Nonspecific amplification of human DNA by Streptococcus pneumoniae LytA primer

Background: Determination of various analytical parameters is essential for the validation of primers used for in-house nucleic acid amplification tests. While standardising a high-resolution melt analysis (HRMA) for detection of Streptococcus pneumoniae in acute pyogenic meningitis, we encountered non-specific amplification of certain base pair sequences of human DNA by Centers for Disease Control & Prevention, USA recommended S. pneumoniae LytA primer. Materials and Methods: HRMA was standardised using DNA extracted from an ATCC strain of S. pneumoniae using SP LytA F373 primer and Type-it HRMTM polymerase chain reaction kit in Rotor-Gene Q Thermal Cycler according to the manufacturer's instructions. Specificity of the primers was determined in dry and wet laboratory experiments against diverse related and unrelated microbial pathogens by HRMA and on DNA extracted from unspiked clinical samples negative for SP DNA. Sensitivity was determined by calculating lower limit of detection threshold in experiments with spiked samples. The amplicon from spiked experiments was sequenced and analysed through Gene Bank. Results: Our dry/wet laboratory experiments showed two separate curves and different Tm values indicating certain non-specific amplification by the primer. Basic Local Alignment Search Tool (BLAST) analysis of the amplicon obtained in the spiked experiment showed sequences of human chromosome 20 associated with Homo sapiens protein tyrosine phosphatase, receptor type T gene. The problem was resolved by stopping the reaction at 30th Ct cycle and observing the Tm values. Conclusion: Since HRMA is done without a specific probe, one should be aware of non-specific amplifications while using primers for HRMA of human clinical samples.

Síndrome de deleção 22q11.2 e cardiopatias congênitas / 22q11.2 deletion syndrome and congenital heart defects

OBJETIVO: Revisar as características clínicas, etiológicas e diagnósticas da síndrome de deleção 22q11 e sua associação com as cardiopatias congênitas. FONTES DOS DADOS: Foram pesquisados artigos científicos presentes nos portais Medline, Lilacs e SciELO, utilizando-se descritores específicos como "22q11", "DiGeorge syndrome", "velocardiofacial syndrome", "congenital heart defects" e "cardio-vascular malformations". O período adotado para a revisão foi de 1980 a 2009. SÍNTESE DOS DADOS: As malformações cardíacas são os defeitos congênitos observados mais frequentemente ao nascimento e representam um problema importante de Saúde Pública. Dentre suas principais causas conhecidas destaca-se a síndrome de deleção 22q11, também chamada de síndrome de DiGeorge, síndrome velocardiofacial e CATCH22. Trata-se de uma doença autossômica domi-nante caracterizada por um fenótipo altamente variável, o que dificulta em muito seu reconhecimento clínico. Além disso, a maior parte dos pacientes apresenta uma microdeleção identificada principalmente por técnicas de citogenética molecular, como a hibridização in situ fluorescente, pouco disponíveis em nosso meio. De forma similar a outras síndromes, a síndrome de deleção 22q11 associa-se a certos defeitos cardíacos específicos, no caso os do tipo conotruncal. Apesar disso, não há ainda na literatura um consenso sobre quais os pacientes com car-diopatia congênita que deveriam ser investigados para a síndrome de deleção 22q11. CONCLUSÕES: Cardiologistas e cirurgiões cardíacos, espe-cialmente pediátricos, devem estar cientes das peculiaridades e dos cuidados dispensados à síndrome de deleção 22q11. Os indivíduos com a síndrome apresentam comumente alterações envolvendo vários sistemas, o que pode levar a dificuldades e a complicações durante seu manejo clínico e cirúrgico.

OBJECTIVE: To review clinical, etiological and diagnostic characteristics of the 22q11 deletion syndrome and its as-sociation with congenital heart defects. DATA SOURCES: Medline, Lilacs and SciELO databases were searched from 1980 to 2009 using specific descrip-tors as "22q11", "DiGeorge syndrome", "velocardiofacial syndrome", "congenital heart defects" and "cardiovascular malformations". DATA SYNTHESIS: Heart malformations are the most fre-quent congenital defects at birth and represent an important Public Health problem. The 22q11 deletion syndrome, also called DiGeorge syndrome, velocardiofacial syndrome and CATCH22, stands out as one of the main known causes of congenital heart defects. This is an autosomal dominant genetic disease characterized by a highly variable phenotype, which renders its difficult clinical identification. In addition, the majority of the patients present a microdeletion identified mainly by molecular cytogenetic techniques as fluorescent in situ hybridization, which are rarely available in Brazil. Similarly to other syndromes, 22q11 deletion syndrome is associated to some specific heart defects, espe-cially conotruncal. It is still not clear which patients with congenital heart defect should be screened for 22q11 dele-tion syndrome. CONCLUSIONS: Cardiologists and cardiac surgeons, particu-larly the pediatric ones, must be aware about the features and health care related to 22q11 deletion syndrome. Subjects with the syndrome very often present abnormalities of mul-tiple systems, that could result in difficulties and complica-tions during their clinical and surgical course.

Association study between the genetic polymorphism of 15 STR loci and the crime of rape / 中华行为医学与脑科学杂志

Objective To investigate the relationship between rapists and related allele genes based on the analysis of 15 short tandem repeats (STRs) loci genetic polymorphism. Methods The method of Genome-wide scan was being used. Buccal swab samples of 129 rapists and 156 random populations were collected and PCR compound amplification was carried out with the aid of AmpFISTR Identifiler system. Then the products were subjected to electrophoresis and gene detection with AB13100 type gene analysis system so as to calculate and compare the alleles of 15 STRs gene frequency in the two groups. Results All the 15 STRs loci allele gene frequency in rapists and random population was found to coincide with Hardy-Weinberg law(P>0. 05). Allele 28 of D21S11 (rapists: 1.55% ,control group:5. 13%) ,allele22 of FGA(rapists:24.03% ,control group:16.99%),allele23 of FGA(rapists: 17.05% ,control group:26.28%) ,allele 10 of TH01(rapists:1.16% ,control group:4.17%) ,allele 8 of TPOX(rapists:55.77% ,control group:63.77%),allele 12 of TPOX(rapists:4.26% ,control group: 1.28%) were different between the two groups (P< 0.05) .while it is no differ significantly in other STRs loci allele gene(P >0.05). Conclusion Allele 28 of D21 S11,allele 22 and 23 of FGA, allele 10 of TH01, allele 8 and 12 of TPOX may be associated with the violent crime of rape. It is suggested that there are existing sensitive or resistance genes about the violent crime of rape in chromosome 2,4,11,21.

Identification of a Novel Deletion Region in 3q29 Microdeletion Syndrome by Oligonucleotide Array Comparative Genomic Hybridization / 대한진단검사의학회지

BACKGROUND: The 3q29 microdeletion syndrome is a genomic disorder characterized by mental retardation, developmental delay, microcephaly, and slight facial dysmorphism. In most cases, the microdeletion spans a 1.6-Mb region between low-copy repeats (LCRs). We identified a novel 4.0- Mb deletion using oligonucleotide array comparative genomic hybridization (array CGH) in monozygotic twin sisters. METHODS: G-banded chromosome analysis was performed in the twins and their parents. Highresolution oligonucleotide array CGH was performed using the human whole genome 244K CGH microarray (Agilent Technologies, USA) followed by validation using FISH, and the obtained results were analyzed using the genome database resources. RESULTS: G-banding revealed that the twins had de novo 46,XX,del(3)(q29) karyotype. Array CGH showed a 4.0-Mb interstitial deletion on 3q29, which contained 39 genes and no breakpoints flanked by LCRs. In addition to the typical characteristics of the 3q29 microdeletion syndrome, the twins had attention deficit-hyperactivity disorder, strabismus, congenital heart defect, and gray hair. Besides the p21-activated protein kinase (PAK2) and discs large homolog 1 (DLG1) genes, which are known to play a critical role in mental retardation, the hairy and enhancer of split 1 (HES1) and antigen p97 (melanoma associated; MFI2) genes might be possible candidate genes associated with strabismus, congenital heart defect, and gray hair. CONCLUSIONS: The novel 4.0-Mb 3q29 microdeletion found in the twins suggested the occurrence of genomic rearrangement mediated by mechanisms other than nonallelic homologous recombination. Molecular genetic and functional studies are required to elucidate the contribution of each gene to a specific phenotype.

Preparation of Microcells For Use in Production of Transchromosomic Animals / 生物化学与生物物理进展

Microcell mediated chromosome transfer (MMCT) is a challenging technique for introducing exogenous chromosomes into interested mammalian cells. Combined with the somatic cell nuclear transfer technique, MMCT has been employed for producing transchromosomic animals of medical and agricultural value. Producing high quality of microcells is a key step in the success of MMCT. Eamamined by fluorescin staining and Giemsa staining, 0.2 mg/L colcemid was considered suitable for inducing high percentage of micronuclei in A9 (neo12) cells, without causing death of a mass of cells. Microcells were produced by centrifugation of micronucleated A9 (neo12) cells in Percoll density gradient containing 20 mg/L Cytochalasin B at 39 000 g. The resulting mixture of microcells, whole cells, karyoplasts and cytoplast fragments was filtered through 8 μm and 5 μm size membrane pores sequentially to obtain pure preparation of microcells. Microcells were then characterized by Giemsa staining and microcell PCR was first applied for examination of the quality of microcell preparation. The result showed that microcells containing our interest chromosomes-human chromosome 12 were equally distributed in the preparation, the preparation was suitable for use in generation of transchromosomic animals.

Chromosomal localization and neural distribution of voltage dependent calcium channel alpha1A and alpha1E subunit genes / 대한해부학회지

Fluorescent in situ hybridization using human genomic DNA probes was performed to localize genes encoding the alpha1A and alpha1E of voltage dependent calcium channels (VDCCs) in the human chromosome and the mRNA expression of these two alpha1 subunits of VDCC was demonstrated in the 18 day old embryo (E18) and adult rat brain by in situ hybridization histochemistry. The genes for the VDCC alpha1A and alpha1E were specifically localized on human chromosome 19p13.1 and 1q25, respectively. In 18 days old rat embryos, the mRNAs of the VDCC alpha1A and alpha1E were predominently expressed in the nervous system including brain and spinal cord. In adult rat brain, the expression pattern of each subunit was extremely different. The expression of alpha1A mRNA was strong in the purkinje cells of cerebellum and CA3 area of hippocampus, relatively high level of expression was found in the dentate gyrus, CA1 area of hippocampus, superficial layer of cerebral cortex and olfactory mitral cells. Whereas alpha1E was highly expressed in the dentate gyrus, CA1-3 area of hippocampus, medial habenula nucleus of thalamus and olfactory mitral and internal granule cells and relatively high level of expression was found in the Purkinje cells of cerebellum, cerebral cortex and caudate-putamen. Until now, no neurological disorder has been mapped to 1q25, location of VDCC alpha1E gene. Recently, it has been reported that mutation of VDCC alpha1A gene causes episodic ataxia type 2 (EA-2) and spinocerebellar ataxia 6 (SCA6). These reports comfirm the our experimental results of chromosomal mapping and prominent cerebellar expression of VDCC a1A gene.