Monitoring 5'-End Resection at Site-Specific Double-Strand Breaks by Southern Blot Analysis

DNA double-strand break (DSB) is one of the most deleterious types of DNA lesions threatening genome integrity. Cells have evolved several exquisite pathways to repair these breaks. Homologous recombination (HR) is an essential DSB repair mechanism that utilizes an intact homologous sequence as a template to repair DSBs with high fidelity. To initiate the HR repair, the 5'-ends of DSBs have to be nucleolytically cleaved by nucleases to generate 3'-single-strand DNA (ssDNA). Exposed 3'-ssDNA recruits the ssDNA binding protein complex RPA to activate the DNA damage checkpoint. RPA is subsequently replaced by Rad51 recombinase to form Rad51 nucleoprotein filament that catalyzes strand invasion and formation of the D-loop. Processing of 5'-ends (called resection) is a crucial step that determines the choice of repair pathways. Here we introduce an assay for monitoring the dynamics of resection at different locations from a site-specific DSB in yeast.

Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses

Geminiviruses constitute a family of plant viruses with characteristic twinned quasi-icosahedral virions and a small circular DNA genome. Geminiviruses, especially begomoviruses, cause substantial economic losses in tropical and subtropical regions globally. Geminiviruses use the host's transcriptional mechanisms to synthesize their mRNAs. They are considered as an attractive model to understand the transcription mechanism of their host plants. Experiments were conducted to identify transcriptional start sites (TSSs) of the three begomoviruses, i.e., Cotton leaf curl Multan virus (CLCuMuV), Corchorus yellow vein virus (CoYVV), and Ramie mosaic virus (RamV). We first rub-inoculated Rice stripe tenuivirus (RSV), a segmented negative-sense RNA virus that uses cap-snatching to produce capped viral mRNAs, into N. benthamiana. After the inoculation, RSV-infected N. benthamiana were super-infected by CoYVV, CLCuMuV, or RamV, respectively. The capped-RNA leaders snatched by RSV were obtained by determining the 5'-ends of RSV mRNA with high throughput sequencing. Afterwards, snatched capped-RNA leaders of RSV were mapped onto the genome of each begomovirus and those matching the begomoviral genome were considered to come from the 5' ends of assumed begomoviral mRNAs. In this way, TSSs of begomoviruses were obtained. After mapping these TSSs onto the genome of the respective begomovirus, it was found very commonly that a begomovirus can use many different TSSs to transcribe the same gene, producing many different mRNA isoforms containing the corresponding open reading frames (ORFs).

Analysis of Human Mitochondrial DNA Content by Southern Blotting and Nonradioactive Probe Hybridization

A single cell can contain several thousand copies of the mitochondrial DNA genome or mtDNA. Tools for assessing mtDNA content are necessary for clinical and toxicological research, as mtDNA depletion is linked to genetic disease and drug toxicity. For instance, mtDNA depletion syndromes are typically fatal childhood disorders that are characterized by severe declines in mtDNA content in affected tissues. Mitochondrial toxicity and mtDNA depletion have also been reported in human immunodeficiency virus-infected patients treated with certain nucleoside reverse transcriptase inhibitors. Further, cell culture studies have demonstrated that exposure to oxidative stress stimulates mtDNA degradation. Here we outline a Southern blot and nonradioactive digoxigenin-labeled probe hybridization method to estimate mtDNA content in human genomic DNA samples. © 2019 by John Wiley & Sons, Inc.

Clinical Genetic Testing for Fragile X Syndrome by Polymerase Chain Reaction Amplification and Southern Blot Analyses

Fragile X syndrome (FXS) is characterized by mental retardation and in the vast majority of cases it is caused by expansion of CGG trinucleotide repeats in the 5' untranslated region (or UTR) in the FMR1 gene on the X chromosome. The size and methylation status of CGG repeats are correlated with the clinical phenotype of FMR1-related disorders. The methods used for clinical genetic testing of FXS include polymerase chain reaction (PCR) amplification and Southern blot analyses, which effectively detect alleles with repeats in the normal, intermediate, premutation, and full mutation size ranges, as well as the methylation status of FMR1 promoter region.

Validation of a Screening Method for Dynamic Mutations in the FMR1 Gene

The objectives of this study were to validate the direct triplet-primed PCR method (dTP-PCR) for determination of dynamic mutations in the FMR1 gene, and to compare the results of the dTP-PCR method and Southern blot analysis. The number of CGG repeats in the FMR1 gene was determined by the direct triplet-primed PCR method and by melting curve analysis. The cut-off temperature between normal and permutations of the CGG repeats was determined using control samples with a known number of CGG repeats. All patients are classified into four categories based on the DNA melting curve. The clinical performance of the assay was established by 40 previously analyzed samples, yielding results of 100% sensitivity and 90.48% specificity in detection expansions of CGG (>30) repeats in the FMR1 gene. This method is appropriate for the quick determination of allelic changes in the FMR1 gene, screening a population, and identifying mutations or premutation carriers in a population with intellectual disabilities of an unknown cause.

Alkaline Denaturing Southern Blot Analysis to Monitor Double-Strand Break Processing

Generation of 3' single-stranded DNA (ssDNA) tails at the ends of a double-strand break (DSB) is essential to repair the break through accurate homology-mediated repair pathways. Several methods have been developed to measure ssDNA accumulation at a DSB in the budding yeast Saccharomyces cerevisiae. Here, we describe one of these assays, which is based on the inability of restriction enzymes to cleave ssDNA. Digestion of genomic DNA prepared at different time points after DSB generation leads to the formation of ssDNA fragments whose length increases as the 5' strand degradation proceeds beyond restriction sites. After the separation by electrophoresis on alkaline denaturing agarose gel, these ssDNA fragments can be visualized by hybridization with an RNA probe that anneals with the 3'-undegraded DSB strand. This assay allows a direct and comprehensive visualization of DSB end processing.

Analysis of De Novo Telomere Addition by Southern Blot

Telomere length is maintained in most eukaryotes by the action of a specialized enzyme, the telomerase. However, the complexity of mechanisms regulating telomeric DNA length as well as the heterogeneity in length of each telomere in a population of cells has made it very difficult to understand how telomerase is regulated in vivo. Here, we describe a method developed in Saccharomyces cerevisiae to monitor the addition of telomeric sequences to a single newly generated telomere in vivo. The primary strain consists of a HO endonuclease cleavage site that is placed directly adjacent to an 81-base-pair stretch of telomeric DNA inserted into the ADH4 locus of chromosome VII. Upon cleavage by HO, the de novo DNA end is rapidly healed by the telomerase enzyme and the analysis of this process allows to gain a mechanistic understanding of how telomerase action is regulated in the cell.

An evaluation of new and established methods to determine T-DNA copy number and homozygosity in transgenic plants

Stable transformation of plants is a powerful tool for hypothesis testing. A rapid and reliable evaluation method of the transgenic allele for copy number and homozygosity is vital in analysing these transformations. Here the suitability of Southern blot analysis, thermal asymmetric interlaced (TAIL-)PCR, quantitative (q)PCR and digital droplet (dd)PCR to estimate T-DNA copy number, locus complexity and homozygosity were compared in transgenic tobacco. Southern blot analysis and ddPCR on three generations of transgenic offspring with contrasting zygosity and copy number were entirely consistent, whereas TAIL-PCR often underestimated copy number. qPCR deviated considerably from the Southern blot results and had lower precision and higher variability than ddPCR. Comparison of segregation analyses and ddPCR of T1 progeny from 26 T0 plants showed that at least 19% of the lines carried multiple T-DNA insertions per locus, which can lead to unstable transgene expression. Segregation analyses failed to detect these multiple copies, presumably because of their close linkage. This shows the importance of routine T-DNA copy number estimation. Based on our results, ddPCR is the most suitable method, because it is as reliable as Southern blot analysis yet much faster. A protocol for this application of ddPCR to large plant genomes is provided.

Problem-solving test: Southwestern blotting

Terms to be familiar with before you start to solve the test: Southern blotting, Western blotting, restriction endonucleases, agarose gel electrophoresis, nitrocellulose filter, molecular hybridization, polyacrylamide gel electrophoresis, proto-oncogene, c-abl, Src-homology domains, tyrosine protein kinase, nuclear localization signal, cDNA, deletion mutants, expression plasmid, transfection, RNA polymerase II, promoter, Shine-Dalgarno sequence, polyadenylation element, affinity chromatography, Northern blotting, immunoprecipitation, sodium dodecylsulfate, autoradiography, tandem repeats.

Problem-solving test: digestion of a plasmid with restriction endonucleases

Terms to be familiar with before you start to solve the test: plasmid, restriction endonuclease, agarose gel electrophoresis, ethidium bromide staining, autoradiography, Coomassie staining, Southern blotting, linear and circular DNA, superhelical DNA, exonuclease, modification methylase, palindrome, sticky and blunt ends, nicked circular DNA.

Comparative study of differential gene expression in closely related bacterial species by comparative hybridization

The ability to profile bacterial gene expression has markedly advanced the capacity to understand the molecular mechanisms of pathogenesis, epidemiology, and therapeutics. This advance has been coupled with the development of techniques that enable investigators to identify bacterial specifically expressed genes and promise to open new avenues of functional genomics by allowing researchers to focus on the identified differentially expressed genes. During the past two decades, a number of approaches have been developed to investigate bacterial genes differentially expressed in response to the changing environment, particularly during interaction with their hosts. The most commonly used techniques include in vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays, which fall into two broad classes: mutagenesis-based technologies and hybridization-based technologies. Selective capture of transcribed sequences, a recently emerging method, is a hybridization-based technique. This technique is powerful in analyzing differential gene expression of the bacteria, with the superb ability to investigate the bacterial species with unknown genomic information. Herein, we describe the application of this technique in a comparative study of the gene expression between two closely related bacteria induced or repressed under a variety of conditions.

Characterization of telomeres and telomerase expression in Xiphophorus

Research investigating telomere lengths and telomerase expression in vertebrates has progressively become important due to the association of these two biological endpoints with cellular aging and cancer in humans. Studies that rely upon the traditional use of laboratory mice have been faced with limitations largely due to inbred mice possessing large telomeres and ubiquitous expression of telomerase. Recently, a number of small fish species have been shown to provide potentially informative models for examining the role of telomeres and telomerase within intact vertebrate animals. Xiphophorus fishes represent a new world live-bearing genus that has not previously been assessed for telomere length or telomerase expression. To add to the knowledge base of telomere and telomerase biology in vertebrates we assessed telomere length and telomerase expression among several species of Xiphophorus. The telomere lengths in several organs (gill, brain, eyes, testis, ovary and liver) in three species (Xiphophorus hellerii, Xiphophorus maculatus, Xiphophorus couchianus) and also in F(1) interspecies hybrids were approximately 2-6 kb. This size was consistent within the same organs of the same species, as well as between species and F(1) hybrids. Despite possessing relatively short telomere lengths compared to humans, the consistency of size among Xiphophorus species and organs may allow experimental detection of telomere shortening. The relative expression of telomerase reverse transcriptase (TERT) was determined by quantitative real-time PCR. Expression levels of TERT was measured in seven organs (ovary, testis, liver, gill, brain, heart, skin) from X. maculatus, X. hellerii and in control and ultraviolet light (UVB) exposed skin samples from X. maculatus, X. hellerii, and F(1) interspecies hybrids. TERT gene expression was significantly higher in ovary and testis, while all other organs showed low relative TERT expression. Detectable increases in TERT expression were found in skin samples upon UVB exposure. Our findings suggest that Xiphophorus may serve as a suitable model for future studies investigating the association of telomere length and telomerase expression in regard to aging and disease.

Mutation detection by Southern blotting

Following the discovery of the structure of DNA in 1953, it became clear that scientists needed to be able to distinguish different DNA sequences. In 1975, Edward Southern published details of a new method for detecting DNA fragments based upon their specific sequence [corrected]. An indication of the importance of his work is that the technique was eponymously named after him and that subsequent methods based loosely on similar principles were named using a play on his surname (western and northern blot). The simplicity and effectiveness of the technique led to its universal acceptance as a standard method for identification of DNA sequences. In the modern laboratory where turn-around times assume ever greater importance, the process can seem relatively time-consuming. In some cases, this has led to its replacement by more rapid techniques such as long-range PCR. Nevertheless, more than 30 years after its invention, the Southern blot remains a cornerstone of molecular biology.

[Identification of a repetitive sequence element for DNA fingerprinting in Phytophthora sojae]

OBJECTIVE

Establishment of DNA fingerprinting in Phytophthora sojae and an analysis of genetic relationship of Heilongjiang and Xinjiang populations.

METHODS

Bioinformatics tools were used to search repetitive sequences in P. sojae and Southern blot analysis was employed for DNA fingerprinting analysis of P. sojae populations from Heilongjiang and Xinjiang using the identified repetitive sequence.

RESULTS

A moderately repetitive sequence was identified and designated as PS1227. Southern blot analysis indicated 34 distinct bands ranging in size from 1.5 kb-23 kb, of which 21 were polymorphic among 49 isolates examined. Analysis of single-zoospore progenies showed that the PS1227 fingerprint pattern was mitotically stable. DNA fingerprinting showed that the P. sojae isolates HP4002, SY6 and GJ0105 of Heilongjiang are genetically identical to DW303, 71228 and 71222 of Xinjiang, respectively.

CONCLUSION

A moderately repetitive sequence designated PS1227 which will be useful for epidemiology and population biology studies of P. sojae was obtained, and a PS1227-based DNA fingerprinting analysis provided molecular evidence that P. sojae in Xinjiang was likely introduced from Heilongjiang.

Cognitive/personality pattern and triplet expansion size in adult myotonic dystrophy type 1 (DM1): CTG repeats, cognition and personality in DM1

BACKGROUND

Although central nervous system (CNS) involvement in adult myotonic dystrophy type 1 (DM1) was described long ago, the large number of variables affecting the cognitive and personality profile have made it difficult to determine the effect of DM1 on the brain. The aim of this study was to define the cognitive and personality patterns in adult DM1 patients, and to analyse the relationship between these clinical patterns and their association with the underlying molecular defect.

METHOD

We examined 121 adult DM1 patients with confirmed molecular CTG repeat expansion and 54 control subjects using comprehensive neuropsychological tests and personality assessments with the Millon Clinical Multiaxial Inventory (MCMI)-II. We used a multiple linear regression model to assess the effect of each variable on cognition and personality adjusted to the remainders.

RESULTS

Patients performed significantly worse than controls in tests measuring executive function (principally cognitive inflexibility) and visuoconstructive ability. In the personality profile, some paranoid and aggressive traits were predominant. Furthermore, there was a significant negative correlation between the CTG expansion size and many of the neuropsychological and personality measures. The molecular defect also correlated with patients' daytime somnolence.

CONCLUSIONS

Besides muscular symptomatology, there is significant CTG-dependent involvement of the CNS in adult DM1 patients. Our data indicate that the cognitive impairment predominantly affects the fronto-parietal lobe.

Biomarkers of oxidative stress: methods and measures of oxidative DNA damage (COMET assay) and telomere shortening

Oxidative stress is fast becoming the nutritional and medical buzzword for the twenty-first century. The theoretical importance of oxidative stress in diabetes is highlighted by its potential double impact on metabolic dysfunction on one hand and the vascular system on the other hand. The new concept of oxidative stress, being an important trigger in the onset and progression of diabetes and its complications, emphasizes the need for measurement of markers of oxidation to assess the degree of oxidative stress. While we have been routinely measuring biomarkers in our molecular epidemiology projects, here we discuss the utility of two assays, (a) DNA damage assessment by COMET measurement and (b) telomere length measurement. As DNA damage is efficiently repaired by cellular enzymes, its measurement gives a snapshot view of the level of oxidative stress. The protocol allows for measurement of oxidative DNA damage (FPG-sensitive DNA strand breaks). Telomere length measured by Southern blotting technique allows one to estimate the chronic burden of oxidative stress at the molecular level and is now considered as biomarker of biological aging.

Pharmacogenetics: technologies to detect copy number variations

The human genome is characterized by structural variations, in addition to having expansive areas of tandem repeat sequences and SNPs. Copy number variations (CNVs) in the human genome are the result of insertions, deletions, duplications and complex multisite variants, affecting approximately 10 to 12% of the genome and covering a higher number of nucleotides than SNPs. Several methods are used for the detection of CNVs, including approaches based on hybridization, such as arrays, PCR amplification, FRET and sequencing. These methods can identify microscopic structural variations (> or = 3 Mb in size), as well as submicroscopic structural variations (approximately 1 kb to 3 Mb in size). CNVs can affect drug metabolism and disease susceptibility. Therefore, the effect of variations in the copies of genes on the efficacy and toxicity of therapeutic agents needs to be well established at both pharmacokinetic and pharmacodynamic levels prior to the use of these agents clinically. This review evaluates the techniques for detecting the CNVs available at the time of publication, citing examples from the application of CNVs in clinical pharmacogenetics.

Nonradioactive genomic DNA blots for detection of low abundant sequences in transgenic maize

Sensitive and reproducible genotyping tools are fundamental in interpreting and substantiating genetic data. In cases where alternative assays like PCR are not applicable, a sensitive genomic Southern protocol is needed. Our maize gene discovery work using the RescueMu transgenic lines was such a task. The direct proof of each new germinal insertion event can be assessed only on a genomic DNA hybridization analysis, and therefore we developed the following protocol to screen efficiently through hundreds up to thousands of samples in a relatively short time. The DNA extraction protocol was scaled to accommodate samples processed in a microcentrifuge with consistent yield of approximately 50 microg of high molecular weight DNA. A trained person can easily process several hundred samples in a few days. Once the DNA is extracted, final results can be obtained routinely within a week on approximately 100 or more samples, depending on the capacity of the electrophoresis and hybridization apparatus available. Under our optimized conditions, the method described below generates blots with high sensitivity and low background even after repeated stripping and reprobing. Single to low-copy transgenes as well as maize genomic sequences can be detected consistently. The nonradioactive DNA probes employed are not only safer, compared to the conventional radioactive probes, but also greatly shorten the exposure time. Confident estimation of copy number - as good as quantitative PCR - and visualization of transgene complexity are just a few more advantages of this protocol.

DNA Checkerboard method for bacterial detection of microbiota from teeth and tongue biofilms. A preliminary study

AIM

The aim of this study was to determine the prevalence of 13 bacterial species in the dorsum tongue biofilm and compare its microbiota to that of subgingival samples in healthy adult subjects using DNA Checkerboard hybridization.

METHODS

A total of 40 samples, from subgingival and tongue biofilm, were enrolled into the study. All the samples were harvested and analyzed by DNA Checkerboard method for their content of 13 species of bacteria. Bacterial scores from each subject and location were averaged and the results of both sites were compared using the Wilcoxon signed ranks test.

RESULTS

All the microorganisms evaluated were detected in both tongue and subgingival samples, without significant differences in their prevalence.

CONCLUSIONS

The dorsum of the tongue was colonized by various microorganisms with similar prevalence as found in the subgingival biofilm of healthy individuals, suggesting that the tongue could be a potential microbial reservoir and may play a role in the recolonization of teeth surfaces.

Gene-specific and mitochondrial repair of oxidative DNA damage

The Southern blot gene-specific DNA damage and repair assay is a robust and flexible method for quantifying many kinds of induced damage and repair with high reproducibility. Specific nicking and loss of a restricted DNA fragment at the site of induced damage is visualized by Southern blot and quantified against a control; since the blot is gene specific, only the damage of interest is measured. Here we show how the assay may be adapted to assess mitochondrial DNA (mtDNA) damage. In the mitochondrion, 8-oxoguanine is a significant oxidative lesion; in the laboratory, photoactivated methylene blue may be used to introduce this lesion into cells. Other lesions may also be studied by using different DNA damaging agents. We find that damage induction by methylene blue is consistently far greater in the mitochondrion than the nucleus. Thus advantageously, mitochondrial 8-oxoguanine repair may be studied without mtDNA isolation or preparation, which are processes known to induce DNA damage and skew measurements. This chapter gives detailed instructions for using methylene blue and the gene-specific repair assay to accurately measure mitochondrial oxidative damage and repair rates.

Heteroduplex structures in 16S-23S rRNA intergenic transcribed spacer PCR products reveal ribosomal interoperonic polymorphisms within single Frankia strains

AIMS

Detection of polymorphisms in intergenic transcribed spacer (ITS) 16S-23S rRNA within single Frankia strains.

METHODS AND RESULTS

Polymorphisms in the 16S-23S rRNA ITS were investigated in single-colony subcultures of seven Frankia isolates. Multiple ITS-polymerase chain reaction (PCR) bands were detected solely in isolates BMG5.5 and BMG5.11. The slow-migrating bands in the ITS-PCR agarose gel electrophoresis profiles of the isolates were revealed to be heteroduplexes on the basis of their migration shift in different electrophoretic matrices, southern hybridization and the single-strand DNA mung bean endonuclease digestion. Laser-scanned capillary electrophoresis detected two ITS-PCR fragments differing in length by three and six nucleotide insertions/deletions in strains BMG5.5 and BMG5.11, respectively. Sequence analysis of the cloned ITS showed that in strain BMG5.5 the two ITS differed by the presence of three to four copies of the 3-bp tandem repeat 5'-TGG-3'. In strain BMG5.11, the two ITS differed by the presence of two to three copies of the 6-bp tandem repeat 5'-CTTGGG-3'.

CONCLUSIONS

We demonstrate the occurrence of ITS 16S-23S rRNa polymorphisms within single Frankia strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

We reported the occurrence of ITS 16S-23S rRNA polymorphisms within single Frankia strains from Elaeagnus host group recognized as the more flexible strains within Frankia genus. Furthermore, we underscored the applied interest of strains BMG5.11 and BMG5.5 in future ecological studies using ITS 16S-23S rRNA as molecular marker.

Screening and identification of putative allergens in berry fruits of the Rosaceae family: technical challenges

Cross-reactive proteins in small fruits of the Rosaceae family like strawberry, raspberry and blackberry revealed an unexpected complex IgE-reactivity pattern. Several copies of PR-10 and PR-14 proteins were detected by Southern blots in strawberry, raspberry and blackberry. In raspberry, the highest similarity at the DNA level for PR-10 and PR-14 (Rub i 1 and Rub i 3) was detected to strawberry sequences of Fra a 1 and Fra a 3. At the protein level, Rub i 1 and Rub i 3 showed more than 70% identity with homologous proteins of rosaceous fruits. Furthermore, raspberries contained additional putative allergens, e.g. class III acidic chitinases and cyclophilins. Blackberries were shown to share at least two well-known major fruit allergens with other rosaceous fruits, namely PR-10s and PR-14s homologous proteins. However the IgE-reactive proteins of small fruits are still not extensively investigated. The main challenges in studying small fruit allergens are the complexity of the fruit matrix, the diversity of physico-chemical properties of fruit proteins, the lack of appropriate protein extraction procedures and the missing information about the influence of processing treatments on food components.

Forensic aspects of DNA-based human identity testing

The forensic applications of DNA-based human identity laboratory testing are often underappreciated. Molecular biology has seen an exponential improvement in the accuracy and statistical power provided by identity testing in the past decade. This technology, dependent upon an individual's unique DNA sequence, has cemented the use of DNA technology in the forensic laboratory. This paper will discuss the state of modern DNA-based identity testing, describe the technology used to perform this testing, and describe its use as it relates to forensic applications. We will also compare individual technologies, including polymerase chain reaction (PCR) and Southern Blotting, that are used to detect the molecular differences that make all individuals unique. An increasing reliance on DNA-based identity testing dictates that healthcare providers develop an understanding of the background, techniques, and guiding principles of this important forensic tool.

Extension of the typing in a general-primer-PCR reverse-line-blotting system to detect all 25 cutaneous beta human papillomaviruses

beta-Papillomaviruses (PV) seem to be involved in the pathogenesis of cutaneous squamous cell carcinoma and its early stage actinic keratosis. In this study, typing was extended of a previously described consensus primer-mediated beta- and gamma-cutaneous HPV PCR method followed by reverse-line-blotting (BGC-PCR/RLB) to detect all 25 known beta-PV and to examine their prevalence in actinic keratosis. The typing format of the BGC-PCR assay was extended by adding hybridization probes of six beta-PV (HPV 75, 76, 80, 92, 93, and 96) to the RLB system. Subsequently, tumor and normal skin tissues were collected from 75 patients with actinic keratosis, allowing typing for a total of 25 beta- and 5 gamma-types. The analytical sensitivity was between 10 copies (HPV 75, 80, 92, 93, and 96) and 100 copies (HPV 76). Except for that of HPV 76, none of the added probes showed any cross-hybridization with other beta-HPV. HPV DNA was detected in 45% of actinic keratosis and in 33% of normal skin by BGC-PCR, and at least one of the six added beta-types was present in 19% of actinic keratoses and in 13% of normal skin. Six beta-HPV types were added successfully to the typing format of the BGC-PCR/RLB system. The potential role of these types in the development of non-melanoma skin cancer awaits further studies.

Coexistence of Trypanosoma cruzi genotypes in wild and periodomestic mammals in Chile

Epidemiologic evidence suggests a preferential association of Trypanosoma cruzi genotypes TCI and TCII with marsupials and placental mammals, respectively. We identify T. cruzi genotypes from 117 infected mammals. Minicircle DNA amplified by polymerase chain reaction and hybridization with a panel of four specific probes showed frequencies for the T. cruzi genotypes TCI, TCIIb, TCIId, and TCIIe of 38%, 41%, 26%, and 9%, respectively, in wild mammals. In peridomestic mammals, frequencies for the same clones were 29%, 33%, 43%, and 14%, respectively. As a whole, mixed infections are found in more than 31% of the cases, which indicates the coexistence of multiclonal strains circulating in nature, and the absence of specific associations between T. cruzi genotypes and reservoir hosts, including marsupials. The direct characterization of parasite genotypes emphasizes the importance of obtaining unbiased epidemiologic information from parasite-endemic areas. Results are discussed in the context of competition or facilitation of T. cruzi genotypes within hosts.

Expression of Cyp21a1 and Cyp11b1 in the fetal mouse testis

Fetal Leydig cells and fetal adrenocortical cells may share a common progenitor cell. Both cell types show several similarities, particularly in relation to their primary steroidogenic function. Differences in steroid secretion are largely due to the expression of 21-hydroxylase (CYP21A1) and 11β-hydroxylase (CYP11B1) activity in the adrenal. To determine whether expression of these enzymes defines a clear difference between adrenocortical and Leydig cells, or is further evidence of a link between the cell types, we have measuredCyp21a1andCyp11b1expression and related enzyme activity in the fetal testis. Expression of bothCyp21a1andCyp11b1was clearly detectable in the fetal testis by RT-PCR and Southern blotting. Real-time PCR studies showed thatCyp11b1was expressed only in the fetal/neonatal testis with no expression in the pubertal or post-pubertal animal.Cyp21a1was also predominantly expressed in the fetal testis although some lower expression was also seen in the adult. Expression ofCyp21a1andCyp11b1in neonatal testicular cells was unaffected by incubationin vitrowith human chorionic gonadotrophin or ACTH. Using immunohistochemistry, CYP21A1 was localised to a subset of interstitial steroidogenic cells in the fetal testis although CYP11B1 was not detectable. Incubation studies showed that 21-hydroxylase activity was present in the tissue although 11β-hydroxylase activity could not be detected. Results indicate that a subpopulation of steroidogenic cells in the fetal testis expressCyp21a1and show 21-hydroxylase activity. This may provide further evidence of a link between fetal Leydig cells and adrenocortical cells but does not discount the possibility that these steroidogenic cells represent ‘ectopic’ adrenal cells.

Spread and variability of the integrase gene in Lactobacillus delbrueckii ssp. lactis strains and phages isolated from whey starter cultures

AIMS

To determine the presence, diffusion and variability of the integrase (int) gene in Lactobacillus delbrueckii ssp. lactis isolated from natural whey starters used for the production of Italian hard cheeses.

METHODS AND RESULTS

A PCR-based protocol aimed to amplify an internal fragment of the int gene was optimized taking into account phage genome sequences available from public databases. Thirty-seven of the 39 strains tested showed the presence of the putative int gene. Southern blot hybridization experiments confirmed data obtained by PCR. The presence of the putative int gene was observed also in 20 of 23 Lact. delbrueckii ssp. lactis lytic phages isolated from the same starter cultures used to isolate strains. Phylogenetic analysis of partial int gene revealed a high similarity both within and between strain- and phage-derived sequences. Sixty per cent of the int-positive strains resulted inducible with mitomycin C, and two of them released active phage particles.

CONCLUSIONS

Our preliminary findings seem to suggest that an important number of Lact. delbrueckii ssp. lactis strains associated with the whey starters are lysogenic.

SIGNIFICANCE AND IMPACT OF THE STUDY

Further contribution to obtain a clearer picture of the complex relationship between thermophilic lactic acid bacteria phage and host in whey starters for Italian, hard-cooked cheeses.

Southern blotting

This protocol describes a basic method to perform the Southern blot. Blotting allows the detection of specific molecules among a mixture separated by gel electrophoresis. Molecules are transferred from the gel to a porous membrane by capillary action using absorbent paper to soak solution through the gel and the membrane. For DNA, specific sequences are detected in the membrane by molecular hybridization with labeled nucleic acid probes. The original method, on which this protocol is based, used labeled RNAs to detect specific DNA fragments in genomic DNA that had been digested with restriction endonucleases. This protocol can be completed in 1-5 d and is inexpensive to carry out, as it requires only basic laboratory equipment.

Rapid and high-resolution detection of IgH gene rearrangements using PCR and melting curve analysis

The analytical methods of Southern blot hybridization (SBH) and the polymerase chain reaction (PCR) for complementarity determining region-3 (CDR3) are fundamental for detecting IgH gene rearrangement. However, there are problems stemming from the characteristics of both methods; especially, the long turn around time (TAT) because of the complex process in the SBH, and the low analytical sensitivity for amplicons in the PCR. Thus, to improve the PCR procedure, we investigated the application of detecting the clonal amplicons based on the different melting Temperature (T(m)) in internal melting domains corresponding to the CDR3 hypervariable region. Our new protocol is based on the combination of a LightCycler Technology with high-speed amplification, and Idaho-Technology with rapid and high-resolution melting curve analysis (MCA), designated PCR-MCA. This method can provide the results within 3 h with an analytical sensitivity of 10(-3). The diagnostic sensitivity and specificity relative to the results documented with the SBH analysis were 89.2% and 100%, respectively. This indicates that the new protocol of PCR-MCA is acceptable for clinical testing; especially, PCR-MCA is relevant in terms of the rapid and sensitive detection of IgH clonality within amplicons.

Small chromosomal integration site of classical CTX prophage in Mozambique Vibrio cholerae O1 biotype El Tor strain

An unusual strain of Vibrio cholerae O1 biotype El Tor harbouring multiple tandem copies of classical CTX prophage caused a cholera epidemic in Mozambique in 2004. However, the location of the classical CTX prophage in the genome of the Mozambique strain was unknown. In this study, pulsed field gel electrophoresis (PFGE) of the whole genome along with Southern hybridization experiments indicated that the classical CTX prophage present in the Mozambique strain is located in the small chromosome. To determine the CTX prophage integration site in the small chromosome of Mozambique strain, the 5'and 3' junctions of the prophage and small chromosome were PCR amplified, cloned and sequenced. Sequence analysis indicated that the prophage was integrated in the conserved dif site of the replication terminus region of the Mozambique strain. While using an O1 El Tor isolate VC44 as a control strain, which carries tandem copies of CTX prophage in its small chromosome like the Mozambique strain, it was unexpectedly detected that the strain VC44 also possesses classical cholera toxin B gene allele. Since the strain VC44 was isolated in India in the year 1992, it appears that the Mozambique strain has probably originated from a VC44-like strain.

Virulence potential and genetic diversity ofAeromonas caviae,Aeromonas veronii, andAeromonas hydrophilaclinical isolates from Mexico and Spain: a comparative study

A comparative study of 109 Aeromonas clinical isolates belonging to the 3 species most frequently isolated from patients with diarrhea in Mexico and Spain was performed to investigate the distribution of 3 prominent toxin genes and the gene encoding flagellin of lateral flagella; 4 well-established virulence factors in the genus Aeromonas. The aerolysin–hemolysin toxin genes were the most prevalent, being present in 89% of the total isolates. The ast toxin gene was conspicuously absent from the Aeromonas caviae and Aeromonas veronii groups but was present in 91% of the Aeromonas hydrophila isolates. Both the alt toxin gene and the lafA flagellin gene also had a low incidence in A. caviae and A. veronii. Differences in the prevalence of alt and lafA were observed between isolates from Mexico and Spain, confirming genus heterogeneity according to geographic location. Carriage of multiple toxin genes was primarily restricted to A. hydrophila isolates, suggesting that A. caviae and A. veronii isolates circulating in Mexico and Spain possess a limited array of virulence genes. Enterobacterial repetitive intergenetic consensus – polymerase chain reaction showed that the Aeromonas populations sampled lack dominant clones and were genetically heterogeneous, with A. caviae being the most diverse species. Further surveys of virulence determinants in genetically heterogeneous populations of Aeromonas isolates circulating worldwide are required to enhance the understanding of their capacity to cause disease.

Development of cystic glandular hyperplasia of the endometrium in Mullerian inhibitory substance type II receptor-pituitary tumor transforming gene transgenic mice

The pituitary tumor transforming gene (PTTG)/securin is an oncogene that is involved in cell cycle regulation and sister chromatid separation. PTTG is highly expressed in various tumors including ovarian tumors, suggesting that PTTG may play a role in ovarian tumorigenesis. Overexpression of PTTG resulted in induction of cellular transformation in vitro and tumor formation in nude mice. To ascertain PTTG function in ovarian tumorigenesis, we generated a transgenic mouse model of PTTG by cloning PTTG cDNA downstream of Mullerian inhibitory substance type II receptor gene promoter (MISIIR) in order to target the ovarian surface epithelium. By screening of transgenic animals, we identified five founders (four males and one female). Using the four male founders, we developed four transgenic lines. PTTG expression was increased in ovarian surface epithelium, ovarian granulosa cells, as well as in the pituitary gland. Transgenic females did not develop any visible ovarian tumors at 8-10 months of age; however, there was an overall increase in the corpus luteum mass in transgenic ovary, suggesting increased luteinization. These changes were associated with an increase in serum LH and testosterone levels. In addition, there was a generalized hypertrophy of the myometrium of MISIIR-PTTG transgenic uteri with cystic glandular and hyperplasia of the endometrium. Based on these results, we conclude that the overexpression of PTTG may be required to initiate precancerous conditions but is not sufficient to induce ovarian tumorigenesis and may require another partner to initiate cellular transformation.

Integration of active human β-galactosidase gene (100 kb) into genome using HSV/AAV amplicon vector

Vectors based on herpes simplex virus type-1 (HSV-1) permit delivery of transgenes of up to 150 kb, while the inverted terminal repeats and Rep of the adeno-associated virus (AAV) can confer site-specific integration into the AAVS1 site, which allows sustained expression of a transgene. In this study, combination of the viral elements in HSV/AAV hybrid vectors has been applied for the infectious transfer of the human lysosomal beta-galactosidase (BGAL) gene of 100 kb. Temporary expression and functional activity of beta-galactosidase (beta-gal) could be detected in human beta-gal-deficient patient and glioblastoma (Gli36) cells upon infection with the basic BGAL amplicon vector. Sustained expression of beta-gal was achieved in Gli36 cells infected with rep-plus, but not rep-minus, HSV/AAV hybrid vectors. None of five clones isolated after rep-minus hybrid vector infection showed elevated beta-gal activity or site-specific integration. In contrast, 80% of the rep-plus clones possessed beta-gal activity at least twofold greater than normal levels for up to 4 months of continuous growth, and 33% of the clones exhibited AAVS1-specific integration of the ITR-flanked transgene. One of the rep-plus clones displayed integration of the ITR cassette only at the AAVS1 site, with no sequences outside the cassette detectable and beta-gal activity fourfold above normal levels. These data demonstrate AAVS1-specific integration of an entire genomic locus and expression of the transgene from the endogenous promoter mediated by an HSV/AAV hybrid vector.

Anthocyanin-rich purple potato flake extract has antioxidant capacity and improves antioxidant potential in rats

Anthocyanins from various vegetables and fruits have antioxidant activities, however, the bioactivities of coloured potato anthocyanins are not well studied. We examined the antioxidant capacities of pigmented fractions from purple potato flakes in vitro, and the antioxidant potentials of purple potato flakes in vivo. 1,1-Diphenyl-2-picrylhydrazyl radical scavenging activity of the pigmented fraction from Hokkai no. 92 (H92) potato flakes was higher than that from Kitamurasaki (KM) potato flakes. Extracts equivalent to 600 μg pigmented fractions from KM and H92 potato flakes inhibited linoleic acid oxidation in the order trolox>H92 ≥ KM>control. Rats were fed 25 % KM or H92 potato flake diets for 4 weeks. The major anthocyanin was identified as petanin. Control rats were fed a diet with cornstarch instead of potato flakes for 4 weeks. The serum antioxidant potential level in the H92 group was significantly higher than that in the control group. The degree of hepatic lipid peroxidation in the H92 group was significantly lower than that in the control group. Hepatic Cu/Zn-superoxide dismutase (SOD), Mn-SOD and glutathione peroxidase (GSH-Px) mRNA levels in the H92 group were significantly higher than those in the control group. Similar significant differences in Cu/Zn-SOD and Mn-SOD mRNA levels between the KM and control groups were found. The present results suggest that purple potato flakes have antioxidant functions with regard to radical scavenging activity and inhibition of linoleic acid oxidation, and that they improve the antioxidant potentials in rats by enhancing hepatic Mn-SOD, Cu/Zn-SOD and GSH-Px mRNA expression.

Detection of clonal IGH gene rearrangements: summary of molecular oncology surveys of the College of American Pathologists

CONTEXT

The diagnosis of B-cell lymphoid malignancy can frequently be substantiated by detecting clonal immunoglobulin heavy chain (IGH) gene rearrangements, which is typically done by polymerase chain reaction (PCR) amplification and/or Southern blot analysis.

OBJECTIVE

To characterize current laboratory practice for the assessment of IGH rearrangements and to identify opportunities for improvement.

DESIGN

The data from the Molecular Oncology Proficiency Survey distributed to participating laboratories by the Molecular Pathology Committee of the College of American Pathologists from 1998 through 2003 were analyzed.

RESULTS

Thirty-nine proficiency survey specimens (29 positive and 10 negative for clonal IGH rearrangements) were distributed. For Southern blot analysis, 944 results were reported, with a successful response rate of 95%. For PCR detection, 2349 results were reported, with a successful response rate of 72%. A higher rate of successful responses by PCR was achieved using framework 3 primers in combination with other frameworks (82%) compared with framework 3 primers only (76%) and when fresh/frozen (72%) compared with paraffin-embedded (65%) tissues were analyzed.

CONCLUSIONS

The performance of the participating laboratories was very good, by both Southern blot and PCR analysis. As expected, Southern blot analysis consistently detects a higher proportion of IGH rearrangements than PCR analysis. Further improvement and standardization of the IGH PCR assay is important if it is to replace Southern blot analysis as the standard method. Participation in this survey is a valuable tool for assessing laboratory performance and it directs our attention to areas where we may improve laboratory practice.

Assessment of Southern blot ribotyping for differentiation of Leptospira strains isolated from field rats

A Southern blot ribotyping based on EcoRV and HindIII digestion with two 16S and 23S rDNA probes for differentiating 27 Leptospira serovars was developed. The results between ribotyping and serotyping among 40 leptospiral strains isolated from field rats trapped in the northeastern region of Thailand during 1999-2000, were compared. A combination of Southern blot ribotyping, using EcoRV or HindIII digestion with both 16S and 23S rDNA as the probes, successfully typed 27 Leptospira serovars into 24 ribotypes with the discriminatory index (D) values of 0.99. The 16S- and 23S-EcoRV ribopatterns produced 17 and 9 profiles, respectively, with D values of 0.95 and 0.63, respectively. Ribopatterns of HindIII from both specific probes yielded 17 patterns. The D values of 16S- and 23S-HindIII ribopatterns were 0.94 and 0.93, respectively. With EcoRV digestion, the 16S rDNA probe was more discriminative than the 23S rDNA probe for differentiating Leptospira serovars. Moreover, the 16S-EcoRV (11 profiles), 16S-HindIII (11 profiles), and 23S-HindIII (10 profiles) ribopatterns produced higher numbers of distinct and unique profiles than the 23S-EcoRV (5 profiles). The results showed 100% concordance between ribotyping and serotyping, leading to all 40 isolates being successfully typed. The current study revealed that ribotyping as a quick and powerful tool for differentiating Leptospira serovars, has potential value in epidemiological studies.

Cloning of equine prostaglandin dehydrogenase and its gonadotropin-dependent regulation in theca and mural granulosa cells of equine preovulatory follicles during the ovulatory process

The mammalian ovulatory process is accompanied by a gonadotropin-dependent increase in follicular levels of prostaglandin E2 (PGE2) and PGF2α, which are metabolized by 15-hydroxy prostaglandin dehydrogenase (PGDH). Little is known about ovarian PGDH regulation in non-primate species. The objectives of this study were to characterize the structure of equine PGDH and its regulation in follicles during human chorionic gonadotropin (hCG)-induced ovulation. The full-length equine PGDH was obtained by RT-PCR, 5′- and 3′-rapid amplification of cDNA ends (RACE). Its open reading frame encodes a 266-amino acid protein that is 72–95% homologous to other species. Semi-quantitative RT-PCR/Southern blot were used to study PGDH regulation in follicles isolated 0–39 h post-hCG. Results showed that PGDH mRNA expression was low in follicles obtained at 0 h, increased at 12 and 24 h (P< 0.05), and decreased at 36-h post-hCG. This induction of expression was biphasic, with elevated abundance of transcripts at 12 and 33 h post-hCG (P< 0.05) in mural granulosa and theca cells. Immunohistochemistry and immunoblotting confirmed regulated expression of PGHD protein in both cell types of preovulatory follicles after hCG. High levels of PGDH mRNA were observed in corpus luteum and other non-ovarian tissues tested, except kidney, muscle, brain, and heart. Thus, this study is the first to report the gonadotropin-dependent regulation of PGDH during ovulation in a non-primate species. PGDH induction was biphasic in theca and mural granulosa cells differing from primates in which this induction was monophasic and limited to granulosa cells, suggesting species-specific differences in follicular control of PGDH expression during ovulation.

[Advancement in the methods for gene dosage analysis]

Gene dosage determination is increasingly important for the study of both genome variation and rearrangement associated with complex diseases. Large genomic duplications and deletions are increasingly found as the causes. Methods such as PCR or sequencing are usually qualitative rather than quantitative. Thus, these methods can not detect large genomic duplications or deletions. Therefore, searching for a gene dosage method which is reliable, sensitive and high-throughput becomes imperative. Many high-performance technologies have been developed for gene dosage analyses in the recent years. There are generally three categories of methods including cytogenetic, Southern or dot blotting, or PCR amplification. Recent development in these techniques have been introduced and discussed in this review, which will help people to choose a suitable method for different research.

JC [corrected] virus detection in human tissue specimens

AIM

To clarify the advantages and disadvantages of different detection methods for Jamestown Canyon virus (JCV) in human tissue specimens.

METHODS

Specimens of lung and gastric carcinomas, and normal lung tissue, gastric mucosa, and tonsil were examined for T-antigen, VP and agnoprotein of JCV by nested PCR, Southern blotting and sequencing. JCV load targeting T-antigen was evaluated by real-time PCR, and JCV existence morphologically by immunohistochemistry, in-situ hybridisation (ISH) and PCR. For these experiments, the JCI cell line (JCV cultured neuroblastoma cell line) was employed as positive control.

RESULTS

In lung and gastric carcinomas, T-antigen, VP and agnoprotein of JCV could be detected by nested PCR whose products were confirmed by Southern blots and sequencing. With real-time PCR, frozen samples of gastric carcinomas gave better detection of JCV than their corresponding paraffin-embedded tissues (p<0.05). The positive rate of JCV was high in lung carcinoma, compared with normal lung tissue (p<0.05). It was the same for JCV copies in gastric carcinoma (p<0.05). Only the positive control exhibited JCV in the nucleus by ISH and immunohistochemistry. In-situ PCR showed that JCV genomic DNA was located in the nucleus of the carcinoma cell, some alveolar epithelial cells, and tonsil lymphocytes. In ISH and PCR, NBT/BCIP colouring was stronger than Fuchsin.

CONCLUSIONS

Nested PCR whose amplicons should be confirmed by Southern blot and sequencing was a comparatively sensitive approach to detect JCV genomic DNA in human non-neural tissues. Real-time PCR might be employed to quantify copy number of JCV. In-situ PCR was a good method to observe the JCV location in cells, given appropriate modulation of amplification cycles. Combinations of various approaches will be adopted to explore the oncogenic roles of JCV in malignancies.

Exploratory study of Mycoplasma suis (Eperythrozoon suis ) on four commercial pig farms in southern Brazil

Mycoplasma suis (Eperythrozoon suis) was detected by PCR and Southern blot in 186 pigs (121 sows, 61 piglets and four boars) on four farms in southern Brazil. DNA was extracted from blood samples and a 16S rRNA gene fragment of M suis was amplified by PCR; Southern blot analysis was then performed on all the samples. Twenty-two of the sows (18.2 per cent) were positive by PCR, and 40 (33.1 per cent) were positive by Southern blot; only one piglet and one boar were positive. The packed cell volume and total plasma protein of the pigs and their PCR and Southern blot results were not significantly different on the four farms, but higher proportions of the pigs were positive by Southern blot than by PCR (P<0.05). The packed cell volume and total plasma protein concentrations of the M suis positive and negative sows were not significantly different.

Arc/Arg3.1 is essential for the consolidation of synaptic plasticity and memories

Arc/Arg3.1 is robustly induced by plasticity-producing stimulation and specifically targeted to stimulated synaptic areas. To investigate the role of Arc/Arg3.1 in synaptic plasticity and learning and memory, we generated Arc/Arg3.1 knockout mice. These animals fail to form long-lasting memories for implicit and explicit learning tasks, despite intact short-term memory. Moreover, they exhibit a biphasic alteration of hippocampal long-term potentiation in the dentate gyrus and area CA1 with an enhanced early and absent late phase. In addition, long-term depression is significantly impaired. Together, these results demonstrate a critical role for Arc/Arg3.1 in the consolidation of enduring synaptic plasticity and memory storage.

Nonradioactive northern and Southern analyses from plant samples

Several specific problems are encountered when nonradioactive detection methods are used in conjunction with plant nucleic acids. In this chapter, we describe protocols for the isolation of DNA and RNA from plant leaves and the preparation of probe molecules by either PCR or in vitro transcription with different haptens. Furthermore, standard conditions and possible modifications for hybridization and detection of probes are given.

Human papilloma virus-16/18 cervical infection among women attending a family medical clinic in Riyadh

BACKGROUND

Prevalence information is lacking on human papillomavirus types 16 and 18 (HPV-16/18) infection in cervical tissues of women residing in Riyadh, Saudi Arabia. In addition, there are no observations on progression to cervical intraepithelial neoplasia (CIN).

SUBJECTS AND METHODS

Pap smear and HPV-16/18 DNA detection by PCR followed by Southern blotting was performed on 120 subjects (Saudi and other Arab nationals) during routine gynecological examination. Some HPV-positive subjects were followed for 4 years, by Pap smear every 6 months and by HPV DNA detection at the end of 4 years.

RESULTS

Overall HPV-16/18 prevalence was 31.6%. HPV-16 prevalence alone was 13.3%, HPV-16 as a mixed infection with HPV-18 was 15%, and all HPV-16 was 28.3%. HPV-18 alone was 3.3%, HPV-18 as a mixed infection with HPV-16 was 15%, and all HPV-18 was 18.3%. Ten subjects had cervical abnormalities with the Pap smear test, six of whom were HPV-16/18 positive, 1 with HPV-16, 1 with HPV-18, and 4 with a mixed infection of HPV-16/18. Of all 23 HPV-16/18-positive subjects, either as individual or mixed infection, followed for 4 years, 7 showed abnormal cytology, 6 at initial examination and 1 during follow-up. Of these 7, 6 reverted to normal without treatment and 1 was treated and became normal after 3 years. None of the subjects progressed to CIN-III.

CONCLUSION

A high prevalence of HPV-16/18 was found, but with a low rate of progression to CIN. A significant association with abnormal cytology was found only in patients with HPV-16/18 mixed infection.

The regulation of stearoyl-CoA desaturase gene expression is tissue specific in chickens

Emerging evidence suggests a potential role of stearoyl-CoA desaturase (SCD)-1 in the control of body weight and energy homeostasis. The present study was conducted to investigate the effects of several energy balance-related factors (leptin, cerulenin, food deprivation, genotype, and gender) on SCD gene expression in chickens. In experiment 1, 6-week-old female and male broiler chickens were used. In experiment 2, two groups of 3-week-old broiler chickens were continuously infused with recombinant chicken leptin (8 micro g/kg/h) or vehicle for 6 h. In experiment 3, two groups of 2-week-old broiler chickens received i.v. injections of cerulenin (15 mg/kg) or vehicle. In experiment 4, two broiler chicken lines (fat and lean) were submitted to two nutritional states (food deprivation for 16 or 24 h and feeding ad libitum). At the end of each experiment, tissues were collected for analyzing SCD gene expression. Data from experiment 1 showed that SCD is ubiquitously expressed in chicken tissues with highest levels in the proventriculus followed by the ovary, hypothalamus, kidney, liver, and adipose tissue in female, and hypothalamus, leg muscle, pancreas, liver, and adipose tissue in male. Female chickens exhibited significantly higher SCD mRNA levels in kidney, breast muscle, proventriculus, and intestine than male chickens. However, hypothalamic SCD gene expression was higher in male than in female (P < 0.05). Leptin increased SCD gene expression in chicken liver (P < 0.05), whereas cerulenin decreased SCD mRNA levels in muscle. Both leptin and cerulenin significantly reduced food intake (P < 0.05). Food deprivation for either 16 or 24 h decreased the hepatic SCD gene expression in fat line and lean line chickens compared with their fed counterparts (P < 0.05). The hypothalamic SCD mRNA levels were decreased in both lines only after 24 h of food deprivation (P < 0.05). In conclusion, SCD is ubiquitously expressed in chickens and it is regulated by leptin, cerulenin, nutritional state, and gender in a tissue-specific manner.

Oncogenic role of JC virus in lung cancer

The JC virus (JCV) infects a large proportion of the population world wide and can cause progressive multifocal leucoencephalopathy in the context of immunodeficiency. Recent reports provide evidence that it may also be oncogenic. Here, JCV was examined by targeting its T-antigen in lung carcinomas (n=103) and normal lung tissues (n=18) by nested-PCR followed by Southern blot, real-time PCR, immunohistochemistry, in situ hybridization and in situ PCR. Additionally, expression of Ki-67, caspase-3, beta-catenin, p53, and Rb was analysed by immunohistochemistry on tissue microarrays of lung carcinomas. Copy numbers of JCV were compared with clinicopathological features. Normal lung tissue was positive significantly less frequently, and contained a lower copy number of JCV than lung carcinomas (p<0.05), and copies were lower in lung adenocarcinomas than in squamous, small or large cell carcinomas (p<0.05). In situ PCR and immunolabelling revealed JCV positivity in the nuclei of lung carcinoma cells. The JCV copy number correlated closely with sex, and expression of Ki-67 and membrane beta-catenin (p<0.05), but not with age, tumour size, pleural invasion, lymph node metastasis, expression of caspase-3, cytoplasmic beta-catenin, p53 or Rb, prognosis, smoking or cancer family history (p>0.05). Age and UICC staging were independent prognostic factors for lung carcinoma patients. These data suggest that JCV may be involved in lung carcinogenesis, especially in tumour types other than adenocarcinoma. Lung carcinomas with higher JCV copy numbers display high proliferation and down-regulation of cell adhesion mediated by membrane beta-catenin.