Identification of DNA-protein binding residues through integration of Transformer encoder and Bi-directional Long Short-Term Memory.

DNA-protein binding is crucial for the normal development and function of organisms. The significance of accurately identifying DNA-protein binding sites lies in its role in disease prevention and the development of innovative approaches to disease treatment. In the present study, we introduce a precise and robust identifier for DNA-protein binding residues. In the context of protein representation, we combine the evolutionary information of the protein, represented by its position-specific scoring matrix, with the spatial information of the protein's secondary structure, enriching the overall informational content. This approach initially employs a combination of Bi-directional Long Short-Term Memory and Transformer encoder to jointly extract the interdependencies among residues within the protein sequence. Subsequently, convolutional operations are applied to the resulting feature matrix to capture local features of the residues. Experimental results on the benchmark dataset demonstrate that our method exhibits a higher level of competitiveness when compared to contemporary classifiers. Specifically, our method achieved an MCC of 0.349, SP of 96.50%, SN of 44.03% and ACC of 94.59% on the PDNA-41 dataset.

Ectopic overexpression of mulberry MnT5H2 enhances melatonin production and salt tolerance in tobacco.

Soil salinization severely inhibits plant growth and has become one of the major limiting factors for global agricultural production. Melatonin (N-acetyl-5-methoxytryptamine) plays an important role in regulating plant growth and development and in responding to abiotic stresses. Tryptamine-5-hydroxylase (T5H) is an enzyme essential for the biosynthesis of melatonin in plants. Previous studies have identified the gene MnT5H for melatonin synthesis in mulberry (Morus notabilis), but the role of this gene in response to salinity stress in mulberry is remain unclear. In this study, we ectopically overexpressed MnT5H2 in tobacco (Nicotiana tabacum L.) and treated it with NaCl solutions. Compared to wild-type (WT), melatonin content was significantly increased in the overexpression-MnT5H2 tobacco. Under salt stress, the expression of NtCAT, NtSOD, and NtERD10C and activity of catalase (CAT), peroxidase (POD), and the content of proline (Pro) in the transgenic lines were significantly higher than that in WT. The Malondialdehyde (MDA) content in transgenic tobacco was significantly lower than that of WT. Furthermore, transgenic tobacco seedlings exhibited faster growth in media with NaCl. This study reveals the changes of melatonin and related substance content in MnT5H2-overexpressing tobacco ultimately lead to improve the salt tolerance of transgenic tobacco, and also provides a new target gene for breeding plant resistance to salt.

Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants.

Multiple plant lineages have independently evolved sex chromosomes and variable karyotypes to maintain their sessile lifestyles through constant biological innovation. Morus notabilis, a dioecious mulberry species, has the fewest chromosomes among Morus spp., but the genetic basis of sex determination and karyotype evolution in this species has not been identified. In this study, three high-quality genome assemblies were generated for Morus spp. [including dioecious M. notabilis (male and female) and Morus yunnanensis (female)] with genome sizes of 301-329 Mb and were grouped into six pseudochromosomes. Using a combination of genomic approaches, we found that the putative ancestral karyotype of Morus species was close to 14 protochromosomes, and that several chromosome fusion events resulted in descending dysploidy (2n = 2x = 12). We also characterized a ∼ 6.2-Mb sex-determining region on chromosome 3. Four potential male-specific genes, a partially duplicatedDNA helicase gene (named MSDH) and three Ty3_Gypsy long terminal repeat retrotransposons (named MSTG1/2/3), were identified in the Y-linked area and considered to be strong candidate genes for sex determination or differentiation. Population genomic analysis showed that Guangdong accessions in China were genetically similar to Japanese accessions of mulberry. In addition, genomic areas containing selective sweeps that distinguish domesticated mulberry from wild populations in terms of flowering and disease resistance were identified. Our study provides an important genetic resource for sex identification research and molecular breeding in mulberry.

Calcium poisoning mechanism on the selective catalytic reduction of NOx by ammonia over the γ-Fe2O3 (001) surface.

γ-Fe2O3 has an excellent low-temperature selective catalytic reduction (SCR) deNOx performance, but its resistance to alkaline earth metal calcium (Ca) is poor. In particular, the detailed mechanism of Ca poisoning on the γ-Fe2O3 catalyst at the atomic level is not clear. Hence, the density functional theory method was used in this research to investigate the influence mechanism of Ca poisoning on the NH3-SCR over the γ-Fe2O3 catalyst surface. The findings reveal that NH3, NO, and O2 molecules can bind to the γ-Fe2O3 (001) surface to generate coordinated ammonia, monodentate nitroso, and adsorption oxygen species, respectively. The main active site is Fe1-top. For the γ-Fe2O3 with Ca poisoning, the Ca atom has a high adsorption energy on the surface of γ-Fe2O3 (001), which covers the catalyst surface and reduces the active sites. The presence of Ca atom decreases the adsorption performance of NH3, while slightly improving the NO and O2 adsorption. In particular, the Ca atom restrains the NH3 activation and NH2 formation, which is detrimental to the NH3-SCR process.

Understanding the roles of copper dopant and oxygen vacancy in promoting nitrogen oxides removal over iron-based catalyst surface: A collaborative experimental and first-principles study.

In this work, we proposed a novel strategy of copper (Cu) doping to enhance the nitrogen oxides (NOx) removal efficiency of iron (Fe)-based catalysts at low temperature through a simple citric acid mixing method, which is critical for its practical application. The doping of Cu significantly improves the deNOx performance of Fe-based catalysts below 200 °C, and the optimal catalyst is (Cu0.22Fe1.78)1-δO3, which deNOx efficiency can reach 100% at 160-240 °C. From the macro aspects, the main reasons for the excellent catalytic activity of the (Cu0.22Fe1.78)1-δO3 catalyst are the large number of oxygen vacancies (Ovac), appropriate Fe3+ and Cu2+ contents, stronger surface acidity and redox ability. From the micro aspects, the Ovac plays a key role in enhancing molecular adsorption, oxidation, and the deNOx reaction over the Fe-based catalyst surface, which promoting order is CuOvac > Ovac > Cu. This work provides a new insight for the mechanism study of oxygen vacancy engineering and also accelerates the development of CuFe bimetal composite catalysts at low temperature.

Effect of doping Cr on NH3 adsorption and NO oxidation over the FexOy/AC surface: A DFT-D study.

Activated carbon supported iron-based catalysts (FexOy/AC) show good deNOx efficiency at low temperature. The doping of chromium (Cr) greatly improves the catalyst activity. However, the detailed effect of doping Cr over FexOy/AC surface at molecular level is still a grey area. In this study, the roles of Cr dopant on gas adsorption and NO oxidation were deeply investigated by a DFT-D3 method. Results show that the synergy of Cr-Fe bimetal improves the binding capacity of Fe2O3/AC and Fe3O4/AC surfaces after doping Cr. NH3 can be adsorbed on Cr and Fe sites to form coordinated NH3. Doping Cr greatly improves the NH3 adsorption property on the Fe3O4/AC surface. NO molecule can combine with Cr, Fe, and O sites to form nitrosyl and nitrite. The doping of Cr increases the adsorption performance of NO on the Fe2O3/AC and Fe3O4/AC surfaces, especially for Fe3O4/AC surface. Furthermore, NO can be oxidized to NO2 by adsorption oxygen or active O sites of FexOy clusters. The doping of Cr restrains the formation of insoluble chelating bidentate nitrates and greatly reduces the reaction energy barrier of NO oxidation on the FexOy/AC surface, which can promote the deNOx reaction.

Atmospheric-Pressure Pyrolysis Study of Chlorobenzene Using Synchrotron Radiation Photoionization Mass Spectrometry.

The pyrolysis of chlorobenzene (C6H5Cl) at 760 Torr was studied in the temperature range of 873-1223 K. The pyrolysis products including intermediates and chlorinated aromatics were detected and quantified via synchrotron radiation photoionization mass spectrometry. Furthermore, the photoionization cross sections of chlorobenzene were experimentally measured. On the basis of the experimental results, the decomposition pathways of chlorobenzene were discussed as well as the generation and consumption pathways of the main products. Benzene is the main product of chlorobenzene pyrolysis. Chlorobiphenyl (C12H9Cl), dichlorobiphenyl (C12H8Cl2), and chlorotriphenylene (C18H11Cl) predominated in trace chlorinated aromatic products. Chlorobenzene decomposed initially to form two radicals [chlorophenyl (·C6H4Cl) and phenyl (·C6H5)] and the important intermediate o-benzyne (o-C6H4). The propagation processes of chlorinated aromatics, including polychlorinated naphthalenes and polychlorinated biphenyls, were mainly triggered by chlorobenzene, chlorophenyl, and benzene via the even-numbered-carbon growth mechanism. Besides, the small-molecule products such as acetylene (C2H2), 1,3,5-hexatriyne (C6H2), and diacetylene (C4H2) were formed via the bond cleavage of o-benzyne (o-C6H4).

Heavy metal poisoning resistance of a Co-modified 3Mn10Fe/Ni low-temperature SCR deNOx catalyst.

Heavy metals have a great influence on the deNOx efficiency of catalysts. The 3Mn10Fe/Ni catalyst that used nickel foam (Ni) as the carrier, Mn and Fe as the active components, and Co as a trace auxiliary was prepared using an impregnation method. The catalysts poisoned by Pb or Zn and Co-modified catalysts with Pb or Zn poisoning were studied. The addition of Pb or Zn significantly decreases the deNOx activity of the 3Mn10Fe/Ni catalyst due to the decrease in the content of high-valence metal elements such as Fe3+ and Mn4+, lattice oxygen concentration, reduction performance, acidity, and the number of acid sites. However, after Co modification, the deNOx activity of the poisoned catalysts can be improved effectively because the strong interaction between Pb or Zn and lattice oxygen is weakened, and the contents of lattice oxygen, high valence metal elements, reduction ability, and the number of acid sites increase.

Zacopride Exerts an Antiarrhythmic Effect by Specifically Stimulating the Cardiac Inward Rectifier Potassium Current in Rabbits: Exploration of a New Antiarrhythmic Strategy.

BACKGROUND: Zacopride, a potent antagonist of 5-HT3 receptors and an agonist of 5-HT4 receptors, is a gastrointestinal prokinetic agent. In a previous study, we discovered that zacopride selectively stimulated the inward rectifier potassium current (IK1) in the rat and that agonizing IK1 prevented or eliminated aconitine-induced arrhythmias in rats. OBJECTIVE: Our aims were to confirm that the antiarrhythmic effects of zacopride are mediated by selectively enhancing IK1 in rabbits. METHODS: The effects of zacopride on the function of the main ion channels were investigated using a whole-cell patch-clamp technique in rabbits. Effects of zacopride on cardiac arrhythmias were also explored experimentally both in vivo and in vitro. RESULTS: Zacopride moderately enhanced cardiac IK1 but had no apparent action on voltage-gated sodium current (INa), L- type calcium current (ICa-L), sodium-calcium exchange current (INa/Ca), transient outward potassium current (Ito), or delayed rectifier potassium current (IK) in rabbits. Zacopride also had a marked antiarrhythmic effect in vivo and in vitro. We proved that the resting membrane potential (RMP) was hyperpolarized in the presence of 1 µmol/L zacopride, and the action potential duration (APD) at 90% repolarization (APD90) was shortened by zacopride (0.1-10 µmol/L) in a concentration- dependent manner. Furthermore, zacopride at 1 µmol/L significantly decreased the incidence of drug-induced early afterdepolarization (EAD) in rabbit ventricular myocytes. CONCLUSION: Zacopride is a selective agonist of rabbit cardiac IK1 and that IK1 enhancement exerts potential antiarrhythmic effects.

Investigation of low-temperature selective catalytic reduction of NOx with ammonia over Cr-promoted Fe/AC catalysts.

Fe/activated coke (AC) and Cr-Fe/AC catalysts with AC as a supporter and Cr and Fe as active components were prepared by an impregnation method for low-temperature selective catalytic reduction (SCR) of NO with NH3. The effects of Cr addition and its concentrations on the deNOx performance of Fe/AC catalysts were studied at low temperature. The Cr addition promotes the low-temperature SCR activity of the 8Fe/AC catalyst and the 8Fe6Cr/AC catalyst has the best low-temperature SCR deNOx performance, which the NOx conversions are greater than 90% at 160-240 °C. The 8Fe6Cr/AC catalyst has good water resistance. However, when 100 ppm SO2 was introduced into the reaction gas, its deNOx efficiency drops to 45% at 180 °C. To clarify the specific effects of Cr addition on the NOx conversions and sulfur poisoning, the Cr-Fe/AC catalysts were characterized by X-ray diffraction, BET, H2 temperature-programmed reduction, NH3 temperature-programmed desorption, X-ray photoelectron spectroscopy, and Fourier infrared spectroscopy. The addition of Cr into Fe/AC catalysts greatly increases the BET surface area and the number of weak and medium-strong acid sites on the catalyst surface and improves the ratio of Fe3+/Fe2+. These factors enhance the NOx conversion of 8Fe/AC catalyst. The formed sulfates and hydrogen sulfates cover the active sites on the catalyst surface, which lead to the sulfur poisoning of the 8Fe6Cr/AC catalyst. Graphical abstract.

Promotional effect of Mn modification on DeNOx performance of Fe/nickel foam catalyst at low temperature.

Manganese (Mn)-modified ferric oxide/nickel foam (Fe/Ni) catalysts were prepared using Ni as a carrier, Fe and Mn as active components to study NH3-SCR of NOx at low temperature. The effects of different Fe loads and Mn-modified Fe/Ni catalysts on the DeNOx activity were investigated. Results show that when the amount of Fe is 10%, Fe/Ni catalyst has the highest NOx conversion. For the Mn-modified Fe/Ni catalysts, the NOx conversions firstly increase and then decrease with the Mn loading amount increasing. 3MnFe/Ni catalyst shows high NOx conversions, which reach 98.4-100% at 120-240 °C. The characterization analyses reveal that Mn-modified Fe/Ni catalysts increase the FeOx dispersion on Ni surface, improve significantly the valence ratio of the Fe3+/Fe2+, the content of lattice oxygen which promotes the catalyst storage and exchange oxygen capacity at low temperature, and the number of Brønsted active acid sites on the catalyst surface, and enhance the low-temperature redox capacity. These factors remarkably increase the NOx conversions at low temperature. Especially, 3Mn10Fe/Ni catalyst not only has excellent DeNOx activity but also has better water resistance. However, the anti-SO2 poisoning performance needs to be improved. To further analyze the reason why different catalysts show different DeNOx performance, the reaction kinetics was also explored.

Natural manganese ore catalyst for low-temperature selective catalytic reduction of NO with NH3 in coke-oven flue gas.

Different types of manganese ore raw materials were prepared for use as catalysts, and the effects of different manganese ore raw materials and calcination temperature on the NO conversion were analyzed. The catalysts were characterized by XRF, XRD, BET, XPS, H2-TPR, NH3-TPD, and SEM techniques. The results showed that the NO conversion of calcined manganese ore with a Mn:Fe:Al:Si ratio of 1.51:1.26:0.34:1 at 450 °C reached 80% at 120 °C and 98% at 180~240 °C. The suitable proportions and better dispersibility of active ingredients, larger BET surface area, good reductibility, a lot of acid sites, contents of Mn4+ and Fe3+, and surface-adsorbed oxygen played important roles in improving the NO conversion.