The neutral theory and natural selection in the HLA region

Based on available DNA sequence data in the HLA region of 4 Mb, we review the degree of polymorphism at 39 loci of which most are involved in the immune system. The extent of nucleotide differences per silent site differs greatly from locus to locus. It is exceptionally high at classical MHC loci, intermediate at six MHC-related pseudogenes as well as at some loci in class I and II regions, and low in the class III region. Different exons of individual MHC loci show also different degrees of silent polymorphism; high in the exons encoding for the peptide binding region (PBR) and low in the exons encoding for trans-membranes and cytoplasmic tails. The degree of polymorphism within MHC allelic lineages is not much smaller than that between allelic lineages, contrary to the expectation where intra-allelic sequence exchanges are restricted. The observation that many allelic lineages at the HLA-DRB1 locus are combinations of distinct motifs in the beta pleated sheet and alpha helix of PBR indicates that sequence exchanges occur even within exon 2. Semi-quantitative analysis is presented about the rate of sequence exchanges between selected and linked neutral regions, although more sequence information is necessary to make definite conclusions. The extraordinary MHC polymorphism is viewed from the dual function of MHC molecules that controls the acquired immune system

Divergence, demography and gene loss along the human lineage

Genomic DNA sequences are an irreplaceable source for reconstructing the vanished past of living organisms. Based on updated sequence data, this paper summarizes our studies on species divergence time, ancient population size and functional loss of genes in the primate lineage leading to modern humans (Homo sapiens sapiens). The inter- and intraspecific comparisons of DNA sequences suggest that the human lineage experienced a rather severe bottleneck in the Middle Pleistocene, throughout which period the subdivided African population played a predominant role in shaping the genetic architecture of modern humans. Also, published and newly identified human-specific pseudogenes (HSPs) are enumerated in order to infer their significance for human evolution. Of the 121 candidate genes obtained, authentic HSPs turn out to comprise only 25 olfactory receptor genes, four T cell receptor genes and nine other genes. The fixation of HSPs has been too rare over the past 6–7 Myr to account for species differences between humans and chimpanzees

Frequent gene conversion events between the X and Y homologous chromosomal regions in primates

<p>Abstract</p> <p>Background</p> <p>Mammalian sex-chromosomes originated from a pair of autosomes. A step-wise cessation of recombination is necessary for the proper maintenance of sex-determination and, consequently, generates a four strata structure on the X chromosome. Each stratum shows a specific per-site nucleotide sequence difference (<it>p-</it>distance) between the X and Y chromosomes, depending on the time of recombination arrest. Stratum 4 covers the distal half of the human X chromosome short arm and the <it>p</it>-distance of the stratum is ~10%, on average. However, a 100-kb region, which includes <it>KALX </it>and <it>VCX</it>, in the middle of stratum 4 shows a significantly lower <it>p</it>-distance (1-5%), suggesting frequent sequence exchanges or gene conversions between the X and Y chromosomes in humans. To examine the evolutionary mechanism for this low <it>p</it>-distance region, sequences of a corresponding region including <it>KALX</it>/<it>Y </it>from seven species of non-human primates were analyzed.</p> <p>Results</p> <p>Phylogenetic analysis of this low <it>p</it>-distance region in humans and non-human primate species revealed that gene conversion like events have taken place at least ten times after the divergence of New World monkeys and Catarrhini (<it>i.e</it>., Old World monkeys and hominoids). A <it>KALY</it>-converted <it>KALX </it>allele in white-handed gibbons also suggests a possible recent gene conversion between the X and Y chromosomes. In these primate sequences, the proximal boundary of this low <it>p</it>-distance region is located in a <it>LINE </it>element shared between the X and Y chromosomes, suggesting the involvement of this element in frequent gene conversions. Together with a palindrome on the Y chromosome, a segmental palindrome structure on the X chromosome at the distal boundary near <it>VCX</it>, in humans and chimpanzees, may mediate frequent sequence exchanges between X and Y chromosomes.</p> <p>Conclusion</p> <p>Gene conversion events between the X and Y homologous regions have been suggested, mainly in humans. Here, we found frequent gene conversions in the evolutionary course of primates. An insertion of a <it>LINE </it>element at the proximal end of the region may be a cause for these frequent conversions. This gene conversion in humans may also be one of the genetic causes of Kallmann syndrome.</p

Genomic structure and evolution of multigene families: “Flowers” on the human genome

We report the results of an extensive investigation of genomic structures in the human genome, with a particular focus on relatively large repeats (>50 kb) in adjacent chromosomal regions. We named such structures “Flowers” because the pattern observed on dot plots resembles a flower. We detected a total of 291 Flowers in the human genome. They were predominantly located in euchromatic regions. Flowers are gene-rich compared to the average gene density of the genome. Genes involved in systems receiving environmental information, such as immunity and detoxification, were overrepresented in Flowers. Within a Flower, the mean number of duplication units was approximately four. The maximum and minimum identities between homologs in a Flower showed different distributions; the maximum identity was often concentrated to 100% identity, while the minimum identity was evenly distributed in the range of 78% to 100%. Using a gene conversion detection test, we found frequent and/or recent gene conversion events within the tested Flowers. Interestingly, many of those converted regions contained protein-coding genes. Computer simulation studies suggest that one role of such frequent gene conversions is the elongation of the life span of gene families in a Flower by the resurrection of pseudogenes

The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius

It is postulated that chickens (Gallus gallus domesticus) became domesticated from wild junglefowls in Southeast Asia nearly 10,000 years ago. Based on 19 individual samples covering various chicken breeds, red junglefowl (G. g. gallus), and green junglefowl (G. varius), we address the origin of domestic chickens, the relative roles of ancestral polymorphisms and introgression, and the effects of artificial selection on the domestic chicken genome. DNA sequences from 30 introns at 25 nuclear loci are determined for both diploid chromosomes from a majority of samples. The phylogenetic analysis shows that the DNA sequences of chickens, red and green junglefowls formed reciprocally monophyletic clusters. The Markov chain Monte Carlo simulation further reveals that domestic chickens diverged from red junglefowl 58,000±16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci

Efficacy and safety of garenoxacin tablets on clinically diagnosed atypical pneumonia: Postmarketing surveillance in Japan

We performed a postmarketing surveillance study to determine the efficacy and safety of the oral quinolone antibacterial agent garenoxacin (Geninax R Tablets 200 mg) against atypical pneumonia. Between October 2009 and July 2011, patients with community-acquired pneumonia visited 26 facilities in Japan; we collected survey forms from 105 of these patients who were suspected of having atypical pneumonia based on the Japanese Respiratory Society Guidelines for the Management of Community-Acquired Pneumonia in Adults. We examined the safety in 105 patients and the efficacy in 71 patients. 1. The efficacy rates among patients suspected of having atypical pneumonia and those with a confirmed diagnosis of atypical pneumonia were 94.8% (55/58 patients) and 92.3% (12/13 patients), respectively. The efficacy rate was 4/4 for patients in whom Chlamydophila pneumoniae was detected (including 1 patient with a polymicrobial infection with another bacterial strain) and 90% (9/10 patients) for patients in whom Mycoplasma pneumoniae was detected (garenoxacin was ineffective in 1 of 2 patients with a polymicrobial infection with another bacterial strain). 2. The incidence of adverse drug reactions (including abnormal laboratory tests) was 4.8% (5/105 patients). Among the adverse drug reactions, gastrointestinal disorders, infection and infestation, nervous system disorder, and skin and subcutaneous tissue disorder were observed in 2.9% of patients (3/105), 1.0% (1/105), 1.0% (1/105), and 1.0% (1/105), respectively. In conclusion, garenoxacin showed an efficacy rate of greater than 90% for suspected atypical pneumonia and confirmed atypical pneumonia. Garenoxacin is considered to be useful in daily practice

Methylation of the KEAP1 gene promoter region in human colorectal cancer

<p>Abstract</p> <p>Background</p> <p>The Keap1-Nrf2 pathway has been reported to be impaired in several cancers. However, the status of Keap1-Nrf2 system in human colorectal cancer (CRC) has not been elucidated.</p> <p>Methods</p> <p>We used colorectal cancer (CRC) cell lines and surgical specimens to investigate the methylation status of the <it>KEAP1 </it>promoter region as well as expression of Nrf2 and its downstream antioxidative stress genes, <it>NQO-1 </it>and <it>AKR1C1</it>.</p> <p>Results</p> <p>DNA sequencing analysis indicated that all mutations detected were synonymous, with no amino acid substitutions. We showed by bisulfite genomic sequencing and methylation-specific PCR that eight of 10 CRC cell lines had hypermethylated CpG islands in the <it>KEAP1 </it>promoter region. HT29 cells with a hypermethylated <it>KEAP1 </it>promoter resulted in decreased mRNA and protein expression but unmethylated Colo320DM cells showed higher expression levels. In addition, treatment with the DNA methyltransferase inhibitor 5-Aza-dC combined with the histone deacetylase inhibitor trichostatin A (TSA) increased <it>KEAP1 </it>mRNA expression. These result suggested that methylation of the <it>KEAP1 </it>promoter regulates its mRNA level. Time course analysis with the Nrf2-antioxidant response element (ARE) pathway activator t-BHQ treatment showed a rapid response within 24 h. HT29 cells had higher basal expression levels of <it>NQO-1 </it>and <it>AKR1C1 </it>mRNA than Colo320DM cells. Aberrant promoter methylation of <it>KEAP1 </it>was detected in 53% of tumor tissues and 25% of normal mucosae from 40 surgical CRC specimens, indicating that cancerous tissue showed increased methylation of the <it>KEAP1 </it>promoter region, conferring a protective effect against cytotoxic anticancer drugs.</p> <p>Conclusion</p> <p>Hypermethylation of the <it>KEAP1 </it>promoter region suppressed its mRNA expression and increased nuclear Nrf2 and downstream ARE gene expression in CRC cells and tissues.</p

Evolutionary origin of peptidoglycan recognition proteins in vertebrate innate immune system

<p>Abstract</p> <p>Background</p> <p>Innate immunity is the ancient defense system of multicellular organisms against microbial infection. The basis of this first line of defense resides in the recognition of unique motifs conserved in microorganisms, and absent in the host. Peptidoglycans, structural components of bacterial cell walls, are recognized by Peptidoglycan Recognition Proteins (PGRPs). PGRPs are present in both vertebrates and invertebrates. Although some evidence for similarities and differences in function and structure between them has been found, their evolutionary history and phylogenetic relationship have remained unclear. Such studies have been severely hampered by the great extent of sequence divergence among vertebrate and invertebrate PGRPs. Here we investigate the birth and death processes of PGRPs to elucidate their origin and diversity.</p> <p>Results</p> <p>We found that (i) four rounds of gene duplication and a single domain duplication have generated the major variety of present vertebrate PGRPs, while in invertebrates more than ten times the number of duplications are required to explain the repertoire of present PGRPs, and (ii) the death of genes in vertebrates appears to be almost null whereas in invertebrates it is frequent.</p> <p>Conclusion</p> <p>These results suggest that the emergence of new <it>PGRP </it>genes may have an impact on the availability of the repertoire and its function against pathogens. These striking differences in PGRP evolution of vertebrates and invertebrates should reflect the differences in the role of their innate immunity. Insights on the origin of <it>PGRP </it>genes will pave the way to understand the evolution of the interaction between host and pathogens and to lead to the development of new treatments for immune diseases that involve proteins related to the recognition of self and non-self.</p