1,721,052 research outputs found
Multiple-breed genomic evaluation by principal component analysis in small size populations
Full text linkIn this study, the effects of breed composition and predictor dimensionality on the accuracy of direct genomic values (DGV) in a multiple breed (MB) cattle population were investigated. A total of 3559 bulls of three breeds were genotyped at 54 001 single nucleotide polymorphisms: 2093 Holstein (H), 749 Brown Swiss (B) and 717 Simmental (S). DGV were calculated using a principal component (PC) approach for either single (SB) or MB scenarios. Moreover, DGV were computed using all SNP genotypes simultaneously with SNPBLUP model as comparison. A total of seven data sets were used: three with a SB each, three with different pairs of breeds (HB, HS and BS), and one with all the three breeds together (HBS), respectively. Editing was performed separately for each scenario. Reference populations differed in breed composition, whereas the validation bulls were the same for all scenarios. The number of SNPs retained after data editing ranged from 36 521 to 41 360. PCs were extracted from actual genotypes. The total number of retained PCs ranged from 4029 to 7284 in Brown Swiss and HBS respectively, reducing the number of predictors by about 85% (from 82% to 89%). In all, three traits were considered: milk, fat and protein yield. Correlations between deregressed proofs and DGV were used to assess prediction accuracy in validation animals. In the SB scenarios, average DGV accuracy did not substantially change when either SNPBLUP or PC were used. Improvement of DGV accuracy were observed for some traits in Brown Swiss, only when MB reference populations and PC approach were used instead of SB-SNPBLUP (+10% HBS, +16%HB for milk yield and +3% HBS and +7% HB for protein yield, respectively). With the exclusion of the abovementioned cases, similar accuracies were observed using MB reference population, under the PC or SNPBLUP models. Random variation owing to sampling effect or size and composition of the reference population may explain the difficulty in finding a defined pattern in the results
Complete CSN1S2 characterization, novel alleles identification and association with milk fatty acids composition in river buffalo
No full textThe αs2-casein is one of the phosphoproteins secreted in all ruminants milk and it is the most hydrophilic of all caseins. However, this important gene (CSN1S2) has not been characterised in detail in buffaloes with only two alleles detected (reported as alleles A and B) and no association studies with milk traits have been carried out unlike what has been achieved for other species of ruminants. In this study, we sequenced the whole gene of two Mediterranean river buffaloes homozygotes for the presence/absence of the nucleotide C (g.7539G>C) realised at donor splice site of the exon 7 and, therefore, responsible for the skipping of the same exon at mRNA level (allele B). A high genetic variability was found all over the two sequenced CSN1S2 alleles. In particular, 74 polymorphic sites were found in introns, 6 in the promoter and 3 SNPs in the coding region (g.11072C>T, g.12803A>T and g.14067A>G) with 2 of them responsible of amino acid replacements. Considering this genetic diversity, those found in the database and the SNP at donor splice site of the exon 7, it is possible to deduce at least eight different alleles (CSN1S2 A, B, B1, B2, C, D, E and F) responsible of seven different possible translations of the buffalo αs2-casein. Haplotype data analysis suggests an evolutionary pathway of buffalo CSN1S2 gene consistent with our proposal that the published allele CSN1S2 A is the ancestral αs2-CN form and the B2 probably arises from interallelic recombination (single crossing) between the alleles D and B (or B1). The allele CSN1S2 C is of new identification, while CSN1S2 B, B1, B2 are deleted alleles because all characterized by the mutation g.7539G>C. Two SNPs (g.7539G>C and g.14067A>G) were genotyped in 747 Italian buffaloes and major alleles had a relative frequency of 0.83 and 0.51, respectively. An association study between these SNPs and milk traits including fatty acids composition was carried out. The SNP g.14067A>G showed a significant association (P<0.05) on the content of palmitic acid in buffalo milk, thus suggesting its use in marker assisted selection programs aiming for the improvement of buffalo milk fatty acid composition
Genome-wide association analysis in Italian Simmental cows for lactation curve traits using a low-density (7K) SNP panel
Full text linkHigh-throughput cow genotyping has opened new perspectives for genome-wide association studies (GWAS). Directly recorded phenotypes and several records per animal could be used. In this study, a GWAS on lactation curve traits of 337 Italian Simmental cows genotyped with the Illumina (San Diego, CA) low-density BeadChip (7K) was carried out. Scores of the first 2 principal components extracted from test-day records (7 for each lactation) for milk yield, fat and protein percentages, and somatic cell score were used as phenotypes. The first component described the average level of the lactation curve, whereas the second summarized its shape. Data were analyzed with a mixed linear model that included fixed effects of herd, calving month, calving year,. parity, SNP genotype, and random effects of animal and permanent environment. All statistically significant markers (Bonferroni corrected) were associated with the average level component (2 for milk yield, 9 for fat percentage, 6 for protein percentages, and 1 for somatic cell score). No markers were found to be associated with the lactation curve shape. Gene discovery was performed using windows of variable size, according to the linkage disequilibrium level of the specific genomic region. Several suggestive candidate genes were identified, some of which already reported to be associated with dairy traits, such as DGAT1. Others were involved in lipid metabolism, in protein synthesis, in the immune response, in cellular processes, and in early development. The large number of genes flagged in the present study suggests interesting perspectives for the use of low-density genotyped females for GWAS, also for novel phenotypes that are not currently considered as breeding goals
Phenotypic and genetic characterization of the occurrence of noncoagulating milk in dairy sheep
No full textMilk coagulation ability is of central importance for the sheep dairy industry because almost all sheep milk is destined for cheese processing. The occurrence of milk with impaired coagulation properties is an obstacle to cheese processing and, in turn, to the profitability of the dairy companies. In this work, we investigated the causes of noncoagulation of sheep milk; specifically, we studied the effect of milk physicochemical properties on milk coagulation status [coagulating and noncoagulating (NC) milk samples, which do or do not coagulate within 30 min, respectively], and whether mid-infrared spectroscopy (MIR) could be used to assess variability in coagulation status. We also investigated the genetic background of milk coagulation ability. Individual milk samples were collected from 996 Sarda ewes farmed in 47 flocks located in Sardinia (Italy). Considered traits were daily milk yield, milk composition traits, and milk coagulation properties (rennet coagulation time, curd firming time, and curd firmness), and MIR spectra were acquired. About 9% of samples did not coagulate within 30 min. A logistic regression approach was used to test the effect of milk-related traits on milk coagulation status. A principal component (PC) analysis was carried out on the milk MIR spectra, and PC scores were then used as covariates in a logistic regression model to assess their relationship with milk coagulation status. Results of the present work demonstrated that the probability of having NC samples increases as milk contents of proteins and chlorides and somatic cell score increase. The analysis of PC extracted from milk spectra that influenced coagulation status highlighted key regions associated with lactose and protein concentrations, and others not associated with routinely collected milk composition traits. These results suggest that the occurrence of NC is mostly related to damage of the epithelium secretory mammary cells, which occurs with the advancement of a lactation or due to unhealthy mammary gland status. Genetic analysis of milk coagulation status and of the extracted PC confirmed the genetic background of the milk coagulability of sheep milk
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
A functional polymorphism influencing the promoter activity of alpaca α-lactalbumin gene (LALBA)
No full textAlpha-lactalbumin (α-La), encoded by LALBA gene, is a Ca2+
binding whey-protein whose key function is to facilitate lactose
synthesis by the galactosyltransferase component, serving as a
regulatory subunit. Other biological functions have been demonstrated
including immune modulation, cell growth regulation,
antimicrobial activity, etc. Gene promoters have transcription
factor (TF) binding sites necessary for gene expression regulation.
Mutations in the promoters may modify the transcription
rates or the mRNA stability, thus affecting the protein yield.
This study aims to sequence the LALBA promoter in alpacas,
identify putative TFs and detect genetic diversity affecting gene
expression.
A DNA fragment (800 bp) spanning the gene promoter until the
exon 1 was amplified and sequenced for 20 alpacas. Multiple
alignments and SNP discovery were accomplished by DNAsis
software, whereas Transfact 7.0 was used for the TF sites search.
Three independent gene reporter assays were achieved by pGL3
specific contructs to test luciferase expression in HEK 293T cells.
Data elaboration was performed using JASP software (p < 0.05,
students’s t-test).
TF binding sites analysis evidenced 16 putative consensus
sequences, including 3 C/EBPα, 3 Sp1, one NF-1, etc. Seven polymorphic
sites were found. Taking as reference the first nucleotide
of the exon 1, one SNP (g.15C > G) was found in the signal peptide,
but it is a silent mutation. The other 6 SNPs were detected
in the promoter (g.-553A > G, g.-428C > T, g.-308C > G, g.-236A > T,
g.-73C > G, g.-51A > G). The SNP g.-553A > G creates a putative
binding site of the TF Sp1. This motif is a well-known enhancer
element for the basal expression of many genes, including milk
proteins.
To assess the SNP effect on the LALBA promoter, we amplified
and cloned a DNA region of 178bp in the pGL3-basic vector from
four homozygous individuals (two g.-553AA and two g.-553GG).
The two different constructs (g.553A and g.-553G), with the pGL3
vector as a control were used to transiently transfect HEK293T
cells. After 48 h, the reporter activity of the variants was measured
using the luciferase assay system. The G variant of this SNP
enhances the promoter activity of the alpaca LALBA (p < 0.01).
Therefore, we suppose an effective role of this binding site in the expression of the α-La in alpaca milk that, consequently, may
affect the functional roles of the protein
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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