Abstract Strobilurins constitute a new class of fungicides that is the most widely used in world. The present study was conducted to investigate aquatic toxicity 3 common strobilurin (kresoxim‐methyl, pyraclostrobin, and trifloxystrobin) Daphnia magna . neonate acute immobilization test showed 48‐h 50% effective concentration (EC50) values kresoxim‐methyl, trifloxystrobin were 443.3 µg/L, 20.9 23.0 respectively. In addition, strobilurins significantly induced activity important...

Abstract Background The p53 tumor suppressor protein is involved in a complicated regulatory network, mediating expression of ~1000 human genes. Recent studies have shown that many vivo binding sites (BSs) reside transposable repeats. relationship between these BSs and functional response elements (REs) remains unknown, however. We sought to understand whether the REs also particularly most-abundant Alu Results analyzed ~160 identified so far found 24 them occur More than half...

The topological landscape of gene interaction networks provides a rich source information for inferring functional patterns genes or proteins. However, it is still challenging task to aggregate heterogeneous biological such as expression and interactions achieve more accurate inference prediction discovery new interactions. In particular, how generate unified vector representation integrate diverse input data key challenge addressed here. We propose scalable robust deep learning framework...

The widespread use of the maize Mutator (Mu) system to generate mutants exploits preference Mu transposons insert into genic regions. However, little is known about specificity insertions within genes. Analysis 79 independently isolated Mu-induced alleles at gl8 locus established that least 75 contain insertions. terminal inverted repeats (TIRs) inserted defined three new transposons: Mu10, 11, and Mu12. A large percentage (>80%) are located in 5' untranslated region (UTR) gene. Ten...

Abstract Recent studies of genome-wide nucleosomal organization suggest that the DNA sequence is one major determinants nucleosome positioning. Although search for underlying patterns encoded in has been going on about 30 years, our knowledge these still remains limited. Based evaluations deformation energy, we developed new scoring functions to predict There are three principal differences between approach and earlier studies: (i) assume length varies from 146 147 bp; (ii) consider...

Objectives: To develop and validate a predictive model for discriminating clinically significant prostate cancer (csPCa) from insignificant (ciPCa). Methods: This retrospective study was performed with 159 consecutively enrolled pathologically confirmed PCa patients two medical centers. The dataset allocated to training group (n = 54) an internal validation 22) one center along external independent 83) another center. A total of 1,188 radiomic features were extracted T2WI, diffusion-weighted...

Abstract Background One of the most challenging tasks for bladder cancer diagnosis is to histologically differentiate two early stages, non-invasive Ta and superficially invasive T1, latter which associated with a significantly higher risk disease progression. Indeed, in considerable number cases, T1 tumors look very similar under microscope, making distinction difficult even experienced pathologists. Thus, there an urgent need favoring system based on machine learning (ML) distinguish...

Functional characterization of single nucleotide variants (SNVs) involves two steps, the first step is to convert DNA protein and second visualize sequences with their structures. As massively parallel sequencing has emerged as a leading technology in genomics, resulting significant increase data volume, direct visualization SNVs together associated sequences/structures new user interface (UI) would be more effective way assess potential effects on function.We have developed BioVR, an...

Linker histones (LHs) bind to the DNA entry/exit points of nucleosomes and demonstrate preference for AT-rich DNA, although recognized sequence patterns remain unknown. These are expected be more pronounced in metazoan with abundant LHs, compared yeast few LHs. To test this hypothesis, we nucleosome core particle (NCP) sequences from chicken, Drosophila yeast, extending them by flanking extracted genomes. We found that known ∼10-bp periodic oscillation elements goes beyond ends nucleosomes,...

The tumor suppressor protein p53 exhibits high affinity to the response elements regulating cell cycle arrest genes (CCA-sites), but relatively low sites associated with apoptosis (Apo-sites). This in vivo tendency cannot be explained solely by p53-DNA binding constants measured vitro. Since can bind nucleosomal DNA, we sought understand if two groups of differ their accessibility when embedded nucleosomes. To this aim, analyzed sequence-dependent bending anisotropy human genomic DNA...

Background . It is important to distinguish the classification of lung adenocarcinoma. A radiomics model was developed predict tumor invasiveness using quantitative and qualitative features pulmonary ground-glass nodules (GGNs) on chest CT. Materials Methods total 599 GGNs [including 202 preinvasive lesions 397 minimally invasive adenocarcinomas (IPAs)] were evaluated univariate, multivariate, logistic regression analyses construct a that predicted GGNs. In primary cohort (comprised patients...

Some unidentified RNA molecules, together with the nucleoid protein HU, were suggested to be involved in structure of Escherichia coli. HU is a conserved known for its role binding DNA and maintaining negative supercoils latter. also binds few RNAs, but full spectrum targets cell not known. To understand any interaction structure, we immunoprecipitated potential HU-RNA complexes from cells examined bound RNAs by hybridization whole-genome tiling arrays. We identified associations between 10...

Nucleosomes often undergo extensive rearrangement when genes are activated for transcription. We have shown previously, using paired-end sequencing of yeast nucleosomes, that major changes in chromatin structure occur by 3-aminotriazole (3AT), an inducer the transcriptional activator Gcn4. Here, we provide a global analysis these data. At genomic level, nucleosomes regularly phased relative to transcription start site. However, subset 234 strongly induced genes, this phasing is much more...

Biomedical interaction networks have incredible potential to be useful in the prediction of biologically meaningful interactions, identification network biomarkers disease, and discovery putative drug targets. Recently, graph neural been proposed effectively learn representations for biomedical entities achieved state-of-the-art results prediction. These methods only consider information from immediate neighbors but cannot a general mixing features at various distances. In this paper, we...

The tumor suppressor protein p53 interacts with DNA in a sequence-dependent manner. Thousands of binding sites have been mapped genome-wide normal and cancer cells. However, the way selectively binds its cognate different types cells is not fully understood. Here, we performed comprehensive analysis 25 published cistromes identified 3,551 6,039 'high-confidence' cells, respectively. Our revealed 2 distinct epigenetic features underlying p53-DNA interactions vivo. First, are associated...

Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ∼147 bp wrapped ∼1.7 times around core histone octamer. linker histone, H1, binds both to the nucleosome, sealing coils, and between directing chromatin folding. Micrococcal nuclease (MNase) digests yield chromatosome, containing H1 ∼160 bp, then converts it particle, no H1. Sequencing nucleosomal...

The spatial organization of nucleosomes in 30-nm fibers remains unknown detail. To tackle this problem, we analyzed all stereochemically possible configurations two-start chromatin with DNA linkers L = 10-70 bp (nucleosome repeat length NRL 157-217 bp). In our model, the energy a fiber is sum elastic linker DNA, steric repulsion, electrostatics, and H4 tail-acidic patch interaction between two stacked nucleosomes. We found families energetically feasible conformations fibers-one observed...