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T L Bailey

Publications and source records attributed to T L Bailey.

At least 19 recordsLinked to original sources
PubMed2005

The transcriptional landscape of the mammalian genome.

This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

3' Untranslated Regions↗
PubMed2004

Xenogenous fertilization of equine oocytes following recovery from slaughterhouse ovaries and in vitro maturation.

The in vitro production (IVP) of equine embryos using currently available protocols has met limited success; therefore investigations into alternative approaches to IVP are justified. The objective of this study was to evaluate the feasibility of xenogenous fertilization and early embryo development of in vitro matured (IVM) equine oocytes. Follicular aspirations followed by slicing of ovarian tissue were performed on 202 equine ovaries obtained from an abattoir. A total of 667 oocytes (3.3 per ovary) were recovered from 1023 follicles (recovery rate, 65%). Oocytes underwent IVM for 41 +/- 2 h (mean +/- S.D.), before being subjected to xenogenous gamete intrafallopian transfer (XGIFT). An average of 13 +/- 0.8 oocytes and 40x10(3) spermatozoa per oocyte were transferred into 20 oviducts of ewes. Fourteen percent of transferred oocytes (36/259) were recovered between 2 and 7 days post-XGIFT and 36% of those recovered displayed embryonic development ranging from the 2-cell to the blastocyst stage. Fertilization following XGIFT was also demonstrated by the detection of zinc finger protein Y (ZFY) loci. Ligation of the uterotubal junction (UTJ), ovarian structures, or the duration of oviductal incubation did not significantly affect the frequency of embryonic development or recovery of oocytes/embryos after XGIFT. In conclusion, equine embryos can be produced in a smaller non-equine species that is easier for handling.

Animals↗
PubMed2002

Milk yield, energy balance, hormone, follicular and oocyte measures in early and mid-lactation Holstein cows.

The purpose of the study was to determine the influence of energy status on metabolic and endocrine measures, follicular development, and the quality of oocytes obtained from cows during early and mid-lactation (ML). We selected Holstein cows at calving to be assigned to the early lactation (EL) group (n = 8), while we assigned cows at about day 90 postpartum to the ML group (n = 7). We obtained blood samples twice weekly from 4 weeks before aspiration to the aspiration periods for metabolite and hormone determinations. We performed ultrasound-guided transvaginal follicular aspiration (TVFA) twice weekly on all cows for a 10-week period. We obtained follicular fluid from the largest follicle > 10 mm in diameter for hormone determinations. We analyzed data by ANOVA, using the general linear model (GLM) procedures. Energy balance was positive (2.43 +/- 0.32 Mcal/kg) for ML cows and negative (-1.55 +/- 0.33 Mcal/kg) for EL cows. Serum progesterone (P4) for ML cows decreased rapidly from the first aspiration session (2.7 +/- 0.1 ng/ml) and reached a nadir at Week 8 (0.33 +/- 0.1 ng/ml), while follicular fluid P4 increased from 0.9 +/- 0.5 to 5.6 +/- 0.05 ng/ml. Serum and follicular fluid P4 remained relatively constant over the entire aspiration period for EL cows. Follicular fluid insulin-like growth factor I (TGF-I) concentrations increased linearly for EL and ML cows, but the increase was more rapid (159 +/- 36 to 200 +/- 36 ng/ml) for ML cows than for EL cows (145 +/- 36 to 164 +/- 36 ng/ml). Serum IGF-I followed the same pattern for ML cows but declined for EL cows. Early lactation cows experienced a rapid decrease in serum nonesterified fatty acids (NEFA; 0.32 +/- 0.2 to 0.22 +/- 0.2 meq/l), while serum NEFA concentrations were relatively stable (0.19 +/- 0.2 to 0.22 +/- 0.2 meq/l) for ML cows over the aspiration period. The number of follicles obtained from the twice weekly aspiration sessions increased linearly for both EL and ML cows (P < 0.05) over the 10-week period. However, the number of follicles increased from 14.2 +/- 0.5 (Day 119) to 18.1 +/- 0.5 (Day 190) in the ML cows, compared to the changes from 14.9 +/- 0.3 (Day 32) to 15.7 +/- 0.5 (Day 90) for the EL cows. These results indicate that cows are physiologically under more production stress during EL, but increasing follicular fluid and serum IGF-I throughout ML may reflect potential differences in follicle and oocyte measures, compared to cows in EL.

Animals↗
PubMed2002

Parity-related changes in bovine follicle and oocyte populations, oocyte quality, and hormones to 90 days postpartum.

Ultrasound-guided transvaginal follicular aspiration was used to obtain oocytes from Holstein cows to study follicular development and oocyte morphology during early lactation. A single aspiration was conducted on each of the 120 cows during wk 1 to 12 postpartum. On the day of aspiration, the number of follicles and their sizes were recorded. The collected oocytes were morphologically classified into four grades. Blood and follicular fluid samples were collected for hormone and metabolite assays. Greater serum nonesterified fatty acids concentrations for first- and second-parity cattle on d 7 implied a more negative energy balance status than for third-parity cattle. The numbers of follicles and oocytes retrieved were affected by linear days postpartum x parity interactions, with second-parity cattle having increases compared with decreases for third-parity cattle. Oocyte quality score was affected by the quadratic days postpartum x parity interaction. First- and second-parity cattle had greater oocyte quality scores from d 20 to 70 postpartum compared with third-parity cattle, but third-parity cattle had greater quality oocytes near the end of the 12-wk period. In contrast to cattle subjected to multiple aspirations, first- and second-parity cattle had higher estradiol and insulin-like growth factor I concentrations in follicular fluid associated with greater numbers of oocytes retrieved than third-parity cattle. This study demonstrated that conditions related to early lactation have a negative effect on oocyte quality and endocrine measures of dairy cattle and that animals of various parities may be differentially affected.

Animals↗
PubMed2000

Impact of follicular aspiration on folliculogenesis as influenced by dietary energy and stage of lactation.

Prolonged dietary energy restriction has been shown to influence the secretion of ovarian hormones and follicular development. Energy balance affects the ability of the cow to support a functional reproductive system during early lactation. Follicular aspiration is a tool that can be used to assess the impact of dietary energy and stage of lactation on follicle development in dairy cattle. Follicular aspiration was conducted twice weekly from d 30 to 100 postpartum in cows fed either 104 or 80% of NRC energy requirements. Oocyte numbers recovered increased linearly from d 30 to 100 postpartum. Cows on high energy diets produced more high quality oocytes, but also produced more poor quality oocytes than cows fed the lower energy diet. Follicles < 5 mm predominated throughout. Cows in early (d 28) and mid (d 117) lactation were used to assess stage of lactation effects on serum and follicular fluid hormones, and quality of oocytes recovered by follicular aspiration procedures for 10 wk. Serum IGF-1 decreased in early lactation cows, but increased in midlactation cows. Follicular fluid progesterone in early lactation cows decreased from 275 to 235 ng/ml, whereas in midlactation cows it increased from 65 to 550 ng/ml at aspiration wk 10. The percentage of high quality ova was higher in early lactation cows (11%) than midlactation cows (6%), but fell to 1% by aspiration wk 7 and increased to 10% by wk 10, whereas percentage of high quality ova in midlactation cows steadily declined to 2% by wk 10. Milk yield and energy balance affect patterns of folliculogenesis in lactating dairy cows.

Animals↗
PubMed1999

Effects of ultrasound-guided transvaginal follicular aspiration on oocyte recovery and hormonal profiles before and after GnRH treatment.

Endocrine changes and recovered oocytes were evaluated during 16 wk of ultrasound-guided transvaginal follicular aspiration (TVFA) and prior to and following administration of GnRH at the cessation of aspiration. Nonlactating previously aspirated (PAC, n = 4) and non-aspirated, (AC, n = 4) Holstein cows were subjected to 16 wk of twice-weekly aspiration. Four control cows (OAC) were aspirated 1 time only at the final TVFA session (wk 16). Jugular blood samples were collected from all cows during aspiration, before and after the final TVFA session, and during an 18-d period following cessation of aspiration. Ovarian activity was monitored in all cows after cessation of aspiration for 18 d. The PAC and AC cows averaged 3.4 +/- 1.2 (+/- SE) and 6.8 +/- 1.2 oocytes per session, respectively. Progesterone concentrations during TVFA did not differ between the PAC and AC (0.8 +/- 0.1 and 0.9 +/- 0.1 ng/mL, respectively). Progesterone concentration in OAC was 4.5 +/- 0.2 ng/mL before TVFA, while the PAC and AC averaged 0.5 +/- 0.2 and 0.3 +/- 0.2 ng/mL, respectively, at 16 wk. At Week 16 LH was 1.0 +/- 0.2 ng/mL and it increased to 7.5 +/- 0.1 ng/mL after GnRH treatment. The LH concentration before the final aspiration session was higher at peak amplitude in PAC than in AC groups and peak length was longer in OAC than in AC cows (P < 0.07). Between 18 and 24 h after the last aspiration there were more LH peaks and greater peak frequencies in PAC than in OAC cows (P < 0.07), and the interval between peaks was longer in PAC and AC cows (P < 0.10) than in OAC cows. Mean FSH concentrations were lower (P < 0.01) for OAC than for PAC and AC groups at 20 and 24 h after the last aspiration. Follicle numbers after GnRH varied most among treatment groups for follicles < 9 mm, with the PAC, AC and OAC averaging 5.1 +/- 1.0, 5.1 +/- 1.0, and 3.8 +/- 1.0 follicles/d, respectively. Progesterone concentrations increased to 1.1 +/- 0.3 ng/mL in PAC cows and 2.5 +/- 0.3 and 3.4 +/- 0.3 ng/mL in AC and OAC groups, respectively, during the 18-d period. These results suggest that long-term TVFA affects progesterone, LH and FSH profiles and ovarian dynamics in cows.

Animals↗
PubMed1999

Family pairwise search with embedded motif models.

MOTIVATION: Statistical models of protein families, such as position-specific scoring matrices, profiles and hidden Markov models, have been used effectively to find remote homologs when given a set of known protein family members. Unfortunately, training these models typically requires a relatively large set of training sequences. Recent work (Grundy, J. Comput. Biol., 5,<479-492, 1998) has shown that, when only a few family members are known, several theoretically justified statistical modeling techniques fail to provide homology detection performance on a par with Family Pairwise Search (FPS), an algorithm that combines scores from a pairwise sequence similarity algorithm such as BLAST. RESULTS: The present paper provides a model-based algorithm that improves FPS by incorporating hybrid motif-based models of the form generated by Cobbler (Henikoff and Henikoff, Protein Sci., 6, 698-705, 1997). For the 73 protein families investigated here, this cobbled FPS algorithm provides better homology detection performance than either Cobbler or FPS alone. This improvement is maintained when BLAST is replaced with the full Smith-Waterman algorithm. AVAILABILITY: http://fps.sdsc.edu

Algorithms↗
PubMed1999

Bovine follicular dynamics, oocyte recovery, and development of oocytes microinjected with a green fluorescent protein construct.

The present study was carried out to 1) evaluate the viability of in vitro fertilized zygotes after microinjection of DNA, 2) assess the influence of oocyte quality upon the development rate of embryos when injected with DNA, and 3) determine the integration frequency of green fluorescent protein DNA into microinjected embryos. Oocytes were aspirated from ovaries of nine nonlactating Holsteins and were categorized into grades A, B, C, and D. At 16 h after in vitro fertilization, approximately half of the pronuclear stage presumptive zygotes were classified as having 1 pronucleus or 2 pronuclei, and they were microinjected with DNA constructs. A potential predictor of DNA integration frequency at d 10 was assessment of the incidence of green fluorescing embryos. The proportion of cleaved embryos that developed to morulae or blastocysts was not different between groups with 1 pronucleus injected (45%), 1 pronucleus uninjected (64%), or 2 pronuclei injected (49%). However, the development of morulae or blastocysts was higher in the group with 2 pronuclei uninjected (69%). The overall developmental score of green fluorescent protein-positive embryos was higher for grade A oocytes (1.3 +/- 0.1) than for grade B (0.8 +/- 0.1), C (0.6 +/- 0.1), or D (0.3 +/- 0.1) oocytes. The results show that production of transgenic bovine blastocysts can occur from the microinjection of a presumptive zygote having only one visible pronucleus. Initial oocyte quality is an important factor in selection of oocytes suitable for microinjection of DNA and for preimplantation development to produce bovine transgenic embryos.

Animals↗
PubMed1999

Effects of energy balance of hormones, ovarian activity, and recovered oocytes in lactating Holstein cows using transvaginal follicular aspiration.

The effects of energy balance on hormonal secretion patterns and the structure of recovered oocytes were evaluated in 20 lactating Holstein cows during two trial periods. Cows were randomly assigned to one of two dietary treatments formulated so that dry matter consumption was 3.6% of body weight (high energy; 1.78 Mcal/kg) or 3.2% of body weight (low energy; 1.52 Mcal/kg). Ovum recovery procedures were conducted twice weekly between d 30 and 100 of lactation. Follicle size and number were recorded. Follicular fluid aspirated from the largest follicle and serum samples were collected for hormone assay. Milk yield averaged 41.6 +/- 0.3 kg/d (mean +/- SE) for high energy fed cows and 32.8 +/- 0.3 kg/d for low energy fed cows. Oocyte numbers increased linearly from d 30 to 100 postpartum. Cows fed high energy diets produced more good (+) oocytes than did cows fed low energy diets.

Animals↗
PubMed1998

Serum immunoglobulin type G concentrations in calves produced by IVF and delivered by elective cesarean section.

Colostrum ingestion by neonatal calves is widely recognized to provide passive transfer of immunity. In this study immunoglobulin absorption from colostrum was evaluated in 54 IVF-produced calves. The IVF calves were delivered by Cesarean section on Days 275 to 277 of gestation, 24 h after the dams had been administered 30 mg dexamethasone. The calves suckled bottles or were force-fed 6 L of colostrum in the first 12 h of life. Colostrum was obtained from the first post-calving milking of recipient dams or from frozen storage reserves if dam secretion was not adequate. Immunoglobulin type G (IgG) content of both sources of colostrum was determined. Serum samples from the calves were collected at 0, 12 and 24 h of age and analyzed for IgG. Twenty dairy calves born vaginally served as the controls and were subjected to the same colostrum management protocol except that the colostrum was obtained only from frozen post-calving milk of dairy cows from the same farm. The control calves were also subjected to the same sampling protocol. The IVF group of calves ingested more IgG (P < 0.0001) and absorbed more IgG by 24 h of age (P < 0.0001) than their control group counterparts. Absorption of IgG was analyzed by comparing the g/kg body weight of IgG with serum IgG values at corresponding times after birth. Colostrum absorption efficiency was the same for both IVF and control groups of calves at 12 and 24 h of age. There was a maximum IgG dose above which additional increases in serum IgG were not realized. The slightly premature, Cesarean delivered IVF calves absorbed IgG from colostrum similarly to control calves delivered vaginally.

Animals↗
PubMed1998

Caliper and ultrasonographic measurements of bovine testicles and a mathematical formula for determining testicular volume and weight in vivo.

This study quantified the relationship between calibrated caliper and ultrasonographic derived measurements of bovine testicles in vivo with actual testicular length, width, volume and weight. The prolate spheroid formula was tested to accurately predict testicular volume and a modification to predict weight. Ten bulls were employed to derive caliper and ultrasound testicle (n = 20) length and width measurements in vivo. Caliper length measurements were more reliable than ultrasound derived lengths, with correlations of r2 = 0.8023; P < 0.05 and r2 = 0.5111; P < 0.05, respectively. Width for both the calipers and ultrasound measurements when compared to actual width measurements were r2 = 0.7313; P < 0.05 and r2 = 0.8310; P < 0.05, respectively. The prolate spheroid formula is reliable in determining testicle (n = 116) volume (r2 = 0.8928; P < 0.05). Testicular volume and weight are highly correlated (r2 = 0.9776; P < 0.05); therefore, a modification of the prolate spheroid formula was used to predict weight (r2 = 0.9084; P < 0.05) against the actual weight. Caliper-derived length and width measurements used in the prediction of volume and weight had correlation coefficients against actual volume and weight of r2 = 0.5497; P < 0.05 and r2 = 0.6340; P < 0.05, respectively. Ultrasound in vivo measurements for prediction of testicular volume and testicular weight had a correlation of r2 = 0.3276; P < 0.05 and r2 = 0.6249; P < 0.05, respectively. A testicular (n = 116) length to width ratio of 1.8:1 (SEM = 0.01) was determined for both slaughterhouse and castrated animals. Caliper measurements are reliable, inexpensive and much simpler to obtain than ultrasound determinations for in vivo testicle length, width, volume and weight. The two-dimensional measurement of length and width would be a more accurate predictor of testicle volume and weight than the one-dimensional measurement of scrotal circumference (SC), especially in bulls with variation in testicular shape.

Animals↗
PubMed1998

Methods and statistics for combining motif match scores.

Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

Algorithms↗
PubMed1998

Combining evidence using p-values: application to sequence homology searches.

MOTIVATION: To illustrate an intuitive and statistically valid method for combining independent sources of evidence that yields a p-value for the complete evidence, and to apply it to the problem of detecting simultaneous matches to multiple patterns in sequence homology searches. RESULTS: In sequence analysis, two or more (approximately) independent measures of the membership of a sequence (or sequence region) in some class are often available. We would like to estimate the likelihood of the sequence being a member of the class in view of all the available evidence. An example is estimating the significance of the observed match of a macromolecular sequence (DNA or protein) to a set of patterns (motifs) that characterize a biological sequence family. An intuitive way to do this is to express each piece of evidence as a p-value, and then use the product of these p-values as the measure of membership in the family. We derive a formula and algorithm (QFAST) for calculating the statistical distribution of the product of n independent p-values. We demonstrate that sorting sequences by this p-value effectively combines the information present in multiple motifs, leading to highly accurate and sensitive sequence homology searches.

Algorithms↗
PubMed1997

Hidden Markov model analysis of motifs in steroid dehydrogenases and their homologs.

The increasing size of protein sequence databases is straining methods of sequence analysis, even as the increased information offers opportunities for sophisticated analyses of protein structure, function, and evolution. Here we describe a method that uses artificial intelligence-based algorithms to build models of families of protein sequences. These models can be used to search protein sequence databases for remote homologs. The MEME (Multiple Expectation-maximization for Motif Elicitation) software package identifies motif patterns in a protein family, and these motifs are combined into a hidden Markvov model (HMM) for use as a database searching tool. Meta-MEME is sensitive and accurate, as well as automated and unbiased, making it suitable for the analysis of large datasets. We demonstrate Meta-MEME on a family of dehydrogenases that includes mammalian 11 beta-hydroxysteroid and 17 beta-hydroxysteroid dehydrogenase and their homologs in the short chain alcohol dehydrogenase family. We chose this dataset because it is large and phylogenetically diverse, providing a good test of the sensitivity and selectivity of Meta-MEME on a protein family of biological interest. Indeed, Meta-MEME identifies at least 350 members of this family in Genpept96 and clearly separates these sequences from non-homologous proteins. We also show how the MEME motif output can be used for phylogenetic analysis.

Algorithms↗
PubMed1997

An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases.

MEME (Multiple Expectation-maximization for Motif Elicitation) is a unique new software tool that uses artificial intelligence techniques to discover motifs shared by a set of protein sequences in a fully automated manner. This paper is the first detailed study of the use of MEME to analyse a large, biologically relevant set of sequences, and to evaluate the sensitivity and accuracy of MEME in identifying structurally important motifs. For this purpose, we chose the short-chain alcohol dehydrogenase superfamily because it is large and phylogenetically diverse, providing a test of how well MEME can work on sequences with low amino acid similarity. Moreover, this dataset contains enzymes of biological importance, and because several enzymes have known X-ray crystallographic structures, we can test the usefulness of MEME for structural analysis. The first six motifs from MEME map onto structurally important alpha-helices and beta-strands on Streptomyces hydrogenans 20beta-hydroxysteroid dehydrogenase. We also describe MAST (Motif Alignment Search Tool), which conveniently uses output from MEME for searching databases such as SWISS-PROT and Genpept. MAST provides statistical measures that permit a rigorous evaluation of the significance of database searches with individual motifs or groups of motifs. A database search of Genpept90 by MAST with the log-odds matrix of the first six motifs obtained from MEME yields a bimodal output, demonstrating the selectivity of MAST. We show for the first time, using primary sequence analysis, that bacterial sugar epimerases are homologs of short-chain dehydrogenases. MEME and MAST will be increasingly useful as genome sequencing provides large datasets of phylogenetically divergent sequences of biomedical interest.

Alcohol Dehydrogenase↗