Genome-wide computational analyses of microRNAs and their targets from Canis familiaris

By computational analyses, we identified 357 miRNA candidates from Canis familiaris genome, among which 300 are homology of characterized human miRNAs, the remains are not reported in any other animal. Of the 357 miRNA genes, 142 are organized into 53 clusters, and two clusters locate in the paternally imprinted region. These dog miRNAs may regulate more than 800 possible targets, which are involved in a wide range of cellular processes. Remarkably, miR-186 resides in the eighth intron of its target gene in the same orientation, suggesting a feedback regulation of miRNA on its host gene.     

Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia

Using a combined computational program, we identified 50 potential microRNAs (miRNAs) in Giardia lamblia, one of the most primitive unicellular eukaryotes. These miRNAs are unique to G. lamblia and no homologues have been found in other organisms; miRNAs, currently known in other species, were not found in G. lamblia. This suggests that miRNA biogenesis and miRNA-mediated gene regulation pathway may evolve independently, especially in evolutionarily distant lineages. A majority (43) of the predicted miRNAs are located at one single locus; however, some miRNAs have two or more copies in the genome. Among the 58 miRNA genes, 28 are located in the intergenic regions whereas 30 are present in the anti-sense strands of the protein-coding sequences. Five predicted miRNAs are expressed in G. lamblia trophozoite cells evidenced by expressed sequence tags or RT-PCR. Thirty-seven identified miRNAs may target 50 protein-coding genes, including seven variant-specific surface proteins (VSPs). Our findings provide a clue that miRNA-mediated gene regulation may exist in the early stage of eukaryotic evolution, suggesting that it is an important regulation system ubiquitous in eukaryotes.     

Computational identification of 48 potato microRNAs and their targets

MicroRNAs (miRNAs) are a new family of small RNA molecules known in animals and plants, whose conservation among species suggests that they bear conserved biological functions. So far, little is known about miRNA in Solanum tuberosum species. Using previously known miRNAs from Arabidopsis, rice and other plant species against expressed sequence tags (ESTs), genomic survey sequence (GSS) and nucleotide databases, we identified 48 potential miRNAs in S. tuberosum. These potato miRNAs may regulate 186 potential targets, which are involved in floral, leaf, root, and stem development, signal transduction, metabolism pathways, and stress responses. To validate the prediction of miRNAs in potato, we performed a RT-PCR analysis and found that potato miRNAs have diverse expression patterns during development.     

Immunoliposomes and their targets

Immunoliposomes have been actively studied over the past two decades. However, researcher’s attention has still been limited to intensive preclinical trials and no one immunoliposomal formulation has passed clinical trials. This fact can be explained by a fear of complications, when mouse monoclonal antibodies are used as delivery vehicles. The situation has radically changed over the past few years. Nonimmunogenic single-chain antibodies have become an accessible research tool. Moreover, antibodies can be easily modified and conjugated with liposomes. Therefore, a vigorous breakthrough in the field of development of newgeneration immuno-liposomal formulations for oncological practice can be expected.     

Electrophilic natural products and their biological targets

The study of biologically active natural products has resulted in seminal contributions to our understanding of living systems. In the case of electrophilic natural products, the covalent nature of their interaction has largely facilitated the identification of their biological binding partners. In this review, we provide a comprehensive compilation of electrophilic natural products from all major chemical classes together with their biological targets. Covering Michael acceptor systems, ring-strained compounds and other electrophiles, such as esters or carbamates, we highlight representative and instructive examples for over 20 electrophilic moieties. The fruitful cooperation of natural product chemistry, medicinal chemistry and chemical biology has produced a collection of well-studied examples for how electrophilic natural products exert their biological functions that range from antibiotic to antitumor effects. Special emphasis is put on the elucidation of their respective biological targets via activity-based protein profiling, which together with the recent advancements in mass spectrometry has been crucial to the success of the field. The wealth of naturally occurring electrophilic moieties and their chemical complexity enables binding of a large variety of biological targets, such as enzymes of all classes, nonenzymatic proteins, DNA and other cellular compounds. With approximately 30,000 genes in the human genome but only 266 confirmed protein drug targets, the study of biologically active, electrophilic natural products has the potential to provide insights into fundamental biological processes and to greatly aid the discovery of new drug targets.     

Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis

Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-coding RNA with ability to regulate gene expression by bind the 3′ UTR region of target mRNA and are evolved at different rates in different plant species. In this study we have utilized homology based computational approach and identified 27 mature miRNAs for the first time from this bio-medically important plant. The phylogenetic tree developed from binary data derived from the data on presence/absence of the identified miRNAs were noticed to be uncertain and biased. Most of the identified miRNAs were highly conserved among the plant species and sequence based phylogeny analysis of miRNAs resolved the above difficulties in phylogeny approach using miRNA. Predicted gene targets of the identified miRNAs revealed their importance in regulation of plant developmental process. Reported miRNAs held sequence conservation in mature miRNAs and the detailed phylogeny analysis of pre-miRNA sequences revealed genus specific segregation of clusters.     

In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species

MicroRNAs are a recently identified class of small regulatory RNAs that target more than 30% protein-coding genes. Elevating evidence shows that miRNAs play a critical role in many biological processes, including developmental timing, tissue differentiation, and response to chemical exposure. In this study, we applied a computational approach to analyze expressed sequence tags, and identified 32 miRNAs belonging to 22 miRNA families, in three earthworm species Eisenia fetida, Eisenia andrei, and Lumbricus rubellus. These newly identified earthworm miRNAs possess a difference of 2-4 nucleotides from their homologous counterparts in Caenorhabditis elegans. They also share similar features with other known animal miRNAs, for instance, the nucleotide U being dominant in both mature and pre-miRNA sequences, particularly in the first position of mature miRNA sequences at the 5' end. The newly identified earthworm miRNAs putatively regulate mRNA genes that are involved in many important biological processes and pathways related to development, growth, locomotion, and reproduction as well as response to stresses, particularly oxidative stress. Future efforts will focus on experimental validation of their presence and target mRNA genes to further elucidate their biological functions in earthworms.     

Hydration, charge, size, and shape characteristics of peptides from their CZE analyses

A CZE model is presented for peptide characterization on the basis of well-established physicochemical equations. The effective mobility is used as basic data in the model to estimate relevant peptide properties such as, for instance, hydration, net and total electrical charge numbers, hydrodynamic size and shape, particle average orientation, and pH-microenvironment from the charge regulation phenomenon. Therefore 102 experimental effective mobilities of different peptides are studied and discussed in relation to previous work. An equation for the estimation of peptide hydration as a function of ionizing, polar, and non-polar amino acid residues is included in the model. It is also shown that the shape-orientation factor of peptides may be either lower or higher than one, and its value depends on a complex interplay among total charge number, molar mass, hydration, and amino acid sequence.     

钒化合物的靶点蛋白及其生物效应

作为一种生物相关的金属元素,基于钒的金属化合物在糖尿病、癌症、阿尔茨海默症、神经炎症等疾病的治疗方面表现出独特的潜在应用价值。现阶段研究表明,钒发挥其生物活性主要源于钒酸根作为磷酸根类似物对细胞内磷酸转移反应的影响,及钒在细胞内经氧化还原转化产生的活性氧物质对相关信号通路的调节;而钒化合物与细胞内靶点蛋白的相互作用亦被认为是发挥其治疗作用的关键因素。本文就钒的化学性质、钒化合物与血清蛋白的结合、钒化合物对细胞内效应靶点蛋白及其作用通路的调控、细胞内金属药物靶点蛋白分析鉴定等几方面,对近年来取得的相关研究的进展进行综述,以系统性阐释钒化合物用于疾病治疗的生物活性机制,并对进一步揭示钒化合物作用机理的探索方向及其药用前景进行展望。     

Synthesis of some novel isatin-thiazole conjugates and their computational and biological studies

Structural Chemistry - The present work describes the synthesis of novel 3-[2-(5-phenyl-1,3-thiazol-2-yl)hydrazinyl]-1,3-dihydro-2H-indol-2-one derivatives 4(a-h) and the characterization of...     

A computational study on some viable targets for gas-phase synthesis of metal complexes of the cyclic (B6C)-2 and their bonding pattern

In this account, a detailed computational study is conducted to verify the geometric, energetic, and electronic properties of the planar cyclic (B 6C) (-2) (as the simplest carrier of hexacoordinate carbon) within some metal complexes. The [M(B 6C)] ((-)) (M = Li, Na, K) and [M(B 6C)] (M = Be, Mg, Ca) series are employed for this purpose. Relevant ab initio calculations at both DFT and post-HF levels vividly demonstrate that this dianion is stabilized considerably in the electric field generated by cations, whereas the geometrical and electronic properties of this ring remain almost intact in these complexes. The complementary topological analysis of charge densities confirms that cyclic (B 6C) (-2) within these complexes exhibits the same topological patterns as the naked dianion, thus confirming the presence of an unusual charge density distribution in this dianion. An electrostatic model is proposed that not only qualitatively but also quantitatively explains the observed computational trends in these complexes. This model successfully traces the polarization of the central carbon atom of the ring in the presence of a hard, multiply charged cation. To facilitate experimental detection, the photoelectron spectra of the [M(B 6C)] ((-)) (M = Li, Na, K) series are computed and the dominant features are extracted. Although considered species are not global minima on their potential energy hypersurfaces, their kinetic stabilities are verified and demonstrated unequivocally.     

A simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function

We devise and apply a simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function. These bonding schemes are close to resonance structures drawn by chemists. Firstly, a CASSCF wave function is computed. Secondly, the CASSCF computation is repeated but now the delocalized complete active space MOs are substituted by Weinhold's localized natural atomic orbitals. In this way the original CASSCF wave function is represented by a sequence of Slater determinants composed of localized natural atomic orbitals. Thus, a standard CASSCF wave function can be reinterpreted in terms of a local picture. To test the method we obtain localized bonding schemes and their weights for the ground and the pi-pi* excited state of ethylene. Moreover, bonding schemes and their weights are derived for the ground, the 1(1)B(u), and the 2(1)Ag pi-pi* excited states of trans-butadiene. The large weight bonding schemes are shown to be a qualitative indicator for the known photochemistry of butadiene. The remarkable stability of the Arduengo carbene is discussed by obtaining bonding schemes that indicate a stabilizing delocalization of the pi electrons. We illustrate that the large weight bonding schemes are in line with the observed reactivity of the Arduengo carbene.     

The assembly state between magnetic nanosensors and their targets orchestrates their magnetic relaxation response

The target-induced clustering of magnetic nanoparticles is typically used for the identification of clinically relevant targets and events. A decrease in the water proton transverse NMR relaxation time, or T(2), is observed upon clustering, allowing the sensitive and accurate detection of target molecules. We have discovered a new mechanistically unique nanoparticle-target interaction resulting in a T(2) increase and demonstrate herein that this increase, and its associated r(2) relaxivity decrease, are also observed upon the interaction of the nanoparticles with ligands or molecular entities. Small molecules, proteins, and a 15-bp nucleic acid sequence were chemically conjugated to polyacrylic-acid-coated iron oxide nanoparticles, and all decreased the original nanoparticle r(2) value. Further experiments established that the r(2) decrease was inversely proportional to the number of ligands bound to the nanoparticle and the molecular weight of the bound ligand. Additional experiments revealed that the T(2)-increasing mechanism was kinetically faster than the conventional clustering mechanism. Most importantly, under conditions that result in T(2) increases, as little as 5.3 fmol of Bacillus anthracis plasmid DNA (pX01 and pX02), 8 pmol of the cholera toxin B subunit (Ctb), and even a few cancer cells in blood were detected. Transition from the binding to the clustering mechanism was observed in the carbohydrate-, Ctb-, and DNA-sensing systems, simply by increasing the target concentration significantly above the nanoparticle concentration, or using Ctb in its pentameric form as opposed to its monomer. Collectively, these results demonstrate that the molecular architectures resulting from the interaction between magnetic nanosensors and their targets directly govern water proton NMR relaxation. We attribute the observed T(2) increases to the bound target molecules partially obstructing the diffusion of solvent water molecules through the superparamagnetic iron oxide nanoparticles' outer relaxation spheres. Finally, we anticipate that this novel interaction can be incorporated into new clinical and field detection applications, due to its faster kinetics relative to the conventional nanoparticle-clustering assays.     

Synthesis of hydroxy and methoxy perylene quinones, their spectroscopic and computational characterization, and their antiviral activity

Hydroxy and methoxy perylene quinones are synthesized in an attempt to isolate the essential spectroscopic and biological features of light-induced antiviral agents such as hypericin and hypocrellin. Unlike their naturally occurring counterparts, these synthetic quinones bear the carbonyl, hydroxyl, and methoxy groups in the "bay region." The hydroxy and methoxy compounds have rich absorption spectra with broad features in the visible (approximately 450-800 nm) and relatively more intense and narrow features at wavelengths < or = 350 nm. High-level ab initio quantum mechanical calculations assign the features in the absorption spectra to electronic transitions from S0 to S2 and to higher-lying electronic states. The calculations indicate that in the ground state the trans dihydroxy isomer is 12.5 kcal/mol lower in energy than the cis dihydroxy isomer and is thus the only species present. The lowest-energy trans methoxy ground state isomer and the lowest-energy cis methoxy ground state isomer are found to be degenerate. An additional cis methoxy isomer 6.3 kcal/mol higher in energy than the global minimum is assumed to contribute to the spectrum and is also considered. Finally, the synthetic compounds exhibit similar light-induced antiviral activity to each other, but significantly less than that of hypericin.