bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel strategy for obtaining kanamycin resistance in Arabidopsis thaliana by silencing an endogenous gene encoding a putative chloroplast transporter
Authors: Aufsatz Werner , Nehlin Lilian , Voronin Viktor , Schmidt Agnes , Matzke Antonius J. M. , Matzke Marjori 
Published: February 2009

AbstractThe use of bacterial antibiotic resistance markers in transgenic plants raises concerns about horizontal gene transfer to soil bacteria. We report here that kanamycin resistance in Arabidopsis thaliana can be achieved by silencing an endogenous gene encoding a putative chloroplast transporter, which presumably imports kanamycin into chloroplasts to interfere with ribosomal RNA. Homologs of the transporter exist in other plant species, suggesting this strategy may be generally useful for selecting transformed plant cells.
Cell lysis methods for high‐throughput screening or miniaturized assays
Authors: Lin Zhanglin , Cai Zhen 
Published: February 2009

AbstractThe widely and routinely used cell lysis techniques are still being evolved to address the technical needs of micro‐scale sample processing, for example in high‐throughput screening or miniaturized assays. This review focuses on several recently emerged mechanical, physical and biological methods designed for lysing cells on small scales for screening or analysis.
Emerging trends in plasma‐free manufacturing of recombinant protein therapeutics expressed in mammalian cells
Authors: Grillberger Leopold , Kreil Thomas R. , Nasr Sonia , Reiter Manfred 
Published: February 2009

AbstractMammalian cells are the expression system of choice for therapeutic proteins, especially those requiring complex post‐translational modifications. Traditionally, these cells are grown in medium supplemented with serum and other animal‐ or human‐derived components to support viability and productivity. Such proteins are also typically added as excipients and stabilizers in the final drug formulation. However, the transmission of hepatitis B in the 1970s and of hepatitis C and HIV in the 1980s through plasma‐derived factor VIII concentrates had catastrophic consequences for hemophilia patients. Thus, due to regulatory concerns about the inherent potential for transmission of infectious agents as well as the heterogeneity and lack of reliability of the serum supply, a trend has emerged to eliminate the use of plasma‐derived additives in the production and formulation of recombinant protein therapeutics. This practice began with products used in the treatment of hemophilia and is progressively expanding throughout the entire industry. The plasma‐free method of producing recombinant therapeutics is accomplished by the use of both cell culture media and final product formulations that do not contain animal‐ or human‐derived additives. A number of recombinant therapeutic proteins for the treatment of several different diseases have been produced by plasma‐free processes, with the objective of improving safety by eliminating blood‐borne pathogens or by reducing immunogenicity. This review describes the factors that drove the development of plasma‐free protein therapeutics and provides examples of advances in manufacturing that have made possible the removal of human and animal‐derived products from all steps of recombinant protein production.
Extracting cancer cell line electrochemical parameters at the single cell level using a microfabricated device
Authors: Alqabandi Jassim A. , Abdel‐Motal Ussama M. , Youcef‐Toumi Kamal 
Published: February 2009

AbstractCancer cells have distinctive electrochemical properties. This work sheds light on the system design aspects and key challenges that should be considered when experimentally analyzing and extracting the electrical characteristics of a tumor cell line. In this study, we developed a cellularbased functional microfabricated device using lithography technology. This device was used to investigate the electrochemical parameters of cultured cancer cells at the single‐cell level. Using impedance spectroscopy analyses, we determined the average specific capacitance and resistance of the membrane of the cancer cell line B16‐F10 to be 1.154 ± 0.29 μF/cm2, and 3.9 ± 1.15 KΩ.cm2 (mean ± SEM, n =14 cells), respectively. The consistency of our findings via different trails manifests the legitimacy of our experimental procedure. Furthermore, the data were compared with a proposed constructed analytical‐circuit model. The results of this work may greatly assist researchers in defining an optimal procedure while extracting electrical properties of cancer cells. Detecting electrical signals at the single cell level could lead to the development of novel approaches for analysis of malignant cells in human tissues and biopsies.
Design of metal‐binding sites onto self‐assembled peptide fibrils
Authors: Kasotakis Emmanouil , Mossou Estelle , Adler‐Abramovich Lihi , Mitchell Edward P. , Forsyth V. Trevor , Gazit Ehud , Mitraki Anna 
Published: February 2009

AbstractThe ability to develop a rational basis for the binding of inorganic materials to specific binding sites within self‐assembling biological scaffolds has important applications in nanobiotechnology. Amyloid‐forming peptides are a class of such scaffolds and show enormous potential as templates for the fabrication of low resistance, conducting nanowires. Here we report the use of a self‐assembling peptide building block as scaffold for the systematic introduction of metal‐binding residues at specific locations within the structure. The octapeptide NSGAITIG (Asparagine‐Serine‐Glycine‐Alanine‐Isoleucine‐Threonine‐Isoleucine‐Glycine) from the fiber protein of adenovirus has been identified in previous structural studies as an elementary fibril‐forming building block. Using this building block as a scaffold, we have designed three new cysteine‐containing octa‐peptides to study their eventual fibril‐forming ability and potential templating of metal nanoparticles. We find that the cysteine substitutions do not alter the fibril‐forming potential of the peptides, and that the fibrils formed bind efficiently to silver, gold, and platinum nanoparticles; furthermore, we report unexpected behavior of serine in nucleating gold and platinum nanoparticles. We find that combination of cysteine and serine residues projecting from adjacent sites on a peptide scaffold represents a potentially useful strategy in nucleating inorganic materials. The ability to reliably produce metal‐coated fibrils is a vital first step towards the exploitation of these fibrils as conducting nanowires with applications in nano‐circuitry. Short, biologically inspired self‐assembling peptide scaffolds derived from natural fibrous proteins with known three‐dimensional structure may provide a viable approach towards the rational design of inorganic nanowires. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 164–172, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Peptidic modulators of protein‐protein interactions: Progress and challenges in computational design
Authors: Rubinstein Mor , Niv Masha Y. 
Published: February 2009

AbstractWith the decline in productivity of drug‐development efforts, novel approaches to rational drug design are being introduced and developed. Naturally occurring and synthetic peptides are emerging as novel promising compounds that can specifically and efficiently modulate signaling pathways in vitro and in vivo. We describe sequence‐based approaches that use peptides to mimic proteins in order to inhibit the interaction of the mimicked protein with its partners. We then discuss a structure‐based approach, in which protein‐peptide complex structures are used to rationally design and optimize peptidic inhibitors. We survey flexible peptide docking techniques and discuss current challenges and future directions in the rational design of peptidic inhibitors. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 505–513, 2009.This article was originally published online as an accepted preprint. The “Published Online”date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Trifluoroethanol reveals helical propensity at analogous positions in cytoplasmic domains of three connexins
Authors: Fort Alfredo G. , Spray David C. 
Published: February 2009

AbstractCytoplasmic domains of gap junction proteins (connexins) are involved in channel gating, voltage and pH sensitivity, and contain binding sites for partner proteins. However, their secondary structure is incompletely characterized and comparisons among the connexins is totally lacking. Circular dichroism (CD) was used to study the conformational properties of synthetic peptides corresponding to the highly divergent amino acid sequences of cytoplasmic domains of connexin (Cx)32, Cx36, and Cx43. We report that whereas peptides were largely unstructured in aqueous buffer, certain peptides in 30% trifluoroethanol (TFE) showed considerable helical content. These structured peptides correspond to analogous regions in each of the three connexin cytoplasmic domains. This first comparative study of conformational properties of connexin cytoplasmic domains reveals protein domains that may play similar roles in channel function and protein‐protein interactions. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 173–182, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Crystal structure of bovine 3‐hydroxyanthranilate 3,4‐dioxygenase
Authors: Đilović Ivica , Gliubich Francesca , Malpeli Giorgio , Zanotti Giuseppe , Matković‐Čalogović Dubravka 
Published: February 2009

Abstract3‐Hydroxyanthranilate 3,4‐dioxygenase, the enzyme that catalyzes the conversion of 3‐hydroxyanthranilate to quinolinic acid, has been extracted and purified from bovine kidney, crystallized and its structure determined at 2.5 Å resolution. The enzyme, which crystallizes in the triclinic P1 space group, is a monomer, characterized by the so‐called cupin fold. The monomer of the bovine enzyme mimics the dimer present in lower species, such as bacteria and yeast, since it is composed of two domains: one of them is equivalent to one monomer, whilst the second domain corresponds to only a portion of it. The active site consists of an iron ion coordinated by two histidine residues, one glutamate and an external ligand, which has been interpreted as a solvent molecule. It is contained in the N‐terminal domain, whilst the function of the C‐terminal domain is possibly structural. The catalytic mechanism very likely has been conserved through all species, since the positions of all residues considered relevant for the reaction are present from bacteria to humans. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1189–1195, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Structural and electrostatic characterization of Pariacoto virus: Implications for viral assembly
Authors: Devkota Batsal , Petrov Anton S. , Lemieux Sébastien , Boz Mustafa Burak , Tang Liang , Schneemann Anette , Johnson John E. , Harvey Stephen C. 
Published: February 2009

AbstractWe present the first all‐atom model for the structure of a T = 3 virus, pariacoto virus (PaV), which is a nonenveloped, icosahedral RNA virus and a member of the Nodaviridae family. The model is an extension of the crystal structure, which reveals about 88% of the protein structure but only about 35% of the RNA structure. New modeling methods, combining coarse‐grained and all‐atom approaches, were required for developing the model. Evaluation of alternative models confirms our earlier observation that the polycationic N‐ and C‐terminal tails of the capsid proteins must penetrate deeply into the core of the virus, where they stabilize the structure by neutralizing a substantial fraction of the RNA charge. This leads us to propose a model for the assembly of small icosahedral RNA viruses: nonspecific binding of the protein tails to the RNA leads to a collapse of the complex, in a fashion reminiscent of DNA condensation. The globular protein domains are excluded from the condensed phase but are tethered to it, so they accumulate in a shell around the condensed phase, where their concentration is high enough to trigger oligomerization and formation of the mature virus. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 530–538, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Isopeptide bonds in bacterial pili and their characterization by X‐ray crystallography and mass spectrometry
Authors: Kang Hae Joo , Middleditch Martin , Proft Thomas , Baker Edward N. 
Published: February 2009

AbstractPili are long, filamentous protein assemblies which extend from the surfaces of many bacteria, and mediate their adhesion to host cells and other matrices. For pathogenic bacteria they are critical to colonization and infection. Whereas the pili of gram‐negative bacteria are formed by noncovalent association of their pilin subunits, those of gram‐positive bacteria are assembled with the aid of sortase enzymes that mediate the formation of covalent isopeptide bonds between successive pilin subunits. Sequence comparisons, mutagenesis and crystallography have implicated specific lysine residues in the formation of these intermolecular bonds and mass spectral analyses of native and modified pili have now provided definitive proof of these linkages. Crystallographic studies of pilin subunits have also led to the unexpected discovery of internal isopeptide crosslinks formed between lysine and asparagine residues. These, too, have been confirmed by mass spectrometry. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1126–1134, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Biochemical correlation of Raman spectra of normal, benign and malignant breast tissues: A spectral deconvolution study
Authors: Chowdary M. V. P. , Kalyan Kumar K. , Mathew Stanley , Rao Lakshmi , Krishna C. Murali , Kurien Jacob 
Published: February 2009

AbstractThe aim of this study was to understand and correlate spectral features and biochemical changes in normal, fibroadenoma and infiltrating ductal carcinoma of breast tissues using Raman spectra that were part of the spectroscopic models developed and evaluated by us earlier. Spectra were subjected to curve fitting and intensities plots of resultant curve resolved bands were computed. This study has revealed that fat (1301 and 1440 cm−1), collagen (1246, 1271, and 1671 cm−1) and DNA (1340 and 1480 cm−1) bands have strong presence in normal, benign and malignant breast tissues, respectively. Intensity plots of various combinations of curved resolved bands were also explored to classify tissue types. Combinations of fat (1301 cm−1) and collagen (1246, 1271, and 1671 cm−1)/amide I; DNA (1340 cm−1) and fat (1301 cm−1); collagen (1271 cm−1) and DNA (1480 cm−1) are found to be good discriminating parameters. These results are in tune with findings of earlier studies carried out on western population as well as our molecular biological understanding of normal tissues and neoplastic processes. Thus the finding of this study further demonstrates the efficacy Raman spectroscopic approaches in diagnostic applications as well as in understanding molecular phenomenon in breast cancers. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 539–546, 2009.This article was originally published online as an accepted preprint. The “Published Online”date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Impact of estradiol on insulin signaling in the rat heart
Authors: Koricanac Goran , Milosavljevic Tijana , Stojiljkovic Mojca , Zakula Zorica , Tepavcevic Snezana , Ribarac‐Stepic Nevena , Isenovic Esma R. 
Published: February 2009

AbstractIt is well known that variation in the concentration of estrogens affects insulin action. In this study we examine the impact of estradiol (E2) on insulin signaling in the rat heart. Ovariectomized female rats were treated with E2 6 h prior to analysis of basal protein and mRNA content of insulin signaling molecules, and additionally with insulin 30 min before the experiment to delineate E2 effects on phosphorylations and molecular associations relevant for insulin signaling. The results show that E2 decreased insulin receptor (IR) tyrosine phosphorylation, while it did not alter IR protein and mRNA content. E2 administration did not change IR substrate 1 (IRS‐1) protein content and tyrosine phosphorylation, while decreased mRNA content and increased its association with the p85 subunit of phosphatidylinositol 3‐kinase (PI3K). E2 decreased protein and mRNA content of IR substrate 2 (IRS‐2), while did not change IRS‐2 tyrosine phosphorylation and IRS‐2 association with p85. The increase of IRS‐1/p85 is accompanied by increase of p85 protein and mRNA levels, and by stimulation of protein kinase B (Akt) Ser473 phosphorylation. In contrast, Akt protein and mRNA content were not changed. In summary, although in some aspects cardiac insulin signaling is obviously improved by E2 treatment (increase of p85 mRNA and protein levels, enhancement of IRS‐1/p85 association and Ser473Akt phosphorylation), the observed decrease of IR tyrosine phosphorylation, IRS‐2 protein content, and IRSs mRNA contents, suggest very complex interplay of beneficial and suppressive effects of E2, both genomic and non‐genomic, in regulation of heart insulin signaling. Copyright © 2009 John Wiley & Sons, Ltd.
Identification of Cytochrome P450s Required for Fumitremorgin Biosynthesis in Aspergillus fumigatus
Authors: Kato Naoki , Suzuki Hirokazu , Takagi Hiroshi , Asami Yukihiro , Kakeya Hideaki , Uramoto Masakazu , Usui Takeo , Takahashi Shunji , Sugimoto Yoshikazu , Osada Hiroyuki 
Published: February 2009

AbstractMissing links in the fumitremorgin biosynthetic pathway have been elucidated as 1) hydroxylation of the tryprostatin B indole ring at C‐6 by FtmC, 2) CN bond formation by FtmE to produce fumitremorgin C, and 3) the subsequent dihydroxylation of fumitremorgin C by FtmG to afford fumitremorgin B. These are also crucial processes for the inhibitory activity of fumitremorgin C against breast cancer resistance protein (BCRP).magnified imageFumitremorgin C, a diketopiperazine mycotoxin produced by Aspergillus fumigatus, is a potent and specific inhibitor of breast cancer resistance protein (BCRP). Elucidation of the fumitremorgin C biosynthetic pathway provides a strategy for new drug design. A structure–activity relationship study based on metabolites related to the ftm gene cluster revealed that the process most crucial for inhibitory activity against BCRP was cyclization to form fumitremorgin C. To determine the gene involved in the cyclization reaction, targeted gene inactivation was performed with candidate genes in the ftm cluster. Analysis of the gene disruptants allowed us to identify ftmE, one of the cytochrome P450 genes in the cluster, as the gene responsible for the key step in fumitremorgin biosynthesis. Additionally, we demonstrated that the other two cytochrome P450 genes, ftmC and ftmG, were involved in hydroxylation of the indole ring and successive hydroxylation of fumitremorgin C, respectively.
Synthesis and Conformational Analysis of Cyclotetrapeptide Mimetic β‐Turn Templates and Validation as 3D Scaffolds
Authors: Gentilucci Luca , Cardillo Giuliana , Tolomelli Alessandra , De Marco Rossella , Garelli Andrea , Spampinato Santi , Spartà Antonino , Juaristi Eusebio 
Published: February 2009

AbstractThe conformations of all stereoisomers of PMRI cyclotetrapeptide mimetics 1–8 are essentially determined by the predisposition of the diamine to stabilize β‐turns. The peptide mimetics can be regarded as 3D scaffolds for designing molecules with a predictable display of the pharmacophores. We used the models for testing novel RGD analogues as αvβ3‐integrin receptor antagonists.magnified image
Dynamic gene and protein expression patterns of the autism‐associated met receptor tyrosine kinase in the developing mouse forebrain
Authors: Judson Matthew C. , Bergman Mica Y. , Campbell Daniel B. , Eagleson Kathie L. , Levitt Pat 
Published: February 2009

AbstractThe establishment of appropriate neural circuitry depends on the coordination of multiple developmental events across space and time. These events include proliferation, migration, differentiation, and survival—all of which can be mediated by hepatocyte growth factor (HGF) signaling through the Met receptor tyrosine kinase. We previously found a functional promoter variant of theMETgene to be associated with autism spectrum disorder, suggesting that forebrain circuits governing social and emotional function may be especially vulnerable to developmental disruptions in HGF/Met signaling. However, little is known about the spatiotemporal distribution of Met expression in the forebrain during the development of such circuits. To advance our understanding of the neurodevelopmental influences of Met activation, we employed complementary Western blotting, in situ hybridization, and immunohistochemistry to comprehensively map Met transcript and protein expression throughout perinatal and postnatal development of the mouse forebrain. Our studies reveal complex and dynamic spatiotemporal patterns of expression during this period. Spatially,Mettranscript is localized primarily to specific populations of projection neurons within the neocortex and in structures of the limbic system, including the amygdala, hippocampus, and septum. Met protein appears to be principally located in axon tracts. Temporally, peak expression of transcript and protein occurs during the second postnatal week. This period is characterized by extensive neurite outgrowth and synaptogenesis, supporting a role for the receptor in these processes. Collectively, these data suggest that Met signaling may be necessary for the appropriate wiring of forebrain circuits, with particular relevance to the social and emotional dimensions of behavior. J. Comp. Neurol. 513:511–531, 2009. © 2009 Wiley‐Liss, Inc.