Nanotube molecular wires as chemical sensors

Chemical sensors based on individual single-walled carbon nanotubes (SWNTs) are demonstrated. Upon exposure to gaseous molecules such as NO(2) or NH(3), the electrical resistance of a semiconducting SWNT is found to dramatically increase or decrease. This serves as the basis for nanotube molecular sensors. The nanotube sensors exhibit a fast response and a substantially higher sensitivity than that of existing solid-state sensors at room temperature. Sensor reversibility is achieved by slow recovery under ambient conditions or by heating to high temperatures. The interactions between molecular species and SWNTs and the mechanisms of molecular sensing with nanotube molecular wires are investigated.

Functional discovery via a compendium of expression profiles

Ascertaining the impact of uncharacterized perturbations on the cell is a fundamental problem in biology. Here, we describe how a single assay can be used to monitor hundreds of different cellular functions simultaneously. We constructed a reference database or "compendium" of expression profiles corresponding to 300 diverse mutations and chemical treatments in S. cerevisiae, and we show that the cellular pathways affected can be determined by pattern matching, even among very subtle profiles. The utility of this approach is validated by examining profiles caused by deletions of uncharacterized genes: we identify and experimentally confirm that eight uncharacterized open reading frames encode proteins required for sterol metabolism, cell wall function, mitochondrial respiration, or protein synthesis. We also show that the compendium can be used to characterize pharmacological perturbations by identifying a novel target of the commonly used drug dyclonine.

Crystalline Ropes of Metallic Carbon Nanotubes

Fullerene single-wall nanotubes (SWNTs) were produced in yields of more than 70 percent by condensation of a laser-vaporized carbon-nickel-cobalt mixture at 1200degreesC. X-ray diffraction and electron microscopy showed that these SWNTs are nearly uniform in diameter and that they self-organize into "ropes," which consist of 100 to 500 SWNTs in a two-dimensional triangular lattice with a lattice constant of 17 angstroms. The x-ray form factor is consistent with that of uniformly charged cylinders 13.8 +/- 0.2 angstroms in diameter. The ropes were metallic, with a single-rope resistivity of <10(-4) ohm-centimeters at 300 kelvin. The uniformity of SWNT diameter is attributed to the efficient annealing of an initial fullerene tubelet kept open by a few metal atoms; the optimum diameter is determined by competition between the strain energy of curvature of the graphene sheet and the dangling-bond energy of the open edge, where growth occurs. These factors strongly favor the metallic (10,10) tube with C5v symmetry and an open edge stabilized by triple bonds.

Fullerene pipes

Single-wall fullerene nanotubes were converted from nearly endless, highly tangled ropes into short, open-ended pipes that behave as individual macromolecules. Raw nanotube material was purified in large batches, and the ropes were cut into 100- to 300-nanometer lengths. The resulting pieces formed a stable colloidal suspension in water with the help of surfactants. These suspensions permit a variety of manipulations, such as sorting by length, derivatization, and tethering to gold surfaces.

Self-oriented regular arrays of carbon nanotubes and their field emission properties

The synthesis of massive arrays of monodispersed carbon nanotubes that are self-oriented on patterned porous silicon and plain silicon substrates is reported. The approach involves chemical vapor deposition, catalytic particle size control by substrate design, nanotube positioning by patterning, and nanotube self-assembly for orientation. The mechanisms of nanotube growth and self-orientation are elucidated. The well-ordered nanotubes can be used as electron field emission arrays. Scaling up of the synthesis process should be entirely compatible with the existing semiconductor processes, and should allow the development of nanotube devices integrated into silicon technology.

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.

Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles

Genome-wide transcript profiling was used to monitor signal transduction during yeast pheromone response. Genetic manipulations allowed analysis of changes in gene expression underlying pheromone signaling, cell cycle control, and polarized morphogenesis. A two-dimensional hierarchical clustered matrix, covering 383 of the most highly regulated genes, was constructed from 46 diverse experimental conditions. Diagnostic subsets of coexpressed genes reflected signaling activity, cross talk, and overlap of multiple mitogen-activated protein kinase (MAPK) pathways. Analysis of the profiles specified by two different MAPKs-Fus3p and Kss1p-revealed functional overlap of the filamentous growth and mating responses. Global transcript analysis reflects biological responses associated with the activation and perturbation of signal transduction pathways.

Drug target validation and identification of secondary drug target effects using DNA microarrays

We describe here a method for drug target validation and identification of secondary drug target effects based on genome-wide gene expression patterns. The method is demonstrated by several experiments, including treatment of yeast mutant strains defective in calcineurin, immunophilins or other genes with the immunosuppressants cyclosporin A or FK506. Presence or absence of the characteristic drug 'signature' pattern of altered gene expression in drug-treated cells with a mutation in the gene encoding a putative target established whether that target was required to generate the drug signature. Drug dependent effects were seen in 'targetless' cells, showing that FK506 affects additional pathways independent of calcineurin and the immunophilins. The described method permits the direct confirmation of drug targets and recognition of drug-dependent changes in gene expression that are modulated through pathways distinct from the drug's intended target. Such a method may prove useful in improving the efficiency of drug development programs.

Widespread aneuploidy revealed by DNA microarray expression profiling

Expression profiling using DNA microarrays holds great promise for a variety of research applications, including the systematic characterization of genes discovered by sequencing projects. To demonstrate the general usefulness of this approach, we recently obtained expression profiles for nearly 300 Saccharomyces cerevisiae deletion mutants. Approximately 8% of the mutants profiled exhibited chromosome-wide expression biases, leading to spurious correlations among profiles. Competitive hybridization of genomic DNA from the mutant strains and their isogenic parental wild-type strains showed they were aneuploid for whole chromosomes or chromosomal segments. Expression profile data published by several other laboratories also suggest the use of aneuploid strains. In five separate cases, the extra chromosome harboured a close homologue of the deleted gene; in two cases, a clear growth advantage for cells acquiring the extra chromosome was demonstrated. Our results have implications for interpreting whole-genome expression data, particularly from cells known to suffer genomic instability, such as malignant or immortalized cells.

Experimental annotation of the human genome using microarray technology

The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

Modulated chemical doping of individual carbon nanotubes

Modulation doping of a semiconducting single-walled carbon nanotube along its length leads to an intramolecular wire electronic device. The nanotube is doped n-type for half of its length and p-type for the other half. Electrostatic gating can tune the system into p-n junctions, causing it to exhibit rectifying characteristics or negative differential conductance. The system can also be tuned into n-type, exhibiting single-electron charging and negative differential conductance at low temperatures. The low-temperature behavior is manifested by a quantum dot formed by chemical inhomogeneity along the tube.

Gate-Controlled Superconducting Proximity Effect in Carbon Nanotubes

The superconducting proximity effect in single-walled carbon nanotubes connected to niobium electrodes was controlled with the use of nearby gates that tune the niobium-nanotube transparency. At 4.2 kelvin, when the transparency was tuned to be high, a dip in the low-bias differential resistance was observed, indicating a proximity effect mediated by Andreev reflection. When the transparency was tuned to be low, signatures of Andreev reflection disappeared and only tunneling conduction was observed. Below approximately 4 kelvin, a narrow peak in differential resistance around zero bias appeared superimposed on the Andreev dip, probably as a result of electron-electron interaction competing with the proximity effect.

The Drosophila schnurri gene acts in the Dpp/TGF beta signaling pathway and encodes a transcription factor homologous to the human MBP family

Decapentaplegic (dpp), a TGF beta-related ligand, plays a key role in Drosophila development. Although dpp receptors have been isolated, the downstream components of the signaling pathway remain to be identified. We have cloned the schnurri (shn) gene and show that it encodes a putative zinc finger transcription factor homologous to the human major histocompatibility complex-binding proteins 1 and 2. Mutations in shn affect multiple events that require dpp signaling as well as the transcription of dpp-responsive genes. Genetic interactions and the strikingly similar phenotypes of mutations in shn and the dpp receptors encoded by thick veins and punt suggest that shn plays a downstream role in dpp signaling.

Mice bearing deletions of retinoic acid receptors demonstrate reduced lung elastin and alveolar numbers

In mammals, including rats and mice, the development of pulmonary alveolar septa is primarily limited to late gestation and the early periods of postnatal life. Before this time, the rat lung contains a relatively large supply of endogenous retinyl ester that, together with its metabolite retinoic acid, has been shown to increase elastin gene expression and the number of alveoli. We have hypothesized that mice bearing a deletion of one or more genes encoding for retinoic acid receptors (which are DNA binding proteins that alter transcription of retinoic acid-responsive genes) may demonstrate abnormalities in retinoid-mediated alveolar formation. Our studies demonstrate that the absence of the retinoic acid receptor-gamma (RARgamma) is associated with a decrease in the steady-state level of tropoelastin messenger RNA in a subpopulation of lung fibroblasts at Postnatal Day 12. RARgamma gene deletion also resulted in a decrease in whole lung elastic tissue and alveolar number, and an increase in mean cord length of alveoli (L(m)) at Postnatal Day 28. The additional deletion of one retinoid X receptor (RXR)alpha allele resulted in a decrease in alveolar surface area and alveolar number, and an increase in L (m). These data indicate that RARgamma is required for the formation of normal alveoli and alveolar elastic fibers in the mouse, and that RAR/RXR heterodimers are involved in alveolar morphogenesis.

Noninvasive Raman spectroscopy in living mice for evaluation of tumor targeting with carbon nanotubes

An optimized noninvasive Raman microscope was used to evaluate tumor targeting and localization of single walled carbon nanotubes (SWNTs) in mice. Raman images were acquired in two groups of tumor-bearing mice. The control group received plain-SWNTs, whereas the experimental group received tumor targeting RGD-SWNTs intravenously. Raman imaging commenced over the next 72 h and revealed increased accumulation of RGD-SWNTs in tumor ( p < 0.05) as opposed to plain-SWNTs. These results support the development of a new preclinical Raman imager.

Establishing best practices and guidance in population modeling: an experience with an internal population pharmacokinetic analysis guidance

This tutorial describes the development of a population pharmacokinetic (Pop PK) analysis guidance within Pfizer, which strives for improved consistency and efficiency, and a more systematic approach to model building. General recommendations from the Pfizer internal guidance and a suggested workflow for Pop PK model building are discussed. A description is also provided for mechanisms by which conflicting opinions were captured and resolved across the organization to arrive at the final guidance.

CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e51; doi:10.1038/psp.2013.26; advance online publication 3 July 2013

Frequency of SCA1, SCA2, SCA3/MJD, SCA6, SCA7, and DRPLA CAG trinucleotide repeat expansion in patients with hereditary spinocerebellar ataxia from Chinese kindreds

OBJECTIVE

To assess the frequency of SCA1 (spinocerebellar ataxia type 1), SCA2, SCA3/MJD (spinocerebellar ataxia type 3/Machado-Joseph disease), SCA6, SCA7, and DRPLA (dentatorubropallidoluysian atrophy) CAG trinucleotide repeat expansions [(CAG)n] among persons diagnosed with hereditary SCA from Chinese families.

PATIENTS AND METHODS

Spinocerebellar ataxia type 1, SCA2, SCA3/MJD, SCA6, SCA7, and DRPLA (CAG)n mutation were detected with the polymerase chain reaction, highly denaturing polyacrylamide gel electrophoresis, and silver staining technique in 167 patients with autosomal dominant SCA from 85 Chinese families and 37 patients with sporadic SCA.

RESULTS

Spinocerebellar ataxia type 1 (CAG)n mutation in 7 patients from 4 kindreds (4.70%) was expanded to 53 to 62 repeats. Spinocerebellar ataxia type 2 (CAG)n mutation in 12 patients from 5 kindreds (5.88%) was expanded to 42 to 47 repeats. Spinocerebellar ataxia type 3/Machado-Joseph disease (CAG)n mutation in 83 patients from 41 kindreds (48.23%) was expanded to 68 to 83 repeats. Sixty-five patients from 35 kindreds (41.19%) and 37 patients with sporadic SCA did not test positive for SCA1, SCA2, SCA3/MJD, SCA6, SCA7, or DRPLA. There was a predictable inverse relationship between the number of CAG repeats and the age at onset for SCA3/MJD and SCA2. Clinically, dementia and hyporeflexia were more frequent in patients with SCA2, while spasticity, hyperreflexia, and Babinski signs were more frequent in patients with SCA3/ MJD, and those might be helpful in clinical work to primarily distinguish patients with SCA3/MJD and SCA2 from others with different types of SCA.

CONCLUSIONS

The frequency of SCA3/MJD is substantially higher than that of SCA1 and SCA2 in patients with autosomal dominant SCA from Chinese kindreds, who are non-Portuguese. Clinical expressions of the various types of SCAs overlap one another; therefore, for clinical study it is important to make a gene diagnosis and genetic classification for patients with SCA.

Diet and exercise in the treatment of obesity: effects of 3 interventions on insulin resistance

BACKGROUND

In short-term studies, diet and exercise both improve insulin sensitivity.

OBJECTIVE

To determine the effects of a 48-week supervised diet and exercise program on weight and insulin sensitivity after initial weight loss and weight maintenance, and then subsequent weight regain over 96 weeks.

METHODS

Forty-five obese women were randomly assigned to 1 of 3 treatment groups: (1) diet alone, (2) diet and aerobic training, and (3) diet and strength training. All subjects received the same 48-week group behavior modification program and diet (approximately 3879 kJ/d [approximately 925 kcal/d] for the first 16 weeks; approximately 6276 kJ/d [approximately 1500 kca/d] thereafter). Exercising subjects were provided 3 supervised exercise sessions per week for the first 28 weeks and 2 sessions weekly until week 48. During weeks 48 to 96, subjects were unsupervised. Oral glucose tolerance tests were performed at baseline and weeks 16, 24, 44, and 96.

RESULTS

Subjects across the 3 conditions achieved a mean weight loss of 13.8 kg by week 16, which was associated with decreased insulin levels (61.8% of baseline) There were no significant differences among groups in changes in body mass index, which is a measure of weight in kilograms divided by the square of the height in meters, weight, glucose tolerance, or insulin levels at weeks 16, 24, and 44. No additional beneficial effect of aerobic or strength exercise on insulin resistance, as reflected by serum insulin levels before and after a glucose load, was demonstrated. The 22 subjects who were studied at week 96 maintained a loss of approximately 10% of initial weight. Insulin levels, however, had returned to pretreatment levels.

CONCLUSIONS

This study confirms the beneficial effect of weight reduction on hyperinsulinemia in obese individuals. Participation in supervised exercise did not result in additional improvement in weight loss or insulin sensitivity. We also observed a marked increase in insulin levels with only partial weight regain. Determining the amount of sustained weight loss necessary for continued improvement in insulin sensitivity will require further study.

Tropomyosin isoforms in intestinal mucosa: production of autoantibodies to tropomyosin isoforms in ulcerative colitis

BACKGROUND & AIMS

Autoantibodies against tropomyosins (TMs) have been reported in ulcerative colitis (UC). In this study the hTM isoforms (hTM1-5) present in intestinal epithelial cells and in smooth muscle were investigated, and the immunoreactivity against hTMs by immunoglobulin G (IgG) produced in vitro by colonic mucosal lymphocytes (LPMCs) from patients with UC, Crohn's disease (CD), and controls was examined.

METHODS

TMs were extracted from colonic and jejunal epithelial cells and smooth muscle, and hTM isoforms were identified using isoform-specific monoclonal antibodies by enzyme-linked immunosorbent assay and transblot analysis. The immunoreactivity of IgG produced by colonic LPMCs was analyzed against the recombinant hTM isoforms.

RESULTS

The major hTM isoforms present in colonic and jejunal epithelial cells are hTM5 and hTM4, whereas intestinal smooth muscle contains the hTM1-3 isoforms. The IgG synthesized in vitro by LPMCs from UC (n = 19) recognized hTM5 and hTM1, more significantly (P < 0.04 to <0.001) when compared with CD (n = 12) and controls (n = 17). However, IgG produced by LPMCs from CD did not show such anti-hTM reactivity. Mucosal anti-hTM IgG mainly belonged to the IgG1 subclass.

CONCLUSIONS

Intestinal epithelial cells and smooth muscle have distinct hTM isoforms. Patients with UC, and not CD, show mucosal autoantibody response against hTM isoforms, particularly hTM5 and hTM1.

Hydrogenation of single-walled carbon nanotubes

Towards the development of a useful mechanism for hydrogen storage, we have studied the hydrogenation of single-walled carbon nanotubes with atomic hydrogen using core-level photoelectron spectroscopy and x-ray absorption spectroscopy. We find that atomic hydrogen creates C-H bonds with the carbon atoms in the nanotube walls, and such C-H bonds can be completely broken by heating to 600 degrees C. We demonstrate approximately 65 +/- 15 at % hydrogenation of carbon atoms in the single-walled carbon nanotubes, which is equivalent to 5.1 +/- 1.2 wt % hydrogen capacity. We also show that the hydrogenation is a reversible process.

Longitudinal changes in pulmonary function and respiratory symptoms in cotton textile workers. A 15-yr follow-up study

To evaluate the chronic effects of exposure to cotton dust, a 15-yr follow-up study in cotton textile workers was performed in Shanghai, China from 1981 to 1996. Testing occurred four times during the 15-yr period. The achieved follow-up rates were 76-88% of the original 447 cotton textile workers, and 70-85% of the original 472 silk textile workers (as a control group). Identical questionnaires, equipment, and methods were used throughout the study. The prevalence of byssinosis increased over time in cotton workers, with 15.3% at the last survey versus 7.6% at the baseline, whereas no byssinosis was found in silk workers. More workers in the cotton group consistently reported symptoms than in the silk group, although symptom reporting varied considerably from survey to survey. Cotton workers had small, but significantly greater, adjusted annual declines in FEV(1) and FVC than did the silk workers. Years worked in cotton mills, high level of exposure to endotoxin, and across-shift drops in FEV(1) were found to be significant determinants for longitudinal change in FEV(1), after controlling for appropriate confounders. Furthermore, there were statistically significant associations between excessive loss of FEV(1) and byssinosis, chest tightness at work, and chronic bronchitis in cotton workers. Workers who consistently (three or four of the surveys) reported byssinosis or chest tightness at work had a significantly greater 15-yr loss of FEV(1). We conclude that long-term exposure to cotton dust is associated with chronic or permanent obstructive impairments. Consistent reporting of respiratory symptoms, including byssinosis and chest tightness at work, is of value to predict the magnitude and severity of chronic impairments in textile workers.