Characterization and psychophysical studies of an air-jet lump display.

Development of tactile displays to enhance palpation of lumps during robot-assisted minimally invasive surgery is challenging due to size and weight constraints, motivating a pneumatic actuation strategy. This work describes the quantitative and psychophysical assessment of an air-jet tactile display that creates a lump percept by directing pressurized air through an aperture onto the finger. The air pressure and aperture size are meant to control the hardness and size, respectively, of the perceived lump. Jet impingement pressure and flow rate were measured by capacitive tactile sensors and mass flow meters at varying aperture sizes and pressures. The air-jet pressure profile width evolves as jet theory predicts and is largely independent of supply pressure (and therefore jet exit velocity). The method of constant stimuli was used to determine the just noticeable differences (JNDs) for the air pressure and aperture size. Qualitative results indicate that subjects perceive the stimulus as a "lump-like" shape. Pressure JNDs ranged from 19.6-24.4 kPag and aperture size JNDs ranged from 0.50-0.66 mm. No significant correlation exists between the supply pressure and changes in perceived lump size. However, pressure JNDs show significant (p < 0.001) inverse correlation with aperture size, with improved discrimination at larger apertures, where a greater finger pad area is stimulated.

[Lysogenic infection of a Shiga toxin 2-converting bacteriophage changes host gene expression, enhances host acid resistance and motility].

Shiga toxin 2 (Stx2)-converting bacteriophages can infect and lysogenize other bacteria in vivo and in vitro, and, thus, contribute to a genotypic heterogeneity of infected host. However, the global transcription patterns accompanying the lysogenic infection of E. coli host have not been clearly resolved. In this study, gene expression profiles of Stx2 phage phi Min27(delta stx::cat) converted and native E. coli MG1655 hosts were compared using microarray assay. The phi Min27(delta stx::cat) conversion had a direct effect on the global expression of bacterial host genes as 166 genes were found to be differentially expressed (104 up-regulated and 62 downregulated). These genes were predominantly responsible for bacterial central metabolism, transport and transcription. It was shown that in addition to the down-regulation of genes involved in synthesis of thiamine and protein transporters, expression of genes associated with bacterial energy production (e.g., fadABDEHIJL, aceK, and acnA) was also suppressed. Conversely, most up-regulated genes were transport genes, flagellar synthesis genes (fliDESTZ), and acid resistance genes (e.g., gadEW, hdeABD, and adiY). Futhermore, conversion of phi Min27(delta stx::cat) was shown to change physiological properties of the host cell. In comparison with the uninfected cells the converted bacteria host had increased acid tolerance and promoted swimming motility on a semisolid agar surface.

A randomised, double blind, placebo controlled study of celecoxib, a selective cyclooxygenase 2 inhibitor, on duodenal polyposis in familial adenomatous polyposis.

BACKGROUND: Non-selective cyclooxygenase (COX) inhibitors (non-steroidal anti-inflammatory drugs) inhibit large bowel carcinogenesis in patients with familial adenomatous polyposis (FAP). Their role in the duodenum of these patients is less certain. The disease modifying activity of specific COX-2 inhibitors has not been explored in humans. PATIENTS AND METHODS: This was a randomised, double blind, placebo controlled study of celecoxib (100 mg twice daily (n=34) or 400 mg twice daily (n=32)) versus placebo (n=17), given orally twice daily for six months to patients with FAP. Efficacy was assessed qualitatively by blinded review of shuffled endoscopy videotapes comparing the extent of duodenal polyposis at entry and at six months and quantitatively by measurement of the percentage change in duodenal area covered by discrete and plaque-like adenomas from photographs of high and low density polyposis. RESULTS: Shuffled and blinded video review showed a statistically significant effect of 400 mg twice daily celecoxib compared with placebo treatment (p=0.033) with all five independent observers scoring a beneficial effect. Overall, patients taking celecoxib 400 mg twice daily showed a 14.5% reduction in involved areas compared with a 1.4% for placebo (p=0.436). However, patients with clinically significant disease at baseline (greater than 5% covered by polyps) showed a 31% reduction in involved areas with celecoxib 400 mg twice daily compared with 8% on placebo (p=0.049). CONCLUSIONS: A panel of five endoscopists found a significant reduction in duodenal polyposis after six months of treatment with celecoxib 400 mg twice daily. COX-2 inhibition may help this otherwise untreatable condition.

Biallelic inactivation of the APC gene is associated with hepatocellular carcinoma in familial adenomatous polyposis coli.

BACKGROUND: Certain primary hepatic tumors have been associated with familial adenomatous polyposis (FAP), a condition caused by germline mutations of the adenomatous polyposis coli (APC) gene. However, a genetic association between FAP and hepatocellular carcinoma (HCC) has not been shown. This study tested the hypothesis that biallelic inactivation of the APC gene contributed to the development of HCC in a patient with FAP and a known germline mutation of the APC gene at codon 208, but no other risk factors for HCC. METHODS: Total RNA and genomic DNA were isolated from the tumor, and in vitro synthesized protein assay and DNA sequencing analysis were used to screen for a somatic mutation in the APC gene. RESULTS: A somatic one-base pair deletion at codon 568 was identified in the wild-type allele of the APC gene. CONCLUSIONS: To the authors' knowledge, this study provides the first evidence that biallelic inactivation of the APC gene may contribute to the development of HCC in patients with FAP.

Regulation of microtubule assembly by human EB1 family proteins.

The EB1 family proteins are highly conserved microtubule-associated proteins. The EB1 protein in yeast has been shown to play an important role in regulating microtubule dynamics and chromosome segregation. Human EB1 family proteins include EB1, RP1 and EBF3. Although EB1 and RP1 have been shown to associate with microtubules, the subcellular localization of endogenous EBF3 had not been characterized. The function of human EB1 family proteins was also not clear. We therefore investigated the cellular localization of EBF3 and the regulation of microtubule organization by EB1 family proteins. As do EB1 and RP1, EBF3 was found to colocalize with microtubules, preferentially at their plus ends, throughout the cell cycle. Moreover, there was a very strong EBF3 signal at the centrosome in interphase cells and at the spindle poles in mitotic cells. When EB1 family proteins were overexpressed, they associated with the entire microtubule cytoskeleton. In addition, EB1 and EBF3 induced microtubule bundling in some cells overexpressing these proteins. These microtubule bundles were more resistant to nocodazole and were more acetylated than regular microtubules. Our results demonstrate for the first time that human EB1 family proteins could regulate microtubule assembly and stability.

Ultraviolet irradiation induces BRCA2 protein depletion through a p53-independent and protein synthesis-dependent pathway.

It has been suggested that BRCA2, the protein product of the breast cancer susceptibility gene BRCA2, is involved in DNA damage repair. It is therefore likely that BRCA2 plays a role in a signaling pathway induced by DNA-damaging agents. To test this possibility, we examined the alteration of the BRCA2 protein level in human cell lines after UV irradiation. We found that UV irradiation down-regulated BRCA2 in a dose-dependent manner in all cell lines tested. The down-regulation of BRCA2 occurred soon (within 4 h) after UV treatment. Surprisingly, down-regulation of BRCA2 by UV does not require functional p53, which has been suggested to be required for the down-regulation of BRCA1 and BRCA2 mRNAs by DNA-damaging agents. Moreover, the proteosome- and calpain-mediated protein degradation pathways do not have an important role in the UV-induced BRCA2 depletion. However, blocking protein synthesis temporally inhibited the depletion of BRCA2 and BRCA1 in some cell lines. Ectopic expression of BRCA2 in cells increased resistance of cells to high-dose UV irradiation. These results demonstrate that BRCA2 is involved in a DNA-damaging signaling pathway induced by UV radiation and that expression of BRCA2 can protect cells from UV-mediated cell death.

Characterization of human MAPRE genes and their proteins.

The MAPRE genes encode the EB1 family proteins. The yeast EB1 protein had been shown to play important roles in microtubule dynamic regulation, cytokinesis, mitotic spindle positioning, and episome segregation. To facilitate functional studies of mammalian EB1 family proteins, we characterized the human MAPRE genes (MAPRE1, MAPRE2, and MAPRE3) and their proteins (EB1, RP1, and EBF3). We found that the three MAPRE genes had similar genomic structures but were on different chromosomes. We showed that EB1 family proteins appeared to be expressed ubiquitously. We identified two EBF3 proteins, which were encoded by alternatively spliced MAPRE3 mRNAs. We demonstrated that there were also two RP1 proteins, which were products of translation from different initiation codons. We showed that the three EB1 family proteins had different abilities to interact with APC in vitro, and we provided the first direct evidence for the association between endogenous EB1 and APC.

Detection of sequence variations in the adenomatous polyposis coli (APC) gene using denaturing high-performance liquid chromatography.

We have evaluated the usefulness of denaturing high performance liquid chromatography (dHPLC) for scanning the adenomatous polyposis coli (APC) gene for point mutations, small deletions, and insertions. Our assay consists of 28 sets of primers to amplify the 15 exons of the APC gene. All PCR reactions were amplified simultaneously using the same reaction conditions in a 96-well format and then analyzed by dHPLC, using empirically determined optimum temperatures for partial fragment denaturation. Previously studied DNA specimens from 47 familial adenomatous polyposis (FAP) patients were analyzed by dHPLC and all mutations were correctly identified and confirmed by sequence analysis. This approach identified a single-base substitution in exon 6 and a 2-bp insertion in exon 15 that initially had not been detected by single-strand conformational polymorphism (SSCP) analysis. A novel mutation in exon 15 of the APC gene, 2065delG (codon 689) that had previously been undetected by the protein truncation test (PTT) was also identified by dHPLC. We present our validation studies of dHPLC technology for APC gene analysis in terms of sensitivity and specificity and compare it to current standard scanning technologies including PTT, SSCP, and conformational sensitive gel electrophoresis (CSGE).

Genomic rearrangements of the APC tumor-suppressor gene in familial adenomatous polyposis.

Germline mutations of the adenomatous polyposis coli (APC) tumor-suppressor gene result in the hereditary colorectal cancer syndrome familial adenomatous polyposis (FAP). Almost all APC mutations that have been identified are single-nucleotide alterations, small insertions, or small deletions that would truncate the protein product of the gene. No well-characterized intragenic rearrangement of APC has been described, and the prevalence of this type of mutation in FAP patients is not clear. We screened 49 potential FAP families and identified 26 different germline APC mutations in 30 families. Four of these mutations were genomic rearrangements resulting from homologous and nonhomologous recombinations mediated by Alu elements. Two of these four rearrangements were complex, involving deletion and insertion of nucleotides. Of these four rearrangements, one resulted in the deletion of exons 11 and 12 and two others resulted in either complete or partial deletion of exon 14. The fourth rearrangement grossly altered the sequence within intron 14. Although this rearrangement did not affect any coding sequence of APC at the genomic DNA level, it caused inappropriate splicing of exon 14. These rearrangements were initially revealed by analyzing cDNAs and could not have been identified by using mutation detection methods that screened each exon individually. The identification of a rearrangement that did not alter any coding exons yet affected the splicing further underscores the importance of using cDNA for mutation analysis. The identification of four genomic rearrangements among 30 mutations suggests that genomic rearrangements are frequent germline APC mutations.

Inactivation of germline mutant APC alleles by attenuated somatic mutations: a molecular genetic mechanism for attenuated familial adenomatous polyposis.

Germline mutations of the adenomatous polyposis coli (APC) tumor-suppressor gene result in familial adenomatous polyposis (FAP). Patients with FAP typically develop hundreds to thousands of benign colorectal tumors and early-onset colorectal cancer. A subset of germline APC mutations results in an attenuated FAP (AFAP) phenotype, in which patients develop fewer tumors and develop them at an older age. Although a genotype-phenotype correlation between the locations of APC germline mutations and the development of AFAP has been well documented, the mechanism for AFAP has not been well defined. We investigated the mechanism for AFAP in patients carrying a mutant APC allele (APC(AS9)) that has a mutation in the alternatively spliced region of exon 9. APC(AS9) was found to down-regulate beta-catenin-regulated transcription, the major tumor-suppressor function of APC, as did the wild-type APC. Mutation analysis showed that both APC(AS9) and the wild-type APC alleles were somatically mutated in most colorectal tumors from these patients. Functional analysis showed that 4666insA, a common somatic mutation in APC(AS9) in these tumors, did not inactivate the wild-type APC. Our results indicate that carriers of APC(AS9) develop fewer colorectal tumors than do typical patients with FAP because somatic inactivation of both APC alleles is necessary for colorectal tumorigenesis. However, these patients develop colorectal tumors more frequently than does the general population because APC(AS9) is inactivated by mutations that do not inactivate the wild-type APC.

The effect of celecoxib, a cyclooxygenase-2 inhibitor, in familial adenomatous polyposis.

BACKGROUND: Patients with familial adenomatous polyposis have a nearly 100 percent risk of colorectal cancer. In this disease, the chemopreventive effects of nonsteroidal antiinflammatory drugs may be related to their inhibition of cyclooxygenase-2. METHODS: We studied the effect of celecoxib, a selective cyclooxygenase-2 inhibitor, on colorectal polyps in patients with familial adenomatous polyposis. In a double-blind, placebo-controlled study, we randomly assigned 77 patients to treatment with celecoxib (100 or 400 mg twice daily) or placebo for six months. Patients underwent endoscopy at the beginning and end of the study. We determined the number and size of polyps from photographs and videotapes; the response to treatment was expressed as the mean percent change from base line. RESULTS: At base line, the mean (+/-SD) number of polyps in focal areas where polyps were counted was 15.5+/-13.4 in the 15 patients assigned to placebo, 11.5+/-8.5 in the 32 patients assigned to 100 mg of celecoxib twice a day, and 12.3+/-8.2 in the 30 patients assigned to 400 mg of celecoxib twice a day (P=0.66 for the comparison among groups). After six months, the patients receiving 400 mg of celecoxib twice a day had a 28.0 percent reduction in the mean number of colorectal polyps (P=0.003 for the comparison with placebo) and a 30.7 percent reduction in the polyp burden (the sum of polyp diameters) (P=0.001), as compared with reductions of 4.5 and 4.9 percent, respectively, in the placebo group. The improvement in the extent of colorectal polyposis in the group receiving 400 mg twice a day was confirmed by a panel of endoscopists who reviewed the videotapes. The reductions in the group receiving 100 mg of celecoxib twice a day were 11.9 percent (P=0.33 for the comparison with placebo) and 14.6 percent (P=0.09), respectively. The incidence of adverse events was similar among the groups. CONCLUSIONS: In patients with familial adenomatous polyposis, six months of twice-daily treatment with 400 mg of celecoxib, a cyclooxygenase-2 inhibitor, leads to a significant reduction in the number of colorectal polyps.

Characterization of BRCA2: temperature sensitivity of detection and cell-cycle regulated expression.

People carrying a mutant BRCA2 gene are susceptible to breast, ovarian, pancreatic and other tumors. Many facets of BRCA2 have been studied, including its mutation in human cancers, its role in mouse embryogenesis and its RNA expression in different tissues and different mouse embryogenesis stages. However, there has been very little characterization of BRCA2 protein. We investigated the biochemical and biological properties of BRCA2 by using a monoclonal antibody we generated against the N-terminal portion of BRCA2. We discovered that the detection of BRCA2 by immunoblot analysis was sensitive to the temperature used to denature the samples before gel electrophoresis. BRCA2 was easily detectable when samples were denatured at low temperature instead of boiling. Although the precise mechanism underlying this observation is not clear yet, this finding will significantly improve our ability to study BRCA2. We examined the expression of BRCA2 using an immunoblot analysis protocol modified according to this observation. We showed that BRCA2 was presented in every human cell lines examined, including Capan-1, which expressed a truncated BRCA2 due to a BRCA2 frameshift mutation. We also showed that the expression of BRCA2 was cell-cycle regulated. Our results suggest that BRCA2 has an important role in cell growth regulation.

TSG101 is not mutated in lung cancer but a shortened transcript is frequently expressed in small cell lung cancer.

TSG101 is a candidate tumor suppressor gene whose deletion in NIH3T3 cells leads to spontaneous lung metastases in nude mice. Aberrant transcripts of TSG101 have been identified in 47% of primary breast carcinomas, without evidence of intragenic deletions at the TSG101 locus on 11p15. To investigate the possible role of TSG101 in lung cancer, which often shows 11p allele loss, we performed transcript analysis and mutational analysis of TSG101 in lung cancer cell lines. Reverse transcriptase RT-PCR and Northern analysis detected a common TSG101 transcript, shortened because of an internal deletion, which was expressed simultaneously with the wild-type transcript in 89% of small cell lung cancer (SCLC) lines. In contrast, the wild-type transcript was expressed alone in normal tissues, primary non-small cell lung cancer (NSCLC) specimens, and the majority of NSCLC cell lines. Sequence of the shortened SCLC transcript was identical to that of the most common aberrant transcript identified in breast cancer, consisting of a deletion of exons 2-4 and part of 1 and 5. Southern analysis of SCLC lines expressing the shortened transcript did not detect any intragenic deletions. Single strand conformational polymorphism (SSCP) analysis and direct sequencing of TSG101 cDNAs also identified no mutations or deletions. These results suggest that TSG101 is not mutated in lung cancer but that aberrant splicing of TSG101 occurs in SCLC.

Alterations of PTEN/MMAC1, a candidate tumor suppressor gene, and its homologue, PTH2, in small cell lung cancer cell lines.

Loss of heterozygosity (LOH) at chromosome 10q23-q25 is frequent in small cell lung cancer (SCLC), indicating the presence of putative tumor suppressor genes. PTEN/ MMAC1, a newly cloned candidate tumor suppressor gene at 10q23, was mutated in multiple human cancers. We investigated whether mutations of PTEN/MMAC1 play an important role in SCLC tumorigenesis. We examined 16 SCLC cell lines for PTEN/MMAC1 mRNA expression by reverse-transcriptase polymerase chain reaction (RT-PCR) and potential mutations by sequencing analysis of the PTEN/MMAC1 coding region. No mutation was observed in PTEN/MMAC1 cDNAs in 15 cell lines expressing PTEN/MMAC1. One SCLC cell line, DMS79, did not have detectable PTEN/ MMAC1 expression. Importantly, we identified a novel homologue of PTEN/MMAC1, termed PTH2, localized to chromosome 9p21-q13 and containing only ten amino acid substitutions compared with the PTEN/MMAC1 coding region. However, because the putative initiation codon for PTEN/MMAC1 gene was changed to arginine in PTH2, the translational initiation site of PTH2 is very likely to differ from that of the PTEN/MMAC1. PTH2 was expressed in two normal lung tissues and two normal colon tissues, but in only four of 16 SCLC cell lines. A missense mutation in PTH2 was identified in a SCLC cell line that did not express PTEN/MMAC1 mRNA. Our data suggest that inactivation of PTEN/ MMAC1 is a rare event in SCLC tumorigenesis. However, the PTEN/MMAC1 homologue PTH2 may play a role in SCLC tumorigenesis.

Changes in BRCA2 expression during progression of the cell cycle.

It has been shown that genetic alterations in BRCA1 and BRCA2 can predispose an individual to develop breast cancer. We investigated the expression of both BRCA2 and BRCA1 during the progression of the cell cycle by northern blot analysis. In MCF-10F (normal breast epithelial cell line) and MCF-7 (breast cancer cell line) cells the expression of BRCA2 RNA was low in G0 and early G1 phases then up-regulated at the G1/S phase junction. Expression of BRCA2 was maintained at relatively high levels when cells progressed through S and G2/M phases. For MCF-7 cells, the level of BRCA2 transcript decreased as cells were released from nocodazole-mediated metaphase arrest. This is consistent with the observation of low but detectable BRCA2 RNA level in G1 phase of the cell cycle. For both cell lines, the patterns of RNA expression of BRCA1 and BRCA2 were similar during the proliferation phase of cell cycle. However, the transcripts from both genes were undetectable in quiescent cells. These results suggest important functions for both BRCA2 and BRCA1 in regulation of cell growth.

APC binds to the novel protein EB1.

Mutations of the APC gene play a critical role in both sporadic and familial forms of colorectal cancer. The vast majority of these mutations result in the loss of the carboxyl terminus of the protein. To further elucidate the function of APC, we searched for cellular proteins that associate with its carboxyl terminus. One million human cDNA clones were screened with the use of the interaction trap two-hybrid system, and 67 clones were found to have a phenotype suggestive of an APC-interacting protein. Nucleotide sequence analysis revealed that 48 of these clones were derived from a single novel named EBI. The association of APC and EB1 proteins was confirmed with in vitro binding assays. mAbs against EB1 were then produced and used to demonstrate the association of APC and EB1 in vivo. The EB1 gene was predicted to encode a 268-amino acid protein without significant homology to proteins with known function. However, searches of nucleotide databases did identify evidence for at least two related human genes and a yeast homologue. This conservation suggests an essential function for EB1 that might provide clues to the mechanism through which APC suppresses colonic neoplasia.

The gene for the APC-binding protein beta-catenin (CTNNB1) maps to chromosome 3p22, a region frequently altered in human malignancies.

beta-Catenin is one of the E-cadherin associated proteins involved in the process of cellular adhesion. It has recently been shown to interact with the APC protein whose gene is known to be mutated in the germline of familial adenomatous polyposis patients. This interaction implies that beta-catenin is a potential regulator of the APC gene. The localization of the human beta-catenin gene (CTNNB1) to chromosome 3p22, by fluorescent in situ hybridization (FISH), has linked the gene to a region that is frequently altered in several human malignancies. The location of the gene and the protein interactions suggest the importance of beta-catenin in the etiology of various human cancers.

Association of the APC tumor suppressor protein with catenins.

Mutations of APC appear to initiate sporadic and inherited forms of human colorectal cancer. Although these mutations have been well characterized, little is known about the function of the APC gene product. Two cellular proteins that associate with APC were identified by nucleotide sequence analysis and peptide mapping as the E-cadherin-associated proteins alpha- and beta-catenin. A 27-residue fragment of APC containing a 15-amino acid repeat was sufficient for the interaction with the catenins. These results suggest an important link between tumor initiation and cell adhesion.

Association between wild type and mutant APC gene products.

Germline mutations of the APC gene are responsible for familial adenomatous polyposis, an autosomal dominant inherited predisposition to colorectal tumors. Mutation of the APC gene is also an early, if not initiating, event for sporadic colorectal tumorigenesis. In both cases, almost all of the currently identified mutations of APC result in the truncation of the protein. In this study, we demonstrate that truncated APC proteins can associate with the wild type APC in vivo. Using in vitro expression and immunoprecipitation, we show that the first 171 residues of APC are sufficient for APC oligomerization and that the first 45 amino acids of APC is necessary for this interaction. These results indicate that most mutant APC proteins should be able to bind to wild type APC protein and perhaps inactivate it in a dominant negative manner.