Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves

Alcohol dependence is a serious public health problem. We studied data from families participating in the Collaborative Study on the Genetics of Alcoholism (COGA) and made available to participants in the Genetic Analysis Workshop 14 (GAW14) in order to search for genes predisposing to alcohol dependence. Using factor analysis, we identified four factors (F1, F2, F3, F4) related to the electroencephalogram traits. We conducted variance components linkage analysis with each of the factors. Our results using the Affymetrix single-nucleotide polymorphism dataset showed significant evidence for a novel linkage of F3 (factor comprised of the three midline channel EEG measures from the target case of the Visual Oddball experiment ttdt2, 3, 4) to chromosome 18 (LOD = 3.45). This finding was confirmed by analyses of the microsatellite data (LOD = 2.73) and Illumina SNP data (LOD = 3.30). We also demonstrated that, in a sample like the COGA data, a dense single-nucleotide polymorphism map provides better linkage signals than low-resolution microsatellite map with quantitative traits.     

Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellites

Alcoholism is a complex disease. As with other common diseases, genetic variants underlying alcoholism have been illusive, possibly due to the small effect from each individual susceptible variant, gene x environment and gene x gene interactions and complications in phenotype definition. We conducted association tests, the family-based association tests (FBAT) and the backward haplotype transmission association (BHTA), on the Collaborative Study of the Genetics of Alcoholism (COGA) data provided by Genetic Analysis Workshop (GAW) 14. Efron's local false discovery rate method was applied to control the proportion of false discoveries. For FBAT, we compared the results based on different types of genetic markers (single-nucleotide polymorphisms (SNPs) versus microsatellites) and different phenotype definitions (clinical diagnoses versus electrophysiological phenotypes). Significant association results were found only between SNPs and clinical diagnoses. In contrast, significant results were found only between microsatellites and electrophysiological phenotypes. In addition, we obtained the association results for SNPs and microsatellites using COGA diagnosis as phenotype based on BHTA. In this case, the results for SNPs and microsatellites are more consistent. Compared to FBAT, more significant markers are detected with BHTA.     

Linkage analysis and association analysis in the presence of linkage using age at onset of COGA alcoholism data

Complex disease mapping usually involves a combination of linkage and association techniques. Linkage analysis can scan the entire genome in a few hundred tests. Association tests may involve an even greater number of tests. However, association tests can localize the susceptibility genes more accurately. Using a recently developed combined linkage and association strategy, we analyzed a subset of the Collaborative Study on the Genetics of Alcoholism (COGA) data for the Genetic Analysis Workshop 14 (GAW14). In this analysis, we first employed linkage analysis based on frailty models that take into account age of onset information to establish which regions along the chromosome are likely to harbor disease susceptibility genes for alcohol dependence. Second, we used an association analysis by exploiting linkage disequilibrium to narrow down the peak regions. We also compare the methods with mean identity-by-descent tests and transmission/disequilibrium tests that do not use age of onset information.     

A genome-wide linkage analysis of alcoholism on microsatellite and single-nucleotide polymorphism data,using alcohol dependence phenotypes and electroencephalogram measures

The Collaborative Study on the Genetics of Alcoholism (COGA) is a large-scale family study designed to identify genes that affect the risk for alcoholism and alcohol-related phenotypes. We performed genome-wide linkage analyses on the COGA data made available to participants in the Genetic Analysis Workshop 14 (GAW 14). The dataset comprised 1,350 participants from 143 families. The samples were analyzed on three technologies: microsatellites spaced at 10 cM, Affymetrix GeneChip Human Mapping 10 K Array (HMA10K) and Illumina SNP-based Linkage III Panel. We used ALDX1 and ALDX2, the COGA definitions of alcohol dependence, as well as electrophysiological measures TTTH1 and ECB21 to detect alcoholism susceptibility loci. Many chromosomal regions were found to be significant for each of the phenotypes at a p-value of 0.05. The most significant region for ALDX1 is on chromosome 7, with a maximum LOD score of 2.25 for Affymetrix SNPs, 1.97 for Illumina SNPs, and 1.72 for microsatellites. The same regions on chromosome 7 (96-106 cM) and 10 (149-176 cM) were found to be significant for both ALDX1 and ALDX2. A region on chromosome 7 (112-153 cM) and a region on chromosome 6 (169-185 cM) were identified as the most significant regions for TTTH1 and ECB21, respectively. We also performed linkage analysis on denser maps of markers by combining the SNPs datasets from Affymetrix and Illumina. Adding the microsatellite data to the combined SNP dataset improved the results only marginally. The results indicated that SNPs outperform microsatellites with the densest marker sets performing the best.     

Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses

We compared linkage analysis results for an alcoholism trait, ALDX1 (DSM-III-R and Feigner criteria) using a nonparametric linkage analysis method, which takes into account allele sharing among several affected persons, for both microsatellite and single-nucleotide polymorphism (SNP) markers (Affymetrix and Illumina) in the Collaborative Study on the Genetics of Alcoholism (COGA) dataset provided to participants at the Genetic Analysis Workshop 14 (GAW14). The two sets of linkage results from the dense Affymetrix SNP markers and less densely spaced Illumina SNP markers are very similar. The linkage analysis results from microsatellite and SNP markers are generally similar, but the match is not perfect. Strong linkage peaks were found on chromosome 7 in three sets of linkage analyses using both SNP and microsatellite marker data. We also observed that for SNP markers, using the given genetic map and using the map by converting 1 megabase pair (1 Mb) to 1 centimorgan (cM), did not change the linkage results. We recommend the use of the 1 Mb-to-1 cM converted map in a first round of linkage analysis with SNP markers in which map integration is an issue.     

Investigation of altering single-nucleotide polymorphism density on the power to detect trait loci and frequency of false positive in nonparametric linkage analyses of qualitative traits

Genome-wide linkage analysis using microsatellite markers has been successful in the identification of numerous Mendelian and complex disease loci. The recent availability of high-density single-nucleotide polymorphism (SNP) maps provides a potentially more powerful option. Using the simulated and Collaborative Study on the Genetics of Alcoholism (COGA) datasets from the Genetics Analysis Workshop 14 (GAW14), we examined how altering the density of SNP marker sets impacted the overall information content, the power to detect trait loci, and the number of false positive results. For the simulated data we used SNP maps with density of 0.3 cM, 1 cM, 2 cM, and 3 cM. For the COGA data we combined the marker sets from Illumina and Affymetrix to create a map with average density of 0.25 cM and then, using a sub-sample of these markers, created maps with density of 0.3 cM, 0.6 cM, 1 cM, 2 cM, and 3 cM. For each marker set, multipoint linkage analysis using MERLIN was performed for both dominant and recessive traits derived from marker loci. Our results showed that information content increased with increased map density. For the homogeneous, completely penetrant traits we created, there was only a modest difference in ability to detect trait loci. Additionally, as map density increased there was only a slight increase in the number of false positive results when there was linkage disequilibrium (LD) between markers. The presence of LD between markers may have led to an increased number of false positive regions but no clear relationship between regions of high LD and locations of false positive linkage signals was observed.     

The collaborative study on the genetics of alcoholism: Sample and clinical data

The collaborative study on the genetics of alcoholism (COGA) is a multi-site, multidisciplinary project with the goal of identifying how genes are involved in alcohol use disorder and related outcomes, and characterizing how genetic risk unfolds across development and in conjunction with the environment and brain function. COGA is a multi-generational family-based study in which probands were recruited through alcohol treatment centers, along with a set of community comparison families. Nearly 18,000 individuals from >2200 families have been assessed over a period of over 30 years with a rich phenotypic battery that includes semi-structured psychiatric interviews and questionnaire measures, along with DNA collection and electrophysiological data on a large subset. Participants range in age from 7 to 97, with many having longitudinal assessments, providing a valuable opportunity to study alcohol use and problems across the lifespan. Here we provide an overview of data collection methods for the COGA sample, and details about sample characteristics and comorbidity. We also review key research findings that have emerged from analyses of the COGA data. COGA data are available broadly to researchers, and we hope this overview will encourage further collaboration and use of these data to advance the field.     

Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure

Single-nucleotide polymorphisms (SNPs) are a class of attractive genetic markers for population genetic studies and for identifying genetic variations underlying complex traits. However, the usefulness and efficiency of SNPs in comparison to microsatellites in different scientific contexts, e.g., population structure inference or association analysis, still must be systematically evaluated through large empirical studies. In this article, we use the Collaborative Studies on Genetics of Alcoholism (COGA) data from Genetic Analysis Workshop 14 (GAW14) to compare the performance of microsatellites and SNPs in the whole human genome in the context of population structure inference. A total of 328 microsatellites and 15,840 SNPs are used to infer population structure in 236 unrelated individuals. We find that, on average, the informativeness of random microsatellites is four to twelve times that of random SNPs for various population comparisons, which is consistent with previous studies. Our results also indicate that for the combined set of microsatellites and SNPs, SNPs constitute the majority among the most informative markers and the use of these SNPs leads to better inference of population structure than the use of microsatellites. We also find that the inclusion of less informative markers may add noise and worsen the results.     

The effect of linkage disequilibrium on linkage analysis of incomplete pedigrees

Dense SNP maps can be highly informative for linkage studies. But when parental genotypes are missing, multipoint linkage scores can be inflated in regions with substantial marker-marker linkage disequilibrium (LD). Such regions were observed in the Affymetrix SNP genotypes for the Genetic Analysis Workshop 14 (GAW14) Collaborative Study on the Genetics of Alcoholism (COGA) dataset, providing an opportunity to test a novel simulation strategy for studying this problem. First, an inheritance vector (with or without linkage present) is simulated for each replicate, i.e., locations of recombinations and transmission of parental chromosomes are determined for each meiosis. Then, two sets of founder haplotypes are superimposed onto the inheritance vector: one set that is inferred from the actual data and which contains the pattern of LD; and one set created by randomly selecting parental alleles based on the known allele frequencies, with no correlation (LD) between markers. Applying this strategy to a map of 176 SNPs (66 Mb of chromosome 7) for 100 replicates of 116 sibling pairs, significant inflation of multipoint linkage scores was observed in regions of high LD when parental genotypes were set to missing, with no linkage present. Similar inflation was observed in analyses of the COGA data for these affected sib pairs with parental genotypes set to missing, but not after reducing the marker map until r2 between any pair of markers was 相似文献   

Synchronization and resynchronization of inseminations in lactating dairy cows with the CIDR insert and the Ovsynch protocol

Pregnancy per artificial insemination (AI) was evaluated in dairy cows (Bos taurus) subjected to synchronization and resynchronization for timed AI (TAI). Cows (n = 718) received prostaglandin F_2α (PGF) on Days –38 and –24 (Days 39 and 53 postpartum), gonadotropin-releasing hormone (GnRH) on Day –10, PGF on Day –3, and GnRH and TAI on Day 0. Between Days –10 and –3, cows received a progesterone intravaginal insert (CIDR group) or no CIDR (Control group). Between Days 14 and 23, cows received a CIDR (Resynch CIDR group) or no CIDR (Resynch control group), GnRH on Day 23, with pregnancy diagnosis on Day 30. Cows in estrus (between Days 0 and 30) were re-inseminated at detected estrus (RIDE). Nonpregnant cows received PGF on Day 30 and GnRH and TAI on Day 33. Plasma progesterone was determined to be low or high on Days –24 and –10. Pregnancy rates were evaluated 30 and 55 d after AI. The CIDR insert included in the Presynch-Ovsynch protocol did not increase overall pregnancy per AI for first service (36.1% and 33.6% for CIDR; 34.1% and 28.8% for Control) but did decrease pregnancy loss (7.0% for CIDR and 15.6% for Control). The CIDR insert increased pregnancy per AI in cows with high progesterone at the time the CIDR insert was applied. Administration of a CIDR insert between Days 14 and 23 of the estrous cycle after first service did not increase overall pregnancy per AI to second service (24.7% and 22.7% for Resynch CIDR; 28.6% and 25.3% for Resynch control). For second service, RIDE cows had lower pregnancy rates in the Resynch CIDR group than in the Resynch control group. Cows with a CL (corpus luteum) at Day 30 had higher pregnancy rates in the Resynch CIDR group than those in the Resynch control group.     

The collaborative study on the genetics of alcoholism: Brain function

Alcohol use disorder (AUD) and related health conditions result from a complex interaction of genetic, neural and environmental factors, with differential impacts across the lifespan. From its inception, the Collaborative Study on the Genetics of Alcoholism (COGA) has focused on the importance of brain function as it relates to the risk and consequences of alcohol use and AUD, through the examination of noninvasively recorded brain electrical activity and neuropsychological tests. COGA's sophisticated neurophysiological and neuropsychological measures, together with rich longitudinal, multi-modal family data, have allowed us to disentangle brain-related risk and resilience factors from the consequences of prolonged and heavy alcohol use in the context of genomic and social-environmental influences over the lifespan. COGA has led the field in identifying genetic variation associated with brain functioning, which has advanced the understanding of how genomic risk affects AUD and related disorders. To date, the COGA study has amassed brain function data on over 9871 participants, 7837 with data at more than one time point, and with notable diversity in terms of age (from 7 to 97), gender (52% female), and self-reported race and ethnicity (28% Black, 9% Hispanic). These data are available to the research community through several mechanisms, including directly through the NIAAA, through dbGAP, and in collaboration with COGA investigators. In this review, we provide an overview of COGA's data collection methods and specific brain function measures assessed, and showcase the utility, significance, and contributions these data have made to our understanding of AUD and related disorders, highlighting COGA research findings.     

The 9-day CIDR-PG protocol: Incorporation of PGF2α pretreatment into a long-term progestin-based estrus synchronization protocol for postpartum beef cows

A pilot experiment was designed to test the hypothesis that administration of PGF_2α before progestin treatment would allow for a reduced duration of progestin treatment in a long-term progestin-based estrus synchronization protocol. A modified presynchronization treatment was compared with a standard long-term controlled internal drug release (CIDR) treatment, and treatments were compared on the basis of ovarian follicular dynamics, estrous response rate, synchrony of estrus expression, and pregnancy rates resulting from timed artificial insemination (TAI) in postpartum beef cows. Estrous was synchronized for 85 cows, with cows assigned to one of two treatments based on age, days postpartum, and body condition score. Cows assigned to the 14-day CIDR-PG protocol received a CIDR insert (1.38 g progesterone) on Day 0, CIDR removal on Day 14, and administration of PGF_2α (25 mg im) on Day 30. Cows assigned to the 9-day CIDR-PG protocol received PGF_2α concurrent with CIDR insertion on Day 5, PGF_2α concurrent with CIDR removal on Day 14, and administration of PGF_2α on Day 30. In both treatments, split-time AI was performed based on estrous response. At 72 hours after PGF_2α (Day 33), cows having expressed estrus received TAI; cows that failed to express estrus by 72 hours received TAI 24 hours later (96 hours after PGF_2α on Day 34), with GnRH (100 μg im) administered to nonestrous cows. Estrus-detection transmitters were used from CIDR removal until AI to determine onset time of estrus expression both after CIDR removal and after PGF_2α. Ovarian ultrasonography was performed at CIDR removal on Day 14, PGF_2α on Day 30, and AI on Days 33 or 34. At CIDR removal on Day 14, diameter of the largest follicle present on the ovary was similar between treatments. The proportion of cows expressing estrus after CIDR removal tended to be higher (P = 0.09) among cows assigned to the 9-day CIDR-PG treatment (93%; 40 of 43) than among cows assigned to the 14-day CIDR-PG treatment (81%; 34 of 42). After PGF_2α, a significantly higher proportion (P = 0.02) of cows expressed estrus after synchronization with the 9-day CIDR-PG treatment (91%; 39 of 43) than the 14-day CIDR-PG treatment (69%; 29 of 42). Consequently, pregnancy rate to TAI tended to be increased (P = 0.09) among the 9-day CIDR-PG treatment (76.7%; 33 of 43) compared with the 14-day CIDR-PG treatment (59.5%; 25 of 42). In summary, a long-term CIDR-based estrous synchronization protocol for postpartum beef cows was enhanced through administration of PGF_2α at CIDR insertion and CIDR removal.     

Study of sexual behaviours with different types of estrus synchronization protocols in Boer goats

There is still a lack of information on estrus synchronization in goats. Understanding the estrus synchronization protocols and the subsequent effects is important to improve the efficiency of assisted reproductive technologies (ARTs) and subsequently would improve the breeding procedures. This study will help in determining the most suitable estrus synchronization protocol and understand better the effect on the sexual behaviour and hormonal effects in goats. A total of 127 Boer does were used and divided into three groups with different duration of CIDR insertion intravaginally either for 14 (two groups) or 9 days (one group). Approximately 0.5 ml Estrumate^® (PG) was administered intramuscularly to all groups at CIDR removal, and only groups PMSG14 and PMSG9 were administered with 200IU of Pregnant Mare Serum Gonadotropin (PMSG) intramuscularly. Estrus signs were observed at 4 h intervals and blood samples were collected for progesterone and luteinizing hormone determination. The percentage of does in estrus within 24 to 72 h post CIDR removal was significantly higher (P<0.05) in groups with PMSG compared to the group without the PMSG. The numbers of does display estrus signs within 24 to 28 h post CIDR removal were significantly higher (P<0.05) in group shorter period (9 days) compared to groups with 14 days CIDR. The P4 concentrations at 24 hours post CIDR removals and LH concentration was not significantly different (P>0.05) in all groups. The time of the LH peak in the group without the PMSG was significantly delayed (P<0.05) when compared to group 9 days CIDR and administered with PMSG. It is recommended to use the treatment for 9 days CIDR since the estrous cycle can be shortened.     

Genome Annotation Resource Fields--GARFIELD: a genome browser for Felis catus

Annotation features from the 1.9-fold whole-genome shotgun (WGS) sequences of domestic cat have been organized into an interactive web application, Genome Annotation Resource Fields (GARFIELD) (http://lgd.abcc.ncifcrf.gov) at the Laboratory of Genomic Diversity and Advanced Biomedical Computing Center (ABCC) at The National Cancer Institute (NCI). The GARFIELD browser allows the user to view annotations on a per chromosome basis with unplaced contigs provided on placeholder chromosomes. Various tracks on the browser allow display of annotations. A Genes track on the browser includes 20 285 regions that align to genes annotated in other mammalian genomes: Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, Bos taurus, and Canis familiaris. Also available are tracks that display the contigs that make up the chromosomes and representations of their GC content and repetitive elements as detected using the RepeatMasker (http://www.repeatmasker.org). Data from the browser can be downloaded in FASTA and GFF format, and users can upload their own data to the display. The Felis catus sequences and their chromosome assignments and additional annotations incorporate data analyzed and produced by a multicenter collaboration between NCI, ABCC, Agencourt Biosciences Corporation, Broad Institute of Harvard and Massachusetts Institute of Technology, National Human Genome Research Institute, National Center for Biotechnology and Information, and Texas A&M.     

The efficacy of controlled internal drug release (CIDR) in synchronizing the follicular wave in dromedary camels (Camelus dromedarius) during the breeding season

The present study aimed to evaluate the efficacy of controlled internal drug release (CIDR) to synchronize the follicular wave in dromedary camels (Camelus dromedarius) during the breeding season through ovarian monitoring, evaluating sexual receptivity, and measuring progesterone (P4) and estradiol (E2) levels during and after CIDR treatment. Sixteen camels received a new CIDR containing 1.9 g of P4 for 14 days. Ultrasound ovarian monitoring was performed on the day of insertion and every 3 days until the CIDR was withdrawn. Ultrasound examinations were continued day in day out after the CIDR was withdrawn for 10 days. According to the ultrasound examinations, the percentages of camels in the breeding (follicles: 12–18 mm) and nonbreeding phases were calculated. Blood samples were collected day after day during the experimental period (24 days) from the day that the CIDR was inserted. The serum P4 and E2 concentrations were analyzed using ELISA kits. The sexual receptivity of the camels was tested daily during the course of the experiment. The results revealed that 2 and 4 days after the CIDR was withdrawn, the percentage of camels in the breeding phase (68.75% and 75.00%, respectively) was significantly (P < 0.05) higher than that in the nonbreeding phase (31.25% and 25.00%, respectively). The percentage of camels that were abstinent during CIDR treatment was significantly (P < 0.05) higher than that observed for those who were incompletely receptive or completely receptive. The P4 levels increased significantly (P < 0.05) 2 days after CIDR insertion (1.73 ng/mL) and reached maximum values (2.94 ng/mL) at Day 12. Significant (P < 0.05) decreases in the P4 levels were observed 2 to 4 days after CIDR withdrawal (1.01 and 0.80 ng/mL, respectively). The P4 levels reached minimum values (0.18–0.22 ng/mL) at Day 20 through the end of the experiment. The E2 levels differed insignificantly during and after CIDR treatment in dromedary camels. In conclusion, the treatment of dromedary camels with CIDR produced a uniform increase in serum concentrations of P4 that could completely prevent sexual receptivity but could not suppress the follicular wave. After CIDR withdrawal, the P4 levels fell and induced the emergence of a new follicular wave, and most of the camels were in the breeding (ovulatory) phase 2 to 4 days after withdrawal. Therefore, CIDR can be used to synchronize the follicular wave in dromedary camels.     

Ultrasonic identification of follicular populations and return to estrus in early postpartum dairy cows given intravaginal progesterone for 15 days

In an attempt to program ovarian function in the early post partum period, 52 lactating Holstein cows were injected with 25 mg prostaglandin F(2alpha) (PGF) and given a CIDR device containing 1.9 g progesterone for 15 d starting on Day 25 post partum. Ovarian follicles were measured by ultrasound on 0, 5, 10 and 15 d after insertion and on alternate days after CIDR removal until estrus. Not all cows were devoid of corpora lutea (CL) during the CIDR (11, 9 and 8 cows had a CL on Days 5, 10 and 15, respectively). There was a CL by day interaction (P<0.01) for the number of 10- to 15-mm follicles per cow; the average number of large follicles (>15 mm) was twice greater (0.75 vs 0.37) for those cows not having a CL during the period of CIDR exposure. The average size of the largest follicle increased to a maximum of 19.3 +/- 0.7 mm by 15 d after insertion in cows not having a CL. Plasma estradiol increased for 10 d after insertion, then decreased to the end of the CIDR period. After removal of the CIDR, 34 cows ovulated, eight cows developed ovarian follicular cysts, and eight cows did not ovulated by 14 d. Cows becoming cystic or not ovulating had a declining number of follicles during the CIDR compared with those cows ovulating (P<0.07). The diameter of the largest follicle in cystic cows was equivalent to noncystic cows until removal of the CIDR, but then it increased markedly. Interval to estrus was longer in cows having more 6- to 9-mm follicles on Day 15 (day of CIDR removal). These results demonstrate the existence and maintenance of a large dominant follicle after CIDR insertion and PGF injection which was influenced apparently by the presence of a CL. Furthermore, subsequent reproductive responses after the CIDR treatment was a function of follicular populations prior to withdrawal of the CIDR device. This system may be appropriate for the study of factors regulating follicular growth and fertility in domestic cattle.     

Effect of CIDR-based protocols for timed-AI on the conception rate and ovarian functions of Japanese Black beef cows in the early postpartum period

Our objectives were to compare: (1) conception rates (in early postpartum Japanese Black beef cows) to timed-artificial insemination (timed-AI) among Ovsynch and Ovsynch plus CIDR protocols, and a protocol that used estradiol benzoate (EB) in lieu of the first GnRH of the Ovsynch plus CIDR; and (2) the effects of these protocols on blood concentrations of ovarian steroids. Cows in the control group (Ovsynch; n=35) underwent a standard Ovsynch protocol (GnRH analogue on Day 0, PGF(2 alpha) analogue on Day 7 and GnRH analogue on Day 9), with timed-AI on Day 10, approximately 20 h after the second GnRH treatment. Cows in the Ovsynch+CIDR group (n=31) received a standard Ovsynch protocol plus a CIDR for 7 days (starting on Day 0). Cows in the third treatment group (EB+CIDR+GnRH; n=41) received 2mg of EB on Day 0 in lieu of the first GnRH treatment, followed by the same treatment as in the Ovsynch+CIDR protocol. The conception rate tended to be greater in the Ovsynch+CIDR group (67.7%, P<0.15) and was greater in the EB+CIDR+GnRH (73.2%, P<0.05) and CIDR-combined (both CIDR-treated groups were combined) groups (70.8%, P<0.05) than in the Ovsynch group (48.6%). Plasma progesterone concentrations were higher on Day 7 (P<0.01) and lower on Days 14, 17 and 21 (P<0.001) in the CIDR-combined group than in the Ovsynch group. Plasma estradiol-17beta concentrations were higher on Day 7 in the Ovsynch group of non-pregnant cows than in the CIDR-combined group of non-pregnant cows and in an all-combined group (all treatment groups combined) of pregnant cows (P<0.01). Furthermore, estradiol-17beta concentrations were lower on Day 9 in the Ovsynch and CIDR-combined groups of non-pregnant cows than in the all-combined group of pregnant cows (P<0.05). In conclusion, both protocols using CIDR improved conception rates following timed-AI in early postpartum suckled Japanese Black beef cows relative to the Ovsynch protocol. Treatment with a CIDR may prevent early maturation of follicles observed in non-pregnant cows treated with the Ovsynch protocol, by maintaining elevated blood progesterone concentrations until PGF(2 alpha) treatment.     

The challenge of detecting genotype-by-methylation interaction: GAW20

Background

GAW20 working group 5 brought together researchers who contributed 7 papers with the aim of evaluating methods to detect genetic by epigenetic interactions. GAW20 distributed real data from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study, including single-nucleotide polymorphism (SNP) markers, methylation (cytosine-phosphate-guanine [CpG]) markers, and phenotype information on up to 995 individuals. In addition, a simulated data set based on the real data was provided.

Results

The 7 contributed papers analyzed these data sets with a number of different statistical methods, including generalized linear mixed models, mediation analysis, machine learning, W-test, and sparsity-inducing regularized regression. These methods generally appeared to perform well. Several papers confirmed a number of causative SNPs in either the large number of simulation sets or the real data on chromosome 11. Findings were also reported for different SNPs, CpG sites, and SNP–CpG site interaction pairs.

Conclusions

In the simulation (200 replications), power appeared generally good for large interaction effects, but smaller effects will require larger studies or consortium collaboration for realizing a sufficient power.

     

Early pregnancy detection and the hormonal characterization of embryonic-fetal mortality in fallow deer (Dama dama)

The objectives of this investigation were to 1) determine serum concentrations of progesterone (P4), estrone sulfate (E1S) and pregnancy-specific protein B (PSPB) from estrus synchronization through mid-gestation in the fallow doe (Dama dama) and 2) characterize the hormonal profiles of does whose embryos or fetuses died in utero. Ten fallow does were synchronized for 14 d with an intravaginal P4-releasing device (CIDR) and were naturally mated after CIDR removal. Blood samples were collected at CIDR insertion, CIDR removal and at intervals through Day 203 post-CIDR removal for analysis of P4, E1S and PSPB by radioimmunoassay (RIA). Ultrasonography was performed on Days 49 and 69 post-CIDR removal. Serum P4 at the time of CIDR insertion was 4.8 +/- 0.6 ng/ml, and at CIDR withdrawal it was 6.2 +/- 0.3 ng/ml. Concentrations of E1S and PSPB were nondetectable at CIDR insertion. Serum E1S was highest at Day 93, and PSPB was first detectable in pregnant does at Days 27 to 30 post-CIDR withdrawal. Ultrasonography on Day 49 revealed that 6 does were pregnant, 2 were not pregnant and 2 others were diagnosed originally as early pregnant. At Day 69, ultrasonography revealed that 6 does (60%) were pregnant and 4 (40%) were not. A comparison of the ultrasonographic and hormonal data indicated that the 2 does diagnosed as early pregnant on Day 49 had conceived but had lost the pregnancy. A third doe which was pregnant on Day 69 lost the fetus later in gestation. Hormonal profiles of does whose embryo or fetus had died were characterized by erratic P4 and E1S profiles, with PSPB becoming undetectable in the 3 does by Days 49, 65 and 80 post-CIDR removal. These data 1) demonstrate the timing for the collection of serum samples for determining early pregnancy in fallow does using 3 hormonal methods and 2) characterize the hormonal profiles of 3 fallow does with embryonic-fetal loss.     

Analysis of the raw starch-binding domain by mutation of a glucoamylase from Aspergillus awamori var. kawachi expressed in Saccharomyces cerevisiae.

Carboxy-terminal deletions were introduced into the raw starch-binding domain (A-515 to R-615) encoded by the gene for glucoamylase I (GAI) from Aspergillus awamori var. kawachi. Genes coding for proteins designated GA596 (A-1 to E-596), GA570 (A-1 to A-570), and GA559 (A-1 to N-559) were constructed and resulted in truncated proteins. All of the mutant genes were expressed heterologously in Saccharomyces cerevisiae. GA596 adsorbed to raw starch and digested it. GA570 and GA559 did not adsorb to raw starch or to an alpha-cyclodextrin-Sepharose CL-4B gel under our experimental conditions. However, GA570 was able to digest raw starch, and the digestion of raw starch by GA570 was inhibited by beta-cyclodextrin. Residue Trp-562 of GAI, which was suggested previously to contribute to formation of an inclusion complex with raw starch, was replaced by Leu (GAW562L), Phe (GAW562F), and Gly (GAW562G). GAW562L and GAW562F adsorbed to raw starch and an alpha-cyclodextrin gel, but GAW562G did not. Although GAW562L digested raw starch to the same extent as wild-type GAI (designated GAY), GAW562F and GAW562G exhibited less ability to digest raw starch. On the basis of our results, it appears that the sequence around Trp-562, PL(W-562)YVTVTLPA, is the minimal sequence necessary for digestion of raw starch and that hydrophobic residue Trp-562 contributes to formation of an inclusion complex. The sequence near Trp-589, which has abundant hydrogen bond-forming residues and the charged amino acid residues needed for stable adsorption to raw starch, probably assists in the formation of the inclusion complex.