An Insight into the Structural Requirements and Pharmacophore Identification of Carbonic Anhydrase Inhibitors to Combat Oxidative Stress at High Altitudes: An In-Silico Approach

Carbonic anhydrases (CA) inhibitory action could be linked to the treatment of a number of ailments, including cancer, osteoporosis, glaucoma, and several neurological problems. For the development of effective CA inhibitors, a variety of heterocyclic rings have been investigated. Furthermore, at high altitudes, oxygen pressure drops, resulting in the formation of reactive oxygen and nitrogen species, and CA inhibitors having role in combating this oxidative stress. Acetazolamide contains thiadiazole ring, which has aroused researchers’ interest because of its CA inhibitory action. In the present study, we used a number of drug design tools, such as pharmacophore modeling, 3D QSAR, docking, and virtual screening on twenty-seven 1,3,4-thiadiazole derivatives that have been described as potential CA inhibitors in the literature. An atom-based 3D-QSAR analysis was carried out to determine the contribution of individual atoms to model generation, while a pharmacophore mapping investigation was carried out to find the common unique pharmacophoric properties required for biological activity. The coefficient of determination for both the training and test sets were statistically significant in the generated model. The best QSAR model was chosen based on the values of R² (0.8757) and Q² (0.7888). A molecular docking study was also conducted against the most potent analogue 4m, which has the highest SP docking score (−5.217) (PDB ID: 6g3v). The virtual screening revealed a number of promising compounds. The screened compound ZINC77699643 interacted with the amino acid residues, Pro201 and Thr199, in the virtual screening study (PDB ID: 6g3v). These interactions demonstrated the significance of the CA inhibitory activity of the compound. Furthermore, ADME study revealed useful information regarding compound’s drug-like properties. Therefore, the findings of the present investigation could aid in the development of more potent CA inhibitors, which could benefit the treatment of oxidative stress at high altitudes.     

地山雀血红蛋白高原低氧适应的分子机制

血红蛋白(hemoglobin,Hb)作为血液循环系统中氧气运输的主要载体,在动物高原低氧适应中发挥关键作用.本文结合基因组、转录物组、分子进化、同源建模和分子动力学计算等分析,探索了高原土著鸟类地山雀血氧亲和力升高的分子机制.结果表明,与大山雀相比(RPKM为0),胚胎特异表达ρ基因在地山雀成体肝中表达较高(RPKM...     

Role of Putrescine in the Regulation of the Expression of the Oxidative Stress Defense Genes of Escherichia coli

The role of putrescine in the adaptive response of Escherichia coligrown aerobically in synthetic M9 medium with glucose to the H₂O₂-induced oxidative stress was studied. Under oxidative stress, the expression of the single-copy reporter gene fusions oxyR"::lacZand katG"::lacZwas found to undergo biphasic changes, which were most pronounced in glucose-starved E. colicells. The concentration-dependent activating effect of putrescine on the expression of the OxyR regulon genes was maximum when theoxyRgene was inhibited by high concentrations of hydrogen peroxide.     

Underlying the Mechanisms of Doxorubicin-Induced Acute Cardiotoxicity: Oxidative Stress and Cell Death

Cancer is a destructive disease that causes high levels of morbidity and mortality. Doxorubicin (DOX) is a highly efficient antineoplastic chemotherapeutic drug, but its use places survivors at risk for cardiotoxicity. Many studies have demonstrated that multiple factors are involved in DOX-induced acute cardiotoxicity. Among them, oxidative stress and cell death predominate. In this review, we provide a comprehensive overview of the mechanisms underlying the source and effect of free radicals and dependent cell death pathways induced by DOX. Hence, we attempt to explain the cellular mechanisms of oxidative stress and cell death that elicit acute cardiotoxicity and provide new insights for researchers to discover potential therapeutic strategies to prevent or reverse doxorubicin-induced cardiotoxicity.     

番茄AT-hook基因家族的鉴定及胁迫条件下的表达分析

AT-hook蛋白家族在植物生长发育、器官构建及逆境胁迫和激素信号应答中发挥重要作用。本研究在番茄基因组范围内,利用生物信息学方法对番茄AT-hook基因家族的成员、分布、结构和功能进行分析。结果表明,番茄AT-hook家族包含32个成员,分为3种类型,其中类型Ⅰ含有13个成员;遗传进化分析表明番茄AT-hook基因成员与拟南芥家族基因具有相似分类。利用实时荧光定量PCR对番茄32个基因开展组织表达分析,结果表明AT-hook基因具有表达差异,主要在根和花中表达较高。氧化胁迫分析结果表明,32个基因受ABA、SA、盐、高温和低温诱导表达,其中部分基因显著上调或下调表达,很可能参与了番茄逆境胁迫条件下的防御应答反应。本研究结果将为番茄AT-hook家族基因的深入研究提供依据,为进一步解析番茄AT-hook基因的功能奠定基础。     

砂仁不同叶位叶片的光合作用和氧化胁迫

衰老时砂仁叶片Pmax降低,这与叶片Gs、Chi含量和可溶性蛋白质含量的降低有关.随着叶片的衰老,NPQ、AQY、F/Fm、φPsIl和qp均降低,热耗散减少,光抑制加剧,衰老后期出现光破坏.但这些参数下降的幅度均小于Pmax下降幅度.光暗反应失衡,活性氧生成增加.衰老初期(老化)叶片MDA含量没有升高,衰老中后期叶片MDA含量显著升高,表明老化叶片能有效地耗散或清除活性氧,衰老叶片则不能,尽管其sOD、APX和POD等抗氧化酶活力显著升高.上述结果表明砂仁叶片老化与氧化胁迫关系不大,衰老与氧化胁迫密切相关.     

Focus: The Science of Stress: Oxidative Stress and Inflammation in Cardiovascular Diseases and Cancer: Role of Non-coding RNAs

High oxidative stress, Th1/Th17 immune response, M1 macrophage inflammation, and cell death are associated with cardiovascular diseases. Controlled oxidative stress, Th2/Treg anti-tumor immune response, M2 macrophage inflammation, and survival are associated with cancer. MiR-21 protects against cardiovascular diseases but may induce tumor growth by retaining the anti-inflammatory M2 macrophage and Treg phenotypes and inhibiting apoptosis. Down-regulation of let-7, miR-1, miR-9, miR-16, miR-20a, miR-22a, miR-23a, miR-24a, miR-26a, miR-29, miR-30a, miR-34a, miR-124, miR-128, miR-130a, miR-133, miR-140, miR-143-145, miR-150, miR-153, miR-181a, miR-378, and miR-383 may aid cancer cells to escape from stresses. Upregulation of miR-146 and miR-223 may reduce anti-tumor immune response together with miR-21 that also protects against apoptosis. MiR-155 and silencing of let-7e, miR-125, and miR-126 increase anti-tumor immune response. MiR expression depends on oxidative stress, cytokines, MYC, and TGF-β, and expression of silencing lncRNAs and circ-RNAs. However, one lncRNA or circ-RNA may have opposite effects by targeting several miRs. For example, PVT1 induces apoptosis by targeting miR-16a and miR-30a but inhibits apoptosis by silencing miR-17. In addition, levels of a non-coding RNA in a cell type depend not only on expression in that cell type but also on an exchange of microvesicles between cell types and tumors. Although we got more insight into the function of a growing number of individual non-coding RNAs, overall, we do not know enough how several of them interact in functional networks and how their expression changes at different stages of disease progression.     

Evolution of the Mitochondrial Genome in Mammals Living at High Altitude: New Insights from a Study of the Tribe Caprini (Bovidae,Antilopinae)

Organisms living at high altitude are exposed to severe environmental stress associated with decreased oxygen pressure, cold temperatures, increased levels of UV radiation, steep slopes, and scarce food supplies, which may have imposed important selective constraints on the evolution of the mitochondrial genome. Within mammals, the tribe Caprini is of particular interest for studying the evolutionary effects of life at high altitude, as most species live in mountain regions, where they developed morphological and physiological adaptations for climbing. In this report, we analyzed the complete mitochondrial genome of 24 ruminants, including 20 species of Caprini. The phylogenetic analyses based on 16,117 nucleotides suggested the existence of a new large clade, here named subtribe Caprina, containing all genera, but Pantholops (Pantholopina), Capricornis, Naemorhedus, and Ovibos (Ovibovina). The alignment of the control region showed that all Caprini have between two and four tandem repeats of ~75 bp in the RS2 region, and that several of these copies emerged from recent and independent duplication events. We proposed therefore that the maintenance of at least two RS2 repeats in the control region of Caprini is positively selected, probably for producing a higher number of D-loop strands 3′-ending at different locations. The analyses of base composition at third-codon positions of protein-coding genes revealed that Caprini have the highest percentage of A nucleotide and the lowest percentage of G nucleotide, a pattern which suggests increased rates of cytosine deamination (C→T transitions) on the H strand of mtDNA. Two nonexclusive hypotheses related to high-altitude life can explain such a mutational pattern: more severe oxidative stress (ROS) and higher metabolic rates. By comparing the relative rates of nonsynonymous and synonymous substitutions in protein-coding genes, we identified that Caprini have higher levels of adaptive variation in the ATPase complex. In addition, we detected several changes in mitochondrial genes that should be tested for their potential role in mountain adaptation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phytoplankton and Zooplankton Associations in a Set of Alpine High Altitude Lakes: Geographic Distribution and Ecology

Species composition and interactions, biomass dominance, geographic distribution and driving variables were investigated for two key elements of the pelagic food web of Alpine lakes, the phytoplankton and the zooplankton, based on a single sampling campaign during summer 2000. Altogether, 70 lakes were surveyed, 49 of which located in three different lake districts of the west and eastern Italian Alps and 21 in the central Austrian Alps (within the uppermost Danube catchment). In addition to the analysis of environmental variables affecting distribution and species structure of the two planktonic compartments, a brief review of the main research lines and hypotheses adopted in the past for the study of phytoplankton and zooplankton in high Alpine lakes is given. The lakes, investigated partly within the European project EMERGE (EVK1-CT-1999-00032) and partly within a regional project in the eastern Alps, comprise a wide range of morphological, chemical and trophic conditions. The phytoplankton communities were found to be diverse and mostly dominated by flagellates (chrysophytes, cryptophytes and dinoflagellates), and only to a lesser extent by non-motile green algae, desmids and centric diatoms. The zooplankton communities were mainly dominated by Alpine cladocerans and copepod species, while rotifers were abundant within one group of Italian lakes (sampled in early summer). The multivariate statistical analyses (CCA) showed that catchment features (i.e. percentage of vegetation cover and geochemical composition) and nitrate concentration are essential drivers for the phytoplankton, whereas for zooplankton also trophic status of the lakes and phytoplankton structure are important. The combined variance analysis of the lake clusters outlined by the multivariate analyses on phytoplankton and zooplankton data, respectively, allowed the identification of four principal lake types (three located on siliceous and one on carbonaceous bedrock), each one characterised by a certain combination of habitat features, which in their turn influence trophic state, and phytoplankton and zooplankton species composition and functionality.     

辣椒锌指蛋白DnaJ-Like基因家族鉴定及对高温胁迫的表达响应

植物DnaJ-Like锌指蛋白（DNAJE）是近年来发现的一类具有重要功能的蛋白,在光合作用、质体发育与运动和植物抗逆及防御反应中发挥重要作用。基于辣椒全基因组数据,对辣椒DNAJE基因家族（CaDNAJE）进行鉴定,利用生物信息学方法对基因和蛋白特征、比较进化、共线性关系及高温胁迫下基因表达模式等进行分析。结果表明,CaDNAJE基因家族有28个成员,不均匀的分布在10条染色体和3个Scaffold上,氨基酸序列长度为99-470 aa,分子量为10.05-52.26 kD,理论等电点（pI）为4.75-9.64,其编码蛋白主要定位在叶绿体和细胞核中;辣椒、番茄和拟南芥的比较进化分析可将其分为GroupⅠ 和GroupⅡ 2个亚族,同一亚族具有类似的蛋白保守motif和基因结构;CaDNAJE基因启动子区包含大量光响应、激素响应和胁迫应答元件;辣椒与拟南芥DNAJE之间存在10对共线性基因,辣椒种内仅有1对;辣椒不同组织转录组分析发现,GroupⅠ 中多数成员在各组织中均有高表达,而GroupⅡ 中除CaDNAJE2、CaDNAJE9等基因存在高表达外,多数基因表达量都很低甚至不表达;高温胁迫下,辣椒叶片过氧化氢含量急速上升后降低,丙二醛含量持续升高,抗氧化物酶活性也有不同程度的提高。同时,高温诱导热激转录因子Hsf和热激蛋白HSP耐热相关基因及CaDNAJE基因高表达,在不同胁迫时期发挥调控作用。推测CaDNAJE基因家族可能参与辣椒响应高温胁迫,提高其耐受力,以降低细胞损伤。     

Caffeic Acid Inhibits the Formation of Advanced Glycation End Products (AGEs) and Mitigates the AGEs‐Induced Oxidative Stress and Inflammation Reaction in Human Umbilical Vein Endothelial Cells (HUVECs)

The advanced glycation end products (AGEs) are the compounds produced by non‐enzymatic glycation reaction of proteins and sugars, which can induce the generation of free radicals and the expression of inflammatory factors, thereby playing an important role in vascular dysfunction in diabetes. To investigate the effects of caffeic acid (CA) on glycation formed by glucose and protein, various spectroscopic techniques and molecular docking methods were carried out. Furthermore, the protective effects of CA on human umbilical vein endothelial cells (HUVECs) damaged by AGEs were detected. The results indicated that CA inhibited AGEs formation in vitro, decreased the expression of IL‐1β, IL‐18, ICAM‐1, VCAM‐1, NLRP3, Caspase‐1 and CRP (C‐reactive protein) and reduced the ROS in HUVECs exposed to AGEs. Our findings suggested that the supplementation with dietary CA could prevent and delay the AGEs‐induced vascular dysfunction in diabetes.     

Alleviation of Liver Dysfunction,Oxidative Stress,and Inflammation Underlines the Protective Effects of Polysaccharides from Cordyceps cicadae on High Sugar/High Fat Diet-Induced Metabolic Syndrome in Rats

This study investigated the protective effects of two polysaccharides (CPA-1 and CPB-2) from Cordyceps cicadae against high fructose/high fat diet (HF/HFD) induced obesity and metabolic disorders in rats. Rats were either fed with normal diet or HF/HFD and treated with CPA-1 and CPB-2 (100 and 300 mg/kg) for 11 weeks. Administration of CPA-1 and CPB-2 significantly and dose dependently reduced body and liver weight, insulin and glucose tolerance, serum insulin and glucose levels. Furthermore, serum and hepatic lipid profiles, liver function enzymes and proinflammatory cytokines (TNF-α, IL-1β and IL-6) were markedly reduced. Additionally, CPA-1 and CPB-2 treatment alleviated hepatic oxidative stress by reducing lipid peroxidation level (MDA) and upregulating glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) and catalase (CAT) activities as well as ameliorated histological alterations through the reduction of hepatic lipid accumulation. These results suggested that the polysaccharides from C. cicadae showed protective effects against HF/HFD induced metabolic disturbances and may be considered as a dietary supplement for treating obesity.     

Postnatal Methylmercury Exposure Induces Hyperlocomotor Activity and Cerebellar Oxidative Stress in Mice: Dependence on the Neurodevelopmental Period

During the early postnatal period the central nervous system (CNS) is extremely sensitive to external agents. The present study aims at the investigation of critical phases where methylmercury (MeHg) induces cerebellar toxicity during the suckling period in mice. Animals were treated with daily subcutaneous injections of MeHg (7 mg/kg of body weight) during four different periods (5 days each) at the early postnatal period: postnatal day (PND) 1–5, PND 6–10, PND 11–15, or PND 16–20. A control group was treated with daily subcutaneous injections of a 150 mM NaCl solution (10 ml/kg of body weight). Subjects exposed to MeHg at different postnatal periods were littermate. At PND 35, behavioral tests were performed to evaluate spontaneous locomotor activity in the open field and motor performance in the rotarod task. Biochemical parameters related to oxidative stress (levels of glutathione and thiobarbituric acid reactive substances, as well as glutathione peroxidase and glutathione reductase activity) were evaluated in cerebellum. Hyperlocomotor activity and high levels of cerebellar thiobarbituric acid reactive substances were observed in animals exposed to MeHg during the PND 11–15 or PND 16–20 periods. Cerebellar glutathione reductase activity decreased in MeHg-exposed animals. Cerebellar glutathione peroxidase activity was also decreased after MeHg exposure and the lowest enzymatic activity was found in animals exposed to MeHg during the later days of the suckling period. In addition, low levels of cerebellar glutathione were found in animals exposed to MeHg during the PND 16–20 period. The present results show that the postnatal exposure to MeHg during the second half of the suckling period causes hyperlocomotor activity in mice and point to this phase as a critical developmental stage where mouse cerebellum is a vulnerable target for the neurotoxic and pro-oxidative effects of MeHg.     

氧化应激在高原重体力劳动过程中急性高原反应发生中的作用

目的：观察氧化应激在高原重体力劳动过程中急性高原反应（AHAR）发生中的作用。方法：由低海拔（1500m）快速进入高原（3700m）并从事重体力劳动的男性官兵96名,年龄18～35岁。根据AHAR症状评分,分为重度AHAR组（A组,n=24）、轻中度AHAR组（B组,n=47）和无AHAR组（C组,n=25）,在该高度逗留50d后下撤前及返回低海拔（1500m）后12h、15d分别测定血清8．异前列腺素F2a（8-iso-PGF2a）、超氧化物歧化酶（SOD）、丙二醛（MDA）,并与低海拔（1500m）50名健康官兵（D组）比较。结果：A组血清8-iso-PGF2a、MDA[分别为（9．53±0．47）μg／L、（8．91±0．39）μmol／L]水平显著高于B组[分别为（8．34±O．42）μg／L、（7．31±0．32）μmol／L]、C组[分别为（7．02±0．48）μg／L、（6．41±0．23）μmol／L和D组[分别为（5．13±0．56）μg／L、（5．48±0．33）μmol／L]（均P〈0．01）,SOD（52．08±3．44）μ／mL水平显著低于B组（62．27±2．54）μ/mL、C组（71．99±3．35）μ/mL和D组（80．78±3．44）μ/mL,（均P〈0．01）,B组与c组之间和C组与D组之间亦有显著性差异（均P〈0．01）。海拔3700mAHAR总计分与血清8-iso-PGF2α、ⅣⅡ）A呈显著正相关（均P〈0．01）,与血清SOD显著负相关（P〈0．01）;8-iso-PGF2α、MDA与SOD显著负相关（均P〈0．01）。海拔3700m50d,血清8-iso-PGF2α、MDA水平显著高于,SOD水平显著低于海拔1500m12h、15d和D组（均P〈0．01）,海拔1500m12h与15d之间有显著性差异（均P〈0．01）,海拔1500m 15d与D组之间无显著性差异。结论：人体在高原低氧并重体力时氧化应激和氧化．抗氧化失衡与AHAR的发病和程度有密切关系,氧化应激和氧化．抗氧化失衡越严重,AHAR越重。返回低海拔后12h有显著改善,15d恢复到正常水平。     

Challenges and Solutions in the Development of Genomic Biomarker Panels: A Systematic Phased Approach

In the post-genome era, high throughput gene expression profiling has been successfully used to develop genomic biomarker panels (GBP) that can be integrated into clinical decision making. The development of GBPs in the context of personalized medicine is a scientifically challenging and resource-intense process. It needs to be accomplished in a systematic phased approach to address biological variation related to a clinical phenotype (e.g. disease etiology, gender, etc.) and minimize technical variation (noise). Here we present the methodological aspects of GBP development based on the experience of the Cardiac Allograft Rejection Gene Expression Observation (CARGO) study, a study that lead to the development of a molecular classifier for rejection screening in heart transplant patients.     

Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review

Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress.     

白菜PLD基因家族全基因组鉴定及对高温胁迫的响应

膜磷脂是产生胞内信号信使的重要来源,磷脂酶Ds(phospholipase D,PLDs)可以催化磷脂产生信号分子磷脂酸(phosphatidic acid, PA),从而响应不同胁迫信号。该研究利用生物信息学方法对白菜PLD基因家族的基因成员进行鉴定及结构域分析,并采用qRT PCR方法对不结球白菜的18个BrPLD基因的表达进行分析,以探讨不结球白菜的BrPLD基因家族对高温胁迫的响应机制。结果表明：(1)共鉴定到18个白菜PLD基因家族成员,其中有2个成员(BrPLD03和BrPLD09)的C2结构域被替换为PH/PX结构域,另有1个基因(BrPLD12)缺少了其N末端保守结构域,由信号肽代替。(2)根据编码蛋白结构域的不同,18个BrPLD基因分为3个亚类,分别为15个C2 BrPLD、2个PH/PX BrPLD和1个SP BrPLD;氨基酸理化性质分析发现,该基因家族编码蛋白多半为酸性蛋白;18个基因分布在除4号和7号之外的8条染色体,且呈现不均匀分布,并发现了BrPLDs蛋白Ca²⁺配位碱基的缺失。(3)qRT PCR检测发现,高温处理下不结球白菜的BrPLD基因的表达量发生明显变化,各基因在耐热和热敏品种中的表达具有差异。(4)对BrPLD基因家族不同功能顺式响应元件的预测发现,所有家族基因含有光应答有关的作用元件,9个基因含有与低温有关的顺式元件,10个基因含有调控干旱相关元件,18个基因均未预测到热胁迫相关顺式响应元件。