Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass ...spectrometry is the primary approach for identification of Kcr sites. However, experimental approaches for identifying Kcr sites are often time-consuming and expensive when compared with computational approaches. To date, several predictors for Kcr site prediction have been developed, most of which are capable of predicting crotonylation sites on either histones alone or mixed histone and nonhistone proteins together. These methods exhibit high diversity in their algorithms, encoding schemes, feature selection techniques and performance assessment strategies. However, none of them were designed for predicting Kcr sites on nonhistone proteins. Therefore, it is desirable to develop an effective predictor for identifying Kcr sites from the large amount of nonhistone sequence data. For this purpose, we first provide a comprehensive review on six methods for predicting crotonylation sites. Second, we develop a novel deep learning-based computational framework termed as CNNrgb for Kcr site prediction on nonhistone proteins by integrating different types of features. We benchmark its performance against multiple commonly used machine learning classifiers (including random forest, logitboost, naïve Bayes and logistic regression) by performing both 10-fold cross-validation and independent test. The results show that the proposed CNNrgb framework achieves the best performance with high computational efficiency on large datasets. Moreover, to facilitate users' efforts to investigate Kcr sites on human nonhistone proteins, we implement an online server called nhKcr and compare it with other existing tools to illustrate the utility and robustness of our method. The nhKcr web server and all the datasets utilized in this study are freely accessible at http://nhKcr.erc.monash.edu/.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Vibrational modes in mechanical resonators provide a promising candidate to interface and manipulate classical and quantum information. The observation of coherent dynamics between distant mechanical ...resonators can be a key step toward scalable phononbased applications. Here we report tunable coherent phonon dynamics with an architecture comprising three graphene mechanical resonators coupled in series, where all resonators can be manipulated by electrical signals on control gates. We demonstrate coherent Rabi oscillations between spatially separated resonators indirectly coupled via an intermediate resonator serving as a phonon cavity. The Rabi frequency fits well with the microwave burst power on the control gate. We also observe Ramsey interference, where the oscillation frequency corresponds to the indirect coupling strength between these resonators. Such coherent processes indicate that information encoded in vibrational modes can be transferred and stored between spatially separated resonators, which can open the venue of on-demand phonon-based information processing.
Natural pyrethrins have been widely used as natural pesticides due to their low mammalian toxicity and environmental friendliness. Previous studies have mainly focused on
, which contains high levels ...of pyrethrins and volatile terpenes that play significant roles in plant defense and pollination. However, there is little information on
due to its lower pyrethrin content and low commercial value. In this study, we measured the transcriptome and metabolites of the leaves (L), flower buds (S1), and fully blossomed flowers (S4) of
. The results show that the expression of pyrethrins and precursor terpene backbone genes was low in the leaves, and then rapidly increased in the S1 stage before decreasing again in the S4 stage. The results also show that pyrethrins primarily accumulated at the S4 stage. However, the content of volatile terpenes was consistently low. This perhaps suggests that, despite
and
having similar gene expression patterns and accumulation of pyrethrins,
attracts pollinators via its large and colorful flowers rather than via inefficient and metabolically expensive volatile terpenes, as in
This is the first instance of de novo transcriptome sequencing reported for
. The present results could provide insights into pyrethrin biosynthetic pathways and will be helpful for further understanding how plants balance the cost-benefit relationship between plant defense and pollination.
Background
Upstream stimulatory factors (USFs) are members of the basic helix-loop-helix leucine zipper transcription factor family, including USF1, USF2, and USF3. The first two members have been ...well studied compared to the third member, USF3, which has received scarce attention in cancer research to date. Despite a recently reported association of its alteration with thyroid carcinoma, its expression has not been previously analyzed.
Methods
We comprehensively analyzed differential levels of USFs expression, genomic alteration, DNA methylation, and their prognostic value across different cancer types and the possible correlation with tumor-infiltrating immune cells and drug response by using different bioinformatics tools.
Results
Our findings established that USFs play an important role in cancers related to the urinary system and justify the necessity for further investigation. We implemented and offer a useful ShinyApp to facilitate researchers’ efforts to inquire about any other gene of interest and to perform the analysis of drug response in a user-friendly fashion at http://zzdlab.com:3838/Drugdiscovery/.
One zinc-based coordination polymer was synthesized by a solvothermal method using zinc nitrate and 1,4-bis(1-imidazolyl)benzene (bib) ligand, {Zn(bib)·(SO4)·(H2O)}n (1). The fluorescence test ...results showed that compound 1 had a good fluorescence quenching effect on antibiotics and metal ions, especially norfloxacin and Fe3+. The limit of detection is calculated to be 7.04 μmol/L for norfloxacin. The results of the anti-interference experiment show that it selectively detect norfloxacin. Meanwhile, compound 1 has a good adsorption effect on methyl orange due to the electrostatic interactions and the different molecular sizes.
One Zn coordination polymer was synthesized under acidic conditions. It had a good fluorescence quenching effect on antibiotics and metal ions, especially to norfloxacin and Fe3+. For other antibiotics, it has a certain degree of selectivity to norfloxacin at low concentration. It has a good adsorption effect on methyl orange dye, which may be mainly attributed to the electrostatic interactions between cationic frameworks and anionic dyes as well as the different molecular sizes of anionic dyes. Display omitted
•One Zn-based coordination polymer was synthesized under acidic conditions.•It has a fluorescence quenching effect on antibiotics, especially to norfloxacin.•Compound 1 could selectively detect norfloxacin in wastewater.•Compound 1 has a certain selectivity to norfloxacin at low concentration.•Compound 1 has a good adsorption effect on methyl orange dye.
We aimed to investigate the clinical characteristics of severe influenza virus-associated pneumonia complicated with bacterial infection in children. We retrospectively analysed data concerning 64 ...paediatric patients with severe influenza virus-associated pneumonia who had been treated at our hospital. The patients were divided into observation (44 patients) and control (20 patients) groups, based on the presence or absence of concomitant bacterial infection, and clinical data were compared between the groups. The mean age in the observation group was 2.71 + or - 1.44 years, 42 (95.45%) were aged less than or equal to 5 years, and 18 (40.9%) had underlying diseases. The mean age in the control group was 4.05 + or - 2.21 years, 13 (65%) were aged less than or equal to 5 years, and 3 (15%) had underlying diseases. There was a statistically significant difference in patient age and the proportion of patients with underlying diseases (P < 0.05). The observation group had higher duration of fever values, a higher number of patients with duration of fever greater than or equal to 7 days, a higher incidence of gasping, and a higher incidence of seizures/consciousness disturbance, and the differences were statistically significant (P < 0.05). Secondary bacterial infections in the observation group were mainly due to gram-negative bacteria, with Haemophilus influenzae and Moraxella catarrhalis being the most common pathogens. The observation group had a higher proportion of patients treated in the paediatric intensive care unit and a longer hospital stay, and the differences were statistically significant (P < 0.05). Severe influenza virus-associated pneumonia complicated with bacterial infection was more common in children aged less than or equal to 5 years. Younger patients with underlying diseases were more susceptible to bacterial infection (mainly due to gram-negative bacteria). The timely administration of neuraminidase inhibitors and antibiotics against susceptible bacteria is likely to help improve cure rates.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The cross-talk between oocyte and somatic cells plays a crucial role in the regulation of follicular development and oocyte maturation. As a result, granulosa cell apoptosis causes follicular ...atresia. In this study, sheep granulosa cells were cultured under thermal stress to induce apoptosis, and melatonin (MT) was examined to evaluate its potential effects on heat-induced granulosa cell injury. The results demonstrated that the Colony Forming Efficiency (CFE) of granulosa cells was significantly decreased (heat 19.70% ± 1.29% vs. control 26.96% ± 1.81%, p < 0.05) and the apoptosis rate was significantly increased (heat 56.16% ± 13.95% vs. control 22.80% ± 12.16%, p < 0.05) in granulosa cells with thermal stress compared with the control group. Melatonin (10⁻⁷ M) remarkably reduced the negative effects caused by thermal stress in the granulosa cells. This reduction was indicated by the improved CFE and decreased apoptotic rate of these cells. The beneficial effects of melatonin on thermal stressed granulosa cells were not inhibited by its membrane receptor antagonist luzindole. A mechanistic exploration indicated that melatonin (10⁻⁷ M) down-regulated p53 and up-regulated Bcl-2 and LHR gene expression of granulosa cells under thermal stress. This study provides evidence for the molecular mechanisms of the protective effects of melatonin on granulosa cells during thermal stress.
The effect of preoxidative treatments on the reducing characteristics of ShenHua (SH) coal char and the evolution of surface nitrogen-containing complexes during the reducing process under different ...temperature conditions were investigated using temperature-programmed reduction (TPR) and X-ray photoelectron spectroscopy (XPS). The SH samples were oxidized to different conversion degrees (0.15, 0.22, 0.32, 0.42, 0.52, 0.73, and 0.89) under an O2 atmosphere, and the reductivity of each char sample was considerably enhanced after the preoxidative treatment. This phenomenon could be attributed to the generation of active sites and oxygen-containing complexes on the SH particle surface during the oxidation process. The preoxidized samples were obviously more reactive than the raw char, and per unit mass almost all the preoxidized samples could consume more NO than SH raw char under the same experimental conditions. The entire TPR process could be divided into the following four sections: (a) the reversible physical adsorption stage, (b) the heterogeneous reaction stage, (c) the multireaction stage, and (d) the equilibrium reaction stage. The primary reaction path at each stage could be summarized using the TPR and XPS results. The evolution of the C(N) and the variation in the elemental distribution (C, O, and N) during the TPR process were investigated by XPS. The results showed that N-Q was the most stable organic structure of the nitrogen-containing complexes on the particle, and the decomposition of N-6, N-5, and N-Q occurred when the reaction temperature reached 1173 K. The total amounts of N-Q, N-6, and N-5 decreased when the reaction temperature exceeded 1173 K, indicating interaction between the nitrogen-containing complexes occurred. Meanwhile, prior to the attachment of NO molecules to the char particle surface and forming C(N), more NO molecules were consumed by CO at this temperature. The results in this research clarified the effect of the conversion degree on the char reductivity and the primary reduction reaction path under different temperature conditions, providing a technical framework for the reducing process of air-staged combustion technology.
The antagonistic effect of selenium (Se) against cadmium (Cd)-induced breast carcinogenesis was reported, but underlying mechanisms were unclear. The aim of this study was to identify the ...epigenetically regulated genes and biological pathways mediating the antagonistic effect. We exposed MCF-7 cells to Cd and Se alone or simultaneously. Cell proliferation was assessed by MTT assay, and differential epigenome (DNA methylation, microRNA, and long non-coding RNA) was obtained by microarrays. We cross-verified the epigenetic markers with differential transcriptome, and the ones modulated by Cd and Se in opposite directions were regarded to mediate the antagonistic effect. The epigenetically regulated genes were validated by using gene expression data in human breast tissues. We further assessed the biological functions of these validated genes. Our results showed that Se alleviated the proliferative effect of Cd on MCF-7 cell. A total of 10 epigenetically regulated genes were regarded to mediate the antagonistic effect, including
APBA2
,
KIAA0895
,
DHX35
,
CPEB3
,
SVIL
,
MYLK
,
ZFYVE28
,
ABLIM2
,
GRB10
, and
PCDH9.
Biological function analyses suggested that these epigenetically regulated genes were involved in multiple cancer-related pathways, such as focal adhesion and PI3K/Akt pathway. In conclusion, we provided evidence that Se antagonized the Cd-induced breast carcinogenesis via epigenetic modification and revealed the critical pathways.
•JN and SH coal were used to study the variation of char surface in oxidation reaction.•TPD and FT-IR results conveyed that the properties of stable complexes were identified.•JN and SH have ...identical chemical structure on char surface during oxidation reaction.•Char conversion ratio had little effect on the distribution of Cwea/Cstr.
Two typical types of bituminous coal (JN and SH) were employed for thorough devolatilization, then the samples were functionalized by O2 at 1073K to different conversion ratios (JN: 0.21, 0.34, 0.40, 0.53 and 0.63; SH: 0.15, 0.22, 0.32, 0.42 and 0.52) before the surface oxygen containing complexes C(O) were qualitatively and semi-quantitatively characterized by Fourier transform infrared spectroscopy (FT-IR) and temperature programmed desorption (TPD). A deconvolution method was applied to analyze the C(O) adsorption in the spectral region of 1800–1000cm−1 in the FT-IR spectra, and the results indicated that the type and thermal stability of these functional groups were as follows: carboxylic (1250K)<phenol (1350K)<ether/anhydride (1550K)<lactone/quinone (1650K). The TPD results demonstrated that more active sites were generated on the particle surface after the oxidative treatment under O2 atmosphere, especially the samples with low conversion degree (J2, S2, and S3), coal type and conversion ratio had small effects on the ratios of metastable stable complexes to stable complexes Cwea(O)/Cstr(O) under the experimental conditions. The oxidized char samples were significantly more reactive than the raw char, and per unit mass of each oxidized sample could reduce more NO than raw char during the temperature programmed reduction (TPR) process, and phenol, ether and anhydride were the main reactants participated in the NO reduction reaction under high-temperature condition (1173–1600K).
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