Ecological-Evaluation of Organotin-Contaminated Sediment.

DTIC Science & Technology

1985-07-01

the potential for bioaccumulation of cadmium, chromium, copper, mercury , silver, pesticides, PCBs, petroleum hydrocarbons, and organotins RESULTS The...tissues were frozen for subsequent bioaccumulation estimates. Tissues and sediment samples were analyzed for cadmium, chromium, copper, mercury , silver...spectroscopy; mercury was analyzed by cold vapor atomic absorption spectroscopy. Pesticides, PCBs, and petroleum hydrocarbons were measured by gas

Contrast-enhanced 3D micro-CT of plant tissues using different impregnation techniques.

PubMed

Wang, Zi; Verboven, Pieter; Nicolai, Bart

2017-01-01

X-ray micro-CT has increasingly been used for 3D imaging of plant structures. At the micrometer resolution however, limitations in X-ray contrast often lead to datasets with poor qualitative and quantitative measures, especially within dense cell clusters of plant tissue specimens. The current study developed protocols for delivering a cesium based contrast enhancing solution to varying plant tissue specimens for the purpose of improving 3D tissue structure characterization within plant specimens, accompanied by new image processing workflows to extract the additional data generated by the contrast enhanced scans. Following passive delivery of a 10% cesium iodide contrast solution, significant increases of 85.4 and 38.0% in analyzable cell volumes were observed in pear fruit hypanthium and tomato fruit outer mesocarp samples. A significant increase of 139.6% in the number of analyzable cells was observed in the pear fruit samples along the added ability to locate and isolate better brachysclereids and vasculature in the sample volume. Furthermore, contrast enhancement resulted in significant improvement in the definition of collenchyma and parenchyma in the petiolule of tomato leaflets, from which both qualitative and quantitative data can be extracted with respect to cell measures. However, contrast enhancement was not achieved in leaf vasculature and mesophyll tissue due to fundamental limitations. Active contrast delivery to apple fruit hypanthium samples did yield a small but insignificant increase in analyzable volume and cells, but data on vasculature can now be extracted better in correspondence to the pear hypanthium samples. Contrast delivery thus improved visualization and analysis the most in dense tissue types. The cesium based contrast enhancing protocols and workflows can be utilized to obtain detailed 3D data on the internal microstructure of plant samples, and can be adapted to additional samples of interest with minimal effort. The resulting datasets can therefore be utilized for more accurate downstream studies that requires 3D data.

A Cancer-Indicative microRNA Pattern in Normal Prostate Tissue

PubMed Central

Hellwinkel, Olaf J. C.; Sellier, Christina; Sylvester, Yu-Mi Jessica; Brase, Jan C.; Isbarn, Hendrik; Erbersdobler, Andreas; Steuber, Thomas; Sültmann, Holger; Schlomm, Thorsten; Wagner, Christina

2013-01-01

We analyzed the levels of selected micro-RNAs in normal prostate tissue to assess their potential to indicate tumor foci elsewhere in the prostate. Histologically normal prostate tissue samples from 31 prostate cancer patients and two cancer negative control groups with either unsuspicious or elevated prostate specific antigen (PSA) levels (14 and 17 individuals, respectively) were analyzed. Based on the expression analysis of 157 microRNAs in a pool of prostate tissue samples and information from data bases/literature, we selected eight microRNAs for quantification by real-time polymerase chain reactions (RT-PCRs). Selected miRNAs were analyzed in histologically tumor-free biopsy samples from patients and healthy controls. We identified seven microRNAs (miR-124a, miR-146a & b, miR-185, miR-16 and let-7a & b), which displayed significant differential expression in normal prostate tissue from men with prostate cancer compared to both cancer negative control groups. Four microRNAs (miR-185, miR-16 and let-7a and let-7b) remained to significantly discriminate normal tissues from prostate cancer patients from those of the cancer negative control group with elevated PSA levels. The transcript levels of these microRNAs were highly indicative for the presence of cancer in the prostates, independently of the PSA level. Our results suggest a microRNA-pattern in histologically normal prostate tissue, indicating prostate cancer elsewhere in the organ. PMID:23459235

Biological Marker Analysis as Part of the CIBERES-RTIC Cancer-SEPAR Strategic Project on Lung Cancer.

PubMed

Monsó, Eduard; Montuenga, Luis M; Sánchez de Cos, Julio; Villena, Cristina

2015-09-01

The aim of the Clinical and Molecular Staging of Stage I-IIp Lung Cancer Project is to identify molecular variables that improve the prognostic and predictive accuracy of TMN classification in stage I/IIp non-small cell lung cancer (NSCLC). Clinical data and lung tissue, tumor and blood samples will be collected from 3 patient cohorts created for this purpose. The prognostic protein signature will be validated from these samples, and micro-RNA, ALK, Ros1, Pdl-1, and TKT, TKTL1 y G6PD expression will be analyzed. Tissue inflammatory markers and stromal cell markers will also be analyzed. Methylation of p16, DAPK, RASSF1a, APC and CDH13 genes in the tissue samples will be determined, and inflammatory markers in peripheral blood will also be analyzed. Variables that improve the prognostic and predictive accuracy of TNM in NSCLC by molecular staging may be identified from this extensive analytical panel. Copyright © 2014 SEPAR. Published by Elsevier Espana. All rights reserved.

Statistical analysis and machine learning algorithms for optical biopsy

NASA Astrophysics Data System (ADS)

Wu, Binlin; Liu, Cheng-hui; Boydston-White, Susie; Beckman, Hugh; Sriramoju, Vidyasagar; Sordillo, Laura; Zhang, Chunyuan; Zhang, Lin; Shi, Lingyan; Smith, Jason; Bailin, Jacob; Alfano, Robert R.

2018-02-01

Analyzing spectral or imaging data collected with various optical biopsy methods is often times difficult due to the complexity of the biological basis. Robust methods that can utilize the spectral or imaging data and detect the characteristic spectral or spatial signatures for different types of tissue is challenging but highly desired. In this study, we used various machine learning algorithms to analyze a spectral dataset acquired from human skin normal and cancerous tissue samples using resonance Raman spectroscopy with 532nm excitation. The algorithms including principal component analysis, nonnegative matrix factorization, and autoencoder artificial neural network are used to reduce dimension of the dataset and detect features. A support vector machine with a linear kernel is used to classify the normal tissue and cancerous tissue samples. The efficacies of the methods are compared.

Quantitatively differentiating microstructural variations of skeletal muscle tissues by multispectral Mueller matrix imaging

NASA Astrophysics Data System (ADS)

Dong, Yang; He, Honghui; He, Chao; Ma, Hui

2016-10-01

Polarized light is sensitive to the microstructures of biological tissues and can be used to detect physiological changes. Meanwhile, spectral features of the scattered light can also provide abundant microstructural information of tissues. In this paper, we take the backscattering polarization Mueller matrix images of bovine skeletal muscle tissues during the 24-hour experimental time, and analyze their multispectral behavior using quantitative Mueller matrix parameters. In the processes of rigor mortis and proteolysis of muscle samples, multispectral frequency distribution histograms (FDHs) of the Mueller matrix elements can reveal rich qualitative structural information. In addition, we analyze the temporal variations of the sample using the multispectral Mueller matrix transformation (MMT) parameters. The experimental results indicate that the different stages of rigor mortis and proteolysis for bovine skeletal muscle samples can be judged by these MMT parameters. The results presented in this work show that combining with the multispectral technique, the FDHs and MMT parameters can characterize the microstructural variation features of skeletal muscle tissues. The techniques have the potential to be used as tools for quantitative assessment of meat qualities in food industry.

Final LDRD report : development of sample preparation methods for ChIPMA-based imaging mass spectrometry of tissue samples.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maharrey, Sean P.; Highley, Aaron M.; Behrens, Richard, Jr.

2007-12-01

The objective of this short-term LDRD project was to acquire the tools needed to use our chemical imaging precision mass analyzer (ChIPMA) instrument to analyze tissue samples. This effort was an outgrowth of discussions with oncologists on the need to find the cellular origin of signals in mass spectra of serum samples, which provide biomarkers for ovarian cancer. The ultimate goal would be to collect chemical images of biopsy samples allowing the chemical images of diseased and nondiseased sections of a sample to be compared. The equipment needed to prepare tissue samples have been acquired and built. This equipment includesmore » an cyro-ultramicrotome for preparing thin sections of samples and a coating unit. The coating unit uses an electrospray system to deposit small droplets of a UV-photo absorbing compound on the surface of the tissue samples. Both units are operational. The tissue sample must be coated with the organic compound to enable matrix assisted laser desorption/ionization (MALDI) and matrix enhanced secondary ion mass spectrometry (ME-SIMS) measurements with the ChIPMA instrument Initial plans to test the sample preparation using human tissue samples required development of administrative procedures beyond the scope of this LDRD. Hence, it was decided to make two types of measurements: (1) Testing the spatial resolution of ME-SIMS by preparing a substrate coated with a mixture of an organic matrix and a bio standard and etching a defined pattern in the coating using a liquid metal ion beam, and (2) preparing and imaging C. elegans worms. Difficulties arose in sectioning the C. elegans for analysis and funds and time to overcome these difficulties were not available in this project. The facilities are now available for preparing biological samples for analysis with the ChIPMA instrument. Some further investment of time and resources in sample preparation should make this a useful tool for chemical imaging applications.« less

Post-Remediation Biomonitoring of Pesticides and Other Contaminants in Marine Waters and Sediment Near the United Heckathorn Superfund Site, Richmond, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

LD Antrim; NP Kohn

This report, PNNL-1 3059 Rev. 1, was published in July 2000 and replaces PNNL-1 3059 which is dated October 1999. The revision corrects tissue concentration units that were reported as dry weight but were actually wet weight, and updates conclusions based on the correct reporting units. Marine sediment remediation at the United Heckathorn Superfund Site was completed in April 1997. Water and mussel tissues were sampled in February 1999 from four stations near Lauritzen Canal in Richmond, California, for Year 2 of post-remediation monitoring of marine areas near the United Heckathom Site. Dieldrin and dichlorodiphenyl trichloroethane (DDT) were analyzed inmore » water samples, tissue samples from resident mussels, and tissue samples from transplanted mussels deployed for 4 months. Concentrations of dieldrin and total DDT in water and total DDT in tissue were compared with Year 1 of post-remediation monitoring, and with preremediation data from the California State Mussel Watch program (tissue s) and the Ecological Risk Assessment for the United Heckathorn Superfund Site (tissues and water). Mussel tissues were also analyzed for polychlorinated biphenyls (PCB), which were detected in sediment samples. Chlorinated pesticide concentrations in water samples were similar to preremediation levels and did not meet remediation goals. Mean dieldrin concentrations in water ranged from 0.62 ng/L to 12.5 ng/L and were higher than the remediation goal (0.14 ng/L) at all stations. Mean total DDT concentrations in water ranged from 14.4 ng/L to 62.3 ng/L and exceeded the remediation goal (0.59 ng/L) at all stations. The highest concentrations of both DDT and dieldrin were found at the Lauritzen Canal/End station. Despite exceedence of the remediation goals, chlorinated pesticide concentrations in Lauritzen Canal water samples were notably lower in 1999 than in 1998. PCBS were not detected in water samples in 1999.« less

Study of gastric cancer samples using terahertz techniques

NASA Astrophysics Data System (ADS)

Wahaia, Faustino; Kasalynas, Irmantas; Seliuta, Dalius; Molis, Gediminas; Urbanowicz, Andrzej; Carvalho Silva, Catia D.; Carneiro, Fatima; Valusis, Gintaras; Granja, Pedro L.

2014-08-01

In the present work, samples of healthy and adenocarcinoma-affected human gastric tissue were analyzed using transmission time-domain THz spectroscopy (THz-TDS) and spectroscopic THz imaging at 201 and 590 GHz. The work shows that it is possible to distinguish between normal and cancerous regions in dried and paraffin-embedded samples. Plots of absorption coefficient α and refractive index n of normal and cancer affected tissues, as well as 2-D transmission THz images are presented and the conditions for discrimination between normal and affected tissues are discussed.

Fluorescence suppression using wavelength modulated Raman spectroscopy in fiber-probe-based tissue analysis.

PubMed

Praveen, Bavishna B; Ashok, Praveen C; Mazilu, Michael; Riches, Andrew; Herrington, Simon; Dholakia, Kishan

2012-07-01

In the field of biomedical optics, Raman spectroscopy is a powerful tool for probing the chemical composition of biological samples. In particular, fiber Raman probes play a crucial role for in vivo and ex vivo tissue analysis. However, the high-fluorescence background typically contributed by the auto fluorescence from both a tissue sample and the fiber-probe interferes strongly with the relatively weak Raman signal. Here we demonstrate the implementation of wavelength-modulated Raman spectroscopy (WMRS) to suppress the fluorescence background while analyzing tissues using fiber Raman probes. We have observed a significant signal-to-noise ratio enhancement in the Raman bands of bone tissue, which have a relatively high fluorescence background. Implementation of WMRS in fiber-probe-based bone tissue study yielded usable Raman spectra in a relatively short acquisition time (∼30  s), notably without any special sample preparation stage. Finally, we have validated its capability to suppress fluorescence on other tissue samples such as adipose tissue derived from four different species.

Terahertz spectroscopy for the study of paraffin-embedded gastric cancer samples

NASA Astrophysics Data System (ADS)

Wahaia, Faustino; Kasalynas, Irmantas; Seliuta, Dalius; Molis, Gediminas; Urbanowicz, Andrzej; Carvalho Silva, Catia D.; Carneiro, Fatima; Valusis, Gintaras; Granja, Pedro L.

2015-01-01

Terahertz (THz) spectroscopy constitute promising technique for biomedical applications as a complementary and powerful tool for diseases screening specially for early cancer diagnostic. The THz radiation is not harmful to biological tissues. As increased blood supply in cancer-affected tissues and consequent local increase in tissue water content makes THz technology a potentially attractive. In the present work, samples of healthy and adenocarcinoma-affected gastric tissue were analyzed using transmission time-domain THz spectroscopy (THz-TDS). The work shows the capability of the technique to distinguish between normal and cancerous regions in dried and paraffin-embedded samples. Plots of absorption coefficient α and refractive index n of normal and cancer affected tissues, are presented and the conditions for discrimination between normal and affected tissues are discussed.

Improved results of LINE-1 methylation analysis in formalin-fixed, paraffin-embedded tissues with the application of a heating step during the DNA extraction process.

PubMed

Wen, Xianyu; Jeong, Seorin; Kim, Younghoon; Bae, Jeong Mo; Cho, Nam Yun; Kim, Jung Ho; Kang, Gyeong Hoon

2017-01-01

Formalin-fixed, paraffin-embedded (FFPE) tissues are important resources for profiling DNA methylation changes and for studying a variety of diseases. However, formalin fixation introduces inter-strand crosslinking, which might cause incomplete bisulfite conversion of unmethylated cytosines, which might lead to falsely elevated measurements of methylation levels in pyrosequencing assays. Long interspersed nucleotide element-1 (LINE-1) is a major constituent of repetitive transposable DNA elements, and its methylation is referred to correlates with global DNA methylation. To identify whether formalin fixation might impact the measured values of methylation in LINE-1 repetitive elements and whether prolonged heat-induced denaturation of DNA might reduce the artificial increases in measured values caused by formalin fixation, we analyzed paired fresh-frozen (FF) and FFPE xenograft tissue samples for their methylation levels in LINE-1 using a pyrosequencing assay. To further confirm the effect of a heating step in the measurement of LINE-1 or single gene methylation levels, we analyzed FFPE tissue samples of gastric cancer and colorectal cancer for their methylation status in LINE-1 and eight single genes, respectively. Formalin fixation led to an increase in the measured values of LINE-1 methylation regardless of the duration of fixation. Prolonged heating of the DNA at 95 °C for 30 min before bisulfite conversion was found (1) to decrease the discrepancy in the measured values between the paired FF and FFPE tissue samples, (2) to decrease the standard deviation of the measured value of LINE-1 methylation levels in FFPE tissue samples of gastric cancer, and (3) to improve the performance in the measurement of single gene methylation levels in FFPE tissue samples of colorectal cancer. Formalin fixation leads to artificial increases in the measured values of LINE-1 methylation, and the application of prolonged heating of DNA samples decreases the discrepancy in the measured values of LINE-1 methylation between paired FF and FFPE tissue samples. The application of prolonged heating of DNA samples improves bisulfite conversion-based measurement of LINE-1 or single gene methylation levels in FFPE tissue samples.

Advantages of tandem LC-MS for the rapid assessment of tissue-specific metabolic complexity using a pentafluorophenylpropyl stationary phase

PubMed Central

Lv, Haitao; Palacios, Gustavo; Hartil, Kirsten; Kurland, Irwin J.

2014-01-01

In this study a UPLC-tandem (Waters Xevo TQ) MRM based MS method was developed for rapid, broad profiling of hydrophilic metabolites from biological samples, in either positive or negative ion modes without the need for an ion pairing reagent, using a reversed-phase pentafluorophenylpropyl (PFPP) column. The developed method was successfully applied to analyze various biological samples from C57BL/6 mice; including urine, duodenum, liver, plasma, kidney, heart, and skeletal muscle. As result, a total 112 of hydrophilic metabolites were detected within 8 min of running time to obtain a metabolite profile of the biological samples. The analysis of this number of hydrophilic metabolites is significantly faster than previous studies. Classification separation for metabolites from different tissues was globally analyzed by PCA, PLS-DA and HCA biostatistical methods. Overall, most of the hydrophilic metabolites were found to have a “fingerprint” characteristic of tissue dependency. In general, a higher level of most metabolites was found in urine, duodenum and kidney. Altogether, these results suggest that this method has potential application for targeted metabolomic analyzes of hydrophilic metabolites in a wide ranges of biological samples. PMID:21322650

Advantages of tandem LC-MS for the rapid assessment of tissue-specific metabolic complexity using a pentafluorophenylpropyl stationary phase.

PubMed

Lv, Haitao; Palacios, Gustavo; Hartil, Kirsten; Kurland, Irwin J

2011-04-01

In this study, a tandem LC-MS (Waters Xevo TQ) MRM-based MS method was developed for rapid, broad profiling of hydrophilic metabolites from biological samples, in either positive or negative ion modes without the need for an ion pairing reagent, using a reversed-phase pentafluorophenylpropyl (PFPP) column. The developed method was successfully applied to analyze various biological samples from C57BL/6 mice, including urine, duodenum, liver, plasma, kidney, heart, and skeletal muscle. As result, a total 112 of hydrophilic metabolites were detected within 8 min of running time to obtain a metabolite profile of the biological samples. The analysis of this number of hydrophilic metabolites is significantly faster than previous studies. Classification separation for metabolites from different tissues was globally analyzed by PCA, PLS-DA and HCA biostatistical methods. Overall, most of the hydrophilic metabolites were found to have a "fingerprint" characteristic of tissue dependency. In general, a higher level of most metabolites was found in urine, duodenum, and kidney. Altogether, these results suggest that this method has potential application for targeted metabolomic analyzes of hydrophilic metabolites in a wide ranges of biological samples.

[Identification and management of intra-operative suspicious tissues in 20 transsphenoidal surgery cases].

PubMed

Liu, Jun-Feng; Ke, Chang-Shu; Chen, Xi; Xu, Yu; Zhang, Hua-Qiu; Chen, Juan; Gan, Chao; Li, Chao-Xi; Lei, Ting

2013-05-01

To determine appropriate protocols for the identification and management of intra operative suspicious tissues during transsphenoidal surgery. Clinical data and pathological reports of 20 patients with intra-operative suspicious tissues during transsphenoidal surgeries were analyzed retrospectively. The methods for discriminating between adenoma and normal pituitary tissues were reviewed. The postoperative pathological reports revealed that adenoma and normal pituitary tissues coexisted in 9 samples, while 5 samples were identified as normal pituitary tissues, 2 as adenoma tissues, and 4 as other tissues. Adenomas were distinguished from normal pituitary tissues on the basis of intra-operative appearance, texture, blood supply and possible existence of boundary. If decisions are difficult to made during surgeries from the appearance of the suspicious tissues, pathological examinations are advised as a guidance for the next steps.

Comparison of pinniped and cetacean prey tissue lipids with lipids of their elasmobranch predator.

PubMed

Davidson, Bruce; Cliff, Geremy

2014-01-01

The great white shark is known to include pinnipeds and cetaceans in its diet. Both groups of marine mammals deposit thick blubber layers around their bodies. Elasmobranchs do not produce adipose tissue, but rather store lipid in their livers, thus a great white predating on a marine mammal will deposit the lipids in its liver until required. Samples from great white liver and muscle, Cape fur seal, Indian Ocean bottlenose dolphin and common dolphin liver, muscle and blubber were analyzed for their lipid and fatty acid profiles. The great white liver and marine mammal blubber samples showed a considerable degree of homogeneity, but there were significant differences when comparing between the muscle samples. Blubber from all three marine mammal species was calculated to provide greater than 95% of lipid intake for the great white shark from the tissues analyzed. Sampling of prey blubber may give a good indication of the lipids provided to the shark predator.

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

PubMed

Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

2016-01-04

Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

Advanced synchronous luminescence system

DOEpatents

Vo-Dinh, Tuan

1997-01-01

A method and apparatus for determining the condition of tissue or otherwise making chemical identifications includes exposing the sample to a light source, and using a synchronous luminescence system to produce a spectrum that can be analyzed for tissue condition.

CLOSED-LOOP STRIPPING ANALYSIS (CLSA) OF ...

EPA Pesticide Factsheets

Synthetic musk compounds have been found in surface water, fish tissues, and human breast milk. Current techniques for separating these compounds from fish tissues require tedious sample clean-upprocedures A simple method for the deterrnination of these compounds in fish tissues has been developed. Closed-loop stripping of saponified fish tissues in a I -L Wheaton purge-and-trap vessel is used to strip compounds with high vapor pressures such as synthetic musks from the matrix onto a solid sorbent (Abselut Nexus). This technique is useful for screening biological tissues that contain lipids for musk compounds. Analytes are desorbed from the sorbent trap sequentially with polar and nonpolar solvents, concentrated, and directly analyzed by high resolution gas chromatography coupled to a mass spectrometer operating in the selected ion monitoring mode. In this paper, we analyzed two homogenized samples of whole fish tissues with spiked synthetic musk compounds using closed-loop stripping analysis (CLSA) and pressurized liquid extraction (PLE). The analytes were not recovered quantitatively but the extraction yield was sufficiently reproducible for at least semi-quantitative purposes (screening). The method was less expensive to implement and required significantly less sample preparation than the PLE technique. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water,

Cancer testis antigen OY-TES-1: analysis of protein expression in ovarian cancer with tissue microarrays.

PubMed

Fan, R; Huang, W; Luo, B; Zhang, Q M; Xiao, S W; Xie, X X

2015-01-01

Revised manuscript accepted for publication March 5, Objectives: The purpose of this study was to determine the potential of cancer testis antigen OY-TES-1 as a vaccine for ovarian cancer (OC). A tissue microarray (TMA) containing 107 samples from OC tissues and 48 samples from OC adjacent tissues was analyzed by immunohistochemistry with the OY-TES-1 polyclonal antibody. The correlation between OY-TES-1 and clinic pathological traits of OC was statistically analyzed. The expression of OY-TES-1 protein was found in 81% (87/107) of OC tissues and 56% (27/48) of OC adjacent tissues. The immunostaining intensity of OY-TES-1 in OC tissues was significantly higher than that in OC adjacent tissues tested (p = 0.040). OC adjacent tissues only demonstrated lower immunostaining intensity, whereas some of OC tissues presented higher immunostaining intensity and majority showed the heterogeneity of protein distribution. There was no statistically significant correlation found between OY-TES-1 expression and any other clinicopathological traits such as age, FIGO stage, pathological grade, and histological type. OY-TES-1 was expressed in OC tissues with a high proportion, and some of OC tissues presented OY-TES-1 expression in high level vs OC adjacent tissues. OY-TES-1 could be an attractive target for immunotherapy for OC in the future.

Post-Remediation Biomonitoring of Pesticides in Marine Waters Near the United Heckathorn Site, Richmond, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antrim, Liam D.; Kohn, Nancy P.

Marine sediment remediation at the United Heckathorn Superfund Site was completed in April 1997. Water and mussel tissues were sampled in January 1998 from four stations near Lauritzen Canal in Richmond, California, for the first post-remediation monitoring of marine areas near the United Heckathorn Site. Dieldrin and DDT were analyzed in water samples, tissue samples from resident mussels, and tissue samples from transplanted mussels deployed for 4 months. Concentrations of dieldrin and total DDT in water and total DDT in tissue were compared to pre-remediation data available from the California State Mussel Watch program (tissues) and the Ecological Risk Assessmentmore » for the United Heckathorn Superfund Site (tissues and water). Biomonitoring results indicated that pesticides were still bioavailable in the water column, and have not been reduced from pre-remediation levels. Annual biomonitoring will continue to assess the effectiveness of remedial actions at the United Heckathorn Site.« less

Biochemical and molecular characterization of thyroid tissue by micro-Raman spectroscopy and gene expression analysis

NASA Astrophysics Data System (ADS)

Neto, Lázaro P. M.; Martin, Aírton A.; Soto, Claudio A. T.; Santos, André B. O.; Mello, Evandro S.; Pereira, Marina A.; Cernea, Cláudio R.; Brandão, Lenine G.; Canevari, Renata A.

2016-02-01

Thyroid carcinomas represent the main endocrine malignancy and their diagnosis may produce inconclusive results. Raman spectroscopy and gene expression analysis have shown excellent results on the differentiation of carcinomas. This study aimed to improve the discrimination between different thyroid pathologies combining of both analyses. A total of 35 thyroid tissues samples including normal tissue (n=10), goiter (n=10), papillary (n=10) and follicular carcinomas (n=5) were analyzed. Confocal Raman spectra was obtain by using a Rivers Diagnostic System, 785 nm laser excitation and CCD detector. The data was processed by the software Labspec5 and Origin 8.5 and analyzed by Minitab® program. The gene expression analysis was performed by qRT-PCR technique for TG, TPO, PDGFB, SERPINA1, LGALS3 and TFF3 genes and statistically analyzed by Mann-Whitney test. The confocal Raman spectroscopy allowed a maximum discrimination of 91.1% between normal and tumor tissues, 84.8% between benign and malignant pathologies and 84.6% among carcinomas analyzed. Significant differences was observed for TG, LGALS3, SERPINA1 and TFF3 genes between benign lesions and carcinomas, and SERPINA1 and TFF3 genes between papillary and follicular carcinomas. Principal component analysis was performed using PC1 and PC2 in the papillary carcinoma samples that showed over gene expression when compared with normal sample, where 90% of discrimination was observed at the Amide 1 (1655 cm-1), and at the tyrosine spectra region (856 cm-1). The discrimination of tissues thyroid carried out by confocal Raman spectroscopy and gene expression analysis indicate that these techniques are promising tools to be used in the diagnosis of thyroid lesions.

Age estimation based on aspartic acid racemization in human sclera.

PubMed

Klumb, Karolin; Matzenauer, Christian; Reckert, Alexandra; Lehmann, Klaus; Ritz-Timme, Stefanie

2016-01-01

Age estimation based on racemization of aspartic acid residues (AAR) in permanent proteins has been established in forensic medicine for years. While dentine is the tissue of choice for this molecular method of age estimation, teeth are not always available which leads to the need to identify other suitable tissues. We examined the suitability of total tissue samples of human sclera for the estimation of age at death. Sixty-five samples of scleral tissue were analyzed. The samples were hydrolyzed and after derivatization, the extent of aspartic acid racemization was determined by gas chromatography. The degree of AAR increased with age. In samples from younger individuals, the correlation of age and D-aspartic acid content was closer than in samples from older individuals. The age-dependent racemization in total tissue samples proves that permanent or at least long-living proteins are present in scleral tissue. The correlation of AAR in human sclera and age at death is close enough to serve as basis for age estimation. However, the precision of age estimation by this method is lower than that of age estimation based on the analysis of dentine which is due to molecular inhomogeneities of total tissue samples of sclera. Nevertheless, the approach may serve as a valuable alternative or addition in exceptional cases.

Spectroscopic optical coherence tomography for ex vivo brain tumor analysis

NASA Astrophysics Data System (ADS)

Lenz, Marcel; Krug, Robin; Dillmann, Christopher; Gerling, Alexandra; Gerhardt, Nils C.; Welp, Hubert; Schmieder, Kirsten; Hofmann, Martin R.

2017-02-01

For neurosurgeries precise tumor resection is essential for the subsequent recovery of the patients since nearby healthy tissue that may be harmed has a huge impact on the life quality after the surgery. However, so far no satisfying methodology has been established to assist the surgeon during surgery to distinguish between healthy and tumor tissue. Optical Coherence Tomography (OCT) potentially enables non-contact in vivo image acquisition at penetration depths of 1-2 mm with a resolution of approximately 1-15 μm. To analyze the potential of OCT for distinction between brain tumors and healthy tissue, we used a commercially available Thorlabs Callisto system to measure healthy tissue and meningioma samples ex vivo. All samples were measured with the OCT system and three dimensional datasets were generated. Afterwards they were sent to the pathology for staining with hematoxylin and eosin and then investigated with a bright field microscope to verify the tissue type. This is the actual gold standard for ex vivo analysis. The images taken by the OCT system exhibit variations in the structure for different tissue types, but these variations may not be objectively evaluated from raw OCT images. Since an automated distinction between tumor and healthy tissue would be highly desirable to guide the surgeon, we applied Spectroscopic Optical Coherence Tomography to further enhance the differences between the tissue types. Pattern recognition and machine learning algorithms were applied to classify the derived spectroscopic information. Finally, the classification results are analyzed in comparison to the histological analysis of the samples.

Association of mutant EGFR L858R and exon 19 concentration in circulating cell-free DNA using droplet digital PCR with response to EGFR-TKIs in NSCLC

PubMed Central

Zhu, Yan-Juan; Zhang, Hai-Bo; Liu, Yi-Hong; Zhu, Ya-Zhen; Chen, Jun; Li, Yong; Bai, Jian-Ping; Liu, Li-Rong; Qu, Yan-Chun; Qu, Xin; Chen, Xian; Zheng, Guang-Juan

2017-01-01

The present study aimed to determine the diagnostic concordance of plasma epidermal growth factor receptor (EGFR) mutation using droplet digital polymerase chain reaction (ddPCR) with tumor tissue samples and the predictive clinical significance of plasma EGFR mutation concentration. Plasma DNA samples from patients with non-small cell lung cancer (NSCLC) were analyzed for EGFR exon 21 codon 858 (L858R) mutation, deletion of exon 19 (ex19del) and exon 20 codon 790 (T790M) mutation using ddPCR. Firstly, the mutations in the plasma samples were compared with the matched tumor samples to determine the concordance. Secondly, image examination follow-ups were analyzed to assess the association between plasma EGFR mutation concentration and patients' response to EGFR-tyrosine kinase inhibitors (TKIs). A total of 51 patients with NSCLC were enrolled, including 48 newly diagnosed patients. Compared with tumor tissue samples, the sensitivity and specificity of ddPCR were 76.19% (16/21) and 96.55% (28/29) for mutant L858R, and 88.89% (8/9) and 100% (41/41) for ex19del, respectively. No patient exhibited the T790M mutation in the tumor tissue or plasma samples. Furthermore, 5 patients with the L858R mutation and 4 patients with ex19del in plasma and tumor tissue samples had been followed up with image examination for ≥3 months following EGFR-TKI treatment. The baseline mutant EGFR concentrations were positively correlated with a reduction in tumor burden (Spearman's r=0.7000, P=0.0358). When analyzed separately, ex19del concentrations (Spearman's r=1.0000, P<0.0001) were also positively correlated with the reduction, while mutant L858R concentrations were not (Spearman's r=0.7000, P=0.1881). In the present study, detection of plasma EGFR mutations using ddPCR exhibited sufficient concordance with tumor tissue sample results. Baseline plasma mutant EGFR and ex19del concentrations were significantly and positively correlated with response to EGFR-TKIs. PMID:28789464

Advanced synchronous luminescence system

DOEpatents

Vo-Dinh, T.

1997-02-04

A method and apparatus are disclosed for determining the condition of tissue or otherwise making chemical identifications includes exposing the sample to a light source, and using a synchronous luminescence system to produce a spectrum that can be analyzed for tissue condition. 14 figs.

Application of biospeckles for assessment of structural and cellular changes in muscle tissue

NASA Astrophysics Data System (ADS)

Maksymenko, Oleksandr P.; Muravsky, Leonid I.; Berezyuk, Mykola I.

2015-09-01

A modified spatial-temporal speckle correlation technique for operational assessment of structural changes in muscle tissues after slaughtering is considered. Coefficient of biological activity as a quantitative indicator of structural changes of biochemical processes in biological tissues is proposed. The experimental results have shown that this coefficient properly evaluates the biological activity of pig and chicken muscle tissue samples. Studying the degradation processes in muscle tissue during long-time storage in a refrigerator by measuring the spatial-temporal dynamics of biospeckle patterns is carried out. The reduction of the bioactivity level of refrigerated muscle tissue samples connected with the initiation of muscle fiber cracks and ruptures, reduction of sarcomeres, nuclei deformation, nuclear chromatin diminishing, and destruction of mitochondria is analyzed.

The value of intraoperative ultrasonography during the resection of relapsed irradiated malignant gliomas in the brain.

PubMed

Mursch, Kay; Scholz, Martin; Brück, Wolfgang; Behnke-Mursch, Julianne

2017-01-01

The aim of this study was to investigate whether intraoperative ultrasonography (IOUS) helped the surgeon navigate towards the tumor as seen in preoperative magnetic resonance imaging and whether IOUS was able to distinguish between tumor margins and the surrounding tissue. Twenty-five patients suffering from high-grade gliomas who were previously treated by surgery and radiotherapy were included. Intraoperatively, two histopathologic samples were obtained a sample of unequivocal tumor tissue (according to anatomical landmarks and the surgeon's visual and tactile impressions) and a small tissue sample obtained using a navigated needle when the surgeon decided to stop the resection. This specimen was considered to be a boundary specimen, where no tumor tissue was apparent. The decision to take the second sample was not influenced by IOUS. The effect of IOUS was analyzed semi-quantitatively. All 25 samples of unequivocal tumor tissue were histopathologically classified as tumor tissue and were hyperechoic on IOUS. Of the boundary specimens, eight were hypoechoic. Only one harbored tumor tissue (P=0.150). Seventeen boundaries were moderately hyperechoic, and these samples contained all possible histological results (i.e., tumor, infiltration, or no tumor). During surgery performed on relapsed, irradiated, high-grade gliomas, IOUS provided a reliable method of navigating towards the core of the tumor. At borders, it did not reliably distinguish between remnants or tumor-free tissue, but hypoechoic areas seldom contained tumor tissue.

Distribution of volatile branched-chain fatty acids in various lamb tissues.

PubMed

Brennand, C P; Lindsay, R C

1992-01-01

Volatile fatty acids (C4-C11) including even-, odd-, and branched-chain members in lamb tissues were quantitatively analyzed. Volatile branched-chain fatty acids (BCFA) were more concentrated in subcutaneous adipose tissue samples (rump, shoulder, breast) than in perinepheric adipose or muscle tissues. Perinepheric adipose tissue contained relatively high quantities of n-chain, even-numbered fatty acids and very low levels of BCFA. Greater variation existed in fatty acid profiles among similar subcutaneous adipose tissues from different lambs than between samples of adipose tissue from different carcass sites from a given lamb sample. 4-Methyl- and 4-ethyloctanoic acids were present at concentrations greatly above threshold levels in all lamb fats tested, and thus upon hydrolysis would contribute species-related flavors to lamb. 4-Methylnonanoic concentrations in lamb fats ranged from nondetectable to greater than the threshold level, and therefore this compound would not always contribute to the species-related flavors of lamb. Lean meat samples contained very low concentrations of 4-methyl- and 4-ethyloctanoic acids. Copyright © 1992. Published by Elsevier Ltd.

Fabrication and characterization of biological tissue phantoms with embedded nanoparticles

NASA Astrophysics Data System (ADS)

Skaptsov, A. A.; Ustalkov, S. O.; Mohammed, A. H. M.; Savenko, O. A.; Novikova, A. S.; Kozlova, E. A.; Kochubey, V. I.

2017-11-01

Phantoms are imitations of biological tissue, which are used for modelling of the light propagation in biological tissues. Carrying out any biophysical experiments requires an indispensable constancy of the initial experiment conditions. The use of solid undegradable phantoms is the basis to obtain reliable reproducible experimental results. The fabrication of biological tissues phantoms containing high absorbance or fluorescence nanoparticles and corresponding to specific mechanical, optical properties is an actual task. This work describes development, fabrication and characterization of such solid tissue phantoms with embedded CdSe/ZnS quantum dots, gold and upconversion nanoparticles. Luminescence of samples with CdSe/ZnS quantum dots and upconversion nanoparticles were recorded. A sample of gold nanorods was analyzed using thermal gravimetric analysis. It can be concluded that the samples are well suited for experiments on laser thermolysis.

Measuring Compartment Size and Gas Solubility in Marine Mammals

DTIC Science & Technology

2014-09-30

analyzed by gas chromatography . Injection of the sample into the gas chromatograph is done using a sample loop to minimize volume injection error. We...1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Measuring Compartment Size and Gas Solubility in Marine...study is to develop methods to estimate marine mammal tissue compartment sizes, and tissue gas solubility. We aim to improve the data available for

Sampling and Analyzing Air Pollution: An Apparatus Suitable for Use in Schools.

ERIC Educational Resources Information Center

Rockwell, Dean M.; Hansen, Tony

1994-01-01

Describes two variations of an air sampler and analyzer that are inexpensive to construct, easy to operate, and designed to be used in an educational program. Variations use vacuum cleaners and aquarium pumps, and white facial tissues serve as filters. Samples of air pollution obtained by this method may be used from early grade school to advanced…

Organochlorine compounds and trace elements in fish tissue and streambed sediment in the Mobile River Basin, Alabama, Mississippi, and Georgia, 1998

USGS Publications Warehouse

Zappia, Humbert

2002-01-01

During the summer of 1998, as part of the National Water-Quality Assessment Program, a survey was conducted to determine which organochlorine compounds and trace elements occur in fish tissues and streambed sediments in the Mobile River Basin, which includes parts of Alabama, Mississippi, Georgia, and Tennessee. The data collected were compared to guidelines related to wildlife, land use, and to 1991 and 1994 National Water-Quality Assessment Program Study-Unit data.Twenty-one sites were sampled in subbasins of the Mobile River Basin. The subbasins ranged in size from about 9 to 22,000 square miles and were dominated by either a single land use or a combination of land uses. The major land-use categories were urban, agriculture, and forest.Organochlorine compounds were widespread spatially in the Mobile River Basin. At least one organochlorine compound was reported at the majority of sampling sites (84 percent) and in a majority of whole-fish (80 percent) and streambed-sediment (52 percent) samples. Multiple organochlorine compounds were reported at 75 percent of the sites where fish tissues were collected and were reported at many of the streambed-sediment sampling sites (45 percent). The majority of concentrations reported, however, were less than 5 micrograms per kilogram in fish-tissue samples and less than 1 microgram per kilogram in streambed-sediment samples.The majority of trace elements analyzed in fish-liver tissue (86 percent) and streambed-sediment (98 percent) samples were reported during this study. Multiple trace elements were reported in all samples and at all sites.Based on comparisons of concentrations of organochlorine compounds and trace elements in fish-tissue and streambed-sediment samples in relation to National Academy of Science and National Academy of Engineering and Canadian tissue guidelines, probable-effects concentrations, and mean probable-effects concentration quotients for streambed sediment, the potential exists for adverse effects to wildlife at 15 (72 percent) of the sites sampled. The potential for adverse effects at these sites is because of the presence of residues or breakdown products related to polychlorinated biphenyls (PCB?s), chlordane, dichlorodiphenyltrichloroethane (DDT), chromium, lead, and zinc.The majority of compounds reported (65 percent) were chlordane, DDT, and PCB?s, or their breakdown products. Concentrations of chlordane and heptachlor epoxide in whole-fish tissue were positively correlated to the amount of urban land use in a basin. Total DDT concentrations in whole-fish tissues were positively correlated to agriculture.The relation of trace elements to land use is not as clear as the relation of organochlorine compounds to land use. This lack of clarity may be due to the possibility of geologic sources of trace elements in the Mobile River Basin and to the ubiquitous nature of many of these trace elements. However, there may be a correlation between the amount of urban land use and concentrations of antimony, cadmium, lead, and zinc in streambed-sediment samples from the Mobile River Basin.Fewer organochlorine compounds and trace elements were reported in samples from the Mobile River Basin than in samples collected during the 1991 and 1994 National Water-Quality Assessment Program studies. Of the organochlorine compounds analyzed nationally, 57 percent were reported in whole-fish tissue samples collected locally and 41 percent were reported in streambed-sediment samples collected locally, whereas 96 percent and 86 percent, respectively, were reported nationally. Of trace elements analyzed nationally, 86 percent were reported in fish-liver tissue locally and 95 percent were reported in streambed-sediment samples locally, whereas 95 percent and 98 percent, respectively, were reported nationally.In general, concentrations of organochlorine compounds and trace elements and the frequency with which they were reported in the Mobile River Basin are similar to or less than t

Transcriptome instability as a molecular pan-cancer characteristic of carcinomas.

PubMed

Sveen, Anita; Johannessen, Bjarne; Teixeira, Manuel R; Lothe, Ragnhild A; Skotheim, Rolf I

2014-08-10

We have previously proposed transcriptome instability as a genome-wide, pre-mRNA splicing-related characteristic of colorectal cancer. Here, we explore the hypothesis of transcriptome instability being a general characteristic of cancer. Exon-level microarray expression data from ten cancer datasets were analyzed, including breast cancer, cervical cancer, colorectal cancer, gastric cancer, lung cancer, neuroblastoma, and prostate cancer (555 samples), as well as paired normal tissue samples from the colon, lung, prostate, and stomach (93 samples). Based on alternative splicing scores across the genomes, we calculated sample-wise relative amounts of aberrant exon skipping and inclusion. Strong and non-random (P < 0.001) correlations between these estimates and the expression levels of splicing factor genes (n = 280) were found in most cancer types analyzed (breast-, cervical-, colorectal-, lung- and prostate cancer). This suggests a biological explanation for the splicing variation. Surprisingly, these associations prevailed in pan-cancer analyses. This is in contrast to the tissue and cancer specific patterns observed in comparisons across healthy tissue samples from the colon, lung, prostate, and stomach, and between paired cancer-normal samples from the same four tissue types. Based on exon-level expression profiling and computational analyses of alternative splicing, we propose transcriptome instability as a molecular pan-cancer characteristic. The affected cancers show strong and non-random associations between low expression levels of splicing factor genes, and high amounts of aberrant exon skipping and inclusion, and vice versa, on a genome-wide scale.

Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age.

PubMed

Craven, Rachel A; Cairns, David A; Zougman, Alexandre; Harnden, Patricia; Selby, Peter J; Banks, Rosamonde E

2013-04-01

Protein profiling of formalin-fixed paraffin-embedded (FFPE) tissues has enormous potential for the discovery and validation of disease biomarkers. The aim of this study was to systematically characterize the effect of length of time of storage of such tissue blocks in pathology archives on the quality of data produced using label-free MS. Normal kidney and clear cell renal cell carcinoma tissues routinely collected up to 10 years prior to analysis were profiled using LC-MS/MS and the data analyzed using MaxQuant. Protein identities and quantification data were analyzed to examine differences between tissue blocks of different ages and assess the impact of technical and biological variability. An average of over 2000 proteins was seen in each sample with good reproducibility in terms of proteins identified and quantification for normal kidney tissue, with no significant effect of block age. Greater biological variability was apparent in the renal cell carcinoma tissue, possibly reflecting disease heterogeneity, but again there was good correlation between technical replicates and no significant effect of block age. These results indicate that archival storage time does not have a detrimental effect on protein profiling of FFPE tissues, supporting the use of such tissues in biomarker discovery studies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ORGANIC COMPOUNDS IN SURFACE SEDIMENTS AND OYSTER TISSUES FROM THE CHESAPEAKE BAY. APPENDICES

EPA Science Inventory

Detailed in the first part of this report is a development and discussion of the methodology used to extract and analyze sediment and oyster tissue samples from Chesapeake Bay for organic compounds. The method includes extraction, fractionation, and subsequent analysis using glas...

Overcoming confounded controls in the analysis of gene expression data from microarray experiments.

PubMed

Bhattacharya, Soumyaroop; Long, Dang; Lyons-Weiler, James

2003-01-01

A potential limitation of data from microarray experiments exists when improper control samples are used. In cancer research, comparisons of tumour expression profiles to those from normal samples is challenging due to tissue heterogeneity (mixed cell populations). A specific example exists in a published colon cancer dataset, in which tissue heterogeneity was reported among the normal samples. In this paper, we show how to overcome or avoid the problem of using normal samples that do not derive from the same tissue of origin as the tumour. We advocate an exploratory unsupervised bootstrap analysis that can reveal unexpected and undesired, but strongly supported, clusters of samples that reflect tissue differences instead of tumour versus normal differences. All of the algorithms used in the analysis, including the maximum difference subset algorithm, unsupervised bootstrap analysis, pooled variance t-test for finding differentially expressed genes and the jackknife to reduce false positives, are incorporated into our online Gene Expression Data Analyzer ( http:// bioinformatics.upmc.edu/GE2/GEDA.html ).

High-resolution analysis of the mechanical behavior of tissue

NASA Astrophysics Data System (ADS)

Hudnut, Alexa W.; Armani, Andrea M.

2017-06-01

The mechanical behavior and properties of biomaterials, such as tissue, have been directly and indirectly connected to numerous malignant physiological states. For example, an increase in the Young's Modulus of tissue can be indicative of cancer. Due to the heterogeneity of biomaterials, it is extremely important to perform these measurements using whole or unprocessed tissue because the tissue matrix contains important information about the intercellular interactions and the structure. Thus, developing high-resolution approaches that can accurately measure the elasticity of unprocessed tissue samples is of great interest. Unfortunately, conventional elastography methods such as atomic force microscopy, compression testing, and ultrasound elastography either require sample processing or have poor resolution. In the present work, we demonstrate the characterization of unprocessed salmon muscle using an optical polarimetric elastography system. We compare the results of compression testing within different samples of salmon skeletal muscle with different numbers of collagen membranes to characterize differences in heterogeneity. Using the intrinsic collagen membranes as markers, we determine the resolution of the system when testing biomaterials. The device reproducibly measures the stiffness of the tissues at variable strains. By analyzing the amount of energy lost by the sample during compression, collagen membranes that are 500 μm in size are detected.

Effects of tissue fixation and dehydration on tendon collagen nanostructure.

PubMed

Turunen, Mikael J; Khayyeri, Hanifeh; Guizar-Sicairos, Manuel; Isaksson, Hanna

2017-09-01

Collagen is the most prominent protein in biological tissues. Tissue fixation is often required for preservation or sectioning of the tissue. This may affect collagen nanostructure and potentially provide incorrect information when analyzed after fixation. We aimed to unravel the effect of 1) ethanol and formalin fixation and 2) 24h air-dehydration on the organization and structure of collagen fibers at the nano-scale using small and wide angle X-ray scattering. Samples were divided into 4 groups: ethanol fixed, formalin fixed, and two untreated sample groups. Samples were allowed to air-dehydrate in handmade Kapton pockets during the measurements (24h) except for one untreated group. Ethanol fixation affected the collagen organization and nanostructure substantially and during 24h of dehydration dramatic changes were evident. Formalin fixation had minor effects on the collagen organization but after 12h of air-dehydration the spatial variation increased substantially, not evident in the untreated samples. Generally, collagen shrinkage and loss of alignment was evident in all samples during 24h of dehydration but the changes were subtle in all groups except the ethanol fixed samples. This study shows that tissue fixation needs to be chosen carefully in order to preserve the features of interest in the tissue. Copyright © 2017 Elsevier Inc. All rights reserved.

A validated UPLC-MS/MS method for the analysis of linezolid and a novel oxazolidinone derivative (PH027) in plasma and its application to tissue distribution study in rabbits.

PubMed

Hedaya, Mohsen A; Thomas, Vidhya; Abdel-Hamid, Mohamed E; Kehinde, Elijah O; Phillips, Oludotun A

2017-01-01

Linezolid is the first approved oxazolidinone antibacterial agent, whereas PH027 is a novel compound of the same class that exhibits good in vitro antibacterial activity. The objective of this study was to develop an UPLC-MS/MS assay for the analysis of linezolid and PH027 in plasma and to apply the method for comparative pharmacokinetic and tissue distribution studies of both compounds. Plasma samples and calibrators were extracted with diethyl ether after addition of the internal standard solution. After evaporation of the ether layer, the residue was reconstituted in mobile phase and injected into UPLC-MS/MS. The mobile phase consisted of 2mM ammonium acetate buffer solution and acetonitrile (70:30) at a flow rate of 0.2ml/min. Separation was achieved using UPLC BEH C 18 column, and quantitative determination of the analytes was performed using multiple-reaction monitoring (MRM) scanning mode. The method was validated by analyzing quality control tissue homogenate samples, and was applied to analyze tissue homogenate samples obtained following IV injections of linezolid and PH027 in rabbits. The developed UPLC-MS/MS method was linear in the concentration range of 50-5000ng/ml. Validation of the method proved that the method's precision, selectivity and stability were all within the acceptable limits. Linezolid and PH027 concentrations were accurately determined in the quality control tissue homogenate samples, and analysis of samples obtained following IV administration of the two compounds showed that the tissue to plasma concentration ratio of PH027 was higher than that of linezolid probably due to its higher lipophilicity. The developed UPLC-MS/MS method for the analysis of linezolid and PH027 in rabbit's plasma can accurately determine the concentrations of these compounds in different tissues. Copyright © 2016 Elsevier B.V. All rights reserved.

Multiview boosting digital pathology analysis of prostate cancer.

PubMed

Kwak, Jin Tae; Hewitt, Stephen M

2017-04-01

Various digital pathology tools have been developed to aid in analyzing tissues and improving cancer pathology. The multi-resolution nature of cancer pathology, however, has not been fully analyzed and utilized. Here, we develop an automated, cooperative, and multi-resolution method for improving prostate cancer diagnosis. Digitized tissue specimen images are obtained from 5 tissue microarrays (TMAs). The TMAs include 70 benign and 135 cancer samples (TMA1), 74 benign and 89 cancer samples (TMA2), 70 benign and 115 cancer samples (TMA3), 79 benign and 82 cancer samples (TMA4), and 72 benign and 86 cancer samples (TMA5). The tissue specimen images are segmented using intensity- and texture-based features. Using the segmentation results, a number of morphological features from lumens and epithelial nuclei are computed to characterize tissues at different resolutions. Applying a multiview boosting algorithm, tissue characteristics, obtained from differing resolutions, are cooperatively combined to achieve accurate cancer detection. In segmenting prostate tissues, the multiview boosting method achieved≥ 0.97 AUC using TMA1. For detecting cancers, the multiview boosting method achieved an AUC of 0.98 (95% CI: 0.97-0.99) as trained on TMA2 and tested on TMA3, TMA4, and TMA5. The proposed method was superior to single-view approaches, utilizing features from a single resolution or merging features from all the resolutions. Moreover, the performance of the proposed method was insensitive to the choice of the training dataset. Trained on TMA3, TMA4, and TMA5, the proposed method obtained an AUC of 0.97 (95% CI: 0.96-0.98), 0.98 (95% CI: 0.96-0.99), and 0.97 (95% CI: 0.96-0.98), respectively. The multiview boosting method is capable of integrating information from multiple resolutions in an effective and efficient fashion and identifying cancers with high accuracy. The multiview boosting method holds a great potential for improving digital pathology tools and research. Copyright © 2017 Elsevier B.V. All rights reserved.

High-throughput simultaneous analysis of RNA, protein, and lipid biomarkers in heterogeneous tissue samples.

PubMed

Reiser, Vladimír; Smith, Ryan C; Xue, Jiyan; Kurtz, Marc M; Liu, Rong; Legrand, Cheryl; He, Xuanmin; Yu, Xiang; Wong, Peggy; Hinchcliffe, John S; Tanen, Michael R; Lazar, Gloria; Zieba, Renata; Ichetovkin, Marina; Chen, Zhu; O'Neill, Edward A; Tanaka, Wesley K; Marton, Matthew J; Liao, Jason; Morris, Mark; Hailman, Eric; Tokiwa, George Y; Plump, Andrew S

2011-11-01

With expanding biomarker discovery efforts and increasing costs of drug development, it is critical to maximize the value of mass-limited clinical samples. The main limitation of available methods is the inability to isolate and analyze, from a single sample, molecules requiring incompatible extraction methods. Thus, we developed a novel semiautomated method for tissue processing and tissue milling and division (TMAD). We used a SilverHawk atherectomy catheter to collect atherosclerotic plaques from patients requiring peripheral atherectomy. Tissue preservation by flash freezing was compared with immersion in RNAlater®, and tissue grinding by traditional mortar and pestle was compared with TMAD. Comparators were protein, RNA, and lipid yield and quality. Reproducibility of analyte yield from aliquots of the same tissue sample processed by TMAD was also measured. The quantity and quality of biomarkers extracted from tissue prepared by TMAD was at least as good as that extracted from tissue stored and prepared by traditional means. TMAD enabled parallel analysis of gene expression (quantitative reverse-transcription PCR, microarray), protein composition (ELISA), and lipid content (biochemical assay) from as little as 20 mg of tissue. The mean correlation was r = 0.97 in molecular composition (RNA, protein, or lipid) between aliquots of individual samples generated by TMAD. We also demonstrated that it is feasible to use TMAD in a large-scale clinical study setting. The TMAD methodology described here enables semiautomated, high-throughput sampling of small amounts of heterogeneous tissue specimens by multiple analytical techniques with generally improved quality of recovered biomolecules.

A flow-proteometric platform for analyzing protein concentration (FAP): Proof of concept for quantification of PD-L1 protein in cells and tissues.

PubMed

Chou, Chao-Kai; Huang, Po-Jung; Tsou, Pei-Hsiang; Wei, Yongkun; Lee, Heng-Huan; Wang, Ying-Nai; Liu, Yen-Liang; Shi, Colin; Yeh, Hsin-Chih; Kameoka, Jun; Hung, Mien-Chie

2018-05-29

Protein expression level is critically related to the cell physiological function. However, current methodologies such as Western blot (WB) and Immunohistochemistry (IHC) in analyzing the protein level are rather semi-quantitative and without the information of actual protein concentration. We have developed a microfluidic technique termed a "flow-proteometric platform for analyzing protein concentration (FAP)" that can measure the concentration of a target protein in cells or tissues without the requirement of a calibration standard, e.g., the purified target molecules. To validate our method, we tested a number of control samples with known target protein concentrations and showed that the FAP measurement resulted in concentrations that well matched the actual concentrations in the control samples (coefficient of determination [R 2 ], 0.998), demonstrating a dynamic range of concentrations from 0.13 to 130 pM of a detection for 2 min. We successfully determined a biomarker protein (for predicting the treatment response of cancer immune check-point therapy) PD-L1 concentration in cancer cell lines (HeLa PD-L1 and MDA-MB-231) and breast cancer patient tumor tissues without any prior process of sample purification and standard line construction. Therefore, FAP is a simple, faster, and reliable method to measure the protein concentration in cells and tissues, which can support the conventional methods such as WB and IHC to determine the actual protein level. Copyright © 2018 Elsevier B.V. All rights reserved.

Automatic recognition and analysis of synapses. [in brain tissue

NASA Technical Reports Server (NTRS)

Ungerleider, J. A.; Ledley, R. S.; Bloom, F. E.

1976-01-01

An automatic system for recognizing synaptic junctions would allow analysis of large samples of tissue for the possible classification of specific well-defined sets of synapses based upon structural morphometric indices. In this paper the three steps of our system are described: (1) cytochemical tissue preparation to allow easy recognition of the synaptic junctions; (2) transmitting the tissue information to a computer; and (3) analyzing each field to recognize the synapses and make measurements on them.

[Transciptome among Mexicans: a large scale methodology to analyze the genetics expression profile of simultaneous samples in muscle, adipose tissue and lymphocytes obtained from the same individual].

PubMed

Bastarrachea, Raúl A; López-Alvarenga, Juan Carlos; Kent, Jack W; Laviada-Molina, Hugo A; Cerda-Flores, Ricardo M; Calderón-Garcidueñas, Ana Laura; Torres-Salazar, Amada; Torres-Salazar, Amanda; Nava-González, Edna J; Solis-Pérez, Elizabeth; Gallegos-Cabrales, Esther C; Cole, Shelley A; Comuzzie, Anthony G

2008-01-01

We describe the methodology used to analyze multiple transcripts using microarray techniques in simultaneous biopsies of muscle, adipose tissue and lymphocytes obtained from the same individual as part of the standard protocol of the Genetics of Metabolic Diseases in Mexico: GEMM Family Study. We recruited 4 healthy male subjects with BM1 20-41, who signed an informed consent letter. Subjects participated in a clinical examination that included anthropometric and body composition measurements, muscle biopsies (vastus lateralis) subcutaneous fat biopsies anda blood draw. All samples provided sufficient amplified RNA for microarray analysis. Total RNA was extracted from the biopsy samples and amplified for analysis. Of the 48,687 transcript targets queried, 39.4% were detectable in a least one of the studied tissues. Leptin was not detectable in lymphocytes, weakly expressed in muscle, but overexpressed and highly correlated with BMI in subcutaneous fat. Another example was GLUT4, which was detectable only in muscle and not correlated with BMI. Expression level concordance was 0.7 (p< 0.001) for the three tissues studied. We demonstrated the feasibility of carrying out simultaneous analysis of gene expression in multiple tissues, concordance of genetic expression in different tissues, and obtained confidence that this method corroborates the expected biological relationships among LEPand GLUT4. TheGEMM study will provide a broad and valuable overview on metabolic diseases, including obesity and type 2 diabetes.

Focused ion beam (FIB)/scanning electron microscopy (SEM) in tissue structural research.

PubMed

Leser, Vladka; Milani, Marziale; Tatti, Francesco; Tkalec, Ziva Pipan; Strus, Jasna; Drobne, Damjana

2010-10-01

The focused ion beam (FIB) and scanning electron microscope (SEM) are commonly used in material sciences for imaging and analysis of materials. Over the last decade, the combined FIB/SEM system has proven to be also applicable in the life sciences. We have examined the potential of the focused ion beam/scanning electron microscope system for the investigation of biological tissues of the model organism Porcellio scaber (Crustacea: Isopoda). Tissue from digestive glands was prepared as for conventional SEM or as for transmission electron microscopy (TEM). The samples were transferred into FIB/SEM for FIB milling and an imaging operation. FIB-milled regions were secondary electron imaged, back-scattered electron imaged, or energy dispersive X-ray (EDX) analyzed. Our results demonstrated that FIB/SEM enables simultaneous investigation of sample gross morphology, cell surface characteristics, and subsurface structures. The same FIB-exposed regions were analyzed by EDX to provide basic compositional data. When samples were prepared as for TEM, the information obtained with FIB/SEM is comparable, though at limited magnification, to that obtained from TEM. A combination of imaging, micro-manipulation, and compositional analysis appears of particular interest in the investigation of epithelial tissues, which are subjected to various endogenous and exogenous conditions affecting their structure and function. The FIB/SEM is a promising tool for an overall examination of epithelial tissue under normal, stressed, or pathological conditions.

Importance of tissue preparation methods in FTIR micro-spectroscopical analysis of biological tissues: 'traps for new users'.

PubMed

Zohdi, Vladislava; Whelan, Donna R; Wood, Bayden R; Pearson, James T; Bambery, Keith R; Black, M Jane

2015-01-01

Fourier Transform Infrared (FTIR) micro-spectroscopy is an emerging technique for the biochemical analysis of tissues and cellular materials. It provides objective information on the holistic biochemistry of a cell or tissue sample and has been applied in many areas of medical research. However, it has become apparent that how the tissue is handled prior to FTIR micro-spectroscopic imaging requires special consideration, particularly with regards to methods for preservation of the samples. We have performed FTIR micro-spectroscopy on rodent heart and liver tissue sections (two spectroscopically very different biological tissues) that were prepared by desiccation drying, ethanol substitution and formalin fixation and have compared the resulting spectra with that of fully hydrated freshly excised tissues. We have systematically examined the spectra for any biochemical changes to the native state of the tissue caused by the three methods of preparation and have detected changes in infrared (IR) absorption band intensities and peak positions. In particular, the position and profile of the amide I, key in assigning protein secondary structure, changes depending on preparation method and the lipid absorptions lose intensity drastically when these tissues are hydrated with ethanol. Indeed, we demonstrate that preserving samples through desiccation drying, ethanol substitution or formalin fixation significantly alters the biochemical information detected using spectroscopic methods when compared to spectra of fresh hydrated tissue. It is therefore imperative to consider tissue preparative effects when preparing, measuring, and analyzing samples using FTIR spectroscopy.

Evaporation process in histological tissue sections for neutron autoradiography.

PubMed

Espector, Natalia M; Portu, Agustina; Santa Cruz, Gustavo A; Saint Martin, Gisela

2018-05-01

The analysis of the distribution and density of nuclear tracks forming an autoradiography in a nuclear track detector (NTD) allows the determination of 10 B atoms concentration and location in tissue samples from Boron Neutron Capture Therapy (BNCT) protocols. This knowledge is of great importance for BNCT dosimetry and treatment planning. Tissue sections studied with this technique are obtained by cryosectioning frozen tissue specimens. After the slicing procedure, the tissue section is put on the NTD and the sample starts drying. The thickness varies from its original value allowing more particles to reach the detector and, as the mass of the sample decreases, the boron concentration in the sample increases. So in order to determine the concentration present in the hydrated tissue, the application of corrective coefficients is required. Evaporation mechanisms as well as various factors that could affect the process of mass variation are outlined in this work. Mass evolution for tissue samples coming from BDIX rats was registered with a semimicro analytical scale and measurements were analyzed with software developed to that end. Ambient conditions were simultaneously recorded, obtaining reproducible evaporation curves. Mathematical models found in the literature were applied for the first time to this type of samples and the best fit of the experimental data was determined. The correlation coefficients and the variability of the parameters were evaluated, pointing to Page's model as the one that best represented the evaporation curves. These studies will contribute to a more precise assessment of boron concentration in tissue samples by the Neutron Autoradiography technique.

Organochlorine compounds in streambed sediment and in biological tissue from streams and their relations to land use, central Arizona

USGS Publications Warehouse

Gebler, Joseph B.

2000-01-01

Streambed-sediment samples from 13 sites and biological-tissue samples from 11 sites in the Gila River Basin in central Arizona were analyzed for 32 organochlorine compounds in streambed sediment and 28 compounds in biological tissue during 1996 as part of the U.S. Geological Survey's National Water-Quality Assessment program. The objectives of the study were to determine the occurrence and distribution of organochlorine compounds and their relation to land use. Sampling sites were categorized on the basis of major land uses in the basin or the source of water in the stream. Because land uses were mixed or had changed over time, some land-use categories were combined. Sites were categorized as forest/rangeland (6), forest/urban (1), urban (4), or agricultural/urban (2). Thirteen organochlorine compounds were detected in streambed-sediment samples, and 10 were detected in tissue samples. The number of compounds found in streambed-sediment samples from individual sites ranged from 0 to 10, and the range for individual tissue samples was 0 to 7. Comparison of the number of detections in streambed-sediment samples to the number of detections in tissue samples from particular sites where both were sampled yielded five instances where more compounds were detected in streambed sediment, six instances where more compounds were detected in tissue, and five instances where the number of detections in streambed sediment and tissue were equal. The frequency of detection of particular compounds for sites where both streambed sediment and tissue were sampled resulted in five compounds being detected more frequently in streambed sediment, five more frequently in tissue, and three compounds that were equally frequent in streambed sediment and in tissue. Few contaminants were detected in samples from the forest/rangeland sites; greater numbers of compounds were detected at the urban sites and at the forest/urban site. The greatest number of compounds and the highest concentrations of many contaminants were detected at agriculture/urban sites. The compound detected most frequently in streambed-sediment and tissue samples was p,p'-DDE. Streambed-sediment guideline values for the protection of aquatic life for p,p'-DDE and total DDT were exceeded at both agricultural/urban sites, The streambed-sediment guideline value for the protection of aquatic life for total chlordane was exceeded at one agricultural/urban site, one urban site, and the forest/urban site. The streambed-sediment guideline value for the protection of aquatic life for total PCB’s was exceeded at one agricultural/urban site. Guideline values for the protection of fish-eating wildlife for total DDT and for toxaphene were exceeded only in samples from the two agricultural/urban sites. The guideline value for the protection of fish-eating wildlife for total PCB’s was equaled or exceeded in samples from two sites—one urban and one agricultural/urban site. Screening values established by the U.S. Environmental Protection Agency for the protection of human health for edible portions of fish were exceeded by total DDT and by toxaphene in fish-tissue samples from both agricultural/urban sites. The human-health criterion for total PCB’s was exceeded in two fish-tissue samples from an agricultural site and from an urban site. Tissue samples analyzed in this study were for whole fish, and thus, concentration data are not entirely comparable to the screening values of the U.S. Environmental Protection Agency. Because these exceedences were an order of magnitude above the criteria, however, it is possible that concentrations in the edible portions of fish from these locations could present a human- health risk. Analyses of samples of edible portions of fish from these locations would be needed to adequately assess the presence or absence of a human-health risk. The similarity of the results of this study to the results of other studies of organochlorine compounds in the environment suggests that there is a correlation between contaminants in sediment and biological-tissue samples and land uses. As with other studies of the occurrence and distribution of organochlorine contaminants in streambed sediments and biological tissue, this study shows that many organochlorine compounds continue to persist in the environment and thus could pose a threat to aquatic life, fish-eating wildlife, and possibly to humans who consume contaminated fish.

Cryopreservation of Cell/Scaffold Tissue-Engineered Constructs

PubMed Central

Costa, Pedro F.; Dias, Ana F.; Reis, Rui L.

2012-01-01

The aim of this work was to study the effect of cryopreservation over the functionality of tissue-engineered constructs, analyzing the survival and viability of cells seeded, cultured, and cryopreserved onto 3D scaffolds. Further, it also evaluated the effect of cryopreservation over the properties of the scaffold material itself since these are critical for the engineering of most tissues and in particular, tissues such as bone. For this purpose, porous scaffolds, namely fiber meshes based on a starch and poly(caprolactone) blend were seeded with goat bone marrow stem cells (GBMSCs) and cryopreserved for 7 days. Discs of the same material seeded with GBMSCs were also used as controls. After this period, these samples were analyzed and compared to samples collected before the cryopreservation process. The obtained results demonstrate that it is possible to maintain cell viability and scaffolds properties upon cryopreservation of tissue-engineered constructs based on starch scaffolds and goat bone marrow mesenchymal cells using standard cryopreservation methods. In addition, the outcomes of this study suggest that the greater porosity and interconnectivity of scaffolds favor the retention of cellular content and cellular viability during cryopreservation processes, when compared with nonporous discs. These findings indicate that it might be possible to prepare off-the-shelf engineered tissue substitutes and preserve them to be immediately available upon request for patients' needs. PMID:22676448

Spectroscopic analysis of bladder cancer tissues using Fourier transform infrared spectroscopy

NASA Astrophysics Data System (ADS)

Al-Muslet, Nafie A.; Ali, Essam E.

2012-03-01

Bladder cancer is one of the most common cancers in Africa. It takes several days to reach a diagnosis using histological examinations of specimens obtained by endoscope, which increases the medical expense. Recently, spectroscopic analysis of bladder cancer tissues has received considerable attention as a diagnosis technique due to its sensitivity to biochemical variations in the samples. This study investigated the use of Fourier transform infrared (FTIR) spectroscopy to analyze a number of bladder cancer tissues. Twenty-two samples were collected from 11 patients diagnosed with bladder cancer from different hospitals without any pretreatment. From each patient two samples were collected, one normal and another cancerous. FTIR spectrometer was used to differentiate between normal and cancerous bladder tissues via changes in spectra of these samples. The investigations detected obvious changes in the bands of proteins (1650, 1550 cm-1), lipids (2925, 2850 cm-1), and nucleic acid (1080, 1236 cm-1). The results show that FTIR spectroscopy is promising as a rapid, accurate, nondestructive, and easy to use alternative method for identification and diagnosis of bladder cancer tissues.

Occurrence and distribution of organochlorine pesticides, polychlorinated biphenyls, and trace elements in fish tissue in the lower Tennessee River basin, 1980-98

USGS Publications Warehouse

Knight, R.R.; Powell, J.R.

2001-01-01

The U.S. Geological Survey, as part of the National Water-Quality Assessment Program, evaluated the occurrence and distribution of organochlorine pesticides, polychlorinated biphenyls, and trace elements in fish tissue in samples collected in the lower Tennessee River Basin study unit. Fish tissue analysis provides a time-averaged measurement of contaminants as well as a direct measurement of the contaminants that bioaccumulate in fish tissue. Bioaccumulation of contaminants in fish tissue may result in concentrations that can affect human, wildlife, or aquatic health. Data for two types of tissue analyses were evaluated to assess the occurrence and distribution of contaminants: whole fish for organochlorine pesticides and polychlorinated biphenyls and fish fillets for organochlorine pesticides, polychlorinated biphenyls, and trace elements. The fish tissue data analyzed for this study cover an 18-year span including data collected in 1998 by the U.S. Geological Survey as part of the National Water-Quality Assessment Program; data collected from 1980 through 1997 by the Tennessee Valley Authority; and data collected from 1992 through 1997 by the Tennessee Department of Environment and Conservation. Concentration data for constituents that are on the U.S. Environmental Protection Agency Priority Pollutant List were summarized and compared against existing action levels or guidelines.From the list of organochlorine pesticide compounds analyzed, p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE), a breakdown product of dichlorodiphenyltrichloroethane (DDT), was the most commonly detected compound with detections at 83 percent of the sites sampled. Eleven p,p'-DDE samples exceeded action levels or guidelines with concentrations ranging from 0.20 to 12.8 milligrams per kilogram. Five other organochlorine compounds, p,p'-dichlorodiphenyldichloroethane (p,p'-DDD), dieldrin, endrin, chlordane, and polychlorinated biphenyls, also exceeded action levels and guidelines, but the detection frequencies at sampling sites generally were less than 70 percent. Mercury, the only trace element to exceed a guideline, was detected at 51 of 102 sites sampled for trace elements. Selenium was detected in fish fillet samples from 70 of 102 sites sampled, which was more sites than for any other trace element; however, selenium did not exceed the 50 micrograms per gram U.S. Environmental Protection Agency screening criteria. Arsenic and cadmium also were detected at 44 and 54 percent of the sampling sites, respectively.

Monitoring temporal microstructural variations of skeletal muscle tissues by multispectral Mueller matrix polarimetry

NASA Astrophysics Data System (ADS)

Dong, Yang; He, Honghui; He, Chao; Ma, Hui

2017-02-01

Mueller matrix polarimetry is a powerful tool for detecting microscopic structures, therefore can be used to monitor physiological changes of tissue samples. Meanwhile, spectral features of scattered light can also provide abundant microstructural information of tissues. In this paper, we take the 2D multispectral backscattering Mueller matrix images of bovine skeletal muscle tissues, and analyze their temporal variation behavior using multispectral Mueller matrix parameters. The 2D images of the Mueller matrix elements are reduced to the multispectral frequency distribution histograms (mFDHs) to reveal the dominant structural features of the muscle samples more clearly. For quantitative analysis, the multispectral Mueller matrix transformation (MMT) parameters are calculated to characterize the microstructural variations during the rigor mortis and proteolysis processes of the skeletal muscle tissue samples. The experimental results indicate that the multispectral MMT parameters can be used to judge different physiological stages for bovine skeletal muscle tissues in 24 hours, and combining with the multispectral technique, the Mueller matrix polarimetry and FDH analysis can monitor the microstructural variation features of skeletal muscle samples. The techniques may be used for quick assessment and quantitative monitoring of meat qualities in food industry.

Determination of oxidation state of iron in normal and pathologically altered human aortic valves

NASA Astrophysics Data System (ADS)

Czapla-Masztafiak, J.; Lis, G. J.; Gajda, M.; Jasek, E.; Czubek, U.; Bolechała, F.; Borca, C.; Kwiatek, W. M.

2015-12-01

In order to investigate changes in chemical state of iron in normal and pathologically altered human aortic valves X-ray absorption spectroscopy was applied. Since Fe is suspected to play detrimental role in aortic valve stenosis pathogenesis the oxidation state of this element has been determined. The experimental material consisted of 10 μm sections of valves excised during routine surgery and from autopsies. The experiment was performed at the MicroXAS beamline of the SLS synchrotron facility in Villigen (Switzerland). The Fe K-edge XANES spectra obtained from tissue samples were carefully analyzed and compared with the spectra of reference compounds containing iron in various chemical structures. The analysis of absorption edge position and shape of the spectra revealed that both chemical forms of iron are presented in valve tissue but Fe3+ is the predominant form. Small shift of the absorption edge toward higher energy in the spectra from stenotic valve samples indicates higher content of the Fe3+ form in pathological tissue. Such a phenomenon suggests the role of Fenton reaction and reactive oxygen species in the etiology of aortic valve stenosis. The comparison of pre-edge regions of XANES spectra for control and stenotic valve tissue confirmed no differences in local symmetry or spin state of iron in analyzed samples.

Digital detection of multiple minority mutants and expression levels of multiple colorectal cancer-related genes using digital-PCR coupled with bead-array.

PubMed

Huang, Huan; Li, Shuo; Sun, Lizhou; Zhou, Guohua

2015-01-01

To simultaneously analyze mutations and expression levels of multiple genes on one detection platform, we proposed a method termed "multiplex ligation-dependent probe amplification-digital amplification coupled with hydrogel bead-array" (MLPA-DABA) and applied it to diagnose colorectal cancer (CRC). CRC cells and tissues were sampled to extract nucleic acid, perform MLPA with sequence-tagged probes, perform digital emulsion polymerase chain reaction (PCR), and produce a hydrogel bead-array to immobilize beads and form a single bead layer on the array. After hybridization with fluorescent probes, the number of colored beads, which reflects the abundance of expressed genes and the mutation rate, was counted for diagnosis. Only red or green beads occurred on the chips in the mixed samples, indicating the success of single-molecule PCR. When a one-source sample was analyzed using mixed MLPA probes, beads of only one color occurred, suggesting the high specificity of the method in analyzing CRC mutation and gene expression. In gene expression analysis of a CRC tissue from one CRC patient, the mutant percentage was 3.1%, and the expression levels of CRC-related genes were much higher than those of normal tissue. The highly sensitive MLPA-DABA succeeds in the relative quantification of mutations and gene expressions of exfoliated cells in stool samples of CRC patients on the same chip platform. MLPA-DABA coupled with hydrogel bead-array is a promising method in the non-invasive diagnosis of CRC.

A comparison of sample preparation strategies for biological tissues and subsequent trace element analysis using LA-ICP-MS.

PubMed

Bonta, Maximilian; Török, Szilvia; Hegedus, Balazs; Döme, Balazs; Limbeck, Andreas

2017-03-01

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is one of the most commonly applied methods for lateral trace element distribution analysis in medical studies. Many improvements of the technique regarding quantification and achievable lateral resolution have been achieved in the last years. Nevertheless, sample preparation is also of major importance and the optimal sample preparation strategy still has not been defined. While conventional histology knows a number of sample pre-treatment strategies, little is known about the effect of these approaches on the lateral distributions of elements and/or their quantities in tissues. The technique of formalin fixation and paraffin embedding (FFPE) has emerged as the gold standard in tissue preparation. However, the potential use for elemental distribution studies is questionable due to a large number of sample preparation steps. In this work, LA-ICP-MS was used to examine the applicability of the FFPE sample preparation approach for elemental distribution studies. Qualitative elemental distributions as well as quantitative concentrations in cryo-cut tissues as well as FFPE samples were compared. Results showed that some metals (especially Na and K) are severely affected by the FFPE process, whereas others (e.g., Mn, Ni) are less influenced. Based on these results, a general recommendation can be given: FFPE samples are completely unsuitable for the analysis of alkaline metals. When analyzing transition metals, FFPE samples can give comparable results to snap-frozen tissues. Graphical abstract Sample preparation strategies for biological tissues are compared with regard to the elemental distributions and average trace element concentrations.

Proteomic analysis of formalin-fixed paraffin embedded tissue by MALDI imaging mass spectrometry

PubMed Central

Casadonte, Rita; Caprioli, Richard M

2012-01-01

Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informational resource for proteomic studies. Multiple FFPE core biopsies can be assembled in a single block to form tissue microarrays (TMAs). We describe a protocol for analyzing protein in FFPE -TMAs using matrix-assisted laser desorption/ionization (MAL DI) imaging mass spectrometry (IMS). The workflow incorporates an antigen retrieval step following deparaffinization, in situ trypsin digestion, matrix application and then mass spectrometry signal acquisition. The direct analysis of FFPE -TMA tissue using IMS allows direct analysis of multiple tissue samples in a single experiment without extraction and purification of proteins. The advantages of high speed and throughput, easy sample handling and excellent reproducibility make this technology a favorable approach for the proteomic analysis of clinical research cohorts with large sample numbers. For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis. PMID:22011652

Evaluation of two outlier-detection-based methods for detecting tissue-selective genes from microarray data.

PubMed

Kadota, Koji; Konishi, Tomokazu; Shimizu, Kentaro

2007-05-01

Large-scale expression profiling using DNA microarrays enables identification of tissue-selective genes for which expression is considerably higher and/or lower in some tissues than in others. Among numerous possible methods, only two outlier-detection-based methods (an AIC-based method and Sprent's non-parametric method) can treat equally various types of selective patterns, but they produce substantially different results. We investigated the performance of these two methods for different parameter settings and for a reduced number of samples. We focused on their ability to detect selective expression patterns robustly. We applied them to public microarray data collected from 36 normal human tissue samples and analyzed the effects of both changing the parameter settings and reducing the number of samples. The AIC-based method was more robust in both cases. The findings confirm that the use of the AIC-based method in the recently proposed ROKU method for detecting tissue-selective expression patterns is correct and that Sprent's method is not suitable for ROKU.

Analysis of Lung Tissue Using Ion Beams

NASA Astrophysics Data System (ADS)

Alvarez, J. L.; Barrera, R.; Miranda, J.

2002-08-01

In this work a comparative study is presented of the contents of metals in lung tissue from healthy patients and with lung cancer, by means of two analytical techniques: Particle Induced X-ray Emission (PIXE) and Rutherford Backscattering Spectrometry (RBS). The samples of cancerous tissue were taken from 26 autopsies made to individuals died in the National Institute of Respiratory Disease (INER), 22 of cancer and 4 of other non-cancer biopsies. When analyzing the entirety of the samples, in the cancerous tissues, there were increments in the concentrations of S (4%), K (635%), Co (85%) and Cu (13%). Likewise, there were deficiencies in the concentrations of Cl (59%), Ca (6%), Fe (26%) and Zn (7%). Only in the cancerous tissues there were appearances of P, Ca, Ti, V, Cr, Mn, Ni, Br and Sr. The tissue samples were classified according to cancer types (adenocarcinomas, epidermoides and of small cell carcinoma), personal habits (smokers and alcoholic), genetic predisposition and residence place. There was a remarkable decrease in the concentration of Ca and a marked increment in the Cu in the epidermoide tissue samples with regard to those of adenocarcinoma or of small cells cancer. Also, decrements were detected in K and increments of Fe, Co and Cu in the sample belonging to people that resided in Mexico City with regard to those that resided in the State of Mexico.

Comparative Testis Tissue Proteomics Using 2-Dye Versus 3-Dye DIGE Analysis.

PubMed

Holland, Ashling

2018-01-01

Comparative tissue proteomics aims to analyze alterations of the proteome in response to a stimulus. Two-dimensional difference gel electrophoresis (2D-DIGE) is a modified and advanced form of 2D gel electrophoresis. DIGE is a powerful biochemical method that compares two or three protein samples on the same analytical gel, and can be used to establish differentially expressed protein levels between healthy normal and diseased pathological tissue sample groups. Minimal DIGE labeling can be used via a 2-dye system with Cy3 and Cy5 or a 3-dye system with Cy2, Cy3, and Cy5 to fluorescently label samples with CyDye flours pre-electrophoresis. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization. This form of quantitative high-resolution proteomics facilitates the comparative analysis and evaluation of tissue protein compositions. Comparing tissue groups under different conditions is crucially important for advancing the biomedical field by characterization of cellular processes, understanding pathophysiological development and tissue biomarker discovery. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of 2-dye and 3-dye DIGE minimal labeling.

Using Digital Image Correlation to Characterize Local Strains on Vascular Tissue Specimens.

PubMed

Zhou, Boran; Ravindran, Suraj; Ferdous, Jahid; Kidane, Addis; Sutton, Michael A; Shazly, Tarek

2016-01-24

Characterization of the mechanical behavior of biological and engineered soft tissues is a central component of fundamental biomedical research and product development. Stress-strain relationships are typically obtained from mechanical testing data to enable comparative assessment among samples and in some cases identification of constitutive mechanical properties. However, errors may be introduced through the use of average strain measures, as significant heterogeneity in the strain field may result from geometrical non-uniformity of the sample and stress concentrations induced by mounting/gripping of soft tissues within the test system. When strain field heterogeneity is significant, accurate assessment of the sample mechanical response requires measurement of local strains. This study demonstrates a novel biomechanical testing protocol for calculating local surface strains using a mechanical testing device coupled with a high resolution camera and a digital image correlation technique. A series of sample surface images are acquired and then analyzed to quantify the local surface strain of a vascular tissue specimen subjected to ramped uniaxial loading. This approach can improve accuracy in experimental vascular biomechanics and has potential for broader use among other native soft tissues, engineered soft tissues, and soft hydrogel/polymeric materials. In the video, we demonstrate how to set up the system components and perform a complete experiment on native vascular tissue.

TOFSIMS-P: a web-based platform for analysis of large-scale TOF-SIMS data.

PubMed

Yun, So Jeong; Park, Ji-Won; Choi, Il Ju; Kang, Byeongsoo; Kim, Hark Kyun; Moon, Dae Won; Lee, Tae Geol; Hwang, Daehee

2011-12-15

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has been a useful tool to profile secondary ions from the near surface region of specimens with its high molecular specificity and submicrometer spatial resolution. However, the TOF-SIMS analysis of even a moderately large size of samples has been hampered due to the lack of tools for automatically analyzing the huge amount of TOF-SIMS data. Here, we present a computational platform to automatically identify and align peaks, find discriminatory ions, build a classifier, and construct networks describing differential metabolic pathways. To demonstrate the utility of the platform, we analyzed 43 data sets generated from seven gastric cancer and eight normal tissues using TOF-SIMS. A total of 87 138 ions were detected from the 43 data sets by TOF-SIMS. We selected and then aligned 1286 ions. Among them, we found the 66 ions discriminating gastric cancer tissues from normal ones. Using these 66 ions, we then built a partial least square-discriminant analysis (PLS-DA) model resulting in a misclassification error rate of 0.024. Finally, network analysis of the 66 ions showed disregulation of amino acid metabolism in the gastric cancer tissues. The results show that the proposed framework was effective in analyzing TOF-SIMS data from a moderately large size of samples, resulting in discrimination of gastric cancer tissues from normal tissues and identification of biomarker candidates associated with the amino acid metabolism.

Histopathology Image Analysis in Two Long-Term Animal Experiments with Helical Flow Total Artificial Heart.

PubMed

Wotke, Jiri; Homolka, Pavel; Vasku, Jaromír; Dobsak, Petr; Palanova, Petra; Mrkvicova, Veronika; Konecny, Petr; Soska, Vladimir; Pohanka, Michal; Novakova, Marie; Yurimoto, Terumi; Saito, Itsuro; Inoue, Yusuke; Isoyama, Takashi; Abe, Yusuke

2016-12-01

Histopathological analysis can provide important information in long-term experiments with total artificial heart (TAH). Recently, a new type of blood pump, the helical flow total artificial heart (HF-TAH) was developed. This study aimed to investigate the changes in selected vital organs in animal experiments with implanted HF-TAH. Samples from lung, liver, and kidneys from two female goats (No. 1301 and No. 1304) with implanted HF-TAH were analyzed. Tissue samples were fixed in 10% formaldehyde and 4 µm thick transverse sections were stained with hematoxylin-eosin (HE). Additional staining was done for detection of connective tissue (Masson-Goldner stain) and for detection of iron (hemosiderin) deposits (Perls stain). Sections were scanned at 100× and 500× magnification with a light microscope. Experiment no. 1301 survived 100 days (cause of termination was heavy damage of the right pump); experimental goat no.1304 survived 68 days and was sacrificed due to severe right hydrodynamic bearing malfunction. Histopathological analysis of liver samples proved signs of chronic venostasis with limited focal necrotic zones. Dilated tubules, proteinaceous material in tubular lumen, and hemosiderin deposits were detected in kidney samples. Contamination of the organs by embolized micro-particles was suspected at the autopsy after discovery of visible damage (scratches) of the pump impeller surface (made from titanium alloy) in both experiments. Sporadic deposits of foreign micro-particles (presumably titanium) were observed in most of the analyzed parenchymal organs. However, the described deposits were not in direct connection with inflammatory reactions in the analyzed tissues. Histopathological analysis showed the presence of minimal contamination of the lung, kidney, and liver tissue samples by foreign material (titanium very likely). The analysis showed only limited pathological changes, especially in liver and kidneys, which might be attributed to the influence of artificial perfusion often observed in chronic TAH experiments. © 2016 Wiley Periodicals, Inc. and International Center for Artificial Organs and Transplantation.

Organochlorine compounds and trace elements in fish tissue and bed sediments in the lower Snake River basin, Idaho and Oregon

USGS Publications Warehouse

Clark, Gregory M.; Maret, Terry R.

1998-01-01

Fish-tissue and bed-sediment samples were collected to determine the occurrence and distribution of organochlorine compounds and trace elements in the lower Snake River Basin. Whole-body composite samples of suckers and carp from seven sites were analyzed for organochlorine compounds; liver samples were analyzed for trace elements. Fillets from selected sportfish were analyzed for organochlorine compounds and trace elements. Bed-sediment samples from three sites were analyzed for organochlorine compounds and trace elements. Twelve different organochlorine compounds were detected in 14 fish-tissue samples. All fish-tissue samples contained DDT or its metabolites. Concentrations of total DDT ranged from 11 micrograms per kilogram wet weight in fillets of yellow perch from C.J. Strike Reservoir to 3,633 micrograms per kilogram wet weight in a whole-body sample of carp from Brownlee Reservoir at Burnt River. Total DDT concentrations in whole-body samples of sucker and carp from the Snake River at C.J. Strike Reservoir, Snake River at Swan Falls, Snake River at Nyssa, and Brownlee Reservoir at Burnt River exceeded criteria established for the protection of fish-eating wildlife. Total PCB concentrations in a whole-body sample of carp from Brownlee Reservoir at Burnt River also exceeded fish-eating wildlife criteria. Concentrations of organochlorine compounds in whole-body samples, in general, were larger than concentrations in sportfish fillets. However, concentrations of dieldrin and total DDT in fillets of channel catfish from the Snake River at Nyssa and Brownlee Reservoir at Burnt River, and concentrations of total DDT in fillets of smallmouth bass and white crappie from Brownlee Reservoir at Burnt River exceeded a cancer risk screening value of 10-6 established by the U.S. Environmental Protection Agency. Concentrations of organochlorine compounds in bed sediment were smaller than concentrations in fish tissue. Concentrations of p,p'DDE, the only compound detected in all three bed-sediment samples, ranged from 1.1 micrograms per kilogram dry weight in C.J. Strike Reservoir to 11 micrograms per kilogram dry weight in Brownlee Reservoir at Burnt River. Data from this study, compared with data collected in the upper Snake River Basin from 1992 to 1994, indicates that, in general, organochlorine concentrations in fish tissue and bed sediment increased from the headwaters of the Snake River in Wyoming downstream to Brownlee Reservoir. The largest trace-element concentrations in fish tissue were in liver samples from carp from Brownlee Reservoir at Burnt River and suckers from the Boise River near Twin Springs. Concentrations of most trace elements were larger in livers than in the sport- fish fillets. However, mercury concentrations were generally larger in the sportfish fillets; they ranged from 0.08 microgram per gram wet weight in yellow perch from C.J. Strike Reservoir to 0.32 microgram per gram wet weight in channel catfish from Brownlee Reservoir at Burnt River. None of the trace-element concentrations in fillets exceeded median international standards or U.S. Food and Drug Administration action levels. Large trace-element concentrations in the upper Snake River Basin were reported in liver samples from suckers from headwater streams, probably a result of historical mining and weathering of metal-rich rocks. Concentrations of most trace elements in the bed-sediment samples were largest in Brownlee Reservoir at Mountain Man Lodge. Concentrations of arsenic, cadmium, chromium, copper, nickel, and zinc in bed sediment from the Mountain Man Lodge site exceeded either the threshold effect level or probable effect level established by the Canadian Government for the protection of benthic life. Arsenic, chromium, copper, and nickel concentrations in bed sediment from Brownlee Reservoir at Burnt River and chromium, copper, and nickel in bed sediment from C.J. Strike Reservoir also exceeded the threshold effect level.

Relationship of In Vivo MR Parameters to Histopathological and Molecular Characteristics of Newly Diagnosed, Nonenhancing Lower-Grade Gliomas.

PubMed

Luks, Tracy L; McKnight, Tracy Richmond; Jalbert, Llewellyn E; Williams, Aurelia; Neill, Evan; Lobo, Khadjia A; Persson, Anders I; Perry, Arie; Phillips, Joanna J; Molinaro, Annette M; Chang, Susan M; Nelson, Sarah J

2018-06-05

The goal of this research was to elucidate the relationship between WHO 2016 molecular classifications of newly diagnosed, nonenhancing lower grade gliomas (LrGG), tissue sample histopathology, and magnetic resonance (MR) parameters derived from diffusion, perfusion, and 1 H spectroscopic imaging from the tissue sample locations and the entire tumor. A total of 135 patients were scanned prior to initial surgery, with tumor cellularity scores obtained from 88 image-guided tissue samples. MR parameters were obtained from corresponding sample locations, and histograms of normalized MR parameters within the T2 fluid-attenuated inversion recovery lesion were analyzed in order to evaluate differences between subgroups. For tissue samples, higher tumor scores were related to increased normalized apparent diffusion coefficient (nADC), lower fractional anisotropy (nFA), lower cerebral blood volume (nCBV), higher choline (nCho), and lower N-acetylaspartate (nNAA). Within the T2 lesion, higher tumor grade was associated with higher nADC, lower nFA, and higher Cho to NAA index. Pathological analysis confirmed that diffusion and metabolic parameters increased and perfusion decreased with tumor cellularity. This information can be used to select targets for tissue sampling and to aid in making decisions about treating residual disease. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Water-quality assessment of the Potomac River Basin: analysis of available pesticide data, 1972-1990

USGS Publications Warehouse

Zappia, Humbert; Fisher, Gary T.

1997-01-01

A study of available data for the period from 1972 to 1990 was conducted to characterize the occurrence and distribution of pesticides in sur-face water, bottom material, ground water, and fish tissue in the Potomac River Basin. The study was conducted by the Potomac River study unit of the U.S. Geological Survey?s National Water-Quality Assessment (NAWQA) program. Exist-ing data coverage was evaluated to guide future data-collection activities. Data from computer data bases and from published and unpublished reports were obtained from local, State, and Fed-eral agencies in the four Potomac River Basin states and the District of Columbia. Data are available for all environmental media, but geo-graphic and temporal coverage are limited. Clusters of data occur in the north-central parts of the basin, with numerous samples at discrete loca-tions in the Shenandoah and Monocacy River Basins, along the mainstem Potomac River, in the Washington, D.C., area, and in streams along the Potomac Estuary. Much of the available surface-water and bottom-material data are from the ear-lier years of the period of interest, the ground-water data are from the middle years, and the fish-tissue data are distributed over much of the period. Overall, temporal coverage is not sufficient for analysis of trends. Comparisons between different sample media are possible in some areas of the Potomac River Basin, particularly in the northern end of the Great Valley. Residual concentrations of some pesticides have been found in surface water, bottom mate-rial, ground water, and fish tissue. Samples have been analyzed for a total of at least 69 pesticides and related compounds in surface water, bottom material, ground water, and fish tissue. Most con-centrations of the pesticides analyzed during the period from 1972 to 1990 were less than or equal to reporting limits. For surface-water samples, 13 out of 41 pes-ticides and related compounds analyzed had concentrations equal to or greater than the report-ing limits. Compounds reported in surface water included 2,4-D, atrazine, aldrin, chlordane, DDT and related compounds, dieldrin, endrin, lindane, prometone, prometryne, and simazine. For bottom material samples, 19 of 31 pesticides and related compounds analyzed had concentrations equal to or greater than the reporting limits. Compounds reported in bottom material included aldrin, chlor-dane, DDT and related compounds, diazinon, dieldrin, endosulfan, endrin, ethion, heptachlor, heptachlor epoxide, lindane, parathion, and tox-aphene. In ground-water samples, 14 of 39 pesticides and related compounds analyzed had concentrations equal to or greater than the report-ing limits. Compounds reported in ground water included 2,4-D, atrazine, chlordane, cyanazine, DDT and related compounds, diazinon, dieldrin, endosulfan, endrin, heptachlor epoxide, malathion, methyl parathion, simazine. For fish- tissue sam-ples, 30 of the 37 pesticides and related compounds analyzed had concentrations equal to or greater than the reporting limits. Compounds reported included aldrin, chlorpyrifos, dacthal, dieldrin, endrin, HCB, heptachlor, heptachlor epoxide, methoxychlor, mirex, PCA, toxaphene, and those compounds related to chlordane, DDT, and lindane.

Microgravity

NASA Image and Video Library

1998-10-10

Dr. Harry Mahtani analyzes the gas content of nutrient media from Bioreactor used in research on human breast cancer. NASA's Marshall Space Flight Center (MSFC) is sponsoring research with Bioreactors, rotating wall vessels designed to grow tissue samples in space, to understand how breast cancer works. This ground-based work studies the growth and assembly of human mammary epithelial cells (HMEC) from breast cancer susceptible tissue. Radiation can make the cells cancerous, thus allowing better comparisons of healthy vs. tunourous tissues.

Office-based narrow band imaging-guided flexible laryngoscopy tissue sampling: A cost-effectiveness analysis evaluating its impact on Taiwanese health insurance program.

PubMed

Fang, Tuan-Jen; Li, Hsueh-Yu; Liao, Chun-Ta; Chiang, Hui-Chen; Chen, I-How

2015-07-01

Narrow band imaging (NBI)-guided flexible laryngoscopy tissue sampling for laryngopharyngeal lesions is a novel technique. Patients underwent the procedure in an office-based setting without being sedated, which is different from the conventional technique performed using direct laryngoscopy. Although the feasibility and effects of this procedure were established, its financial impact on the institution and Taiwanese National Health Insurance program was not determined. This is a retrospective case-control study. From May 2010 to April 2011, 20 consecutive patients who underwent NBI flexible laryngoscopy tissue sampling were recruited. During the same period, another 20 age-, sex-, and lesion-matched cases were enrolled in the control group. The courses for procedures and financial status were analyzed and compared between groups. Office-based NBI flexible laryngoscopy tissue sampling procedure took 27 minutes to be completed, while 191 minutes were required for the conventional technique. Average reimbursement for each case was New Taiwan Dollar (NT$)1264 for patients undergoing office-based NBI flexible laryngoscopy tissue sampling, while NT$10,913 for those undergoing conventional direct laryngoscopy in the operation room (p < 0.001). The institution suffered a loss of at least NT$690 when performing NBI flexible laryngoscopy tissue sampling. Office-based NBI flexible laryngoscopy tissue sampling is a cost-saving procedure for patients and the Taiwanese National Health Insurance program. It also saves the procedure time. However, the net financial loss for the institution and physician would limit its popularization unless reimbursement patterns are changed. Copyright © 2013. Published by Elsevier B.V.

Comparative analysis of laparoscopic and ultrasound-guided biopsy methods for gene expression analysis in transgenic goats.

PubMed

Melo, C H; Sousa, F C; Batista, R I P T; Sanchez, D J D; Souza-Fabjan, J M G; Freitas, V J F; Melo, L M; Teixeira, D I A

2015-07-31

The present study aimed to compare laparoscopic (LP) and ultrasound-guided (US) biopsy methods to obtain either liver or splenic tissue samples for ectopic gene expression analysis in transgenic goats. Tissue samples were collected from human granulocyte colony stimulating factor (hG-CSF)-transgenic bucks and submitted to real-time PCR for the endogenous genes (Sp1, Baff, and Gapdh) and the transgene (hG-CSF). Both LP and US biopsy methods were successful in obtaining liver and splenic samples that could be analyzed by PCR (i.e., sufficient sample sizes and RNA yield were obtained). Although the number of attempts made to obtain the tissue samples was similar (P > 0.05), LP procedures took considerably longer than the US method (P = 0.03). Finally, transgene transcripts were not detected in spleen or liver samples. Thus, for the phenotypic characterization of a transgenic goat line, investigation of ectopic gene expression can be made successfully by LP or US biopsy, avoiding the traditional approach of euthanasia.

Distribution and elimination of [14C] sarafloxacin hydrochloride from tissues of juvenile channel catfish (Ictalurus punctatus)

USGS Publications Warehouse

Gingerich, W.H.; Meinertz, J.R.; Dawson, V.K.; Gofus, J.E.; Delaney, L.J.; Bunnell, P.R.

1995-01-01

The distribution and loss of radioactivity from tissues were determined in 60 juvenile channel catfish (Ictalurus punctatus) following oral dosing with the candidate fish therapeutant Sarafin® ([14C] sarafloxacin hydrochloride) at 10 mg/kg for 5 consecutive days. Twelve groups of 5 fish each were sampled at selected times ranging from 3 to 240 h after the last dose was administered, The concentration and content of sarafloxacin-equivalent activity was determined in liver, gallbladder, kidney, skin, and skinless fillet by sample oxidation and liquid scintillation counting; content of sarafloxacin-equivalent activity was determined in stomach and anterior and posterior intestines, Skinless fillet tissues were also analyzed for sarafloxacin and for potential metabolites by gradient-elution high-performance liquid chromatography (HPLC) with in-line radiometric and fluorescence detection, Loss of radioactivity from the whole body conformed to a bimodal elimination pattern with a rapid initial phase (t1/2=11 h) and a slower secondary phase (t1/2=222 h). Tissue and contents of the gastrointestinal tract (i.e. stomach and anterior and posterior intestines) were a principal depot of activity during the first four sample times (3, 6, 12, and 24 h); the combined head, skeleton, and fins (i.e. residual carcass) were the principal depot of activity in samples taken after 24 h. Of those tissues sampled 3 h after the last dose, relative sarafloxacin concentration was greatest in the liver (4.06 μg equivalents/g) and least in the residual carcass (1.13 μg equivalents/g), Intermediate concentrations were found in the kidney (2.04 μg equivalents/g), skinless fillet (1.71 μg equivalents/ g), and the skin (1.51 μg equivalents/g). Concentrations of sarafloxacin-equivalent residues in edible skinless fillet were consistently among the lowest of all tissues examined. The highest mean concentration of parent-equivalent material in the fillet tissue was found 12 h after administration of the last dose (2.27 μg equivalents/g) and declined thereafter, Sarafloxacin constituted between 80 and 90% of the extractable radioactive residues from the fillet homogenates. No other peaks were resolved in any of the fillet tissue samples analyzed by HPLC with in-line radiometric detection.

Automated Morphological and Morphometric Analysis of Mass Spectrometry Imaging Data: Application to Biomarker Discovery

NASA Astrophysics Data System (ADS)

Picard de Muller, Gaël; Ait-Belkacem, Rima; Bonnel, David; Longuespée, Rémi; Stauber, Jonathan

2017-12-01

Mass spectrometry imaging datasets are mostly analyzed in terms of average intensity in regions of interest. However, biological tissues have different morphologies with several sizes, shapes, and structures. The important biological information, contained in this highly heterogeneous cellular organization, could be hidden by analyzing the average intensities. Finding an analytical process of morphology would help to find such information, describe tissue model, and support identification of biomarkers. This study describes an informatics approach for the extraction and identification of mass spectrometry image features and its application to sample analysis and modeling. For the proof of concept, two different tissue types (healthy kidney and CT-26 xenograft tumor tissues) were imaged and analyzed. A mouse kidney model and tumor model were generated using morphometric - number of objects and total surface - information. The morphometric information was used to identify m/z that have a heterogeneous distribution. It seems to be a worthwhile pursuit as clonal heterogeneity in a tumor is of clinical relevance. This study provides a new approach to find biomarker or support tissue classification with more information. [Figure not available: see fulltext.

An evaluation of a reagentless method for the determination of total mercury in aquatic life

USGS Publications Warehouse

Haynes, Sekeenia; Gragg, Richard D.; Johnson, Elijah; Robinson, Larry; Orazio, Carl E.

2006-01-01

Multiple treatment (i.e., drying, chemical digestion, and oxidation) steps are often required during preparation of biological matrices for quantitative analysis of mercury; these multiple steps could potentially lead to systematic errors and poor recovery of the analyte. In this study, the Direct Mercury Analyzer (Milestone Inc., Monroe, CT) was utilized to measure total mercury in fish tissue by integrating steps of drying, sample combustion and gold sequestration with successive identification using atomic absorption spectrometry. We also evaluated the differences between the mercury concentrations found in samples that were homogenized and samples with no preparation. These results were confirmed with cold vapor atomic absorbance and fluorescence spectrometric methods of analysis. Finally, total mercury in wild captured largemouth bass (n = 20) were assessed using the Direct Mercury Analyzer to examine internal variability between mercury concentrations in muscle, liver and brain organs. Direct analysis of total mercury measured in muscle tissue was strongly correlated with muscle tissue that was homogenized before analysis (r = 0.81, p < 0.0001). Additionally, results using this integrated method compared favorably (p < 0.05) with conventional cold vapor spectrometry with atomic absorbance and fluorescence detection methods. Mercury concentrations in brain were significantly lower than concentrations in muscle (p < 0.001) and liver (p < 0.05) tissues. This integrated method can measure a wide range of mercury concentrations (0-500 ??g) using small sample sizes. Total mercury measurements in this study are comparative to the methods (cold vapor) commonly used for total mercury analysis and are devoid of laborious sample preparation and expensive hazardous waste. ?? Springer 2006.

Conductive carbon tape used for support and mounting of both whole animal and fragile heat-treated tissue sections for MALDI MS imaging and quantitation.

PubMed

Goodwin, Richard J A; Nilsson, Anna; Borg, Daniel; Langridge-Smith, Pat R R; Harrison, David J; Mackay, C Logan; Iverson, Suzanne L; Andrén, Per E

2012-08-30

Analysis of whole animal tissue sections by MALDI MS imaging (MSI) requires effective sample collection and transfer methods to allow the highest quality of in situ analysis of small or hard to dissect tissues. We report on the use of double-sided adhesive conductive carbon tape during whole adult rat tissue sectioning of carboxymethyl cellulose (CMC) embedded animals, with samples mounted onto large format conductive glass and conductive plastic MALDI targets, enabling MSI analysis to be performed on both TOF and FT-ICR MALDI mass spectrometers. We show that mounting does not unduly affect small molecule MSI detection by analyzing tiotropium abundance and distribution in rat lung tissues, with direct on-tissue quantitation achieved. Significantly, we use the adhesive tape to provide support to embedded delicate heat-stabilized tissues, enabling sectioning and mounting to be performed that maintained tissue integrity on samples that had previously been impossible to adequately prepare section for MSI analysis. The mapping of larger peptidomic molecules was not hindered by tape mounting samples and we demonstrate this by mapping the distribution of PEP-19 in both native and heat-stabilized rat brains. Furthermore, we show that without heat stabilization PEP-19 degradation fragments can detected and identified directly by MALDI MSI analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

Organochlorine pesticide levels in female adipose tissue from Puebla, Mexico.

PubMed

Waliszewski, Stefan M; Sanchez, K; Caba, M; Saldariaga-Noreña, H; Meza, E; Zepeda, R; Valencia Quintana, R; Infanzon, R

2012-02-01

The objective of this study was to determine the levels of organochlorine pesticides HCB, α-β-γ-HCH, pp'DDE, op'DDT and pp'DDT in adipose tissue of females living in Puebla, Mexico. Organochlorine pesticides were analyzed in 75 abdominal adipose tissue samples taken during 2010 by autopsy at the Forensic Services of Puebla. The results were expressed as mg/kg on fat basis. In analyzed samples the following pesticides were detected: p,p'-DDE in 100% of samples at mean 1.464 mg/kg; p,p'-DDT in 96.0.% of samples at mean 0.105 mg/kg; op'DDT in 89.3% of monitored samples at mean 0.025 mg/kg and β-HCH in 94.7% of the samples at mean 0.108 mg/kg. To show if organochlorine pesticide levels in monitored female's adipose tissues are age dependant, the group was divided in three ages ranges (13-26, 26-57 and 57-96 years). The mean and median levels of all organochlorine pesticides increase significantly (p < 0.05) from the first to second and from the first to third group. At the same time, the increase of mean and medians levels from the second to third group were not statistically significant (p > 0.05). The present results compared to previous ones from 2008 indicates an increase in the concentrations during the 2010 study, but only the differences for pp'DDE and op'DDT were statistically significant. The 2010 group of females was older compared to the 2008 group. The presence of organochlorine pesticide residues is still observed, indicating uniform and permanent exposure to the pesticides by Puebla inhabitants.

Frozen tissue preparation for high-resolution multiplex histological analyses of human brain specimens.

PubMed

Shao, Fangjie; Jiang, Wenhong; Gao, Qingqing; Li, Baizhou; Sun, Chongran; Wang, Qiyuan; Chen, Qin; Sun, Bing; Shen, Hong; Zhu, Keqing; Zhang, Jianmin; Liu, Chong

2017-10-01

The availability of a comprehensive tissue library is essential for elucidating the function and pathology of human brains. Considering the irreplaceable status of the formalin-fixation-paraffin-embedding (FFPE) preparation in routine pathology and the advantage of ultra-low temperature to preserve nucleic acids and proteins for multi-omics studies, these methods have become major modalities for the construction of brain tissue libraries. Nevertheless, the use of FFPE and snap-frozen samples is limited in high-resolution histological analyses because the preparation destroys tissue integrity and/or many important cellular markers. To overcome these limitations, we detailed a protocol to prepare and analyze frozen human brain samples that is particularly suitable for high-resolution multiplex immunohistological studies. As an alternative, we offered an optimized procedure to rescue snap-frozen tissues for the same purpose. Importantly, we provided a guideline to construct libraries of frozen tissue with minimal effort, cost and space. Taking advantage of this new tissue preparation modality to nicely preserve the cellular information that was otherwise damaged using conventional methods and to effectively remove tissue autofluorescence, we described the high-resolution landscape of the cellular composition in both lower-grade gliomas and glioblastoma multiforme samples. Our work showcases the great value of fixed frozen tissue in understanding the cellular mechanisms of CNS functions and abnormalities.

Trace elements by instrumental neutron activation analysis for pollution monitoring

NASA Technical Reports Server (NTRS)

Sheibley, D. W.

1975-01-01

Methods and technology were developed to analyze 1000 samples/yr of coal and other pollution-related samples. The complete trace element analysis of 20-24 samples/wk averaged 3-3.5 man-hours/sample. The computerized data reduction scheme could identify and report data on as many as 56 elements. In addition to coal, samples of fly ash, bottom ash, crude oil, fuel oil, residual oil, gasoline, jet fuel, kerosene, filtered air particulates, ore, stack scrubber water, clam tissue, crab shells, river sediment and water, and corn were analyzed. Precision of the method was plus or minus 25% based on all elements reported in coal and other sample matrices. Overall accuracy was estimated at 50%.

Metal bioaccumulation in two edible cephalopods in the Gulf of Gabes, South-Eastern Tunisia: environmental and human health risk assessment.

PubMed

Rabaoui, Lotfi; El Zrelli, Radhouan; Balti, Rafik; Mansour, Lamjed; Courjault-Radé, Pierre; Daghbouj, Nabil; Tlig-Zouari, Sabiha

2017-01-01

Samples of Octopus vulgaris and Sepia officinalis were collected from four areas in the Gulf of Gabes, south-eastern Tunisia, and their edible tissues (mantle and arms) were analyzed for cadmium, copper, mercury, and zinc. While the concentrations of metals showed significant differences between the sampling sites, no differences were revealed between the tissues of the two species. The spatial distribution of metals analyzed showed similar pattern for both tissues of the two species, with the highest concentrations found in the central area of Gabes Gulf, and the lowest in the northern and/or southern areas. From a human health risk point of view, the highest values of estimated daily intake, target hazard quotient, and hazard index were found in the central area of Gabes Gulf. Although the results of these indices were, in general, not alarming, the health risks posed by the consumption of cephalopods on local consumers cannot be excluded.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ballachey, B.E.; Kloecker, K.A.

Aliphatic and aromatic hydrocarbons were analyzed in hair, liver and intestinal samples taken from dead sea otters (Enhydra lutris) collected in spring and summer 1989 from Prince William Sound, the Kenai Peninsula and Kodiak Island, along the path of the Exxon Valdez oil spill. Hair showed significant differences in hydrocarbon concentrations among the three locations, but few significant differences were noted for liver or intestine samples. The highest concentrations of both aliphatic and aromatic hydrocarbons were measured in hair samples from Prince William Sound. Hydrocarbon concentrations in intestine and liver samples from the three locations were generally similar and low,more » suggesting that uptake into the tissues was limited, or that hydrocarbons within the tissues had been metabolized by the time samples were collected.« less

Automatic and objective oral cancer diagnosis by Raman spectroscopic detection of keratin with multivariate curve resolution analysis

NASA Astrophysics Data System (ADS)

Chen, Po-Hsiung; Shimada, Rintaro; Yabumoto, Sohshi; Okajima, Hajime; Ando, Masahiro; Chang, Chiou-Tzu; Lee, Li-Tzu; Wong, Yong-Kie; Chiou, Arthur; Hamaguchi, Hiro-O.

2016-01-01

We have developed an automatic and objective method for detecting human oral squamous cell carcinoma (OSCC) tissues with Raman microspectroscopy. We measure 196 independent Raman spectra from 196 different points of one oral tissue sample and globally analyze these spectra using a Multivariate Curve Resolution (MCR) analysis. Discrimination of OSCC tissues is automatically and objectively made by spectral matching comparison of the MCR decomposed Raman spectra and the standard Raman spectrum of keratin, a well-established molecular marker of OSCC. We use a total of 24 tissue samples, 10 OSCC and 10 normal tissues from the same 10 patients, 3 OSCC and 1 normal tissues from different patients. Following the newly developed protocol presented here, we have been able to detect OSCC tissues with 77 to 92% sensitivity (depending on how to define positivity) and 100% specificity. The present approach lends itself to a reliable clinical diagnosis of OSCC substantiated by the “molecular fingerprint” of keratin.

Indirect tissue electrophoresis: a new method for analyzing solid tissue protein.

PubMed

Smith, A C

1988-01-01

1. The eye lens core (nucleus) has been a valuable source of molecular biologic information. 2. In these studies, lens nuclei are usually homogenized so that any protein information related to anatomical subdivisions, or layers, of the nucleus is lost. 3. The present report is of a new method, indirect tissue electrophoresis (ITE), which, when applied to fish lens nuclei, permitted (a) automatic correlation of protein information with anatomic layer, (b) production of large, clear electrophoretic patterns even from small tissue samples and (c) detection of more proteins than in liquid extracts of homogenized tissues. 4. ITE seems potentially applicable to a variety of solid tissues.

Triple Gene Analysis Using Samples Obtained by Endobronchial Ultrasound-guided Transbronchial Needle Aspiration

PubMed Central

Lee, Kyungjong; Um, Sang-Won; Jeong, Byeong-Ho; Yang, Jung Wook; Choi, Yoon-La; Han, Joungho; Kim, Hojoong; Kwon, O Jung

2016-01-01

Objective A mutational analysis of tumor tissue samples is an important part of advanced lung cancer treatment strategies. This study evaluated the efficacy of a triple gene analysis using samples obtained via endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). Methods Either metastatic lymph nodes or primary lung mass samples obtained by EBUS-TBNA were collected between May 2011 and May 2013. We consecutively analyzed epidermal growth factor receptor (EGFR), V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), and anaplastic lymphoma kinase (ALK) fusion genes using remnant tissue samples. Results A total of 109 patients were diagnosed with non-small cell lung cancer (NSCLC). Of these, 70% were adenocarcinoma, 27% squamous cell carcinoma with NSCLC, and 3% were related to other types of lung cancer. EGFR mutations were detected in 23 cases (21.1%), KRAS mutations in 13 cases (11.9%), and ALK fusion genes in 5 cases (4.9%). The ALK fusion genes could not be analyzed in four cases because of insufficient tissue samples remaining after routine histochemistry and an EGFR/KRAS mutation analysis. We found that small biopsy samples from EBUS-TBNA were adequate for performing a triple gene analysis in 97 patients (96%). ALK fusion protein immunohistochemistry (IHC) was 100% consistent with fluorescence in situ hybridization (FISH). Conclusion Small samples obtained by EBUS-TBNA were found to be sufficient for performing a triple gene analysis following routine histology and IHC. ALK IHC showed a very good concordance with FISH for detecting ALK fusion genes. PMID:27803402

Breast Cancer Research at NASA

NASA Technical Reports Server (NTRS)

1998-01-01

Dr. Harry Mahtani analyzes the gas content of nutrient media from Bioreactor used in research on human breast cancer. NASA's Marshall Space Flight Center (MSFC) is sponsoring research with Bioreactors, rotating wall vessels designed to grow tissue samples in space, to understand how breast cancer works. This ground-based work studies the growth and assembly of human mammary epithelial cells (HMEC) from breast cancer susceptible tissue. Radiation can make the cells cancerous, thus allowing better comparisons of healthy vs. tunourous tissues.

Wideband acoustic microscopy of tissue.

PubMed

Daft, C W; Briggs, G D

1989-01-01

A scanning acoustic microscope (SAM) has been used to measure the elastic properties of tissue with a resolution of around 8 mum. This is achieved by broadband excitation of the acoustic lens, and the recording of an undemodulated returning signal. A method of analyzing this information to yield sound velocity, acoustic impedance, section thickness, and acoustic attenuation is described. Results from a sample of skin tissue are presented and compared with data from a computer simulation of the experiment.

Evaluation of arsenic speciation in rainbow trout and fathead minnows from dietary exposure

EPA Science Inventory

The concentration of total arsenic and various arsenic species were measured in food and fish tissue samples from two dietary arsenic exposures to juvenile fish. For arsenic speciation, samples were extracted with 10% MeOH and analyzed by HPLC/ICPMS. Total arsenic concentration...

Applications of Raman spectroscopy in life science

NASA Astrophysics Data System (ADS)

Martin, Airton A.; T. Soto, Cláudio A.; Ali, Syed M.; Neto, Lázaro P. M.; Canevari, Renata A.; Pereira, Liliane; Fávero, Priscila P.

2015-06-01

Raman spectroscopy has been applied to the analysis of biological samples for the last 12 years providing detection of changes occurring at the molecular level during the pathological transformation of the tissue. The potential use of this technology in cancer diagnosis has shown encouraging results for the in vivo, real-time and minimally invasive diagnosis. Confocal Raman technics has also been successfully applied in the analysis of skin aging process providing new insights in this field. In this paper it is presented the latest biomedical applications of Raman spectroscopy in our laboratory. It is shown that Raman spectroscopy (RS) has been used for biochemical and molecular characterization of thyroid tissue by micro-Raman spectroscopy and gene expression analysis. This study aimed to improve the discrimination between different thyroid pathologies by Raman analysis. A total of 35 thyroid tissues samples including normal tissue (n=10), goiter (n=10), papillary (n=10) and follicular carcinomas (n=5) were analyzed. The confocal Raman spectroscopy allowed a maximum discrimination of 91.1% between normal and tumor tissues, 84.8% between benign and malignant pathologies and 84.6% among carcinomas analyzed. It will be also report the application of in vivo confocal Raman spectroscopy as an important sensor for detecting advanced glycation products (AGEs) on human skin.

Low prevalence of transcriptionally active human papilloma virus in Indian patients with HNSCC and leukoplakia.

PubMed

Bhosale, Priyanka G; Pandey, Manishkumar; Desai, Rajiv S; Patil, Asawari; Kane, Shubhada; Prabhash, Kumar; Mahimkar, Manoj B

2016-11-01

In the present study, we comprehensively analyzed the prevalence of transcriptionally active human papilloma virus (HPV) in tissue samples of Indian patients with leukoplakia, predominantly hyperplastic lesions and head and neck squamous cell carcinoma (HNSCC). In addition, saliva samples from patients with HNSCC were screened for HPV detection. P16 overexpression was analyzed by immunohistochemistry. Tissue samples of leukoplakia (n = 121) and HNSCC (n = 427) and saliva from patients with HNSCC (n = 215) were tested for HPV using nested polymerase chain reaction. Positive samples were sequenced for subtyping. The presence of HPV E6/E7 mRNA was confirmed by RNA in situ hybridization. P16 expression and HPV DNA were not detected in any of the leukoplakia specimens. Of the 427 HNSCC tumors, 9 showed p16 overexpression and 7/427 cases were positive for HPV16 DNA, in saliva or tissue. E6/E7 mRNA positivity was observed in 8 HNSCC samples, primarily from patients with no habit of tobacco consumption. The prevalence of high-risk HPV was restricted to oropharynx and larynx, with very little concordance between p16 overexpression and HPV positivity. All patients with HPV-positive saliva samples had transcriptionally active HPV present in their tumors. The presence of HPV DNA does not necessarily reflect transcriptionally active virus in tumors; hence, it is important to consider this fact while categorizing HPV-associated tumors. Copyright © 2016 Elsevier Inc. All rights reserved.

Bladder cancer diagnosis during cystoscopy using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Grimbergen, M. C. M.; van Swol, C. F. P.; Draga, R. O. P.; van Diest, P.; Verdaasdonk, R. M.; Stone, N.; Bosch, J. H. L. R.

2009-02-01

Raman spectroscopy is an optical technique that can be used to obtain specific molecular information of biological tissues. It has been used successfully to differentiate normal and pre-malignant tissue in many organs. The goal of this study is to determine the possibility to distinguish normal tissue from bladder cancer using this system. The endoscopic Raman system consists of a 6 Fr endoscopic probe connected to a 785nm diode laser and a spectral recording system. A total of 107 tissue samples were obtained from 54 patients with known bladder cancer during transurethral tumor resection. Immediately after surgical removal the samples were placed under the Raman probe and spectra were collected and stored for further analysis. The collected spectra were analyzed using multivariate statistical methods. In total 2949 Raman spectra were recorded ex vivo from cold cup biopsy samples with 2 seconds integration time. A multivariate algorithm allowed differentiation of normal and malignant tissue with a sensitivity and specificity of 78,5% and 78,9% respectively. The results show the possibility of discerning normal from malignant bladder tissue by means of Raman spectroscopy using a small fiber based system. Despite the low number of samples the results indicate that it might be possible to use this technique to grade identified bladder wall lesions during endoscopy.

Light propagation in tissues with controlled optical properties

NASA Astrophysics Data System (ADS)

Tuchin, Valery V.; Maksimova, Irina L.; Zimnyakov, Dmitry A.; Kon, Irina L.; Mavlyutov, Albert H.; Mishin, Alexey A.

1997-10-01

Theoretical and computer modeling approaches, such as Mie theory, radiative transfer theory, diffusion wave correlation spectroscopy, and Monte Carlo simulation were used to analyze tissue optics during a process of optical clearing due to refractive index matching. Continuous wave transmittance and forward scattering measurement as well as intensity correlation experiments were used to monitor tissue structural and optical properties. As a control, tissue samples of the human sclera were taken. Osmotically active solutions, such as Trazograph, glucose, and polyethylene glycol, were used as chemicals. A characteristic time response of human scleral optical clearing the range 3 to 10 min was determined. The diffusion coefficients describing the permeability of the scleral samples to Trazograph were experimentally estimated; the average value was DT approximately equals (0.9 +/- 0.5) X 10-5 cm2/s. The results are general and can be used to describe many other fibrous tissues.

Digital Detection of Multiple Minority Mutants and Expression Levels of Multiple Colorectal Cancer-Related Genes Using Digital-PCR Coupled with Bead-Array

PubMed Central

Huang, Huan; Li, Shuo; Sun, Lizhou; Zhou, Guohua

2015-01-01

To simultaneously analyze mutations and expression levels of multiple genes on one detection platform, we proposed a method termed “multiplex ligation-dependent probe amplification–digital amplification coupled with hydrogel bead-array” (MLPA–DABA) and applied it to diagnose colorectal cancer (CRC). CRC cells and tissues were sampled to extract nucleic acid, perform MLPA with sequence-tagged probes, perform digital emulsion polymerase chain reaction (PCR), and produce a hydrogel bead-array to immobilize beads and form a single bead layer on the array. After hybridization with fluorescent probes, the number of colored beads, which reflects the abundance of expressed genes and the mutation rate, was counted for diagnosis. Only red or green beads occurred on the chips in the mixed samples, indicating the success of single-molecule PCR. When a one-source sample was analyzed using mixed MLPA probes, beads of only one color occurred, suggesting the high specificity of the method in analyzing CRC mutation and gene expression. In gene expression analysis of a CRC tissue from one CRC patient, the mutant percentage was 3.1%, and the expression levels of CRC-related genes were much higher than those of normal tissue. The highly sensitive MLPA–DABA succeeds in the relative quantification of mutations and gene expressions of exfoliated cells in stool samples of CRC patients on the same chip platform. MLPA–DABA coupled with hydrogel bead-array is a promising method in the non-invasive diagnosis of CRC. PMID:25880764

Use of electron microprobe x-ray analysis for determination of low calcium concentrations across leaves deficient in calcium

NASA Technical Reports Server (NTRS)

Barta, D. J.; Tibbitts, T. W.

1991-01-01

An electron microprobe with wavelength-dispersive x-ray spectrometry (WDS) was found to be useful for the determination of Ca concentrations in leaf tissue deficient in Ca. WDS effectively detected Ca concentrations as low as 0.2 mg/g dry wt in the presence of high levels of K and Mg (120 and 50 mg/g dry wt, respectively). Leaf specimens were prepared for analysis by quick-freezing in liquid nitrogen and freeze-drying at -20 degrees C to maintain elemental integrity within the tissue. Because dry material was analyzed, sample preparation was simple and samples could be stored for long periods before analysis. A large beam diameter of 50 gm was used to minimize tissue damage under the beam and analyze mineral concentrations within several cells at one time. Beam penetration was between 50 and 55 microns, approximately one-third of the thickness of the leaf. For analysis of concentrations in interveinal areas, analyses directed into the abaxial epidermis were found most useful. However, because of limited beam penetration, analyses of veinal areas would require use of cross sections [correction of crosssections]. Solid mineral standards were used for instrument standardization. To prevent measurement errors resulting from differences between the matrix of the mineral standards and the analyzed tissue, concentrations in leaves were corrected using gelatin standards prepared and analyzed under the same conditions. WDS was found to be useful for documenting that very low Ca levels occur in specific areas of lettuce leaves exhibiting the Ca deficiency injury termed tipburn.

Determination of 240Pu/239Pu isotopic ratios in human tissues collected from areas around the Semipalatinsk Nuclear Test Site by sector-field high resolution ICP-MS.

PubMed

Yamamoto, M; Oikawa, S; Sakaguchi, A; Tomita, J; Hoshi, M; Apsalikov, K N

2008-09-01

Information on the 240Pu/239Pu isotope ratios in human tissues for people living around the Semipalatinsk Nuclear Test Site (SNTS) was deduced from 9 sets of soft tissues and bones, and 23 other bone samples obtained by autopsy. Plutonium was radiochemically separated and purified, and plutonium isotopes (239Pu and 240Pu) were determined by sector-field high resolution inductively coupled plasma-mass spectrometry. For most of the tissue samples from the former nine subjects, low 240Pu/239Pu isotope ratios were determined: bone, 0.125 +/- 0.018 (0.113-0.145, n = 4); lungs, 0.063 +/- 0.010 (0.051-0.078, n = 5); and liver, 0.148 +/- 0.026 (0.104-0.189, n = 9). Only 239Pu was detected in the kidney samples; the amount of 240Pu was too small to be measured, probably due to the small size of samples analyzed. The mean 240Pu/239Pu isotope ratio for bone samples from the latter 23 subjects was 0.152 +/- 0.034, ranging from 0.088 to 0.207. A significant difference (a two-tailed Student's t test; 95% significant level, alpha = 0.05) between mean 240Pu/239Pu isotope ratios for the tissue samples and for the global fallout value (0.178 +/- 0.014) indicated that weapons-grade plutonium from the atomic bombs has been incorporated into the human tissues, especially lungs, in the residents living around the SNTS. The present 239,240Pu concentrations in bone, lung, and liver samples were, however, not much different from ranges found for human tissues from other countries that were due solely to global fallout during the 1970's-1980's.

CT imaging during microwave ablation: Analysis of spatial and temporal tissue contraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Dong; Brace, Christopher L., E-mail: clbrace@wisc.edu

Purpose: To analyze the spatial distribution and temporal development of liver tissue contraction during high-temperature ablation by using intraprocedural computed tomography (CT) imaging. Methods: A total of 46 aluminum fiducial markers were positioned in a 60 × 45 mm grid, in a single plane, around a microwave ablation antenna in each of six ex vivo bovine liver samples. Ablations were performed for 10 min at 100 W. CT data of the liver sample were acquired every 30 s during ablation. Fiducial motion between acquisitions was tracked in postprocessing and used to calculate measures of tissue contraction and contraction rates. Themore » spatial distribution and temporal evolution of contraction were analyzed. Results: Fiducial displacement indicated that the zone measured postablation was 8.2 ± 1.8 mm (∼20%) smaller in the radial direction and 7.1 ± 1.0 mm (∼10%) shorter in the longitudinal direction than the preablation tissue dimension. Therefore, the total ablation volume was reduced from its preablation value by approximately 45%. Very little longitudinal contraction was noted in the distal portion of the ablation zone. Central tissues contracted more than 60%, which was near an estimated limit of ∼70% based on initial water content. More peripheral tissues contracted only 15% in any direction. Contraction rates peaked during the first 60 s of heating with a roughly exponential decay over time. Conclusions: Ablation zones measured posttreatment are significantly smaller than the pretreatment tissue dimensions. Tissue contraction is spatially dependent, with the greatest effect occurring in the central ablation zone. Contraction rate peaks early and decays over time.« less

Detecting quinoxaline-2-carboxylic acid in animal tissues by using sensitive rapid enzyme-linked immunosorbent assay and time-resolved fluoroimmunoassay.

PubMed

Le, Tao; Yu, Huan; Niu, Xiaodong

2015-05-15

An indirect competitive enzyme-linked immunosorbent assay (ic-ELISA) and time-resolved fluoroimmunoassay (TR-FIA) based on an anti-N-butylquinoxaline-2-carboxamide (BQCA) monoclonal antibody were standardized and validated for quinoxaline-2-carboxylic acid (QCA) screening in animal tissues and its performance were compared to HPLC. The sensitivities obtained for edible tissue extracts were 1.62 and 1.12 ng ml(-1) for ic-ELISA and TR-FIA detection, respectively. Two samples were spiked with QCA and analyzed by both methods. The recovery values ranged from 92.6% to 112.2% and the coefficients of variation were less than 15% for QCA spiking into swine tissue samples at concentrations of 2.5-50.0 μg kg(-1). Excellent correlations (r(2)=0.987-0.996) of the ic-ELISA/HPLC and TR-FIA/HPLC data were observed for processed samples. The results demonstrated that the ic-ELISA and TR-FIA methods were rapid and accurate for the residue detection of QCA in animal tissues. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluation of Two Outlier-Detection-Based Methods for Detecting Tissue-Selective Genes from Microarray Data

PubMed Central

Kadota, Koji; Konishi, Tomokazu; Shimizu, Kentaro

2007-01-01

Large-scale expression profiling using DNA microarrays enables identification of tissue-selective genes for which expression is considerably higher and/or lower in some tissues than in others. Among numerous possible methods, only two outlier-detection-based methods (an AIC-based method and Sprent’s non-parametric method) can treat equally various types of selective patterns, but they produce substantially different results. We investigated the performance of these two methods for different parameter settings and for a reduced number of samples. We focused on their ability to detect selective expression patterns robustly. We applied them to public microarray data collected from 36 normal human tissue samples and analyzed the effects of both changing the parameter settings and reducing the number of samples. The AIC-based method was more robust in both cases. The findings confirm that the use of the AIC-based method in the recently proposed ROKU method for detecting tissue-selective expression patterns is correct and that Sprent’s method is not suitable for ROKU. PMID:19936074

Detection of cocaine and benzoylecgonine in formalin fixed rat tissues.

PubMed

Hilal, Ahmet; Dağlioğlu, Nebīle; Battal, Dīlek; Yener, Fadīle; Dağlioğlu, Kenan

2009-09-01

The stability of drugs in formalin solution is an important factor in forensic investigation. Tissues (liver, lung, kidney, brain) taken from rats, which have been poisoned acutely with cocaine, were preserved in two different conditions, analyzed by GC-MS, and then compared. Organs of the first group were preserved and stored at -20 degrees C without adding formalin, whereas the organs of the second group were preserved and stored in formalin solution at room temperature (25 degrees C). Serum samples were taken immediately after poisoning and studied as well. In specimens stored at -20 degrees C, cocaine and its metabolite benzoylecgonine were detected in the tissues. Only benzoylecgonine was detected both in tissues and their formalin solution. It was observed that the distribution of cocaine in tissues had differed depending on the preservation conditions. The formalin solution in which benzoylecgonine was mostly detected was from liver. As a result, cocaine was detected in tissues stored at -20 degrees C. It is recommended that both the formalin-fixed tissues and formalin solution should be analyzed concurrently to assure the accurate results (LOD = 3 ng/ml).

Increased Expression of Cathelicidin by Direct Activation of Protease-Activated Receptor 2: Possible Implications on the Pathogenesis of Rosacea

PubMed Central

Kim, Ji Young; Kim, Yoon Jee; Lim, Beom Jin; Sohn, Hyo Jung; Shin, Dongyun

2014-01-01

Purpose Recent findings of increased cathelicidin protein and its proteolytic fragments in rosacea suggest a pathogenic role for cathelicidin in this disease. The relationship between cathelicidin and protease-activated receptor 2 (PAR-2) is therefore of interest, as PAR-2, expressed principally in keratinocytes, regulates pro-inflammatory cytokine expression in the skin. The purpose of this study was to determine the relationship between expression of PAR-2 and cathelicidin in rosacea and to test the effect of direct PAR-2 activation on cathelicidin expression in keratinocytes. Materials and Methods Samples from 40 patients with clinicopathologic diagnosis of rosacea and facial skin tissue samples from 20 patients with no specific findings or milium without inflammation were retrieved. Intensities of immunohistochemical staining for PAR-2 and cathelicidin were compared between normal and rosacea-affected skin tissues. Additionally, correlations between PAR-2 and cathelicidin staining intensities within rosacea patients were analyzed. In cultured keratinocytes, changes in PAR-2, cathelicidin, and vascular endothelial growth factor (VEGF) mRNA and protein were analyzed after treatment with PAR-2 activating peptide (AP). Results Cathelicidin expression was significantly higher in rosacea skin tissues than in normal tissues (p<0.001), while PAR-2 expression was not significantly higher in rosacea tissues than in normal skin tissues. A positive correlation between PAR-2 and cathelicidin within rosacea samples was observed (R=0.330, p=0.037). After treatment of PAR-2 AP, both mRNA and protein levels for PAR-2, cathelicidin, and VEGF significantly increased in cultured keratinocytes, compared with PAR-2 control peptide treatment. Conclusion PAR-2 may participate in the pathogenesis of rosacea through activation of cathelicidin LL-37, a mediator of innate immune responses in the skin. PMID:25323904

Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences

PubMed Central

Hong, Mineui; Bang, Heejin; Van Vrancken, Michael; Kim, Seungtae; Lee, Jeeyun; Park, Se Hoon; Park, Joon Oh; Park, Young Suk; Lim, Ho Yeong; Kang, Won Ki; Sun, Jong-Mu; Lee, Se Hoon; Ahn, Myung-Ju; Park, Keunchil; Kim, Duk Hwan; Lee, Seunggwan; Park, Woongyang; Kim, Kyoung-Mee

2017-01-01

To generate accurate next-generation sequencing (NGS) data, the amount and quality of DNA extracted is critical. We analyzed 1564 tissue samples from patients with metastatic or recurrent solid tumor submitted for NGS according to their sample size, acquisition method, organ, and fixation to propose appropriate tissue requirements. Of the 1564 tissue samples, 481 (30.8%) consisted of fresh-frozen (FF) tissue, and 1,083 (69.2%) consisted of formalin-fixed paraffin-embedded (FFPE) tissue. We obtained successful NGS results in 95.9% of cases. Out of 481 FF biopsies, 262 tissue samples were from lung, and the mean fragment size was 2.4 mm. Compared to lung, GI tract tumor fragments showed a significantly lower DNA extraction failure rate (2.1 % versus 6.1%, p = 0.04). For FFPE biopsy samples, the size of biopsy tissue was similar regardless of tumor type with a mean of 0.8 × 0.3 cm, and the mean DNA yield per one unstained slide was 114 ng. We obtained highest amount of DNA from the colorectum (2353 ng) and the lowest amount from the hepatobiliary tract (760.3 ng) likely due to a relatively smaller biopsy size, extensive hemorrhage and necrosis, and lower tumor volume. On one unstained slide from FFPE operation specimens, the mean size of the specimen was 2.0 × 1.0 cm, and the mean DNA yield per one unstained slide was 1800 ng. In conclusions, we present our experiences on tissue requirements for appropriate NGS workflow: > 1 mm2 for FF biopsy, > 5 unstained slides for FFPE biopsy, and > 1 unstained slide for FFPE operation specimens for successful test results in 95.9% of cases. PMID:28477007

Backscatter and attenuation properties of mammalian brain tissues

NASA Astrophysics Data System (ADS)

Wijekularatne, Pushpani Vihara

Traumatic Brain Injury (TBI) is a common category of brain injuries, which contributes to a substantial number of deaths and permanent disability all over the world. Ultrasound technology plays a major role in tissue characterization due to its low cost and portability that could be used to bridge a wide gap in the TBI diagnostic process. This research addresses the ultrasonic properties of mammalian brain tissues focusing on backscatter and attenuation. Orientation dependence and spatial averaging of data were analyzed using the same method resulting from insertion of tissue sample between a transducer and a reference reflector. Apparent backscatter transfer function (ABTF) at 1 to 10 MHz, attenuation coefficient and backscatter coefficient (BSC) at 1 to 5 MHz frequency ranges were measured on ovine brain tissue samples. The resulting ABTF was a monotonically decreasing function of frequency and the attenuation coefficient and BSC generally were increasing functions of frequency, results consistent with other soft tissues such as liver, blood and heart.

Evaluation of metal content in perch of the Ob River basin

NASA Astrophysics Data System (ADS)

Osipova, N. A.; Stepanova, K. D.; Matveenko, I. A.

2015-11-01

The geochemical features of river perch in the River Ob basin have been studied (the upper and middle reaches of the Ob River and the lower reach of the Tom River). The contents of Ag, Bi, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Sn, W, Zn, Hg in perch's soft tissue are defined by the methods of ICP AES and stripping voltammetry, that of mercury in bones - by the atomic absorption method using mercury analyzer PA-915+. The distribution series of metal absolute concentrations in perch's soft tissue from the Ob River basin are plotted: Fe > Zn > Cu > Mn, typical for uncontaminated or slightly metal contaminated water bodies. In soft tissue of the studied samples the metal content does not exceed the permissible values. The mercury content in bones of studied samples is in the range 0,036-0,556 mg/kg. The mercury concentration is higher in bones in comparison with soft tissue in all samples.

Assessing Amide Proton Transfer (APT) MRI Contrast Origins in 9 L Gliosarcoma in the Rat Brain Using Proteomic Analysis.

PubMed

Yan, Kun; Fu, Zongming; Yang, Chen; Zhang, Kai; Jiang, Shanshan; Lee, Dong-Hoon; Heo, Hye-Young; Zhang, Yi; Cole, Robert N; Van Eyk, Jennifer E; Zhou, Jinyuan

2015-08-01

To investigate the biochemical origin of the amide photon transfer (APT)-weighted hyperintensity in brain tumors. Seven 9 L gliosarcoma-bearing rats were imaged at 4.7 T. Tumor and normal brain tissue samples of equal volumes were prepared with a coronal rat brain matrix and a tissue biopsy punch. The total tissue protein and the cytosolic subproteome were extracted from both samples. Protein samples were analyzed using two-dimensional gel electrophoresis, and the proteins with significant abundance changes were identified by mass spectrometry. There was a significant increase in the cytosolic protein concentration in the tumor, compared to normal brain regions, but the total protein concentrations were comparable. The protein profiles of the tumor and normal brain tissue differed significantly. Six cytosolic proteins, four endoplasmic reticulum proteins, and five secreted proteins were considerably upregulated in the tumor. Our experiments confirmed an increase in the cytosolic protein concentration in tumors and identified several key proteins that may cause APT-weighted hyperintensity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Emin, David, E-mail: emin@unm.edu; Akhtari, Massoud; Ellingson, B. M.

We analyze the transient-dc and frequency-dependent electrical conductivities between blocking electrodes. We extend this analysis to measurements of ions’ transport in freshly excised bulk samples of human brain tissue whose complex cellular structure produces blockages. The associated ionic charge-carrier density and diffusivity are consistent with local values for sodium cations determined non-invasively in brain tissue by MRI (NMR) and diffusion-MRI (spin-echo NMR). The characteristic separation between blockages, about 450 microns, is very much shorter than that found for sodium-doped gel proxies for brain tissue, >1 cm.

Optical imaging of oral pathological tissue using optical coherence tomography and synchrotron radiation computed microtomography

NASA Astrophysics Data System (ADS)

Cânjǎu, Silvana; Todea, Carmen; Sinescu, Cosmin; Negrutiu, Meda L.; Duma, Virgil; Mǎnescu, Adrian; Topalǎ, Florin I.; Podoleanu, Adrian Gh.

2013-06-01

The efforts aimed at early diagnosis of oral cancer should be prioritized towards developing a new screening instrument, based on optical coherence tomography (OCT), to be used directly intraorally, able to perform a fast, real time, 3D and non-invasive diagnosis of oral malignancies. The first step in this direction would be to optimize the OCT image interpretation of oral tissues. Therefore we propose plastination as a tissue preparation method that better preserves three-dimensional structure for study by new optical imaging techniques. The OCT and the synchrotron radiation computed microtomography (micro-CT) were employed for tissue sample analyze. For validating the OCT results we used the gold standard diagnostic procedure for any suspicious lesion - histopathology. This is a preliminary study of comparing features provided by OCT and Micro-CT. In the conditions of the present study, OCT proves to be a highly promising imaging modality. The use of x-ray based topographic imaging of small biological samples has been limited by the low intrinsic x-ray absorption of non-mineralized tissue and the lack of established contrast agents. Plastination can be used to enhance optical imagies of oral soft tissue samples.

Ultra-sensitive high performance liquid chromatography-laser-induced fluorescence based proteomics for clinical applications.

PubMed

Patil, Ajeetkumar; Bhat, Sujatha; Pai, Keerthilatha M; Rai, Lavanya; Kartha, V B; Chidangil, Santhosh

2015-09-08

An ultra-sensitive high performance liquid chromatography-laser induced fluorescence (HPLC-LIF) based technique has been developed by our group at Manipal, for screening, early detection, and staging for various cancers, using protein profiling of clinical samples like, body fluids, cellular specimens, and biopsy-tissue. More than 300 protein profiles of different clinical samples (serum, saliva, cellular samples and tissue homogenates) from volunteers (normal, and different pre-malignant/malignant conditions) were recorded using this set-up. The protein profiles were analyzed using principal component analysis (PCA) to achieve objective detection and classification of malignant, premalignant and healthy conditions with high sensitivity and specificity. The HPLC-LIF protein profiling combined with PCA, as a routine method for screening, diagnosis, and staging of cervical cancer and oral cancer, is discussed in this paper. In recent years, proteomics techniques have advanced tremendously in life sciences and medical sciences for the detection and identification of proteins in body fluids, tissue homogenates and cellular samples to understand biochemical mechanisms leading to different diseases. Some of the methods include techniques like high performance liquid chromatography, 2D-gel electrophoresis, MALDI-TOF-MS, SELDI-TOF-MS, CE-MS and LC-MS techniques. We have developed an ultra-sensitive high performance liquid chromatography-laser induced fluorescence (HPLC-LIF) based technique, for screening, early detection, and staging for various cancers, using protein profiling of clinical samples like, body fluids, cellular specimens, and biopsy-tissue. More than 300 protein profiles of different clinical samples (serum, saliva, cellular samples and tissue homogenates) from healthy and volunteers with different malignant conditions were recorded by using this set-up. The protein profile data were analyzed using principal component analysis (PCA) for objective classification and detection of malignant, premalignant and healthy conditions. The method is extremely sensitive to detect proteins with limit of detection of the order of femto-moles. The HPLC-LIF combined with PCA as a potential proteomic method for the diagnosis of oral cancer and cervical cancer has been discussed in this paper. This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Coupled Analysis of In Vitro and Histology Tissue Samples to Quantify Structure-Function Relationship

PubMed Central

Acar, Evrim; Plopper, George E.; Yener, Bülent

2012-01-01

The structure/function relationship is fundamental to our understanding of biological systems at all levels, and drives most, if not all, techniques for detecting, diagnosing, and treating disease. However, at the tissue level of biological complexity we encounter a gap in the structure/function relationship: having accumulated an extraordinary amount of detailed information about biological tissues at the cellular and subcellular level, we cannot assemble it in a way that explains the correspondingly complex biological functions these structures perform. To help close this information gap we define here several quantitative temperospatial features that link tissue structure to its corresponding biological function. Both histological images of human tissue samples and fluorescence images of three-dimensional cultures of human cells are used to compare the accuracy of in vitro culture models with their corresponding human tissues. To the best of our knowledge, there is no prior work on a quantitative comparison of histology and in vitro samples. Features are calculated from graph theoretical representations of tissue structures and the data are analyzed in the form of matrices and higher-order tensors using matrix and tensor factorization methods, with a goal of differentiating between cancerous and healthy states of brain, breast, and bone tissues. We also show that our techniques can differentiate between the structural organization of native tissues and their corresponding in vitro engineered cell culture models. PMID:22479315

Elemental composition of some essential cations in human ocular tissue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panessa-Warren, B.J.; Kraner, H.W.; Warren, J.B.

1983-01-01

To obtain data on the baseline elemental content in normal adult sensory retina, RPE and iris, normal non-diabetic eyes were analyzed and these results were used for comparison to similarly prepared samples from diabetic donor eyes. To determine if the concentrations of the cations, Ca, Ba and Zn were altered by the age, alimentation and exposure to light of the donor, tissue from children (from 25 weeks gestation to 8-1/2 years old) was also analyzed by x-ray fluorescence spectroscopy, proton induced x-ray emission spectroscopy, and light and electron (scanning and transmission) microscopy.

Cell and tissue microarray technologies for protein and nucleic acid expression profiling.

PubMed

Cardano, Marina; Diaferia, Giuseppe R; Falavigna, Maurizio; Spinelli, Chiara C; Sessa, Fausto; DeBlasio, Pasquale; Biunno, Ida

2013-02-01

Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform.

Pulp tissue dissolution capacity of QMix 2in1 irrigation solution.

PubMed

Arslan, Dilara; Guneser, Mehmet Burak; Kustarci, Alper; Er, Kursat; Siso, Seyda Herguner

2015-01-01

The aim of this study was to evaluate the tissue dissolution efficacy of four root canal irrigation solutions (sodium hypochlorite [NaOCl], chlorhexidine gluconate [CHX], Octenidine [OCT], and QMix 2in1) on bovine pulp tissue. Fifty bovine pulp tissue samples, each weighing 6.55 mg, were prepared and randomly divided into four experimental groups and one control group (n = 10) according to the dissolution irrigants used: (1) 5.25% NaOCl group; (2) 2% CHX group; (3) OCT group; (4) QMix 2in1 group; and (5) control group (saline solution). These samples were then placed into special bovine dentin reservoir models and immersed for 1 h with each test solution (0.1 mL of each) at room temperature. The pulp samples were then blotted dry and weighed again. The percentage of weight loss was calculated. Statistically analyzed with one-way analysis of variance and post-hoc Tukey tests (P = 0.05). Saline solution did not dissolve the bovine pulp tissue. All groups, except OCT, dissolved pulp samples more effectively than the control group (P < 0.05). The highest tissue dissolution was observed in 5.25% NaOCl group (P < 0.05). No statistically significant difference was found between the tissue-dissolving effect between QMix 2in1 and those of 2% CHX. Within the limitations of this in vitro study, NaOCl exhibited the best tissue-dissolving effect out of all solutions tested. CHX and QMix 2in1 were able to dissolve pulp tissue but less than NaOCl. OCT and saline solutions could not exhibit significantly tissue-dissolving effectiveness. This study shown that QMix 2in1 has little capacity to dissolve pulp tissue therefore used alone is not sufficient for this purpose.

Pulp tissue dissolution capacity of QMix 2in1 irrigation solution

PubMed Central

Arslan, Dilara; Guneser, Mehmet Burak; Kustarci, Alper; Er, Kursat; Siso, Seyda Herguner

2015-01-01

Objective: The aim of this study was to evaluate the tissue dissolution efficacy of four root canal irrigation solutions (sodium hypochlorite [NaOCl], chlorhexidine gluconate [CHX], Octenidine [OCT], and QMix 2in1) on bovine pulp tissue. Materials and Methods: Fifty bovine pulp tissue samples, each weighing 6.55 mg, were prepared and randomly divided into four experimental groups and one control group (n = 10) according to the dissolution irrigants used: (1) 5.25% NaOCl group; (2) 2% CHX group; (3) OCT group; (4) QMix 2in1 group; and (5) control group (saline solution). These samples were then placed into special bovine dentin reservoir models and immersed for 1 h with each test solution (0.1 mL of each) at room temperature. The pulp samples were then blotted dry and weighed again. The percentage of weight loss was calculated. Statistically analyzed with one-way analysis of variance and post-hoc Tukey tests (P = 0.05). Results: Saline solution did not dissolve the bovine pulp tissue. All groups, except OCT, dissolved pulp samples more effectively than the control group (P < 0.05). The highest tissue dissolution was observed in 5.25% NaOCl group (P < 0.05). No statistically significant difference was found between the tissue-dissolving effect between QMix 2in1 and those of 2% CHX. Conclusions: Within the limitations of this in vitro study, NaOCl exhibited the best tissue-dissolving effect out of all solutions tested. CHX and QMix 2in1 were able to dissolve pulp tissue but less than NaOCl. OCT and saline solutions could not exhibit significantly tissue-dissolving effectiveness. This study shown that QMix 2in1 has little capacity to dissolve pulp tissue therefore used alone is not sufficient for this purpose. PMID:26430374

A new model for ancient DNA decay based on paleogenomic meta-analysis

PubMed Central

Ware, Roselyn; Smith, Oliver; Collins, Matthew

2017-01-01

Abstract The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics. PMID:28486705

Capillary electrophoresis - Mass spectrometry metabolomics analysis revealed enrichment of hypotaurine in rat glioma tissues.

PubMed

Gao, Peng; Ji, Min; Fang, Xueyan; Liu, Yingyang; Yu, Zhigang; Cao, Yunfeng; Sun, Aijun; Zhao, Liang; Zhang, Yong

2017-11-15

Glioma is one of the most lethal brain malignancies with unknown etiologies. Many metabolomics analysis aiming at diverse kinds of samples had been performed. Due to the varied adopted analytical platforms, the reported disease-related metabolites were not consistent across different studies. Comparable metabolomics results are more likely to be acquired by analyzing the same sample types with identical analytical platform. For tumor researches, tissue samples metabolomics analysis own the unique advantage that it can gain more direct insight into disease-specific pathological molecules. In this light, a previous reported capillary electrophoresis - mass spectrometry human tissues metabolomics analysis method was employed to profile the metabolome of rat C6 cell implantation gliomas and the corresponding precancerous tissues. It was found that 9 metabolites increased in the glioma tissues. Of them, hypotaurine was the only metabolite that enriched in the malignant tissues as what had been reported in the relevant human tissues metabolomics analysis. Furthermore, hypotaurine was also proved to inhibit α-ketoglutarate-dependent dioxygenases (2-KDDs) through immunocytochemistry staining and in vitro enzymatic activity assays by using C6 cell cultures. This study reinforced the previous conclusion that hypotaurine acted as a competitive inhibitor of 2-KDDs and proved the value of metabolomics in oncology studies. Copyright © 2017. Published by Elsevier Inc.

Mathematical modeling of the malignancy of cancer using graph evolution.

PubMed

Gunduz-Demir, Cigdem

2007-10-01

We report a novel computational method based on graph evolution process to model the malignancy of brain cancer called glioma. In this work, we analyze the phases that a graph passes through during its evolution and demonstrate strong relation between the malignancy of cancer and the phase of its graph. From the photomicrographs of tissues, which are diagnosed as normal, low-grade cancerous and high-grade cancerous, we construct cell-graphs based on the locations of cells; we probabilistically generate an edge between every pair of cells depending on the Euclidean distance between them. For a cell-graph, we extract connectivity information including the properties of its connected components in order to analyze the phase of the cell-graph. Working with brain tissue samples surgically removed from 12 patients, we demonstrate that cell-graphs generated for different tissue types evolve differently and that they exhibit different phase properties, which distinguish a tissue type from another.

Water-quality assessment of the Rio Grande Valley, Colorado, New Mexico and Texas; organic compounds and trace elements in bed sediment and fish tissue, 1992-93

USGS Publications Warehouse

Carter, L.F.; Anderholm, S.K.

1997-01-01

The occurrence and distribution of contaminants in aquatic systems are major components of the National Water-Quality Assessment (NAWQA) Program. Bed-sediment samples were collected at 18 sites in the Rio Grande Valley study unit between September 1992 and March 1993 to characterize the geographic distribution of organic compounds, including chlorinated insecticides, polychlorinated biphenyls (PCB's), and other chlorinated hydrocarbons, and also trace elements. Two-millimeter-size- fraction sediment was analyzed for organic compounds and less than 63-micron-size-fraction sediment was analyzed for trace elements. Concentrations of p,p'-DDE were detected in 33 percent of the bed-sediment samples. With the exception of DDT-related compounds, no other organochlorine insecticides or polychlorinated biphenyls were detected in samples of bed sediment. Whole-body fish samples were collected at 11 of the bed- sediment sites and analyzed for organic compounds. Organic compounds were reported more frequently in samples of fish, and more types of organic compounds were found in whole-body fish samples than in bed-sediment samples. Concentrations of p,p'-DDE were detected in 91 percent of whole-body fish samples. Polychlorinated biphenyls, cis-chlordane, trans-chlordane, trans- nonachlor, and hexachlorobenzene were other organic compounds detected in whole-body samples of fish from at least one site. Because of the extent of mineralized areas in the Rio Grande Basin arsenic, cadmium, copper, lead, mercury, selenium, and zinc concentrations in bed-sediment samples could represent natural conditions at most sites. However, a combination of natural conditions and human activities appears to be associated with elevated trace-element concentrations in the bed-sediment sample from the site Rio Grande near Creede, Colorado, because this sample exceeded the background trace-element concentrations calculated for this study. Fish-liver samples were collected at 12 of the bed-sediment sites and analyzed for trace elements. Certain trace elements were detected at higher concentrations in fish-liver samples than in bed-sediment samples from the same site. Both bed-sediment and fish-tissue samples are necessary for a complete environmental assessment of the occurrence and distribution of trace elements.

Mercury concentrations of food products and of soils in North Dakota

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deitz, F.D.; Sell, J.L.; Buchanan, M.L.

1973-01-01

Recent discovery of high levels of mercury (Hg) in waterfowl in the state prompted a Hg survey of agricultural products in North Dakota. Milk, eggs, soil, pork and beef tissue (longissimis dorsi and liver) were among the products analyzed. Tissue samples were subjected to wet-oxidation using concentrated HNO/sub 3/ and H/sub 2/SO/sub 4/ acids with vanadium pentoxide as a catalyst. Subsequently, Hg in the digests was determined by the cold-vapor technique, utilizing atomic absorption spectrophotometry. The milk samples analyzed average 0.8 ng/ml (ppb) with a range of 0.0 to 7.0 ng/ml. Beef longissimis dorsi samples average 4.5 ng/g with amore » range of 0.0 to 18.8 ng/g while liver samples from the same animals average 10.1 ng/g (range of 0.0 to 29.5 ng/g). Pork longissimis dorsi samples averaged 5.4 ng/g with a range of 0.0 to 12.5 ng/g while liver samples from the same animals average 12.9 ng/g (range of 0.0 to 26.2 ng/g). Eggs and soil samples had an average mercury content of 15.8 ng/g and 32.7 ng/g respectively.« less

VIROLOGICAL AND SEROLOGICAL DIAGNOSIS OF RABIES IN BATS FROM AN URBAN AREA IN THE BRAZILIAN AMAZON.

PubMed

Oliveira, Rubens Souza de; Costa, Lanna Jamile Corrêa da; Andrade, Fernanda Atanaena Gonçalves de; Uieda, Wilson; Martorelli, Luzia Fátima Alves; Kataoka, Ana Paula de Arruda Geraldes; Rosa, Elizabeth Salbé Travassos da; Vasconcelos, Pedro Fernando da Costa; Pereira, Armando de Souza; Carmo, Antônio Ismael Barros do; Fernandes, Marcus Emanuel Barroncas

2015-12-01

The outbreaks of rabies in humans transmitted by Desmodus rotundus in 2004 and 2005, in the northeast of the Brazilian State of Para, eastern Amazon basin, made this a priority area for studies on this zoonosis. Given this, the present study provides data on this phenomenon in an urban context, in order to assess the possible circulation of the classic rabies virus (RABV) among bat species in Capanema, a town in the Amazon basin. Bats were collected, in 2011, with mist nets during the wet and dry seasons. Samples of brain tissue and blood were collected for virological and serological survey, respectively. None of the 153 brain tissue samples analyzed tested positive for RABV infection, but 50.34% (95% CI: 45.67-55.01%) of the serum samples analyzed were seropositive. Artibeus planirostris was the most common species, with a high percentage of seropositive individuals (52.46%, 95% CI: 52.31 52.60%). Statistically, equal proportions of seropositive results were obtained in the rainy and dry seasons (c2 = 0.057, d.f. = 1, p = 0.88). Significantly higher proportions of males (55.96%, 95% CI: 48.96-62.96%) and adults (52.37%, 95% CI: 47.35-57.39%) were seropositive. While none of the brain tissue samples tested positive for infection, the high proportion of seropositive specimens indicates that RABV may be widespread in this urban area.

Sample processing, protocol, and statistical analysis of the time-of-flight secondary ion mass spectrometry (ToF-SIMS) of protein, cell, and tissue samples.

PubMed

Barreto, Goncalo; Soininen, Antti; Sillat, Tarvo; Konttinen, Yrjö T; Kaivosoja, Emilia

2014-01-01

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly being used in analysis of biological samples. For example, it has been applied to distinguish healthy and osteoarthritic human cartilage. This chapter discusses ToF-SIMS principle and instrumentation including the three modes of analysis in ToF-SIMS. ToF-SIMS sets certain requirements for the samples to be analyzed; for example, the samples have to be vacuum compatible. Accordingly, sample processing steps for different biological samples, i.e., proteins, cells, frozen and paraffin-embedded tissues and extracellular matrix for the ToF-SIMS are presented. Multivariate analysis of the ToF-SIMS data and the necessary data preprocessing steps (peak selection, data normalization, mean-centering, and scaling and transformation) are discussed in this chapter.

[Herpes simplex virus and malignancies of female genital organs].

PubMed

Cokić-Damjanović, J; Horvat, E; Balog, A

2001-01-01

Primary herpes simplex virus (HSV) infections of female genital tract usually end with remission, while the virus remains in the organism--almost in the sacral ganglion in a latent form, protected from humoral and cellular immunity. Stress induces the virus and the result is recurrent genital infection. Frequent exacerbations damage some parts of vital cellular structures without cytolysis, but stimulate malignant transformations. Vulvar (portio vaginalis uteri) and endometrial tumor tissue samples were analyzed for HSV by direct and indirect fluorescent antibody technique (FAT). Pre and postoperative sera samples were analyzed for presence of anti-HSV antibodies--IgM and IgG by Elisa-Enzygnost method. Acellular filtrates obtained by ultrasonic destruction of malignant tissues were used as inoculum for rabbit corneal scarification. Out of 63 tissue samples, 42 were positive for HSV antigen i.e. 67.3%. According to location 50% of vulvar, 76% PVU and 65% of endometrial tissues were positive. This antigen induces production of virus specific antibodies. Two types of antigens are known: the so-called T-antigen persisting in the cell nucleus and cell-surface antigen--product of the viral genome and can be evidenced by immunofluorescence method. Anti HSV antibodies were present in 63 preoperative serum samples and belonged to IgG group, but not one to IgM, implying a long and chronic course of infection excluding acute primary. Out of 38 postoperative serums the titer of antibodies decreased in 36 evidently, but in two samples remained unchanged. Two samples of endometrial and one from PVU origin contained HSV antigen type one. In the remaining 16 samples HSV 2 antigen was present. Rabbit corneal scarification was the proof of complete infectious virus in malignant tissues. Acellular filtrate of malignant tissues served as inoculum. Corneas of examined rabbits showed a mild inflammation after 24 hours which disappeared in the next 24 hours. We could not isolate the infectious virus by rabbit corneal scarification. Instead of herpetic changes, mild inflammation was evident. This abortive, incomplete symptomatology was probably caused by nonstructural early protein, which is a product of viral genome incorporated in malignant cells. On the basis of our results, we can conclude that HSV can have, beside other factors, a very important, maybe an initial role in development of malignant changes of female genital tract, not only on vulva and PVU, but on endometrium as well. HSV I can cause genital infections and have some role in malignant changes as well as HSV 2. However, complete infective virion couldn't be isolated from malignant tissues.

Influence of sample preparation and reliability of automated numerical refocusing in stain-free analysis of dissected tissues with quantitative phase digital holographic microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Lenz, Philipp; Bettenworth, Dominik; Krausewitz, Philipp; Domagk, Dirk; Ketelhut, Steffi

2015-05-01

Digital holographic microscopy (DHM) has been demonstrated to be a versatile tool for high resolution non-destructive quantitative phase imaging of surfaces and multi-modal minimally-invasive monitoring of living cell cultures in-vitro. DHM provides quantitative monitoring of physiological processes through functional imaging and structural analysis which, for example, gives new insight into signalling of cellular water permeability and cell morphology changes due to toxins and infections. Also the analysis of dissected tissues quantitative DHM phase contrast prospects application fields by stain-free imaging and the quantification of tissue density changes. We show that DHM allows imaging of different tissue layers with high contrast in unstained tissue sections. As the investigation of fixed samples represents a very important application field in pathology, we also analyzed the influence of the sample preparation. The retrieved data demonstrate that the quality of quantitative DHM phase images of dissected tissues depends strongly on the fixing method and common staining agents. As in DHM the reconstruction is performed numerically, multi-focus imaging is achieved from a single digital hologram. Thus, we evaluated the automated refocussing feature of DHM for application on different types of dissected tissues and revealed that on moderately stained samples highly reproducible holographic autofocussing can be achieved. Finally, it is demonstrated that alterations of the spatial refractive index distribution in murine and human tissue samples represent a reliable absolute parameter that is related of different degrees of inflammation in experimental colitis and Crohn's disease. This paves the way towards the usage of DHM in digital pathology for automated histological examinations and further studies to elucidate the translational potential of quantitative phase microscopy for the clinical management of patients, e.g., with inflammatory bowel disease.

Expression of the membrane mucins MUC4 and MUC15, potential markers of malignancy and prognosis, in papillary thyroid carcinoma.

PubMed

Nam, Kee-Hyun; Noh, Tae-Woong; Chung, So-Hyang; Lee, So Hee; Lee, Mi Kyung; Hong, Soon Won; Chung, Woong Youn; Lee, Eun Jig; Park, Cheong Soo

2011-07-01

Papillary thyroid carcinoma (PTC) is the most frequent carcinoma of the thyroid gland and has a relatively good prognosis. However, it is important to identify PTC characteristics that indicate high risk for recurrence and metastasis. To date, overexpression of the membrane mucin, MUC1, has been investigated as a key molecular event in the pathogenesis of aggressive PTC. However, other membrane-associated mucins, matrix metalloproteinase-13 (MMP-13) and tissue inhibitor of metalloproteinase-13 (TIMP-3), have not been studied yet. The aim of this study was to evaluate the expression levels of MUC4, MUC15, MMP-13, and TIMP-3 and their prognostic significance in PTC. We analyzed MUC4, MUC15, MMP-13, and TIMP-3 expression in 10 PTC and 10 normal thyroid tissue samples using real-time reverse transcription-polymerase chain reaction. Tissue array blocks were obtained from 98 PTC cases. Tumor regions and nontumor regions were analyzed in tissue array blocks and immunohistochemistry studies were conducted using sectioned slides. Semiquantitative scores were correlated with clinicopathological factors of 98 PTC patients. MUC4- and MUC15-specific mRNA was increased by 78-fold and 4.75-fold, respectively, in PTC samples compared with normal thyroid tissues. MMP-13 and TIMP-3 gene expression levels were decreased by approximately 0.39-fold and 0.53-fold, respectively. By immunohistochemistry, MUC4 and MUC15 expression levels were increased in PTC samples compared with normal thyroid tissues (p < 0.001). MMP-13 and TIMP-3 expression levels were decreased in PTC samples compared with normal thyroid tissues (p < 0.001). High MUC4 scores were significantly correlated with small tumor size and papillary thyroid microcarcinoma subtype. High MUC15 scores were significantly correlated with age (≥45 years), distant metastasis, and multifocality. MUC4 and MUC15 were overexpressed in PTC, and high MUC15 expression was associated with high malignant potential. MUC15 may serve as a prognostic marker and potential novel therapeutic target in PTC.

Tissue distribution of enrofloxacin after intramammary or simulated systemic administration in isolated perfused sheep udders.

PubMed

López Cadenas, Cristina; Fernández Martínez, Nélida; Sierra Vega, Matilde; Diez Liébana, Maria J; Gonzalo Orden, Jose M; Sahagún Prieto, Ana M; García Vieitez, Juan J

2012-11-01

To determine the tissue distribution of enrofloxacin after intramammary or simulated systemic administration in isolated perfused sheep udders by measuring its concentration at various sample collection sites. 26 udders (obtained following euthanasia) from 26 healthy lactating sheep. For each isolated udder, 1 mammary gland was perfused with warmed, gassed Tyrode solution. Enrofloxacin (1 g of enrofloxacin/5 g of ointment) was administered into the perfused gland via the intramammary route or systemically via the perfusion fluid (equivalent to a dose of 5 mg/kg). Samples of the perfusate were obtained every 30 minutes for 180 minutes; glandular tissue samples were obtained at 2, 4, 6, and 8 cm from the teat base after 180 minutes. The enrofloxacin content of the perfusate and tissue samples was analyzed via high-performance liquid chromatography with UV detection. After intramammary administration, maximun perfusate enrofloxacin concentration was detected at 180 minutes and, at this time, mean tissue enrofloxacin concentration was detected and mean tissue enrofloxacin concentration was 123.80, 54.48, 36.72, and 26.42 μg/g of tissue at 2, 4, 6, and 8 cm from the teat base, respectively. Following systemic administration, perfusate enrofloxacin concentration decreased with time and, at 180 minutes, tissue enrofloxacin concentrations ranged from 40.38 to 35.58 μg/g of tissue. By 180 minutes after administration via the intramammary or systemic route in isolated perfused sheep mammary glands, mean tissue concentration of enrofloxacin was greater than the minimum inhibitory concentration required to inhibit growth of 90% of many common mastitis pathogens in sheep. Use of either route of administration (or in combination) appears suitable for the treatment of acute mastitis in sheep.

Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets.

PubMed

Zhu, Ying; Dou, Maowei; Piehowski, Paul D; Liang, Yiran; Wang, Fangjun; Chu, Rosalie K; Chrisler, Will; Smith, Jordan N; Schwarz, Kaitlynn C; Shen, Yufeng; Shukla, Anil K; Moore, Ronald J; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T

2018-06-24

Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution due to the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 µm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-µm-thick rat brain cortex tissue sections with diameters of 50, 100, and 200 µm, respectively. We also analyzed 100-µm-diameter sections corresponding to 10-18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

[Extraction and analysis of chemical components of essential oil in Thymus vulgaris of tissue culture].

PubMed

Li, Xiao-Dong; Yang, Li; Xu, Shi-Qian; Li, Jian-Guo; Cheng, Zhi-Hui; Dang, Jian-Zhang

2011-10-01

To extract the essential oils from the Seedlings, the Aseptic Seedlings and the Tissue Culture Seedlings of Thymus vulgaris and analyze their chemical components and the relative contents. The essential oils were extracted by steam distillation, the chemical components and the relative contents were identified and analyzed by gas chromatography-mass spectrometry (GC/MS) and peak area normalization method. The main chemical components of essential oil in these three samples had no significant difference, they all contained the main components of essential oil in Thymus vulgaris: Thymol, Carvacrol, o-Cymene, gamma-Terpinene, Caryophyllene et al. and only had a slight difference in the relative content. This study provides important theoretical foundation and data reference for further study on production of essential oil in thyme by tissue culture technology.

Thyroid peroxidase (TPO) expressed in thyroid and breast tissues shows similar antigenic properties.

PubMed

Godlewska, Marlena; Arczewska, Katarzyna D; Rudzińska, Magdalena; Łyczkowska, Anna; Krasuska, Wanda; Hanusek, Karolina; Ruf, Jean; Kiedrowski, Mirosław; Czarnocka, Barbara

2017-01-01

Thyroid peroxidase (TPO) is essential for physiological function of the thyroid gland. The high prevalence of thyroid peroxidase antibodies (TPOAbs) in patients with breast cancer and their protective role had previously been demonstrated, indicating a link between breast cancer and thyroid autoimmunity. Recently, TPO was shown to be present in breast cancer tissue samples but its antigenicity has not been analyzed. In this study, we investigated TPO expression levels in a series of fifty-six breast cancer samples paired with normal (peri-tumoral) tissue and its antigenic activity using a panel of well-characterized murine anti-human TPOAbs. We have shown that TPO transcripts were present in both normal and cancer tissue samples, although the amounts in the latter were reduced. Additionally, we observed that TPO levels are lower in more advanced cancers. TPO protein expression was confirmed in all tissue samples, both normal and cancerous. We also found that the antigenicity of the immunodominant regions (IDRs) in breast TPO resembles that of thyroid TPO, which is crucial for effective interactions with human TPOAbs. Expression of TPO in breast cancer together with its antigenic activity may have beneficial effects in TPOAb-positive breast cancer patients. However, further studies are needed to confirm the beneficial role of TPOAbs and to better understand the underlying mechanism.

Evaluation of microwave and ultrasound extraction procedures for arsenic speciation in bivalve mollusks by liquid chromatography-inductively coupled plasma-mass spectrometry

NASA Astrophysics Data System (ADS)

Santos, Clarissa M. M.; Nunes, Matheus A. G.; Barbosa, Isa S.; Santos, Gabriel L.; Peso-Aguiar, Marlene C.; Korn, Maria G. A.; Flores, Erico M. M.; Dressler, Valderi L.

2013-08-01

Liquid chromatography-inductively coupled plasma-mass spectrometry (LC-ICP-MS) was used for arsenic speciation analysis in tissues of bivalve mollusks (Anomalocardia brasiliana sp. and Macoma constricta sp.). Microwave and ultrasound radiation, combined with different extraction conditions (solvent, sample amount, time, and temperature), were evaluated for As-species extraction from the mollusks' tissues. Accuracy, extraction efficiency, and the stability of As species were evaluated by analyzing certified reference materials (DORM-2, dogfish muscle; BCR-627, tuna fish tissue; and SRM 1566b, oyster tissue) and analyte recovery tests. The best conditions were found to be microwave-assisted extraction using 200 mg of samples and water at 80 °C for 6 min. The agreement of As-species concentration in samples ranged from 97% to 102%. Arsenobetaine (AsB) was the main species present in bivalve mollusk tissues, while monomethylarsonic acid (MMA) and arsenate (As(V)) were below the limit of quantification (0.001 and 0.003 μg g- 1, respectively). Two unidentified As species also were detected and quantified. The sum of the As-species concentration was in agreement (90 to 104%), with the total As content determined by ICP-MS after sample digestion.

Expression profiling of microRNAs in human bone tissue from postmenopausal women.

PubMed

De-Ugarte, Laura; Serra-Vinardell, Jenny; Nonell, Lara; Balcells, Susana; Arnal, Magdalena; Nogues, Xavier; Mellibovsky, Leonardo; Grinberg, Daniel; Diez-Perez, Adolfo; Garcia-Giralt, Natalia

2018-01-01

Bone tissue is composed of several cell types, which express their own microRNAs (miRNAs) that will play a role in cell function. The set of total miRNAs expressed in all cell types configures the specific signature of the bone tissue in one physiological condition. The aim of this study was to explore the miRNA expression profile of bone tissue from postmenopausal women. Tissue was obtained from trabecular bone and was analyzed in fresh conditions (n = 6). Primary osteoblasts were also obtained from trabecular bone (n = 4) and human osteoclasts were obtained from monocyte precursors after in vitro differentiation (n = 5). MicroRNA expression profiling was obtained for each sample by microarray and a global miRNA analysis was performed combining the data acquired in all the microarray experiments. From the 641 miRNAs detected in bone tissue samples, 346 (54%) were present in osteoblasts and/or osteoclasts. The other 46% were not identified in any of the bone cells analyzed. Intersection of osteoblast and osteoclast arrays identified 101 miRNAs shared by both cell types, which accounts for 30-40% of miRNAs detected in these cells. In osteoblasts, 266 miRNAs were detected, of which 243 (91%) were also present in the total bone array, representing 38% of all bone miRNAs. In osteoclasts, 340 miRNAs were detected, of which 196 (58%) were also present in the bone tissue array, representing 31% of all miRNAs detected in total bone. These analyses provide an overview of miRNAs expressed in bone tissue, broadening our knowledge in the microRNA field.

Glycomics expression analysis of sulfated glycosaminoglycans of human colorectal cancer tissues and non-neoplastic mucosa by electrospray ionization mass spectrometry.

PubMed

Marolla, Ana Paula Cleto; Waisberg, Jaques; Saba, Gabriela Tognini; Waisberg, Daniel Reis; Margeotto, Fernando Beani; Pinhal, Maria Aparecida da Silva

2015-01-01

To determine the presence of glycosaminoglycans in the extracellular matrix of connective tissue from neoplastic and non-neoplastic colorectal tissues, since it has a central role in tumor development and progression. Tissue samples from neoplastic and non-neoplastic colorectal tissues were obtained from 64 operated patients who had colorectal carcinoma with no distant metastases. Expressions of heparan sulphate, chondroitin sulphate, dermatan sulphate and their fragments were analyzed by electrospray ionization mass spectrometry, with the technique for extraction and quantification of glycosaminoglycans after proteolysis and electrophoresis. The statistical analysis included mean, standard deviation, and Student'st test. The glycosaminoglycans extracted from colorectal tissue showed three electrophoretic bands in agarose gel. Electrospray ionization mass spectrometry showed characteristic disaccharide fragments from glycosaminoglycans, indicating their structural characterization in the tissues analyzed. Some peaks in the electrospray ionization mass spectrometry were not characterized as fragments of sugars, indicating the presence of fragments of the protein structure of proteoglycans generated during the glycosaminoglycan purification. The average amount of chondroitin and dermatan increased in the neoplastic tissue compared to normal tissue (p=0.01). On the other hand, the average amount of heparan decreased in the neoplastic tissue compared to normal tissue (p= 0.03). The method allowed the determination of the glycosaminoglycans structural profile in colorectal tissue from neoplastic and non-neoplastic colorectal tissue. Neoplastic tissues showed greater amounts of chondroitin sulphate and dermatan sulphate compared to non-neoplastic tissues, while heparan sulphate was decreased in neoplastic tissues.

System and method for controlling depth of imaging in tissues using fluorescence microscopy under ultraviolet excitation following staining with fluorescing agents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levenson, Richard; Demos, Stavros

A method is disclosed for analyzing a thin tissue sample and adapted to be supported on a slide. The tissue sample may be placed on a slide and exposed to one or more different exogenous fluorophores excitable in a range of about 300 nm-200 nm, and having a useful emission band from about 350 nm-900 nm, and including one or more fluorescent dyes or fluorescently labeled molecular probes that accumulate in tissue or cellular components. The fluorophores may be excited with a first wavelength of UV light between about 200 nm-290 nm. An optical system collects emissions from the fluorophoresmore » at a second wavelength, different from the first wavelength, which are generated in response to the first wavelength of UV light, to produce an image for analysis.« less

Cell and Tissue Microarray Technologies for Protein and Nucleic Acid Expression Profiling

PubMed Central

Cardano, Marina; Diaferia, Giuseppe R.; Falavigna, Maurizio; Spinelli, Chiara C.; Sessa, Fausto; DeBlasio, Pasquale

2013-01-01

Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform. PMID:23172795

Comparison of liquid chromatographic and bioassay procedures for determining depletion of intramuscularly injected tylosin.

PubMed

Moats, W A; Harris, E W; Steele, N C

1985-01-01

Crossbred pigs weighing 80-110 kg were injected intramuscularly in the ham with 8.8 mg/kg tylosin. Animals were slaughtered in groups of 3 at intervals of 4 h, and 1, 2, 4, and 8 days after injection, and samples of blood, injected muscle, uninjected muscle, liver, and kidney were analyzed by liquid chromatography (LC) and by bioassay using Sarcina lutea as the test organism. The LC method was far more sensitive with a detection limit of less than 0.1 ppm, while the detection limit by bioassay was about 0.5 ppm in tissue. Results by bioassay and LC sometimes differed considerably for tissue samples. Residues in all tissues were below the tolerance limit of 0.2 ppm at 24 h, except in the injected muscle in one animal. Residues were not detected in any tissue of any animal at 48 h after treatment.

Device for high spatial resolution chemical analysis of a sample and method of high spatial resolution chemical analysis

DOEpatents

Van Berkel, Gary J.

2015-10-06

A system and method for analyzing a chemical composition of a specimen are described. The system can include at least one pin; a sampling device configured to contact a liquid with a specimen on the at least one pin to form a testing solution; and a stepper mechanism configured to move the at least one pin and the sampling device relative to one another. The system can also include an analytical instrument for determining a chemical composition of the specimen from the testing solution. In particular, the systems and methods described herein enable chemical analysis of specimens, such as tissue, to be evaluated in a manner that the spatial-resolution is limited by the size of the pins used to obtain tissue samples, not the size of the sampling device used to solubilize the samples coupled to the pins.

Comparison of human papillomavirus detection between freshly frozen tissue and paraffin embedded tissue of invasive cervical cancer

PubMed Central

2010-01-01

Background Human Papillomavirus (HPV) detection results comparing paraffin embedded cervical tissue and other cervical specimens have been done with varying degrees of agreement. However, studies comparing freshly frozen specimens and paraffin embedded specimens of invasive cervical carcinomas are lacking. The aim of the study was to compare HPV detection using SPF10 broad-spectrum primers PCR followed by DEIA and genotyping by LiPA25 (version 1) between freshly frozen cervical tissue samples and paraffin embedded blocks of cervical tissue from the same patient. There were 171 pairs of paraffin embedded and freshly frozen samples analyzed from cervical carcinoma cases from Kampala, Uganda. Results 88.9% (95% CI: 83.2%-93.2%) of paraffin embedded samples were HPV positive compared with 90.1% (95% CI: 84.6%-94.1%) of freshly frozen samples, giving an overall agreement in HPV detection between fresh tissue and paraffin embedded tissue at 86.0% (95% CI: 79.8%-90.8%). Although the proportion of HPV positive cases in freshly frozen tissue was higher than those in paraffin blocks, the difference was not statistically significant (p > 0.05). In both types of tissues, single HPV infections were predominant, with HPV16 accounting for 47% of positive cases. Comparison in the overall agreement, taking into accounts not only positivity in general, but also HPV types, showed a 65% agreement (complete agreement of 59.7%, partial agreement of 5.3%) and complete disagreement of 35.0%. HPV detection in squamous cell carcinomas (SCC) and adenocarcinomas (ADC) was similar in fresh tissue or paraffin blocks (p ≥ 0.05). p16 immunostaining in samples that had at least one HPV negative results showed that 24 out of 25 cases had an over-expressed pattern. Conclusions HPV DNA detection was lower among ADC as compared to SCC. However, such differences were minimized when additional p16 testing was added, suggesting that the technical issues may largely explain the HPV negative cases. PMID:20846370

The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease.

PubMed

Pragman, Alexa A; Lyu, Tianmeng; Baller, Joshua A; Gould, Trevor J; Kelly, Rosemary F; Reilly, Cavan S; Isaacson, Richard E; Wendt, Chris H

2018-01-09

Oral taxa are often found in the chronic obstructive pulmonary disease (COPD) lung microbiota, but it is not clear if this is due to a physiologic process such as aspiration or experimental contamination at the time of specimen collection. Microbiota samples were obtained from nine subjects with mild or moderate COPD by swabbing lung tissue and upper airway sites during lung lobectomy. Lung specimens were not contaminated with upper airway taxa since they were obtained surgically. The microbiota were analyzed with 16S rRNA gene qPCR and 16S rRNA gene hypervariable region 3 (V3) sequencing. Data analyses were performed using QIIME, SourceTracker, and R. Streptococcus was the most common genus in the oral, bronchial, and lung tissue samples, and multiple other taxa were present in both the upper and lower airways. Each subject's own bronchial and lung tissue microbiota were more similar to each other than were the bronchial and lung tissue microbiota of two different subjects (permutation test, p = 0.0139), indicating more within-subject similarity than between-subject similarity at these two lung sites. Principal coordinate analysis of all subject samples revealed clustering by anatomic sampling site (PERMANOVA, p = 0.001), but not by subject. SourceTracker analysis found that the sources of the lung tissue microbiota were 21.1% (mean) oral microbiota, 8.7% nasal microbiota, and 70.1% unknown. An analysis using the neutral theory of community ecology revealed that the lung tissue microbiota closely reflects the bronchial, oral, and nasal microbiota (immigration parameter estimates 0.69, 0.62, and 0.74, respectively), with some evidence of ecologic drift occurring in the lung tissue. This is the first study to evaluate the mild-moderate COPD lung tissue microbiota without potential for upper airway contamination of the lung samples. In our small study of subjects with COPD, we found oral and nasal bacteria in the lung tissue microbiota, confirming that aspiration is a source of the COPD lung microbiota.

Assessment of Regenerative Capacity in the Dolphin

DTIC Science & Technology

2010-10-10

liposuction ; cells released during the digestion of the adipose tissue were analyzed for cytology, assayed for the total number of colony-forming cells... liposuction was used to harvest subcutaneous adipose from the nuchal pad of six dolphins at the Navy Marine Mammal Program (NMMP). Adipose samples...and aid in the placement of the liposuction cannula in the adipose depot. The difference between the various layers of muscle and adipose tissue

Association between promoter hypermethylation of the DACT2 gene and tumor stages in breast cancer.

PubMed

Marusa Borgonio-Cuadra, Veronica; Miranda-Duarte, Antonio; Rojas-Toledo, Xochitl; Garcia-Hernandez, Normand; Alfredo Sierra-Ramirez, Jose; Cardenas-Garcia, Maura; Elena Hernandez-Caballero, Marta

2018-01-01

Aberrant methylation of CpG islands in the promoter is a hallmark of cancer, leading to transcriptional silencing of tumor suppressor genes. The aim of this work was to evaluate the promoter methylation status of the DACT2 gene in breast cancer (BC) tissue and to analyze its possible effect on tumor type or grade. CpG island from the DACT2 promoter in region -240 to -14 from transcriptional start site (TSS) were obtained. Through the use of sodium bisulfite DNA conversion analysis, followed by detection with MSP (methylation specific PCR), we analyzed 79 BC and 15 adjacent healthy samples. T he c ases a nalyzed w ere i n s tage I ( 2.5%), I I (38%), or III (59.5%). The most frequent tumor type was invasive ductal carcinoma (71.4%). Methylation analysis comparing tumor tissues with adjacent non-cancerous tissues showed statistical significance. Methylation was observed in 32.9% (26/79) of the samples; no methylation was found in adjacent healthy tissue. DACT2 methylation was associated with tumor stage I-II (p=0.03) and stage III (p=0.004). An association was found of DACT2 promoter methylation with advanced tumor stages. This gene has been suggested as a potential biomarker, however, more investigation is required to validate this function.

Spectral grading and Gleason grading of malignant prostate tissue using Stokes shift spectra

NASA Astrophysics Data System (ADS)

Al Salhi, M.; Masilamani, V.; Rabah, D.; Farhat, K.; Liu, C. H.; Pu, Y.; Alfano, R. R.

2012-01-01

Gleason score is the most common method of grading the virulence of prostate malignancy and is based on the pathological assessment of morphology of cellular matrix. Since this involves the excision of the tissue, we are working on a new, minimally invasive, non contact, procedure of spectral diagnosis of prostate malignancy. In this preliminary in vitro study reported here, we have analyzed 27 tissue samples (normal control =7: benign=8: malignant =12) by Stokes' shift spectra (SSS) to establish a one- to- one correlation between spectral grading and Gleason grading.

The airway antigen sampling system: respiratory M cells as an alternative gateway for inhaled antigens.

PubMed

Kim, Dong-Young; Sato, Ayuko; Fukuyama, Satoshi; Sagara, Hiroshi; Nagatake, Takahiro; Kong, Il Gyu; Goda, Kaoru; Nochi, Tomonori; Kunisawa, Jun; Sato, Shintaro; Yokota, Yoshifumi; Lee, Chul Hee; Kiyono, Hiroshi

2011-04-01

In this study, we demonstrated a new airway Ag sampling site by analyzing tissue sections of the murine nasal passages. We revealed the presence of respiratory M cells, which had the ability to take up OVA and recombinant Salmonella typhimurium expressing GFP, in the turbinates covered with single-layer epithelium. These M cells were also capable of taking up respiratory pathogen group A Streptococcus after nasal challenge. Inhibitor of DNA binding/differentiation 2 (Id2)-deficient mice, which are deficient in lymphoid tissues, including nasopharynx-associated lymphoid tissue, had a similar frequency of M cell clusters in their nasal epithelia to that of their littermates, Id2(+/-) mice. The titers of Ag-specific Abs were as high in Id2(-/-) mice as in Id2(+/-) mice after nasal immunization with recombinant Salmonella-ToxC or group A Streptococcus, indicating that respiratory M cells were capable of sampling inhaled bacterial Ag to initiate an Ag-specific immune response. Taken together, these findings suggest that respiratory M cells act as a nasopharynx-associated lymphoid tissue-independent alternative gateway for Ag sampling and subsequent induction of Ag-specific immune responses in the upper respiratory tract.

Reducing the orientation influence of Mueller matrix measurements for anisotropic scattering media

NASA Astrophysics Data System (ADS)

Sun, Minghao; He, Honghui; Zeng, Nan; Du, E.; He, Yonghong; Ma, Hui

2014-09-01

Mueller matrix polarimetry techniques contain rich micro-structural information of samples, such as the sizes and refractive indices of scatterers. Recently, Mueller matrix imaging methods have shown great potentials as powerful tools for biomedical diagnosis. However, the orientations of anisotropic fibrous structures in tissues have prominent influence on Mueller matrix measurements, resulting in difficulties for extracting micro-structural information effectively. In this paper, we apply the backscattering Mueller matrix imaging technique to biological samples with different microstructures, such as chicken heart muscle, bovine skeletal muscle, porcine liver and fat tissues. Experimental results show that the directions of the muscle fibers have prominent influence on the Mueller matrix elements. In order to reduce the orientation influence, we adopt the rotation-independent MMT and RLPI parameters, which were proposed in our previous studies, to the tissue samples. Preliminary results in this paper show that the orientation-independent parameters and their statistic features are helpful for analyzing the tissues to obtain their micro-structural properties. Since the micro-structure variations are often related to the pathological changes, the method can be applied to microscope imaging techniques and used to detect abnormal tissues such as cancer and other lesions for diagnosis purposes.

Water-quality assessment of part of the Upper Mississippi River Basin, Minnesota and Wisconsin: Organochlorine compounds in streambed sediments and fish tissues, 1995-97

USGS Publications Warehouse

McNellis, R.P.; Fallon, J.D.; Lee, K.E.

2001-01-01

Streambed sediments and fish tissues were collected in part of the Upper Mississippi River Basin to assess the presence and distribution of organochlorine compounds (OCs) including PCBs. A total of 13 OCs were detected among 14 of 27 streambed sediment sampling locations. In fish tissues analyzed, 9 OCs were detected among 17 of 24 sites sampled. Eight OCs were detected in both fish and streambed sediment samples, they were: cis-chlordane, o,p'-DDD; p,p'-DDD; p,p'-DDE; p,p'-DDT; hexachlorobenzene; transnonachlor; and PCBs. The most frequently detected OCs were: p,p'-DDE; and p,p'-DDD in streambed sediment and p,p'-DDE and PCBs in fish tissues. No OCs were detected in streambed sediment at agricultural sites; however, the agricultural sites had 17 detections of OCs in fish tissue. Urban streams had concentrations of total DDT and metabolites in streambed sediment that exceed guidelines for classification of sites with high probabilities of adverse effects to aquatic organisms. Total DDT was the only OC within an urban land use that exceeded guidelines for piscivorous wildlife.

Expression levels of matrix metalloproteinase-9 in human gastric carcinoma.

PubMed

Chen, Su-Zuan; Yao, Huai-Qi; Zhu, Sen-Zhi; Li, Qiu-Yuan; Guo, Guang-Hua; Yu, Jing

2015-02-01

The present report investigated the correlation between the expression levels of matrix metalloproteinase (MMP)-9 in gastric carcinoma patients and the clinicopathological characteristics. Forty-five samples of gastric carcinoma and distal gastric mucosa tissue, and 10 samples of healthy gastric mucosa tissue were analyzed using semi-quantitative polymerase chain reaction, as well as immunohistochemical and hematoxylin and eosin staining. MMP-9 protein levels in serum samples from the same patients were quantified by enzyme-linked immunosorbent assay. The present report identified that MMP-9 expression was markedly higher in the gastric carcinoma tissue (86.67%) than in the adjacent healthy tissue (10.00%). A positive association was identified between the level of MMP-9 protein expression and the depth of cancer invasion (P<0.05). Furthermore, the preoperative serum levels of the MMP-9 protein in the gastric carcinoma tissue were correlated with the tumor-node-metastasis stage and occurrence of lymph node metastasis (P<0.01). Data from the present report indicates that MMP-9 may be key in gastric carcinoma malignancy, and implies that MMP-9 may serve as a novel biomarker in the diagnosis and prognosis of gastric carcinoma.

Biological Sampling and Analysis in Sinclair and Dyes Inlets, Washington: Chemical Analyses for 2007 Puget Sound Biota Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandenberger, Jill M.; Suslick, Carolynn R.; Johnston, Robert K.

2008-10-09

Evaluating spatial and temporal trends in contaminant residues in Puget Sound fish and macroinvertebrates are the objectives of the Puget Sound Ambient Monitoring Program (PSAMP). In a cooperative effort between the ENVironmental inVESTment group (ENVVEST) and Washington State Department of Fish and Wildlife, additional biota samples were collected during the 2007 PSAMP biota survey and analyzed for chemical residues and stable isotopes of carbon (δ13C) and nitrogen (δ15N). Approximately three specimens of each species collected from Sinclair Inlet, Georgia Basin, and reference locations in Puget Sound were selected for whole body chemical analysis. The muscle tissue of specimens selected formore » chemical analyses were also analyzed for δ13C and δ15N to provide information on relative trophic level and food sources. This data report summarizes the chemical residues for the 2007 PSAMP fish and macro-invertebrate samples. In addition, six Spiny Dogfish (Squalus acanthias) samples were necropsied to evaluate chemical residue of various parts of the fish (digestive tract, liver, embryo, muscle tissue), as well as, a weight proportional whole body composite (WBWC). Whole organisms were homogenized and analyzed for silver, arsenic, cadmium, chromium, copper, nickel, lead, zinc, mercury, 19 polychlorinated biphenyl (PCB) congeners, PCB homologues, percent moisture, percent lipids, δ13C, and δ15N.« less

Transplacental transfer of persistent organic pollutants in La Plata dolphins (Pontoporia blainvillei; Cetartiodactyla, Pontoporiidae).

PubMed

Barbosa, Ana Paula Moreno; Méndez-Fernandez, Paula; Dias, Patrick Simões; Santos, Marcos César Oliveira; Taniguchi, Satie; Montone, Rosalinda Carmela

2018-08-01

Persistent organic pollutants (POPs) accumulate in the fat tissue of living organisms and are found in relatively high concentrations in animals at the top of the food chain, such as dolphins. The ability of these compounds to interact with the endocrine system of marine mammals constitutes a risk for the reproduction and conservation of species. The La Plata dolphin, Pontoporia blainvillei, is exclusive to the southwestern Atlantic Ocean and is classified on the IUCN red list as a vulnerable species. Blubber, liver, kidney and muscle samples from four P. blainvillei mother-fetus pairs were analyzed to evaluate the transfer of POPs to fetal tissues through the placenta. The presence of POPs in fetal tissues indicates the maternal transfer of compounds. In the pregnant females, blubber was the tissue with POP highest concentration, followed by the liver, kidneys and muscles. In the fetuses, POP accumulation mainly occurred in the blubber followed by the muscles, liver and kidneys. Polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDTs) were found in all tissues analyzed and had the highest concentrations among all compounds. The main PCB congeners in the fetal samples had five to seven chlorine atoms. The only polybrominated diphenyl ether (PBDE) in the fetal samples was 47 and was found only in blubber. The main DDT metabolite in the fetuses was p,p'-DDE. POP transfer via the placenta occurs in the first months of gestation and increases with fetal development, according to fetus/mother (F/M) ratio: HCB>DDT>PCB>PBDE>Mirex, which may follow the order of the octanol/water partition coefficient (K ow ) values. Copyright © 2018 Elsevier B.V. All rights reserved.

Mercury, lead, and cadmium in blue crabs, Callinectes sapidus, from the Atlantic coast of Florida, USA: a multipredator approach.

PubMed

Adams, Douglas H; Engel, Marc E

2014-04-01

Blue crabs, Callinectes sapidus, from the Atlantic coast of Florida were analyzed for total mercury, methylmercury, lead, and cadmium. Paired samples of two tissue types were analyzed for each crab, (1) muscle tissue (cheliped and body muscles) and (2) whole-body tissue (all organs, muscle tissue and connective tissue), for evaluation of the concentration of metals available to human consumers as well as estuarine predators. There were clear patterns of tissue-specific partitioning for each metal. Total mercury was significantly greater in muscle tissue (mean=0.078 µg/g) than in whole-body tissue (mean=0.055 µg/g). Conversely, whole-body concentrations of lead and cadmium (means=0.131 and 0.079 µg/g, respectively) were significantly greater than concentrations in muscle (means=0.02 and 0.029 µg/g, respectively). There were no significant correlations between any metal contaminant and crab size. Cadmium levels were significantly greater in the muscle tissue of females, but, no other sex-related differences were seen for other metals or tissue types. Methylmercury composed 93-100% of the total mercury in tissues. Compared to previous blue crab studies from different regions of the United States, mean concentrations of mercury, lead, and cadmium were relatively low, although isolated groups or individual blue crabs accumulated high metal concentrations. © 2013 Published by Elsevier Inc.

Micro-quantity tissue digestion for metal measurements by use of a microwave acid-digestion bomb.

PubMed

Nicholson, J R; Savory, M G; Savory, J; Wills, M R

1989-03-01

We describe a simple and convenient method for processing small amounts of tissue samples for trace-metal measurements by atomic absorption spectrometry, by use of a modified Parr microwave digestion bomb. Digestion proceeds rapidly (less than or equal to 90 s) in a sealed Teflon-lined vessel that eliminates contamination or loss from volatilization. Small quantities of tissue (5-100 mg dry weight) are digested in high-purity nitric acid, yielding concentrations of analyte that can be measured directly without further sample manipulation. We analyzed National Institute of Standards and Technology bovine liver Standard Reference Material to verify the accuracy of the technique. We assessed the applicability of the technique to analysis for aluminum in bone by comparison with a dry ashing procedure.

Biomarkers of the Hedgehog/Smoothened pathway in healthy volunteers

PubMed Central

Kadam, Sunil K; Patel, Bharvin K R; Jones, Emma; Nguyen, Tuan S; Verma, Lalit K; Landschulz, Katherine T; Stepaniants, Sergey; Li, Bin; Brandt, John T; Brail, Leslie H

2012-01-01

The Hedgehog (Hh) pathway is involved in oncogenic transformation and tumor maintenance. The primary objective of this study was to select surrogate tissue to measure messenger ribonucleic acid (mRNA) levels of Hh pathway genes for measurement of pharmacodynamic effect. Expression of Hh pathway specific genes was measured by quantitative real time polymerase chain reaction (qRT-PCR) and global gene expression using Affymetrix U133 microarrays. Correlations were made between the expression of specific genes determined by qRT-PCR and normalized microarray data. Gene ontology analysis using microarray data for a broader set of Hh pathway genes was performed to identify additional Hh pathway-related markers in the surrogate tissue. RNA extracted from blood, hair follicle, and skin obtained from healthy subjects was analyzed by qRT-PCR for 31 genes, whereas 8 samples were analyzed for a 7-gene subset. Twelve sample sets, each with ≤500 ng total RNA derived from hair, skin, and blood, were analyzed using Affymetrix U133 microarrays. Transcripts for several Hh pathway genes were undetectable in blood using qRT-PCR. Skin was the most desirable matrix, followed by hair follicle. Whether processed by robust multiarray average or microarray suite 5 (MAS5), expression patterns of individual samples showed co-clustered signals; both normalization methods were equally effective for unsupervised analysis. The MAS5- normalized probe sets appeared better suited for supervised analysis. This work provides the basis for selection of a surrogate tissue and an expression analysis-based approach to evaluate pathway-related genes as markers of pharmacodynamic effect with novel inhibitors of the Hh pathway. PMID:22611475

Characterization of the mechanical properties of resected porcine organ tissue using optical fiber photoelastic polarimetry.

PubMed

Hudnut, Alexa W; Babaei, Behzad; Liu, Sonya; Larson, Brent K; Mumenthaler, Shannon M; Armani, Andrea M

2017-10-01

Characterizing the mechanical behavior of living tissue presents an interesting challenge because the elasticity varies by eight orders of magnitude, from 50Pa to 5GPa. In the present work, a non-destructive optical fiber photoelastic polarimetry system is used to analyze the mechanical properties of resected samples from porcine liver, kidney, and pancreas. Using a quasi-linear viscoelastic fit, the elastic modulus values of the different organ systems are determined. They are in agreement with previous work. In addition, a histological assessment of compressed and uncompressed tissues confirms that the tissue is not damaged during testing.

Liquid microjunction surface sampling coupled with high-pressure liquid chromatography-electrospray ionization-mass spectrometry for analysis of drugs and metabolites in whole-body thin tissue sections.

PubMed

Kertesz, Vilmos; Van Berkel, Gary J

2010-07-15

In this work, a commercially available autosampler was adapted to perform direct liquid microjunction (LMJ) surface sampling followed by a high-pressure liquid chromatography (HPLC) separation of the extract components and detection with electrospray ionization mass spectrometry (ESI-MS). To illustrate the utility of coupling a separation with this direct liquid extraction based surface sampling approach, four different organs (brain, lung, kidney, and liver) from whole-body thin tissue sections of propranolol dosed and control mice were examined. The parent drug was observed in the chromatograms of the surface sampling extracts from all the organs of the dosed mouse examined. In addition, two isomeric phase II metabolites of propranolol (an aliphatic and an aromatic hydroxypropranolol glucuronide) were observed in the chromatograms of the extracts from lung, kidney, and liver. Confirming the presence of one or the other or both of these glucuronides in the extract from the various organs was not possible without the separation. These drug and metabolite data obtained using the LMJ surface sampling/HPLC-MS method and the results achieved by analyzing similar samples by conventional extraction of the tissues and subsequent HPLC-MS analysis were consistent. The ability to directly and efficiently sample from thin tissue sections via a liquid extraction and then perform a subsequent liquid phase separation increases the utility of this liquid extraction surface sampling approach.

Detection of Leishmania in Unaffected Mucosal Tissues of Patients with Cutaneous Leishmaniasis Caused by Leishmania (Viannia) Species

PubMed Central

Figueroa, Roger Adrian; Lozano, Leyder Elena; Romero, Ibeth Cristina; Cardona, Maria Teresa; Prager, Martin; Pacheco, Robinson; Diaz, Yira Rosalba; Tellez, Jair Alexander; Saravia, Nancy Gore

2016-01-01

Background Leishmania (Viannia) species are the principal cause of mucosal leishmaniasis. The natural history and pathogenesis of mucosal disease are enigmatic. Parasitological evaluation of mucosal tissues has been constrained by the invasiveness of conventional sampling methods. Methods We evaluated the presence ofLeishmania in the mucosa of 26 patients with cutaneous leishmaniasis and 2 patients with mucocutaneous leishmaniasis. Swab samples of the nasal mucosa, tonsils, and conjunctiva were analyzed using polymerase chain reaction with LV-B1 primers and Southern blot hybridization. Results Two patients with mucocutaneous leishmaniasis and 21 (81%) of 26 patients with cutaneous leishmaniasis had Leishmania kinetoplast minicircle DNA (kDNA) in mucosal tissues. kDNA was amplified from swab samples of nasal mucosa from 14 (58%) of 24 patients, tonsils from 13 (46%) of 28 patients, and conjunctiva from 6 (25%) of 24 patients. kDNA was detected in the mucosa of patients with cutaneous disease caused by Leishmania panamensis, Leishmania guyanensis, and Leishmania braziliensis. Conclusion The asymptomatic presence of parasites in mucosal tissues may be common in patients with Leishmania (Viannia) infection. PMID:19569974

Effects of dietary Pb on accumulation, histopathology, and digestive enzyme activities in the digestive system of tilapia (Oreochromis niloticus).

PubMed

Dai, Wei; Du, Huahua; Fu, Linglin; Jin, Chengguan; Xu, Zirong; Liu, Huitao

2009-02-01

With the increasing occurrence of dietary lead (Pb) contamination in aquatic environment, threat of the dietary Pb toxicity to aquatic organisms attracted more attention. In this study, after being exposed to dietary Pb at concentrations of 0, 100, 400, and 800-microg/g dry weight for 60 days, the groups of tilapia (Oreochromis niloticus) were sacrificed and sampled to analyze the effects of dietary Pb on accumulation, histopathology, and digestive enzyme activities in tissues of the digestive system. The results showed that the Pb accumulation in tissues increased with the dietary Pb concentrations. Moreover, Pb accumulated in sampled tissues in the following order: intestine > stomach > liver. By observation of liver histological sections in optical microscope, lesions could be detected in the Pb-contaminated groups. It was also demonstrated that the inhibitory effect of dietary Pb on digestive enzyme activities was dietary Pb concentration dependent. Different degrees of inhibition of enzyme activities were exhibited in sampled tissues. It was indicated that digestive enzyme activities in the digestive system might be considered as the potential biomarkers of dietary Pb contamination in tilapia.

Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types.

PubMed

Plessy, Charles; Desbois, Linda; Fujii, Teruo; Carninci, Piero

2013-02-01

Tissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual cells. Here, we describe microfluidics technologies that utilize a combination of molecular biology and miniaturized labs on chips to study gene expression at the single cell level. We discuss how the characterization of the transcriptome of each cell in a sample will open a new field in gene expression analysis, population transcriptomics, that will change the academic and biomedical analysis of complex samples by defining them as quantified populations of single cells. Copyright © 2013 WILEY Periodicals, Inc.

Molecular glycopathology by capillary electrophoresis: Analysis of the N-glycome of formalin-fixed paraffin-embedded mouse tissue samples.

PubMed

Donczo, Boglarka; Szarka, Mate; Tovari, Jozsef; Ostoros, Gyorgyi; Csanky, Eszter; Guttman, Andras

2017-06-01

Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing. Structural assignment of the oligosaccharides was accomplished by the help of the GUcal software and the associated database, based on the mobility shifts after treatments with the corresponding exoglycosidase reaction mixtures. Sixteen major N-linked carbohydrate structures were sequenced from the mouse lung FFPE tissue glycome and identified, as high mannose (3) neutral biantennary (3) sialylated monoantennary (1) and sialylated bianennary (9) oligosaccharides. Two of these latter ones also possessed alpha(1-3) linked galactose residues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Post-Remediation Biomonitoring of Pesticides in Marine Waters Near the United Heckathorn Superfund Site, Richmond, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

LD Antrim; NP Kohn

This report, PNNL-11911 Rev. 1, was published in July 2000 and replaces PNNL-11911, which was published in September 1998. The revision corrects tissue concentration units that were reported as dry weight but were actually wet weight, and updates conclusions based on the correct reporting units. Marine sediment remediation at the United Heckathorn Superfund Site was completed in April 1997. Water and mussel tissues were sampled in January 1998 from four stations near Lauritzen Canal in Richmond, California, for the first post-remediation monitoring of marine areas near the United Heckathorn Site. Dieldrin and DDT were analyzed in water samples, tissue samplesmore » from resident mussels, and tissue samples from transplanted mussels deployed for 4 months. Concentrations of dieldrin and total DDT in water and total DDT in tissue were compared to pre-remediation data available from the California State Mussel Watch program (tissues) and the Ecological Risk Assessment for the United Heckathorn Superfund Site (tissues and water). Chlorinated pesticide concentrations in water samples were similar to pre-remediation levels and did not meet remediation goals. Mean dieldrin concentrations in water ranged from 0.65 ng/L to 18.1 ng/L and were higher than the remediation goal (0.14 ng/L) at all stations. Mean total DDT concentrations in water ranged from 0.65 ng/L to 103 ng/L and exceeded the remediation goal of 0.59 ng/L. The highest concentrations of both pesticides were found in Lauritzen Canal, and the lowest levels were from the Richmond Inner Harbor Channel water. Unusual amounts of detritus in the water column at the time of sampling, particularly in Lauritzen Canal, could have contributed to the elevated pesticide concentrations and poor analytical precision.« less

Selenium and mining in the Powder River Basin, Wyoming: Phase III - a preliminary survey of selenium concentrations in deer mice (Peromyscus maniculatus) livers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raisbeck, M.L.; Vance, G.F.; Steward, D.G.

1995-09-01

Samples of liver tissue from deer mice trapped on not-yet-mined areas and reclaimed areas at five surface coal mines in the Powder River Basin of northeastern Wyoming were analyzed for selenium. The overall mean concentration of selenium in wet weight liver tissue was 1.685 ppm. The mean value from not-yet-mined areas was 1.437 ppm; the mean value from reclaimed areas was 1.910 ppm (significant at p<0.1016). When one not-yet-mined outlier was removed, significance rose to p<0.0004. Mine-to-mine comparison of samples stratified by type (that is, by not-yet-mined or reclaimed), showed average tissue concentrations from the reclaimed area of Mine 1more » were also higher (p<0.0143) then not-yet-mined area samples at Mine 1. No statistically significant differences were found between mines for samples from not-yet-mined areas, and no statistically significant differences were found between Mines 2, 3, 4, and 5 for samples from reclaimed areas. Multiple analysis of variance using the factors: site (mine) and type (not-yet-mined or reclaimed) was not significantly significant (p<0.2115). Simple linear regression showed that selenium concentrations in dry tissue could easily be predicted from wet tissue selenium (r2=0.9775), demonstrating that percent water in the samples was relatively constant. Animal body weight in general was not a predictor for either wet or dry tissue selenium concentrations, but was related to body weight at the higher tissue concentrations of selenium encountered in samples from the reclaimed area at Mine 1. Mouse body weights at Mine 1 were higher on the reclaimed area than mouse body weights from the not-yet-mined area.« less

Tissue identification during Pneumoperitoneum in laparoscopy

NASA Astrophysics Data System (ADS)

Chang, Yin; Tseng, Chi-Yang

2015-03-01

Pneumoperitoneum is the beginning procedure of laparoscopy to enlarge the abdominal cavity in order to allow the surgical instruments to insert for surgical purpose. However, the insertion of Veress needle is a blind fashion that could cause blood vessels or visceral injury without attention and results in undetectable internal bleeding. Seriously it may cause a life-threatened complication. We have developed a method that can monitor the tissue reflective spectrum, which can be used for tissue discrimination, in real time during the puncture of the Veress needle. The system includes a modified Veress needle which containes an optical bundle, a light spectrum analyzing and control unit. Therefore, the tissue reflective spectrum can be vivid observed and analyzed through the fiber optical technology during the procedure of the Veress needle insertion. In this study, we have measured the reflective spectra of various porcine abdominal tissues. The features of their spectra were analyzed and characterized to build up the data base and create an algorithm for tissue discrimination in laparoscopy. The results showed that the correlation coefficient (r) of the reflective spectrum can be 0.79-0.95 for the wavelength range of 350-1000 nm and 0.85-0.98 for the wavelength range of 350-650 nm in the same tissue of various samples which were obtained from different days. An alternative way for tissue discrimination is achieved through a decision making tree according to the characteristics of tissue spectrum. For single blind test the success rate is nearly 100%. It seems that both the algorithms mentioned above for tissue discrimination are all very promising. Therefore, these algorithms will be applied to in vivo study in animal in the near future.

Positron Spectroscopy Investigation of Normal Brain Section and Brain Section with Glioma Derived from a Rat Glioma Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, SH.; Ballmann, C.; Quarles, C. A.

2009-03-10

The application of positron annihilation lifetime spectroscopy (PALS) and Doppler broadening spectroscopy (DBS) to the study of animal or human tissue has only recently been reported [G. Liu, et al. phys. stat. sol. (C) 4, Nos. 10, 3912-3915 (2007)]. We have initiated a study of normal brain section and brain section with glioma derived from a rat glioma model. For the rat glioma model, 200,000 C6 cells were implanted in the basal ganglion of adult Sprague Dawley rats. The rats were sacrificed at 21 days after implantation. The brains were harvested, sliced into 2 mm thick coronal sections, and fixedmore » in 4% formalin. PALS lifetime runs were made with the samples soaked in formalin, and there was not significant evaporation of formalin during the runs. The lifetime spectra were analyzed into two lifetime components. While early results suggested a small decrease in ortho-Positronium (o-Ps) pickoff lifetime between the normal brain section and brain section with glioma, further runs with additional samples have showed no statistically significant difference between the normal and tumor tissue for this type of tumor. The o-Ps lifetime in formalin alone was lower than either the normal tissue or glioma sample. So annihilation in the formalin absorbed in the samples would lower the o-Ps lifetime and this may have masked any difference due to the glioma itself. DBS was also used to investigate the difference in positronium formation between tumor and normal tissue. Tissue samples are heterogeneous and this needs to be carefully considered if PALS and DBS are to become useful tools in distinguishing tissue samples.« less

Detection of pesticides and dioxins in tissue fats and rendering oils using laser-induced breakdown spectroscopy (LIBS).

PubMed

Multari, Rosalie A; Cremers, David A; Scott, Thomas; Kendrick, Peter

2013-03-13

In laser-induced breakdown spectroscopy (LIBS), a series of powerful laser pulses are directed at a surface to form microplasmas from which light is collected and spectrally analyzed to identify the surface material. In most cases, no sample preparation is needed, and results can be automated and made available within seconds to minutes. Advances in LIBS spectral data analysis using multivariate regression techniques have led to the ability to detect organic chemicals in complex matrices such as foods. Here, the use of LIBS to differentiate samples contaminated with aldrin, 1,2,3,4,6,7,8-heptachlorodibenzo-p-dioxin, chlorpyrifos, and dieldrin in the complex matrices of tissue fats and rendering oils is described. The pesticide concentrations in the samples ranged from 0.005 to 0.1 μg/g. All samples were successfully differentiated from each other and from control samples. Sample concentrations could also be differentiated for all of the pesticides and the dioxin included in this study. The results presented here provide first proof-of-principle data for the ability to create LIBS-based instrumentation for the rapid analysis of pesticide and dioxin contamination in tissue fat and rendered oils.

Phytoremediation of wastewater containing lead (Pb) in pilot reed bed using Scirpus grossus.

PubMed

Tangahu, Bieby Voijant; Abdullah, Siti Rozaimah Sheikh; Basri, Hassan; Idris, Mushrifah; Anuar, Nurina; Mukhlisin, Muhammad

2013-01-01

Phytoremediation is a technology to clean the environment from heavy metals contamination. The objectives of this study are to threat Pb contaminated wastewater by using phytoremediation technology and to determine if the plant can be mention as hyperaccumulator. Fifty plants of Scirpus grossus were grown in sand medium and 600 L spiked water in various Pb concentration (10, 30 and 50 mg/L) was exposed. The experiment was conducted with single exposure method, sampling time on day-1, day-14, day-28, day-42, day-70, and day-98. The analysis of Pb concentration in water, sand medium and inside the plant tissue was conducted by ICP-OES. Water samples were filtered and Pb concentration were directly analyzed, Pb in sand samples were extracted by EDTA method before analyzed, and Pb in plant tissues were extracted by wet digestion method and analyzed. The results showed that on day-28, Pb concentration in water decreased 100%, 99.9%, 99.7%, and the highest Pb uptake by plant were 1343, 4909, 3236 mg/kg for the treatment of 10, 30, and 50 mg/L respectively. The highest BC and TF were 485,261 on day-42 and 2.5295 on day-70 of treatment 30 mg/L, it can be mentioned that Scirpus grossus is a hyperaccumulator.

The landscape of genomic imprinting across diverse adult human tissues

PubMed Central

Baran, Yael; Subramaniam, Meena; Biton, Anne; Tukiainen, Taru; Tsang, Emily K.; Rivas, Manuel A.; Pirinen, Matti; Gutierrez-Arcelus, Maria; Smith, Kevin S.; Kukurba, Kim R.; Zhang, Rui; Eng, Celeste; Torgerson, Dara G.; Urbanek, Cydney; Li, Jin Billy; Rodriguez-Santana, Jose R.; Burchard, Esteban G.; Seibold, Max A.; MacArthur, Daniel G.; Montgomery, Stephen B.; Zaitlen, Noah A.; Lappalainen, Tuuli

2015-01-01

Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project. We characterize imprinting in 42 genes, including both novel and previously identified genes. Tissue specificity of imprinting is widespread, and gender-specific effects are revealed in a small number of genes in muscle with stronger imprinting in males. IGF2 shows maternal expression in the brain instead of the canonical paternal expression elsewhere. Imprinting appears to have only a subtle impact on tissue-specific expression levels, with genes lacking a systematic expression difference between tissues with imprinted and biallelic expression. In summary, our systematic characterization of imprinting in adult tissues highlights variation in imprinting between genes, individuals, and tissues. PMID:25953952

Increased Expression of Herpes Virus-Encoded hsv1-miR-H18 and hsv2-miR-H9-5p in Cancer-Containing Prostate Tissue Compared to That in Benign Prostate Hyperplasia Tissue

PubMed Central

Shinn, Helen Ki; Yan, Chunri; Kim, Tae-Hwan; Kim, Sang Tae; Kim, Won Tae; Lee, Ok-Jun; Moon, Sung-Kwon; Kim, Nam-Hyung; Kim, Jayoung; Cha, Eun-Jong

2016-01-01

Purpose: Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections. PMID:27377944

Increased Expression of Herpes Virus-Encoded hsv1-miR-H18 and hsv2-miR-H9-5p in Cancer-Containing Prostate Tissue Compared to That in Benign Prostate Hyperplasia Tissue.

PubMed

Yun, Seok Joong; Jeong, Pildu; Kang, Ho Won; Shinn, Helen Ki; Kim, Ye-Hwan; Yan, Chunri; Choi, Young-Ki; Kim, Dongho; Ryu, Dong Hee; Ha, Yun-Sok; Kim, Tae-Hwan; Kwon, Tae Gyun; Kim, Jung Min; Suh, Sang Heon; Kim, Seon-Kyu; Kim, Seon-Young; Kim, Sang Tae; Kim, Won Tae; Lee, Ok-Jun; Moon, Sung-Kwon; Kim, Nam-Hyung; Kim, Isaac Yi; Kim, Jayoung; Cha, Hee-Jae; Choi, Yung-Hyun; Cha, Eun-Jong; Kim, Wun-Jae

2016-06-01

Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections.

Water-quality assessment of the Albemarle-Pamlico drainage basin, North Carolina and Virginia; trace elements in Asiatic clam (Corbicula fluminea) soft tissues and redbreast sunfish (Lepomis auritus) livers, 1992-93

USGS Publications Warehouse

Ruhl, P.M.; Smith, K.E.

1996-01-01

The analysis of potential contaminants in biological tissues is an important part of many water-quality assessment programs, including the National Water-Quality Assessment (NAWQA) Program. Tissue analyses often are used to provide information about (1) direct threats to ecosystem integrity, and (2) the occurrence and distribution of potential contaminants in the environment. During 1992-93, trace elements in Asiatic clam (Corbicula fluminea) soft tissues and redbreast sunfish (Lepomis auritus) livers were analyzed to obtain information about the occurrence and distribution of trace element contaminants in the Albemarle-Pamlico Drainage Basin of North Carolina and Virginia. The investigation was conducted as part of the NAWQA Program. All but 3 of the 22 trace elements that were analyzed were detected. Although all 10 of the U.S. Environmental Protection Agency (U.S. EPA) priority pollutants were detected in the tissues sampled, they were present in relatively low concentrations. Concentrations of U.S. EPA priority pollutants in Asiatic clams collected in the Albemarle-Pamlico Drainage Basin are similar to concentrations observed in other NAWQA study units in the southeastern United States. Mercury (a U.S. EPA priority pollutant) was widely detected, being present in 29 of 30 tissue samples, but concentrations did not exceed the FDA action level for mercury of a risk-based screening value for the general public. Mercury concentrations in Asiatic clams were similar to concentrations in other NAWQA study areas in the Southeast.

Transcriptional Profiling of Synovial Macrophages Using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid Arthritis.

PubMed

Mandelin, Arthur M; Homan, Philip J; Shaffer, Alexander M; Cuda, Carla M; Dominguez, Salina T; Bacalao, Emily; Carns, Mary; Hinchcliff, Monique; Lee, Jungwha; Aren, Kathleen; Thakrar, Anjali; Montgomery, Anna B; Bridges, S Louis; Bathon, Joan M; Atkinson, John P; Fox, David A; Matteson, Eric L; Buckley, Christopher D; Pitzalis, Costantino; Parks, Deborah; Hughes, Laura B; Geraldino-Pardilla, Laura; Ike, Robert; Phillips, Kristine; Wright, Kerry; Filer, Andrew; Kelly, Stephen; Ruderman, Eric M; Morgan, Vince; Abdala-Valencia, Hiam; Misharin, Alexander V; Budinger, G Scott; Bartom, Elizabeth T; Pope, Richard M; Perlman, Harris; Winter, Deborah R

2018-06-01

Currently, there are no reliable biomarkers for predicting therapeutic response in patients with rheumatoid arthritis (RA). The synovium may unlock critical information for determining efficacy, since a reduction in the numbers of sublining synovial macrophages remains the most reproducible biomarker. Thus, a clinically actionable method for the collection of synovial tissue, which can be analyzed using high-throughput strategies, must become a reality. This study was undertaken to assess the feasibility of utilizing synovial biopsies as a precision medicine-based approach for patients with RA. Rheumatologists at 6 US academic sites were trained in minimally invasive ultrasound-guided synovial tissue biopsy. Biopsy specimens obtained from patients with RA and synovial tissue from patients with osteoarthritis (OA) were subjected to histologic analysis, fluorescence-activated cell sorting, and RNA sequencing (RNA-seq). An optimized protocol for digesting synovial tissue was developed to generate high-quality RNA-seq libraries from isolated macrophage populations. Associations were determined between macrophage transcriptional profiles and clinical parameters in RA patients. Patients with RA reported minimal adverse effects in response to synovial biopsy. Comparable RNA quality was observed from synovial tissue and isolated macrophages between patients with RA and patients with OA. Whole tissue samples from patients with RA demonstrated a high degree of transcriptional heterogeneity. In contrast, the transcriptional profile of isolated RA synovial macrophages highlighted different subpopulations of patients and identified 6 novel transcriptional modules that were associated with disease activity and therapy. Performance of synovial tissue biopsies by rheumatologists in the US is feasible and generates high-quality samples for research. Through the use of cutting-edge technologies to analyze synovial biopsy specimens in conjunction with corresponding clinical information, a precision medicine-based approach for patients with RA is attainable. © 2018, American College of Rheumatology.

Bi-PROF

PubMed Central

Gries, Jasmin; Schumacher, Dirk; Arand, Julia; Lutsik, Pavlo; Markelova, Maria Rivera; Fichtner, Iduna; Walter, Jörn; Sers, Christine; Tierling, Sascha

2013-01-01

The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 102-104 sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer. PMID:23803588

A new model for ancient DNA decay based on paleogenomic meta-analysis.

PubMed

Kistler, Logan; Ware, Roselyn; Smith, Oliver; Collins, Matthew; Allaby, Robin G

2017-06-20

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Micro-polarimetry for pre-clinical diagnostics of pathological changes in human tissues

NASA Astrophysics Data System (ADS)

Golnik, Andrzej; Golnik, Natalia; Pałko, Tadeusz; Sołtysiński, Tomasz

2008-05-01

The paper presents a practical study of several methods of image analysis applied to polarimetric images of regular and malignant human tissues. The images of physiological and pathologically changed tissues from body and cervix of uterus, intestine, kidneys and breast were recorded in transmitted light of different polarization state. The set up of the conventional optical microscope with CCD camera and rotating polarizer's were used for analysis of the polarization state of the light transmitted through the tissue slice for each pixel of the camera image. The set of images corresponding to the different coefficients of the Stockes vectors, a 3×3 subset of the Mueller matrix as well as the maps of the magnitude and in-plane direction of the birefringent components in the sample were calculated. Then, the statistical analysis and the Fourier transform as well as the autocorrelation methods were used to analyze spatial distribution of birefringent elements in the tissue samples. For better recognition of tissue state we proposed a novel method that takes advantage of multiscale image data decomposition The results were used for selection of the optical characteristics with significantly different values for regular and malignant tissues.

Glycomics expression analysis of sulfated glycosaminoglycans of human colorectal cancer tissues and non-neoplastic mucosa by electrospray ionization mass spectrometry

PubMed Central

Marolla, Ana Paula Cleto; Waisberg, Jaques; Saba, Gabriela Tognini; Waisberg, Daniel Reis; Margeotto, Fernando Beani; Pinhal, Maria Aparecida da Silva

2015-01-01

ABSTRACT Objective To determine the presence of glycosaminoglycans in the extracellular matrix of connective tissue from neoplastic and non-neoplastic colorectal tissues, since it has a central role in tumor development and progression. Methods Tissue samples from neoplastic and non-neoplastic colorectal tissues were obtained from 64 operated patients who had colorectal carcinoma with no distant metastases. Expressions of heparan sulphate, chondroitin sulphate, dermatan sulphate and their fragments were analyzed by electrospray ionization mass spectrometry, with the technique for extraction and quantification of glycosaminoglycans after proteolysis and electrophoresis. The statistical analysis included mean, standard deviation, and Student’s t test. Results The glycosaminoglycans extracted from colorectal tissue showed three electrophoretic bands in agarose gel. Electrospray ionization mass spectrometry showed characteristic disaccharide fragments from glycosaminoglycans, indicating their structural characterization in the tissues analyzed. Some peaks in the electrospray ionization mass spectrometry were not characterized as fragments of sugars, indicating the presence of fragments of the protein structure of proteoglycans generated during the glycosaminoglycan purification. The average amount of chondroitin and dermatan increased in the neoplastic tissue compared to normal tissue (p=0.01). On the other hand, the average amount of heparan decreased in the neoplastic tissue compared to normal tissue (p= 0.03). Conclusion The method allowed the determination of the glycosaminoglycans structural profile in colorectal tissue from neoplastic and non-neoplastic colorectal tissue. Neoplastic tissues showed greater amounts of chondroitin sulphate and dermatan sulphate compared to non-neoplastic tissues, while heparan sulphate was decreased in neoplastic tissues. PMID:26761548

In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer.

PubMed

Lee, Deanna; Das Gupta, Jaydip; Gaughan, Christina; Steffen, Imke; Tang, Ning; Luk, Ka-Cheung; Qiu, Xiaoxing; Urisman, Anatoly; Fischer, Nicole; Molinaro, Ross; Broz, Miranda; Schochetman, Gerald; Klein, Eric A; Ganem, Don; Derisi, Joseph L; Simmons, Graham; Hackett, John; Silverman, Robert H; Chiu, Charles Y

2012-01-01

XMRV, or xenotropic murine leukemia virus (MLV)-related virus, is a novel gammaretrovirus originally identified in studies that analyzed tissue from prostate cancer patients in 2006 and blood from patients with chronic fatigue syndrome (CFS) in 2009. However, a large number of subsequent studies failed to confirm a link between XMRV infection and CFS or prostate cancer. On the contrary, recent evidence indicates that XMRV is a contaminant originating from the recombination of two mouse endogenous retroviruses during passaging of a prostate tumor xenograft (CWR22) in mice, generating laboratory-derived cell lines that are XMRV-infected. To confirm or refute an association between XMRV and prostate cancer, we analyzed prostate cancer tissues and plasma from a prospectively collected cohort of 39 patients as well as archival RNA and prostate tissue from the original 2006 study. Despite comprehensive microarray, PCR, FISH, and serological testing, XMRV was not detected in any of the newly collected samples or in archival tissue, although archival RNA remained XMRV-positive. Notably, archival VP62 prostate tissue, from which the prototype XMRV strain was derived, tested negative for XMRV on re-analysis. Analysis of viral genomic and human mitochondrial sequences revealed that all previously characterized XMRV strains are identical and that the archival RNA had been contaminated by an XMRV-infected laboratory cell line. These findings reveal no association between XMRV and prostate cancer, and underscore the conclusion that XMRV is not a naturally acquired human infection.

The effects of CD147 on the cell proliferation, apoptosis, invasion, and angiogenesis in glioma.

PubMed

Yin, Haoyuan; Shao, Ying; Chen, Xuan

2017-01-01

To analyze the effects of extracellular matrix metalloproteinase inducer (CD147) on glioma proliferation, apoptosis, invasion, and angiogenesis. Tissue samples were obtained from 101 glioma cases while normal brain tissues were obtained from 30 brain injury cases. Immunohistochemical assay was performed to detect the expressions of CD147, CD34, and VEGF in tissue samples. QRT-PCR was performed to detect the relative expression of CD147 mRNA in human glioma cell lines. CD147 siRNA was transfected into glioma cell line U251. Cell proliferation, apoptosis, invasion, and angiogenesis were tested by MTT, flow cytometry, Transwell assay, and vasculogenic mimicry assay, respectively. Expressions of relative proteins were analyzed with western blot. CD147 was positively expressed with the percentage of 0, 37.5, 44.8, 67.9, and 85.7 % in normal tissues and glioma tissues with WHO grades I-IV, respectively, and the scores of MVDand VEGF were associated with the expression of CD147. CD147 was significantly upregulated in the human glioma cell lines (P < 0.05). Downregulated the expression of CD147 suppressed cell proliferation, blocked cell cycle, induced apoptosis, inhibited cell invasion and angiogenesis in glioma cells in vitro. The expression of CD147 was significantly associated with WHO tumor grade and angiogenesis; silencing of CD147 contributed to inhibition of glioma proliferation, invasion, and angiogenesis. Our study provided firm evidence that CD 147 is a potential glioma target for anti-angiogenic therapies.

Enhanced epithelial to mesenchymal transition (EMT) and upregulated MYC in ectopic lesions contribute independently to endometriosis.

PubMed

Proestling, Katharina; Birner, Peter; Gamperl, Susanne; Nirtl, Nadine; Marton, Erika; Yerlikaya, Gülen; Wenzl, Rene; Streubel, Berthold; Husslein, Heinrich

2015-07-22

Epithelial to mesenchymal transition (EMT) is a process in which epithelial cells lose polarity and cell-to-cell contacts and acquire the migratory and invasive abilities of mesenchymal cells. These abilities are thought to be prerequisites for the establishment of endometriotic lesions. A hallmark of EMT is the functional loss of E-cadherin (CDH1) expression in epithelial cells. TWIST1, a transcription factor that represses E-cadherin transcription, is among the EMT inducers. SNAIL, a zinc-finger transcription factor, and its close relative SLUG have similar properties to TWIST1 and are thus also EMT inducers. MYC, which is upregulated by estrogens in the uterus by an estrogen response cis-acting element (ERE) in its promoter, is associated with proliferation in endometriosis. The role of EMT and proliferation in the pathogenesis of endometriosis was evaluated by analyzing TWIST1, CDH1 and MYC expression. CDH1, TWIST1, SNAIL and SLUG mRNA expression was analyzed by qRT-PCR from 47 controls and 74 patients with endometriosis. Approximately 42 ectopic and 62 eutopic endometrial tissues, of which 30 were matched samples, were collected during the same surgical procedure. We evaluated TWIST1 and MYC protein expression by immunohistochemistry (IHC) in the epithelial and stromal tissue of 69 eutopic and 90 ectopic endometrium samples, of which 49 matched samples were analyzed from the same patient. Concordant expression of TWIST1/SNAIL/SLUG and CDH1 but also of TWIST1 and MYC was analyzed. We found that TWIST1, SNAIL and SLUG are overexpressed (p < 0.001, p = 0.016 and p < 0.001) in endometriosis, while CDH1 expression was concordantly reduced in these samples (p < 0.001). Similar to TWIST1, the epithelial expression of MYC was also significantly enhanced in ectopic endometrium compared to eutopic tissues (p = 0.008). We found exclusive expression of either TWIST1 or MYC in the same samples (p = 0.003). Epithelial TWIST1 is overexpressed in endometriosis and may contribute to the formation of endometriotic lesions by inducing epithelial to mesenchymal transition, as CDH1 was reduced in ectopic lesions. We found exclusive expression of either TWIST1 or MYC in the same samples, indicating that EMT and proliferation contribute independently of each other to the formation of endometriotic lesions.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients.

PubMed

Schlick, Bettina; Massoner, Petra; Lueking, Angelika; Charoentong, Pornpimol; Blattner, Mirjam; Schaefer, Georg; Marquart, Klaus; Theek, Carmen; Amersdorfer, Peter; Zielinski, Dirk; Kirchner, Matthias; Trajanoski, Zlatko; Rubin, Mark A; Müllner, Stefan; Schulz-Knappe, Peter; Klocker, Helmut

2016-01-01

Chronic inflammation is frequently observed on histological analysis of malignant and non-malignant prostate specimens. It is a suspected supporting factor for prostate diseases and their progression and a main cause of false positive PSA tests in cancer screening. We hypothesized that inflammation induces autoantibodies, which may be useful biomarkers. We aimed to identify and validate prostate inflammation associated serum autoantibodies in prostate cancer patients and evaluate the expression of corresponding autoantigens. Radical prostatectomy specimens of prostate cancer patients (N = 70) were classified into high and low inflammation groups according to the amount of tissue infiltrating lymphocytes. The corresponding pre-surgery blood serum samples were scrutinized for autoantibodies using a low-density protein array. Selected autoantigens were identified in prostate tissue and their expression pattern analyzed by immunohistochemistry and qPCR. The identified autoantibody profile was cross-checked in an independent sample set (N = 63) using the Luminex-bead protein array technology. Protein array screening identified 165 autoantibodies differentially abundant in the serum of high compared to low inflammation patients. The expression pattern of three corresponding antigens were established in benign and cancer tissue by immunohistochemistry and qPCR: SPAST (Spastin), STX18 (Syntaxin 18) and SPOP (speckle-type POZ protein). Of these, SPAST was significantly increased in prostate tissue with high inflammation. All three autoantigens were differentially expressed in primary and/or castration resistant prostate tumors when analyzed in an inflammation-independent tissue microarray. Cross-validation of the inflammation autoantibody profile on an independent sample set using a Luminex-bead protein array, retrieved 51 of the significantly discriminating autoantibodies. Three autoantibodies were significantly upregulated in both screens, MUT, RAB11B and CSRP2 (p>0.05), two, SPOP and ZNF671, close to statistical significance (p = 0.051 and 0.076). We provide evidence of an inflammation-specific autoantibody profile and confirm the expression of corresponding autoantigens in prostate tissue. This supports evaluation of autoantibodies as non-invasive markers for prostate inflammation.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients

PubMed Central

Schlick, Bettina; Massoner, Petra; Lueking, Angelika; Charoentong, Pornpimol; Blattner, Mirjam; Schaefer, Georg; Marquart, Klaus; Theek, Carmen; Amersdorfer, Peter; Zielinski, Dirk; Kirchner, Matthias; Trajanoski, Zlatko; Rubin, Mark A.; Müllner, Stefan; Schulz-Knappe, Peter; Klocker, Helmut

2016-01-01

Background Chronic inflammation is frequently observed on histological analysis of malignant and non-malignant prostate specimens. It is a suspected supporting factor for prostate diseases and their progression and a main cause of false positive PSA tests in cancer screening. We hypothesized that inflammation induces autoantibodies, which may be useful biomarkers. We aimed to identify and validate prostate inflammation associated serum autoantibodies in prostate cancer patients and evaluate the expression of corresponding autoantigens. Methods Radical prostatectomy specimens of prostate cancer patients (N = 70) were classified into high and low inflammation groups according to the amount of tissue infiltrating lymphocytes. The corresponding pre-surgery blood serum samples were scrutinized for autoantibodies using a low-density protein array. Selected autoantigens were identified in prostate tissue and their expression pattern analyzed by immunohistochemistry and qPCR. The identified autoantibody profile was cross-checked in an independent sample set (N = 63) using the Luminex-bead protein array technology. Results Protein array screening identified 165 autoantibodies differentially abundant in the serum of high compared to low inflammation patients. The expression pattern of three corresponding antigens were established in benign and cancer tissue by immunohistochemistry and qPCR: SPAST (Spastin), STX18 (Syntaxin 18) and SPOP (speckle-type POZ protein). Of these, SPAST was significantly increased in prostate tissue with high inflammation. All three autoantigens were differentially expressed in primary and/or castration resistant prostate tumors when analyzed in an inflammation-independent tissue microarray. Cross-validation of the inflammation autoantibody profile on an independent sample set using a Luminex-bead protein array, retrieved 51 of the significantly discriminating autoantibodies. Three autoantibodies were significantly upregulated in both screens, MUT, RAB11B and CSRP2 (p>0.05), two, SPOP and ZNF671, close to statistical significance (p = 0.051 and 0.076). Conclusions We provide evidence of an inflammation-specific autoantibody profile and confirm the expression of corresponding autoantigens in prostate tissue. This supports evaluation of autoantibodies as non-invasive markers for prostate inflammation. PMID:26863016

Quantitatively characterizing the microstructural features of breast ductal carcinoma tissues in different progression stages by Mueller matrix microscope.

PubMed

Dong, Yang; Qi, Ji; He, Honghui; He, Chao; Liu, Shaoxiong; Wu, Jian; Elson, Daniel S; Ma, Hui

2017-08-01

Polarization imaging has been recognized as a potentially powerful technique for probing the microstructural information and optical properties of complex biological specimens. Recently, we have reported a Mueller matrix microscope by adding the polarization state generator and analyzer (PSG and PSA) to a commercial transmission-light microscope, and applied it to differentiate human liver and cervical cancerous tissues with fibrosis. In this paper, we apply the Mueller matrix microscope for quantitative detection of human breast ductal carcinoma samples at different stages. The Mueller matrix polar decomposition and transformation parameters of the breast ductal tissues in different regions and at different stages are calculated and analyzed. For more quantitative comparisons, several widely-used image texture feature parameters are also calculated to characterize the difference in the polarimetric images. The experimental results indicate that the Mueller matrix microscope and the polarization parameters can facilitate the quantitative detection of breast ductal carcinoma tissues at different stages.

DNA Electrochemistry Shows DNMT1 Methyltransferase Hyperactivity in Colorectal Tumors.

PubMed

Furst, Ariel L; Barton, Jacqueline K

2015-07-23

DNMT1, the most abundant human methyltransferase, is responsible for translating the correct methylation pattern during DNA replication, and aberrant methylation by DNMT1 has been linked to tumorigenesis. We have developed a sensitive signal-on electrochemical assay for the measurement of DNMT1 activity in crude tissue lysates. We have further analyzed ten tumor sets and have found a direct correlation between DNMT1 hyperactivity and tumorous tissue. In the majority of samples analyzed, the tumorous tissue has significantly higher DNMT1 activity than the healthy adjacent tissue. No such correlation is observed in measurements of DNMT1 expression by qPCR, DNMT1 protein abundance by western blotting, or DNMT1 activity using a radiometric DNA labeling assay. DNMT1 hyperactivity can result from both protein overexpression and enzyme hyperactivity. DNMT1 activity measured electrochemically provides a direct measure of activity in cell lysates and, as a result, provides a sensitive and early indication of cancerous transformation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Thyroid peroxidase (TPO) expressed in thyroid and breast tissues shows similar antigenic properties

PubMed Central

Godlewska, Marlena; Arczewska, Katarzyna D.; Rudzińska, Magdalena; Łyczkowska, Anna; Krasuska, Wanda; Hanusek, Karolina; Ruf, Jean; Kiedrowski, Mirosław

2017-01-01

Background Thyroid peroxidase (TPO) is essential for physiological function of the thyroid gland. The high prevalence of thyroid peroxidase antibodies (TPOAbs) in patients with breast cancer and their protective role had previously been demonstrated, indicating a link between breast cancer and thyroid autoimmunity. Recently, TPO was shown to be present in breast cancer tissue samples but its antigenicity has not been analyzed. Methods In this study, we investigated TPO expression levels in a series of fifty-six breast cancer samples paired with normal (peri-tumoral) tissue and its antigenic activity using a panel of well-characterized murine anti-human TPOAbs. Results We have shown that TPO transcripts were present in both normal and cancer tissue samples, although the amounts in the latter were reduced. Additionally, we observed that TPO levels are lower in more advanced cancers. TPO protein expression was confirmed in all tissue samples, both normal and cancerous. We also found that the antigenicity of the immunodominant regions (IDRs) in breast TPO resembles that of thyroid TPO, which is crucial for effective interactions with human TPOAbs. Conclusions Expression of TPO in breast cancer together with its antigenic activity may have beneficial effects in TPOAb-positive breast cancer patients. However, further studies are needed to confirm the beneficial role of TPOAbs and to better understand the underlying mechanism. PMID:28575127

[GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value].

PubMed

Skorodumova, L O; Babalyan, K A; Sultanov, R; Vasiliev, A O; Govorov, A V; Pushkar, D Y; Prilepskaya, E A; Danilenko, S A; Generozov, E V; Larin, A K; Kostryukova, E S; Sharova, E I

2016-11-01

There is a clear need in molecular markers for prostate cancer (PC) risk stratification. Alteration of DNA methylation is one of processes that occur during ÐÑ progression. Methylation-sensitive PCR with high resolution melting curve analysis (MS-HRM) can be used for gene methylation analysis in routine laboratory practice. This method requires very small amounts of DNA for analysis. Numerous results have been accumulated on DNA methylation in PC samples analyzed by the Infinium HumanMethylation450 BeadChip (HM450). However, the consistency of MS-HRM results with chip hybridization results has not been examined yet. The aim of this study was to assess the consistency of results of GSTP1, APC and RASSF1 gene methylation analysis in ÐÑ biopsy samples obtained by MS-HRM and chip hybridization. The methylation levels of each gene determined by MS-HRM were statistically different in the group of PC tissue samples and the samples without signs of tumor growth. Chip hybridization data analysis confirmed the results obtained with the MS-HRM. Differences in methylation levels between tumor tissue and histologically intact tissue of each sample determined by MS-HRM and chip hybridization, were consistent with each other. Thus, we showed that the assessment of GSTP1, APC and RASSF1 gene methylation analysis using MS-HRM is suitable for the design of laboratory assays that will differentiate the PC tissue from the tissue without signs of tumor growth.

Tissue preservation with mass spectroscopic analysis: Implications for cancer diagnostics.

PubMed

Hall, O Morgan; Peer, Cody J; Figg, William D

2018-05-17

Surgical intervention is a common treatment modality for localized cancer. Post-operative analysis involves evaluation of surgical margins to assess whether all malignant tissue has been resected because positive surgical margins lead to a greater likelihood of recurrence. Secondary treatments are utilized to minimize the negative effects of positive surgical margins. Recently, in Science Translational Medicine, Zhang et al describe a new mass spectroscopic technique that could potentially decrease the likelihood of positive surgical margins. Their nondestructive in vivo tissue sampling leads to a highly accurate and rapid cancer diagnosis with great precision between healthy and malignant tissue. This new tool has the potential to improve surgical margins and accelerate cancer diagnostics by analyzing biomolecular signatures of various tissues and diseases.

Multilaboratory trial for determination of ceftiofur residues in bovine and swine kidney and muscle, and bovine milk.

PubMed

Hornish, Rex E; Hamlow, Philip J; Brown, Scott A

2003-01-01

A multilaboratory trial for determining ceftiofur-related residues in bovine and swine kidney and muscle, and bovine milk was conducted following regulatory guidelines of the U.S. Food and Drug Administration, Center for Veterinary Medicine. The methods convert all desfuroylceftiofur-related residues containing the intact beta-lactam ring to desfuroylceftiofur acetamide to establish ceftiofur residues in tissues. Four laboratories analyzed 5 sets of samples for each tissue. Each sample set consisted of a control/blank sample and 3 control samples fortified with ceftiofur at 0.5 Rm, Rm, and 2 Rm, respectively, where Rm is the U.S. tolerance assigned for ceftiofur residue in each tissue/matrix: 0.100 microg/mL for milk, 8.0 microg/g for kidney (both species), 1.0 microg/g for bovine muscle, and 2.0 microg/g for swine muscle. Each sample set also contained 2 samples of incurred-residue tissues (one > Rm and one < Rm) from animals treated with ceftiofur hydrochloride. All laboratories completed the method trial after a familiarization phase and test of system suitability in which they demonstrated > 80% recovery in pretrial fortified test samples. Results showed that the methods met all acceptable performance criteria for recovery, accuracy, and precision. Although sample preparation was easy, solid-phase extraction cartridge performance must be carefully evaluated before samples are processed. The liquid chromatography detection system was easily set up; however, the elution profile may require slight modifications. The procedures could clearly differentiate between violative (> Rm) and nonviolative (< Rm) ceftiofur residues. Participating laboratories found the procedures suitable for ceftiofur residue determination.

Clinicopathological significance of c-MYC in esophageal squamous cell carcinoma.

PubMed

Lian, Yu; Niu, Xiangdong; Cai, Hui; Yang, Xiaojun; Ma, Haizhong; Ma, Shixun; Zhang, Yupeng; Chen, Yifeng

2017-07-01

Esophageal squamous cell carcinoma is one of the most common malignant tumors. The oncogene c-MYC is thought to be important in the initiation, promotion, and therapy resistance of cancer. In this study, we aim to investigate the clinicopathologic roles of c-MYC in esophageal squamous cell carcinoma tissue. This study is aimed at discovering and analyzing c-MYC expression in a series of human esophageal tissues. A total of 95 esophageal squamous cell carcinoma samples were analyzed by the western blotting and immunohistochemistry techniques. Then, correlation of c-MYC expression with clinicopathological features of esophageal squamous cell carcinoma patients was statistically analyzed. In most esophageal squamous cell carcinoma cases, the c-MYC expression was positive in tumor tissues. The positive rate of c-MYC expression in tumor tissues was 61.05%, obviously higher than the adjacent normal tissues (8.42%, 8/92) and atypical hyperplasia tissues (19.75%, 16/95). There was a statistical difference among adjacent normal tissues, atypical hyperplasia tissues, and tumor tissues. Overexpression of the c-MYC was detected in 61.05% (58/95) esophageal squamous cell carcinomas, which was significantly correlated with the degree of differentiation (p = 0.004). The positive rate of c-MYC expression was 40.0% in well-differentiated esophageal tissues, with a significantly statistical difference (p = 0.004). The positive rate of c-MYC was 41.5% in T1 + T2 esophageal tissues and 74.1% in T3 + T4 esophageal tissues, with a significantly statistical difference (p = 0.001). The positive rate of c-MYC was 45.0% in I + II esophageal tissues and 72.2% in III + IV esophageal tissues, with a significantly statistical difference (p = 0.011). The c-MYC expression strongly correlated with clinical staging (p = 0.011), differentiation degree (p = 0.004), lymph node metastasis (p = 0.003), and invasion depth (p = 0.001) of patients with esophageal squamous cell carcinoma. The c-MYC was differentially expressed in a series of human esophageal tissues, and the aberrant c-MYC expression could be a potential factor in carcinogenesis and progression of esophageal squamous cell carcinoma. There was a statistical signification for c-MYC in esophageal squamous cell carcinoma patients to analyze clinicopathological features. It possibly becomes a new diagnostic indicator of esophageal squamous cell carcinoma.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

PubMed

Bova, G Steven; Eltoum, Isam A; Kiernan, John A; Siegal, Gene P; Frost, Andra R; Best, Carolyn J M; Gillespie, John W; Emmert-Buck, Michael R

2005-01-01

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of pancreatic malignancy and other biological phenomena. This chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed-over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification. High-quality tissue microdissection does not necessarily mean high-quality samples to analyze. The quality of biomaterials obtained for analysis is highly dependent on steps upstream and downstream from tissue microdissection. We provide protocols for each of these steps, and encourage you to improve upon these. It is worth the effort of every laboratory to optimize and document its technique at each stage of the process, and we provide a starting point for those willing to spend the time to optimize. In our view, poor documentation of tissue and cell type of origin and the use of nonoptimized protocols is a source of inefficiency in current life science research. Even incremental improvement in this area will increase productivity significantly.

Measurement of stable isotopic enrichment and concentration of long-chain fatty acyl-carnitines in tissue by HPLC-MS.

PubMed

Sun, Dayong; Cree, Melanie G; Zhang, Xiao-Jun; Bøersheim, Elisabet; Wolfe, Robert R

2006-02-01

We have developed a new method for the simultaneous measurements of stable isotopic tracer enrichments and concentrations of individual long-chain fatty acyl-carnitines in muscle tissue using ion-pairing high-performance liquid chromatography-electrospray ionization quadrupole mass spectrometry in the selected ion monitoring (SIM) mode. Long-chain fatty acyl-carnitines were extracted from frozen muscle tissue samples by acetonitrile/methanol. Baseline separation was achieved by reverse-phase HPLC in the presence of the volatile ion-pairing reagent heptafluorobutyric acid. The SIM capability of a single quadrupole mass analyzer allows further separation of the ions of interest from the sample matrixes, providing very clean total and selected ion chromatograms that can be used to calculate the stable isotopic tracer enrichment and concentration of long-chain fatty acyl-carnitines in a single analysis. The combination of these two separation techniques greatly simplifies the sample preparation procedure and increases the detection sensitivity. Applying this protocol to biological muscle samples proves it to be a very sensitive, accurate, and precise analytical tool.

Comparison of inferred fractions of n-3 and n-6 polyunsaturated fatty acids in feral domestic cat diets with those in commercial feline extruded diets.

PubMed

Backus, Robert C; Thomas, David G; Fritsche, Kevin L

2013-04-01

To compare presumed fatty acid content in natural diets of feral domestic cats (inferred from body fat polyunsatrated fatty acids content) with polyunsaturated fatty acid content of commercial feline extruded diets. Subcutaneous and intra-abdominal adipose tissue samples (approx 1 g) from previously frozen cadavers of 7 adult feral domestic cats trapped in habitats remote from human activity and triplicate samples (200 g each) of 7 commercial extruded diets representing 68% of market share obtained from retail stores. Lipid, triacylglycerol, and phospholipid fractions in adipose tissue samples and ether extracts of diet samples were determined by gas chromatography of methyl esters. Triacylglycerol and phospholipid fractions in the adipose tissue were isolated by thin-layer chromatography. Diet samples were also analyzed for proximate contents. For the adipose tissue samples, with few exceptions, fatty acids fractions varied only moderately with lipid fraction and site from which tissue samples were obtained. Linoleic, α-linolenic, arachidonic, eicosapentaenoic, and docosahexaenoic acid fractions were 15.0% to 28.2%, 4.5% to 18.7%, 0.9% to 5.0%, < 0.1% to 0.2%, and 0.6% to 1.7%, respectively. As inferred from the adipose findings, dietary fractions of docosahexaenoic and α-linolenic acid were significantly greater than those in the commercial feline diets, but those for linoleic and eicosapentaenoic acids were not significantly different. The fatty acid content of commercial extruded feline diets differed from the inferred content of natural feral cat diets, in which dietary n-3 and possibly n-6 polyunsaturated fatty acids were more abundant. The impact of this difference on the health of pet cats is not known.

Determination of PCBs in fish using enzyme-linked immunosorbent assay (ELISA)

USGS Publications Warehouse

Lasrado, J.A.; Santerre, C.R.; Zajicek, J.L.; Stahl, J.R.; Tillitt, D.E.; Deardorff, D.

2003-01-01

Polychlorinated biphenyls (PCBs) were determined in fish tissue using an enzyme-linked immunosorbent assay (ELISA). Standard curves for Aroclor 1248, 1254, and 1260 in catfish tissue were developed with ranges from 0.05 to 0.5 ppm and 0.5 to 5.0 ppm. Wild fish were initially analyzed using gas chromatography/electron-capture detection (GC/ECD) and those having residues within the standard curve ranges were analyzed with ELISA. Results obtained using ELISA and GC/ECD were not significantly different (p < 0.05) from 0.05 to 0.5 ppm. From 0.5 to 5.0 ppm, the standard curve for Aroclor 1254 was the best predictor of total PCB in wild fish samples.

Determination of mercury in fish tissue using a minianalyzer based on cold vapor atomic absorption spectrometry at the 184.9 nm line.

PubMed

Rizea, Maria-Cristina; Bratu, Maria-Cristina; Danet, Andrei Florin; Bratu, Adrian

2007-09-01

A sensitive method was proposed and optimized for the determination of total mercury in fish tissue by using wet digestion, followed by cold vapor atomic absorption spectrometry (CVAAS) at the main resonance line of mercury (184.9 nm). The measurements were made using a new type of a non-dispersive mercury minianalyzer. This instrument was initially designed and built for atmospheric mercury-vapor detection. For determining mercury in aqueous samples, the minianalyzer was linked with a mercury/hydride system, Perkin Elmer Model MHS-10. To check the method, the analyzed samples were spiked with a standard solution of mercury. The recoveries of mercury spiked to wet fish tissue were >90% for 0.5 - 0.8 g samples. The results showed a better sensitivity (about 2.5 times higher) when using the mercury absorption line at 184.9 nm compared with the sensitivity obtained by conventional CVAAS at 253.7 nm.

Re-generation of tissue about an animal-based scaffold: AMS studies of the fate of the scaffold

NASA Astrophysics Data System (ADS)

Rickey, Frank A.; Elmore, David; Hillegonds, Darren; Badylak, Stephen; Record, Rae; Simmons-Byrd, Abby

2000-10-01

Small intestinal submucosa (SIS) is an unusual tissue, which shows great promise for the repair of damaged tissues in humans. When the SIS is used as a surgical implant, the porcine-derived material is not rejected by the host immune system, and in fact stimulates the constructive re-modeling of damaged tissue. In dogs, these SIS scaffolds have been used to grow new arteries, tendons, and urinary bladders. Moreover, the SIS scaffold tissue seems to disappear from the implant region after a few months. The fate of this SIS tissue is of considerable importance if it is to be used in human tissue repair. SIS is obtained from pigs. We have labeled the SIS in several pigs by intraveneous administration of 14C enriched proline from the age of three weeks until they reach market weight. The prepared SIS was then implanted in dogs as scaffolds for urinary bladder patches. During the remaining life of each dog, blood, urine and feces samples were collected on a regular schedule. AMS analyses of these specimens were performed to measure the elimination rate of the SIS. At different intervals, the dogs were sacrificed. Tissue samples were analyzed by AMS to determine the whole-body distribution of the labeled SIS.

Rapid intra-operative diagnosis of kidney cancer by attenuated total reflection infrared spectroscopy of tissue smears.

PubMed

Pucetaite, Milda; Velicka, Martynas; Urboniene, Vidita; Ceponkus, Justinas; Bandzeviciute, Rimante; Jankevicius, Feliksas; Zelvys, Arunas; Sablinskas, Valdas; Steiner, Gerald

2018-05-01

Herein, a technique to analyze air-dried kidney tissue impression smears by means of attenuated total reflection infrared (ATR-IR) spectroscopy is presented. Spectral tumor markers-absorption bands of glycogen-are identified in the ATR-IR spectra of the kidney tissue smear samples. Thin kidney tissue cryo-sections currently used for IR spectroscopic analysis lack such spectral markers as the sample preparation causes irreversible molecular changes in the tissue. In particular, freeze-thaw cycle results in degradation of the glycogen and reduction or complete dissolution of its content. Supervised spectral classification was applied to the recorded spectra of the smears and the test spectra were classified with a high accuracy of 92% for normal tissue and 94% for tumor tissue, respectively. For further development, we propose that combination of the method with optical fiber ATR probes could potentially be used for rapid real-time intra-operative tissue analysis without interfering with either the established protocols of pathological examination or the ordinary workflow of operating surgeon. Such approach could ensure easier transition of the method to clinical applications where it may complement the results of gold standard histopathology examination and aid in more precise resection of kidney tumors. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison of ESR1 Mutations in Tumor Tissue and Matched Plasma Samples from Metastatic Breast Cancer Patients.

PubMed

Takeshita, Takashi; Yamamoto, Yutaka; Yamamoto-Ibusuki, Mutsuko; Tomiguchi, Mai; Sueta, Aiko; Murakami, Keiichi; Omoto, Yoko; Iwase, Hirotaka

2017-10-01

ESR1 mutation in circulating cell-free DNA (cfDNA) is emerging as a noninvasive biomarker of acquired resistance to endocrine therapy, but there is a paucity of data comparing the status of ESR1 gene in cfDNA with that in its corresponding tumor tissue. The objective of this study is to validate the degree of concordance of ESR1 mutations between plasma and tumor tissue. ESR1 ligand-binding domain mutations Y537S, Y537N, Y537C, and D538G were analyzed using droplet digital PCR in 35 patients with metastatic breast cancer (MBC) (35 tumor tissue samples and 67 plasma samples). Of the 35 paired samples, 26 (74.3%) were concordant: one patient had detectable ESR1 mutations both plasma (ESR1 Y537S/Y537N) and tumor tissue (ESR1 Y537S/Y537C), and 25 had WT ESR1 alleles in both. Nine (25.7%) had discordance between the plasma and tissue results: five had mutations detected only in their tumor tissue (two Y537S, one Y537C, one D538G, and one Y537S/Y537N/D538G), and four had mutations detected only in their plasma (one Y537S, one Y537N, and two Y537S/Y537N/D538G). Furthermore, longitudinal plasma samples from 19 patients were used to assess changes in the presence of ESR1 mutations during treatment. Eleven patients had cfDNA ESR1 mutations over the course of treatment. A total of eight of 11 patients with MBC with cfDNA ESR1 mutations (72.7%) had the polyclonal mutations. We have shown the independent distribution of ESR1 mutations between plasma and tumor tissue in 35 patients with MBC. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Ontology-based, Tissue MicroArray oriented, image centered tissue bank

PubMed Central

Viti, Federica; Merelli, Ivan; Caprera, Andrea; Lazzari, Barbara; Stella, Alessandra; Milanesi, Luciano

2008-01-01

Background Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly managed, if possible with an infrastructure able to support tissue sharing between institutes. Moreover, the available frameworks oriented to Tissue MicroArray provide good storage for clinical patient, sample treatment and block construction information, but their utility is limited by the lack of data integration with biomolecular information. Results In this work we propose a Tissue MicroArray web oriented system to support researchers in managing bio-samples and, through the use of ontologies, enables tissue sharing aimed at the design of Tissue MicroArray experiments and results evaluation. Indeed, our system provides ontological description both for pre-analysis tissue images and for post-process analysis image results, which is crucial for information exchange. Moreover, working on well-defined terms it is then possible to query web resources for literature articles to integrate both pathology and bioinformatics data. Conclusions Using this system, users associate an ontology-based description to each image uploaded into the database and also integrate results with the ontological description of biosequences identified in every tissue. Moreover, it is possible to integrate the ontological description provided by the user with a full compliant gene ontology definition, enabling statistical studies about correlation between the analyzed pathology and the most commonly related biological processes. PMID:18460177

Three-Dimensional Anthropometric Database of Attractive Caucasian Women: Standards and Comparisons.

PubMed

Galantucci, Luigi Maria; Deli, Roberto; Laino, Alberto; Di Gioia, Eliana; D'Alessio, Raoul; Lavecchia, Fulvio; Percoco, Gianluca; Savastano, Carmela

2016-10-01

The aim of this paper is to develop a database to determine a new biomorphometric standard of attractiveness. Sampling was carried out using noninvasive three-dimensional relief methods to measure the soft tissues of the face. These anthropometric measurements were analyzed to verify the existence of any canons with respect to shape, size, and measurement proportions which proved to be significant with regard to the aesthetics of the face. Finally, the anthropometric parameters obtained were compared with findings described in the international literature.The study sample was made up competitors in the Miss Italy 2010 and 2009 beauty contest. The three-dimensional (3D) scanning of soft tissue surfaces allowed 3D digital models of the faces and the spatial 3D coordinates of 25 anthropometric landmarks to be obtained and used to calculate linear and angular measurements. A paired Student t test for the analysis of the means allowed 3 key questions in the study of biomorphometric parameters of the face to be addressed through comparison with the data available in the literature.The question of statistical evidence for the samples analyzed being members of the populations samples reported in literature was also addressed.The critical analysis of the data helped to identify the anthropometric measurements of the upper, middle, and lower thirds of the face, variations in which have a major influence on the attractiveness of the face. These changes involve facial width, height, and depth. Changes in measurements of length, angles, and proportions found in the sample considered were also analyzed.

Tissue and organ donation for research in forensic pathology: the MRC Sudden Death Brain and Tissue Bank.

PubMed

Millar, T; Walker, R; Arango, J-C; Ironside, J W; Harrison, D J; MacIntyre, D J; Blackwood, D; Smith, C; Bell, J E

2007-12-01

Novel methodological approaches to the investigation of brain and non-central nervous system disorders have led to increased demand for well-characterized, high quality human tissue samples, particularly from control cases. In the setting of the new Human Tissue legislation, we sought to determine whether relatives who have been suddenly bereaved are willing to grant authorization for research use of post mortem tissue samples and organs in sufficient numbers to support the establishment of a brain and tissue bank based in the forensic service. Research authorization was sought from families on the day prior to forensic post mortem examination followed up by written confirmation. We have to date selected individuals who have died suddenly (age range 1-89 years) and who were likely to have normal brains or who had displayed symptoms of a CNS disorder of interest to researchers, including psychiatric disorders. One hundred and eleven families have been approached during the first 2 years of this project. Research use of tissue samples was authorized by 96% of families and 17% agreed to whole brain donation. Audit of families' experience does not suggest that they are further distressed by being approached. Respondents expressed a clear view that the opportunity for research donation should be open to all bereaved families. Despite the sometimes long post mortem intervals, the quality of tissue samples is good, as assessed by a range of markers including Agilent BioAnalyzer quantification of RNA integrity (mean value 6.4). We conclude that the vast majority of families are willing to support research use of post mortem tissues even in the context of sudden bereavement and despite previous adverse publicity. The potential for acquisition of normal CNS and non-CNS tissues and of various hard-to-get CNS disorders suggests that efforts to access the forensic post mortem service for research material are eminently worthwhile. (c) 2007 Pathological Society of Great Britain and Ireland

Recurrence of Marfan syndrome as a result of parental germ-line mosaicism for an FBN1 mutation.

PubMed Central

Rantamäki, T; Kaitila, I; Syvänen, A C; Lukka, M; Peltonen, L

1999-01-01

Mutations in the FBN1 gene cause Marfan syndrome (MFS), a dominantly inherited connective tissue disease. Almost all the identified FBN1mutations have been family specific, and the rate of new mutations is high. We report here a de novo FBN1mutation that was identified in two sisters with MFS born to clinically unaffected parents. The paternity and maternity were unequivocally confirmed by genotyping. Although one of the parents had to be an obligatory carrier for the mutation, we could not detect the mutation in the leukocyte DNA of either parent. To identify which parent was a mosaic for the mutation we analyzed several tissues from both parents, with a quantitative and sensitive solid-phase minisequencing method. The mutation was not, however, detectable in any of the analyzed tissues. Although the mutation could not be identified in a sperm sample from the father or in samples of multiple tissue from the mother, we concluded that the mother was the likely mosaic parent and that the mutation must have occurred during the early development of her germ-line cells. Mosaicism confined to germ-line cells has rarely been reported, and this report of mosaicism for the FBN1 mutation in MFS represents an important case, in light of the evaluation of the recurrence risk in genetic counseling of families with MFS. PMID:10090884

Distinct expression patterns of the E3 ligase SIAH-1 and its partner Kid/KIF22 in normal tissues and in the breast tumoral processes.

PubMed

Bruzzoni-Giovanelli, Heriberto; Fernandez, Plinio; Veiga, Lucía; Podgorniak, Marie-Pierre; Powell, Darren J; Candeias, Marco M; Mourah, Samia; Calvo, Fabien; Marín, Mónica

2010-02-09

SIAH proteins are the human members of an highly conserved family of E3 ubiquitin ligases. Several data suggest that SIAH proteins may have a role in tumor suppression and apoptosis. Previously, we reported that SIAH-1 induces the degradation of Kid (KIF22), a chromokinesin protein implicated in the normal progression of mitosis and meiosis, by the ubiquitin proteasome pathway. In human breast cancer cells stably transfected with SIAH-1, Kid/KIF22 protein level was markedly reduced whereas, the Kid/KIF22 mRNA level was increased. This interaction has been further elucidated through analyzing SIAH and Kid/KIF22 expression in both paired normal and tumor tissues and cell lines. It was observed that SIAH-1 protein is widely expressed in different normal tissues, and in cells lines but showing some differences in western blotting profiles. Immunofluorescence microscopy shows that the intracellular distribution of SIAH-1 and Kid/KIF22 appears to be modified in human tumor tissues compared to normal controls. When mRNA expression of SIAH-1 and Kid/KIF22 was analyzed by real-time PCR in normal and cancer breast tissues from the same patient, a large variation in the number of mRNA copies was detected between the different samples. In most cases, SIAH-1 mRNA is decreased in tumor tissues compared to their normal counterparts. Interestingly, in all breast tumor tissues analyzed, variations in the Kid/KIF22 mRNA levels mirrored those seen with SIAH-1 mRNAs. This concerted variation of SIAH-1 and Kid/KIF22 messengers suggests the existence of an additional level of control than the previously described protein-protein interaction and protein stability regulation. Our observations also underline the need to re-evaluate the results of gene expression obtained by qRT-PCR and relate it to the protein expression and cellular localization when matched normal and tumoral tissues are analyzed.

Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hewitson, Laura; Thissen, James B.; Gardner, Shea N.

In 2010, researchers reported that the two US-licensed rotavirus vaccines contained DNA or DNA fragments from porcine circovirus (PCV). Although PCV, a common virus among pigs, is not thought to cause illness in humans, these findings raised several safety concerns. In this study, we sought to determine whether viruses, including PCV, could be detected in ileal tissue samples of children vaccinated with one of the two rotavirus vaccines. A broad spectrum, novel DNA detection technology, the Lawrence Livermore Microbial Detection Array (LLMDA), was utilized, and confirmation of viral pathogens using the polymerase chain reaction (PCR) was conducted. The LLMDA technologymore » was recently used to identify PCV from one rotavirus vaccine. Ileal tissue samples were analyzed from 21 subjects, aged 15–62 months. PCV was not detected in any ileal tissue samples by the LLMDA or PCR. LLMDA identified a human rotavirus A from one of the vaccinated subjects, which is likely due to a recent infection from a wild type rotavirus. LLMDA also identified human parechovirus, a common gastroenteritis viral infection, from two subjects. Additionally, LLMDA detected common gastrointestinal bacterial organisms from the Enterobacteriaceae , Bacteroidaceae , and Streptococcaceae families from several subjects. This study provides a survey of viral and bacterial pathogens from pediatric ileal samples, and may shed light on future studies to identify pathogen associations with pediatric vaccinations.« less

Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination

DOE PAGES

Hewitson, Laura; Thissen, James B.; Gardner, Shea N.; ...

2014-01-01

In 2010, researchers reported that the two US-licensed rotavirus vaccines contained DNA or DNA fragments from porcine circovirus (PCV). Although PCV, a common virus among pigs, is not thought to cause illness in humans, these findings raised several safety concerns. In this study, we sought to determine whether viruses, including PCV, could be detected in ileal tissue samples of children vaccinated with one of the two rotavirus vaccines. A broad spectrum, novel DNA detection technology, the Lawrence Livermore Microbial Detection Array (LLMDA), was utilized, and confirmation of viral pathogens using the polymerase chain reaction (PCR) was conducted. The LLMDA technologymore » was recently used to identify PCV from one rotavirus vaccine. Ileal tissue samples were analyzed from 21 subjects, aged 15–62 months. PCV was not detected in any ileal tissue samples by the LLMDA or PCR. LLMDA identified a human rotavirus A from one of the vaccinated subjects, which is likely due to a recent infection from a wild type rotavirus. LLMDA also identified human parechovirus, a common gastroenteritis viral infection, from two subjects. Additionally, LLMDA detected common gastrointestinal bacterial organisms from the Enterobacteriaceae , Bacteroidaceae , and Streptococcaceae families from several subjects. This study provides a survey of viral and bacterial pathogens from pediatric ileal samples, and may shed light on future studies to identify pathogen associations with pediatric vaccinations.« less

Characterization of PD-L1 expression in Chinese non-small cell lung cancer patients with PTEN expression as a means for tissue quality screening.

PubMed

Zhang, Xu-Chao; Cao, Xu; Sun, Chun; Xie, Zhi; Guo, Jian-Jun; Yang, Jin-Ji; Yang, Xue-Ning; Dai, Hang-Jun; Li, Su-Chun; Xu, Xin-Ran; Zuo, Yun-Xia; Chen, Meng; Koeppen, Hartmut; He, Jing; Kiermaier, Astrid; Shames, David; Cheng, Gang; Wu, Yi-Long

2018-03-01

The goal of this study is to evaluate PD-L1 prevalence and its association with major clinical characteristics in Chinese non-small cell lung cancer (NSCLC) patients to inform the clinical development of anti-PD1/PD-L1 agents in this population. We used phosphatase and tensin homolog (PTEN) expression through IHC as a surrogate tissue quality marker to screen surgical NSCLC samples in tissue microarray (TMA; 172 cases) or whole-section (268 cases) format. The samples were then analyzed with a clinically validated PD-L1 IHC assay. The results were correlated with baseline characteristics and clinical outcomes. PTEN IHC showed that 108 TMA samples and 105 whole-section samples qualified for PD-L1 IHC. With a clinically relevant cutoff, 41.7% of the TMA samples were PD-L1 positive. PD-L1 level was much lower in EGFR-mutant patients and seemed to be a favorable prognostic factor for both overall survival (OS) and recurrence-free survival (RFS). These findings were confirmed in the whole-section samples except that their survival data were not mature enough for correlation analysis. In summary, PD-L1 expression was detected in approximately 40% of PTEN-qualified Chinese NSCLC samples, negatively correlated with EGFR mutation and seemed to be a favorable prognostic factor for both OS and RFS. Notably, the different results from PTEN-qualified and PTEN-disqualified samples underscore the importance of tissue quality control prior to biomarker testing.

A Multivariate Evaluation of Factors Affecting the Quality of Freshly Frozen Tissue Specimens.

PubMed

Wang, Tong-Hong; Chen, Chin-Chuan; Liang, Kung-Hao; Chen, Chi-Yuan; Chuang, Wen-Yu; Ueng, Shir-Hwa; Chu, Pao-Hsien; Huang, Chung-Guei; Chen, Tse-Ching; Hsueh, Chuen

2017-08-01

Well-prepared and preserved freshly frozen specimens are indispensable materials for clinical studies. To manage specimen quality and to understand the factors potentially affecting specimen quality during preservation processes, we analyzed the quality of RNA and genomic DNA of various tissues collected between 2002 and 2011 in Linkou Chang Gung Memorial Hospital, Taiwan. During this period, a total of 1059 freshly frozen specimens from eight major cancer categories were examined. It was found that preservation duration, organ origin, and tissue type could all influence the quality of RNA samples. The increased preservation period correlated with decreased RNA quality; the brain, breast, and stomach RNA specimens displayed faster degradation rates than those of other organs, and RNA specimens isolated from tumor tissues were apparently more stable than those of other tissues. These factors could all be used as quality predictors of RNA quality. In contrast, almost all analyses revealed that the genomic DNA samples had good quality, which was not influenced by the aforementioned factors. The results assisted us in determining preservation factors that affect specimen quality, which could provide evidence for improving processes of sample collection and preservation. Furthermore, the results are also useful for researchers to adopt as the evaluation criteria for choosing specimen collection and preservation strategies.

Hyperspectral stimulated emission depletion microscopy and methods of use thereof

DOEpatents

Timlin, Jerilyn A; Aaron, Jesse S

2014-04-01

A hyperspectral stimulated emission depletion ("STED") microscope system for high-resolution imaging of samples labeled with multiple fluorophores (e.g., two to ten fluorophores). The hyperspectral STED microscope includes a light source, optical systems configured for generating an excitation light beam and a depletion light beam, optical systems configured for focusing the excitation and depletion light beams on a sample, and systems for collecting and processing data generated by interaction of the excitation and depletion light beams with the sample. Hyperspectral STED data may be analyzed using multivariate curve resolution analysis techniques to deconvolute emission from the multiple fluorophores. The hyperspectral STED microscope described herein can be used for multi-color, subdiffraction imaging of samples (e.g., materials and biological materials) and for analyzing a tissue by Forster Resonance Energy Transfer ("FRET").

A method to estimate the fractional fat volume within a ROI of a breast biopsy for WAXS applications: Animal tissue evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Robert Y., E-mail: rx-tang@laurentian.ca; McDonald, Nancy, E-mail: mcdnancye@gmail.com; Laamanen, Curtis, E-mail: cx-laamanen@laurentian.ca

Purpose: To develop a method to estimate the mean fractional volume of fat (ν{sup ¯}{sub fat}) within a region of interest (ROI) of a tissue sample for wide-angle x-ray scatter (WAXS) applications. A scatter signal from the ROI was obtained and use of ν{sup ¯}{sub fat} in a WAXS fat subtraction model provided a way to estimate the differential linear scattering coefficient μ{sub s} of the remaining fatless tissue. Methods: The efficacy of the method was tested using animal tissue from a local butcher shop. Formalin fixed samples, 5 mm in diameter 4 mm thick, were prepared. The two mainmore » tissue types were fat and meat (fibrous). Pure as well as composite samples consisting of a mixture of the two tissue types were analyzed. For the latter samples, ν{sub fat} for the tissue columns of interest were extracted from corresponding pixels in CCD digital x-ray images using a calibration curve. The means ν{sup ¯}{sub fat} were then calculated for use in a WAXS fat subtraction model. For the WAXS measurements, the samples were interrogated with a 2.7 mm diameter 50 kV beam and the 6° scattered photons were detected with a CdTe detector subtending a solid angle of 7.75 × 10{sup −5} sr. Using the scatter spectrum, an estimate of the incident spectrum, and a scatter model, μ{sub s} was determined for the tissue in the ROI. For the composite samples, a WAXS fat subtraction model was used to estimate the μ{sub s} of the fibrous tissue in the ROI. This signal was compared to μ{sub s} of fibrous tissue obtained using a pure fibrous sample. Results: For chicken and beef composites, ν{sup ¯}{sub fat}=0.33±0.05 and 0.32 ± 0.05, respectively. The subtractions of these fat components from the WAXS composite signals provided estimates of μ{sub s} for chicken and beef fibrous tissue. The differences between the estimates and μ{sub s} of fibrous obtained with a pure sample were calculated as a function of the momentum transfer x. A t-test showed that the mean of the differences did not vary from zero in a statistically significant way thereby validating the methods. Conclusions: The methodology to estimate ν{sup ¯}{sub fat} in a ROI of a tissue sample via CCD x-ray imaging was quantitatively accurate. The WAXS fat subtraction model allowed μ{sub s} of fibrous tissue to be obtained from a ROI which had some fat. The fat estimation method coupled with the WAXS models can be used to compare μ{sub s} coefficients of fibroglandular and cancerous breast tissue.« less

Evaluation of a multiplex real-time PCR assay for detecting pathogens in cardiac valve tissue in patients with endocarditis.

PubMed

Fernández, Angel L; Varela, Eduardo; Martínez, Lucía; Martínez, Amparo; Sierra, Juan; González-Juanatey, José R; Regueiro, Benito

2010-10-01

With a novel real-time multiplex polymerase chain reaction test, the LightCycler SeptiFast® test, 25 bacterial and fungal species can be identified directly in blood. The SeptiFast® test has been used for rapid etiologic diagnosis in infectious endocarditis using blood samples but has not been evaluated directly on cardiac vegetations in patients being treated for infectious endocarditis. We prospectively analyzed 15 samples of heart valve tissue with active infectious endocarditis using the SeptiFast® test and compared the test's sensitivity with that of blood culture, valve tissue culture, and the SeptiFast® test in blood. The sensitivity of the SeptiFast test in heart valve tissue was 100%. The test results confirmed the diagnosis obtained using blood culture in 13 cases and identified the pathogen in 2 cases where blood culture tested negative. The sensitivity of the SeptiFast® test in heart valve tissue was greater than that obtained with conventional culture of vegetations or with the SeptiFast test in blood.

Cadmium contamination of tissues and organs of delphinids species (Stenella attenuata)--influence of biological and ecological factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andre, J.M.; Amiard, J.C.; Amiard-Triquet, C.

1990-12-01

Based on a sample of 27 dolphins (Stenella attenuata) captured in the Eastern tropical zone of the Pacific Ocean, this study was carried out to analyze the cadmium accumulation levels and distribution in 12 organs or tissue samples. The average cadmium concentrations were between 0.2 mg Cd.kg-1 in the brain and muscle and 48 mg Cd.kg-1 in the kidneys. For most of organs and tissues the average values were between 1 and 5 mg Cd.kg-1. Kidneys, liver, muscle, and intestine contained almost 85% of the total cadmium burden of all tissues considered in this study. Most of the biological andmore » ecological factors taken into account (age, sex, total weight, and length of the dolphins, weight of the organs, place and date of capture) interacted with the cadmium concentrations and burdens in the collected organs or tissues. Three factors appear to be of prime importance: age, body weight, and geographical location of the area of capture.« less

Preferential expression of cystein-rich secretory protein-3 (CRISP-3) in chronic pancreatitis.

PubMed

Liao, Q; Kleeff, J; Xiao, Y; Guweidhi, A; Schambony, A; Töpfer-Petersen, E; Zimmermann, A; Büchler, M W; Friess, H

2003-04-01

Chronic pancreatitis (CP) is a progressive inflammatory process resulting in exocrine and endocrine pancreatic insufficiency in advanced stages. Cysteine-rich secretory protein (CRISP-3) has been identified as a defense-associated molecule with predominant expression in the salivary gland, pancreas and prostate. In this study, we investigated CRISP-3 expression in normal pancreatic tissues, chronic pancreatitis tissues, pancreatic cancer tissues and pancreatic cancer cell lines, as well as in other gastrointestinal organs. 15 normal pancreatic tissues, 14 chronic pancreatitis tissues and 14 pancreatic cancer tissues as well as three pancreatic cancer cell lines were analyzed. Moreover, hepatocellular carcinoma and esophageal, stomach and colon cancers were also analyzed together with the corresponding normal controls. CRISP-3 was expressed at moderate to high levels in chronic pancreatitis tissues and at moderate levels in pancreatic cancer tissues but at low levels in normal pancreatic tissues, and was absent in three pancreatic cancer cell lines. CRISP-3 expression was below the level of detection in all cancerous gastrointestinal tissues and in all normal tissues except 2 of 16 colon tissue samples. CRISP-3 mRNA signals and immunoreactivity were strongly present in the cytoplasm of degenerating acinar cells and in small proliferating ductal cells in CP tissues and CP-like lesions in pancreatic cancer tissues. In contrast, CRISP-3 expression was weak to absent in the cytoplasm of cancer cells as well as in acinar cells and ductal cells in pancreatic cancer tissues and normal pancreatic tissues. These results reveal that the distribution of CRISP-3 in gastrointestinal tissues is predominantly in the pancreas. High levels of CRISP-3 in acinar cells dedifferentiating into small proliferating ductal cells in CP and CP-like lesions in pancreatic cancer suggests a role of this molecule in the pathophysiology of CP.

Selenium levels in human breast carcinoma tissue are associated with a common polymorphism in the gene for SELENOP (Selenoprotein P).

PubMed

Ekoue, Dede N; Zaichick, Sofia; Valyi-Nagy, Klara; Picklo, Matthew; Lacher, Craig; Hoskins, Kent; Warso, Michael A; Bonini, Marcelo G; Diamond, Alan M

2017-01-01

Selenium supplementation of the diets of rodents has consistently been shown to suppress mammary carcinogenesis and some, albeit not all, human epidemiological studies have indicated an inverse association between selenium and breast cancer risk. In order to better understand the role selenium plays in breast cancer, 30 samples of tumor tissue were obtained from women with breast cancer and analyzed for selenium concentration, the levels of several selenium-containing proteins and the levels of the MnSOD anti-oxidant protein. Polymorphisms within the genes for these same proteins were determined from DNA isolated from the tissue samples. There was a wide range of selenium in these tissues, ranging from 24 to 854ng/gm. The selenium levels in the tissues were correlated to the genotype of the SELENOP selenium carrier protein, but not to other proteins whose levels have been reported to be responsive to selenium availability, including GPX1, SELENOF and SBP1. There was an association between a polymorphism in the gene for MnSOD and the levels of the encoded protein. These studies were the first to examine the relationship between selenium levels, genotypes and protein levels in human tissues. Furthermore, the obtained data provide evidence for the need to obtain data about the effects of selenium in breast cancer by examining samples from that particular tissue type. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance

PubMed Central

Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-01-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (P<0.001) and decreased overall survival (P<0.001). Based on a multivariate analysis, Mena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC. PMID:29113241

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance.

PubMed

Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-11-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (P<0.001) and decreased overall survival (P<0.001). Based on a multivariate analysis, Mena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC.

Altered intragenic DNA methylation of HOOK2 gene in adipose tissue from individuals with obesity and type 2 diabetes

PubMed Central

Fernández-Bayón, Gustavo; Morales-Sánchez, Paula; Sanz, Lourdes; Turienzo, Estrella; González, Juan José; Martinez-Faedo, Ceferino; Suarez-Gutiérrez, Lorena; Ares, Jessica; Díaz-Naya, Lucia; Martin-Nieto, Alicia; Fernández-Morera, Juan L.; Fraga, Mario F.

2017-01-01

Aims/Hypothesis Failure in glucose response to insulin is a common pathology associated with obesity. In this study, we analyzed the genome wide DNA methylation profile of visceral adipose tissue (VAT) samples in a population of individuals with obesity and assessed whether differential methylation profiles are associated with the presence of type 2 diabetes (T2D). Methods More than 485,000 CpG genome sites from VAT samples from women with obesity undergoing gastric bypass (n = 18), and classified as suffering from type 2 diabetes (T2D) or not (no type 2 diabetes, NT2D), were analyzed using DNA methylation arrays. Results We found significant differential methylation between T2D and NT2D samples in 24 CpGs that map with sixteen genes, one of which, HOOK2, demonstrated a significant correlation between differentially hypermethylated regions on the gene body and the presence of type 2 diabetes. This was validated by pyrosequencing in a population of 91 samples from both males and females with obesity. Furthermore, when these results were analyzed by gender, female T2D samples were found hypermethylated at the cg04657146-region and the cg 11738485-region of HOOK2 gene, whilst, interestingly, male samples were found hypomethylated in this latter region. Conclusion The differential methylation profile of the HOOK2 gene in individuals with T2D and obesity might be related to the attendant T2D, but further studies are required to identify the potential role of HOOK2 gene in T2D disease. The finding of gender differences in T2D methylation of HOOK2 also warrants further investigation. PMID:29228058

Femtosecond irradiation of chicken corneas analyzed by digital holographic microscopy

NASA Astrophysics Data System (ADS)

Fimia, A.; Gomariz, M.; Murciano, A.; Acebal, P.; Madrigal, R.; Carretero, L.; Alió, J. L.; Rodriguez, A.; Fernández, E.

2012-06-01

Digital Holographic Microscopy (DHM) is a potentially non-invasive new technology which can be applied in many areas from applied imaging science to biomedical optics. DHM is an interferometric technique that gives us a number of important advantages such as the possibility to acquire holograms at high speed, to obtain complete information about amplitude and phase and to use image processing techniques. In this sense, DHM offers rapid 3D imaging with a theoretically higher resolution than OCT (Optical Coherent Tomography). By this technique optical path measurements with sensitivities in the nanometer range of reflective and transparent objects can be obtained. In this work, we use DHM to study the effect of ablation using 4.5 nJ pulses on chicken corneas. For this, a titanium sapphire laser at 800 nm and 76 MHz frequency (Vitesse, Coherent Inc. USA) was focused to its diffraction-limited spot size by a 10x objective of 0.3 numerical aperture. The width of the pulse (170 fs) at the sample was measured by spectral techniques. The average beam power at the sample was 340 mW and all the system was mechanically driven by a XY synchronization unit that controls the speed of the sample movement. The speed of the sample was varied between 1-50 μm/s. The studied chicken corneal tissue was previously processed by Trypan dye in order to visualize the irradiated area. The photodisrupted zone was analyzed by a HDM technique by illuminating it using a laser diode source (λ=683 nm) linearly polarized in a modified Mach-Zehnder with an off-axis geometry configuration. The reflected object wave by the tissue surface (specimen) interferes with the reference wave and a CCD camera records the hologram. As a result, the influence of the speed of photodisruption in the depth of the ablated corneas was analyzed. Therefore, it is possible to analyze thermal and photoirradiated effects on corneal tissues which allow us the possibility to optimize the interaction of intratissue and the intratissue target region of interest.

Osteoconductive composite graft based on bacterial synthesized hydroxyapatite nanoparticles doped with different ions: From synthesis to in vivo studies.

PubMed

Ahmadzadeh, Elham; Talebnia, Farid; Tabatabaei, Meisam; Ahmadzadeh, Hossein; Mostaghaci, Babak

2016-07-01

To repair damaged bone tissues, osteoconductive bone graft substitutes are required for enhancement of the regenerative potential of osteoblast cells. Nanostructured hydroxyapatite is a bioactive ceramic used for bone tissue engineering purposes. In this study, carbonate hydroxyapatite (cHA) and zinc-magnesium substituted hydroxyapatite (Zn-Mg-HA) nanoparticles were synthesized via biomineralization method using Enterobacter aerogenes. The structural phase composition and the morphology of the samples were analyzed using appropriate powder characterization methods. Next, a composite graft was fabricated by using polyvinyl alcohol and both cHA and Zn-Mg-HA samples. In vivo osteogenic potential of the graft was then investigated in a rabbit tibial osteotomy model. Histological, radiological and morphological studies showed that the graft was mineralized by the newly formed bone tissue without signs of inflammation or infection after 4 weeks of implantation. These histomorphometric results suggest that the fabricated graft can function as a potent osteoconductive bone tissue substitute. Copyright © 2016 Elsevier Inc. All rights reserved.

Cancer related gene alterations can be detected with next-generation sequencing analysis of bile in diffusely infiltrating type cholangiocarcinoma.

PubMed

Lee, Chang Hun; Wang, Hong En; Seo, Seung Young; Kim, Seong Hun; Kim, In Hee; Kim, Sang Wook; Lee, Soo Teik; Kim, Dae Ghon; Han, Myung Kwan; Lee, Seung Ok

2016-08-01

Genome-wide association study in diffusely infiltrating type cholangiocarcinoma (CC) can be limited due to the difficulty of obtaining tumor tissue. We aimed to evaluate the genomic alterations of diffusely infiltrating type CC using next-generation sequencing (NGS) of bile and to compare the variations with those of mass-forming type CC. A total of 24 bile samples obtained during endoscopic retrograde cholangiopancreatography (ERCP) and 17 surgically obtained tumor tissue samples were evaluated. Buffy coat and normal tissue samples were used as controls for a somatic mutation analysis. After extraction of genomic DNA, NGS analysis was performed for 48 cancer related genes. There were 27 men and 14 women with a mean age of 65.0±11.8years. The amount of extracted genomic DNA from 3cm(3) of bile was 66.0±84.7μg and revealed a high depth of sequencing coverage. All of the patients had genomic variations, with an average number of 19.4±2.8 and 22.3±3.3 alterations per patient from the bile and tumor tissue, respectively. After filtering process, damaging SNPs (8 sites for each type of CC) were predicted by analyzing tools, and their target genes showed relevant differences between the diffusely infiltrating and mass-forming type CC. Finally, in somatic mutation analysis, tumor-normal paired 14 tissue and 6 bile samples were analyzed, genomic alterations of EGFR, FGFR1, ABL1, PIK3CA, and CDKN2A gene were seen in the diffusely infiltrating type CC, and TP53, KRAS, APC, GNA11, ERBB4, ATM, SMAD4, BRAF, and IDH1 were altered in the mass-forming type CC group. STK11, GNAQ, RB1, KDR, and SMO genes were revealed in both groups. The NGS analysis was feasible with bile sample and diffusely infiltrating type CC revealed genetic differences compared with mass-forming type CC. Genome-wide association study could be performed using bile sample in the patients with CC undergoing ERCP and a different genetic approach for accurate diagnosis, pathogenesis study, and targeted therapy will be needed in diffusely infiltrating type CC. Copyright © 2016 Elsevier Inc. All rights reserved.

Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer.

PubMed

Karahan, Gurbet; Sayar, Nilufer; Gozum, Gokcen; Bozkurt, Betul; Konu, Ozlen; Yulug, Isik G

2015-06-01

Ribosomal RNA (rRNA) expression, one of the most important factors regulating ribosome production, is primarily controlled by a CG-rich 45 S rDNA promoter. However, the DNA methylation state of the 45 S rDNA promoter, as well as its effect on rRNA gene expression in types of human cancers is controversial. In the present study we analyzed the methylation status of the rDNA promoter (-380 to +53 bp) as well as associated rRNA expression levels in breast cancer cell lines and breast tumor-normal tissue pairs. We found that the aforementioned regulatory region was extensively methylated (74-96%) in all cell lines and in 68% (13/19 tumor-normal pairs) of the tumors. Expression levels of rRNA transcripts 18 S, 28 S, 5.8 S and 45 S external transcribed spacer (45 S ETS) greatly varied in the breast cancer cell lines regardless of their methylation status. Analyses of rRNA transcript expression levels in the breast tumor and normal matched tissues showed no significant difference when normalized with TBP. On the other hand, using the geometric mean of the rRNA expression values (GM-rRNA) as reference enabled us to identify significant changes in the relative expression of rRNAs in the tissue samples. We propose GM-rRNA normalization as a novel strategy to analyze expression differences between rRNA transcripts. Accordingly, the 18S rRNA/GM-rRNA ratio was significantly higher whereas the 5.8S rRNA/GM-rRNA ratio was significantly lower in breast tumor samples than this ratio in the matched normal samples. Moreover, the 18S rRNA/GM-rRNA ratio was negatively correlated with the 45 S rDNA promoter methylation level in the normal breast tissue samples, yet not in the breast tumors. Significant correlations observed between the expression levels of rRNA transcripts in the normal samples were lost in the tumor samples. We showed that the expression of rRNA transcripts may not be based solely on promoter methylation. Carcinogenesis may cause dysregulation of the correlation between spliced rRNA expression levels, possibly due to changes in rRNA processing, which requires further investigation.

Organic Compounds and Trace Elements in Fish Tissue and Bed Sediment in the Delaware River Basin, New Jersey, Pennsylvania, New York, and Delaware, 1998-2000

USGS Publications Warehouse

Romanok, Kristin M.; Fischer, Jeffrey M.; Riva-Murray, Karen; Brightbill, Robin; Bilger, Michael

2006-01-01

As part of the National Water-Quality Assessment (NAWQA) program activities in the Delaware River Basin (DELR), samples of fish tissue from 21 sites and samples of bed sediment from 35 sites were analyzed for a suite of organic compounds and trace elements. The sampling sites, within subbasins ranging in size from 11 to 600 square miles, were selected to represent 5 main land-use categories in the DELR -forest, low-agricultural, agricultural, urban, and mixed use. Samples of both fish tissue and bed sediment were also collected from 4 'large-river' sites that represented drainage areas ranging from 1,300 to 6,800 square miles, areas in which the land is used for a variety of purposes. One or more of the organochlorine compounds-DDT and chlordane metabolites, polychlorinated biphenyls (total PCBs), and dieldrin- were detected frequently in samples collected over a wide geographic area. One or more of these compounds were detected in fish-tissue samples from 92 percent of the sites and in bed-sediment samples from 82 percent of the sites. Concentrations of total DDT, total chlordanes, total PCBs, and dieldrin in whole white suckers and in bed sediment were significantly related to urban/industrial basin characteristics, such as percentage of urban land use and population density. Semi-volatile organic compounds (SVOCs)-total polycyclic aromatic hydrocarbons (PAHs), total phthalates, and phenols- were detected frequently in bed-sediment samples. All three types of SVOCs were detected in samples from at least one site in each land-use category. The highest detection rates and concentrations typically were in samples from sites in the urban and mixed land-use categories, as well as from the large-river sites. Concentrations of total PAHs and total phthalates in bed-sediment samples were found to be statistically related to percentages of urban land use and to population density in the drainage areas represented by the sampling sites. The samples of fish tissue and bed sediment collected throughout the DELR were analyzed for a large suite of trace elements, but results of the analyses for eight elements-arsenic, cadmium, chromium, copper, lead, nickel, mercury, and zinc- that are considered contaminants of concern are described in this report. One or more of the eight trace elements were detected in samples from every fish tissue and bed-sediment sampling site, and all of the trace elements were detected in samples from 97 percent of the bed-sediment sites. The concentrations of organic compounds and trace elements in the DELR samples were compared to applicable guidelines for the protection of wildlife and other biological organisms. Concentrations of total DDT, total chlordanes, total PCBs, and dieldrin in fish-tissue samples from 14 sites exceeded one or more of the Wildlife Protective Guidelines established by the New York State Department of Environmental Conservation. Concentrations of one or more organic compounds in samples from 16 bed-sediment sites exceeded the Threshold Effects Concentrations (TEC) of the Canadian Sediment Quality Guidelines, and concentrations of one or more of the eight trace elements in samples from 38 bed-sediment sites exceeded the TEC. (The TEC is the concentration below which adverse biological effects in freshwater ecosystems are expected to be rare.) Concentrations of organic compounds in samples from some bed-sediment sites exceeded the Canadian Probable Effects Concentrations (PEC), and concentrations of trace elements in samples from 18 sites exceeded the PEC. (The PEC is the concentration above which adverse effects to biological organisms are expected to occur frequently). Concentrations of organic compounds and trace elements in samples from the DELR were compared to similar data from other NAWQA study units in the northeastern United States and also data from the Mobile River (Alabama) Basin and the Northern Rockies Intermontane Basin study units. Median concentrations of to

MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue: Identifying Reference MicroRNAs and Variability.

PubMed

Boisen, Mogens Karsbøl; Dehlendorff, Christian; Linnemann, Dorte; Schultz, Nicolai Aagaard; Jensen, Benny Vittrup; Høgdall, Estrid Vilma Solyom; Johansen, Julia Sidenius

2015-12-29

Archival formalin-fixed paraffin-embedded (FFPE) cancer tissue samples are a readily available resource for microRNA (miRNA) biomarker identification. No established standard for reference miRNAs in FFPE tissue exists. We sought to identify stable reference miRNAs for normalization of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen/FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean miRNA expression was tested using linear regression. Variability was described using correlation coefficients and linear mixed effects models. Normalization effects were determined by changes in standard deviation and by hierarchical clustering. We created lists of 20 miRNAs with the best correlation to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global miRNA expression in PC (50% reduction over 20 years) but not in CRC. Formalin fixation for 2-6 days decreased miRNA expression 30-65%. Normalization using global mean expression reduced variability for technical and biological replicates while normalization using the expression of the identified reference miRNAs reduced variability only for biological replicates. Normalization only had a minor impact on clustering results. We identified suitable reference miRNAs for future miRNA expression experiments using CRC- and PC FFPE tissue samples. Formalin fixation decreased miRNA expression considerably, while the effect of increasing sample age was estimated to be negligible in a clinical setting.

Fluorescence Spectroscopy as a Tool for the Assessment of Liver Samples with Several Stages of Fibrosis.

PubMed

Fabila-Bustos, Diego A; Arroyo-Camarena, Úrsula D; López-Vancell, María D; Durán-Padilla, Marco A; Azuceno-García, Itzel; Stolik-Isakina, Suren; Valor-Reed, Alma; Ibarra-Coronado, Elizabeth; Hernández-Quintanar, Luis F; Escobedo, Galileo; de la Rosa-Vázquez, José M

2018-03-01

During the last years, fluorescence spectroscopy has been used as a potential tool for the evaluation and characterization of tissues with different disease conditions due to its low cost, high sensitivity, and minimally or noninvasive character. In this study, fluorescence spectroscopy was used to study 19 paraffin blocks containing human liver tissue from biopsies. All samples were previously analyzed by two senior pathologists in a single-blind trial. After their evaluation, four liver samples were classified as nonfibrosis (F0), four as initial fibrosis (F1-F2), four as advanced fibrosis (F3), and six as cirrhosis (F4). The fluorescence was induced at different wavelengths as follows: 330, 365, and 405 nm using a portable fiber-optic system. The fluorescence spectra were recorded in the range of 400-750 nm. A distinctive correlation between the shape of each spectrum and the level of fibrosis in the liver sample was detected. A multi-variate statistical analysis based on principal component analysis followed by linear discrimination analysis was applied to develop algorithms able to distinguish different stages of fibrosis based on the characteristics of fluorescence spectra. Pairwise comparisons were performed: F0 versus F1-F2, F1-F2 versus F3, F3 versus F4, and F1-F2 versus F4. The algorithms applied to each set of data yielded values of sensitivity and specificity that were higher than 90% and 95%, respectively, in all the analyzed cases. With this study, it is concluded that fluorescence spectroscopy can be used as a complementary tool for the assessment of liver fibrosis in liver tissue samples, which sets the stage for subsequent clinical trials.

Comparative study of pharmacokinetics and tissue distribution of osthole in rats after oral administration of pure osthole and Libanotis buchtormensis supercritical extract.

PubMed

Shi, Juan; Fu, Qiang; Chen, Wang; Yang, Hai-Ping; Liu, Jing; Wang, Xiao-Meng; He, Xu

2013-01-09

Libanotis buchtormensis is the source of an important traditional medicine from Shaanxi province of China used in the treatment of many illnesses. Libanotis buchtormensis supercritical extract (LBSE) has analgesic, sedative and anti-inflammatory qualities. Osthole is one of the major bioactive components of LBSE; it is known for its significant anti-tumor, analgesic, and anti-inflammatory properties, it also alleviates hyperglycemia. The purpose of the present study was to compare the pharmacokinetics and tissue distribution of osthole in Sprague-Dawley (SD) rats after oral administration of pure osthole and LBSE. The two preparations were administered at the same osthole dose (approximately 130 mg/kg). The results should provide some guidance for the clinical applications of Libanotis buchtormensis. Comparative pharmacokinetics and tissue distribution of osthole in SD rats after oral administration of pure osthole and LBSE were analyzed using reversed-phase high-performance liquid chromatography (RP-HPLC). All pharmacokinetic data were analyzed using 3P97 software. Samples of blood and internal organs (heart, liver, spleen, lungs and kidney) were collected and pretreated according to the experimental schedule. After pretreatment, plasma and tissue samples were extracted using ether-ethyl acetate mixture (3:1, v/v). The concentration of osthole in the plasma and tissues were determined using the RP-HPLC method. The procedure described in this paper shows good precision and stability and is suitable for the osthole assays in biological samples. We found that the average plasma concentration-time profile of osthole after oral administration of osthole and LBSE showed a single peak. There were also clear differences between plasma concentrations of osthole after oral administration of pure osthole and LBSE. Non-osthole ingredients in LBSE showed some pharmacokinetic interactions with osthole and hence decreased its absorption levels (p<0.05). Our results show different tissue distribution of osthole in the single and composite administration regimens. This study compares the pharmacokinetic characteristics and tissue distribution of osthole in rats after oral administration of pure osthole and LBSE; the results might be useful in clinical application of this traditional Chinese herbal medicine. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

PIXE analysis of tumors and localization behavior of a lanthanide in nude mice

NASA Astrophysics Data System (ADS)

Chang, Pei-Jiun; Yang, Czau-Siung; Chou, Ming-Ji; Wei, Chau-Chin; Hsu, Chu-Chung; Wang, Chia-Yu

1984-04-01

We have used particle induced X-ray emission (PIXE) to analyze the elemental compositions and uptakes of a lanthanide, yttrium in this report, in tumors and normal tissues of nude mice. A small amount of yttrium nitrate was injected into nude mice with tumors. Samples of normal and malignant tissues taken from these mice were bombarded by the 2 MeV proton beam from a 3 MeV Van de Graaff accelerator with a Ge detector system to determine the relative elemental compositions of tissues and the relative concentrations of yttrium taken up by these tissues. We found that the uptakes of yttrium by tumors were at least five times more than those by normal tissues. Substantial differences were often observed between the trace element weight (or concentration) pattern of the cancerous and normal tissues. The present result is compared with human tissues.

Morphology of mucosa-associated lymphoid tissue in odontocetes.

PubMed

Silva, Fernanda M O; Guimarães, Juliana P; Vergara-Parente, Jociery E; Carvalho, Vitor L; Carolina, Ana; Meirelles, O; Marmontel, Miriam; Oliveira, Bruno S S P; Santos, Silvanise M; Becegato, Estella Z; Evangelista, Janaina S A M; Miglino, Maria Angelica

2016-09-01

This study describes the mucosa-associated lymphoid tissue (MALT) in odontocetes from the Brazilian coast and freshwater systems. Seven species were evaluated and tissue samples were analyzed by light, scanning and transmission electron microscopy, and immunohistochemistry. Laryngeal tonsil was a palpable oval mass located in the larynx, composed of a lymphoepithelial complex. Dense collections of lymphocytes were found in the skin of male fetus and calf. Clusters of lymphoid tissue were found in the uterine cervix of a reproductively active juvenile female and along the pulmonary artery of an adult female. Lymphoid tissues associated with the gastrointestinal tract were characterized by diffusely arranged or organized lymphocytes. The anal tonsil was composed of an aggregate of lymphoid tissue occurring exclusively in the anal canal, being composed of squamous epithelium branches. MALT was present in different tissues and organic systems of cetaceans, providing constant protection against mucosal pathogens present in their environment. © 2016 Wiley Periodicals, Inc.

Mechanical characterization of human brain tumors from patients and comparison to potential surgical phantoms.

PubMed

Stewart, Daniel C; Rubiano, Andrés; Dyson, Kyle; Simmons, Chelsey S

2017-01-01

While mechanical properties of the brain have been investigated thoroughly, the mechanical properties of human brain tumors rarely have been directly quantified due to the complexities of acquiring human tissue. Quantifying the mechanical properties of brain tumors is a necessary prerequisite, though, to identify appropriate materials for surgical tool testing and to define target parameters for cell biology and tissue engineering applications. Since characterization methods vary widely for soft biological and synthetic materials, here, we have developed a characterization method compatible with abnormally shaped human brain tumors, mouse tumors, animal tissue and common hydrogels, which enables direct comparison among samples. Samples were tested using a custom-built millimeter-scale indenter, and resulting force-displacement data is analyzed to quantify the steady-state modulus of each sample. We have directly quantified the quasi-static mechanical properties of human brain tumors with effective moduli ranging from 0.17-16.06 kPa for various pathologies. Of the readily available and inexpensive animal tissues tested, chicken liver (steady-state modulus 0.44 ± 0.13 kPa) has similar mechanical properties to normal human brain tissue while chicken crassus gizzard muscle (steady-state modulus 3.00 ± 0.65 kPa) has similar mechanical properties to human brain tumors. Other materials frequently used to mimic brain tissue in mechanical tests, like ballistic gel and chicken breast, were found to be significantly stiffer than both normal and diseased brain tissue. We have directly compared quasi-static properties of brain tissue, brain tumors, and common mechanical surrogates, though additional tests would be required to determine more complex constitutive models.

Transforming growth factor beta-1 expression in macrophages of human chronic periapical diseases.

PubMed

Liang, Z-Z; Li, J; Huang, S-G

2017-03-30

The objective of this study was to observe the distribution of macrophages (MPs) expressing transforming growth factor beta-1 (TGF-β1) in tissue samples from patients with different human chronic periapical diseases. In this study, samples were collected from 75 volunteers, who were divided into three groups according to classified standards, namely, healthy control (N = 25), periapical granuloma (N = 25), and periapical cyst (N = 25). The samples were fixed in 10% buffered formalin for more than 48 h, dehydrated, embedded, and stained with hematoxylin and eosin for histopathology. Double immunofluorescence was conducted to analyze the expression of TGF-β-CD14 double-positive MPs in periapical tissues. The number of double-positive cells (cells/mm 2 ) were significantly higher in the chronic periapical disease tissues (P < 0.01) compared to that in the control tissue; in addition, the density of TGF-β1-CD14 double positive cells was significantly higher in the periapical cyst group than in the periapical granuloma group (P < 0.01). The number of TGF-β1 expressing macrophages varied with human chronic periapical diseases. The TGF-β1-CD14 double-positive cells might play an important role in the pathology of human chronic periapical diseases.

Microbiota of human breast tissue.

PubMed

Urbaniak, Camilla; Cummins, Joanne; Brackstone, Muriel; Macklaim, Jean M; Gloor, Gregory B; Baban, Chwanrow K; Scott, Leslie; O'Hanlon, Deidre M; Burton, Jeremy P; Francis, Kevin P; Tangney, Mark; Reid, Gregor

2014-05-01

In recent years, a greater appreciation for the microbes inhabiting human body sites has emerged. In the female mammary gland, milk has been shown to contain bacterial species, ostensibly reaching the ducts from the skin. We decided to investigate whether there is a microbiome within the mammary tissue. Using 16S rRNA sequencing and culture, we analyzed breast tissue from 81 women with and without cancer in Canada and Ireland. A diverse population of bacteria was detected within tissue collected from sites all around the breast in women aged 18 to 90, not all of whom had a history of lactation. The principal phylum was Proteobacteria. The most abundant taxa in the Canadian samples were Bacillus (11.4%), Acinetobacter (10.0%), Enterobacteriaceae (8.3%), Pseudomonas (6.5%), Staphylococcus (6.5%), Propionibacterium (5.8%), Comamonadaceae (5.7%), Gammaproteobacteria (5.0%), and Prevotella (5.0%). In the Irish samples the most abundant taxa were Enterobacteriaceae (30.8%), Staphylococcus (12.7%), Listeria welshimeri (12.1%), Propionibacterium (10.1%), and Pseudomonas (5.3%). None of the subjects had signs or symptoms of infection, but the presence of viable bacteria was confirmed in some samples by culture. The extent to which these organisms play a role in health or disease remains to be determined.

FT-IR spectroscopy study on cutaneous neoplasie

NASA Astrophysics Data System (ADS)

Crupi, V.; De Domenico, D.; Interdonato, S.; Majolino, D.; Maisano, G.; Migliardo, P.; Venuti, V.

2001-05-01

In this work we report a preliminary study of Fourier transform infrared spectroscopy on normal and neoplastic human skin samples suffering from two kinds of cancer, namely epithelioma and basalioma. The analyzed skin samples have been drawn from different parts of the human body, after biopsies. By performing a complex band deconvolution due to the complexity of the tissue composition, the analysis within the considered frequency region (900-4000 cm -1) of the collected IR spectra, allowed us, first of all, to characterize the presence of the pathologies and to show clear different spectral features passing from the normal tissue to the malignant one in particular within the region (1500-2000 cm -1) typical of the lipid bands.

[Periodontal microbiota and microorganisms isolated from heart valves in patients undergoing valve replacement surgery in a clinic in Cali, Colombia].

PubMed

Moreno, Sandra; Parra, Beatriz; Botero, Javier E; Moreno, Freddy; Vásquez, Daniel; Fernández, Hugo; Alba, Sandra; Gallego, Sara; Castillo, Gilberto; Contreras, Adolfo

2017-12-01

Periodontitis is an infectious disease that affects the support tissue of the teeth and it is associated with different systemic diseases, including cardiovascular disease. Microbiological studies facilitate the detection of microorganisms from subgingival and cardiovascular samples. To describe the cultivable periodontal microbiota and the presence of microorganisms in heart valves from patients undergoing valve replacement surgery in a clinic in Cali. We analyzed 30 subgingival and valvular tissue samples by means of two-phase culture medium, supplemented blood agar and trypticase soy agar with antibiotics. Conventional PCR was performed on samples of valve tissue. The periodontal pathogens isolated from periodontal pockets were: Fusobacterium nucleatum (50%), Prevotella intermedia/ nigrescens (40%), Campylobacter rectus (40%), Eikenella corrodens (36.7%), Gram negative enteric bacilli (36.7%), Porphyromonas gingivalis (33.3%), and Eubacterium spp. (33.3%). The pathogens isolated from the aortic valve were Propionibacterium acnes (12%), Gram negative enteric bacilli (8%), Bacteroides merdae (4%), and Clostridium bifermentans (4%), and from the mitral valve we isolated P. acnes and Clostridium beijerinckii. Conventional PCR did not return positive results for oral pathogens and bacterial DNA was detected only in two samples. Periodontal microbiota of patients undergoing surgery for heart valve replacement consisted of species of Gram-negative bacteria that have been associated with infections in extraoral tissues. However, there is no evidence of the presence of periodontal pathogens in valve tissue, because even though there were valve and subgingival samples positive for Gram-negative enteric bacilli, it is not possible to maintain they corresponded to the same phylogenetic origin.

Liquid Microjunction Surface Sampling Coupled with High-Pressure Liquid Chromatography-Electrospray Ionization-Mass Spectrometry for Analysis of Drugs and Metabolites in Whole-Body Thin Tissue Sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kertesz, Vilmos; Van Berkel, Gary J

2010-01-01

In this work, a commercially available autosampler was adapted to perform direct liquid microjunction (LMJ) surface sampling followed by a high-pressure liquid chromatography (HPLC) separation of the extract components and detection with electrospray ionization mass spectrometry (ESI-MS). To illustrate the utility of coupling a separation with this direct liquid extraction based surface sampling approach, four different organs (brain, lung, kidney, and liver) from whole-body thin tissue sections of propranolol dosed and control mice were examined. The parent drug was observed in the chromatograms of the surface sampling extracts from all the organs of the dosed mouse examined. In addition, twomore » isomeric phase II metabolites of propranolol (an aliphatic and an aromatic hydroxypropranolol glucuronide) were observed in the chromatograms of the extracts from lung, kidney, and liver. Confirming the presence of one or the other or both of these glucuronides in the extract from the various organs was not possible without the separation. These drug and metabolite data obtained using the LMJ surface sampling/HPLC-MS method and the results achieved by analyzing similar samples by conventional extraction of the tissues and subsequent HPLC-MS analysis were consistent.« less

The relationship between flesh quality and numbers of Kudoa thyrsites plasmodia and spores in farmed Atlantic salmon, Salmo salar L.

PubMed

Dawson-Coates, J A; Chase, J C; Funk, V; Booy, M H; Haines, L R; Falkenberg, C L; Whitaker, D J; Olafson, R W; Pearson, T W

2003-08-01

Atlantic salmon, Salmo salar L., were exposed to Kudoa thyrsites (Myxozoa, Myxosporea)-containing sea water for 15 months, and then harvested and assessed for parasite burden and fillet quality. At harvest, parasites were enumerated in muscle samples from a variety of somatic and opercular sites, and mean counts were determined for each fish. After 6 days storage at 4 degrees C, fillet quality was determined by visual assessment and by analysis of muscle firmness using a texture analyzer. Fillet quality could best be predicted by determining mean parasite numbers and spore counts in all eight tissue samples (somatic and opercular) or in four fillet samples, as the counts from opercular samples alone showed greater variability and thus decreased reliability. The variability in both plasmodia and spore numbers between tissue samples taken from an individual fish indicated that the parasites were not uniformly distributed in the somatic musculature. Therefore, to best predict the probable level of fillet degradation caused by K. thyrsites infections, multiple samples must be taken from each fish. If this is performed, a mean plasmodia count of 0.3 mm(-2) or a mean spore count of 4.0 x 10(5) g(-1) of tissue are the levels where the probability of severe myoliquefaction becomes a significant risk.

Comparative study of chitosan and chitosan-gelatin scaffold for tissue engineering

NASA Astrophysics Data System (ADS)

Kumar, Pawan; Dehiya, Brijnandan S.; Sindhu, Anil

2017-12-01

A number of orthopedic disorders and bone defect issues are solved by scaffold-based therapy in tissue engineering. The biocompatibility of chitosan (polysaccharide) and its similarity with glycosaminoglycan makes it a bone-grafting material. The current work focus on the synthesis of chitosan and chitosan-gelatin scaffold for hard tissue engineering. The chitosan and chitosan-gelatin scaffold have shown improved specific surface area, density, porosity, mechanical properties, biodegradability and absorption. These scaffolds can lead to the development or artificial fabrication of hard tissue alternates. The porous scaffold samples were prepared by freeze-drying method. The microstructure, mechanical and degradable properties of chitosan and chitosan-gelatin scaffolds were analyzed and results revealed that the scaffolds prepared from chitosan-gelatin can be utilized as a useful matrix for tissue engineering.

Characterization of the quality of water, bed sediment, and fish in Mittry Lake, Arizona, 2014–15

USGS Publications Warehouse

Hermosillo, Edyth; Coes, Alissa L.

2017-03-01

Water, bed-sediment, and fish sampling was conducted in Mittry Lake, Arizona, in 2014–15 to establish current water-quality conditions of the lake. The parameters of temperature, dissolved-oxygen concentration, specific conductance, and alkalinity were measured in the field. Water samples were collected and analyzed for dissolved major ions, dissolved trace elements, dissolved nutrients, dissolved organic carbon, dissolved pesticides, bacteria, and suspended-sediment concentrations. Bed-sediment and fish samples were analyzed for trace elements, halogenated compounds, total mercury, and methylmercury.U.S. Environmental Protection Agency secondary maximum contaminant levels in drinking water were exceeded for sulfate, chloride, and manganese in the water samples. Trace-element concentrations were relatively similar between the inlet, middle, and outlet locations. Concentrations for nutrients in all water samples were below the Arizona Department of Environmental Quality’s water-quality standards for aquatic and wildlife uses, and all bacteria levels were below the Arizona Department of Environmental Quality’s recommended recreational water-quality criteria. Three out of 81 pesticides were detected in the water samples.Trace-element concentrations in bed sediment were relatively consistent between the inlet, middle, and outlet locations. Lead, manganese, nickel, and zinc concentrations, however, decreased from the inlet to outlet locations. Concentrations for lead, nickel, and zinc in some bed-sediment samples exceeded consensus-based sediment-quality guidelines probable effect concentrations. Eleven out of 61 halogenated compounds were detected in bed sediment at the inlet location, whereas three were detected at the middle location, and five were detected at the outlet location. No methylmercury was detected in bed sediment. Total mercury was detected in bed sediment at concentrations below the consensus-based sediment-quality guidelines probable effect concentration.Sixteen trace elements were detected in at least one of the fish-tissue samples, and trace-element concentrations were relatively consistent between the three fish-tissue samples. Seven halogenated compounds were detected in at least one of the whole-body fish samples; four to five compounds were detected in each fish. One fish-tissue sample exceeded the U.S. Environmental Protection Agency human health consumption criteria for methylmercury.

Concentrations of selected organochlorine compounds in fish tissue in the Mississippi Embayment Study Unit : Arkansas, Kentucky, Louisiana, Mississippi, Missouri, and Tennessee, 1995-99

USGS Publications Warehouse

Femmer, Suzanne R.; Coupe, Richard H.; Justus, B.G.; Kleiss, Barbara A.

2004-01-01

Whole fish were collected at 52 sites during 1995-99 to evaluate the occurrence and distribution of selected organochlorine compounds in the Mississippi Embayment Study Unit. Samples were collected as part of the U.S. Geological Survey National Water Quality Assessment Program. From 5 to 8 fish were collected at each site; the fish were composited, and an aliquot of the tissue was analyzed for 28 organo-chlorine compounds, which included pesticides, pesticide degradates, and polychlorinated biphenyls. The use of these organochlorine compounds has been discontinued or severely restricted within the United States, but the continued detection of these compounds or their degradates in the air, water, soil, and biota in national surveys, coupled with known environmental problems associated with these compounds (such as a long half-life and the propensity to accumulate in living tissue), is cause for continued interest in their environmental fate. At least one organochlorine compound was detected in every fish-tissue sample, and as many as 15 different compounds were detected in some. The most frequently detected com-pounds were the degradates of p,p'-dichlorodiphenyltrichlo-roethane (p,p'-DDT); p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE) was detected in every sample above the method reporting limit, and p,p'-dichlorodiphenyldichloroethane (p,p'-DDD), was detected in 94 percent of the samples. Polychlorinated biphenyl compounds and dieldrin were detected in 83 and 78 percent of fish-tissue samples, respectively. Because these were whole fish samples, the results are not directly comparable to human health standards, which are based on fish fillets. Comparison of these results, however, to the guidelines for the protection of fish-eating wildlife indicates that concentrations of the p,p'-DDT degradates and toxaphene continue to be of environmental concern.

Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

PubMed

Calacal, Gayvelline C; Apaga, Dame Loveliness T; Salvador, Jazelyn M; Jimenez, Joseph Andrew D; Lagat, Ludivino J; Villacorta, Renato Pio F; Lim, Maria Cecilia F; Fortun, Raquel D R; Datar, Francisco A; De Ungria, Maria Corazon A

2015-11-01

The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples. Routinely, femur shafts are obtained from recovered bodies for human identification because the calcium matrix protects the DNA contained in the osteocytes. In the Philippines, there is difficulty in collecting femur samples after natural disasters or even human-made disasters, because these events are usually characterized by a large number of fatalities. Identification of casualties is further delayed by limitation in human and material resources. Hence, it is imperative to test other types of biological samples that are easier to collect, transport, process and store. We analyzed DNA that were obtained from body fluid, bone marrow, muscle tissue, clavicle, femur, metatarsal, patella, rib and vertebral samples from five recently deceased untreated male cadavers and seven male human remains that were embalmed, buried for ∼ 1 month and then exhumed. The bodies had undergone different environmental conditions and were in various stages of putrefaction. A DNA extraction method utilizing a detergent-washing step followed by an organic procedure was used. The utility of bone marrow and vitreous fluid including bone marrow and vitreous fluid that was transferred on FTA(®) cards and subjected to autosomal STR and Y-STR DNA typing were also evaluated. DNA yield was measured and the presence or absence of PCR inhibitors in DNA extracts was assessed using Plexor(®)HY. All samples were amplified using PowerPlex(®)21 and PowerPlexY(®)23 systems and analyzed using the AB3500 Genetic Analyzer and the GeneMapper(®) ID-X v.1.2 software. PCR inhibitors were consistently detected in bone marrow, muscle tissue, rib and vertebra samples. Amplifiable DNA was obtained in a majority of the samples analyzed. DNA recovery from 0.1g biological material was adequate for successful genotyping of most of the non-bone and bone samples. Complete DNA profiles were generated from bone marrow, femur, metatarsal and patella with 0.1 ng DNA template. Using 0.5 ng DNA template resulted in increased allele recovery and improved intra- and inter-locus peak balance. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer.

PubMed

Kündig, Pascale; Giesen, Charlotte; Jackson, Hartland; Bodenmiller, Bernd; Papassotirolopus, Bärbel; Freiberger, Sandra Nicole; Aquino, Catharine; Opitz, Lennart; Varga, Zsuzsanna

2018-05-08

Intra-tumoral heterogeneity has been recently addressed in different types of cancer, including breast cancer. A concept describing the origin of intra-tumoral heterogeneity is the cancer stem-cell hypothesis, proposing the existence of cancer stem cells that can self-renew limitlessly and therefore lead to tumor progression. Clonal evolution in accumulated single cell genomic alterations is a further possible explanation in carcinogenesis. In this study, we addressed the question whether intra-tumoral heterogeneity can be reliably detected in tissue-micro-arrays in breast cancer by comparing expression levels of conventional predictive/prognostic tumor markers, tumor progression markers and stem cell markers between central and peripheral tumor areas. We analyzed immunohistochemical expression and/or gene amplification status of conventional prognostic tumor markers (ER, PR, HER2, CK5/6), tumor progression markers (PTEN, PIK3CA, p53, Ki-67) and stem cell markers (mTOR, SOX2, SOX9, SOX10, SLUG, CD44, CD24, TWIST) in 372 tissue-micro-array samples from 72 breast cancer patients. Expression levels were compared between central and peripheral tumor tissue areas and were correlated to histopathological grading. 15 selected cases additionally underwent RNA sequencing for transcriptome analysis. No significant difference in any of the analyzed between central and peripheral tumor areas was seen with any of the analyzed methods/or results that showed difference. Except mTOR, PIK3CA and SOX9 (nuclear) protein expression, all markers correlated significantly (p < 0.05) with histopathological grading both in central and peripheral areas. Our results suggest that intra-tumoral heterogeneity of stem-cell and tumor-progression markers cannot be reliably addressed in tissue-micro-array samples in breast cancer. However, most markers correlated strongly with histopathological grading confirming prognostic information as expression profiles were independent on the site of the biopsy was taken.

Comparative analysis of Trichuris muris surface using conventional, low vacuum, environmental and field emission scanning electron microscopy.

PubMed

Lopes Torres, Eduardo José; de Souza, Wanderley; Miranda, Kildare

2013-09-23

The whipworm of the genus Trichuris Roederer, 1791, is a nematode of worldwide distribution and comprises species that parasitize humans and other mammals. Infections caused by Trichuris spp. in mammals can lead to various intestinal diseases of human and veterinary interest. The morphology of Trichuris spp. and other helminths has been mostly studied using conventional scanning electron microscopy of chemically fixed, dried and metal-coated specimens, although this kind of preparation has been shown to introduce a variety of artifacts such as sample shrinking, loss of secreted products and/or hiding of small structures due to sample coating. Low vacuum (LVSEM) and environmental scanning electron microscopy (ESEM) have been applied to a variety of insulator samples, also used in the visualization of hydrated and/or live specimens in their native state. In the present work, we used LVSEM and ESEM to analyze the surface of T. muris and analyze its interaction with the host tissue using freshly fixed or unfixed hydrated samples. Analysis of hydrated samples showed a set of new features on the surface of the parasite and the host tissue, including the presence of the secretory products of the bacillary glands on the surface of the parasite, and the presence of mucous material and eggs on the intestinal surface. Field emission scanning electron microscopy (FESEM) was also applied to reveal the detailed structure of the glandular chambers in fixed, dried and metal coated samples. Taken together, the results show that analysis of hydrated samples may provide new insights in the structural organization of the surface of helminth parasites and its interaction with the infected tissue, suggesting that the application of alternative SEM techniques may open new perspectives for analysis in taxonomy, morphology and host-parasite interaction fields. Copyright © 2013 Elsevier B.V. All rights reserved.

Evaluation of Protein Profiles From Treated Xenograft Tumor Models Identifies an Antibody Panel for Formalin-fixed and Paraffin-embedded (FFPE) Tissue Analysis by Reverse Phase Protein Arrays (RPPA)*

PubMed Central

Bader, Sabine; Zajac, Magdalena; Friess, Thomas; Ruge, Elisabeth; Rieder, Natascha; Gierke, Berthold; Heubach, Yvonne; Thomas, Marlene; Pawlak, Michael

2015-01-01

Reverse phase protein arrays (RPPA) are an established tool for measuring the expression and activation status of multiple proteins in parallel using only very small amounts of tissue. Several studies have demonstrated the value of this technique for signaling pathway analysis using proteins extracted from fresh frozen (FF) tissue in line with validated antibodies for this tissue type; however, formalin fixation and paraffin embedding (FFPE) is the standard method for tissue preservation in the clinical setting. Hence, we performed RPPA to measure profiles for a set of 300 protein markers using matched FF and FFPE tissue specimens to identify which markers performed similarly using the RPPA technique in fixed and unfixed tissues. Protein lysates were prepared from matched FF and FFPE tissue specimens of individual tumors taken from three different xenograft models of human cancer. Materials from both untreated mice and mice treated with either anti-HER3 or bispecific anti-IGF-1R/EGFR monoclonal antibodies were analyzed. Correlations between signals from FF and FFPE tissue samples were investigated. Overall, 60 markers were identified that produced comparable profiles between FF and FFPE tissues, demonstrating significant correlation between the two sample types. The top 25 markers also showed significance after correction for multiple testing. The panel of markers covered several clinically relevant tumor signaling pathways and both phosphorylated and nonphosphorylated proteins were represented. Biologically relevant changes in marker expression were noted when RPPA profiles from treated and untreated xenografts were compared. These data demonstrate that, using appropriately selected antibodies, RPPA analysis from FFPE tissue is well feasible and generates biologically meaningful information. The identified panel of markers that generate similar profiles in matched fixed and unfixed tissue samples may be clinically useful for pharmacodynamic studies of drug effect using FFPE tissues. PMID:26106084

Physiological comparisons of plasma and tissue metrics of selected inland and coastal steelhead kelts.

USGS Publications Warehouse

Penney, Zachary L.; Moffitt, Christine M.; Jones, Bryan; Marston, Brian

2016-01-01

The physiological status of migrating steelhead kelts (Oncorhynchus mykiss) from the Situk River, Alaska, and two tributaries of the Clearwater River, Idaho, was evaluated to explore potential differences in post-spawning survival related to energy reserves. Blood plasma samples were analyzed for metrics related to nutritional and osmotic status, and samples of white muscle tissue collected from recent mortalities at weirs were analyzed for proximate constituents. Female kelts from the Situk River had significantly higher plasma cholesterol, triglycerides, glucose and calcium concentrations, all of which suggested higher lipid and energy stores. Additional support for energy limitation in kelts was provided by evaluating the presence of detectable proteins in the plasma. Most all kelts sampled from the Situk River populations had detectable plasma proteins, in contrast to kelts sampled from the Clearwater River tributary populations where 27 % of kelts from one tributary, and 68 % of the second tributary were below the limits of detection. We found proximate constituents of kelt mortalities were similar between the Situk and Clearwater River populations, and the lipid fraction of white muscle averaged 0.1 and 0.2 %. Our findings lend support to the hypothesis that energetic limitations likely affect post-spawn survival in the Clearwater River kelts.

Intensive hypermethylation of the CpG island of Ras association domain family 1A in hepatitis B virus-associated hepatocellular carcinomas.

PubMed

Zhong, Sheng; Yeo, Winnie; Tang, Mandy W; Wong, Nathalie; Lai, Paul B S; Johnson, Phillip J

2003-08-15

The human Ras association domain family 1A gene (RASSF1A) is a newly isolated tumor suppressor gene. In this study, we analyzed the methylation status of the promoter region of RASSF1A using bisulfite sequencing and PCR-RFLP in four liver cancer cell lines (Hep3B, HepG(2), SK-HEP-1, and Huh-7) and a cohort of 43 hepatitis B virus-associated hepatocellular carcinoma (HCC) tissues and their corresponding nontumor tissue specimens. The methylation of the CpG islands in the RASSF1A promoter was not detected in 4 samples of normal liver tissue or 10 samples of peripheral blood mononuclear cells from normal subjects. However, the CpG islands were completely methylated, and transcription of the RASSF1A was silenced in the four cell lines. Treatment with the DNA methylation inhibitor 5-aza-2'-deoxycytidine reactivated the expression of RASSF1A in the Hep3B and HepG2 cells. In 41 of 43 (95%) HCC specimens studied, the promoter region of RASSF1A was intensively methylated at its CpG sites. Although heterogeneous methylation was also detected in 16 of the 23 (70%) corresponding nontumorous tissues analyzed, the level of methylation was significantly lower than in the corresponding tumor tissues. HCC has the highest incidence of promoter methylation of RASSF1A among all malignancies yet reported suggesting that hypermethylation of the CpG island promoter of RASSF1A may play an important pathological role in this tumor.

Characterization of canine mitochondrial protein expression in natural and induced forms of idiopathic dilated cardiomyopathy.

PubMed

Lopes, Rosana; Solter, Philip F; Sisson, D David; Oyama, Mark A; Prosek, Robert

2006-06-01

To map canine mitochondrial proteins and identify qualitative and quantitative differences in heart mitochondrial protein expression between healthy dogs and dogs with naturally occurring and induced dilated cardiomyopathy (DCM). Left ventricle samples were obtained from 7 healthy dogs, 7 Doberman Pinschers with naturally occurring DCM, and 7 dogs with induced DCM. Fresh and frozen mitochondrial fractions were isolated from the left ventricular free wall and analyzed by 2-dimensional electrophoresis. Protein spots that increased or decreased in density by >or= 2-fold between groups were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometry. Within narrow pH gradients of control canine heart mitochondrial samples, a total of 1,528 protein spots were revealed. Forty subunits of heart mitochondrial proteins that differ significantly from control tissues were altered in tissue specimens from dogs with naturally occurring and induced forms of DCM. The most affected heart mitochondrial proteins in both groups were those of oxidative phosphorylation (55%). Upregulation of manganese superoxide dismutase was suggestive of heart oxidative injury in tissue specimens from dogs with both forms of DCM. Evidence of apoptosis was associated with overexpression of the heart mitochondrial voltage-dependent anion channel-2 protein and endonuclease G in tissue specimens from dogs with induced DCM. Alterations of heart mitochondrial proteins related to oxidative phosphorylation dysfunction were more prevalent in tissue specimens from dogs with induced or naturally occurring DCM, compared with those of control dogs.

Determination of niclosamide residues in rainbow trout (Oncorhynchus mykiss) and channel catfish (Ictalurus punctatus) fillet tissue by high-performance liquid chromatography

USGS Publications Warehouse

Schreier, Theresa M.; Dawson, V.K.; Cho, Yirang; Spanjers, N.J.; Boogaard, M.A.

2000-01-01

Bayluscide [the ethanolamine salt of niclosamide (NIC)] is a registered piscicide used in combination with 3-(trifluoromethyl)-4-nitrophenol (TFM) to control sea lamprey populations in streams tributary to the Great Lakes. A high-performance liquid chromatography (HPLC) method was developed for the determination of NIC residues in muscle fillet tissues of fish exposed to NIC and TFM during sea lamprey control treatments. NIC was extracted from fortified channel catfish and rainbow trout fillet tissue with a series of acetone extractions and cleaned up on C-18 solid-phase extraction cartridges. NIC concentrations were determined by HPLC with detection at 360 and 335 nm for rainbow trout and catfish, respectively. Recovery of NIC from rainbow trout (n = 7) fortified at 0.04 mu g/g was 77 +/- 6.5% and from channel catfish (n = 7) fortified at 0.02 mu g/g was 113 +/- 11%. NIC detection limit was 0.0107 mu g/g for rainbow trout and 0.0063 mu g/g for catfish. Percent recovery of incurred radioactive residues by this method from catfish exposed to [C-14]NIC was 89.3 +/- 4.1%. Percent recoveries of NIC from fortified storage stability tissue samples for rainbow trout (n = 3) analyzed at 5 and 7.5 month periods were 78 +/- 5.1 and 68 +/- 2.4%, respectively. Percent recoveries of NIC from fortified storage stability tissue samples for channel catfish (n = 3) analyzed at 5 and 7.5 month periods were 88 +/- 13 and 76 +/- 21%, respectively.

Advantages of analyzing postmortem brain samples in routine forensic drug screening-Case series of three non-natural deaths tested positive for lysergic acid diethylamide (LSD).

PubMed

Mardal, Marie; Johansen, Sys Stybe; Thomsen, Ragnar; Linnet, Kristian

2017-09-01

Three case reports are presented, including autopsy findings and toxicological screening results, which were tested positive for the potent hallucinogenic drug lysergic acid diethylamide (LSD). LSD and its main metabolites were quantified in brain tissue and femoral blood, and furthermore hematoma and urine when available. LSD, its main metabolite 2-oxo-3-hydroxy-LSD (oxo-HO-LSD), and iso-LSD were quantified in biological samples according to a previously published procedure involving liquid-liquid extraction and ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). LSD was measured in the brain tissue of all presented cases at a concentration level from 0.34-10.8μg/kg. The concentration level in the target organ was higher than in peripheral blood. Additional psychoactive compounds were quantified in blood and brain tissue, though all below toxic concentration levels. The cause of death in case 1 was collision-induced brain injury, while it was drowning in case 2 and 3 and thus not drug intoxication. However, the toxicological findings could help explain the decedent's inability to cope with brain injury or drowning incidents. The presented findings could help establish reference concentrations in brain samples and assist in interpretation of results from forensic drug screening in brain tissue. This is to the author's knowledge the first report of LSD, iso-LSD, and oxo-HO-LSD measured in brain tissue samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Wistar rats immature testicular tissue vitrification and heterotopic grafting.

PubMed

Benvenutti, Larissa; Salvador, Rafael Alonso; Til, David; Senn, Alfred Paul; Tames, David Rivero; Amaral, Nicole Louise Lângaro; Amaral, Vera Lúcia Lângaro

2018-04-25

To evaluate the efficiency of two vitrification protocols for rat immature testicular tissue and heterotopic transplantation. Twenty-four pre-pubertal Wistar rats were divided into three groups (n=8). After orchiectomy, testicular fragments (3mm) from Groups 1 and 2 were vitrified with different cryoprotectant concentration solutions, using sterile inoculation loops as support. After warming up, the fragments were submitted to cell viability assessment by Trypan blue and histological evaluation. Vitrified (Groups 1 and 2) and fresh (Group 3) fragments were grafted to the animals periauricular region. After 8 weeks of grafting, the implant site was histologically analyzed. The viability recovery rate from Group 1 (72.09%) was higher (p=0.02) than that from Group 2 (59.19%). Histological analysis showed similar tubular integrity between fresh fragments from Groups 1 and 3. Group 2 samples presented lower tubular integrity. We ran histological analyses in the grafts from the Groups. In all groups, it was possible to see the implant site, however, no fragment of testicular tissue or signs of inflammation were histologically found in most samples from Groups 1 and 3. In one sample from Group 2, we found degenerated seminiferous tubules with necrosis and signs of an inflammatory process. In another sample from Group 2, we found seminiferous tubules in the implant site. The vitrification of pre-pubertal testicular tissue of rats showed little damage to cell viability through histological analysis when we used cryoprotectants in a lower concentration. Heterotopic transplantation could not preserve the structural organization of the testicular tissue.

Defining the molecular signatures of human right heart failure.

PubMed

Williams, Jordan L; Cavus, Omer; Loccoh, Emefah C; Adelman, Sara; Daugherty, John C; Smith, Sakima A; Canan, Benjamin; Janssen, Paul M L; Koenig, Sara; Kline, Crystal F; Mohler, Peter J; Bradley, Elisa A

2018-03-01

Right ventricular failure (RVF) varies significantly from the more common left ventricular failure (LVF). This study was undertaken to determine potential molecular pathways that are important in human right ventricular (RV) function and may mediate RVF. We analyzed mRNA of human non-failing LV and RV samples and RVF samples from patients with pulmonary arterial hypertension (PAH), and post-LVAD implantation. We then performed transcript analysis to determine differential expression of genes in the human heart samples. Immunoblot quantification was performed followed by analysis of non-failing and failing phenotypes. Inflammatory pathways were more commonly dysregulated in RV tissue (both non-failing and failing phenotypes). In non-failing human RV tissue we found important differences in expression of FIGF, TRAPPAC, and CTGF suggesting that regulation of normal RV and LV function are not the same. In failing RV tissue, FBN2, CTGF, SMOC2, and TRAPP6AC were differentially expressed, and are potential targets for further study. This work provides some of the first analyses of the molecular heterogeneity between human RV and LV tissue, as well as key differences in human disease (RVF secondary to pulmonary hypertension and LVAD mediated RVF). Our transcriptional data indicated that inflammatory pathways may be more important in RV tissue, and changes in FIGF and CTGF supported this hypothesis. In PAH RV failure samples, upregulation of FBN2 and CTGF further reinforced the potential significance that altered remodeling and inflammation play in normal RV function and failure. Copyright © 2018 Elsevier Inc. All rights reserved.

An electrical impedance tomography (EIT) multi-electrode needle-probe device for local assessment of heterogeneous tissue impeditivity.

PubMed

Meroni, Davide; Maglioli, Camilla Carpano; Bovio, Dario; Greco, Francesco G; Aliverti, Andrea

2017-07-01

Electrical Impedance Tomography (EIT) is an image reconstruction technique applied in medicine for the electrical imaging of living tissues. In literature there is the evidence that a large resistivity variation related to the differences of the human tissues exists. As a result of this interest for the electrical characterization of the biological samples, recently the attention is also focused on the identification and characterization of the human tissue, by studying the homogeneity of its structure. An 8 electrodes needle-probe device has been developed with the intent of identifying the structural inhomogeneities under the surface layers. Ex-vivo impeditivity measurements, by placing the needle-probe in 5 different patterns of fat and lean porcine tissue, were performed, and impeditivity maps were obtained by EIDORS open source software for image reconstruction in electrical impedance. The values composing the maps have been analyzed, pointing out a good tissue discrimination, and the conformity with the real images. We conclude that this device is able to perform impeditivity maps matching to reality for position and orientation. In all the five patterns presented is possible to identify and replicate correctly the heterogeneous tissue under test. This new procedure can be helpful to the medical staff to completely characterize the biological sample, in different unclear situations.

Effect of luminescence transport through adipose tissue on measurement of tissue temperature by using ZnCdS nanothermometers

NASA Astrophysics Data System (ADS)

Volkova, Elena K.; Yanina, Irina Yu.; Sagaydachnaya, Elena; Konyukhova, Julia G.; Kochubey, Vyacheslav I.; Tuchin, Valery V.

2018-02-01

The spectra of luminescence of ZnCdS nanoparticles (ZnCdS NPs) were measured and analyzed in a wide temperature range: from room to human body and further to a hyperthermic temperature resulting in tissue morphology change. The results show that the signal of luminescence of ZnCdS NPs placed within the tissue is reasonably good sensitive to temperature change and accompanied by phase transitions of lipid structures of adipose tissue. It is shown that the presence of a phase transition in adipose tissue upon its heating (polymorphic transformations of lipids) leads to a nonmonotonic temperature dependence of the intensity of luminescence for the nanoparticles introduced into adipose tissue. This is due to a change in the light scattering by the tissue. The light scattering of adipose tissue greatly distorts the results of temperature measurements. The application of these nanoparticles is possible for temperature measurements in very thin or weakly scattering samples.

Qualitative tissue differentiation by analysing the intensity ratios of atomic emission lines using laser induced breakdown spectroscopy (LIBS): prospects for a feedback mechanism for surgical laser systems.

PubMed

Kanawade, Rajesh; Mahari, Fanuel; Klämpfl, Florian; Rohde, Maximilian; Knipfer, Christian; Tangermann-Gerk, Katja; Adler, Werner; Schmidt, Michael; Stelzle, Florian

2015-01-01

The research work presented in this paper focuses on qualitative tissue differentiation by monitoring the intensity ratios of atomic emissions using 'Laser Induced Breakdown Spectroscopy' (LIBS) on the plasma plume created during laser tissue ablation. The background of this study is to establish a real time feedback control mechanism for clinical laser surgery systems during the laser ablation process. Ex-vivo domestic pig tissue samples (muscle, fat, nerve and skin) were used in this experiment. Atomic emission intensity ratios were analyzed to find a characteristic spectral line for each tissue. The results showed characteristic elemental emission intensity ratios for the respective tissues. The spectral lines and intensity ratios of these specific elements varied among the different tissue types. The main goal of this study is to qualitatively and precisely identify different tissue types for tissue specific laser surgery. © 2015 The Authors. Journal of Biophotonics published by WILEY-VCH Verlag.

Tissue Multiplatform-Based Metabolomics/Metabonomics for Enhanced Metabolome Coverage.

PubMed

Vorkas, Panagiotis A; Abellona U, M R; Li, Jia V

2018-01-01

The use of tissue as a matrix to elucidate disease pathology or explore intervention comes with several advantages. It allows investigation of the target alteration directly at the focal location and facilitates the detection of molecules that could become elusive after secretion into biofluids. However, tissue metabolomics/metabonomics comes with challenges not encountered in biofluid analyses. Furthermore, tissue heterogeneity does not allow for tissue aliquoting. Here we describe a multiplatform, multi-method workflow which enables metabolic profiling analysis of tissue samples, while it can deliver enhanced metabolome coverage. After applying a dual consecutive extraction (organic followed by aqueous), tissue extracts are analyzed by reversed-phase (RP-) and hydrophilic interaction liquid chromatography (HILIC-) ultra-performance liquid chromatography coupled to mass spectrometry (UPLC-MS) and nuclear magnetic resonance (NMR) spectroscopy. This pipeline incorporates the required quality control features, enhances versatility, allows provisional aliquoting of tissue extracts for future guided analyses, expands the range of metabolites robustly detected, and supports data integration. It has been successfully employed for the analysis of a wide range of tissue types.

The landscape of genomic imprinting across diverse adult human tissues.

PubMed

Baran, Yael; Subramaniam, Meena; Biton, Anne; Tukiainen, Taru; Tsang, Emily K; Rivas, Manuel A; Pirinen, Matti; Gutierrez-Arcelus, Maria; Smith, Kevin S; Kukurba, Kim R; Zhang, Rui; Eng, Celeste; Torgerson, Dara G; Urbanek, Cydney; Li, Jin Billy; Rodriguez-Santana, Jose R; Burchard, Esteban G; Seibold, Max A; MacArthur, Daniel G; Montgomery, Stephen B; Zaitlen, Noah A; Lappalainen, Tuuli

2015-07-01

Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project. We characterize imprinting in 42 genes, including both novel and previously identified genes. Tissue specificity of imprinting is widespread, and gender-specific effects are revealed in a small number of genes in muscle with stronger imprinting in males. IGF2 shows maternal expression in the brain instead of the canonical paternal expression elsewhere. Imprinting appears to have only a subtle impact on tissue-specific expression levels, with genes lacking a systematic expression difference between tissues with imprinted and biallelic expression. In summary, our systematic characterization of imprinting in adult tissues highlights variation in imprinting between genes, individuals, and tissues. © 2015 Baran et al.; Published by Cold Spring Harbor Laboratory Press.

Circular RNA hsa_circ_0000745 may serve as a diagnostic marker for gastric cancer.

PubMed

Huang, Mei; He, Yi-Ren; Liang, Li-Chuan; Huang, Qiang; Zhu, Zhi-Qiang

2017-09-14

To determine whether circular RNAs (circRNAs) are involved in pathological processes of gastric cancer (GC). Three circRNAs with differential expression in GC and colorectal cancer were randomly selected for validation by quantitative reverse transcription-polymerase chain reaction (qRT-PCR), using 20 pairs of gastric tissues and normal tissues. Based on the predicted circRNA-miRNA network, we then focused on hsa_circ_0000745, which was found to be down-regulated in 20 GC tissues compared with normal tissues. The hsa_circ_0000745 levels were further analyzed by qRT-PCR in 60 GC tissues and paired adjacent non-tumor tissues, as well as 60 plasma samples from GC patients and 60 plasma samples from healthy controls. The associations between the levels of hsa_circ_0000745 and the clinicopathological features of GC patients were statistically assessed. A receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of hsa_circ_0000745 in GC. Hsa_circ_0000745 was down-regulated in GC tissues vs non-tumorous tissues ( P < 0.001) and in plasma samples from patients with GC vs healthy controls ( P < 0.001). The expression level of hsa_circ_0000745 in GC tissues correlated with tumor differentiation, while the expression level in plasma correlated with tumor-node-metastasis stage. The area under the ROC curve (AUC) of hsa_circ_0000745 in plasma was 0.683, suggesting good diagnostic value. Plasma hsa_circ_0000745 level combined with carcinoembryogenic antigen (CEA) level increased the AUC to 0.775. Hsa_circ_0000745 plays an important role in GC and its expression level in plasma in combination with CEA level is a promising diagnostic marker for this malignancy.

Post-remediation biomonitoring of pesticides and other contaminants in marine waters and sediment near the United Heckathorn Superfund Site, Richmond, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

LD Antrim; NP Kohn

Marine sediment remediation at the United Heckathorn Superfund Site was completed in April 1997. Water and mussel tissues were sampled in February 1999 from four stations near Lauritzen Canal in Richmond, California, for Year 2 of post-remediation monitoring of marine areas near the United Heckathorn Site. Dieldrin and dichlorodiphenyl trichloroethane (DDT) were analyzed in water samples, tissue samples from resident mussels, and tissue samples from transplanted mussels deployed for 4 months. Concentrations of dieldrin and total DDT in water and total DDT in tissue were compared with Year 1 of post-remediation monitoring, and with preremediation data from the California Statemore » Mussel Watch program (tissues) and the Ecological Risk Assessment for the United Heckathorn Superfund Site (tissues and water). Mussel tissues were also analyzed for polychlorinated biphenyls (PCB), which were detected in sediment samples. Chlorinated pesticide concentrations in water samples were similar to preremediation levels and did not meet remediation goals. Mean dieidrin concentrations in water ranged from 0.62 rig/L to 12.5 ng/L and were higher than the remediation goal (0.14 ng/L) at all stations. Mean total DDT concentrations in water ranged from 14.4 ng/L to 62.3 ng/L and exceeded the remediation goal (0.59 ng/L) at all stations. The highest concentrations of both pesticides were found at the Lauritzen Canal/End station. Despite exceedence of the remediation goals, chlorinated pesticide concentrations in Lauritzen Canal water samples were notably lower in 1999 than in 1998. Tissue samples from biomonitoring organisms (mussels) provide an indication of the longer-term integrated exposure to contaminants in the water column, which overcomes the limitations of grab samples of water. Biomonitoring results indicated that the bioavailability of chlorinated pesticides has been reduced from preremediation levels both in the dredged area and throughout Richmond Harbor. Total DDT and dieldrin concentrations in mussel tissues were dramatically lower than measured levels from preremediation surveys and also lower than Year 1 levels from post-remediation biomonitoring. The lowest levels were found at the Richmond Inner Harbor Channel station (4.1 {micro}g/kg total DDT and 0.59 {micro}g/kg dieldrin, wet weight; mean of resident and transplant mussels). Mean chlorinated pesticide concentrations were highest at Lauritzen Canal/End (82 {micro}g/kg total DDT and 7.1 {micro}g/kg dieldrin, wet weight), followed by Lauritzen Canal/Mouth (22 {micro}/kg total DDT and 1.7 {micro}g/kg dieldrin, wet weight) and Santa Fe Channel/End (7.5 {micro}g/kg total DOT and 0.61 {micro}g/kg dieldrin, wet weight). These levels are 95% to 99% lower than those recorded by the California State Mussel Watch program prior to EPA's response actions. The levels of PCBs in mussel tissue were also reduced by 93% to 97% from preremediation levels. Surface sediment concentrations of dieldrin and DDT in November 1998 were highest in samples from the head or north end of Lauritzen Canal and progressively lower toward the mouth, or south end. Total DDT ranged from 130 ppm (dry weight) at the north end to 3 ppm at the south end. Dieldrin concentrations decreased from 3,270 ppb (dry weight) at the north end to 52 ppb at the south end. These results confirmed elevated pesticide concentrations in sediments collected from Lauritzen Channel by Anderson et al. (1999). The pesticide concentrations were lower than maximum concentrations found in the 1993 Remedial Investigation but comparable to the median levels measured before remediation was completed. Sediment analyses also showed the presence of elevated PCB aroclor 1254, and very high levels of polynuclear aromatic hydrocarbons (PAH) in Lauritzen Channel.« less

Glutamine Provides Effective Protection against Deltamethrin-Induced Acute Hepatotoxicity in Rats But Not Against Nephrotoxicity

PubMed Central

Gündüz, Ercan; Ülger, Burak Veli; İbiloğlu, İbrahim; Ekinci, Aysun; Dursun, Recep; Zengin, Yılmaz; İçer, Mustafa; Uslukaya, Ömer; Ekinci, Cenap; Güloğlu, Cahfer

2015-01-01

Background The aim of this study was to investigate the protective effects of L-glutamine (GLN) against liver and kidney injury caused by acute toxicity of deltamethrin (DLM). Material/Methods Thirty-two rats were indiscriminately separated into 4 groups with 8 rats each: control group (distilled water; 10 ml/kg, perorally [p.o.]), DLM group (35 mg/kg p.o. one dose.), GLN group (1.5 gr/kg, p.o. single dose.) and DLM (35 mg/kg p.o. one dose.) + GLN group (1.5 gr/kg, p.o. one dose after 4 hours.). Testing for total antioxidant status (TAS), total oxidant status (TOS), interleukin-1 beta (IL-1β), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6) analyses were performed on tissue samples, and alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), urea, and creatinine were analyzed on serum samples. Liver and kidney samples were histopathologically analyzed. Results The TOS level in liver was significantly higher in the DLM group than in the control group, and the level in DLM+GLN group was considerably lower than in the DLM group. The TAS level in the DLM+GLN group was considerably higher than in the control and DLM groups. The TAS level in kidney tissues was considerably lower in the DLM group than in controls, but was similar to other groups. Histopathological analyses of liver tissues established a significant difference between DLM and DLM+GLN groups in terms of grade 2 hepatic injury. However, no significant difference was found between DLM and DLM+GLN groups in terms of kidney injury. Conclusions Glutamine leads to significant improvement in deltamethrin-induced acute hepatotoxicity in terms of histopathologic results, tissue oxidative stress parameters, and serum liver function marker enzymes. PMID:25890620

Concentrations of selected trace elements in fish tissue and streambed sediment in the Clark Fork-Pend Oreille and Spokane River basins, Washington, Idaho, and Montana, 1998

USGS Publications Warehouse

Maret, Terry R.; Skinner, K.D.

2000-01-01

Fish tissue and bed sediment samples were collected from 16 stream sites in the Northern Rockies Intermontane Basins study area in 1998 as part of the U.S. Geological Survey National Water-Quality Assessment Program. Bed sediment samples were analyzed for 45 trace elements, and fish livers and sportfish fillets were analyzed for 22 elements to characterize the occurrence and distribution of these elements in relation to stream characteristics and land use activities. Nine trace elements of environmental concern—arsenic, cadmium, chromium, copper, lead, mercury, nickel, selenium, and zinc—were detected in bed sediment, but not all of these elements were detected in fish tissue. Trace-element concentrations were highest in bed sediment samples collected at sites downstream from significant natural mineral deposits and (or) mining activities. Arsenic, cadmium, copper, lead, mercury, and zinc in bed sediment at some sites were elevated relative to national median concentrations, and some concentrations were at levels that can adversely affect aquatic biota. Although trace-element concentrations in bed sediment exceeded various guidelines, no concentrations in sportfish fillets exceeded U.S. Environmental Protection Agency screening values for the protection of human health. Correlations between most trace-element concentrations in bed sediment and fish tissue (liver and fillet) were not significant (r0.05). Concentrations of arsenic, cadmium, copper, lead, mercury, nickel, selenium, and zinc in bed sediment were significantly correlated (r=0.53 to 0.88, p2=0.95 and 0.99, p<0.001) that corresponded to trace-element enrichment categories. These strong relations warrant further study using mine density as an explanatory variable to predict trace-element concentrations in bed sediment.

Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences

USGS Publications Warehouse

Barker, F. Keith; Oyler-McCance, Sara; Tomback, Diana F.

2015-01-01

Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.

Clinical significance of CD44 expression in children with hepatoblastoma.

PubMed

Cai, H-Y; Yu, B; Feng, Z-C; Qi, X; Wei, X-J

2015-10-27

The aim of this study was to investigate the expression of CD44 and its clinical significance in children suffering from hepatoblastoma (HB). CD44 expression was detected with immunohistochemistry staining in 30 samples from hepatoblastoma children and 10 normal liver tissue samples from normal children. The data obtained was statistically analyzed using the chi-square test, using the SPSS (v.11.0) software. The rate of CD44 expression was significantly higher (66.7%) in hepatoblastoma tissues than in normal liver tissues (χ(2) = 4.848, P < 0.05). The rate of CD44 expression was significantly higher in children with stage III or IV hepatoblastoma (83.3%) than that in children with stage I and II hepatoblastoma (χ(2) ＝ 5.625, P < 0.05) (41.7%). Therefore, CD44 expression might play an important role in the pathogenesis, progression, and prognosis of HB in children.

Comparative anti-microbial efficacy of Azadirachta indica irrigant with standard endodontic irrigants: A preliminary study

PubMed Central

Dutta, Arindam; Kundabala, Mala

2014-01-01

Objective: The anti-microbial efficacy of 2.5% sodium hypochlorite (SHC) and 0.2% chlorhexidine gluconate were compared with an experimental irrigant formulated from the Neem tree, Azadirachta indica A. Juss. Materials and Methods: A sample of 36 single rooted anterior teeth with periapical radiolucency and absence of response to vitality tests that required root canal treatment were selected for this study. The test irrigants and their combinations were assigned to five different groups and saline served as the control. Access cavities were prepared using an aseptic technique and samples collected for both anaerobic culture and Gram stained smears, followed by irrigation and sample collection again. The number of organisms were expressed in colony forming units/ml after 72 h of incubation; the smears were analyzed for their microbial loads and tissue clearance and assessed as per defined criteria. Results: Our results found the maximum reduction in microbial loads, when analyzed by culture method, with a combination of SHC and the experimental neem irrigant. Maximum tissue clearance on the Gram Stained smears was also found with the same combination. Conclusion: Neem irrigant has anti-microbial efficacy and can be considered for endodontic use. PMID:24778508

Multispectral Mueller polarimetric imaging detecting residual cancer and cancer regression after neoadjuvant treatment for colorectal carcinomas

NASA Astrophysics Data System (ADS)

Pierangelo, Angelo; Manhas, Sandeep; Benali, Abdelali; Fallet, Clément; Totobenazara, Jean-Laurent; Antonelli, Maria-Rosaria; Novikova, Tatiana; Gayet, Brice; De Martino, Antonello; Validire, Pierre

2013-04-01

This work is devoted to a first exploration of Mueller polarimetric imaging for the detection of residual cancer after neoadjuvant treatment for the rectum. Three samples of colorectal carcinomas treated by radiochemotherapy together with one untreated sample are analyzed ex vivo before fixation in formalin by using a multispectral Mueller polarimetric imaging system operated from 500 to 700 nm. The Mueller images, analyzed using the Lu-Chipmann decomposition, show negligible diattenuation and retardation. The nonirradiated rectum exhibits a variation of depolarization with cancer evolution stage. At all wavelengths on irradiated samples, the contrast between the footprint of the initial tumor and surrounding healthy tissue is found to be much smaller for complete tumor regression than when a residual tumor is present, even at volume fractions of the order of 5%. This high sensitivity is attributed to the modification of stromal collagen induced by the cancer. The depolarization contrast between treated cancer and healthy tissue is found to increase monotonously with the volume fraction of residual cancer in the red part of the spectrum. Polarimetric imaging is a promising technique for detecting short-time small residual cancers, which is valuable information for pathological diagnosis and patient management by clinicians.

Compound parabolic concentrator probe for efficient light collection in spectroscopy of biological tissue

NASA Astrophysics Data System (ADS)

Tanaka, Kazunori; Pacheco, Marcos T. T.; Brennan, James F., III; Itzkan, Irving; Berger, Andrew J.; Dasari, Ramachandra R.; Feld, Michael S.

1996-02-01

We describe a compound parabolic concentrator (CPC)-based probe for enhanced signal collection in the spectroscopy of biological tissues. Theoretical considerations governing signal enhancement compared with conventional collection methods are given. A ray-tracing program was used to analyze the throughput of CPC's with shape deviations and surface imperfections. A modified CPC shape with 99% throughput was discovered. A 4.4-mm-long CPC was manufactured and incorporated into an optical fiber-based near-infrared Raman spectrometer system. For human tissue samples, light collection was enhanced by a factor of 7 compared with collection with 0.29-NA optical fibers.

Micro-scale elemental partition in tissues of the aquatic plant Lemna minor L. exposed to highway drainage water

NASA Astrophysics Data System (ADS)

Mendes Godinho, R.; Raimundo, J.; Vale, C.; Anes, B.; Brito, P.; Alves, L. C.; Pinheiro, T.

2013-07-01

In the scope of a monitoring program to assess the environmental impact of automobile traffic over one main bridge in Lisbon, both water and duckweed (Lemna minor L.) were sampled from the road drainage tanks and analyzed for chemical elements. Plants uptake Cr, Mn, Cu, and Zn metals from rain water draining the bridge road. Nuclear microprobe elemental maps of cryosections of L. minor tissues showed that incorporated elements were internalized in fronds of the plant. This approach at micrometer level allows a better knowledge of the elemental tissue partitioning in this biomonitor organism.

Precision Medicine Approaches to Diabetic Kidney Disease: Tissue as an Issue.

PubMed

Gluck, Caroline; Ko, Yi-An; Susztak, Katalin

2017-05-01

Precision medicine approaches, that tailor medications to specific individuals has made paradigm-shifting improvements for patients with certain cancer types. Such approaches, however, have not been implemented for patients with diabetic kidney disease. Precision medicine could offer new avenues for novel diagnostic, prognostic and targeted therapeutics development. Genetic studies associated with multiscalar omics datasets from tissue and cell types of interest of well-characterized cohorts are needed to change the current paradigm. In this review, we will discuss precision medicine approaches that the nephrology community can take to analyze tissue samples to develop new therapeutics for patients with diabetic kidney disease.

Gas-liquid chromatographic determination of kepone in field-collected avian tissues and eggs

USGS Publications Warehouse

Stafford, C.J.; Reichel, W.L.; Swineford, D.M.; Prouty, R.M.; Gay, M.L.

1978-01-01

A procedure is described for determining Kepone (decachlorooctahydro-1,3,4-metheno-2H-cyclobuta [cd] pentalene-2-one) residues in avian egg, liver, and tissue. Samples were extracted with benzene-isopropanol, and the extract was cleaned up with fuming H2SO4-concentrated H2SO4. Kepone was separated from organochlorine pesticides and polychlorinated biphenyls on a Florisil column and analyzed by electron capture gas-liquid chromatography (GLC). The average recovery from spiked tissues was 86%. The analyses performed on 14 bald eagle carcasses and livers, 3 bald eagle eggs, and 14 osprey eggs show measurable levels which indicate that Kepone accumulates in the tissues of fish-eating birds. Residues were confirmed by GLC-mass spectrometry.

OpenMSI Arrayed Analysis Tools v2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

BOWEN, BENJAMIN; RUEBEL, OLIVER; DE ROND, TRISTAN

2017-02-07

Mass spectrometry imaging (MSI) enables high-resolution spatial mapping of biomolecules in samples and is a valuable tool for the analysis of tissues from plants and animals, microbial interactions, high-throughput screening, drug metabolism, and a host of other applications. This is accomplished by desorbing molecules from the surface on spatially defined locations, using a laser or ion beam. These ions are analyzed by a mass spectrometry and collected into a MSI 'image', a dataset containing unique mass spectra from the sampled spatial locations. MSI is used in a diverse and increasing number of biological applications. The OpenMSI Arrayed Analysis Tool (OMAAT)more » is a new software method that addresses the challenges of analyzing spatially defined samples in large MSI datasets, by providing support for automatic sample position optimization and ion selection.« less

Microfluidics for rapid detection of isocitrate dehydrogenase 1 mutation for intraoperative application.

PubMed

Aibaidula, Abudumijiti; Zhao, Wang; Wu, Jin-Song; Chen, Hong; Shi, Zhi-Feng; Zheng, Lu-Lu; Mao, Ying; Zhou, Liang-Fu; Sui, Guo-Dong

2016-06-01

OBJECT Conventional methods for isocitrate dehydrogenase 1 (IDH1) detection, such as DNA sequencing and immunohistochemistry, are time- and labor-consuming and cannot be applied for intraoperative analysis. To develop a new approach for rapid analysis of IDH1 mutation from tiny tumor samples, this study used microfluidics as a method for IDH1 mutation detection. METHODS Forty-seven glioma tumor samples were used; IDH1 mutation status was investigated by immunohistochemistry and DNA sequencing. The microfluidic device was fabricated from polydimethylsiloxane following standard soft lithography. The immunoanalysis was conducted in the microfluidic chip. Fluorescence images of the on-chip microcolumn taken by the charge-coupled device camera were collected as the analytical results readout. Fluorescence signals were analyzed by NIS-Elements software to gather detailed information about the IDH1 concentration in the tissue samples. RESULTS DNA sequencing identified IDH1 R132H mutation in 33 of 47 tumor samples. The fluorescence signal for IDH1-mutant samples was 5.49 ± 1.87 compared with 3.90 ± 1.33 for wild type (p = 0.005). Thus, microfluidics was capable of distinguishing IDH1-mutant tumor samples from wild-type samples. When the cutoff value was 4.11, the sensitivity of microfluidics was 87.9% and the specificity was 64.3%. CONCLUSIONS This new approach was capable of analyzing IDH1 mutation status of tiny tissue samples within 30 minutes using intraoperative microsampling. This approach might also be applied for rapid pathological diagnosis of diffuse gliomas, thus guiding personalized resection.

Microbiome Heterogeneity Characterizing Intestinal Tissue and Inflammatory Bowel Disease Phenotype.

PubMed

Tyler, Andrea D; Kirsch, Richard; Milgrom, Raquel; Stempak, Joanne M; Kabakchiev, Boyko; Silverberg, Mark S

2016-04-01

Inflammatory bowel disease has been associated with differential abundance of numerous organisms when compared to healthy controls (HCs); however, few studies have investigated variability in the microbiome across intestinal locations and how this variability might be related to disease location and phenotype. In this study, we have analyzed the microbiome of a large cohort of individuals recruited at Mount Sinai Hospital in Toronto, Canada. Biopsies were taken from subjects with Crohn's disease, ulcerative colitis, and HC, and also individuals having undergone ileal pouch-anal anastomosis for treatment of ulcerative colitis or familial adenomatous polyposis. Microbial 16S rRNA was sequenced using the Illumina MiSeq platform. We observed a great deal of variability in the microbiome characterizing different sampling locations. Samples from pouch and afferent limb were comparable in microbial composition. When comparing sigmoid and terminal ileum samples, more differences were observed. The greatest number of differentially abundant microbes was observed when comparing either pouch or afferent limb samples to sigmoid or terminal ileum. Despite these differences, we were able to observe modest microbial variability between inflammatory bowel disease phenotypes and HCs, even when controlling for sampling location and additional experimental factors. Most detected associations were observed between HCs and Crohn's disease, with decreases in specific genera in the families Ruminococcaceae and Lachnospiraceae characterizing tissue samples from individuals with Crohn's disease. This study highlights important considerations when analyzing the composition of the microbiome and also provides useful insight into differences in the microbiome characterizing these seemingly related phenotypes.

Toll like receptor expression induced by exercise in obesity and metabolic syndrome: A systematic review.

PubMed

Rada, Isabel; Deldicque, Louise; Francaux, Marc; Zbinden-Foncea, Hermann

2018-01-01

Obesity and metabolic syndrome are disorders that correlate with the activation of pro-inflammatory pathways and cytokine production, to which Toll like receptors (TLR) contribute. Exercise may act as an anti-inflammatory modulator, but there is no consensus about the role of the TLR in this tuning. The present styudy aims to systematically review the current evidence on exercise-induced TLR regulation in animals and humans suffering from obesity and metabolic syndrome. Pubmed and Scopus databases were searched for publications from 1990 to September 2015. Search terms included: "Toll like Receptor", "TLR", "exercise", "obesity", "diabetes", and "metabolic syndrome". Elegibility criteria comprised: randomized control trials, cross-sectional and cohort studies; human or animal models with metabolic syndrome; any type of exercise; TLR expression measurement in any tissue by a clearly reported technique. The quality of selected studies was assessed using a modified version of the Downs and Black Quality Assessment Checklist. Data of study design; population; exercise type, timing and training elements; measurement technique, tissue analyzed and main outcome were extracted and categorized to facilitate data synthesis. 17 studies were included, of which 11 publications obtained a high, 5 a moderate and 1 a low score for quality assessment. A total of 8 human studies were analyzed: 6 studies used endurance continuous or interval training protocols, 1 study resistance training and the remaining study was performed following a marathon race. Blood cells were analyzed in seven studies, of which four studies sampled peripheral blood mononuclear cells (PBMC), three analyzed whole blood and one study sampled skeletal muscle. Nine animal studies were included: 8 used endurance training and 1 acute aerobic exercise. A variety of tissues samples were explored such as PBMC, skeletal muscle, adipose, vascular and nervous tissue. Globally, the animal studies showed a marked tendency towards a down-regulation of TLR2 and 4 expression accompagnied with, a reduced activation of nuclear factorkappaB (NF-κB) signaling and cytokine production, and an improvement in insulin sensitivity and body composition. While animal studies showed a marked tendency towards TLR2 and 4 down-regulation after chronic endurance exercise, the current evidence in human is not sufficiently robust to conclude any role of TLR in the anti-inflammatory properties of exercise. Copyright © 2016 International Society of Exercise and Immunology. All rights reserved.

The Antimicrobial Peptide Lysozyme Is Induced after Multiple Trauma

PubMed Central

Klüter, Tim; Fitschen-Oestern, Stefanie; Lippross, Sebastian; Weuster, Matthias; Pufe, Thomas; Tohidnezhad, Mersedeh; Beyer, Andreas; Seekamp, Andreas; Varoga, Deike

2014-01-01

The antimicrobial peptide lysozyme is an important factor of innate immunity and exerts high potential of antibacterial activity. In the present study we evaluated the lysozyme expression in serum of multiple injured patients and subsequently analyzed their possible sources and signaling pathways. Expression of lysozyme was examined in blood samples of multiple trauma patients from the day of trauma until 14 days after trauma by ELISA. To investigate major sources of lysozyme, its expression and regulation in serum samples, different blood cells, and tissue samples were analysed by ELISA and real-time PCR. Neutrophils and hepatocytes were stimulated with cytokines and supernatant of Staphylococcus aureus. The present study demonstrates the induction and release of lysozyme in serum of multiple injured patients. The highest lysozyme expression of all tested cells and tissues was detected in neutrophils. Stimulation with trauma-related factors such as interleukin-6 and S. aureus induced lysozyme expression. Liver tissue samples of patients without trauma show little lysozyme expression compared to neutrophils. After stimulation with bacterial fragments, lysozyme expression of hepatocytes is upregulated significantly. Toll-like receptor 2, a classic receptor of Gram-positive bacterial protein, was detected as a possible target for lysozyme induction. PMID:25258475

Micro and bulk analysis of prostate tissues classified as hyperplasia

NASA Astrophysics Data System (ADS)

Kwiatek, W. M.; Banaś, A.; Banaś, K.; Cinque, G.; Dyduch, G.; Falkenberg, G.; Kisiel, A.; Marcelli, A.; Podgórczyk, M.

2007-07-01

BPH (Benign Prostatic Hyperplasia) is the most common benign neoplasm (non cancerous enlargement of the prostate gland), whose prevalence increases with age. The gland, when increased in size, exerts pressure on the urethra, causing obstruction to urine flow. The latter may result in severe urinary tract and kidney conditions. In this work prostate samples from patients diagnosed with BPH were analyzed using synchrotron radiation. Micro-analysis of the hyperplastic samples was carried out on the L-beam line at HASYLAB, DESY (Germany), while bulk analysis on selected samples was performed at the DRX2 beamline at LNF, Frascati (Italy). Microanalysis with a mono-energetic beam 15 μm in diameter confirmed that concentrations of certain elements, such as S, Mn, Cu, Fe and Zn, are good indicators of pathological disorders in prostate tissue that may be considered effective tracers of developing compliant. The concentrations of Mn, Cu, Fe and Zn are higher in hyperplastic tissues, as compared to normal ones, while for sulphur the opposite is observed. Additionally, Fe and S K-edge XANES (X-ray Absorption Near Edge Structure) spectroscopy experiments were carried out in order to determine the chemical speciation of these elements in our samples.

Relative mRNA expression of prostate-derived E-twenty-six factor and E-twenty-six variant 4 transcription factors, and of uridine phosphorylase-1 and thymidine phosphorylase enzymes, in benign and malignant prostatic tissue

PubMed Central

CAVAZZOLA, LUCIANE ROSTIROLA; CARVALHAL, GUSTAVO FRANCO; DEVES, CANDIDA; RENCK, DAIANA; ALMEIDA, RICARDO; SANTOS, DIóGENES SANTIAGO

2015-01-01

Prostate cancer is the most frequent urological tumor, and the second most common cancer diagnosed in men. Incidence and mortality are variable and appear to depend on behavioral factors and genetic predisposition. The prostate-derived E-twenty-six factor (PDEF) and E-twenty-six variant 4 (ETV4) transcription factors, and the thymidine phosphorylase (TP) and uridine phosphorylase-1 (UP-1) enzymes, are reported to be components of the pathways leading to tumorigenesis and/or metastasis in a number of tumors. The present study aimed to analyze the mRNA expression levels of these proteins in prostatic cancerous and benign tissue, and their association with clinical and pathological variables. Using quantitative reverse transcription polymerase chain reaction, the mRNA expression levels of PDEF, ETV4, TP and UP-1 were studied in 52 tissue samples (31 of benign prostatic hyperplasia and 21 of prostate adenocarcinomas) obtained from patients treated by transurethral resection of the prostate or by radical prostatectomy. Relative expression was assessed using the ∆-CT method. Data was analyzed using Spearman's tests for correlation. P<0.05 was considered to indicate a statistically significant difference. The results revealed that PDEF, ETV4, UP-1 and TP were expressed in 85.7, 90.5, 95.2 and 100% of the prostate cancer samples, and in 90.3, 96.8, 90.3 and 96.8% of the benign samples, respectively. PDEF and ETV4 exhibited a significantly higher relative expression level in the tumor samples compared with their benign counterparts. The relative expression of TP and UP-1 did not differ significantly between benign and cancerous prostate tissues. The relative expression of TP was moderately and significantly correlated with the expression of ETV4 in the benign tissues. The relative expression of UP-1 was significantly lower in T3 compared with T1 and T2 cancers. These findings indicate that PDEF, ETV4, TP and UP-1 are typically expressed in benign and malignant prostatic tissues. Further studies are necessary to define the role of these proteins as therapeutic targets in prostate cancer. PMID:26137165

Reagent Precoated Targets for Rapid In-Tissue Derivatization of the Anti-Tuberculosis Drug Isoniazid Followed by MALDI Imaging Mass Spectrometry

NASA Astrophysics Data System (ADS)

Manier, M. Lisa; Reyzer, Michelle L.; Goh, Anne; Dartois, Veronique; Via, Laura E.; Barry, Clifton E.; Caprioli, Richard M.

2011-08-01

Isoniazid (INH) is an important component of front-line anti-tuberculosis therapy with good serum pharmacokinetics but unknown ability to penetrate tuberculous lesions. However, endogenous background interferences hinder our ability to directly analyze INH in tissues. Chemical derivatization has been successfully used to measure isoniazid directly from tissue samples using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). MALDI targets were pretreated with trans-cinnamaldehyde (CA) prior to mounting tissue slices. Isoniazid present in the tissues was efficiently derivatized and the INH-CA product measured by MS/MS. Precoating of MALDI targets allows the tissues to be directly thaw-mounted and derivatized, thus simplifying the preparation. A time-course series of tissues from tuberculosis infected/INH dosed animals were assayed and the MALDI MS/MS response correlates well with the amount of INH determined to be in the tissues by high-performance liquid chromatography (HPLC)-MS/MS.

Environmental contaminants in California condors

USGS Publications Warehouse

Wiemeyer, Stanley N.; Scott, J.M.; Anderson, M.P.; Bloom, P.H.; Stafford, C.J.

1988-01-01

Five wild Califorinia condors (Gymnogyps californianus) that died in 1980-86 were necropsied and tissues were analyzed for environmental contaminants. Three died of lead (Pb) poisoning, 1 presumably of cyanide (CN) poisoning, and 1 nestling of handling shock. Organochlorine concentrations were low in 4 condors that were analyzed for these contaminants. Blood samples from 14 wild and 14 captive condors were analyzed primarily for Pb. Five of 14 wild condors sampled had elevated (> 0.70 ppm) concentrations of Pb in blood whereas Pb concentrations in all captive condors were low. Lead levels in individual birds often fluctuated over time. Lead exposure, especially poisoning, was a major factor affecting the wild California condor population during 1982-86. The probable source of Pb was bullet fragments in carrion on which condors were feeding.

CONNECTICUT RIVER FISH TISSUE CONTAMINANT STUDY (2000): ECOLOGICAL AND HUMAN HEALTH RISK SCREENING

EPA Science Inventory

The study targeted commonly caught recreational fish, as well as other fish that are important in the river food chain. Smallmouth bass, white suckers and yellow perch were collected during 2000 from the mainstem of the Connecticut River and composite samples were analyzed for t...

p16 promoter hypermethylation: A useful serum marker for early detection of gastric cancer

PubMed Central

Abbaszadegan, Mohammad Reza; Moaven, Omeed; Sima, Hamid Reza; Ghafarzadegan, Kamran; A'rabi, Azadeh; Forghani, Mohammad Naser; Raziee, Hamid Reza; Mashhadinejad, Ali; Jafarzadeh, Mostafa; Esmaili-Shandiz, Ehsan; Dadkhah, Ezzat

2008-01-01

AIM: To determine p16 promoter hypermethylation in gastric tumoral tissue and serum samples, its impact on p16-protein expression, and correlation with clinical and histological features. METHODS: Samples were obtained from 52 histologically confirmed cases of gastric adenocarcinoma. Gastric tissue and serum of 50 age- and sex-matched individuals with normal gastroscopy and biopsy were obtained as control samples. Methylation-specific polymerase chain reaction (MSP) was used to evaluate methylation status of p16 promoter. p16-protein expression was analyzed by immunohistochemical staining on paraffin-embedded sections. RESULTS: Methylation was detected in 44.2% (23/52) of tumoral tissues. 60.9% of them were also methylated in serum, i.e., 26.9% of all patients (14/52). Methylation was not detected in tissue and sera of control samples. p16-protein expression was decreased in 61.5% of cases (32/52), and was significantly associated with promoter hypermethylation (P < 0.001). Methylation was significantly more frequent in higher pathological grades (P < 0.05). Methylation was not associated with other clinicopathological features and environmental factors including H pylori infection and smoking. CONCLUSION: p16 promoter hypermethylation is an important event in gastric carcinogenesis. It is the principle mechanism of p16 gene silencing. It is related to malignant tumor behavior. Detection of DNA methylation in serum may be a biomarker for early detection of gastric cancer. PMID:18395906

Detection of border disease virus (BDV) genotype 3 in Italian goat herds.

PubMed

Rosamilia, A; Grattarola, C; Caruso, C; Peletto, S; Gobbi, E; Tarello, V; Caroggio, P; Dondo, A; Masoero, L; Acutis, P L

2014-03-01

In January 2011, cases of abortion, stillbirth and weak live kids were reported in two goat herds in northern Italy. Samples from 18 kids found dead, 12 fetuses, and two stillborn kids were analyzed for pestivirus antigen using an ELISA kit and a border disease virus (BDV)-specific RT-PCR. Positive results were obtained in six kids and one fetus. Phylogenetic analysis based on 225 bp of the 5'UTR fragment of the BDV genome from positive samples showed that the goats were infected with BDV genotype 3. Serum and blood samples collected from all animals in both herds were analyzed using competitive ELISA to detect p80 antibodies and RT-PCR to detect viraemia. Pestivirus antibodies were detected in 61/67 goats in herd A and in 38/169 in herd B. A persistently infected (PI) goat was found in herd A. The PI animal was submitted to the laboratory for BDV diagnosis with Ag-ELISA, viral isolation, and nested RT-PCR on tissue samples from the spleen, kidney, brain, liver, lung, ileocaecal valve, mesenteric lymph nodes, and skin. All of the tests were positive for BDV in each of the tissues analyzed. The BDV sequence of the PI was identical to BDV sequences found in other positive animals. This is the first description of a BDV PI goat and the first evidence of BDV genotype 3 circulation in Italy. The study raises questions about the real impact this virus has on breeding goats. Copyright © 2013 Elsevier Ltd. All rights reserved.

Implementation of Amplicon Parallel Sequencing Leads to Improvement of Diagnosis and Therapy of Lung Cancer Patients.

PubMed

König, Katharina; Peifer, Martin; Fassunke, Jana; Ihle, Michaela A; Künstlinger, Helen; Heydt, Carina; Stamm, Katrin; Ueckeroth, Frank; Vollbrecht, Claudia; Bos, Marc; Gardizi, Masyar; Scheffler, Matthias; Nogova, Lucia; Leenders, Frauke; Albus, Kerstin; Meder, Lydia; Becker, Kerstin; Florin, Alexandra; Rommerscheidt-Fuss, Ursula; Altmüller, Janine; Kloth, Michael; Nürnberg, Peter; Henkel, Thomas; Bikár, Sven-Ernö; Sos, Martin L; Geese, William J; Strauss, Lewis; Ko, Yon-Dschun; Gerigk, Ulrich; Odenthal, Margarete; Zander, Thomas; Wolf, Jürgen; Merkelbach-Bruse, Sabine; Buettner, Reinhard; Heukamp, Lukas C

2015-07-01

The Network Genomic Medicine Lung Cancer was set up to rapidly translate scientific advances into early clinical trials of targeted therapies in lung cancer performing molecular analyses of more than 3500 patients annually. Because sequential analysis of the relevant driver mutations on fixated samples is challenging in terms of workload, tissue availability, and cost, we established multiplex parallel sequencing in routine diagnostics. The aim was to analyze all therapeutically relevant mutations in lung cancer samples in a high-throughput fashion while significantly reducing turnaround time and amount of input DNA compared with conventional dideoxy sequencing of single polymerase chain reaction amplicons. In this study, we demonstrate the feasibility of a 102 amplicon multiplex polymerase chain reaction followed by sequencing on an Illumina sequencer on formalin-fixed paraffin-embedded tissue in routine diagnostics. Analysis of a validation cohort of 180 samples showed this approach to require significantly less input material and to be more reliable, robust, and cost-effective than conventional dideoxy sequencing. Subsequently, 2657 lung cancer patients were analyzed. We observed that comprehensive biomarker testing provided novel information in addition to histological diagnosis and clinical staging. In 2657 consecutively analyzed lung cancer samples, we identified driver mutations at the expected prevalence. Furthermore we found potentially targetable DDR2 mutations at a frequency of 3% in both adenocarcinomas and squamous cell carcinomas. Overall, our data demonstrate the utility of systematic sequencing analysis in a clinical routine setting and highlight the dramatic impact of such an approach on the availability of therapeutic strategies for the targeted treatment of individual cancer patients.

Using Fourier transform IR spectroscopy to analyze biological materials

PubMed Central

Baker, Matthew J; Trevisan, Júlio; Bassan, Paul; Bhargava, Rohit; Butler, Holly J; Dorling, Konrad M; Fielden, Peter R; Fogarty, Simon W; Fullwood, Nigel J; Heys, Kelly A; Hughes, Caryn; Lasch, Peter; Martin-Hirsch, Pierre L; Obinaju, Blessing; Sockalingum, Ganesh D; Sulé-Suso, Josep; Strong, Rebecca J; Walsh, Michael J; Wood, Bayden R; Gardner, Peter; Martin, Francis L

2015-01-01

IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing. PMID:24992094

Prolyl hydroxylation in elastin is not random.

PubMed

Schmelzer, Christian E H; Nagel, Marcus B M; Dziomba, Szymon; Merkher, Yulia; Sivan, Sarit S; Heinz, Andrea

2016-10-01

This study aimed to investigate the prolyl and lysine hydroxylation in elastin from different species and tissues. Enzymatic digests of elastin samples from human, cattle, pig and chicken were analyzed using mass spectrometry and bioinformatics tools. It was confirmed at the protein level that elastin does not contain hydroxylated lysine residues regardless of the species. In contrast, prolyl hydroxylation sites were identified in all elastin samples. Moreover, the analysis of the residues adjacent to prolines allowed the determination of the substrate site preferences of prolyl 4-hydroxylase. It was found that elastins from all analyzed species contain hydroxyproline and that at least 20%-24% of all proline residues were partially hydroxylated. Determination of the hydroxylation degrees of specific proline residues revealed that prolyl hydroxylation depends on both the species and the tissue, however, is independent of age. The fact that the highest hydroxylation degrees of proline residues were found for elastin from the intervertebral disc and knowledge of elastin arrangement in this tissue suggest that hydroxylation plays a biomechanical role. Interestingly, a proline-rich domain of tropoelastin (domain 24), which contains several repeats of bioactive motifs, does not show any hydroxyproline residues in the mammals studied. The results show that prolyl hydroxylation is not a coincidental feature and may contribute to the adaptation of the properties of elastin to meet the functional requirements of different tissues. The study for the first time shows that prolyl hydroxylation is highly regulated in elastin. Copyright © 2016 Elsevier B.V. All rights reserved.

Core needle biopsy guidance based on EMOCT imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Iftimia, Nicusor V.; Park, Jesung; Maguluri, Gopi

2016-03-01

We present a novel method, based on encoder mapping OCT imaging, for real-time guidance of core biopsy procedures. This method provides real-time feedback to the interventional radiologist, such that he/she can reorient the needle during the biopsy and sample the most representative area of the suspicious mass that is being investigated. This aspect is very important for tailoring therapy to the specific cancer based on biomarker analysis, which will become one of the next big advances in our search for the optimal cancer therapy. To enable individualized treatment, the genetic constitution and the DNA repair status in the affected areas is needed for each patient. Thus, representative sampling of the tumor is needed for analyzing various biomarkers, which are used as a tool to personalize cancer therapy. The encoder-based OCT enables samping of large size masses and provides full control on the imaging probe, which is passed through the bore of the biopsy guidance needle. The OCT image is built gradually, based on the feedback of an optical encoder which senses the incremental movement of the needle with a few microns resolution. Tissue mapping is independent of the needle speed, while it is advanced through the tissue. The OCT frame is analyzed in real-time and tissue cellularity is reported in a very simple manner (pie chart). Our preliminary study on a rabbit model of cancer has demonstrated the capability of this technology for accurately differentiating between viable cancer and heterogeneous or necrotic tissue.

Intraoperative metastases detection by laser-induced fluorescence spectroscopy

NASA Astrophysics Data System (ADS)

Vari, Sandor G.; Papazoglou, Theodore G.; van der Veen, Maurits J.; Fishbein, Michael C.; Young, J. D.; Chandra, Mudjianto; Papaioannou, Thanassis; Beeder, Clain; Shi, Wei-Qiang; Grundfest, Warren S.

1991-06-01

The authors studied the ability of Laser Induced Fluorescence Spectroscopy (LIFS) for the intraoperative identification of metastases using a photosensitizing agent Photofrin IIr to enhance spectroscopic detection. A He-Cd laser source (442 nm) was used to produce low-power illumination of tissue via a hand-held 400 micrometers fiberoptic probe. Through the same fiber, reflected and emitted light was returned to an optical multi-channel analyzer (OMA III) for analysis. Spectroscopic signals were displayed on a screen for immediate examination. Lobund Wistar rats, inoculated with Pollard rat adenocarcinoma cells, were used as an animal model. Photofrin IIr was administered intraperitoneal 24 or 48 hours prior to surgical exploration in doses varying from 0.75-7.5 mg/kg. Metastases detection was performed during abdominal exploration directed to ipsilateral and contralateral inguinal, iliac, para-aortic and renal lymph nodes. Nineteen tissue samples, identified as abnormal by LIFS, were removed for histologic analysis; 11 of these samples were larger than 5mm and histologic examination revealed malignancy in all cases. While LIFS signals showed malignancy in 8 tissue samples with dimensions less than 5mm, histology confirmed this in only 3. However, serial histologic sections were not performed. From the initial results, it was concluded that LIFS detection of malignant tissue is feasible and enhanced by the addition of Photofrin IIr. LIFS may be a promising technique for the intraoperative detection of primary malignant and metastatic tissue.

Biological response in vitro of skeletal muscle cells treated with different intensity continuous and pulsed ultrasound fields

NASA Astrophysics Data System (ADS)

Abrunhosa, Viviane M.; Mermelstein, Claudia S.; Costa, Manoel L.; Costa-Felix, Rodrigo P. B.

2011-02-01

Therapeutic ultrasound has been used in physiotherapy to accelerate tissue healing. Although the ultrasonic wave is widely used in clinical practice, not much is known about the biological effects of ultrasound on cells and tissues. This study aims to evaluate the biological response of ultrasound in primary cultures of chick myogenic cells. To ensure the metrological reliability of whole measurement process, the ultrasound equipment was calibrated in accordance with IEC 61689:2007. The skeletal muscle cells were divided in four samples. One sample was used as a control group and the others were submitted to different time and intensity and operation mode of ultrasound: 1) 0.5 W/cm2 continuous for 5 minutes, 2) 0.5 W/cm2 pulsed for 5 minutes, 3) 1.0 W/cm2 pulsed for 10 minutes. The samples were analyzed with phase contrast optical microscopy before and after the treatment. The results showed alignment of myogenic cells in the sample treated with 0.5 W/cm2 continuous during 5 minutes when compared with the control group and the other samples. This study is a first step towards a metrological and scientific based protocol to cells and tissues treatment under different ultrasound field exposures.

Development of a highly sensitive and specific enzyme-linked immunosorbent assay (ELISA) for the detection of phenylethanolamine A in tissue and feed samples and confirmed by liquid chromatography tandem mass spectrometry (LC-MS/MS).

PubMed

Cao, Biyun; He, Guangzhao; Yang, Hong; Chang, Huafang; Li, Shuqun; Deng, Anping

2013-10-15

Phenylethanolamine A (PA) is a new emerged β-adrenergic agonist illegally used as feed additives for growth promotion. In this study, a highly sensitive and specific indirect competitive enzyme-linked immunosorbent assay (ELISA) for the detection of PA in tissue and feed samples was developed and confirmed by liquid chromatography tandem mass spectrometry (LC-MS/MS). By reduction of nitryl group to amino group, the PA derivative was synthesized and coupled to carrier proteins with diazobenzidine method. The antisera obtained from four immunized rabbits were characterized in terms of sensitivity and specificity. All antisera displayed high sensitivity with IC50 values lower than 0.48 ng mL(-1). The most sensitive ELISA was established with IC50 and limit of detection (LOD) values of 0.049 ng mL(-1) and 0.003 ng mL(-1), respectively. The cross-reactivity (CR) values of the antisera with three frequently used β-adrenergic agonists (clenbuterol, salbutamol and ractopamine) were lesser than 0.39%; there was no CR of the antisera with other six compounds including two structurally related substances (isoproterenol, phenylephrine). To investigate the accuracy and precision of the assay, swine kidney, liver, meat and feed samples were fortified with PA at different content and analyzed by ELISA. Acceptable recovery rates of 92.2-113.7% and intra-assay coefficients of variation of 3.8-10.9% (n=3) were achieved. Seven spiked samples were simultaneously analyzed by ELISA and LC-MS/MS. There was a high correlation coefficient of 0.9956 (n=7) between the two methods. The proposed ELISA proven to be a feasible quantitative/screening method for PA analysis in tissue and feed samples with the properties of high sensitivity and specificity, high sample throughput and low expensive. © 2013 Elsevier B.V. All rights reserved.

Mechanical characterization of human brain tumors from patients and comparison to potential surgical phantoms

PubMed Central

Rubiano, Andrés; Dyson, Kyle; Simmons, Chelsey S.

2017-01-01

While mechanical properties of the brain have been investigated thoroughly, the mechanical properties of human brain tumors rarely have been directly quantified due to the complexities of acquiring human tissue. Quantifying the mechanical properties of brain tumors is a necessary prerequisite, though, to identify appropriate materials for surgical tool testing and to define target parameters for cell biology and tissue engineering applications. Since characterization methods vary widely for soft biological and synthetic materials, here, we have developed a characterization method compatible with abnormally shaped human brain tumors, mouse tumors, animal tissue and common hydrogels, which enables direct comparison among samples. Samples were tested using a custom-built millimeter-scale indenter, and resulting force-displacement data is analyzed to quantify the steady-state modulus of each sample. We have directly quantified the quasi-static mechanical properties of human brain tumors with effective moduli ranging from 0.17–16.06 kPa for various pathologies. Of the readily available and inexpensive animal tissues tested, chicken liver (steady-state modulus 0.44 ± 0.13 kPa) has similar mechanical properties to normal human brain tissue while chicken crassus gizzard muscle (steady-state modulus 3.00 ± 0.65 kPa) has similar mechanical properties to human brain tumors. Other materials frequently used to mimic brain tissue in mechanical tests, like ballistic gel and chicken breast, were found to be significantly stiffer than both normal and diseased brain tissue. We have directly compared quasi-static properties of brain tissue, brain tumors, and common mechanical surrogates, though additional tests would be required to determine more complex constitutive models. PMID:28582392

A mixture model-based approach to the clustering of microarray expression data.

PubMed

McLachlan, G J; Bean, R W; Peel, D

2002-03-01

This paper introduces the software EMMIX-GENE that has been developed for the specific purpose of a model-based approach to the clustering of microarray expression data, in particular, of tissue samples on a very large number of genes. The latter is a nonstandard problem in parametric cluster analysis because the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. A feasible approach is provided by first selecting a subset of the genes relevant for the clustering of the tissue samples by fitting mixtures of t distributions to rank the genes in order of increasing size of the likelihood ratio statistic for the test of one versus two components in the mixture model. The imposition of a threshold on the likelihood ratio statistic used in conjunction with a threshold on the size of a cluster allows the selection of a relevant set of genes. However, even this reduced set of genes will usually be too large for a normal mixture model to be fitted directly to the tissues, and so the use of mixtures of factor analyzers is exploited to reduce effectively the dimension of the feature space of genes. The usefulness of the EMMIX-GENE approach for the clustering of tissue samples is demonstrated on two well-known data sets on colon and leukaemia tissues. For both data sets, relevant subsets of the genes are able to be selected that reveal interesting clusterings of the tissues that are either consistent with the external classification of the tissues or with background and biological knowledge of these sets. EMMIX-GENE is available at http://www.maths.uq.edu.au/~gjm/emmix-gene/

Overexpression of neuromedin U is correlated with regional metastasis of head and neck squamous cell carcinoma

PubMed Central

Wang, Lei; Chen, Chen; Li, Fen; Hua, Qing-Quan; Chen, Shiming; Xiao, Bokui; Dai, Mengyuan; Li, Man; Zheng, Anyuan; Yu, Di; Hu, Zhang Wei; Tao, Zezhang

2016-01-01

Regional metastasis is an important prognostic factor for patients with head and neck squamous cell carcinoma (HNSCC). Neuromedin U (Nmu) is a secreted neuropeptide, named due to its potent uterine contraction-inducing activity. The aim of the present study was to analyze the significance of Nmu in the regional metastasis of HNSCC. The characteristics of 240 patients recruited from the Department of Otolaryngology Head and Neck Surgery, Renmin Hospital of Wuhan University (Wuhan, China) were summarized retrospectively. The positive rate of neck dissection was analyzed according to the material. The expression levels of Nmu in human tumor samples were analyzed using immunohistochemistry. Subsequently, the expression of Nmu was investigated using a tissue microassay to analyze the association between Nmu protein expression and Tumor Node Metastasis (TNM) status. The positive rate of neck dissection was 51.4% in the study sample. The expression levels of Nmu in primary tumors with regional metastasis were higher, compared with those without metastasis. There was increased protein expression of Nmu in the advanced tumor tissues. The data obtained in the present study demonstrated that the expression of Nmu was correlated with regional metastasis and TNM status. Overexpression of Nmu may be involved in the process of regional metastasis of HNSCC, and may serve as a novel and valuable biomarker for predicting regional metastasis in patients with HNSCC. PMID:27279246

In vitro autoradiography of carcinoembryonic antigen in tissue from patients with colorectal cancer using multifunctional antibody TF2 and 67/68Ga-labeled haptens by pretargeting

PubMed Central

Hall, Håkan; Velikyan, Irina; Blom, Elisabeth; Ulin, Johan; Monazzam, Azita; Påhlman, Lars; Micke, Patrick; Wanders, Alkwin; McBride, William; Goldenberg, David M.; Långström, Bengt

2012-01-01

The carcinoembryonic antigen (CEA) was visualized in vitro in tissue from patients with colorectal cancer with trivalent bispecific antibody TF2 and two hapten molecules, [67/68Ga]Ga-IMP461 and [67/68Ga]Ga-IMP485 by means of pretargeting. Colorectal cancer tissue samples obtained from surgery at Uppsala University Hospital, were frozen fresh and cryosectioned. The two hapten molecules comprising 1,4,7-triazacyclononanetriacetic acid chelate moiety (NOTA) were labeled with 67Ga or 68Ga. The autoradiography was conducted by incubating the tissue samples with the bispecific antibody TF2, followed by washing and incubation with one of the radiolabeled hapten molecules. After washing, drying and exposure to phosphor imager plates, the autoradiograms were analyzed and compared to standard histochemistry (hematoxylin-eosin). Pronounced binding was found in the tissue from colorectal cancer using the bispecific antibody TF2 and either of the haptens [67/68Ga]Ga-IMP461 and [67/68Ga]Ga-IMP485. Distinct binding was also detected in the epithelium of most samples of neighboring tissue, taken at a minimum of 10 cm from the site of the tumor. It is concluded that pretargeting CEA with the bispecific antibody TF2 followed by the addition of 67/68Ga-labeled hapten is extremely sensitive for visualizing this marker for colorectal cancer. This methodology is therefore a very specific complement to other histochemical techniques in the diagnosis of biopsies or in samples taken from surgery. Use of the pretargeting technique in vivo may also be an advance in diagnosing patients with colorectal cancer, either using 67Ga and SPECT or 68Ga and PET. PMID:23133809

Evaluating the efficiency of environmental monitoring programs

USGS Publications Warehouse

Levine, Carrie R.; Yanai, Ruth D.; Lampman, Gregory G.; Burns, Douglas A.; Driscoll, Charles T.; Lawrence, Gregory B.; Lynch, Jason; Schoch, Nina

2014-01-01

Statistical uncertainty analyses can be used to improve the efficiency of environmental monitoring, allowing sampling designs to maximize information gained relative to resources required for data collection and analysis. In this paper, we illustrate four methods of data analysis appropriate to four types of environmental monitoring designs. To analyze a long-term record from a single site, we applied a general linear model to weekly stream chemistry data at Biscuit Brook, NY, to simulate the effects of reducing sampling effort and to evaluate statistical confidence in the detection of change over time. To illustrate a detectable difference analysis, we analyzed a one-time survey of mercury concentrations in loon tissues in lakes in the Adirondack Park, NY, demonstrating the effects of sampling intensity on statistical power and the selection of a resampling interval. To illustrate a bootstrapping method, we analyzed the plot-level sampling intensity of forest inventory at the Hubbard Brook Experimental Forest, NH, to quantify the sampling regime needed to achieve a desired confidence interval. Finally, to analyze time-series data from multiple sites, we assessed the number of lakes and the number of samples per year needed to monitor change over time in Adirondack lake chemistry using a repeated-measures mixed-effects model. Evaluations of time series and synoptic long-term monitoring data can help determine whether sampling should be re-allocated in space or time to optimize the use of financial and human resources.

Pesticide concentrations in snail kite eggs and nestlings in Florida

USGS Publications Warehouse

Sykes, P.W.

1985-01-01

From 1970-1977, unhatched snail kite eggs and young that were found dead at nests in Florida were analyzed by gas chromatography for residues of organochlorine pollutants. The 1970 and 1974 material showed measurable amounts of p,p'-DDE, p,p'-DDD, p,p'-DDT, and dieldrin. Dieldrin and polychlorinated biphenyl (PCB) residues were less than 0.1 ppm in the eggs and were detected in only one sample of muscle tissue at 0.11 ppm. Concentrations in ppm wet weight of p,p'-DDE, p,p' DDD, p,p'-DDT, dieldrin, and PCB for two samples of muscle and three of brain tissue (all 1977 material) were not detected at the limit of quantification (0.05 ppm).

Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate

PubMed Central

Jasinska, Anna J.; Zelaya, Ivette; Service, Susan K.; Peterson, Christine B.; Cantor, Rita M.; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A.; Fears, Scott; Furterer, Allison E.; Huang, Yu S.; Ramensky, Vasily; Schmitt, Christopher A.; Svardal, Hannes; Jorgensen, Matthew J.; Kaplan, Jay R.; Villar, Diego; Aken, Bronwen L.; Flicek, Paul; Nag, Rishi; Wong, Emily S.; Blangero, John; Dyer, Thomas D.; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M.; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K.; Jentsch, J. David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P.; Freimer, Nelson B.

2017-01-01

By analyzing multi-tissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalogue of expression quantitative trait loci (eQTLs) in a non-human primate model. This catalogue contains more genome-wide significant eQTLs, per sample, than comparable human resources, and reveals sex and age-related expression patterns. Findings include a master regulatory locus that likely plays a role in immune function, and a locus regulating hippocampal long non-coding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders. PMID:29083405

Preservation of Multiple Mammalian Tissues to Maximize Science Return from Ground Based and Spaceflight Experiments.

PubMed

Choi, Sungshin; Ray, Hami E; Lai, San-Huei; Alwood, Joshua S; Globus, Ruth K

2016-01-01

Even with recent scientific advancements, challenges posed by limited resources and capabilities at the time of sample dissection continue to limit the collection of high quality tissues from experiments that can be conducted only infrequently and at high cost, such as in space. The resources and time it takes to harvest tissues post-euthanasia, and the methods and duration of long duration storage, potentially have negative impacts on sample quantity and quality, thereby limiting the scientific outcome that can be achieved. The goals of this study were to optimize methods for both sample recovery and science return from rodent experiments, with possible relevance to both ground based and spaceflight studies. The first objective was to determine the impacts of tissue harvest time post-euthanasia, preservation methods, and storage duration, focusing on RNA quality and enzyme activities in liver and spleen as indices of sample quality. The second objective was to develop methods that will maximize science return by dissecting multiple tissues after long duration storage in situ at -80°C. Tissues of C57Bl/6J mice were dissected and preserved at various time points post-euthanasia and stored at -80°C for up to 11 months. In some experiments, tissues were recovered from frozen carcasses which had been stored at -80°C up to 7 months. RNA quantity and quality was assessed by measuring RNA Integrity Number (RIN) values using an Agilent Bioanalyzer. Additionally, the quality of tissues was assessed by measuring activities of hepatic enzymes (catalase, glutathione reductase and GAPDH). Fresh tissues were collected up to one hour post-euthanasia, and stored up to 11 months at -80°C, with minimal adverse effects on the RNA quality of either livers or RNAlater-preserved spleens. Liver enzyme activities were similar to those of positive controls, with no significant effect observed at any time point. Tissues dissected from frozen carcasses that had been stored for up to 7 months at -80°C had variable results, depending on the specific tissue analyzed. RNA quality of liver, heart, and kidneys were minimally affected after 6-7 months of storage at -80°C, whereas RNA degradation was evident in tissues such as small intestine, bone, and bone marrow when they were collected from the carcasses frozen for 2.5 months. These results demonstrate that 1) the protocols developed for spaceflight experiments with on-orbit dissections support the retrieval of high quality samples for RNA expression and some protein analyses, despite delayed preservation post-euthanasia or prolonged storage, and 2) many additional tissues for gene expression analysis can be obtained by dissection even following prolonged storage of the tissue in situ at -80°C. These findings have relevance both to high value, ground-based experiments when sample collection capability is severely constrained, and to spaceflight experiments that entail on-orbit sample recovery by astronauts.

HPLC and TLC methods for analysis of [18F]FDG and its metabolites from biological samples.

PubMed

Rokka, Johanna; Grönroos, Tove J; Viljanen, Tapio; Solin, Olof; Haaparanta-Solin, Merja

2017-03-24

The most used positron emission tomography (PET) tracer, 2-[ 18 F]fluoro-2-deoxy-d-glucose ([ 18 F]FDG), is a glucose analogue that is used to measure tissue glucose consumption. Traditionally, the Sokoloff model is the basis for [ 18 F]FDG modeling. According to this model, [ 18 F]FDG is expected to be trapped in a cell in the form of [ 18 F]FDG-6-phosphate ([ 18 F]FDG-6-P). However, several studies have shown that in tissues, [ 18 F]FDG metabolism goes beyond [ 18 F]FDG-6-P. Our aim was to develop radioHPLC and radioTLC methods for analysis of [ 18 F]FDG metabolites from tissue samples. The radioHPLC method uses a sensitive on-line scintillation detector to detect radioactivity, and the radioTLC method employs digital autoradiography to detect the radioactivity distribution on a TLC plate. The HPLC and TLC methods were developed using enzymatically in vitro-produced metabolites of [ 18 F]FDG as reference standards. For this purpose, three [ 18 F]FDG metabolites were synthesized: [ 18 F]FDG-6-P, [ 18 F]FD-PGL, and [ 18 F]FDG-1,6-P2. The two methods were evaluated by analyzing the [ 18 F]FDG metabolic profile from rodent ex vivo tissue homogenates. The HPLC method with an on-line scintillation detector had a wide linearity in a range of 5Bq-5kBq (LOD 46Bq, LOQ 139Bq) and a good resolution (Rs ≥1.9), and separated [ 18 F]FDG and its metabolites clearly. The TLC method combined with digital autoradiography had a high sensitivity in a wide range of radioactivity (0.1Bq-2kBq, LOD 0.24Bq, LOQ 0.31Bq), and multiple samples could be analyzed simultaneously. As our test and the method validation with ex vivo samples showed, both methods are useful, and at best they complement each other in analysis of [ 18 F]FDG and its radioactive metabolites from biological samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Dense populations of the microsporidian Enterocytozoon hepatopenaei (EHP) in feces of Penaeus vannamei exhibiting white feces syndrome and pathways of their transmission to healthy shrimp.

PubMed

Tang, Kathy F J; Han, Jee Eun; Aranguren, Luis Fernando; White-Noble, Brenda; Schmidt, Margeaux M; Piamsomboon, Patharapol; Risdiana, Eris; Hanggono, Bambang

2016-10-01

White feces syndrome (WFS) is an emerging problem for penaeid shrimp farming industries in SE Asia countries, Thailand, Malaysia, Vietnam, Indonesia, China, and in India. This occurrence of this syndrome is usually first evidenced by the appearance of white fecal strings floating on surface of the shrimp ponds. The gross signs of affected shrimp include the appearance of a whitish hindgut and loose carapace, and it is associated with reduced feeding and growth retardation. To investigate the nature of the white feces syndrome, samples of white feces and shrimp hepatopancreas tissue were collected from Penaeus vannamei in affected farms in Indonesia, and these were examined histologically. Within the white feces, we found densely packed spores of the microsporidian Enterocytozoon hepatopenaei (abbreviated as EHP) and relatively fewer numbers of rod-shaped bacteria. From WFS ponds, hepatopancreas samples form 30 individual shrimp were analyzed by histology and in situ hybridization. The results showed that all of the shrimp examined were infected with EHP accompanied by septic hepatopancreatic necrosis (SHPN). Midgut epithelial cells were also infected and this increased the number of tissue types being affected by EHP. By PCR, EHP was detected in all the samples analyzed from WFS-affected ponds, but not in those sampled from healthy shrimp ponds. To determine the modes of transmission for this parasite, we performed feeding and cohabitation bioassays, the results showed that EHP can be transmitted through per os feeding of EHP-infected hepatopancreas tissue to healthy shrimp and through cohabitation ofinfected and healthy shrimp. In addition, we found the use of Fumagillin-B, an antimicrobial agent, was ineffective in either reducing or eliminating EHP in infected shrimp. Copyright © 2016 Elsevier Inc. All rights reserved.

Health implications of radionuclide levels in cattle raised near U mining and milling facilities in Ambrosia Lake, New Mexico

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapham, S.C.; Millard, J.B.; Samet, J.M.

1989-03-01

This study was conducted to determine radionuclide tissue levels in cattle raised near U mining and milling facilities. Ambrosia Lake, New Mexico, has been the site of extensive U mining for 30 y and contains several underground U mines, a processing mill, and two large U tailings piles. Ten cows were purchased from two grazing areas in Ambrosia Lake and ten control animals were purchased from Crownpoint, New Mexico. Muscle, liver, kidney, and bone tissue taken from these animals, and environmental samples, including water, grasses and soil collected from the animals' grazing areas, were analyzed for /sup 238/U, /sup 234/U,more » /sup 230/Th, /sup 226/Ra, /sup 210/Pb, and /sup 210/Po. Mean radionuclide levels in cattle tissue and environmental samples from Ambrosia Lake were higher in almost every comparison than those found in respective controls. Liver and kidney tissues were particularly elevated in /sup 226/Ra and /sup 210/Po. Radiation dose commitments from eating cattle tissue with these radionuclide concentrations were calculated. We concluded that the health risk to the public from eating exposed cattle is minimal, unless large amounts of this tissue, especially liver and kidney, are ingested.« less

Classification of microscopic images of breast tissue

NASA Astrophysics Data System (ADS)

Ballerini, Lucia; Franzen, Lennart

2004-05-01

Breast cancer is the most common form of cancer among women. The diagnosis is usually performed by the pathologist, that subjectively evaluates tissue samples. The aim of our research is to develop techniques for the automatic classification of cancerous tissue, by analyzing histological samples of intact tissue taken with a biopsy. In our study, we considered 200 images presenting four different conditions: normal tissue, fibroadenosis, ductal cancer and lobular cancer. Methods to extract features have been investigated and described. One method is based on granulometries, which are size-shape descriptors widely used in mathematical morphology. Applications of granulometries lead to distribution functions whose moments are used as features. A second method is based on fractal geometry, that seems very suitable to quantify biological structures. The fractal dimension of binary images has been computed using the euclidean distance mapping. Image classification has then been performed using the extracted features as input of a back-propagation neural network. A new method that combines genetic algorithms and morphological filters has been also investigated. In this case, the classification is based on a correlation measure. Very encouraging results have been obtained with pilot experiments using a small subset of images as training set. Experimental results indicate the effectiveness of the proposed methods. Cancerous tissue was correctly classified in 92.5% of the cases.

Image analysis of representative food structures: application of the bootstrap method.

PubMed

Ramírez, Cristian; Germain, Juan C; Aguilera, José M

2009-08-01

Images (for example, photomicrographs) are routinely used as qualitative evidence of the microstructure of foods. In quantitative image analysis it is important to estimate the area (or volume) to be sampled, the field of view, and the resolution. The bootstrap method is proposed to estimate the size of the sampling area as a function of the coefficient of variation (CV(Bn)) and standard error (SE(Bn)) of the bootstrap taking sub-areas of different sizes. The bootstrap method was applied to simulated and real structures (apple tissue). For simulated structures, 10 computer-generated images were constructed containing 225 black circles (elements) and different coefficient of variation (CV(image)). For apple tissue, 8 images of apple tissue containing cellular cavities with different CV(image) were analyzed. Results confirmed that for simulated and real structures, increasing the size of the sampling area decreased the CV(Bn) and SE(Bn). Furthermore, there was a linear relationship between the CV(image) and CV(Bn) (.) For example, to obtain a CV(Bn) = 0.10 in an image with CV(image) = 0.60, a sampling area of 400 x 400 pixels (11% of whole image) was required, whereas if CV(image) = 1.46, a sampling area of 1000 x 100 pixels (69% of whole image) became necessary. This suggests that a large-size dispersion of element sizes in an image requires increasingly larger sampling areas or a larger number of images.

Long-term stability and temporal trends of organic contaminants in four collections of mussel tissue frozen standard reference materials.

PubMed

Schantz, Michele M; Pugh, Rebecca S; Pol, Stacy S Vander; Wise, Stephen A

2015-04-01

The stability of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and chlorinated pesticides in frozen mussel tissue Standard Reference Materials (SRMs) stored at -80 °C was assessed by analyzing samples of SRM 1974, SRM 1974a, and SRM 1974b Organics in Mussel Tissue (Mytilus edulis) periodically over 25 y, 20 y, and 12 y, respectively. The most recent analyses were performed during the certification of the fourth release of this material, SRM 1974c. Results indicate the concentrations of these persistent organic pollutants have not changed during storage at -80 °C. In addition, brominated diphenyl ethers (BDEs) were quantified in each of the materials during this study. The stability information is important for on-going monitoring studies collecting large quantities of samples for future analyses (i.e., formally established specimen banking programs). Since all four mussel tissue SRMs were prepared from mussels collected at the same site in Dorchester Bay, MA, USA, the results provide a temporal trend study for these contaminants over a 17 year period (1987 to 2004).

Evaluation of residual radioactivity in human tissues associated with weapons testing at the nevada test site. Technical report, 1 June 1981-31 March 1989

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wrenn, M.E.; Singh, N.P.; Paschoa, A.S.

1992-11-01

Residual radioactivity consisting of 239 Pu were measured by radiochemistry and alpha spectrometry in samples of bone and soft tissues from 100 autopsies or surgeries from northern and southwestern Utah and from control areas in Colorado and Pennsylvania. Based upon the isotopic ratio 240 Pu/239 Pu contamination was attributable to atmospheric weapons tests at the Nevada Test Site (NTS). In addition, 110 thyroid tissue samples obtained from tissue blocks made at autopsy of veterans dying at the VA hospital in Salt Lake City in the 1940's and 1950's were measured for 129 I (half life 16 million year) and 127more » I (stable) by neutron activation. The results were analyzed by year of death, by periods before and during atmospheric nuclear weapons testing at the NTS and by origin of usual residence. A model was developed to relate thyroid dose from 131 I to the measured 124/127 I ratios, and thyroid dose estimates were made based upon the measured ratios.« less

RAS testing of liquid biopsy correlates with the outcome of metastatic colorectal cancer patients treated with first-line FOLFIRI plus cetuximab in the CAPRI-GOIM trial.

PubMed

Normanno, N; Esposito Abate, R; Lambiase, M; Forgione, L; Cardone, C; Iannaccone, A; Sacco, A; Rachiglio, A M; Martinelli, E; Rizzi, D; Pisconti, S; Biglietto, M; Bordonaro, R; Troiani, T; Latiano, T P; Giuliani, F; Leo, S; Rinaldi, A; Maiello, E; Ciardiello, F

2018-01-01

Liquid biopsy is an alternative to tissue for RAS testing in metastatic colorectal carcinoma (mCRC) patients. Little information is available on the predictive role of liquid biopsy RAS testing in patients treated with first-line anti-EGFR monoclonal antibody-based therapy. In the CAPRI-GOIM trial, 340 KRAS exon-2 wild-type mCRC patients received first-line cetuximab plus FOLFIRI. Tumor samples were retrospectively assessed by next generation sequencing (NGS). Baseline plasma samples were analyzed for KRAS and NRAS mutations using beads, emulsion, amplification, and magnetics digital PCR (BEAMing). Discordant cases were solved by droplet digital PCR (ddPCR) or deep-sequencing. A subgroup of 92 patients with available both NGS data on tumor samples and baseline plasma samples were included in this study. Both NGS analysis of tumor tissue and plasma testing with BEAMing identified RAS mutations in 33/92 patients (35.9%). However, 10 cases were RAS tissue mutant and plasma wild-type, and additional 10 cases were tissue wild-type and plasma mutant, resulting in a concordance rate of 78.3%. Analysis of plasma samples with ddPCR detected RAS mutations in 2/10 tissue mutant, plasma wild-type patients. In contrast, in all tissue wild-type and plasma mutant cases, ddPCR or deep-sequencing analysis of tumor tissue confirmed the presence of RAS mutations at allelic frequencies ranging between 0.15% and 1.15%. The median progression-free survival of RAS mutant and wild-type patients according to tissue (7.9 versus 12.6 months; P = 0.004) and liquid biopsy testing (7.8 versus 13.8 moths; P < 0.001) were comparable. Similar findings were observed for the median overall survival of RAS mutant and wild-type patients based on tissue (22.1 versus 35.8 months; P = 0.016) and plasma (19.9 versus 35.8 months; P = 0.013) analysis. This study indicates that RAS testing of liquid biopsy results in a similar outcome when compared with tissue testing in mCRC patients receiving first-line anti-EGFR monoclonal antibodies. © The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Distinct expression patterns of the E3 ligase SIAH-1 and its partner Kid/KIF22 in normal tissues and in the breast tumoral processes

PubMed Central

2010-01-01

SIAH proteins are the human members of an highly conserved family of E3 ubiquitin ligases. Several data suggest that SIAH proteins may have a role in tumor suppression and apoptosis. Previously, we reported that SIAH-1 induces the degradation of Kid (KIF22), a chromokinesin protein implicated in the normal progression of mitosis and meiosis, by the ubiquitin proteasome pathway. In human breast cancer cells stably transfected with SIAH-1, Kid/KIF22 protein level was markedly reduced whereas, the Kid/KIF22 mRNA level was increased. This interaction has been further elucidated through analyzing SIAH and Kid/KIF22 expression in both paired normal and tumor tissues and cell lines. It was observed that SIAH-1 protein is widely expressed in different normal tissues, and in cells lines but showing some differences in western blotting profiles. Immunofluorescence microscopy shows that the intracellular distribution of SIAH-1 and Kid/KIF22 appears to be modified in human tumor tissues compared to normal controls. When mRNA expression of SIAH-1 and Kid/KIF22 was analyzed by real-time PCR in normal and cancer breast tissues from the same patient, a large variation in the number of mRNA copies was detected between the different samples. In most cases, SIAH-1 mRNA is decreased in tumor tissues compared to their normal counterparts. Interestingly, in all breast tumor tissues analyzed, variations in the Kid/KIF22 mRNA levels mirrored those seen with SIAH-1 mRNAs. This concerted variation of SIAH-1 and Kid/KIF22 messengers suggests the existence of an additional level of control than the previously described protein-protein interaction and protein stability regulation. Our observations also underline the need to re-evaluate the results of gene expression obtained by qRT-PCR and relate it to the protein expression and cellular localization when matched normal and tumoral tissues are analyzed. PMID:20144232

Determination of sulfonamides in animal tissues by modified QuEChERS and liquid chromatography tandem mass spectrometry.

PubMed

Wen, Ching-Hsuan; Lin, Shu-Ling; Fuh, Ming-Ren

2017-03-01

In this study, the salting-out solvent extraction and dispersive solid-phase extraction (dSPE) clean-up steps in QuEChERS (quick, easy, cheap, effective, rugged, and safe) method were optimized to reduce matrix effect and efficiently extract target sulfonamides from a variety of edible animal tissues. The extracted sulfonamides were then analyzed using liquid chromatography tandem mass spectrometry (LC-MS/MS). Good extraction recoveries (74.0-100.3% in five different sources of animal tissues; n=3) with acceptable matrix effect (<10%, except for liver samples) were obtained using the proposed method. For the first time, a commercial ND-lipids cartridge was used to remove hydrophobic matrix components from fat-rich animal tissues in the clean-up step of QuEChERS. In addition, good linearity (0.125-12.5ngg -1 ) was observed using matrix-matched calibration (in beef). Limits of detection (LODs) were estimated at 0.01-0.03ngg -1 in beef, pork, and chicken samples. For beef tripe and pig liver samples, the LODs were in the range of 0.02-0.04ngg -1 . Good intra-day/inter-day precision (1.0-10.5%/0.4-8.0%) and accuracy (95.2-107.2%/97.8-102.1%) were also achieved using the modified QuEChERS for sample pretreatment. The applicability of the modified QuEChERS-LC-MS/MS method was demonstrated by determining the occurrence of target sulfonamides in various edible animal tissues for potential food safety analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Real-Time Reverse-Transcription Quantitative Polymerase Chain Reaction Assay Is a Feasible Method for the Relative Quantification of Heregulin Expression in Non-Small Cell Lung Cancer Tissue.

PubMed

Kristof, Jessica; Sakrison, Kellen; Jin, Xiaoping; Nakamaru, Kenji; Schneider, Matthias; Beckman, Robert A; Freeman, Daniel; Spittle, Cindy; Feng, Wenqin

2017-01-01

In preclinical studies, heregulin ( HRG ) expression was shown to be the most relevant predictive biomarker for response to patritumab, a fully human anti-epidermal growth factor receptor 3 monoclonal antibody. In support of a phase 2 study of erlotinib ± patritumab in non-small cell lung cancer (NSCLC), a reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay for relative quantification of HRG expression from formalin-fixed paraffin-embedded (FFPE) NSCLC tissue samples was developed and validated and described herein. Test specimens included matched FFPE normal lung and NSCLC and frozen NSCLC tissue, and HRG -positive and HRG -negative cell lines. Formalin-fixed paraffin-embedded tissue was examined for functional performance. Heregulin distribution was also analyzed across 200 NSCLC commercial samples. Applied Biosystems TaqMan Gene Expression Assays were run on the Bio-Rad CFX96 real-time PCR platform. Heregulin RT-qPCR assay specificity, PCR efficiency, PCR linearity, and reproducibility were demonstrated. The final assay parameters included the Qiagen FFPE RNA Extraction Kit for RNA extraction from FFPE NSCLC tissue, 50 ng of RNA input, and 3 reference (housekeeping) genes ( HMBS, IPO8 , and EIF2B1 ), which had expression levels similar to HRG expression levels and were stable among FFPE NSCLC samples. Using the validated assay, unimodal HRG distribution was confirmed across 185 evaluable FFPE NSCLC commercial samples. Feasibility of an RT-qPCR assay for the quantification of HRG expression in FFPE NSCLC specimens was demonstrated.

Characterization of articular cartilage by combining microscopic analysis with a fibril-reinforced finite-element model.

PubMed

Julkunen, Petro; Kiviranta, Panu; Wilson, Wouter; Jurvelin, Jukka S; Korhonen, Rami K

2007-01-01

Load-bearing characteristics of articular cartilage are impaired during tissue degeneration. Quantitative microscopy enables in vitro investigation of cartilage structure but determination of tissue functional properties necessitates experimental mechanical testing. The fibril-reinforced poroviscoelastic (FRPVE) model has been used successfully for estimation of cartilage mechanical properties. The model includes realistic collagen network architecture, as shown by microscopic imaging techniques. The aim of the present study was to investigate the relationships between the cartilage proteoglycan (PG) and collagen content as assessed by quantitative microscopic findings, and model-based mechanical parameters of the tissue. Site-specific variation of the collagen network moduli, PG matrix modulus and permeability was analyzed. Cylindrical cartilage samples (n=22) were harvested from various sites of the bovine knee and shoulder joints. Collagen orientation, as quantitated by polarized light microscopy, was incorporated into the finite-element model. Stepwise stress-relaxation experiments in unconfined compression were conducted for the samples, and sample-specific models were fitted to the experimental data in order to determine values of the model parameters. For comparison, Fourier transform infrared imaging and digital densitometry were used for the determination of collagen and PG content in the same samples, respectively. The initial and strain-dependent fibril network moduli as well as the initial permeability correlated significantly with the tissue collagen content. The equilibrium Young's modulus of the nonfibrillar matrix and the strain dependency of permeability were significantly associated with the tissue PG content. The present study demonstrates that modern quantitative microscopic methods in combination with the FRPVE model are feasible methods to characterize the structure-function relationships of articular cartilage.

Secretory Leukocyte Protease Inhibitor Expression and High-Risk HPV Infection in Anal Lesions of HIV-Positive Patients.

PubMed

Nicol, Alcina F; Brunette, Laurie L; Nuovo, Gerard J; Grinsztejn, Beatriz; Friedman, Ruth K; Veloso, Valdiléa G; Cunha, Cynthia B; Coutinho, José R; Vianna-Andrade, Cecilia; Oliveira, Nathalia S; Woodham, Andrew W; DA Silva, Diane M; Kast, W Martin

2016-09-01

The aim of this study was to evaluate secretory leukocyte protease inhibitor (SLPI) expression in anal biopsies from HIV-positive (HIV+) individuals, and compare that to anal intraepithelial neoplasia (AIN) diagnoses and human papillomavirus (HPV) status. This is a cross-sectional study of a cohort of 54 HIV+ (31 males and 23 females) from an AIDS clinic in Rio de Janeiro, Brazil. The study material consisted of anorectal tissue biopsies obtained from HIV+ subjects, which were used to construct tissue microarray paraffin blocks for immunohistochemical analysis of SLPI expression. Biopsies were evaluated by an expert pathologist and classified as low-grade AIN1, high-grade AIN2/3, or normal squamous epithelium. In addition, DNA from the biopsies was extracted and analyzed for the presence of low- or high-risk HPV DNA. Histologically, normal squamous epithelium from the anorectal region showed strong positive SLPI staining in 17/20 (85%) samples. In comparison, 9/17 (53%) dysplastic squamous epithelial samples from AIN1 patients showed strong SLPI staining, and only 5/17 (29%) samples from AIN2/3 patients exhibited strong SPLI staining, which both were significantly fewer than those from normal tissue (P = 0.005). Furthermore, there was a significantly higher proportion of samples in which oncogenic high-risk HPV genotypes were detected in low SLPI-expressing tissues than that in tissues with high SLPI expression (P = 0.040). Taken together these results suggest that low SLPI expression is associated with high-risk HPV infections in the development of AIN.

Trypsin and MALDI matrix pre-coated targets simplify sample preparation for mapping proteomic distributions within biological tissues by imaging mass spectrometry

PubMed Central

Zubair, Faizan; Laibinis, Paul E.; Swisher, William G.; Yang, Junhai; Spraggins, Jeffrey M.; Norris, Jeremy L.; Caprioli, Richard M.

2017-01-01

Prefabricated surfaces containing α-cyano-4-hydroxycinnamic acid and trypsin have been developed to facilitate enzymatic digestion of endogenous tissue proteins prior to matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). Tissue sections are placed onto slides that were previously coated with α-cyano-4-hydroxycinnamic acid and trypsin. After incubation to promote enzymatic digestion, the tissue is analyzed by MALDI IMS to determine the spatial distribution of the tryptic fragments. The peptides detected in the MALDI IMS dataset were identified by Liquid chromatography-tandem mass spectrometry/mass spectrometry. Protein identification was further confirmed by correlating the localization of unique tryptic fragments originating from common parent proteins. Using this procedure, proteins with molecular weights as large as 300 kDa were identified and their distributions were imaged in sections of rat brain. In particular, large proteins such as myristoylated alanine-rich C-kinase substrate (29.8 kDa) and spectrin alpha chain, non-erythrocytic 1 (284 kDa) were detected that are not observed without trypsin. The pre-coated targets simplify workflow and increase sample throughput by decreasing the sample preparation time. Further, the approach allows imaging at higher spatial resolution compared with robotic spotters that apply one drop at a time. PMID:27676701

Extraction and analysis methods for the determination of pyrethroid insecticides in surface water, sediments and biological tissues at environmentally relevant concentrations.

PubMed

Mekebri, A; Crane, D B; Blondina, G J; Oros, D R; Rocca, J L

2008-05-01

The aim of this study was to develop and validate chemical methods for measuring pyrethroid insecticides at environmentally relevant concentrations in different matrices. The analytes included six synthetic pyrethroids with the highest agricultural and commercial structural uses in California: bifenthrin, cyfluthrin, cypermethrin, esfenvalerate/fenvalerate, lambda-cyhalothrin, permethrin, and their corresponding stereoisomers, which includes enantiomers, diastereomers and racemic mixtures. Fortified water samples were extracted for analysis of synthetic pyrethroids using liquid-liquid extraction, while fortified sediment and fish tissue samples were extracted using pressurized fluid extraction followed by gel permeation chromatography (GPC) to remove matrix interferences. A florisil column was used for additional cleanup and fractionation of sediment and tissue extracts. Extracts were analyzed using dual column high resolution gas chromatography with electron capture detection (GC/ECD) and confirmation was obtained with gas chromatography mass spectrometry using a quadrupole ion trap detector in MS-MS mode. Method detection limits (MDLs) have been established for water (1-3 ng/L), sediment (0.5-4 ng/g dry weight) and tissue (1-3 ng/g fresh weight). Mean percent recoveries of fortified blanks and samples ranged from 75 to 115% with relative standard deviation (RSD) values less than 20% for all target compounds.

Chronic alcohol abuse in men alters bone mechanical properties by affecting both tissue mechanical properties and microarchitectural parameters.

PubMed

Cruel, M; Granke, M; Bosser, C; Audran, M; Hoc, T

2017-06-01

Alcohol-induced secondary osteoporosis in men has been characterized by higher fracture prevalence and a modification of bone microarchitecture. Chronic alcohol consumption impairs bone cell activity and results in an increased fragility. A few studies highlighted effects of heavy alcohol consumption on some microarchitectural parameters of trabecular bone. But to date and to our knowledge, micro- and macro-mechanical properties of bone of alcoholic subjects have not been investigated. In the present study, mechanical properties and microarchitecture of trabecular bone samples from the iliac crest of alcoholic male patients (n=15) were analyzed and compared to a control group (n=8). Nanoindentation tests were performed to determine the tissue's micromechanical properties, micro-computed tomography was used to measure microarchitectural parameters, and numerical simulations provided the apparent mechanical properties of the samples. Compared to controls, bone tissue from alcoholic patients exhibited an increase of micromechanical properties at tissue scale, a significant decrease of apparent mechanical properties at sample scale, and significant changes in several microarchitectural parameters. In particular, a crucial role of structure model index (SMI) on mechanical properties was identified. 3D microarchitectural parameters are at least as important as bone volume fraction to predict bone fracture risk in the case of alcoholic patients. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Pathological changes in Alzheimer"s brain evaluated with fluorescence emission analysis (FEA)

NASA Astrophysics Data System (ADS)

Christov, Alexander; Ottman, Todd; Grammas, Paula

2004-07-01

Development of AD is associated with cerebrovascular deposition of amyloid beta (Aβ) as well as a progressive increase in vasular collagen content. Both AΒ and collagen are naturally fluorescent compounds when exposed to UV light. We analyzed autofluorescence emitted from brain tissue samples and isolated brain resistance vessels harvested postmortem from patients with Alzheimer's disease (AD) and age-matched controls. Fluorescence emission, excited at 355 nm with an Nd:YAG laser, was measured using a fiber-optic based fluorescence spectroscopic system for tissue analysis. Significantly higher values of fluorescence emission intensity (P<0.001) in the spectral region from 465 to 490 nm were detected in brain resistance vessel samples from AD patients compared to the normal individuals. Results from western blot analysis showed elevated levels of type I and type III collagen, and reduced levels of type IV collagen in resistance vessels from AD patients, compared to control samples. In addition, using direct scanning of the cortical suface for fluoresxcence emission by the laser-induced fluorescence spectroscopy system we detected a significantly (P<0.05) higher level of apoptosis in AD brain tissue compared to age-matched controls. Fluorescence emission analysis (FEA) appears to be a sensitive technique for detecting structural changes in AD brain tissue.

Lysine hydroxylation of collagen in a fibroblast cell culture system

NASA Technical Reports Server (NTRS)

Uzawa, Katsuhiro; Yeowell, Heather N.; Yamamoto, Kazushi; Mochida, Yoshiyuki; Tanzawa, Hideki; Yamauchi, Mitsuo

2003-01-01

The lysine (Lys) hydroxylation pattern of type I collagen produced by human fibroblasts in culture was analyzed and compared. Fibroblasts were cultured from normal human skin (NSF), keloid (KDF), fetal skin (FDF), and skin tissues of Ehlers-Danlos syndrome type VIA and VIB patients (EDS-VIA and -VIB). The type I collagen alpha chains with or without non-helical telopeptides were purified from the insoluble matrix and analyzed. In comparison with NSFs, KDF and FDF showed significantly higher Lys hydroxylation, particularly in the telopeptide domains of both alpha chains. Both EDS-VIA and -VIB showed markedly lower Lys hydroxylation in the helical domains of both alpha chains whereas that in the telopeptides was comparable with those of NSFs. A similar profile was observed in the tissue sample of the EDS-VIB patient. These results demonstrate that the Lys hydroxylation pattern is domain-specific within the collagen molecule and that this method is useful to characterize the cell phenotypes in normal/pathological connective tissues.

Polyesterurethane and acellular matrix based hybrid biomaterial for bladder engineering.

PubMed

Horst, Maya; Milleret, Vincent; Noetzli, Sarah; Gobet, Rita; Sulser, Tullio; Eberli, Daniel

2017-04-01

Poly(lactic-co-glycolic acid) (PLGA) based biomaterials for soft tissue engineering have inherent disadvantages, such as a relative rigidity and a limited variability in the mechanical properties and degradation rates. In this study, a novel electrospun biomaterial based on degradable polyesterurethane (PEU) (DegraPol ® ) was investigated for potential use for bladder engineering in vitro and in vivo. Hybrid microfibrous PEU and PLGA scaffolds were produced by direct electrospinning of the polymer onto a bladder acellular matrix. The scaffold morphology of the scaffold was analyzed, and the biological performance was tested in vitro and in vivo using a rat cystoplasty model. Anatomical and functional outcomes after implantation were analyzed macroscopically, histologically and by cystometry, respectively. Scanning electron microscopy analysis showed that PEU samples had a lower porosity (p < 0.001) and were slightly thinner (p = 0.009) than the PGLA samples. Proliferation and survival of the seeded smooth muscle cells in vitro were comparable on PEU and PLGA scaffolds. After 8 weeks in vivo, the PEU scaffolds exhibited no shrinkage. However, cystometry of the reconstructed bladders exhibited a slightly greater functional bladder capacity in the PLGA group. Morphometric analyses revealed significantly better tissue healing (p < 0.05) and, in particular, better smooth muscle regeneration, as well as a lower rate of inflammatory responses at 8 weeks in the PEU group. Collectively, the results indicated that PEU-hybrid scaffolds promote bladder tissue formation with excellent tissue integration and a low inflammatory reaction in vivo. PEU is a promising biomaterial, particularly with regard to functional tissue engineering of the bladder and other hollow organs. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 658-667, 2017. © 2015 Wiley Periodicals, Inc.

Determination of diagnostic standards on saturated soil extracts for cut roses grown in greenhouses.

PubMed

Franco-Hermida, John Jairo; Quintero, María Fernanda; Cabrera, Raúl Iskander; Guzman, José Miguel

2017-01-01

This work comprises the theoretical determination and validation of diagnostic standards for the analysis of saturated soil extracts for cut rose flower crops (Rosa spp.) growing in the Bogota Plateau, Colombia. The data included 684 plant tissue analyses and 684 corresponding analyses of saturated soil extracts, all collected between January 2009 and June 2013. The tissue and soil samples were selected from 13 rose farms, and from cultivars grafted on the 'Natal Briar' rootstock. These concurrent samples of soil and plant tissues represented 251 production units (locations) of approximately 10,000 m2 distributed across the study area. The standards were conceived as a tool to improve the nutritional balance in the leaf tissue of rose plants and thereby define the norms for expressing optimum productive potential relative to nutritional conditions in the soil. To this end, previously determined diagnostic standard for rose leaf tissues were employed to obtain rates of foliar nutritional balance at each analyzed location and as criteria for determining the diagnostic norms for saturated soil extracts. Implementing this methodology to foliar analysis, showed a higher significant correlation for diagnostic indices. A similar behavior was observed in saturated soil extracts analysis, becoming a powerful tool for integrated nutritional diagnosis. Leaf analyses determine the most limiting nutrients for high yield and analyses of saturated soil extracts facilitate the possibility of correcting the fertigation formulations applied to soils or substrates. Recommendations are proposed to improve the balance in soil-plant system with which the possibility of yield increase becomes more probable. The main recommendations to increase and improve rose crop flower yields would be: continuously check pH values of SSE, reduce the amounts of P, Fe, Zn and Cu in fertigation solutions and carefully analyze the situation of Mn in the soil-plant system.

Serum immunoreactivity of cancer/testis antigen OY-TES-1 and its tissues expression in glioma.

PubMed

Li, Xisheng; Yan, Jun; Fan, Rong; Luo, Bin; Zhang, Qingmei; Lin, Yongda; Zhou, Sufang; Luo, Guorong; Xie, Xiaoxun; Xiao, Shaowen

2017-05-01

OY-TES-1 is a member of the cancer/testis antigen family that is expressed in healthy testis tissue and certain types of cancerous tissue. The present study aimed to analyze the expression pattern of OY-TES-1 and serum anti-OY-TES-1 antibody concentration in patients with glioma. OY-TES-1 mRNA was detected in 28/36 (78%) of glioma cases using conventional reverse transcription polymerase chain reaction (RT-PCR) analysis. RT-quantitative-PCR revealed that OY-TES-1 was expressed at a higher level in glioma tissues compared with normal adult tissues (with the exception of testis tissue). Anti-OY-TES-1 antibodies were present in the serum of 5/36 (14%) of patients with glioma, but absent in all the serum samples from 107 healthy donors. Immunohistochemical analysis demonstrated that OY-TES-1 protein was expressed in all glioma tissues from patients with anti-OY-TES-1 antibody seropositivity. These results suggest that OY-TES-1 is a novel candidate for glioma immunotherapy.

DNA Methylation Patterns in Normal Tissue Correlate more Strongly with Breast Cancer Status than Copy-Number Variants.

PubMed

Gao, Yang; Widschwendter, Martin; Teschendorff, Andrew E

2018-05-04

Normal tissue at risk of neoplastic transformation is characterized by somatic mutations, copy-number variation and DNA methylation changes. It is unclear however, which type of alteration may be more informative of cancer risk. We analyzed genome-wide DNA methylation and copy-number calls from the same DNA assay in a cohort of healthy breast samples and age-matched normal samples collected adjacent to breast cancer. Using statistical methods to adjust for cell type heterogeneity, we show that DNA methylation changes can discriminate normal-adjacent from normal samples better than somatic copy-number variants. We validate this important finding in an independent dataset. These results suggest that DNA methylation alterations in the normal cell of origin may offer better cancer risk prediction and early detection markers than copy-number changes. Copyright © 2018. Published by Elsevier B.V.

Liquid-chromatographic determination of sarafloxacin residues in channel catfish muscle-tissue

USGS Publications Warehouse

Meinertz, J.R.; Dawson, V.K.; Gingerich, W.H.; Cheng, B.; Tubergen, M.M.

1994-01-01

A liquid chromatographic method is described for the determination of sarafloxacin hydrochloride residues i n channel catfish (ictalurus punctatus) fillets. Sarafloxacin was extracted from fillet tissue with acetonitrile=water (1 + 1). The extract was centrifuged and the supernatant was partitioned with hexane. The aqueous fraction was filtered through a 0.45 Mum filter and evaporated to dryness. The sample was redissolved with 20% acetonitrile-methanol (3 + 2) and 80% trifluoroacetic acid (0.1%), Centrifuged, and filtered to remove proteins. Samples were analyzed by chromatography with gradient elution on a c18 column and with fluorescence detection (excitation at 280 nm and emission above 389 nm). Mean recoveries ranged from 85.4 To 104%, and relative standard deviations ranged from 1.06 To 5.58% In samples spiked at concentrations of 10.0-863.8 Ng/g. The method detection limit for sarafloxacin was 1.4 Ng/g.

Endoscopic OCT for in-vivo imaging of precancer and cancer states of human mucosa

NASA Astrophysics Data System (ADS)

Sergeev, Alexander M.; Gelikonov, Valentin M.; Gelikonov, Grigory V.; Feldchtein, Felix I.; Kuranov, Roman V.; Gladkova, Natalia D.; Shakhova, Natalia M.; Kuznetzova, Irina N.; Snopova, Ludmila; Denisenko, Arkady; Almasov, Valentin

1998-01-01

First results of endoscopic applications of optical coherence tomography for in vivo studies of human mucosa in gastrointestinal and genital tracts are presented. A novel endoscopic OCT system has ben created that is based on the integration of a sampling arm of an all-optical-fiber interferometer into standard endoscopic devices using their biopsy channel to transmit low-coherence radiation to investigated tissue. We have studied mucous membranes of esophagus, stomach and uterine cervix as typical localization for carcinomatous processes. Images of tumor tissues versus healthy tissues have been recorded and analyzed. Violations of well-defined stratified healthy mucosa structure in cancerous tissue is distinctly seen by EOCT, thus making this technique promising for early diagnosis of tumors and precise guiding of excisional biopsy.

Establishment of a nested-ASP-PCR method to determine the clarithromycin resistance of Helicobacter pylori.

PubMed

Luo, Xiao-Feng; Jiao, Jian-Hua; Zhang, Wen-Yue; Pu, Han-Ming; Qu, Bao-Jin; Yang, Bing-Ya; Hou, Min; Ji, Min-Jun

2016-07-07

To investigate clarithromycin resistance positions 2142, 2143 and 2144 of the 23SrRNA gene in Helicobacter pylori (H. pylori) by nested-allele specific primer-polymerase chain reaction (nested-ASP-PCR). The gastric tissue and saliva samples from 99 patients with positive results of the rapid urease test (RUT) were collected. The nested-ASP-PCR method was carried out with the external primers and inner allele-specific primers corresponding to the reference strain and clinical strains. Thirty gastric tissue and saliva samples were tested to determine the sensitivity of nested-ASP-PCR and ASP-PCR methods. Then, clarithromycin resistance was detected for 99 clinical samples by using different methods, including nested-ASP-PCR, bacterial culture and disk diffusion. The nested-ASP-PCR method was successfully established to test the resistance mutation points 2142, 2143 and 2144 of the 23SrRNA gene of H. pylori. Among 30 samples of gastric tissue and saliva, the H. pylori detection rate of nested-ASP-PCR was 90% and 83.33%, while the detection rate of ASP-PCR was just 63% and 56.67%. Especially in the saliva samples, nested-ASP-PCR showed much higher sensitivity in H. pylori detection and resistance mutation rates than ASP-PCR. In the 99 RUT-positive gastric tissue and saliva samples, the H. pylori-positive detection rate by nested-ASP-PCR was 87 (87.88%) and 67 (67.68%), in which there were 30 wild-type and 57 mutated strains in gastric tissue and 22 wild-type and 45 mutated strains in saliva. Genotype analysis showed that three-points mixed mutations were quite common, but different resistant strains were present in gastric mucosa and saliva. Compared to the high sensitivity shown by nested-ASP-PCR, the positive detection of bacterial culture with gastric tissue samples was 50 cases, in which only 26 drug-resistant strains were found through analyzing minimum inhibitory zone of clarithromycin. The nested-ASP-PCR assay showed higher detection sensitivity than ASP-PCR and drug sensitivity testing, which could be performed to evaluate clarithromycin resistance of H. pylori.

Establishment of a nested-ASP-PCR method to determine the clarithromycin resistance of Helicobacter pylori

PubMed Central

Luo, Xiao-Feng; Jiao, Jian-Hua; Zhang, Wen-Yue; Pu, Han-Ming; Qu, Bao-Jin; Yang, Bing-Ya; Hou, Min; Ji, Min-Jun

2016-01-01

AIM: To investigate clarithromycin resistance positions 2142, 2143 and 2144 of the 23SrRNA gene in Helicobacter pylori (H. pylori) by nested-allele specific primer-polymerase chain reaction (nested-ASP-PCR). METHODS: The gastric tissue and saliva samples from 99 patients with positive results of the rapid urease test (RUT) were collected. The nested-ASP-PCR method was carried out with the external primers and inner allele-specific primers corresponding to the reference strain and clinical strains. Thirty gastric tissue and saliva samples were tested to determine the sensitivity of nested-ASP-PCR and ASP-PCR methods. Then, clarithromycin resistance was detected for 99 clinical samples by using different methods, including nested-ASP-PCR, bacterial culture and disk diffusion. RESULTS: The nested-ASP-PCR method was successfully established to test the resistance mutation points 2142, 2143 and 2144 of the 23SrRNA gene of H. pylori. Among 30 samples of gastric tissue and saliva, the H. pylori detection rate of nested-ASP-PCR was 90% and 83.33%, while the detection rate of ASP-PCR was just 63% and 56.67%. Especially in the saliva samples, nested-ASP-PCR showed much higher sensitivity in H. pylori detection and resistance mutation rates than ASP-PCR. In the 99 RUT-positive gastric tissue and saliva samples, the H. pylori-positive detection rate by nested-ASP-PCR was 87 (87.88%) and 67 (67.68%), in which there were 30 wild-type and 57 mutated strains in gastric tissue and 22 wild-type and 45 mutated strains in saliva. Genotype analysis showed that three-points mixed mutations were quite common, but different resistant strains were present in gastric mucosa and saliva. Compared to the high sensitivity shown by nested-ASP-PCR, the positive detection of bacterial culture with gastric tissue samples was 50 cases, in which only 26 drug-resistant strains were found through analyzing minimum inhibitory zone of clarithromycin. CONCLUSION: The nested-ASP-PCR assay showed higher detection sensitivity than ASP-PCR and drug sensitivity testing, which could be performed to evaluate clarithromycin resistance of H. pylori. PMID:27433095

CMG2 Expression Is an Independent Prognostic Factor for Soft Tissue Sarcoma Patients

PubMed Central

Wedler, Alice; Rot, Swetlana; Keßler, Jacqueline; Kehlen, Astrid; Holzhausen, Hans-Jürgen; Bache, Matthias; Würl, Peter; Kappler, Matthias

2017-01-01

The capillary morphogenesis gene 2 (CMG2), also known as the anthrax toxin receptor 2 (ANTXR2), is a transmembrane protein putatively involved in extracellular matrix (ECM) adhesion and tissue remodeling. CMG2 promotes endothelial cell proliferation and exhibits angiogenic properties. Its downregulation is associated with a worsened survival of breast carcinoma patients. Aim of this study was to analyze the CMG2 mRNA and protein expression in soft tissue sarcoma and their association with patient outcome. CMG2 mRNA was measured in 121 tumor samples of soft tissue sarcoma patients using quantitative real-time PCR. CMG2 protein was evaluated in 52 tumor samples by ELISA. CMG2 mRNA was significantly correlated with the corresponding CMG2 protein expression (rs = 0.31; p = 0.027). CMG2 mRNA expression was associated with the mRNA expressions of several ECM and tissue remodeling enzymes, among them CD26 and components of the uPA system. Low CMG2 mRNA expression was correlated with a worsened patients’ disease-specific survival in Kaplan-Meier analyses (mean patient survival was 25 vs. 96 months; p = 0.013), especially in high-stage tumors. A decreased CMG2 expression is a negative prognostic factor for soft tissue sarcoma patients. CMG2 may be an interesting candidate gene for the further exploration of soft tissue sarcoma genesis and progression. PMID:29215551

Factors for C-Kit Expression in Cardiac Outgrowth Cells and Human Heart Tissue.

PubMed

Matsushita, Satoshi; Minematsu, Kazuo; Yamamoto, Taira; Inaba, Hirotaka; Kuwaki, Kenji; Shimada, Akie; Yokoyama, Yasutaka; Amano, Atsushi

2017-12-12

We determined the factors associated with the expression of c-kit in the heart and the proliferation of c-kit-positive (c-kit pos ) cardiac stem cells among the outgrowth cells cultured from human cardiac explants.Samples of the right atrium (RA), left atrium (LA), and left ventricle obtained from patients during open-heart surgery were processed for cell culture of outgrowth cells and tissue analysis. The total number of growing cells and the population of c-kit pos cells were measured and compared with c-kit expression in native tissues and characteristics of the patients according to the region of the heart.We analyzed 452 samples from 334 patients. Atrial fibrillation (AF) in the patients reduced the number of outgrowth cells from the RA and LA, and aging was a co-factor for the LA. The c-kit pos population from the RA was associated with serum brain natriuretic peptide (BNP). C-kit expression in native tissue was also associated with BNP expression. However, we observed no relationship in expression between outgrowth cells and native tissue. In addition, the RA tissue provided the highest number of c-kit pos cells, and the left ventricle provided the lowest.C-kit was weakly expressed in response to damage. In addition, no correlation between outgrowth cells and native tissue was found for c-kit expression.

CMG2 Expression Is an Independent Prognostic Factor for Soft Tissue Sarcoma Patients.

PubMed

Greither, Thomas; Wedler, Alice; Rot, Swetlana; Keßler, Jacqueline; Kehlen, Astrid; Holzhausen, Hans-Jürgen; Bache, Matthias; Würl, Peter; Taubert, Helge; Kappler, Matthias

2017-12-07

The capillary morphogenesis gene 2 (CMG2), also known as the anthrax toxin receptor 2 (ANTXR2), is a transmembrane protein putatively involved in extracellular matrix (ECM) adhesion and tissue remodeling. CMG2 promotes endothelial cell proliferation and exhibits angiogenic properties. Its downregulation is associated with a worsened survival of breast carcinoma patients. Aim of this study was to analyze the CMG2 mRNA and protein expression in soft tissue sarcoma and their association with patient outcome. CMG2 mRNA was measured in 121 tumor samples of soft tissue sarcoma patients using quantitative real-time PCR. CMG2 protein was evaluated in 52 tumor samples by ELISA. CMG2 mRNA was significantly correlated with the corresponding CMG2 protein expression (r s = 0.31; p = 0.027). CMG2 mRNA expression was associated with the mRNA expressions of several ECM and tissue remodeling enzymes, among them CD26 and components of the uPA system. Low CMG2 mRNA expression was correlated with a worsened patients' disease-specific survival in Kaplan-Meier analyses (mean patient survival was 25 vs. 96 months; p = 0.013), especially in high-stage tumors. A decreased CMG2 expression is a negative prognostic factor for soft tissue sarcoma patients. CMG2 may be an interesting candidate gene for the further exploration of soft tissue sarcoma genesis and progression.

Histopathological Analysis of PEEK Wear Particle Effects on the Synovial Tissue of Patients

PubMed Central

Jansson, V.; Giurea, A.

2016-01-01

Introduction. Increasing interest developed in the use of carbon-fiber-reinforced-poly-ether-ether-ketones (CFR-PEEK) as an alternative bearing material in knee arthroplasty. The effects of CFR-PEEK wear in in vitro and animal studies are controversially discussed, as there are no data available concerning human tissue. The aim of this study was to analyze human tissue containing CFR-PEEK as well as UHMWPE wear debris. The authors hypothesized no difference between the used biomaterials. Methods and Materials. In 10 patients during knee revision surgery of a rotating-hinge-knee-implant-design, synovial tissue samples were achieved (tibial inserts: UHMWPE; bushings and flanges: CFR-PEEK). One additional patient received revision surgery without any PEEK components as a control. The tissue was paraffin-embedded, sliced into 2 μm thick sections, and stained with hematoxylin and eosin in a standard process. A modified panoptical staining was also done. Results. A “wear-type” reaction was seen in the testing and the control group. In all samples, the UHMWPE particles were scattered in the tissue or incorporated in giant cells. CFR-PEEK particles were seen as conglomerates and only could be found next to vessels. CFR-PEEK particles showed no giant-cell reactions. In conclusion, the hypothesis has to be rejected. UHMWPE and PEEK showed a different scatter-behavior in human synovial tissue. PMID:27766256

Donor screening for hepatitis B virus infection in a cell and tissue bank.

PubMed

Solves, P; Mirabet, V; Alvarez, M; Vila, E; Quiles, F; Villalba, J V; Montoro, J A; Soler, M A; Roig, R J

2008-12-01

Hepatitis B virus (HBV) has been transmitted by tissue transplantation. In order to reduce the risk of HBV transmission, testing for antibody to HBV core antigen (anti-HBc) is used in addition to testing for hepatitis B surface antigen (HBsAg) in many blood centers and tissue banks. We retrospectively analyzed the results of HBV assays in tissue donors. All tissue donors were tested for HBsAg and anti-HBc. All anti-HBc positive sera were tested for the antibody to HBsAg (anti-HBs). From July 2006, an HBV nucleic acid testing (NAT) assay was also performed. A total of 6855 tissue donors from January 1999 till July 2007 were tested for HBV assays: 4756 women and 2099 men. Positive HBsAg was found in 23 (0.36%) living donors, while no multiorgan or cord blood (CB) donor was found to be positive for HBsAg. Positive anti-HBc was found in 80 multiorgan donors (12.94%), 599 living donors (17.84%), and 103 CB donors (3.57%) (P<0.005), while isolated anti-HBc was found in 12 multiorgan (1.94%), in 126 living tissue donors (3.75%), and in 8 CB donors (0.28%). A total of 1310 donors were analyzed for single-sample DNA HBV NAT assay. We consider that anti-HBc and NAT assays must both still be performed in addition to HBsAg assay for HBV screening in tissue donors. All these tests will be useful in order to define an algorithm for safe and efficient management of the tissue bank.

Avian toxicologic diagnosis

USGS Publications Warehouse

Sigurdson, C.J.; Franson, J.C.; Fudge, A.M.

2000-01-01

This chapter describes the sources and pathophysiology of some potential poisons that affect birds and summarizes useful laboratory tests. The diagnosis of poisoning in birds, as in mammals, requires a complete and accurate history, careful observation of clinical signs, and a thorough necropsy evaluation. Appropriate sample handling and analysis, based on consultation with the diagnostic toxicologist, are critical (Table 19--1). Veterinary toxicology laboratories are becoming increasingly specialized, with only certain laboratories capable of analyzing for drug residues or anticoagulants, for example. Although a local laboratory may not be able to fulfill a specific test request, they may recommend an alternative laboratory or may be willing to forward the sample. As a general rule in suspect poisoning cases, large tissue samples of liver, kidney, brain, and subcutaneous fat and of crop, proventriculus, and ventriculus contents should be collected at necropsy and frozen. Appropriate samples should be submitted frozen, with the remainder held in the freezer for possible later testing. A second set of tissues should be placed in 10% formalin for histopathologic examination.

A comparison of ARMS-Plus and droplet digital PCR for detecting EGFR activating mutations in plasma

PubMed Central

Zhang, Xinxin; Chang, Ning; Yang, Guohua; Zhang, Yong; Ye, Mingxiang; Cao, Jing; Xiong, Jie; Han, Zhiping; Wu, Shuo; Shang, Lei; Zhang, Jian

2017-01-01

In this study, we introduce a novel amplification refractory mutation system (ARMS)-based assay, namely ARMS-Plus, for the detection of epidermal growth factor receptor (EGFR) mutations in plasma samples. We evaluated the performance of ARMS-Plus in comparison with droplet digital PCR (ddPCR) and assessed the significance of plasma EGFR mutations in predicting efficacy of EGFR-tyrosine kinase inhibitor (TKI) regimen. A total of 122 advanced non-small cell lung cancer (NSCLC) patients were enrolled in this study. The tumor tissue samples from these patients were evaluated by conventional ARMS PCR method to confirm their EGFR mutation status. For the 116 plasma samples analyzed by ARMS-Plus, the sensitivity, specificity, and concordance rate were 77.27% (34/44), 97.22% (70/72), and 89.66% (104/116; κ=0.77, P<0.0001), respectively. Among the 71 plasma samples analyzed by both ARMS-Plus and ddPCR, ARMS-Plus showed a higher sensitivity than ddPCR (83.33% versus 70.83%). The presence of EGFR activating mutations in plasma was not associated with the response to EGFR-TKI, although further validation with a larger cohort is required to confirm the correlation. Collectively, the performance of ARMS-Plus and ddPCR are comparable. ARMS-Plus could be a potential alternative to tissue genotyping for the detection of plasma EGFR mutations in NSCLC patients. PMID:29340107

Trace elements and organic compounds in streambed sediment and fish tissue of coastal New England streams, 1998-99

USGS Publications Warehouse

Chalmers, Ann

2002-01-01

Streambed sediment and fish tissue were collected at 14 river sites in eastern New England during low-flow conditions in 1998 and 1999 as part of the New England Coastal Basins (NECB) study of the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program. Sampling sites were selected over a range of urban settings. Population densities at selected sites ranged from 26 to 3,585 people per square mile, and urban land use ranged from 1 to 68 percent. The streambed sediment samples were analyzed for a total of 141 contaminants, including 45 trace elements, 32 organochlorine compounds, and 64 semi-volatile organic compounds. The fish tissue samples were analyzed for 22 trace elements and 28 organochlorine compounds. Concentrations of selected contaminants in both streambed sediment and fish tissue correlated more strongly with population density than with other watershed characteristics. Cadmium, copper, lead, mercury, zinc, total polycyclic aromatic hydrocarbons (PAHs), total polychlorinated biphenyls (PCBs), dichloro diphenyl trichloroethane and metabolites (DDTM), and total chlordane in streambed sediment all showed strong positive correlations with population density (rho = 0.71 to 0.85, p value = 0.005 to <0.001). Correlations between population density and selected contaminants in fish tissue were less significant than with streambed sediment (rho = 0.62 to 0.72, p value = 0.03 to 0.008). Organic carbon concentrations were correlated with concentrations of arsenic, selenium, total PAHs, total PCBs, and DDTM in streambed sediment. The relation between concentrations of contaminants in streambed sediment and fish tissue was stronger for organochlorine compounds (rho = 0.75 to 0.55, p = 0.005 to 0.065) than for trace elements (rho = 0.63 to 0.53, p = 0.029 to 0.069). The NECB study area had the highest median concentrations of lead, mercury, total PAHs, total PCBs, and DDTM in streambed sediment and the highest median concentration of PCBs in fish tissue compared to 45 other NAWQA study units across the Nation. Concentrations of many of these constituents in streambed sediment also were frequently above the consensus-based Sediment-Quality Guidelines for the protection of wildlife, suggesting they are a threat to the health of aquatic biota in New England.

Therapy of Prostate Cancer Using a Human Antibody Targeting the Type 1 Insulin-Like Growth Factor Receptor (IGF-IR)

DTIC Science & Technology

2009-09-01

euthanized, tumors harvested and portions processed for IHC, Western blot, flow cytometry , culture, and RNA analysis. If not enough tissue is available...temperature for 60 minutes. Samples were analyzed by flow cytometry using a BD FACScan. Data were analyzed with CellQuestPRO software. Evaluation of BrdUrd...were approved by the University of Washington Institutional Animal Care and Use Committee (IACUC). Flow cytometry . To measure tumor IGF-IR expression

Simulation of a compact analyzer-based imaging system with a regular x-ray source

NASA Astrophysics Data System (ADS)

Caudevilla, Oriol; Zhou, Wei; Stoupin, Stanislav; Verman, Boris; Brankov, J. G.

2017-03-01

Analyzer-based Imaging (ABI) belongs to a broader family of phase-contrast (PC) X-ray techniques. PC measures X-ray deflection phenomena when interacting with a sample, which is known to provide higher contrast images of soft tissue than other X-ray methods. This is of high interest in the medical field, in particular for mammogram applications. This paper presents a simulation tool for table-top ABI systems using a conventional polychromatic X-ray source.

Polychlorinated dibenzo-p-dioxins and dibenzofurans detected in bivalve samples from the NOAA National Status and Trends Program.

PubMed

Wade, Terry L; Sweet, Stephen T; Sericano, José L; Defreitas, Debra A; Lauenstein, Gunnar G

2014-04-30

Bivalve samples from 142 sites were analyzed to determine the concentration and toxicity equivalents (TEQ) of dioxins and furans (D/F) as part of the NOAA National Status and Trends Program. The total concentration of 17 D/F ranged from not detected to 203 pg/g wet weight of tissue. Octachlorinated dibenzo-p-dioxin, OCDD, had a concentration range from not detected to 189 pg/g and a mean concentration of 8.65 pg/g. OCDD was the dominant D/F compound detected and accounted for, on average, over 70% of the total D/F concentration. The TEQ (compared to 2,3,7,8-TCDD) ranged from 0.12 to 7.32 pg TEQ/g. The TEQ for 39% of the bivalves analyzed were below 0.238 pg TEQ/g. TEQ above human consumption advisory concentration of 1.2 pg TEQ/g were found in 9.3% of the samples analyzed. TEQ for D/F indicate very limited human health concerns from consumption of bivalves at most of the locations sampled. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simple high-performance liquid chromatography method for formaldehyde determination in human tissue through derivatization with 2,4-dinitrophenylhydrazine.

PubMed

Yilmaz, Bilal; Asci, Ali; Kucukoglu, Kaan; Albayrak, Mevlut

2016-08-01

A simple high-performance liquid chromatography method has been developed for the determination of formaldehyde in human tissue. FA Formaldehyde was derivatized with 2,4-dinitrophenylhydrazine. It was extracted from human tissue with ethyl acetate by liquid-liquid extraction and analyzed by high-performance liquid chromatography. The calibration curve was linear in the concentration range of 5.0-200 μg/mL. Intra- and interday precision values for formaldehyde in tissue were <6.9%, and accuracy (relative error) was better than 6.5%. The extraction recoveries of formaldehyde from human tissue were between 88 and 98%. The limits of detection and quantification of formaldehyde were 1.5 and 5.0 μg/mL, respectively. Also, this assay was applied to liver samples taken from a biopsy material. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

MARS spectral molecular imaging of lamb tissue: data collection and image analysis

NASA Astrophysics Data System (ADS)

Aamir, R.; Chernoglazov, A.; Bateman, C. J.; Butler, A. P. H.; Butler, P. H.; Anderson, N. G.; Bell, S. T.; Panta, R. K.; Healy, J. L.; Mohr, J. L.; Rajendran, K.; Walsh, M. F.; de Ruiter, N.; Gieseg, S. P.; Woodfield, T.; Renaud, P. F.; Brooke, L.; Abdul-Majid, S.; Clyne, M.; Glendenning, R.; Bones, P. J.; Billinghurst, M.; Bartneck, C.; Mandalika, H.; Grasset, R.; Schleich, N.; Scott, N.; Nik, S. J.; Opie, A.; Janmale, T.; Tang, D. N.; Kim, D.; Doesburg, R. M.; Zainon, R.; Ronaldson, J. P.; Cook, N. J.; Smithies, D. J.; Hodge, K.

2014-02-01

Spectral molecular imaging is a new imaging technique able to discriminate and quantify different components of tissue simultaneously at high spatial and high energy resolution. Our MARS scanner is an x-ray based small animal CT system designed to be used in the diagnostic energy range (20-140 keV). In this paper, we demonstrate the use of the MARS scanner, equipped with the Medipix3RX spectroscopic photon-processing detector, to discriminate fat, calcium, and water in tissue. We present data collected from a sample of lamb meat including bone as an illustrative example of human tissue imaging. The data is analyzed using our 3D Algebraic Reconstruction Algorithm (MARS-ART) and by material decomposition based on a constrained linear least squares algorithm. The results presented here clearly show the quantification of lipid-like, water-like and bone-like components of tissue. However, it is also clear to us that better algorithms could extract more information of clinical interest from our data. Because we are one of the first to present data from multi-energy photon-processing small animal CT systems, we make the raw, partial and fully processed data available with the intention that others can analyze it using their familiar routines. The raw, partially processed and fully processed data of lamb tissue along with the phantom calibration data can be found at http://hdl.handle.net/10092/8531.

A prototype for unsupervised analysis of tissue microarrays for cancer research and diagnostics.

PubMed

Chen, Wenjin; Reiss, Michael; Foran, David J

2004-06-01

The tissue microarray (TMA) technique enables researchers to extract small cylinders of tissue from histological sections and arrange them in a matrix configuration on a recipient paraffin block such that hundreds can be analyzed simultaneously. TMA offers several advantages over traditional specimen preparation by maximizing limited tissue resources and providing a highly efficient means for visualizing molecular targets. By enabling researchers to reliably determine the protein expression profile for specific types of cancer, it may be possible to elucidate the mechanism by which healthy tissues are transformed into malignancies. Currently, the primary methods used to evaluate arrays involve the interactive review of TMA samples while they are viewed under a microscope, subjectively evaluated, and scored by a technician. This process is extremely slow, tedious, and prone to error. In order to facilitate large-scale, multi-institutional studies, a more automated and reliable means for analyzing TMAs is needed. We report here a web-based prototype which features automated imaging, registration, and distributed archiving of TMAs in multiuser network environments. The system utilizes a principal color decomposition approach to identify and characterize the predominant staining signatures of specimens in color space. This strategy was shown to be reliable for detecting and quantifying the immunohistochemical expression levels for TMAs.

Preparation of A Spaceflight: Apoptosis Search in Sutured Wound Healing Models.

PubMed

Riwaldt, Stefan; Monici, Monica; Graver Petersen, Asbjørn; Birk Jensen, Uffe; Evert, Katja; Pantalone, Desiré; Utpatel, Kirsten; Evert, Matthias; Wehland, Markus; Krüger, Marcus; Kopp, Sascha; Frandsen, Sofie; Corydon, Thomas; Sahana, Jayashree; Bauer, Johann; Lützenberg, Ronald; Infanger, Manfred; Grimm, Daniela

2017-12-03

To prepare the ESA (European Space Agency) spaceflight project "Wound healing and Sutures in Unloading Conditions", we studied mechanisms of apoptosis in wound healing models based on ex vivo skin tissue cultures, kept for 10 days alive in serum-free DMEM/F12 medium supplemented with bovine serum albumin, hydrocortisone, insulin, ascorbic acid and antibiotics at 32 °C. The overall goal is to test: (i) the viability of tissue specimens; (ii) the gene expression of activators and inhibitors of apoptosis and extracellular matrix components in wound and suture models; and (iii) to design analytical protocols for future tissue specimens after post-spaceflight download. Hematoxylin-Eosin and Elastica-van-Gieson staining showed a normal skin histology with no signs of necrosis in controls and showed a normal wound suture. TdT-mediated dUTP-biotin nick end labeling for detecting DNA fragmentation revealed no significant apoptosis. No activation of caspase-3 protein was detectable. FASL , FADD , CASP3 , CASP8 , CASP10 , BAX , BCL2 , CYC1 , APAF1 , LAMA3 and SPP1 mRNAs were not altered in epidermis and dermis samples with and without a wound compared to 0 day samples (specimens investigated directly post-surgery). BIRC5 , CASP9 , and FN1 mRNAs were downregulated in epidermis/dermis samples with and/or without a wound compared to 0 day samples. BIRC2 , BIRC3 were upregulated in 10 day wound samples compared to 0 day samples in epidermis/dermis. RELA/FAS mRNAs were elevated in 10 day wound and no wound samples compared to 0 day samples in dermis. In conclusion, we demonstrate that it is possible to maintain live skin tissue cultures for 10 days. The viability analysis showed no significant signs of cell death in wound and suture models. The gene expression analysis demonstrated the interplay of activators and inhibitors of apoptosis and extracellular matrix components, thereby describing important features in ex vivo sutured wound healing models. Collectively, the performed methods defining analytical protocols proved to be applicable for post-flight analyzes of tissue specimens after sample return.

Two alternative DNA extraction methods to improve the detection of Mycobacterium-tuberculosis-complex members in cattle and red deer tissue samples.

PubMed

Fell, Shari; Bröckl, Stephanie; Büttner, Mathias; Rettinger, Anna; Zimmermann, Pia; Straubinger, Reinhard K

2016-09-15

Bovine tuberculosis (bTB), which is caused by Mycobacterium bovis and M. caprae, is a notifiable animal disease in Germany. Diagnostic procedure is based on a prescribed protocol that is published in the framework of German bTB legislation. In this protocol small sample volumes are used for DNA extraction followed by real-time PCR analyses. As mycobacteria tend to concentrate in granuloma and the infected tissue in early stages of infection does not necessarily show any visible lesions, it is likely that DNA extraction from only small tissue samples (20-40 mg) of a randomly chosen spot from the organ and following PCR testing may result in false negative results. In this study two DNA extraction methods were developed to process larger sample volumes to increase the detection sensitivity of mycobacterial DNA in animal tissue. The first extraction method is based on magnetic capture, in which specific capture oligonucleotides were utilized. These nucleotides are linked to magnetic particles and capture Mycobacterium-tuberculosis-complex (MTC) DNA released from 10 to 15 g of tissue material. In a second approach remaining sediments from the magnetic capture protocol were further processed with a less complex extraction protocol that can be used in daily routine diagnostics. A total number of 100 tissue samples from 34 cattle (n = 74) and 18 red deer (n = 26) were analyzed with the developed protocols and results were compared to the prescribed protocol. All three extraction methods yield reliable results by the real-time PCR analysis. The use of larger sample volume led to a sensitivity increase of DNA detection which was shown by the decrease of Ct-values. Furthermore five samples which were tested negative or questionable by the official extraction protocol were detected positive by real time PCR when the alternative extraction methods were used. By calculating the kappa index, the three extraction protocols resulted in a moderate (0.52; protocol 1 vs 3) to almost perfect agreement (1.00; red deer sample testing with all protocols). Both new methods yielded increased detection rates for MTC DNA detection in large sample volumes and consequently improve the official diagnostic protocol.

Identification of forensic samples by using an infrared-based automatic DNA sequencer.

PubMed

Ricci, Ugo; Sani, Ilaria; Klintschar, Michael; Cerri, Nicoletta; De Ferrari, Francesco; Giovannucci Uzielli, Maria Luisa

2003-06-01

We have recently introduced a new protocol for analyzing all core loci of the Federal Bureau of Investigation's (FBI) Combined DNA Index System (CODIS) with an infrared (IR) automatic DNA sequencer (LI-COR 4200). The amplicons were labeled with forward oligonucleotide primers, covalently linked to a new infrared fluorescent molecule (IRDye 800). The alleles were displayed as familiar autoradiogram-like images with real-time detection. This protocol was employed for paternity testing, population studies, and identification of degraded forensic samples. We extensively analyzed some simulated forensic samples and mixed stains (blood, semen, saliva, bones, and fixed archival embedded tissues), comparing the results with donor samples. Sensitivity studies were also performed for the four multiplex systems. Our results show the efficiency, reliability, and accuracy of the IR system for the analysis of forensic samples. We also compared the efficiency of the multiplex protocol with ultraviolet (UV) technology. Paternity tests, undegraded DNA samples, and real forensic samples were analyzed with this approach based on IR technology and with UV-based automatic sequencers in combination with commercially-available kits. The comparability of the results with the widespread UV methods suggests that it is possible to exchange data between laboratories using the same core group of markers but different primer sets and detection methods.

Real time analysis of brain tissue by direct combination of ultrasonic surgical aspiration and sonic spray mass spectrometry.

PubMed

Schäfer, Karl-Christian; Balog, Júlia; Szaniszló, Tamás; Szalay, Dániel; Mezey, Géza; Dénes, Júlia; Bognár, László; Oertel, Matthias; Takáts, Zoltán

2011-10-15

Direct combination of cavitron ultrasonic surgical aspirator (CUSA) and sonic spray ionization mass spectrometry is presented. A commercially available ultrasonic surgical device was coupled to a Venturi easy ambient sonic-spray ionization (V-EASI) source by directly introducing liquified tissue debris into the Venturi air jet pump. The Venturi air jet pump was found to efficiently nebulize the suspended tissue material for gas phase ion production. The ionization mechanism involving solely pneumatic spraying was associated with that of sonic spray ionization. Positive and negative ionization spectra were obtained from brain and liver samples reflecting the primary application areas of the surgical device. Mass spectra were found to feature predominantly complex lipid-type constituents of tissues in both ion polarity modes. Multiply charged peptide anions were also detected. The influence of instrumental settings was characterized in detail. Venturi pump geometry and flow parameters were found to be critically important in ionization efficiency. Standard solutions of phospholipids and peptides were analyzed in order to test the dynamic range, sensitivity, and suppression effects. The spectra of the intact tissue specimens were found to be highly specific to the histological tissue type. The principal component analysis (PCA) and linear discriminant analysis (LDA) based data analysis method was developed for real-time tissue identification in a surgical environment. The method has been successfully tested on post-mortem and ex vivo human samples including astrocytomas, meningeomas, metastatic brain tumors, and healthy brain tissue. © 2011 American Chemical Society

Raman spectroscopic analysis of human skin tissue sections ex-vivo: evaluation of the effects of tissue processing and dewaxing

NASA Astrophysics Data System (ADS)

Ali, Syed M.; Bonnier, Franck; Tfayli, Ali; Lambkin, Helen; Flynn, Kathleen; McDonagh, Vincent; Healy, Claragh; Clive Lee, T.; Lyng, Fiona M.; Byrne, Hugh J.

2013-06-01

Raman spectroscopy coupled with K-means clustering analysis (KMCA) is employed to elucidate the biochemical structure of human skin tissue sections and the effects of tissue processing. Both hand and thigh sections of human cadavers were analyzed in their unprocessed and formalin-fixed, paraffin-processed (FFPP), and subsequently dewaxed forms. In unprocessed sections, KMCA reveals clear differentiation of the stratum corneum (SC), intermediate underlying epithelium, and dermal layers for sections from both anatomical sites. The SC is seen to be relatively rich in lipidic content; the spectrum of the subjacent layers is strongly influenced by the presence of melanin, while that of the dermis is dominated by the characteristics of collagen. For a given anatomical site, little difference in layer structure and biochemistry is observed between samples from different cadavers. However, the hand and thigh sections are consistently differentiated for all cadavers, largely based on lipidic profiles. In dewaxed FFPP samples, while the SC, intermediate, and dermal layers are clearly differentiated by KMCA of Raman maps of tissue sections, the lipidic contributions to the spectra are significantly reduced, with the result that respective skin layers from different anatomical sites become indistinguishable. While efficient at removing the fixing wax, the tissue processing also efficiently removes the structurally similar lipidic components of the skin layers. In studies of dermatological processes in which lipids play an important role, such as wound healing, dewaxed samples are therefore not appropriate. Removal of the lipids does however accentuate the spectral features of the cellular and protein components, which may be more appropriate for retrospective analysis of disease progression and biochemical analysis using tissue banks.

Improved method for quantifying the avicide 3-chloro-p-toluidine hydrochloride in bird tissues using a deuterated surrogate/GC/MS method.

PubMed

Stahl, Randal S; Custer, Thomas W; Pochop, Patricia A; Johnston, John J

2002-02-13

A method using a deuterated surrogate of the avicide 3-chloro-p-toluidine hydrochloride (CPTH) was developed to quantify the CPTH residues in the gastrointestinal (GI) tract and breast muscle tissues in birds collected in CPTH-baited sunflower and rice fields. This method increased the range of a previous surrogate/gas chromatography/mass spectroscopy method from 0-2 to 0-20 microg/g in tissue samples and greatly simplified the extraction procedure. The modified method also sought to increase recoveries over a range of matrix effects introduced by analyzing tissues from birds collected in the field, where the GI tract contents would be affected by varying diet. The new method was used to determine the CPTH concentration in GI tract samples fortified with CPTH-treated rice bait to simulate the consumption of varying amounts of treated bait by two nontargeted bird species, pigeon (Columbia livia) and house sparrow (Passer domesticus). The new method was then used to examine the CPTH concentrations in the gizzard contents of the targeted bird species, red-winged black bird (Agelaius phoeniceus) and brown-headed cowbird (Molothrus ater), that were collected after feeding at a treated bait site. The method proved sufficiently sensitive to quantify CPTH in the breast muscle tissues and the gizzard contents of red-winged blackbirds and brown-headed cowbirds during an operational baiting program. The levels of CPTH determined for these birds in both tissue samples were determined to be highly correlated. The appearance of CPTH in the breast muscle tissue immediately after feeding was not anticipated. The potential secondary hazard posed by the targeted birds to potential scavengers and predators was also evaluated.

Stable phenotype of B-cell subsets following cryopreservation and thawing of normal human lymphocytes stored in a tissue biobank.

PubMed

Rasmussen, Simon Mylius; Bilgrau, Anders Ellern; Schmitz, Alexander; Falgreen, Steffen; Bergkvist, Kim Steve; Tramm, Anette Mai; Baech, John; Jacobsen, Chris Ladefoged; Gaihede, Michael; Kjeldsen, Malene Krag; Bødker, Julie Støve; Dybkaer, Karen; Bøgsted, Martin; Johnsen, Hans Erik

2015-01-01

Cryopreservation is an acknowledged procedure to store vital cells for future biomarker analyses. Few studies, however, have analyzed the impact of the cryopreservation on phenotyping. We have performed a controlled comparison of cryopreserved and fresh cellular aliquots prepared from individual healthy donors. We studied circulating B-cell subset membrane markers and global gene expression, respectively by multiparametric flow cytometry and microarray data. Extensive statistical analysis of the generated data tested the concept that "overall, there are no phenotypic differences between cryopreserved and fresh B-cell subsets." Subsequently, we performed an uncontrolled comparison of tonsil tissue samples. By multiparametric flow analysis, we documented no significant changes following cryopreservation of subset frequencies or membrane intensity for the differentiation markers CD19, CD20, CD22, CD27, CD38, CD45, and CD200. By gene expression profiling following cryopreservation, across all samples, only 16 out of 18708 genes were significantly up or down regulated, including FOSB, KLF4, RBP7, ANXA1 or CLC, DEFA3, respectively. Implementation of cryopreserved tissue in our research program allowed us to present a performance analysis, by comparing cryopreserved and fresh tonsil tissue. As expected, phenotypic differences were identified, but to an extent that did not affect the performance of the cryopreserved tissue to generate specific B-cell subset associated gene signatures and assign subset phenotypes to independent tissue samples. We have confirmed our working concept and illustrated the usefulness of vital cryopreserved cell suspensions for phenotypic studies of the normal B-cell hierarchy; however, storage procedures need to be delineated by tissue-specific comparative analysis. © 2014 Clinical Cytometry Society.

Improved method for quantifying the avicide 3-chloro-p-toluidine hydrochloride in bird tissues using a deuterated surrogate/GC/MS method

USGS Publications Warehouse

Stahl, R.S.; Custer, T.W.; Pochop, P.A.; Johnston, J.J.

2002-01-01

A method using a deuterated surrogate of the avicide 3-chloro-p-toluidine hydrochloride (CPTH) was developed to quantify the CPTH residues in the gastrointestinal (Gl) tract and breast muscle tissues in birds collected in CPTH-baited sunflower and rice fields. This method increased the range of a previous surrogate/gas chromatography/mass spectroscopy method from 0-2 to 0-20mug/g in tissue samples and greatly simplified the extraction procedure. The modified method also sought to increase recoveries over a range of matrix effects introduced by analyzing tissues from birds collected in the field, where the GI tract contents would be affected by varying diet. The new method was used to determine the CPTH concentration In GI tract samples fortified with CPTH-treated rice bait to simulate the consumption of varying amounts of treated bait by two nontargeted bird species, pigeon (Columbia livia) and house sparrow (Passer domesticus). The new method was then used to examine the CPTH concentrations in the gizzard contents of the targeted bird species, red-winged black bird (Agelaius phoeniceus) and brown-headed cowbird (Molothrus ater) that were collected after feeding at a treated bait site. The method proved sufficiently sensitive to quantify CPTH in the breast muscle tissues and the gizzard contents of red-winged blackbirds and brown-headed cowbirds during an operational baiting program. The levels of CPTH determined for these birds in both tissue samples were determined to be highly correlated. The appearance of CPTH in the breast muscle tissue immediately after feeding was not anticipated. The potential secondary hazard posed by the targeted birds to potential scavengers and predators was also evaluated.

Diamond, titanium dioxide, titanium silicon oxide, and barium strontium titanium oxide nanoparticles as matrixes for direct matrix-assisted laser desorption/ionization mass spectrometry analysis of carbohydrates in plant tissues.

PubMed

Gholipour, Yousef; Giudicessi, Silvana L; Nonami, Hiroshi; Erra-Balsells, Rosa

2010-07-01

Nanoparticles (NPs) of diamond, titanium dioxide, titanium silicon oxide, barium strontium titanium oxide, and silver (Ag) were examined for their potential as MALDI matrixes for direct laser desorption/ionization of carbohydrates, especially fructans, from plant tissue. Two sample preparation methods including solvent-assisted and solvent-free (dry) NPs deposition were performed and compared. All examined NPs except for Ag could desorb/ionize standard sucrose and fructans in positive and in negative ion mode. Ag NPs yielded good signals only for nonsalt-doped samples that were measured in the negative ion mode. In the case of in vivo studies, except for Ag, all NPs studied could desorb/ionize carbohydrates from tissue in both the positive and negative ion modes. Furthermore, compared to the results obtained with soluble sugars extracted from plant tissues, fructans with higher molecular weight intact molecular ions could be detected when the plant tissues were directly profiled. The limit of detection (LOD) of fructans and the ratios between signal intensities and fructan concentrations were analyzed. NPs had similar LODs for standard fructan triose (1-kestose) in the positive ion mode and better LODs in the negative ion mode when compared with the common crystalline organic MALDI matrixes used for carbohydrates (2,5-dihydroxybenzoic acid and nor-harmane) or carbon nanotubes. Solvent-free NP deposition on tissues partially improves the signal acquisition. Although lower signal-to-noise ratio sugar signals were acquired from the tissues when compared to the solvent-assisted method, the reproducibility averaged over all sample was more uniform.

Stable Phenotype Of B-Cell Subsets Following Cryopreservation and Thawing of Normal Human Lymphocytes Stored in a Tissue Biobank.

PubMed

Rasmussen, Simon Mylius; Bilgrau, Anders Ellern; Schmitz, Alexander; Falgreen, Steffen; Bergkvist, Kim Steve; Tramm, Anette Mai; Baech, John; Jacobsen, Chris Ladefoged; Gaihede, Michael; Kjeldsen, Malene Krag; Bødker, Julie Støve; Dybkaer, Karen; Bøgsted, Martin; Johnsen, Hans Erik

2014-09-20

Background Cryopreservation is an acknowledged procedure to store vital cells for future biomarker analyses. Few studies, however, have analyzed the impact of the cryopreservation on phenotyping. Methods We have performed a controlled comparison of cryopreserved and fresh cellular aliquots prepared from individual healthy donors. We studied circulating B-cell subset membrane markers and global gene expression, respectively by multiparametric flow cytometry and microarray data. Extensive statistical analysis of the generated data tested the concept that "overall, there are phenotypic differences between cryopreserved and fresh B-cell subsets". Subsequently, we performed a consecutive uncontrolled comparison of tonsil tissue samples. Results By multiparametric flow analysis, we documented no significant changes following cryopreservation of subset frequencies or membrane intensity for the differentiation markers CD19, CD20, CD22, CD27, CD38, CD45, and CD200. By gene expression profiling following cryopreservation, across all samples, only 16 out of 18708 genes were significantly up or down regulated, including FOSB, KLF4, RBP7, ANXA1 or CLC, DEFA3, respectively. Implementation of cryopreserved tissue in our research program allowed us to present a performance analysis, by comparing cryopreserved and fresh tonsil tissue. As expected, phenotypic differences were identified, but to an extent that did not affect the performance of the cryopreserved tissue to generate specific B-cell subset associated gene signatures and assign subset phenotypes to independent tissue samples. Conclusions We have confirmed our working concept and illustrated the usefulness of vital cryopreserved cell suspensions for phenotypic studies of the normal B-cell hierarchy; however, storage procedures need to be delineated by tissue specific comparative analysis. © 2014 Clinical Cytometry Society. Copyright © 2014 Clinical Cytometry Society.

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements.

PubMed

Korsch, Michael; Marten, Silke-Mareike; Dötsch, Andreas; Jáuregui, Ruy; Pieper, Dietmar H; Obst, Ursula

2016-12-01

Cementing dental restorations on implants poses the risk of undetected excess cement. Such cement remnants may favor the development of inflammation in the peri-implant tissue. The effect of excess cement on the bacterial community is not yet known. The aim of this study was to analyze the effect of two different dental cements on the composition of the microbial peri-implant community. In a cohort of 38 patients, samples of the peri-implant tissue were taken with paper points from one implant per patient. In 15 patients, the suprastructure had been cemented with a zinc oxide-eugenol cement (Temp Bond, TB) and in 23 patients with a methacrylate cement (Premier Implant Cement, PIC). The excess cement found as well as suppuration was documented. Subgingival samples of all patients were analyzed for taxonomic composition by means of 16S amplicon sequencing. None of the TB-cemented implants had excess cement or suppuration. In 14 (61%) of the PIC, excess cement was found. Suppuration was detected in 33% of the PIC implants without excess cement and in 100% of the PIC implants with excess cement. The taxonomic analysis of the microbial samples revealed an accumulation of oral pathogens in the PIC patients independent of the presence of excess cement. Significantly fewer oral pathogens occurred in patients with TB compared to patients with PIC. Compared with TB, PIC favors the development of suppuration and the growth of periodontal pathogens. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Monitoring of organochlorine pesticide residue levels in adipose tissue of Veracruz, Mexico inhabitants.

PubMed

Waliszewski, Stefan M; Caba, M; Herrero-Mercado, M; Saldariaga-Noreña, H; Meza, E; Zepeda, R; Martínez-Valenzuela, C; Infanzon, R; Hernández-Chalate, F

2011-11-01

The objective of the present study was to monitor the levels of organochlorine pesticides HCB, α-β-γ-HCH, pp'DDE, op'DDT and pp'DDT in 150 adipose tissue samples of Veracruz, Mexico inhabitants. In analyzed samples, the following pesticides were detected: p,p'-DDE in 100% of the samples at mean 1.643 mg/kg; p,p'-DDT in 99.3.% of the samples at mean 0.227 mg/kg; β-HCH in 97.3% of the samples at mean 0.063 mg/kg; and op'DDT in 93.3% of the samples at mean 0.022 mg/kg. Comparing mean, median and geometric mean concentrations of organochlorine pesticides shows a decrease in values from mean to median and to geometric mean which points out a prevalence of lower concentrations among the total samples and the existence of occasional cases of extreme exposure expressed in range values. The pooled samples divided according to sex, showed only significant differences of pp'DDE median concentrations between sexes. The other organochlorine pesticides indicated no statistical differences between sexes, including the pp'DDE/pp'DDT ratio. The samples grouped according to age, showed that the third tertile was more contaminated for both sexes, indicating age as a positively associated factor with organochlorine pesticide levels in adipose tissue of Veracruz inhabitants. Comparing organochlorine pesticide levels between 2008 and 2010 years, a decreased tendency for β-HCH, pp'DDE, Σ-DDT and pp'DDE/pp'DDT ratio levels was observed.

Water quality, sediment characteristics, aquatic habitat, geomorphology, and mussel population status of the Clinch River, Virginia and Tennessee, 2009-2011

USGS Publications Warehouse

Krstolic, Jennifer L.; Johnson, Gregory C.; Ostby, Brett J.K.

2013-01-01

Chemical, physical, and biological data were collected during 2009-2011 as part of a study of the Clinch River in Virginia and Tennessee. The data from this study, data-collection methods, and laboratory analytical methods used in the study are documented in this report. The study was conducted to describe the conditions of the Clinch River and to determine if there are measurable differences in chemical, physical, or biological characteristics in a segment of the river where freshwater mussel populations are in decline, have low density, richness, little to no recruitment, and lack endangered species (low-quality reach) compared to a segment of the river where mussel assemblages have relatively high density, richness, evidence of recruitment, and support endangered species (high-quality reach). Five continuous water-quality monitors were installed and operated on the mainstem of the Clinch River and two tributaries. Discrete water-quality sample sets were collected during base-flow and stormflow conditions two sites on the Clinch River and on the Guest River, a tributary to the Clinch River predominantly in the Appalachian Plateaus Physiographic Province. Base-flow water-quality samples were collected in July and August 2011 at 15 sites along the mainstem of the Clinch River. Other analyses included longitudinal sampling along the mainstem of the Clinch River at 10 sites to evaluate bed-sediment chemistry, habitat condition, and mollusk community status. In situ freshwater mussel growth and mortality experiments were conducted with hatchery propogated Villosa iris (rainbow mussels). Tissue from the V. iris as well as tissue from 16 Actinonaias pectorosa mussels were analyzed for trace metals, and V. iris mussel tissue was analyzed for organic compounds. Data collected during this investigation were analyzed by various U.S. Geological Survey or U.S. Fish and Wildlife Service laboratories.

Investigation of the efficacy of ultrafast laser in large bowel excision

NASA Astrophysics Data System (ADS)

Mohanan, Syam Mohan P. C.; Beck, Rainer J.; Góra, Wojciech S.; Perry, Sarah L.; Shires, Mike; Jayne, David; Hand, Duncan P.; Shephard, Jonathan D.

2017-02-01

Local resection of early stage tumors in the large bowel via colonoscopy has been a widely accepted surgical modality for colon neoplasm treatment. The conventional electrocautery techniques used for the resection of neoplasia in the mucosal or submucosal layer of colon tissue has been shown to create obvious thermal necrosis to adjacent healthy tissues and lacks accuracy in resection. Ultrafast picosecond (ps) laser ablation using a wavelength of 1030 or 515 nm is a promising surgical tool to overcome the limitations seen with conventional surgical techniques. The purpose of this initial study is to analyze the depth of ablation or the extent of coagulation deployed by the laser as a function of pulse energy and fluence in an ex-vivo porcine model. Precise control of the depth of tissue removal is of paramount importance for bowel surgery where bowel perforation can lead to morbidity or mortality. Thus we investigate the regimes that are optimal for tissue resection and coagulation through plasma mediated ablation of healthy colon tissue. The ablated tissue samples were analyzed by standard histologic methods and a three dimensional optical profilometer technique. We demonstrate that ultrafast laser resection of colonic tissue can minimize the region of collateral thermal damage (<50 μm) with a controlled ablation depth. This surgical modality allows potentially easier removal of early stage lesions and has the capability to provide more control to the surgeon in comparison with a mechanical or electrocautery device.

[Arf6, RalA and BIRC5 protein expression in non small cell lung cancer].

PubMed

Knizhnik, A V; Kovaleva, O B; Laktionov, K K; Mochal'nikova, V V; Komel'kov, A V; Chevkina, E M; Zborovskaia, I B

2011-01-01

Evaluation of tumor markers expression pattern which determines individual progression parameters is one of the major topics in molecular oncopathology research. This work presents research on expression analysis of several Ras-Ral associated signal transduction pathway proteins (Arf6, RalA and BIRC5) in accordance with clinical criteria in non small cell lung cancer patients. Using Western-blot analysis and RT-PCR Arf6, RalA and BIRC5 expression has been analyzed in parallel in 53 non small cell lung cancer samples of different origin. Arf6 protein expression was elevated in 55% non small cell lung cancer tumor samples in comparison with normal tissue. In the group of squamous cell lung cancer Arf6 expression elevation was observed more often. RalA protein expression was decreased in comparison to normal tissue samples in 64% of non small cell lung cancer regardless to morphological structure. Correlation between RalA protein expression decrease and absence of regional metastases was revealed for squamous cell lung cancer. BIRC5 protein expression in tumor samples versus corresponding normal tissue was 1.3 times more often elevated in the squamous cell lung cancer group (in 76% tumor samples). At the same time elevation of BIRC5 expression was fixed only in 63% of adenocarcinoma tumor samples. A statistically significant decrease (p = 0.0158) of RalA protein expression and increase (p = 0.0498) of Arf6 protein expression in comparison with normal tissue was found for T1-2N0M0 and T1-2N1-2M0 groups of squamous cell lung cancer correspondingly.

Investigation of ultrashort-pulsed laser on dental hard tissue

NASA Astrophysics Data System (ADS)

Uchizono, Takeyuki; Awazu, Kunio; Igarashi, Akihiro; Kato, Junji; Hirai, Yoshito

2007-02-01

Ultrashort-pulsed laser (USPL) can ablate various materials with precious less thermal effect. In laser dentistry, to solve the problem that were the generation of crack and carbonized layer by irradiating with conventional laser such as Er:YAG and CO II laser, USPL has been studied to ablate dental hard tissues by several researchers. We investigated the effectiveness of ablation on dental hard tissues by USPL. In this study, Ti:sapphire laser as USPL was used. The laser parameter had the pulse duration of 130 fsec, 800nm wavelength, 1KHz of repetition rate and the average power density of 90~360W/cm2. Bovine root dentin plates and crown enamel plates were irradiated with USPL at 1mm/sec using moving stage. The irradiated samples were analyzed by SEM, EDX, FTIR and roughness meter. In all irradiated samples, the cavity margin and wall were sharp and steep, extremely. In irradiated dentin samples, the surface showed the opened dentin tubules and no smear layer. The Ca/P ratio by EDX measurement and the optical spectrum by FTIR measurement had no change on comparison irradiated samples and non-irradiated samples. These results confirmed that USPL could ablate dental hard tissue, precisely and non-thermally. In addition, the ablation depths of samples were 10μm, 20μm, and 60μm at 90 W/cm2, 180 W/cm2, and 360 W/cm2, approximately. Therefore, ablation depth by USPL depends on the average power density. USPL has the possibility that can control the precision and non-thermal ablation with depth direction by adjusting the irradiated average power density.

Raman fiber-optical method for colon cancer detection: Cross-validation and outlier identification approach

NASA Astrophysics Data System (ADS)

Petersen, D.; Naveed, P.; Ragheb, A.; Niedieker, D.; El-Mashtoly, S. F.; Brechmann, T.; Kötting, C.; Schmiegel, W. H.; Freier, E.; Pox, C.; Gerwert, K.

2017-06-01

Endoscopy plays a major role in early recognition of cancer which is not externally accessible and therewith in increasing the survival rate. Raman spectroscopic fiber-optical approaches can help to decrease the impact on the patient, increase objectivity in tissue characterization, reduce expenses and provide a significant time advantage in endoscopy. In gastroenterology an early recognition of malign and precursor lesions is relevant. Instantaneous and precise differentiation between adenomas as precursor lesions for cancer and hyperplastic polyps on the one hand and between high and low-risk alterations on the other hand is important. Raman fiber-optical measurements of colon biopsy samples taken during colonoscopy were carried out during a clinical study, and samples of adenocarcinoma (22), tubular adenomas (141), hyperplastic polyps (79) and normal tissue (101) from 151 patients were analyzed. This allows us to focus on the bioinformatic analysis and to set stage for Raman endoscopic measurements. Since spectral differences between normal and cancerous biopsy samples are small, special care has to be taken in data analysis. Using a leave-one-patient-out cross-validation scheme, three different outlier identification methods were investigated to decrease the influence of systematic errors, like a residual risk in misplacement of the sample and spectral dilution of marker bands (esp. cancerous tissue) and therewith optimize the experimental design. Furthermore other validations methods like leave-one-sample-out and leave-one-spectrum-out cross-validation schemes were compared with leave-one-patient-out cross-validation. High-risk lesions were differentiated from low-risk lesions with a sensitivity of 79%, specificity of 74% and an accuracy of 77%, cancer and normal tissue with a sensitivity of 79%, specificity of 83% and an accuracy of 81%. Additionally applied outlier identification enabled us to improve the recognition of neoplastic biopsy samples.

Quantification of various growth factors in different demineralized bone matrix preparations.

PubMed

Wildemann, B; Kadow-Romacker, A; Haas, N P; Schmidmaier, G

2007-05-01

Besides autografts, allografts, and synthetic materials, demineralized bone matrix (DBM) is used for bone defect filling and treatment of non-unions. Different DBM formulations are introduced in clinic since years. However, little is known about the presents and quantities of growth factors in DBM. Aim of the present study was the quantification of eight growth factors important for bone healing in three different "off the shelf" DBM formulations, which are already in human use: DBX putty, Grafton DBM putty, and AlloMatrix putty. All three DBM formulations are produced from human donor tissue but they differ in the substitutes added. From each of the three products 10 different lots were analyzed. Protein was extracted from the samples with Guanidine HCL/EDTA method and human ELISA kits were used for growth factor quantification. Differences between the three different products were seen in total protein contend and the absolute growth factor values but also a large variability between the different lots was found. The order of the growth factors, however, is almost comparable between the materials. In the three investigated materials FGF basic and BMP-4 were not detectable in any analyzed sample. BMP-2 revealed the highest concentration extractable from the samples with approximately 3.6 microg/g tissue without a significant difference between the three DBM formulations. In DBX putty significantly more TGF-beta1 and FGFa were measurable compared to the two other DBMs. IGF-I revealed the significantly highest value in the AlloMatrix and PDGF in Grafton. No differences were accessed for VEGF. Due to the differences in the growth factor concentration between the individual samples, independently from the product formulation, further analyzes are required to optimize the clinical outcome of the used demineralized bone matrix. Copyright 2006 Wiley Periodicals, Inc.

Quantitative analysis of in vivo mucosal bacterial biofilms.

PubMed

Singhal, Deepti; Boase, Sam; Field, John; Jardeleza, Camille; Foreman, Andrew; Wormald, Peter-John

2012-01-01

Quantitative assays of mucosal biofilms on ex vivo samples are challenging using the currently applied specialized microscopic techniques to identify them. The COMSTAT2 computer program has been applied to in vitro biofilm models for quantifying biofilm structures seen on confocal scanning laser microscopy (CSLM). The aim of this study was to quantify Staphylococcus aureus (S. aureus) biofilms seen via CSLM on ex situ samples of sinonasal mucosa, using the COMSTAT2 program. S. aureus biofilms were grown in frontal sinuses of 4 merino sheep as per a previously standardized sheep sinusitis model for biofilms. Two sinonasal mucosal samples, 10 mm × 10 mm in size, from each of the 2 sinuses of the 4 sheep were analyzed for biofilm presence with Baclight stain and CSLM. Two random image stacks of mucosa with S. aureus biofilm were recorded from each sample, and analyzed using COMSTAT2 software that translates image stacks into a simplified 3-dimensional matrix of biofilm mass by eliminating surrounding host tissue. Three independent observers analyzed images using COMSTAT2 and 3 repeated rounds of analyses were done to calculate biofilm biomass. The COMSTAT2 application uses an observer-dependent threshold setting to translate CSLM biofilm images into a simplified 3-dimensional output for quantitative analysis. Intraclass correlation coefficient (ICC) between thresholds set by the 3 observers for each image stacks was 0.59 (p = 0.0003). Threshold values set at different points of time by a single observer also showed significant correlation as seen by ICC of 0.80 (p < 0.001). COMSTAT2 can be applied to quantify and study the complex 3-dimensional biofilm structures that are recorded via CSLM on mucosal tissue like the sinonasal mucosa. Copyright © 2011 American Rhinologic Society-American Academy of Otolaryngic Allergy, LLC.

Accounting for tissue heterogeneity in infrared spectroscopic imaging for accurate diagnosis of thyroid carcinoma subtypes.

PubMed

Martinez-Marin, David; Sreedhar, Hari; Varma, Vishal K; Eloy, Catarina; Sobrinho-Simões, Manuel; Kajdacsy-Balla, André; Walsh, Michael J

2017-07-01

Fourier transform infrared (FT-IR) microscopy was used to image tissue samples from twenty patients diagnosed with thyroid carcinoma. The spectral data were then used to differentiate between follicular thyroid carcinoma and follicular variant of papillary thyroid carcinoma using principle component analysis coupled with linear discriminant analysis and a Naïve Bayesian classifier operating on a set of computed spectral metrics. Classification of patients' disease type was accomplished by using average spectra from a wide region containing follicular cells, colloid, and fibrosis; however, classification of disease state at the pixel level was only possible when the extracted spectra were limited to follicular epithelial cells in the samples, excluding the relatively uninformative areas of fibrosis. The results demonstrate the potential of FT-IR microscopy as a tool to assist in the difficult diagnosis of these subtypes of thyroid cancer, and also highlights the importance of selectively and separately analyzing spectral information from different features of a tissue of interest.

Novel Multiplex MethyLight Protocol for Detection of DNA Methylation in Patient Tissues and Bodily Fluids

PubMed Central

Olkhov-Mitsel, Ekaterina; Zdravic, Darko; Kron, Ken; van der Kwast, Theodorus; Fleshner, Neil; Bapat, Bharati

2014-01-01

Aberrant DNA methylation is a hallmark of cancer and is an important potential biomarker. Particularly, combined analysis of a panel of hypermethylated genes shows the most promising clinical performance. Herein, we developed, optimized and standardized a multiplex MethyLight assay to simultaneously detect hypermethylation of APC, HOXD3 and TGFB2 in DNA extracted from prostate cancer (PCa) cell lines, archival tissue specimens, and urine samples. We established that the assay is capable of discriminating between fully methylated and unmethylated alleles with 100% specificity and demonstrated the assay as highly accurate and reproducible as the singleplex approach. For proof of principle, we analyzed the methylation status of these genes in tissue and urine samples of PCa patients as well as PCa-free controls. These data show that the multiplex MethyLight assay offers a significant advantage when working with limited quantities of DNA and has potential applications in research and clinical settings. PMID:24651255

Ex vivo photometric and polarimetric multilayer characterization of human healthy colon by multispectral Mueller imaging.

PubMed

Pierangelo, Angelo; Manhas, Sandeep; Benali, Abdelali; Fallet, Clément; Antonelli, Maria-Rosaria; Novikova, Tatiana; Gayet, Brice; Validire, Pierre; De Martino, Antonello

2012-06-01

Healthy human colon samples were analyzed ex vivo with a multispectral imaging Mueller polarimeter operating from 500 to 700 nm in a backscattering configuration with diffuse light illumination impinging on the innermost tissue layer, the mucosa. The intensity and polarimetric responses were taken on whole tissues first and after progressive exfoliation of the outer layers afterwards. Moreover, these measurements were carried out with two different substrates (one bright and the other dark) successively placed beneath each sample, allowing a reasonably accurate evaluation of the contributions to the overall backscattered light by the various layers. For the shorter investigated wavelengths (500 to 550 nm) the major contribution comes from mucosa and submucosa, while for the longer wavelengths (650 to 700 nm) muscular tissue and fat also contribute significantly. The depolarization has also been studied and is found to be stronger in the red part of the spectrum, mainly due to the highly depolarizing power of the muscular and fat layers.

Bioaccumulation of Cd, Pb and Zn in the edible and inedible tissues of three sturgeon species in the Iranian coastline of the Caspian Sea.

PubMed

Mashroofeh, Abdulreza; Bakhtiari, Alireza Riyahi; Pourkazemi, Mohammad; Rasouli, Sana

2013-01-01

The accumulations of Cd, Pb and Zn were determined in edible and inedible tissues of Persian sturgeon (Acipenser persicus; n=27), stellate sturgeon (Acipenser stellatus; n=5) and beluga (Huso huso; n=4) collected from coastal waters of the South Caspian Sea from March to April 2011. Concentrations of metals evaluated in the caviar, muscle, liver, kidney, gills, ovary and heart of the three species of sturgeons have been assessed using the flame and graphite furnace atomic absorption spectrophotometer. Concentrations of Zn, Pb and Cd in the edible and inedible tissues were apparently different among the three species of sturgeons. Especially, beluga heart showed the highest concentrations of Zn and Pb and Cd in Persian sturgeon liver. The analyzed metals were found in the caviar and muscle samples of Persian sturgeon and likewise muscle samples two other sturgeon species at mean concentrations under the permissible limits proposed by MAFF (2000). Copyright © 2012 Elsevier Ltd. All rights reserved.

Expression of plakophilin 3 in diffuse malignant pleural mesothelioma.

PubMed

Mašić, Silvija; Brčić, Luka; Krušlin, Božo; Šepac, Ana; Pigac, Biserka; Stančić-Rokotov, Dinko; Jakopović, Marko; Seiwerth, Sven

2018-05-03

Diffuse malignant pleural mesothelioma (DMPM) is the most common primary malignant pleural neoplasm still posing major diagnostic, prognostic and therapeutic challenges. Plakophilins are structural proteins considered to be important for cell stability and adhesion in both tumor and normal tissues. Plakophilin 3 is a protein present in desmosomes of stratified and simple epithelia of normal tissues with presence in malignant cells of various tumors where it participates in the process of tumorigenesis. The aim of this study was to investigate the expression of plakophilin 3 protein in DMPM, but also to study its prognostic significance and relation to histologically accessible parameters of aggressive growth. Archival samples of tissue with established diagnosis of DMPM and samples of normal pleural tissue were used. Tumor samples were classified into three histological types of DMPM (epithelioid, sarcomatoid and biphasic). Additional subclassification of epithelioid mesotheliomas into nine patterns based on the prevalent histological component of the tumor was then performed. After immunohistochemical staining, cytoplasmic and membrane immunopositivity of tumor cells was assesed by scoring the intensity of the staining from 0 (no staining) to 4 (very strong staining). Prognostic value and expression of plakophilin 3 with consideration to histologically estimated aggression in tumor growth were then statistically analyzed using non- parametric tests. The results demonstrated higher level of plakophilin 3 expression in tumor samples with histologically more aggressive tumor growth, but no significant prognostic value. According to our study, plakophilin 3 appears to be involved in tumor invasion in malignant mesothelioma.

Extraction of high-quality DNA from ethanol-preserved tropical plant tissues.

PubMed

Bressan, Eduardo A; Rossi, Mônica L; Gerald, Lee T S; Figueira, Antonio

2014-04-24

Proper conservation of plant samples, especially during remote field collection, is essential to assure quality of extracted DNA. Tropical plant species contain considerable amounts of secondary compounds, such as polysaccharides, phenols, and latex, which affect DNA quality during extraction. The suitability of ethanol (96% v/v) as a preservative solution prior to DNA extraction was evaluated using leaves of Jatropha curcas and other tropical species. Total DNA extracted from leaf samples stored in liquid nitrogen or ethanol from J. curcas and other tropical species (Theobroma cacao, Coffea arabica, Ricinus communis, Saccharum spp., and Solanum lycopersicon) was similar in quality, with high-molecular-weight DNA visualized by gel electrophoresis. DNA quality was confirmed by digestion with EcoRI or HindIII and by amplification of the ribosomal gene internal transcribed spacer region. Leaf tissue of J. curcas was analyzed by light and transmission electron microscopy before and after exposure to ethanol. Our results indicate that leaf samples can be successfully preserved in ethanol for long periods (30 days) as a viable method for fixation and conservation of DNA from leaves. The success of this technique is likely due to reduction or inactivation of secondary metabolites that could contaminate or degrade genomic DNA. Tissue conservation in 96% ethanol represents an attractive low-cost alternative to commonly used methods for preservation of samples for DNA extraction. This technique yields DNA of equivalent quality to that obtained from fresh or frozen tissue.

Activation of RAS family genes in urothelial carcinoma.

PubMed

Boulalas, I; Zaravinos, A; Karyotis, I; Delakas, D; Spandidos, D A

2009-05-01

Bladder cancer is the fifth most common malignancy in men in Western society. We determined RAS codon 12 and 13 point mutations and evaluated mRNA expression levels in transitional cell carcinoma cases. Samples from 30 human bladder cancers and 30 normal tissues were analyzed by polymerase chain reaction/restriction fragment length polymorphism and direct sequencing to determine the occurrence of mutations in codons 12 and 13 of RAS family genes. Moreover, we used real-time reverse transcriptase-polymerase chain reaction to evaluate the expression profile of RAS genes in bladder cancer specimens compared to that in adjacent normal tissues. Overall H-RAS mutations in codon 12 were observed in 9 tumor samples (30%). Two of the 9 patients (22%) had invasive bladder cancer and 7 (77%) had noninvasive bladder cancer. One H-RAS mutation (11%) was homozygous and the remaining 89% were heterozygous. All samples were WT for K and N-RAS oncogenes. Moreover, 23 of 30 samples (77%) showed over expression in at least 1 RAS family gene compared to adjacent normal tissue. K and N-RAS had the highest levels of over expression in bladder cancer specimens (50%), whereas 27% of transitional cell carcinomas demonstrated H-RAS over expression relative to paired normal tissues. Our results underline the importance of H-RAS activation in human bladder cancer by codon 12 mutations. Moreover, they provide evidence that increased expression of all 3 RAS genes is a common event in bladder cancer that is associated with disease development.

Extraction of high-quality DNA from ethanol-preserved tropical plant tissues

PubMed Central

2014-01-01

Background Proper conservation of plant samples, especially during remote field collection, is essential to assure quality of extracted DNA. Tropical plant species contain considerable amounts of secondary compounds, such as polysaccharides, phenols, and latex, which affect DNA quality during extraction. The suitability of ethanol (96% v/v) as a preservative solution prior to DNA extraction was evaluated using leaves of Jatropha curcas and other tropical species. Results Total DNA extracted from leaf samples stored in liquid nitrogen or ethanol from J. curcas and other tropical species (Theobroma cacao, Coffea arabica, Ricinus communis, Saccharum spp., and Solanum lycopersicon) was similar in quality, with high-molecular-weight DNA visualized by gel electrophoresis. DNA quality was confirmed by digestion with EcoRI or HindIII and by amplification of the ribosomal gene internal transcribed spacer region. Leaf tissue of J. curcas was analyzed by light and transmission electron microscopy before and after exposure to ethanol. Our results indicate that leaf samples can be successfully preserved in ethanol for long periods (30 days) as a viable method for fixation and conservation of DNA from leaves. The success of this technique is likely due to reduction or inactivation of secondary metabolites that could contaminate or degrade genomic DNA. Conclusions Tissue conservation in 96% ethanol represents an attractive low-cost alternative to commonly used methods for preservation of samples for DNA extraction. This technique yields DNA of equivalent quality to that obtained from fresh or frozen tissue. PMID:24761774

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues.

PubMed

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health.Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper,we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameter scan provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues

NASA Astrophysics Data System (ADS)

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health. Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper, we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameters can provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

LC-MS/MS quantification of free and Fab-bound colchicine in plasma, urine and organs following colchicine administration and colchicine-specific Fab fragments treatment in Göttingen minipigs.

PubMed

Fabresse, Nicolas; Allard, Julien; Sardaby, Marine; Thompson, Adrian; Clutton, R Eddie; Eddleston, Michael; Alvarez, Jean-Claude

2017-08-15

Clinical evaluation of a colchicine specific antigen-binding fragment (Fab) in order to treat colchicine poisoning required the development of an accurate method allowing quantification of free and Fab-bound colchicine in plasma and urine, and free colchicine in tissues, to measure colchicine redistribution after Fab administration. Three methods have been developed for this purpose, and validated in plasma, urine and liver: total colchicine was determined after denaturation of Fab by dilution in water and heating; free colchicine was separated from Fab-bound colchicine by filtration with 30KDa micro-filters; tissues were homogenized in a tissue mixer. Deuterated colchicine was used as internal standard. Samples were extracted by liquid-liquid extraction and analyzed with a LC-MS/MS. LOQ were 0.5ng/mL in plasma and urine for free and total colchicine and 5pg/mg in tissues. The methods were linear in the 0.5-100ng/mL range in plasma and urine, and 5-300pg/mg in tissues with determination coefficients>0.99. Precision and accuracy of QC samples presented a CV<9.4%. The methods require only 200μL of sample and allow a high throughput due to short analytical run (2min). These methods were successfully applied to a pig intoxicated with colchicine and treated with colchicine specific Fab fragments. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative analysis of drug distribution by ambient mass spectrometry imaging method with signal extinction normalization strategy and inkjet-printing technology.

PubMed

Luo, Zhigang; He, Jingjing; He, Jiuming; Huang, Lan; Song, Xiaowei; Li, Xin; Abliz, Zeper

2018-03-01

Quantitative mass spectrometry imaging (MSI) is a robust approach that provides both quantitative and spatial information for drug candidates' research. However, because of complicated signal suppression and interference, acquiring accurate quantitative information from MSI data remains a challenge, especially for whole-body tissue sample. Ambient MSI techniques using spray-based ionization appear to be ideal for pharmaceutical quantitative MSI analysis. However, it is more challenging, as it involves almost no sample preparation and is more susceptible to ion suppression/enhancement. Herein, based on our developed air flow-assisted desorption electrospray ionization (AFADESI)-MSI technology, an ambient quantitative MSI method was introduced by integrating inkjet-printing technology with normalization of the signal extinction coefficient (SEC) using the target compound itself. The method utilized a single calibration curve to quantify multiple tissue types. Basic blue 7 and an antitumor drug candidate (S-(+)-deoxytylophorinidine, CAT) were chosen to initially validate the feasibility and reliability of the quantitative MSI method. Rat tissue sections (heart, kidney, and brain) administered with CAT was then analyzed. The quantitative MSI analysis results were cross-validated by LC-MS/MS analysis data of the same tissues. The consistency suggests that the approach is able to fast obtain the quantitative MSI data without introducing interference into the in-situ environment of the tissue sample, and is potential to provide a high-throughput, economical and reliable approach for drug discovery and development. Copyright © 2017 Elsevier B.V. All rights reserved.

Tomographic reconstruction of melanin structures of optical coherence tomography via the finite-difference time-domain simulation

NASA Astrophysics Data System (ADS)

Huang, Shi-Hao; Wang, Shiang-Jiu; Tseng, Snow H.

2015-03-01

Optical coherence tomography (OCT) provides high resolution, cross-sectional image of internal microstructure of biological tissue. We use the Finite-Difference Time-Domain method (FDTD) to analyze the data acquired by OCT, which can help us reconstruct the refractive index of the biological tissue. We calculate the refractive index tomography and try to match the simulation with the data acquired by OCT. Specifically, we try to reconstruct the structure of melanin, which has complex refractive indices and is the key component of human pigment system. The results indicate that better reconstruction can be achieved for homogenous sample, whereas the reconstruction is degraded for samples with fine structure or with complex interface. Simulation reconstruction shows structures of the Melanin that may be useful for biomedical optics applications.

Accumulation profiles of parabens and their metabolites in fish, black bear, and birds, including bald eagles and albatrosses.

PubMed

Xue, Jingchuan; Kannan, Kurunthachalam

2016-09-01

Although several studies have reported the ubiquitous occurrence of parabens in human specimens and the environment, little is known about the accumulation of these estrogenic chemicals in fish and birds. In this study, accumulation profiles of six parabens and their metabolites were determined in 254 tissue (including liver, kidney, egg, and plasma) samples from 12 species of fish and seven species of birds collected from inland, coastal, and remote aquatic ecosystems. In addition, liver and kidney tissues from black bears were analyzed. Methyl paraben (MeP) was found in a majority of the tissues, with the highest concentration (796ng/g (wet weight [wet wt])) found in the liver of a bald eagle from Michigan. 4-Hydroxy benzoate (HB) was the major metabolite, found in 91% of the tissue samples analyzed at concentrations as high as 68,600ng/g, wet wt, which was found in the liver of a white-tailed sea eagle from the Baltic Sea coast. The accumulation pattern of MeP and 4-HB varied, depending on the species. The mean concentrations of MeP measured in fishes from Michigan, New York, and Florida waters were <2.01 (fillet), 152 (liver), and 32.0 (liver) ng/g, wet wt, respectively, and the corresponding 4-HB concentrations were 39.5, 10,500, and 642ng/g, wet wt. The mean hepatic and renal concentrations of 4-HB in black bears were 1,720 and 1,330ng/g, wet wt, respectively. The concentrations of MeP and 4-HB were significantly positively correlated with each other in various tissues and species, which suggested a common source of exposure to these compounds in fish and birds. Trace concentrations of MeP and 4-HB also were found in the tissues of albatrosses from Midway Atoll, Northwestern Pacific Ocean, which suggested widespread distribution of these compounds in the marine environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Efficacy of low-level laser therapy on scar tissue.

PubMed

Freitas, Carla P; Melo, Cristina; Alexandrino, Ana M; Noites, Andreia

2013-06-01

Physiotherapy has a very important role in the maintenance of the integumentary system integrity. There is very few evidence in humans. Nevertheless, there are some studies about tissue regeneration using low-level laser therapy (LLLT). To analyze the effectiveness of LLLT on scar tissue. Seventeen volunteers were stratified by age of their scars, and then randomly assigned to an experimental group (EG) - n = 9 - and a placebo group (PG) - n = 8. Fifteen sessions were conducted to both the groups thrice a week. However, in the PG, the laser device was switched off. Scars' thickness, length, width, macroscopic aspect, pain threshold, pain perception, and itching were measured. After 5 weeks, there were no statistically significant differences in any variable between both the groups. However, analyzing independently each group, EG showed a significant improvement in macroscopic aspect (p = 0.003) using LLLT. Taking into account the scars' age, LLLT showed a tendency to decrease older scars' thickness in EG. The intervention with LLLT appears to have a positive effect on the macroscopic scars' appearance, and on old scars' thickness, in the studied sample. However, it cannot be said for sure that LLLT has influence on scar tissue.

Dead in the water--are we killing the hospital autopsy with poor consent practices?

PubMed

Henry, Jaimie; Nicholas, Nick

2012-07-01

It is now a recognized fact that the practice of conducting a consent (or hospital) post-mortem examination is in decline. There have been many reasons put forth to explain this demise, but the quality of the consenting process is frequently cited as having a high impact. This article focuses on consent practices for post-mortem examinations in England and Wales, and considers if our consent techniques are adversely affecting post-mortem examination uptake. We examine the regulatory compliance of trusts with their statutory obligations by analyzing the Human Tissue Authority's compliance and inspection reports. We further analyze 21 publicly available NHS Trust policies on post-mortem examination consent procedures, and consider whether these are fit for the purpose of meeting the dual needs of clinicians and the bereaved. Despite more Human Tissue Authority inspections, there is a disproportionate rise in enforcement actions, with up to 48% of sampled Trusts exhibiting shortcomings in their legal duties. Additionally, only 52.4% of sampled trusts follow the Human Tissue Authority best-practice model, with 23.8% having no documented procedures. Despite the well founded evidence base for best-practice models, consent practices for post-mortem examinations remains poor and is likely to have a gross adverse effect on the rate of post-mortem examinations. We recommend that NHS Trusts rigorously review their protocols and introduce a team-approach between clinicians and trained bereavement staff in core-consent teams, as the Human Tissue Authority suggests, whilst at the same time placing a strong emphasis on education for junior and senior colleagues alike.

The challenge of on-tissue digestion for MALDI MSI- a comparison of different protocols to improve imaging experiments.

PubMed

Diehl, Hanna C; Beine, Birte; Elm, Julian; Trede, Dennis; Ahrens, Maike; Eisenacher, Martin; Marcus, Katrin; Meyer, Helmut E; Henkel, Corinna

2015-03-01

Mass spectrometry imaging (MSI) has become a powerful and successful tool in the context of biomarker detection especially in recent years. This emerging technique is based on the combination of histological information of a tissue and its corresponding spatial resolved mass spectrometric information. The identification of differentially expressed protein peaks between samples is still the method's bottleneck. Therefore, peptide MSI compared to protein MSI is closer to the final goal of identification since peptides are easier to measure than proteins. Nevertheless, the processing of peptide imaging samples is challenging due to experimental complexity. To address this issue, a method development study for peptide MSI using cryoconserved and formalin-fixed paraffin-embedded (FFPE) rat brain tissue is provided. Different digestion times, matrices, and proteases were tested to define an optimal workflow for peptide MSI. All practical experiments were done in triplicates and analyzed by the SCiLS Lab software, using structures derived from myelin basic protein (MBP) peaks, principal component analysis (PCA) and probabilistic latent semantic analysis (pLSA) to rate the experiments' quality. Blinded experimental evaluation in case of defining countable structures in the datasets was performed by three individuals. Such an extensive method development for peptide matrix-assisted laser desorption/ionization (MALDI) imaging experiments has not been performed so far, and the resulting problems and consequences were analyzed and discussed.

Clinical Implications of Promoter Hypermethylation in RASSF1A and MGMT in Retinoblastoma1

PubMed Central

Choy, Kwong Wai; Lee, Tom C; Cheung, Kin Fai; Fan, Dorothy S P; Lo, Kwok Wai; Beaverson, Katherine L; Abramson, David H; Lam, Dennis S C; Yu, Christopher B O; Pang, Chi Pui

2005-01-01

Abstract We investigated the epigenetic silencing and genetic changes of the RAS-associated domain family 1A (RASSF1A) gene and the O6-methylguanine-DNA methyltransferase (MGMT) gene in retinoblastoma. We extracted DNA from microdissected tumor and normal retina tissues of the same patient in 68 retinoblastoma cases. Promoter methylation in RASSF1A and MGMT was analyzed by methylation-specific PCR, RASSF1A sequence alterations in all coding exons by direct DNA sequencing, and RASSF1A expression by RT-PCR. Cell cycle staging was analyzed by flow cytometry. We detected RASSF1A promoter hypermethylation in 82% of retinoblastoma, in tumor tissues only but not in adjacent normal retinal tissue cells. There was no expression of RASSF1A transcripts in all hypermethylated samples, but RASSF1A transcripts were restored after 5-aza-2′-deoxycytidine treatment with no changes in cell cycle or apoptosis. No mutation in the RASSF1A sequence was found. MGMT hypermethylation was present in 15% of theretinoblastoma samples, and the absence of MGMT hypermethylation was associated (P = .002) with retinoblastoma at advanced Reese-Ellsworth tumor stage. Our results revealed a high RASSF1A hypermethylation frequency in retinoblastoma. The correlation of MGMT inactivation by promoter hypermethylation with lower-stage diseases indicated that MGMT hypermethylation provides useful prognostic information. Epigenetic mechanism plays an important role in the progression of retinoblastoma. PMID:15799820

Determination of malachite green residues in the eggs, fry, and adult muscle-tissue of rainbow-trout (Oncorhynchus-mykiss)

USGS Publications Warehouse

Allen, John L.; Gofus, J.E.; Meinertz, Jeffery R.

1994-01-01

Malachite green, an effective antifungal therapeutant used in fish culture, is a known teratogen. We developed a method to simultaneously detect both the chromatic and leuco forms of malachite green residues in the eggs, fry, and adult muscle tissue of rainbow trout (oncorhynchus mykiss). Homogenates of these tissues were fortified with [c-14] malachite green chloride and extracted with 1% (v/v) acetic acid in acetonitrile or in methanol. The extracts were partitioned with chloroform, dried, redissolved in mobile phase, and analyzed by liquid chromatography (lc) with postcolumn oxidation of leuco malachite green to the chromatic form. Lc fractions were collected every 30 s for quantitation by scintillation counting. Recoveries of total [c-14] malachite green chloride residue were 85 and 98% in eggs fortified with labeled malachite green at concentrations of 0.5 And 1.00 Mug/g, respectively; 68% in fry similarly fortified at a concentration of 0.65 Mug/g; and 66% in muscle homogenate similarly fortified at a level of 1.00 Mug/g. The method was tested under operational conditions by exposing adult rainbow trout to 1.00 Mg/l [c-14] malachite green chloride bath for 1 h. Muscle samples analyzed by sample oxidation and scintillation counting contained 1.3 And 0.5 Mug/g total malachite green chloride residues immediately after exposure and after a 5-day withdrawal period, respectively.

Effect of lipid extraction on analyses of stable carbon and stable nitrogen isotopes in coastal organisms of the Aleutian archipelago

USGS Publications Warehouse

Ricca, M.A.; Miles, A.K.; Anthony, R.G.; Deng, X.; Hung, S.S.O.

2007-01-01

We tested whether extracting lipids reduced confounding variation in ??13C and ??15N values by analyzing paired lipid-extracted (LE) and non-lipid-extracted (NLE) samples of bald eagle (Haliaeetus leucocephalus (L., 1766)) whole eggs, muscle tissue from nine seabird and one terrestrial bird species, muscle tissue from four marine fish species, and blue mussels (Mytilus edulis L., 1758) collected from the Aleutian archipelago, Alaska. Lipid extraction significantly increased ??13C by an average of 2.0??? in whole eggs, 0.8??? in avian muscle, 0.2??? in fish muscle, and 0.6??? in blue mussels. Lower ??13C values in NLE samples covaried positively with lipid content across all sample types. Lower ??13C values in NLE samples were not correlated with lipid content within bald eagle eggs and blue mussels, but covaried positively with percent lipid in avian and fish muscles. Neither lipid extraction nor percent lipid significantly changed ??15N values for any sample type. Lower ??13C values in most NLE avian and fish muscle tissues should not confound interpretation of pelagic versus nearshore sources of primary production, but lipid extraction may be necessary when highly precise estimates of ??13C are needed. Lipid extraction may not be necessary when only ??15N is of interest. ?? 2007 NRC.

Water-quality assessment of part of the upper Mississippi River basin, Minnesota and Wisconsin: Design and implementation of water-quality studies, 1995-98

USGS Publications Warehouse

Stark, James R.; Fallon, J.D.; Fong, A.L.; Goldstein, R.M.; Hanson, P.E.; Kroening, S.E.; Lee, K.E.

1999-01-01

This report describes the design, site-selection, and implementation of the study. Methods used to collect, process, and analyze samples; characterize sites; and assess habitat are described. A comprehensive list of sample sites is provided. Sample analyses for water-quality studies included chlorophyll a, major inorganic constituents, nutrients, trace elements, tritium, radon, environmental isotopes, organic carbon, pesticides, volatile organic compounds, and other synthetic and naturallyoccurring organic compounds. Aquatic-biological samples included fish, benthic macroinvertebrates, and algal enumeration and identification, as well as synthetic-organic compounds and trace elements in fish tissue.

Excessive radiofrequency application: effects on capsular tissue in an animal model.

PubMed

Wolf, Brian R; Heiner, Anneliese D; Albright, John P; Nepola, James V

2005-01-01

Capsular attenuation has been seen after thermal capsulorrhaphy surgery. The purpose of this study was to evaluate the mechanical, histologic, and morphologic effects on capsular tissue after cumulative applications of radiofrequency energy. Ovine patellofemoral capsular tissue was treated with 1, 2, 4, or 8 applications of bipolar radiofrequency energy and then analyzed. No acute capsular ablation or destruction was seen grossly, even in the 8-application group. No definitive visual clues that excessive radiofrequency energy had been applied were seen. There was significant shrinkage and loss of tensile stiffness for all thermal application groups. Given the small sample sizes, post-application failure load, percent relaxation, and stiffness were not observed to be significantly different among the groups. Cumulative applications produced minimal further tissue shrinkage but were accompanied by larger, though not statistically significant, mechanical property losses and increased depth of tissue penetration. These findings suggest that there is no benefit to repeated applications of radiofrequency energy to capsular tissue.

VARIATIONS IN CARBOHYDRATE-PHOSPHORUS EXCHANGE IN MUSCLE TISSUE INDUCED BY $gamma$-IRRADIATION (in Russian)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silaev, M.P.

1962-01-01

Normal female rabbits, 2.5 to 3.0 kilograms in weight, were given a Co/ sup 60/ gamma dose of 800 r. Tissue samples of the Musculus longissimus dorsi were analyzed for glycogen content by the anthranone method, for monosacharrides, inorganic phosphate, adenosine phosphate, and lactic acid. The maximum drop in glycogen content was found to occur 24 hours after the irradiation. A whole-body dose of 800 r resulted in a significant drop in total carbohydrate content (both monosacharride content and glycogen content). The content of adenosinephosphate remained essentially unchanged. Irradiated muscle tissue, stored at --5 to +3 deg C decomposed moremore » rapidly than normal tissue. The content of glycogen was lower, and the free phosphate content was higher than in normal tissue. The adenosinephosphate decomposed more readily in the irradiated tissue. These differences in autolytic processes may be due to shifts in fermentative activity as a result of irradiation. (TTT).« less

Tryptophan as key biomarker to detect gastrointestinal tract cancer using non-negative biochemical analysis of native fluorescence and Stokes Shift spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Leana; Zhou, Yan; Liu, Cheng-hui; Zhou, Lixin; He, Yong; Pu, Yang; Nguyen, Thien An; Alfano, Robert R.

2015-03-01

The objective of this study was to find out the emission spectral fingerprints for discrimination of human colorectal and gastric cancer from normal tissue in vitro by applying native fluorescence. The native fluorescence (NFL) and Stokes shift spectra of seventy-two human cancerous and normal colorectal (colon, rectum) and gastric tissues were analyzed using three selected excitation wavelengths (e.g. 300 nm, 320 nm and 340 nm). Three distinct biomarkers, tryptophan, collagen and reduced nicotinamide adenine dinucleotide hydrate (NADH), were found in the samples of cancerous and normal tissues from eighteen subjects. The spectral profiles of tryptophan exhibited a sharp peak in cancerous colon tissues under a 300 nm excitation when compared with normal tissues. The changes in compositions of tryptophan, collagen, and NADH were found between colon cancer and normal tissues under an excitation of 300 nm by the non-negative basic biochemical component analysis (BBCA) model.

Evaluating differential nuclear DNA yield rates and osteocyte numbers among human bone tissue types: A synchrotron radiation micro-CT approach.

PubMed

Andronowski, Janna M; Mundorff, Amy Z; Pratt, Isaac V; Davoren, Jon M; Cooper, David M L

2017-05-01

Molecular human identification has conventionally focused on DNA sampling from dense, weight-bearing cortical bone tissue, typically from femora or tibiae. A comparison of skeletal elements from three contemporary individuals demonstrated that elements with high quantities of cancellous bone yielded nuclear DNA at the highest rates, suggesting that preferentially sampling cortical bone may be suboptimal (Mundorff & Davoren, 2014). Despite these findings, the reason for the differential DNA yields between cortical and cancellous bone tissues remains unknown. The primary goal of this work is to ascertain whether differences in bone microstructure can be used to explain differential nuclear DNA yield among bone tissue types observed by Mundorff and Davoren (2014), with a focus on osteocytes and the three-dimensional (3D) quantification of their associated lacunae. Osteocytes and other bone cells are recognized to house DNA in bone tissue, thus examining the density of their lacunae may explain why nuclear DNA yield rates differ among bone tissue types. Lacunae were visualized and quantified using synchrotron radiation-based micro-Computed Tomographic imaging (SR micro-CT). Volumes of interest (VOIs) from cortical and cancellous bone tissues (n=129) were comparatively analyzed from the three skeletons sampled for Mundorff and Davoren's (2014) study. Analyses tested the primary hypothesis that the abundance and density of osteocytes (inferred from their lacunar spaces) vary between cortical and cancellous bone tissue types. Results demonstrated that osteocyte lacunar abundance and density vary between cortical and cancellous bone tissue types, with cortical bone VOIs containing a higher lacunar abundance and density. We found that the osteocyte lacunar density values are independent of nuclear DNA yield, suggesting an alternative explanation for the higher nuclear DNA yields from bones with greater quantities of cancellous bone tissue. The use of SR micro-CT allowed for a scale of analysis that revealed a high range of variation in lacunar abundance in both tissue types. Moreover, high-resolution SR micro-CT imaging revealed potential soft tissue remnants within marrow spaces not visible macroscopically. It is hypothesized that soft tissue remnants observed among the trabeculae of skeletal elements with high quantities of cancellous bone tissue are responsible for the high nuclear DNA yields. These findings have significant implications for bone-sample selection for nuclear DNA analysis in a forensic context when skeletal remains are recovered from the ground surface. Copyright © 2017 Elsevier B.V. All rights reserved.

Water Quality, Fish Tissue, and Bed Sediment Monitoring in Waterbodies of Fort Chaffee Maneuver Training Center, Arkansas, 2002-2004

USGS Publications Warehouse

Justus, B.G.; Stanton, Gregory P.

2005-01-01

The Fort Chaffee Maneuver Training Center is a facility used to train as many as 50,000 Arkansas National Guardsmen each year. Due to the nature of ongoing training and also to a poor understanding of environmental procedures that were practiced in the World War II era, areas within Fort Chaffee have the potential to be sources of a large number of contaminants. Because some streams flow on to Fort Chaffee, there is also the potential for sources that are off post to affect environmental conditions on post. This study evaluates constituent concentrations in water, fish tissue, and bed sediment collected from waterbodies on Fort Chaffee between September 2002 and July 2004. Constituent concentrations detected in the three media and measured at nine stream sites and four lake sites were compared to national and regional criteria when available. Two of the larger streams, Big and Vache Grasse Creeks, were sampled at multiple sites. All three sampled media were analyzed for insecticides, PCBs, explosives, and trace elements. Additionally, water samples were analyzed for nutrients and herbicides. The different constituents detected in the three sample media (water, fish tissue, and bed sediment) indicate that land-use activities both on and off post are influencing environmental conditions. Contaminants such as explosives that were sometimes detected in water samples have an obvious relation to military training; however, the occurrence and locations of some nutrients, insecticides, and trace elements suggest that land use both on and off post also could be influencing environmental conditions to some degree. Constituent concentrations at sites on Vache Grasse Creek, and particularly the most upstream site, which was located immediately downstream from an off-post wastewater-treatment facility, indicate that environmental conditions were being influenced by an off-post source. The most upstream site on Vache Grasse Creek had both the highest number of detections and the highest concentrations detected of all sites sampled. Event-mean storm concentrations and storm loads calculated from storm-flow samples at two sites each for Big and Vache Grasse Creeks indicate that storm loads were highest at the two Vache Grasse Creek sites for 24 of the 25 constituents detected. Further evaluation by normalizing storm loads at Big Creek to storm loads at Vache Grasse Creek by stream flow indicate that event loads at Vache Grasse Creek were about two or more times higher than those on Big Creek for 15 of the 25 constituents measured. Low concentrations of arsenic and lead were detected in water samples, but all detections for the two trace elements occurred in samples collected at the upstream site on Vache Grasse Creek. The nickel concentration in fish livers collected from the upstream site on Vache Grasse Creek was 45 percent higher than the median of a national study of 145 sites. Mercury concentrations in edible fish tissue, which are a widespread concern in the United States, exceeded an USEPA criterion for methylmercury of 300 ?g/kg in four of nine samples; however, concentrations are typical of mercury concentrations in fish tissues for the State of Arkansas. Constituent concentrations at some sites indicate that environmental conditions are being influenced by on-post activities. Of the 55 (excluding total organic carbon) organic constituents analyzed in water samples, only 10 were detected above the minimum detection limit but four of those were explosives. Bed-sediment samples from one site located on Grayson Creek, and nearest the administrative and residential (cantonment) area, had detections for arsenic, copper, lead, manganese, nickel, and zinc that were above background concentrations, and concentrations for arsenic and nickel at this site exceeded lowest effect level criteria established by the U.S. Environmental Protection Agency. The site on Grayson Creek also had the only detections of DDT metabolites in bed sedi

In vivo endoscopic OCT imaging of precancer and cancer states of human mucosa

NASA Astrophysics Data System (ADS)

Sergeev, Alexander M.; Gelikonov, V. M.; Gelikonov, G. V.; Feldchtein, Felix I.; Kuranov, R. V.; Gladkova, N. D.; Shakhova, N. M.; Snopova, L. B.; Shakhov, A. V.; Kuznetzova, I. A.; Denisenko, A. N.; Pochinko, V. V.; Chumakov, Yu P.; Streltzova, O. S.

1997-12-01

First results of endoscopic applications of optical coherence tomography for in vivo studies of human mucosa in respiratory, gastrointestinal, urinary and genital tracts are presented. A novel endoscopic OCT (EOCT) system has been created that is based on the integration of a sampling arm of an all-optical-fiber interferometer into standard endoscopic devices using their biopsy channel to transmit low-coherence radiation to investigated tissue. We have studied mucous membranes of esophagus, larynx, stomach, urinary bladder, uterine cervix and body as typical localization for carcinomatous processes. Images of tumor tissues versus healthy tissues have been recorded and analyzed. Violations of well-defined stratified healthy mucosa structure in cancered tissue are distinctly seen by EOCT, thus making this technique promising for early diagnosis of tumors and precise guiding of excisional biopsy.

Integrated endoscopic OCT system and in-vivo images of human internal organs

NASA Astrophysics Data System (ADS)

Sergeev, Alexander M.; Gelikonov, Valentin M.; Gelikonov, Grigory V.; Feldchtein, Felix I.; Kuranov, Roman V.; Gladkova, Natalia D.; Shakhova, Natalia M.; Snopova, Ludmila; Shakhov, Andrei; Kuznetzova, Irina N.; Denisenko, Arkady; Pochinko, Vitaly; Chumakov, Yuri; Almasov, Valentin

1998-04-01

First results of endoscopic applications of optical coherence tomography (OCT) for in vivo studies of human mucosa in respiratory, gastrointestinal, urinary and genital tracts are presented. A novel endoscopic OCT (EOCT) system has been created that is based on the integration of a sampling arm of an all-optical-fiber interferometer into standard endoscopic devices using their biopsy channel to transmit low-coherence radiation to investigated tissue. We have studied mucous membranes of esophagus, larynx, stomach, urinary bladder, uterine cervix and endometrium as typical localization for carcinomatous processes. Images of tumor tissues versus healthy tissues have been recorded and analyzed. Violations of well-defined stratified healthy mucosa structure in cancered tissue is distinctly seen by EOCT, thus making this technique promising for early diagnosis of tumors and precise guiding of excisional biopsy.

Maintenance of head and neck tumor on-chip: gateway to personalized treatment?

PubMed Central

Bower, Ruth; Green, Victoria L; Kuvshinova, Elena; Kuvshinov, Dmitriy; Karsai, Laszlo; Crank, Stephen T; Stafford, Nicholas D; Greenman, John

2017-01-01

Aim: Head and neck squamous cell carcinomas (HNSCC) are solid tumors with low overall survival (40–60%). In a move toward personalized medicine, maintenance of tumor biopsies in microfluidic tissue culture devices is being developed. Methodology/results: HNSCC (n = 15) was dissected (5–10 mg) and either analyzed immediately or cultured in a microfluidic device (37°C) for 48 h. No difference was observed in morphology between pre- and postculture specimens. Dissociated samples were analyzed using trypan blue exclusion (viability), propidium iodide flow cytometry (death) and MTS assay (proliferation) with no significant difference observed highlighting tissue maintenance. Computational fluid dynamics showed laminar flow within the system. Conclusion: The microfluidic culture system successfully maintained HNSCC for 48 h, the culture system will allow testing of different treatment modalities with response monitoring. PMID:28670466

Time trend tendency (1988-2014 years) of organochlorine pesticide levels in the adipose tissue of Veracruz inhabitants.

PubMed

Calderón-Garcidueñas, Ana Laura; Waliszewski, Stefan M; Ruiz-Ramos, Rubén; Del Carmen Martinez-Valenzuela, María

2018-03-10

The population that lives in areas where organochlorine pesticides were spread in the past is still exposed to them through contaminated food, particulate matter, and vapors. Due to their lipophilic properties and resistance to metabolic reactions, they accumulate in tissues and fluids rich in lipids. The aim of the study was to monitor the concentrations of organochlorine pesticides in forensic adipose tissue samples of adult inhabitants of Veracruz City, Mexico, and compare their time trend levels from 1988 to 2014. During the study, hexachlorobenzene (HCB); lindane; β-hexachorocyclohexane; p,p'-dichlorodiphenyldichloroethylene (pp'DDE); p,p'-dichlorodiphenyldichloroethane (p,p'-DDT); and o,p'-dichlorodiphenyldichloroethane (o,p'-DDT) were determined. Our survey was divided into two periods: first, from the years 1988 to 1999, during which DDT was allowed to fight malaria and dengue vectors and the second from the years 2001 to 2014, after the DDT ban. A total of 1435 samples were analyzed. There were substantial differences in the forecasted time trend values of p,p'-DDE and p,p'-DDT in human adipose tissue samples in the two different periods. During the first period, p,p'-DDE decrease time trend was 1.198 mg/kg on lipid base per year; for the second one, decrease was 0.128 mg/kg on lipid base per year. p,p'-DDT decreased 0.507 mg/kg on lipid base during the first period and 0.039 mg/kg on lipid base for the second. The different concentrations may be explained by the cessation of fresh exposure after the first period and a more equilibrated decontamination tendency during the second period. This model was useful to show the decrease in the concentration of pesticides in human adipose tissue samples.

Secretory leukocyte protease inhibitor expression and high-risk HPV infection in anal lesions of HIV positive patients

PubMed Central

NUOVO, Gerard J.; GRINSZTEJN, Beatriz; FRIEDMAN, Ruth K.; VELOSO, Valdiléa G.; CUNHA, Cynthia B.; COUTINHO, José R.; VIANNA-ANDRADE, Cecilia; OLIVEIRA, Nathalia S.; WOODHAM, Andrew W.; DA SILVA, Diane M.; KAST, W. Martin

2016-01-01

Objective The aim of the current study was to evaluate secretory leukocyte protease inhibitor (SLPI) expression in anal biopsies from HIV-positive (HIV+) individuals, and compare that to anal intraepithelial neoplasia (AIN) diagnoses and human papillomavirus (HPV) status. Design This is a cross-sectional study of a cohort of 54 HIV+ (31 males and 23 females) from an AIDS clinic in Rio de Janeiro, Brazil. Methods The study material consisted of anorectal tissue biopsies obtained from HIV+ subjects, which were used to construct tissue microarray paraffin blocks for immunohistochemical analysis of SLPI expression. Biopsies were evaluated by an expert pathologist and classified as low-grade anal intraepithelial neoplasia (AIN1), high-grade anal intraepithelial neoplasia (AIN2/3), or normal squamous epithelium. Additionally, DNA from the biopsies was extracted and analyzed for the presence of low- or high-risk HPV DNA. Results Histologically normal squamous epithelium from the anorectal region showed strong positive SLPI staining in 17/20 (85%) samples. In comparison, 9/17 (53%) dysplastic squamous epithelial samples from AIN1 patients showed strong SLPI staining, and only 5/17 (29%) samples from AIN2-3 patients exhibited strong SPLI staining, which both were significantly fewer than those from normal tissue (p=0.005). Furthermore, there was a significantly higher proportion of samples in which oncogenic high-risk HPV genotypes were detected in low SLPI expressing tissues than that in tissues with high SLPI expression (p=0.040). Conclusion Taken together these results suggest that low SLPI expression is associated with high-risk HPV infections in the development of AIN. PMID:27149102

Chromatographic analysis of tryptophan metabolites

PubMed Central

Sadok, Ilona; Gamian, Andrzej

2017-01-01

The kynurenine pathway generates multiple tryptophan metabolites called collectively kynurenines and leads to formation of the enzyme cofactor nicotinamide adenine dinucleotide. The first step in this pathway is tryptophan degradation, initiated by the rate‐limiting enzymes indoleamine 2,3‐dioxygenase, or tryptophan 2,3‐dioxygenase, depending on the tissue. The balanced kynurenine metabolism, which has been a subject of multiple studies in last decades, plays an important role in several physiological and pathological conditions such as infections, autoimmunity, neurological disorders, cancer, cataracts, as well as pregnancy. Understanding the regulation of tryptophan depletion provide novel diagnostic and treatment opportunities, however it requires reliable methods for quantification of kynurenines in biological samples with complex composition (body fluids, tissues, or cells). Trace concentrations, interference of sample components, and instability of some tryptophan metabolites need to be addressed using analytical methods. The novel separation approaches and optimized extraction protocols help to overcome difficulties in analyzing kynurenines within the complex tissue material. Recent developments in chromatography coupled with mass spectrometry provide new opportunity for quantification of tryptophan and its degradation products in various biological samples. In this review, we present current accomplishments in the chromatographic methodologies proposed for detection of tryptophan metabolites and provide a guide for choosing the optimal approach. PMID:28590049

Analysis of Apoptosis in Ultraviolet-Induced Sea Cucumber (Stichopus japonicus) Melting Using Terminal Deoxynucleotidyl-Transferase-Mediated dUTP Nick End-Labeling Assay and Cleaved Caspase-3 Immunohistochemistry.

PubMed

Yang, Jing-Feng; Gao, Rong-Chun; Wu, Hai-Tao; Li, Peng-Fei; Hu, Xian-Shu; Zhou, Da-Yong; Zhu, Bei-Wei; Su, Yi-Cheng

2015-11-04

The sea cucumber body wall melting phenomenon occurs under certain circumstances, and the mechanism of this phenomenon remains unclear. This study investigated the apoptosis in the ultraviolet (UV)-induced sea cucumber melting phenomenon. Fresh sea cucumbers (Stichopus japonicus) were exposed to UV radiation for half an hour at an intensity of 0.056 mW/cm(2) and then held at room temperature for melting development. The samples were histologically processed into formalin-fixed paraffin-embedded tissues. The apoptosis of samples was analyzed with the terminal deoxynucleotidyl-transferase-mediated dUTP nick end-labeling (TUNEL) assay and cleaved caspase-3 immunohistochemistry. The emergence of TUNEL-positive cells speeds up between 0.5 and 2 h after UV irradiation. Cleaved caspase-3 positive cells were obviously detected in sample tissues immediately after the UV irradiation. These results demonstrated that sea cucumber melting induced by UV irradiation was triggered by the activation of caspase-3 followed by DNA fragmentation in sea cucumber tissue, which was attributed to apoptosis but was not a consequence of autolysis activity.

Circulating tumor DNA functions as an alternative for tissue to overcome tumor heterogeneity in advanced gastric cancer.

PubMed

Gao, Jing; Wang, Haixing; Zang, Wanchun; Li, Beifang; Rao, Guanhua; Li, Lei; Yu, Yang; Li, Zhongwu; Dong, Bin; Lu, Zhihao; Jiang, Zhi; Shen, Lin

2017-09-01

Overcoming tumor heterogeneity is a major challenge for personalized treatment of gastric cancer, especially for human epidermal growth factor receptor-2 targeted therapy. Analysis of circulating tumor DNA allows a more comprehensive analysis of tumor heterogeneity than traditional biopsies in lung cancer and breast cancer, but little is known in gastric cancer. We assessed mutation profiles of ctDNA and primary tumors from 30 patients with advanced gastric cancer, then performed a comprehensive analysis of tumor mutations by multiple biopsies from five patients, and finally analyzed the concordance of HER2 amplification in ctDNA and paired tumor tissues in 70 patients. By comparing with a single tumor sample, ctDNA displayed a low concordance of mutation profile, only approximately 50% (138/275) somatic mutations were found in paired tissue samples, however, when compared with multiple biopsies, most DNA mutations in ctDNA were also shown in paired tumor tissues. ctDNA had a high concordance (91.4%, Kappa index = 0.784, P < 0.001) of HER2 amplification with tumor tissues, suggesting it might be an alternative for tissue. It implied that ctDNA-based assessment could partially overcome the tumor heterogeneity, and might serve as a potential surrogate for HER2 analysis in gastric cancer. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

Accumulation of pesticides in pacific chorus frogs (Pseudacris regilla) from California's Sierra Nevada Mountains, USA

USGS Publications Warehouse

Smalling, Kelly L.; Fellers, Gary M.; Kleeman, Patrick M.; Kuivila, Kathryn

2013-01-01

Pesticides are receiving increasing attention as potential causes of amphibian declines, acting singly or in combination with other stressors, but limited information is available on the accumulation of current-use pesticides in tissue. The authors examined potential exposure and accumulation of currently used pesticides in pond-breeding frogs (Pseudacris regilla) collected from 7 high elevations sites in northern California. All sites sampled are located downwind of California's highly agricultural Central Valley and receive inputs of pesticides through precipitation and/or dry deposition. Whole frog tissue, water, and sediment were analyzed for more than 90 current-use pesticides and pesticide degradates using gas chromatography–mass spectrometry. Two fungicides, pyraclostrobin and tebuconazole, and one herbicide, simazine, were the most frequently detected pesticides in tissue samples. Median pesticide concentration ranged from 13 µg/kg to 235 µg/kg wet weight. Tebuconazole and pyraclostrobin were the only 2 compounds observed frequently in frog tissue and sediment. Significant spatial differences in tissue concentration were observed, which corresponded to pesticide use in the upwind counties. Data generated indicated that amphibians residing in remote locations are exposed to and capable of accumulating current-use pesticides. A comparison of P. regilla tissue concentrations with water and sediment data indicated that the frogs are accumulating pesticides and are potentially a more reliable indicator of exposure to this group of pesticides than either water or sediment.

Quantitative assessment of soft tissue deformation using digital speckle pattern interferometry: studies on phantom breast models.

PubMed

Karuppanan, Udayakumar; Unni, Sujatha Narayanan; Angarai, Ganesan R

2017-01-01

Assessment of mechanical properties of soft matter is a challenging task in a purely noninvasive and noncontact environment. As tissue mechanical properties play a vital role in determining tissue health status, such noninvasive methods offer great potential in framing large-scale medical screening strategies. The digital speckle pattern interferometry (DSPI)-based image capture and analysis system described here is capable of extracting the deformation information from a single acquired fringe pattern. Such a method of analysis would be required in the case of the highly dynamic nature of speckle patterns derived from soft tissues while applying mechanical compression. Soft phantoms mimicking breast tissue optical and mechanical properties were fabricated and tested in the DSPI out of plane configuration set up. Hilbert transform (HT)-based image analysis algorithm was developed to extract the phase and corresponding deformation of the sample from a single acquired fringe pattern. The experimental fringe contours were found to correlate with numerically simulated deformation patterns of the sample using Abaqus finite element analysis software. The extracted deformation from the experimental fringe pattern using the HT-based algorithm is compared with the deformation value obtained using numerical simulation under similar conditions of loading and the results are found to correlate with an average %error of 10. The proposed method is applied on breast phantoms fabricated with included subsurface anomaly mimicking cancerous tissue and the results are analyzed.

A comparative study of three tissue-cultured Dendrobium species and their wild correspondences by headspace gas chromatography-mass spectrometry combined with chemometric methods.

PubMed

Chen, Nai-Dong; You, Tao; Li, Jun; Bai, Li-Tao; Hao, Jing-Wen; Xu, Xiao-Yuan

2016-10-01

Plant tissue culture technique is widely used in the conservation and utilization of rare and endangered medicinal plants and it is crucial for tissue culture stocks to obtain the ability to produce similar bioactive components as their wild correspondences. In this paper, a headspace gas chromatography-mass spectrometry method combined with chemometric methods was applied to analyze and evaluate the volatile compounds in tissue-cultured and wild Dendrobium huoshanense Cheng and Tang, Dendrobium officinale Kimura et Migo and Dendrobium moniliforme (Linn.) Sw. In total, 63 volatile compounds were separated, with 53 being identified from the three Dendrobium spp. Different provenances of Dendrobiums had characteristic chemicals and showed remarkable quantity discrepancy of common compositions. The similarity evaluation disclosed that the accumulation of volatile compounds in Dendrobium samples might be affected by their provenance. Principal component analysis showed that the first three components explained 85.9% of data variance, demonstrating a good discrimination between samples. Gas chromatography-mass spectrometry techniques, combined with chemometrics, might be an effective strategy for identifying the species and their provenance, especially in the assessment of tissue-cultured Dendrobium quality for use in raw herbal medicines. Copyright © 2016. Published by Elsevier B.V.

The lipid-reactive oxygen species phenotype of breast cancer. Raman spectroscopy and mapping, PCA and PLSDA for invasive ductal carcinoma and invasive lobular carcinoma. Molecular tumorigenic mechanisms beyond Warburg effect.

PubMed

Surmacki, Jakub; Brozek-Pluska, Beata; Kordek, Radzislaw; Abramczyk, Halina

2015-04-07

Vibrational signatures of human breast tissue (invasive ductal carcinoma and invasive lobular carcinoma) were used to identify, characterize and discriminate structures in normal (noncancerous) and cancerous tissues by confocal Raman imaging, Raman spectroscopy and IR spectroscopy. The most important differences between normal and cancerous tissues were found in regions characteristic for vibrations of carotenoids, fatty acids, proteins, and interfacial water. Particular attention was paid to the role played by unsaturated fatty acids and their derivatives. K-means clustering and basis analysis followed by PCA and PLSDA is employed to analyze Raman spectroscopic maps of human breast tissue and for a statistical analysis of the samples (82 patients, 164 samples). Raman maps successfully identify regions of carotenoids, fatty acids, and proteins. The intensities, frequencies and profiles of the average Raman spectra differentiate the biochemical composition of normal and cancerous tissues. The paper demonstrates that Raman imaging has reached a clinically relevant level in regard to breast cancer diagnosis applications. The sensitivity and specificity obtained directly from PLSLD and cross validation are equal to 90.5% and 84.8% for calibration and 84.7% and 71.9% for cross-validation respectively.

Chromatographic methods for determination of macrolide antibiotic residues in tissues and milk of food-producing animals.

PubMed

Moats, W A

1985-01-01

Tylosin, an antibiotic developed specifically for agricultural use, and erythromycin are the main macrolide antibiotics used in animal production. Two-dimensional thin layer chromatography has been used for detection of tylosin in poultry meat, eggs, and milk and for erythromycin in poultry meat. Detection limits reported are, for tylosin, 0.1 ppm in poultry meat, 0.05 ppm in egg, and 0.01 ppm in milk, and for erythromycin, 0.25 ppm in poultry meat. Liquid chromatography (LC) has also been used for determination of tylosin in milk, blood, and tissues of animals. Samples (milk, blood serum, or tissue homogenates in water or pH 2.2 buffer) were deproteinized with acetonitrile, tylosin was partitioned into methylene chloride, and the extracts were concentrated and dissolved in acetonitrile. Chromatography was done on a reverse phase end-capped C18 column using 0.002-0.005 M ammonium dihydrogen phosphate-acetonitrile-methanol (10 + 60 + 30-5 + 80 + 15). Solvent composition was varied with the type of sample analyzed. The method will detect 0.1 ppm tylosin in tissues and less in milk and blood serum. The LC method was more sensitive than microbiological assays for detection of tylosin in tissues of treated swine; recoveries of tylosin by the LC method were frequently several-fold higher.

Statistical Survey of Persistent Organic Pollutants: Risk Estimations to Humans and Wildlife through Consumption of Fish from U.S. Rivers

EPA Science Inventory

U.S. EPA conducted a national statistical survey of fish tissue contamination at 540 river sites (representing 82 954 river km) in 2008–2009, and analyzed samples for 50 persistent organic pollutants (POPs), including 21 PCB congeners, 8 PBDE congeners, and 21 organoc...

Effects of SNPs from the differentially expressed swine odorant binding protein (OBP) gene on average daily gain

USDA-ARS?s Scientific Manuscript database

The objective of this study was to analyze genetic mutations in the swine odorant binding protein (OBP), map them on the swine genome, and to investigate the association between genetic variants and growth traits. The tissue sample of intramuscular fat from 10 individuals for each growth stage (0, 9...

Evaluation of biomolecular distributions in rat brain tissues by means of ToF-SIMS using a continuous beam of Ar clusters.

PubMed

Nakano, Shusuke; Yokoyama, Yuta; Aoyagi, Satoka; Himi, Naoyuki; Fletcher, John S; Lockyer, Nicholas P; Henderson, Alex; Vickerman, John C

2016-06-08

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) provides detailed chemical structure information and high spatial resolution images. Therefore, ToF-SIMS is useful for studying biological phenomena such as ischemia. In this study, in order to evaluate cerebral microinfarction, the distribution of biomolecules generated by ischemia was measured with ToF-SIMS. ToF-SIMS data sets were analyzed by means of multivariate analysis for interpreting complex samples containing unknown information and to obtain biomolecular mapping indicated by fragment ions from the target biomolecules. Using conventional ToF-SIMS (primary ion source: Bi cluster ion), it is difficult to detect secondary ions beyond approximately 1000 u. Moreover, the intensity of secondary ions related to biomolecules is not always high enough for imaging because of low concentration even if the masses are lower than 1000 u. However, for the observation of biomolecular distributions in tissues, it is important to detect low amounts of biological molecules from a particular area of tissue. Rat brain tissue samples were measured with ToF-SIMS (J105, Ionoptika, Ltd., Chandlers Ford, UK), using a continuous beam of Ar clusters as a primary ion source. ToF-SIMS with Ar clusters efficiently detects secondary ions related to biomolecules and larger molecules. Molecules detected by ToF-SIMS were examined by analyzing ToF-SIMS data using multivariate analysis. Microspheres (45 μm diameter) were injected into the rat unilateral internal carotid artery (MS rat) to cause cerebral microinfarction. The rat brain was sliced and then measured with ToF-SIMS. The brain samples of a normal rat and the MS rat were examined to find specific secondary ions related to important biomolecules, and then the difference between them was investigated. Finally, specific secondary ions were found around vessels incorporating microspheres in the MS rat. The results suggest that important biomolecules related to cerebral microinfarction can be detected by ToF-SIMS.

Molecular analysis of Mycobacterium isolates from extrapulmonary specimens obtained from patients in Mexico

PubMed Central

Alvarado-Esquivel, Cosme; García-Corral, Nora; Carrero-Dominguez, David; Enciso-Moreno, José Antonio; Gurrola-Morales, Teodoro; Portillo-Gómez, Leopoldo; Rossau, Rudi; Mijs, Wouter

2009-01-01

Background Little information is available on the molecular epidemiology in Mexico of Mycobacterium species infecting extrapulmonary sites in humans. This study used molecular methods to determine the Mycobacterium species present in tissues and body fluids in specimens obtained from patients in Mexico with extrapulmonary disease. Methods Bacterial or tissue specimens from patients with clinical or histological diagnosis of extrapulmonary tuberculosis were studied. DNA extracts from 30 bacterial cultures grown in Löwenstein Jensen medium and 42 paraffin-embedded tissues were prepared. Bacteria were cultured from urine, cerebrospinal fluid, pericardial fluid, gastric aspirate, or synovial fluid samples. Tissues samples were from lymph nodes, skin, brain, vagina, and peritoneum. The DNA extracts were analyzed by PCR and by line probe assay (INNO-LiPA MYCOBACTERIA v2. Innogenetics NV, Gent, Belgium) in order to identify the Mycobacterium species present. DNA samples positive for M. tuberculosis complex were further analyzed by PCR and line probe assay (INNO-LiPA Rif.TB, Innogenetics NV, Gent, Belgium) to detect mutations in the rpoB gene associated with rifampicin resistance. Results Of the 72 DNA extracts, 26 (36.1%) and 23 (31.9%) tested positive for Mycobacterium species by PCR or line probe assay, respectively. In tissues, M. tuberculosis complex and M. genus were found in lymph nodes, and M. genus was found in brain and vagina specimens. In body fluids, M. tuberculosis complex was found in synovial fluid. M. gordonae, M. smegmatis, M. kansasii, M. genus, M. fortuitum/M. peregrinum complex and M. tuberculosis complex were found in urine. M. chelonae/M. abscessus was found in pericardial fluid and M. kansasii was found in gastric aspirate. Two of M. tuberculosis complex isolates were also PCR and LiPA positive for the rpoB gene. These two isolates were from lymph nodes and were sensitive to rifampicin. Conclusion 1) We describe the Mycobacterium species diversity in specimens derived from extrapulmonary sites in symptomatic patients in Mexico; 2) Nontuberculous mycobacteria were found in a considerable number of patients; 3) Genotypic rifampicin resistance in M. tuberculosis complex infections in lymph nodes was not found. PMID:19272158

Engineering vascularized soft tissue flaps in an animal model using human adipose–derived stem cells and VEGF+PLGA/PEG microspheres on a collagen-chitosan scaffold with a flow-through vascular pedicle

PubMed Central

Zhang, Qixu; Hubenak, Justin; Iyyanki, Tejaswi; Alred, Erik; Turza, Kristin C.; Davis, Greg; Chang, Edward I.; Branch-Brooks, Cynthia D.; Beahm, Elisabeth K.; Butler, Charles E.

2015-01-01

Insufficient neovascularization is associated with high levels of resorption and necrosis in autologous and engineered fat grafts. We tested the hypothesis that incorporating angiogenic growth factor into a scaffold–stem cell construct and implanting this construct around a vascular pedicle improves neovascularization and adipogenesis for engineering soft tissue flaps. Poly(lactic-co-glycolic-acid/polyethylene glycol (PLGA/PEG) microspheres containing vascular endothelial growth factor (VEGF) were impregnated into collagen-chitosan scaffolds seeded with human adipose-derived stem cells (hASCs). This setup was analyzed in vitro and then implanted into isolated chambers around a discrete vascular pedicle in nude rats. Engineered tissue samples within the chambers were harvested and analyzed for differences in vascularization and adipose tissue growth. In vitro testing showed that the collagen-chitosan scaffold provided a supportive environment for hASC integration and proliferation. PLGA/PEG microspheres with slow-release VEGF had no negative effect on cell survival in collagen-chitosan scaffolds. In vivo, the system resulted in a statistically significant increase in neovascularization that in turn led to a significant increase in adipose tissue persistence after 8 weeks versus control constructs. These data indicate that our model—hASCs integrated with a collagen-chitosan scaffold incorporated with VEGF-containing PLGA/PEG microspheres supported by a predominant vascular vessel inside a chamber—provides a promising, clinically translatable platform for engineering vascularized soft tissue flap. The engineered adipose tissue with a vascular pedicle could conceivably be transferred as a vascularized soft tissue pedicle flap or free flap to a recipient site for the repair of soft-tissue defects. PMID:26410787

Engineering vascularized soft tissue flaps in an animal model using human adipose-derived stem cells and VEGF+PLGA/PEG microspheres on a collagen-chitosan scaffold with a flow-through vascular pedicle.

PubMed

Zhang, Qixu; Hubenak, Justin; Iyyanki, Tejaswi; Alred, Erik; Turza, Kristin C; Davis, Greg; Chang, Edward I; Branch-Brooks, Cynthia D; Beahm, Elisabeth K; Butler, Charles E

2015-12-01

Insufficient neovascularization is associated with high levels of resorption and necrosis in autologous and engineered fat grafts. We tested the hypothesis that incorporating angiogenic growth factor into a scaffold-stem cell construct and implanting this construct around a vascular pedicle improves neovascularization and adipogenesis for engineering soft tissue flaps. Poly(lactic-co-glycolic-acid/polyethylene glycol (PLGA/PEG) microspheres containing vascular endothelial growth factor (VEGF) were impregnated into collagen-chitosan scaffolds seeded with human adipose-derived stem cells (hASCs). This setup was analyzed in vitro and then implanted into isolated chambers around a discrete vascular pedicle in nude rats. Engineered tissue samples within the chambers were harvested and analyzed for differences in vascularization and adipose tissue growth. In vitro testing showed that the collagen-chitosan scaffold provided a supportive environment for hASC integration and proliferation. PLGA/PEG microspheres with slow-release VEGF had no negative effect on cell survival in collagen-chitosan scaffolds. In vivo, the system resulted in a statistically significant increase in neovascularization that in turn led to a significant increase in adipose tissue persistence after 8 weeks versus control constructs. These data indicate that our model-hASCs integrated with a collagen-chitosan scaffold incorporated with VEGF-containing PLGA/PEG microspheres supported by a predominant vascular vessel inside a chamber-provides a promising, clinically translatable platform for engineering vascularized soft tissue flap. The engineered adipose tissue with a vascular pedicle could conceivably be transferred as a vascularized soft tissue pedicle flap or free flap to a recipient site for the repair of soft-tissue defects. Copyright © 2015 Elsevier Ltd. All rights reserved.

A reconnaissance study of halogenated organic compounds in catfish from the lower Mississippi river and its major tributaries

USGS Publications Warehouse

Leiker, T.J.; Rostad, C.E.; Barnes, C.R.; Pereira, W.E.

1991-01-01

Blue catfish, (Ictarurus furcatus), black bullhead catfish, (Ictalurus melas), channel catfish (Ictalurus punctatus), and flathead catfish (Pylodictus olivaris), were collected along a 1200 mile river reach of the Mississippi River and its major tributaries. Tissue samples were extracted and analyzed by fused silica capillary gas chromatography/mass spectrometry (GC/MS) to determine the concentrations of hydrophobic organic halogenated contaminants that have bioconcentrated within the tissues. The compounds identified in the tissue include chlordane, polychlorinated biphenyls (PCBs), DDT and its metabolites along with several other chlorinated pesticides. The data indicates that the southern reach of the river system appears to be more contaminated than the middle and upper reaches of the study area.

Detection of K-ras gene mutation by liquid biopsy in patients with pancreatic cancer.

PubMed

Kinugasa, Hideaki; Nouso, Kazuhiro; Miyahara, Koji; Morimoto, Yuki; Dohi, Chihiro; Tsutsumi, Koichiro; Kato, Hironari; Matsubara, Takehiro; Okada, Hiroyuki; Yamamoto, Kazuhide

2015-07-01

Cell-free circulating tumor DNA (ctDNA) in serum has been considered to be a useful candidate for noninvasive cancer diagnosis. The current study was designed to estimate the clinical usefulness of genetic analysis for ctDNA by digital polymerase chain reaction in patients with pancreatic cancer. The authors compared K-ras mutations detected in endoscopic ultrasound-guided fine-needle aspiration biopsy tissue DNA and in ctDNA from 75 patients with pancreatic cancer. K-ras mutations in the serum of 66 independent, consecutive patients with pancreatic cancer were also analyzed and the authors compared the results with survival rates. The frequencies of the mutations in tissue samples at G12V, G12D, and G12R in codon 12 were 28 of 75 samples (37.3%), 22 of 75 samples (29.3%), and 6 of 75 samples (8.0%), respectively. Conversely, the rates of the mutations in ctDNA were 26 of 75 samples (34.6%), 29 of 75 samples (38.6%), and 4 of 75 samples (5.3%), respectively. Overall, the K-ras mutation rates in tissue and ctDNA were 74.7% and 62.6%, respectively, and the concordance rate between them was 58 of 75 samples (77.3%). Survival did not appear to differ by the presence of K-ras mutations in tissue DNA, but the survival of patients with K-ras mutations in ctDNA was significantly shorter than that of patients without mutations in both a development set (P = .006) and an independent validation set (P = .002). The difference was especially evident in cases with a G12V mutation. Analysis of ctDNA is a new useful procedure for detecting mutations in patients with pancreatic cancer. This noninvasive method may have great potential as a new strategy for the diagnosis of pancreatic cancer as well as for predicting survival. © 2015 American Cancer Society.

Relative IGF-1 and IGF-2 gene expression in maternal and fetal tissues from diabetic swine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolverton, C.K.; Leaman, D.W.; White, M.E.

1990-02-26

Fourteen pregnant, crossbred gilts were utilized in this study. Seven gilts were injected with alloxan (50 mg/kg) at day 75 of gestation to induce diabetes. Gilts underwent caesarean section on day 105 of gestation. Samples were collected from maternal skeletal muscle, adipose tissue, uterus and endometrium; and from fetal skeletal muscle, adipose tissue, placenta, liver, lung, kidney, heart, brain and spleen. Tissues were frozen in liquid nitrogen for later analysis of IGF-1 and IGF-2 gene expression. Samples were pooled and total RNA was isolated using the guanidine isothiocynate method. Total mRNA was analyzed by dot blot hybridization. Blots were probedmore » with {sup 32}P-cDNA for porcine IGF-1 and rat IGF-2. IGF-1 gene expression in maternal tissues was unaffected by diabetes. Maternal diabetes increased IGF-2 mRNA in maternal adipose tissue but exhibited no effect in muscle or uterus. Expression of IGF-2 by maternal endometrium was decreased by diabetes. Maternal diabetes induced an increase in IGF-1 gene expression in muscle and placenta while causing an increase in IGF-2 expression in fetal liver and placenta. IGF-2 mRNA was lower in lung from fetuses of diabetic mothers than in controls. These results suggest that maternal diabetes alters IGF-1 and IGF-2 gene expression in specific tissues and differential regulation of these genes appears to exist in the mother and developing fetus.« less

A highly sensitive method for analysis of 7-dehydrocholesterol for the study of Smith-Lemli-Opitz syndrome[S

PubMed Central

Liu, Wei; Xu, Libin; Lamberson, Connor; Haas, Dorothea; Korade, Zeljka; Porter, Ned A.

2014-01-01

We describe a highly sensitive method for the detection of 7-dehydrocholesterol (7-DHC), the biosynthetic precursor of cholesterol, based on its reactivity with 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD) in a Diels-Alder cycloaddition reaction. Samples of biological tissues and fluids with added deuterium-labeled internal standards were derivatized with PTAD and analyzed by LC-MS. This protocol permits fast processing of samples, short chromatography times, and high sensitivity. We applied this method to the analysis of cells, blood, and tissues from several sources, including human plasma. Another innovative aspect of this study is that it provides a reliable and highly reproducible measurement of 7-DHC in 7-dehydrocholesterol reductase (Dhcr7)-HET mouse (a model for Smith-Lemli-Opitz syndrome) samples, showing regional differences in the brain tissue. We found that the levels of 7-DHC are consistently higher in Dhcr7-HET mice than in controls, with the spinal cord and peripheral nerve showing the biggest differences. In addition to 7-DHC, sensitive analysis of desmosterol in tissues and blood was also accomplished with this PTAD method by assaying adducts formed from the PTAD “ene” reaction. The method reported here may provide a highly sensitive and high throughput way to identify at-risk populations having errors in cholesterol biosynthesis. PMID:24259532

Development and validation of a multiplex reaction analyzing eight miniSTRs of the X chromosome for identity and kinship testing with degraded DNA.

PubMed

Castañeda, María; Odriozola, Adrián; Gómez, Javier; Zarrabeitia, María T

2013-07-01

We report the development of an effective system for analyzing X chromosome-linked mini short tandem repeat loci with reduced-size amplicons (less than 220 bp), useful for analyzing highly degraded DNA samples. To generate smaller amplicons, we redesigned primers for eight X-linked microsatellites (DXS7132, DXS10079, DXS10074, DXS10075, DXS6801, DXS6809, DXS6789, and DXS6799) and established efficient conditions for a multiplex PCR system (miniX). The validation tests confirmed that it has good sensitivity, requiring as little as 20 pg of DNA, and performs well with DNA from paraffin-embedded tissues, thus showing potential for improved analysis and identification of highly degraded and/or very limited DNA samples. Consequently, this system may help to solve complex forensic cases, particularly when autosomal markers convey insufficient information.

Clinicopathological features and pituitary homeobox 1 gene expression in the progression and prognosis of cutaneous malignant melanoma.

PubMed

Barut, Figen; Udul, Perihan; Kokturk, Furuzan; Kandemir, Nilufer Onak; Keser, Sevinc Hallac; Ozdamar, Sukru Oguz

2016-10-01

The evidence that PITX1 (pituitary homeobox 1) is a significant tumor suppressor in human cancer remains largely circumstantial, but it clearly warrants further study as little is known about the tumor-inhibitory roles of PITX1 in cutaneous malignant melanoma. The aims of this study were to investigate PITX1 gene expression in patients with cutaneous malignant melanoma and to evaluate its potential relevance to clinicopathological characteristics and tumor cell proliferation. Clinicopathological findings of patients with cutaneous malignant melanoma were analyzed retrospectively. PITX1 and Ki-67 expression were detected by immunohistochemistry in malignant melanoma and healthy tissue samples from each patient. Labeling indices were calculated based on PITX1 gene and Ki-67 expression. The correlation between PITX1and Ki-67 expressions was analyzed in cutaneous malignant melanoma cases. The relationship between PITX1 expression intensity and clinicopathological characteristics was also analyzed. PITX1 expression was observed in all (100%) normal healthy skin tissue samples. In addition, PITX1 expression was found in 56 (80%) and was absent in 14 (20%) of the 70 cutaneous malignant melanoma cases. Ki-67 positive expression was only detected in the 14 (20%) PITX1-negative cases. PITX1-positive tumor cells were observed on the surface, but Ki-67 positive tumor cells were observed in deeper zones of the tumor nests. PITX1 expression was downregulated in human cutaneous malignant melanoma lesions compared with healthy skin tissue, but Ki-67 expression was upregulated in concordance with the progression of cutaneous malignant melanoma. PITX1 expression may be involved in tumor progression and is a potential tumor suppressor gene and prognostic marker for cutaneous malignant melanoma. Copyright © 2016. Published by Elsevier Taiwan.

Tissue dissolution ability of sodium hypochlorite activated by photon-initiated photoacoustic streaming technique.

PubMed

Guneser, Mehmet Burak; Arslan, Dilara; Usumez, Aslihan

2015-05-01

The aim of this study was to evaluate the effect of the photon-initiated photoacoustic streaming (PIPS) technique on the pulp tissue-dissolving capacity of sodium hypochlorite (NaOCl) and compare it with the EndoActivator System (Dentsply Tulsa Dental Specialties, Tulsa, OK) and the Er:YAG laser with an endodontic fiber tip. Bovine pulp tissue samples (45 ± 15 mg) and dentin powder (10 mg) were placed in 1.5-mL Eppendorf tubes with 1 mL 5.25% NaOCl (Wizard; Rehber Kimya, Istanbul, Turkey) or distilled water (control) for 5 minutes with activation by the EndoActivator System, the Er:YAG laser with an endodontic fiber tip, and the PIPS technique. Nonactivated NaOCl served as the positive control. All testing procedures were performed at room temperature. The tissue samples were weighed before and after treatment, and the percentage of weight loss was calculated. The differences were statistically analyzed. The highest rate of tissue dissolution was observed in the NaOCl + Er:YAG group (P < .05). The NaOCl + PIPS group dissolved more bovine pulp tissue than the nonactivated NaOCl group (P < .05). There was no statistically significant difference between the rates of tissue dissolution of the NaOCl + EA and the nonactivated NaOCl groups (P > .05). NaOCl activation with the Er:YAG laser with an endodontic fiber tip was the most effective in bovine pulp tissue dissolution. The PIPS technique also promoted superior tissue-dissolving effects when compared with no activation. However, the EndoActivator System had no direct effect on tissue dissolution. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Colon Cancer Associated Transcript-1 (CCAT1) Expression in Adenocarcinoma of the Stomach.

PubMed

Mizrahi, Ido; Mazeh, Haggi; Grinbaum, Ronit; Beglaibter, Nahum; Wilschanski, Michael; Pavlov, Vera; Adileh, Muchamad; Stojadinovic, Alexander; Avital, Itzhak; Gure, Ali Osmay; Halle, David; Nissan, Aviram

2015-01-01

Long non-coding RNAs (lncRNAs) have been shown to have functional roles in cancer biology and are dys-regulated in many tumors. Colon Cancer Associated Transcript -1 (CCAT1) is a lncRNA, previously shown to be significantly up-regulated in colon cancer. The aim of this study is to determine expression levels of CCAT1 in gastric carcinoma (GC). Tissue samples were obtained from patients undergoing resection for gastric carcinoma (n=19). For each patient, tumor tissue and normal appearing gastric mucosa were taken. Normal gastric tissues obtained from morbidly obese patients, undergoing laparoscopic sleeve gastrectomy served as normal controls (n=19). A human gastric carcinoma cell line (AGS) served as positive control. RNA was extracted from all tissue samples and CCAT1 expression was analyzed using quantitative real time-PCR (qRT-PCR). Low expression of CCAT1 was identified in normal gastric mucosa samples obtained from morbidly obese patients [mean Relative Quantity (RQ) = 1.95±0.4]. AGS human gastric carcinoma cell line showed an elevated level of CCAT1 expression (RQ=8.02). Expression levels of CCAT1 were approximately 10.8 fold higher in GC samples than in samples taken from the negative control group (RQ=21.1±5 vs. RQ=1.95±0.4, respectively, p<0.001). Interestingly, CCAT1 expression was significantly overexpressed in adjacent normal tissues when compared to the negative control group (RQ = 15.25±2 vs. RQ=1.95±0.4, respectively, p<0.001). Tissues obtained from recurrent GC cases showed the highest expression levels (RQ = 88.8±31; p<0.001). Expression levels increased with tumor stage (T4- 36.4±15, T3- 16.1±6, T2- 4.7±1), however this did not reach statistical significance (p=0.2). There was no difference in CCAT1 expression between intestinal and diffuse type GC (RQ=22.4±7 vs. 22.4±16, respectively, p=0.9). Within the normal gastric tissue samples, no significant difference in CCAT1 expression was observed in helicobacter pylori negative and positive patients (RQ= 2.4±0.9 vs. 0.93±0.2, respectively, p=0.13). CCAT1 is up-regulated in gastric cancer, and may serve as a potential bio-marker for early detection and surveillance.

Studies on the Presence of Mycotoxins in Biological Samples: An Overview

PubMed Central

Escrivá, Laura; Font, Guillermina; Manyes, Lara

2017-01-01

Mycotoxins are fungal secondary metabolites with bioaccumulation levels leading to their carry-over into animal fluids, organs, and tissues. As a consequence, mycotoxin determination in biological samples from humans and animals has been reported worldwide. Since most mycotoxins show toxic effects at low concentrations and considering the extremely low levels present in biological samples, the application of reliable detection methods is required. This review summarizes the information regarding the studies involving mycotoxin determination in biological samples over the last 10 years. Relevant data on extraction methodology, detection techniques, sample size, limits of detection, and quantitation are presented herein. Briefly, liquid-liquid extraction followed by LC-MS/MS determination was the most common technique. The most analyzed mycotoxin was ochratoxin A, followed by zearalenone and deoxynivalenol—including their metabolites, enniatins, fumonisins, aflatoxins, T-2 and HT-2 toxins. Moreover, the studies were classified by their purpose, mainly focused on the development of analytical methodologies, mycotoxin biomonitoring, and exposure assessment. The study of tissue distribution, bioaccumulation, carry-over, persistence and transference of mycotoxins, as well as, toxicokinetics and ADME (absorption, distribution, metabolism and excretion) were other proposed goals for biological sample analysis. Finally, an overview of risk assessment was discussed. PMID:28820481

CDH4 suppresses the progression of salivary adenoid cystic carcinoma via E-cadherin co-expression.

PubMed

Xie, Jian; Feng, Yan; Lin, Ting; Huang, Xiao-Yu; Gan, Rui-Huan; Zhao, Yong; Su, Bo-Hua; Ding, Lin-Can; She, Lin; Chen, Jiang; Lin, Li-Song; Lin, Xu; Zheng, Da-Li; Lu, You-Guang

2016-12-13

The cadherin-4 gene (CDH4) of the cadherin family encodes non-epithelial R-cadherin (R-cad); however, the function of this gene in different types of cancer remains controversial. In this study, we found higher expression of CDH4 mRNA in a salivary adenoid cystic carcinoma (SACC) cell line with low metastatic potential (SACC-83) than in a cell line with high metastatic potential (SACC-LM). By analyzing 67 samples of SACC tissues and 40 samples of paraneoplastic normal tissues, we found R-cad highly expressed in 100% of normal paraneoplastic tissue but only expressed in 64% of SACC tumor tissues (P<0.001). Knockdown of CDH4 expression in vitro promoted the growth, mobility and invasion of SACC cells, and in vivo experiments showed that decreased CDH4 expression enhanced SACC tumorigenicity. Furthermore, CDH4 suppression resulted in down-regulation of E-cadherin (E-cad), which is encoded by CDH1 gene and is a well-known tumor suppressor gene by inhibition of cell proliferation and migration. These results indicate that CDH4 may play a negative role in the growth and metastasis of SACC via co-expression with E-cadherin.

Skeletal muscle proteins: a new approach to delimitate the time since death.

PubMed

Foditsch, Elena Esra; Saenger, Alexandra Maria; Monticelli, Fabio Carlo

2016-03-01

Skeletal muscle tissue is proposed as a forensic model tissue with strong potential, as it is easily accessible and its true-to-life state structure and function is well known. Despite this strong potential, skeletal muscle degradation studies are rare. The aim of this study was to test if a skeletal muscle-based protein analysis is applicable to delimitate the time since death. Under standard conditions, two pigs were stored either at 22 °C for 5 days or 4 °C for 21 days. Their Mm. biceps femori were sampled periodically for analyses of ten skeletal muscle proteins postmortem. All analyzed proteins can serve as markers for a delimitation of the time since death. Desmin, nebulin, titin, and SERCA 1 displayed distinct protein patterns at certain points of time. The other five proteins, α-actinin, calsequestrin-1, laminin, troponin T-C, and SERCA 2, showed no degradation patterns within the analyzed postmortem time frame. Referring to specific skeletal muscle proteins, results showed short-term stabilities for just a minority of analyzed proteins, while the majority of investigated proteins displayed characteristics as long-term markers. Due to specific patterns and the possibility to determine definite constraints of the presence, absence, or pattern alterations of single proteins, the feasibility of porcine skeletal muscle as forensic model tissue is outlined and the potential of skeletal muscle as forensic model tissue is underlined, especially with respect to later postmortem phases, which so far lack feasible methods to delimitate the time since death.

Trace elements and organic compounds in sediment and fish tissue from the Great Salt Lake basins, Utah, Idaho, and Wyoming, 1998-99

USGS Publications Warehouse

Waddell, Kidd M.; Giddings, Elise M.

2004-01-01

A study to determine the occurrence and distribution of trace elements, organochlorine pesticides, polychlorinated biphenyls (PCBs), and semivolatile organic compounds in sediment and in fish tissue was conducted in the Great Salt Lake Basins study unit of the National Water-Quality Assessment (NAWQA) program during 1998-99. Streambed-sediment and fish-tissue samples were collected concurrently at 11 sites and analyzed for trace-element concentration. An additional four sites were sampled for streambed sediment only and one site for fish tissue only. Organic compounds were analyzed from streambed-sediment and fish-tissue samples at 15 sites concurrently.Bed-sediment cores from lakes, reservoirs, and Farmington Bay collected by the NAWQA program in 1998 and by other researchers in 1982 were used to examine historical trends in trace-element concentration and to determine anthropogenic sources of contaminants. Cores collected in 1982 from Mirror Lake, a high-mountain reference location, showed an enrichment of arsenic, cadmium, copper, lead, tin, and zinc in the surface sediments relative to the deeper sediments, indicating that enrichment likely began after about 1900. This enrichment was attributed to atmospheric deposition during the period of metal-ore mining and smelting. A core from Echo Reservoir, in the Weber River Basin, however, showed a different pattern of trace-element concentration that was attributed to a local source. This site is located downstream from the Park City mining district, which is the most likely historical source of trace elements. Cores collected in 1998 from Farmington Bay show that the concentration of lead began to increase after 1842 and peaked during the mid-1980s and has been in decline since. Recent sediments deposited during 1996-98 indicate a 41- to 62-percent reduction since the peak in the mid-1980s.The concentration of trace elements in streambed sediment was greatest at sites that have been affected by historic mining, including sites on Little Cottonwood Creek in the Jordan River basin, Silver Creek in the Weber River basin, and the Weber River below the confluence with Silver Creek. There was significant correlation of lead concentrations in streambed sediment and fish tissue, but other trace elements did not correlate well. Streambed sediment and fish tissue collected from sites in the Bear River basin, which is predominantly rangeland and agriculture, generally had low concentrations of most elements.Sediment-quality guidelines were used to assess the relative toxicity of streambed-sediment sites to aquatic communities. Sites affected by mining exceeded the Probable Effect Concentration (PEC), the concentration at which it is likely there will be a negative effect on the aquatic community, for arsenic, cadmium, copper, lead, silver, mercury, and zinc. Sites that were not affected by mining did not exceed these criteria. Concentrations of trace elements in samples collected from the Great Salt Lake Basins study unit (GRSL) are high compared to those of samples collected nationally with the NAWQA program. Nine of 15 streambed-sediment samples and 11 of 14 fish-tissue samples had concentrations of at least one trace element greater than the concentration of 90 percent of the samples collected nationally during 1993-2000.Organic compounds that were examined in streambed sediment and fish-tissue samples also were examined in bed-sediment cores. A bed-sediment core from Farmington Bay of Great Salt Lake showed an increase in total polycyclic aromatic hydrocarbon (PAH) concentrations coincident with the increase in population in Salt Lake Valley, which drains into this bay. Analysis of streambed-sediment samples showed that the highest concentrations of PAHs were detected at urban sites, including two sites in the lower Jordan River (the Jordan River flows into Farmington Bay), the Weber River at Ogden Bay, and the Provo River near Provo. Other organic compounds detected in streambed sediment in the lower Jordan River were PCBs, DDT compounds, and chlordane compounds.Organic compounds were detected more frequently in fish tissue than in streambed sediment. Chlordane compounds and PCBs were detected more frequently at urban sites. DDT compounds were detected at 13 of 15 sites including urban and agricultural sites. Concentrations of total DDT in fish tissue exceeded the guideline for protection of fish-eating wildlife at two urban sites. The concentration of organic compounds in the GRSL study unit is low compared with that of samples collected nationally.

Total mercury distribution in different tissues of six species of freshwater fish from the Kpong hydroelectric reservoir in Ghana.

PubMed

Atta, Alhassan; Voegborlo, Ray Bright; Agorku, Eric Selorm

2012-05-01

Total mercury concentrations were determined in seven tissues of 38 fish samples comprising six species from the Kpong hydroelectric reservoir in Ghana by cold vapour atomic absorption spectrometry technique using an automatic mercury analyzer. Mercury concentration in all the tissues ranged from 0.005 to 0.022 μg/g wet weight. In general, the concentration of mercury in all the tissues were decreasing in the order; liver > muscle > intestine > stomach > gonad > gill > swim bladder. Mercury concentration was generally greater in the tissues of high-trophic-level fish such as Clarotes laticeps, Mormyrops anguilloides and Chrysichthys aurutus whereas low-trophic-level fish such as Oreochromis niloticus recorded low mercury concentration in their tissues. The results obtained for total mercury concentration in the muscle tissues analysed in this study are below the WHO/FAO threshold limit of 0.5 μg/g. This suggests that the exposure of the general public to Hg through fish consumption can be considered negligible.

Serum immunoreactivity of cancer/testis antigen OY-TES-1 and its tissues expression in glioma

PubMed Central

Li, Xisheng; Yan, Jun; Fan, Rong; Luo, Bin; Zhang, Qingmei; Lin, Yongda; Zhou, Sufang; Luo, Guorong; Xie, Xiaoxun; Xiao, Shaowen

2017-01-01

OY-TES-1 is a member of the cancer/testis antigen family that is expressed in healthy testis tissue and certain types of cancerous tissue. The present study aimed to analyze the expression pattern of OY-TES-1 and serum anti-OY-TES-1 antibody concentration in patients with glioma. OY-TES-1 mRNA was detected in 28/36 (78%) of glioma cases using conventional reverse transcription polymerase chain reaction (RT-PCR) analysis. RT-quantitative-PCR revealed that OY-TES-1 was expressed at a higher level in glioma tissues compared with normal adult tissues (with the exception of testis tissue). Anti-OY-TES-1 antibodies were present in the serum of 5/36 (14%) of patients with glioma, but absent in all the serum samples from 107 healthy donors. Immunohistochemical analysis demonstrated that OY-TES-1 protein was expressed in all glioma tissues from patients with anti-OY-TES-1 antibody seropositivity. These results suggest that OY-TES-1 is a novel candidate for glioma immunotherapy. PMID:28529561

TFDP3 was expressed in coordination with E2F1 to inhibit E2F1-mediated apoptosis in prostate cancer.

PubMed

Ma, Yueyun; Xin, Yijuan; Li, Rui; Wang, Zhe; Yue, Qiaohong; Xiao, Fengjing; Hao, Xiaoke

2014-03-10

TFDP3 has been previously identified as an inhibitor of E2F molecules. It has been shown to suppress E2F1-induced apoptosis dependent P53 and to play a potential role in carcinogenesis. However, whether it indeed helps cancer cells tolerate apoptosis stress in cancer tissues remains unknown. TFDP3 expression was assessed by RT-PCR, in situ hybridization and immunohistochemistry in normal human tissues, cancer tissues and prostate cancer tissues. The association between TFDP3 and E2F1 in prostate cancer development was analyzed in various stages. Apoptosis was evaluated with annexin-V and propidium iodide staining and flow-cytometry. The results show that, in 96 samples of normal human tissues, TFDP3 could be detected in the cerebrum, esophagus, stomach, small intestine, bronchus, breast, ovary, uterus, and skin, but seldom in the lung, muscles, prostate, and liver. In addition, TFDP3 was highly expressed in numerous cancer tissues, such as brain-keratinous, lung squamous cell carcinoma, testicular seminoma, cervical carcinoma, skin squamous cell carcinoma, gastric adenocarcinoma, liver cancer, and prostate cancer. Moreover, TFDP3 was positive in 23 (62.2%) of 37 prostate cancer samples regardless of stage. Furthermore, immunohistochemistry results show that TFDP3 was always expressed in coordination with E2F1 at equivalent expression levels in prostate cancer tissues, and was highly expressed particularly in samples of high stage. When E2F1 was extrogenously expressed in LNCap cells, TFDP3 could be induced, and the apoptosis induced by E2F1 was significantly decreased. It was demonstrated that TFDP3 was a broadly expressed protein corresponding to E2F1 in human tissues, and suggested that TFDP3 is involved in prostate cancer cell survival by suppressing apoptosis induced by E2F1. Copyright © 2013 Elsevier B.V. All rights reserved.

Gastric Cancer-Specific Protein Profile Identified Using Endoscopic Biopsy Samples via MALDI Mass Spectrometry

PubMed Central

Kim, Hark Kyun; Reyzer, Michelle L.; Choi, Il Ju; Kim, Chan Gyoo; Kim, Hee Sung; Oshima, Akira; Chertov, Oleg; Colantonio, Simona; Fisher, Robert J.; Allen, Jamie L.; Caprioli, Richard M.; Green, Jeffrey E.

2012-01-01

To date, proteomic analyses on gastrointestinal cancer tissue samples have been performed using surgical specimens only, which are obtained after a diagnosis is made. To determine if a proteomic signature obtained from endoscopic biopsy samples could be found to assist with diagnosis, frozen endoscopic biopsy samples collected from 63 gastric cancer patients and 43 healthy volunteers were analyzed using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. A statistical classification model was developed to distinguish tumor from normal tissues using half the samples and validated with the other half. A protein profile was discovered consisting of 73 signals that could classify 32 cancer and 22 normal samples in the validation set with high predictive values (positive and negative predictive values for cancer, 96.8% and 91.3%; sensitivity, 93.8%; specificity, 95.5%). Signals overexpressed in tumors were identified as α-defensin-1, α-defensin-2, calgranulin A, and calgranulin B. A protein profile was also found to distinguish pathologic stage Ia (pT1N0M0) samples (n = 10) from more advanced stage (Ib or higher) tumors (n = 48). Thus, protein profiles obtained from endoscopic biopsy samples may be useful in assisting with the diagnosis of gastric cancer and, possibly, in identifying early stage disease. PMID:20557134

Analysis of the effectiveness of Sodium Hypochlorite decontamination of cadaveric human tissues at retrieval.

PubMed

Paolin, Adolfo; Trojan, Diletta; Carniato, Antonio; Tasca, Fabio; Massarin, Ervino; Tugnoli, Alessandro; Cogliati, Elisa

2016-12-01

Bacterial contamination of tissues retrieved from cadaveric donors is a common feature worldwide, and every tissue bank, albeit using different methods, conducts decontamination to guarantee safe tissues suitable for clinical use. The effectiveness of the methods used to eradicate pathogens differs. In order to reduce the tissue bioburden at retrieval, we have introduced a new method involving rinsing tissues in a sodium hypochlorite solution. To test its effectiveness we analyzed two comparable groups of tissues: Group A: 1881 tissues, all rinsed with isotonic saline solution after retrieval, and Group B: 1968 tissues immersed in an isotonic saline solution containing sodium hypochlorite (final concentration 0.1 %) for different lengths of time and subsequently rinsed with isotonic saline. The rinsing solution of each tissue was then sampled for microbiological cultures in both groups. The resultant overall contamination rate was 40.5 % for Group A and 6.7 % for Group B, with an 82.8 % difference in the reduction of contamination between the two groups. This was especially the case for commensal skin bacteria in musculoskeletal tissue, which accounted for over half the overall contamination. Our data highlighted that decontamination with sodium hypochlorite was helpful in reducing the bacterial bioburden in tissues retrieved from cadaveric donors.

Transplantation of human fetal tissue for neurodegenerative diseases: validation of a new protocol for microbiological analysis and bacterial decontamination.

PubMed

Piroth, Tobias; Pauly, Marie-Christin; Schneider, Christian; Wittmer, Annette; Möllers, Sven; Döbrössy, Máté; Winkler, Christian; Nikkhah, Guido

2014-01-01

Restorative cell therapy concepts in neurodegenerative diseases are aimed at replacing lost neurons. Despite advances in research on pluripotent stem cells, fetal tissue from routine elective abortions is still regarded as the only safe cell source. Progenitor cells isolated from distinct first-trimester fetal CNS regions have already been used in clinical trials and will be used again in a new multicenter trial funded by the European Union (TRANSEURO). Bacterial contamination of human fetal tissue poses a potential risk of causing infections in the brain of the recipient. Thus, effective methods of microbial decontamination and validation of these methods are required prior to approval of a neurorestorative cell therapy trial. We have developed a protocol consisting of subsequent washing steps at different stages of tissue processing. Efficacy of microbial decontamination was assessed on rat embryonic tissue incubated with high concentrations of defined microbe solutions including representative bacterial and fungal species. Experimental microbial contamination was reduced by several log ranks. Subsequently, we have analyzed the spectrum of microbial contamination and the effect of subsequent washing steps on aborted human fetal tissue; 47.7% of the samples taken during human fetal tissue processing were positive for a microbial contamination, but after washing, no sample exhibited bacterial growth. Our data suggest that human fetal tissue for neural repair can carry microbes of various species, highlighting the need for decontamination procedures. The decontamination protocol described in this report has been shown to be effective as no microbes could be detected at the end of the procedure.

The Impact of Repeated Freeze-Thaw Cycles on the Quality of Biomolecules in Four Different Tissues.

PubMed

Ji, Xiaoli; Wang, Min; Li, Lingling; Chen, Fang; Zhang, Yanyang; Li, Qian; Zhou, Junmei

2017-10-01

High-quality biosamples are valuable resources for biomedical research. However, some tissues are stored without being sectioned into small aliquots and have to undergo repeated freeze-thaw cycles throughout prolonged experimentation. Little is known regarding the effects of repeated freeze-thaw cycles on the quality of biomolecules in tissues. The aim of this study was to evaluate the impact of repeated freeze-thaw (at room temperature or on ice) cycles on biomolecules and gene expression in four different types of tissues. Each fresh tissue was sectioned into seven aliquots and snap-frozen before undergoing repeated freeze-thaw cycles at room temperature or on ice. Biomolecules were extracted and analyzed. Both relative and absolute quantification were used to detect the changes in gene expression. The results indicated that the impact of repeated freeze-thaw cycles on RNA integrity varied by tissue type. Gene expression, including the housekeeping gene, was affected in RNA-degraded samples according to absolute quantification rather than relative quantification. Furthermore, our results suggest that thawing on ice could protect RNA integrity compared with thawing at room temperature. No obvious degradation of protein or DNA was observed with repeated freeze-thaw cycles either at room temperature or on ice. This research provides ample evidence for the necessity of sectioning fresh tissues into small aliquots before snap-freezing, thus avoiding degradation of RNA and alteration of gene expression resulting from repeated freeze-thaw cycles. For frozen tissue samples that were already in storage and had to be used repeatedly during their lifecycle, thawing on ice or sectioned at ultralow temperature is recommended.

Detection of Francisella tularensis within infected mouse tissues by using a hand-held PCR thermocycler.

PubMed

Emanuel, Peter A; Bell, Ryan; Dang, Jessica L; McClanahan, Rebecca; David, John C; Burgess, Robert J; Thompson, Joseph; Collins, Lisa; Hadfield, Ted

2003-02-01

The diagnosis of human cases of tularemia often relies upon the demonstration of an antibody response to Francisella tularensis or the direct culturing of the bacteria from the patient. Antibody response is not detectable until 2 weeks or more after infection, and culturing requires special media and suspicion of tularemia. In addition, handling live Francisella poses a risk to laboratory personnel due to the highly infectious nature of this pathogen. In an effort to develop a rapid diagnostic assay for tularemia, we investigated the use of TaqMan 5' hydrolysis fluorogenic PCR to detect the organism in tissues of infected mice. Mice were infected to produce respiratory tularemia. The fopA and tul4 genes of F. tularensis were amplified from infected spleen, lung, liver, and kidney tissues sampled over a 5-day period. The samples were analyzed using the laboratory-based Applied Biosystems International 7900 and the Smiths Detection-Edgewood BioSeeq, a hand-held portable fluorescence thermocycler designed for use in the field. A comparison of culturing and PCR for detection of bacteria in infected tissues shows that culturing was more sensitive than PCR. However, the results for culture take 72 h, whereas PCR results were available within 4 h. PCR was able to detect infection in all the tissues tested. Lung tissue showed the earliest response at 2 days when tested with the ABI 7900 and in 3 days when tested with the BioSeeq. The results were in agreement between the ABI 7900 and the BioSeeq when presented with the same sample. Template preparation may account for the loss of sensitivity compared to culturing techniques. The hand-held BioSeeq thermocycler shows promise as an expedient means of forward diagnosis of infection in the field.

Detection of Francisella tularensis within Infected Mouse Tissues by Using a Hand-Held PCR Thermocycler

PubMed Central

Emanuel, Peter A.; Bell, Ryan; Dang, Jessica L.; McClanahan, Rebecca; David, John C.; Burgess, Robert J.; Thompson, Joseph; Collins, Lisa; Hadfield, Ted

2003-01-01

The diagnosis of human cases of tularemia often relies upon the demonstration of an antibody response to Francisella tularensis or the direct culturing of the bacteria from the patient. Antibody response is not detectable until 2 weeks or more after infection, and culturing requires special media and suspicion of tularemia. In addition, handling live Francisella poses a risk to laboratory personnel due to the highly infectious nature of this pathogen. In an effort to develop a rapid diagnostic assay for tularemia, we investigated the use of TaqMan 5′ hydrolysis fluorogenic PCR to detect the organism in tissues of infected mice. Mice were infected to produce respiratory tularemia. The fopA and tul4 genes of F. tularensis were amplified from infected spleen, lung, liver, and kidney tissues sampled over a 5-day period. The samples were analyzed using the laboratory-based Applied Biosystems International 7900 and the Smiths Detection-Edgewood BioSeeq, a hand-held portable fluorescence thermocycler designed for use in the field. A comparison of culturing and PCR for detection of bacteria in infected tissues shows that culturing was more sensitive than PCR. However, the results for culture take 72 h, whereas PCR results were available within 4 h. PCR was able to detect infection in all the tissues tested. Lung tissue showed the earliest response at 2 days when tested with the ABI 7900 and in 3 days when tested with the BioSeeq. The results were in agreement between the ABI 7900 and the BioSeeq when presented with the same sample. Template preparation may account for the loss of sensitivity compared to culturing techniques. The hand-held BioSeeq thermocycler shows promise as an expedient means of forward diagnosis of infection in the field. PMID:12574268

Distribution of enrofloxacin and its active metabolite, using an in vivo ultrafiltration sampling technique after the injection of enrofloxacin to pigs.

PubMed

Messenger, K M; Papich, M G; Blikslager, A T

2012-10-01

The objective of this study was to determine the pharmacokinetics (PK) of enrofloxacin in pigs and compare to the tissue interstitial fluid (ISF). Six healthy, young pigs were administered 7.5 mg/kg enrofloxacin subcutaneously (SC). Blood and ISF samples were collected from preplaced intravenous catheters and ultrafiltration sampling probes placed in three different tissue sites (intramuscular, subcutaneous, and intrapleural). Enrofloxacin concentrations were measured using high-pressure liquid chromatography with fluorescence detection, PK parameters were analyzed using a one-compartment model, and protein binding was determined using a microcentrifugation system. Concentrations of the active metabolite ciprofloxacin were negligible. The mean ± SD enrofloxacin plasma half-life, volume of distribution, clearance, and peak concentration were 26.6 ± 6.2 h (harmonic mean), 6.4 ± 1.2 L/kg, 0.18 ± 0.08 L/kg/h, and 1.1 ± 0.3 μg/mL, respectively. The half-life of enrofloxacin from the tissues was 23.6 h, and the maximum concentration was 1.26 μg/mL. Tissue penetration, as measured by a ratio of area-under-the-curve (AUC), was 139% (± 69%). Plasma protein binding was 31.1% and 37.13% for high and low concentrations, respectively. This study demonstrated that the concentration of biologically active enrofloxacin in tissues exceeds the concentration predicted by the unbound fraction of enrofloxacin in pig plasma. At a dose of 7.5 mg/kg SC, the high tissue concentrations and long half-life produce an AUC/MIC ratio sufficient for the pathogens that cause respiratory infections in pigs. © 2011 Blackwell Publishing Ltd.

Printing metal-spiked inks for LA-ICP-MS bioimaging internal standardization: comparison of the different nephrotoxic behavior of cisplatin, carboplatin, and oxaliplatin.

PubMed

Moraleja, Irene; Esteban-Fernández, Diego; Lázaro, Alberto; Humanes, Blanca; Neumann, Boris; Tejedor, Alberto; Luz Mena, M; Jakubowski, Norbert; Gómez-Gómez, M Milagros

2016-03-01

The study of the distribution of the cytostatic drugs cisplatin, carboplatin, and oxaliplatin along the kidney may help to understand their different nephrotoxic behavior. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) allows the acquisition of trace element images in biological tissues. However, results obtained are affected by several variations concerning the sample matrix and instrumental drifts. In this work, an internal standardization method based on printing an Ir-spiked ink onto the surface of the sample has been developed to evaluate the different distributions and accumulation levels of the aforementioned drugs along the kidney of a rat model. A conventional ink-jet printer was used to print fresh sagittal kidney tissue slices of 4 μm. A reproducible and homogenous deposition of the ink along the tissue was observed. The ink was partially absorbed on top of the tissue. Thus, this approach provides a pseudo-internal standardization, due to the fact that the ablation sample and internal standard take place subsequently and not simultaneously. A satisfactory normalization of LA-ICP-MS bioimages and therefore a reliable comparison of the kidney treated with different Pt-based drugs were achieved even for tissues analyzed on different days. Due to the complete ablation of the sample, the transport of the ablated internal standard and tissue to the inductively coupled plasma-mass spectrometry (ICP-MS) is practically taking place at the same time. Pt accumulation in the kidney was observed in accordance to the dosages administered for each drug. Although the accumulation rate of cisplatin and oxaliplatin is high in both cases, their Pt distributions differ. The strong nephrotoxicity observed for cisplatin and the absence of such side effect in the case of oxaliplatin could explain these distribution differences. The homogeneous distribution of oxaliplatin in the cortical and medullar areas could be related with its higher affinity for cellular transporters such as MATE2-k.

Differential Expression of c-fos Proto-Oncogene in Normal Oral Mucosa versus Squamous Cell Carcinoma

PubMed Central

Krishna, Akhilesh; Bhatt, Madan Lal Brahma; Singh, Vineeta; Singh, Shraddha; Gangwar, Pravin Kumar; Singh, Uma Shankar; Kumar, Vijay; Mehrotra, Divya

2018-01-01

Background: The c-Fos nuclear protein dimerizes with Jun family proteins to form the transcription factor AP-1 complex which participates in signal transduction and regulation of normal cellular processes. In tumorigenesis, c-Fos promotes invasive growth through down-regulation of tumor suppressor genes but its role in oral carcinogenesis is not clear. Objectives: This study concerned c-fos gene expression in normal and malignant tissues of the oral cavity, with attention to associations between expression status and clinico-pathological profiles of OSCC patients. Method: A total of 65 histopathologically confirmed OSCC tissue samples were included in case group along with an equal number of age and sex-matched normal tissue samples of oral cavity for the control group. c-Fos protein and m-RNA expressions were analyzed using immunohistochemistry and qRT-PCR, respectively. Results: A significant low expression of c-Fos protein was observed in OSCC cases than normal control subjects (p= <0.001). The mean percent positivity of c-Fos protein in cases vs. controls was 24.91± 2.7 vs. 49.68± 2.2 (p= <0.001). Most OSCC tissue samples showed weak or moderate c-Fos expression whereas 53.8% of normal tissue sections presented with strong immunostaining. Moreover, the relative m-RNA expression for the c-fos gene was significantly decreased in case group (0.93± 0.48) as compared to the control group (1.22± 0.87). Majority of c-Fos positive cases were diagnosed with well developed tumor. The mean percent positivity of c-Fos protein was significantly lower in higher grade tumor as compared with normal oral mucosa (p= < 0.001). Conclusion: The present study suggested that the c-fos gene is downregulated in oral carcinomas. The disparity of c-Fos protein levels in different pathological grades of tumor and normal oral tissue samples may indicate that loss of c-Fos expression is related with the progression of OSCC. PMID:29582647

Structural and functional studies of bioobjects prepared from femoral heads

NASA Astrophysics Data System (ADS)

Kirilova, I. A.; Sharkeev, Yu. P.; Podorozhnaya, V. T.; Popova, K. S.; Uvarkin, P. V.

2015-11-01

Results of examination of physicomechanical characteristics of samples of medial femoral head cuts are presented. The samples of medial femoral head cuts resected in 6 patients with coxarthrosis in primary endoprosthetic replacement of a coxofemoral joint have been tested for micro- and nanohardness. Young's modulus and elemental composition of bone tissue have been investigated. To estimate the architectonics of cancellous tissue of the femoral head, adjacent cuts of the same patient have been analyzed. The porosity of bone tissue was estimated from macroscopic images obtained using macrophotography. The total porosity is calculated as the ratio of the total length of straight line segments overlapping pores to the total length of secants. A three-point bending test of the samples has shown that their strength changed from 0.187 to 1.650 MPa and their elasticity modulus changes from 1.69 to 8.15 MPa. The microhardness of the samples changes in the range 220-265 MPa and the average microhardness of medial femoral head cuts is 240 MPa. The elemental composition of medial femoral head cuts is represented by basic Ca, P, O, Na and Mg elements as well as by Sn, S, Fe, Cr, and C in microamounts. The atomic Ca to P ratio for bone tissue is 1.55. It is revealed that pores of the upper part of the femoral head have a more regular shape and in the lower part they are more elongated along the cut and occupy a larger volume. The lower part of the femoral head has a higher porosity (39 and 33%) than the upper part (34 and 30%). The total porosity of all samples does not exceed 37%.

Validation of reference genes aiming accurate normalization of qRT-PCR data in Dendrocalamus latiflorus Munro.

PubMed

Liu, Mingying; Jiang, Jing; Han, Xiaojiao; Qiao, Guirong; Zhuo, Renying

2014-01-01

Dendrocalamus latiflorus Munro distributes widely in subtropical areas and plays vital roles as valuable natural resources. The transcriptome sequencing for D. latiflorus Munro has been performed and numerous genes especially those predicted to be unique to D. latiflorus Munro were revealed. qRT-PCR has become a feasible approach to uncover gene expression profiling, and the accuracy and reliability of the results obtained depends upon the proper selection of stable reference genes for accurate normalization. Therefore, a set of suitable internal controls should be validated for D. latiflorus Munro. In this report, twelve candidate reference genes were selected and the assessment of gene expression stability was performed in ten tissue samples and four leaf samples from seedlings and anther-regenerated plants of different ploidy. The PCR amplification efficiency was estimated, and the candidate genes were ranked according to their expression stability using three software packages: geNorm, NormFinder and Bestkeeper. GAPDH and EF1α were characterized to be the most stable genes among different tissues or in all the sample pools, while CYP showed low expression stability. RPL3 had the optimal performance among four leaf samples. The application of verified reference genes was illustrated by analyzing ferritin and laccase expression profiles among different experimental sets. The analysis revealed the biological variation in ferritin and laccase transcript expression among the tissues studied and the individual plants. geNorm, NormFinder, and BestKeeper analyses recommended different suitable reference gene(s) for normalization according to the experimental sets. GAPDH and EF1α had the highest expression stability across different tissues and RPL3 for the other sample set. This study emphasizes the importance of validating superior reference genes for qRT-PCR analysis to accurately normalize gene expression of D. latiflorus Munro.

Structural and functional studies of bioobjects prepared from femoral heads

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirilova, I. A., E-mail: IKirilova@niito.ru; Podorozhnaya, V. T., E-mail: VPodorognaya@niito.ru; Sharkeev, Yu. P., E-mail: sharkeev@ispms.tsc.ru

2015-11-17

Results of examination of physicomechanical characteristics of samples of medial femoral head cuts are presented. The samples of medial femoral head cuts resected in 6 patients with coxarthrosis in primary endoprosthetic replacement of a coxofemoral joint have been tested for micro- and nanohardness. Young’s modulus and elemental composition of bone tissue have been investigated. To estimate the architectonics of cancellous tissue of the femoral head, adjacent cuts of the same patient have been analyzed. The porosity of bone tissue was estimated from macroscopic images obtained using macrophotography. The total porosity is calculated as the ratio of the total length ofmore » straight line segments overlapping pores to the total length of secants. A three-point bending test of the samples has shown that their strength changed from 0.187 to 1.650 MPa and their elasticity modulus changes from 1.69 to 8.15 MPa. The microhardness of the samples changes in the range 220–265 MPa and the average microhardness of medial femoral head cuts is 240 MPa. The elemental composition of medial femoral head cuts is represented by basic Ca, P, O, Na and Mg elements as well as by Sn, S, Fe, Cr, and C in microamounts. The atomic Ca to P ratio for bone tissue is 1.55. It is revealed that pores of the upper part of the femoral head have a more regular shape and in the lower part they are more elongated along the cut and occupy a larger volume. The lower part of the femoral head has a higher porosity (39 and 33%) than the upper part (34 and 30%). The total porosity of all samples does not exceed 37%.« less

Mitigation of enniatins in edible fish tissues by thermal processes and identification of degradation products.

PubMed

Tolosa, J; Font, G; Mañes, J; Ferrer, E

2017-03-01

Emerging mycotoxins, such as enniatins and beauvericin, are common contaminants in vegetal matrices, but recently, the occurrence of mycotoxins in foodstuffs from animal origin has been also reported as they can be present in edible tissues of animals fed with contaminated feedstuffs. Sea bass, sea bream, Atlantic salmon and rainbow trout from aquaculture analyzed in the present survey showed contamination by emerging Fusarium mycotoxins enniatins (ENs). ENs were extracted from raw and cooked fish with acetonitrile and analyzed by Liquid Chromatography coupled to Mass Spectrometry. In this study, the stability of ENs was evaluated during food processing by the application of different cooking methods (broiling, boiling, microwaving and baking treatments). All treated samples showed a reduction in mycotoxin levels with different percentages depending on the type of EN and the fish species. Thus, the reduction obtained ranged from 30 to 100%. The thermal treatments have shown to be a good strategy to mitigate ENs content in edible fish tissues. On the other hand, some ENs degradation products originated during the application of thermal treatments were identified. Copyright © 2017 Elsevier Ltd. All rights reserved.

Intra-operative probe for brain cancer: feasibility study

NASA Astrophysics Data System (ADS)

Vu Thi, M. H.; Charon, Y.; Duval, M. A.; Lefebvre, F.; Menard, L.; Pitre, S.; Pinot, L.; Siebert, R.

2007-07-01

The present work aims a new medical probe for surgeons devoted to brain cancers, in particular glioblastoma multiforme. Within the last years, our group has started the development of a new intra-operative beta imaging probe. More recently, we took an alternative approach for the same application: a fluorescence probe. In both cases the purpose is to differentiate normal from tumor brain tissue. In a first step, we developed set-ups capable to measure autofluorescence. They are based on a dedicated epi-fluorescence design and on specific fiber optic probes. Relative signal amplitude, spectral shape and fluorescence lifetime measurements are foreseen to distinguish normal and cancer tissue by analyzing fluorophores like NADH, lipopigments and porphyrines. The autofluorescence spectra are recorded in the 460-640 nm range with a low resolution spectrometer. For lifetime measurements a fast detector (APD) is used together with a TCSPC-carte. Intrinsic wavelength- and time-resolutions are a few nm and 200 ps, respectively. Different samples have been analyzed to validate our new detection system and to allow a first configuration of our medical fluorescence probe. First results from the tissue measurements are shown.

Acaricide Residues in Laying Hens Naturally Infested by Red Mite Dermanyssus gallinae

PubMed Central

Marangi, Marianna; Morelli, Vincenzo; Pati, Sandra; Camarda, Antonio; Cafiero, Maria Assunta; Giangaspero, Annunziata

2012-01-01

In the poultry industry, control of the red mite D. gallinae primarily relies worldwide on acaricides registered for use in agriculture or for livestock, and those most widely used are carbamates, followed by amidines, pyrethroids and organophosphates. Due to the repeated use of acaricides - sometimes in high concentrations - to control infestation, red mites may become resistant, and acaricides may accumulate in chicken organs and tissues, and also in eggs. To highlight some situations of misuse/abuse of chemicals and of risk to human health, we investigated laying hens, destined to the slaughterhouse, for the presence of acaricide residues in their organs and tissues. We used 45 hens from which we collected a total of 225 samples from the following tissues and organs: skin, fat, liver, muscle, hearth, and kidney. In these samples we analyzed the residual contents of carbaryl and permethrin by LC-MS/MS. Ninety-one (40.4%) samples were positive to carbaryl and four samples (1.7%) were positive to permethrin. Concentrations of carbaryl exceeding the detection limit (0.005 ppm) were registered in the skin and fat of birds from two farms (p<0.01), although these concentrations remained below the maximum residue limit (MRLs) (0.05 ppm) (p<0.01). All organs/tissues of hens from a third farm were significantly more contaminated, with skin and muscle samples exceeding the MRL (0.05 ppm) (p<0.01) of carbaryl in force before its use was banned. Out of 45 chickens tested, 37 (82.2%) were found to be contaminated by carbaryl, and 4 (8.8%) by permethrin. The present study is the first report on the presence of pesticides banned by the EU (carbaryl) or not licensed for use (permethrin) in the organs and tissues of laying hens, which have been treated against red mites, and then slaughtered for human consumption at the end of their life cycle. PMID:22363736

Acaricide residues in laying hens naturally infested by red mite Dermanyssus gallinae.

PubMed

Marangi, Marianna; Morelli, Vincenzo; Pati, Sandra; Camarda, Antonio; Cafiero, Maria Assunta; Giangaspero, Annunziata

2012-01-01

In the poultry industry, control of the red mite D. gallinae primarily relies worldwide on acaricides registered for use in agriculture or for livestock, and those most widely used are carbamates, followed by amidines, pyrethroids and organophosphates. Due to the repeated use of acaricides--sometimes in high concentrations--to control infestation, red mites may become resistant, and acaricides may accumulate in chicken organs and tissues, and also in eggs. To highlight some situations of misuse/abuse of chemicals and of risk to human health, we investigated laying hens, destined to the slaughterhouse, for the presence of acaricide residues in their organs and tissues. We used 45 hens from which we collected a total of 225 samples from the following tissues and organs: skin, fat, liver, muscle, hearth, and kidney. In these samples we analyzed the residual contents of carbaryl and permethrin by LC-MS/MS.Ninety-one (40.4%) samples were positive to carbaryl and four samples (1.7%) were positive to permethrin. Concentrations of carbaryl exceeding the detection limit (0.005 ppm) were registered in the skin and fat of birds from two farms (p<0.01), although these concentrations remained below the maximum residue limit (MRLs) (0.05 ppm) (p<0.01). All organs/tissues of hens from a third farm were significantly more contaminated, with skin and muscle samples exceeding the MRL (0.05 ppm) (p<0.01) of carbaryl in force before its use was banned. Out of 45 chickens tested, 37 (82.2%) were found to be contaminated by carbaryl, and 4 (8.8%) by permethrin. The present study is the first report on the presence of pesticides banned by the EU (carbaryl) or not licensed for use (permethrin) in the organs and tissues of laying hens, which have been treated against red mites, and then slaughtered for human consumption at the end of their life cycle.

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections.

PubMed

Rudkjøbing, Vibeke Børsholt; Thomsen, Trine Rolighed; Xu, Yijuan; Melton-Kreft, Rachael; Ahmed, Azad; Eickhardt, Steffen; Bjarnsholt, Thomas; Poulsen, Steen Seier; Nielsen, Per Halkjær; Earl, Joshua P; Ehrlich, Garth D; Moser, Claus

2016-11-08

Necrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold standard for identification of pathogens is culture; however molecular methods for identification of microorganisms may provide a more rapid result and may be able to identify additional microorganisms that are not detected by culture. In this study, tissue samples (n = 20) obtained after debridement of 10 patients with NSTI were analyzed by standard culture, fluorescence in situ hybridization (FISH) and multiple molecular methods. The molecular methods included analysis of microbial diversity by 1) direct 16S and D2LSU rRNA gene Microseq 2) construction of near full-length 16S rRNA gene clone libraries with subsequent Sanger sequencing for most samples, 3) the Ibis T5000 biosensor and 4) 454-based pyrosequencing. Furthermore, quantitative PCR (qPCR) was used to verify and determine the relative abundance of Streptococcus pyogenes in samples. For 70 % of the surgical samples it was possible to identify microorganisms by culture. Some samples did not result in growth (presumably due to administration of antimicrobial therapy prior to sampling). The molecular methods identified microorganisms in 90 % of the samples, and frequently detected additional microorganisms when compared to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods. Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also made including infection by a) Acinetobacter baumannii, b) Streptococcus pneumoniae, and c) fungi, mycoplasma and Fusobacterium necrophorum. The study emphasizes that many pathogens can be involved in NSTIs, and that no specific "NSTI causing" combination of species exists. This means that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially for fulminant life-threatening infections such as NSTI.

Ectopic High Expression of E2-EPF Ubiquitin Carrier Protein Indicates a More Unfavorable Prognosis in Brain Glioma.

PubMed

Zhang, Xiaohui; Zhao, Fangbo; Zhang, Shujun; Song, Yichun

2017-04-01

Ubiquitination of proteins meant for elimination is a primary method of eukaryotic cellular protein degradation. The ubiquitin carrier protein E2-EPF is a key degradation enzyme that is highly expressed in many tumors. However, its expression and prognostic significance in brain glioma are still unclear. The aim of this study was to reveal how the level of E2-EPF relates to prognosis in brain glioma. Thirty low-grade and 30 high-grade brain glioma samples were divided into two tissue microarrays each. Levels of E2-EPF protein were examined by immunohistochemistry and immunofluorescence. Quantitative real-time polymerase chain reaction was used to analyze the level of E2-EPF in 60 glioma and 3 normal brain tissue samples. The relationship between E2-EPF levels and prognosis was analyzed by Kaplan-Meier survival curves. E2-EPF levels were low in normal brain tissue samples but high in glioma nuclei. E2-EPF levels gradually increased as glioma grade increased (p < 0.05). Ectopic E2-EPF levels in high-grade glioma were significantly higher than in low-grade glioma (p < 0.01). The 5-year survival rate of glioma patients with high E2-EPF levels was shorter than in patients with low expression (p < 0.05). Furthermore, the 5-year survival rate of patients with ectopic E2-EPF was significantly shorter than patients with only nuclear E2-EPF (p < 0.01). These results suggest that higher E2-EPF levels, especially ectopic, are associated with higher grade glioma and shorter survival. E2-EPF levels may play a key role in predicting the prognosis for patients with brain glioma.

LC-MS/MS-based quantification of kynurenine metabolites, tryptophan, monoamines and neopterin in plasma, cerebrospinal fluid and brain.

PubMed

Fuertig, René; Ceci, Angelo; Camus, Sandrine M; Bezard, Erwan; Luippold, Andreas H; Hengerer, Bastian

2016-09-01

The kynurenine (KYN) pathway is implicated in diseases such as cancer, psychiatric, neurodegenerative and autoimmune disorders. Measurement of KYN metabolite levels will help elucidating the involvement of the KYN pathway in the disease pathology and inform drug development. Samples of plasma, cerebrospinal fluid or brain tissue were spiked with deuterated internal standards, processed and analyzed by LC-MS/MS; analytes were chromatographically separated by gradient elution on a C18 reversed phase analytical column without derivatization. We established an LC-MS/MS method to measure 11 molecules, namely tryptophan, KYN, 3-OH-KYN, 3-OH-anthranilic acid, quinolinic acid, picolinic acid, kynurenic acid, xanthurenic acid, serotonin, dopamine and neopterin within 5.5 min, with sufficient sensitivity to quantify these molecules in small sample volumes of plasma, cerebrospinal fluid and brain tissue.

Cancer-adipose tissue interaction and fluid flow synergistically modulate cell kinetics, HER2 expression, and trastuzumab efficacy in gastric cancer.

PubMed

Akutagawa, Takashi; Aoki, Shigehisa; Yamamoto-Rikitake, Mihoko; Iwakiri, Ryuichi; Fujimoto, Kazuma; Toda, Shuji

2018-04-25

Early local tumor invasion in gastric cancer results in likely encounters between cancer cells and submucosal and subserosal adipose tissue, but these interactions remain to be clarified. Microenvironmental mechanical forces, such as fluid flow, are known to modulate normal cell kinetics, but the effects of fluid flow on gastric cancer cells are poorly understood. We analyzed the cell kinetics and chemosensitivity in gastric cancer using a simple in vitro model that simultaneously replicated the cancer-adipocyte interaction and physical microenvironment. Gastric cancer cells (MKN7 and MKN74) were seeded on rat adipose tissue fragment-embedded discs or collagen discs alone. To generate fluid flow, samples were placed on a rotatory shaker in a CO 2 incubator. Proliferation, apoptosis, invasion, and motility-related molecules were analyzed by morphometry and immunostaining. Proteins were evaluated by western blot analysis. Chemosensitivity was investigated by trastuzumab treatment. Adipose tissue and fluid flow had a positive synergistic effect on the proliferative potential and invasive capacity of gastric cancer cells, and adipose tissue inhibited apoptosis in these cells. Adipose tissue upregulated ERK1/2 signaling in gastric cancer cells, but downregulated p38 signaling. Notably, adipose tissue and fluid flow promoted membranous and cytoplasmic HER2 expression and modulated chemosensitivity to trastuzumab in gastric cancer cells. We have demonstrated that cancer-adipocyte interaction and physical microenvironment mutually modulate gastric cancer cell kinetics. Further elucidation of the microenvironmental regulation in gastric cancer will be very important for the development of strategies involving molecular targeted therapy.

Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples.

PubMed

Zhao, Qi; Liu, Yuanning; Zhang, Ning; Hu, Menghan; Zhang, Hao; Joshi, Trupti; Xu, Dong

2018-01-01

In recent years, an increasing number of studies have reported the presence of plant miRNAs in human samples, which resulted in a hypothesis asserting the existence of plant-derived exogenous microRNA (xenomiR). However, this hypothesis is not widely accepted in the scientific community due to possible sample contamination and the small sample size with lack of rigorous statistical analysis. This study provides a systematic statistical test that can validate (or invalidate) the plant-derived xenomiR hypothesis by analyzing 388 small RNA sequencing data from human samples in 11 types of body fluids/tissues. A total of 166 types of plant miRNAs were found in at least one human sample, of which 14 plant miRNAs represented more than 80% of the total plant miRNAs abundance in human samples. Plant miRNA profiles were characterized to be tissue-specific in different human samples. Meanwhile, the plant miRNAs identified from microbiome have an insignificant abundance compared to those from humans, while plant miRNA profiles in human samples were significantly different from those in plants, suggesting that sample contamination is an unlikely reason for all the plant miRNAs detected in human samples. This study also provides a set of testable synthetic miRNAs with isotopes that can be detected in situ after being fed to animals.

Selection of internal reference genes for normalization of quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis in the canine brain and other organs.

PubMed

Park, Sang-Je; Huh, Jae-Won; Kim, Young-Hyun; Lee, Sang-Rae; Kim, Sang-Hyun; Kim, Sun-Uk; Kim, Heui-Soo; Kim, Min Kyu; Chang, Kyu-Tae

2013-05-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive technique for quantifying gene expression. To analyze qRT-PCR data accurately, suitable reference genes that show consistent expression patterns across different tissues and experimental conditions should be selected. The objective of this study was to obtain the most stable reference genes in dogs, using samples from 13 different brain tissues and 10 other organs. 16 well-known candidate reference genes were analyzed by the geNorm, NormFinder, and BestKeeper programs. Brain tissues were derived from several different anatomical regions, including the forebrain, cerebrum, diencephalon, hindbrain, and metencephalon, and grouped accordingly. Combination of the three different analyses clearly indicated that the ideal reference genes are ribosomal protien S5 (RPS5) in whole brain, RPL8 and RPS5 in whole body tissues, RPS5 and RPS19 in the forebrain and cerebrum, RPL32 and RPS19 in the diencephalon, GAPDH and RPS19 in the hindbrain, and MRPS7 and RPL13A in the metencephalon. These genes were identified as ideal for the normalization of qRT-PCR results in the respective tissues. These findings indicate more suitable and stable reference genes for future studies of canine gene expression.

Raman spectroscopy and immunohistochemistry for schwannoma characterization: a case study

NASA Astrophysics Data System (ADS)

Neto, Lazaro P. M.; das Chagas, Maurilio J.; Carvalho, Luis Felipe C. S.; Ferreira, Isabelle; dos Santos, Laurita; Haddad, Marcelo; Loddi, Vinicius; Martin, Airton A.

2016-03-01

The schwannomas is a tumour of the tissue that covers nerves, called the nerve sheath. Schwannomas are often benign tumors of the Schwan cells, which are the principal glia of the peripheral nervous system (PNS). Preoperative diagnosis of this lesion usually is difficult, therefore, new techniques are being studied as pre surgical evaluation. Among these, Raman spectroscopy, that enables the biochemical identification of the tissue analyzed by their optical properties, may be used as a tool for schwannomas diagnosis. The aim of this study was to discriminate between normal nervous tissue and schwannoma through the confocal Raman spectroscopy and Raman optical fiber-based techniques combined with immunohistochemical analysis. Twenty spectra were analyzed from a normal nerve tissue sample (10) and schwannoma (10) by Holospec f / 1.8 (Kayser Optical Systems) coupled to an optical fiber with a 785nm laser line source. The data were pre-processed and vector normalized. The average analysis and standard deviation was performed associated with cluster analysis. AML, 1A4, CD34, Desmin and S-100 protein markers were used for immunohistochemical analysis. Immunohistochemical analysis was positive only for protein S-100 marker which confirmed the neural schwanomma originality. The immunohistochemistry analysis were important to determine the source of the injury, whereas Raman spectroscopy were able to differentiated tissues types indicating important biochemical changes between normal and benign neoplasia.

Substance P and neprilysin in chronic pancreatitis.

PubMed

Mascetta, G; di Mola, F F; Tavano, F; Selvaggi, F; Giese, N; Bassi, C; Büchler, M W; Friess, H; di Sebastiano, P

2012-01-01

We aimed to analyze substance P (SP) and neprilysin (NEP), the membrane metallopeptidase that degrades SP, in chronic pancreatitis (CP). SP and NEP mRNA levels were analyzed by qRT-PCR in tissue samples from 30 patients with CP and 8 organ donors. In addition, SP serum levels were determined before and after surgery in the same patients, by means of a competitive ELISA assay. Genetic and epigenetic analyses of the NEP gene were also performed. SP mRNA expression levels were higher in CP tissues compared to controls (p = 0.0152), while NEP mRNA showed no significant differences between CP and healthy subjects (p = 0.2102). In CP patients, SP serum levels correlated with those in tissue, and after surgical resection SP serum levels were reduced compared to the preoperative values. Failure of NEP to overexpress in CP tissues was associated with significant miR-128a overexpression (p = 0.02), rather than with mutations in the NEP coding region or the presence of hypermethylation sites in the NEP promoter region. Tissue and serum levels of SP were increased in CP, while NEP levels remained unaltered. In an SP/NEP-mediated pathway, it would appear that NEP fails to provide adequate surveillance of SP levels. Failure of NEP to overexpress could be associated with miRNA regulation. Copyright © 2012 S. Karger AG, Basel.

Occurrence of contaminants of emerging concern along the California coast (2009-10) using passive sampling devices.

PubMed

Alvarez, David A; Maruya, Keith A; Dodder, Nathan G; Lao, Wenjian; Furlong, Edward T; Smalling, Kelly L

2014-04-30

Three passive sampling devices (PSDs), polar organic chemical integrative samplers (POCIS), polyethylene devices (PEDs), and solid-phase microextraction (SPME) samplers were used to sample a diverse set of chemicals in the coastal waters of San Francisco Bay and the Southern California Bight. Seventy one chemicals (including fragrances, phosphate flame retardants, pharmaceuticals, PAHs, PCBs, PBDEs, and pesticides) were measured in at least 50% of the sites. The chemical profile from the San Francisco Bay sites was distinct from profiles from the sites in the Southern California Bight. This distinction was not due to a single compound or class, but by the relative abundances/concentrations of the chemicals. Comparing the PSDs to mussel (Mytilus spp.) tissues, a positive correlation exists for the 25 and 26 chemicals in common for the PEDs and SPME, respectively. Diphenhydramine was the only common chemical out of 40 analyzed in both POCIS and tissues detected at a common site. Published by Elsevier Ltd.

Occurrence of contaminants of emerging concern along the California coast (2009-10) using passive sampling devices

USGS Publications Warehouse

Alvarez, David A.; Maruya, Keith A.; Dodder, Nathan G.; Lao, Wenjian; Furlong, Edward T.; Smalling, Kelly L.

2014-01-01

Three passive sampling devices (PSDs), polar organic chemical integrative samplers (POCIS), polyethylene devices (PEDs), and solid-phase microextraction (SPME) samplers were used to sample a diverse set of chemicals in the coastal waters of San Francisco Bay and the Southern California Bight. Seventy one chemicals (including fragrances, phosphate flame retardants, pharmaceuticals, PAHs, PCBs, PBDEs, and pesticides) were measured in at least 50% of the sites. The chemical profile from the San Francisco Bay sites was distinct from profiles from the sites in the Southern California Bight. This distinction was not due to a single compound or class, but by the relative abundances/concentrations of the chemicals. Comparing the PSDs to mussel (Mytilus spp.) tissues, a positive correlation exists for the 25 and 26 chemicals in common for the PEDs and SPME, respectively. Diphenhydramine was the only common chemical out of 40 analyzed in both POCIS and tissues detected at a common site.

Data on occurrence of selected trace metals, organochlorines, and semivolatile organic compounds in edible fish tissues from Lake Worth, Fort Worth, Texas, 1999

USGS Publications Warehouse

Moring, J. Bruce

2002-01-01

A public-health assessment conducted for the Texas Department of Health and the Agency for Toxic Substances and Disease Registry concluded that exposure to contaminants through the aquatic food chain is an indeterminate human-health hazard in Lake Worth, Fort Worth, Texas. In 1999, the U.S. Geological Survey, in cooperation with the U.S. Air Force and in collaboration with the Texas Department of Health, collected samples of edible fish tissues from Lake Worth for analysis of selected trace metals, organochlorines, and semivolatile organic compounds to support a human-health risk assessment. Left-side, skin-off fillet samples were collected from 10 individuals each of channel catfish, common carp, freshwater drum (gaspergou), largemouth bass, and white crappie but only from five smallmouth buffalo. The U.S. Geological Survey National Water Quality Laboratory analyzed the samples for 22 trace metals, 40 organochlorine pesticides and polychlorinated biphenyls, and 75 semivolatile organic compounds.

Analysis of the distribution and expression of claudin-1 tight junction protein in the oral cavity.

PubMed

Ouban, Abderrahman; Ahmed, Atif

2015-07-01

Claudins are the main sealing proteins of the intercellular tight junctions and play an important role in cancer cell progression and dissemination. The authors have previously shown that overexpression of claudin-1 is associated with angiolymphatic and perineural invasion, consistent with aggressive tumor behavior and with advanced stage disease in oral squamous cell carcinomas (OSCCs). Our goal in this study was to examine claudin-1 expression in a tissue microarray of OSCCs taken from multiple sites within the oral cavity. This study examined and compared the expression of claudin-1 by immunohistochemistry in 60 tissue samples (49 OSCCs and 10 cases of non-neoplastic tissue, single core per case) were analyzed for claudin-1 expression by immunohistochemistry. The tumors included SCCs from the tongue (n=28), the cheek (n=9), gingival (n=4), lip (n=3), and oral cavity (n=5). Nonmalignant normal oral mucosa from the tongue (unmatched cases, n=2). Cancer adjacent tissue samples were taken from the tongue (n=6), gingival (n=2), and palate (n=1). This study demonstrates the expression of claudin-1 protein across a sample of OSCCs originating from multiple locations in the oral cavity. The highest expression of claudin-1 was observed in well-differentiated OSCCs, whereas poorly differentiated OSCCs exhibited mostly negative staining for claudin-1. In addition, we hereby report differential pattern of expression among tumors of different sites within the oral cavity, and between benign and cancerous samples. Our understanding of the exact function and role of claudin-1 in tumorigenesis is expanding exponentially.

TaqMan real-time RT-PCR detection of infectious salmon anaemia virus (ISAV) from formalin-fixed paraffin-embedded Atlantic salmon Salmo salar tissues.

PubMed

Godoy, M G; Kibenge, F S; Kibenge, M J; Olmos, P; Ovalle, L; Yañez, A J; Avendaño-Herrera, R

2010-05-18

The objective of this study was to evaluate the application of a TaqMan real-time reverse transcriptase PCR (RT-PCR) assay for the detection of infectious salmon anaemia virus (ISAV) in formalin-fixed paraffin-embedded (FFPE) fish tissues from Atlantic salmon Salmo salar with and without clinical signs of infection, and to compare it with histological and immunohistochemical (IHC) techniques. Sixteen fish samples obtained in 2007 and 2008 from 4 different farms in Chile were examined. The real-time RT-PCR allowed the detection of ISAV in FFPE samples from 9 of 16 fish, regardless of the organs analyzed, whereas 4 of the real-time RT-PCR negative fish were positive as indicated by histological examination and 3 of the real-time RT-PCR positive fish were negative as indicated by immunohistochemistry evaluation. The presence of ISAV in RT-PCR positive samples was confirmed by amplicon sequencing. This work constitutes the first report on the use of real-time RT-PCR for the detection of ISAV in FFPE sections. The assay is very useful for the examination of archival wax-embedded tissues, and allows for both prospective and retrospective evaluation of tissue samples for the presence of ISAV. However, the method only confirms the presence of the pathogen and should be used in combination with histopathology, which is a more precise tool. The combination of both techniques would be invaluable for confirmatory diagnosis of infectious salmon anaemia (ISA), which is essential for solving salmon farm problems.

Chromatically encoded high-speed photography of cavitation bubble dynamics inside inhomogeneous ophthalmic tissue

NASA Astrophysics Data System (ADS)

Tinne, N.; Matthias, B.; Kranert, F.; Wetzel, C.; Krüger, A.; Ripken, T.

2016-03-01

The interaction effect of photodisruption, which is used for dissection of biological tissue with fs-laser pulses, has been intensively studied inside water as prevalent sample medium. In this case, the single effect is highly reproducible and, hence, the method of time-resolved photography is sufficiently applicable. In contrast, the reproducibility significantly decreases analyzing more solid and anisotropic media like biological tissue. Therefore, a high-speed photographic approach is necessary in this case. The presented study introduces a novel technique for high-speed photography based on the principle of chromatic encoding. For illumination of the region of interest within the sample medium, the light paths of up to 12 LEDs with various emission wavelengths are overlaid via optical filters. Here, MOSFET-electronics provide a LED flash with a duration <100 ns; the diodes are externally triggered with a distinct delay for every LED. Furthermore, the different illumination wavelengths are chromatically separated again for detection via camera chip. Thus, the experimental setup enables the generation of a time-sequence of <= 12 images of a single cavitation bubble dynamics. In comparison to conventional time-resolved photography, images in sample media like water and HEMA show the significant advantages of this novel illumination technique. In conclusion, the results of this study are of great importance for the fundamental evaluation of the laser-tissue interaction inside anisotropic biological tissue and for the optimization of the surgical process with high-repetition rate fs-lasers. Additionally, this application is also suitable for the investigation of other microscopic, ultra-fast events in transparent inhomogeneous materials.

Thermographic study of laser on arteries.

PubMed

Mnitentag, J; Marques, E F; Ribeiro, M P; Braga, G A; Navarro, M R; Veratti, A B; Armelin, E; Macruz, R; Jatene, A D

1987-01-01

We analyzed the different effects of CO2, Nd-YAG, and argon lasers on aorta by using a Thermovision infrared system that registered the laser interaction with mongrel dog aorta. The images (thermograms) obtained were processed by a computer, which associated each area of the same temperature with a determined color. These thermograms were compared to histological analysis of the respective samples and the following results were obtained: (1) After the application of each laser there is very little propagation of heat in tissue. (2) The CO2 laser makes tissue reach 100 degrees C in less than 0.05 seconds. (3) The heat dissipation time was higher with the Nd-YAG laser due to higher scattering on tissue. Based on this research we conclude that the CO2 laser was best absorbed, the Nd-YAG laser penetrated human tissue with the best results, and the argon laser had the most significant backscattering.

Preparation and Respirometric Assessment of Mitochondria Isolated from Skeletal Muscle Tissue Obtained by Percutaneous Needle Biopsy

PubMed Central

Bharadwaj, Manish S.; Tyrrell, Daniel J.; Lyles, Mary F.; Demons, Jamehl L.; Rogers, George W.; Molina, Anthony J. A.

2015-01-01

Respirometric profiling of isolated mitochondria is commonly used to investigate electron transport chain function. We describe a method for obtaining samples of human Vastus lateralis, isolating mitochondria from minimal amounts of skeletal muscle tissue, and plate based respirometric profiling using an extracellular flux (XF) analyzer. Comparison of respirometric profiles obtained using 1.0, 2.5 and 5.0 μg of mitochondria indicate that 1.0 μg is sufficient to measure respiration and that 5.0 μg provides most consistent results based on comparison of standard errors. Western blot analysis of isolated mitochondria for mitochondrial marker COX IV and non-mitochondrial tissue marker GAPDH indicate that there is limited non-mitochondrial contamination using this protocol. The ability to study mitochondrial respirometry in as little as 20 mg of muscle tissue allows users to utilize individual biopsies for multiple study endpoints in clinical research projects. PMID:25741892

Express diagnostics of intact and pathological dental hard tissues by optical PNC method

NASA Astrophysics Data System (ADS)

Masychev, Victor I.; Alexandrov, Michail T.

2000-03-01

The results of hard tooth tissues research by the optical PNC- method in experimental and clinical conditions are presented. In the experiment under 90 test-sample of tooth slices with thickness about 1 mm (enamel, dentine and cement) were researched. The results of the experiment were processed by the method of correlation analyze. Clinical researches were executed on teeth of 210 patients. The regions of tooth tissue diseases with initial, moderate and deep caries were investigated. Spectral characteristics of intact and pathologically changed tooth tissues are presented and their peculiar features are discussed. The results the optical PNC- method application while processing tooth carious cavities are presented in order to estimate efficiency of the mechanical and antiseptic processing of teeth. It is revealed that the PNC-method can be used as for differential diagnostics of a degree dental carious stage, as for estimating of carefulness of tooth cavity processing before filling.

Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits?

USDA-ARS?s Scientific Manuscript database

It has been more than 10 years since the concept of the ionome, all of the mineral nutrients in a cell tissue or organism, was introduced. In the intervening years, ionomics, high throughput elemental profiling, has been used to analyze over 400,000 samples from at least 7 different organisms. There...

Determination of relative protein degradation activity at different life stages in rainbow trout (Oncorhynchus mykiss) fed fishmeal or plant based diets.

USDA-ARS?s Scientific Manuscript database

Rainbow trout were reared on a diet formulated to supply the required protein from either fishmeal or protein meal sources. From liver and muscle tissue samples RNA and protein were isolated and analyzed for the expression of a number of muscle regulatory and protein degradation genes and enzymatic...

Increased tenascin C and Toll-like receptor 4 levels in visceral adipose tissue as a link between inflammation and extracellular matrix remodeling in obesity.

PubMed

Catalán, Victoria; Gómez-Ambrosi, Javier; Rodríguez, Amaia; Ramírez, Beatriz; Rotellar, Fernando; Valentí, Victor; Silva, Camilo; Gil, María J; Salvador, Javier; Frühbeck, Gema

2012-10-01

Obesity is associated with an altered inflammatory and extracellular matrix (ECM) profile. Tenascin C (TNC) is an ECM glycoprotein with proinflammatory effects. We aimed to explore the expression levels of TNC in adipose tissue analyzing the contribution of adipocytes and stromovascular fraction cells (SVFC) as well as its impact on inflammation and ECM regulation. We also analyzed the effect of the stimulation with TNF-α and lipopolysaccharide (LPS) on both SVFC and adipocytes. Samples obtained from 75 subjects were used in the study. Expression levels of TNC, TLR4, MMP2, and MMP9 were analyzed in visceral adipose tissue (VAT) as well as in both adipocytes and SVFC. In addition, Tnc expression was measured in two mice models of obesity. We show, for the first time, that VAT expression levels of TNC are increased in normoglycemic and type 2 diabetic obese patients (P<0.01) as well as in obese patients with nonalcoholic steatohepatitis (P<0.01). Furthermore, expression levels of Tnc in epididymal adipose tissue from two different mice models of obesity were significantly increased (P<0.01). TNC and TLR4 were mainly expressed by SVFC, and its expression was significantly enhanced (P<0.01) by TNF-α treatment. LPS treatment also increased mRNA levels of TNC. Moreover, the addition of exogenous TNC induced (P<0.05) TLR4 and CCL2 mRNA expression in human adipocyte cultures. These findings indicate that TNC is involved in the etiopathology of obesity via visceral adipose tissue inflammation representing a link with ECM remodeling.

Prevalence of human papilloma virus in marginal periodontium and its association with periodontitis: A cross sectional study.

PubMed

Jacob, Anila; Janam, Presanthila; Babu Vijayamma, Janki Mohan

2014-07-01

Bacterial pathogens in dental plaque are necessary for the development of periodontitis but this etiology alone does not explain all its clinicopathologic features. Researchers have proven the role of certain viruses like herpes virus in periodontal disease which implies that other viral agents like human papilloma virus may also be involved. This cross-sectional study was conducted to determine the proportion of patients with human papilloma virus (HPV-16) in marginal periodontium by analyzing DNA from the gingival tissue sample and to understand its association with periodontitis. 102 systemically healthy patients between the age group of 15 and 70 years reporting to the Department of Periodontology who required surgical intervention (flap surgery for patients with periodontitis and crown lengthening for healthy patients) with internal bevel gingivectomy were selected. After scaling and root planning, gingival tissue was collected during the respective surgical procedure. DNA was isolated and amplified using specific primers for HPV-16 by polymerase chain reaction (PCR). The amplified products were checked by agarose gel electrophoresis. No HPV DNA was detected in the 102 samples analyzed. Marginal periodontium does not contain HPV in this study population and hence there was no association between HPV and periodontitis.

Authentication of meat products: determination of animal feeding by parallel GC-MS analysis of three adipose tissues.

PubMed

Sivadier, Guilhem; Ratel, Jérémy; Bouvier, Frédéric; Engel, Erwan

2008-11-12

Authentication of farm animal rearing conditions, especially the type of feeding, is a key issue in certification of meat quality and meat products. The purpose of this article was to analyze in parallel the volatile fraction of three adipose tissues excised from 16 lambs in order to authenticate two animal diets: pasture (n = 8) and concentrate (n = 8). On the basis of growth rate and anatomical location, three different lamb adipose tissues were analyzed: perirenal fat (PRF), caudal subcutaneous fat (CSCF), and heart fat (HF). An initial experiment was used to optimize the extraction of volatile compounds from the adipose tissues. Using a lipid liquid phase extraction, heating the ground tissue to 70 degrees C, was shown to be the best sample preparation mode before dynamic headspace-gas chromatography-mass spectrometry (DH-GC-MS) analysis to achieve a good representation of the starting material, while getting a good extraction and reproducibility. Next, the application of an instrumental drifts correction procedure to DH-GC-MS data enabled the identification of 130 volatile compounds that discriminate the two diets in one or several of the three tissues: 104 were found in PRF, 75 in CSCF, and 70 in HF. Forty-eight of these diet tracers, including 2,3-octanedione, toluene, terpenes, alkanes, alkenes, and ketones, had previously been identified as ruminant pasture-diet tracers and can be considered generic of this type of animal feeding. Moreover, 49 of the 130 compounds could identify diets in only one tissue, suggesting that complementary analysis of several tissues is superior for diet identification. Finally, multivariate discriminant analyses confirmed that the discrimination was improved when PRF, CSCF, and HF were considered simultaneously, even if HF contributed minimal information.

Rapid in situ detection of alkaloids in plant tissue under ambient conditions using desorption electrospray ionization.

PubMed

Talaty, Nari; Takáts, Zoltán; Cooks, R Graham

2005-12-01

Desorption electrospray ionization (DESI) mass spectrometry is applied to the in situ detection of alkaloids in the tissue of poison hemlock (Conium maculatum), jimsonweed (Datura stramonium) and deadly nightshade (Atropa belladonna). The experiment is carried out by electrospraying micro-droplets of solvent onto native or freshly-cut plant tissue surfaces. No sample preparation is required and the mass spectra are recorded under ambient conditions, in times of a few seconds. The impact of the sprayed droplets on the surface produces gaseous ions from organic compounds originally present in the plant tissue. The effects of operating parameters, including the electrospray high voltage, heated capillary temperature, the solvent infusion rate and the carrier gas pressure on analytical performance are evaluated and optimized. Different types of plant material are analyzed including seeds, stems, leaves, roots and flowers. All the previously reported alkaloids have been detected in C. maculatum, while fifteen out of nineteen known alkaloids for D. stramonium and the principal alkaloids of A. belladonna were also identified. All identifications were confirmed by tandem mass spectrometry. Results obtained show similar mass spectra, number of alkaloids, and signal intensities to those obtained when extraction and separation processes are performed prior to mass spectrometric analysis. Evidence is provided that DESI ionization occurs by both a gas-phase ionization process and by a droplet pick-up mechanism. Quantitative precision of DESI is compared with conventional electrospray ionization mass spectrometry (after sample workup) and the RSD values for the same set of 25 dicotyledonous C. maculatum seeds (one half of each seed analyzed by ESI and the other by DESI) are 9.8% and 5.2%, respectively.

Quantitative determination of selenium and mercury, and an ICP-MS semi-quantitative scan of other elements in samples of eagle tissues collected from the Pacific Northwest--Summer 2011

USGS Publications Warehouse

May, Thomas; Walther, Mike; Brumbaugh, William

2013-01-01

Eagle tissues from dead eagle carcasses were collected by U.S. Fish and Wildlife Service personnel at various locations in the Pacific Northwest as part of a study to document the occurrence of metal and metalloid contaminants. A group of 182 eagle tissue samples, consisting of liver, kidney, brain, talon, feather, femur, humerus, and stomach contents, were quantitatively analyzed for concentrations of selenium and mercury by atomic absorption techniques, and for other elements by semi-quantitative scan with an inductively coupled plasma-mass spectrometer. For the various tissue matrices analyzed by an ICP-MS semiquantitative scan, some elemental concentrations (micrograms per gram dry weight) were quite variable within a particular matrix; notable observations were as follows: lead concentrations ranged from 0.2 to 31 in femurs, 0.1 to 29 in humeri, 0.1 to 54 in talons, less than (<) 0.05 to 120 in livers, <0.05 to 34 in kidneys, and 0.05 to 8 in brains; copper concentrations ranged from 5 to 9 in feathers, 8 to 47 in livers, 7 to 43 in kidneys, and 7 to 28 in brains; cadmium concentrations ranged from 0.1 to 10 in kidneys. In stomach contents, concentrations of vanadium ranged from 0.08 to 5, chromium 2 to 34, manganese 1 to 57, copper 2 to 69, arsenic <0.05 to 6, rubidium 1 to 13, and barium <0.5 to 18. Selenium concentrations from highest to lowest based on the matrix mean were as follows: kidney, liver, feather, brain, stomach content, talon, femur, and humerus. For mercury, the highest to lowest concentrations were feather, liver, talon, brain, stomach content, femur, and humerus.

The G protein-coupled estrogen receptor 1 (GPER/GPR30) does not predict survival in patients with ovarian cancer

PubMed Central

2012-01-01

Background Even though ovarian tumors are not generally considered estrogen-sensitive, estrogens may still have an impact on ovarian tumor progression. The recently identified trans-membrane estrogen receptor GPER is involved in rapid estrogen signaling. Furthermore, it binds selective estrogen receptor modulators with agonistic effect, which could explain tamoxifen controversies. Methods GPER mRNA was assayed with quantitative real-time PCR (qPCR) in 42 primary ovarian tumors and 7 ovarian cancer cell lines. ERα and ERβ mRNA were analyzed for comparison. GPER protein was semi-quantified with densitometric scanning of Western blots and its tissue distribution analyzed with immunohistochemistry (IHC) in 40 ovarian tumors. In addition, IHC was evaluated in a tissue microarray (TMA) of 150 primary malignant ovarian tumors. Results All tumor samples contained GPER mRNA. The content of mRNA was not different between benign and malignant tumors, but one third of malignant samples over-expressed GPER mRNA. The content of ERα mRNA was higher in malignant than in benign tumors, whereas ERβ mRNA was higher in benign than in malignant tumors. GPER mRNA was detected in all seven ovarian cancer cell lines with highest levels in TOV21G and TOV112D cells. Similar expression pattern was seen for ERβ mRNA. Western blot demonstrated GPER protein in all tumor samples. Semi-quantification showed no difference between benign and malignant tumors, but about one third of malignant samples over-expressed GPER protein. GPER staining was localized mainly in epithelial cells. In the TMA study we found no correlation between GPER staining and clinical stage, histological grade or patient survival. Conclusions GPER mRNA as well as GPER protein is present in both benign and malignant ovarian tumor tissue. About one third of malignant tumors over-expressed both GPER mRNA and protein. This, however, correlated neither with histological or clinical parameters nor with patient survival. PMID:22424333

Identification of miRNAs Expression Profile in Gastric Cancer Using Self-Organizing Maps (SOM)

PubMed Central

Gomes, Larissa Luz; Moreira, Fabiano Cordeiro; Hamoy, Igor Guerreiro; Santos, Sidney; Assumpção, Paulo; Santana, Ádamo L.; Ribeiro-dos-Santos, Ândrea

2014-01-01

In this paper, an unsupervised artificial neural network was implemented to identify the patters of specific signatures. The network was based on the differential expression of miRNAs (under or over expression) found in healthy or cancerous gastric tissues. Among the tissues analyzes, the neural network evaluated 514 miRNAs of gastric tissue that exhibited significant differential expression. The result suggested a specific expression signature nine miRNAs (hsa-mir-21, hsa-mir-29a, hsa-mir-29c, hsa-mir-148a, hsa-mir-141, hsa-let-7b, hsa-mir-31, hsa-mir-451, and hsa-mir-192), all with significant values (p-value < 0.01 and fold change > 5) that clustered the samples into two groups: healthy tissue and gastric cancer tissue. The results obtained “in silico” must be validated in a molecular biology laboratory; if confirmed, this method may be used in the future as a risk marker for gastric cancer development. PMID:24966529

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ballachey, B.E.; Kloecker, K.A.

Ten moderately to heavily oiled sea otters were collected in Prince William Sound during the Exxon Valdez oil spill and up to seven tissues from each were analyzed for hydrocarbons. Aliphatic and aromatic hydrocarbons were detected in all tissues. Concentrations of aromatic hydrocarbons in fat samples were an order of magnitude higher than in other tissues. The patterns of distribution of these hydrocarbons suggested crude oil as the source of contamination. However, there was variation among oiled otters in the concentrations of individual hydrocarbons, which may be due to differing proximate causes of mortality and varying lengths of time andmore » sea otters survived following oil exposure. The concentrations of both aliphatic and aromatic hydrocarbons in the tissues of the ten oiled sea otters generally were higher than in tissues from 7 sea otters with no external oiling that were collected from prince William Sound in 1989 and 1990, or from 12 sea otters collected from an area in southeast Alaska which had not experienced an oil spill.« less

Elemental concentration analysis in prostate tissues using total reflection X-ray fluorescence

NASA Astrophysics Data System (ADS)

Leitão, R. G.; Palumbo, A.; Souza, P. A. V. R.; Pereira, G. R.; Canellas, C. G. L.; Anjos, M. J.; Nasciutti, L. E.; Lopes, R. T.

2014-02-01

Prostate cancer (PCa) currently represents the second most prevalent malignant neoplasia in men, representing 21% of all cancer cases. Benign Prostate Hyperplasia (BPH) is an illness prevailing in men above the age of 50, close to 90% after the age of 80. The prostate presents a high zinc concentration, about 10-fold higher than any other body tissue. In this work, samples of human prostate tissues with cancer, BPH and normal tissue were analyzed utilizing total reflection X-ray fluorescence spectroscopy using synchrotron radiation technique (SR-TXRF) to investigate the differences in the elemental concentrations in these tissues. SR-TXRF analyses were performed at the X-ray fluorescence beamline at Brazilian National Synchrotron Light Laboratory (LNLS), in Campinas, São Paulo. It was possible to determine the concentrations of the following elements: P, S, K, Ca, Fe, Cu, Zn and Rb. By using Mann-Whitney U test it was observed that almost all elements presented concentrations with significant differences (α=0.05) between the groups studied.

Core needle biopsy of soft tissue tumors, CEUS vs US guided: a pilot study.

PubMed

Coran, Alessandro; Di Maggio, Antonio; Rastrelli, Marco; Alberioli, Enrico; Attar, Shady; Ortolan, Paolo; Bortolanza, Carlo; Tosi, Annalisa; Montesco, Maria Cristina; Bezzon, Elisabetta; Rossi, Carlo Riccardo; Stramare, Roberto

2015-12-01

The purpose of this study was to evaluate the usefulness of contrast-enhanced ultrasonography (CEUS) in the bioptic sampling of soft tissue tumors (STT) compared with unenhanced ultrasonography alone. This is a prospective longitudinal study of 40 patients subjected to ultrasonography (US)-guided core needle biopsy (CNB) to characterize a suspected STT. Three series of bioptic samplings were carried out on each patient, respectively using unenhanced US alone and CEUS in both the areas of the tumor enhanced or not by the contrast medium. All bioptic samples underwent a histological evaluation and the results were analyzed by comparing the histology of the biopsy with the definitive diagnosis in 15 surgically excised samples. 27 (67.5 %) of the 40 patients completed the entire study procedure; in 19 cases (70.3 %) the three bioptic samplings gave unanimous results, also when compared to the surgical specimen; in seven cases (25.9 %) use of CEUS allowed to obtain additional or more accurate information about the mass in question, compared to simple US guidance without contrast; in one patient (3.7 %) sampling obtained using unenhanced ultrasonography guidance and in the areas enhanced by the contrast agent had precisely the same results of the surgical specimen. CEUS, due to its ability to evaluate microvascular areas, has proven to be a promising method in guiding bioptic sampling of soft tissue tumor, directing the needle to the most significant areas of the tumor. Given the small number of patients evaluated in our study, to achieve statistically significant results, it would be appropriate to obtain a larger sample size, since the very first results seem to be encouraging and to justify the increase of the population.

Radiation-Induced Changes in Serum Lipidome of Head and Neck Cancer Patients

PubMed Central

Jelonek, Karol; Pietrowska, Monika; Ros, Malgorzata; Zagdanski, Adam; Suchwalko, Agnieszka; Polanska, Joanna; Marczyk, Michal; Rutkowski, Tomasz; Skladowski, Krzysztof; Clench, Malcolm R.; Widlak, Piotr

2014-01-01

Cancer radiotherapy (RT) induces response of the whole patient’s body that could be detected at the blood level. We aimed to identify changes induced in serum lipidome during RT and characterize their association with doses and volumes of irradiated tissue. Sixty-six patients treated with conformal RT because of head and neck cancer were enrolled in the study. Blood samples were collected before, during and about one month after the end of RT. Lipid extracts were analyzed using MALDI-oa-ToF mass spectrometry in positive ionization mode. The major changes were observed when pre-treatment and within-treatment samples were compared. Levels of several identified phosphatidylcholines, including (PC34), (PC36) and (PC38) variants, and lysophosphatidylcholines, including (LPC16) and (LPC18) variants, were first significantly decreased and then increased in post-treatment samples. Intensities of changes were correlated with doses of radiation received by patients. Of note, such correlations were more frequent when low-to-medium doses of radiation delivered during conformal RT to large volumes of normal tissues were analyzed. Additionally, some radiation-induced changes in serum lipidome were associated with toxicity of the treatment. Obtained results indicated the involvement of choline-related signaling and potential biological importance of exposure to clinically low/medium doses of radiation in patient’s body response to radiation. PMID:24747595

Analysis of disease-associated protein expression using quantitative proteomics—fibulin-5 is expressed in association with hepatic fibrosis.

PubMed

Bracht, Thilo; Schweinsberg, Vincent; Trippler, Martin; Kohl, Michael; Ahrens, Maike; Padden, Juliet; Naboulsi, Wael; Barkovits, Katalin; Megger, Dominik A; Eisenacher, Martin; Borchers, Christoph H; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

2015-05-01

Hepatic fibrosis and cirrhosis are major health problems worldwide. Until now, highly invasive biopsy remains the diagnostic gold standard despite many disadvantages. To develop noninvasive diagnostic assays for the assessment of liver fibrosis, it is urgently necessary to identify molecules that are robustly expressed in association with the disease. We analyzed biopsied tissue samples from 95 patients with HBV/HCV-associated hepatic fibrosis using three different quantification methods. We performed a label-free proteomics discovery study to identify novel disease-associated proteins using a subset of the cohort (n = 27). Subsequently, gene expression data from all available clinical samples were analyzed (n = 77). Finally, we performed a targeted proteomics approach, multiple reaction monitoring (MRM), to verify the disease-associated expression in samples independent from the discovery approach (n = 68). We identified fibulin-5 (FBLN5) as a novel protein expressed in relation to hepatic fibrosis. Furthermore, we confirmed the altered expression of microfibril-associated glycoprotein 4 (MFAP4), lumican (LUM), and collagen alpha-1(XIV) chain (COL14A1) in association to hepatic fibrosis. To our knowledge, no tissue-based quantitative proteomics study for hepatic fibrosis has been performed using a cohort of comparable size. By this means, we add substantial evidence for the disease-related expression of the proteins examined in this study.

The effects of sample preparation on measured concentrations of eight elements in edible tissues of fish from streams contaminated by lead mining

USGS Publications Warehouse

Schmitt, Christopher J.; Finger, Susan E.

1987-01-01

The influence of sample preparation on measured concentrations of eight elements in the edible tissues of two black basses (Centrarchidae), two catfishes (Ictaluridae), and the black redhorse,Moxostoma duquesnei (Catostomidae) from two rivers in southeastern Missouri contaminated by mining and related activities was investigated. Concentrations of Pb, Cd, Cu, Zn, Fe, Mn, Ba, and Ca were measured in two skinless, boneless samples of axial muscle from individual fish prepared in a clean room. One sample (normally-processed) was removed from each fish with a knife in a manner typically used by investigators to process fish for elemental analysis and presumedly representative of methods employed by anglers when preparing fish for home consumption. A second sample (clean-processed) was then prepared from each normally-processed sample by cutting away all surface material with acid-cleaned instruments under ultraclean conditions. The samples were analyzed as a single group by atomic absorption spectrophotometry. Of the elements studied, only Pb regularly exceeded current guidelines for elemental contaminants in foods. Concentrations were high in black redhorse from contaminated sites, regardless of preparation method; for the other fishes, whether or not Pb guidelines were exceeded depended on preparation technique. Except for Mn and Ca, concentrations of all elements measured were significantly lower in cleanthan in normally-processed tissue samples. Absolute differences in measured concentrations between clean- and normally-processed samples were most evident for Pb and Ba in bass and catfish and for Cd and Zn in redhorse. Regardless of preparation method, concentrations of Pb, Ca, Mn, and Ba in individual fish were closely correlated; samples that were high or low in one of these four elements were correspondingly high or low in the other three. In contrast, correlations between Zn, Fe, and Cd occurred only in normallyprocessed samples, suggesting that these correlations resulted from high concentrations on the surfaces of some samples. Concentrations of Pb and Ba in edible tissues of fish from contaminated sites were highly correlated with Ca content, which was probably determined largely by the amount of tissue other than muscle in the sample because fish muscle contains relatively little Ca. Accordingly, variation within a group of similar samples can be reduced by normalizing Pb and Ba concentrations to a standard Ca concentration. When sample size (N) is large, this can be accomplished statistically by analysis of covariance; whenN is small, molar ratios of [Pb]/[Ca] and [Ba]/[Ca] can be computed. Without such adjustments, unrealistically large Ns are required to yield statistically reliable estimates of Pb concentrations in edible tissues. Investigators should acknowledge that reported concentrations of certain elements are only estimates, and that regardless of the care exercised during the collection, preparation, and analysis of samples, results should be interpreted with the awareness that contamination from external sources may have occurred.

[Determination of trace Cs, Th and U in ten kinds of human autopsy tissues by ICP-MS].

PubMed

Wang, Jing-yu; Zhu, Hong-da; Ouyang, Li; Liu, Ya-qiong; Wang, Xiao-yan; Huang, Zhuo; Wang, Nai-fen; Liu, Hu-sheng

2004-09-01

This paper studied the trace elements Cs, Th and U in ten kinds of human autopsy tissues by ICP-MS. The instrumental operating conditions were optimized for the measurement of Cs, Th and U. Rhodium (Rh) was used as an internal standard element to compensate matrix effect. Detection limits for Th, U and Cs were 5.7-17.8 pg x mL(-1). The recoveries for spiking liver samples were 96%-107%, and their RSDs were 4.8%-8.9%. Reference materials of NIST SRM 8414 Bovine and NIST SRM 1486 Bone Meal were analyzed by the described method, and the analytical results agreed well with the reference values. Human autopsy tissues samples were digested by mixed acid (HNO3 + HClO4). The determination of Cs, Th and U in lung, liver, bone, heart, stomach, spleen, muscle, kidney, thyroid gland and intestinum tenue was performed by ICP-MS without separation and enrichment procedures. The obtained results indicated that this method is rapid, sensitive and accurate; the distribution of the three elements is different from one to another human organ sample; the main organ targets for Th and U are lungs and kidneys; and a coordinated variation of Cs, Th and U concentration in lungs was found in the samples collected from Hebei and Sichuan provinces.

Can we trust intraoperative culture results in nonunions?

PubMed

Palmer, Michael P; Altman, Daniel T; Altman, Gregory T; Sewecke, Jeffrey J; Ehrlich, Garth D; Hu, Fen Z; Nistico, Laura; Melton-Kreft, Rachel; Gause, Trent M; Costerton, John W

2014-07-01

To identify the presence of bacterial biofilms in nonunions comparing molecular techniques (multiplex polymerase chain reaction and mass spectrometry, fluorescent in situ hybridization) with routine intraoperative cultures. Thirty-four patients with nonunions were scheduled for surgery and enrolled in this ongoing prospective study. Intraoperative specimens were collected from removed implants, surrounding tissue membrane, and local soft tissue followed by standard culture analysis, Ibis's second generation molecular diagnostics (Ibis Biosystems), and bacterial 16S rRNA-based fluorescence in situ hybridization (FISH). Confocal microscopy was used to visualize the tissue specimens reacted with the FISH probes, which were chosen based on the Ibis analysis. Thirty-four patient encounters were analyzed. Eight were diagnosed as infected nonunions by positive intraoperative culture results. Ibis confirmed the presence of bacteria in all 8 samples. Ibis identified bacteria in a total of 30 of 34 encounters, and these data were confirmed by FISH. Twenty-two of 30 Ibis-positive samples were culture-negative. Four samples were negative by all methods of analysis. No samples were positive by culture, but negative by molecular techniques. Our preliminary data indicate that molecular diagnostics are more sensitive for identifying bacteria than cultures in cases of bony nonunion. This is likely because of the inability of cultures to detect biofilms and bacteria previously exposed to antibiotic therapy. Diagnostic Level I. See Instructions for Authors for a complete description of levels of evidence.

Metabolic Pathway Signatures Associated with Urinary Metabolite Biomarkers Differentiate Bladder Cancer Patients from Healthy Controls.

PubMed

Kim, Won Tae; Yun, Seok Joong; Yan, Chunri; Jeong, Pildu; Kim, Ye Hwan; Lee, Il Seok; Kang, Ho Won; Park, Sunghyouk; Moon, Sung Kwon; Choi, Yung Hyun; Choi, Young Deuk; Kim, Isaac Yi; Kim, Jayoung; Kim, Wun Jae

2016-07-01

Our previous high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry study identified bladder cancer (BCA)-specific urine metabolites, including carnitine, acylcarnitines, and melatonin. The objective of the current study was to determine which metabolic pathways are perturbed in BCA, based on our previously identified urinary metabolome. A total of 135 primary BCA samples and 26 control tissue samples from healthy volunteers were analyzed. The association between specific urinary metabolites and their related encoding genes was analyzed. Significant alterations in the carnitine-acylcarnitine and tryptophan metabolic pathways were detected in urine specimens from BCA patients compared to those of healthy controls. The expression of eight genes involved in the carnitine-acylcarnitine metabolic pathway (CPT1A, CPT1B, CPT1C, CPT2, SLC25A20, and CRAT) or tryptophan metabolism (TPH1 and IDO1) was assessed by RT-PCR in our BCA cohort (n=135). CPT1B, CPT1C, SLC25A20, CRAT, TPH1, and IOD1 were significantly downregulated in tumor tissues compared to normal bladder tissues (p<0.05 all) of patients with non-muscle invasive BCA, whereas CPT1B, CPT1C, CRAT, and TPH1 were downregulated in those with muscle invasive BCA (p<0.05), with no changes in IDO1 expression. Alterations in the expression of genes associated with the carnitine-acylcarnitine and tryptophan metabolic pathways, which were the most perturbed pathways in BCA, were determined.

A mass balance of tri-hexabrominated diphenyl ethers in lactating cows.

PubMed

Kierkegaard, Amelie; De Wit, Cynthia A; Asplund, Lillemor; McLachlan, Michael S; Thomas, Gareth O; Sweetman, Andrew J; Jones, Kevin C

2009-04-01

Beef and dairy products can be important vectors of human exposure to polybrominated diphenylethers (BDEs), and hence an understanding of BDE transfer from feed to cows' milk and tissue is important for BDE exposure assessment The fate of tri- to hexaBDEs in lactating cows exposed to a naturally contaminated diet was studied by analyzing feed, feces, and milk samples from a mass balance study. Tissue distribution was studied in one cowslaughtered afterthe experiment The carryover rates from feed to milk ranged from 0.15 to 0.35 for the major congeners. Lower values were observed for several of the tetrabrominated congeners, and this was attributed to metabolism. The dietary absorption efficiency decreased with increasing octanol-water partition coefficient of the BDE congener. The absorption behavior was consistent with a model based on chemical lipophilicity, but agreed less well with a model based on effective molecular diameter, and it violated Lipinski's "rule of 5". The lipid normalized concentrations were similar in all tissues analyzed including liver and milk, suggesting that tissue distribution is governed by partitioning into lipids. Overall, the behavior of the tri- to hexaBDEs was consistent with that observed for other classes of halogenated aromatic contaminants such as PCBs and PCDD/Fs, but it differed markedly from the behavior of the hepta- decaBDEs.

A method for analyzing electrical impedance spectroscopy data from breast cancer patients

PubMed Central

Kim, Bong Seok; Isaacson, David; Xia, Hongjun; Kao, Tzu-Jen; Newell, Jonathan C; Saulnier, Gary J

2008-01-01

Research on freshly-excised malignant breast tissues and surrounding normal tissues in an in vitro impedance cell has shown that breast tumors have different conductivity and permittivity from normal or non-malignant tissues. This contrast may provide a basis for breast cancer detection using electrical impedance imaging. This paper describes a procedure for collecting electrical impedance spectroscopy data simultaneously and in register with tomosynthesis data from patients. We describe the methods used to analyze the data in order to determine if the electrodes are making contact with the breast of the patient. Canonical voltage patterns are applied and used to synthesize the data that would have resulted from constant voltage patterns applied to each of two parallel mammography plates. A type of Cole–Cole plot is generated and displayed from each of the currents measured on each of the electrodes for each of the frequencies (5, 10, 30, 100 and 300 kHz) of applied voltages. We illustrate the potential usefulness of these displays in distinguishing breast cancer from benign lesions with the Cole–Cole plots for two patients—one having cancer and one having a benign lesion—by comparing these graphs with electrical impedance spectra previously found by Jossinet and Schmitt in tissue samples taken from a variety of patients. PMID:17664638

A method for analyzing electrical impedance spectroscopy data from breast cancer patients.

PubMed

Kim, Bong Seok; Isaacson, David; Xia, Hongjun; Kao, Tzu-Jen; Newell, Jonathan C; Saulnier, Gary J

2007-07-01

Research on freshly-excised malignant breast tissues and surrounding normal tissues in an in vitro impedance cell has shown that breast tumors have different conductivity and permittivity from normal or non-malignant tissues. This contrast may provide a basis for breast cancer detection using electrical impedance imaging. This paper describes a procedure for collecting electrical impedance spectroscopy data simultaneously and in register with tomosynthesis data from patients. We describe the methods used to analyze the data in order to determine if the electrodes are making contact with the breast of the patient. Canonical voltage patterns are applied and used to synthesize the data that would have resulted from constant voltage patterns applied to each of two parallel mammography plates. A type of Cole-Cole plot is generated and displayed from each of the currents measured on each of the electrodes for each of the frequencies (5, 10, 30, 100 and 300 kHz) of applied voltages. We illustrate the potential usefulness of these displays in distinguishing breast cancer from benign lesions with the Cole-Cole plots for two patients--one having cancer and one having a benign lesion--by comparing these graphs with electrical impedance spectra previously found by Jossinet and Schmitt in tissue samples taken from a variety of patients.

X-ray Phase Contrast Allows Three Dimensional, Quantitative Imaging of Hydrogel Implants

PubMed Central

Appel, Alyssa A.; Larson, Jeffery C.; Jiang, Bin; Zhong, Zhong; Anastasio, Mark A.; Brey, Eric M.

2015-01-01

Three dimensional imaging techniques are needed for the evaluation and assessment of biomaterials used for tissue engineering and drug delivery applications. Hydrogels are a particularly popular class of materials for medical applications but are difficult to image in tissue using most available imaging modalities. Imaging techniques based on X-ray Phase Contrast (XPC) have shown promise for tissue engineering applications due to their ability to provide image contrast based on multiple X-ray properties. In this manuscript, we investigate the use of XPC for imaging a model hydrogel and soft tissue structure. Porous fibrin loaded poly(ethylene glycol) hydrogels were synthesized and implanted in a rodent subcutaneous model. Samples were explanted and imaged with an analyzer-based XPC technique and processed and stained for histology for comparison. Both hydrogel and soft tissues structures could be identified in XPC images. Structure in skeletal muscle adjacent could be visualized and invading fibrovascular tissue could be quantified. There were no differences between invading tissue measurements from XPC and the gold-standard histology. These results provide evidence of the significant potential of techniques based on XPC for 3D imaging of hydrogel structure and local tissue response. PMID:26487123

Whole Transcriptome Sequencing Enables Discovery and Analysis of Viruses in Archived Primary Central Nervous System Lymphomas

PubMed Central

DeBoever, Christopher; Reid, Erin G.; Smith, Erin N.; Wang, Xiaoyun; Dumaop, Wilmar; Harismendy, Olivier; Carson, Dennis; Richman, Douglas; Masliah, Eliezer; Frazer, Kelly A.

2013-01-01

Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV), JC polyomavirus (JCV), and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples. PMID:24023918

Standardization and validation of real time PCR assays for the diagnosis of histoplasmosis using three molecular targets in an animal model.

PubMed

López, Luisa F; Muñoz, César O; Cáceres, Diego H; Tobón, Ángela M; Loparev, Vladimir; Clay, Oliver; Chiller, Tom; Litvintseva, Anastasia; Gade, Lalitha; González, Ángel; Gómez, Beatriz L

2017-01-01

Histoplasmosis is considered one of the most important endemic and systemic mycoses worldwide. Until now few molecular techniques have been developed for its diagnosis. The aim of this study was to develop and evaluate three real time PCR (qPCR) protocols for different protein-coding genes (100-kDa, H and M antigens) using an animal model. Fresh and formalin-fixed and paraffin-embedded (FFPE) lung tissues from BALB/c mice inoculated i.n. with 2.5x106 Histoplasma capsulatum yeast or PBS were obtained at 1, 2, 3, 4, 8, 12 and 16 weeks post-infection. A collection of DNA from cultures representing different clades of H. capsulatum (30 strains) and other medically relevant pathogens (36 strains of related fungi and Mycobacterium tuberculosis) were used to analyze sensitivity and specificity. Analytical sensitivity and specificity were 100% when DNAs from the different strains were tested. The highest fungal burden occurred at first week post-infection and complete fungal clearance was observed after the third week; similar results were obtained when the presence of H. capsulatum yeast cells was demonstrated in histopathological analysis. In the first week post-infection, all fresh and FFPE lung tissues from H. capsulatum-infected animals were positive for the qPCR protocols tested except for the M antigen protocol, which gave variable results when fresh lung tissue samples were analyzed. In the second week, all qPCR protocols showed variable results for both fresh and FFPE tissues. Samples from the infected mice at the remaining times post-infection and uninfected mice (controls) were negative for all protocols. Good agreement was observed between CFUs, histopathological analysis and qPCR results for the 100-kDa and H antigen protocols. We successfully standardized and validated three qPCR assays for detecting H. capsulatum DNA in fresh and FFPE tissues, and conclude that the 100-kDa and H antigen molecular assays are promising tests for diagnosing this mycosis.

Determination of diagnostic standards on saturated soil extracts for cut roses grown in greenhouses

PubMed Central

Cabrera, Raúl Iskander

2017-01-01

This work comprises the theoretical determination and validation of diagnostic standards for the analysis of saturated soil extracts for cut rose flower crops (Rosa spp.) growing in the Bogota Plateau, Colombia. The data included 684 plant tissue analyses and 684 corresponding analyses of saturated soil extracts, all collected between January 2009 and June 2013. The tissue and soil samples were selected from 13 rose farms, and from cultivars grafted on the 'Natal Briar' rootstock. These concurrent samples of soil and plant tissues represented 251 production units (locations) of approximately 10,000 m2 distributed across the study area. The standards were conceived as a tool to improve the nutritional balance in the leaf tissue of rose plants and thereby define the norms for expressing optimum productive potential relative to nutritional conditions in the soil. To this end, previously determined diagnostic standard for rose leaf tissues were employed to obtain rates of foliar nutritional balance at each analyzed location and as criteria for determining the diagnostic norms for saturated soil extracts. Implementing this methodology to foliar analysis, showed a higher significant correlation for diagnostic indices. A similar behavior was observed in saturated soil extracts analysis, becoming a powerful tool for integrated nutritional diagnosis. Leaf analyses determine the most limiting nutrients for high yield and analyses of saturated soil extracts facilitate the possibility of correcting the fertigation formulations applied to soils or substrates. Recommendations are proposed to improve the balance in soil-plant system with which the possibility of yield increase becomes more probable. The main recommendations to increase and improve rose crop flower yields would be: continuously check pH values of SSE, reduce the amounts of P, Fe, Zn and Cu in fertigation solutions and carefully analyze the situation of Mn in the soil-plant system. PMID:28542547

High-accuracy biodistribution analysis of adeno-associated virus variants by double barcode sequencing.

PubMed

Marsic, Damien; Méndez-Gómez, Héctor R; Zolotukhin, Sergei

2015-01-01

Biodistribution analysis is a key step in the evaluation of adeno-associated virus (AAV) capsid variants, whether natural isolates or produced by rational design or directed evolution. Indeed, when screening candidate vectors, accurate knowledge about which tissues are infected and how efficiently is essential. We describe the design, validation, and application of a new vector, pTR-UF50-BC, encoding a bioluminescent protein, a fluorescent protein and a DNA barcode, which can be used to visualize localization of transduction at the organism, organ, tissue, or cellular levels. In addition, by linking capsid variants to different barcoded versions of the vector and amplifying the barcode region from various tissue samples using barcoded primers, biodistribution of viral genomes can be analyzed with high accuracy and efficiency.

Organochlorine compounds in bed sediment and fish tissue in the South Platte River Basin, USA, 1992-1993

USGS Publications Warehouse

Tate, C.M.; Heiny, J.S.

1996-01-01

Bed-sediment and fish-tissue samples were collected in the South Platte River Basin to determine the occurrence and distribution of organochlorine compounds in the basin. During August-November 1992 and August 1993, bed sediment (23 sites) and fish tissue (subset of 19 sites) were sampled and analyzed for 32 organochlorine compounds in bed sediment and 27 compounds in fish tissue. More types of organochlorine compounds were detected in fish tissue than in bed sediment. Total DDT, p,p???-DDE, o,p???-DDE, p,p???-DDD, total PCS, Dacthal??, dieldrin, cis-chlordane, cis-nonachlor, trans-nonachlor, and p,p???-DDT were detected in fish tissue at >25% of the sites; p,p???-DDE, total DDT, cis-chlordane, and trans-chlordane were detected in bed sediment at >25% of the sites. Organochlorine concentrations in bed sediment and fish tissue were related to land-use settings. Few organochlorine compounds were detected at minimally impacted sites located in rangeland, forest, and built-up land-use settings. Chlordane-related compounds and p,p???-methoxychlor in bed sediment and fish tissue, endrin in fish tissue, and endosulfan I in bed sediment were associated with urban and mixed (urban and agricultural) sites. Dacthal?? in bed sediment and fish tissue was associated with agricultural sites. The compounds HCB, ??-HCH, PCA, and toxaphene were detected only at mixed land-use sites. Although DDT and DDT-metabolites, dieldrin, and total PCB were detected in urban, mixed, and agricultural land-use settings, highest mean concentrations were detected at mixed land-use sites. Mixed land-use sites had the greatest number of organochlorine compounds detected in fish tissue, whereas urban and mixed sites had the greatest number of organochlorine compounds detected in bed sediment. Measuring concentrations of organochlorine compounds in bed sediment and fish tissue at the same site offers a more complete picture of the persistence of organochlorine compounds in the environment and their relation to land-use settings.

Characterization of Mycobacterium tuberculosis Complex DNAs from Egyptian Mummies by Spoligotyping

PubMed Central

Zink, Albert R.; Sola, Christophe; Reischl, Udo; Grabner, Waltraud; Rastogi, Nalin; Wolf, Hans; Nerlich, Andreas G.

2003-01-01

Bone and soft tissue samples from 85 ancient Egyptian mummies were analyzed for the presence of ancient Mycobacterium tuberculosis complex DNA (aDNA) and further characterized by spoligotyping. The specimens were obtained from individuals from different tomb complexes in Thebes West, Upper Egypt, which were used for upper social class burials between the Middle Kingdom (since ca. 2050 BC) and the Late Period (until ca. 500 BC). A total of 25 samples provided a specific positive signal for the amplification of a 123-bp fragment of the repetitive element IS6110, indicating the presence of M. tuberculosis DNA. Further PCR-based tests for the identification of subspecies failed due to lack of specific amplification products in the historic tissue samples. Of these 25 positive specimens, 12 could be successfully characterized by spoligotyping. The spoligotyping signatures were compared to those in an international database. They all show either an M. tuberculosis or an M. africanum pattern, but none revealed an M. bovis-specific pattern. The results from a Middle Kingdom tomb (used exclusively between ca. 2050 and 1650 BC) suggest that these samples bear an M. africanum-type specific spoligotyping signature. The samples from later periods provided patterns typical for M. tuberculosis. This study clearly demonstrates that spoligotyping can be applied to historic tissue samples. In addition, our results do not support the theory that M. tuberculosis originated from the M. bovis type but, rather, suggest that human M. tuberculosis may have originated from a precursor complex probably related to M. africanum. PMID:12517873

Quantitative assessment of soft tissue deformation using digital speckle pattern interferometry: studies on phantom breast models

PubMed Central

Karuppanan, Udayakumar; Unni, Sujatha Narayanan; Angarai, Ganesan R.

2017-01-01

Abstract. Assessment of mechanical properties of soft matter is a challenging task in a purely noninvasive and noncontact environment. As tissue mechanical properties play a vital role in determining tissue health status, such noninvasive methods offer great potential in framing large-scale medical screening strategies. The digital speckle pattern interferometry (DSPI)–based image capture and analysis system described here is capable of extracting the deformation information from a single acquired fringe pattern. Such a method of analysis would be required in the case of the highly dynamic nature of speckle patterns derived from soft tissues while applying mechanical compression. Soft phantoms mimicking breast tissue optical and mechanical properties were fabricated and tested in the DSPI out of plane configuration set up. Hilbert transform (HT)-based image analysis algorithm was developed to extract the phase and corresponding deformation of the sample from a single acquired fringe pattern. The experimental fringe contours were found to correlate with numerically simulated deformation patterns of the sample using Abaqus finite element analysis software. The extracted deformation from the experimental fringe pattern using the HT-based algorithm is compared with the deformation value obtained using numerical simulation under similar conditions of loading and the results are found to correlate with an average %error of 10. The proposed method is applied on breast phantoms fabricated with included subsurface anomaly mimicking cancerous tissue and the results are analyzed. PMID:28180134

NOAA National Status and Trends Program Twelfth Round Intercomparison Exercise Results for Trace Metals in Marine Sediments and Biological Tissues. National Status and Trends Program for marine environmental quality: Technical memo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willie, S.

1998-11-01

The report summarizes the results of the Twelfth Round Intercomparison for Trace Metals in Marine Sediments and Biological Tissues under the directive of the NOAA National Status and Trends Program. A total of forty-four participants were included in the exercise, including NOAA, USEPA, state, Austrailian, Canadian, Mexican and Argentinean laboratories. Two samples were sent by NRC to each participant, a marine sediment collected on the east coast of Canada and a freeze-dried mussel tissue. Laboratories were also asked to analyze two certified reference materials (CRMs) MESS-2 and CRM 2976. The elements to be determined were Al, Cr, Fe, Ni, Cu,more » Zn, As, Se, Ag, Cd, Sn, Hg, and Pb for both matrices, plus Be, Si, Mn, Sb, and Tl for the sediments. An accepted mean and confidence interval was calculated for each analyte in the two unknown samples, laboratory biases were identified and an overall rating of superior, good, fair or others were assigned to each laboratory.« less

Real-time optical coherence tomography observation of retinal tissue damage during laser photocoagulation therapy on ex-vivo porcine samples

NASA Astrophysics Data System (ADS)

Steiner, P.; Považay, B.; Stoller, M.; Morgenthaler, P.; Inniger, D.; Arnold, P.; Sznitman, R.; Meier, Ch.

2015-07-01

Retinal laser photocoagulation represents a widely used treatment for retinal pathologies such as diabetic chorioretinopathy or diabetic edema. For effective treatment, an appropriate choice of the treatment energy dose is crucial to prevent excessive tissue damage caused by over-irradiation of the retina. In this manuscript we investigate simultaneous and time-resolved optical coherence tomography for its applicability to provide feedback to the ophthalmologist about the introduced retinal damage during laser photocoagulation. Time-resolved and volumetric optical coherence tomography data of 96 lesions on ex-vivo porcine samples, set with a 577 nm laser prototype and irradiance of between 300 and 8800 W=cm2 were analyzed. Time-resolved scans were compared to volumetric scans of the lesion and correlated with ophthalmoscopic visibility. Lastly, image parameters extracted from optical coherence tomography Mscans, suitable for lesion classification were identified. Results presented in this work support the hypothesis that simultaneous optical coherence tomography provides valuable information about the extent of retinal tissue damage and may be used to guide retinal laser photocoagulation in the future.

Contents of chemical elements in stomach during prenatal development: different age-dependent dynamical changes and their significance

PubMed Central

Hou, Shao-Fan; Li, Hai-Rong; Wang, Li-Zhen; Li, De-Zhu; Yang, Lin-Sheng; Li, Chong-Zheng

2003-01-01

AIM: To observe dynamic of different chemical elements in stomach tissue during fetal development. METHODS: To determine contents of the 21 chemical elements in each stomach samples from fetus aging four to ten months. The content values were compared to those from adult tissue samples, and the values for each month group were also analyzed for dynamic changes. RESULTS: Three representations were found regarding the relationship between contents of the elements and ages of the fetus, including the positive correlative (K), reversely correlative (Na, Ca, P, Al, Cu, Zn, Fe, Mn, Cr, Sr, Li, Cd, Ba, Se) and irrelevant groups (Mg, Co, Ni, V, Pb, Ti). CONCLUSION: The chemical elements’ contents in stomach tissues were found to change dynamically with the stomach weights. The age-dependent representations for different chemical elements during the prenatal development may be of some significance for assessing development of fetal stomach and some chemical elements. The data may be helpful for the nutritional balance of fetus and mothers during prenatal development and even the perinatal stages. PMID:12717857

Nociceptive role of substance-P in the knee joint of a patient with congenital insensitivity to pain.

PubMed

Derwin, K A; Glover, R A; Wojtys, E M

1994-01-01

This case report describes the immunocytochemical examination of tissue from a 9-year-old black child diagnosed with congenital insensitivity to pain at age 5. A recent fall and resulting patella fracture required surgical treatment. Biopsies of the distal pole and surrounding soft tissue, as well as a sample of his patellofemoral joint fluid, were taken at the time of partial patellectomy and analyzed for substance-P (SP). Morphologic staining of the patella showed a grossly degenerated patellofemoral articular surface. Examination of tissue sections stained either immunocytochemically with diaminobenzidine DAB or by a rhodamine fluorescent labeling technique showed no evidence of SP-positive nerve fibers. Furthermore, only a trace amount of SP (7.29 pg/ml) was detected in a sample of the patient's knee joint synovial fluid. This patient's absence of pain sensation in conjunction with the absence of SP nerve fibers in stained patella sections and identification of only trace levels of SP in his synovial fluid, further implicates this neuropeptide in nociceptive innervation of diarthrodial joints.

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

PubMed Central

Friis-Nielsen, Jens; Vinner, Lasse; Hansen, Thomas Arn; Richter, Stine Raith; Fridholm, Helena; Herrera, Jose Alejandro Romero; Lund, Ole; Brunak, Søren; Izarzugaza, Jose M. G.; Mourier, Tobias; Nielsen, Lars Peter

2016-01-01

Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition. PMID:26818667

International Cartilage Repair Society (ICRS) Recommended Guidelines for Histological Endpoints for Cartilage Repair Studies in Animal Models and Clinical Trials

PubMed Central

Hoemann, Caroline; Kandel, Rita; Roberts, Sally; Saris, Daniel B.F.; Creemers, Laura; Mainil-Varlet, Pierre; Méthot, Stephane; Hollander, Anthony P.; Buschmann, Michael D.

2011-01-01

Cartilage repair strategies aim to resurface a lesion with osteochondral tissue resembling native cartilage, but a variety of repair tissues are usually observed. Histology is an important structural outcome that could serve as an interim measure of efficacy in randomized controlled clinical studies. The purpose of this article is to propose guidelines for standardized histoprocessing and unbiased evaluation of animal tissues and human biopsies. Methods were compiled from a literature review, and illustrative data were added. In animal models, treatments are usually administered to acute defects created in healthy tissues, and the entire joint can be analyzed at multiple postoperative time points. In human clinical therapy, treatments are applied to developed lesions, and biopsies are obtained, usually from a subset of patients, at a specific time point. In striving to standardize evaluation of structural endpoints in cartilage repair studies, 5 variables should be controlled: 1) location of biopsy/sample section, 2) timing of biopsy/sample recovery, 3) histoprocessing, 4) staining, and 5) blinded evaluation with a proper control group. Histological scores, quantitative histomorphometry of repair tissue thickness, percentage of tissue staining for collagens and glycosaminoglycan, polarized light microscopy for collagen fibril organization, and subchondral bone integration/structure are all relevant outcome measures that can be collected and used to assess the efficacy of novel therapeutics. Standardized histology methods could improve statistical analyses, help interpret and validate noninvasive imaging outcomes, and permit cross-comparison between studies. Currently, there are no suitable substitutes for histology in evaluating repair tissue quality and cartilaginous character. PMID:26069577

Untargeted UPLC-MS Profiling Pipeline to Expand Tissue Metabolome Coverage: Application to Cardiovascular Disease

PubMed Central

2015-01-01

Metabolic profiling studies aim to achieve broad metabolome coverage in specific biological samples. However, wide metabolome coverage has proven difficult to achieve, mostly because of the diverse physicochemical properties of small molecules, obligating analysts to seek multiplatform and multimethod approaches. Challenges are even greater when it comes to applications to tissue samples, where tissue lysis and metabolite extraction can induce significant systematic variation in composition. We have developed a pipeline for obtaining the aqueous and organic compounds from diseased arterial tissue using two consecutive extractions, followed by a different untargeted UPLC-MS analysis method for each extract. Methods were rationally chosen and optimized to address the different physicochemical properties of each extract: hydrophilic interaction liquid chromatography (HILIC) for the aqueous extract and reversed-phase chromatography for the organic. This pipeline can be generic for tissue analysis as demonstrated by applications to different tissue types. The experimental setup and fast turnaround time of the two methods contributed toward obtaining highly reproducible features with exceptional chromatographic performance (CV % < 0.5%), making this pipeline suitable for metabolic profiling applications. We structurally assigned 226 metabolites from a range of chemical classes (e.g., carnitines, α-amino acids, purines, pyrimidines, phospholipids, sphingolipids, free fatty acids, and glycerolipids) which were mapped to their corresponding pathways, biological functions and known disease mechanisms. The combination of the two untargeted UPLC-MS methods showed high metabolite complementarity. We demonstrate the application of this pipeline to cardiovascular disease, where we show that the analyzed diseased groups (n = 120) of arterial tissue could be distinguished based on their metabolic profiles. PMID:25664760

An evaluation of mercury levels in Louisiana fish: trends and public health issues.

PubMed

Katner, Adrienne; Sun, Mei-Hung; Suffet, Mel

2010-11-01

To characterize statewide fish tissue mercury levels in edible finfish the first comprehensive analysis of Louisiana's fish tissue mercury database was conducted. Analyses were based on fifteen years of fish tissue mercury data collected from 368 waterbodies between 1994 and 2008 (n=14,344). The overall objectives of this study were to establish baseline fish tissue mercury levels; and evaluate species-specific temporal and spatial trends in fish tissue mercury levels. Fish tissue mercury levels ranged from 0.001 ppm (the detection limit) to 5.904 ppm for king mackerel; with an overall geometric mean of 0.218 ppm. Ninety-five percent of samples had mercury levels below the FDA's action level of 1.0 ppm for methylmercury in commercial food. Forty-four percent of all samples had mercury levels above the U.S. EPA's methylmercury fish tissue criterion of 0.3 ppm for sportfish. Species of potential concern include cobia, king mackerel, blackfin tuna, greater amberjack, spotted bass, bowfin, largemouth bass and freshwater drum. There was a significant but small decline in statewide length-adjusted largemouth bass mercury levels between 1994-1999 to 2003-2008 (p<0.05). The highest fish mercury levels were observed in Pearl, Calcasieu, Mermentau, Ouachita, Pontchartrain and Sabine basins. Length-adjusted largemouth bass mercury levels were significantly higher in wetlands and rivers/streams vs. lakes; and in wetlands vs. estuaries (p<0.05). Data were analyzed from a public health perspective to make recommendations for optimizing monitoring and outreach. Copyright © 2010 Elsevier B.V. All rights reserved.

Vitamin D receptor levels in colorectal cancer. Possible role of BsmI polymorphism.

PubMed

Parisi, Eva; Reñé, Josep Maria; Cardús, Anna; Valcheva, Petya; Piñol-Felis, Carme; Valdivielso, José Manuel; Fernández, Elvira

2008-07-01

A high expression of vitamin D receptor (VDR) in colorectal cancer (CRC) tumoral tissue has been related to a good prognosis and it has been proposed that it could be a good biological marker of CRC progression. Nevertheless, there are no previous studies that compare the VDR expression in tumoral towards normal tissue of the same CRC patient in relation to VDR BsmI genotype. We collected normal and tumoral tissue samples, as well as blood samples, from CRC patients (n=170) and controls (n=122). VDR genotyping was performed and BsmI homozygous patients were selected (CRC=50, Cont=32). VDR mRNA and protein levels were analyzed. We also measured 25-Hydroxyvitamin D serum levels. We found no differences in the polymorphism distribution in tumoral versus normal tissue (control: BB=15.7%, bb=41.3%, Bb=43%; CRC: BB=14.2%, bb=41.9%, Bb=43.9%). Furthermore, VDR levels decreased in colonic cancer tissue (mean: 3.03) versus normal mucosa (11.62) from the same patient (p<0.001), but this decrease was similar in both genotypes. There were differences in 25-Hydroxyvitamin D(3) levels between the CRC and the control group (CRC=8.65 ng/ml, Cont=18.15 ng/ml). In conclusion, we found a decrease in VDR levels in tumoral compared with normal mucosa from the same patient. This difference is independent of the BsmI polymorphism.

A Derivatization and Validation Strategy for Determining the Spatial Localization of Endogenous Amine Metabolites in Tissues using MALDI Imaging Mass Spectrometry

PubMed Central

Manier, M. Lisa; Spraggins, Jeffrey M.; Reyzer, Michelle L.; Norris, Jeremy L.; Caprioli, Richard M.

2014-01-01

Imaging mass spectrometry (IMS) studies increasingly focus on endogenous small molecular weight metabolites and consequently bring special analytical challenges. Since analytical tissue blanks do not exist for endogenous metabolites, careful consideration must be given to confirm molecular identity. Here we present approaches for the improvement in detection of endogenous amine metabolites such as amino acids and neurotransmitters in tissues through chemical derivatization and matrix-assisted laser desorption/ionization (MALDI) IMS. Chemical derivatization with 4-hydroxy-3-methoxycinnamaldehyde (CA) was used to improve sensitivity and specificity. CA was applied to the tissue via MALDI sample targets precoated with a mixture of derivatization reagent and ferulic acid (FA) as a MALDI matrix. Spatial distributions of chemically derivatized endogenous metabolites in tissue were determined by high-mass resolution and MSn imaging mass spectrometry. We highlight an analytical strategy for metabolite validation whereby tissue extracts are analyzed by high-performance liquid chromatography (HPLC)-MS/MS to unambiguously identify metabolites and distinguish them from isobaric compounds. PMID:25044893

Analysis of DNA Methylation Status in Bodily Fluids for Early Detection of Cancer

PubMed Central

Yokoi, Keigo; Yamashita, Keishi; Watanabe, Masahiko

2017-01-01

Epigenetic alterations by promoter DNA hypermethylation and gene silencing in cancer have been reported over the past few decades. DNA hypermethylation has great potential to serve as a screening marker, a prognostic marker, and a therapeutic surveillance marker in cancer clinics. Some bodily fluids, such as stool or urine, were obtainable without any invasion to the body. Thus, such bodily fluids were suitable samples for high throughput cancer surveillance. Analyzing the methylation status of bodily fluids around the cancer tissue may, additionally, lead to the early detection of cancer, because several genes in cancer tissues are reported to be cancer-specifically hypermethylated. Recently, several studies that analyzed the methylation status of DNA in bodily fluids were conducted, and some of the results have potential for future development and further clinical use. In fact, a stool DNA test was approved by the U.S. Food and Drug Administration (FDA) for the screening of colorectal cancer. Another promising methylation marker has been identified in various bodily fluids for several cancers. We reviewed studies that analyzed DNA methylation in bodily fluids as a less-invasive cancer screening. PMID:28358330

Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy.

PubMed

Kearney, Mary F; Anderson, Elizabeth M; Coomer, Charles; Smith, Luke; Shao, Wei; Johnson, Nicholas; Kline, Christopher; Spindler, Jonathan; Mellors, John W; Coffin, John M; Ambrose, Zandrea

2015-11-11

Determining the anatomic compartments that contribute to plasma HIV-1 is critical to understanding the sources of residual viremia during combination antiretroviral therapy (ART). We analyzed viral DNA and RNA populations in the plasma and tissues from macaques infected with SIV containing HIV-1 RT (RT-SHIV) to identify possible sources of persistent viremia and to investigate the effect of ART on viral replication in tissues. Tissues were collected at necropsy from four pigtailed macaques infected for 30 weeks with a diverse population of RT-SHIV. Two animals (6760 and 8232) were untreated and two animals (8030 and 8272) were treated with efavirenz, tenofovir, and emtricitabine for 20 weeks. A total of 1800 single-genome RT-SHIV pol and env DNA and RNA sequences were analyzed from the plasma, PBMCs, axillary and mesenteric lymph nodes, spleen, thymus, small intestine, bone marrow, lung, and brain. Analyses of intracellular DNA and RNA populations revealed that the majority of proviruses in tissues from untreated animal 8232 were not expressed, whereas a greater proportion of proviruses in tissues were expressed from 6760. Few intracellular RNA sequences were detected in treated animals and most contained inactivating mutations, such as frame shifts or large deletions. Phylogenetics showed that RT-SHIV DNA populations in tissues were not different from virus in contemporary plasma samples in the treated or untreated animals, demonstrating a lack of anatomic compartmentalization and suggesting that plasma viremia is derived from multiple tissue sources. No sequence divergence was detected in the plasma or between tissues in the treated animals after 20 weeks of ART indicating a lack of ongoing replication in tissues during treatment. Virus populations in plasma and tissues did not differ significantly in either treated or untreated macaques, suggesting frequent exchange of virus or infected cells between tissues and plasma, consistent with non-compartmentalized and widely disseminated infection. There was no genetic evidence of ongoing replication in tissues during suppressive ART.

Organochlorine pesticide levels in adipose tissue of pregnant women in Veracruz, Mexico.

PubMed

Herrero-Mercado, Margarita; Waliszewski, S M; Valencia-Quintana, R; Caba, M; Hernández-Chalate, F; García-Aguilar, E; Villalba, R

2010-06-01

DDT and Lindane (gamma-HCH) which were used until 1999 in Mexico, have provided great benefits in the combat of vectors that spread infection-borne diseases and in agriculture for crop protection. The persistence in the environment and their accumulative properties results in bioconcentration in lipid rich tissues of the human body that reflect the extent of environmental pollution. Human adipose tissue samples were taken during 2009 from abdominal cavities of 69 pregnant women by cesarean surgery and from 34 samples of control donors by autopsy in Veracruz State. The samples were analyzed by gas chromatography with ECD. The results of mean levels (mg/kg on fat basis) were higher in controls compared to pregnant women beta-HCH 0.064 vs 0.027; pp'DDE 1.187 vs. 0.745; op'DDT 0.016 vs. 0.011; pp'DDT 0.117 vs. 0.099 and Sigma-DDT 1.337 vs. 0.854. The pregnant women group was divided according to age: up to 20, 20-30, and more than 30 years, and presented an increase for the more persistent pesticides with age in terms of mean concentrations and a more pronounced higher correlation in medians levels. Pairing Body Mass Index to organochlorine pesticide mean levels revealed no correlation between these factors in pregnant women.

Laser-initiated decomposition products of indocyanine green (ICG) and carbon black sensitized biological tissues

NASA Astrophysics Data System (ADS)

Kokosa, John M.; Przyjazny, Andrzej; Bartels, Kenneth E.; Motamedi, Massoud; Hayes, Donald J.; Wallace, David B.; Frederickson, Christopher J.

1997-05-01

Organic dyes have found increasing use a s sensitizers in laser surgical procedures, due to their high optical absorbances. Little is known, however, about the nature of the degradation products formed when these dyes are irradiated with a laser. Previous work in our laboratories has shown that irradiation of polymeric and biological tissues with CO2 and Nd:YAG lasers produces a host of volatile and semivolatile by-products, some of which are known to be potential carcinogens. This work focuses on the identification of the chemical by-products formed by diode laser and Nd:YAG laser irradiation of indocyanine green (ICG) and carbon black based ink sensitized tissues, including bone, tendon and sheep's teeth. Samples were mounted in a 0.5-L Pyrex sample chamber equipped with quartz optical windows, charcoal filtered air inlet and an outlet attached to an appropriate sample trap and a constant flow pump. By-products were analyzed by GC/MS and HPLC. Volatiles identified included benzene and formaldehyde. Semi-volatiles included traces of polycyclic aromatics, arising from the biological matrix and inks, as well as fragments of ICG and the carbon ink components. The significance of these results will be discussed, including the necessity of using appropriate evacuation devices when utilizing lasers for surgical procedures.

Global Gene Expression Profiling in Lung Tissues of Rat Exposed to Lunar Dust Particles

NASA Technical Reports Server (NTRS)

Yeshitla, Samrawit A.; Lam, Chiu-Wing; Kidane, Yared H.; Feiveson, Alan H.; Ploutz-Snyder, Robert; Wu, Honglu; James, John T.; Meyers, Valerie E.; Zhang, Ye

2014-01-01

The Moon's surface is covered by a layer of fine, potential reactive dust. Lunar dust contain about 1-2% respirable very fine dust (less than 3 micrometers). The habitable area of any lunar landing vehicle and outpost would inevitably be contaminated with lunar dust that could pose a health risk. The purpose of the study is to analyze the dynamics of global gene expression changes in lung tissues of rats exposed to lunar dust particles. F344 rats were exposed for 4 weeks (6h/d; 5d/wk) in nose-only inhalation chambers to concentrations of 0 (control air), 2.1, 6.8, 21, and 61 mg/m3 of lunar dust. Animals were euthanized at 1 day and 13 weeks after the last inhalation exposure. After being lavaged, lung tissue from each animal was collected and total RNA was isolated. Four samples of each dose group were analyzed using Agilent Rat GE v3 microarray to profile global gene expression of 44K transcripts. After background subtraction, normalization, and log transformation, t tests were used to compare the mean expression levels of each exposed group to the control group. Correction for multiple testing was made using the method of Benjamini, Krieger, and Yekuteli (1) to control the false discovery rate. Genes with significant changes of at least 1.75 fold were identified as genes of interest. Both low and high doses of lunar dust caused dramatic, dose-dependent global gene expression changes in the lung tissues. However, the responses of lung tissue to low dose lunar dust are distinguished from those of high doses, especially those associated with 61mg/m3 dust exposure. The data were further integrated into the Ingenuity system to analyze the gene ontology (GO), pathway distribution and putative upstream regulators and gene targets. Multiple pathways, functions, and upstream regulators have been identified in response to lunar dust induced damage in the lung tissue.

Comparison of a bioassay and a liquid chromatography-fluorescence-mass spectrometry(n) method for the detection of incurred enrofloxacin residues in chicken tissues.

PubMed

Schneider, M J; Donoghue, D J

2004-05-01

Regulatory monitoring for most antibiotic residues in edible poultry tissues is often accomplished with accurate, although expensive and technically demanding, chemical analytical techniques. The purpose of this study is to determine if a simple, inexpensive bioassay could detect fluoroquinolone (FQ) residues in chicken muscle above the FDA established tolerance (300 ppb) comparable to a liquid chromatography-fluorescencemass spectrometry(n) method. To produce incurred enrofloxacin (ENRO) tissues (where ENRO is incorporated into complex tissue matrices) for the method comparison, 40-d-old broilers (mixed sex) were orally dosed through drinking water for 3 d at the FDA-approved dose of ENRO (50 ppm). At the end of each day of the 3-d dosing period and for 3 d postdosing, birds were sacrificed and breast and thigh muscle collected and analyzed. Both methods were able to detect ENRO at and below the tolerance level in the muscle, with limits of detection of 26 ppb (bioassay), 0.1 ppb for ENRO, and 0.5 ppb for the ENRO metabolite, ciprofloxacin (liquid chromatography-fluorescence-mass spectrometry(n)). All samples that had violative levels of antibiotic were detected by the bioassay. These results support the use of this bioassay as a screening method for examining large numbers of samples for regulatory monitoring. Positive samples should then be examined by a more extensive method, such as liquid chromatography-fluorescence-mass spectrometry(n), to provide confirmation of the analyte.

Exposure of insects and insectivorous birds to metals and other elements from abandoned mine tailings in three Summit County drainages, Colorado

USGS Publications Warehouse

Custer, Christine M.; Yang, C.; Crock, J.G.; Shearn-Bochsler, V.; Smith, K.S.; Hageman, P.L.

2009-01-01

Concentrations of 31 metals, metalloids, and other elements were measured in insects and insectivorous bird tissues from three drainages with different geochemistry and mining histories in Summit Co., Colorado, in 2003, 2004, and 2005. In insect samples, all 25 elements that were analyzed in all years increased in both Snake and Deer Creeks in the mining impacted areas compared to areas above and below the mining impacted areas. This distribution of elements was predicted from known or expected sediment contamination resulting from abandoned mine tailings in those drainages. Element concentrations in avian liver tissues were in concordance with levels in insects, that is with concentrations higher in mid-drainage areas where mine tailings were present compared to both upstream and downstream locations; these differences were not always statistically different, however. The lack of statistically significant differences in liver tissues, except for a few elements, was due to relatively small sample sizes and because many of these elements are essential and therefore well regulated by the bird's homeostatic processes. Most elements were at background concentrations in avian liver tissue except for Pb which was elevated at mid-drainage sites to levels where ??-aminolevulinic acid dehydratase activity was inhibited at other mining sites in Colorado. Lead exposure, however, was not at toxic levels. Fecal samples were not a good indication of what elements birds ingested and were potentially exposed to. ?? Springer Science+Business Media B.V. 2008.

Multiplexed color-coded probe-based gene expression assessment for clinical molecular diagnostics in formalin-fixed paraffin-embedded human renal allograft tissue.

PubMed

Adam, Benjamin; Afzali, Bahman; Dominy, Katherine M; Chapman, Erin; Gill, Reeda; Hidalgo, Luis G; Roufosse, Candice; Sis, Banu; Mengel, Michael

2016-03-01

Histopathologic diagnoses in transplantation can be improved with molecular testing. Preferably, molecular diagnostics should fit into standard-of-care workflows for transplant biopsies, that is, formalin-fixed paraffin-embedded (FFPE) processing. The NanoString(®) gene expression platform has recently been shown to work with FFPE samples. We aimed to evaluate its methodological robustness and feasibility for gene expression studies in human FFPE renal allograft samples. A literature-derived antibody-mediated rejection (ABMR) 34-gene set, comprised of endothelial, NK cell, and inflammation transcripts, was analyzed in different retrospective biopsy cohorts and showed potential to molecularly discriminate ABMR cases, including FFPE samples. NanoString(®) results were reproducible across a range of RNA input quantities (r = 0.998), with different operators (r = 0.998), and between different reagent lots (r = 0.983). There was moderate correlation between NanoString(®) with FFPE tissue and quantitative reverse transcription polymerase chain reaction (qRT-PCR) with corresponding dedicated fresh-stabilized tissue (r = 0.487). Better overall correlation with histology was observed with NanoString(®) (r = 0.354) than with qRT-PCR (r = 0.146). Our results demonstrate the feasibility of multiplexed gene expression quantification from FFPE renal allograft tissue. This represents a method for prospective and retrospective validation of molecular diagnostics and its adoption in clinical transplantation pathology. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Climatic signals registered as Carbon isotopic values in Metasequoia leaf tissues: A statistical analysis

NASA Astrophysics Data System (ADS)

Yang, H.; Blais, B.; Perez, G.; Pagani, M.

2006-12-01

To examine climatic signals registered as carbon isotopic values in leaf tissues of C3 plants, we collected mature leaf tissues from sun and shade leaves of Metasequoia trees germinated from the 1947 batch of seeds from China and planted along a latitudinal gradient of the United States. Samples from 40 individual trees, along with fossilized material from the early Tertiary of the Canadian Arctic, were analyzed for C and concentration and isotopic values using EA-IRMS after the removal of free lipids. The generated datasets were then merged with climate data compiled from each tree site recorded as average values over the past thirty years (1971-2002, NOAA database). When the isotope data were cross plotted against each geographic and climatic indicator, Latitude, Mean Annual Temperature (MAT), Average Summer Mean Temperature (ASMT)(June-August), Mean Annual Precipitation (MAP), and Average Summer Mean Precipitation (ASMP) respectively correlation patterns were revealed. The best correlating trend was obtained between temperature parameters and C isotopic values, and this correlation is stronger in the northern leaf samples than the southern samples. We discovered a strong positive correlation between latitude and the offset of C isotopic values between shade and sun leaves. This investigation represents a comprehensive examination on climatic signals registered as C isotopic values on a single species that is marked by single genetic source. The results bear implications on paleoclimatic interpretations of C isotopic signals obtained from fossil plant tissues.

Inflammatory cytokine expression following the use of bipolar electrocoagulation, ultracision harmonic scalpel and cold knife biopsy.

PubMed

Litta, Pietro; Saccardi, Carlo; Gizzo, Salvatore; Conte, Lorena; Ambrosi, Giulia; Sissi, Claudia; Palumbo, Manlio

2015-08-01

Electrical surgical devices may determine tissue damage through lateral thermal spread and activation of inflammatory processes. Several tissue effects are associated with the use of different surgical instruments. The aim of the present study was to compare tissue damage following the application of cold knife biopsy, bipolar electrocoagulation and the ultracision harmonic scalpel, through the analysis of inflammatory gene mediator expression. Three fragments of the round ligament (length 0.5 cm) were obtained from 22 females who had undergone total or subtotal laparoscopic hysterectomy using three different modes of resection: Cold knife biopsy, bipolar electrocoagulation and ultracision harmonic scalpel. The tissue fragments were examined by quantitative polymerase chain reaction (qPCR) analysis of selected cytokines. Gene expression analysis demonstrated large standard deviations due to individual variability among patients and indicated variability in the concentrations of cytokines in the three different samples. The quantity of cytokine mRNA in the cold knife biopsy samples was generally greater than those obtained by other techniques. Tumor necrosis factor-α expression was significantly higher in the sample obtained with the ultracision harmonic scalpel and bipolar electrocoagulation (P=0.033) when compared with cold knife biopsy. The inflammatory response was analyzed by the quantification of gene expression through the use of qPCR. The ultracision harmonic scalpel and bipolar electrocoagulation triggered the inflammatory cascade and resulted in an increased production of cytokines compared with cold knife biopsy.

AT1 expression in human urethral stricture tissue.

PubMed

Siregar, Safendra; Parardya, Aga; Sibarani, Jupiter; Romdan, Tjahjodjati; Adi, Kuncoro; Hernowo, Bethy S; Yantisetiasti, Anglita

2017-01-01

Urethral stricture has a high recurrence rate. There is a common doctrine stating that "once a stricture, always a stricture". This fibrotic disease pathophysiology, pathologically characterized by excessive production, deposition and contraction of extracellular matrix is unknown. Angiotensin II type 1 (AT 1 ) receptor primarily induces angiogenesis, cellular proliferation and inflammatory responses. AT 1 receptors are also expressed in the fibroblasts of hypertrophic scars, whereas angiotensin II (AngII) regulates DNA synthesis in hypertrophic scar fibroblasts through a negative cross talk between AT 1 and angiotensin II type 2 (AT 2 ) receptors, which might contribute to the formation and maturation of human hypertrophic scars. This study was conducted to determine the expression of AT 1 receptors in urethral stricture tissues. Urethral stricture tissues were collected from patients during anastomotic urethroplasty surgery. There were 24 tissue samples collected in this study with 2 samples of normal urethra for the control group. Immunohistochemistry study was performed to detect the presence of AT 1 receptor expression. Data were analyzed using Mann-Whitney U test, and statistical analysis was performed with SPSS version 20. This study showed that positive staining of AT 1 receptor was found in all urethral stricture tissues (n=24). A total of 8.33% patients had low intensity, 41.67% had moderate intensity and 50% had high intensity of AT 1 receptors, while in the control group, 100% patients had no intensity of AT 1 receptors. Using the Mann-Whitney U test, it was found that urethral stricture tissue had a higher intensity of AT 1 receptors than normal urethral tissue with a p -value = 0.012. The results showed that AT 1 receptor had a higher intensity in the urethral stricture tissue and that AT 1 receptor may play an important role in the development of urethral stricture.

Determination of friction coefficient in unconfined compression of brain tissue.

PubMed

Rashid, Badar; Destrade, Michel; Gilchrist, Michael D

2012-10-01

Unconfined compression tests are more convenient to perform on cylindrical samples of brain tissue than tensile tests in order to estimate mechanical properties of the brain tissue because they allow homogeneous deformations. The reliability of these tests depends significantly on the amount of friction generated at the specimen/platen interface. Thus, there is a crucial need to find an approximate value of the friction coefficient in order to predict a possible overestimation of stresses during unconfined compression tests. In this study, a combined experimental-computational approach was adopted to estimate the dynamic friction coefficient μ of porcine brain matter against metal platens in compressive tests. Cylindrical samples of porcine brain tissue were tested up to 30% strain at variable strain rates, both under bonded and lubricated conditions in the same controlled environment. It was established that μ was equal to 0.09±0.03, 0.18±0.04, 0.18±0.04 and 0.20±0.02 at strain rates of 1, 30, 60 and 90/s, respectively. Additional tests were also performed to analyze brain tissue under lubricated and bonded conditions, with and without initial contact of the top platen with the brain tissue, with different specimen aspect ratios and with different lubricants (Phosphate Buffer Saline (PBS), Polytetrafluoroethylene (PTFE) and Silicone). The test conditions (lubricant used, biological tissue, loading velocity) adopted in this study were similar to the studies conducted by other research groups. This study will help to understand the amount of friction generated during unconfined compression of brain tissue for strain rates of up to 90/s. Copyright © 2012 Elsevier Ltd. All rights reserved.