bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Weeder for the Discovery of Conserved Transcription Factor Binding Sites
Authors: Pavesi Giulio , Pesole Graziano 
Published: September 2006

AbstractOne of the greatest challenges facing modern molecular biology is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of motifs involved in the regulation of gene expression at transcriptional and post‐transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors with their corresponding binding sites. Weeder is a software package freely available for noncommercial users as a stand‐alone or Web‐based application for the automatic discovery of conserved motifs in a set of related DNA sequences from coregulated genes. The motifs found are likely to represent instances of binding sites for some common transcription factor regulating the genes of the set. The program has been designed to make its usage as simple as possible and to require very little prior knowledge about the length and conservation of the motifs to be found.
An Introduction to Modeling Structure from Sequence
Authors: Petsko Gregory A. 
Published: September 2006

AbstractThe underlying premise behind all attempts to determine a large number of diverse protein structures is that the total number of protein domain folds is much smaller, by many orders of magnitude, than the total number of sequences; in other words, many sequences adopt essentially the same fold. If the fold of a protein could be recognized from sequence information alone, then a complete database of all possible folds would allow the structure corresponding to any sequence to be modeled. The growth of structure determination has turned most biochemists and biologists into consumers of structural information. As the demand for such information continues to outstrip the supply, all aspects of structure modeling assume increasing importance. This unit provides an introduction to modeling structure from its sequence and surveys the currently available methods described in the subsequent units of this chapter.
Getting a Tree Fast: Neighbor Joining, FastME, and Distance‐Based Methods
Authors: Desper Richard , Gascuel Olivier 
Published: September 2006

AbstractNeighbor Joining (NJ), FastME, and other distance‐based programs including BIONJ, WEIGHBOR, and (to some extent) FITCH, are fast methods to build phylogenetic trees. This makes them particularly effective for large‐scale studies or for bootstrap analysis, which require runs on multiple data sets. Like maximum likelihood methods, distance methods are based on a sequence evolution model that is used to estimate the matrix of pairwise evolutionary distances. Computer simulations indicate that the topological accuracy of FastME is best, followed by FITCH, WEIGHBOR, and BIONJ, while NJ is worse. Moreover, FastME is even faster than NJ with large data sets. Best‐distance methods are equivalent to parsimony in most cases, but become more accurate when the molecular clock is strongly violated or in the presence of long (e.g., outgroup) branches. This unit describes how to use distance‐based methods, focusing on NJ (the most popular) and FastME (the most efficient today). It also describes how to estimate evolutionary distances from DNA and proteins, how to perform bootstrap analysis, and how to use CLUSTAL to compute both a sequence alignment and a phylogenetic tree.
Using MSDchem to Search the PDB Ligand Dictionary
Authors: Dimitropoulos Dimitris , Ionides John , Henrick Kim 
Published: September 2006

AbstractThe PDB ligand dictionary is the chemical reference database of all the small building block molecules (e.g., amino acids, nucleic acids, and bound ligands) in the Protein Data Bank (PDB) referenced by a distinct three‐letter code identifier. Since PDB files have only three‐dimensional coordinate data, the role of the dictionary that of a reference resource for the actual chemical properties of small molecules, shared consistently across all PDB entries. The ligand dictionary is maintained in all sites of the Worldwide Protein Data Bank (wwPDB), the Research Collaboratory for Structural Bioinformatics (RCSB) in U.S., the Macromolecular Structure Database (MSD) in Europe, and the Protein Data Bank in Japan (PDBj), and it is exchanged on a regular basis. The MSD group at the European BioInformatics Institute (EBI) extends the dictionary into the MSDchem ligand database, which utilizes chemo‐informatics packages and incorporates additional curation work. MSDchem is publicly available on the Web through the MSDchem search system, the functionality of which is described in more detail in this unit.
Murine Models of Streptococcus pyogenes Infection
Authors: Roberts Samantha , Scott June R. , Husmann Linda K. , Zurawski Christine A. 
Published: September 2006

AbstractThis unit describes procedures for testing virulence of Streptococcus pyogenes in mice. S. pyogenes is an important human pathogen and causes one of the most common childhood diseases. The syndromes that result from S. pyogenes infection are diverse, ranging from mild, superficial throat or skin infection to severe, invasive disea/se that is often lethal. Thus, a greater understanding of the virulence factors of this bacterium and development of modalities to prevent or relieve the infections it causes are important. Since S. pyogenes is a strictly human pathogen (with the exception of a single strain), the value of all animal models is limited. This unit describes a model for long‐term throat colonization following the natural route of infection (inhalation), one for pneumonia and systemic dissemination following intratracheal inoculation, and one for systemic dissemination following the more natural route of skin infection. In addition, methods are presented for culturing S. pyogenes from tissues of the infected animal.
A new approach for in vitro regeneration of tomato plants devoid of exogenous plant growth hormones
Authors: Plana Dagmara , Fuentes Alejandro , Alvarez Marta , Lara Regla M. , Alvarez Félix , Pujol Merardo 
Published: September 2006

AbstractMany available methodologies for in vitro regeneration of commercial tomato varieties promote not only the production of normal shoots but also individual leaves, shoots without apical meristems and vitrified structures. All these abnormal formations influence and diminish the regeneration efficiency. At the basis of this phenomenon lies callus development. We optimized an alternative procedure by which the regeneration occurs without abnormal shoot formation. The portion including the proximal part of hypocotyls and the radicle was cultured on medium consisting of Murashige and Skoog salts, 4 mg/L thiamine, 100 mg/L mio‐inositol and 3% sucrose. After two‐three weeks, 60% explants showed adventitious shoot formation. No changes in the morphological characteristics of regenerated plants and fruits were observed as compared with parents. Karyotypic analysis of regenerated plants showed no variations in chromosome number. The optimized procedure offers the advantage of tomato plant regeneration avoiding callus formation, which enables normal plant recovery with an efficiency ranging from 1.45 ± 0.05 to 2.57 ± 0.06 shoots per explant in Campbell‐28, Amalia, Lignon, and Floradel cultivars.
New insights into mechanisms of growth and β‐carotene production in Blakeslea trispora
Authors: Böhme Karen , Richter Christin , Pätz Reinhard 
Published: September 2006

AbstractBlakeslea trispora (Mucorales) has economic importance because of its ability to produce large amounts of β‐carotene. To shed light on the actual point of induction and to shorten the following production process, germination and growth of its two mating types, (–) and (+), were observed separately, and the mating point was investigated in lab scale experiments. The (–) mating type showed much faster germination than the (+) type on solid medium and in Erlenmeyer flasks. However, after a first period, the (–) mating type grew clearly slower than the (+) type. In addition, the (–) type branched more vividly than the (+) type. A ratio of 30:1 of (–) and (+) type at an age of 20 h was found to achieve highest β‐carotene yields. Our results provide a comprehensive overview of Blakeslea trispora growth and its product synthesis.
Expression of green fluorescent protein in pollen of oilseed rape (Brassica napus L.) and its utility for assessing pollen movement in the field
Authors: Moon Hong S. , Halfhill Matthew D. , Hudson Laura C. , Millwood Reginald J. , Stewart C. Neal 
Published: September 2006

AbstractTransgene movement via pollen is an important component of gene flow from transgenic plants. Here, we present proof‐of‐concept studies that demonstrate the monitoring of short distant movement of pollen expressing a genetically encoded fluorescent tag in oilseed rape (Brassica napus L. cv. Westar). Transgenic oilseed rape plants were produced using Agrobacterium‐mediated transformation method with the pBINDC1 construct containing a green fluorescent protein (GFP) variant, mGFP5‐ER, under the control of the pollen‐specific LAT59 promoter from tomato. Transgenic pollen was differentiated from non‐transgenic pollen in vivo by a unique spectral signature, and was shown to be an effective tool to monitor pollen movement in the greenhouse and field. GFP‐tagged pollen also served as a practical marker to determine the zygosity of plants. In a greenhouse pollen flow study, more pollen was captured at closer distances from the source plant plot with consistent wind generated by a fan. Under field conditions, GFP transgenic pollen grains were detected up to a distance of 15 m, the farthest distance from source plants assayed. GFP‐tagged pollen was easily distinguishable from non‐transgenic pollen using an epifluorescence microscope.
Evaluation of anti‐methicillin‐resistant Staphylococcus aureus (MRSA) activity and synergy of some bioactive plant extracts
Authors: Aqil Farrukh , Ahmad Iqbal , Owais Mohd 
Published: September 2006

AbstractAnti‐methicillin‐resistant Staphylococcus aureus (MRSA) activity of ethanolic extracts of four medicinal plants namely Acorus calamus (rhizome) Hemidesmus indicus (stem), Holarrhena antidysenterica (bark), and Plumbago zeylanica (root), were detected with inhibition zone size ranged from 11 to 44 mm and minimum inhibitory concentration (MIC) varied from 0.32 to 3.25 mg/mL. Further, ethyl acetate, acetone and methanol fractions of above plants demonstrated antibacterial activity. The potency of these fractions based on zone of inhibition and MIC value was relatively higher in P. zeylanica (ethylacetate fraction), followed by acetone fractions of H. indicus, A. calamus, and H. antidysenterica. Time kill assay with most promising fractions of these plant extracts, demonstrated concentration‐dependent killing of MRSA within 9–12 h of incubation. Interestingly, synergistic interaction among alcoholic extracts and some fractions of above four plants was evident against MRSA. Further, synergistic interaction of these extracts was detected with one or more antibiotics tested (tetracycline, chloramphenicol, ciprofloxacin, cefuroxime and ceftidizime). The findings also validate the traditional uses of above plants against infectious diseases. Phytochemical studies demonstrated flavonoids and phenols as major active constituents. Further investigations are needed to characterize the active principle and its interaction mechanism with antibiotics.
XVSAP1 from Xerophyta viscosa improves osmotic‐, salinity‐ and high‐temperature‐stress tolerance in Arabidopsis
Authors: Garwe Dahlia , Thomson Jennifer A. , Mundree Sagadevan G. 
Published: September 2006

AbstractXVSAP1, a gene isolated from a dehydrated Xerophyta viscosa cDNA library, was transformed into Arabidopsis thaliana by Ti plasmid‐mediated transformation under the control of a cauliflower mosaic virus 35S promoter, a nos terminator and bar gene selection. Expression of XVSAP1 in Arabidopsis led to constitutive accumulation of the corresponding protein in the leaves. Transgenic Arabidopsis grown in tissue culture maintained higher growth rates during osmotic, high‐salinity and high temperature stress, respectively. Non‐transgenic plants had shorter roots, leaf expansion was inhibited and leaves were more chlorotic than those of the transgenic plants. This study demonstrates that XVSAP1 has a significant impact on dehydration, salinity and high‐temperature stress tolerance in Arabidopsis.
Use of virus vectors for the expression in plants of active full‐length and single chain anti‐coronavirus antibodies
Authors: Alamillo Josefa M. , Monger Wendy , Sola Isabel , García Beatriz , Perrin Yolande , Bestagno Marco , Burrone Oscar R. , Sabella Patricia , Plana‐Durán Joan , Enjuanes Luis , Lomonossoff George P. , García Juan A. 
Published: September 2006

AbstractTo extend the potential of antibodies and their derivatives to provide passive protection against enteric infections when supplied orally in crude plant extracts, we have expressed both a small immune protein (SIP) and a full‐length antibody in plants using two different plant virus vectors based on potato virus X (PVX) and cowpea mosaic virus (CPMV). The agr;SIP molecule consisted of a single chain antibody (scFv) specific for the porcine coronavirus, transmissible gastroenteritis virus (TGEV) linked to the α‐CH3 domain from human IgA. To express the full‐length IgA, the individual light and heavy chains from the TGEV‐specific mAb 6A.C3 were inserted into separate PVX constructs and plants were co‐infected with both constructs. Western blot analysis revealed the efficient expression of both the SIP and IgA molecules. Analysis of crude plant extracts revealed that both the plant‐expressed αSIP and IgA molecules could bind to and neutralize TGEV in tissue culture, indicating that active molecules were produced. Oral administration of crude extracts from antibody‐expressing plant tissue to 2‐day‐old piglets showed that both the αSIP and full‐length IgA molecules can provide in vivo protection against TGEV.
Production of biopharmaceuticals and vaccines in plants via the chloroplast genome
Authors: Daniell Henry 
Published: September 2006

AbstractTransgenic plants offer many advantages, including low cost of production (by elimination of fermenters), storage and transportation; heat stability; and absence of human pathogens. When therapeutic proteins are orally delivered, plant cells protect antigens in the stomach through bioencapsulation and eliminate the need for expensive purification and sterile injections, in addition to development of both systemic and mucosal immunity. Chloroplast genetic engineering offers several advantages, including high levels of transgene expression, transgene containment via maternal inheritance and multi‐gene expression in a single transformation event. Hyper‐expression of vaccine antigens against cholera, tetanus, anthrax, plague or canine parvovirus (4–31% of total soluble protein, tsp) in transgenic chloroplasts (leaves) or non‐green plastids (carrots, tomato), as well as the availability of antibiotic‐free selectable markers or the ability to excise selectable marker genes, facilitate oral delivery. Hyper‐expression of several therapeutic proteins, including human serum albumin (11.1% tsp), somatotropin (7% tsp), interferon‐gamma (6% tsp), anti‐microbial peptide (21.5% tsp), facilitates efficient and economic purification. Also, the presence of chaperones and enzymes in chloroplasts facilitate assembly of complex multi‐subunit proteins and correct folding of human blood proteins with proper disulfide bonds. Functionality of chloroplast‐derived vaccine antigens and therapeutic proteins has been demonstrated by several assays, including the macrophage lysis assay, GM1‐ganglioside binding assay, protection of HeLa cells or human lung carcinoma cells against encephalomyocarditis virus, systemic immune response, protection against pathogen challenge, and growth or inhibition of cell cultures. Thus, transgenic chloroplasts are ideal bioreactors for production of functional human and animal therapeutic proteins in an environmentally friendly manner.
Protein‐free transfection of CHO host cells with an IgG‐fusion protein: Selection and characterization of stable high producers and comparison to conventionally transfected clones
Authors: Lattenmayer Christine , Loeschel Martina , Schriebl Kornelia , Steinfellner Willibald , Sterovsky Thomas , Trummer Evelyn , Vorauer‐Uhl Karola , Müller Dethardt , Katinger Hermann , Kunert Renate 
Published: September 2006

AbstractIn order to improve the current techniques of cell cultivation in the absence of serum, we have developed a protein‐free transfection protocol for CHO cells, based on the Nucleofector™ technology. After starting with a heterogeneous pool of primary transfectants which express the fusion protein EpoFc, we isolated single clones and compared them with parallel clones generated by lipofection in serum‐dependent cultivation. Our intensive characterization program was based on determination of specific productivity (qp) and analysis of genetic parameters. In two nucleofection experiments, transfection with 5 µg of DNA resulted in best productivities of the primary cell pools. After subcloning, the qp could be raised up to 27 pg · cells−1 · day−1. While the serum‐dependent transfectants exhibited specific productivities up to 57 pg · cells−1 · day−1 in serum‐dependent cultivation, a significant decrease that resulted in the range of qp of the protein‐free transfectants was observed after switching to protein‐free conditions. Investigation of genetic parameters revealed higher mRNA levels and gene copy numbers (GCN) for the protein‐free adapted serum‐dependent transfectants. Therefore, we assume that problems during protein‐free adaptation (PFA) lead to a less efficient translation machinery after serum deprivation. We describe the generation of stable‐producing recombinant CHO clones by protein‐free transfection of a protein‐free adapted host cell line, which reduces the risk of adverse clonal changes after PFA. The main advantage of this approach is the earlier predictability of clone behavior, which makes the generation of production clones by protein‐free transfection, a viable and highly efficient strategy for recombinant cell line development. Biotechnol. Bioeng. 2007;96:1118–1126. © 2006 Wiley Periodicals, Inc.
Sialic acid and oxidizability of lipid and proteins and antioxidant status in patients with coronary artery disease
Authors: Serdar Zehra , Yeşilbursa Dilek , Dirican Melahat , Sarandöl Emre , Serdar Akın 
Published: September 2006

AbstractThe aim of this study was to investigate the possible relationship between serum total sialic acid (TSA) concentration, recently shown to be a cardiovascular risk factor, and lipid and protein oxidation and antioxidant status and the severity of coronary artery disease (CAD) according to the obstructive vessel number in patients. The study was carried out on a total of 200 patients (142 men and 58 women) who were hospitalized for elective coronary angiographic evaluation with complaint of typical angina pectoris. According to the results of angiography, 150 patients had angiographically proven CAD (CAD group) and 50 patients had a history suggestive of angina pectoris but normal coronary angiograms (control group). The CAD group was further divided into single‐, double‐ and triple‐vessel disease groups according to the number of vessels involved. Lipid parameters were determined by routine laboratory methods. Plasma malondialdehyde (MDA) and vitamin E concentrations were determined by high‐performance liquid chromatography. TSA and other oxidant and antioxidant parameters were studied spectrophotometrically. Our results demonstrated significant increases both in TSA levels and in indicators of oxidative stress in the patients with CAD compared with the controls. However, antioxidant parameters were decreased in the patients with CAD. We found strong positive correlations between TSA and plasma MDA, Δ‐MDA which represents the degree of oxidative modification of apolipoprotein B‐containing lipoproteins, serum protein carbonyls and apolipoprotein B and weak correlations between TSA and low density lipoprotein cholesterol, triacylglycerol, paraoxonase, glutathione peroxidase (GPx), vitamin C and vitamin E. In conclusion, TSA is related to markers of lipid and protein oxidation, paraoxonase and GPx activities, vitamin C and E levels and the severity of CAD. Copyright © 2006 John Wiley & Sons, Ltd.
Modulation of Unconventional Fluorescence of Novel Photochromic Perimidine Spirodimers
Authors: Davis Riju , Tamaoki Nobuyuki 
Published: September 2006

AbstractFluorescence modulation by a class of photochromic perimidine spirodimers, which exhibit a characteristic fluorescence associated with their photochromic reactions, has been described. Upon irradiation using 365 nm light, these non‐fluorescent spiro molecules undergo a thermally‐reversible ring opening at their spiro junction resulting in the generation of strong fluorescence. The fluorescing species is distinctly different from both the stable ring‐closed and the ring‐opened compounds, though it appears to have been formed from and remains in equilibrium with the photochemically generated ring‐opened form. While the fluorescing species possesses a narrow absorption band with its maximum centered at 500 nm, the ring‐opened form exhibits a broad absorption across the visible region with two maxima centered at 410 and 650 nm, respectively. After initiating the photochromic reactions in these molecules using 365 nm light, purely photochemically‐controlled fluorescence modulation can be carried out using two wavelengths in the visible region, that is, 500 and 700 nm, while the equilibrium concentration of the ring‐opened form and the fluorescing species is controlled. Fluorescence modulation is attained also by controlling the ratio of the ring‐closed and ring‐opened forms by photochemical ring‐opening and thermal ring‐closing reactions. The study on the effect of substitution of these molecules suggests that by extending the conjugation of the perimidine core in the ring‐opened form the molecule is rendered non‐fluorescent and hence it can be assumed that the perimidine core forms the fluorescing entity of the molecule.
Synthesis of the First Chiral Bidendate Bis(trifluoromethyl)phosphane Ligand through Stabilization of the Bis(trifluoromethyl)phosphanide Anion in the Presence of Acetone
Authors: Hoge Berthold , Thösen Christoph , Pantenburg Ingo 
Published: September 2006

AbstractLewis acid/Lewis base adduct formation of the P(CF3)2− ion and acetone leads to a reduced negative hyperconjugation and, therefore, limits the CF bond activation. The resulting increased thermal stability of the P(CF3)2− ion in the presence of acetone allows selective substitutions and enables the synthesis of the first example of a chiral, bidentate bis(trifluoromethyl)phosphane ligand: a DIOP derivative, [(2,2‐dimethyl‐1,3‐dioxolane‐4,5‐diyl)bis(methylene)]bis(diphenylphosphane), in which the phenyl groups at the phosphorus atoms are replaced by strong electron‐withdrawing trifluoromethyl groups. The resulting high electron‐acceptor strength of the synthesized bidentate (CF3)2P ligand is demonstrated by a structural and vibrational study of the corresponding tetracarbonyl–molybdenum complex. The stabilization of the P(CF3)2− ion in the presence of acetone is based on the formation of a dynamic Lewis acid/Lewis base couple, (CF3)2PC(CH3)2O−. Although there is no spectroscopic evidence for the formation of the formulated alcoholate ion, the intermediate formation of (CF3)2PC(CH3)2O− could be proved through the reaction with (CF3)2PP(CF3)2, which yields the novel phosphane–phosphinite ligand (CF3)2PC(CH3)2OP(CF3)2. This ligand readily forms square‐planar Pt(II) complexes upon treatment with solid PtCl2.