A fluorescence-based screen for ribosome binding antibiotics.

The development of new antibacterial agents has become necessary to treat the large number of emerging bacterial strains resistant to current antibiotics. Despite the different methods of resistance developed by these new strains, the A-site of the bacterial ribosome remains an attractive target for new antibiotics. To develop new drugs that target the ribosomal A-site, a high-throughput screen is necessary to identify compounds that bind to the target with high affinity. To this end, we present an assay that uses a novel fluorescein-conjugated neomycin (F-neo) molecule as a binding probe to determine the relative binding affinity of a drug library. We show here that the binding of F-neo to a model Escherichia coli ribosomal A-site results in a large decrease in the fluorescence of the molecule. Furthermore, we have determined that the change in fluorescence is due to the relative change in the pK(a) of the probe resulting from the change in the electrostatic environment that occurs when the probe is taken from the solvent and localized into the negative potential of the A-site major groove. Finally, we demonstrate that F-neo can be used in a robust, highly reproducible assay, determined by a Z'-factor greater than 0.80 for 3 consecutive days. The assay is capable of rapidly determining the relative binding affinity of a compound library in a 96-well plate format using a single channel electronic pipette. The current assay format will be easily adaptable to a high-throughput format with the use of a liquid handling robot for large drug libraries currently available and under development.

Meeting the challenge of interpreting high-resolution single nucleotide polymorphism array data in prenatal diagnosis: does increased diagnostic power outweigh the dilemma of rare variants?

OBJECTIVE: Several studies have already shown the superiority of chromosomal microarray analysis (CMA) compared with conventional karyotyping for prenatal investigation of fetal ultrasound abnormality. This study used very high-resolution single nucleotide polymorphism (SNP) arrays to determine the impact on detection rates of all clinical categories of copy number variations (CNVs), and address the issue of interpreting and communicating findings of uncertain or unknown clinical significance, which are to be expected at higher frequency when using very high-resolution CMA. DESIGN: Prospective validation study. SETTING: Tertiary clinical genetics centre. POPULATION: Women referred for further investigation of fetal ultrasound anomaly. METHODS: We prospectively tested 104 prenatal samples using both conventional karyotyping and high-resolution arrays. MAIN OUTCOME MEASURES: The detection rates for each clinical category of CNV. RESULTS: Unequivocal pathogenic CNVs were found in six cases, including one with uniparental disomy (paternal UPD 14). A further four cases had a 'likely pathogenic' finding. Overall, CMA improved the detection of 'pathogenic' and 'likely pathogenic' abnormalities from 2.9% (3/104) to 9.6% (10/104). CNVs of 'unknown' clinical significance that presented interpretational difficulties beyond results from parental investigations were detected in 6.7% (7/104) of samples. CONCLUSIONS: Increased detection sensitivity appears to be the main benefit of high-resolution CMA. Despite this, in this cohort there was no significant benefit in terms of improving detection of small pathogenic CNVs. A potential disadvantage is the high detection rate of CNVs of 'unknown' clinical significance. These findings emphasise the importance of establishing an evidence-based policy for the interpretation and reporting of CNVs, and the need to provide appropriate pre- and post-test counselling.

The course of posttraumatic stress symptoms and functional impairment following a disaster: what is the lasting influence of acute versus ongoing traumatic events and stressors?

PURPOSE: Ongoing traumatic events and stressors, rather than acute sources of trauma, may shape long-term post-disaster mental health. The purpose of this study was to compare the influence of acute hurricane-related exposures and ongoing post-hurricane exposures on the short- and long-term course of posttraumatic stress symptoms (PTSS) and functional impairment (FI). METHODS: A random sample of adults (n = 658) in Galveston and Chambers Counties, Texas, was selected 2-6 months after Hurricane Ike and interviewed 3 times over 18 months. Hurricane-related exposures included traumatic events such as death of a family member due to the hurricane and stressors such as loss/damage to personal property due to the hurricane. Post-hurricane exposures included traumatic events such as sexual assault and stressors such as divorce or serious financial problems. RESULTS: Experiencing an acute hurricane-related traumatic event or stressor was associated with initial post-hurricane PTSS [RR = 1.92 (95% CI = 1.13-3.26) and RR = 1.62 (1.36-1.94), respectively] and FI [RR = 1.76; (1.05-2.97) and RR = 1.74 (1.46-2.08)], respectively, and acute hurricane-related stressors were associated with a higher rate of increase in FI over time [RR = 1.09; (1.01-1.19)]. In contrast, ongoing post-hurricane daily stressors were not associated within initial PTSS and FI, but were associated with PTSS and FI at the second and third interviews. CONCLUSIONS: While immediate postdisaster interventions may influence short-term mental health, investment in the prevention of ongoing stressors may be instrumental to manage long-term mental health status.

Pathogenic aberrations revealed exclusively by single nucleotide polymorphism (SNP) genotyping data in 5000 samples tested by molecular karyotyping.

BACKGROUND: Several recent studies have demonstrated the use of single nucleotide polymorphism (SNP) arrays for the investigation of intellectual disability, developmental delay, autism or congenital abnormalities. In addition to LogR 'copy number' data, these arrays provide SNP genotyping data for gene level autozygosity mapping, estimating low levels of mosaicism, assessing long continuous stretches of homozygosity (LCSH), detection of uniparental disomy, and 'autozygous' regions. However, there remains little specific information on the clinical utility of this genotyping data. METHODS: Molecular karyotyping, using SNP array, was performed on 5000 clinical samples. RESULTS: Clinically significant 'LogR neutral' genotyping abnormalities were detected in 0.5% of cases. Among these were a single case of chimerism, 12 cases with low level chromosome mosaicism, and 11 cases with an LCSH associated with uniparental disomy. In addition, the genotyping data revealed several LCSH associated with clinically relevant 'recessive type' genetic defects. CONCLUSIONS: These results demonstrate the utility of SNP genotyping data for detection of clinically significant abnormalities, including chimerism/mosaicism and recessive Mendelian disorders associated with autozygosity. The incidence of clinically significant low level mosaicism inferred from these cases suggests that this has hitherto been underestimated and chromosome mosaicism frequently occurs in the absence of indicative clinical features. The growing appreciation among clinicians and demand for SNP genotyping data poses significant challenges for the interpretation of LCSH, especially where there is no detailed phenotypic description to direct laboratory analysis. Finally, reporting of unexpected or hidden consanguinity revealed by SNP array analysis raises potential ethical and legal issues.

Toward in situ monitoring of water contamination by nitroenergetic compounds.

We have previously described the application of novel porous organosilicate materials to the preconcentration of nitroenergetic targets from aqueous solution prior to HPLC analysis. The performance of the sorbents and the advantages of these types of materials over commercially available solid phase extraction sorbents have been demonstrated. Here, the development of systems for application of those sorbents to in situ monitoring is described. Considerations such as column pressure, particulate filtration, and component durability are discussed. The diameter of selected column housings, the sorbent bed depth, and the frits utilized significantly impact the utility of the sorbent columns in the prototype system. The impact of and necessity for improvements in the morphological characteristics of the sorbents as they relate to reduction in column pressure are detailed. The results of experiments utilizing a prototype system are presented. Data demonstrating feasibility for use of the sorbents in preconcentration prior to ion mobility spectrometry is also presented.

Enkephalin-induced depression of single neurons in brain areas with opiate receptors--antagonism by naloxone.

Enkephalin, applied microiontophoretically, depressed spontaneous and glutamate-induced firing of single neurons in frontal cortex, caudate nucleus, and periaqueductal gray matter, where enkephalin and high concentrations of opiate receptors are found. Many of the depressions were blocked by the specific narcotic antagonist naloxone. The data are compatible with a neurotransmitter or neuromodulator role for this new brain pentapeptide.

Events in the evolution of pre-proinsulin.

An extensive computer-assisted analysis of known pre-proinsulin coding sequences has shown correlations that can be interpreted as evidence for an intron-mediated juxtaposition of exons in the evolution of these genes. The evidence includes the discovery that the regions of the pre-proinsulin genes that code for the signal peptide consist of nearly tandem repeating units of nine base pairs. This pattern reappears in the C region of the genes after a large intron that occurs in three of the four genes analyzed. A model is proposed in which primordial insulin was coded for by two separate minigenes arising from a gene duplication, each with identical or nearly identical signal peptide coding regions. The minigenes fused into one transcriptional unit mediated by the large intron, and the signal peptide coding region of one of the putative minigenes evolved into the latter portion of the C peptide coding region.

Multiple forms of an inositol polyphosphate 5-phosphatase form signaling complexes with Shc and Grb2.

BACKGROUND: Shc and Grb2 form a complex in cells in response to growth factor stimulation and link tyrosine kinases to Ras during the resulting signaling process. Shc and Grb2 each contain domains that mediate interactions with other unidentified intracellular proteins. For example, the Shc PTB domain binds to 130 kDa and 145 kDa tyrosine-phosphorylated proteins in response to stimulation of cells by growth factors, cytokines and crosslinking of antigen receptors. The Grb2 SH3 domains bind to an unidentified 116 kDa protein in T cells. We have identified three proteins, of 110 kDa, 130 kDa and 145 kDa, as a new family of molecules encoded by the same gene. In vivo studies show that these proteins form signal transduction complexes with Shc and with Grb2. RESULTS: The 130 kDa and 145 kDa tyrosine-phosphorylated proteins that associate with the Shc PTB domain were purified by conventional chromatographic methods. Partial peptide and cDNA sequences corresponding to these proteins, termed SIP-145 and SIP-130 (SIP for signaling inositol polyphosphate 5-phosphatase), identified them as SH2 domain-containing products of a single gene and as members of the inositol polyphosphate 5-phosphatase family. The SIP-130 and SIP-145 proteins and inositol polyphosphate 5-phosphatase activity associated with Shc in vivo in response to B-cell activation. By using an independent approach, expression cloning, we found that the Grb2 SH3 domains bind specifically to SIP-110, a 110 kDa splice variant of SIP-145 and SIP-130, which lacks the SH2 domain. The SIP proteins hydrolyzed phosphatidylinositol (3,4,5)-trisphosphate (PtdIns (3,4,5)-P3) and Ins (1,3,4,5)-P4, but not PtdIns (4,5)-P2 or Ins (1,4,5)-P3. CONCLUSIONS: These findings strongly implicate the inositol polyphosphate 5-phosphatases in Shc- and Grb2-mediated signal transduction. Furthermore, SIP-110, SIP-130 and SIP-145 prefer 3-phosphorylated substrates, suggesting a link to the phosphatidylinositol 3-kinase signaling pathway.

The apparent permeability coefficient for proton flux through phosphatidylcholine vesicles is dependent on the direction of flux.

A dioleoylphosphatidylcholine unilamellar vesicle model system was used to determine proton permeability. The fluorescence of the pH reporter group, pyranine, trapped within vesicles with a difference in pH across the bilayer, was digitized and analyzed with numerical integration. When H+ flux was initiated by the acidification of the external buffer (acid jump), the apparent H+ permeability was found to be a linear function of the reciprocal of the internal H+ concentration with the slope inversely proportional to the initial size of the H+ gradient. When flux was initiated by the alkalinization of the external buffer (base jump), the apparent permeability coefficient was constant for each external H+ concentration. However, the value of the apparent permeability was linearly dependent on the reciprocal of the external H+. The possibility that carbonates (carbon dioxide, carbonic acid, bicarbonate and carbonate) could be acting as proton carriers was tested by adding millimolar concentrations of bicarbonate to solutions greatly reduced in carbonates. The slopes of the graphs of apparent permeability coefficient vs. reciprocal H+ were linear functions of added bicarbonate concentration for both acid and base jump conditions. These observations were interpreted in terms of a model suggesting that carbonic acid or carbon dioxide together with bicarbonate was an efficient proton carrier across phospholipid bilayers.

Characterization of CO2/carbonic acid mediated proton flux through phosphatidylcholine vesicles as model membranes.

The apparent proton permeability coefficient for phospholipid vesicles measured in our laboratory (Norris, F. A. and Powell, G. L. (1990) Biochim. Biophys. Acta 1030, 165-171) for proton flux initiated by rapidly lowering of the external pH (acid jump) was a linear function of the reciprocal internal proton concentration. This behavior was ascribed to the presence of the weak acid carriers, carbonic acid/CO2/bicarbonate. In the present work, a theoretical description, appropriate for proton transport by any weak acid carrier, has been developed which lends itself to novel graphical treatment permitting the separate estimation of the permeability coefficients for protons, hydroxide ions and bicarbonate. The proton permeability coefficient determined by this method was 1.8 x 10(-5) (S.E. 1.3 x 10(-5)) cm/s; that for hydroxide ion was 3.8 x 10(-5) (S.E. 5.6 x 10(-6)) cm/s and a lower limit for the permeability of bicarbonate ion, 4.3 x 10(-6) (S.E. 3.6 x 10(-7) cm/s, can be set. The presence of negative surface charge on the lipid bilayer increased the observed proton permeability coefficient in accordance with Gouy-Chapman theory. The charge was introduced by preparing vesicles containing increasing amounts of negatively charged dioleoylphosphatidylglycerol. The observed proton permeability coefficient increased and the observed permeability coefficients for hydroxide ion and bicarbonate decreased. The addition of the lipophilic cations, valinomycin-K+ and tetrabutylammonium ion increased the slope of P vs. 1/[Hi+]. These changes are analogous to those reported for the permeant weak acid uncouplers FCCP and CCCP. These studies demonstrated that CO2/carbonic acid was an effective carrier of protons across phospholipid model membranes.

The 1.6 A structure of Kunitz-type domain from the alpha 3 chain of human type VI collagen.

The C-terminal Kunitz-type domain from the alpha 3 chain of human type VI collagen (C5), a single 58 amino acid residue chain with three disulfide bridges, was cloned, expressed and crystallized in a monoclonic form, space group P2(1), with a = 25.7 A, b = 38.2 A, c = 28.8 A and beta = 109 degrees. The structure was resolved by molecular replacement, using Alzheimer's protein precursor inhibitor and bovine pancreatic trypsin inhibitor three-dimensional structures as search models. The molecule with one sulfate ion and 43 associated water molecules was refined by XPLOR to an R-factor of 18.9% at 1.6 A. The molecule was not degraded by trypsin and did not inhibit trypsin or tested serine proteases. As opposed to the other Kunitz family members, C5 demonstrates left-handed chirality of the Cys14-Cys38 disulfide bond. Inversion of the Thr13 carbonyl and bulky side-chains at the interface with trypsin in a model of the C5-trypsin complex may explain the lack of inhibition of trypsin.

Tubular particles in a case of recurrent lymphocytic meningitis followed by amyotrophic lateral sclerosis.

A patient suffered recurrent episodes of aseptic lymphocytic meningitis for many years and then developed amyotrophic lateral sclerosis (ALS). Immune-complexes were deposited in the renal glomerular basement membrane and mesangia. The necropsy study revealed both lymphocytic meningitis and ALS. Study of the motor neurons with the electron microscope revealed proliferation of endoplasmic reticulum, small cytoplasmolytic areas and focal neurofibrillar accumulations in axons. Interwoven, serpentine 10-15 nm. tubules first appeared with ER proliferation and, presumably at a later stage, were sometimes present in large masses. These tubules might be virus material but virus cultures, including tissue culture, and animal inoculations have thus far been negative.

Trial of oral physostigmine in amyotrophic lateral sclerosis.

We evaluated a double-blind, placebo-controlled, and double-crossover trial of oral physostigmine salicylate for a 9-month period in 13 of 25 patients with sporadic amyotrophic lateral sclerosis (ALS). A large dropout rate of 48% was secondary to eight deaths and four exclusions attributed to the incapability to swallow the tablets (physostigmine) and capsules (lecithin) or to attend the clinic. Parameters used for assessment of the drug efficacy included body weight, ALS score, Jamar grip strength, forced vital capacity, and maximum voluntary ventilation. It revealed slight benefit in reduced loss of grip strength compared with the pretrial and placebo periods. However, the rates of decline for body weight, ALS score, forced vital capacity, maximum voluntary ventilation, and megascore did not differ significantly between the pretrial, placebo, and physostigmine periods. We therefore concluded that overall no significant alteration in the clinical course was gained by oral physostigmine therapy in the 13 patients with ALS who were included in this study.

Distribution of alpha interferon in serum and cerebrospinal fluid after systemic administration.

After intravenous infusion of recombinant leukocyte interferon (rIFN-alpha A) to four subjects with an indwelling reservoir, serial serum and cerebrospinal fluid samples were taken over 48 hr and were analyzed for interferon by an enzyme immunoassay method (ELISA). On separate occasions, 18 and 50 X 10(6) of rIFN-alpha A were infused over 10 min. Maximum serum concentrations of rIFN-alpha A ranged from 6720 to 11,000 pg/ml and from 32,900 to 43,400 pg/ml after the 18 and 50 X 10(6) U doses. There was no measurable concentration of rIFN-alpha A in the cerebrospinal fluid of subjects who received 18 X 10(6) U doses. In three of four subjects who received 50 X 10(6) U rIFN-alpha A, concentrations ranged from 17 to 70 pg/ml that were measurable no earlier than 1 hr after the start of the infusion and that in two cases were measurable throughout 24 hr.

Purification and characterization of the trefoil peptide human spasmolytic polypeptide (hSP) produced in yeast.

Recombinant human spasmolytic polypeptide (r-hSP) has been produced in relatively large amounts in Saccharomyces cerevisiae. The two intronless trefoil domains of the hSP-DNA were cloned separately by PCR from human genomic DNA, and the remaining parts of the gene synthesized. Recombinant plasmids were constructed to encode a fusion protein consisting of a hybrid leader sequence and the hSP sequence. The leader sequence serves to direct the fusion protein into the secretory pathway of the cell and to expose it to the Kex 2 processing enzyme system. The secreted r-hSP was found in a glycosylated and an non-glycosylated form. The two forms of r-hSP were purified from the yeast fermentation broth by a combination of ion-exchange chromatography and preparative HPLC. The overall yield from 8 litres of fermentation broth was 160 mg r-hSP and 219 mg glycosylated r-hSP corresponding to 50% and 34%, respectively. The structure of the r-hSP and the glycosylated r-hSP was determined by amino acid analysis and carbohydrate composition analysis as well as by peptide mapping, amino acid sequencing and mass spectrometric analysis.

The secretion of glucagon by transformed yeast strains.

Saccharomyces cerevisiae strains were transformed with plasmids coding for modified mating factor alpha 1 leader sequences followed by glucagon. Glucagon-containing peptides which were secreted into the fermentation broth were isolated and their amino acid sequences determined. The yeast strain transformed with the sequence coding for the complete mating factor alpha 1 leader sequence preceding the glucagon gene (MT556) secreted glucagon plus glucagon extended at its N-terminal by parts of the leader sequence. The yeast strain transformed with the sequence coding for a truncated mating factor alpha 1 leader sequence before the glucagon gene (MT615) secreted glucagon. These observations suggest that S. cerevisiae is a suitable vehicle for the efficient expression of plasmids coding for polypeptides similar to glucagon (e.g. VIP, secretin, GIP).

Expression, purification and characterization of a Kunitz-type protease inhibitor domain from human amyloid precursor protein homolog.

The Kunitz-type protease inhibitor domain from a recently identified homolog of the Alzheimer amyloid precursor protein (APPH KPI) was expressed in yeast, purified and characterized. Its inhibition profile towards several serine proteases was studied and compared to that of APP KPI, the Kunitz domain from the Alzheimer amyloid precursor protein. APPH KPI was shown to inhibit proteases with trypsin-like specificity with an inhibitor profile resembling that of the APP KPI domain. The KPI domains from APP and APPH inhibited trypsin (Ki = 0.02 nM), and plasma kallikrein (Ki = 86 nM) with approximal equal affinity. In comparison to APP KPI (Ki = 82 nM) the KPI domain of the homolog, APPH KPI, (Ki = 8.8 nM) was a more potent inhibitor of glandular kallikrein. APPH KPI was a less potent inhibitor of chymotrypsin than APP KPI (Ki = 78 nM as compared to Ki = 6 nM), plasmin (Ki = 81 nM as compared to 42 nM), and factor XIa (Ki = 14 nM as compared to Ki = 0.7 nM). The affinity of factor XIa for APPH KPI is sufficiently high to allow for an interaction in the blood. It is, however, well possible that the physiological protease ligand for the receptor-like APPH protein has yet to be identified.

Expression of protein-tyrosine phosphatases in the major insulin target tissues.

Protein-tyrosine phosphatases (PTPs) are key regulators of the insulin receptor signal transduction pathway. We have performed a detailed analysis of PTP expression in the major human insulin target tissues or cells (liver, adipose tissue, skeletal muscle and endothelial cells). To obtain a representative picture, all tissues were analyzed by PCR using three different primer sets corresponding to conserved regions of known PTPs. A total of 24 different PTPs were identified. A multiprobe RNase protection assay was developed to obtain a semiquantitative measure of the expression levels of selected PTPs. Surprisingly, PTP-LAR, previously suggested to be a major regulator of the insulin receptor tyrosine kinase, was expressed in extremely low levels in skeletal muscle, whereas the related receptor-type PTP-sigma and PTP-alpha were expressed in relatively high levels in all four tissues. The low levels of LAR PTP mRNA in skeletal muscle were further confirmed by Northern blot analysis.

Amyotrophic lateral sclerosis. Impairment of neuromuscular transmission.

Neuromuscular transmission was studied in the ulnar-hypothenar group in 55 patients with amyotrophic lateral sclerosis. A decremental response was found in 67.0%. The decrement was larger and present more often in muscles showing atrophy. In addition, muscles with frequent fasciculations showed a larger decrement than the ones with rare fasciculation. A temperature effect similar to that in myasthenia gravis was observed, with a reduction of the decrement following local cooling of the muscles. Administration of edrophonium chloride improved the synaptic defect. Posttetanic exhaustion was observed as well. It is thought that the defect of neuromuscular transmission is due to a decreased trophic function of the neuron followed by morphological changes at the endplate.

Trial of baclofen in amyotrophic lateral sclerosis.

A trial of the antispastic drug baclofen was made in amyotrophic lateral sclerosis. Some patients noted reduction of tonus and spasticity; but others had no benefit, nor was the course of the disease altered by long-term administration of baclofen. No major side effects occurred.