Helical preferences of alanine,glycine, and aminoisobutyric homopeptides

The stability between helical conformations of homopeptides of alanine, glycine, and aminoisobutyric acid has been studied by means of quantum-mechanical methods. The influence of peptide length on the relative stability between helical conformations has also been analyzed by means of systematic studies for peptides of size up to 11 residues. Finally, the influence of the solvent has been examined by using self-consistent reaction field methods. The results provide a detailed picture of the modulation exerted by these factors on the helical preferences of these peptides. © 1997 Wiley-Liss Inc.     

Identification of 5 β-cholestane-3 α, 7 α, 12 α, 25, 26-pentol in cerebrotendinous xanthomatosis

An unrecognized pentahydroxy bile alcohol has been isolated from the bile and feces of patients with cerebrotendinous xanthomatosis (CTX). Its structure, 5 β-cholestane-3 α, 7 α, 12 α, 25, 26-pentol has been deduced by spectroscopic methods and confirmed by comparison with a synthetic analog.     

Research with animals: requirement, responsibility, welfare

Recognition of unacceptable cruelty to animals in pasttimes such as bull-baiting, dates in Britain from the early 19th century. The Society for the Prevention of Cruelty to Animals was founded in 1824. Several bills to curb cruelty were discussed in Parliament, and the Cruel and Improper Treatment of Cattle Act was passed in 1822. Other Acts have followed over the years. Cruelty in the form of painful scientific experiments, including dissection of living, conscious animals, vivisection, was proscribed by the Cruelty to Animals Act 1876. That Act required anyone wishing to experiment with animals to obtain a licence from the Secretary of State. Conditions for issue of licences were strict and remain so to this day. The Act is still valid, and is enforced by the Home Office, with its medical and veterinary Inspectors. The Cruelty to Animals Act 1876 allows experiments on animals under strictly controlled conditions. Experiments must have the clear objective of improving the welfare of man and/or animals. Benefits from experiments carried out under the Act have been enormous, covering every aspect of diagnosis, treatment, and prophylaxis in human and veterinary medicine. Coincidentally, the welfare of laboratory animals has also been greatly improved. There has always been some opposition to the use of animals in biomedical research. The subject is emotive but, by and large, discussion has been rational and within the law. In recent years, however, the morality of using experimental animals has been examined more closely. The possibility of replacing them by alternative methods has been investigated. Where these alternatives are applicable, they are used and further research on them continues. The questioning of animal experiments has emphasized the need to look constantly at animal welfare to ensure humane treatment of all animals, especially those restricted in a laboratory or on a farm. Attention has been drawn in this work to our existing laws protecting animals, but new legislation is being demanded, not only by some lay welfare groups but also by scientists. Hence, it has become very important to discuss various ways of ensuring animal welfare, including by legislation, especially with those knowledgeable in laboratory animal science and animal experiments.(ABSTRACT TRUNCATED AT 400 WORDS)     

Azotobacter vinelandii ferredoxin I: cloning, sequencing, and mutant analysis

The structure of Azotobacter vinelandii ferredoxin I (AvFdI) has been extensively characterized by a variety of techniques. Although its physiological function is unknown, it has long been implicated as being involved in electron donation to nitrogenase. Here we report that the AvFdI gene (fdxA) has been cloned from an EcoRI digest lambda library using a synthetic oligonucleotide probe and that its sequence has been determined. The amino acid sequence deduced from the DNA sequence is identical to the previously published protein sequence. Analysis of the promoter region indicates that AvFdI is not a nif specific gene product. A mutant of A. vinelandii has been constructed which is identical to the wild-type, at the DNA level, except that the fdxA gene has been interrupted by insertion of a kanamycin cartridge. This mutant, called LM100, does not synthesize AvFdI but does synthesize the Fe and MoFe proteins of nitrogenase and grows at wild-type rates under N2-fixing conditions. This demonstrates that AvFdI is not required for N2 fixation by A. vinelandii. There is a small acidic protein, which is present in wild-type A. vinelandii, whose level is dramatically increased in LM100. The nature of this protein is under further investigation.     

Mechanistic aspects in the biogenic synthesis of extracellular metal nanoparticles by peptides,bacteria, fungi,and plants

Metal nanoparticles have been studied and applied in many areas including the biomedical, agricultural, electronic fields, etc. Several products of colloidal silver are already on the market. Research on new, eco-friendly and cheaper methods has been initiated. Biological production of metal nanoparticles has been studied by many researchers due to the convenience of the method that produces small particles stabilized by protein. However, the mechanism involved in this production has not yet been elucidated although hypothetical mechanisms have been proposed in the literature. Thus, this review discusses the various mechanisms provided for the biological synthesis of metal nanoparticles by peptides, bacteria, fungi, and plants. One thing that is clear is that the mechanistic aspects in some of the biological systems need more detailed studies.     

Retraction: SODD promotes glucose uptake of colorectal cancer cells via AKT pathway by Rui Zhang,Jibin Li,Xiaofei Yan,Keer Jin,Wenya Li,Jian Xu,Jian Zhao,Jinghui Bai,Xiaohui Su

The above article, published online on 31 October 2017 in Wiley Online Library ( https://doi.org/10.1002/cbin.10907 ), has been withdrawn by agreement with the journal Editor, Sergio Schenkman, and John Wiley & Sons Ltd. The withdrawal has been agreed because the authors have not provided a signed Copyright Transfer Agreement.     

Differences in structure, physiological stability, electrochemistry, cytotoxicity, DNA and protein binding properties between two Ru(III) complexes

A novel Ru(III) complex, mer-[RuCl(3)(CH(3)CN)(dpq)] (1), has been synthesized and characterized by X-ray diffraction, where dpq=dipyrido[3,2-d:2',3'-f]quinoxaline. Its chemical and biological properties have been intensively compared with those of mer-[RuCl(3)(DMSO)(dpq)] (DMSO=dimethyl sulfoxide) (2). It has been found that the stability in buffered solutions and the reduction potential for the Ru(III)/Ru(II) couple can be modulated by changing the small molecule bonded to the Ru(III) center. Interactions of 1 with DNA have been investigated by DNA melting experiments, DNA competitive binding with EB (ethidium bromide), plasmid DNA cleavage experiments and viscosity measurements. The interaction of 1 and 2 with BSA (bovine serum albumin) has also been studied using fluorescent quenching method. The experimental results show that 1 exerts higher affinity towards DNA and BSA than 2 does. The cytotoxicity of 1 has been evaluated by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) method, and 2 shows slightly higher anticancer potency than 1 does against all the cell lines screened. Attempts are made to clarify the possible antitumor mechanisms of these two complexes by analyzing the experimental results presented.     

Diabetes, metallothionein, and zinc interactions: a review

Epidemiological evidence, associating diabetes with zinc (Zn) deficiencies, has resulted in numerous research studies describing the effects of Zn and associated metallothionein (MT), on reducing diabetic complications associated with oxidative stress. MT has been found to have a profound effect on the reduction of oxidative stress induced by the diabetic condition. Over expression of MT in various metabolic organs has also been shown to reduce hyperglycaemia-induced oxidative stress, organ specific diabetic complications, and DNA damage in diabetic experimental animals, which have been further substantiated by the results from MT-knockout mice. Additionally, supplementation with Zn has been shown to induce in vivo MT synthesis in experimental animals and to reduce diabetes related complications in both humans and animal models. Although the results are promising, some caution regarding this topic is however necessary, due to the fact that the majority of the studies done have been animal based. Hence more human intervention trials are needed regarding the positive effects of MT and Zn before firm conclusions can be made regarding their use in the treatment of diabetes.     

Ethnobotany and phytochemistry of yarrow,Achillea millefolium,compositae

The data reported in the literature concerning the uses and composition of yarrow,Achillea millefolium aggr., Compositae, are compiled and discussed. Historically, this plant has been extensively used as a herbal remedy for numerous afflictions by many cultures on several continents. It has also been the subject of a considerable number of scientific investigations. It has, however, not been previously reviewed. Analysis of available information demonstrates the value of continued phytochemical investigations of folklore remedies.     

3D domain swapping, protein oligomerization, and amyloid formation

In 3D domain swapping, first described by Eisenberg, a structural element of a monomeric protein is replaced by the same element from another subunit. This process requires partial unfolding of the closed monomers that is then followed by adhesion and reconstruction of the original fold but from elements contributed by different subunits. If the interactions are reciprocal, a closed-ended dimer will be formed, but the same phenomenon has been suggested as a mechanism for the formation of open-ended polymers as well, such as those believed to exist in amyloid fibrils. There has been a rapid progress in the study of 3D domain swapping. Oligomers higher than dimers have been found, the monomer-dimer equilibrium could be controlled by mutations in the hinge element of the chain, a single protein has been shown to form more than one domain-swapped structure, and recently, the possibility of simultaneous exchange of two structural domains by a single molecule has been demonstrated. This last discovery has an important bearing on the possibility that 3D domain swapping might be indeed an amyloidogenic mechanism. Along the same lines is the discovery that a protein of proven amyloidogenic properties, human cystatin C, is capable of 3D domain swapping that leads to oligomerization. The structure of domain-swapped human cystatin C dimers explains why a naturally occurring mutant of this protein has a much higher propensity for aggregation, and also suggests how this same mechanism of 3D domain swapping could lead to an open-ended polymer that would be consistent with the cross-beta structure, which is believed to be at the heart of the molecular architecture of amyloid fibrils.     

Staphylococcal enterotoxin type E: isolation, purification, identification

Homogeneous protein of staphylococcal enterotoxin type E has been isolated. The technique of isolation, permitting 48% yield of active material, includes concentration by ammonium sulfate precipitation, ion exchange chromatography on DEAE-cellulose and gel-filtration on sephacryl S-200. The molecular mass of the isolated protein is 32 Kd. Antigenic affinity of staphylococcal toxins types A and E has been established by immunochemical analysis.     

Identification of prodrug,active drug,and metabolites in an ADEPT clinical study

Antibody-directed enzyme prodrug therapy (ADEPT) involves two phases. The first is an antibody-enzyme conjugate that localizes to tumor. The second phase is a prodrug that is administered when the enzyme-conjugate has cleared from blood and other nontumor tissues. In the pilot-scale clinical trial, the prodrug has been measured—in the plasma of patients, by liquid chromatography (HPLC) and by liquid chromatography-mass spectrometry (LC-MS). Active drug has been detected and metabolites identified. An indirect measurement of enzyme-conjugate in the plasma of patients has also been developed.     

Studies of reversible inhibition,irreversible inhibition,and activation of alkaline phosphatase by capillary electrophoresis

Reversible inhibition, irreversible inhibition, and activation of calf intestinal alkaline phosphatase (EC 3.1.3.1) have been studied by capillary electrophoresis. The capillary electrophoretic enzyme-inhibitor assays were based on electrophoretic mixing of inhibitor and enzyme zones in a substrate-filled capillary. Enzyme inhibition was indicated by a decrease in product formation detected in the capillary by laser-induced fluorescence. Reversible enzyme inhibitors could be quantified by Michaelis-Menten treatment of the electrophoretic data. Reversible, competitive inhibition of alkaline phosphatase by sodium vanadate and sodium arsenate has been examined, and reversible, noncompetitive inhibition by theophylline has been studied. The K(i) values determined for these reversible inhibitors using capillary electrophoresis are within the range of values reported in the literature for the same enzyme-inhibitor combinations. Irreversible inhibition of alkaline phosphatase by EDTA at concentrations of 1.0mM and above has been observed. Activation of alkaline phosphatase has also been observed for EDTA at concentrations from 20 to 400 microM.     

1, 4-alpha-Glucan phosphorylase from Klebsiella pneumoniae purification, subunit structure and amino acid composition.

1. A 1,4-alpha-glucan phosphorylase from Klebsiella pneumoniae has been purified about 80-fold with an over-all yield greater than 35%. The purified enzyme has been shown to be homogeneous by gel electrophoresis at different pH-values, by isoelectric focusing, by dodecylsulfate electrophoresis and by ultracentrifugation. 2. The molecular weight of the native enzyme has been determined to be 180 000 by ultra-centrifugation studies, in good agreement with the value of 189 000 estimated by gel permeation chromatography. 3. The enzyme dissociates in the presence of 0.1% dodecylsulfate or 5 M guanidine hydrochloride into polypeptide chains. The molecular weight of these polypeptide chains has been found to be 88 000 by dodecylsulfate polyacrylamide gel electrophoresis and 99 000 by sedimentation equilibrium studies, indicating that the native enzyme is composed of two polypeptide chains. 4. The enzyme contains pyridoxalphosphate with a stoichiometry of two moles per 180 000 g protein, confirming that the 1,4-alpha-glucan phosphorylase from Klebsiella pneumoniae is a dimeric enzyme. 5. The amino acid composition of the enzyme has been determined, and its correspondence to that of 1,4-alpha-glucan phosphorylases from other sources is discussed. 6. The pI of the enzyme has been shown to be 5.3 and its pH-optimum to be about pH 5.9. The enzyme is stable in the range from pH 5.9 to 10.5.     

Cloning, expression, purification, and characterization of Leishmania major dihydroorotate dehydrogenase

Leishmania major Friedlin (LmjF) is a protozoan parasite whose genomic sequence has been recently elucidated. Here we have cloned, overexpressed, purified, and characterized the product of the gene from LmjF chromosome 16: LmjF16.0530, which encodes a protein with putative dihydroorotate dehydrogenase activity. Dihydroorotate dehydrogenase (DHODH) is a flavoprotein that catalyses the oxidation of L-dihydroorotate to orotate, the fourth sequential step in the de novo pyrimidine nucleotide synthesis pathway. The predicted enzyme from L. major was cloned and expressed in Escherichia coli strain BL21(DE3) as a histidine-tag fusion protein and purified to homogeneity using affinity chromatography. The final product was homogeneous in SDS-PAGE gel electrophoresis. The dihydroorotate oxidase activity has been assayed and the steady-state kinetic mechanism has been determined using fumarate as the oxidizing substrate. The catalysis by LmDHODH enzyme proceeds by a Ping-Pong Bi-Bi mechanism and the kinetic parameters Km were calculated to be 90 and 418 microM for dihydroorotate and fumarate, respectively, and Vmax was calculated to be 11 micromol min-1 mg-1. Our results confirmed that the product of the gene LmjF16.0530, whose function has previously been predicted based on homology to known proteins, can therefore be positively assigned as L. major DHODH.     

Pattern cladism, homology, and theory-neutrality

Pattern cladists purport to classify biological taxa in a way that is theory-neutral. The idea of a theory-neutral science is, however, philosophically problematic; and, while pattern cladists' commitment to theory-neutrality has been subject to scrutiny by both phylogenetic cladists and some philosophers, virtually no attention has been paid to the core issue of whether observation of patterns in nature is a means to theory-neutrality. This essay critically examines pattern cladists' claim to construct a theory-neutral cladistic taxonomy by relying on observation. Special attention is paid to the observations of patterns involving homologous traits.     

Cloning of tlrD, a fourth resistance gene, from the tylosin producer, Streptomyces fradiae

In addition to tlrA, tlrB and tlrC, which were previously cloned by others, a fourth antibiotic-resistance gene (tlrD) has been isolated from Streptomyces fradiae, a producer of tylosin (Ty), and cloned in Streptomyces lividans. Like tlrA, tlrD encodes an enzyme that methylates the N6-amino group of the A2058 nucleoside within 23S ribosomal RNA. However, whereas the tlrA protein dimethylates that nucleoside, the tlrD product generates N6-monomethyladenosine. The genes also differ in their mode of expression: tlrA is inducible, whereas tlrD is apparently expressed constitutively, and it has been confirmed that the tlrA-encoded enzyme can add a second methyl group to 23S rRNA that has already been monomethylated by the tlrD-encoded enzyme. Presumably, that is what happens in S. fradiae.     

Studies of fossil brachiopods of Mongolia: Ordovician,Silurian, Devonian,Carboniferous, and Permian

Fossil brachiopods from the Ordovician, Silurian, Devonian, Carboniferous, and Permian deposits of Mongolia have been studied for the last forty-five years by the Joint Soviet-Mongolian (later RussianMongolian) Paleontological and Geological Expeditions. New data on the taxonomic composition, stratigraphic and geographic distribution of the brachiopod assemblages have been obtained. The brachiopod systematics has been further refined and detailed, and the stratigraphic and correlation scales and biogeographic reconstructions have been elaborated for the Paleozoic of Mongolia.     

The interrelationships of chromosome banding patterns in procyonids, viverrids, and felids.

The Giemsa banding patterns of the chromosomes of 4 species of Procyonidae, 13 of Viverridae, and 6 of Felidae have been studied. The patterns have all been related to the basic felid karyotype. Each procyonid and viverrid has a distinctive karyotype, whereas some felids have indistinguishable karyotypes even when banded. Extensive interfamilial G-banding conservatism has been demonstrated, with many chromosomes being "shared" by all three families. A chromosome identification and karyotyping system for the Carnivora has been devised to facilitate comparison of data from future studies. Phylogenetic implications of the findings have been discussed.     

Thermal behaviour,phase diagram,and spectroscopic properties of rac-indobufen and its enantiomers

The binary phase diagram of the enantiomers of indobufen, 1 (Ibustrin), an antithrombotic drug, has been investigated by differential scanning calorimetry (DSC); 1 is a racemic compound (racemate) with melting point lower than that of the enantiomers. Its thermal behaviour (DSC) has been examined and is discussed in comparison with other physical methods (IR spectroscopy and X-ray powder diffraction). Absolute configuration has been assigned to the enantiomers by ¹H-NMR correlations. © 1995 Wiley-Liss, Inc.