BACKGROUND: Long terminal repeats (LTRs) represent important parts of LTR retrotransposons and retroviruses found in high copy numbers in a majority of eukaryotic genomes. LTRs contain regulatory sequences essential for the life cycle of the retrotransposon. Previous experimental and sequence studies have provided only limited information about LTR structure and composition, mostly from model systems. To enhance our understanding of these key sequence modules, we focused on the contrasts between LTRs of various retrotransposon families and other genomic regions. Furthermore, this approach can be utilized for the classification and prediction of LTRs. RESULTS: We used machine learning methods suitable for DNA sequence classification and applied them to a large dataset of plant LTR retrotransposon sequences. We trained three machine learning models using (i) traditional model ensembles (Gradient Boosting), (ii) hybrid convolutional/long and short memory network models, and (iii) a DNA pre-trained transformer-based model using k-mer sequence representation. All three approaches were successful in classifying and isolating LTRs in this data, as well as providing valuable insights into LTR sequence composition. The best classification (expressed as F1 score) achieved for LTR detection was 0.85 using the hybrid network model. The most accurate classification task was superfamily classification (F1=0.89) while the least accurate was family classification (F1=0.74). The trained models were subjected to explainability analysis. Positional analysis identified a mixture of interesting features, many of which had a preferred absolute position within the LTR and/or were biologically relevant, such as a centrally positioned TATA-box regulatory sequence, and TG..CA nucleotide patterns around both LTR edges. CONCLUSIONS: Our results show that the models used here recognized biologically relevant motifs, such as core promoter elements in the LTR detection task, and a development and stress-related subclass of transcription factor binding sites in the family classification task. Explainability analysis also highlighted the importance of 5'- and 3'- edges in LTR identity and revealed need to analyze more than just dinucleotides at these ends. Our work shows the applicability of machine learning models to regulatory sequence analysis and classification, and demonstrates the important role of the identified motifs in LTR detection.
- Klíčová slova
- CNN-LSTM, DNABERT, Deep learning, Eukaryote, Regulatory mechanisms, Repeat, SHAP score, Sequence analysis, TFBS, Transcription factor binding sites, Transposable elements,
- Publikační typ
- časopisecké články MeSH
In most studied eukaryotes, chromosomes are monocentric, with centromere activity confined to a single region. However, the rush family (Juncaceae) includes species with both monocentric (Juncus) and holocentric (Luzula) chromosomes, where centromere activity is distributed along the entire chromosome length. Here, we combine chromosome-scale genome assembly, epigenetic analysis, immuno-FISH and super-resolution microscopy to study the transition to holocentricity in Luzula sylvatica. We report repeat-based holocentromeres with an irregular distribution of features along the chromosomes. Luzula sylvatica holocentromeres are predominantly associated with two satellite DNA repeats (Lusy1 and Lusy2), while CENH3 also binds satellite-free gene-poor regions. Comparative repeat analysis suggests that Lusy1 plays a crucial role in centromere function across most Luzula species. Furthermore, synteny analysis between L. sylvatica (n = 6) and Juncus effusus (n = 21) suggests that holocentric chromosomes in Luzula could have arisen from chromosome fusions of ancestral monocentric chromosomes, accompanied by the expansion of CENH3-associated satellite repeats.
- MeSH
- centromera * genetika MeSH
- chromozomy rostlin * genetika MeSH
- DNA rostlinná genetika MeSH
- genom rostlinný MeSH
- hybridizace in situ fluorescenční MeSH
- molekulární evoluce MeSH
- repetitivní sekvence nukleových kyselin genetika MeSH
- satelitní DNA * genetika MeSH
- syntenie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA rostlinná MeSH
- satelitní DNA * MeSH
Due to high biocompatibility, miniaturization, optical transparency and low production cost together with high radiation hardness the diamond-based sensors are considered promising for radiation medicine and biomedicine in general. Here we present detection of fibroblast cell culture properties by nanocrystalline diamond solution-gated field-effect transistors (SG-FET), including effects of gamma irradiation. We show that blank nanocrystalline diamond field-effect biosensors are stable at least up to 300 Gy of γ irradiation. On the other hand, gate current of the diamond SG-FET biosensors with fibroblastic cells increases exponentially over an order of magnitude with increasing radiation dose. Extracellular matrix (ECM) formation is also detected and analyzed by correlation of electronic sensor data with optical, atomic force, fluorescence, and scanning electron microscopies.
- Klíčová slova
- Atomic force microscopy, Biosensors, Cells, Diamond thin films, Field-effect transistors, Gamma irradiation, Proteins,
- MeSH
- biosenzitivní techniky * MeSH
- diamant * MeSH
- extracelulární matrix MeSH
- fibroblasty MeSH
- mikroskopie elektronová rastrovací MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- diamant * MeSH
Centromere drive model describes an evolutionary process initiated by centromeric repeats expansion, which leads to the recruitment of excess kinetochore proteins and consequent preferential segregation of an expanded centromere to the egg during female asymmetric meiosis. In response to these selfish centromeres, the histone protein CenH3, which recruits kinetochore components, adaptively evolves to restore chromosomal parity and counter the detrimental effects of centromere drive. Holocentric chromosomes, whose kinetochores are assembled along entire chromosomes, have been hypothesized to prevent expanded centromeres from acquiring a selective advantage and initiating centromere drive. In such a case, CenH3 would be subjected to less frequent or no adaptive evolution. Using codon substitution models, we analyzed 36 CenH3 sequences from 35 species of the holocentric family Cyperaceae. We found 10 positively selected codons in the CenH3 gene [six codons in the N-terminus and four in the histone fold domain (HFD)] and six branches of its phylogeny along which the positive selection occurred. One of the positively selected codons was found in the centromere targeting domain (CATD) that directly interacts with DNA and its mutations may be important in centromere drive suppression. The frequency of these positive selection events was comparable to the frequency of positive selection in monocentric clades with asymmetric female meiosis. Taken together, these results suggest that preventing centromere drive is not the primary adaptive role of holocentric chromosomes, and their ability to suppress it likely depends on their kinetochore structure in meiosis.
- Klíčová slova
- CenH3, asymmetric meiosis, centromere drive, holocentric chromosomes, meiotic drive, monocentric chromosomes, symmetric meiosis,
- Publikační typ
- časopisecké články MeSH
We show the influence of osteoblastic SAOS-2 cells on the transfer characteristics of nanocrystalline diamond solution-gated field-effect transistors (SGFET) prepared on glass substrates. Channels of these fully transparent SGFETs are realized by hydrogen termination of undoped diamond film. After cell cultivation, the transistors exhibit about 100× increased leakage currents (up to 10nA). During and after the cell delamination, the transistors return to original gate currents. We propose a mechanism where this triggering effect is attributed to ions released from adhered cells, which depends on the cell adhesion morphology, and could be used for cell culture monitoring.
- Klíčová slova
- Field-effect transistors, Leakage currents, Nanocrystalline diamond, Osteoblastic cells,
- MeSH
- akční potenciály * MeSH
- biosenzitivní techniky přístrojové vybavení MeSH
- buněčná adheze * MeSH
- diamant chemie MeSH
- elektronické tranzistory * MeSH
- ionty MeSH
- lidé MeSH
- nádorové buňky kultivované MeSH
- nádory kostí * MeSH
- osteosarkom * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- diamant MeSH
- ionty MeSH
The authors show that nanocrystalline diamond (NCD) thin films prepared by microwave plasma enhanced chemical vapor deposition apparatus with a linear antenna delivery system are well compatible with epithelial cells (5637 human bladder carcinoma) and significantly improve the cell adhesion compared to reference glass substrates. This is attributed to better adhesion of adsorbed layers to diamond as observed by atomic force microscopy (AFM) beneath the cells. Moreover, the cell morphology can be adjusted by appropriate surface treatment of diamond by using hydrogen and oxygen plasma. Cell bodies, cytoplasmic rims, and filopodia were characterized by Peakforce AFM. Oxidized NCD films perform better than other substrates under all conditions (96% of cells adhered well). A thin adsorbed layer formed from culture medium and supplemented with fetal bovine serum (FBS) covered the diamond surface and played an important role in the cell adhesion. Nevertheless, 50-100 nm large aggregates formed from the RPMI medium without FBS facilitated cell adhesion also on hydrophobic hydrogenated NCD (increase from 23% to 61%). The authors discuss applicability for biomedical uses.
- MeSH
- buněčná adheze * MeSH
- diamant chemie MeSH
- epitelové buňky cytologie fyziologie ultrastruktura MeSH
- lidé MeSH
- mikroskopie atomárních sil MeSH
- nádorové buněčné linie MeSH
- nanostruktury chemie MeSH
- tvar buňky MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- diamant MeSH
Diamond is recognized as an attractive material for merging solid-state and biological systems. The advantage of diamond field-effect transistors (FET) is that they are chemically resistant, bio-compatible, and can operate without gate oxides. Solution-gated FETs based on H-terminated nanocrystalline diamond films exhibiting surface conductivity are employed here for studying effects of fetal bovine serum (FBS) proteins and osteoblastic SAOS-2 cells on diamond electronic properties. FBS proteins adsorbed on the diamond FETs permanently decrease diamond conductivity as reflected by the -45 mV shift of the FET transfer characteristics. Cell cultivation for 2 days results in a further shift by another -78 mV. We attribute it to a change of diamond material properties rather than purely to the field-effect. Increase in gate leakage currents (by a factor of 4) indicates that the FBS proteins also decrease the diamond-electrolyte electronic barrier induced by C-H surface dipoles. We propose a model where the proteins replace ions in the very vicinity of the H-terminated diamond surface.
- MeSH
- adsorpce MeSH
- biosenzitivní techniky přístrojové vybavení metody MeSH
- buněčné linie MeSH
- diamant chemie MeSH
- elektrochemie metody MeSH
- elektronické tranzistory * MeSH
- ionty MeSH
- krevní proteiny chemie MeSH
- lidé MeSH
- mikroskopie elektronová rastrovací MeSH
- nanočástice chemie ultrastruktura MeSH
- povrchové vlastnosti MeSH
- roztoky MeSH
- skot MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- diamant MeSH
- ionty MeSH
- krevní proteiny MeSH
- roztoky MeSH
