Molecular cloning and physical mapping of the Neurospora crassa 74-OR23-1A mitochondrial genome

Summary To provide for thorough sampling of the Neurospora crassa mitochondrial genome for evolutionary studies, recombinant plasmids containing each of the EcoRI digestion fragments of the genome were assembled and used to map the locations of 89 additional restriction endonuclease cleavage sites, representing 10 newly mapped enzymes and 2 previously unmapped HincII sites. Data used to locate new restriction sites were obtained from digestions of whole mitochondrial DNA, digestions of the cloned EcoRI mitochondrial DNA fragments and hybridizations between new restriction fragments and the cloned fragments. Length measurements of the total genome and of EcoRI fragment 1 are larger than commonly reported.     

Molecular cloning and complete nucleotide sequence of the genome of Japanese encephalitis virus Beijing-1 strain

The genomic RNA of the Japanese encephalitis virus (JEV) Beijing-1 strain was reversely transcribed and the synthesized cDNA was molecularly cloned. Six continuous cDNA clones that cover the entire virus genome were established and sequenced to determine the complete nucleotide sequence of the JEV RNA. The precise genomic size was estimated as 10,965 bases long. With flanking 95 bases at the 5 and 583 bases at the 3 non-coding regions, one long open reading frame (ORF) was revealed encoding a virus polyprotein with 3,429 amino acid residues. Because of sequence homologies observed between JEV and other flaviviruses, the genome organization of JEV appears to be identical with other flaviviruses. Genetic variation detected among flavivirus genomes is consistent with the established serological relatedness between JEV and other members of flaviviruses. The secondary structure of the JEV genome is deduced and discussed concerning its involvement in genome replication.     

Analysis of the genome of molluscum contagiosum virus by restriction endonuclease analysis and molecular cloning

Virions of molluscum contagiosum virus (MCV), a member of the poxviridae, were isolated directly from lesions of individual patients and characterized by restriction enzyme analysis. The comparative analysis of the cleavage patterns and Southern blot hybridization of 14 independently isolated virus samples revealed that MCV isolates can be classified into two different types. The majority of MCV isolated from clinically typical skin lesions (13 of 14) showed similar DNA cleavage patterns and were termed MCV type 1, whereas one isolate derived from a vaginal lesion showed a completely different DNA cleavage pattern and therefore was termed MCV type 2. For detailed investigation of the viral genome, a defined gene library of MCV DNA sequences was established. The Bam HI DNA fragments of the viral genome of MCV type 1 prototype isolate 1/80 was inserted into the bacterial plasmid vector pAT153. With the exception of terminal fragments (fragments A and B) of the viral genome, all other DNA fragments were cloned. All cloned Bam HI DNA fragments were individually identified by digestion of the recombinant plasmid DNA with different restriction enzymes and screened by hybridization of plasmid DNA to viral DNA.     

Identification, cloning, and R-loop mapping of the polyhedrin gene from the multicapsid nuclear polyhedrosis virus of Orgyia pseudotsugata

Polyadenylated RNA was isolated from Orgyia pseudotsugata larvae 8-10 days postinfection with the multicapsid nuclear polyhedrosis virus. This RNA was centrifuged through a sucrose gradient and fractions enriched for polyhedrin mRNA were identified by in vitro translation. Complementary DNA made to this RNA hybridized predominantly to a 5-kb fragment of XhoI-digested viral DNA. This fragment was cloned into the plasmid pACYC177 and mapped with restriction endonucleases. A SalI subclone with a 2.5-kb insert derived from the cloned XhoI fragment was found to select by hybridization only polyhedrin mRNA as determined by the size of the in vitro translation product and its precipitation by anti-polyhedrin antibodies. The orientation of the polyhedrin gene and the region of the insert encoding the N terminus of the polyhedrin protein were determined by DNA sequencing. R-Loop mapping indicated polyhedrin mRNA is 980 +/- 75 bases long and contains about 250 nucleotides not represented in the final protein. The polyhedrin gene had no observable intervening sequences.     

Molecular cloning and expression of the epidermolytic toxin A gene of Staphylococcus aureus

The gene coding for serotype A of epidermolytic (exfoliative) toxin has been cloned from Staphylococcus aureus in Escherichia coli phage lambda and plasmid vectors. The coding sequence for eta was localised by subcloning and transposon Tn5 mutagenesis experiments. The eta gene was probably expressed from its natural promoter in E. coli. The protein synthesised in E. coli was located predominantly in the periplasm. It was immunochemically indistinguishable from the toxin purified from S. aureus culture supernatants and had the same molecular weight. Furthermore, subcutaneous injection of this material caused epidermal splitting (the Nikolsky reaction) showing that it was biologically active. An eta shuttle plasmid was transformed into protoplasts of S. aureus. The level of expression of toxin in strain 8325-4 was shown to be dependent on the integrity of the agr gene which is known to be required for the expression of several exoproteins.     

Molecular cloning and characterization of retrovirus-like intracisternal type A particle genes (IAP) present in the Chinese hamster genome

Endogenous retrovirus-like sequences that are homologous to the multigenic murine and Syrian hamster intracisternal type A particle (IAP) genes can be detected in very few copies in the Chinese hamster (CH) genome. They were cloned from a CHO gene library and two recombinants, harboring the major IAP-like DNA genes characterized by Southern blot hybridization after DNA digestion with several restriction enzymes. The IAP DNA inserts of the two clones analyzed were 4.70 and 8.04 kb respectively, allowing us to construct a physical map of our Chinese hamster clone that represents an almost complete IAP element.     

Molecular cloning and complete nucleotide sequence of genomic RNA of the AIK-C strain of attenuated measles virus

Twelve cDNA clones covering the entire genome of the AIK-C strain of a seed for live measles vaccine were obtained, and the nucleotide sequences were determined. The full viral genomic RNA consists of 15,894 nucleotides. Comparisons of the nucleotide sequence and the deduced amino acid sequence between the AIK-C and other Edmonston strains revealed the following changes: 56 nucleotide differences and one C residue insertion, 31 amino acid changes, and 19 silent mutations.     

Genomic characterization of molluscum contagiosum virus type 1: Identification of the repetitive DNA sequences in the viral genome

The genomes (188 kbp) of the prototypeMolluscum contagiosum virus type 1 (MCV-1) and a variant strain (MCV-1v) were characterized by construction of the physical maps of the viral DNA for the restriction enzymesBamHI,ClaI,EcoRI, andHindIII using a defined gene library harboring the DNA sequences of the MCV-1 genome and by DNA-DNA hybridizations. It was found that the genomes of both MCV strains are identical, with the exception of very few changes in the DNA fragmentation patterns of restriction endonucleaseBamHI as a consequence of naturally occurring nucleotide exchanges in the genome of the variant strain. Detailed hybridization experiments revealed the existence of repetitive DNA sequences, which are located within the terminal regions of the viral genome at the map coordinates 0 to 0.027 and 0.973 to 1.     

Efficient cloning of hepatitis B virus DNA from single-stranded replicative intermediates and its application to S1 mapping of viral RNA in human liver tissue

An efficient method for cloning subgenomic fragments of the hepatitis B virus (HBV) was developed, utilizing its abundant single-stranded replicative intermediates. The total genomic DNA obtained from the liver tissue of patients with chronic HBV infection was treated by using the Klenow fragment of E. coli DNA polymerase I without adding any exogenous primers. Single-stranded replicative intermediates were efficiently converted to double-stranded linear DNA, one end of which terminated at (or near to) the direct repeat 1 (DR1) sequence of the HBV genome. By screening less than 1,000 recombinants from a DNA library after this treatment, we obtained a subgenomic HBV fragment of 2.0 kilobases. We then analysed HBV RNA in human liver tissue by S1 mapping. It was possible to map HBV RNA only when a DNA probe from the same tissue was used.     

Molecular epidemiology of adenovirus type 7 in Israel: Identification of two new genome types,Ad7k and Ad7d2

The molecular epidemiology of Adenovirus type 7 in Israel was investigated. Fifty-seven adenovirus isolates identified as serotypes 7 or 7a which were recovered from patients in Israel between 1968 and 1995 were analyzed by restriction enzymes digestion using BamHI for primary discrimination and identification of genome types and by six additional enzymes: BstEII, HpaI, BglI, BglII, BclI, and XbaI for confirmation and determination of genomic subtypes. Four digestion patterns were identified with BamHI; one of them was new. Using BstEII, two patterns were obtained, one of them new. Digestion with the other five enzymes yielded known patterns. The analysis revealed four different genomic types and subtypes, which circulated in Israel in different years: subtype 7a1; type 7b, a type with a new BamHI pattern which was designated type 7K, and a subtype with a new BstEII pattern which differed from type 7d by one restriction site and was designated type 7d2. Twenty-two isolates from 1968 through 1975 and from 1984 were Ad7a1. Three isolates from 1973–1974 were Ad7b. Five isolates from 1968 through 1973 were Ad7K and 27 isolates from 1992 through 1995 were Ad7d2. This demonstrates the temporal change in the circulating genome types with up to three genome types cocirculating in 1 year (1973). The two new types, Ad7k and Ad7d2 could have evolved in Israel or could have been imported by travellers and immigrants from neighboring or distant countries. J. Med. Virol. 54:291–299, 1998. © 1998 Wiley-Liss, Inc.     

Molecular cloning and characterization of the genome of wound tumor virus: a tumor-inducing plant reovirus

The double-stranded RNA genome of the tumor-inducing plant pathogen, wound tumor virus, was converted to double-stranded DNA and cloned into plasmid pBR322. Multiple apparent full-length copies of 9 of the 12 wound tumor virus genome segments were identified. The entire sequence of cloned genome segment S12, the smallest of the genome segments, was determined. This genome segment was found to be 851 nucleotides in length and to possess a single long open reading frame that extends 178 codons from the first AUG triplet (residues 35-37): information sufficient to encode a protein of the size estimated for the smallest of the previously identified wound tumor virus primary gene products, Pns 12. Sequence data obtained from analysis of cloned cDNA copies of several genome segments and from direct analysis of the 3' termini of the double-stranded genome RNAs revealed that each wound tumor virus genome segment possesses the common terminal sequences: (+) 5'GGUAUU ... UGAU 3' (-) 3'CCAUAA ... ACUA 5'.     

The mitochondrial genome of the basidiomycete Agrocybe aegerita: molecular cloning,physical mapping and gene location

Summary The mtDNA of a wild-type strain of Agrocybe aegerita was purified from mitochondria isolated by cellular fractionation. A representative library was constructed in E. coli by molecular cloning at the HindIII restriction site of pBR322. Southern hybridizations between total DNA of the fungal strain and cloned mitochondrial insert probes were used to establish the restriction map of the mtDNA molecule. Its size was assessed at about 80 500 bp. Four structural genes (for Cox 1, Cox 2, Atp 6, and Atp 8) were located on the map by heterologous hybridizations with oligonucleote probes specific for yeast mitochondrial genes. The location of the genes coding for the large and the small RNAs of the mitochondrial ribosome was determined by hybridization with the E. coli rrnB operon. A comparison of A. aegerita mtDNA organization with that of both phylogenetically close and distant fungi is discussed.     

Genetic homogeneity,high-resolution mapping,and mutation analysis of the urofacial (Ochoa) syndrome and exclusion of the glutamate oxaloacetate transaminase gene (GOT1) in the critical region as the disease gene

The urofacial (Ochoa) syndrome (UFS) is a rare autosomal recessive disorder characterized by abnormal facial expression and urinary abnormalities. Previously, we mapped the gene to a genomic interval of approximately 1 cM on chromosome region 10q23-24, using families from Columbia. Here we demonstrate genetic homogeneity of the syndrome through homozygosity mapping in American patients with Irish heritage. We established a physical map and identified novel polymorphic markers in the UFS critical region. Haplotype analysis using the new markers mapped the UFS gene within one YAC clone of 1,410 kb. We also determined the precise location of the gene encoding for glutamate oxaloacetate transaminase (GOT1) within the new UFS critical region and determined its genomic structure. However, mutation analysis excluded GOT1 as a candidate for the UFS gene. Am. J. Med. Genet. 84:454–459, 1999. © 1999 Wiley-Liss, Inc.     

Structure of the cloned Locusta migratoria mitochondrial genome: restriction mapping and sequence of its ND-1 (URF-1) gene

Summary We have cloned the entire mitochondrial genome of Locusta migratoria in four fragments and characterised by restriction mapping. In addition, we have sequenced a 1,095 kb region containing the ND-1 (URF-1) gene. The inferred primary structure of the protein is highly homologous to its Drosophila counterpart (68%). The gene is flanked at the 5 end by the tRNA _CUN ^leu gene, interrupted by the sequence TTG. The 3 end is flanked by the tRNA _ser ^UCN gene, followed by a sequence homologous to the 3 end of D. yakuba cytochrome b. The relative position of the genes is conserved between Locusta and Drosophila, thus indicating conservation of mitochondrial gene order in insects.     

胰岛素样生长因子-1及内皮素-1水平与胎儿宫内发育受限发病的关系

目的 探讨胰岛素样生长因子-1(IGF-1)及内皮素-1 (ET-1)与胎儿宫内发育受限(FGR)发病的关系.方法 应用放射免疫分析法和酶联免疫吸附试验,分别测定21例FGR患儿脐血、孕妇(FGR组)血清及羊水中IGF-1和ET-1水平,同期住院的正常晚期妊娠妇女34例(正常妊娠组)作为对照.结果 (1)FGR组孕妇血清IGF-1为112.16±7.02μg/L,低于正常妊娠组的207.07±8.25μg/L,两者比较,差异有显著性(P＜0.01);FGR组脐血清IGF-1为16.27±7.38μg/L,低于正常妊娠组的44.89±6.44μg/L,两者比较, 差异有极显著性(P＜0.001);FGR组羊水中IGF-1 与正常妊娠组无明显差异(P＞0.05);(2)FGR组脐血清ET-1为79.34±3.67μg/L,高于正常妊娠组的43.96±4.16μg/L,两者比较,差异有显著性(P＜0.01);FGR组羊水中ET-1水平(21.96±1.89μg/L)明显高于正常妊娠组(10.41±2.13μg/L),两组相比有显著差异(P＜0.01);而FGR组孕妇血清ET-1与正常妊娠组相比无明显差异(P＞0.05).结论 IGF-1及ET-1在FGR的发病中可能起到重要作用有关.     

Cloning and expression in Escherichia coli and Staphylococcus aureus of the beta-lysin determinant from Staphylococcus aureus: evidence that bacteriophage conversion of beta-lysin activity is caused by insertional inactivation of the beta-lysin determinant

The beta-lysin determinant (Hlb) from Staphylococcus aureus CN6708 was cloned in Escherichia coli K-12 using the bacteriophage replacement vector lambda L47.1. The Hlb determinant was localised to a 1250 base pair DNA sequence by cloning fragments from a Hlb+ recombinant phage into the plasmid vectors pACYC184 and pBR322 in E. coli K-12, and by the subsequent construction and analysis of several sub-clones, in vitro deletion and Tn5 insertion mutations. E. coli cells harbouring Hlb+ plasmids expressed readily detectable levels of beta-lysin and sphingomyelinase activity, which were located in the cytoplasm. Two polypeptides of molecular weight 38,000 and 33,000 which were encoded by the Hlb determinant were detected in E. coli minicells, but only the 33,000 dalton protein was detected in immunoblotting experiments with specific anti-beta-lysin serum. Hybridisation analysis with probes made from the cloned Hlb determinant and from DNA of the staphylokinase-converting phage phi 13, indicated that bacteriophage conversion of S. aureus to loss of beta-lysin activity is due to insertion of phi 13 DNA into or adjacent to the beta-lysin determinant. A shuttle plasmid was used to transfer the cloned Hlb determinant into a beta-lysin negative strain of S. aureus where the wild-type chromosomal determinant was inactivated by lysogenic conversion. Beta-lysin activity was readily detected in supernatants of S. aureus harbouring the cloned determinant.     

Molecular analysis of HLA-DRB1, DQA1, DQB1, DQ promoter polymorphism and extended class I/class II haplotypes in the Seri Indians from Northwest Mexico

The study of the genetics of the Major Histocompatibility Complex (MHC) in Amerindians is of great value in understanding the origins and migrations of these native groups, as well as the impact of immunogenetics on the epidemiology of diseases affecting these populations. We analyzed, using Polymerase Chain Reaction and Sequence Specific Oligonucleotide Probes (PCR-SSOP), DRB1, DQA1, DQB1 alleles and the promoter regions of DQA1 and DQB1 genes in 31 unrelated and 24 related Seri, a Mexican Indian group, from the state of Sonora (Northwest Mexico). The class II genotypes of this population were found to be in genetic equilibrium. The allele frequency (AF) of the prevalent DRB1 alleles were DRB1*0407 (48.4%), DRB1*0802 (33.9%) and DRB1*1402 (16.1%). The most frequent DQA1 and DQB1 alleles were DQA1*03011 (AF = 50.00%), DQA1*0401 (AF = 33.87%) and DQA1*0501 (AF = 16.13%); DQB1*0302 (AF = 50.00%), DQB1*0402 (33.87%) and DQB1*0301 (16.13%); which were in combination with DRB1*0407, DRB1*0802 and DRB1*1402, respectively. Three QAP and three QBP alleles were present (QAP 3.1, 4.1, 4.2; QBP 3.1, 3.21, 4.1) associated with the typical published DQA1 and DQB1 alleles. Four class II haplotypes were present in family members: DRB1*0407-QAP-3.1-DQA1*03011-QBP-3.21-DQB1*0302; DRB1*0802-QAP-4.2-DQA1*0401-QBP-4.1-DQB1*0402; DRB1*1402-QAP-4.1-DQA1*0501-QBP-3.1-DQB1*0301 and DRB1*0701-QAP-2.1-DQA1*0201-QBP-2.1-DQB1*0201. The family data were used to confirm extended haplotypes. A total of 21 haplotypes were found when A* and B* loci were also considered. The three most frequent combinations included A*0201-B*3501-DRB1*0407, A*3101-B*5101-DRB1*0802, and A*0201-B*40-DRB1*1402.