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Genetic analyses of temperature-sensitive mutations in baculovirus late expression factors.

Two temperature-sensitive mutants of Autographa californica nuclear polyhedrosis virus were characterized with respect to late and very late gene expression. Cells infected with ts317 or ts538 at the nonpermissive temperature revealed slightly reduced intracellular levels of late structural gene products including gp64 envelope, vp39 capsid, and p6.9 DNA binding proteins. However, with the exception of gp64, there was a dramatic reduction in extracellular levels of the structural proteins, suggesting that assembly or transport of extracellular virions was impaired. Electron microscopy confirmed the dramatic effect the mutations exhibited on viral morphogenesis. The ts538 mutation was physically mapped to the 60-65 mu region and DNA sequence analysis identified a single nucleotide alteration converting Leu to Phe in amino acid 105 of the late expression factor called lef-4. The mutation was positively correlated with the temperature-sensitive phenotype by analysis of DNA from ts+ revertants generated by marker rescue. Transient expression assays confirmed that lef-4 was required for activation of the late vp39 gene in virus infected cells. The defect in activation of the ts317 and ts538 polyhedrin genes could be overcome by coinfection with helper virus indicating that the mutations affected functions involved in activating the very late class of baculovirus genes as well. These results demonstrated a clear functional differentiation between genes regulating viral DNA replication which was normal in the mutant infected cells and those regulating late gene expression and extracellular virus production which were defective in these same infected cells.

Animals↗

A novel missense mutation (Asn5-->Ile) in lecithin: cholesterol acyltransferase (LCAT) gene in a Japanese patient with LCAT deficiency.

We identified a novel missense mutation in the lecithin:cholesterol acyltransferase gene in a new case of lecithin:cholesterol acyltransferase (LCAT) deficiency. The patient was a 64-year-old diabetic Japanese male who showed an extremely low level of serum high-density lipoprotein-cholesterol, corneal opacities, anemia, and proteinuria. Both the patient's LCAT activity and mass were markedly low. DNA sequence analysis of the LCAT gene showed an A-to-T transition at base 97 in exon 1, and predicted a change in asparagine to isoleucine at the 5th amino acid of the protein. Restriction analysis of polymerase chain reaction-amplified DNA using Ase I showed that the patient was homozygous for this mutation. Our results suggested that asparagine 5 was an important amino acid and substitution with isoleucine caused marked reduction of LCAT activity and mass, resulting in LCAT deficiency.

Amino Acid Sequence↗

SVARAP and aSVARAP: simple tools for quantitative analysis of nucleotide and amino acid variability and primer selection for clinical microbiology.

BACKGROUND: Simple computerized methods that analyse variability along alignments of nucleotide or amino acid sequences can be very useful in a clinical microbiology laboratory for two main purposes. First, to optimize primer selection, which is critical for the identification of infectious pathogens based on gene sequencing: primers must target conserved nucleotide regions bordering highly variable areas to ensure discrimination of species. Second, it can be of interest to reveal mutations associated with drug resistance of pathogen agents. Our aim was therefore to test easy and cost-free tools (SVARAP and aSVARAP) that require short hands-on work, little expertise, and which allow visual interpretation and statistical analysis of results. RESULTS: We first tested SVARAP to improve a strategy of identification of streptococci species of the Viridans Group targeting the groESL gene. Two regions with < 500 nucleotides were identified, one being significantly more discriminant than one of a similar length used in a previous study (mean number of nucleotide differences between species, 113 (range: 12-193) vs. 77 (range: 14-109); p < 10-3). Secondly, aSVARAP was tested on reverse transcriptase (RT) sequences from 129 HIV-1 clinical strains to identify natural polymorphisms and drug-selected mutations emerging under nucleoside RT inhibitor (NRTI)-selective pressure. It revealed eleven of the 18 RT mutations considered in a reference HIV-1 genotypic NRTI-resistance interpretation algorithm. CONCLUSION: SVARAP and aSVARAP are simple, versatile and helpful tools for analysis of sequence variability, and are currently being used in real practice in our clinical microbiology laboratory.

Amino Acid Sequence↗

Detection of sequence variation in the HVII region of the human mitochondrial genome in 689 individuals using immobilized sequence-specific oligonucleotide probes.

We have developed a rapid, immobilized probe-based assay for the detection of sequence variation in the hypervariable segment II (HVII) of the mitochondrial DNA (mtDNA) control region. Using a panel of 17 sequence-specific oligonucleotide (SSO) probes immobilized on nylon membrane strips, we typed 689 individuals from four population groups. The genetic diversity value for each population was calculated from the frequency data, and the frequencies of distinct "mitotypes" in each group were determined. We performed DNA sequence analysis of 129 samples to characterize the sequences associated with "blanks" (absence of probe signals) and weak probe signals. Out of 689 samples, we observed five heteroplasmic samples (excluding the variable C-stretch beginning at position 303) using the immobilized SSO probe panel. The SSO probe strips were used for the analysis of shed hairs and bloodstains from several criminal cases in Sweden, one of which is described here. We conclude that this mtDNA typing system is useful for human identification and significantly decreases casework turnaround time.

Base Sequence↗

Complete genome analysis of the mandarin fish infectious spleen and kidney necrosis iridovirus.

The nucleotide sequence of the infectious spleen and kidney necrosis virus (ISKNV) genome was determined and found to comprise 111,362 bp with a G+C content of 54.78%. It contained 124 potential open reading frames (ORFs) with coding capacities ranging from 40 to 1208 amino acids. The analysis of the amino acid sequences deduced from the individual ORFs revealed that 35 of the 124 potential gene products of ISKNV show significant homology to functionally characterized proteins of other species. Some of the putative gene products of ISKNV showed significant homologies to proteins in the GenBank/EMBL/DDBJ databases including enzymes and structural proteins involved in virus replication, transcription, protein modification, and virus-host interaction. In addition, one major repeated sequence showing significant homology to the Red Sea bream iridovirus (RSIV) genome was identified. Based on the information obtained from biological properties (including histopathology, tissue tropisms, natural host range, and geographic distribution), physiochemical and physical properties, and genome analysis, we suggest that ISKNV, RSIV, sea bass iridovirus, grouper iridovirus, and African lampeye iridovirus may belong to a new genus of the Iridoviridae family and are tentatively referred to as cell hypertrophy iridoviruses.

Amino Acid Sequence↗

Characterization of the Euplotes crassus macronuclear rDNA and its potential as a DNA transformation vehicle.

We have cloned the macronuclear linear DNA molecule carrying the ribosomal RNA genes from the ciliated protozoan Euplotes crassus. DNA sequence analysis was carried out to locate coding regions and to determine whether sequences that have been mutated to confer antibiotic resistance are conserved in the E. crassus genes. The beginning and end of the primary transcript were mapped. In order to determine whether conserved sequences that might serve as replication origins were present, the 5' and 3' non-coding sequences from E. crassus were compared to the corresponding sequences from the macronuclear linear rDNA molecules from the following euplotid species: Euplotes vannus, Euplotes minuta, Euplotes raikovii and Euplotes rariseta. A DNA transformation construct was made by generating a putative anisomycin resistant mutation along with a mutation generating a restriction site polymorphism. Microinjection of the construct into the developing macronucleus of mated cells resulted in exconjugant cell lines with increased resistance to anisomycin. The injected rDNA with the restriction site polymorphism is detectable in the anisomycin resistant cells and appears to represent a minor fraction of the rDNA.

Animals↗

Characterization of cDNA clones for differentially expressed genes in embryos of dormant and nondormant Avena fatua L. caryopses.

The molecular regulation of seed dormancy was investigated using differential display to visualize and isolate cDNAs representing differentially expressed genes during early imbibition of dormant and nondormant Avena fatua L. embryos. Of about 3000 cDNA bands examined, 5 cDNAs hybridized with mRNAs exhibiting dormancy-associated expression patterns during the first 48 h of inhibition, while many more nondormancy-associated cDNAs were observed. Dormancy-associated clone AFD1 hybridized with a 1.5 kb mRNA barely detectable in dry dormant and nondormant embryos that became more abundant in dormant embryos after 24 h of imbibition. Clone AFD2 hybridized with two mRNAs, a 1.3 kb message constitutively expressed in dormant and nondormant embryos and a 0.9 kb message present at higher levels in dormant embryos after 3 h of imbibition. Nondormancy-associated clones AFN1, AFN2 and AFN3 hybridized with 1.5 kb, 1.7 kb and 1.1 kb mRNAs, respectively, that were more abundant in nondormant embryos during imbibition. Expression patterns of some mRNAs in dormant embryos induced to germinate by GA3 treatment were different than water controls, but were not identical to those observed in nondormant embryos. DNA sequence analysis revealed 76% sequence identity between clone AFN3 and a Citrus sinensis glutathione peroxidase-like cDNA, while significant sequence similarities with known genes were not found for other clones. Southern hybridization analyses showed that all clones represent low (1 to 4) copy number genes.

Blotting, Northern↗

A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem.

A unique transfer RNA has been identified in human and bovine mitochondria that lacks the "dihydrouridine" loop and stem structure. This tRNA is mitochondrially coded as shown by DNA sequence analysis of the human and bovine mitochondrial DNA. Sequence analysis of the RNA shows that it is post-transcriptionally modified by the addition of CCA at the 3' terminus and that at least one base is modified. As predicted by its anticodon (GCU, corresponding to the serine codons AGU/C) this tRNA can be aminoacylated with serine when purified mitochondria are incubated in a medium containing 3H-serine.

Animals↗

Characterization of a repetitive DNA element in a brown algal virus.

We describe a family of repetitive sequences found in viruses infecting the brown alga Feldmannia sp. Previously we have demonstrated that the dsDNA genomes of viruses infecting one Feldmannia sp. isolate exist as two size classes of 160 and 179 kb. Repetitive sequences within these genomes were first demonstrated based on the anomalous hybridization among five BamHI fragments from digested virus DNA. Sequence analysis of one of those fragments, B2.4, revealed the presence of 173-bp direct repeats. The restriction maps of the cross-hybridizing BamHI fragments in the two FsV (Feldmannia sp. virus) genome size classes show that these repeats are not widely dispersed, rather they are confined to a small region of each virus genome. We estimate the number of these repeats in the 179-kb genome to be about 109 and in the 169-kb genome to be about 41. In the 179-kb genome, the repeats are contained within a 22-kb region, about 12% of that virus genome, and in the 160-kb genome the repeats are contained within a 10-kb region, about 6% of the genome. The difference in repeat numbers can account for 62% of the size difference between the two size classes of the FsV genome.

Base Sequence↗

Addition of non-genomically encoded nucleotides to the 3'-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA.

The 3'-termini of maize mitochondrial RNAs were characterized by ligation of an anchor oligonucleotide, reverse transcription and amplification. DNA sequence analysis of cDNA clones for tRNA(Ser) and 18S rRNA confirmed the expected 3'-terminal nucleotides and demonstrated the accuracy and fidelity of the protocol. Analysis of cDNAs for rps12, cox2 and atp9 indicated that non-genomically encoded nucleotides were present at the 3'-terminus. rps12 cDNAs exhibited the highest degree of modification, with 94% of 35 cDNA clones analyzed containing one to four non-genomically encoded C or A residues; 83% of these cDNAs terminated with the trinucleotide CCA. DNA sequence and transcript mapping analyses demonstrated that four positions exhibited modified 3'-termini within a small region of the 3' flank of rps12 transcripts. These transcript termini represented low abundance, truncated forms of rps12 mRNAs which may be intermediates in degradation. cox2 mRNAs are also modified at a truncated position. Sixty percent of the cox2 cDNAs were modified with 1-5 nt that most frequently included A and C residues, but also included a few G and T residues. Non-genomically encoded nucleotides were detected in 27% of the atp9 cDNAs as a single C or A residue.

3' Untranslated Regions↗

Genetic heterogeneity of M type 3 group A streptococci causing severe infections in Tayside, Scotland.

To explain the worldwide increase in the frequency of severe infections by group A streptococci, molecular techniques are increasingly being employed to evaluate the genetic relationships of strains. We used restriction endonuclease analysis, pulsed-field gel electrophoresis (PFGE), the PCR, ribotyping, and DNA sequence analysis in a study of 13 group A streptococci isolated from a cluster of cases of serious infections over a 3-month period in Tayside, Scotland. Eight of the strains were M type 3; molecular characterization identified two subclones. The first, displaying PFGE profile 4, has been observed in Northern Scotland and has been circulating in New Zealand for over a decade. The second subclone has been documented only in the United Kingdom; it was first seen in 1993 in Scotland. Sequence analysis of emm-3 genes further differentiated the PFGE 4 subclone. DNA sequence analysis of virulence factors supports the suggestion that they may have recently been acquired by horizontal gene transfer.

Bacterial Typing Techniques↗

Cloning and sequencing of the central region of the flagellin gene from the Gram-positive bacterium Clostridium tyrobutyricum ATCC 25755.

The purpose of this study was to sequence the central part of the coding region of the Clostridium tyrobutyricum fiagellin gene to improve the immunoenzymatic counting of cells after milk filtration. The coding region was amplified by PCR, and the amplified products were cloned. A DNA sequence analysis of positive clones gave us 1,131 nucleotides with a partial calculated flagellin molecular mass of 40,143 Da. The flagellar filament protein sequence exhibited high levels of homology to sequences of flagellin protein from other bacteria in both N- and C-terminal parts, but little homology in the central domain. A PCR-restriction fragment length polymorphism analysis of amplified C. tyrobutyricum flagellin gene products confirmed the variability of the central domain. The flagellin mRNA was determined to be 1.1 kb in size, which suggests a monocistronic mRNA. Furthermore, the deduced protein flagellin contains eleven potential N-glycosylation sites and one sequence rich in serine, which could be modified by O-glycosylation.

Amino Acid Sequence↗

Extreme DNA sequence variation in isolates of Aspergillus fumigatus.

DNA sequence analysis of the alkaline protease gene was used to investigate two Aspergillus fumigatus strains isolated from ostriches (QLD1 and NSW3) and one environmental isolate (FRR 1266) that have shown genetic variation in previous analyses. The results showed that the QLD1 sequence was virtually identical to the published sequences for three human isolates but NSW3 differed in > 6% and FRR 1266 in > 10% of the nucleotides that were analysed. An RFLP assay was designed to determine the distribution of these (and other) genetic variants among environmental and clinical isolates of A. fumigatus.

Amino Acid Sequence↗

Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.

The human (nuclear) genome encodes at least 79 mitochondrial ribosomal proteins (MRPs), which are imported into the mitochondria. Using a comprehensive approach, we find 41 of these give rise to 120 pseudogenes in the genome. The majority of the MRP pseudogenes are of processed origin and can be aligned to match the entire coding region of the functional MRP mRNAs. One processed pseudogene was found to have originated from an alternatively spliced mRNA transcript. We also found two duplicated pseudogenes that are transcribed in the cell as confirmed by screening the human EST database. We observed a significant correlation between the number of processed pseudogenes and the gene CDS length (R = -0.40; p < 0.001), i.e., the relatively shorter genes tend to have more processed pseudogenes. There is also a weaker correlation between the number of processed pseudogenes and the gene CDS GC content. Our study provides a catalogue of human MRP pseudogenes, which will be useful in the study of functional MRP genes. It also provides a molecular record of the evolution of these genes. More details are available at http://pseudogene.org/.

Animals↗

Identification of androgen receptor protein and 5alpha-reductase mRNA in human ocular tissues.

BACKGROUND/AIMS: Androgens have been reported to influence the structural organisation, functional activity, and/or pathological features of many ocular tissues. In addition, these hormones have been proposed as a topical therapy for such conditions as dry eye syndromes, corneal wound healing, and high intraocular pressure. To advance our understanding of androgen action in the eye, the purpose of the present study was twofold: firstly, to determine whether tissues of the anterior and posterior segments contain androgen receptor protein, which might make them susceptible to hormone effects following topical application; and, secondly, to examine whether these tissues contain the mRNA for types 1 and/or 2 5alpha-reductase, an enzyme that converts testosterone to the very potent metabolite, dihydrotestosterone. METHODS: Human ocular tissues and cells were obtained and processed for histochemical and molecular biological procedures. Androgen receptor protein was identified by utilising specific immunoperoxidase techniques. The analysis of type 1 and type 2 5alpha-reductase mRNAs was performed by the use of RT-PCR, agarose gel electrophoresis, and DNA sequence analysis. All immunohistochemical evaluations and PCR amplifications included positive and negative controls. RESULTS: These findings show that androgen receptor protein exists in the human lacrimal gland, meibomian gland, cornea, bulbar and forniceal conjunctivae, lens epithelial cells, and retinal pigment epithelial cells. In addition, our results demonstrate that the mRNAs for types 1 and 2 5alpha-reductase occur in the human lacrimal gland, meibomian gland, bulbar conjunctiva, cornea, and RPE cells. CONCLUSION: These combined results indicate that multiple ocular tissues may be target sites for androgen action.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗

A block coding method that leads to significantly lower entropy values for the proteins and coding sections of Haemophilus influenzae.

A simple statistical block code in combination with the LZW-based compression utilities gzip and compress has been found to increase by a significant amount the level of compression possible for the proteins encoded in Haemophilus influenzae, the first fully sequenced genome. The method yields an entropy value of 3.665 bits per symbol (bps), which is 0.657 bps below the maximum of 4.322 bps and an improvement of 0.452 bps over the best known to date of 4.118 bps using Matsumoto, Sadakane, and Imai's lza-CTW algorithm. Calculations based on a compact inverse genetic code show that the genome has a maximum entropy of 1.757 bps for the coding regions, with a possibly lower actual entropy. These results hint at the existence of hitherto unexplored redundancies that do not show up in Markov models and are indicative of more internal structure than suspected in both the protein and the genome.

Algorithms↗

Using faecal DNA sampling and GIS to monitor hybridization between red wolves (Canis rufus) and coyotes (Canis latrans).

The US Fish and Wildlife Service's (USFWS) Red Wolf Recovery Program recognizes hybridization with coyotes as the primary threat to red wolf recovery. Efforts to curb or stop hybridization are hampered in two ways. First, hybrid individuals are difficult to identify based solely on morphology. Second, managers need to effectively search 6000 km(2) for the presence of coyotes and hybrids. We develop a noninvasive method to screen large geographical areas for coyotes and hybrids with maternal coyote ancestry by combining mitochondrial DNA sequence analysis of faeces (scat) and geographic information system (GIS) technology. This method was implemented on the Alligator River National Wildlife Refuge (1000 km(2)) in northeastern North Carolina. A total of 956 scats were collected in the spring of 2000 and 2001 and global positioning system (GPS) coordinates were recorded. Seventy-five percent of the scats were assigned to species and five coyote/hybrid scats were detected. Placement of scat location coordinates on a map of the experimental population area revealed that four of the coyote/hybrid scats were detected within the home ranges of sterilized hybrids. The other coyote/hybrid scat indicated the presence of a previously unknown individual. We suggest this method be expanded to include more of the experimental population area and be optimized for use with nuclear markers to improve detection of hybrid and back-crossed individuals.

Animals↗

An efficient homologous recombination vector pTV(I) contains a hot spot for increased recombinant protein expression in Chinese hamster ovary cells.

We employed reverse genetics to clone a 5.0 kb genomic DNA hot spot HIRPE (hot spot for increased recombinant protein expression) flanking the plasmid integration site from a recombinant Chinese hamster ovary (CHO) cell line. DNA sequence analysis of the 5.0 kb fragment revealed that HIRPE is enriched for repetitive elements, Alu-like sequences and matrix-associated regions that are known to be linked with transcriptionally active regions in a number of mammalian systems. The construction of a homologous recombination vector, pTV1, containing the 5.0 kb HIRPE genomic DNA, a recombinant gene human CTLA4-Ig, and the dhfr gene as a positive selection marker is described. It was observed that the pTV1 vector targeted the CTLA4Ig gene to a preferred locus in the CHO genome contributing to high recombinant gene expression in transfected CHO cells. Preliminary studies suggest that similar to the observation with the parental cell line, pTV1-generated transfectomas that were analyzed appear to harbor an inverted duplication of the genomic DNA at the plasmid integration site.

Abatacept↗