A New Hybrid Model of Amino Acid Substitution for Protein Functional Classification

In this paper, a new hybrid model of amino acid substitution is developed and compared with the others in previous works. The results show that the new hybrid model can characterize the protein sequences very well by calculating Fisher weights, which can denote how much the variants contribute to the classification.

Cinnamicaldehyde regulates the expression of tight junction proteins and amino acid transporters in intestinal porcine epithelial cells

Background： Cinnamicaldehyde（CA） is a key flavor compound in cinnamon essential oil possessing various bioactivities. Tight junction（TJ） proteins are vital for the maintenance of intestinal epithelial barrier function,transport, absorption and utilization of dietary amino acids and other nutrients. In this study, we tested the hypothesis that CA may regulate the expression of TJ proteins and amino acid transporters in intestinal porcine epithelial cells（IPEC-1） isolated from neonatal pigs.Results： Compared with the control, cells incubated with 25 μmol/L CA had increased transepithelial electrical resistance（TEER） and decreased paracellular intestinal permeability. The beneficial effect of CA on mucosal barrier function was associated with enhanced protein abundance for claudin-4, zonula occludens（ZO）-1, ZO-2, and ZO-3. Immunofluorescence staining showed that 25 μmol/L CA promoted the localization of claudin-1 and claudin-3 to the plasma membrane without affecting the localization of other TJ proteins, including claudin-4, occludin,ZO-1, ZO-2, and ZO-3, compared with the control cells. Moreover, protein abundances for rBAT, xCT and LAT2 in IPEC-1 cells were enhanced by 25 μmol/L CA, while that for EAAT3 was not affected.Conclusions： CA improves intestinal mucosal barrier function by regulating the distribution of claudin-1 and claudin-3 in enterocytes, as well as enhancing protein abundance for amino acid transporters rBAT, xCT and LAT2 in enterocytes. Supplementation with CA may provide an effective nutritional strategy to improve intestinal integrity and amino acid transport and absorption in piglets.

Framework nucleic Acid-MicroRNA mediated hepatic differentiation and functional hepatic spheroid development for treating acute liver failure

The specific induction of hepatic differentiation presents a significant challenge in developing alternative liver cell sources and viable strategies for clinical therapy of acute liver failure (ALF). The past decade has witnessed the blossom of microRNAs in regenerative medicine. Herein, microRNA 122-functionalized tetrahedral framework nucleic acid (FNA-miR-122) has emerged as an unprecedented and potential platform for directing the hepatic differentiation of adipose-derived mesenchymal stem cells (ADMSCs), which offers a straightforward and cost-effective method for generating functional hepatocyte-like cells (FNA-miR-122-iHep). Additionally, we have successfully established a liver organoid synthesis strategy by optimizing the co-culture of FNA-miR-122-iHep with endothelial cells (HUVECs), resulting in functional Hep:HUE-liver spheroids. Transcriptome analysis not only uncovered the potential molecular mechanisms through which miR-122 influences hepatic differentiation in ADMSCs, but also clarified that Hep:HUE-liver spheroids could further facilitate hepatocyte maturation and improved tissue-specific functions, which may provide new hints to be used to develop a hepatic organoid platform. Notably, compared to transplanted ADMSCs and Hep-liver spheroid, respectively, both FNA-miR-122-iHep-based single cell therapy and Hep:HUE-liver spheroid-based therapy showed high efficacy in treating ALF in vivo. Collectively, this research establishes a robust system using microRNA to induce ADMSCs into functional hepatocyte-like cells and to generate hepatic organoids in vitro, promising a highly efficient therapeutic approach for ALF.

Gut microbiota remodeling drived by dietary millet protein prevents the metabolic syndrome

Metabolic syndrome(Met S)is a chronic disease associated with the disturbance of gut microbiota homeostasis.Metabolites derived from gut microbes play essential roles in Met S prevention and therapy.Here,we focused on the inhibitory effect of the extract of millet bran protein(EMBP)on a high-fat diet(HFD)-induced Met S,aiming to identify gut microbiota and their metabolites that involve in the anti-Met S activity of EMBP.The obesity,chronic inflammation,insulin resistance in Met S mouse models were abolished after EMBP treatment.The protective mechanism of EMBP against HFD-induced Met S may depend on improved gut barrier function.Using microbiome analysis,we found that EMBP supplementation improved gut microbiome dysbiosis in Met S mice,specifically upregulating Bacteroides acidifaciens.The fecal microbiota transplantation(FMT)also demonstrated this phenomenon.In addition,metabolomic analysis showed that EMBP mediates metabolic profiling reprogramming in Met S mice.Notably,a microbiota-derived metabolite,gamma-aminobutyric acid(GABA),is enriched by EMBP.In addition,exogenous GABA treatment produced a similar protective effect to EMBP by improving NRF2-dependent gut barrier function to protect HFDinduced Met S.The results suggest that EMBP suppress host Met S by remodeling of gut microbiota as an effective candidate for next-generation medicine food dual purpose dietary supplement to intervene in MetS.

Effects of Three Humic Acid Foliar Fertilizers on Quality and Photosynthetic Characteristics of Hawthorn

[Objectives]To investigate the effects of three foliar fertilizers on photosynthetic characteristics,fruit quality and yield of hawthorn.[Methods]Taking hawthorn foliar fertilization as the reference,the photosynthetic rate,transpiration rate,intercellular CO 2 concentration,stomatal conductance and single fruit weight of hawthorn leaves were measured under different concentrations of foliar fertilizer.[Results]The results showed that the photosynthetic rate,transpiration rate and stomatal conductance of hawthorn leaves increased significantly,while the intercellular CO 2 concentration decreased.Specifically,the fish protein peptide foliar fertilizer performed best,with net photosynthetic rate and transpiration rate increased by 57.22%and 57.51%,respectively.All the three foliar fertilizers significantly reduced the intercellular CO 2 concentration.In addition,fertilization significantly increased the single fruit weight of hawthorn,and the effect of fermented fulvic acid foliar fertilizer was the most significant,with the highest growth rate of 68.49%.[Conclusions]Spraying foliar fertilizer significantly increased the content of Vc,titratable acid,anthocyanin and soluble solids of hawthorn fruit,among which fermented fulvic acid foliar fertilizer had the optimal effect.

Effects of 4PU-30 on leaf senescence and degration of protein and nucleic acid in rice

4PU—30[N—phenyl—’N—(2—chloro—4—pyridyl) urea] is a new type of plant growth regulator with cytokinin properties. It has been confirmed to delay rice leaf senescence effectively. In order to elucidate the physiological role of 4PU—30 in delaying senescence, the changes of protein, nucleic acid contents, and the related activities of degradative enzymes were studied. Shanyou 63, an indica hybrid rice was used for this experiment. In the in vitro experiment, two full—developed leaves from the top during heading stage were collected and cut into 5.0cm segments, They were floated on the surface of distilled water containing 0.1mg/14PU—30 and incubated in darkness at 30 C. The leaves floated on distilled water were used as control.It was observed that chlorophyll content in controlled leaves declined rapidly started from the second day and dropped by 93.4% on the 6th day while that in leaves treated with 4PU—30 declined by 41.4% only. During senescence, specific activities of hemoglobin—digesting

Evaluation on performance of MM/PBSA in nucleic acid-protein systems

The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding energy by the standard MM/PBSA is not always good,especially in highly charged systems.In this work,we take the protein-nucleic acid complexes as an example,and showed that the use of screening electrostatic energy(instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA.In particular,the Pearson correlation coefficient of dataset Ⅱ in the modified MM/PBSA(i.e.,screening MM/PBSA) is about 0.52,much better than that(<0.33)in the standard MM/PBSA.Further,we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA.The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.

Smart antioxidant function enhancing(SAFE)nucleic acid therapy for ROS-related chronic diseases and comorbidities

Reactive oxygen species(ROS)-mediated oxidative stress exacerbates chronic diseases such as organ damage and neurodegenerative disorders.The Keap1-Nrf2-ARE pathway is a widely distributed endogenous antioxidant system.However,ROS under redox homeostasis regulates a wide range of life activities.Therefore,smart scavenging of excess ROS under pathological conditions is essential to treat chronic diseases safely.This study reports a smart antioxidant function enhancement(SAFE)strategy.On-demand release of nucleic acid drugs in a pathological ROS environment smartly activates the endogenous antioxidant system,thereby smartly alleviating oxidative stress in an exogenous antioxidant-independent manner.Through structural modulation and ligand modification,we develop SAFE nanoparticles based on nanohybrid complexes(SAFE-complex)adapted to brain delivery of nucleic acid drugs.SAFE-complex with homogeneous monodisperse structure efficiently treat ROS-related neurodegenerative diseases while protecting the major organ from oxidative stress damage.Moreover,SAFE-complex can stabilize storage in the form of freeze-dried powder.These data indicate that SAFE nanoparticles hold promise for treating ROS-related chronic diseases and comorbidities through rational transformation.

Comparative Influence of Dehulling on the Composition, Antioxidative and Functional Properties of Sorrel (<i>Hibiscus sabdariffa</i>L.) Seed

Although animal proteins provide indispensable amino acids that the body requires for normal growth, maintenance and function, their expensiveness makes them unaffordable especially for most families in the developing countries. This has given impetus to extensive research into under-utilized protein-rich oilseeds such as sorrel as possible alternate sources of good quality protein for tackling the challenge of protein-energy malnutrition which is fast becoming a global challenge. Sorrel seed may hold great potentials as a source of good quality protein, however the presence of hard seed coat, bitter after-taste and associated antinutritional factors have limited its use as protein supplement for humans and food ingredient. This study therefore compared the effect of dehulling sorrel seed to boiling, germination and roasting. This was with the aim of enhancing its utilization as protein source for human nutrition and functional ingredient in food product development. Flours obtained were analyzed for their proximate, mineral, antinutrient, amino and fatty acids composition;in vitro starch and protein digestibility, and functional and antioxidative properties. Protein content (ranged from 24.93% - 32.91%) significantly increased due to processing;dehulling alone accounted for a percentage increase of 32.01%. Similarly, dehulling increased all essential amino acids (except isoleucine and valine) at percentage which ranged from 3.63% - 61.17% whereas other processing methods caused significant reductions. Lysine, leucine, valine, arginine and phenylalanine were the most abundant essential amino acids, while methionine and cystine were the first and second limiting amino acids. Palmitic, linoleic, oleic and stearic acids were the most abundant fatty acids. Mineral composition was K > Ca > Mg > Na > Fe > Zn > Mn. Dehulled seed flour had highest in vitro protein digestibility (75.87%). Improved amino acid composition, antioxidative and functional properties of sorrel seed flour due to dehulling may indicate the potential of this flour to serve as a protein supplement and functional ingredient for food product development.

典型饲用氨基酸的太赫兹光谱检测与密度泛函理论指认分析

为探索用于畜禽饲喂低蛋白日粮的典型氨基酸太赫兹波段指纹特性及其与分子结构相关性,本文基于太赫兹时域光谱技术和密度泛函理论(DFT)对蛋氨酸等6种饲用氨基酸开展了实验测量和理论振动计算分析。首先,制备了氨基酸实验样本,测量了它们在0.5~2.0 THz的太赫兹吸收光谱,发现:蛋氨酸在1.48和1.54 THz、赖氨酸在0.95和1.67 THz、色氨酸在1.2和1.4 THz、苏氨酸在1.42 THz、组氨酸在1.4 THz、异亮氨酸在1.41和1.51 THz处呈现明显吸收特性;然后,利用GaussView软件构建了6种氨基酸单分子结构,应用DFT理论的B3LYP杂化泛函方法,结合6-311G(d,p)基组优化结构,计算获得其太赫兹波段的频谱特征,发现:蛋氨酸在1.51 THz、赖氨酸在0.89和1.68 THz、色氨酸在0.67和1.39 THz、苏氨酸在1.4 THz、组氨酸在1.4 THz、异亮氨酸在1.56和1.75 THz处有一定吸收,与实际实验测量吸收峰位基本吻合;最后,利用Gaussian软件分析了6种氨基酸在0.5~2.0 THz波段各吸收峰处的振动模式,发现:蛋氨酸1.51 THz处吸收峰源自其甲基团的面内摇摆振动;赖氨酸0.89和1.68 THz处吸收峰源自其羧基官能团的旋转和氨基官能团的面内摇摆振动;色氨酸1.39 THz处吸收峰源自其羧基官能团的面外弯曲振动;苏氨酸1.4 THz处吸收峰源自其羧基官能团的面外弯曲和氨基官能团的面内摇摆振动;组氨酸1.4 THz处吸收峰源自其氨基官能团的面内摇摆和整体摇摆振动;异亮氨酸1.56 THz处吸收峰源自其甲基团和氨基官能团的整体摇摆和羧基官能团的面外摇摆振动、1.75 THz处吸收峰源自其甲基团的整体摇摆和羧基官能团的面外摇摆振动。该研究为利用太赫兹光谱技术开展典型饲用氨基的快速定性定量研究提供理论参考。

内蒙古3种生态型华北驼绒藜蛋白质组成分析及功能特性研究

试验旨在研究内蒙古3种生态型华北驼绒藜蛋白质组成及功能特性,为华北驼绒藜的质量评价及开发利用提供参考。提取驼绒藜叶片粗蛋白进行定性和定量测定,对其氨基酸组成及含量进行测定;并对粗蛋白功能特性进行研究。结果表明:(1)3种生态型驼绒藜叶片粗蛋白含量(16%~23%)较高,均含有氨基酸17种,其中必需氨基酸7种,非必需氨基酸8种,半必需氨基酸2种。(2)3种生态型驼绒藜叶片粗蛋白的功能特性基本一致,粗蛋白疏水性为35~37μg/mg;1,1-二苯基-2-三硝基苯肼(DPPH)自由基清除能力随粗蛋白浓度增加而增强,当粗蛋白浓度为0.1 mg/mL时,DPPH自由基清除能力达30%~37%;总巯基和游离巯基含量均较高,分别为37~44μmol/g和18~20μmol/g;在碱性环境下的溶解度明显高于酸性条件下,当pH=3时,溶解度均最小;乳化性为12~14 m2/g,乳化稳定性为42%~47%;具有很高的持水性(平均为5.25 g/g)和持油性(平均为4.66 g/g);粗蛋白起泡性为67%~69%,起泡稳定性为35%~38%。由此可见,内蒙古3种生态型华北驼绒藜蛋白质组成及功能特性相近,营养丰富,均具有较高的饲用价值。

齐刺环跳穴干预坐骨神经损伤大鼠海马IL-1β、IL-6、TNF-α及GFAP表达影响的实验研究

目的 通过观察齐刺环跳穴对坐骨神经损伤大鼠海马白细胞介素-1β(Interleukin-1β,IL-1β)、白细胞介素-6(Interleukin-6,IL-6)、肿瘤坏死因子-α(Tumor Necrosis Factor-alpha, TNF-α)及胶质纤维酸性蛋白(Glial Fibrillary Acidic Protein, GFAP)表达的影响,探讨齐刺环跳穴治疗坐骨神经痛的中枢镇痛机制。方法 60只SD大鼠随机分为假手术组、模型组、齐刺组、单刺组及药物组,每组12只,采用钳夹法制备大鼠坐骨神经损伤模型。造模第2天开始进行针刺及药物干预,连续14 d。观察各组大鼠干预前后坐骨神经功能指数(Sciatic nerve Function Index, SFI)、热缩足反射潜伏期(Paw Withdrawal Latency, PWL)的变化,ELISA法检测海马组织IL-1β、IL-6、TNF-α蛋白表达水平,实时定量PCR法及免疫组化法检测海马组织GFAP表达水平。结果 干预前,与假手术组比较,其余各组大鼠PWL值、SPI值显著降低(P<0.01),与模型组比较,齐刺组干预后大鼠PWL值、SPI值显著改善(P<0.01)。ELISA法、RT-PCR法及免疫组化检测结果显示,模型组、齐刺组、单刺组、药物组IL-1β、IL-6、TNF-α、GFAP表达较假手术组显著升高(P<0.01);与模型组相比,齐刺组、单刺组、药物组IL-1β、IL-6、TNF-α、GFAP表达显著下降,齐刺组表达低于单刺组及药物组(P<0.01)。结论 齐刺环跳穴缓解坐骨神经痛的镇痛机制可能与下调海马炎症因子表达,抑制星形胶质细胞活化,从而降低中枢痛觉敏化程度有关。

CRISPR/Cas-等温扩增技术在食源性病原菌检测中的研究进展

食源性病原菌引起的食品安全事件引起广泛关注,为保证食品安全,采取有效的检测手段至关重要。新兴的簇状规则间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)及其关联蛋白(CRISPR-associated protein,Cas)组成的CRISPR/Cas系统是广泛存在于细菌和古细菌中的一种获得性免疫系统,可高效、特异性识别并切割外源核酸,与传统技术相比在检测病原菌方面更为高效。本文基于CRISPR/Cas生物传感系统-等温扩增技术联用的相关研究进行综述,对CRISPR/Cas系统的分类、原理以及与等温扩增耦合后在食源性病原菌检测方面的研究进展进行概述,并对其在即时检测应用中的前景以及所面临的挑战进行深入探讨,以期为CRISPR/Cas生物传感系统的进一步发展提供参考。

A possible mode of the specific recognition of nucleic acids by proteins

Seven sets of protein target sites, which occur in several gene promoters, have been analyzed. The results suggest that there is a possible mode of specific recognition of double-helical nucleic acids by proteins. This recognition mode is related to a special topological property of double-helical DNA, which is termed base spatial pattern (BSP) of DNA segment. BSP is the spatial topological property determined only by the spatial arrangement of the bases on double-helical DNA segment.

Functional Xeno Nucleic Acids for Biomedical Application

Functional nucleic acids(FNAs)refer to a type of oligonucleotides with functions over the traditional genetic roles of nucleic acids,which have been widely applied in screening,sensing and imaging fields.However,the potential application of FNAs in biomedical field is still restricted by the unsatisfactory stability,biocompatibility,biodistribution and immunity of natural nucleic acids(DNA/RNA).Xeno nucleic acids(XNAs)are a kind of nucleic acid analogues with chemically modified sugar groups that possess improved biological properties,including improved biological stability,increased binding affinity,reduced immune responses,and enhanced cell penetration or tissue specificity.In the last two decades,scientists have made great progress in the research of functional xeno nucleic acids,which makes it an emerging attractive biomedical application material.In this review,we summarized the design of functional xeno nucleic acids and their applications in the biomedical field.

肠脂肪酸结合蛋白在肠黏膜屏障损伤相关疾病中的作用研究进展

肠道是人体持续暴露于外部环境的最大器官之一,发挥着重要的物理及化学屏障作用保护人体免受致病菌侵害,肠黏膜屏障作为肠道的重要组成部分,其完整性对维持肠道微生态平衡起关键作用,肠黏膜屏障破坏可导致肠道菌群失调及易位,与多种疾病的发生发展相关。肠脂肪酸结合蛋白(intestinal fatty acid binding protein,I‑FABP)是脂肪酸结合蛋白家族中的一种,对肠道损伤具有特异性,在肠道发生损伤、缺血、肠黏膜屏障损伤及通透性增加时会迅速释放入血液循环,I‑FABP水平升高是反映肠道损伤的重要标志物,临床上很多疾病常合并肠道功能障碍,本文主要对I‑FABP的结构特征、功能及其与肠黏膜屏障相关疾病的关系进行综述。

Cold Acclimation-Induced Changes in Total Soluble Protein, RNA, DNA, RNase and Freezing Resistance in Populus tomentosa Cuttings

The changes in the contents of total soluble protein and RNA, the activity of RNase in leaves and branches of Populus tomentosa cuttings at various periods (viz: cold acclimation, deacclimation, chilling stress and the recovery after chilling stress), and the survival rate and the freezing resistance of cuttings during cold acclimation at -3℃ were investigated. Results showed that cold acclimation not only increased the contents of total soluble protein and RNA, the survival rates and the freezing resistance of cuttings, decreased the activity of RNase, but also reduced the declining degree of total soluble protein and RNA contents, and the increasing level of RNase caused by chilling stress as compared with the controls. In addition, cold acclimation augmented the increase in the level of total soluble protein and RNA, and facilitated the decrease of RNase during the recovery periods. Further analysis found that the DNA content of all treatments kept relative stability at various periods. The changes in total soluble protein, RNA and RNase were closely related to the freezing resistance of cuttings. It appears that the increase of RNA content caused by cold acclimation induced decrease of RNase activity may be involved in the accumulation of total soluble protein and the induction of freezing resistance of cuttings.

CRISPR/Cas12a技术在动物疫病检测方面的应用

CRISPR/Cas系统是由簇状规则间隔的短回文重复序列(CRISPR)和CRISPR相关蛋白(Cas)组成的一种基因编辑技术,可以特异地切割和识别靶标核酸基因。该技术具有检测速度快、灵敏度高和特异性强的优势,因此被广泛应用于动物疫病检测领域。本文就CRISPR/Cas12a结合等温核酸扩增技术和可视化技术在动物疫病检测中的应用进行综述,并对其应用前景进行展望,以期为我国的养殖业和进境动物疫病的监测提供技术支撑。

ICP-MS在生物医学领域中的应用进展

电感耦合等离子体质谱(ICP-MS)是一种强大的痕量、超痕量元素和同位素分析仪器,具有干扰少、检出限低、分辨率高、检测速度快、多元素同时分析等优势而被广泛应用于生物医学领域。本文简要概述了近年来基于元素标记策略的ICP-MS方法和(或)ICP-MS联用技术在核酸、蛋白质定量检测以及其它与人体健康和疾病相关元素测定的进展。针对目前存在的问题给出了可行建议,并对ICP-MS的发展前景做出了展望。

金属离子对二甲亚砜依赖的RNA切割型脱氧核酶催化活性的影响

在高浓度有机溶剂中工作的RNA切割型脱氧核酶(RNA-cleaving DNAzyme,RCD)及其构筑的分子器件不仅拓展了DNA作为酶的能力,还可将功能核酸推进新的应用领域.本文研究了一个需要二甲亚砜才能工作的RCD(命名为E3)对金属离子的需求,发现二价金属离子对其催化活性至关重要,活性顺序为Zn^(2+),Mg^(2+)>Fe^(2+)>Pb^(2+)>Mn^(2+)>Co^(2+).以Mg^(2+)或Zn^(2+)为辅因子,表征了E3的速率-pH值关系及其与二者的结合比例.E3的催化速率-pH曲线在Mg^(2+)存在下为“钟形”,高速率的pH值范围为7.0~9.0;Zn^(2+)存在下为“尖峰”,速率最高时pH=7.0;E3与Mg^(2+)和Zn^(2+)的数量结合比例均为1∶1.另外,E3以Fe^(2+)为辅因子时易失活,Fe^(2+)被氧化成Fe^(3+)是失活的关键,加入还原剂可使其复活.进一步研究发现,Cu^(2+),Fe^(3+)和Ni^(2+)等金属离子可抑制Mg^(2+)或Zn^(2+)的作用,使E3的催化活性急剧降低.本文研究结果为理解E3的性质及催化机制提供了有用信息.