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Lebedeva TV, Huang A, Janzen M, Lau M, Yu N. Identification of novel HLA class I alleles using single allele sequencing. ACTA ACUST UNITED AC 2003; 62:433-5. [PMID: 14617051 DOI: 10.1034/j.1399-0039.2003.00106.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Three new HLA-A and five HLA-B alleles reported in this paper have been characterized by direct sequencing of PCR product obtained by group-specific amplification of potential new alleles. Four new alleles, B*5133, B*5134, B*1574 and B*5807, carry motifs observed in previously identified HLA-B alleles and may have evolved via gene conversion. Four alleles, A*2438, A*3405, A*2437 and B*520104, display polymorphisms at positions previously considered constant. All new alleles were identified either by an unexpected sequence specific oligonucleotide probe hybridization pattern or by sequence-based typing, and later confirmed by single allele sequencing.
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Beconi M, Mao A, Creighton M, Hop CECA, Chiu SHL, Eydelloth R, Franklin R, Tang F, Yu N, Vincent S. Species and gender differences in the formation of an active metabolite of a substituted 2,4-thiazolidinedione insulin sensitizer. Xenobiotica 2003; 33:767-87. [PMID: 12893525 DOI: 10.1080/0049825031000108333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
1. The metabolism of a substituted 2,4-thiazolidinedione (P1) with dual PPARalpha/gamma activity was evaluated in male and female rats, dogs and monkeys. A para-hydroxylated metabolite (M1) with potent PPARgamma-selective agonist, was a major circulating drug-related component in female rats, dogs and monkeys, but not in male rats (M1-to-P1 exposure ratio of <1, 3-5, 5 and 5-11 in male rat, monkey, female rat, and dog, respectively). 2. M1 (%) formed in vitro (5, 53, 57-65, 67 and 67% in male rat, monkey, female rat, dog, and human liver microsomes, respectively), rank ordered with M1 (%) formed in vivo (24-45, 53-57, 78, 75-85%, for male rat, monkey, female rat and dog, respectively, after oral administration of P1). 3. The plasma clearance of M1 was higher in male rats (32 ml min(-1) kg(-1) compared with 6, 7 and 2 ml min(-1) kg(-1) in female rat, male monkey and male dogs, respectively). 4. The low amounts of M1 observed in male rats, with the appearance of products of the cleavage of the propyl group between the phenyl groups was probably due to the presence of the sex-specific CYP2C11, which cleaves P1 at the propyl bridge. None of the CYPs present in female rats cleaved P1 at this site and M1 was only produced by CYP2C6. In humans, only CYP2C8 and the polymorphic CYP2C19 produced M1.
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Li X, Sun J, Yu N, Sun Y, Tan Z, Jiang S, Li N, Zhou C. Glutamate induced modulation of free Ca(2+) in isolated inner hair cells of the guinea pig cochlea. Hear Res 2001; 161:29-34. [PMID: 11744278 DOI: 10.1016/s0378-5955(01)00330-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To explore the possible involvement of glutamate (Glu) in modulation of inner hair cell (IHC) functions, the glutamate (Glu) induced changes in intracellular free Ca(2+) ([Ca(2+)]i) concentration in isolated IHCs and outer hair cells (OHCs) of the guinea pig cochlea were investigated with fluo-3, a fluorescent probe for intracellular Ca(2+). Their unique flask shape identified the IHCs with a distinct neck and spherical base with a large spherical nucleus. Normal cell shapes could be maintained for about 2 h. Fluorescence of fluo-3 was distributed in the whole isolated IHC with brighter staining nuclei. Static [Ca(2+)]i remained constant within the observation period in the absence of Glu. In the presence of a low concentration of Glu (3.85 microM), there was an increase of [Ca(2+)]i in IHCs, whereas no obvious [Ca(2+)]i change was found in OHCs. The increase of the fluorescence in IHCs reached peak level at 180 s and then gradually reduced at 400 s after the administration of Glu. The increases of [Ca(2+)]i were observed in nine of 10 IHCs, but one IHC did not show any change. For 10 of the observed OHCs, seven showed no [Ca(2+)]i change, and three showed minor reduction of [Ca(2+)]i. The increase of the Glu concentration resulted in a corresponding change of [Ca(2+)]i in the IHCs after three times administration of Glu. These results suggest that Glu acts on the IHCs presynaptic autoreceptor in a positive feedback manner.
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Glover KJ, Whiles JA, Wu G, Yu N, Deems R, Struppe JO, Stark RE, Komives EA, Vold RR. Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules. Biophys J 2001; 81:2163-71. [PMID: 11566787 PMCID: PMC1301688 DOI: 10.1016/s0006-3495(01)75864-x] [Citation(s) in RCA: 242] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Several complementary physical techniques have been used to characterize the aggregate structures formed in solutions containing dimyristoylphosphatidylcholine (DMPC)/dihexanoylphosphatidylcholine (DHPC) at ratios of < or =0.5 and to establish their morphology and lipid organization as that of bicelles. (31)P NMR studies showed that the DMPC and DHPC components were highly segregated over a wide range of DMPC/DHPC ratios (q = 0.05-0.5) and temperatures (15 degrees C and 37 degrees C). Only at phospholipid concentrations below 130 mM did the bicelles appear to undergo a change in morphology. These results were corroborated by fluorescence data, which demonstrated the inverse dependence of bicelle size on phospholipid concentration as well as a distinctive change in phospholipid arrangement at low concentrations. In addition, dynamic light scattering and electron microscopy studies supported the hypothesis that the bicellar phospholipid aggregates are disk-shaped. The radius of the planar domain of the disk was found to be directly proportional to the ratio of DMPC/DHPC and inversely proportional to the total phospholipid concentration when the DMPC/DHPC ratio was held constant at 0.5. Taken together, these results suggest that bicelles with low q retain the morphology and bilayer organization typical of their liquid-crystalline counterparts, making them useful membrane mimetics.
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Bernstein CN, Kraut A, Blanchard JF, Rawsthorne P, Yu N, Walld R. The relationship between inflammatory bowel disease and socioeconomic variables. Am J Gastroenterol 2001; 96:2117-25. [PMID: 11467642 DOI: 10.1111/j.1572-0241.2001.03946.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Inflammatory bowel diseases (IBD) are chronic diseases associated with considerable morbidity. This morbidity may have an impact on the ability of patients to remain employed, on their marital status, and on their ability to complete a course of higher education. It has long been held that IBD patients are of a higher socioeconomic status and more educated than the general population. Our aim was to determine the relationship between IBD and employment, income, disability, education, and marital status in two population-based data sets based in the province of Manitoba, Canada. METHODS Two studies are reported here. In study A, we surveyed persons with IBD, using the population-based University of Manitoba IBD Database, created in 1995-1996. We compared these IBD patients to the general population with respect to employment, education, and marital status using data from the 1996 National Population Health Survey. IBD patients were queried as to their socioeconomic status as of the time of diagnosis and also at the time of the survey (1995-1996). In study B, we used a database that linked health care and census variables to determine differences in employment, income, occupation, and marital status among individuals who met the administrative definition of IBD (created in forming the University of Manitoba IBD Database, based on ICD-9-CM codes 555 for Crohn's disease and 556 for ulcerative colitis) compared with the rest of working-age population. RESULTS In study A we found that, compared with the general population, patients with IBD were more likely to be unemployed. Crohn's disease appeared to affect employment more than ulcerative colitis. IBD patients, however, had a low rate of reporting themselves as disabled (1.3%). Among those married when diagnosed with IBD, approximately 10% of men and up to 20% of women were no longer married 5 yr later. More patients with IBD were married in 1995 compared with the general population; however, more were also divorced. Fewer patients with IBD achieved postsecondary education. In study B, we found that individuals with IBD were twice as likely to be out of the labor force as were controls. Sedentary occupations were twice as likely to be associated with IBD. The income, education level, and marital status of IBD patients were not significantly different from those of controls. CONCLUSIONS Individuals with IBD at some time in the course of their illness are more likely not to be working than are those in the general population. Based on employment status and job classification, as well as income and education, IBD patients are not of a higher socioeconomic status as previously reported. IBD patients are at least as likely as the general population to be married.
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Bernstein CN, Kraut A, Blanchard JF, Rawsthorne P, Yu N, Walld R. The relationship between inflammatory bowel disease and socioeconomic variables. Am J Gastroenterol 2001. [PMID: 11467642 DOI: 10.1111/j.1572-] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Inflammatory bowel diseases (IBD) are chronic diseases associated with considerable morbidity. This morbidity may have an impact on the ability of patients to remain employed, on their marital status, and on their ability to complete a course of higher education. It has long been held that IBD patients are of a higher socioeconomic status and more educated than the general population. Our aim was to determine the relationship between IBD and employment, income, disability, education, and marital status in two population-based data sets based in the province of Manitoba, Canada. METHODS Two studies are reported here. In study A, we surveyed persons with IBD, using the population-based University of Manitoba IBD Database, created in 1995-1996. We compared these IBD patients to the general population with respect to employment, education, and marital status using data from the 1996 National Population Health Survey. IBD patients were queried as to their socioeconomic status as of the time of diagnosis and also at the time of the survey (1995-1996). In study B, we used a database that linked health care and census variables to determine differences in employment, income, occupation, and marital status among individuals who met the administrative definition of IBD (created in forming the University of Manitoba IBD Database, based on ICD-9-CM codes 555 for Crohn's disease and 556 for ulcerative colitis) compared with the rest of working-age population. RESULTS In study A we found that, compared with the general population, patients with IBD were more likely to be unemployed. Crohn's disease appeared to affect employment more than ulcerative colitis. IBD patients, however, had a low rate of reporting themselves as disabled (1.3%). Among those married when diagnosed with IBD, approximately 10% of men and up to 20% of women were no longer married 5 yr later. More patients with IBD were married in 1995 compared with the general population; however, more were also divorced. Fewer patients with IBD achieved postsecondary education. In study B, we found that individuals with IBD were twice as likely to be out of the labor force as were controls. Sedentary occupations were twice as likely to be associated with IBD. The income, education level, and marital status of IBD patients were not significantly different from those of controls. CONCLUSIONS Individuals with IBD at some time in the course of their illness are more likely not to be working than are those in the general population. Based on employment status and job classification, as well as income and education, IBD patients are not of a higher socioeconomic status as previously reported. IBD patients are at least as likely as the general population to be married.
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Yu N, Margulis CJ, Coker DF. Influence of Solvation Environment on Excited State Avoided Crossings and Photodissociation Dynamics. J Phys Chem B 2001. [DOI: 10.1021/jp0108925] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sun W, Ding D, Jin X, Richard JS, Li X, Yu N. [Study on voltage-sensitive current of spiral ganglion cells in mice organ of Corti culture]. ZHONGHUA ER BI YAN HOU KE ZA ZHI 2001; 36:178-82. [PMID: 12761918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
OBJECTIVE To investigate the property of voltage-sensitive current in cochlear spiral ganglion cells of the C57BL/10J mice, an inbred strain which develops early onset hearing loss. METHODS Organotypic cultures of organ of Corti were prepared from neonatal mice 0-5 days of age. Whole-cell current and voltage clamp techniques were used to study Na+, K+ and Ca2+ currents of the spiral ganglion cells in culture. RESULTS Cultures were maintained for 8-48 hours before use. Ganglion cells were identified first through their anatomical positions and finally through fast negative Na+ current. Spontaneous action potentials were recorded from some ganglion cells (4 out of 39). When present, spontaneous rates were around 20 spikes/sec, and might be as high as 135 spikes/sec. The mean resting potential was (-55 +/- 5) mV (n = 39). Under voltage clamp conditions, transient inward currents (negative) and outward (positive), steady-state voltage-dependent currents were recorded in normal HBSS. Rapid inward currents were totally blocked by 300 nM TTX applied locally to the culture. Inward currents recovered quickly after TTX wash out suggesting that the transient inward current was carried by Na+. The mean maximum amplitude of Na+ current was (-2.0 +/- 1.1) nA (n = 39) recorded in HBSS. Adding TEA (10 mmol/L) and 4-AP (0.15 mmol/L) to the bath solution or replacing K+ with Ca+ in the pipette solution partly blocked the sustained outward current. This suggests that the outward current was carried by K+. The mean maximum amplitude of K+ was (3.0 +/- 1.3) nA (n = 39) with 140 mM K+ in the pipette. Inward Ca2+ current was recorded in Ba2+ solution which mean peak amplitude was (-1.0 +/- 0.7) nA (n = 20). Ca2+ currents were reversibly blocked by 100 microM Cd2+. CONCLUSION Whole cell recordings from spiral ganglion neurons can be obtained from organotypic cultures of the organ of Corti. Fast Na+ current, sustained K+ current and L-type Ca2+ current were recorded in the spiral ganglion cells cultured for 1-2 days. Whole cell recording showed that cochlea spiral ganglion cells can generate spontaneous action potential one day after birth and the firing rates could reach levels equal to those recorded in vivo.
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Kale TA, Raab C, Yu N, Dean DC, Distefano MD. A photoactivatable prenylated cysteine designed to study isoprenoid recognition. J Am Chem Soc 2001; 123:4373-81. [PMID: 11457220 DOI: 10.1021/ja0012016] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein prenylation, involving the alkylation of a specific C-terminal cysteine with a C(15) or C(20) isoprenoid unit, is an essential posttranslational modification required by most GTP-binding proteins for normal biological activity. Despite the ubiquitous nature of this modification and numerous efforts aimed at inhibiting prenylating enzymes for therapeutic purposes, the function of prenylation remains unclear. To explore the role the isoprenoid plays in mediating protein-protein recognition, we have synthesized a photoactivatable, isoprenoid-containing cysteine analogue (2) designed to act as a mimic of the C-terminus of prenylated proteins. Photolysis experiments with 2 and RhoGDI (GDI), a protein which interacts with prenylated Rho proteins, suggest that the GDI is in direct contact with the isoprenoid moiety. These results, obtained using purified GDI as well as Escherichia coli (E. coli) crude extract containing GDI, suggest that this analogue will be an effective and versatile tool for the investigation of putative isoprenoid binding sites in a variety of systems. Incorporation of this analogue into peptides or proteins should allow for even more specific interactions between the photoactivatable isoprenoid and any number of isoprenoid binding proteins.
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Li X, Sun J, Yu N, Sun Y, Tan Z, Jiang S, Li N, Zhou C. [Glutamate induced modulation of free Ca2+ in isolated inner hair cells of the guinea pig cochlea]. ZHONGHUA ER BI YAN HOU KE ZA ZHI 2001; 36:101-4. [PMID: 12761973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
OBJECTIVE To investigate the modulation effect of glutamate (Glu) on intracellular free Ca2+ concentration([Ca2+]i) of inner hair cell (IHC). METHODS Using the laser scanning confocal microscope (LSCM), the exogenous Glu-induced changes in [Ca2+]i of isolated 10 IHCs and 10 OHCs of guinea pig cochlea were observed with fluo-3, a fluorescent probe for [Ca2+]i. RESULTS The IHCs were identified by their unique flask shape with a distinct neck and spherical base and a large spherical nucleus. In most cases, normal cell shapes could be maintained about two hours after isolation. The images of [Ca2+]i from LSCM were similar to those from inverted microscopy. Fluorescence of Fluo-3 distributed in the isolated IHCs with brighter staining in the nucleus. In the presence of low concentration of Glu (3.85 mumol/L), there was an increase of [Ca2+]i in IHCs, whereas no change in OHCs was found. Of the 10 IHCs, increases of [Ca2+]i were observed in 9 and no change in 1. Of the 10 OHCs, 7 showed no [Ca2+]i change and only 3 showed minor reduction of [Ca2+]i. An increase of the Glu concentration (21.88 mumol/L) induced a corresponding increase of [Ca2+]i in IHCs, but eventually resulted in a gradual decrease of [Ca2+]i with a distortion of the normal shape, which indicated that the IHCs were degenerated and swelling. CONCLUSION These results suggested that exogenous Glu is capable of modulating [Ca2+]i of IHC and may be act on autoreceptor in a positive feedback manner. Excessive Glu induced the accumulation of IHC [Ca2+]i which finally resulted in the degeneration and edema of IHC and the reduction of IHC [Ca2+]i.
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Bernstein CN, Blanchard JF, Rawsthorne P, Yu N. The prevalence of extraintestinal diseases in inflammatory bowel disease: a population-based study. Am J Gastroenterol 2001; 96:1116-22. [PMID: 11316157 DOI: 10.1111/j.1572-0241.2001.03756.x] [Citation(s) in RCA: 478] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The aim of this study was to determine the prevalence of the major extraintestinal manifestations of inflammatory bowel disease (IBD) and their relation to disease diagnosis and gender. METHODS We used the population-based University of Manitoba IBD Database, which includes longitudinal files on all subjects of all health system contacts identified by International Classification of Diseases, 9th Revision, Clinical Modification codes for visit diagnosis. We extracted a cohort from our database, which included subjects with a known diagnosis of IBD for at least 10 yr. We then determined how many contacts each subject had for each of the following extraintestinal IBD-associated immune diseases: primary sclerosing cholangitis, ankylosing spondylitis, iritis/uveitis, pyoderma gangrenosum, and erythema nodosum. We calculated the prevalence of the extraintestinal diseases using an administrative definition of having at least five health system contacts for the diagnosis in question. This administrative definition has previously been validated in Crohn's disease and ulcerative colitis (UC). RESULTS A total of 6.2% of patients with IBD had one of six major extraintestinal diseases studied in this report. Only 0.3% of patients had multiple extraintestinal diseases. Iritis/uveitis was the most common extraintestinal disease of all assessed (2.2% of women and 1.1% of men). Iritis/uveitis was more common among women, particularly those with UC (3.8%). Primary sclerosing cholangitis was most common among men with UC (3%). Ankylosing spondylitis was more common among men, and the highest rate was seen among men with Crohn's disease (2.7%). Pyoderma gangrenosum was more common in Crohn's (1.2%) with no gender predilection. Erythema nodosum was similarly present in Crohn's and UC but was more common among women (1.9%). CONCLUSIONS The associations of immune mediated diseases in extraintestinal sites may help us to further our understanding of IBD pathogenesis, and it may help us in developing a paradigm of disease subsets.
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Noreen HJ, Yu N, Setterholm M, Ohashi M, Baisch J, Endres R, Fernandez-Vina M, Heine U, Hsu S, Kamoun M, Mitsuishi Y, Monos D, Perlee L, Rodriguez-Marino S, Smith A, Yang SY, Shipp K, Hegland J, Hurley CK. Validation of DNA-based HLA-A and HLA-B testing of volunteers for a bone marrow registry through parallel testing with serology. TISSUE ANTIGENS 2001; 57:221-9. [PMID: 11285130 DOI: 10.1034/j.1399-0039.2001.057003221.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A total of 42,160 individuals were typed for HLA-A and HLA-B by both serology and PCR-based typing. The HLA assignments included all of the known serological equivalents. The majority of the individuals (99.9%) were from U.S. minority population groups. The serologic typing was performed between 1993 and 1997 at the time of recruitment for the National Bone Marrow Program (NMDP) registry. The polymerase chain reaction (PCR)-based typing was carried out in two phases. In phase I, DNA typing was performed by PCR using sequence-specific oligonucleotide probes (PCR-SSOP) or PCR using sequence-specific primers (PCR-SSP) without knowledge of the serologic assignments. Discrepancies were identified between the serologic and DNA assignments in 24% of the volunteers (8% of volunteers differed for only HLA-A assignments, 13% for HLA-B, and 3% for both HLA-A and -B) and a potential explanation was assigned each discrepant serology/DNA pair. In phase II, a random sampling scheme was used to select a statistically significant number of individuals for repeat DNA typing from each of these categories. The categories included antigens missed by serology, nonexpressed (null) alleles, PCR amplification failures, misassignment of antigens and nomenclature issues. Only a single individual was found to carry a null allele. DNA-based testing correctly typed nearly 99% of the donors at HLA-A, more than 98% at HLA-B, and more than 97% at both HLA-A and -B validating this methodology for registry typing.
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Yu N, Zhao Z, Fu YX, Sambuughin N, Ramsay M, Jenkins T, Leskinen E, Patthy L, Jorde LB, Kuromori T, Li WH. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol Biol Evol 2001; 18:214-22. [PMID: 11158380 DOI: 10.1093/oxfordjournals.molbev.a003795] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human DNA variation is currently a subject of intense research because of its importance for studying human origins, evolution, and demographic history and for association studies of complex diseases. A approximately 10-kb region on chromosome 1, which contains only four small exons (each <155 bp), was sequenced for 61 humans (20 Africans, 20 Asians, and 21 Europeans) and for 1 chimpanzee, 1 gorilla, and 1 orangutan. We found 52 polymorphic sites among the 122 human sequences and 382 variant sites among the human, chimpanzee, gorilla, and orangutan sequences. For the introns sequenced (8,991 bp), the nucleotide diversity (pi) was 0.058% among all sequences, 0.076% among the African sequences, 0.047% among the Asian sequences, and 0.045% among the European sequences. A compilation of data revealed that autosomal regions have, on average, the highest pi value (0.091%), X-linked regions have a somewhat lower pi value (0.079%), and Y-linked regions have a very low pi value (0.008%). The lower polymorphism in the present region may be due to a lower mutation rate and/or selection in the gene containing these introns or in genes linked to this region. The present region and two other 10-kb noncoding regions all show a strong excess of low-frequency variants, indicating a relatively recent population expansion. This region has a low mutation rate, which was estimated to be 0.74 x 10 per nucleotide per year. An average estimate of approximately 12,600 for the long-term effective population size was obtained using various methods; the estimate was not far from the commonly used value of 10,000. Fu and Li's tests rejected the assumption of an equilibrium neutral Wright-Fisher population, largely owing to the high proportion of low-frequency variants. The age of the most recent common ancestor of the sequences in our sample was estimated to be more than 1 Myr. Allowing for some unrealistic assumptions in the model, this estimate would still suggest an age of more than 500,000 years, providing further evidence for a genetic history of humans much more ancient than the emergence of modern humans. The fact that many unique variants exist in Europe and Asia also suggests a fairly long genetic history outside of Africa and argues against a complete replacement of all indigenous populations in Europe and Asia by a small Africa stock. Moreover, the ancient genetic history of humans indicates no severe bottleneck during the evolution of humans in the last half million years; otherwise, much of the ancient genetic history would have been lost during a severe bottleneck. We suggest that both the "Out of Africa" and the multiregional models are too simple to explain the evolution of modern humans.
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Yu N. Dosage of buserelin. THE JOURNAL OF REPRODUCTIVE MEDICINE 2000; 45:964-5. [PMID: 11127117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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Jin D, Yang S, Yu N, Chen J, Shi Z. [Thoracolumbar injuries: pathomorphology of and a new classification]. ZHONGHUA WAI KE ZA ZHI [CHINESE JOURNAL OF SURGERY] 2000; 38:811-4. [PMID: 11832169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To introduce a new classification of thoracolumbar injuries. METHODS Three modes were used to classify the injuries according to the mechanisms of injuries: Type A, flexion-compression fractures; Type B, vertical compression fractures; Type C, distraction injuries. Two groups were used to distinguish the fractures in one type according to the pathomorphological differences and the clinical incidence: Group A, with a more clinical incidence, and Group B, with a less clinical incidence. Three subgroups were used to divide the injuries in one group in consideration of the severity of the fracture instability and the fracture displacement: fracture, subluxation, and dislocation. RESULTS A new classification of thoracolumbar fractures was established. CONCLUSION The new classification is more systemic and more convenient.
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Oppmann B, Lesley R, Blom B, Timans JC, Xu Y, Hunte B, Vega F, Yu N, Wang J, Singh K, Zonin F, Vaisberg E, Churakova T, Liu M, Gorman D, Wagner J, Zurawski S, Liu Y, Abrams JS, Moore KW, Rennick D, de Waal-Malefyt R, Hannum C, Bazan JF, Kastelein RA. Novel p19 protein engages IL-12p40 to form a cytokine, IL-23, with biological activities similar as well as distinct from IL-12. Immunity 2000; 13:715-25. [PMID: 11114383 DOI: 10.1016/s1074-7613(00)00070-4] [Citation(s) in RCA: 2054] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A novel sequence discovered in a computational screen appears distantly related to the p35 subunit of IL-12. This factor, which we term p19, shows no biological activity by itself; instead, it combines with the p40 subunit of IL-12 to form a novel, biologically active, composite cytokine, which we term IL-23. Activated dendritic cells secrete detectable levels of this complex. IL-23 binds to IL-12R beta 1 but fails to engage IL-12R beta 2; nonetheless, IL-23 activates Stat4 in PHA blast T cells. IL-23 induces strong proliferation of mouse memory (CD4(+)CD45Rb(low)) T cells, a unique activity of IL-23 as IL-12 has no effect on this cell population. Similar to IL-12, human IL-23 stimulates IFN-gamma production and proliferation in PHA blast T cells, as well as in CD45RO (memory) T cells.
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Zhao Z, Jin L, Fu YX, Ramsay M, Jenkins T, Leskinen E, Pamilo P, Trexler M, Patthy L, Jorde LB, Ramos-Onsins S, Yu N, Li WH. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc Natl Acad Sci U S A 2000; 97:11354-8. [PMID: 11005839 PMCID: PMC17204 DOI: 10.1073/pnas.200348197] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human DNA sequence variation data are useful for studying the origin, evolution, and demographic history of modern humans and the mechanisms of maintenance of genetic variability in human populations, and for detecting linkage association of disease. Here, we report worldwide variation data from a approximately 10-kilobase noncoding autosomal region. We identified 75 variant sites in 64 humans (128 sequences) and 463 variant sites among the human, chimpanzee, and orangutan sequences. Statistical tests suggested that the region is selectively neutral. The average nucleotide diversity (pi) across the region was 0.088% among all of the human sequences obtained, 0.085% among African sequences, and 0.082% among non-African sequences, supporting the view of a low nucleotide diversity ( approximately 0.1%) in humans. The comparable pi value in non-Africans to that in Africans indicates no severe bottleneck during the evolution of modern non-Africans; however, the possibility of a mild bottleneck cannot be excluded because non-Africans showed considerably fewer variants than Africans. The present and two previous large data sets all show a strong excess of low frequency variants in comparison to that expected from an equilibrium population, indicating a relatively recent population expansion. The mutation rate was estimated to be 1.15 x 10(-9) per nucleotide per year. Estimates of the long-term effective population size N(e) by various statistical methods were similar to those in other studies. The age of the most recent common ancestor was estimated to be approximately 1.29 million years ago among all of the sequences obtained and approximately 634,000 years ago among the non-African sequences, providing the first evidence from a noncoding autosomal region for ancient human histories, even among non-Africans.
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Yu N, Li W. No fixed nucleotide difference between Africans and Non-Africans at the pyruvate dehydrogenase E1 alpha-subunit locus. Genetics 2000; 155:1481-3. [PMID: 10960278 PMCID: PMC1461154 DOI: 10.1093/genetics/155.3.1481] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Yu N, Zheng C, Zhang YP, Li WH. Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 2000; 16:85-95. [PMID: 10877942 DOI: 10.1006/mpev.2000.0776] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e. , represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau. On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister taxa of one steppe dweller and one shrub dweller is very low. These findings support the hypothesis that pikas have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution.
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Hurley CK, Maiers M, Ng J, Wagage D, Hegland J, Baisch J, Endres R, Fernandez-Vina M, Heine U, Hsu S, Kamoun M, Mitsuishi Y, Monos D, Noreen H, Perlee L, Rodriguez-Marino S, Smith A, Stastny P, Trucco M, Yang SY, Yu N, Holsten R, Hartzman RJ, Setterholm M. Large-scale DNA-based typing of HLA-A and HLA-B at low resolution is highly accurate specific and reliable. TISSUE ANTIGENS 2000; 55:352-8. [PMID: 10852387 DOI: 10.1034/j.1399-0039.2000.550409.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
DNA-based typing of HLA class I alleles of the HLA-A and HLA-B loci using sequence-specific oligonucleotide primers and/or probes has been used for the large-scale typing of individuals for the National Marrow Donor Program unrelated donor registry. Typing was performed by 16 laboratories at a low level of resolution (e.g. A*01, B*07). The results of blinded quality control analysis for the first 12 months of the project show the typing to be highly accurate, specific and reliable. The total error rate based on 11,545 HLA-A and 11,428 HLA-B assignments was 1.1% for HLA-A and 1.9% for HLA-B. This level of accuracy is particularly remarkable because the quality control samples could not be distinguished from 64,180 donor samples tested at the same time by the laboratories.
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Li B, Yu J, Suntharalingam M, Kennedy AS, Amin PP, Chen Z, Yin R, Guo S, Han T, Wang Y, Yu N, Song G, Wang L. Comparison of three treatment options for single brain metastasis from lung cancer. Int J Cancer 2000; 90:37-45. [PMID: 10725856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Whole brain radiotherapy (WBRT), stereotactic radiosurgery (SRS), and the combination of both treatment methods were used for the management of single brain metastasis from lung cancer. The purpose of this study is to compare these three different treatment options in terms of local response, survival, and quality of life. From June 1995 to July 1998, 70 lung cancer patients with new diagnosed single brain metastasis were treated with either WBRT alone (n = 29), or SRS alone (n = 23), or the combination of both methods (n = 18). Multiple endpoints, including survival, freedom from local progression (FFLP), freedom from new brain metastasis (FFNBM), local control, Karnofsky performance status (KPS), and causes of death, were measured from the date of treatment completion and compared using univariate and multivariate analyses. For patients treated with WBRT-alone, SRS-alone, and SRS+WBRT, the median survivals were 5.7, 9.3, and 10.6 months, the median FFLP were 4.0, 6.9, and 8.6 months, the median FFNBM were 4.1, 6.7, and 8.6 months, and the local response rates were 55.6, 87.0, and 88.9%, respectively. Four of the 29 patients treated with WBRT-alone continued with progression of disease. The post treatment KPS showed improvement in 41.4, 82.6, and 88.9% of patients treated with WBRT-alone, SRS-alone, and SRS+WBRT, respectively. The progression of new and/or recurred metastatic brain tumor as the cause of death accounted for 51.7%, 50. 0%, and 28.3% of the patients treated with WBRT-alone, SRS-alone, and SRS+WBRT, respectively. Univariate analyses showed that the significant differences among the three treatment arms were observed based on all of the above mentioned endpoints. However, the comparison between SRS-alone and SRS+WBRT groups indicated that adding WBRT only improves FFNBM (P = 0.0392). Cox regression analyses revealed no significant difference in both of the KPS (P = 0.1082) and causes of death (P = 0.081) among the three arms. Both SRS alone and SRS+WBRT seem better in prolonging life and improving quality of life than WBRT alone for patients with single brain metastasis from lung cancer. But the combined therapy did not show significant advantage over SRS alone in improving survival, enhancing local control, and quality of life except for a more favorable FFNBM. Further investigation via a randomized trial is needed to access the value of adding WBRT to SRS in the management of this group of patients. Int. J. Cancer (Radiat. Oncol. Invest.) 90, 37-45 (2000).
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Billaud JN, Selway D, Yu N, Phillips TR. Replication rate of feline immunodeficiency virus in astrocytes is envelope dependent: implications for glutamate uptake. Virology 2000; 266:180-8. [PMID: 10612672 DOI: 10.1006/viro.1999.0079] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Feline immunodeficiency virus (FIV) induces neurological abnormalities in domestic cats. Previously, we demonstrated that two disparate strains of FIV (FIV-34TF10 and FIV-PPR) varied greatly in the ability to replicate in feline cortical astrocytes. To investigate the impact of the env region on the replication efficiency of these strains, we constructed two env chimera viruses, FIV-34TF10-PPRenv and FIV-PPR-34TF10env, to infect feline cortical astrocytes in vitro. Although all of these viruses infected cortical astrocytes, the efficiency of replication depended on strain, and the env region played an essential role. The viruses containing the env of 34TF10, FIV-34TF10, and FIV-PPR-34TF10env had the greatest replication rate, whereas the viruses containing the env of PPR replicated at a lower level. Other viral regions had modulatory effects on the replication rate, with the FIV-PPR genome providing a slight replication advantage over the FIV-34TF10 genome. We also monitored the effects of these viruses on an important astrocyte function, glutamate uptake; all viruses significantly decreased this activity, but only the viruses containing the env of PPR significantly impaired glutamate uptake without altering the culture viability. These results may be particularly relevant in the context of lentivirus-induced central nervous system disease in which a selective breakdown of astroglial function may contribute to neurodegeneration.
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Yu N, Roy SK. Development of primordial and prenatal follicles from undifferentiated somatic cells and oocytes in the hamster prenatal ovary in vitro: effect of insulin. Biol Reprod 1999; 61:1558-67. [PMID: 10570003 DOI: 10.1095/biolreprod61.6.1558] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Fetal hamster ovaries were cultured for up to 16 days in the presence or absence of various dosages of insulin to evaluate the induction of folliculogenesis in vitro. In the absence of insulin, a few primordial follicle-like structures appeared by the 4th day, and distinct primary follicles (stage 1) appeared by the 12th day of culture. The organelles in the oocytes and adjacent granulosa cells developed along with follicular growth. Moreover, gap junctions between the oocyte and somatic cell plasma membrane also developed as early as 8 days in culture. In the presence of 0.2 microg/ml insulin, primary follicles developed after 8 days, and approximately 4% secondary follicles with 2-3 layers of granulosa cells appeared after 16 days of culture. However, higher dosages (> 0.2 microg/ml) of insulin retarded primary follicle formation and induced the formation of primordial follicles with larger oocytes. An increased number of larger oocytes with a few granulosa cells accumulated at the periphery of the ovary. The results indicate that although primordial and primary follicles can develop after 12 days in vitro in the absence of exogenous insulin, the latter is required for timely progression of follicular development through primary and secondary stages.
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Yu N, Li X, Hu B. [The effects of salicylate on noise-induced hearing loss in the guinea pig]. ZHONGHUA ER BI YAN HOU KE ZA ZHI 1999; 34:344-6. [PMID: 12764841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
OBJECTIVE To investigate the effects of salicylate on noise-induced hearing loss (NIHL) in guinea pigs. METHODS The animals were allocated into four groups (salicylate + noise, saline + noise, noise only and salicylate only) and were exposed to a 4 kHz octave band noise at 105 dB SPL for 2 hours for 5 consecutive days. Dynamic changes of ABR thresholds evoked by clicks were monitored. After physiological examination, the cochleae were processed for the morphological examination by light microscopy. RESULTS Mean thresholds of ABRs in the experimental group obtained on 5th day of the noise exposure was positively lower than the control groups (P < 0.05). The similar trends of ABR changes were found during other exposure days and after exposure, but the differences were not statistically significant. In the experimental group, there were 37.00 +/- 8.89 hair cell loses as assessed by nucleus staining, and 3.20 +/- 1.07 hair cells with nuclear deformation. The noise group had 74.11 +/- 10.28 hair cell loses and 10.43 +/- 9.71 hair cells with nuclear deformation, whereas the saline group had 63.60 +/- 7.97 hair cell loses and 20.80 +/- 15.48 hair cells with nuclear deformation. The difference between two groups was significant (P < 0.05). CONCLUSION The results suggest that administration of salicylate facilitates the recovery of cochlear hearing and reduces damage to hair cells after noise exposure.
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Yu N, Guan C, Liu Y, Yang X. [Clinical value of 99mTc-MIBI imaging, 131I whole body scan and HTG determination for the follow-up of patients with differentiated thyroid carcinoma after 131I therapy]. HUA XI YI KE DA XUE XUE BAO = JOURNAL OF WEST CHINA UNIVERSITY OF MEDICAL SCIENCES = HUAXI YIKE DAXUE XUEBAO 1999; 30:437-9. [PMID: 11387963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The purpose of this study was to make a comparative evaluation of 99mTc-MIBI imaging, 131I whole body scan and HTG determination in use for the follow-up of patients with differentiated thyroid carcinoma (DTC) after 131I therapy. Fifty-three patients with DTC had undergone surgical treatment and 131I ablation. Clinical examinations showed that 22 of them had metastases or recurrences. In the follow-up of all the patients, the HTG determination, the 99mTc-MIBI imaging and the 131I-WBS were performed in sequence after the discontinuance of the administration of thyroxin for 4-6 weeks. The results showed that the sensitivity, specificity and accuracy of 99mTc-MIBI imaging were 86.36%, 87.10% and 86.79% respectively; those for HTG were 68.18%, 100% and 86.79% and those for 131I-WBS were 63.64%, 100% and 84.91% respectively. The total sensitivity of the three examinations was 100%; the total specificity and total accuracy were 87.10% and 92.45% respectively. The data of this study suggest that 99mTc-MIBI imaging is a highly sensitive method and the combined use of the three examinations can improve the sensitivity and accuracy of diagnosis for patients with DTC.
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