Multiscale Persistent Functions for Biomolecular Structure Characterization

In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al. in Pattern Recognit 48(2):391–401, 2015; Merelli et al. in Entropy 17(10):6872–6892, 2015; Rucco et al. in: Proceedings of ECCS 2014, Springer, pp 117–128, 2016), a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our MPE can be used in conformational entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of an MRF built from angular distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. It is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the intermediate range. Moreover, by comparing with traditional entropies from various grid sizes, bond angle-based methods and a persistent homology-based support vector machine method (Cang et al. in Mol Based Math Biol 3:140–162, 2015), we find that our MPE method gives the best results in terms of average true positive rate in a classic protein structure classification test. More interestingly, all-alpha and all-beta protein classes can be clearly separated from each other with zero error only in our model. Finally, a special protein structure index (PSI) is proposed, for the first time, to describe the “regularity” of protein structures. Basically, a protein structure is deemed as regular if it has a consistent and orderly configuration. Our PSI model is tested on a database of 110 proteins; we find that structures with larger portions of loops and intrinsically disorder regions are always associated with larger PSI, meaning an irregular configuration, while proteins with larger portions of secondary structures, i.e., alpha-helix or beta-sheet, have smaller PSI. Essentially, PSI can be used to describe the “regularity” information in any systems.     

Availability of Essential Elements in Nutrient Supplements Used as Antidiabetic Herbal Formulations

Five brands of antidiabetic herbal formulations as tablets, Diabetex, Divya Madhu Nashini, Jambrushila, Diabeticin, and Madhumeh Nashini, from different pharmacies were analyzed for six minor (Na, K, Ca, Cl, Mg, and P) and 20 trace (As, Ba, Br, Ce, Co, Cr, Cs, Cu, Fe, Hg, La, Mn, Rb, Sb, Sc, Se, Sm, Th, V, and Zn) elements by thermal neutron irradiation followed by high-resolution gamma ray spectrometry. Further Ni, Cd, and Pb were determined by atomic absorption spectrophotometry. Most elements vary in a narrow range by a factor of 2–4 while a few others vary in a wide range, e.g., Na (0.05–0.67 mg/g), Mn (26.7–250 μg/g), and V (0.26–2.50 μg/g). All the five brands contain K, Cl, Mg, P, and Ca as minor constituents along with mean trace amounts of Cr (2.11 ± 0.67 μg/g), Cu (15.7 ± 7.11 μg/g), Fe (459 ± 171 μg/g), Mn (143 ± 23 μg/g), Se (238 ± 112 ng/g), and V (0.99 ± 0.93 μg/g). Jambrushila is enriched in Na, Ca, Mg, Cl, Fe, Cu, Se, and Zn, essential nutrients responsible for curing diabetes. Dietary intake of Mn, Fe, and Cu are greater than 10% of the recommended dietary allowance, whereas that for Zn and Se is less than 2%. Mean contents of toxic elements (As, Cd, Hg, and Pb) were found below permissible limits except in Jambrushila. Cr and Zn were inversely correlated with r = −0.81, whereas Rb and Cs exhibit linear correlation (r = 0.93) in five brands. C, H, N analysis showed C ∼ 55%, H ∼ 12%, and N ∼ 2% with a total of ∼70% organic matter. However, thermal decomposition studies at 700°C suggest less than 5% nonvolatile metal oxides. Herbal formulations contain minor and trace elements in bioavailable forms that favorably influence glucose tolerance and possibly increase the body’s ability to ameliorate development of diabetes.     

Biomolecular Characterization of Wild Sicilian Oregano: Phytochemical Screening of Essential Oils and Extracts,and Evaluation of Their Antioxidant Activities

An extensive survey of wild Sicilian oregano was made. A total of 57 samples were collected from various sites, followed by taxonomic characterization from an agronomic perspective. Based on morphological and production characteristics obtained from the 57 samples, cluster analysis was used to divide the samples into homogeneous groups, to identify the best biotypes. All samples were analyzed for their phytochemical content, applying a cascade‐extraction protocol and hydrodistillation, to obtain the non volatile components and the essential oils, respectively. The extracts contained thirteen polyphenol derivatives, i.e., four flavanones, seven flavones, and two organic acids. Their qualitative and quantitative characterization was carried out by LC/MS analyses. The essential oils were characterized using a combination of GC‐FID and GC/MS analyses; a total of 81 components were identified. The major components of the oils were thymol, p‐cymene, and γ‐terpinene. Cluster analysis was carried out on both phytochemical profiles and resulted in the division of the oregano samples into different chemical groups. The antioxidant activity of the essential oils and extracts was investigated by the Folin? Ciocalteau (FC) colorimetric assay, by UV radiation‐induced peroxidation in liposomal membranes (UV‐IP test), and by determining the O ‐scavenging activity.     

Cytotoxicity and Antioxidative Effects of Herbal and Fruit Extracts In Vitro

Many studies have been carried out on bioactivities of individual herbs/fruits using in cosmetics or as a diet products, however, no collective study on their comparative antioxidant activities against oxidative damage or on cytotoxicity effect has been reported. The aim of this work was study the cytotoxicity and antioxidative activity of eight extracts with hypothetical antioxidative influence in vitro. To further elucidate of a possible role of herbals/fruits extracts on cell protection was used on the healthy and UV-A damaged mouse fibroblast cells. The cell viability was detect using MTT assay. Kinetic production of reactive oxygen species, identification of cell death, cell cycle and gene expression C-FOS were measured. Intracellular and mitochondrial transmembrane potential was evaluate with JC-1 fluorescence probe. Comet assay was employed to detect the UV-A induced DNA damage. The results indicated that using the extracts decreased ROS production. It can lead to greatly enhance and promote the viability of cells. As the most effective antioxidant in quenching of the ROS, in cell viability and DNA presentation was determined Prunella Vulgaris. However, one of them (Wheat Germ Oil) caused increased production of ROS and low cell viability.     

Antioxidant and Antidiabetic Properties of Extracts from Three Underutilized Food Plants of North East India

Three underutilized leafy vegetables Sarcochlamys pulcherrima (Roxb.) Gaudich (SP), Ipomoea aquatica Forssk. (IA) and Zanthoxylum rhetsa (Roxb.) DC (ZR) were extracted with different solvents viz. 95 % ethyl alcohol, methanol and hot water. The extracts were evaluated for their antioxidant potential via DPPH, ABTS and FRAP assay along with electroanalytical studies using cyclic voltammetry. The antidiabetic potential was determined by recording their α-amylase and α-glucosidase inhibitory assay. The total phenolic content (TPC), total flavonoid content (TFC) and the liquid chromatography-mass spectrometry (LC/MS) based phytochemical profiles of the extracts were also determined. All three extracts of SP exhibited significant antioxidant capacity. The antidiabetic potential of the IA and ZR extracts was found to be higher than or at par with that of standard acarbose. LC/MS studies reveal the presence of hitherto reported antioxidant and antidiabetic compounds like gamma-aminobutyric acid, cinnamic acid, caffeic acid, α-viniferin, piperlonguminine, niacin, kaempferol, etc., in the extracts.     

Characterization of a Putative Ancestor of Coxsackievirus B5

Like other RNA viruses, coxsackievirus B5 (CVB5) exists as circulating heterogeneous populations of genetic variants. In this study, we present the reconstruction and characterization of a probable ancestral virion of CVB5. Phylogenetic analyses based on capsid protein-encoding regions (the VP1 gene of 41 clinical isolates and the entire P1 region of eight clinical isolates) of CVB5 revealed two major cocirculating lineages. Ancestral capsid sequences were inferred from sequences of these contemporary CVB5 isolates by using maximum likelihood methods. By using Bayesian phylodynamic analysis, the inferred VP1 ancestral sequence dated back to 1854 (1807 to 1898). In order to study the properties of the putative ancestral capsid, the entire ancestral P1 sequence was synthesized de novo and inserted into the replicative backbone of an infectious CVB5 cDNA clone. Characterization of the recombinant virus in cell culture showed that fully functional infectious virus particles were assembled and that these viruses displayed properties similar to those of modern isolates in terms of receptor preferences, plaque phenotypes, growth characteristics, and cell tropism. This is the first report describing the resurrection and characterization of a picornavirus with a putative ancestral capsid. Our approach, including a phylogenetics-based reconstruction of viral predecessors, could serve as a starting point for experimental studies of viral evolution and might also provide an alternative strategy for the development of vaccines.The group B coxsackieviruses (CVBs) (serotypes 1 to 6) were discovered in the 1950s in a search for new poliovirus-like viruses (33, 61). Infections caused by CVBs are often asymptomatic but may occasionally result in severe diseases of the heart, pancreas, and central nervous system (99). CVBs are small icosahedral RNA viruses belonging to the Human enterovirus B (HEV-B) species within the family Picornaviridae (89). In the positive single-stranded RNA genome, the capsid proteins VP1 to VP4 are encoded within the P1 region, whereas the nonstructural proteins required for virus replication are encoded within the P2 and P3 regions (4). The 30-nm capsid has an icosahedral symmetry and consists of 60 copies of each of the four structural proteins. The VP1, VP2, and VP3 proteins are surface exposed, whereas the VP4 protein lines the interior of the virus capsid (82). The coxsackievirus and adenovirus receptor (CAR), a cell adhesion molecule of the immunoglobulin superfamily, serves as the major cell surface attachment molecule for all six serotypes of CVB (5, 6, 39, 60, 98). Some strains of CVB1, CVB3 and CVB5 also interact with the decay-accelerating factor (DAF) (CD55), a member of the family of proteins that regulate the complement cascade. However, the attachment of CVBs to DAF alone does not permit the infection of cells (6, 7, 59, 85).Picornaviruses exist as genetically highly diverse populations within their hosts, referred to as quasispecies (20, 57). This genetic plasticity enables these viruses to adapt rapidly to new environments, but at the same time, it may compromise the structural integrity and enzymatic functionality of the virus. The selective constraints imposed on the picornavirus genome are reflected in the different regions used for different types of evolutionary studies. The highly conserved RNA-dependent RNA polymerase (3D^pol) gene is used to establish phylogenetic relationships between more-distantly related viruses (e.g., viruses belonging to different genera) (38), whereas the variable genomic sequence encoding the VP1 protein is used for the classification of serotypes (13, 14, 69, 71, 72).In 1963, Pauling and Zuckerkandl proposed that comparative analyses of contemporary protein sequences can be used to predict the sequences of their ancient predecessors (73). Experimental reconstruction of ancestral character states has been applied to evolutionary studies of several different proteins, e.g., galectins (49), G protein-coupled receptors (52), alcohol dehydrogenases (95), rhodopsins (15), ribonucleases (46, 88, 110), elongation factors (32), steroid receptors (10, 96, 97), and transposons (1, 45, 87). In the field of virology, reconstructed ancestral or consensus protein sequences have been used in attempts to develop vaccine candidates for human immunodeficiency virus type 1 (21, 51, 66, 81) but rarely to examine general phenotypic properties.In this study, a CVB5 virus with a probable ancestral virion (CVB5-P1anc) was constructed and characterized. We first analyzed in detail the evolutionary relationships between structural genes of modern CVB5 isolates and inferred a time scale for their evolutionary history. An ancestral virion sequence was subsequently inferred by using a maximum likelihood (ML) method. This sequence was then synthesized de novo, cloned into a replicative backbone of an infectious CVB5 cDNA clone, and transfected into HeLa cells. The hypothetical CVB5-P1anc assembled into functional virus particles that displayed phenotypic properties similar to those of contemporary clinical isolates. This is the first report describing the reconstruction and characterization of a fully functional picornavirus with a putative ancestral capsid.     

Phytochemical Content,Antidiabetic, Anticholinergic,and Antioxidant Activities of Endemic Lecokia cretica Extracts

The aim of this work was to investigate the enzyme inhibition, antioxidant activity, and phenolic compounds of Lecokia cretica (Lam .) DC. Acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and α‐glycosidase enzymes were strongly inhibited by the L. cretica extracts. IC₅₀ values for the three enzymes were found as 3.21 mg/mL, 2.1 mg/mL, and 2.07 mg/mL, respectively. Antioxidant activities were examined in both aqueous and ethanol (EtOH) extracts using CUPRAC, FRAP, and DPPH method. Also, the phenolic compounds of the endemic plant were identified and quantified by using HPLC/MS/MS. According to the results, the extracts have remarkable antioxidant activities. The most abundant phenolic acids of L. cretica in EtOH extract were determined as quinic acid (12.76 mg/kg of crude extract), chlorogenic acid (3.39 mg/kg), and malic acid (2.38 mg/kg).     

Essential Oils and Herbal Extracts as Antimicrobial Agents in Cosmetic Emulsion

The cosmetic industry adapts to the needs of consumers seeking to limit the use of preservatives and develop of preservative-free or self-preserving cosmetics, where preservatives are replaced by raw materials of plant origin. The aim of study was a comparison of the antimicrobial activity of extracts (Matricaria chamomilla, Aloe vera, Calendula officinalis) and essential oils (Lavandulla officinallis, Melaleuca alternifolia, Cinnamomum zeylanicum) with methylparaben. Extracts (2.5 %), essential oils (2.5 %) and methylparaben (0.4 %) were tested against Pseudomonas aeruginosa ATCC 27853, Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29213, Candida albicans ATCC 14053. Essentials oils showed higher inhibitory activity against tested microorganism strain than extracts and methylparaben. Depending on tested microorganism strain, all tested extracts and essential oils show antimicrobial activity 0.8–1.7 and 1–3.5 times stronger than methylparaben, respectively. This shows that tested extracts and essential oils could replace use of methylparaben, at the same time giving a guarantee of microbiological purity of the cosmetic under its use and storage.     

杨树基因组AMT转运蛋白的生物信息学特性

本研究中,通过隐马尔科夫模型(HMM)和杨树蛋白质库搜索,共找到17个杨树铵转运体蛋白(PtAMTs).利用生物信息学方法,我们对杨树家族17条AMT蛋白序列的系统发生和AMT基因组定位进行分析,然后对其氨基酸组成成分、理化性质以及二级结构进行预测和分析,同时还分析了杨树与拟南芥、水稻、番茄、百脉根和欧洲油菜的AMT基因家族之间的联系.二级结构预测结果发现不同成员间氨基酸数目、氨基酸序列间的疏水性存在一定的差异;α-螺旋和无规则卷曲为主要二级结构组成部分.同源性比对分析表明,PtAMT基因家族主要分为2个亚家族,AMT1 (11个成员)和AMT2 (6个成员),基因结果分析表明AMT2亚家族成员不含内含子.杨树AMT蛋白的亚细胞定位分析表明PtAMT主要定位于膜结构上.电子表达图谱分析结果表明:只有XP_002309151和 XP_002334025基因有对应的EST序列,并有相应的电子表达谱,并主要在花蕾表达.     

Bead Aggregation Assays for the Characterization of Putative Cell Adhesion Molecules

Cell-cell adhesion is fundamental to multicellular life and is mediated by a diverse array of cell surface proteins. However, the adhesive interactions for many of these proteins are poorly understood. Here we present a simple, rapid method for characterizing the adhesive properties of putative homophilic cell adhesion molecules. Cultured HEK293 cells are transfected with DNA plasmid encoding a secreted, epitope-tagged ectodomain of a cell surface protein. Using functionalized beads specific for the epitope tag, the soluble, secreted fusion protein is captured from the culture medium. The coated beads can then be used directly in bead aggregation assays or in fluorescent bead sorting assays to test for homophilic adhesion. If desired, mutagenesis can then be used to elucidate the specific amino acids or domains required for adhesion. This assay requires only small amounts of expressed protein, does not require the production of stable cell lines, and can be accomplished in 4 days.     

Genetic Characterization of a Putative Densovirus from the Mealybug Planococcus citri

Total genomic DNA preparations from the citrus mealybug, Planococcus citri, contained a DNA band corresponding to 5.5 kilobases. This DNA was a linear molecule and was cloned into pUC18. Nucleotide sequence determination indicated that it was the replicative form of a densovirus, most closely related to the virus from Periplaneta fuliginosa (smokybrown cockroach). Received: 25 April 2001 / Accepted: 3 May 2001     

七种中草药提取物抗肿瘤活性部位的筛选研究初报

选取叶下珠、珠子草、千里光、鸦胆子、使君子、冬青和猫爪藤等7种中草药进行提取和初步分离,筛选出有抗肿瘤效果的活性部位,并对其进行初步分析。采用MTT法,以7种中草药醇提物的不同分离部位分别对人肝癌、胃癌、卵巢癌等肿瘤细胞株进行体外增殖抑制作用研究,并以人正常肝细胞株为模型对照跟踪筛选活性部位。结果表明,从7种中草药醇提物中,均获得对肿瘤细胞株具有体外增殖抑制作用的化学分离部位,其中叶下珠和珠子草的乙酸乙酯层和正丁醇层的活性最显著,千里光的乙酸乙酯层、鸦胆子的正丁醇层、使君子和冬青的氯仿层活性次之,猫爪藤氯仿层和冬青的乙酸乙酯层活性较差,其他部位无活性。     

Herbal Extracts as Potential Antioxidant,Anti-Aging,Anti-Inflammatory,and Whitening Cosmeceutical Ingredients

The aim of this research was to investigate and compare the antioxidant, anti-tyrosinase, anti-aging, and anti-inflammatory activities of 16 herbal extracts for topical application in cosmetic/cosmeceutical products. Herbal plant materials were extracted by infusion in boiled water for 15 min. The total phenolic content and total flavonoid content of each extract were investigated by the Folin-Ciocalteu and aluminum chloride methods, respectively. Antioxidant activities were investigated using 2,2’-diphenyl-1-picrylhydrazyl and a ferric reducing antioxidant power assay. Anti-tyrosinase and anti-aging activities were investigated using an in vitro enzymatic-spectrophotometric method. Anti-inflammatory activities were investigated using an enzyme-linked immunosorbent assay. The findings show that the Stevia rebaudiana extract has the most significant levels of both phenols and flavonoids (p<0.05). The S. rebaudiana, Rosa damascene, and Phyllanthus emblica extracts possessed the most significant antioxidant activities (p<0.05) and a promising whitening effect with moderate anti-tyrosinase activities. Furthermore, the Echinacea purpurea extract possessed the most significant anti-collagenase (78.5±0.0 %), anti-elastase (69.0±1.4 %), and anti-hyaluronidase activity (64.2±0.3 %). The Morus alba extract possessed the most significant anti-inflammatory activity since it could inhibit the secretion of interleukin-6 and tumor necrosis factor-α (p<0.05). Therefore, these herbal extracts have promising skin benefits and have potential for use as active ingredients in cosmetic/cosmeceutical products.     

Investigating Terephthalate Biodegradation: Structural Characterization of a Putative Decarboxylating cis-Dihydrodiol Dehydrogenase

As a highly coveted precursor molecule, terephthalate (Tph) continues to be used extensively for the production of polyethylene Tph bottles, polyester films, and textile fibers worldwide. Based on its detrimental physiological effects, Tph is now recognized as a serious environmental pollutant. While amenable to biodegradation and, in fact, traditionally neutralized by aerobic microbiological processes, our current lack of understanding of the enzymatic degradation of Tph at the molecular level presents a major impediment in the development of robust bioremediation strategies. The biodegradation of Tph proceeds through a single metabolic intermediate (a cis-dihydrodiol), which is subsequently converted to the end product (protocatechuate) by a decarboxylating cis-dihydrodiol dehydrogenase (TphB). Using iodide single‐wavelength anomalous dispersion, we report the first structural characterization of TphB to 1.85 Å resolution. Contrary to prior speculations, a fluorescent scan unambiguously shows that TphB coordinates Zn^2 + and not Fe^2 +. The molecular architecture of TphB provides a rationale to the primary‐level divergence observed between TphB and other cis-dihydrodiol dehydrogenases while explaining its intriguingly close evolutionary clustering with non-dihydrodiol dehydrogenases belonging to the isocitrate/isopropylmalate family of enzymes. Sequence and structural analyses reveal a putative substrate-binding pocket proximal to the bound Zn^2 +. In silico substrate modeling in this putative binding pocket suggests a mechanistic sequence relying on H291, K295, and Zn^2 + as core mediators of catalytic turnover. Overall, this study reveals novel structural and mechanistic insights into a decarboxylating cis-dihydrodiol dehydrogenase that mediates one of the two catalytic steps in the biodegradation of the environmental pollutant Tph.     

几种常用中草药抗氧化活性研究(英文)

当归、黄芪、银杏叶、益母草、野甘草是中国传统中药材,几千年来一直为中国人民所认可,在中国和世界都具有重要的科研和药用价值。本研究采用HO&#183;清除及对肝微粒体和亚油酸脂质过氧化抑制的方法,测定五种草药精油和水煮提取物的抗氧化活性;采用Folin—Ciocalteu试剂法测定它们的总酚含量;用肝细胞体外培养法测定它们的细胞毒性并对它们的作用机制进行分析。结果发现五种草药提取物都具有一定的抗氧化活性,尤其是益母草、野甘草、银杏叶的水煮提取物活性较强,其抗氧化活性与总酚含量存在较好的线形关系。此外,本论文还为研究这些草药的一些抗病机制提供参考依据。     

Isolation and Characterization of a Putative Class E Gene from Taihangia rupestris

Studies In model plants showed that SEPALLATA （SEP） genes are required for the Identification of floral organs and the determination of floral meristems In Arabidopsis. In this paper a SEP homolog, TrSEP3, was Isolated from a China-specific species, Taihangla rupestrisi Yü et LI. Phylogenetlc analysis showed that the gene belongs to the SEP3-clade of SEP （previous AGL2） subfamily. In situ hybridization was used to reveal the potential functional specification, and the results showed that TrSEP3 expression was first observed in floral meristems and then confined to the floral primordla of the three inner whorls. In the matured flower, TrSEP3 was strongly expressed In the tips of pistils and weak In stamens and petals. The evolution force analysis shows that TrSEP3 might undergo a relaxed negative selection. These results suggested that TrSEP3 may not only function In determining the identity of floral merlstems and the primordia of three inner whorls, but also function In matured reproductive organs.     

Proteomic Characterization of Colorectal Cancer Tissue from Patients Identifies Novel Putative Protein Biomarkers

Colorectal cancer (CRC) is one of the leading causes of cancer-related death over the world. There is a great need for biomarkers capable of early detection and as targets for treatment. Differential protein expression was investigated with two-dimensional gel electrophoresis (2D-PAGE) followed by identification with liquid chromatography–tandem mass spectrometry (LC-MS/MS) in CRC patient tissue from (i) the peripheral part of the tumor, (ii) the central part of the tumor as well as from (iii) a non-involved part of the colorectal tissue. The expression patterns of six identified proteins were further evaluated by one-dimensional Western blot (1D-WB) analysis of the CRC tissue. Proteins that were perturbed in expression level in the peripheral or in the central part of the tumor as compared with the non-involved part included S100A11, HNRNPF, HNRNPH1 or HNRNPH2, GSTP1, PKM and FABP1. These identified markers may have future diagnostic potential or may be novel treatment targets after further evaluation in larger patient cohorts.