Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses.

BACKGROUND: Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye. RESULTS: In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened. CONCLUSIONS: The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.

Rapid detection of lung cancer based on serum Raman spectroscopy and a support vector machine: a case-control study.

BACKGROUND: Early screening and detection of lung cancer is essential for the diagnosis and prognosis of the disease. In this paper, we investigated the feasibility of serum Raman spectroscopy for rapid lung cancer screening. METHODS: Raman spectra were collected from 45 patients with lung cancer, 45 with benign lung lesions, and 45 healthy volunteers. And then the support vector machine (SVM) algorithm was applied to build a diagnostic model for lung cancer. Furthermore, 15 independent individuals were sampled for external validation, including 5 lung cancer patients, 5 benign lung lesion patients, and 5 healthy controls. RESULTS: The diagnostic sensitivity, specificity, and accuracy were 91.67%, 92.22%, 90.56% (lung cancer vs. healthy control), 92.22%,95.56%,93.33% (benign lung lesion vs. healthy) and 80.00%, 83.33%, 80.83% (lung cancer vs. benign lung lesion), repectively. In the independent validation cohort, our model showed that all the samples were classified correctly. CONCLUSION: Therefore, this study demonstrates that the serum Raman spectroscopy analysis technique combined with the SVM algorithm has great potential for the noninvasive detection of lung cancer.

Enhanced Methane Storage in Graphene Oxide Induced by an External Electric Field: A Study by MD Simulations and DFT Calculation.

To improve the methane (CH4) storage performance of graphene oxide (GO), molecular dynamics (MD) simulations and density functional theory (DFT) calculation were employed to investigate the effect of electric field (EF) on the adsorption and desorption performances of monolayer graphene modified with three oxygen-containing functional groups (hydroxyl, carboxyl, and epoxy) as the CH4 storage material. Through the calculation and analysis of the radial distribution function (RDF), adsorption energy, adsorption weight percentage, and the amount of CH4 released, the mechanisms of influence on adsorption and desorption performances caused by an external EF were revealed. The study results showed that the external EF can significantly enhance the adsorption energy of CH4 on hydroxylated graphene (GO-OH) and carboxylated graphene (GO-COOH), making it easier to adsorb CH4, and improve the adsorption capacity. Whereas the EF severely weakened the adsorption energy of CH4 on epoxy-modified graphene (GO-COC) and reduced the adsorption capacity of GO-COC. For the desorption process, applying the EF can decrease the CH4 release of GO-OH and GO-COOH but increase the CH4 release of GO-COC. To sum up, when an EF is present, the adsorption properties of -COOH and -OH and desorption properties of -COC will be improved, but the desorption properties of -COOH and -OH and the adsorption properties of -COC will be weakened. The findings in this study are expected to propose a novel non-chemical method to improve the storage capacity of GO for CH4.

Influence of an External Electric Field on Electronic and Optical Properties of a g-C3N4/TiO2 Heterostructure: A First-Principles Perspective.

In this study, calculations based on density functional theory (DFT) were utilized to examine how electrostatic fields affect the electrical and optical characteristics of g-C3N4/TiO2 heterostructures. The binding energy, density of states, difference in charge density, and optical absorption spectra of the heterostructure were calculated and analyzed to reveal the mechanism of the influence of the external electric field (EF) on the properties of the heterostructure. The results show that the binding energy of the heterogeneous structure is reduced due to the imposed electric field in X- and Y-directions, and the optical absorption spectrum is slightly enhanced, but the BG and charge transfer number are basically unchanged. On the contrary, applying the electric field in the Z-direction increases the binding energy of the heterogeneous structure, decreases the BG, increases the number of charge transfers, and red shifts the optical absorption spectrum, which improves the photocatalytic ability of the g-C3N4/TiO2 heterostructure.

Histone demethylases in neurodevelopment and neurodegenerative diseases.

Neurodevelopment can be precisely regulated by epigenetic mechanisms, including DNA methylations, noncoding RNAs, and histone modifications. Histone methylation was a reversible modification, catalyzed by histone methyltransferases and demethylases. So far, dozens of histone lysine demethylases (KDMs) have been discovered, and they (members from KDM1 to KDM7 family) are important for neurodevelopment by regulating cellular processes, such as chromatin structure and gene transcription. The role of KDM5C and KDM7B in neural development is particularly important, and mutations in both genes are frequently found in human X-linked mental retardation (XLMR). Functional disorders of specific KDMs, such as KDM1A can lead to the development of neurodegenerative diseases, including Alzheimer's disease (AD) and Parkinson's disease (PD). Several KDMs can serve as potential therapeutic targets in the treatment of neurodegenerative diseases. At present, the function of KDMs in neurodegenerative diseases is not fully understood, so more comprehensive and profound studies are needed. Here, the role and mechanism of histone demethylases were summarized in neurodevelopment, and the potential of them was introduced in the treatment of neurodegenerative diseases.

Development and Analysis of Multi-Degree-of-Freedom Piezoelectric Actuator Based on Elephant Trunk Structure.

In most of the piezoelectric stacked motors studied, the stator usually adopts two compound modes to drive the rotor to do step motion. This design method not only improves the utilization rate of the stator but also improves the torque output to a certain extent and increases the output displacement. In this study, a new type of multi-degree of freedom piezoelectric actuator is proposed for the utilization of a stator. The actuator realizes three compound vibration modes of bending-longitudinal-bending on a single stator, which changes the two compound modes of longitudinal bending and also changes the single motion mode of the stepper motor along a straight line. The rotor is set as a ball to drive it to rotate. The designed motor presents a different driving signal under which the rotor will no longer be accompanied by a return displacement. The finite element method is used to complete the design analysis, and the experimental analysis of the designed motor is carried out after the prototype is made. The multi-degree-of-freedom piezoelectric actuator can achieve a speed of 8.56 mm/c and a driving load of 1200 g at a voltage of 400 v and a working frequency of 42.7 kHz.

Copper-catalyzed reactions of α,ß-unsaturated N-tosylhydrazones with diaryliodonium salts to construct N-arylpyrazoles and diaryl sulfones.

Herein, an economical copper-catalyzed reaction of α,ß-unsaturated N-tosylhydrazones with diaryliodonium salts to construct both N-arylpyrazoles and diaryl sulfones has been developed. Both the p-toluenesulfonyl anion and the 3-arylpyrazole intermediates were formed in situ from N-tosylhydrazones. Subsequently, the former reacted rapidly with diaryliodonium salts to give diaryl sulfones and aryl iodide intermediates, and the latter reacted with aryl iodide to give N-arylpyrazoles under copper-catalyzed conditions. Using unsymmetrical mesityl phenyliodonium salts as substrates, mesityl p-toluenesulfide was obtained as the major product. This reaction took full advantage of the "waste" part of substrates to form an extra diaryl sulfone.

Circular RNAs: novel regulators of resistance to systemic treatments in breast cancer.

Systematic treatments including chemotherapy, endocrine therapy, and HER2-targeted therapy are important therapeutic approaches to breast cancer. However, drug resistance is a major barrier to achieving a cure in breast cancer (BC) patients. Hence, it is urgent to gain insight into the drug-resistance mechanisms in order to improve the prognosis of BC patients. Genetic alternations, epigenetic alternations, and other non-genetic mechanisms such as BC stem-like cells, metabolic reprogramming, and tumor microenvironment contribute to drug resistance of BC. With the development of single-cell sequencing of circulating tumor cell and next-generation sequencing of matched pre- and post- progression tumor biopsies or ctDNA from BC patients with drug resistance, new mechanisms of resistance are being discovered. An increasing number of microRNAs and long non-coding RNAs have been found to be associated with the drug resistance of BC. However, there are few reports on the role of circular RNAs (circRNAs) as master regulators of drug resistance. Therefore, there is still much to say in the field of drug resistance-related circRNAs. In this review, we mainly focus on literature evidence for the detailed mechanisms associated with systematic treatments' resistance of BC and how circRNAs intensify or weaken drug resistance. Exogenous expression of tumor suppressive circRNAs or knockdown of oncogenic circRNAs has been verified to reverse drug resistance of BC cells, which highlights that circRNAs may function as potential biomarkers and/or therapeutic targets of BC. Treatment targeting abnormally expressed circRNAs alone or combined with other systemic treatments may be a promising approach to conquering drug resistance.

Microbe-focused glycan array screening platform.

Interactions between glycans and glycan binding proteins are essential for numerous processes in all kingdoms of life. Glycan microarrays are an excellent tool to examine protein-glycan interactions. Here, we present a microbe-focused glycan microarray platform based on oligosaccharides obtained by chemical synthesis. Glycans were generated by combining different carbohydrate synthesis approaches including automated glycan assembly, solution-phase synthesis, and chemoenzymatic methods. The current library of more than 300 glycans is as diverse as the mammalian glycan array from the Consortium for Functional Glycomics and, due to its microbial focus, highly complementary. This glycan platform is essential for the characterization of various classes of glycan binding proteins. Applications of this glycan array platform are highlighted by the characterization of innate immune receptors and bacterial virulence factors as well as the analysis of human humoral immunity to pathogenic glycans.

Damage Detection for Conveyor Belt Surface Based on Conditional Cycle Generative Adversarial Network.

The belt conveyor is an essential piece of equipment in coal mining for coal transportation, and its stable operation is key to efficient production. Belt surface of the conveyor is vulnerable to foreign bodies which can be extremely destructive. In the past decades, much research and numerous approaches to inspect belt status have been proposed, and machine learning-based non-destructive testing (NDT) methods are becoming more and more popular. Deep learning (DL), as a branch of machine learning (ML), has been widely applied in data mining, natural language processing, pattern recognition, image processing, etc. Generative adversarial networks (GAN) are one of the deep learning methods based on generative models and have been proved to be of great potential. In this paper, a novel multi-classification conditional CycleGAN (MCC-CycleGAN) method is proposed to generate and discriminate surface images of damages of conveyor belt. A novel architecture of improved CycleGAN is designed to enhance the classification performance using a limited capacity images dataset. Experimental results show that the proposed deep learning network can generate realistic belt surface images with defects and efficiently classify different damaged images of the conveyor belt surface.

COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19.

MOTIVATION: The coronavirus disease 2019 (COVID-19) caused by a new type of coronavirus has been emerging from China and led to thousands of death globally since December 2019. Despite many groups have engaged in studying the newly emerged virus and searching for the treatment of COVID-19, the understanding of the COVID-19 target-ligand interactions represents a key challenge. Herein, we introduce COVID-19 Docking Server, a web server that predicts the binding modes between COVID-19 targets and the ligands including small molecules, peptides and antibodies. RESULTS: Structures of proteins involved in the virus life cycle were collected or constructed based on the homologs of coronavirus, and prepared ready for docking. The meta-platform provides a free and interactive tool for the prediction of COVID-19 target-ligand interactions and following drug discovery for COVID-19. AVAILABILITY AND IMPLEMENTATION: http://ncov.schanglab.org.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Synthesis, Characterization of Spirocyclic λ3 -Iodanes and Their Application to Prepare 4,1-Benzoxazepine-2,5-diones and 1,3-Diynes.

Herein, a [3+2] cycloaddition of aza-oxyallylic cations with ethynylbenziodoxolones for synthesis of new λ3 -iodanes containing spirocyclic 4-oxazolidinone has been developed. This cyclic λ3 -iodanes display stability in air and excellent solubility in organic solvent. Using them as substrate, both the 4,1-benzoxazepine-2,5-diones and symmetrical 1,3-diynes derivatives were afforded in high yield under copper(I)-catalyzed conditions.

Monocarboxylate transporter 1 promotes proliferation and invasion of renal cancer cells by mediating acetate transport.

One hallmark of renal cell carcinoma (RCC) is metabolic reprogramming, which involves elevation of glycolysis and upregulation of lipid metabolism. However, the mechanism of metabolic reprogramming is incompletely understood. Monocarboxylate transporter 1 (MCT1) promotes transport for lactate and pyruvate, which are crucial for cell metabolism. The aim of present study was to investigate the function of MCT1 on RCC development and its mechanism on metabolic reprogramming. The results showed that MCT1 messenger RNA and protein levels significantly increased in cancer tissues of ccRCC compared to normal tissue. MCT1 was further found to mainly located in the cell membrane of RCC. The knockdown of MCT1 by RNAi significantly inhibited proliferation and migration of 786-O and ACHN cells. MCT1 also induced the expressions of proliferation marker Ki-67 and invasion marker SNAI1. Moreover, we also showed that acetate treatment could upregulate the expression of MCT1, but not other MCT isoforms. On the other hand, MCT1 was involved in acetate transport and intracellular histone acetylation. In summary, this study revealed that MCT1 is abnormally high in ccRCC and promotes cancer development. The regulatory effect of MCT1 on cell proliferation and invasion maybe mediated by acetate transport.

Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types.

Orthoptera is the most diverse order of polyneopterans, and the forewing and hindwing of its members exhibit extremely variability from full length to complete loss in many groups; thus, this order provides a good model for studying the effects of insect flight ability on the evolutionary constraints on and evolutionary rate of the mitochondrial genome. Based on a data set of mitochondrial genomes from 171 species, including 43 newly determined, we reconstructed Orthoptera phylogenetic relationships and estimated the divergence times of this group. The results supported Caelifera and Ensifera as two monophyletic groups, and revealed that Orthoptera originated in the Carboniferous (298.997 Mya). The date of divergence between the suborders Caelifera and Ensifera was 255.705 Mya, in the late Permian. The major lineages of Acrididae seemed to have radiated in the Cenozoic, and the six patterns of rearrangement of 171 Orthoptera mitogenomes mostly occurred in the Cretaceous and Cenozoic. Based on phylogenetic relationships and ancestral state reconstruction, we analysed the evolutionary selection pressure on and evolutionary rate of mitochondrial protein-coding genes (mPCGs). The results indicated that during approximately 300 Mya of evolution, these genes experienced purifying selection to maintain their function. Flightless orthopteran insects accumulated more non-synonymous mutations than flying species and experienced more relaxed evolutionary constraints. The different wing types had different evolutionary rates, and the mean evolutionary rate of Orthoptera mitochondrial mPCGs was 13.554 × 10-9 subs/s/y. The differences in selection pressures and evolutionary rates observed between the mitochondrial genomes suggested that functional constraints due to locomotion play an important role in the evolution of mitochondrial DNA in orthopteran insects with different wing types.

Histone demethylase KDM6B regulates human podocyte differentiation in vitro.

Podocytes are terminally differentiated and highly specialized glomerular cells, which have an essential role as a filtration barrier against proteinuria. Histone methylation has been shown to influence cell development, but its role in podocyte differentiation is less understood. In this study, we first examined the expression pattern of histone demethylase KDM6B at different times of cultured human podocytes in vitro We found that the expression of KDM6B and podocyte differentiation markers WT1 and Nephrin are increased in the podocyte differentiation process. In cultured podocytes, KDM6B knockdown with siRNA impaired podocyte differentiation and led to expression down-regulation of WT1 and Nephrin. The treatment of podocytes with GSK-J4, a specific KDM6B inhibitor, can also obtain similar results. Overexpression of WT1 can rescue differentiated phenotype impaired by disruption of KDM6B ChIP (chromatin immunoprecipitation) assay further indicated that KDM6B can bind the promoter region of WT1 and reduce the histone H3K27 methylation. Podocytes in glomeruli from nephrotic patients exhibited increased KDM6B contents and reduced H3K27me3 levels. These data suggest a role for KDM6B as a regulator of podocyte differentiation, which is important for the understanding of podocyte function in kidney development and related diseases.

Histone demethylase KDM6B regulates 1,25-dihydroxyvitamin D3-induced senescence in glioma cells.

Vitamin D is a fat-soluble vitamin and plays an important role in calcium absorption and bone development, whose lack can cause a variety of diseases, including cancer. Human epidemiological studies suggested that vitamin D3 deficiency might increase glioma incidence, but molecular mechanism is less understood. In this study, we show that 1,25-dihydroxyvitamin D3 (the active form of vitamin D3) induces senescence of glioma cells and increases the expression of senescence markers, INK4A and cyclin-dependent kinase inhibitor 1A (CDKN1A). 1,25-Dihydroxyvitamin D3 also upregulates the expression of histone demethylase, KDM6B. Knockdown of KDM6B attenuates 1,25-dihydroxyvitamin D3-induced senescence and upregulation of INK4A and CDKN1A. KDM6B promotes the transcription of INK4A by eliminating the trimethylation of repressive marker H3K27me3 near its promoter. This study reveals a new regulatory mechanism involved in vitamin D3 inhibition on gliomas, which is beneficial to prevention and adjuvant therapy of glioma.

Directing cellular information flow via CRISPR signal conductors.

The complex phenotypes of eukaryotic cells are controlled by decision-making circuits and signaling pathways. A key obstacle to implementing artificial connections in signaling networks has been the lack of synthetic devices for efficient sensing, processing and control of biological signals. By extending sgRNAs to include modified riboswitches that recognize specific signals, we can create CRISPR-Cas9-based 'signal conductors' that regulate transcription of endogenous genes in response to external or internal signals of interest. These devices can be used to construct all the basic types of Boolean logic gates that perform logical signal operations in mammalian cells without needing the layering of multiple genetic circuits. They can also be used to rewire cellular signaling events by constructing synthetic links that couple different signaling pathways. Moreover, this approach can be applied to redirect oncogenic signal transduction by controlling simultaneous bidirectional (ON-OFF) gene transcriptions, thus enabling reprogramming of the fate of cancer cells.

Spreading of Cell Aggregates on Zwitterion-Modified Chitosan Films.

The sulfobetaine (SB) moiety, which comprises a quaternary ammonium group linked to a negatively charged sulfonate ester, is known to impart nonfouling properties to interfaces coated with polysulfobetaines or grafted with SB-polymeric brushes. Increasingly, evidence emerges that the SB group is, overall, a better antifouling group than the phosphorylcholine (PC) moiety extensively used in the past. We report here the synthesis of a series of SB-modified chitosans (CH-SB) carrying between 20 and 40 mol % SB per monosaccharide unit. Chitosan (CH) itself is a naturally derived copolymer of glucosamine and N-acetyl-glucosamine linked with a ß-1,4 bond. Analysis by quartz crystal microbalance with dissipation (QCM-D) indicates that CH-SB films (thickness ∼ 20 nm) resist adsorption of bovine serum albumin (BSA) with increasing efficiency as the SB content of the polymer augments (surface coverage ∼ 15 µg cm-2 for films of CH with 40 mol % SB). The cell adhesivity of CH-SB films coated on glass was assessed by determining the spreading dynamics of CT26 cell aggregates. When placed on chitosan films, known to be cell-adhesive, the CT26 cell aggregates spread by forming a cell monolayer around them. The spreading of CT26 cell aggregates on zwitterion-modified chitosans films is thwarted remarkably. In the cases of CH-SB30 and CH-SB40 films, only a few isolated cells escape from the aggregates. The extent of aggregate spreading, quantified based on the theory of liquid wetting, provides a simple in vitro assay of the nonfouling properties of substrates toward specific cell lines. This assay can be adopted to test and compare the fouling characteristics of substrates very different from the chemical viewpoint.

A base-promoted cascade reaction of α,ß-unsaturated N-tosylhydrazones with o-hydroxybenzyl alcohols: highly regioselective synthesis of N-sec-alkylpyrazoles.

An efficient method for the synthesis of N-sec-alkylpyrazoles through a base-promoted cascade cyclization/Michael addition reaction of α,ß-unsaturated N-tosylhydrazones with ortho-hydroxybenzyl alcohols has been developed. The desired products containing di- or triaryl groups at the same carbon atom were afforded in good to excellent yields with excellent regioselectivities (>20 : 1). Moreover, a three-component reaction of ortho-hydroxybenzyl alcohols, α,ß-unsaturated N-tosylhydrazones and saturated N-tosylhydrazones also took place to afford pyrazoles in good yields. This reaction offers a new route to triarylmethanes with a simple operation and is applicable for large-scale synthesis.

Ultrasound-assisted aqueous extraction of total flavonoids and hydroxytyrosol from olive leaves optimized by response surface methodology.

Olive leaves were often extracted with methanol or ethanol at different proportions. In this study, ultrasound-assisted aqueous extraction was adopted for olive leaf extraction. The yields of total flavonoids (TF) and hydroxytyrosol (HT) were optimized by central composite experimental design. Two second-order polynomial equations were established to quantify the relationship between the responses and the processing parameters. Under the optimal condition of extracting at 60 °C for 60 min with the solvent-to-material ratio of 40, TF and HT amounted to 57.31 ± 0.35 and 1.80 ± 0.02 mg/g dry leaves (DL), respectively. The scavenging rate of all extracts against α, α-diphenyl-ß-picrylhydrazyl (DPPH) and hydroxyl free radicals was screened. The integrated scores, representing both active ingredients and antioxidant capacity of the extracts, were calculated by principle component analysis (PCA). The optimal extract gained the highest score in PCA. In addition, compared to the extracts from 80% methanol to 44% ethanol, the ultrasound-assisted aqueous extract was richer in TF, HT, and polyphenols, while it also presented stronger ferric reducing antioxidant power (FRAP), but poorer strength to quench hydroxyl radicals. The study indicated that the aqueous extract of olive leaves may present broad potential opportunities in health-care sector.