Women's most frequent type of cancer is breast cancer, second only to lung cancer. This paper summarizes changes in genomics and epigenetics and incremental biological activities. A tumour develops through a series of phases involving a separate abnormal gene. Even though many diseases cause DNA mutations, most treatments are designed to relieve symptoms rather than change the DNA. Clustering short palindromic repeats (CRISPR) or Cas9 is the primary approach for discovering and confirming tumorigenic genomic targets. A Kohonen neural network with an expression programming model was developed for gene selection. The main problem in genetic selection is reducing the number of features chosen while maintaining accuracy. This purpose is accomplished systematically. In the end, the approach method performed better than the existing quantum squirrel-inspired algorithm and the recurrent neural network oppositional call search algorithm for genetic selection. The KNNet-EPM model used an expression programming approach to identify gene biomarkers for breast cancer. This method was achieved with RAE of 42%, sensitivity of 93%, f1 score of 88%, accuracy of 98%, kappa score of 83%, specificity of 92% and MAE of 30%.
- MeSH
- algoritmy MeSH
- karcinogeneze MeSH
- lidé MeSH
- nádory plic * MeSH
- nádory prsu * diagnóza genetika MeSH
- umělá inteligence MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought responses in the field remain largely unknown. Here, we addressed this by utilizing an interdisciplinary approach involving field water status phenotyping, sampling, and gene expression analyses. Overall, changes at the transcriptional level were reflected in plant spectral traits amenable to field-level physiological measurements, although changes in photosynthesis-related pathways were found likely to be under more complex post-transcriptional control. Examining homoeologous genes with a 1:1:1 relationship across the A, B, and D genomes (triads), we revealed a complex genomic architecture for drought responses under field conditions, involving gene homoeolog specialization, multiple gene clusters, gene families, miRNAs, and transcription factors coordinating these responses. Our results provide a new focus for genomics-assisted breeding of drought-tolerant wheat cultivars.
Transcription factors (TFs) fine-tune the host defense transcriptome in response to pathogen invasions. No information is available on Zingiber zerumbet (Zz) TFs involved in defense response against Pythium myriotylum. Here, we provide a global identification, characterization, and temporal expression profiling of Zz TFs following an incompatible interaction with P. myriotylum using a transcriptome sequencing approach. We identified a total of 903 TFs belonging to 96 families based on their conserved domains. Evolutionary analysis clustered the Zz TFs according to their phylogenetic affinity, providing glimpses of their functional diversities. High throughput expression array analysis highlighted a complex interplay between activating and repressing transcription factors in fine-tuning Zz defense response against P. myriotylum. The high differential modulation of TFs involved in cell wall fortification, lignin biosynthesis, and SA/JA hormone crosstalk allows us to envisage that this mechanism plays a central role in restricting P. myriotylum proliferation in Zz. This study lays a solid foundation and provides valuable resources for the investigation of the evolutionary history and biological functions of Zz TF genes involved in defense response.
- MeSH
- fyziologický stres MeSH
- imunita rostlin * MeSH
- molekulární evoluce MeSH
- Pythium patogenita MeSH
- responzivní elementy MeSH
- rostlinné proteiny genetika metabolismus MeSH
- transkripční faktory genetika metabolismus MeSH
- transkriptom * MeSH
- zázvorníkovité genetika imunologie mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
We report a series of microarray-based leaf and crown transcriptome comparisons involving three barley cultivars (cvs. Luxor, Igri and Atlas 68) which express differing degrees of frost tolerance. The transcripts were obtained following the exposure of seedlings to low (above and below zero) temperatures, aiming to identify those genes and signalling/metabolic pathways which are associated with frost tolerance. Both the leaves and the crowns responded to low temperature by the up-regulation of a suite of abscisic acid (ABA)-responsive genes, most of which have already been recognized as components of the plant low temperature response. The inter-cultivar comparison indicated that genes involved in maintaining the leaf's capacity to synthesize protein and to retain chloroplast activity were important for the expression of frost tolerance. In the crown, the repression of genes associated with nucleosome assembly and transposon regulation were the most relevant transcriptional changes associated with frost tolerance, highlighting the role of gene repression in the cold acclimation response.
- MeSH
- down regulace MeSH
- ječmen (rod) genetika metabolismus MeSH
- listy rostlin genetika metabolismus MeSH
- mapování chromozomů MeSH
- nukleozomy genetika metabolismus MeSH
- reakce na chladový šok MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné geny MeSH
- rostlinné proteiny genetika metabolismus MeSH
- transkripční elongační faktory genetika metabolismus MeSH
- transkriptom MeSH
- upregulace MeSH
- zmrazování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.
- MeSH
- chromozomy chemie genetika MeSH
- fyzikální mapování chromozomů metody MeSH
- genom lidský MeSH
- genomika metody MeSH
- genová knihovna MeSH
- karyotyp MeSH
- lidé MeSH
- malování chromozomů metody MeSH
- mitóza MeSH
- průtoková cytometrie metody MeSH
- rostliny chemie genetika MeSH
- sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů metody MeSH
- struktury chromozomu chemie genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
We report a series of microarray-based comparisons of gene expression in the leaf and crown of the winter barley cultivar Luxor, following the exposure of young plants to various periods of low (above and below zero) temperatures. A transcriptomic analysis identified genes which were either expressed in both the leaf and crown, or specifically in one or the other. Among the former were genes responsible for calcium and abscisic acid signalling, polyamine synthesis, late embryogenesis abundant proteins and dehydrins. In the crown, the key organ for cereal overwintering, cold treatment induced transient changes in the transcription of nucleosome assembly genes, and especially H2A and HTA11, which have been implicated in cold sensing in Arabidopsis thaliana. In the leaf, various heat-shock proteins were induced. Differences in expression pattern between the crown and leaf were frequent for genes involved in certain pathways responsible for osmolyte production (sucrose and starch, raffinose, γ-aminobutyric acid metabolism), sugar signalling (trehalose metabolism) and secondary metabolism (lignin synthesis). The action of proteins with antifreeze activity, which were markedly induced during hardening, was demonstrated by a depression in the ice nucleation temperature.
- MeSH
- aklimatizace genetika MeSH
- GABA genetika metabolismus MeSH
- genetická transkripce MeSH
- histony genetika MeSH
- ječmen (rod) genetika metabolismus MeSH
- lignin biosyntéza genetika MeSH
- listy rostlin genetika metabolismus MeSH
- metabolismus sacharidů genetika MeSH
- nízká teplota MeSH
- nukleozomy metabolismus MeSH
- proteiny teplotního šoku genetika MeSH
- regulace genové exprese u rostlin MeSH
- roční období MeSH
- stanovení celkové genové exprese MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The effect of recalcitrant soil and water pollutant 2,4,6-trinitrotoluen (TNT) on gene expression in Arabidopsis thaliana rosettes and roots was studied separately for the first time using microarrays. Seven-day exposure to TNT resulted in 170 up- and 122 down-regulated genes in the rosettes and 61 up- and 51 down-regulated genes in the roots (expression difference > 1.5-fold; p[t test] < 0.05). TNT concentration, 5 µg/ml, was selected according to the dose response analysis and study of TNT uptake from liquid media. Although many TNT induced genes fell into ontology groups annotated as response to biotic and abiotic stresses in rosettes and roots, only a small overlap of TNT effects on transcriptome was observed between rosettes and roots. The rosettes exhibited induction of several genes associated with toxin metabolism, such as UDP-glycosyltransferases and ATP-binding cassette (ABC) family transporters. On the other side, no genes known to be involved in TNT transformation were found to be up-regulated in the roots. The genes coding for enzymes involved in the cell wall modifications were abundantly up-regulated in roots. Microarray data indicated that after a relatively long incubation with TNT (7 days), metabolism of this xenobiotic proceeded mainly in aerial parts, while its translocation into cell walls still took place in the roots. Results obtained by microarray hybridization were validated by quantitative real-time reverse-transcription PCR. Nitrate reductase 1, several glycosyltransferases and ABC transporters, sucrose-proton symporter 2, thioredoxin-dependent peroxidase 2, and gamma-glutamyltransferase are discussed for their potential to enhance detoxification and toleration capability of plants to TNT.
- MeSH
- Arabidopsis anatomie a histologie účinky léků metabolismus fyziologie MeSH
- membránové transportní proteiny genetika metabolismus MeSH
- metabolická inaktivace MeSH
- mikročipová analýza MeSH
- molekulární struktura MeSH
- proteiny huseníčku genetika metabolismus MeSH
- regulace genové exprese u rostlin MeSH
- stanovení celkové genové exprese MeSH
- transferasy genetika metabolismus MeSH
- trinitrotoluen farmakokinetika farmakologie MeSH
- výbušné látky farmakokinetika farmakologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
