes autoproteolysis. This proteolysis is abolished when the predicted active site serine residue is altered to alanine by site-directed mutagenesis. In human cell lines, it is present as two polypeptides of 38 and 40 kDa. HumHtrA2 cleaves beta-casein with an inhibitor profile similar to that previously described for E. coli HtrA, in addition to an increase in beta-casein turnover when the assay temperature is raised from 37 to 45 degrees C. The biochemical and sequence similarities between humHtrA2 and its bacterial homologues, in conjunction with its nuclear location and upregulation in response to tunicamycin and heat shock suggest that it is involved in mammalian stress response pathways.

Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain

We report the x-ray crystal structure of the methylesterase CheB, a phosphorylation-activated response regulator involved in reversible modification of bacterial chemotaxis receptors. Methylesterase CheB and methyltransferase CheR modulate signaling output of the chemotaxis receptors by controlling the level of receptor methylation. The structure of CheB, which consists of an N-terminal regulatory domain and a C-terminal catalytic domain joined by a linker, was solved by molecular replacement methods using independent search models for the two domains. In unphosphorylated CheB, the N-terminal domain packs against the active site of the C-terminal domain and thus inhibits methylesterase activity by directly restricting access to the active site. We propose that phosphorylation of CheB induces a conformational change in the regulatory domain that disrupts the domain interface, resulting in a repositioning of the domains and allowing access to the active site. Structural similarity between the two companion receptor modification enzymes, CheB and CheR, suggests an evolutionary and/or functional relationship. Specifically, the phosphorylated N-terminal domain of CheB may facilitate interaction with the receptors, similar to the postulated role of the N-terminal domain of CheR. Examination of surfaces in the N-terminal regulatory domain of CheB suggests that despite a common fold throughout the response regulator family, surfaces used for protein-protein interactions differ significantly. Comparison between CheB and other response regulators indicates that analogous surfaces are used for different functions and conversely, similar functions are mediated by different molecular surfaces.

Ionic mechanisms of adenosine actions in pacemaker cells from rabbit heart

1. Whole-cell and patch clamp techniques have been applied to cells isolated from the rabbit sino-atrial (S-A) node to study the ionic mechanism(s) of adenosine-induced slowing of cardiac pacemaker activity. 2. Viable spontaneously active cells were isolated from the central region of the S-A node of the rabbit heart by an enzymatic dispersion procedure similar to that reported by Giles & van Ginneken (1985) and van Ginneken & Giles (1988). In these spontaneously beating cells application of adenosine caused a dose-dependent slowing accompanied by a small hyperpolarization of the maximum diastolic potential. Relatively high doses of adenosine (greater than 20 microM) caused complete arrest, associated with a hyperpolarization of 12-15 mV. 3. In corresponding whole-cell voltage clamp experiments adenosine activated a time-independent potassium current, IK(ADO), which at -50 mV is approximately 30 pA in normal Tyrode solution and 50 pA in high [K+]o (20 mM) Tyrode solution. This current is similar to the one identified previously in guinea-pig atrium (Belardinelli & Isenberg, 1983a; Kurachi, Nakajima & Sugimoto, 1986). 4. Patch clamp recordings of the single-channel events underlying IK(ADO) showed that they have a conductance of approximately 25.0 +/- 1.9 pS. The whole-cell or macroscopic current, IK(ADO), and the adenosine-induced single-channel events exhibit strong inward-going rectification. 5. Adenosine in doses (10 microM) which significantly activate IK(ADO) failed to produce any measurable effect on the calcium current, ICa, in these isolated cardiac pacemaker cells. However, after ICa has been enhanced by the addition of isoprenaline, adenosine (1-10 microM) caused a significant inhibition: it reduced ICa back to approximately the control levels. 6. A similar 'indirect' effect of adenosine was observed on If, the slow time- and voltage-dependent inward current which is activated by hyperpolarizing these S-A node cells. Adenosine (10(-5) M) failed to influence the control or basal If; however, after If was enhanced by isoprenaline, adenosine markedly inhibited it. 7. These results provide explanations for both the direct and the indirect effects of adenosine in mammalian cardiac pacemaker tissue: activation of IK(ADO), and of a time-independent background potassium current and inhibition of ICa and If, respectively. Since it is known that there is significant adrenergic tone in the mammalian S-A node both the indirect and the direct effects of adenosine may be of physiological importance.

The mouse and human homologs of DMC1, the yeast meiosis-specific homologous recombination gene, have a common unique form of exon-skipped transcript in meiosis

Genetic recombination in meiosis plays an important role in generating diversity of genetic information. In yeast an Escherichia coli RecA-like gene, DMC1, is expressed in meiotic prophase and its product co-localizes with Rad51 protein on zygotene chromosomes. We have cloned the mouse and human homologs of the yeast DMC1 gene. The predicted human and mouse DMC1 proteins showed 54.1% sequence identity with yeast Dmc1 protein. The domain II region, highly conserved in the E.coli RecA-like protein family, was also found in the mammalian DMC1 proteins, including the two ATP binding motifs and DNA binding sites with the region. In situ hybridization analysis revealed expression of the mouse Dmc1 gene in testicular germ cells in meiosis; RT-PCR showed expression in embryonal ovaries. These findings suggest that DMC1 plays an important role in meiotic homologous recombination. From both the man and mouse we have isolated an alternative spliced form of Dmc1 cDNA (Dmc1-d), which is deleted for a region between the two motifs involved in nucleotide binding. Since the alternatively spliced Dmc1-d transcript was detected in both male and female germ cells, the encoded protein DMC1-D may have a novel role in mammalian genetic recombination in meiosis.

Chromosome localization and genomic structure of the KiSS-1 metastasis suppressor gene (KISS1)

The identification and sequence of KiSS-1 (HGMW-approved symbol, KISS1), a human malignant melanoma metastasis-suppressor gene, was recently published. In this report, we present a corrected genomic sequence, genomic structure, and refined chromosomal location for KiSS-1. The genomic organization of the sequence reveals a gene consisting of four exons. The first two exons are not translated; the third exon contains 38 5' noncoding bases followed by the translational start site and another 100 translated bases. The terminal exon contains a further 332 translated bases, the translational stop codon, and the polyadenylation signal. The gene maps to chromosome 1q32 as determined by radiation hybrid mapping and FISH analysis. The relatively simple organization of this gene will facilitate analyses for mutations and abnormal expression in human tumors.

Evidence for an extraterrestrial impact 12,900 years ago that contributed to the megafaunal extinctions and the Younger Dryas cooling

A carbon-rich black layer, dating to approximately 12.9 ka, has been previously identified at approximately 50 Clovis-age sites across North America and appears contemporaneous with the abrupt onset of Younger Dryas (YD) cooling. The in situ bones of extinct Pleistocene megafauna, along with Clovis tool assemblages, occur below this black layer but not within or above it. Causes for the extinctions, YD cooling, and termination of Clovis culture have long been controversial. In this paper, we provide evidence for an extraterrestrial (ET) impact event at approximately equal 12.9 ka, which we hypothesize caused abrupt environmental changes that contributed to YD cooling, major ecological reorganization, broad-scale extinctions, and rapid human behavioral shifts at the end of the Clovis Period. Clovis-age sites in North American are overlain by a thin, discrete layer with varying peak abundances of (i) magnetic grains with iridium, (ii) magnetic microspherules, (iii) charcoal, (iv) soot, (v) carbon spherules, (vi) glass-like carbon containing nanodiamonds, and (vii) fullerenes with ET helium, all of which are evidence for an ET impact and associated biomass burning at approximately 12.9 ka. This layer also extends throughout at least 15 Carolina Bays, which are unique, elliptical depressions, oriented to the northwest across the Atlantic Coastal Plain. We propose that one or more large, low-density ET objects exploded over northern North America, partially destabilizing the Laurentide Ice Sheet and triggering YD cooling. The shock wave, thermal pulse, and event-related environmental effects (e.g., extensive biomass burning and food limitations) contributed to end-Pleistocene megafaunal extinctions and adaptive shifts among PaleoAmericans in North America.

The development and validation of a predictive index for postpartum depression

A sample of over 6000 women was recruited in the last trimester of pregnancy and administered a 40-item self-report questionnaire designed to detect the presence of factors that were likely to increase the risk of postpartum depression. The mental state of almost 5000 of these women was determined at around 6 to 8 weeks postpartum. By conducting a series of logistic regressions on two-thirds of this sample the original set of variables was reduced to a predictive index of 17 items with weighted scores calculated for each. This index was then applied to the remaining one-third of the sample as a validating procedure and specificity and sensitivity calculated. The index offers a system for the prediction of postpartum depression that could be of use in both research and clinical practice.

Development of child-centered disease-specific questionnaires for living with asthma

Contemporary developments in the management of chronic diseases such as diabetes and asthma offer possibilities for optimal control, but patients increasingly need to take on responsibilities for self care. Health professionals require comprehensive assessments of outcome that include data reflecting patients' perceptions of their disorder and its management. Disease-specific, patient-centered questionnaires for evaluation of adults' health-related quality of life are available for diabetes and asthma. Little progress is evident in relation to pediatric instruments. This paper describes the development of such an instrument for measurement of 8- to 11-year-olds' perceptions of their asthma--the CAQ-B Psychometric characteristics of the CAQ-B are reported: principal axis factor analysis resulted in the derivation of four subscales reflecting children's perceptions of both active and passive aspects of living with asthma, together with their perceptions of its severity and any associated distress. Preliminary explorations with CAQ-B included comparisons of parents', doctors', and children's ratings of severity; comparisons of data from asthmatic and nonasthmatic children; comparisons of data from boys and girls.

Nanodiamonds in the Younger Dryas boundary sediment layer

We report abundant nanodiamonds in sediments dating to 12.9 +/- 0.1 thousand calendar years before the present at multiple locations across North America. Selected area electron diffraction patterns reveal two diamond allotropes in this boundary layer but not above or below that interval. Cubic diamonds form under high temperature-pressure regimes, and n-diamonds also require extraordinary conditions, well outside the range of Earth's typical surficial processes but common to cosmic impacts. N-diamond concentrations range from approximately 10 to 3700 parts per billion by weight, comparable to amounts found in known impact layers. These diamonds provide strong evidence for Earth's collision with a rare swarm of carbonaceous chondrites or comets at the onset of the Younger Dryas cool interval, producing multiple airbursts and possible surface impacts, with severe repercussions for plants, animals, and humans in North America.

Cytoplasmic catalytic subunit of protein kinase A mediates cross-repression by NF-kappa B and the glucocorticoid receptor

Negative transcriptional regulation or cross-coupling between NF-kappa B (RelA) and the glucocorticoid receptor (GR) is proposed to play a regulatory role in human physiology and disease. Despite previous advances, the biochemical basis of this phenomenon remains a subject of controversy. We show here that the inhibition of GR activity by RelA does not require the RelA DNA binding, transactivation, or nuclear localization domains. Surprisingly, RelA repression of GR is abolished by mutation of the conserved protein kinase A (PKA) site at amino acid residue 276 of RelA. We show that GR associates in vivo and in vitro with the catalytic subunit of PKA (PKAc) in a ligand-independent manner and that GR transcription depends on PKA signaling. Indeed, we demonstrated that GR-mediated inhibition of NF-kappa B transactivation is PKAc-dependent. In contrast to previous models, we suggest that the cross-coupling requires a cytoplasmic step and is regulated by a PKAc-associated signaling.

The New York High-Risk Project: anhedonia, attentional deviance, and psychopathology

In the New York High-Risk Project (NYHRP) we followed subjects at risk for schizophrenic or affective disorders and low-risk controls from childhood to adulthood, with the goal of identifying early predictors of later schizophrenia-related psychopathology. In this article, we focus on two potential predictors: the Physical Anhedonia Scale administered in adolescence and the Attention Deviance Index obtained in childhood. Subjects of this report are 161 members of the NYHRP's first sample (sample A), who had scores on both attention and anhedonia and had followup clinical assessments in adulthood. We used a path analysis model and several separate regression analyses to examine the relationships of the parent diagnostic groups, attentional dysfunction, and anhedonia to each other and to each of three psychopathological outcomes: schizophrenia and schizophrenia-related psychoses, major affective disorder, and social isolation in nonpsychotic subjects. Subject groups did not differ in anhedonia scores but did differ in childhood attentional dysfunction, psychosis, and social isolation, all of which are more common in subjects at risk for schizophrenia. In these subjects at risk for schizophrenia, but not in the other two groups of subjects, childhood attentional dysfunction is related to anhedonia, social isolation, and possibly nonparanoid psychosis. Anhedonia is associated with social isolation and with psychosis in females. Several other gender effects are also noted.

Inducible gene expression in mammalian cells and transgenic mice

Advances in biomedicine have accentuated the need to develop methods to deliberately modulate gene activity. In addition to improved versions of the system based on components of the tetracycline resistance operon, several strategies have recently emerged to control gene function at the transcriptional level. Particularly promising are approaches based on non-mammalian steroid hormones, and on small molecules that bind immunophilins.

Tamoxifen for the prevention of breast cancer: psychosocial impact on women participating in two randomized controlled trials

PURPOSE

The purpose of this study was to evaluate the psychosocial implications of tamoxifen versus placebo in women who are at increased risk of breast cancer.

PATIENTS AND METHODS

The 488 women in the psychosocial study were recruited from participants in two placebo-controlled, double-blind, randomized, controlled trials that investigated the efficacy of tamoxifen in the prevention of breast cancer in women who are at high familial risk. During a 5-year period, repeated assessments were made of anxiety, psychological distress, and sexual functioning using standardized questionnaires before treatment at baseline and at 6-month intervals during the trial.

RESULTS

Questionnaire completion over 5 years was good, with 71.1% of women returning at least 8 of 10 follow-up assessments. Although scores from individuals showed considerable fluctuation and variation over time, changes in anxiety, mood, and sexual functioning were not associated with treatment group. The number of symptoms reported at 48 months via a self-report checklist were not associated with treatment group, but vasomotor symptoms were more frequent among tamoxifen-treated women. Symptoms of low energy, breast sensitivity, and visual blurring were reported most frequently in the placebo group.

CONCLUSION

In general, these results are comparable to those from the National Surgical Adjuvant Breast and Bowel Project psychosocial study despite differences in study populations, methodology, and instruments. The long-term use of tamoxifen and other selective estrogen response modulators as preventive agents in high-risk groups has been questioned, but we found no evidence of treatment-related side effects that affect women's psychosocial and sexual functioning.

A major trauma centre is a specialty hospital not a hospital of specialties

BACKGROUND

High estimates of preventable death rates have renewed the impetus for national regionalization of trauma care. Institution of a specialist multidisciplinary trauma service and performance improvement programme was hypothesized to have resulted in improved outcomes for severely injured patients.

METHODS

This was a comparative analysis of data from the Royal London Hospital (RLH) trauma registry and Trauma Audit and Research Network (England and Wales), 2000-2005. Preventable mortality was evaluated by prospective analysis of the RLH performance improvement programme.

RESULTS

Mortality from critical injury at the RLH was 48 per cent lower in 2005 than 2000 (17.9 versus 34.2 per cent; P = 0.001). Overall mortality rates were unchanged for acute hospitals (4.3 versus 4.4 per cent) and other multispecialty hospitals (8.7 versus 7.3 per cent). Secondary transfer mortality in critically injured patients was 53 per cent lower in the regional network than the national average (5.2 versus 11.0 per cent; P = 0.001). Preventable death rates fell from 9 to 2 per cent (P = 0.040) and significant gains were made in critical care and ward bed utilization.

CONCLUSION

Institution of a specialist trauma service and performance improvement programme was associated with significant improvements in outcomes that exceeded national variations.

Neisseria meningitidis produces iron-regulated proteins related to the RTX family of exoproteins

A monoclonal antibody (A4.85) which reacted with Fe-regulated proteins of Neisseria meningitidis, was used to isolate a lambda gt11 clone from N. meningitidis FAM20. Chromosomal fragments flanking the fragment expressing the A4.85 epitope were cloned, and their DNA sequences revealed a 3,345-bp open reading frame predicting a 122-kDa protein. This gene was named frpA (Fe-regulated protein). A computer similarity search of GenBank revealed high levels of similarity to members of the RTX family of cytotoxins, especially in a region of tandem 9-amino-acid repeats. These repeats are found in all members of the RTX family; similar repeats were present 13 times in the predicted FrpA protein. Antigenic relatedness between the meningococcal proteins and the RTX proteins was demonstrated by the reactivity of A4.85 with Escherichia coli hemolysin (HlyA) and Bordetella pertussis adenylate cyclase-hemolysin (CyaA). Similarly, FrpA was recognized by 9D4, a monoclonal antibody directed against B. pertussis CyaA. In addition to the frpA gene, a second gene (frpC) produced a larger RTX-related protein. The frpA and frpC loci were mutagenized in strain FAM20, resulting in the loss of RTX-related proteins. A 120-kDa protein was expressed from the reconstructed frpA gene in E. coli. The biological function of FrpA is unknown, but its similarity to other RTX toxins suggests that it may play an important role in the pathogenesis of meningococcal infection.

Conservation of structure and function among histidine-containing phosphotransfer (HPt) domains as revealed by the crystal structure of YPD1

In Saccharomyces cerevisiae, the SLN1-YPD1-SSK1 phosphorelay system controls a downstream mitogen-activated protein (MAP) kinase in response to hyperosmotic stress. YPD1 functions as a phospho-histidine protein intermediate which is required for phosphoryl group transfer from the sensor kinase SLN1 to the response regulator SSK1. In addition, YPD1 mediates phosphoryl transfer from SLN1 to SKN7, the only other response regulator protein in yeast which plays a role in response to oxidative stress and cell wall biosynthesis. The X-ray structure of YPD1 was solved at a resolution of 2.7 A by conventional multiple isomorphous replacement with anomalous scattering. The tertiary structure of YPD1 consists of six alpha-helices and a short 310-helix. A four-helix bundle comprises the central core of the molecule and contains the histidine residue that is phosphorylated. Structure-based comparisons of YPD1 to other proteins having a similar function, such as the Escherichia coli ArcB histidine-containing phosphotransfer (HPt) domain and the P1 domain of the CheA kinase, revealed that the helical bundle and several structural features around the active-site histidine residue are conserved between the prokaryotic and eukaryotic kingdoms. Despite limited amino acid sequence homology among HPt domains, our analysis of YPD1 as a prototypical family member, indicates that these phosphotransfer domains are likely to share a similar fold and common features with regard to response regulator binding and mechanism for histidine-aspartate phosphoryl transfer.

Comparative in vitro activities of ten antimicrobial agents against bacterial enteropathogens

The in vitro susceptibilities of 50 strains of Salmonella spp., 80 strains of Shigella spp., and 50 enterotoxigenic Escherichia coli, 14 Yersinia enterocolitica, 6 Aeromonas hydrophila, 4 Plesiomonas shigelloides, 9 Vibrio parahaemolyticus, and 30 Campylobacter jejuni strains that were recently isolated from worldwide sources were determined for 10 antimicrobial agents. The antimicrobial agents tested included ampicillin, bicozamycin, doxycycline, enoxacin (CI-919), erythromycin, furazolidone, amdinocillin, norfloxacin, trimethoprim, and trimethoprim-sulfamethoxazole. Ampicillin resistance occurred frequently in strains of Salmonella and Shigella spp. and enterotoxigenic E. coli strains. The most active agents against all of the bacteria tested were enoxacin and norfloxacin. Furazolidone and amdinocillin were also highly active against the majority of strains. Trimethoprim and trimethoprim-sulfamethoxazole were inhibitory at low concentrations against all test except C. jejuni isolates. The in vitro results of this study confirm the high prevalence of bacterial resistance to ampicillin. However, this work also identifies four antimicrobial agents, enoxacin, furazolidone, norfloxacin, and amdinocillin, that would be appropriate for further testing in clinical trials.

High-performance liquid chromatographic analysis of complex N-linked glycans derivatized with 2-aminoacridone

2-Aminoacridone (2-AMAC) has been used to derivatize mixtures of N-linked oligosaccharides released from alpha(1)-acid glycoprotein and immunoglobulin G. In each case, the HPLC profile obtained for the derivatized glycans was compared to that obtained after digestion with sialidase and a two-enzyme array system made up of sialidase and alpha-fucosidase, prior to derivatization by 2-AMAC. These studies are rapid and provide a wealth of preliminary information about the degree of sialylation and core fucosylation in the corresponding parent glycans. Moreover, collection of glycans from one single injection has provided enough material for molecular weight determination by MALDI-MS analysis. In this study we have also carried out limited MS-MS studies on enriched fractions of 2-AMAC-glycans using a nanospray orthogonal quadrupole time-of-flight mass spectrometer.