High-density genome scan in Crohn disease shows confirmed linkage to chromosome 14q11-12

Epidemiological studies have shown that genetic factors contribute to the pathogenesis of the idiopathic inflammatory bowel diseases (IBD), Crohn disease (CD) and ulcerative colitis (UC). Recent genome scans and replication studies have identified replicated linkage between CD and a locus on chromosome 16 (the IBD1 locus), replicated linkage between IBD (especially UC) and a locus on chromosome 12q (the IBD2 locus), and replicated linkage between IBD (especially CD) and a locus on chromosome 6p (the IBD3 locus). Since the estimated locus-specific lambdas values for the regions of replicated linkage do not account for the overall lambdas in CD, and since the published genome scans in IBD show at least nominal evidence for linkage to regions on all but two chromosomes, we performed an independent genome scan using 751 microsatellite loci in 127 CD-affected relative pairs from 62 families. Single-point nonparametric linkage analysis using the GENEHUNTER-PLUS program shows evidence for linkage to the adjacent D14S261 and D14S283 loci on chromosome 14q11-12 (LOD = 3.00 and 1.70, respectively), and the maximal multipoint LOD score is observed at D14S261 (LOD = 3.60). In the multipoint analysis, nominal evidence for linkage (P<.05) is observed near D2S117 (LOD = 1.25), near D3S3045 (LOD = 1.31), between D7S40 and D7S648 (LOD = 0.91), and near D18S61 (LOD = 1.15). Our finding of significant linkage to D14S261 and the finding of suggestive linkage to the same locus in an independent study (multipoint LOD = 2.8) satisfies criteria for confirmed linkage, so we propose that the region of interest on chromosome 14q11-12 should be designated the IBD4 locus.     

Genetic and physical mapping of a rice blast resistance locus,Pi-CO39(t), that corresponds to the avirulence gene AVR1-CO39 of Magnaporthe grisea

We have identified, genetically mapped and physically delineated the chromosomal location of a new rice blast resistance locus, designated Pi-CO39(t). This locus confers resistance to Magnaporthe grisea isolates carrying the AVR1-CO39 avirulence locus. The AVR1-CO39 locus is conserved in non-rice (cereals and grasses)-infecting isolates of M. grisea, making Pi-CO39(t) useful for engineering M. grisea resistance in rice and other cereals. The resistance in the rice line CO39 was inherited as a single dominant locus in segregating populations derived from F(2) and F(3) crosses between disease-resistant (CO39) and susceptible (51583) rice genotypes. Microsatellite, RFLP and resistance gene analog (RGA) markers were used to map the Pi-CO39(t) locus to a 1.2-cM interval between the probenazole-responsive ( RPR1) gene (0.2 cM) and RFLP marker S2712 (1.0 cM) on the short arm of rice chromosome 11. RFLP markers G320 and F5003, and resistance gene analogs RGA8, RGA38 and RGACO39 were tightly linked to the Pi-CO39(t) locus (no recombination detected in a sample of ~2400 gametes). A large-insert genomic library of CO39 was constructed in the binary plant transformation vector pCLD04541. A library screen using RGA8, RGA38 and probes derived from the ends of CO39 clones, as well as BAC end probes from the corresponding locus in the rice cv. Nipponbare, resulted in the assembly of three CO39 contigs of 180 kb, 110 kb and 145 kb linked to the Pi-CO39(t) locus. A 650-kb contig was also constructed representing the susceptible locus, pi-CO39(t), in the Nipponbare genome. The two genomes are highly divergent with respect to additions, deletions and translocations at the Pi-CO39(t) locus, as revealed by the presence or absence of mapping markers.     

Comparison of follicular dynamics and hormone concentrations between the 7-day and 5-day CO-Synch + CIDR program in primiparous beef cows

The objectives were to compare follicular dynamics, preovulatory estradiol concentrations, and progesterone concentrations between the 7-day (7CO, n = 15) and 5-day (5CO, n = 13) CO-Synch + controlled internal drug release device (CIDR) program in primiparous suckled beef cows. On Day −7 (7CO) or Day −5 (5CO), GnRH (100 μg) was administered (GnRH-1) and a CIDR was inserted. On Day 0, hour 0, CIDR was removed and cows received PGF_2α (25 mg) at hours 0 and 12. Animals were administered GnRH (100 μg, GnRH-2) at either hour 60 (7CO) or 72 (5CO). Follicular growth and ovulation to both GnRH-1 and GnRH-2 were evaluated using ultrasonography. Concentrations of estradiol were determined in blood samples taken at hours 0, 36, 60, and 72 (5CO). Blood samples were collected on Days 5, 8, and 14 for progesterone quantification. Ovulation rate to GnRH-1 did not differ between the 7CO (11/15) and 5CO (8/13) treatments, and for all dependent variables the statistical model included treatment, ovulation to GnRH-1, and their interaction. Diameter (mm) of the ovulatory follicle did not differ between treatments (13.4 ± 0.3) but was greater (P < 0.05) in cows that responded to GnRH-1 (13.8 ± 0.3) than those did not (12.6 ± 0.6). Maximum estradiol concentrations tended (P = 0.06) to be greater in the 5CO (7.3 ± 0.5 pg/mL) than 7CO (6.1 ± 0.7 pg/mL) treatment and tended to be greater (P = 0.08) in cows that responded to GnRH-1 (7.1 ± 0.5 pg/mL) than those did not (5.6 ± 0.9 pg/mL). Three cows in the 7CO treatment failed to develop a CL after GnRH-2. There was a treatment by response to GnRH-1 interaction (P < 0.05) for progesterone concentrations. In cows that did not respond to GnRH-1 in the 7CO treatment, progesterone concentrations were less (P < 0.05) than in those that responded to GnRH-1 in the 7CO treatment and tended (P = 0.09) to be less than in cows in the 5CO treatment that did not respond to GnRH-1. In conclusion, these findings demonstrate that failure to respond to GnRH-1 is detrimental to estradiol and progesterone concentrations with a 7-day interval between GnRH-1 and PGF_2α but of little consequence when this interval is shortened to 5 days.     

Autosomal dominant aniridia linked to the chromosome 11p13 markers catalase and D11S151 in a large Dutch family

In a large pedigree with autosomal dominant aniridia, we found close linkage between the aniridia locus AN2 and the markers catalase (CAT) (zeta = 7.27 at theta = 0.00) and D11S151 (zeta = 3.86 at theta = 0.10) flanking the AN2 locus on 11p13. Positive lod scores were also obtained for the 11p13----11p14 markers D11S16 and FSHB with the linkage group CAT/AN2/D11S151. We conclude that the autosomal dominant aniridia in this family is due to a mutation at the AN2 locus on 11p13. We have excluded linkage (zeta less than -2 at theta less than 0.18) between the aniridia and the chromosome 2p25 marker D2S1 (linked to ACP1).     

Assignment of the YT blood group locus to chromosome 7q.

The antithetical antigens YT1 and YT2 constitute the YT blood group system (International Society of Blood Transfusion system number 11). Despite being serologically well defined, the YT blood group locus (YT) has not secured a chromosomal location. In our report, peak lods of 3.61 at theta = 0.00 for YT:COL1A2 and of 3.31 at theta = 0.00 for YT:D7S13 allow us to assign YT to the long arm of chromosome 7.     

Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals

From a total of 524 microsatellite loci considered in nearly 40 000 individuals of 78 species, freshwater fish displayed levels of population genetic variation (mean heterozygosity, h=0·46, and mean numbers of alleles per locus, a=7·5) roughly similar to those of non-piscine animals (h=0·58 and a=7·1). In contrast, local population samples of marine fish displayed on average significantly higher heterozygosities (h=0·79) and nearly three times the number of alleles per locus (a=20·6). Anadromous fish were intermediate to marine and freshwater fish (h=0·68 and a=11·3). Results parallel earlier comparative summaries of allozyme variation in marine, anadromous, and freshwater fishes and probably are attributable in part to differences in evolutionarily effective population sizes typifying species inhabiting these realms.     

A linkage study of cystic fibrosis in extended multigenerational pedigrees.

The linkage of polymorphic DNA markers on chromosome 7 to cystic fibrosis (CF) was examined in two pedigrees and a number of smaller nuclear families. The pedigrees are multigenerational and together consist of more than 300 members including 30 affected individuals, while the nuclear families each have two generations and either two or three children with CF. Tight linkage was observed between the CF locus and the met oncogene locus theta = 0, zeta = 15.45), pJ3.11 (theta = 0, zeta = 10.07), and 7C22 (theta = 0, zeta = 6.64) in both the pedigrees and nuclear families with no evidence for recombination between CF and any of the DNA markers. Weaker linkage between the CF locus and the locus for the serum enzyme activity marker paraoxonase (PON) was detected, theta = 0.18, zeta = 0.76. The two pedigrees were sufficiently informative to detect significant linkage between CF and each of the three DNA markers previously shown to be tightly linked to the CF locus. These results establish a locus for CF in these pedigrees in the region of chromosome 7 nearest the three DNA markers met, pJ3.11, and 7C22 and are consistent with locus homogeneity for the defect causing CF in these populations and others that have been examined to date.     

Synthesis and reactivity of coordinatively unsaturated osmium and ruthenium stannyl complexes

Treatment of MHCl(CO)(PPh₃)₃ (M=Ru, Os) with (CH₂=CH)SnR₃ is a good general route to the coordinatively unsaturated osmium and ruthenium stannyl complexes M(SnR₃)Cl(CO)(PPh₃)₂ (1: M=Ru, R=Me; 2: M=Ru, R = n-butyl; 3: M=Ru, R = p-tolyl; 4: M=Os, R=Me). These coordinatively unsaturated complexes readily add CO and CN-p-tolyl to form the coordinatively saturated compounds M(SnR₃)Cl(CO)L(PPh₃)₂ (5: M=Ru, R=Me, L=CO; 6: M=;Ru, R = n-butyl, L=CO; 7: M=Ru, R = p-tolyl, L=CO; 8: M=Os, R=Me, L=CO; 9: M=Ru, R=Me, L=CN-p-tolyl; 10: M=Ru, R = n-butyl, L=CN-p-tolyl; 11: M=Os, R=Me, L=CN-p-tolyl). In addition, the chloride ligand in Ru(SnR₃)Cl(CO)(PPh₃)₂ proves to be labile and treatment with the potentially bidentate anionic ligands, dimethyldithiocarbamate or diethyldithiocarbamate, affords the coordinatively saturated compounds Ru(SnR₃)(η²-S₂CNR′₂)(CO)(PPh₃)₂ (12: R=Me, R′ = Me; 13: R=Me, R′ = Et; 14: R = n-butyl, R′ = Me; 15: R = p-tolyl, R′ = Me; 16: R = p-tolyl, R′ = Et). Chloride is also displaced by carboxylates forming the six-coordinate compounds Ru(SnR₃)(η²-O₂CR′)(CO)(PPh₃)₂ (17: R=Me, R′ = H; 18: R=Me, R′ = Me; 19: R=Me, R′ = Ph; 20: R = n-butyl, R′ = Me; 21: R = p-tolyl, R′ = Me). IR and ¹H NMR spectral data for all the new compounds and ³¹P and ¹¹⁹Sn NMR spectral data for selected compounds are reported.     

Confirmation of chromosome 7q11 locus for predisposition to intracranial aneurysm

A significant linkage of intracranial aneurysm (IA) has recently been reported to chromosomal region 7q11 (MLS=3.22) in a genomic search of 85 Japanese nuclear families with at least two affected siblings (104 sib pairs). This region contains the elastin gene (ELN, OMIM 130160), which is a functional candidate gene for IA. We have replicated this finding through linkage analyses in 13 extended pedigrees from Utah, comprising 39 IA cases. We genotyped three markers flanking ELN and performed two-point and multipoint parametric analyses, employing simple dominant and recessive models. Analyses utilizing a recessive affecteds-only model yielded significant confirmation of linkage to the region (best evidence, multipoint TLOD=2.34, at D7S2421, corrected P=0.001). This study is the first to confirm the linkage of the 7q11 locus for IA.     

End-tidal carbon dioxide tension reflects arterial carbon dioxide tension in the heat-stressed human with and without simulated hemorrhage

End-tidal carbon dioxide tension (Pet(CO(2))) is reduced during an orthostatic challenge, during heat stress, and during a combination of these two conditions. The importance of these changes is dependent on Pet(CO(2)) being an accurate surrogate for arterial carbon dioxide tension (Pa(CO(2))), the latter being the physiologically relevant variable. This study tested the hypothesis that Pet(CO(2)) provides an accurate assessment of Pa(CO(2)) during the aforementioned conditions. Comparisons between these measures were made: 1) after two levels of heat stress (N = 11); 2) during combined heat stress and simulated hemorrhage [via lower-body negative pressure (LBNP), N = 8]; and 3) during an end-tidal clamping protocol to attenuate heat stress-induced reductions in Pet(CO(2)) (N = 7). Pet(CO(2)) and Pa(CO(2)) decreased during heat stress (P < 0.001); however, there was no group difference between Pa(CO(2)) and Pet(CO(2)) (P = 0.36) nor was there a significant interaction between thermal condition and measurement technique (P = 0.06). To verify that this nonsignificant trend for the interaction was not due to a type II error, Pet(CO(2)) and Pa(CO(2)) at three distinct thermal conditions were also compared using paired t-tests, revealing no difference between Pa(CO(2)) and Pet(CO(2)) while normothermic (P = 0.14) and following a 1.0 ± 0.2°C (P = 0.21) and 1.4 ± 0.2°C (P = 0.28) increase in internal temperature. During LBNP while heat stressed, measures of Pet(CO(2)) and Pa(CO(2)) were similar (P = 0.61). Likewise, during the end-tidal carbon dioxide clamping protocol, the increases in Pet(CO(2)) (7.5 ± 2.8 mmHg) and Pa(CO(2)) (6.6 ± 3.4 mmHg) were similar (P = 0.31). These data indicate that mean Pet(CO(2)) reflects mean Pa(CO(2)) during the evaluated conditions.     

Use of heavy-metal clusters in the design of N-succinimidyl ester acylation reagents for side-chain-specific labeling of proteins.

New heavy transition metal carbonyl markers for protein labeling, containing an "Mn(CO)11" (M = Ru, Os, n = 3; M = Ir, n = 4) moiety, were prepared by reaction of "lightly stabilized" clusters with an N-succinimidyl ester functionalized phosphine, namely N-succinimidyl 3-diphenylphosphine-propionate (DPPS). The reaction of Os3(CO)11(DPPS) with the model amino acid beta-alanine was performed and led to the expected amide. From the reaction of Mn(CO)11(DPPS) with bovine serum albumin (BSA) in mixed organic/aqueous medium, conjugates bearing a fairly high number of metal carbonyl fragments were obtained, thus demonstrating the usefulness of this class of reagents for the selective and covalent graft of heavy metal clusters to side chain of proteins.     

Family study on the polymorphisms of the sixth and seventh components (C6 and C7) of human complement: linkage and haplotype analyses

Genetic polymorphisms of the sixth and seventh complement components (C6 and C7) have been studied in Japanese family material using polyacrylamide gel isoelectric focusing followed by immunoblotting. Three common and four rare alleles were observed at the locus for C6. Inheritance of the two rare C6 variants, M11 and B3, was first confirmed. Three common C7 allotypes were classified as C7 1, C7 2, and C7 4, respectively. Linkage analysis confirmed the close linkage between the loci for C6 and C7. The maximum lod score was 8.43 at phi = 0 (95% confidence limits: phi = 0 and phi = .07). No significant linkage disequilibrium was found between C6 and C7 in directly determined haplotypes of unrelated parents.     

Evidence That the Saethre-Chotzen Syndrome Locus Lies between D7S664 and D7S507, by Genetic Analysis and Detection of a Microdeletion in a Patient

The locus for Saethre-Chotzen syndrome, a common autosomal dominant disorder of craniosynostosis and digital anomalies, was previously mapped to chromosome 7p between D7S513 and D7S516. We used linkage and haplotype analyses to narrow the disease locus to an 8-cM region between D7S664 and D7S507. The tightest linkage was to locus D7S664 ( = 7.16, θ = .00). Chromosomes from a Saethre-Chotzen syndrome patient with t(2;7) (p23;p22) were used for in situ hybridization with YAC clones containing D7S664 and D7S507. The D7S664 locus was found to lie distal to the 7p22 breakpoint, and the D7S507 locus was deleted from the translocation chromosomes. These genetic and physical mapping data independently show that the disease locus resides in this interval.     

Loss of heterozygosity on chromosome 11p13 in primary bladder carcinoma

Although the occurrence of bladder cancer is common, the molecular events underlying the pathogenesis of this cancer remain ill-defined. A loss of heterozygosity (LOH) at specific chromosomal loci may predispose individuals to the development of bladder cancer but this has not been examined in detail. Furthermore, the role that deletion or inactivation of putative tumour suppressor genes might play in the genesis of bladder cancer has not been established. In this study, allelic deletion analysis on the short arm of chromosome 17 of patients with primary bladder tumours failed to show deletion at 17p13 (0/7), a region known to contain the p53 tumour suppressor gene. Chromosome 11p15 showed allelic deletion at the IGF2 locus (2/7: 29%) and the PTH locus (1/11: 9%). However, no deletion was observed at the CALCA locus (0/6). LOH at 11p13, a region containing the Wilm's tumour suppressor gene (WT1), was also studied. Analysis of LOH at 11p13 showed deletion at the CAT locus (13/18: 72%), the J/D11S414 locus (5/15: 33%), the WT1 locus (7/14: 50%) and the FSHB locus (6/16: 38%). The significance of these findings is discussed.     

ADIPOQ,KCNJ11 and TCF7L2 polymorphisms in type 2 diabetes in Kyrgyz population: A case‐control study

The aim of this study was to ascertain the polymorphic markers profile of ADIPOQ, KCNJ11 and TCF7L2 genes in Kyrgyz population and to analyze the association of polymorphic markers and combinations of ADIPOQ gene's G276T locus, KCNJ11 gene's Glu23Lys locus and TCF7L2 gene's VS3C>T locus with type two diabetes (T2D) in Kyrgyz population. In this case‐control study, 114 T2D patients 109 non‐diabetic participants were genotyped using polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP). Two individual polymorphisms (ADIPOQ rs1501299, KCNJ11 rs5219) were found to be associated with T2D. We found two (Lys23Lys/CC and Glu23Lys/CT) of the overall nine combinations, which were more prevalent in T2D group compared to controls (χ² = 4.21, P = 0.04). Lys23Lys/CC combination was associated with a 2.65‐fold increased likelihood of T2D (OR = 2.65, 95% CI 1.12‐6.28), whereas the Glu23Lys/CT combination also increased such likelihood (OR = 3.88, 95% CI 1.27‐11.91). This study demonstrated some association of 276T allele and ADIPOQ gene G276T heterozygous genotype as well as KCNJ11 gene 23Lys allele with T2D in ethnic Kyrgyz, but study results should be interpreted with caution because of the limited statistical power.     

High-resolution mapping of the blood pressure QTL on chromosome 7 using Dahl rat congenic strains

It was previously shown using Dahl salt-sensitive (S) and salt-resistant (R) rats that a blood pressure quantitative trait locus (QTL) was present on rat chromosome 7. In the present work, this QTL was localized to a region less than 0.54 cM in size on the linkage map using a series of congenic strains. This region was contained in a single yeast artificial chromosome that was 220 kb long. This small segment still contained the primary candidate locus Cyp11b1 (11beta-hydroxylase), but the adjacent candidate genes Cyp11b2 (aldosterone synthase) and Cyp11b3 were ruled out. It is concluded that 11beta-hydroxylase, through its known genetic variants altering the production of 18-hydroxy-11-deoxy corticosterone, is very likely to account for the blood pressure QTL on chromosome 7 in the Dahl rat model of hypertension. This QTL accounts for about 23 mm Hg under the condition of 2% NaCl diet for 24 days.     

A further study of a possible locus for schizophrenia on the X chromosome

Several studies suggest that the X chromosome may contain a gene for schizophrenia. In the present study, we recruited 142 male schizophrenic patients and their biological mothers from all parts of the United Kingdom to detect a genetic association for the SYP/CACNA1F locus in the Xp11 region and the FACL4 locus in the Xq22.3-Xq23 region. The haplotype-based haplotype relative risk (HHRR) analysis showed allelic association for rs2071316 (chi2=6.85, P=0.009) and rs5905724 (chi2=5.3, P=0.021) at the CACNA1F locus, but not for rs5943414 and rs1324805 at the FACL4 locus and rs3817678 at the SYP locus. The haplotype analysis showed a weak association for the rs3817678-rs2071316-rs5905724 haplotypes (chi2=12.19, df=4, P=0.016) but did not show such an association for the rs5943414-rs1324805 haplotypes (chi2=3.96, df=2, P=0.138). Because the linkage disequilibrium signal was detected only at the CACNA1F locus, this gene should perhaps be considered as being a candidate for schizophrenia although further work is needed to draw firm conclusions.