scholarly journals Differentiation of lines of Sychevka cattle using marker genes

2020 ◽  
pp. 87-93
Author(s):  
Dmitry Nikolaevich Koltsov ◽  
Mikhail Eliseevich Gontov ◽  
Valentina Ivanovna Dmitrieva
Keyword(s):  
Genetic Differentiation ◽  
Genetic Markers ◽  
Genetic Similarity ◽  
Marker Gene ◽  
Wide Distribution ◽  
Genetic Differences ◽  
Marker Genes ◽  
Present Stage ◽  
Concentration Degree ◽  
Breed Improvement

The results of genetic differentiation of 10 main genealogical groups of sires of the breed of Sychevka cattle of the Smolensk region, using as genetic markers the genes of the B-locus of erythrocyte antigens of blood groups (n = 2949). At the present stage of breed improvement, 56 marker genes of the EAB locus were found in the studied animals, of which 16 are common to all lines and related groups. The most common are: b, G2Y2E'1Q', I1Y2E'3G'G'', I1Y2I', O1I'Q', O2A'2J'2K'O', Q', Y1A'1. Lines and related groups were differentiated by the level of marker gene concentration, degree of homozygosity, and genetic similarity. The coefficient of genetic similarity (r) between different lines ranged from 0.58 to 0.85. The high similarity between animals of individual lines and the wide distribution of identical inherited material marked with the G2Y2E'1Q' allele indicate that there are no genetic differences between them. The lines that originate from sires of Sychevska and Holstein origin do not have significant genetic differences between them (r = 0.9). It is proposed to direct breeding work using genetic markers to increase the genetic differentiation of existing and breeding new lines.

scholarly journals Epidemiological Association of DifferentCampylobacter jejuniGroups with Metabolism-Associated Genetic Markers

2011 ◽  
Vol 77 (7) ◽  
pp. 2359-2365 ◽  
Author(s):  
Andreas E. Zautner ◽  
Sahra Herrmann ◽  
Jasmin Corso ◽  
A. Malik Tareen ◽  
Thomas Alter ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Marker Gene ◽  
Host Adaptation ◽  
Source Tracking ◽  
Marker Genes ◽  
Gene Marker ◽  
Animal Source ◽  
Genetic Detection ◽  
Effective Source ◽  
Epidemiological Association

ABSTRACTIn this study, multilocus sequence typing (MLST) was combined with the genetic detection of six genetic markers,ansB,dmsA,ggt,cj1585c,cjj81176-1367/71(cj1365c), and the two-gene markertlp7(cj0951cpluscj0952c), to assess if their presence correlated with differentC. jejuniclonal groups. Using a collection of 266C. jejuniisolates from (in decreasing order of sample size) humans, chickens, cattle, and turkeys, it was further investigated whether the resulting genotypes correlated with the isolation source. We found combinations of the six marker genes to be mutually exclusive, and their patterns of presence or absence correlated to some degree with animal source. Together with MLST results, the obtained genotypes could be segregated into six groups. An association was identified foransB,dmsA, andggtwith the MLST-clonal complexes (MLST-CC) 22, 42, 45, and 283, which formed the most prominent group, in which chickens were the most prevalent animal source. Two other groups, characterized by the presence ofcj1585c,cjj81176-1367/71, and the two-gene markertlp7, associated with either MLST-CC 21 or 61, were overrepresented in isolates of bovine origin. Mutually exclusive marker gene combinations were observed foransB,dmsA, andggt, typically found in CC 45 and the related CC 22, 42, and 283, whereas the other three marker genes were found mostly in CC 21, 48, and 206. The presence of the two-gene markertlp7, which is typical for MLST 21 and 53 as well as for MLST-CC 61, strongly correlates with a bovine host; this is interpreted as an example of host adaptation. In cases ofC. jejunioutbreaks, these genetic markers could be helpful for more effective source tracking.

scholarly journals Multi-view feature selection for identifying gene markers: a diversified biological data driven approach

2020 ◽  
Vol 21 (S18) ◽  
Author(s):  
Sudipta Acharya ◽  
Laizhong Cui ◽  
Yi Pan
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Selection ◽  
Marker Gene ◽  
Biological Data ◽  
Protein Interaction Data ◽  
Marker Genes ◽  
Data Sets ◽  
Gene Markers ◽  
Multi Objective

Abstract Background In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene expression data sets. In that context, designing an efficient feature selection algorithm exploiting knowledge from multiple potential biological resources may be an effective way to understand the spectrum of cancer or other diseases with applications in specific epidemiology for a particular population. Results In the current article, we design the feature selection and marker gene detection as a multi-view multi-objective clustering problem. Regarding that, we propose an Unsupervised Multi-View Multi-Objective clustering-based gene selection approach called UMVMO-select. Three important resources of biological data (gene ontology, protein interaction data, protein sequence) along with gene expression values are collectively utilized to design two different views. UMVMO-select aims to reduce gene space without/minimally compromising the sample classification efficiency and determines relevant and non-redundant gene markers from three cancer gene expression benchmark data sets. Conclusion A thorough comparative analysis has been performed with five clustering and nine existing feature selection methods with respect to several internal and external validity metrics. Obtained results reveal the supremacy of the proposed method. Reported results are also validated through a proper biological significance test and heatmap plotting.

PPIT: an R package for inferring microbial taxonomy from nifH sequences

2021 ◽  
Author(s):  
Bennett J Kapili ◽  
Anne E Dekas
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Query Sequence ◽  
Marker Gene ◽  
R Package ◽  
Supplementary Information ◽  
Marker Genes ◽  
Pairwise Identity ◽  
Metabolic Marker ◽  
Microbial Taxonomy

Abstract Motivation Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. Results We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. Availability PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. Supplementary information Supplementary data are available at Bioinformatics online.

Recombination and deletion of sequences in shuttle vector plasmids in mammalian cells

1985 ◽  
Vol 5 (9) ◽  
pp. 2265-2271
Author(s):  
S Chakrabarti ◽  
S Joffe ◽  
M M Seidman
Keyword(s):  
Shuttle Vector ◽  
Marker Gene ◽  
Simian Virus 40 ◽  
Repeated Sequences ◽  
Marker Genes ◽  
Insertion Mutagenesis ◽  
Direct Repeats ◽  
African Green Monkey Kidney ◽  
Alu Sequence ◽  
Insertion Mutants

Shuttle vector plasmids were constructed with directly repeated sequences flanking a marker gene. African green monkey kidney (AGMK) cells were infected with the constructions, and after a period of replication, the progeny plasmids were recovered and introduced into bacteria. Those colonies with plasmids that had lost the marker gene were identified, and the individual plasmids were purified and characterized by restriction enzyme digestion. Recombination between the repeated elements generated a plasmid with a precise deletion and a characteristic restriction pattern, which distinguished the recombined molecules from those with other defects in the marker gene. Recombination among the following different sequences was measured in this assay: (i) the simian virus 40 origin and enhancer region, (ii) the AGMK Alu sequence, and (iii) a sequence from plasmid pBR322. Similar frequencies of recombination among these sequences were found. Recombination occurred more frequently in Cos1 cells than in CV1 cells. In these experiments, the plasmid population with defective marker genes consisted of the recombined molecules and of the spontaneous deletion-insertion mutants described earlier. The frequency of the latter class was unaffected by the presence of the option for recombination represented by the direct repeats. Both recombination and deletion-insertion mutagenesis were stimulated by double-strand cleavage between the repeated sequences and adjacent to the marker, and the frequency of the deletion-insertion mutants in this experiment was again independent of the presence of the direct repeats. We concluded that although recombination and deletion-insertion mutagenesis were both stimulated by double-strand cleavage, the molecules which underwent the two types of change were drawn from separate pools.

scholarly journals Cellular resolution anatomical and molecular atlases for prenatal human brains

2021 ◽  
Author(s):  
Song-Lin Ding ◽  
Joshua J. Royall ◽  
Phil Lesnar ◽  
Benjamin A.C. Facer ◽  
Kimberly A. Smith ◽  
...  
Keyword(s):  
Human Brain ◽  
Hippocampal Formation ◽  
Marker Gene ◽  
Brain Structures ◽  
Marker Genes ◽  
Subcortical Structures ◽  
Cellular Resolution ◽  
Reliable Marker ◽  
Human Brains ◽  
Developmental Features

Increasing interest in studies of prenatal human brain development, particularly using new single-cell genomics and anatomical technologies to create cell atlases, creates a strong need for accurate and detailed anatomical reference atlases. In this study, we present two cellular-resolution digital anatomical atlases for prenatal human brain at post-conceptional weeks (PCW) 15 and 21. Both atlases were annotated on sequential Nissl-stained sections covering brain-wide structures on the basis of combined analysis of cytoarchitecture, acetylcholinesterase staining and an extensive marker gene expression dataset. This high information content dataset allowed reliable and accurate demarcation of developing cortical and subcortical structures and their subdivisions. Furthermore, using the anatomical atlases as a guide, spatial expression of 37 and 5 genes from the brains respectively at PCW 15 and 21 was annotated, illustrating reliable marker genes for many developing brain structures. Finally, the present study uncovered several novel developmental features, such as the lack of an outer subventricular zone in the hippocampal formation and entorhinal cortex, and the apparent extension of both cortical (excitatory) and subcortical (inhibitory) progenitors into the prenatal olfactory bulb. These comprehensive atlases provide useful tools for visualization, targeting, imaging and interpretation of brain structures of prenatal human brain, and for guiding and interpreting the next generation of cell census and connectome studies.

scholarly journals Hypertrophy of Adipose Tissues in Quail Embryos by in ovo Injection of All-Trans Retinoic Acid

2021 ◽  
Vol 12 ◽  
Author(s):  
Dong-Hwan Kim ◽  
Joonbum Lee ◽  
Sanggu Kim ◽  
Hyun S. Lillehoj ◽  
Kichoon Lee
Keyword(s):  
Retinoic Acid ◽  
Vitamin A ◽  
Marker Gene ◽  
Marker Genes ◽  
Health Issues ◽  
Fat Cell ◽  
In Ovo ◽  
Adipose Tissues ◽  
Trans Retinoic Acid ◽  
All Trans Retinoic Acid

Excessive adipose accretion causes health issues in humans and decreases feed efficiency in poultry. Although vitamin A has been known to be involved in adipogenesis, effects of all-trans retinoic acid (atRA), as a metabolite of vitamin A, on embryonic adipose development have not been studied yet. Avian embryos are developing in confined egg environments, which can be directly modified to study effects of nutrients on embryonic adipogenesis. With the use of quail embryos, different concentrations of atRA (0 M to 10 μM) were injected in ovo at embryonic day (E) 9, and adipose tissues were sampled at E14. Percentages of fat pad weights in embryo weights were significantly increased in the group injected with 300 nM of atRA. Also, among three injection time points, E5, E7, or E9, E7 showed the most significant increase in weight and percentage of inguinal fat at E14. Injection of atRA at E7 increased fat cell size in E14 embryos with up-regulation of pro-adipogenic marker genes (Pparγ and Fabp4) and down-regulation of a preadipocyte marker gene (Dlk1) in adipose tissues. These data demonstrate that atRA promotes hypertrophic fat accretion in quail embryos, implying important roles of atRA in embryonic development of adipose tissues.

scholarly journals A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

2019 ◽  
Vol 7 (6) ◽  
pp. 161 ◽  
Author(s):  
Ming-Hsin Tsai ◽  
Yen-Yi Liu ◽  
Von-Wun Soo ◽  
Chih-Chieh Chen
Keyword(s):  
Microbial Diversity ◽  
Large Scale ◽  
Gene Selection ◽  
Marker Gene ◽  
Genome Comparison ◽  
Marker Genes ◽  
Species Classification ◽  
Genome Wide ◽  
A Genome ◽  
Comparison Approach

Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.

Genetic Differences between Bull-Breeding Herds

1955 ◽  
Vol 1955 ◽  
pp. 94-101 ◽  
Author(s):  
Alan Robertson ◽  
A. T. G. McArthur
Keyword(s):  
Great Britain ◽  
Artificial Insemination ◽  
Genetic Difference ◽  
Genetic Differences ◽  
Breeding Value ◽  
Production Data ◽  
Dominant Group ◽  
Breed Type ◽  
Points Of View ◽  
Breed Improvement

In the analysis of the causes of variation between cows of a given breed in milk production, differences between herds pose some difficult problems. The nature of this variation is of importance from several points of view in the discussion of breed improvement. The situation is complicated by the fact that the herds of any breed type do not form a uniform group but can be classified roughly into a sort of ‘social structure’ (Robertson and Asker, 1951). The discussion of variation between all herds of a given breed type can then be broken down into the variation between strata and that between herds in the same stratum. From the analysis of production data from herds using artificial insemination (Robertson and Rendel, 1954; Korkman, 1953) there is evidence that the genetic component is a small proportion of the total variance in these herds; and also that in Great Britain the genetic difference in yield between the dominant group of herds (which provide many of the bulls used in A.I.) and the herds using A.I. is small. This is in agreement with studies on breed structure. In this paper we shall discuss the genetic differences between members of the small group of important herds which dominate each breed. These usually supply a high proportion of the bulls used. If we have good estimates of the breeding values of such bulls from the production records of their progeny, we can then examine the different breeding herds according to the breeding value of the bulls bred in them. Evidence of this type has been presented for Jersey bulls in New Zealand (Castle, 1952) but without statistical analysis of the results, although inspection suggests that there are definite differences between studs.

scholarly journals Myeloperoxidase-Oxidized LDLs Enhance an Anti-Inflammatory M2 and Antioxidant Phenotype in Murine Macrophages

2016 ◽  
Vol 2016 ◽  
pp. 1-20 ◽  
Author(s):  
Valérie Pireaux ◽  
Aude Sauvage ◽  
Benoît Bihin ◽  
Martine Van Steenbrugge ◽  
Alexandre Rousseau ◽  
...  
Keyword(s):  
Macrophage Polarization ◽  
Mrna Level ◽  
Marker Gene ◽  
Lipid Peroxides ◽  
The Other ◽  
Raw 264.7 Cells ◽  
Marker Genes ◽  
Murine Bone Marrow ◽  
Marker Gene Expression ◽  
Anti Inflammatory

Macrophages and oxidized LDLs play a key role in atherogenesis but their heterogeneity has been neglected up to now. Macrophages are prone to polarization and subsets of polarized macrophages have been described in atheromas. LDLs can be oxidized not only chemically by copper (Ox-LDLs) but also enzymatically by myeloperoxidase (MpOx-LDLs) resulting in oxidized LDLs poor in lipid peroxides. The effects of physiologically relevant myeloperoxidase-oxidized LDLs on macrophage polarization or on polarized macrophages remain largely unknown. In this study, the effects of LDLs on macrophage polarization were investigated by monitoring the expression of M1 and M2 genes following stimulation with native LDLs, Ox-LDLs, or MpOx-LDLs in RAW 264.7 cells. Except forMRC1, which is induced only by Ox-LDLs, MpOx-LDLs induced an overexpression of most of the selected marker genes at the mRNA level. MpOx-LDLs also modulate marker gene expression in polarized macrophages favoring notably anti-inflammatoryArg1expression in M2 cells and also in the other phenotypes. Noteworthy, MpOx-LDLs were the most efficient to accumulate lipids intracellularly in (un)polarized macrophages whatever the phenotype. These data were largely confirmed in murine bone marrow-derived macrophages. Our data suggest that MpOx-LDLs were the most efficient to accumulate within cells and to enhance an anti-inflammatory and antioxidant phenotype in M2 cells and also in the other macrophage phenotypes.

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