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1

Animal genome mapping projects

100%
Fredholm M.
Biotechnologia
|
1996
|
issue 2
13-19
EN
During the latest years many examples have been provided illustrating that gene maps can be utilized fer search aiming at (i) isolation causing oe having an influence on certain diseases, (ii) studying the genomic organization an evolutionary relationship of mammalian species, and (iii) eveloping animal models of human disease.
2

Chromosomal localization of a novel repetitive sequence in the Chenopodium quinoa genome

80%
Kolano B., Plucienniczak A., Kwasniewski M., Maluszynska J.
Journal of Applied Genetics
|
2008
|
vol. 49
|
issue 4
313-320
EN
In this study, a novel repetitive sequence pTaq10 was isolated from the Taq I digest of the genomic DNA of the pseudocereal Chenopodium quinoa. Sequence analysis indicated that this 286-bp monomer is not homologous to any known retroelement sequence. FISH and Southern blot analysis showed that this sequence is characterized by an interspersed genomic organization. After FISH, hybridization signals were observed as small dots spread throughout all of the chromosomes. pTaq hybridization signals were excluded from 45S rRNA gene loci, but they partly overlapped with 5S rDNA loci. pTaq10 is not a species-specific sequence, as it was also detected in C. berlandieri.
3

Mutagenesis of mouse embryonic stem (ES) cells

80%
Grundland C.
Biotechnologia
|
1999
|
issue 1
94-105
EN
Embryonic stem (ES) cells derived from preimplantation mouse embryo provide a powerful tool for genome manipulation in mammals. The two principal genetic approaches are used to modify genomes of embryonic stem cells, which may be introduced into blastocyst to produce chimeras, and these animals transmit the genetic alteration into the next generation. One approach, targeted mutagenesis, is designed to disrupt the function of specific murine genes that are known by their homology to genes of other organisms. The other approach, gene trapping by randomly insertional mutagenesis, is designed to identify novel, developmentally regulated genes in mouse embryos. In vivo screens allow for the identification and studying of genes that are expressed either within specific tissue or in spatiotemporal patterns. As an alternative to in vivo gene study, gene expression within specific cell types may be monitored in different ES cell cultures.
4

Identification of transcriptionally active regions with genome tiling microarrays

80%
Zmienko A., Guzowska-Nowowiejska M., Plader W., Figlerowicz M.
Biotechnologia
|
2008
|
issue 4
101-114
EN
Genome tiling microarrays, covering whole genomic sequence, have gained increasing popularity in transcript mapping studies. Functional analysis of model eucaryotic and procaryotic genomes proved their sensitivity and versatility in discovering actively transcribed regions of the genomes. Many novel proteins coding genes, miRNA coding genes, antisense transcripts and other non-protein coding regulatory RNAs, transcribed from introns, intergenic and centromeric regions have been identified this way. Their expression can often be linked to specific developmental stages, organs or stress response in plants and animals, giving further insight into processes which were considered to be already well characterized.
5

CRISPR elements in the Thermococcales: evidence for associated horizontal gene transfer in Pyrococcus furiosus

80%
Portillo M. C., Gonzalez J. M.
Journal of Applied Genetics
|
2009
|
vol. 50
|
issue 4
421-430
EN
The presence and distribution of CRISPR (clustered regularly interspaced short palindrome repeat) elements in the archaeal order Thermococcales were analyzed. Four complete genome sequences from the species Pyrococcus abyssi, P. furiosus, P. horikoshii, and Thermococcus kodakaraensis were studied. A fragment of the genome of P. furiosus was flanked by CRISPR elements upstream and by a single element downstream. The composition of the gene sequences contained in this genome fragment (positions 699013 to 855319) showed significant differences from the other genes in the P. furiosus genome. Differences were observed in the GC content at the third codon positions and the frequency of codon usage between the genes located in the analyzed fragment and the other genes in the P. furiosus genome. These results represent the first evidence suggesting that repeated CRISPR elements can be involved in horizontal gene transfer and genomic differentiation of hyperthermophilic Archaea.
6

Nutrigenomics concepts

80%
Koziolkiewicz M.
Biotechnologia
|
2009
|
issue 4
9-34
EN
The term nutrigenomics refers to the effect of diet on gene expression, while the term nutrigenetics refers to the influence of genetic variation (single nucleotide polymorphisms and/or copy number variation) on the response to a specific diet, functional food or diet supplement. Nutrigenomics and nutrigenetics become an important new research areas because there is growing evidence that diet can influence the long-term risk for metabolic, degenerative or cancer diseases. Various nutrients can influence DNA and chromatine structure, regulation of transcription and signal transduction. Understanding of the diet-gene interactions will allow to redefine current concepts of preventive medicine or dietetics and improve functional food production.
7

From sequence to function ? looking for genes and their annotations

80%
Baczkowski K., Mackiewicz P., Kowalczuk M., Banaszak J., Cebrat S.
Biotechnologia
|
2005
|
issue 3
22-44
EN
Today, we have very powerful and effective machines and methods to sequence and analyze DNA sequences. Almost every week, new genomes are added to sequence databases. However, those data are useless without additional annotations. Genes need to be found and their functions defined. Experimental work is too slow to analyze each sequence of a potential gene but computational methods facilitate such analyses. Here, we review the methodology, potential problems and constraints in genes finding and their annotation. We describe some new approaches including comparative genomics.
8

Chicken (Gallus gallus) ? the recent achievments in animal genomics

80%
Slawinska A., Siwek M.
Biotechnologia
|
2010
|
issue 3
36-46
EN
Chicken (Gallus gallus) is one of the most important animal species worldwide. As a significant contributor to food industry, it provides eggs and meat, which are important sources of animal protein in human diet. Moreover, chicken has a unique genomic architecture, which has been investigated for many years. This paper summarizes the most recent achievements in the field of chicken genomics. Among domestic animals chicken was the first to be selected for genome sequencing. Nowadays extensive chicken genetic and genomic resources such as genetic maps (STR, SNP), RH panel, EST, nucleotide sequence, QTLs and genes are known and publicly available. Finally, high-throughput microarrays (60K SNP array and 44K gene expression array) have been designed for the chicken genome as a modern tool applied in genome-wide association studies and functional genomics.
9

Flow cytometry applied in plant biotechnology

80%
Sliwinska E.
Biotechnologia
|
2002
|
issue 1
122-128
EN
Flow cytometry (FCM) is a rapid and exact method for estimating the nuclear DNA content. Thus, it can be used for ploidy screening of different plant materials cultured in vitro (plantlets, callus, cell suspensions and somatic embryos) as well as haploids and somatic hybrids. In addition, it can be applied as a tool to analyse the events of genetic transformation. The application of FCM in biotechnology will be discussed.
10

Morphogenic potential of plant cell and its genetic conditions

80%
Rybczynski J. J., Mikula A.
Biotechnologia
|
2000
|
issue 2
41-54
EN
The aim of the presented review is to analyse the possibilities of creating highly morphogenic Triticum aestivum genome using generative hybridisation of various wheat forms and its relatives.
11

Polymorphism of nine canine-derived microsatellites in farm silver foxes (Vulpes fulvus)

70%
Zajac M., Klukowska J., Slomski R., Switonski M.
Journal of Applied Genetics
|
2000
|
vol. 41
|
issue 1
43-50
EN
Polymorphism of nine canine-derived microsatellites (CPH1, CPH3, CPH6, CPH11, 2004, 2010, 2140,2168 and 2319) was studied in a group of 91 unrelated silver foxes kept on a commercial farm. Among the studied microsatellites two appeared to be dimorphic (CPH1 and 2140) and another two (2010 and 2319) were highly polymorphic, with PIC (Polymorphic Information Content) values of 0.775 and 0.692, respectively. Other five microsatellites demonstrated medium polymorphism and the PIC values ranged from 0.548 to 0.616. It was calculated that if all the studied markers were applied for paternity testing, then combined exclusion probability would be 0.989. Microsatellite polymorphisms in the silver fox, blue fox and dog were compared and tendency toward longer alleles in the dog was revealed. It was confirmed that canine-derived microsatellites can be successfully applied for parentage control and genome mapping in silver foxes.
12

Monte Carlo simulation of genome viability with paralog replacement

70%
Cebrat S., Stauffer D.
Journal of Applied Genetics
|
2002
|
vol. 43
|
issue 3
391-395
EN
Recent analyses of genome content have revealed that many single functions, even in haploid organisms, can be executed by more than one gene. As a result, experimental disruption of many individual genes does not exert lethal effects on the organism or even any visible change in the phenotype of the organism with a knockedout gene. Our analysis shows that such genetic redundancy allows for an appreciably higher mutation load in the genome simulations before the viability of the whole organism is destroyed.
13

Molecular characterization of novel low-molecular-weight glutenin genes in Aegilops longissima

70%
Huang Z., Long H., Jiang Q.-T., Wei Y.-M., Yan Z.-H., Zheng Y.-L.
Journal of Applied Genetics
|
2010
|
vol. 51
|
issue 1
9-18
EN
Extensive genetic variations of low-molecular-weight glutenin subunits (LMW-GS) and their coding genes were found in the wild diploid A- and D-genome donors of common wheat. In this study, we reported the isolation and characterization of 8 novel LMW-GS genes from Ae.longissima Schweinf. & Muschl., a species of the section Sitopsis of the genus Aegilops, which is closely related to the B genome of common wheat. Based on the N-terminal domain sequences, the 8 genes were divided into 3 groups. A consensus alignment of the extremely conserved domains with known gene groups and the subsequent cluster analysis showed that 2 out of the 3 groups of LMW-GS genes were closely related to those from the B genome, and the remaining was related to those from A and D genomes of wheat and Ae. tauschii. Using 3 sets of gene-group-specific primers, PCRs in diploid, tetraploid and hexaploid wheats and Ae. tauschii failed to obtain the expected products, indicating that the 3 groups of LMW-GS genes obtained in this study were new members of LMW-GS multi-gene families. These results suggested that the Sitopsis species of the genus Aegilops with novel gene variations could be used as valuable gene resources of LMW-GS. The 3 sets of group-specific primers could be utilized as molecular markers to investigate the introgression of novel alien LMW-GS genes from Ae. longissima into wheat.
14

New insights into phylogeny from genomic point of view

70%
Sobczynski M., Mackiewicz P., Mackiewicz D., Smolarczyk K., Cebrat S.
Biotechnologia
|
2005
|
issue 3
102-117
EN
Availability of fully sequenced genomes contributes to the development of new science named phylogenomics which opens new possibilities of phylogenetic analyses and study of genome evolution based on the whole information coded in genomic DNA. The advantages and disadvantages of the new methods are described. Despite many phenomena such as lineage-specific gene loss, gene duplication and horizontal gene transfer disturbing phylogenetic analyses, the new methods are able to extract some phylogenetic signals in the analysed genomes and construct reliable phylogenetic trees. The genome-based studies support not only the three-domain concept of Tree of Life but they identify previously undetected major clades of prokaryotes as well.
15

C-banding analysis of eight species of Kengyilia (Poaceae: Triticeae)

70%
Zeng J., Cao G., Liu J., Zhang H.-Q., Zhou Y.-H.
Journal of Applied Genetics
|
2008
|
vol. 49
|
issue 1
11-21
EN
To characterize chromosomes and the interspecific relationships within the genus Kengyilia, 8 species were used for Giemsa C-banding analysis. Results indicated that the species differed in C-banding patterns. K. gobicola, K. alatavica and K. batalinii had distinct centromeric bands and no banded chromosomes, while K. hirsuta, K. longiglumis, K. melanthera, K. rigidula and K. thoroldiana had more abundant and diagnostic C-bands with interstitial and terminal bands.
16

FISH mapping in cattle (Bos taurus L.) is not yet out of fashion

70%
De_ L. L., Molteni L., Parma P.
Journal of Applied Genetics
|
2010
|
vol. 51
|
issue 4
497-499
EN
Physical mapping of genes by fluorescence in situ hybridization (FISH) seems to be out of fashion in species whose assembled genome sequences are available. However, in this work we evidence the existence of errors in gene location in the Btau_4.0 assembly. We show that DFNA5 and CHCHD6 genes are located on BTA4 and BTA22, respectively, instead of BTA10 and BTA3, as displayed by Btau_4.0. This report emphasizes the need to verify the data on physical localization of genes in the cattle genome (at least by taking into account comparative data reported in available papers) and the need to improve the cattle genome assembly. Our results indicate that FISH mapping in cattle is still useful.
17

Molecular cytogenetic characterization of eight small supernumerary marker chromosomes originating from chromosomes 2, 4, 8, 18, and 21 in three patients

70%
Pietrzak J., Mrasek K., Obersztyn E., Stankiewicz P., Kosyakova N., Weise A., Cheung S. W., Ca W. W., vo_ E. F., Mazurczak T., Bocian E., Liehr T.
Journal of Applied Genetics
|
2007
|
vol. 48
|
issue 2
167-175
EN
Small supernumerary marker chromosomes (sSMCs) are a morphologically heterogeneous group of additional structurally abnormal chromosomes that cannot be identified unambiguously by conventional banding techniques alone. Molecular cytogenetic methods enable detailed characterization of sSMCs; however, in many cases interpretation of their clinical significance is problematic. The aim of our study was to characterize precisely sSMCs identified in three patients with dysmorphic features, psychomotor retardation and multiple congenital anomalies. We also attempted to correlate the patients' genotypes with phenotypes by inclusion of data from the literature. The sSMCs were initially detected by G-banding analysis in peripheral blood lymphocytes in these patients and were subsequently characterized using multicolor fluorescence in situ hybridization (M-FISH), (sub)centromere-specific multicolor FISH (cenM-FISH, subcenM-FISH), and multicolor banding (MCB) techniques. Additionally, the sSMCs in two patients were also studied by hybridization to whole-genome bacterial artificial chromosome (BAC) arrays (array-CGH) to map the breakpoints on a single BAC clone level. In all three patients, the chromosome origin, structure, and euchromatin content of the sSMCs were determined. In patient RS, only a neocentric r(2)(q35q36) was identified. It is a second neocentric sSMC(2) in the literature and the first marker chromosome derived from the terminal part of 2q. In the other two patients, two sSMCs were found, as M-FISH detected additional sSMCs that could not be characterized in G-banding analysis. In patient MK, each of four cell lines contained der(4)(:p11.1->.q12:) accompanied by a sSMC(18): r(18)(:p11.2->q11.1::p11.2->q11.1:), inv dup(18)(:p11.1->q11.1::q11.1->p11.1:), or der(18) (:p11.2->q11.1::q11.1->p11.1:). In patient NP, with clinical features of trisomy 8p, three sSMCs were characterized: r(8)(:p12->q11.1::q11.1->p21:) der(8) (:p11.22->q11.1::q11.1->p21::p21->p11.22:) and der(21)(:p11.1->q21.3:). The BAC array results confirmed the molecular cytogenetic results and refined the breakpoints to the single BAC clone resolution. However, the complex mosaic structure of the marker chromosomes derived from chromosomes 8 and 18 could only be identified by molecular cytogenetic methods. This study confirms the usefulness of multicolor FISH combined with whole-genome arrays for comprehensive analyses of marker chromosomes.
18

A review of asthma genetics: gene expression studies and recent candidates

61%
Malerba G., Pignatti P. F.
Journal of Applied Genetics
|
2005
|
vol. 46
|
issue 1
93-104
EN
Recent evidence indicates an important role of inflammation pathways, airways remodeling and epithelium activation in asthma genetics. In particular, transcriptome studies have detected differentially expressed genes involved in eosinophil apoptosis, the arginase pathway, response to allergens or interleukins, and to inhaled corticosteroids. Candidate gene and genome wide studies have localized genetic regions involved in the disease, such as the A1AR and CLCA1 genes (chromosome 1), IL-1RN and DPP10 (2q14), HLA-G and TNF- (6p21), GPRA (7p14), FcRI and GSTP1 (11q13), NOS1, IFNG, STAT6, VDR, and other genes (12q13-26), PHF11 and flanking genes (13q14), AACT and PTGDR (14q), and ADAM33 (20p13). The role of these and other genetic determinants has to be confirmed in future, preferably longitudinal, studies.
19

Cytogenetic analysis of genome structure of polyploids

61%
Maluszynska J.
Biotechnologia
|
2001
|
issue 1
35-41
EN
Polyploidization is a widespread and important process in the plant evolution and in individual plant development. Polyploids are used in plant breeding programs for improving different crop varieties. Genome spontaneously becomes autoplyploid via chromosomal nondisjunction in mitosis or meiosis, endoreduplication, cell fusion or inhibition of cytokinesis. Polyploids also occur among regenerated plants from in vitro culture or during transformation process. Comparative molecular and cytogenetic genome investigations have revealed that many plant species recognised as diploids are in fact polyploids. Molecular cytogenetics methods, especially genomic in situ hybridization (GISH), allow for distinguishing ancestral genomes and chromosomal rearrangements appearing in the course of evolution or/and biotechnological manipulations.
20

The influence of rye cytoplasm on meiotic stability of tetraploid Secalotriticum

61%
Apolinarska B.
Journal of Applied Genetics
|
2003
|
vol. 44
|
issue 2
129-137
EN
Chromosome pairing in tetraploid Secalotriticum was analysed. In the studied plants wheat chromosomes in PMCs during metaphase I showed a higher degree of pairing, in comparison to the rye genome. This is reflected in a very low frequency of univalents and a higher frequency of ring bivalents. The occurrence of wheat univalents was dependent on wheat mixogenome. In plants with an unstabilized fourth homoeologous group, a heteromorphic bivalent 4A-4B was observed in 39.9% of PMCs, whereas in plants with an unstabilized seventh homoeologous group, chromosome 7A-7B pairing was found in all analysed cells. Rye univalents were present in all plants studied. The highest mean frequency of univalents and rod bivalents, both in wheat and in rye genomes, were recorded in plants whose first homoeologous group contained chromosome 1A. The mean number of terminal chiasmata per chromosome amounted to 1.78 in the wheat genome and 1.36 in the rye genome. It may be concluded that the plasmagenes in Secalotriticum did not increase the meiotic stability of the rye genome and also did not stabilize plant fertility.
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