Mouse DNA Research Articles

Urine sample used for detection of Toxoplasma gondii infection by loop-mediated isothermal amplification (LAMP)

In this study, a loop-mediated isothermal amplification (LAMP) assay was established to detect Toxoplasma gondii DNA in mice infected with T. gondii PRU strain. This LAMP assay was based on the sequence of highly repetitive B1 gene. The detection limit of T. gondii LAMP assay was 1 pg of T. gondii DNA, which was evaluated using 10-fold serially diluted DNA of cultured parasites. The LAMP assay was also highly specific for T. gondii and able to detect T. gondii DNA in urine of mice treated with dexamethasone at 90 day post infection (p.i.), although this assay could not detect the DNA in mice urine 2-6 days p.i. These results demonstrated that LAMP is effective for evaluation of therapy effectiveness for T. gondii infection. The established LAMP assay may represent a useful and practical tool for the routine diagnosis and therapeutic evaluation of human toxoplasmosis.

Co-Immunization with Multimeric Scaffolds and DNA Rapidly Induces Potent Autologous HIV-1 Neutralizing Antibodies and CD8+ T Cells

To obtain proof of concept for HIV vaccines, we generated recombinant multimeric particles displaying the HIV-1 Envelope (Env) third hypervariable region (V3) as an N-terminal fusion protein on the E2 subunit of the pyruvate dehydrogenase complex of Geobacillus stearothermophilus. The E2 scaffold self-assembles into a 60-mer core that is 24 nm in diameter, with a molecular weight of 1.5 MDa, similar to a virus like particle with up to 60 copies of a heterologous protein accessible on the surface. Env(V3)-E2 multimers were tested alone and in combination with Env(gp160) DNA in mice and rabbits. Following two or more co-immunizations with Env(V3)-E2 and Env gp160 DNA, all 18 rabbits developed potent autologous neutralizing antibodies specific for V3 in six weeks. These neutralizing antibodies were sustained for 16 weeks without boosting, and comparable responses were obtained when lipopolysaccharide, a contaminant from expression in E. coli, was removed. Co-immunizations of Env(V3)-E2 and DNA expressing gp160 elicited moderate CD8-specific responses and Env-specific antibodies in mice. Co-immunization with DNA and E2 was superior to individual or sequential vaccination with these components in eliciting both neutralizing antibodies in rabbits and CD8+ T cell responses in mice. Co-immunization with DNA and multimeric E2 scaffolds appears to offer a highly effective means of eliciting rapid, specific, and sustained immune responses that may be a useful approach for other vaccine targets.

Multiplex polymerase chain reaction (PCR) and fluorescence-based capillary electrophoresis for identification of deer species from antlers

Multiplex polymerase chain reaction (PCR) and fluorescence-based capillary electrophoresis (CE) of blood and tissue samples have been used to distinguish between deer species such as red deer, sika deer, wapiti and reindeer. We constructed 4 species-specific primers by using the D-loop of mitochondrial DNA and cytochrome b as an internal PCR control. The amplified species-specific product lengths of 199, 299, 245 and 375 bp for red deer, sika deer, wapiti subspecies and reindeer, respectively were detected from mitochondrial D-loop DNA fragments. The specificity was confirmed by analysis of blood and tissue samples of 4 deer antlers and 8 other samples of mammalian DNA (mouse, rat, pig, chicken, cat, cow, dog and human DNA). The specificity and accuracy of the multiple primers for identification were assessed at various concentrations and from mixed samples. In this study, we established a method for the identification of deer species using deer antlers. Key words: Deer antler, identification, mitochondrial DNA, multiplex polymerase chain reaction (PCR).

Multiplex time-reducing quantitative polymerase chain reaction assay for determination of telomere length in blood and tissue DNA

In this paper we describe a multiplex time-reducing quantitative polymerase chain reaction (qPCR) method for determination of telomere length. This multiplex qPCR assay enables two pairs of primers to simultaneously amplify telomere and single copy gene (albumin) templates, thus reducing analysis time and labor compared with the previously established singleplex assay. The chemical composition of the master mix and primers for the telomere and albumin were systematically optimized. The thermal cycling program was designed to ensure complete separation of the melting processes of the telomere and albumin. Semi-log standard curves of DNA concentration versus cycle threshold (C (t)) were established, with a linear relationship over an 81-fold DNA concentration range. The well-performed intra-assay (RSD range 2.4-4.7%) and inter-assay (RSD range: 3.1-5.0%) reproducibility were demonstrated to ensure measurement stability. Using wild-type, Lewis lung carcinoma and H22 liver carcinoma C57BL/6 mouse models, significantly different telomere lengths among different DNA samples were not observed in wild-type mice. However, the relative telomere lengths of the tumor DNA in the two strains of tumor-bearing mice were significantly shorter than the lengths in the surrounding non-tumor DNA of tumor-bearing mice and the tissue DNA of wild-type mice. These results suggest that the shortening of telomere lengths may be regarded as an important indicator for cancer control and prevention. Quantification of telomere lengths was further confirmed by the traditional Southern blotting method. This method could be successfully used to reduce the time needed for rapid, precise measurement of telomere lengths in biological samples.

Comparison of antigen expression from plasmid DNA in tumor-free and antigen-expressing tumor-bearing mice

Reduced antigen expression after DNA vaccination could be a factor that limits its therapeutic effects in antigen-expressing tumor-bearing hosts. To examine whether the presence of an antigen-positive tumor results in the destroy of antigen-expressing cells, pCMV-OVA plasmid expressing ovalbumin (OVA), a model antigen, was intradermaly injected to tumor-free mice and those bearing an EG7-OVA tumor, which stably expresses OVA. For a quantitative evaluation of the elimination of antigen-expressing cells, a plasmid independently expressing firefly luciferase and OVA (pCMV-Luc/OVA) was injected to mice that had been untreated or administered with pCMV-OVA, and luciferase activity was measured one week after the administration. In both tumor-free and tumor-bearing mice, a pre-injection of pCMV-OVA reduced the luciferase expression from pCMV-OVA/Luc compared with a pre-injection of an empty plasmid, suggesting that an immune response to antigen-expressing cells is induced. In tumor-bearing mice, OVA-specific humoral and cellular immune responses were detected even before the vaccination, but such responses had no significant effects on the luciferase expression from pCMV-OVA/Luc. These results indicate that DNA vaccination can induce antigen-specific immune response even in tumor-bearing mice, although it is not strong enough to reject the tumor burden.

Cyclophosphamide-induced nephrotoxicity, genotoxicity, and damage in kidney genomic DNA of Swiss albino mice: the protective effect of Ellagic acid

Cyclophosphamide (CPM), an alkylating agent is used as an immunosuppressant in rheumatoid arthritis and in the treatment of several cancers as well. In this study, Ellagic acid (EA), a naturally occurring plant polyphenol, was evaluated for its antigenotoxicity and antioxidant efficacy against the CPM-induced renal oxidative stress and genotoxicity in Swiss albino mice. The mice were given a prophylactic treatment of EA orally at a dose of 50 and 100 mg/kg body weight (b wt) for seven consecutive days before the administration of a single intraperitoneal (i.p.) injection of CPM at 50 mg/kg b wt. The modulatory effects of EA on CPM-induced nephrotoxicity and genotoxicity were investigated by assaying oxidative stress biomarkers, serum kidney toxicity markers, DNA fragmentation, alkaline unwinding assay, micronuclei (MN) assay, and by histopathological examination of kidney tissue. A single intraperitoneal administration of CPM in mice increased malondialdehyde level with depletion in glutathione content, antioxidant enzymes activities, viz. glutathione peroxidase, glutathione reductase, catalase, quinone reductase, induced DNA strand breaks, and MN induction. EA oral administration at both doses caused significant reduction in their levels, restoration in the activities of antioxidant enzymes, reduction in MN formation, and DNA fragmentation. Serum toxicity marker enzymes like BUN, creatinine, and LDH were also increased after CPM treatment which was significantly decreased in EA pretreated groups. Present findings suggest a prominent role of EA against CPM-induced renal injury, DNA damage, and genotoxicity.

Analysis of some conventional ab initio gene finders using human and mouse DNA sequences

An evaluation of the prediction accuracy of five ab initio gene prediction programs (that is, FGENESH, Genscan, HMMgene, GeneMark.hmm and FGENES) was conducted by the use of 110 human and mouse orthologous sequences. As expected, all programs presented different predictions with various ranges of accuracy. According to our results, FGENESH and Genscan generally had the maximum power to produce more reliable results in both nucleotide and exon levels than others. Although, both FGENES and GenMark.hmm predicted the highest number of exons (966 and 946 exons, respectively), when exon sensitivity ( ESn ), exon specificity ( ESp ) and ( ESn +ESp /2) were considered, their overall accurate performance descended and was clustered in the lowest positions. It was also determined that all programs have lower power in predicting initial and terminal exons, as compared to internal exons, which suggested that such programs cannot accurately determine translational start sites (TSS) and translational stop codons (TSC) as internal exons, whose boundaries are highlighted by acceptor and donor sites. Apart from the species difference, it was finally recognized that the programs, FGENESH and GeneMark.hmm, presented much more sensitivity in detecting genes with low guanine-cytosine (GC) content.

XMRV and prostate cancer—a 'final' perspective

XMRV was first described in 2006, when it was identified in samples isolated from prostate cancer tissues. However, studies have since shown that XMRV arose in the laboratory and was formed by genetic recombination between two viral genomes carried in the germline DNA of mice used during serial transplantation of the CWR22 prostate cancer xenograft. These new findings strongly imply that XMRV does not circulate in humans, but is only present in the laboratory. Thus, there is no reason to believe that it has any role in the etiology of prostate cancer or other diseases.

Damaging effects of water-borne cadmium chloride on DNA of lung cells of immature mice

We investigated the effects of cadmium on lung cell DNA in immature mice. The mice were randomly divided into four groups: control group, low-dose group (1/100 LD(50)), middle-dose group (1/50 LD(50)), and high-dose group (1/25 LD(50)); they were supplied with cadmium chloride or control water for 40 days. Lung cells collected from sacrificed mice were used to evaluate the extent of DNA damage by comet assay. The ratio of tailing cells, DNA tail length, DNA comet length, DNA tail moment, DNA olive tail moment, and percentage of DNA in the comet tail were measured. The rate of tailing lung cells exposed to cadmium increased significantly; the low-concentration group had significantly (P < 0.05) higher rates, and the middle- and high-concentration groups had higher (P < 0.01) rates compared to the control. DNA tail length, DNA comet length, DNA tail moment, and DNA olive tail moment all increased with the increase in cadmium doses, but compared with those of the control group, no significant differences in low-dose group were found (P > 0.05), and the differences in middle- and high-dose groups were all highly significant (P < 0.01). The degree of DNA damage also increased with the increase of the cadmium concentrations. We conclude that cadmium significantly increases DNA damage in lung cells of immature mice in a dose-dependent manner.

Locating CpG Islands with Kullback-Leibler Divergence

A CpG island is a short contiguous DNA subsequence that is rich in CG dinucleotides. CpG islands are often located around the promoters of housekeeping genes and have been found associated with certain tissue-specific genes. This observation indicates that they can be used as markers to identify genes. The information about the locations of CpG islands can also help us understand a gene regulation process called methylation. In this report, we propose a statistical method for locating CpG islands. Our method employs the Kullback-Leibler divergence. We use the given DNA sequence to determine a window size and a shift size for computing the divergence values along a DNA segment. A region in the proximity of a CpG island should contain consecutive windows with high divergence values. The distribution of the Kullback-Leibler divergence values can be suitably fitted by a truncated Pareto distribution. We estimate the parameters of the truncated Pareto distribution via the maximum likelihood principle. Then the fitted distribution is applied to locate regions with a divergence value exceeding a threshold level of significance. To assess the accuracy of our method, we compare our results to the putative CpG islands found in four well-studied mouse and human DNA sequences. The comparison suggests our approach consistently yields reliable predictions of CpG island locations.

Loop-Mediated Isothermal Amplification Assay Targeting the 47-Kda Gene of Orientia tsutsugamushi: A Rapid and Sensitive Alternative to Real-Time PCR

A sensitive, specific and rapid diagnostic test for the detection of Orientia tsutsugamushi, the causative agent of scrub typhus, is necessary to accurately and promptly diagnose patients and ensure that they receive proper treatment. A Loop-Mediated Isothermal Amplification (LAMP) assay targeting the 47-kDa gene of tsutsugamushi was developed. The LAMP assay was capable of detecting eleven different strains of Orientia at levels comparable to that of the quantitative PCR based method of detection. Ten patient specimens, confirmed to be positive for Orientia by two different PCR methods, were tested and nine out of ten were determined to be positive by LAMP. In terms of specificity, the assay was able to differentiate between Orientia and other phylogenetically similar bacteria as well as mouse and human host DNA. In addition to being sensitive and specific, the LAMP reaction was completed in 1 hour, demonstrating that it is a highly time-efficient method of diagnosing scrub typhus.

Detection of Murine Leukemia Virus or Mouse DNA in Commercial RT-PCR Reagents and Human DNAs

The xenotropic murine leukemia virus (MLV)-related viruses (XMRV) have been reported in persons with prostate cancer, chronic fatigue syndrome, and less frequently in blood donors. Polytropic MLVs have also been described in persons with CFS and blood donors. However, many studies have failed to confirm these findings, raising the possibility of contamination as a source of the positive results. One PCR reagent, Platinum Taq polymerase (pol) has been reported to contain mouse DNA that produces false-positive MLV PCR results. We report here the finding of a large number of PCR reagents that have low levels of MLV sequences. We found that recombinant reverse-transcriptase (RT) enzymes from six companies derived from either MLV or avian myeloblastosis virus contained MLV pol DNA sequences but not gag or mouse DNA sequences. Sequence and phylogenetic analysis showed high relatedness to Moloney MLV, suggesting residual contamination with an RT-containing plasmid. In addition, we identified contamination with mouse DNA and a variety of MLV sequences in commercially available human DNAs from leukocytes, brain tissues, and cell lines. These results identify new sources of MLV contamination and highlight the importance of careful pre-screening of commercial specimens and diagnostic reagents to avoid false-positive MLV PCR results.

No evidence of non‐homologous insertions in mouse model of MDD created by replacement of homologous mouse DNA sequence with pathogenic 6‐base human CREB1 promoter sequence

We have recently reported the creation and initial characterization of the first etiology-based recombinant mouse model of major depressive disorder (MDD). This was achieved by replacing the corresponding mouse DNA sequence with a 6-base DNA sequence from the human CREB1 promoter that is associated with the development of MDD in families identified by probands with recurrent, early-onset MDD. The current study explored whether the desired homologous recombination event at the mouse Creb1 gene that resulted in the creation of the mouse model was also accompanied by insertions of the targeting vector at unintended non-homologous locations in the mouse genome. No evidence of insertions of targeting vector sequence was observed at regions other than the mouse Creb1 gene.

Enhancement of Hepatitis B Virus Replication by Androgen and Its Receptor in Mice

Hepatitis B virus (HBV) is an important pathogen that chronically infects more men than women. To understand the molecular mechanism of this gender disparity, we analyzed HBV replication in transgenic mice that carried the HBV genome with or without the ability to express the HBV X protein (HBx). We found that gender had no effect on HBV surface antigen (HBsAg), DNA, and RNA levels in mice before puberty, but its effect on HBV after puberty was apparent, with HBV replicating approximately twice more efficiently in male mice than in female mice whether or not HBx was expressed. The castration of male mice resulted in a reduction of HBV HBsAg, DNA, and RNA levels, which could be partially restored by the injection of the androgen agonist R1881, indicating a positive role of androgen in HBV replication. The introduction of HBV genomic DNA and androgen receptor (AR) short hairpin RNA (shRNA) into the liver of naïve mice by hydrodynamic injection revealed that the effect of androgen on HBV was dependent on its receptor, which apparently could also stimulate HBV replication via an androgen-independent pathway. Further studies indicated that the two previously identified androgen response elements (AREs) in the HBV genome could indeed mediate the effect of androgen on HBV RNA transcription and DNA replication in vivo. These effects of androgen and its receptor on HBV thus provide an explanation for why men have a higher risk of HBV infection than women.

Real-time PCR-based assay to quantify the relative amount of human and mouse tissue present in tumor xenografts

BackgroundXenograft samples used to test anti-cancer drug efficacies and toxicities in vivo contain an unknown mix of mouse and human cells. Evaluation of drug activity can be confounded by samples containing large amounts of contaminating mouse tissue. We have developed a real-time quantitative polymerase chain reaction (qPCR) assay using TaqMan technology to quantify the amount of mouse tissue that is incorporated into human xenograft samples.ResultsThe forward and reverse primers bind to the same DNA sequence in the human and the mouse genome. Using a set of specially designed fluorescent probes provides species specificity. The linearity and sensitivity of the assay is evaluated using serial dilutions of single species and heterogeneous DNA mixtures. We examined many xenograft samples at various in vivo passages, finding a wide variety of human:mouse DNA ratios. This variation may be influenced by tumor type, number of serial passages in vivo, and even which part of the tumor was collected and used in the assay.ConclusionsThis novel assay provides an accurate quantitative assessment of human and mouse content in xenograft tumors. This assay can be performed on aberrantly behaving human xenografts, samples used in bioinformatics studies, and periodically for tumor tissue frequently grown by serial passage in vivo.

Acute pyelonephritis and renal scarring are caused by dysfunctional innate immunity in mCxcr2 heterozygous mice

The CXCR1 receptor and chemokine CXCL8 (IL-8) support neutrophil-dependent clearance of uropathogenic Escherichia coli from the urinary tract. CXCR1 is reduced in children prone to pyelonephritis, and heterozygous hCXCR1 polymorphisms are more common in this patient group than in healthy individuals, strongly suggesting a disease association. Since murine CXCR2 (mCXCR2) is functionally similar to human CXCR1, we determined effects of gene heterozygosity on the susceptibility to urinary tract infection by infecting heterozygous (mCxcr2+/−) mice with uropathogenic Escherichia coli. Clearance of infection and tissue damage were assessed as a function of innate immunity in comparison to that in knockout (mCxcr2−/−) and wild-type (mCxcr2+/+) mice. Acute sepsis-associated mortality was increased and bacterial clearance drastically impaired in heterozygous compared to wild-type mice. Chemokine and neutrophil responses were delayed along with evidence of neutrophil retention and unresolved kidney inflammation 1 month after infection. This was accompanied by epithelial proliferation and subepithelial fibrosis. The heterozygous phenotype was intermediate, between knockout and wild-type mice, but specific immune cell infiltrates that accompany chronic infection in knockout mice were not found. Hence, the known heterozygous CXCR1 polymorphisms may predispose patients to acute pyelonephritis and urosepsis.

Murine Gammaretrovirus Group G3 Was Not Found in Swedish Patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Fibromyalgia

BackgroundThe recent report of gammaretroviruses of probable murine origin in humans, called xenotropic murine retrovirus related virus (XMRV) and human murine leukemia virus related virus (HMRV), necessitated a bioinformatic search for this virus in genomes of the mouse and other vertebrates, and by PCR in humans.ResultsThree major groups of murine endogenous gammaretroviruses were identified. The third group encompassed both exogenous and endogenous Murine Leukemia Viruses (MLVs), and most XMRV/HMRV sequences reported from patients suffering from myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Two sensitive real-time PCRs for this group were developed. The predicted and observed amplification range for these and three published XMRV/HMRV PCRs demonstrated conspicuous differences between some of them, partly explainable by a recombinatorial origin of XMRV. Three reverse transcription real-time PCRs (RTQPCRs), directed against conserved and not overlapping stretches of env, gag and integrase (INT) sequences of XMRV/HMRV were used on human samples. White blood cells from 78 patients suffering from ME/CFS, of which 30 patients also fulfilled the diagnostic criteria for fibromyalgia (ME/CFS/FM) and in 7 patients with fibromyalgia (FM) only, all from the Gothenburg area of Sweden. As controls we analyzed 168 sera from Uppsala blood donors. We controlled for presence and amplifiability of nucleic acid and for mouse DNA contamination. To score as positive, a sample had to react with several of the XMRV/HMRV PCRs. None of the samples gave PCR reactions which fulfilled the positivity criteria.ConclusionsXMRV/HMRV like proviruses occur in the third murine gammaretrovirus group, characterized here. PCRs developed by us, and others, approximately cover this group, except for the INT RTQPCR, which is rather strictly XMRV specific. Using such PCRs, XMRV/HMRV could not be detected in PBMC and plasma samples from Swedish patients suffering from ME/CFS/FM, and in sera from Swedish blood donors.

Frequent detection of infectious xenotropic murine leukemia virus (XMLV) in human cultures established from mouse xenografts

Purpose: To investigate the frequency of xenotropic murine leukemia virus (MLV) presence in human cell lines established from mouse xenografts and to search for the evidence of horizontal viral spread to other cell lines. Methodology: We examined xenograft tumor cell lines from 7 independent laboratories and 128 non-xenografted tumor cell lines. Cell line DNA was examined for mouse DNA contamination, and by three Taqman qPCR assays targeting the gag, env or pol regions of MLV. Sequencing was used for viral strain identification. Supernatant fluids were tested for reverse transcriptase (RT) activity. Results: Six of 23 (26%) mouse DNA free xenograft cultures were strongly positive for MLV and their sequences had greater than 99% homology to known MLV strains. Four of five available supernatant fluids from these viral positive cultures were strongly positive for RT activity. Three of these supernatant fluids were studied to confirm the infectivity of the released virions for other human culture cells. Of the 78 non-xenograft derived cell lines maintained in the xenograft culture-containing facilities, 13 (17%) were positive for MLV, including XMRV, a virus strain first identified in human tissues. By contrast, all 50 cultures maintained in a xenograft culture-free facility were negative for viral sequences. Conclusions: Human cultures derived after mouse xenografting frequently contain and release highly infectious xenotropic MLV viruses. Laboratories working with xenograft-derived human cultures should be aware of the risk of contamination with potentially biohazardous human-tropic mouse viruses and their horizontal spread to other cultures.

Species identification and authentification of human and rodent cell cultures using polymerase chain reaction analysis of vomeronasal receptor genes

Cell culture and the use of cell lines are routinely used in basic scientific research. It is therefore imperative for researchers to ensure the origin of the cell lines used and that they are routinely re-analysed for contamination and misidentification. Inter-species contamination is relatively frequent, and the most commonly used cell lines are of human, mouse and rat derivation. We have developed simple species specific primer assays based on genomic sequence differences in vomeronasal receptor gene family members to discriminate between human, mouse and rat DNA using standard agarose gel electrophoresis. Furthermore, these PCR assays are able to identify the species composition within an inter-species mixed population. This approach therefore provides a valuable tool to enable a rapid, simple and relatively inexpensive determination of the authentication and contamination of cell cultures.

Regulation of POU4F3 gene expression in hair cells by 5′ DNA in mice

The POU-domain transcription POU4F3 is expressed in the sensory cells of the inner ear. Expression begins shortly after commitment to the hair cell (HC) fate, and continues throughout life. It is required for terminal HC differentiation and survival. To explore regulation of the murine Pou4f3 gene, we linked enhanced green fluorescent protein (eGFP) to 8.5 kb of genomic sequence 5' to the start codon in transgenic mice. eGFP was uniformly present in all embryonic and neonatal HCs. Expression of eGFP was also observed in developing Merkel cells and olfactory neurons as well as adult inner and vestibular HCs, mimicking the normal expression pattern of POU4F3 protein, with the exception of adult outer HCs. Apparently ectopic expression was observed in developing inner ear neurons. On a Pou4f3 null background, the transgene produced expression in embryonic HCs which faded soon after birth both in vivo and in vitro. Pou4f3 null HCs treated with caspase 3 and 9 inhibitors survived longer than untreated HCs, but still showed reduced expression of eGFP. The results suggest the existence of separate enhancers for different HC types, as well as strong autoregulation of the Pou4f3 gene. Bioinformatic analysis of four divergent mammalian species revealed three highly conserved regions within the transgene: 400 bp immediately 5' to the Pou4f3 ATG, a short sequence at -1.3 kb, and a longer region at -8.2 to -8.5 kb. The latter contained E-box motifs that bind basic helix-loop-helix (bHLH) transcription factors, including motifs activated by ATOH1. Cotransfection of HEK293 or VOT-E36 cells with ATOH1 and the transgene as a reporter enhanced eGFP expression when compared with the transgene alone. Chromatin immunoprecipitation of the three highly conserved regions revealed binding of ATOH1 to the distal-most conserved region. The results are consistent with regulation of Pou4f3 in HCs by ATOH1 at a distal enhancer.