Genetic diversity within and between tandemly arrayed copies of the Gp63 gene occurs in laboratory isolates of
Leishmania spp., but the extent to which this represents natural genetic diversity has ...not been assessed. Here, the Gp63 locus is examined in 58 fresh isolates of
L. peruviana, and clones derived from them, collected throughout the Peruvian Andes. Extensive polymorphism is observed, both in size of Gp63 containing chromosomes, and for restriction-fragment-length polymorphisms (RFLPs) at the Gp63 locus. All clones within an isolate are identical, including those with two distinct Gp63-hybridising chromosomal-sized pulsed-field gel electrophoresis (PFGE) bands, consistent with diploidy but with size differences in homologous chromosomes. For RFLP analysis, three enzymes were selected to cut within the coding region (
PstI), in the intergenic region (
SalI) and outside (
EcoRI) the Gp63 gene cluster.
PstI gave identical banding patterns across all isolates/clones. For
EcoRI and
SalI, all clones within an isolate were identical, but isolates were polymorphic for fragments at 13 (2–30 kb) and 8 (2.6–8.8 kb) different molecular mass locations generating 19 and 16 distinct RFLP patterns or genotypes for each enzyme, respectively.
EcoRI restriction patterns, analysed by PFGE, were consistent with the presence of two clusters of Gp63 genes on each homologous chromosome, one contained within
EcoRI fragments large enough to carry from 3 to 10 copies of the Gp63 gene, the second on fragments which could carry 1 or 2 copies of the gene.
SalI patterns indicated variable restriction sites within clusters, but not within every intergenic region. A hierarchical analysis of variance of allele frequencies, expressed in terms of Wright's
F-statistic, indicated significant barriers to gene flow at all levels, valleys within regions (north/south), villages within valleys, and individuals within villages. This extreme polymorphism at the Gp63 locus of
L. peruviana demonstrates the great potential for generation of genetic diversity in parasite populations.
The generation of expressed sequence tags (ESTs) has proven to be an efficient method for gene identification and classification in protozoan parasites such as Plasmodium falciparum, Trypanosoma ...brucei and Toxoplasma gondii. The presence of a 5' spliced-leader sequence on most trypanosomatid mRNAs and some nematode mRNAs has been used to identify the 5' terminus in some cDNAs from a conventional cDNA library and to construct a spliced-leader cDNA library. Here we report an EST analysis of a directionally cloned, full-length, spliced-leader cDNA constructed from promastigotes of Leishmania major.
Abstract
Background
Serrated polyps are recognized as precursors of colorectal cancer in general population and have recently been reported in patients with ulcerative colitis (UC). However, their ...prevalence and detailed characteristics remain unclear.
Methods
The prevalence and clinicopathological and biological characteristics of serrated polyps in patients with UC were retrospectively examined in a single tertiary inflammatory bowel disease centre in Japan from 2000 to 2020.
Results
In total, 252 neoplasms, including 36 serrated polyps (26 in colitis-affected segments, 10 in colitis-unaffected segments), were identified in 187 patients with UC. The proportion of serrated polyps was significantly higher from 2010 to 2020 (35/213, 17%) than from 2000 to 2009 (1/39, 3%; p = 0.023). Serrated polyps in colitis-affected segments were common in patients with extensive colitis (88%), a history of persistent active colitis (58%), and a long duration of UC (12.1 years). Serrated polyps in colitis-affected segments were more common in men (88%). Of 26 serrated polyps in colitis-affected segments, 15, 6, and 5 were categorized as sessile serrated lesion (SSL)-like dysplasia, traditional serrated adenoma (TSA)-like dysplasia, and serrated dysplasia not otherwise specified (SD NOS), respectively. SSL-like dysplasia was common in the proximal colon (67%) and with BRAF mutation (62%), whereas TSA-like dysplasia and SD NOS were common in the distal colon (100% and 80%) and with KRAS mutations (100% and 75%). CpG island hypermethylation phenotype-positive status was observed in 60% cases of TSA-like dysplasia but in only 25% cases of SSL-like dysplasia and SD NOS.
Conclusion
Serrated polyps have recently been increasing in patients with UC. Serrated polyps in colitis-affected segments were common in men with extensive and longstanding colitis, suggesting that chronic inflammation is involved in the development of serrated polyps in patients with UC.
Restriction-map variation was studied in 126 copies of the G6pd region in X chromosome lines of Drosophila melanogaster from North America, Europe, and Africa. Special attention was focused on the ...distribution of variation relative to the geographically variable polymorphism for two electrophoretic variants. Nucleotide heterozygosity as determined by eight six-cutter restriction enzymes for the 13-kb region is estimated, on the basis of the worldwide sample, to be 0.065%, which is the lowest value reported for any comparable region in the D. melanogaster genome. Significant linkage disequilibrium between electrophoretic alleles and restriction-site variation is observed for several sites. In contrast to published studies of other genetic regions, there are large insertions that reach significant frequencies and are found across considerable geographic distances. There is a clustering of this variation inside the first large intervening sequence of the G6PD gene.
We present a strategy for assembling a physical map of the genome of Drosophila melanogaster based on yeast artificial chromosomes (YACs). In this paper we report 500 YACs containing inserts of ...Drosophila DNA averaging 200 kb that have been assigned positions on the physical map by means of in situ hybridization with salivary gland chromosomes. The cloned DNA fragments have randomly sheared ends (DY clones) or ends generated by partial digestion with either NotI (N clones) or EcoRI (E clones). Relative to the euchromatic portion of the genome, the size distribution and genomic positions of the clones reveal no significant bias in the completeness or randomness of genome coverage. The 500 mapped euchromatic clones contain an aggregate of approximately 100 million base pairs of DNA, which is approximately one genome equivalent of Drosophila euchromatin.
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has ...an unusual population structure dominated by three clonal lineages that predominate in North America and Europe, (Types I, II, and III). These lineages were founded by common ancestors approximately10,000 yr ago. The recent origin and widespread distribution of the clonal lineages is attributed to the circumvention of the sexual cycle by a new mode of transmission-asexual transmission between intermediate hosts. Asexual transmission appears to be multigenic and although the specific genes mediating this trait are unknown, it is predicted that all members of the clonal lineages should share the same alleles. Genetic mapping studies suggested that chromosome Ia was unusually monomorphic compared with the rest of the genome. To investigate this further, we sequenced chromosome Ia and chromosome Ib in the Type I strain, RH, and the Type II strain, ME49. Comparative genome analyses of the two chromosomal sequences revealed that the same copy of chromosome Ia was inherited in each lineage, whereas chromosome Ib maintained the same high frequency of between-strain polymorphism as the rest of the genome. Sampling of chromosome Ia sequence in seven additional representative strains from the three clonal lineages supports a monomorphic inheritance, which is unique within the genome. Taken together, our observations implicate a specific combination of alleles on chromosome Ia in the recent origin and widespread success of the clonal lineages of T. gondii.
Towards a Drosophila genome map Hartl, D L; Ajioka, J W; Cai, H ...
Trends in genetics,
02/1992, Letnik:
8, Številka:
2
Journal Article
Recenzirano
A physical map of the genome of Drosophila melanogaster has been created using 965 yeast artificial chromosome (YAC) clones assigned to locations in the cytogenetic map by in situ hybridization with ...the polytene salivary gland chromosomes. Clones with insert sizes averaging about 200 kb, totaling 1.7 genome equivalents, have been mapped. More than 80% of the euchromatic genome is included in the mapped clones, and 75% of the euchromatic genome is included in 161 cytological contigs ranging in size up to 2.5 Mb (average size 510 kb). On the other hand, YAC coverage of the one-third of the genome constituting the heterochromatin is incomplete, and clones containing long tracts of highly repetitive simple satellite DNA sequences have not been recovered.
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