Pooled Tissue Samples Research Articles

A fast method for the quantitation of key metabolites of the methionine pathway in liver tissue by high-resolution mass spectrometry and hydrophilic interaction ultra-performance liquid chromatography

We developed an assay for the extraction and simultaneous quantitation of five key metabolites of the methionine metabolic pathway in liver tissue. The metabolites included were 5'-methylthioadenosine, methionine, homocysteine, S-adenosyl-L-homocysteine, and S-adenosyl-L-methionine. The metabolites were extracted using a bead-based homogenization method, and quantitation was carried out using hydrophilic interaction chromatography and time-of-flight mass spectrometry. The extraction procedure was optimized by testing the effect of various solvent combinations. The chromatographic method was optimized for peak shape, signal intensity, and carry-over. With a total chromatographic run time of 5 min, this assay is suitable for the analysis of large sample sets. Time-of-flight mass spectrometry provided high mass accuracy which, combined with isotope pattern matching and use of chemical standards, guarantees high specificity. Moreover, by operating the mass spectrometer in enhanced duty cycle mode the signal strength for the analytes increased three- to tenfold in comparison with the generic full-scan mode. For quantitation, a matrix-spiked calibration method was used. The lowest analyte levels detected and quantified using our method were within the range of concentrations found in the liver. The inter-day coefficients of variance for the analytes were between 5 and 15% in pooled tissue samples. Interestingly, the CVs between individual liver tissue aliquots were about twice as high. Additional experiments suggested that this higher variability was caused by uneven distribution of the analytes within the liver. In conclusion, an optimized and robust assay is now available for the extraction and quantification of key metabolites in the methionine metabolic pathway.

Detection of the Newcastle disease virus and its effect on development of post-vaccination immunity in a commercial flock of laying hens

The aim of this study was to monitor the concentration of antibodies against Newcastle disease after vaccination of laying hens at the beginning and in the end of the laying period. The study was carried out in one commercial flock of laying hens in Opatovice in the Czech Republic in the years 2008-2010. A total of 280 samples of blood sera were taken from laying hens coming from four poultry houses. The sera were tested by the haemagglutination inhibition test according to the OIE Manual. Virological testing was conducted as a consequence of atypical results of serological testing. Newcastle disease virus RNA was proved by the RT-nested PCR method in the pooled tissue samples of 5 hens, in the samples of intestines with ileocaecal tonsila, in trachea and also in one swab sample from the environment of one house. Based on sequencing analysis and subsequent phylogenetic analysis, the virus was identified as a low pathogenic strain of paramyxovirus (PMV-1). This low pathogenic strain did not have any impact on the health of laying hens.

Peste des petits ruminantsvirus detected in tissues from an Asiatic lion (Panthera leo persica) belongs to Asian lineage IV

In this study, peste des petits ruminants virus (PPRV) was detected in frozen pooled tissue samples from a dead Asiatic lion (Panthera leo persica). The samples were negative for canine distemper virus and positive for PPRV nucleic acids when tested with one-step RT-PCR using the appropriate virus-specific primers. Subsequent amplification, cloning, and sequencing of the partial nucleocapsid, matrix, and fusion genes confirmed the presence of PPRV nucleic acid. Comparative sequence and phylogenetic analyses of the structural genes of the isolated virus confirmed that the virus belonged to Asian lineage IV and was closely related to PPRV circulating in India.

NovelChlamydia-like Organisms as Cause of Bovine Abortions, UK

Novel<i>Chlamydia</i>-like Organisms as Cause of Bovine Abortions, UK

A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples

One important goal of genomics is to explore the extent of alternative splicing in the transcriptome and generate a comprehensive catalog of splice forms. New computational and experimental approaches have led to an increase in the number of predicted alternatively spliced transcripts; however, validation of these predictions has not kept pace. In this work, we systematically explore different methods for the validation of cassette exons predicted by computational methods or tiling microarrays. Our goal was to find a procedure that is cost effective, sensitive and specific. We examined three ways of priming the reverse transcription (RT) reaction—poly-dT priming, random priming and pooled exon-specific priming. We also examined two strategies for PCR amplification—flanking PCR, which uses primers that hybridize to the constitutive exons flanking the predicted exon, and a semi-nested PCR with a primer that targets the predicted exon. We found that the combination of RT using a pool of gene-specific primers followed by semi-nested PCR resulted in a significant increase in sensitivity over the most commonly used methodology (97% of the test set was detected versus 14%). Our method was also highly specific—no false positives were detected using a test set of true negatives. Finally, we demonstrate that this method is able to detect alternative exons with a high sensitivity from whole-organism RNA, allowing all tissues to be sampled in a single experiment. The protocol developed here is an accurate and cost-effective way to validate predictions of alternative splicing.

Isolation ofMycobacterium aviumsubspeciesparatuberculosisfrom non-ruminant wildlife living in the sheds and on the pastures of Greek sheep and goats

This study aimed to: (1) investigate whether non-ruminant wildlife interfacing with dairy sheep and goats of four Greek flocks endemically infected with Mycobacterium avium subspecies paratuberculosis (MAP) harboured MAP and (2) genetically compare the strains isolated from the wildlife to those isolated from the small ruminants of these flocks. We cultured and screened, by polymerase chain reaction (PCR), pooled-tissue samples from 327 wild animals of 11 species for the MAP-specific IS900 insertion sequence. We also cultured faecal samples from 100 sheep or goats from each of the four flocks. MAP was detected in samples from 11 sheep, 12 goats, two mice, two rats, a hare and a fox. Only one rat had histopathological findings. Genetic typing categorized 21 isolates as cattle-type strains and two, from a house mouse and a goat respectively, as sheep-type strains; this is the first report of a rodent harbouring a sheep-type strain. The MAP types that were most frequently isolated amongst the sheep and goats of each flock were also the ones isolated from sympatric rodents; those isolated from the fox and hare also belonged to the predominant ruminant strains.

Identification of prostate cancer mRNA markers by averaged differential expression and their detection in biopsies, blood, and urine

The advent of serum prostate-specific antigen (PSA) as a biomarker has enabled early detection of prostate cancer and, hence, improved clinical outcome. However, a low PSA is not a guarantee of disease-free status, and an elevated PSA is frequently associated with a negative biopsy. Therefore, our goal is to identify molecular markers that can detect prostate cancer with greater specificity in body fluids such as urine or blood. We used the RT-PCR differential display method to first identify mRNA transcripts differentially expressed in tumor vs. patient-matched nontumor prostate tissue. This analysis led to the identification of 44 mRNA transcripts that were expressed differentially in some but not all tumor specimens examined. To identify mRNA transcripts that are differentially expressed in most tumor specimens, we turned to differential display of pooled tissue samples, a technique we name averaged differential expression (ADE). We performed differential display of mRNA from patient-matched nontumor vs. tumor tissue, each pooled from 10 patients with various Gleason scores. Differentially expressed mRNA transcripts identified by ADE were fewer in number, but were expressed in a greater percentage of tumors (>75%) than those identified by differential display of mRNA from individual patient samples. Differential expression of these mRNA transcripts was also detected by RT-PCR in mRNA isolated from urine and blood samples of prostate cancer patients. Our findings demonstrate the principle that specific cDNA probes of frequently differentially expressed mRNA transcripts identified by ADE can be used for the detection of prostate cancer in urine and blood samples.

Improved comparative proteome analysis based on two‐dimensional gel electrophoresis

The purpose of this study was to test the extent to which differences in spot intensity can be reliably recognized between two groups of two-dimensional electrophoresis gels (pH 4-7, visualized with ruthenium fluorescent stain) each loaded with different amounts of protein from rat brain (power analysis). Initial experiments yielded only unsatisfactory results: 546 spots were matched from two groups of 6 gels each loaded with 200 microg and 250 microg protein, respectively. Only 72 spots were higher (p<0.05), while 58 spots were significantly lower in the 250-microg group. The construction of new apparatuses that allowed the simultaneous processing of 24 gels throughout all steps between rehydration and staining procedure considerably lowered the between-gel variation. This resulted in the detection of significant differences in spot intensities in 77-90% of all matched spots on gel groups with a 25% difference in protein load. This applied both when protein from 24 biological replicates was loaded onto two groups of 12 gels and when two pooled tissue samples were each loaded onto 6 gels. At a difference of 50% in protein load, more than 90% of all spots differed significantly between two experimental groups.

Differential expression of nuclear receptor coregulators in mouse tissues

Nuclear receptor coregulators, including co-activators, co-repressors and co-activator binding proteins, play an important role in nuclear receptor activation and target gene transcription. Coregulators are diverse proteins with various functional domains, which can bind directly or indirectly to canonical nuclear receptors and form protein complexes on respective target gene responsive elements, to regulate transcription. The activation of nuclear receptor in vivo is regulated at different levels. Competition between different nuclear receptors for common limiting coregulators is one among those. For a clear understanding of the differential expression of common nuclear receptor coregulators and their role in regulation of nuclear receptor function in normal mice, we have analyzed the gene expression of nuclear receptor co-activators PBP/TRAP220, PRIP/ASC-2, CBP, SRC-1/p160, PRIC285, PRIC320 and co-activator binding proteins CARM-1 and PIMT at mRNA level by quantitative PCR (QPCR). The cDNAs for QPCR were derived from pooled tissue samples of C57BL/6J mice. Our results clearly showed differential expression of these genes in vivo, in that brain abundantly expresses SRC-1, CBP, PIMT and PRIC320 and testis expresses the most PBP. CARM-1 and PRIP were expressed more in both brain and testis. Heart and skeletal muscle expressed more CARM-1 and modest amount of PIMT, CBP and PBP. PRIC285 is highly expressed in liver, small intestine and adipose tissues. This study will help us to better understand the function of these coregulators and the complexity of nuclear receptor activation in vivo. (This work was supported by NIH)

Surveillance of wildlife for Mycobacterium bovis infection using culture of pooled tissue samples from ferrets (Mustela furo)

AIM: To compare culture results of homogenates of pooled lymph nodes from individual ferrets with and without macroscopic lesions of bovine tuberculosis for the presence of Mycobacterium bovis, and to determine whether homogenates from 10–30 ferrets could be combined and cultured without loss of sensitivity as a possible method for improving cost-effectiveness of surveillance for M. bovis infection in wildlife populations. METHODS: Numbers of colony forming units (cfu) of M. bovis present in cultures of homogenates of pooled lymph nodes from individual ferrets known to be infected and having no visible lesions (NVL) or macroscopic lesions consistent with bovine tuberculosis were determined. Prevalences of M. bovis infection in populations of ferrets in the Marlborough region of the South Island of New Zealand were determined by culturing homogenates of pooled lymph nodes from individual animals. Samples from homogenates from North Canterbury were combined to form pools representing 10, 20 and 30 animals and also cultured for M. bovis. RESULTS: Fewer M. bovis cfu were isolated from ferrets with NVL (mean=0.77 log10) compared with ferrets with macroscopic lesions (mean=3.22 log10; p<0.05). The mean prevalence of infection in eight different surveys involving 427 ferrets from the Marlborough region was 18% (range 8–44%), which included a small number of animals with macroscopic lesions of tuberculosis. Pooling of samples from up to 30 different ferrets with NVL did not reduce the sensitivity of detecting M. bovis-infected populations. CONCLUSION: Culturing of pools of lymph node samples detected a significant proportion of M. bovis-infected ferrets that would otherwise have gone unnoticed based on samples that had only macroscopic lesions. Culturing of samples pooled from up to 30 different ferrets could provide significant cost savings in surveys of wildlife for the presence of M. bovis infection without any apparent loss of sensitivity.

Prevalence and diversity of Arcobacter spp. isolated from the internal organs of spontaneous porcine abortions in Denmark

A study was conducted to determine the prevalence and possible significance of campylobacteria in pig abortions in Denmark. Surface-cauterised liver and kidney samples from 55 aborted pig fetuses submitted to the Danish Veterinary Laboratory were taken and a sensitive isolation procedure used to examine pooled tissue samples for Campylobacter, Arcobacter and Helicobacter spp. Routine microbiological, immunological, and histopathological examinations were also performed to identify concurrent infections or histopathological changes. The abortions tested negative for established abortifacient pathogens ( Brucella, Leptospira, PPV, PRRSV), but Arcobacter spp. were recovered from 23/55 abortions. Co-infections with Streptococcus suis, Escherichia coli, and haemolytic streptococci were observed in 7/23 Arcobacter-positive fetuses, and in 4/32 Arcobacter-negative fetuses. Histopathological analyses identified placentitis, pneumonia, hepatitis and encephalitis among the study group. However, no obvious pathologic features were solely associated with Arcobacter-positive cases, nor were Arcobacter-like bacteria observed in tissue samples. Protein profile analyses of the 27 Arcobacter isolates identified 11 as A. cryaerophilus and 10 as A. skirrowii. Six strains could not be classified into any existing species and were phenotypically distinct, thus, potentially representing at least one new species. The identification results showed that multiple taxa could be found in a single fetus, and in distinct aborted fetuses from a single sow. The high prevalence of arcobacters in Danish pig abortions may account for at least some of the >90% of cases in which no established abortifacient agent is detected, but further studies are needed to define the role of each species, especially where co-infections with other bacteria are present.

Experimental Inoculation of European Starlings (Sturnus vulgaris) and American Crows (Corvus brachyrhynchos) with Mycobacterium bovis

The purpose of this series of pilot studies was to determine whether the passerine species studied are susceptible to infection with Mycobacterium bovis. Separate experiments were conducted on wild-caught starlings (Sturnus vulgaris) and American crows (Corvus brachyrhynchos). In each experiment, four birds were challenged intraperitoneally and four were challenged orally with microorganisms. Challenge dose was 1 x 10(5) colony-forming units of M. bovis cultured from a white-tailed deer (Odocoileus virginianus) case in Michigan. Birds were euthanatized at 1 and 2 mo postinoculation. Histologic lesions suggestive of mycobacteriosis, without the presence of acid-fast bacilli, were noted in all experimental groups. Mycobacterial cultures performed on pooled tissue samples were positive for M. bovis in only some of the intraperitoneal inoculates of each species.

Differential expression of cholesteryl ester transfer protein in the liver and plasma of fasted and fed transgenic mice

Because cholesteryl ester transfer protein (CETP) is considered a potential target in the treatment of atherosclerosis, several reports have focused on the regulation of this enzyme, and there is evidence that insulin may be a regulatory factor. The present study examines the differential expression of the human CETP gene between physiologic conditions that are accompanied by low (fasted) and high (fed) insulin levels. CETP expression was examined in plasma and tissues of transgenic mice expressing the human CETP minigene after 12 hours of fasting ( n = 20) or ad libitum feeding ( n = 20) with normal mouse chow. Plasma cholesteryl ester transfer activity (CETA) was 20% higher in fed than in fasted mice, reflecting higher levels of CETP ( P < 0.05). This observation was accompanied by higher liver mRNA in fed mice (100%, P < 0.05), as determined by ribonuclease protection assays, as well as by higher CETA (23%, P < 0.05) and CETP mass (29%, P < 0.05) in the particulate fraction of liver homogenates. These parameters of liver CETP expression correlated well with each other, as well as with plasma CETA. CETP in the liver particulate fraction was found as a doublet (approximately 70 and 65 kDa), which resolved to a single band (approximately 60 kDa) upon deglycosylation. No differences in CETP expression were observed in pooled adipose tissue samples from fed and fasted mice. Insulin and glucose were not related to any plasma or tissue parameter of CETP expression. In summary, the concerted, differential expression of CETP in the liver of fed and fasted transgenic mice appears to contribute to higher plasma CETP levels in fed mice, but the precise role of insulin and glucose in regulating CETP expression under fasted and fed conditions needs to be defined.

Molecular individuality: polymorphism of salivary gland proteins in three species of ixodid tick.

Pooled tissue samples are frequently used in biochemical studies involving parasites in order to ensure that there is sufficient material for experimentation. A pooled sample is considered to represent the overall phenotypic characteristics of the investigated population. However, this will not be the case if there is a significant degree of molecular polymorphism among individuals in the sampled population. Here we demonstrate marked differences in the protein profile of salivary glands among individuals from three species of ixodid tick (Rhipicephalus appendiculatus, Amblyomma variegatum, Ixodes ricinus), and show that pooling the tissue of several individuals masks substantial qualitative differences among the individuals. Our observations indicate that much greater caution is needed in general when using pooled samples if the molecular diversity within the population is not clearly defined.

Mutagenicity of the potent rat hepatocarcinogen 6BT to the liver of transgenic (lacI) rats: consideration of a reduced mutation assay protocol.

6-(p-dimethylaminophenylazo)benzothiazole (6BT) is an unusually potent rat hepatocarcinogen, producing large malignant liver tumours after only 2-3 months of dietary administration in a riboflavin-deficient diet. This azocarcinogen has been evaluated in a Big Blue F344 transgenic rat (lacI) gene mutation assay. In a reproduction of the early stages of the carcinogenesis bioassay of this agent, rats were maintained on a riboflavin-deficient diet and were given 10 consecutive daily doses of 6BT (10 mg/kg) by oral gavage. The animals were killed and the livers examined 11 days after the final dose. The livers of 6BT-treated rats showed evidence of hepatocellular hypertrophy in centrolobular areas, with some indication of an increased incidence of mitotic figures. An approximately 10-fold increase in the mutation frequency of DNA isolated from an aliquot of the combined liver homogenates of 6BT-treated rats was observed over that obtained from an equivalent aliquot from control animals. Examination of DNA samples isolated from the livers of individual animals confirmed that 6BT was mutagenic in Big Blue rat livers. These data extend the sensitivity of this transgenic assay to include azo hepatocarcinogens. The determination of mutation frequencies using pooled tissue samples represented a major resource-saving adaptation of the assay protocol in the present study; the general advantages and disadvantages of this practice are discussed.

Demonstration of renin mRNA, angiotensinogen mRNA, and angiotensin converting enzyme mRNA expression in the human eye: evidence for an intraocular renin-angiotensin system.

All components necessary for the formation of angiotensin II, the biologically active product of the renin-angiotensin system (RAS), have been demonstrated in ocular tissue or vitreous and subretinal fluid. The tissue concentrations of renin were too high to be explained by admixture of blood. This raises the possibility of an intraocular RAS, independent of the RAS in the circulation. In the present study, gene expression of RAS components in different parts of enucleated human eyes was investigated as evidence for tissue specific production. By using pooled tissue samples renin mRNA could be detected with the RNAse protection assay in retinal pigment epithelium (RPE) choroid, but not in neural retina or sclera. With reverse transcription polymerase chain reaction (RT-PCR), renin mRNA was detected in individual samples of RPE choroid and neural retina, and not anterior uveal tract or sclera. Angiotensinogen and angiotensin converting enzyme (ACE) gene expression could be demonstrated by RT-PCR in individual RPE choroid and neural retina samples and marginally in sclera samples. These results support the concept of intraocular synthesis of angiotensin II, independent of renin, angiotensin, and ACE in the circulation. Since gene expression was highest in ocular parts, which are highly vascularised, local angiotensin II may be involved in blood supply and/or pathological vascular processes such as neovascularisation in diabetic retinopathy.

Excitotoxic Injury Stimulates Glial Fibrillary Acidic Protein mRNA Expression in Perinatal Rat Brain

To study the molecular mechanisms contributing to glial fibrillary acidic protein (GFAP) accumulation after neuronal injury in the developing brain, we used a reproducible and pharmacologically modifiable model of excitotoxic injury, intracerebral injection of N-methyl-d-aspartate (NMDA) in Postnatal Day 7 rats. Injection of NMDA into the posterior striatum elicits dose-dependent ipsilateral injury to striatum, hippocampus, and overlying cortex; treatment with the noncompetitive NMDA antagonist MK-801 is neuroprotective. To examine regionally specific changes in GFAP mRNA expression after lesioning, GFAP mRNA content was assayed, by Northern analysis, in pooled tissue samples of striatum, hippocampus, and cortex, derived from the injected and contralateral hemispheres of animals killed 1-16 days after lesioning with NMDA (12.5 nmol), and in samples derived from lesioned animals and littermates treated with MK-801. In addition, in situ hybridization assays were done to visualize the anatomic distribution of GFAP mRNA expression in NMDA-lesioned (n = 5) and lesioned/MK-801-treated animals (n = 3) 5 days postinjection. There was a marked rise in GFAP mRNA in lesioned cortex within 24 h, and increases were sustained over the next 2 weeks. In contrast, in striatum and hippocampus, in which severe histologic damage evolves, at 24 h postlesioning there was little stimulation of GFAP mRNA expression. Subsequently, 5-16 days postinjury increases in GFAP mRNA were detected in both brain regions. In animals examined 5 days postlesioning, MK-801 treatment markedly attenuated stimulation of GFAP mRNA expression. In situ hybridization assays revealed a marked increase in GFAP mRNA unilaterally, in cortex, hippocampus, and striatum; in similarly lesioned animals treated with MK-801, there was no evidence of tissue injury, and no increase in GFAP mRNA was apparent. Thus, in perinatal rodent brain, focal excitotoxic injury predictably stimulates GFAP mRNA expression in a temporally and regionally specific fashion.

Repeated sequences as genetic markers in pooled tissue samples.

We show, using the PDR1 element of pea, that dispersed repeated sequences of moderate copy number can be used simply and efficiently to generate markers linked to a trait of interest. Inspection of hybridization patterns of repeated sequences to DNA mixtures of pooled genotypes is a sensitive way of detecting such markers. The large number of bands in tracks of digests of these mixtures allows the simultaneous sampling of loci at many places in the genome, and the many unlinked loci serve as internal controls. It is also shown that intensity ratios calculated from these band differences can be used to give a rough estimate of linkage distance.

Mucus protection and airway peroxidation following nitrogen dioxide exposure in the rat.

In the current study, biochemical measures of lipid peroxidation following 4-h inhalation exposure to 76 mg/m3 (40 ppm) nitrogen dioxide were correlated with measures of deposition and tissue antioxidant levels in the nasal cavity and the trachea of the Fischer rat. In addition, respiratory-tract mucus samples were collected via esophageal cannulation and nasopharyngeal lavage over known time periods, and were analyzed for phospholipid (PL) content to provide an index of the unsaturated lipids (UL) that they may contain. UL are thought to be important in the scavenging of oxidants by the mucous lining layer. Nasal deposition efficiency, as measured in the surgically isolated upper respiratory tract under unidirectional flow conditions, averaged 25%, corresponding to an absolute deposition rate of 41 nmol/min. Vitamin E levels averaged 1.7, 5.9, and 0.7 nmol/mumol PL in nasal, tracheal, and pulmonary tissues, respectively. The level in the trachea was significantly (p less than 0.005) higher than in the other tissues. As estimated from the increase in lavage PL content over 1 h, the overall mucous PL transport rate was less than 0.013 nmol/min, suggesting the PL of the mucous lining layer could not offer significant protection against the inhaled NO2. Conjugated dienes were detected in two of four pooled nasal tissue samples. Thiobarbituric acid-reactive material levels in tracheal tissues were significantly elevated over control levels by NO2 (p less than 0.05). Thus, despite the relatively high vitamin E levels, 4-h NO2 exposure appeared to result in lipid peroxidation in the trachea and, perhaps, in the nasal airways of the rat, a result that correlated with the apparent lack of oxidant-scavenging species in the mucus lining these airways.

Occurrence and distribution of neuropeptides in the human skin. An immunocytochemical and immunochemical study on normal skin and blister fluid from inflamed skin

The content and distribution of substance P (SP), somatostatin, vasoactive intestinal peptide (VIP), calcitonin gene-related peptide (CGRP) and neuropeptide Y (NPY) in human skin were investigated. Radioimmunoassay was performed on pooled tissue samples from several regions (fingers, toes, axillas and thighs) and on tissue fluid from spontaneous blisters on inflamed skin. Immunocytochemical localization showed all peptides examined except somatostatin to be present in nerve fibers. Nerve fibers storing SP and CGRP, which were found to coexist, were mostly present as free nerve endings in the superficial part of dermis and in epidermis. SP/CGRP fibers were most abundant in fingers and toes. VIP fibers and NPY fibers were localized in the deeper parts of dermis around blood vessels and acini of sweat glands. Also fibers containing these neuropeptides were most common in fingertips and toes. VIP occurred in relatively high amounts also in skin from axilla whereas NPY in this region was below detection limit. Immunoreactive somatostatin was found in low concentrations in tissue extracts and was not present in amounts sufficient for reliable immunostaining. Fluid from spontaneous blisters on inflamed skin contained detectable amounts of all neuropeptides.