mtDNA Single-Nucleotide Variants Associated with Type 2 Diabetes.

Type 2 diabetes (T2D) is a chronic systemic disease with a complex etiology, characterized by insulin resistance and mitochondrial dysfunction in various cell tissues. To explore this relationship, we conducted a secondary analysis of complete mtDNA sequences from 1261 T2D patients and 1105 control individuals. Our findings revealed significant associations between certain single-nucleotide polymorphisms (SNPs) and T2D. Notably, the variants m.1438A>G (rs2001030) (controls: 32 [27.6%], T2D: 84 [72.4%]; OR: 2.46; 95%CI: 1.64-3.78; p < 0.001), m.14766C>T (rs193302980) (controls: 498 [36.9%], T2D: 853 [63.1%]; OR: 2.57, 95%CI: 2.18-3.04, p < 0.001), and m.16519T>C (rs3937033) (controls: 363 [43.4%], T2D: 474 [56.6%]; OR: 1.24, 95%CI: 1.05-1.47, p = 0.012) were significantly associated with the likelihood of developing diabetes. The variant m.16189T>C (rs28693675), which has been previously documented in several studies across diverse populations, showed no association with T2D in our analysis (controls: 148 [13.39] T2D: 171 [13.56%]; OR: 1.03; 95%CI: 0.815-1.31; p = 0.83). These results provide evidence suggesting a link between specific mtDNA polymorphisms and T2D, possibly related to association rules, topological patterns, and three-dimensional conformations associated with regions where changes occur, rather than specific point mutations in the sequence.

Genome-Wide SNP Signal Intensity Scanning Revealed Genes Differentiating Cows with Ovarian Pathologies from Healthy Cows.

Hypoplasia and ovarian cysts are the most common ovarian pathologies in cattle. In this genome-wide study we analyzed the signal intensity of 648,315 Single Nucleotide Polymorphisms (SNPs) and identified 1338 genes differentiating cows with ovarian pathologies from healthy cows. The sample consisted of six cows presenting an ovarian pathology and six healthy cows. SNP signal intensities were measured with a genotyping process using the Axiom Genome-Wide BOS 1 SNPchip. Statistical tests for equality of variance and mean were applied to SNP intensities, and significance p-values were obtained. A Benjamini-Hochberg multiple testing correction reveled significant SNPs. Corresponding genes were identified using the Bovine Genome UMD 3.1 annotation. Principal Components Analysis (PCA) confirmed differentiation. An analysis of Copy Number Variations (CNVs), obtained from signal intensities, revealed no evidence of association between ovarian pathologies and CNVs. In addition, a haplotype frequency analysis showed no association with ovarian pathologies. Results show that SNP signal intensity, which captures not only information for base-pair genotypes elucidation, but the amount of fluorescence nucleotide synthetization produced in an enzymatic reaction, is a rich source of information that, by itself or in combination with base-pair genotypes, might be used to implement differentiation, prediction and diagnostic procedures, increasing the scope of applications for Genotyping Microarrays.

The effect of short term peripheral parenteral nutrition on treatment outcomes and mortality in critically ill pediatric canine patients.

BACKGROUND: Peripheral parenteral nutrition (PPN) is increasingly considered as an alternative to central parenteral nutrition (CPN) given the higher cost and more frequent clinical complications associated with the latter. However, the assessment of potential risks and benefits of PPN in critically ill pediatric canine patients has not been extensively performed. In this study, we aimed to explore the effect of short-term, hypocaloric PPN on weight loss, length of hospital stay, the incidence of complications, adverse effects, and mortality in critically ill pediatric canine patients. RESULTS: Between August 2015 and August 2018, a total of 59 critically ill pediatric canine patients aged from 1 to 6 months admitted at the Veterinary Sciences Research Institute of the Autonomous University of Baja California were included in this non-randomized clinical trial. Canine pediatric patients were initially allocated to 3 groups: 11 in group 1 receiving parenteral nutrition (PN) supplementation equivalent to 40% of the resting energy requirement (RER), 12 in group 2 receiving supplementation of 50% of the RER, and 36 in group 3 receiving no PN supplementation. After establishing that there was no significant difference between 40 and 50% of PN supplementation, these groups were not separated for downstream analysis. Similar lengths of hospital stays were noted among study subjects who received PN supplementation and those who did not (4.3 ± 1.5 vs. 5.0 ± 1.5, days, p = 0.097). No metabolic-, sepsis- or phlebitis-related complications were observed in any animal in the PPN supplemented group. Higher mortality (19.4% vs. 0%, p = 0.036), and a greater percentage of weight loss (9.24% vs. 0%, p <  0.001) were observed in patients who received no supplementation. CONCLUSION: Even though short-term, hypocaloric PPN did not reduce the length of hospital stay, it was associated with lower mortality and resulted in mitigation of weight loss. In contrast to previous studies evaluating central and peripheral parenteral nutrition protocols, we observed a lower frequency of metabolic, septic, and phlebitis complications using a 40-50% parenteral nutrition treatment. The parenteral nutrition therapeutic intervention used in our study may reduce PN-related adverse effects and promote a favorable disease outcome in critically ill canine patients. Larger studies will be needed to confirm these observations.

Canine thoracic radiographic images as an educational dataset for distance learning and research on vertebral heart score.

Distance learning is a rapidly spreading form of education worldwide and it plays a crucial role to provide access to millions of people in developing countries. However, the benefits of online learning extend far beyond and became increasingly popular also in medical schools, including veterinary medicine [1,2]. In these new teaching settings, high-quality, validated and easily accessible multimedia materials are of great importance, especially in specific fields, such as radiology, where graphic resources can greatly support learning [3]. The dataset presented along with this article reviews examples of 153 canine latero-lateral thoracic radiographic medical images taken and collected at the Small Animal Veterinary Teaching Hospital, Veterinary Sciences Research Institute, Autonomous University of Baja California. serves as a basis for teaching VHS calculation. Images on this dataset contain all relevant anatomical structures in the determination of VHS, which makes them optimal images for practice in calculating VHS and teaching this procedure. The number of cardiothoracic radiographic images presented here can be a great support in learning the calculation of VHS, especially when combined with distance competency-based educators' support. Acquired heart diseases in the dog are very common, clinical evidence of degenerative valvular disease is detected in approximately 30% of dogs aged 13 years and older [4]. The prevalence of Dilated Cardiomyopathy (DCM) is remarkably high in certain breeds, approximately 25% of Irish Wolfhounds, 33% of female Doberman Pinschers, and 50% of male Doberman Pinschers are diagnosed with DCM [5]. Thoracic radiography is a key component in cardiovascular evaluation, which is used to calculate the vertebral heart score (VHS). VHS measurement has been described as one of the most objective methods for assessing cardiomegaly in dogs. VHS, in addition to thorough patient history and physical examination, can be very efficient to raise clinical suspicion of underlying heart disease. The measurement is based on cardiac height and width and is normalized to overall body size by comparison to vertebral body length. ln addition to the initial assessment of heart size, the VHS method is also useful for monitoring changes in heart size in response to treatment or to assess the progression of cardiomegaly over time in canine patients [6]Fig. 1. Importantly, considerable breed and individual variation exist with VHS and dogs can have values that fall outside of the normal range even without any cardiac disease. Thus, while the VHS method is a very informative tool, it should not be used as the only means of diagnosing cardiac disease in any given patient [7].

Risk factors and association of body composition components for lumbar disc herniation in Northwest, Mexico.

The goal of this study was to investigate the association of body composition components and to elucidate whether any of these components is a risk factor for Lumbar Disc Herniation (LDH). The group of study consisted of 90 adults involved in a physical activity program due to overweight and obesity. 19 adults with medical diagnostic through Magnetic Resonance Imaging with LDH. Body composition data was obtained with a bioelectrical impedance analyzer. Descriptive statistics and principal components analysis permitted to analyze the information's structure and to visualize information clusters. A logistic regression analysis allowed us to find the association between some of the variables of body composition with LDH. The Degree of Obesity, Body Mass Index, Visceral Fat Area and the Abdominal Circumference resulted associated (P values of 0.0388, 0.0171, 0.0055 and 0.0032, respectively). The application of Odd Ratio allowed us to declare the Visceral Fat Area and Abdominal Circumference as risk factors to develop Lumbar Disk Herniation. Our results provide a new record for future studies, and support for prescription of physical activity and changes in diet, to correct or prevent the development of LDH in the population of Baja California.

High-resolution haplotype block structure in the cattle genome.

BACKGROUND: The Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup species (Anoa and Water Buffalo). Within the larger set of SNPs we targeted 101 high density regions spanning up to 7.6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use. RESULTS: From the 101 targeted high-density regions on bovine chromosomes 6, 14, and 25, between 57 and 95% of the SNPs were informative in the individual breeds. The regions of high LD extend up to ~100 kb and the size of haplotype blocks ranges between 30 bases and 75 kb (10.3 kb average). On the scale from 1-100 kb the extent of LD and haplotype block structure in cattle has high similarity to humans. The estimation of effective population sizes over the previous 10,000 generations conforms to two main events in cattle history: the initiation of cattle domestication (~12,000 years ago), and the intensification of population isolation and current population bottleneck that breeds have experienced worldwide within the last ~700 years. Haplotype block density correlation, block boundary discordances, and haplotype sharing analyses were consistent in revealing unexpected similarities between some beef and dairy breeds, making them non-differentiable. Clustering techniques permitted grouping of breeds into different clades given their similarities and dissimilarities in genetic structure. CONCLUSION: This work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples. Several novel results were obtained. First, cattle and human share a high similarity in LD and haplotype block structure on the scale of 1-100 kb. Second, unexpected similarities in haplotype block structure between dairy and beef breeds make them non-differentiable. Finally, our findings suggest that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in Bos taurus breeds, and ~580,000 SNPs would be necessary to characterize the haplotype block structure across the complete cattle genome.

Analysis of copy number variations in Mexican Holstein cattle using axiom genome-wide Bos 1 array.

Recently, for copy number variation (CNV) analysis, bovine researchers have focused mainly on the use of genome-wide SNP genotyping arrays. One of the highest densities commercially available SNPchips for cattle is the Affymetrix axiom genome-wide Bos 1, which assays 648,315 informative SNPs across the whole bovine genome. Here, we describe the microarray data, quality controls and validation implemented in a study published in Genetics and Molecular Research Journal in 2015 [1]. The microarray raw data has been deposited into Gene Expression Omnibus under accession #GSE54813.

High density LD-based structural variations analysis in cattle genome.

Genomic structural variations represent an important source of genetic variation in mammal genomes, thus, they are commonly related to phenotypic expressions. In this work, ∼ 770,000 single nucleotide polymorphism genotypes from 506 animals from 19 cattle breeds were analyzed. A simple LD-based structural variation was defined, and a genome-wide analysis was performed. After applying some quality control filters, for each breed and each chromosome we calculated the linkage disequilibrium (r2) of short range (≤ 100 Kb). We sorted SNP pairs by distance and obtained a set of LD means (called the expected means) using bins of 5 Kb. We identified 15,246 segments of at least 1 Kb, among the 19 breeds, consisting of sets of at least 3 adjacent SNPs so that, for each SNP, r2 within its neighbors in a 100 Kb range, to the right side of that SNP, were all bigger than, or all smaller than, the corresponding expected mean, and their P-value were significant after a Benjamini-Hochberg multiple testing correction. In addition, to account just for homogeneously distributed regions we considered only SNPs having at least 15 SNP neighbors within 100 Kb. We defined such segments as structural variations. By grouping all variations across all animals in the sample we defined 9,146 regions, involving a total of 53,137 SNPs; representing the 6.40% (160.98 Mb) from the bovine genome. The identified structural variations covered 3,109 genes. Clustering analysis showed the relatedness of breeds given the geographic region in which they are evolving. In summary, we present an analysis of structural variations based on the deviation of the expected short range LD between SNPs in the bovine genome. With an intuitive and simple definition based only on SNPs data it was possible to discern closeness of breeds due to grouping by geographic region in which they are evolving.