Molecular dynamics simulation of the effect of temperature on the conformation of ubiquitin protein.

CONTENT: Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond. METHODS: All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8 nm, a setting that allowed > 0.8 nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100 kJ/mol·nm with a 0.01 nm step size. Minimization was followed by 30 ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10 ns without any restraint using an integral time step of 1 fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5 nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2 nm.

In vitro and in silico analyses reveal the interaction between LysM receptor-like kinase3 of Solanum tuberosum and the carbohydrate elicitor Riclin octaose.

As a carbohydrate elicitor, Riclin octaose (Rioc) activates the pattern-triggered immunity of Solanum tuberosum L., while how the plant perceives Rioc is unknown. Here, a pattern recognition receptor StLYK3 (LysM receptor-like kinase3) whose transcription level was significantly up-regulated after Rioc elicitation was investigated in vitro and in silico. The nucleotide that encoded the ectodomain of StLYK3 (StLYK3-ECD) was heterologously expressed in the Pichia pastoris strain GS115. The purified StLYK3-ECD had the molecular weight of 25.08 kDa and pI of 5.69. Afterwards interaction between StLYK3-ECD and Rioc was analyzed by isothermal titration calorimetry. The molar ratio of ligand to receptor, dissociation constant, and enthalpy were 1.28 ± 0.04, 26.7 ± 3.1 µM, and -45.0 ± 1.8 kJ mol-1 , respectively. Besides, molecular dynamics results indicated that StLYK3-ECD contained three carbohydrate-binding motifs and the first two motifs probably contributed to the interaction with Rioc via hydrogen bond and van de Waals' forces. Amino acids containing hydroxyl, amidic, and sulfhydryl groups took the main portion in the docking site. Moreover, replacing the 92nd threonyl (T) of StLYK3-ECD with valyl (V) resulted in the alteration of the preferred docking site. The dissociation constant drastically increased to 841.6 ± 232.4 µM. In conclusion, StLYK3 was a potential receptor of Rioc.

Application of adaptive laboratory evolution to improve the tolerance of Rhodotorula strain to methanol in crude glycerol and development of an effective method for cell lysis.

Rhodotorula toruloides can utilize crude glycerol as the low-cost carbon source for lipid production, but its growth is subjected to inhibition by methanol in crude glycerol. Here, transcriptome profiling demonstrated that 1004 genes were significantly regulated in the strain R. toruloides TO2 under methanol stress. Methanol impaired the function of membrane transport and subsequently weakened the utilization of glycerol, activities of the primary metabolism and functions of nucleus and ribosome. Afterwards the tolerance of TO2 to methanol was improved by using two-round adaptive laboratory evolution (ALE). The final strain M2-ale had tolerance up to 3.5% of methanol. 1 H NMR-based metabolome analysis indicated that ALE not only improved the tolerance of M2-ale to methanol but also tuned the carbon flux towards the biosynthesis of glycerolipid-related metabolites. The biomass and lipid titer of M2-ale reached 14.63 ± 0.45 g L-1 and 7.06 ± 0.44 g L-1 at 96 h in the crude glycerol medium, which increased up to 17.69% and 31.39%, respectively, comparing with TO2. Afterwards, an effective method for cell lysis was developed by combining sonication and enzymatic hydrolysis (So-EnH). The lytic effect of So-EnH was validated by using confocal imaging and flow cytometry. At last, lipid recovery rate reached 95.4 ± 2.7% at the optimized condition.

Development and validation of a multianalyte method for quantification of aflatoxins and bongkrekic acid in rice and noodle products using PRiME-UHPLC-MS/MS method.

An analytical method based on PRiME (process, robustness, improvements, matrix effects, ease of use) HLB purification followed by the ultra-high liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) detection has been developed for the determination aflatoxin B1, B2, G1 and G2 and bongkrekic acid in rice and noodle products. Five toxins were separated on a Waters BEH C18 column by gradient elution, scanned by ESI+ and ESI- dynamic switching and detected with MRM mode. LOD, LOQ, matrix effects, accuracy and precision of the developed method were investigated. Under the optimal sample pretreatment conditions, high sensitivity (LOQs: 0.20-0.40 µg/kg), good recoveries (80.5%-106.6%) and acceptable precision (2.4%-7.2%) were obtained for the analysis of the four aflatoxins and bongkrekic acid. This method was successfully applied to the analysis of rice and noodle products, demonstrating its applicability and suitability for the routine analysis of aflatoxins and bongkrekic acid in rice and noodle products.

Fragmentation pathway of hypophosphite (H2PO2-) in mass spectrometry and its determination in flour and flour products by LC-MS/MS.

The fragmentation pathway of H2PO2- in MS was obtained by Orbitrap HRMS and the reverse confirmation was carried out by the neutral loss detection experiment. The results showed that H2PO2- with even electron ion would produce the neutral loss of 2H and form a new even electron ion with a pair of lone-pair electrons. Based on this, a LC-MS/MS method was developed for the determination of H2PO2- in flour and flour products. The H2PO2- was separated on an Acclaim Trinity P1 composite ion exchange column, and then detected by MS/MS under MRM mode. Finally, the developed method was validated in terms of the linearity, selectivity, accuracy, precision and matrix effect. The method showed a good linearity (R2＞0.999) in the concentration range of 50 âˆ¼ 1500 µg/L. The LOD and LOQ for H2PO2- were 10.0 mg/kg and 30.0 mg/kg, respectively. The average recoveries and RSDs (n = 6) were 93.0%∼102.9% and 2.6 âˆ¼ 5.6%, respectively.

Banana-peel-derived magnetic porous carbon as effective adsorbent for the enrichment of six bisphenols from beverage and water samples.

Functionalized magnetic nanoporous carbon derived from banana peel was synthesized through carbonization, porogenesis, carboxylation and magnetization using banana peel and was successfully used as a magnetic solid phase extraction (MSPE) material for the enrichment of six bisphenols (BPs) from beverage and water samples. After the optimization of MSPE process, the enrichment factors of six target analytes were in the range of 74-112 for water samples, and 15-22 for beverage samples. Then, high-performance liquid chromatography-quadrupole-Orbitrap high-resolution mass spectrometry (HPLC-Q Orbitrap-HRMS) was used for the separation and determination of the target analytes. Results showed that the extraction recoveries for 6 BPs were in the range of 71.9-108.4% with an RSD of 2.5-7.5% (n = 6). These results demonstrated that the as-prepared material could efficiently enrich some aromatic compounds and the proposed method is reliable and robust for the determination of BPs in water and beverage samples.

Effect of calcium-based sorbents on the reduction of chlorinated contaminants during municipal solid waste thermal treatment.

Chlorinated contaminants are a cause of significant concern in the development of municipal solid waste (MSW) thermal treatment techniques. This study investigates the efficacy of two calcium (Ca)-based in-furnace additives, calcium oxide (CaO), and calcined dolomite (CD), at reducing the levels of chlorinated contaminants during MSW thermal treatment. The results reveal that Ca-based additives could effectively reduce the chlorine (Cl) content by more than 76.8% and 37.3% in the gas and tar phases, respectively. The total concentration and the international total equivalent (I-TEQ) value of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzo-p-furans (PCDD/Fs) were significantly higher under the incineration condition than pyrolysis and gasification conditions. Adding CaO could reduce the total concentration and the I-TEQ value of PCDD/Fs by more than 43.4% and 36.7%, respectively. The reduction effect on PCDD/Fs was more significant in the gaseous phase and the tar phase than the solid phase. CD was more effective than CaO at reducing the chlorinated contaminants, including hydrogen chloride, Cl in the tar phase, and PCDD/Fs. Thus, adding Ca-based sorbents in the furnace during MSW pyrolysis and gasification can effectively reduce PCDD/Fs generation. Based on the experimental results, the mechanism of Ca-based sorbents on the high-temperature homogeneous reaction of PCDD/Fs formation was analysed.

Perchlorate occurrence in foodstuffs and water: Analytical methods and techniques for removal from water - A review.

Perchlorate (ClO4-), a type of contaminant with high diffusivity and durability, has been widely detected in water and foodstuffs, arousing a global concern. It can interfere with normal function of the human thyroid gland, affecting human health. Therefore, determination of perchlorate in water and foodstuffs, and removal from water are important. This review focuses on the occurrence of perchlorate, mainly in water and foodstuffs, and provides an overview of analytical methods for determination of perchlorate over the last two decades. In addition, merits and drawbacks of the various methods have been considered. This review also highlights the most commonly used approaches for removal of perchlorate from water. Finally, current trends and future perspectives in determination of perchlorate and removal from water are proposed. This review provided a comprehensive understanding of perchlorate occurrence and its removal from water, and had practical significance in reducing the harm of perchlorate to human.

Structure, preparation, modification, and bioactivities of ß-glucan and mannan from yeast cell wall: A review.

In order to solve the antibiotic resistance, the research on antibiotic substitutes has received an extensive attention. Many studies have shown that ß-glucan and mannan from yeast cell wall have the potential to replace antibiotics for the prevention and treatment of animal diseases, thereby reducing the development and spread of antibiotic-resistant bacterial pathogens. ß-Glucan and mannan had a variety of biological functions, including improving the intestinal environment, stimulating innate and acquired immunity, adsorbing mycotoxins, enhancing antioxidant capacity, and so on. The biological activities of ß-glucan and mannan can be improved by chemically modifying its primary structure or reducing molecular weight. In this paper, the structure, preparation, modification, and biological activities of ß-glucan and mannan were reviewed, which provided future perspectives of ß-glucan and mannan.

The impact of COVID-19 on small and medium-sized enterprises (SMEs): Evidence from two-wave phone surveys in China.

This paper examines the short-term and mid-term impact of COVID-19 restrictions on SMEs, based on two waves of phone interviews with a previously surveyed large SME sample in China. The outbreak of COVID-19 and the resultant lockdowns took a heavy toll on SMEs. Afflicted by problems of logistics blocks, labor shortages, and drops in demand, 80% of SMEs were temporarily closed at the time of the first wave of interviews in February 2020. After reining in COVID-19, authorities largely eased lockdown restrictions in April. Consequently, most SMEs had reopened by the time of the second round of surveys in May. However, many firms, particularly export firms, were running at partial capacity, primarily due to inadequate demand. Moreover, around 19% of incorporated enterprises and 25% of self-employed businesses had permanently closed between the two waves of surveys.

Determination of bongkrekic acid and isobongkrekic acid in rice noodles by HPLC-Orbitrap HRMS technology using magnetic halloysite nanotubes.

The existing extraction and detection methods of bongkrekic acid (BKA) and isobongkrekic acid (IBKA) are complex, time-consuming and solvent-consuming. In this work, a simple and fast pre-concentration procedure based on Fe3O4/HNTs was developed for the determination of BKA and IBKA in rice noodles using HPLC-Orbitrap HRMS. The structure and morphology of Fe3O4/HNTs was characterized by means of XRD, SEM, FT-IR and VSM. Parameters affecting the extraction efficiency including adsorbent amount, pH, extraction time, type and volume of eluent were investigated by employing the response surface method. Results indicated that the proposed method had favorable linearity in the concentration range of 2-200 µg/L with a correlation coefficient >0.998. Method LOD and LOQ were 0.3 µg/kg and 1.0 µg/kg, respectively. Finally, the method was successfully applied to determine BKA and IBKA in rice noodle samples from southern China with recoveries ranging from 79.8% to 102.6% and relative standard deviation (RSD) of 4.2%-7.1%.

Chemical composition and larvicidal activity against Aedes mosquitoes of essential oils from Arisaema fargesii.

BACKGROUND: Dengue fever is caused by the spread of dengue virus by Aedes mosquito vectors. Currently, the most effective way to control dengue is by preventing mosquitoes from spreading the disease. Arisaema fargesii is a Chinese herbal medicine commonly used to repel mosquitoes. In our laboratory, anti-mosquito chemical components were extracted from A. fargesii, and the effects of these substances on mosquito larvae were examined. RESULTS: In total, 48 compounds corresponding to 98.79% of the total oil were identified and the major compounds identified were linalool (12.38%), carvacrol (8.27%), eugenol (5.21%), and ß-selinene (5.36%). Essential oil had larvicidal activity against Ae. aegypti and Ae. albopictus with LC50 values of 40.49 mg/L, 47.01 mg/L, respectively. The LC50 values of carvacrol, eugenol, linalool and ß-selinene were 32.78, 56.34, 70.56, 136.03 mg/L against Ae. aegypti larvae, and 39.08, 52.07, 82.34, 151.74 mg/L, respectively, against Ae. albopictus larvae. Biochemical assays of Aedes larvae showed that the activities of acetylcholinesterase (AChE), monooxygenases (MO), glutathione-S-transferase (GST), p-Nitrophenyl acetate (p-NPA) esterase, α-esterase and ß-esterase were significantly affected by carvacrol. Essential oil induced the detoxification mechanism for the action of GST and MO. CONCLUSION: The result indicates that essential oil of A. fargesii and its isolated constituent have good inhibitory effects on the defense enzymes of Aedes mosquito larvae. A. fargesii essential oil can be used to control Aedes mosquito larvae to prevent the spread of dengue fever. © 2019 Society of Chemical Industry.

Effects of dietary yeast hydrolysate on the growth, antioxidant response, immune response and disease resistance of largemouth bass (Micropterus salmoides).

A 56-day growth trial was conducted to investigate the effects of dietary yeast hydrolysate on the growth performance, antioxidation, immune response and resistance against Aeromonas hydrophila in largemouth bass. Four experimental diets were prepared with yeast hydrolysate levels of 0% (Y0), 1.5% (Y1.5), 3.0% (Y3.0) and 4.5% (Y4.5). Each diet was randomly assigned to triplicate 150-L tanks and each tank was stocked with 30 largemouth bass (initial body weight, IBW = 7.71 ±â€¯0.02 g). A challenge test was carried out after the feeding trial by injecting A. hydrophila intraperitoneally for 4-day observation. The results showed that the FBW and WGR in Y1.5 group were significantly higher than those in Y0 group (P < 0.05) and the feed conversion ratio (FCR) got the lowest value in Y1.5 group. And the hydrolysate supplement significantly increased the 4-day cumulative survival rate after the bacterial challenge (P < 0.05). The plasma malondialdehyde was lower in the yeast hydrolysate supplement groups in both pre- and post-challenge test (P < 0.05), while the plasma C3 increased (P < 0.05). In post-challenge test, the plasma superoxide dismutase (SOD) and catalase (CAT) activities increased in the Y1.5 and Y3.0 groups respectively (P < 0.05), and plasma lysozyme in Y1.5 group and the plasma IgM in Y3.0 group were higher than those in others respectively (P < 0.05). For the q-PCR results, in post-challenge test, the hepatic hep2 expression level in Y1.5 and Y4.5 groups were both significantly higher than those in others (P < 0.05), as well as il-8 in Y3.0 group. The spleen hif-1alpha and tgf-beta1 expression levels in Y4.5 group were all significantly lower than those in others (P < 0.05), while the gilt was significantly higher (P < 0.05) in the post-challenge test. And the expression levels of spleen tnf-alpah1 in Y1.5 and Y3.0 groups and il-8 in Y3.0 group were all significantly higher than those in other groups (P < 0.05) in the post-challenge test. The head kidney gilt expression level was significantly higher in the yeast hydrolysate supplement groups compared with the Y0 group (P < 0.05), and the head kidney il-8 expression level in Y1.5 group was significant higher than those in other groups in post-challenge test (P < 0.05). The present results indicated dietary yeast hydrolysate improved the antioxidant ability and enhanced the immune response of largemouth bass without negative effect on growth. And 1.5% or 3.0% of dietary yeast hydrolysate was recommended for largemouth bass based on the present results.

Effects of dietary supplementation with yeast glycoprotein on growth performance, intestinal mucosal morphology, immune response and colonic microbiota in weaned piglets.

Antibiotics are commonly provided to weaned piglets; however, this practice has become controversial due to the increased occurrences of microbial resistance, and alternatives are needed. This study aimed to investigate the effects of dietary supplementation with yeast glycoprotein (YG) on growth performance, intestinal mucosal morphology, immune response and colonic microbiota in weaned piglets. A total of 240 weaned piglets (d 23 ± 2) from 16 pens (15 piglets per pen) were randomly allocated to an antibiotics group (25% quinocetone 200 mg kg-1 and 4% enduracidin 800 mg kg-1 of the basal diet) or a YG group (800 mg kg-1 YG of the basal diet), respectively. The trial lasted 14 days, and at the end of the trial, one piglet per pen was chosen to collect plasma, intestinal tissue and colonic digesta samples. The results indicate that piglets fed diets containing YG tended to show increased final body weight (0.05 < P < 0.1), increased average daily gain (P < 0.05) and decreased F/G (P < 0.05) when compared with the antibiotics group. Moreover, intestinal permeability showed that YG led to an improvement in the intestinal development via decreasing serum content of DAO (P < 0.01). Histological evaluations showed that YG contributed to the improvement of the intestinal development via increasing villous height (P < 0.05) and the villous height to crypt depth ratio (P < 0.01), and decreasing crypt depth (P < 0.01) and villous width (P < 0.05) in the ileum. Intestinal integrity also showed that YG was conducive to improvement of the intestinal development via upregulating the m-RNA expression of occludin (P < 0.05) in the duodenal and jejunal mucosa. Interestingly, YG supplementation downregulated the m-RNA expression of IL-12 (P < 0.05), upregulated the m-RNA expression of Hsp-70 (P < 0.05) in the duodenal mucosa, downregulated the m-RNA expression of Hsp-70 (P < 0.05) and IFN-γ (P < 0.05), upregulated the m-RNA expression of Hsp-90 (P < 0.05) in the jejunal mucosa, and upregulated the m-RNA expression of Hsp-70 (P < 0.05) in the ileal mucosa. On the other hand, colonic microbiota results showed that YG supplementation increased the relative abundance of Lactobacillus (P < 0.05) in the genus level. Colonic metabolite results showed that YG supplementation decreased the content of acetate (P < 0.05). Taken together, it is speculated that YG would be a potent alternative to prophylactic antibiotics in improving the gut health in weaned piglets.

Chemical composition and antimicrobial activities of essential oil from Wedelia urticifolia growing wild in Hunan Province, China.

The essential oil obtained from Wedelia urticifolia growing in Hunan Province, China, was analyzed for the first time by capillary GC and GC-MS. A total of 67 constituents, representing 98.68% in essential oil were identified. The major constituents of the oil were: α-pinene (8.85%), limonene (6.38%), carvacrol (6.15%), caryophyllene (6.08%), spathulenol (5.49%), sabinene (5.36%), camphor (4.34%). Antimicrobial potential of oil against bacterial strains (Pseudomonas aeruginosa, Escherichia coli and Bacillus subtilis, and Staphylococcus aureus), yeast strains (Hansenula anomala and Saccharomy cescerevisiae) and molds (Aspergillus niger, Chaetomium globosum, Mucor racemosus, and Monascus anka) was determined by disc diffusion method and broth micro dilution method, respectively. The oil exhibited promising antimicrobial effect as a diameter of zones of inhibition (16.8-24.9 mm). Minimum inhibitory concentration values of oil were ranged 62.5-1000 µg/mL.

Improvement of Source Number Estimation Method for Single Channel Signal.

Source number estimation methods for single channel signal have been investigated and the improvements for each method are suggested in this work. Firstly, the single channel data is converted to multi-channel form by delay process. Then, algorithms used in the array signal processing, such as Gerschgorin's disk estimation (GDE) and minimum description length (MDL), are introduced to estimate the source number of the received signal. The previous results have shown that the MDL based on information theoretic criteria (ITC) obtains a superior performance than GDE at low SNR. However it has no ability to handle the signals containing colored noise. On the contrary, the GDE method can eliminate the influence of colored noise. Nevertheless, its performance at low SNR is not satisfactory. In order to solve these problems and contradictions, the work makes remarkable improvements on these two methods on account of the above consideration. A diagonal loading technique is employed to ameliorate the MDL method and a jackknife technique is referenced to optimize the data covariance matrix in order to improve the performance of the GDE method. The results of simulation have illustrated that the performance of original methods have been promoted largely.

Dynamic Digital Channelizer Based on Spectrum Sensing.

The ability to efficiently channelize a received signal with dynamic sub-channel bandwidths is a key requirement of software defined radio (SDR) systems. The digital channelizer, which is used to split the received signal into a number of sub-channels, plays an important role in SDR systems. In this paper, a design of dynamic digital channelizer is presented. The proposed method is novel in that it employs a cosine modulated filter bank (CMFB) to divide the received signal into multiple frequency sub-bands and a spectrum sensing technique, which is mostly used in cognitive radio, is introduced to detect the presence of signal of each sub-band. The method of spectrum sensing is carried out based on the eigenvalues of covariance matrix of received signal. The ratio of maximum-minimum eigenvalue of each sub-band is vulnerable to noise fluctuation. This paper suggests an optimized method to calculate the ratio of maximum-minimum eigenvalue. The simulation results imply that the design of digital channelizer can effectively separate the received signal with dynamically changeable sub-channel signals.