No abstract available.
Genome* ; Humans* ; Pan troglodytes*

An increasing number of primate genomes are being sequenced. A direct comparison of repeat elements in human genes and their corresponding chimpanzee orthologs will not only give information on their evolution, but also shed light on the major evolutionary events that shaped our species. We have developed REPEATOME to enable visualization and subsequent comparisons of human and chimpanzee repeat elements. REPEATOME (http://www.repeatome.org/) provides easy access to a complete repeat element map of the human genome, as well as repeat element-associated information. It provides a convenient and effective way to access the repeat elements within or spanning the functional regions in human and chimpanzee genome sequences. REPEATOME includes information to compare repeat elements and gene structures of human genes and their counterparts in chimpanzee. This database can be accessed using comparative search options such as intersection, union, and difference to find lineage-specific or common repeat elements. REPEATOME allows researchers to perform visualization and comparative analysis of repeat elements in human and chimpanzee.
Genome ; Genome, Human ; Humans* ; Pan troglodytes* ; Primates

OBJECTIVETo understand the genetic polymorphism and population difference of locus DYF155S1 on human Y chromosome.

METHODSUsing minisatellite variant repeat mapping-polymerase chain reaction (MVR-PCR), automated fluorescence detection, DNA sequence analysis, the authors studied the locus DYF155S1 of two chimpanzee and 10 human subjects from each of the following 8 groups: Northern China Hans, Southern China Hans, the Zang (Tibetan) nationality, the Uighur nationality, Japanese, Korean, Black African, White African.

RESULTSIn this study, loci DYF155S1 and DYF155S2 have been detected. There is no difference in all of the samples on the locus DYF155S2; each sample contains one type 4 repeat unit, which is the ancestor gene of locus DYF155S1. On locus DYF155S1, each individual has its specific DNA sequence. The arrangement of the repeat units differs greatly in races: arrangement 3134 in the yellow race, arrangement 134 in the white race, and arrangement null3a1a4a4 in the black race were most common. The average number of the type 4 repeat unit in the white race is much higher than that in the yellow race. The authors also found two new types of repeat unit: type 6 and type 7. Type 6 is the result of the T22A substitution on type 1, which was observed in Japanese (3 samples). Type 7 is resulted from the T22A substitution on type 3, which was observed in the Zang nationality (4 samples), Southern China Hans(1 sample), and Korean (1 sample).

CONCLUSIONLocus DYF155S1 has great genetic polymorphism and obvious population difference. Its significance should receive more attention in forensic science and human genetics research.

The comparative analysis of the human and primate genomes including the chimpanzee can reveal unique types of information impossible to obtain from comparing the human genome with the genomes of other vertebrates. PrimateDB is an open depository server that provides primate genome information for the comparative genome research. The database also provides an easy access to variable information within/between the primate genomes and supports analyzed information, such as annotation and retroelements and phylogeny. The comparative analyses of more primate genomes are also being included as the long-term objective.
Genome* ; Genome, Human ; Humans ; Pan troglodytes ; Phylogeny ; Primates* ; Retroelements ; Vertebrates

More and more new human enteroviruses (HEVs) types were identified with the broad application of the molecular serotyping methods for enteroviruses. Since enterovirus 71 (EV71) was first reported in 1969, numerous epidemic outbreaks associated with new enteroviruses have occurred all around the world, and pose a significant threat to public health . The epidemics of hand, foot and mouth disease (HFMD) caused by EV71 infection in China have raised great concern of global scholars. This paper reviewed research progress in recent years of the molecular typing, evolution, epidemiology, and pathogenesis attributable to new enterovirus types.
Animals ; Enterovirus ; classification ; genetics ; isolation & purification ; Enterovirus Infections ; veterinary ; virology ; Haplorhini ; Humans ; Pan troglodytes ; Phylogeny ; Primate Diseases ; virology

Comparing 231 genes on chimpanzee chromosome 22 with their orthologous on human chromosome 21, we have found that 15 orthologs have indels within their coding sequences. It was rather surprising that significant number of genes have changed by indel, despite the shorter time since their divergence and led us hypothesize that indels and structural changes may represent one of the major mechanism of proteome evolution in the higher primates. Human T-complex protein 10 like (TCP10L) is a representative having indel within its coding sequence. Gene structure of human TCP10L compared with chimpanzee TCP10L gene showed 16 base pair difference in genomic DNA. As a result of the indel, frame shift mutation occurs in coding sequence (CDS) and human TCP10L express longer polypeptide of 21 amino acid residues than that of chimpanzee. Our prediction found that the indel may affect to dramatic change of secondary protein structure between human and chimpanzee TCP10L. Especially, the structural changes in the C-terminal region of TCP10L protein may affect on the interacting potential to other proteins rather than DNA binding function of the protein. Through these changes, TCP10L might influence gene expression profiles in liver and testis and subsequently influence the physiological changes required in primate evolution.
Base Pairing ; Chromosomes, Human ; Chromosomes, Human, Pair 22 ; Clinical Coding ; DNA ; Frameshift Mutation ; Genomics* ; Humans* ; Liver ; Pan troglodytes* ; Primates ; Protein Structure, Secondary ; Proteome ; Testis ; Transcriptome

Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.
Alu Elements ; Coat Protein Complex I ; DNA ; DNA Transposable Elements ; Endogenous Retroviruses ; Genetic Variation ; Genome ; Humans ; Long Interspersed Nucleotide Elements ; Pan troglodytes ; Primates ; Recombination, Genetic ; Tromethamine

Previously, we constructed a humanized antibody (HuS10) that binds to the common a antigenic determinant on the S protein of HBV. In this study, we evaluated its HBV-neutralizing activity in chimpanzees. A study chimpanzee was intravenously administered with a single dose of HuS10, followed by intravenous challenge with the adr subtype of HBV, while a control chimpanzee was only challenged with the virus. The result showed that the control chimpanzee was infected by the virus, and thus serum HBV surface antigen (HBsAg) became positive from the 14th to 20th week and actively acquired serum anti-HBc and anti-HBs antibodies appeared from the 19th and 23rd week, respectively. However, in the case of the study chimpanzee, serum HBsAg became positive from the 34th to 37th week, while actively acquired serum anti-HBc and anti-HBs antibodies appeared from the 37th and 40th week, respectively, indicating that HuS10 neutralized the virus in vivo and thus delayed the HBV infection. This novel humanized antibody will be useful in the immunoprophylaxis of HBV infection.
Animals ; CHO Cells ; Cricetinae ; Cricetulus ; Hepatitis B/blood/immunology/virology ; Hepatitis B Antibodies/blood/*immunology ; Hepatitis B Surface Antigens/*immunology ; Hepatitis B virus/*immunology ; Neutralization Tests ; Pan troglodytes/blood/*immunology/*virology

The immune response-related genes have been suggested to be the most favorable genes for positive selection during evolution. Comparing the entire DNA sequence of chimpanzee chromosome 22 (PTR22) with human chromosome 21 (HSA21), we have identified 15 orthologs having indel in their coding sequences. Among them, interferon-alpha receptor-1 gene (IFNAR1), an immuneresponse- related gene, is subjected to comparative genomic analysis. Chimpanzee IFNAR1 showed the same genomic structure as human IFNAR1 (11 exons and 10 introns) except the 3 bp insertion in exon 4. The sequence alignment of IFNAR1 coding sequence indicated that "ISPP" amino acid sequence motif is highly conserved in chimpanzee and other animals including mouse and chicken. However, the human IFNAR1 shows that one proline residue is missing in the sequence motif. The homology modeling of the IFNAR1 structures suggests that the proline deletion in human IFNAR1 leads to the formation of the following alpha-helix, whereas two sequential prolines in chimpanzee IFNAR1 inhibit it. As a result, human IFNAR1 may adopt a characteristic structure distinct from chimpanzee IFNAR1. This human specific trait could contribute to specific immune response in the most optimized manner for humans. Further molecular biological studies on the IFNAR1 will help us to gain insights into the molecular implication of species specific host-pathogen interaction in primate evolution.
Amino Acid Sequence ; Animals ; Base Sequence ; Chickens ; Chromosomes, Human ; Chromosomes, Human, Pair 22 ; Clinical Coding ; Exons ; Genomics* ; Host-Pathogen Interactions ; Humans* ; Interferon-alpha* ; Mice ; Pan troglodytes* ; Primates ; Proline ; Sequence Alignment