Microbial Community Characteristics Largely Unaffected by X-Ray Computed Tomography of Sediment Cores

X-ray computed tomography (CT) scanning is used to study the physical characteristics of soil and sediment cores, allowing scientists to analyze stratigraphy without destroying core integrity. Microbiologists often work with geologists to understand the microbial properties in such cores; however, we do not know whether CT scanning alters microbial DNA such that DNA sequencing, a common method of community characterization, changes as a result of X-ray exposure. Our objective was to determine whether CT scanning affects the estimates of the composition of microbial communities that exist in cores. Sediment cores were extracted from a salt marsh and then submitted for CT scanning. We observed a minimal effect of CT scanning on microbial community composition in the sediment cores either when the cores were examined shortly after recovery from the field or after the cores had been stored for several weeks. In contrast, properties such as sediment layer and marsh location did affect microbial community structure. While we observed that CT scanning did not alter microbial community composition as a whole, we identified a few amplicon sequence variants (13 out of 7,037) that showed differential abundance patterns between scanned and unscanned samples among paired sample sets. Our overall conclusion is that the CT-scanning conditions typically used to obtain images for geological core characterization do not significantly alter microbial community structure. We stress that minimizing core exposure to X-rays is important if cores are to be studied for biological properties. Future investigations might consider variables, such as the length and energy of radiation exposure, the volume of the core, or the degree, to which microbial communities are stressed as important factors in assessing the impact of X-rays on microbes in geological cores.

Enabling 3D hepatocyte spheroids for microphysiometry

Advances in the areas of tissue engineering and microfabrication techniques have enabled promising in vitro platforms, known as Organs-on-Chips, with the aim of mimicking complex in vivo conditions for more accurate toxicology studies. To analyze the physiological change induced by chemicals or toxic substances continuously, sensors can be used in order to measure the intracellular and extracellular environment of single cells, cell constructs, or tissue, and therefore the integration of monitoring techniques into 3D tissue culture platforms provides an essential step for the next generation Organ-on-Chip platforms. However, current in vitro platforms are not capable of combining the culture of 3D models with monitoring techniques. To address this, a novel spheroid encapsulation is designed for fluidic contact between 3D models in microwells and Intelligent Mobile Lab for In Vitro Diagnostics (IMOLA-IVD) BioChip sensors while preventing spheroid fusion. In this work, spheroid culturing protocols were developed for optimized spheroid growth and an evaluation of spheroid integrity on different porous layers was performed in order to provide a defined spheroid encapsulation on BioChip sensors.

An automated microphysiological assay for toxicity evaluation

Screening a newly developed drug, food additive or cosmetic ingredient for toxicity is a critical preliminary step before it can move forward in the development pipeline. Due to the sometimes dire consequences when a harmful agent is overlooked, toxicologists work under strict guidelines to effectively catalogue and classify new chemical agents. Conventional assays involve long experimental hours and many manual steps that increase the probability of user error; errors that can potentially manifest as inaccurate toxicology results. Automated assays can overcome many potential mistakes that arise due to human error. In the presented work, we created and validated a novel, automated platform for a microphysiological assay that can examine cellular attributes with sensors measuring changes in cellular metabolic rate, oxygen consumption, and vitality mediated by exposure to a potentially toxic agent. The system was validated with low buffer culture medium with varied conductivities that caused changes in the measured impedance on integrated impedance electrodes.

Label-free monitoring of whole cell vitality

The Intelligent Mobile Lab (IMOLA) delivers metabolic and morphological parameters of living cells in a label-free and real time way. It represents a key technology for the development of new cell-based assays. Electrochemical microsensors are used to measure the extracellular acidification (pH), cellular respiration (pO2), changes in cell number and morphology (electric impedance) in a controlled environment. These parameters are closely linked to the intracellular signaling network of the living cells. They are thus likely to respond sensitively to changes in cellular vitality. A wide spectrum of cell types can be tested with the system, including adherent and suspended cells, continuous cell lines, primary cells or tissue samples. The platform is described in detail and applications in the field's oncology, toxicology and environmental monitoring are shown.

Polarization influence on reflectance measurements in the spatial frequency domain

In this work, we quantify the influence of crossed polarizers on reflectance measurements in the spatial frequency domain. The use of crossed polarizers is a very common approach for suppression of specular surface reflections. However, measurements are typically evaluated using a non-polarized scalar theory. The consequences of this discrepancy are the focus of our study, and we also quantify the related errors of the derived optical properties. We used polarized Monte Carlo simulations for forward calculation of the reflectance from different samples. The samples' scatterers are assumed to be spherical, allowing for the calculation of the scattering functions by Mie theory. From the forward calculations, the reduced scattering coefficient [Formula: see text] and the absorption coefficient μa were derived by means of a scalar theory, as commonly used. Here, we use the analytical solution of the scalar radiative transfer equation. With this evaluation approach, which does not consider polarization, we found large errors in [Formula: see text] and μa in the range of 25% and above. Furthermore, we investigated the applicability of the use of a reference measurement to reduce these errors as suggested in literature. We found that this method is not able to generally improve the accuracy of measurements in the spatial frequency domain. Our general recommendation is to apply a polarized theory when using crossed polarizers.

Intron/exon organization and polymorphisms of the PLK3/PRK gene in human lung carcinoma cell lines

PLK3/PRK, a conserved polo family protein serine/threonine kinase, plays a significant role at the onset of mitosis and mitotic progression. Recently, PLK3/PRK has been shown to induce apoptosis when overexpressed in cell lines and is also implicated in cell proliferation and tumor development. Forty lung tumor cell lines were used for single-strand confirmation polymorphism (SSCP) analysis and DNA sequencing to examine the mutational status of PLK3/PRK. No missense or nonsense mutations were revealed in the lung carcinoma cell lines examined. However, three polymorphisms were identified as: a G to A at position 720, an A to G at 1053, and a G to C at 1275. Intron/exon boundaries were determined by amplification of genomic DNA with PLK3/PRK exon-specific primers. The amplification products with increased size relative to the cDNA were sequenced. Fifteen exons throughout the open reading frame were characterized. None of the introns were exceptionally large, typically ranging from 100-300 basepairs in length. These results suggest that although PLK3/PRK expression is downregulated in a majority of lung carcinoma samples, mutational inactivation of the coding sequence of the PLK3/PRK gene appears to be a rare event in lung cancer.

Examination of p53 alterations and cytokeratin expression in sputa collected from patients prior to histological diagnosis of squamous cell carcinoma

Mutations in the p53 gene are detected in greater than 50% of squamous cell carcinomas of the lung and to a lesser extent in adenocarcinomas. The p53 protein is also overexpressed in a relatively high percentage of preinvasive lesions of the bronchial epithelium. However, unlike tumor tissue, immunoreactivity does not necessarily imply that cells in preinvasive lesions carry a mutant p53 allele. In some cases, overexpression may result from a cellular checkpoint reaction to a toxic or mutagenic substance such as exposure to tobacco smoke. In any case, p53 overexpression in preinvasive lesions may serve as a biomarker for high risk assessment of lung cancer and other tumors in the aerodigestive tract. A study was designed to retrospectively analyze p53 overexpression in cells from sputum samples collected prior to histological tumor diagnosis. The rationale was based on the observation that both preinvasive and tumor cells from the bronchial epithelium are exfoliated into the airways and can be detected based on morphology in sputa. Two sets of cases were chosen: 1) patients whose first primary tumor was a squamous cell carcinoma containing a mutant p53 allele with overexpression observed in most of the tumor cells; and 2) patients whose squamous cell tumor did not contain a mutant p53 allele. Cells which stained positive for p53 expression were observed in sputum samples collected from all six patients whose tumors were positive for a mutant p53 allele. Also p53 positive cells were detected on sputum slides for two of the five cases where the tumor DNA did not contain a mutation and/or tumor cells which overexpress p53 were not detected in tissue sections. Although cells which stained positive for p53 were present in sputum from patients whose tumors contained a missense mutation, the presence of p53 overexpression was not specific for tumors which contain an altered p53 allele since overexpression was detected in sputum cells from patients whose tumor DNA did not contain a p53 mutation and/or tumor cells which stained positive for p53 were not observed in tissue sections. However, the p53 positive cells in sputa collected from the latter group of patients could have been exfoliated from other lesions which contained a mutant p53 allele. The accumulation of p53 in some sputum cells was concomitant with expression of simple epithelial type cytokeratins (CK) 8 and 18 or at least one of the other cytokeratins detected by a broad spectrum (PAN) CK antibody mixture. These data imply that most of the sputum cells which overexpress p53 are epithelial cells. Moreover, our results are consistent, at least in part, with other observations that cells which overexpress p53 in dyplasias and hyperplasias express CK 8, 18. We will continue to explore the possibility that expression of cytokeratins 8, 18 and/or other cytokeratins in conjunction with p53 overexpression and/or morphological criteria could define a new class of atypical cells which are predisposed to cancer development.

Ovarian carcinoma in situ with germline BRCA1 mutation and loss of heterozygosity at BRCA1 and TP53

BACKGROUND

The two-hit hypothesis for the genesis of cancer predicts that cancer can develop when the wild-type allele of a tumor suppressor gene is lost in an individual with a germline mutation in that gene. Neither loss of heterozygosity (LOH) for BRCA1 nor mutations of the TP53 (also known as p53) gene have been documented prior to invasion in ovarian cancers arising in women with germline BRCA1 mutations. Such documentation is difficult because lesions are rarely identified in ovarian epithelium. We, therefore, looked for LOH at microsatellite polymorphisms linked to the BRCA1 and TP53 tumor suppressor loci in an incidental carcinoma in situ of the ovary removed prophylactically from a woman with a germline BRCA1 mutation.

METHODS

By use of laser-capture microdissection, we obtained pure populations of atypical ovarian epithelial cells and normal stromal cells. DNA was extracted, amplified with primers flanking polymorphic microsatellites linked to BRCA1 (D17S855 and D17S579) and TP53 (TP53 and D17S786), and analyzed for LOH at these microsatellites. We also tested for p53 expression in the abnormal epithelium by immunohistochemistry.

RESULTS

Both of the markers linked to TP53 showed LOH, as did an intragenic BRCA1-linked marker (D17S855). The other microsatellite marker for BRCA1 was uninformative. Immunohistochemical staining with an antibody to p53 showed strong immunoreactivity confined to the atypical epithelium.

CONCLUSIONS

BRCA1, as well as TP53, can undergo LOH prior to stromal invasion in BRCA1-associated ovarian cancer. Strong immunoreactivity for p53 suggests the presence of mutated p53 in these cells as well. These findings suggest that loss of function of these two tumor suppressor genes occurs early in ovarian carcinogenesis in BRCA1 mutation carriers.

Alterations in exon 4 of the p53 gene in gastric carcinoma

BACKGROUND & AIMS

Our long-term goal was to evaluate the role of p53 in the prognosis of gastric cancer. We previously showed a discrepancy between p53 expression and the presence of mutations when only exons 5-9 were examined. We then evaluated exon 4.

METHODS

DNA was sequenced from 217 gastric cancers to detect exon 4 alterations. Codon 72 was examined by restriction enzyme digestion.

RESULTS

Mutations were present in 3.2% of tumors. In addition, 2 polymorphic sites were found at codons 36 and 72. Polymorphisms at codon 36 were only found in 2 patients. In contrast, the codon 72 polymorphism was very frequent. The genotype frequency was arg/arg (54%), arg/pro (33%), and pro/pro (14%). The genotype of the polymorphic site varied with race (P = 0.001): 64% of whites had the arg/arg genotype, compared with 24% of blacks. The difference in genotype by site, sex, or histological tumor type was not statistically significant (P = 0.067).

CONCLUSIONS

There are several exon 4 alterations in gastric cancers. These include the rare mutations and the very rare codon 36 polymorphism. The most common change is the codon 72 polymorphism, the genotype of which differs significantly with race. The more common arg/arg genotype in whites may explain why whites are more prone to develop cardiac cancer, whereas the more common proline allele in blacks may explain why they are more prone to develop antral cancers. Further studies are required to determine whether the codon 72 polymorphism affects patient predisposition to gastric cancer.

PRK, a cell cycle gene localized to 8p21, is downregulated in head and neck cancer

The human PRK gene encodes a protein serine/threonine kinase of the polo family and plays an essential role in regulating meiosis and mitosis. We have previously shown that PRK expression is downregulated in a significant fraction of lung carcinomas. Our current studies reveal that PRK mRNA expression is downregulated in a majority (26 out of 35 patients) of primary head and neck squamous-cell carcinomas (HNSCC) compared with adjacent uninvolved tissues from the same patients, regardless of stage. In addition, PRK transcripts were undetectable in one of the two HNSCC cell lines analyzed. Ectopic expression of PRK, but not a PRK deletion construct, in transformed A549 fibroblast cells suppresses their proliferation. Furthermore, fluorescence in situ hybridization analyses show that the PRK gene localizes to chromosome band 8p21, a region that exhibits a high frequency of loss of heterozygosity in a variety of human cancers, including head and neck cancers, and that is proposed to contain two putative tumor suppressor genes. Considering that PRK plays an important role in the regulation of the G2/M transition and cell cycle progression, our current studies suggest that deregulated expression of PRK may contribute to tumor development. Genes Chromosomes Cancer 27:332-336, 2000.

Patterns of instability of expanded CAG repeats at the ERDA1 locus in general populations

A highly polymorphic CAG repeat locus, ERDA1, was recently described on human chromosome 17q21.3, with alleles as large as 50-90 repeats and without any disease association in the general population. We have studied allelic distribution at this locus in five human populations and have characterized the mutational patterns by direct observation of 731 meioses. The data show that large alleles (>/=40 CAG repeats) are generally most common in Asian populations, less common in populations of European ancestry, and least common among Africans. We have observed a high intergenerational instability (46. 3%+/-5.1%) of the large alleles. Although the mutation rate is not dependent on parental sex, paternal transmissions have predominantly resulted in contractions, whereas maternal transmissions have yielded expansions. Within this class of large alleles, the mutation rate increases concomitantly with increasing allele size, but the magnitude of repeat size change does not depend on the size of the progenitor allele. Sequencing of specific alleles reveals that the intermediate-sized alleles (30-40 repeats) have CAT/CAC interruptions within the CAG-repeat array. These results indicate that expansion and instability of trinucleotide repeats are not exclusively disease-associated phenomena. The implications of the existence of massively expanded alleles in the general populations are not yet understood.

Report and abstracts of the Sixth International Workshop on chromosome 9

A meeting on chromosome 9 was held on Tuesday, 27 October 1998 in Denver, with 38 participants (see appendix). Since the last meeting several of the positional cloning efforts on chromosome 9q have come to fruition, and the most detailed discussion was on 9p. Dr Ian Dunham from the Sanger Centre explained the strategy to be used for sequencing chromosome 9, and encouraged collaboration in the preparatory mapping. He indicated that some priority could be given to those regions where people in the field had a strong interest and could identify relevant PAC clones. At this short meeting it was clearly not possible to construct a comprehensive map of chromosome 9, and it was decided that efforts should be made to maintain links to sources of information on the chromosome 9 web page (http:@www.gene.ucl.ac.uk/chr9/). The discussions at the meeting are summarized in four sections: 9p, 9cen-q31, 9q32-9q34 and comparative mapping. Many of the posters presented at the meeting were also presented at the ASHG meeting (28-31 October 1998). They are listed here and are published in The American Journal of Human Genetics, vol. 63 (supplement). Abstracts for posters presented only at this meeting are appended to this report.

Saccomanno smear slides and Megafunnel slides for sputum specimens. A comparison

OBJECTIVE

To compare Megafunnel slides to standard Saccomanno smear slides of sputum specimens and evaluate the use of Megafunnel slides for retrospective studies.

STUDY DESIGN

Papanicolaou-stained Saccomanno smear and Megafunnel slides (Shandon Lipshaw, Inc., Shandon Inc., Pittsburgh, Pennsylvania, U.S.A.) of 65 clinical sputum specimens from 51 patients were compared for cellular morphology, staining, background and cytologic diagnosis. Recovery of diagnostic cells was quantitated using 10 of these specimens. Megafunnel slides prepared from the clinical sputum samples were immunocytochemically stained. Diagnostic cells were quantitated both before removal from 64 archived Saccomanno smear slides and after placement of these cells onto 238 Megafunnel slides.

RESULTS

Saccomanno smear slides and Megafunnel slides of clinical specimens were similar in morphology, background, staining, diagnosis and cell recovery. Megafunnel slides were superior for multiple immunocytochemical stains. The production of multiple Megafunnel slides from archival smear slides provided a method of performing numerous retrospective studies.

CONCLUSION

Megafunnel slides compared favorably to Saccomanno smear slides in the quality of specimens but are more expensive and labor intensive to prepare. However, the reduction in screening time by cytotechnologists may be advantageous. Additionally, their potential use for immunocytochemistry, fluorescence in situ hybridization, or other special clinical and research analyses is very promising.

Genotype/phenotype discordance for human arylamine N-acetyltransferase (NAT2) reveals a new slow-acetylator allele common in African-Americans

Carcinogenic arylamines are acetylated by the hepatic N-acetyltransferase. This enzyme is polymorphic in humans and in some epidemiological studies, the slow-acetylator phenotype has been associated with higher risk of bladder cancer and lower risk of colorectal cancer. The presence of two germline copies of any of several mutant alleles of the NAT2 gene produces a slow-acetylation phenotype. We used a PCR-RFLP technique to identify three known slow-acetylator alleles (M1, M2 and M3). Comparison of results from PCR-RFLP genotyping with caffeine metabolism phenotyping in 42 individuals suggested that an additional slow-acetylator allele was present in our sampled population. We sequenced the NAT2 gene for several discordant slow-acetylator individuals and found a G > A base-change in codon 64 that caused a Arg > Glu amino acid substitution. This sequence change, termed the 'M4' allele, was found in all of the discordant individuals in our population and apparently causes a slow-acetylation phenotype. In addition, we have determined that NAT2 allele frequencies in 372 Caucasian-Americans (WT = 0.25, M1 = 0.45, M2 = 0.28, M3 = 0.02, and M4 = 0.00) and in 128 African-Americans (WT = 0.36, M1 = 0.30, M2 = 0.22, M3 = 0.02 and M4 = 0.09) are significantly different (P < 0.0001). The M4 allele was not found in 372 unrelated Caucasians and appears to be of African origin.