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1.
J Dairy Sci ; 2024 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-39033913

RESUMEN

Lameness in dairy cattle is a clinical sign of impaired locomotion, mainly caused by painful foot lesions, compromising the US dairy industry's economic, environmental, and social sustainability goals. Combining technology and on farm data may be a more precise and less labor-intensive lameness detection tool, particularly for early detection. The objective of this observational study was to describe the association between average weekly autonomous camera-based (AUTO) locomotion scores and hoof trimming (HT) data. The AUTO data were collected from 3 farms from April 2022 to March 2023. Historical farm HT data were collected from March 2016 to March 2023 and used to determine cow lesion history and date of HT event. The HT events were categorized as a regular HT (TRIM; n = 2290) or a HT with a lesion recorded (LESION; n = 670). Events with LESION were sub-categorized based on lesion category: digital dermatitis (DD; n = 276), sole ulcer (SU; n = 79), white line disease (WLD; n = 141), and other (n = 174). The data also contained the leg of the LESION, classified as front left (FL; n = 54), front right (FR; n = 146), rear left (RL; n = 281), or rear right (RR; n = 183) leg with 6 events missing the leg. Cows' HT histories were classified as follows: cows with no previous recorded instance of any lesion were classified as TRIM0 (n = 1554). The first instance of any hoof lesion was classified as LESION1 (n = 238). This classification was retained until a subsequent TRIM occurred - recorded as TRIM1 (n = 632). The next unique instance of any lesion following a TRIM1 was classified as LESION2 (n = 86). Any LESION events occurring after LESION1 or LESION2 without a subsequent TRIM were considered a hoof lesion recurrence and classified as LESIONRE1 (n = 164) and LESIONRE2 (n = 22), respectively. TRIM events after LESION2 or LESION2RE (n = 104) or LESION events after LESIONRE1 or LESIONRE2 were classified as LESION_OTHER (n = 160). The AUTO scores from -28 to -1 days prior to the HT event were summarized into weekly scores and included if cows had at least 1 observation per week in the 4 weeks before the event. For all weeks, LESION cows had a higher median AUTO score than TRIM cows. Cows with TRIM0 had the lowest and most consistent median weekly score compared to LESION and other TRIM classifications. Before HT cows with TRIM0 and TRIM1, both had median score increases of 1 across the 4 weeks, while the LESION categories had an increase of 4 to 8. Scores increased with each subsequent LESION event compared to the previous LESION event. Cows with SU lesions had the highest median score across the 4 weeks, WLD had the largest score increase, and DD had the lowest median score and score increase. When grouping a LESION event by leg the hoof lesion was found on, the AUTO scores for four groups displayed comparable median values. Due to the difference between TRIM and LESION events, this technology shows potential for the early detection of hoof lesions.

2.
J Dairy Sci ; 107(10): 8084-8099, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-38876215

RESUMEN

Feed efficiency is important for economic profitability of dairy farms; however, recording daily DMI is expensive. Our objective was to investigate the potential use of milk mid-infrared (MIR) spectral data to predict proxy phenotypes for DMI based on different cross-validation schemes. We were specifically interested in comparisons between a model that included only MIR data (model M1); a model that incorporated different energy sink predictors, such as body weight, body weight change, and milk energy (model M2); and an extended model that incorporated both energy sinks and MIR data (model M3). Models M2 and M3 also included various cow-level variables (stage of lactation, age at calving, parity) such that any improvement in model performance from M2 to M3, whether through a smaller root mean squared error (RMSE) or a greater squared predictive correlation (R2), could indicate a potential benefit of MIR to predict residual feed intake. The data used in our study originated from a multi-institutional project on the genetics of feed efficiency in US Holsteins. Analyses were conducted on 2 different trait definitions based on different period lengths: averaged across weeks versus averaged across 28 d. Specifically, there were 19,942 weekly records on 1,812 cows across 46 experiments or cohorts and 3,724 28-d records on 1,700 cows across 43 different cohorts. The cross-validation analyses involved 3 different k-fold schemes. First, a 10-fold cow-independent cross-validation was conducted whereby all records from any one cow were kept together in either training or test sets. Similarly, a 10-fold experiment-independent cross-validation kept entire experiments together, whereas a 4-fold herd-independent cross-validation kept entire herds together in either training or test sets. Based on cow-independent cross-validation for both weekly and 28-d DMI, adding MIR predictors to energy sinks (model M3 vs. M2) significantly (P < 10-10) reduced average RMSE to 1.59 kg and increased average R2 to 0.89. However, adding MIR to energy sinks (M3) to predict DMI either within an experiment-independent or herd-independent cross-validation scheme seemed to demonstrate no merit (P > 0.05) compared with an energy sink model (M2) for either R2 or RMSE (respectively, 0.68 and 2.55 kg for M2 in herd-independent scheme). We further noted that with broader cross-validation schemes (i.e., from cow-independent to experiment-independent to herd-independent schemes), the mean and slope bias increased. Given that proxy DMI phenotypes for cows would need to be almost entirely generated in herds having no DMI or training data of their own, herd-independent cross-validation assessments of predictive performance should be emphasized. Hence, more research on predictive algorithms suitable for broader cross-validation schemes and a more earnest effort on calibration of spectrophotometers against each other should be considered.


Asunto(s)
Lactancia , Leche , Animales , Bovinos , Leche/metabolismo , Leche/química , Femenino , Alimentación Animal/análisis , Ingestión de Alimentos , Fenotipo , Peso Corporal
3.
J Dairy Sci ; 106(12): 9095-9104, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37678782

RESUMEN

The use of milk Fourier transform mid-infrared (FT-MIR) spectrometry to develop management and breeding tools for dairy farmers and industry is growing and supported by the availability of numerous new predicted phenotypes to assess the nutritional quality of milk and its technological properties, but also the animal health and welfare status and its environmental fingerprint. For genetic evaluations, having a long-term and representative spectral dairy herd improvement (DHI) database improves the reliabilities of estimated breeding values (EBV) from these phenotypes. Unfortunately, most of the time, the raw spectral data used to generate these estimations are not stored. Moreover, many reference measurements of those phenotypes, needed during the FT-MIR calibration step, are available from past research activities but lack spectra records. So, it is impossible to use them to improve the FT-MIR models. Consequently, there is a strong interest in imputing those missing spectra. The innovative objective of this study was to use the existing large spectral DHI database to estimate missing spectra by selecting probable spectra using, as the match criteria, common dairy traits recorded for a long time by DHI organizations. We tested 4 match criteria combinations. Combination 1 required to have equal fat and protein contents between the sample for which a spectrum was to be estimated and the reference samples in the DHI database. Combination 2 also required an equal urea content. Combination 3 requested equal fat, protein, and lactose contents. Finally, combination 4 included all criteria. When more than one spectrum was found during the search, their average was the estimated spectrum for the query sample. Concretely, this study estimated missing spectra for 1,700 samples using 2,000,000 spectral DHI records. For assessing the effect of this spectral estimation on the prediction quality, FT-MIR equations were used to predict 11 phenotypes, selected as their quantification used different FT-MIR regions. They were related to the milk fat and mineral composition, lactoferrin content, quantity of eructed methane, body weight (BW), and dry matter intake. The accuracy between predictions obtained from actual and estimated spectra was evaluated by calculating the mean absolute error (MAE). The criteria in the fourth and second combinations were too strict to estimate a spectrum for most samples. Indeed, for many samples, no spectra with the same values for those matching criteria was found. The third match criteria combination had a poorer prediction performance for all studied traits and spectral absorptions than the first combination due to fewer matched samples available to compute the missing spectrum. By allowing a range for matching lactose content (±0.1 g/dL milk), we showed that this new combination increased the number of selected samples to compute missing spectra and predict better the infrared absorption at different wavenumbers, especially those related to the lactose quantification. The prediction performance was further improved by performing queries on the entire Walloon DHI spectral database (6,625,570 spectra), and it varied among the studied phenotypes. Without considering the traits used for the matching, the best predictions were obtained for the content of saturated fatty acids (MAE = 0.15 g/dL milk) and BW (MAE = 12.80 kg). Yet, the predictions for the unsaturated fatty acids were less accurate (MAE = 0.13 and 0.018 g/dL milk for monounsaturated and polyunsaturated fatty acids), likely because of the poorer predictions of spectral regions related to long-chain fatty acids. Similarly, poorer predictions were observed for the amount of methane eructed by dairy cows (MAE = 47.02 g/d), likely because it is not directly related to fat content or composition. Prediction accuracies for the remaining traits were also low. In conclusion, we observed that increasing the number of relevant matching criteria helps improve the quality of FT-MIR predicted phenotypes and the number of spectra used during the search. So, it would be of great interest to test in the future the suitability of the developed methodology with large-scale international spectral databases to improve the reliability of EBV from these FT-MIR-based phenotypes and the robustness of FT-MIR predictive models.


Asunto(s)
Lactosa , Leche , Bovinos , Femenino , Animales , Leche/química , Análisis de Fourier , Lactosa/análisis , Reproducibilidad de los Resultados , Espectrofotometría Infrarroja/veterinaria , Ácidos Grasos/análisis , Metano/análisis , Lactancia
4.
J Dairy Sci ; 105(7): 5954-5971, 2022 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-35636997

RESUMEN

Residual feed intake (RFI) and feed saved (FS) are important feed efficiency traits that have been increasingly considered in genetic improvement programs. Future sustainability of these genetic evaluations will depend upon greater flexibility to accommodate sparsely recorded dry matter intake (DMI) records on many more cows, especially from commercial environments. Recent multiple-trait random regression (MTRR) modeling developments have facilitated days in milk (DIM)-specific inferences on RFI and FS, particularly in modeling the effect of change in metabolic body weight (MBW). The MTRR analyses, using daily data on the core traits of DMI, MBW, and milk energy (MilkE), were conducted separately for 2,532 primiparous and 2,379 multiparous US Holstein cows from 50 to 200 DIM. Estimated MTRR variance components were used to derive genetic RFI and FS and DIM-specific genetic partial regressions of DMI on MBW, MilkE, and change in MBW. Estimated daily heritabilities of RFI and FS varied across lactation for both primiparous (0.05-0.07 and 0.11-0.17, respectively) and multiparous (0.03-0.13 and 0.10-0.17, respectively) cows. Genetic correlations of RFI across DIM varied (>0.05) widely compared with FS (>0.54) within either parity class. Heritability estimates based on average lactation-wise measures were substantially larger than daily heritabilities, ranging from 0.17 to 0.25 for RFI and from 0.35 to 0.41 for FS. The partial genetic regression coefficients of DMI on MBW (0.11 to 0.16 kg/kg0.75 for primiparous and 0.12 to 0.14 kg/kg0.75 for multiparous cows) and of DMI on MilkE (0.45 to 0.68 kg/Mcal for primiparous and 0.36 to 0.61 kg/Mcal for multiparous cows) also varied across lactation. In spite of the computational challenges encountered with MTRR, the model potentially facilitates an efficient strategy for harnessing more data involving a wide variety of data recording scenarios for genetic evaluations on feed efficiency.


Asunto(s)
Lactancia , Leche , Alimentación Animal/análisis , Animales , Peso Corporal/genética , Bovinos/genética , Ingestión de Alimentos/genética , Femenino , Lactancia/genética , Leche/metabolismo , Fenotipo , Embarazo
5.
Bioelectromagnetics ; 28(6): 471-6, 2007 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-17492762

RESUMEN

Thirty-two pregnant Holstein heifers weighing 499 +/- 45 kg, at 3.1 +/- .7 months of gestation and 21 +/- 2.0 months of age were confined and exposed to 30 microT magnetic fields (MFs) and a 12 h light/12 h dark light cycle. The heifers were divided into two replicates of 16 animals. Each replicate was divided into two groups of eight animals each, one group the non-exposed and the second, the exposed group. The animals were subjected to the different treatments for 4 weeks. After 4 weeks, the animals switched treatment, the exposed group becoming the non-exposed group and vice versa. Then the treatment continued for 4 more weeks. Catheters were inserted into the jugular vein, and blood samples were collected twice a week to estimate the concentration of progesterone (P4), melatonin (MLT), prolactin (PRL), and insulin-like growth factor 1 (IGF-1). Feed consumption was measured daily. The results indicated that exposure of pregnant heifers to MF similar to those encountered underneath a 735 kV high tension electrical power line for 20 h/day during a period of 4 weeks produces slight effects. This is evidenced by statistically significant higher body weight (1.2%), higher weekly body weight gain (30%), and decreases in the concentration of PRL (15%) and IGF-1 (4%) in blood serum. The absence of abnormal clinical signs and the absolute magnitude of the significant changes detected during MF exposure, make it plausible to preclude any major animal health hazard.


Asunto(s)
Campos Electromagnéticos , Hormonas/sangre , Exposición Materna , Preñez/sangre , Preñez/efectos de la radiación , Animales , Bovinos , Industria Lechera , Relación Dosis-Respuesta en la Radiación , Femenino , Embarazo , Dosis de Radiación
6.
Bioelectromagnetics ; 25(7): 508-15, 2004 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-15376244

RESUMEN

Two experiments were conducted to test the hypothesis that electric and magnetic field (EMF) exposure may result in endocrine responses similar to those observed in animals exposed to long days. In the first experiment, 16 lactating, pregnant Holstein cows were assigned to two replicates according to a crossover design with treatment switchback. All animals were confined to wooden metabolic cages and maintained under short day photoperiods (8 h light/16 h dark). Treated animals were exposed to a vertical electric field of 10 kV/m and a horizontal magnetic field of 30 microT (EMF) for 16 h/day for 4 weeks. In a second, similar experiment, 16 nonlactating, nonpregnant Holstein cows subjected to short days were exposed to EMF, using a similar protocol, for periods corresponding to the duration of one estrous cycle. In the first experiment, circulating MLT concentrations during the light period showed a small numerical decrease during EMF exposure (P < .05). Least-square means for the 8 h light period were 9.9 versus 12.4 pg/ml, SE = 1.3. Melatonin concentrations during the dark period were not affected by the treatment. A similar trend was observed in the second experiment, where MLT concentrations during the light period tended to be lower (8.8 pg/ml vs. 16.3 pg/ml, P < .06) in the EMF exposed group, and no effects were observed during the dark period. Plasma prolactin (PRL) was increased in the EMF exposed group (16.6 vs. 12.7 ng/ml, P < .02) in the first experiment. In the second experiment, the overall PRL concentrations found were lower, and the mean plasma PRL concentration was not affected by treatment. These experiments provide evidence that EMF exposure may modify the response of dairy cows to photoperiod.


Asunto(s)
Campos Electromagnéticos , Melatonina/efectos de la radiación , Fotoperiodo , Prolactina/efectos de la radiación , Animales , Bovinos , Estudios Cruzados , Oscuridad , Electricidad , Exposición a Riesgos Ambientales , Ciclo Estral , Femenino , Lactancia , Magnetismo , Melatonina/sangre , Embarazo , Prolactina/sangre , Distribución Aleatoria
7.
Bioelectromagnetics ; 25(4): 308-12, 2004 May.
Artículo en Inglés | MEDLINE | ID: mdl-15114640

RESUMEN

Sixteen pregnant Holstein heifers weighing 521 +/- 46 kg, at 3.3 +/- 0.7 months of gestation and 2.2 +/- 2.0 months of age were confined to wooden metabolism cages and were exposed to a vertical electric field (EF) of 10.0 +/- 0.4 kV/m and an artificial light cycle of 12 h light-12 h dark. The heifers were divided into two replicates of eight each. Each replicate was divided into two groups of four animals each, one group becoming the non-exposed and the second, the EF exposed group. The exposed group were housed in metabolism cages in an area where EF were generated, and the non-exposed group, in metabolism cages located in the adjacent area where the EF was less than 2% of that present in the exposed area. The test animals were subject to the different treatments for 4 weeks continuously. After 4 weeks, the animals switched treatment, the exposed group becoming the non-exposed group and vice-versa. Then the treatment continued for 4 more weeks. Catheters were inserted into the jugular vein of the animals, and blood samples were collected on twice a week to estimate the serum concentration of progesterone (P4), melatonin (MLT), prolactin (PRL), and insulin-like growth factor-1 (IGF-1). Feed consumption was measured daily and feed samples were collected twice a week. The results indicated that exposure of dairy cattle to EF similar to those encountered directly underneath a 735 kV high tension electrical power line carrying a maximum load of current, cannot be associated with any variation in the experimental variables mentioned above. An exception to this, is the variation in MLT, which was associated with the EF exposure. Due to the inconsistency of the MLT response in the different replicates, caution should be exercised in the interpretation of this phenomenon.


Asunto(s)
Campos Electromagnéticos , Factor I del Crecimiento Similar a la Insulina/metabolismo , Melatonina/sangre , Progesterona/sangre , Prolactina/sangre , Animales , Bovinos , Femenino , Embarazo
8.
Bioelectromagnetics ; 24(8): 557-63, 2003 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-14603475

RESUMEN

Milk production is the main agricultural income in the province of Québec, and the electrical distribution network traverses the rural dairy production region. This study evaluates the hypothesis that electric and magnetic fields may affect dairy production. Sixteen multiparous nonpregnant lactating Holstein cows (weighing 662 +/- 65 kg and with 150.4 +/- 40 days of lactation) were confined to wooden metabolic crates during the experiment with a 12:12 h light:dark cycle. The cows were divided into two replicates of eight cows each and exposed to a vertical EF of 10 kV/m and an uniform horizontal MF of 30 microT at 60 Hz. Replicate one was exposed for three periods. Each period was represented by an estrous cycle ranging from 24 to 27 days. During the first period, the electric and magnetic fields (E&MF) were off; during the second period they were on; and during the final period, they were off. The second replicate was exposed for three periods also, but the exposure protocol was reversed (first period, on; second period, off; last period, on). Exposure to E&MF (on) resulted in an average decrease of 4.97, 13.78, and 16.39% in milk yield, fat corrected milk yield, and milk fat, respectively; and an increase of 4.75% in dry matter intake.


Asunto(s)
Relación Dosis-Respuesta en la Radiación , Ingestión de Alimentos/fisiología , Ingestión de Alimentos/efectos de la radiación , Campos Electromagnéticos , Eyección Láctea/fisiología , Eyección Láctea/efectos de la radiación , Leche/metabolismo , Modelos Biológicos , Animales , Bovinos , Electricidad , Femenino , Embarazo , Preñez/fisiología , Preñez/efectos de la radiación , Dosis de Radiación , Irradiación Corporal Total
9.
Anim Reprod Sci ; 77(1-2): 11-20, 2003 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-12654524

RESUMEN

To study the effects of exposure to extremely low frequency (ELF) electric and magnetic fields (EMF) on the estrous cycle of dairy cows under short-day photoperiod, 16 non-lactating, non-pregnant Holstein cows were exposed to a vertical electric field of 10 kV/m and a horizontal magnetic field of 30 microT for 16 h per day in a cross-over design consisting of two sequences. Each sequence included three periods, and each period corresponded to the duration of one estrous cycle. All animals were maintained under short photoperiod (8 h light/16 h dark) during the trial. Exposure to EMF had an impact on the duration of a complete estrous cycle (P<0.01) and on the duration of the luteal phase (P<0.01). The mean duration of one cycle was 19.5+/-0.4 for the control and 21.3+/-0.4 days for the exposed animals, respectively. The mean duration of the luteal phase was 15.4+/-0.4 days for the control and 17.2+/-0.4 days for the exposed group. The total area under the progesterone (P(4)) curve, the amplitude of the curve or the slope of the P(4) rise at the onset of the luteal phase were not affected by EMF exposure. Results indicate that exposure to EMF may increase the duration of the estrous cycle.


Asunto(s)
Bovinos/fisiología , Campos Electromagnéticos/efectos adversos , Ciclo Estral , Fotoperiodo , Animales , Femenino , Fase Luteínica , Progesterona/sangre , Factores de Tiempo
10.
J Dairy Sci ; 85(11): 2843-9, 2002 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-12487451

RESUMEN

Electric and magnetic fields (EMF) are generated by the transmission of electricity through high tension lines traversing rural areas. Previous studies showed increased dry matter intake (DMI) and fat corrected milk in dairy cows exposed to EMF. Because EMF exposure has been shown to suppress pineal release of melatonin in some species, it was hypothesized that EMF effects resemble those of exposure to long days. Previous studies have shown that DMI and milk production increase in dairy cattle in response to long day photoperiods, and this has been observed in association with increased circulating insulin-like growth factor 1 (IGF-1), but not growth hormone (GH). The hypothesis that EMF act by modifying the response to photoperiod was tested by subjecting dairy cows to controlled EMF exposure while keeping them under short-day conditions. Sixteen lactating, pregnant Holstein cows were exposed to a vertical electric field of 10 kV/m and a horizontal magnetic field of 30 microT in a crossover design with treatment switchback. Two groups of eight cows each were exposed to EMF for 16 h/d in either oftwo sequences. Each sequence consisted of three consecutive 28-d periods. All animals were maintained under short day conditions (8 h light, 16 h dark) during the trial. DMI and plasma IGF-1 were increased (P < 0.01) during EMF exposure (17.03 vs.16.04 kg/d, SE = 0.4; 137 +/- 6 ng/ml vs 126 +/- 6, respectively). The mean GH concentration was not affected, but a treatment x hour interaction was detected, with GH lower for the EMF exposed animals during the first 16 h of the sampling period, and higher for the last 8 h. Overall, the yield of milk or its components was not affected by EMF exposure, but milk yield was significantly higher for the exposed animals during wk 4 of treatment.


Asunto(s)
Bovinos/fisiología , Ingestión de Alimentos , Campos Electromagnéticos , Hormona del Crecimiento/sangre , Factor I del Crecimiento Similar a la Insulina/análisis , Lactancia/fisiología , Animales , Exposición a Riesgos Ambientales , Femenino , Melatonina/sangre , Leche/metabolismo , Fotoperiodo , Embarazo , Prolactina/sangre
11.
Nat Biotechnol ; 19(4): 342-7, 2001 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-11283592

RESUMEN

We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.


Asunto(s)
Expresión Génica , Hibridación in Situ/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Oligonucleótidos/química , Células Cultivadas , Cromatografía Líquida de Alta Presión , ADN Complementario/metabolismo , Humanos , Procesamiento de Imagen Asistido por Computador , Células Jurkat , Células K562 , Oligonucleótidos/síntesis química , Sistemas de Lectura Abierta , Reacción en Cadena de la Polimerasa , ARN Complementario/metabolismo , ARN Mensajero/metabolismo , Reproducibilidad de los Resultados , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Saccharomyces cerevisiae , Sensibilidad y Especificidad , Factores de Tiempo , Transcripción Genética , Tretinoina/química , Células Tumorales Cultivadas
12.
Nature ; 409(6822): 922-7, 2001 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-11237012

RESUMEN

The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.


Asunto(s)
Cromosomas Humanos Par 22 , Biología Computacional , Genoma Humano , Análisis de Secuencia por Matrices de Oligonucleótidos , Algoritmos , Empalme Alternativo , Línea Celular , ADN Complementario , Exones , Proyecto Genoma Humano , Humanos , Sondas de Oligonucleótidos
13.
Nat Genet ; 25(3): 333-7, 2000 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-10888885

RESUMEN

Expression profiling using DNA microarrays holds great promise for a variety of research applications, including the systematic characterization of genes discovered by sequencing projects. To demonstrate the general usefulness of this approach, we recently obtained expression profiles for nearly 300 Saccharomyces cerevisiae deletion mutants. Approximately 8% of the mutants profiled exhibited chromosome-wide expression biases, leading to spurious correlations among profiles. Competitive hybridization of genomic DNA from the mutant strains and their isogenic parental wild-type strains showed they were aneuploid for whole chromosomes or chromosomal segments. Expression profile data published by several other laboratories also suggest the use of aneuploid strains. In five separate cases, the extra chromosome harboured a close homologue of the deleted gene; in two cases, a clear growth advantage for cells acquiring the extra chromosome was demonstrated. Our results have implications for interpreting whole-genome expression data, particularly from cells known to suffer genomic instability, such as malignant or immortalized cells.


Asunto(s)
Aneuploidia , Cromosomas Fúngicos , Saccharomyces cerevisiae/genética , ADN de Hongos/análisis , Expresión Génica , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos
14.
Bioelectromagnetics ; 20(6): 358-64, 1999 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-10453063

RESUMEN

Eight multiparous, nonlactating pregnant Holstein cows (at 198 +/- 35 days of gestation and weighing 608 + 24 kg) and seven nonlactating nonpregnant ovariectomized heifers (weighing 370 + 29 kg) were confined to wooden metabolism crates in an electric and magnetic field chamber. Subarachnoidal catheters were inserted before the activation of the electric and magnetic fields. For 30 days, cows and heifers were continuously exposed in separate trials to electric and magnetic fields (60 Hz, 10 kV/m, and 30 microT). Blood plasma and cerebrospinal fluid samples were collected for 3 consecutive days before the exposure period, the last 3 days of the exposure period, and for 3 days starting 5 days after the exposure period. Concentrations of Ca, Mg, Cu, Zn, Fe, Mn, Na, P, and K in blood plasma and cerebrospinal fluid were determined. Exposure to electric and magnetic fields resulted in decreased concentrations of Mg in blood plasma and in increased concentrations of Ca and P and decreased concentrations of Fe and Mn in cerebrospinal fluid.


Asunto(s)
Bovinos/sangre , Bovinos/líquido cefalorraquídeo , Campos Electromagnéticos/efectos adversos , Oligoelementos/sangre , Oligoelementos/líquido cefalorraquídeo , Animales , Calcio/sangre , Calcio/líquido cefalorraquídeo , Femenino , Hierro/sangre , Hierro/líquido cefalorraquídeo , Magnesio/sangre , Magnesio/líquido cefalorraquídeo , Manganeso/sangre , Manganeso/líquido cefalorraquídeo , Fósforo/sangre , Fósforo/líquido cefalorraquídeo , Embarazo
15.
Neurochem Res ; 23(12): 1527-31, 1998 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-9821157

RESUMEN

Eight multiparous non-lactating pregnant Holstein cows at 198 +/- 35 d of gestation, weighing 608 +/- 24 kg, were confined to wooden metabolic cages in an electric and magnetic field chamber with a 12:12 h light:dark cycle. Subarachnoidal catheters were installed 5 d before the activation of the electric and magnetic fields. The cows were exposed to electric and magnetic fields (60 Hz, 10 kV/m and 30 microT) continuously except for the feeding and cleaning time for an average of 21.44 +/- 1.4 h per day for a period of 30 d. Cerebrospinal fluid samples were collected on three consecutive days before an exposure period of 30 d, on the last 3 d of the exposure period, and for 3 d starting 5 d after the exposure period. The concentrations of beta-endorphin, tryptophan, 5-hydroxyindoleacetic acid, homovanillic acid, 3-methoxy-4-hydroxyphenylethyleneglycol and quinolinic acid in cerebrospinal fluid were determined. There was a significant increase in quinolinic acid, and a trend towards an increase in tryptophan, findings consistent with a weakening of the blood-brain barrier due to exposure to the electric and magnetic fields.


Asunto(s)
Aminas Biogénicas/líquido cefalorraquídeo , Bovinos/líquido cefalorraquídeo , Campos Electromagnéticos , Ácido Quinolínico/líquido cefalorraquídeo , betaendorfina/líquido cefalorraquídeo , Animales , Industria Lechera , Femenino , Ácido Homovanílico/líquido cefalorraquídeo , Ácido Hidroxiindolacético/líquido cefalorraquídeo , Metoxihidroxifenilglicol/líquido cefalorraquídeo , Triptófano/líquido cefalorraquídeo
16.
Nat Med ; 4(11): 1293-301, 1998 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-9809554

RESUMEN

We describe here a method for drug target validation and identification of secondary drug target effects based on genome-wide gene expression patterns. The method is demonstrated by several experiments, including treatment of yeast mutant strains defective in calcineurin, immunophilins or other genes with the immunosuppressants cyclosporin A or FK506. Presence or absence of the characteristic drug 'signature' pattern of altered gene expression in drug-treated cells with a mutation in the gene encoding a putative target established whether that target was required to generate the drug signature. Drug dependent effects were seen in 'targetless' cells, showing that FK506 affects additional pathways independent of calcineurin and the immunophilins. The described method permits the direct confirmation of drug targets and recognition of drug-dependent changes in gene expression that are modulated through pathways distinct from the drug's intended target. Such a method may prove useful in improving the efficiency of drug development programs.


Asunto(s)
Calcineurina/genética , Ciclosporina/farmacología , Regulación Fúngica de la Expresión Génica , Inmunofilinas/genética , Inmunosupresores/farmacología , Saccharomyces cerevisiae/genética , Tacrolimus/farmacología , Diseño de Fármacos , Regulación Fúngica de la Expresión Génica/efectos de los fármacos , Genotipo , Modelos Biológicos , Mutación , Reacción en Cadena de la Polimerasa , Reproducibilidad de los Resultados , Saccharomyces cerevisiae/efectos de los fármacos , Transducción de Señal
17.
Bioelectromagnetics ; 19(7): 438-43, 1998.
Artículo en Inglés | MEDLINE | ID: mdl-9771588

RESUMEN

Sixteen multiparous nonpregnant lactating Holstein cows (each weighing 662 +/- 65 kg in 150.4 +/- 40 day of lactation) were confined to wooden metabolic cages with 12:12 h light:dark cycle during the experiment. The cows were divided into two sequences of eight cows each and exposed to electric and magnetic fields (EMF) in an exposure chamber. This chamber produced a vertical electric field of 10 kV/m and a uniform horizontal magnetic field of 30 microT at 60 Hz. One sequence was exposed for three estrous cycles of 24 to 27 days. During the first estrous cycle, the electric and magnetic fields were off; during the second estrous cycle, they were on; and during the third estrous cycle, they were off. The second sequence was also exposed for three 24 to 26 days estrous cycles, but the exposure to the fields was reversed (first estrous cycle, on; second estrous cycle, off; third estrous cycle, on). The length of each exposure period (21 to 27 days) varied according to the estrous cycle length. No differences were detected in plasma progesterone concentrations and area under the progesterone curve during estrous cycles between EMF nonexposed and exposed periods (2.28 +/- 0.17 and 2.25 +/- 0.17; and 24.5 +/- 1.9 vs. 26.4 +/- 1.9 ng/ml, respectively). However, estrous cycle length, determined by the presence of a functional corpus luteum detected by concentrations of progesterone equal to or more than 1 ng/ml plasma, was shorter in nonexposed cows than when they were exposed to EMF (22.0 +/- 0.9 vs. 25.3 +/- 1.4 days).


Asunto(s)
Electricidad , Estro/sangre , Magnetismo , Progesterona/sangre , Animales , Bovinos , Femenino , Factores de Tiempo
18.
J Dairy Sci ; 81(3): 722-7, 1998 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-9565875

RESUMEN

Sixteen multiparous, pregnant, lactating Holstein cows (weighing 600 +/- 50 kg, at 184.8 +/- 52 d of lactation, and at 101.9 +/- 43 d of gestation) were confined to wooden metabolism cages and exposed to a vertical electric field of 10 kV/m and a uniform horizontal magnetic field of 30 microT. The trial was conducted using a switchback statistical design. Cows were divided into two sequence groups of 8 cows each. One sequence group was exposed for three periods of 28 d each. The electric and magnetic fields were off during the first period, on during the second period, and off during the final period. The second sequence group was exposed for three periods also, but the activity of the fields was reversed (on during the first period, off during the second period, and on during the third period). On d 25 of each exposure period, blood samples were obtained every 0.5 h for 14 h starting at 1700 h to determine melatonin concentration. Nocturnal melatonin concentrations did not show any variation that could be attributed to exposure to electric and magnetic fields.


Asunto(s)
Bovinos/sangre , Ritmo Circadiano , Campos Electromagnéticos/efectos adversos , Melatonina/sangre , Animales , Femenino , Lactancia , Embarazo
19.
J Dairy Sci ; 79(9): 1549-54, 1996 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-8899520

RESUMEN

Sixteen multiparous Holstein cows (weighing 600 +/- 50 kg, in 184.8 +/- 52 d of lactation, and at 101.9 +/- 43 d of gestation) were confined to wooden metabolic cages and exposed to a vertical electric field of 10 kV/ m and to a uniform horizontal magnetic field of 30 microT (microtesla). The trial was conducted as a switch-back statistical design. Cows were divided into two replicates of 8 cows each. One replicate was exposed for three periods of 28 d each. During the first period, the electric and magnetic fields were off; during the second period, they were on; and, during the final period, they were off. The second replicate was exposed for three periods also, but the activity of the fields was reversed (first period, on; second period, off; and third period, on). Blood samples were obtained twice weekly for the determination of cortisol and progesterone and once weekly for the determination of pH and blood gases. Milk samples were collected once weekly to determine milk components (fat, protein, SNF, and SCC). Milk yield and feed consumption were measured daily. Most of the variables studied (bicarbonate, pH, O2 and CO2 partial pressures, cortisol concentration in blood, uncorrected milk yield, and milk components other than milk fat) showed no variation that could be attributed to exposure to electric and magnetic fields. Associations were found between the electric and magnetic fields and increased DMI, 4% FCM yield, milk fat content, and plasma progesterone.


Asunto(s)
Bovinos/fisiología , Campos Electromagnéticos/efectos adversos , Lactancia , Animales , Dióxido de Carbono/sangre , Ingestión de Alimentos , Femenino , Hidrocortisona/sangre , Concentración de Iones de Hidrógeno , Leche/química , Oxígeno/sangre , Presión Parcial , Progesterona/sangre
20.
J Reprod Fertil ; 95(1): 167-73, 1992 May.
Artículo en Inglés | MEDLINE | ID: mdl-1625232

RESUMEN

Fifteen sows were assigned to three groups of five each, according to gestational age (109 days, 114 days or labour). Two fetuses per sow were chosen at random, and amnion, allantochorion, amniochorion, amniotic fluid and fetal urine were collected. Tissues were enzymatically dispersed and incubated for 1, 2, 3 or 4 h and the prostaglandin (PG) content of the supernatant medium was measured by radioimmunoassay. In general, all placental cell types produced at least three times more prostaglandin E (PGE) and 6-keto-PGF1 alpha than PGF. Production did not vary across gestational age, except that production of 6-keto-PGF1 alpha was lower in cells collected during labour, resulting in a relative increase in PGF and PGE. Aminochorion cells had a lower de novo capacity to synthesize PG than did allantochorion or amniochorion, whereas treatment of allantochorion with preterm amniotic fluid, preterm or term fetal urine resulted in increased PG output. These results demonstrate that porcine placental cells can synthesize and metabolize prostaglandin in late gestation but suggest that their capacity to produce PGI2 (as measured by 6-keto-PGF1 alpha) is lower than for other prostaglandins during labour.


Asunto(s)
Placenta/metabolismo , Prostaglandinas/biosíntesis , Porcinos/metabolismo , 6-Cetoprostaglandina F1 alfa/biosíntesis , Alantoína/metabolismo , Amnios/metabolismo , Animales , Células Cultivadas , Corion/metabolismo , Dinoprost/análogos & derivados , Dinoprost/biosíntesis , Femenino , Edad Gestacional , Placenta/citología , Embarazo , Prostaglandinas E/biosíntesis , Prostaglandinas F/biosíntesis
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