Association between / 中国当代儿科杂志

OBJECTIVES@#To study the association of β2-drenergic receptor (@*METHODS@#A total of 143 children with asthma who attended the hospital from October 2016 to October 2020 were enrolled as the asthma group, among whom 61 children had mild symptoms (mild group) and 82 children had moderate-to-severe symptoms (moderate-to-severe group). A total of 137 healthy children were enrolled as the control group. Peripheral venous blood samples were collected from the two groups. The SNaPshot SNP technique was used to analyze the SNP and haplotypes of the @*RESULTS@#Polymorphisms were observed in the @*CONCLUSIONS@#SNP/haplotype of the

Exploration of the pathogenesis for a SRY-negative male with 46,XX disorder of sex development / 中华医学遗传学杂志

OBJECTIVE@#To explore the pathogenesis for a SRY-negative male with 46,XX disorder of sex development (DSD).@*METHODS@#Peripheral blood samples of the patient and his family members were subjected to chromosomal karyotyping, routine PCR, real-time fluorescence quantitative PCR, whole exome sequencing and whole genome sequencing. The data was analyzed with NextGENe software.@*RESULTS@#Both the proband and his brother presented a 46,XX karyotype with negative SRY gene, while their father presented normal phenotype and karyotype with positive SRY gene. No pathogenic variant associated with sex development was detected by whole exome sequencing, while a 243 kb duplication was detected by whole genome sequencing in the 5' upstream region of the SOX9 gene in the proband, his brother and father. The same duplication was not found in his sister and mother.@*CONCLUSION@#The 243 kb duplication at the 5' upstream of the SOX9 gene may predispose to the 46,XX DSD in this family. It is speculated that there exist an unknown core regulatory element in the upstream of the SOX9, and its duplication may trigger expression of SOX9 and initiate testicular differentiation in the absence of SRY gene.

ADN, disco duro de la vida / DNA, life's hard drive

A lo largo de los últimos dos siglos la medicina se vio nutrida con los descubrimientos bioquímicos que impulsaron el entendimiento de los mecanismos isiopatológicos y facilitó el desarrollo de la terapéutica. En cambio, en el presente siglo entramos a la era de la genómica y del "big data", por lo que el estudio de las funciones del ADN como dispositivo de almacenamiento de información es esencial para la comprensión de la nueva medicina genómica personalizada, de precisión. En la presente revisión, se analiza el ADN como un dispositivo informático con tres funciones: almacenamiento, expresión y transmisión de la información acumulada a lo largo de la ilogenia en forma de secuencias de nucleótidos. Se describe cada una de estas funciones comparándolas con la información manejada por una computadora o una sociedad, y se brindan ejemplos de patologías que surgen ante el fallo de alguna de las funciones. La revisión bibliográica es amplia e incluye los artículos más relevantes, tanto históricos como del estado del arte, correspondientes a cada tema...(AU)

Putative 3-nitrotyrosine detoxifying genes identified in the yeast Debaryomyces hansenii: in silico search of regulatory sequences responsive to salt and nitrogen stress

Background: During salt stress, the yeast Debaryomyces hansenii synthesizes tyrosine as a strategy to avoid the oxidation of proteins. Tyrosine reacts with nitrogen radicals to form 3-nitrotyrosine. 3-nitrotyrosine prevents the effects of associated oxidative stress and thus contributes to the high halotolerace of the yeast. However, the mechanism of how D. hansenii counteracts the presence of this toxic compound is unclear. In this work, we evaluated D. hansenii's capacity to assimilate 3-nitrotyrosine as a unique nitrogen source and measured its denitrase activity under salt stress. To identify putative genes related to the assimilation of 3-nitrotyrosine, we performed an in silico search in the promoter regions of D. hansenii genome. Results: We identified 15 genes whose promoters had binding site sequences for transcriptional factors of sodium, nitrogen, and oxidative stress with oxidoreductase and monooxygenase GO annotations. Two of these genes, DEHA2E24178g and DEHA2C00286g, coding for putative denitrases and having GATA sequences, were evaluated by RT-PCR and showed high expression under salt and nitrogen stress. Conclusions: D. hansenii can grow in the presence of 3-nitrotyrosine as the only nitrogen source and has a high specific denitrase activity to degrade 3-nitrotyrosine in 1 and 2 M NaCl stress conditions. The results suggest that given the lack of information on transcriptional factors in D. hansenii, the genes identified in our in silico analysis may help explain 3-nitrotyrosine assimilation mechanisms.

Persistent α-Fetoprotein Elevation in Healthy Adults and Mutational Analysis of α-Fetoprotein Promoter, Enhancer, and Silencer Regions

BACKGROUND/AIMS: α-Fetoprotein (AFP) is normally 1 year, and 20 controls with low AFP levels (<0.61 to 2.9 ng/mL) were included in the study. AFP levels were collected from the families of two of the patients. We sequenced five regions that are critical for AFP expression: a promoter, two enhancers, and two silencers. RESULTS: One of the two cases in which family information was represented is the first case of hereditary persistence of AFP in South Korea. Mutations related to AFP overexpression were not found in the transcription regulatory regions among the four patients. CONCLUSIONS: Persistent AFP elevation is a heterogeneous condition with or without a hereditary pattern and may be caused by factors outside of transcription regulatory region changes. Further research on the mechanism of AFP elevation is needed.

ZRS mutations in two Chinese Han families featuring triphalangeal thumbs and preaxial polydactyly / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To identify the causative mutations in two Chinese Han families featuring triphalangeal thumbs (TPT) and preaxial polydactyly (PPD).</p><p><b>METHODS</b>Blood samples were collected from 9 members (2 affected) from family 1 and 14 members (7 affected) from family 2. After genomic DNA was extracted, the ZPA regulatory sequence (ZRS) region was analyzed with real-time quantitative PCR (qPCR) and Sanger sequencing. For family 1, haplotypes compassing the ZRS were also analyzed with short tandem repeats (STR) and single nucleotide changes.</p><p><b>RESULTS</b>No copy number mutation around the ZRS region was found in both families. Two heterogeneous mutations in the ZRS (406A>G and 105C>G) were found to co-segregate with the TPT/PPD malformation in family 1 and 2, respectively. Neither mutation was detected in 200 healthy individuals. Haplotype analysis and Sanger sequencing of family 1 indicated that the first TPT/PPD patient in the family was both germline and somatic mosaic for the 406A>G mutation.</p><p><b>CONCLUSION</b>Two pathogenic ZRS mutations, 105C>G and 406A>G, have been identified in two Chinese Han families with TPT/PPD, among which the 406A>G mutation was de novo.</p>

Características de las residencias de terapia intensiva pediátrica de la República Argentina: Encuesta nacional / Characteristics of pediatric intensive care residency programs in Argentina: A national survey

Introducción. La residencia de terapia intensiva pediátrica (TIP) tiene pocos años de desarrollo en nuestro país. Conocer su situación brinda la posibilidad de establecer estrategias para contribuir al desarrollo y capacitación de profesionales. Objetivos. 1) Describir las características de las residencias de TIP del país. 2) Evaluar si existen características que se relacionen con una mayor ocupación de las vacantes. 3) Explorar la inserción laboral en el hospital formador de los residentes. Diseño. Descriptivo, observacional. Encuesta nacional. Criterios de inclusión. Residencias de TIP funcionales entre el 1/4/2014 y el 31/5/2014. Resultados. Se analizaron 31 residencias. Solo 11/31 tenían volumen de internación anual >400 pacientes. No había normas y/o criterios de atención en 9/31. En 17/31, el programa estuvo adecuado al marco de referencia nacional. Hubo 13/31 que no contaban con jefe ni instructor de residentes. Fueron acreditadas por el Ministerio de Salud 5/31. Hubo 65 vacantes; el número aumentó en los últimos 4 años; la ocupación disminuyó de 59% en 2009 a 30% en 2013. El 60% de los residentes tuvo inserción laboral en la TIP formadora. El análisis de regresión logística multivariado identificó la variable ingresos anuales > 400 pacientes como predictora independiente de ocupación de vacantes > 60%. Conclusiones. 1) Hay un déficit en la ocupación de cargos. 2) El número de residencias acreditadas es escaso. 3) Las unidades de cuidados intensivos pediátricos con mayor número de ingresos se asociaron a una mayor cobertura de vacantes. 4) Más de la mitad de los residentes se insertaron laboralmente en la TIP formadora.

Introduction. Pediatric intensive care residency programs have been in place in Argentina for just a few years. Knowing their status offers the possibility to establish strategies to help with professional development and training. Objectives. 1) To describe the characteristics of pediatric intensive care residency programs across Argentina. 2) To assess whether certain characteristics are related to a higher vacancy filling rate. 3) To assess job placement in the hospital where residents are trained. Design. Descriptive, observational study. National survey. Inclusion criteria. Pediatric intensive care residency programs in place between April 1st, 2014 and May 31st, 2014. Results. Thirty-one residency programs were analyzed. Only 11/31 had an annual hospitalization volume >400patients. There were no guidelines and/or criteria for care in 9/31. The program suited the national reference frameworkin17/31. There was no head ofresidents or resident trainer in 13/31. Only 5/31 had been certified by the Ministry of Health. There were 65 vacancies; this number increased in the past four years; vacancy filling rate decreased from 59% in 2009 to 30% in 2013. Sixty percent of residents got a job in the pediatric intensive care unit where they were trained. A multivariate logistic regression analysis identified the outcome measure annual hospitalization volume >400 patients as an independent predictor of vacancy filling rate >60%. Conclusions. 1) Vacancy filling is deficient. 2) The number of certified residency programs is scarce. 3) Pediatric intensive care units with a higher number of hospitalizations were associated with a higher vacancy filling rate. 4) More than half of residents got a job in the pediatric intensive care unit where they were trained.

Genetic Architecture of Transcription and Chromatin Regulation

DNA microarray and next-generation sequencing provide data that can be used for the genetic analysis of multiple quantitative traits such as gene expression levels, transcription factor binding profiles, and epigenetic signatures. In particular, chromatin opening is tightly coupled with gene transcription. To understand how these two processes are genetically regulated and associated with each other, we examined the changes of chromatin accessibility and gene expression in response to genetic variation by means of quantitative trait loci mapping. Regulatory patterns commonly observed in yeast and human across different technical platforms and experimental designs suggest a higher genetic complexity of transcription regulation in contrast to a more robust genetic architecture of chromatin regulation.

Understanding Epistatic Interactions between Genes Targeted by Non-coding Regulatory Elements in Complex Diseases

Genome-wide association studies have proven the highly polygenic architecture of complex diseases or traits; therefore, single-locus-based methods are usually unable to detect all involved loci, especially when individual loci exert small effects. Moreover, the majority of associated single-nucleotide polymorphisms resides in non-coding regions, making it difficult to understand their phenotypic contribution. In this work, we studied epistatic interactions associated with three common diseases using Korea Association Resource (KARE) data: type 2 diabetes mellitus (DM), hypertension (HT), and coronary artery disease (CAD). We showed that epistatic single-nucleotide polymorphisms (SNPs) were enriched in enhancers, as well as in DNase I footprints (the Encyclopedia of DNA Elements [ENCODE] Project Consortium 2012), which suggested that the disruption of the regulatory regions where transcription factors bind may be involved in the disease mechanism. Accordingly, to identify the genes affected by the SNPs, we employed whole-genome multiple-cell-type enhancer data which discovered using DNase I profiles and Cap Analysis Gene Expression (CAGE). Assigned genes were significantly enriched in known disease associated gene sets, which were explored based on the literature, suggesting that this approach is useful for detecting relevant affected genes. In our knowledge-based epistatic network, the three diseases share many associated genes and are also closely related with each other through many epistatic interactions. These findings elucidate the genetic basis of the close relationship between DM, HT, and CAD.

Adrenergic Genetic Mechanisms in Hypertension and Hypertensive Kidney Disease

Catecholamine secretory traits were significantly heritable, as were stress-induced blood pressure changes. Tyrosine hydroxylase (TH) is the rate-limiting enzyme in catecholamine biosynthesis. In the tyrosine hyroxylase promoter, significant associations were found for urinary catecholamine excretion and for blood pressure response to stress. TH promoter haplotype 2 (TGGG) showed pleiotropy, increasing both norepinephrine excretion and blood pressure during stress. In hypertension, 2 independent case-control studies (1,266 subjects with 53% women and 927 subjects with 24% women) replicated the effect of C-824T in the determination of blood pressure. Chromogranin A (CHGA) plays a fundamental role in the biogenesis of catecholamine secretory granules. Changes in the storage and release of CHGA in clinical and experimental hypertension prompted us to study whether genetic variation at the CHGA locus might contribute to alterations in autonomic function, and hence hypertension and its target organ consequences such as hypertensive kidney disease (nephrosclerosis). Systematic polymorphism discovery across the human CHGA locus revealed such regulatory regions as the proximal promoter and 3'-UTR. In chromaffin cell-transfected CHGA 3'-UTR and promoter/luciferase reporter plasmids, the functional consequences of the regulatory/non-coding allelic variants were documented. Variants in both the proximal promoter and the 3'-UTR displayed statistical associations with hypertension and hypertensive end stage renal disease. Therefore, I would like to review the common genetic variation in TH and CHGA as a cause of inter-individual variation in sympathetic activity, and ultimately blood pressure and hypertensive kidney disease.

Association of MCP-1 polymorphism with cardiovascular disease risk factors in Korean elderly / 한국영양학회지

Monocyte chemoattractant protein-1 (MCP-1) plays an important role in cardiovascular disease (CVD). Genetic polymorphism in the regulatory regions of MCP-1 could affect MCP-1 expression. The purpose of the study was to explore the possible association of MCP-1 -2518 A/G genetic polymorphism and CVD risk factors in the elderly Korean population. Dietary, anthropometric, and biochemical factors were assessed in 168 subjects. The frequency of A/A, G/A, and G/G genotypes was 14.2%, 45.8%, and 40.0%, respectively. The blood level of MCP-1 was significantly higher in subjects with A/A genotype. The MCP-1 level was significantly higher in A/A genotype with hypercholesterolemia than in other genotypes. Meat intake and percent energy from lipids were significantly positively correlated with the MCP-1 level, especially, stronger in A/A genotype. In the stepwise discriminant analysis, TNF-alpha level, meat intake, HDL-C were associated with MCP-1 in all subjects (model R2 = 24%). TNF-alpha level, sugar intake, cholesterol intake, and meat intake affected MCP-1 in A/A genotype (model R2 = 82%), but not in G/A or G/G. In conclusion, subjects possessing A/A genotype exhibited higher levels of MCP-1 than other genotypes in Korean elders. Further, meat, sugar, and cholesterol intakes affected the MCP-1 level. Therefore, the decrement of meat, sugar, and cholesterol intakes helps to normalize the MCP-1 level and can decrease CVD risk in A/A genotype.

Transcriptional Mechanisms of Drug Addiction

Regulation of gene expression is considered a plausible mechanism of drug addiction given the stability of behavioral abnormalities that define an addicted state. Numerous transcription factors, proteins that bind to regulatory regions of specific genes and thereby control levels of their expression, have been implicated in the addiction process over the past decade or two. Here we review the growing evidence for the role played by several prominent transcription factors, including a Fos family protein (DeltaFosB), cAMP response element binding protein (CREB), and nuclear factor kappa B (NFkappaB), among several others, in drug addiction. As will be seen, each factor displays very different regulation by drugs of abuse within the brain's reward circuitry, and in turn mediates distinct aspects of the addiction phenotype. Current efforts are geared toward understanding the range of target genes through which these transcription factors produce their functional effects and the underlying molecular mechanisms involved. This work promises to reveal fundamentally new insight into the molecular basis of addiction, which will contribute to improved diagnostic tests and therapeutics for addictive disorders.

Preliminary functional analysis of intron in chalcone synthase gene from Scutellaria baicalensis / 中国中药杂志

<p><b>OBJECTIVE</b>To study the function of the chalcone synthese gene introns in Scutellaria baicalensis, and clarify preliminarily their role in abiotic stress.</p><p><b>METHOD</b>The CHS introns with specific primers were cloned and bioinformatic method was applied to predict the cis-elements in the intron of CHS. The introns were subcloned into binary vector, pCAMBIA-1301 before being transferred to tobacco. Then the activity of GUS of the transgenic tobacco seeds was analyzed.</p><p><b>RESULT</b>Seven cis-elements were found in the introns. Under the dark and high temperature GUS expression rose at the first (3 h), but then declined (9 h). ABA and MeJA regulated insignificantly the GUS activity in normal temperature; treatment of 10% PEG induced GUS expression.</p><p><b>CONCLUSION</b>CHS introns could be play a role in the regulation of S. baicalensis phenylpropanoid biosynthetic pathway.</p>

Study on the relationship between TK gene regulated by enhanced suicide gene vector and telomerase activity in nasopharyngeal carcinoma cells / 临床耳鼻咽喉头颈外科杂志

OBJECTIVE@#To explore the relationship between TK gene expression regulated by enhanced suicide gene vector and telomerase activity in nasopharyngeal carcinoma cells.@*METHOD@#The reformed reconstructed enhanced vector, pGL3-basic-EGFP-TK-hTRETp-CMV enhancer, and hTERT mono-promoter vector, pGL3-basic-EGFP-TK-hTRETp(as controls), were transfected into telomerase(+) nasopharyngeal carcinoma 5-8F cell lines, telomerase(+) human breast cancer MCF-7 cell lines and telomerase(-) normal vascular endothelium cell lines respectively. TK gene green fluorescent protein was observed by fluorescence microscope. The expression of TK gene mRNA was measured by the real-time fluorescent quantified PCR and the telomerase activity was determined by the method of TRAP argentation in malignant tumour cells pre- and post-transfected by enhanced vector. Meanwhile the relationship between TK and telomerase was analyzed.@*RESULT@#(1) A strong TK gene fluorescent show and TK mRNA expression were displayed after the enhanced suicide gene vector was transfected into nasopharyngeal carcinoma 5-8F cell lines and human breast cancer MCF-7 cell line, which were more stronger than those of mono-promoter group, pGL3-basic-EGFP-TK-hTRETp, and ECV cells transfected by enhanced suicide gene vector. Meanwhile,real-time fluorescent quantified PCR showed that the A value of enhanced vector group was higher than that of controls. (2) Telomerase activity after transfection of enhanced vector and GCV was lower than those before by the method of TRAP argentation in nasopharyngeal carcinoma cell lines,but no change in normal control cells after transfection of enhanced vector and GCV. (3) After adding GCV, the obvious inhibitory effect of tumour cells growth induced by pGL3-basic-EGFP-TK-hTRETp-CMV enhancer were observed in nasopharyngeal carcinoma 5-8F cell lines and human breast cancer MCF-7 cell line, which was higher than those of mono-promoter, pGL3-basic-EGFP-TK-hTRETp, pGL3-basic-EGFP3 and blank controls, but without inhibitory effect in ECV cells transfected by enhanced vector.@*CONCLUSION@#TK gene expression is regulated by hTERT promoter and CMV enhancer, and then the telomerase activity is reduced and the cancer cells are specifically killed. But it is unclear how the telomerase are down-regulated by TK gene.

Synthetic circuits, devices and modules

The aim of synthetic biology is to design artificial biological systems for novel applications. From an engineering perspective, construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field. Here, we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements, synthetic circuits and their assemblies into devices and modules. Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.

Identification of Causal and/or Rare Genetic Variants for Complex Traits by Targeted Resequencing in Population-based Cohorts

Genome-wide association studies (GWASs) have greatly contributed to the identification of common variants responsible for numerous complex traits. There are, however, unavoidable limitations in detecting causal and/or rare variants for traits in this approach, which depends on an LD-based tagging SNP microarray chip. In an effort to detect potential casual and/or rare variants for complex traits, such as type 2 diabetes (T2D) and triglycerides (TGs), we conducted a targeted resequencing of loci identified by the Korea Association REsource (KARE) GWAS. The target regions for resequencing comprised whole exons, exon-intron boundaries, and regulatory regions of genes that appeared within 1 Mb of the GWA signal boundary. From 124 individuals selected in population-based cohorts, a total of 0.7 Mb target regions were captured by the NimbleGen sequence capture 385K array. Subsequent sequencing, carried out by the Roche 454 Genome Sequencer FLX, generated about 110,000 sequence reads per individual. Mapping of sequence reads to the human reference genome was performed using the SSAHA2 program. An average of 62.2% of total reads was mapped to targets with an average 22X-fold coverage. A total of 5,983 SNPs (average 846 SNPs per individual) were called and annotated by GATK software, with 96.5% accuracy that was estimated by comparison with Affymetrix 5.0 genotyped data in identical individuals. About 51% of total SNPs were singletons that can be considered possible rare variants in the population. Among SNPs that appeared in exons, which occupies about 20% of total SNPs, 304 nonsynonymous singletons were tested with Polyphen to predict the protein damage caused by mutation. In total, we were able to detect 9 and 6 potentially functional rare SNPs for T2D and triglycerides, respectively, evoking a further step of replication genotyping in independent populations to prove their bona fide relevance to traits.

Enhanced thymidine kinase gene vector and its killing effect on nasopharyngeal carcinoma in vitro and in vivo / 中华耳鼻咽喉头颈外科杂志

<p><b>OBJECTIVE</b>To construct a modified and enhanced thymidine kinase (TK) vector regulated by human telomerase catalytic subunit promoter (hTERT) promoter and cytomegalovirus (CMV) enhancer and its killing effect on nasopharyngeal carcinoma in vitro and in vivo and its safety in vivo.</p><p><b>METHODS</b>The pGL3-basic, as basic vector template, was linked and constructed into TK vector regulated by hTERT promoter and CMV enhancer with mono-promoter vector as control. Enhanced TK expression was confirmed by fluorescent microscopy and real time fluorescent quantitative PCR. Telomerase activity was measured by stretch PCR. Tumour killing effects were examined by MTT and Boyden areola. The effects of enhanced TK on the invasiveness of tumor cell NPC 5-8F and the growth of xenograft implanted in nude mice were investigated.</p><p><b>RESULTS</b>Compared with non-enhanced vector, TK expressed by the enhanced vector significantly increased in NPC 5-8F and MCF-7 cells, telomerase activity was positive in human in NPC 5-8F cells and breast cancer MCF-7 cells and negative in control human blood vessel endothelium ECV-304 cells. After ganciclovir(GCV) treatment, NPC 5-8F cell survival rate and invasiveness decreased and tumor progress of NPC xenograft implanted in nude mice was inhibited, without obvious toxicity effects on mouse liver and kidney.</p><p><b>CONCLUSIONS</b>The enhanced TK vector regulated by hTERT promoter and CMV enhancer can obviously and specifically inhibit and kill nasopharyngeal carcinoma cells in culture and nasopharyngeal carcinoma xenograft in nude mice in vivo, without obviously toxic side effects on nude mice. The targeted and enhanced TK gene vector with high performance may be a new tumour targeted gene therapy strategy clinically to aim directly at most malignant tumours including nasopharyngeal carcinoma, with more extensive anti-cancer spectrum.</p>

Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter / 基因组蛋白质组与生物信息学报·英文版

A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites (TFBSs) in mammalian promoter regions using human, mouse and rat sequence alignments. We found that the score distributions of most binding site models did not follow the Gaussian distribution required by many statistical methods. Therefore, we performed an empirical test to establish the optimal threshold for each model. We gauged our computational predictions by comparing with previously known TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32%. Almost all known sites overlapped with predicted sites, and several new putative TFBSs were also identified. We validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, we applied our computational approach to the prediction of putative TFBSs within the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http://bfgl.anri.barc.usda.gov/tfbsConsSites.

The regulatory effect of the first intron and 3'-regulatory region of ovalbumin gene on transgene expression / 生物工程学报

We studied the influence of the first intron and 3'-regulatory region of ovalbumin gene (ov) on oviduct-specific transgene expression. The 3'-regulatory region in the oviduct-specific expression vector containing human tissue kallikrein (hK1) cDNA was replaced with bovine growth hormone (BGH) poly A, and the first intron was deleted by restriction enzyme digestion, resulting in five new vectors pOV2K, pOV3K, pOV4K, pOV5K and pOV6K. After mixing with polyethylenimine, we injected same copies of the five vectors via wing vein route into laying hens and compared their expression levels by quantitative assay for enzymatic activities in the egg whites. Among the five vectors tested, the pOV2K containing both the 5'- and 3'-regulatory regions expressed highest level of rhK1 activity, followed by pOV3K with the 3'-regulatory region replaced with BGH poly A, and then by the first intron-shortened vectors pOV4K, pOV5K and pOV6K. These data suggest that both the first intron and 3'-regulatory region of ov gene have enhancing effect on transgene expression in oviduct cells, which should be included in oviduct-specific expression vectors.

Parsing regulatory DNA: general tasks, techniques, and the PhyloGibbs approach.

In this review, we discuss the general problem of understanding transcriptional regulation from DNA sequence and prior information. The main tasks we discuss are predicting local regions of DNA, cis-regulatory modules (CRMs) that contain binding sites for transcription factors (TFs), and predicting individual binding sites. We review various existing methods, and then describe the approach taken by PhyloGibbs, a recent motif-finding algorithm that we developed to predict TF binding sites, and PhyloGibbs-MP, an extension to PhyloGibbs that tackles other tasks in regulatory genomics, particularly prediction of CRMs.