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[Mitochondrial DNA mutations in lung cancer].

BACKGROUND AND OBJECTIVE: Mitochondiral DNA (mtDNA) mutations has been identified in various cancers, but their significance was unknown. This study aimed to detect mtDNA mutations in lung cancer, and to investigate their roles in the carcinogenesis of human lung. METHODS: Total DNA (including nuclear DNA and mtDNA) was extracted from the tumor tissues, corresponding distal non-cancerous lung tissues, and peripheral lymphocytes derived from 58 patients with lung cancer. Fifty-eight overlapping fragments and covering complete sequence of mtDNA were amplified by nested PCR, and the PCR products were sequenced directly with the cycle sequencing methods. The mtDNA mutations in the tumor tissue were determined by comparing with corresponding and peripheral lymphocytes. RESULTS: Sixty-six mutations were identified in 36 cases (62.1%) of lung cancer, including 58 point mutations, 4 insertions, and 4 deletions. These mutations were dispersedly distributed in the full length of mtDNA. The frequency of mutation in D-loop is the highest, in which 18 mutations were detected. No mutation hot spot was found in peptide-coding regions. Among 43 point mutations identified in protein-coding region, 20 were silent mutations. In 8 patients, identical mutations were detected both in the tumor tissues and corresponding distal non-cancerous tissues. CONCLUSION: Most of mtDNA mutations in the lung cancers investigated were occurred randomly and might have no impact on carcinogenesis; whereas the homoplasmic mutations may provide a potential diagnostic marker for lung cancer.

Aged↗

Deregulation of p73 isoform equilibrium in benign prostate hyperplasia and prostate cancer.

p73, a p53 homologue important for growth suppression, differentiation and induction of apoptosis, utilizes different promoters and undergoes alternative splicing to produce several isoforms differing in their ability to overlap p53 functions. Using reverse transcriptase-polymerase chain reaction (RT-PCR) to assess the mRNA levels of p53, p73 (total and isoforms specific for exons 2 and 13), MDM2, CDKN1A and beta2-microglobulin as internal control, we analyzed 35 prostate carcinomas and 44 benign prostate hyperplasias (BPH) compared to 14 normal prostates. Shift of p73 isoform mRNA levels from exon 13 lacking to exon 13 containing copies was observed in 80% of prostate cancer cases and in 52.3% of BPH specimens, and from exon 2 containing to exon 2 lacking (p73Deltaexon2) transcripts in 45.7% of cancer cases, but only in 9.1% of BPH samples. From these findings we deduce that p73 isoform balance is disrupted in prostate cancer and BPH, suggesting that this disequilibrium could play an important role in both prostate hyperplasia and malignancy.

Adult↗

[Construction of recombinant yellow fever virus 17D containing 2A fragment as a vaccine vector].

The Yellow Fever (YF) vaccine, an attenuated yellow fever 17D (YF-17D) live vaccine, is one of the most effective and safest vaccines in the world and is regarded as one of the best candidates for viral expression vector. We here first reported in China the construction and characterization of the recombinant expression vector of yellow fever 17D which contained the proteinase 2A fragment of foot-and-mouth disease virus (FMDV). Three cDNA fragments representing the full-length YF-17D genome, named 5'-end cDNA (A), 3'-end cDNA (B) and middle cDNA (C), were obtained by reverse transcription polymerase chain reaction (RT-PCR), together with the introduction of SP6 enhancer, necessary restriction sites and overlaps for homologous recombination in yeast. Fragment A and B were then introduced into pRS424 in turn by DNA recombination, followed by transfection of fragment C and the recombinant pRS424 containing A and B (pRS-A-B) into yeast. A recombinant vector containing full length cDNA of YF-17D (pRS-YF) was obtained by screening on medium lack of tryptophan and uracil. A recombinant YF-17D expression vector containing FMDV-2A gene fragment (pRS-YF-2A1) was then constructed by methods of DNA recombination and homologous recombination in yeast described above. In vitro transcription of the recombinant vector pRS-YF-2A1 was then carried out and introduced into BHK-21 cells by electroporation. Results of indirect immunofluorescence assay (IFA) and titer determination showed a stable infectious recombinant virus was gotten, whose features such as growth curve were similar to those of the parental YF-17D. The results suggest that the recombinant vector pRS-YF-2A1, by introduction of heterogenous genes via 2A region, is potential to be an effective live vaccine expression vector.

Animals↗

Amplification of a Cryptosporidium parvum gene fragment encoding thymidylate synthase.

Currently, there is no effective therapy for cryptosporidiosis and it is unclear why antifolate drugs which are effective treatments for infections caused by closely related parasites are not also effective against Cryptosporidium parvum. In protozoa, the target of these drugs, dihydrofolate reductase (DHFR), exists as a bifunctional enzyme also manifesting thymidylate synthase (TS) activity and is encoded by a fused DHFR-TS gene. In order to prepare a probe to isolate the C. parvum DHFR-TS gene we have used degenerate oligonucleotides whose sequences are based on strongly conserved regions of TS protein sequence to prime the polymerase chain reaction (PCR) with C. parvum DNA. The PCR amplified a 375-bp DNA fragment which was cloned and sequenced; the deduced amino acid sequence had significant identity with known TS sequences, including strict conservation of all phylogenetically invariant TS amino acid residues. The cloned PCR fragment was used as a probe to isolate a number of overlapping clones from a C. parvum genomic library which were definitively shown to be of cryptosporidial origin by genomic Southern and molecular karyotype analyses. The deduced protein sequence of C. parvum TS was most similar to the bifunctional TS enzymes of Plasmodium chabaudi and Plasmodium falciparum.

Amino Acid Sequence↗

EasyExonPrimer: automated primer design for exon sequences.

UNLABELLED: EasyExonPrimer is a web-based software that automates the design of PCR primers to amplify exon sequences from genomic DNA. EasyExonPrimer is written in Perl and uses Primer3 to design PCR primers based on the genome builds and annotation databases available at the University of California, Santa Cruz (UCSC) Genome Browser database (http://genome.ucsc.edu/). It masks repeats and known single nucleotide polymorphism (SNP) sites in the genome and designs standardised primers using optimised conditions. Users can input genes by RefSeq mRNA ID, gene name or keyword. The primer design is optimised for large-scale resequencing of exons. For exons larger than 1 kb, the user has the option of breaking the exon sequence down into overlapping smaller fragments. All primer pairs are then verified using the In-Silico PCR software to test for uniqueness in the genome. We have designed >1000 pairs of primers for 90 genes; 95% of the primer pairs successfully amplified exon sequences under standard PCR conditions without requiring further optimisation. AVAILABILITY: EasyExonPrimer is available from http://129.43.22.27/~primer/. The source code is also available upon request. CONTACT: Xiaolin Wu (forestwu@mail.nih.gov).

Algorithms↗

[Cloning and sequencing of complete TT virus genome from Beijing isolate of China].

OBJECTIVE: To obtain the complete TT virus genome from a Beijing isolate of China. METHODS: PCR was performed for amplifying the TT virus genome from serum of a patient with non A-G hepatitis. Five overlapped fragments, that are 199 bp (1-199), 1 267 bp (90-1356), 878 bp (1354-2231),1129 bp(2178-3306),'434 bp(3306-3739), respectively, were obtained. These PCR products were sequenced by standard method. RESULTS: The complete TT virus genome of Beijing isolate consists of 3 739 nucleotides involving two ORFs. The first ORF locates at 589-2902 nt, encoding 770 amino acids, the second ORF locates at 107-715 nt, encoding 202 amino acids. 5' and 3' terminus of the genome are non-coding regions including 106 bp and 837 bp respectively. In this genome, A is 31.2%, C 25.4%, G 22.5% and T 20.9%. The homology of Beijing isolate and Japanese TT virus was more than 95% at both nucleotide and amino acid levels. CONCLUSIONS: We successfully cloned and sequenced the complete TT virus genome from a Chinese patient. This Beijing TT virus isolate and that reported by Japan all belong to a same genotype.

Amino Acid Sequence↗

Development and evaluation of a species diagnostic polymerase chain reaction-restriction fragment-length polymorphism procedure for cryptic members of the Culex sitiens (Diptera: Culicidae) subgroup in Australia and the southwest Pacific.

Members of the Culex sitiens subgroup are important vectors of arboviruses, including Japanese encephalitis virus, Murray Valley encephalitis virus and Ross River virus. Of the eight described species, Cx. annulirostris Skuse, Cx. sitiens Wiedemann, and Cx. palpalis Taylor appear to be the most abundant and widespread throughout northern Australia and Papua New Guinea (PNG). Recent investigations using allozymes have shown this subgroup to contain cryptic species that possess overlapping adult morphology. We report the development of a polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) procedure that reliably separates these three species. This procedure utilizes the sequence variation in the ribosomal DNA ITS1 and demonstrates species-specific PCR-RFLP profiles from both colony and field collected material. Assessment of the consistency of this procedure was undertaken on mosquitoes sampled from a wide geographic area including Australia, PNG, and the Solomon Islands. Overlapping adult morphology was observed for Cx. annulirostris and Cx. palpalis in both northern Queensland and PNG and for all three species at one site in northwest Queensland.

Animals↗

[Gene rearrangement studies in Hashimoto's thyroiditis and primary lymphoma of thyroid].

OBJECTIVE: To study the immunoglobulin gene rearrangement patterns in Hashimoto's thyroiditis (HT) and primary thyroid lymphoma (PTL), and to analyze the relationship between the two diseases. METHODS: Formalin-fixed and paraffin-embedded tissues of 11 cases of PTL and 38 cases of HT as well as their clinical data, were retrieved. The latter group was further subcategorized into classic HT and suspicious PTL. Gene rearrangement studies for immunoglobulin heavy chains and light chains were carried out by polymerase chain reaction (PCR) using VH, FR3A and FR3kappa primers. RESULTS: There was an increasing trend in immunoglobulin gene rearrangement rate for classic HT (10.7%), suspicious PTL (40.0%) and PTL (72.7%) groups. In general, a female predilection was observed. This sex predilection however was less obvious in the PTL group. There was no relationship between serum antibody (both thyroglobulin and thyroid peroxidase) titers and gene rearrangement patterns. CONCLUSIONS: HT and PTL show morphologic overlaps and may not be clearly distinguished on the basis of light microscopy alone. PCR-based immunoglobulin gene rearrangement study may be helpful in the detection of cases with early lymphomatous transformation of HT.

Female↗

Species specific identification of the Neofabraea pathogen complex associated with pome fruits using PCR and multiplex DNA amplification.

Five species of pathogenic fungi belong to Neofabraea. One of these, N. krawtzewii (syn. N. populi), is responsible for bark lesions on poplar (Populus) trees. The other four species cause post-harvest bull's eye rot of pome fruits, and at least two of these also cause bark cankers on pome fruit trees. Morphological variation among these species is slight, and overlap in geographic range sometimes occurs. As a consequence, identification based on conventional criteria can be tenuous. PCR primers with putative species specificity were developed following genetic analysis of the beta-tubulin gene for isolates of each of the five species of Neofabraea. PCR conditions required to achieve specificity of the primer sets were determined, and a multiplex PCR protocol was developed to optimize their diagnostic utility on apple fruits. A protocol with higher annealing temperatures in the initial PCR cycles followed by lower temperatures in later cycles gave complete species-specificity when the primer sets were used individually and in multiplex, resulting in successful detection of the pathogens from axenic culture and infected apple fruits.

Ascomycota↗

The cDNA-derived amino acid sequence of hemoglobin I from Lucina pectinata.

The tropical clam Lucina pectinata contains a unique hemoglobin (HbI) which serves to transport H2S to autotrophic bacteria. The cDNA-derived amino acid sequence was obtained from overlapping clones containing the cDNA that codes for HbI. The reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) methods were employed to synthesize the cDNA fragments. An initial 354-bp cDNA clone encoding 118 amino acid residues of HbI was amplified from total RNA by RT-PCR using degenerate oligonucleotides. Gene-specific primers derived from the HbI-partial cDNA sequence were used for obtaining the 5' and 3' ends of the cDNA by RACE. The length of the HbI cDNA, estimated from sequence analysis of overlapping clones, was 1322 bp for the full-length cDNA. The coding region of the full-length cDNA codes for 143 amino acid residues. The most conserved amino acid residues in HbI from Lucina pectinata were identified by a multiple alignment with nonvertebrate globin sequences.

Amino Acid Sequence↗

Adaptation of the interspersed repetitive sequence polymerase chain reaction to the isolation of mouse DNA probes from somatic cell hybrids on a hamster background.

A strategy for the rapid isolation of DNA probes from radiation-fusion Chinese hamster cell hybrids containing overlapping portions of the murine X chromosome based on the interspersed repetitive sequence polymerase chain reaction (IRS-PCR) previously used with human somatic cell hybrids has been developed. This specific amplification of mouse DNA on a hamster background depends on the use of primers directed to the B2 short interspersed repeat element family and the R repeat, from the long interspersed repeat element family, L1. Two sets of amplification conditions, which gave specific amplification of mouse DNA from either a mouse X-monochromosomal hybrid or irradiation-fusion hybrids having reduced X content, were defined. The mouse X-only chromosome hybrid yielded approximately 20 discrete reproducible bands, while the irradiation-fusion hybrids yielded between 1 and 10 discrete products. Comparison of different irradiation-fusion hybrids has allowed the definition of both specific and shared products corresponding to different regions within the overlapping X-chromosome fragments present within these hybrids. Use of such hybrids and the IRS-PCR technique has allowed the isolation of probes corresponding to the central region of the mouse X chromosome that contains the X-inactivation center. The method should be widely applicable to the isolation of mouse DNA sequences from mouse hybrid cell lines on either human or Chinese hamster backgrounds.

Animals↗

Functional type I PTH/PTHrP receptor in freshly isolated newborn rat keratinocytes: identification by RT-PCR and immunohistochemistry.

The presence of identical or distinct type I parathyroid hormone (PTH)/parathyroid hormone-related peptide (PTHrP) receptors in keratinocytes is still a matter of debate. We studied the expression and functionality of PTHrP receptors in freshly isolated keratinocytes from newborn rat skin. Four overlapping primers, amplifying different regions in the rat PTH receptor, were used for reverse transcriptase-polymerase chain reaction (RT-PCR). The first region corresponded to the N-terminal extracellular region and the first transmembrane domain (S/M1), the second region amplified the connecting intracellular and extracellular loops transmembrane domain (E2/M5), the third spanned the range from the transmembrane to the intracellular domain (M4/T), and the fourth region amplified the C-terminal tail (M6/7/T). The PCR products from the keratinocyte RNA were identical to those from kidney RNA of the same rats. The cloned four transcripts showed 100% of homologies with the cDNA sequence from bone ROS cells. Keratinocytes, freshly isolated or present in situ in the epidermis, recognized an anti-PTH receptor antibody (PTH-II) directed against the receptor extracellular domain. Western blotting showed the same protein patterns in keratinocytes, kidney, and ROS cell extracts. Low doses of PTHrP(1-34) (10(-12)-10(-9) M) increased the cell number studied by [3H]thymidine incorporation and DNA content. Treatment with the PTH/PTHrP receptor antagonist [Asn10, Leu11, D Trp12] PTHrP(7-34) or two different PTH receptor antibodies inhibited the increase in cell proliferation induced by PTHrP(1-34). All these findings indicate that newborn rat epidermis and keratinocytes express functional PTHrP receptors, which are identical to type I PTH/PTHrP receptor and are recognized by PTHrP(1-34).

Animals↗

A long distance RT-PCR able to amplify the Pestivirus genome.

A method to amplify long genomic regions (up to approximately 12.3 kb) from pestiviruses in one RT-PCR is described. The difficulty in designing conserved Pestivirus primers for the amplification of genomes from highly divergent isolates simply by means of overlapping segments is demonstrated using new bioinformatic tools. An alternative procedure consisting of optimizing the length of the genomic cDNA fragments and their subsequent amplification by polymerase chain reaction (PCR) using a limited set of specific primers is described. The amplification of long DNA fragments from a variety of sources, including genomic, mitochondrial, and viral DNAs as well as cDNA produced by reverse transcription (RT) has been achieved using this methodology, known as long distance PCR. In the case of viruses, it is necessary to obtain viral particles from infected cells prior to RT procedures. This work provides improvements in four steps of long distance RT-PCR (L-RT-PCR): (i) preparation of a viral stock, (ii) preparation of template RNA, (iii) reverse transcription and (iv) amplification of the cDNA by LD-PCR. The usefulness of L-RT-PCR is discussed in the light of current knowledge on pestivirus diversity. The genomic sequence of Singer_Arg reference strain obtained using this method is presented and characterized.

Animals↗

PCR Sampling of disease resistance-like sequences from a disease resistance gene cluster in soybean.

Clusters of Resistance-like genes (RLGs) have been identified from a variety of plant species. In soybean, RLG-specific primers and BAC-fingerprinting were used to develop a contig of overlapping BACs for a cluster of RLGs on soybean linkage group J. The resistance genes Rps2 ( Phytophthora stem and root rot) and Rmd-c (powdery mildew) and the ineffective nodulation gene Rj2 were previously mapped to this region of linkage group J. PCR hybridization was used to place two TIR/NBD/LRR cDNAs on overlapping BACs from this contig. Both of the cDNAs were present on BAC 34P7. Fingerprinting of this BAC suggested as many as twelve different RLGs were present. Given the high nucleotide identity shared between cDNAs LM6 and MG13 (>90%), direct sequencing of this region would be difficult. More sequence information was needed about the RLGs within this region before sequencing could be undertaken. By comparing the genomic sequences of cDNAs LM6 and MG13 we identified conserved regions from which oligonucleotide primers specific to BAC 34P7 RLGs could be designed. The nine primer pairs spanned the genomic sequence of LM6 and produced overlapping RLG products upon amplification of BAC 34P7. Amplification products from 12 different RLGs were identified. On average, nucleotide identity between RLG sequences was greater than 95%. Examination of RLG sequences also revealed evidence of additions, deletions and duplications within targeted regions of these genes. Using previously mapped cDNAs we were able to quickly and inexpensively access multiple RLGs within a single specific cluster.

Journal Article↗

[Cloning and sequencing of a Chinese complete TTV gene].

OBJECTIVE: To obtain the complete TT virus gene from a Chinese isolate. METHODS: Long-PCR was performed for amplifying the TTV gene from the serum of a Chinese with non-A to non-G hepatitis. Three overlapped DNA fragments were obtained, which contained 199 bp (1-199), 3 269 bp (38 approximately 3 306) and 434 bp (3 306 approximately 3 739) separately. These PCR products were sequenced by the standard method. RESULTS: The complete TTV gene (named as TTV CHN1) consisting of 3 739 nucleotides contained two ORFs. The first ORF located at 589 approximately 2 901 nt, coding 770 amino acids; the second located at 107 approximately 715 nt, coding 202 amino acids. In this genome, G is 22.25%, C 25.54%, A 31.26% and T 20.97%. The homology of Chinese and Japanese TTV genes was more than 94% at both nucleotide and amino acid levels. There exists a hyper-variation region (HVR) spanning at 1 380 approximately 1 800 bp. In this region, the HVR homology of Chinese and Japanese TTV genes was 88% and 81% at nucleotide and amino acid levels, respectively. CONCLUSION: Chinese and Japanese TTV isolates belong to the same genotype. There exists a hyper-variation region (HVR) spanning at 1 380 approximately 1 800 bp.

Amino Acid Sequence↗

A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment.

A genomic 38 kbp segment on the c1750 cosmid clone containing the cdc2 gene, located in the left arm of chromosome II from Schizosaccharomyces pombe, was sequenced. The segment was found to have five previously known genes, pht1, cdc2, his3, act1 and mei4. Among 11 coding sequences (CDSs) predicted by the gene finding software INTRON.PLOT., four CDSs, pi007, pi010, pi014 and pi016, had considerable similarity to 40S ribosomal protein, glycosyltransferase, cdc2-related protein kinase and alpha-1, 2-mannosyltransferase, respectively. Another unusually huge open reading frame (ORF) (pi011), consisting of 2233 amino acids, existed, having significant homology to alpha-amylase, granule-bound glycogen synthase and the Sz. pombe YS 1110 clone product at the N-terminal, middle and C-terminal regions, respectively. All the predicted 11 CDSs were experimentally analysed by RACE PCR. The sequencing of the RACE products revealed that there were two small overlaps at the 3' untranslated regions (UTRs) between pi004 and pi005 (17 bp) and between pi007 and pi008 (2 bp). The distances between 5' end of the 5'UTR and the putative translation initiation codon varied from 10 to 302 nucleotides (nt) among the nine CDSs successfully analysed by 5'-RACE. The expression level of each CDS on this clone was determined. Among the 16 genes on this clone, the previously determined genes, pht1, cdc2, his3 and act1, were found to be most highly expressed. Finally, cDNAs of all the newly identified genes were detected by RACE, proving the actual expression of these genes. The nucleotide sequence has been submitted to the EMBL database under Accession No. AB004534.

Base Sequence↗

Extensive analysis of the 13q14 region in human prostate tumors: DNA analysis and quantitative expression of genes lying in the interval of deletion.

BACKGROUND: Loss of heterozygosity (LOH) on chromosome arm 13q14 is one of the most consistent genetic alterations in sporadic prostate cancer. This alteration may be involved in prostate oncogenesis through inactivation of one or more tumor suppressor genes (TSGs). Candidate gene expression is an approach to focus the search for TSGs in this region. METHODS: We tested 41 human sporadic prostate tumors for 13q14 LOH by using seven polymorphic markers overlapping the critical region and used a real-time quantitative RT-PCR assay to study the same tumors for expression of the 31 genes located in this genomic region (localized by the Human Genome Project Working Draft). RESULTS: Allelic loss on at least one locus was found in 18 (41%) of the 41 tumor DNAs. Only four genes (ITM2B, CHC1L, KIAA0970, and LOC51131), located in the region most frequently deleted in prostate carcinoma, showed a significant difference in expression between normal and neoplastic prostate tissues. CONCLUSIONS: Given their location in the LOH hotspot, as indicated by our genomic analysis, ITM2B, CHC1L, KIAA0970, and LOC51131 are candidate tumor suppressor genes in this region. ITM2B that showed a significant association (P < 0.005) between expression and LOH at the corresponding locus could, furthermore, be the main target of the observed LOH at 13q in prostate tumors.

Adenocarcinoma↗

An 800-kb region of deletion at 13q14 in human prostate and other carcinomas.

Deletions of regions at 13q14 have been detected by various genetic approaches in human cancers including prostate cancer. Several studies have defined one region of loss of heterozygosity (LOH) at 13q14 that seems to reside in a DNA segment of 7.1 cM between genetic markers D13S263 and D13S153. To define the smallest region of overlap (SRO) for deletion at 13q14, we first applied tissue microdissection and multiplex PCR to detect homozygous deletion and/or hemizygous deletion at 13q14 in 134 prostate cancer specimens from 114 patients. We detected deletions at markers D13S1227, D13S1272, and A005O48 in 13 (10%) of these tumor specimens. Of the 13 tumors with deletions, 12 were either poorly differentiated primary tumors or metastases of prostate cancer. To fine-map the deletion region, we then constructed a high-resolution YAC/BAC/STS/EST physical map based on experimental and database analyses. Several markers encompassing the deletion region were analyzed for homozygous deletion and/or hemizygous deletion in 61 cell lines/xenografts derived from human cancers of the prostate, breast, ovary, endometrium, cervix, and bladder, and a region of deletion was defined by duplex PCR assay between markers A005X38 and WI-7773. We also analyzed LOH at 13q14 in the 61 cell lines/xenografts using the homozygosity mapping of deletion approach and 26 microsatellite markers. We found 24 (39%) of the cell lines/xenografts to show LOH at 13q14 and defined a region of LOH by markers M1 and M5. Combination of homozygous or hemizygous deletion and LOH results defined the SRO for deletion to be an 800-kb DNA interval between A005X38 and M5. There are six known genes located in or close to the SRO for deletion. This region of deletion is at least 2 Mb centromeric to the RB1 tumor-suppressor gene and the leukemia-associated genes 1 and 2, each of which is located at 13q14. These data suggest that the 800-kb DNA segment with deletion contains a gene whose deletion may be important for the development of prostate and other cancers. This study also provides a framework for the fine-mapping, cloning, and identification of a novel tumor-suppressor gene at 13q14.

Adult↗