Towards an Analytical Biology.

This article draws a perspective on the increasingly unavoidable question of whether steps can be taken in genomics and biology at large to move them more rapidly towards more analytical and deductive biology, akin to similar developments that occurred in other natural sciences, such as physics and chemistry, centuries ago. It provides a summary of recent advances in other relevant sciences in the last 3 decades that are likely to pull it in that direction in the next decade or so, as well as what methods and tools will make it possible.

[Study of gene expression in patients with peripheral artery disease]. / Izuchenie ékspressii genov u patsientov s zabolevaniiami perifericheskikh arterii.

Currently, there are no widely used available techniques for reliable prognosis of the onset and course of peripheral artery disease. Working out of optimal test systems including genetic ones for assessment of risks for the development of the disease, its progression or development of complications in patients with peripheral atherosclerosis is an important mission of modern medicine. This article deals with a promising technique of genetic studies in patients with peripheral artery disease, i. e., study of gene expression. Also provided herein is a literature review devoted to the main techniques used for the analysis of the profile of gene expression. This is followed by evaluating the possibility of using DNA chips, as well as describing the state of the art and unsolved problems of studying gene expression in patients with peripheral artery disease.

Development of a highly sensitive PCR/DNA chip method to detect mycoplasmas in a veterinary modified live vaccine.

Mycoplasmas are potential contaminants that introduce undesirable changes in mammalian cell cultures. They frequently contaminate cell substrates and other starting materials used for manufacturing cell-derived biologics, such as vaccines and pharmaceutical products. Mycoplasma purity testing of live vaccines, active ingredients, raw material, and seed lots is required during vaccine production. Previously, testing using a time-consuming, costly 28-day culture assay, which lacks sensitivity for species that do not grow in culture, was required in the European Pharmacopoeia (Ph. Eur). But now nucleic acid amplification techniques (NATs) can be used. NATs provide rapid results and are sensitive. We evaluated the sensitivity and specificity of a commercially-available NAT to detect individual mycoplasma DNA in a veterinary modified live vaccine using five reference strains recommended by the Ph. Eur. Our results showed that this NAT-based method can be used to detect mycoplasma in spiked live vaccine, without interference from the vaccine components, with a limit of detection of 10 CFU/mL, as required by the Ph. Eur. Its specificity was demonstrated since no mycoplasmas were detected in non-spiked vaccine. This method is undergoing validation as a replacement for the conventional culture method in the production of veterinary live vaccines.

Comparison of the performance of the NucliSENS EasyQ HPV E6/E7 mRNA assay and HPV DNA chip for testing squamous cell lesions of the uterine cervix.

This study aims to evaluate the clinical performance of the NucliSENS EasyQ assay and compare it with HPV DNA genotyping for the detection of high-grade squamous intraepithelial lesions (HSIL) and cancer in a Korean population. In 188 total thin prep samples, the remaining fluid after cytology slide preparation was tested with Goodgene HPV DNA chips and the NucliSENS EasyQ HPV E6/E7 messenger RNA (mRNA) assay. The sensitivity and specificity of each test were calculated with HSIL and squamous cell carcinoma (SCC) as the disease endpoint. Out of the 188 samples, 139 (74%) were positive for DNA of 14 HPV types, while 57 (30%) cases were positive for E6/E7 mRNA. The DNA test was positive in cytology cases of SCC, HSIL, and atypical squamous cell. The mRNA test yielded results of 75%, 74%, 60%, 56%, and 29% positivity in abnormal cytology cases of SCC, HSIL, atypical squamous cells - cannot exclude HSIL, atypical squamous cells of undetermined significance, and low-grade squamous intraepithelial lesion, respectively. In normal cytology cases, the positivity rates were 9% and 53% for the mRNA and DNA tests, respectively. For detection of HSIL and SCC, the sensitivity of the mRNA test was 74.36% and that of the DNA test was 100%, while the specificities of the tests were 85% and 40.83%, respectively. These findings suggest that the HPV E6/E7 mRNA assay can overcome the shortcoming of low specificity of DNA assays for clinical detection of high-grade cervical lesions and malignancies.

Bioinformatics analysis of mice Agouti gene polymorphism / 中国实验动物学报

Purpose Polymorphisms of candidate gene Agouti was analyzed in order to reveal the molecular mech -anisms of coat color difference in chromosome engineering mice .Methods Firstly, differences of mouse coat color was detected by color measurement spectrophotometer .Then, candidate gene Agouti was found by whole genome scanning based on DNA chip.Finally, cDNA and amino acid sequence polymorphisms were analyzed , as well as the influence of protein properties and function after mutation was predicted by bioinformatics software .Results There are five SNPs in the Agou-ti cDNA sequences , resulting in three missense mutations in the amino acid sequence of Agouti signaling protein .Bioinfor-matics analysis revealed that one βsheet deletion in the secondary structure of the mutant protein , as well as tertiary struc-ture changed , leading to decrease of binding ability .Conclusion A novel missense mutation is found in candidate Agouti gene.It plays critical role in receptor binding activity , and may reflect on mice coat color changing from light gray to dark gray eventually .

Substitute of Animals in Drug Research: An Approach Towards Fulfillment of 4R's.

The preclinical studies for drug screening involve the use of animals which is very time consuming and expensive and at times leads to suffering of the used organism. Animal right activists around the world are increasingly opposing the use of animals. This has forced the researchers to find ways to not only decrease the time involved in drug screening procedures but also decrease the number of animals used and also increase the humane care of animals. To fulfill this goal a number of new in vitro techniques have been devised which are called 'Alternatives' or 'Substitutes' for use of animals in research involving drugs. These 'Alternatives' are defined as the adjuncts which help to decrease the use as well as the number of animals in biomedical research. Russell and Burch have defined these alternatives by three R's - Reduction, Refinement and Replacement. These alternative strategies include physico-chemical methods and techniques utilizing tissue culture, microbiological system, stem cells, DNA chips, micro fluidics, computer analysis models, epidemiological surveys and plant-tissue based materials. The advantages of these alternatives include the decrease in the number of animals used, ability to obtain the results quickly, reduction in the costs and flexibility to control the variables of the experiment. However these techniques are not glittering gold and have their own shortcomings. The disadvantages include the lack of an appropriate alternative to study the whole animal's metabolic response, inability to study transplant models and idiosyncratic responses and inability to study the body's handling of drugs and its subsequent metabolites. None-the-less these aalternative methods to certain extent help to reduce the number of animals required for research. But such alternatives cannot eliminate the need for animals in research completely. Even though no animal model is a complete set of replica for a process within a human body, the intact animal does provide a better model of the complex interaction of the physiological processes.

Analysis of HPV-other Samples by Performing HPV DNA Sequencing

BACKGROUND: HPV-other samples are designated as being positive on HPV-PCR, but negative when using specific HPV hybridization probes. We wanted to determine the types on the HPV-other samples by performing sequencing, and to know the pathologic status of the uterine cervix according to the HPV type detected on sequencing. METHODS: For HPV genotying, we used the commercially available HPV DNA Chip test, which contains 15 types of high-risk HPV and 9 types of low-risk HPV. The HPV DNA sequencing was performed for the HPV-other samples of 209 patients who subsequently underwent cervical biopsy. RESULTS: For 204 of the 209 samples, the HPV types detected by sequencing were absent types at used HPV DNA chip. For the remaining 5 samples, sequencing was impossible due to mixed peaks. HPV-81 (19.6%), HPV-61 (18.6%), HPV-62 (16.7%) and HPV-84 (13.9%) were frequently detected. For the HPV-81, -62, -71, and -72 samples, most of the samples displayed normal or LSIL. However, HPV-84 and -61 were more associated with HSIL or worse, as compared to the other types. Conclusion: HPV-81, -61, -62 and -84 were frequently found on sequencing analysis of the HPV-other samples. The pathologic status was diverse, according to the HPV type detected on sequencing.

Prevalence and Genotype Distribution of Cervical Human Papillomavirus DNA in Korean Women: A Multicenter Study

Background: DNA prevalence and type distribution of human papillomavirus (HPV) varies geographically. We investigated HPV prevalence and type distribution in Korean women using the MyHPV DNA chip testing. Methods: A total of 2,368 women from five regions of the country underwent Pap smear examination and MyHPV chip testing. Results: Overall HPV positivity was 15.8% and 78.4% in women with normal and abnormal cytology, respectively. High-risk HPV infection was strongly correlated with cytological atypia. In women with abnormal cytology, the five most common HPV types were 16, 58, 18, 52, and 56/53, and HPV16 was significantly the most common type in most geographical regions. After HPV16, HPV58, and 52 were the next most frequently detected types. Women with normal cytology, in contrast, showed heterogeneity in HPV type distribution. High-grade intraepithelial lesions infected with HPV16, 18, 31 or 45 are more likely to progress to carcinoma. Conclusions: The HPV chip test can provide useful data regarding HPV positivity and type. The most common HPV type in Korean women with abnormal cytology is HPV16, with HPV58 and 52 being frequently present. Our data may have important implications for vaccination programs and the development of cervical screening.

Hepatocyte nuclear factor 1-alpha mutation in normal glucose-tolerant subjects and early-onset type 2 diabetic patients

BACKGROUND/AIMS: The prevalence of diabetes in Korea is reported to be approximately 10%, but cases of maturity-onset diabetes of the young (MODY) are rare in Korea. A diagnostic technique for autosomal dominant MODY is being actively sought. In this regard, we used a DNA chip to investigate the frequency of mutations of the MODY3 gene (hepatocyte nuclear factor-1alpha) in Korean patients with early-onset type 2 diabetes. METHODS: The genomic DNA of 30 normal individuals [age, 24.9+/-8.6 years] and 25 patients with early-onset type 2 diabetes (age, 27+/-5.9 years) was extracted, and the MODY3 gene was amplified. The amplified DNA was hybridized onto a MODY3 chip, which has oligonucleotides of 15-25 bases, representing wild-type and mutant MODY3 sequences in both forward and reverse orientations, immobilized on its surface. RESULTS: Among the normal subjects, there was no mutation of MODY3. Among those with early-onset type 2 diabetes, there was one case of MODY3 mutation. CONCLUSIONS: Our results indicate that MODY3 mutations are not rare in Korean early-onset type 2 diabetes patients in Korea and suggest that MODY3 mutations in patients with early-onset type 2 diabetes need to be further evaluated.