Differential expression of OCT4 pseudogenes in pluripotent and tumor cell lines

Objective: The human OCT4 gene, the most important pluripotency marker, can generate at least three different transcripts [OCT4A, OCT4B, and OCT4B1] by alternative splicing. OCT4A is the main isoform responsible for the stemness property of embryonic stem [ES] cells. There also exist eight processed OCT4 pseudogenes in the human genome with high homology to the OCT4A, some of which are transcribed in various cancers. Recent conflicting reports on OCT4 expression in tumor cells and tissues emphasize the need to discriminate the expression of OCT4A from other variants as well as OCT4 pseudogenes

Materials and Methods: In this experimental study, DNA sequencing confirmed the authenticity of transcripts of OCT4 pseudogenes and their expression patterns were investigated in a panel of different human cell lines by reverse transcription-polymerase chain reaction [RT-PCR]

Results: Differential expression of OCT4 pseudogenes in various human cancer and pluripotent cell lines was observed. Moreover, the expression pattern of OCT4-pseudogene 3 [OCT4-pg3] followed that of OCT4A during neural differentiation of the pluripotent cell line of NTERA-2 [NT2]. Although OCT4-pg3 was highly expressed in undifferentiated NT2 cells, its expression was rapidly down-regulated upon induction of neural differentiation

Analysis of protein expression of OCT4A, OCT4-pg1, OCT4-pg3, and OCT4-pg4 by Western blotting indicated that OCT4 pseudogenes cannot produce stable proteins. Consistent with a newly proposed competitive role of pseudogene microRNA docking sites, we detected miR-145 binding sites on all transcripts of OCT4 and OCT4 pseudogenes

Conclusion: Our study suggests a potential coding-independent function for OCT4 pseudogenes during differentiation or tumorigenesis

A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease

A pseudogene, designated as "ps(5.8S+ITS-2)", paralogous to the 5.8S gene and internal transcribed spacer (ITS)-2 of the nuclear ribosomal DNA (rDNA), has been recently found in many triatomine species distributed throughout North America, Central America and northern South America. Among characteristics used as criteria for pseudogene verification, secondary structures and free energy are highlighted, showing a lower fit between minimum free energy, partition function and centroid structures, although in given cases the fit only appeared to be slightly lower. The unique characteristics of "ps(5.8S+ITS-2)" as a processed or retrotransposed pseudogenic unit of the ghost type are reviewed, with emphasis on its potential functionality compared to the functionality of genes and spacers of the normal rDNA operon. Besides the technical problem of the risk for erroneous sequence results, the usefulness of "ps(5.8S+ITS-2)" for specimen classification, phylogenetic analyses and systematic/taxonomic studies should be highlighted, based on consistence and retention index values, which in pseudogenic sequence trees were higher than in functional sequence trees. Additionally, intraindividual, interpopulational and interspecific differences in pseudogene amount and the fact that it is a pseudogene in the nuclear rDNA suggests a potential relationships with fitness, behaviour and adaptability of triatomine vectors and consequently its potential utility in Chagas disease epidemiology and control.

Prevalence of oral cancer self-examination among elderly people treated under Brazil's Unified Health System: household health survey / Prevalência de autoexame bucal é maior entre idosos assistidos no Sistema Único de Saúde: inquérito domiciliar

The aim of this study was to examine the prevalence of oral cancer self-examinationamong the elderly and confirm whether prevalence was higher among users of the dental services provided by Brazil's Unified Health System (SUS, acronym in Portuguese). A transversal study of elderly people aged between 65 and 74 years living in a large-sized Brazilian municipality was conducted using simple random sampling. Logistic regression was conducted and results were corrected for sample design and unequal weighting using the SPSS(r) software. The study assessed 740 individuals. A total of 492 met the inclusion criteria, of which 101 (22.4%) reported having performed an oral cancer self-examination. Prevalence was higher among users of the dental services provided by the SUS, higher-income individuals, people with higher levels of education, individuals that used a removable dental prosthesis, and people who had not experienced discomfort attributed to oral condition, and lower among people who sought regular and periodic dental treatment and individuals who did not have a drinking habit. This type of self-care should be encouraged by public health policies which respond to the needs of the elderly, with emphasis on users of private and philanthropic services, and other services outside the public health network.

Este estudo objetivou identificar a prevalência do autoexame bucal entre idosos e constatar se essa prevalência foi maior entre usuários de serviços odontológicos prestados pelo Sistema Único de Saúde (SUS). Estudo transversal conduzido a partir de amostragem probabilística complexa por conglomerados, entre idosos (65-74 anos) de um município brasileiro de grande porte populacional. Foi realizada regressão logística binária, as estimativas foram corrigidas pelo efeito de desenho e por ponderações, utilizando-se o SPSS(r). Dentre os 740 avaliados, atenderam aos critérios de inclusão 492 idosos e, destes, 101 (22,4%) relataram a prática do autoexame bucal. Esta prática foi maior entre idosos usuários dos serviços odontológicos prestados no SUS, entre aqueles com maior renda per capita, os com maior escolaridade, aqueles que utilizavam prótese dentária removível e entre os que não tiveram impactos decorrentes das desordens bucais; foi menor entre os que usaram serviços odontológicos por rotina e os que não possuíam hábito etilista. A prevalência do autoexame bucal entre idosos foi baixa e maior entre aqueles usuários do SUS. O estímulo à adesão a este autocuidado deve ser considerado nas políticas de saúde do idoso vigentes, especialmente entre usuários de serviços particulares, supletivos e filantrópicos.

CYP21A2 Mutation Analysis in Korean Patients With Congenital Adrenal Hyperplasia Using Complementary Methods: Sequencing After Long-Range PCR and Restriction Fragment Length Polymorphism Analysis With Multiple Ligation-Dependent Probe Amplification Assay

CYP21A2 mutation analysis of congenital adrenal hyperplasia (CAH) is challenging because of the genomic presence of a homologous CYP21A2 pseudogene and the significant incidence of pseudogene conversion and large deletions. The objective of this study was to accurately analyze the CYP21A2 genotype in Korean CAH patients using a combination of complementary methods. Long-range PCR and restriction fragment length polymorphism analyses were performed to confirm valid amplification of CYP21A2 and to detect large gene conversions and deletions before direct sequencing. Multiple ligation-dependent probe amplification (MLPA) analysis was conducted concurrently in 14 CAH-suspected patients and six family members of three patients. We identified 27 CYP21A2 mutant alleles in 14 CAH-suspected patients. The c.293-13A>G (or c.293-13C>G) was the most common mutation, and p.Ile173Asn was the second, identified in 25% and 17.9% of alleles, respectively. A novel frame-shift mutation of c.492delA (p.Glu 164Aspfs*24) was detected. Large deletions were detected by MLPA in 10.7% of the alleles. Mutation studies of the six familial members for three of the patients aided in the identification of haplotypes. In summary, we successfully identified CYP21A2 mutations using both long-range PCR and sequencing and dosage analyses. Our data correspond relatively well with the previously reported mutation spectrum analysis.

Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome

Many other human species appeared in evolution in the last 6 million years that have not been able to survive to modern times and are broadly known as archaic humans, as opposed to the extant modern humans. It has always been considered fascinating to compare the modern human genome with that of archaic humans to identify modern human-specific sequence variants and figure out those that made modern humans different from their predecessors or cousin species. Neanderthals are the latest humans to become extinct, and many factors made them the best representatives of archaic humans. Even though a number of comparisons have been made sporadically between Neanderthals and modern humans, mostly following a candidate gene approach, the major breakthrough took place with the sequencing of the Neanderthal genome. The initial genome-wide comparison, based on the first draft of the Neanderthal genome, has generated some interesting inferences regarding variations in functional elements that are not shared by the two species and the debated admixture question. However, there are certain other genetic elements that were not included or included at a smaller scale in those studies, and they should be compared comprehensively to better understand the molecular make-up of modern humans and their phenotypic characteristics. Besides briefly discussing the important outcomes of the comparative analyses made so far between modern humans and Neanderthals, we propose that future comparative studies may include retrotransposons, pseudogenes, and conserved non-coding regions, all of which might have played significant roles during the evolution of modern humans.

Identification and function analysis of pseudogenes / 生物工程学报

Pseudogenes, which have long been described as "fossils", play a very important role in eukaryotic genomes. Recently, studies on the so called "junk gene" have attracted more attention. Far from being silent, pseudogenes participate in various biological activities, including being a part in the transcription process, or participating in the formation of small interfering RNA (siRNA) which regulated gene expression by means of the RNA-interference pathway. Recent studies have also shown that pseudogenes regulate tumor suppression through competing for the microRNA (miRNA) with their parent genes. However, a deeper understanding of function analysis of pseudogenes depends on the comprehensive and accurate identification. With the sequencing completion of many genomes and the innovation of bioinformatics tools, efficient and precise identification of pseudogenes have become available in a genome-wide scale. Our review focused particularly on the method of pseudogene identification, the mechanism of its regulatory roles and its potential to be applied in directed evolution. Besides, the promising research direction of pseudogenes was proposed.

Study on expression of PTEN gene and its pseudogene PTENP1 in acute leukemia and correlation between them / 中华血液学杂志

<p><b>OBJECTIVE</b>To investigate the expression of PTEN (phosphatase and tension homology deletion on chromosome 10, PTEN) and its pseudogene PTENP1 in acute leukemia (AL) and correlation between them, and to explore the role of PTENP1 on the PTEN expression in AL cells.</p><p><b>METHODS</b>PTEN and PTENP1 mRNA expression were evaluated in bone marrow (BM) samples from 138 newly diagnosed AL patients and 15 healthy controls by quantitative real-time RT-PCR (qRT-PCR). pCDH1-PTENP1 3'UTR-GFP lentivirus vectors were constructed. 293T cells were transfected by calcium phosphate precipitation to produce retrovirus. HL-60 cell line was infected with the retroviral vectors expressing pCDH1-GFP and pCDH1-PTENP1 3'UTR-GFP respectively. The flow cell sorter was used to sort the HL-60 with GFP positively expressed. The mRNA expression of PTEN and PTENP1 was detected by qRT-PCR, the expression of PTEN protein by western blot, and the impact of PTENP13'UTR on the proliferation of HL-60 cells by MTT assay.</p><p><b>RESULTS</b>AML patients showed significantly lower PTEN and PTENP1 mRNA expression in BM compared to healthy controls. Correlation analysis showed that the expression of PTEN and PTENP1 mRNA were positively correlated (P < 0.05). The 108 cases of PTENP1(+) AML were classified according to the prognostic classification of 2011 NCCN Clinical Practice Guidelines in AML, there was no difference among different subgroups. HL-60 cell line was infected with the retroviral vectors expressing pCDH1-GFP (control group) and pCDH1-PTENP1 3'UTR-GFP respectively. Compared with the control group, PTENP1 mRNA level of HL-60 infected with the retroviral vectors expressing pCDH1-PTENP1 3'UTR-GFP increased significantly, and PTEN mRNA level also increased. While the PTEN protein level and the cell growth rate of the PTENP1 3'UTR group didn't change significantly.</p><p><b>CONCLUSION</b>PTEN and PTENP1 mRNA expression level of BM cells from AL patients is significantly lower. There is a positive correlation between expression of PTEN and PTENP1 mRNA. PTENP1 may regulate the expression of PTEN in mRNA level.</p>

Molecular characterization of the feline T-cell receptor gamma alternate reading frame protein (TARP) ortholog

T-cell receptor gamma alternate reading frame protein (TARP) is expressed by human prostate epithelial, prostate cancer, and mammary cancer cells, but is not found in normal mammary tissue. To date, this protein has only been described in humans. Additionally, no animal model has been established to investigate the potential merits of TARP as tumor marker or a target for adoptive tumor immunotherapy. In this study conducted to characterize feline T-cell receptor gamma sequences, constructs very similar to human TARP transcripts were obtained by RACE from the spleen and prostate gland of cats. Transcription of TARP in normal, hyperplastic, and neoplastic feline mammary tissues was evaluated by conventional RT-PCR. In felines similarly to the situation reported in humans, a C-region encoding two open reading frames is spliced to a J-region gene. In contrast to humans, the feline J-region gene was found to be a pseudogene containing a deletion within its recombination signal sequence. Our findings demonstrated that the feline TARP ortholog is transcribed in the prostate gland and mammary tumors but not normal mammary tissues as is the case with human TARP.

Identification of Mycobacterium tuberculosis complex based on amplification and sequencing of the oxyR pseudogene from stored Ziehl-Neelsen-stained sputum smears in Brazil

A cross-sectional analysis of stored Ziehl-Neelsen (ZN)-stained sputum smear slides (SSS) obtained from two public tuberculosis referral laboratories located in Juiz de Fora, Minas Gerais, was carried out to distinguish Mycobacterium bovis from other members of the Mycobacterium tuberculosis complex (MTC). A two-step approach was used to distinguish M. bovis from other members of MTC: (i) oxyR pseudogene amplification to detect MTC and, subsequently, (ii) allele-specific sequencing based on the polymorphism at position 285 of this gene. The oxyR pseudogene was successfully amplified in 100 of 177 (56.5 percent) SSS available from 99 individuals. No molecular profile of M. bovis was found. Multivariate analysis indicated that acid-fast bacilli (AFB) results and the source laboratory were associated (p < 0.05) with oxyR pseudogene amplification. SSS that were AFB++ SSS showed more oxyR pseudogene amplification than those with AFB0, possibly due to the amount of DNA. One of the two source laboratories presented a greater chance of oxyR pseudogene amplification, suggesting that differences in sputum conservation between laboratories could have influenced the preservation of DNA. This study provides evidence that stored ZN-SSS can be used for the molecular detection of MTC.

Genômica comparativa de procariotos: análise da variabilidade em funções enzimáticas / Comparative genomics of prokaryotes: analysis of variability in enzymatic functions

Esta tese trata de abordagens computacionais para a análise comparativa de genomas em larga escala e da análise da variabilidade em funções enzimática de procariotos. Este trabalho apresenta um banco de dados denominado ProteinWorldDB, que representa um esforço importante para criar um conjunto de dados consistente e confiável de comparações entre o conteúdo protéico codificado por centenas de genomas completamente sequenciados, usando uma abordagem rigorosa baseada em programação dinâmica. Além disto, este trabalho descreve uma metodologia aprimorada para detecção e anotação de pseudogenes em procariotos (e outros organismos com organização genômica similar), e uma análise da ocorrência, distribuição e padrões de extinção de enzimas análogas preditas em procariotos. A base de dados ProteinWorldDB oferece à comunidade científica a oportunidade de minerar dados comparativos calculados de forma precisa e usar a informação disponível – e.g. índices de similaridade (e suas estimativas estatísticas) entre pares ou grupos de proteínas, proteínas ortólogas e parálogas inferidas, genes taxonomicamente restritos (únicos), entre outras – como ponto de partida para análises subsequentes. Nossa metodologia para a detecção e anotação de pseudogenes em procariotos, baseada em comparações entre sequências codificantes e regiões intergênicas de genomas-alvos, apresenta duas inovações importantes: a reconstrução da sequência remanescente a partir de todos os fragmentos encontrados, não somente a partir do mais similar e a determinação de limiares de similaridade adequados ao conjunto de dados analisados, com base em validações estatísticas. A aplicação deste método na busca de pseudogenes na via glicolítica/gliconeogênese de centenas de procariotos resultou em um número expressivo de novos pseudogenes identificados, mostrando a necessidade de se incluir mecanismos de busca sistemática de pseudogenes nos fluxos de anotação genômica de procariotos. A análise da ocorrência, distribuição e padrões de extinção de enzimas análogas preditas na via gicolítica/gliconeogênese de centenas de procariotos nos revelou um quadro complexo, difícil de ser interpretado, mesmo quando apenas um pequeno grupo de espécies selecionadas foi utilizado. Um estudo mais detalhado, relacionando os resultados obtidos ao estilo de vida, filogenia, estrutura e organização genômicas destas espécies, será necessária para tentar responder às questões fundamentais que nos colocamos: como surgem as enzimas análogas e, sobretudo, por que, aparentemente, ocorreram tantos eventos de origem independente de atividades enzimáticas durante a evolução, e por que existem diferentes formas análogas coexistindo no mesmo organismo? A manutenção de duas ou mais formas análogas poderia proporcionar flexibilidade metabólica e, portanto, uma vantagem seletiva, dependendo do ambiente e estilo de vida do organismo; ou, ainda, distintas formas poderiam competir pela execução de uma mesma função e, neste caso, sendo uma das formas mais competitivas que a outra, a desfuncionalização da forma menos competitiva poderia representar uma vantagem seletiva, já que o gasto energético com a biossíntese da enzima seria eliminado. Seria possível considerar enzimas análogas como indivíduos e seus grupos como populações, todos em competição por um nicho metabólico em particular? Neste caso, seria plausível imaginar que enzimas mais competitivas teriam uma vantagem seletiva sobre formas alterativas menos competitvas e, consequentemente, dispensar-se-iam entre os diversos genomas bacterianos, com o passar do tempo.

Genômica comparativa de procariotos: análise de variabilidade em funções enzimáticas / Comparative genomics of prokaryotes: analysis of variability in enzymatic functions

Esta tese trata de abordagens computacionais para a análise comparativa de genomas em larga escala e da análise da variabilidade em funções enzimática de procariotos. Este trabalho apresenta um banco de dados denominado ProteinWorldDB, que representa um esforço importante para criar um conjunto de dados consistente e confiável de comparações entre o conteúdo protéico codificado por centenas de genomas completamente seqüeciados, usando uma abordagem rigorosa baseada em programação dinâmica. Além disto, este trabalho descreve uma metodologia aprimorada para detecção e anotação de pseudogenes em procariotos (e outros organismos com organização genômica similar), e uma análise da ocorrência, distribuição e padrões de extinção de enzimas análogas preditas em procariotos. A base de dados ProteinWorldDB oferece à comunidade científica a oportunidade de minerar dados comparativos calculados de forma precisa e usar a informação disponível – e.g. índices de similaridade (e suas estimativas estatísticas) entre pares ou grupos de proteínas, proteínas ortólogas e parálogas inferidas, genes taxonomicamente restritos (únicos), entre outras – como ponto de partida para análises subseqüentes. Nossa metodologia para a detecção e anotação de pseudogenes em procariotos, baseada em comparações entre seqüências codificantes e regiões intergênicas de genomas-alvos, apresenta duas inovações importantes: a reconstrução da seqüência remanescente a partir de todos os fragmentos encontrados, não somente a partir do mais similar e a determinação de limiares de similaridade adequados ao conjunto de dados analisados, com base em validações estatísticas. A aplicação deste método na busca de pseudogenes na via glicolítica/gliconeogênese de centenas de procariotos resultou em um número expressivo de novos pseudogenes identificados, mostrando a necessidade de se incluir mecanismos de busca sistemática de pseudogenes nos fluxos de anotação genômica de procariotos...

Mutations of the steroid 21-hydroxylase gene among Filipino patients with congenital adrenal hyperplasia

Congenital adrenal hyperplasia (CAH), an autosomal recessive disorder, is due to deficiency of the enzymes involved in adrenal steroidogenesis. Phenotypic manifestations vary as a result of the degree of glucocorticoid or mineralocorticoid deficiency and androgen excess present. Among Filipinos, the estimated crude incidence of CAH is approximately 1 in 7,000, which is higher than what is reported in most populations. More than 90% of all cases result from a 21-hydroxylase (21-OH) (cytochrome P450c21) enzyme deficiency involving two 21-OH genes, the active gene (CYP21) and a pseudogene (CYP21P). Studies have shown that mutations result from unequal crossover during meiosis which leads to complete deletion of the gene, gene conversion events or to point mutations. To date, there are no published data on the types of mutations present among Filipinos diagnosed with congenital adrenal hyperplasia. The objective of this study is to describe the profile of Filipino patients diagnosed with CAH and to determine the disease-causing alleles in the 21-OH gene of these patients. Using a method of combined differential polymerase chain reaction and amplification created restriction site approach, direct probing for the presence of known mutations in exons 1,3,4,6,7,8 and intron 2 of the CYP21 and CYP21P genes among Filipino patients with CAH was performed. A total of 12 unrelated CAH patients were examined. A majority of these cases had a premature splicing error mutation at nucleotide 656 of intron 2. The determination of the most frequent alleles in our population can facilitate rapid screening for mutations in the 21-OH gene and lead to a definitive diagnosis of CAH.

An incontinentia pigmenti family with deletion in both NEMO gene and pseudogene DeltaNEMO / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To detect the genomic deletion mutation in the NEMO gene of a family with incontinentia pigmenti (IP; MIM 308310).</p><p><b>METHODS</b>A pedigree of IP was investigated. By using long PCR, the Delta4-10 deletion in NEMO gene was tested with specific primers In2/JF3R, and Delta4-10 deletion in pseudogene DeltaNEMO was investigated with primers Rev-2/JF3R. NEMO gene of 80 normal controls was also tested.</p><p><b>RESULTS</b>The deletion of exons 4-10 in both NEMO gene and the pseudogene DeltaNEMO was detected in all the patients in the family, but was not found in the normal individuals in this IP family and 80 unrelated controls.</p><p><b>CONCLUSION</b>The study showed that the family with IP, which showed anticipation, was caused by NEMODelta4-10 deletion in the NEMO gene. Long PCR analysis is proven to be an efficient tool for identification of NEMO rearrangements. It could provide useful information for the genetic counseling of the family involved.</p>

Recent integrations of mammalian Hmg retropseudogenes.

We propose that select retropseudogenes of the high mobility group nonhistone chromosomal protein genes have recently integrated into mammalian genomes on the basis of the high sequence identity of the copies to the cDNA sequences derived from the original genes. These include the Hmg1 gene family in mice and the Hmgn2 family in humans. We investigated orthologous loci of several strains and species of Mus for presence or absence of apparently young Hmg1 retropseudogenes. Three of four analysed elements were specific to Mus musculus, two of which were not fixed, indicative of recent evolutionary origins. Additionally, we datamined a presumptive subfamily (Hmgz) of mouse Hmg1, but only identified one true element in the GenBank database, which is not consistent with a separate subfamily status. Two of four analysed Hmgn2 retropseudogenes were specific for the human genome, whereas a third was identified in human, chimpanzee and gorilla genomes, and a fourth additionally found in orangutan but absent in African green monkey. Flanking target-site duplications were consistent with LINE integration sites supporting LINE machinery for their mechanism of amplification. The human Hmgn2 retropseudogenes were full length, whereas the mouse Hmg1 elements were either full length or 3'-truncated at specific positions, most plausibly the result of use of alternative polyadenylation sites. The nature of their recent amplification success in relation to other retropseudogenes is unclear, although availability of a large number of transcripts during gametogenesis may be a reason. It is apparent that retropseudogenes continue to shape mammalian genomes, and may provide insight into the process of retrotransposition, as well as offer potential use as phylogenetic markers.

Killer Cell Immunoglobulin-like Receptor (KIR) Analysis in Adult Korean Patients with Acute Myeloid Leukemia / 대한혈액학회지

BACKGROUND: The prevalent natural killer (NK) cells induce alloreaction against leukemic cells during post-transplant. NK cell alloreactivity depends on the compatibility of killer cell immunoglobulin-like receptors (KIR) epitopes for graft-versus-host disease. Genotypic expressions of inhibitory or activating KIR in patients with acute myelogenous leukemia (AML) and their HLA-matched sibling donors, as a model for Korean KIR haplotype diversity and NK alloreactivity, were investigated. METHODS: Ninety-two patients in complete remission and their 76 HLA-matched sibling donors were enrolled in this study. All the patients were scheduled to receive allogeneic hematopoietic stem cell transplantations (HSCT). KIR PCR-SSP typing was performed for 19 different kinds of KIR genes and pseudogenes. The PCR data representing the KIR genotypes from both the patients and donors were compared. RESULTS: We found 43 Korean KIR haplotypes. Thirty-three variable haplotypes for the AML patients, in addition to 25 haplotypes for the normal HSCT donors, were demonstrated. Of note, the expressions of specific genes such as 2DL2 (P=0.026), 2DS2 (P=0.042), and 2DS4 (P=0.037) revealed remarkable differences between the patients and the normal donors. Korean HLA-identical sibling pairs showed 38% KIR matches in terms of the gene content and allelic polymorphism. Although the KIR gene content was the same between the patients and the donors, 40% of those matched pairs of patients and donors showed allelic polymorphism, specifically in the context of 2DL5 and 2DS4 genes. CONCLUSION: These results indicate that the expressions of donor inhibitory and activating repertoire of KIR genotypes, even in the HLA-matched sibling setting, are unique parameters to be considered when we perform allogeneic sibling HSCT.

Comparative analysis of human masculinity

To study rapidly evolving male specific Y (MSY) genes we retrieved and analyzed nine such genes. VCY, HSFY and RBMY were found to have functional X gametologs, but the rest did not. Using chimpanzee orthologs for XKRY, CDY, HSFY, PRY, and TSPY, the average silent substitution is estimated as 0.017 +/- 0.006/site and the substitution rate is 1.42 x 10(-9)/site/year. Except for VCY, all other loci possess two or more pseudogenes on the Y chromosome. Sequence differences from functional genes show that BPY2, DAZ, XKRY, and RBMY each have one pseudogene for each one that is human specific, while others were generated well before the human-chimpanzee split, by means of duplication, retro-transposition or translocation. Some functional MSY gene duplication of VCY, CDY and HSFY, as well as X-linked VCX and HSFX duplication, occurred in the lineage leading to humans; these duplicates have accumulated nucleotide substitutions that permit their identification.

Biodegradation of cypermethrin by pseudomonas in a batch activated sludge process

The biodegradation of Cypermethrin [20 to 125 mg/L] in an effluent using batch activated sludge was studied. Degradation was found to occur to a great extent only in the presence of Pseudomonas [IES-Ps-1] culture. Under aerobic conditions using mechanical aerators, Cypermethrin [20 mg/L] was almost completely degraded in just over 48 h at ambient temperature. Further loading of organic compound in subsequent experiments demonstrated that IES-PS-1was capable to degrade 82% Cypermethrin at 40 mg/L dose in approximately 48 h. When the concentration was increased to 80 mg/L, 50% degradation of this compound was observed. Over this time period the cells could utilize only 17% of Cypermethrin when it was given 125 mg/L, respectively. These findings indicate that increased concentration of Cypermethrin has a marked effect on biodegradation performance of IES-Ps-1 with a modest increased in the duration of lag phase, but did not lead to complete inhibition or cell death. These results proved that IES-Ps-1 is responsible for Cypermethrin degradation. Such finding may be useful in designing a scale-up in situ or on-site hazardous waste bioremediation process for field application

Genotype of Steroid 21-Hydroxylase Gene and Clinical Characteristics in Patients with Congenital Adrenal Hyperplasia 21-Hydroxylase Deficiency / 대한소아내분비학회지

PURPOSE: This study was undertaken to characterize clinical features of congenital adrenal hyperplasia (CAH) with steroid 21-hydroxylase deficiency, identify appropriate dose of hydrocortisone to normalize endocrine abnormalities, and correlate between clinical phenotype and genotype of the patients. METHODS: Endocrine and molecular evaluations were carried out in 42 patients at Asan Medical Center during the periods of December-1990 through July-2004. Endocrine laboratory study included the assay of plasma 17-hydroxyprogesterone (17-OHP), ACTH, androstenedione, testosterone, renin, and aldosterone by immunoradiometric assay (IRMA). Mutation study was performed by deletion analysis using specific polymerase chain reaction (PCR) for active gene (CYP21A2) with combination of pseudogene (CYP21A1P) primers as well as direct DNA sequencing of active gene. Auxological parameters, endocrine profiles and bone age by Greulich-Pyle method were monitored during treatment with hydrocortisone in 30 patients. Their medical records have been analyzed retrospectively. The patients were categorized as salt wasting type (SW) and simple virilization type (SV) depending on their clinical features. Auxological, endocrinological parameters, dose of hydrocortisone and genotype were statistically compared between these two group using SPSS 11.5 version. RESULTS: Of the 30 patients, 24 patients were SW and 6 patients were SV. In the cases of SW, the boys were 0.17+/-0.08 years old and the girls were 0.08+/-0.08 years old at diagnosis. Initial ratio of bone age to chronologic age (BA/CA ratio) of the boys was 1.01+/-0.49 and of the girls was 2.25+/-2.67. In the cases of SV, the boys were 6.17+/-0.42 years old and the girls were 6.91+/-10.83 years old at diagnosis. Initial BA/CA ratio of the boys was 2.33+/-0.17 and of the girls was 1.64+/-0.80. Serum 17-OHP, ACTH and renin were normalized in all patients by hydrocortisone treatment. The dosage of hydrocortisone needed to normalize endocrinological features was 22.9+/-8.0 mg/m2/day in boys and 18.0+/-4.0 mg/m2/day in girls in the SW group, 12.5+/-3.8 mg/m2/day in boys and 18.4+/-0.7 mg/m2/day in girls in the SV group. Nineteen types of CYP21 mutation was observed in 42 patients. Q318X, R356W, c.293-13 A>G and null mutation were observed in the SW group. CONCLUSION: The age at the diagnosis in SV was older than in SW. In SV, bone age was older than chronologic age at diagnosis. However, finally measured BA/CA ratio and the dosage of hydrocortisone were not different in two clinical types. There was genotype-phenotype correlation in CAH patients with 21-hydroxylase deficiency.

The structure, expression and function prediction of DAZAP2, a down-regulated gene in multiple myeloma / 基因组蛋白质组与生物信息学报·英文版

In our previous studies, DAZAP2 gene expression was down-regulated in untreated patients of multiple myeloma (MM). For better studying the structure and function of DAZAP2, a full-length cDNA was isolated from mononuclear cells of a normal human bone marrow, sequenced and deposited to Genbank (AY430097). This sequence has an identical ORF (open reading frame) as the NM_014764 from human testis and the D31767 from human cell line KG-1. Phylogenetic analysis and structure prediction reveal that DAZAP2 homologues are highly conserved throughout evolution and share a polyproline region and several potential SH2/SH3 binding sites. DAZAP2 occurs as a single-copy gene with a four-exon organization. We further noticed that the functional DAZAP2 gene is located on Chromosome 12 and its pseudogene gene is on Chromosome 2 with electronic location of human chromosome in Genbank, though no genetic abnormalities of MM have been reported on Chromosome 12. The ORF of human DAZAP2 encodes a 17-kDa protein, which is highly similar to mouse Prtb. The DAZAP2 protein is mainly localized in cytoplasm with a discrete pattern of punctuated distribution. DAZAP2 may associate with carcinogenesis of MM and participate in yet-to-be identified signaling pathways to regulate proliferation and differentiation of plasma cells.

High Correlation between Alu Elements and the Conversion of 3' UTR of mRNAs Processed Pseudogenes

Even though it represents 6 13% of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over 80 % of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about 10% of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.