bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amyloid fibril formation by the CAD domain of caspase‐activated DNase
Authors: Uegaki Koichi , Nakamura Tsutomu , Yamamoto Hitoshi , Kobayashi Atsuko , Odahara Takayuki , Harata Kazuaki , Hagihara Yoshihisa , Ueyama Norikazu , Yamazaki Toshio , Yumoto Noboru 
Published: June 2005

AbstractCaspase‐activated DNase (CAD) is a key protein in the process of apoptosis that degrades DNA through the action of caspases. Its N‐terminal region, the CAD domain (CAD‐CD), is highly conserved among CAD family proteins and is responsible for the interaction with its inhibitor. We report here that CAD‐CD spontaneously aggregates to form amyloid fibrils, without a lag time, under the conditions of low pH (below 4) and the presence of anions. Interestingly, the secondary structure of CAD‐CD in the fibril state comprised not only β‐sheet but also α‐helix, as found in CD, FTIR, and x‐ray fiber diffraction experiments. Aromatic side chains have a defined orientation and are in the hydrophobic environment occurring with the CAD‐CD fibrillogenesis. These findings provide new insights into the architecture of amyloid fibrils. © 2005 Wiley Periodicals, Inc. Biopolymers 79: 39–47, 2005This 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
Efficient one‐step production of astaxanthin by the microalga Haematococcus pluvialis in continuous culture
Authors: Río Esperanza Del , Acién F. Gabriel , García‐Malea M. Carmen , Rivas Joaquín , Molina‐Grima Emilio , Guerrero Miguel G. 
Published: June 2005

AbstractThe performance of Haematococcus pluvialis in continuous photoautotrophic culture has been analyzed, especially from the viewpoint of astaxanthin production. To this end, chemostat cultures of Haematococcus pluvialis were carried out at constant light irradiance, 1,220 μE/m2 · s, and dilution rate, 0.9/d, but varying the nitrate concentration in the feed medium reaching the reactor, from 1.7 to 20.7 mM. Both growth and biomass composition were affected by the nitrate supply. With saturating nitrate, the biomass productivity was high, 1.2 g/L · d, but astaxanthin accumulation did not take place, the C/N ratio of the biomass being 5.7. Under moderate nitrate limitation, biomass productivity was decreased, as also did biomass concentration at steady state, whereas accumulation of astaxanthin developed and the C/N ratio of the biomass increased markedly. Astaxanthin accumulation took place in cells growing and dividing actively, and its extent was enhanced in response to the limitation in nitrate availability, with a recorded maximum for astaxanthin cellular level of 0.8% of dry biomass and of 5.6 mg/L · d for astaxanthin productivity. The viability of a significant continued generation of astaxanthin‐rich H. pluvialis cells becomes thus demonstrated, as also does the continuous culture option as an alternative to current procedures for the production of astaxanthin using this microalga. The intensive variable controlling the behavior of the system has been identified as the specific nitrate input, and a mathematical model developed that links growth rate with both irradiance and specific nitrate input. Moreover, a second model for astaxanthin accumulation, also as a function of irradiance and specific nitrate input, was derived. The latter model takes into account that accumulation of astaxanthin is only partially linked to growth, being besides inhibited by excess nitrate. Simulations performed fit experimental data and emphasize the contention that astaxanthin can be efficiently produced under continuous mode by adjustment of the specific nitrate input, predicting even higher values for astaxanthin productivity. The developed models represent a powerful tool for management of such an astaxanthin‐generating continuous process, and could allow the development of improved systems for the production of astaxanthin‐rich Haematococcus cells. © 2005 Wiley Periodicals, Inc.
High‐level transient expression of recombinant protein in lettuce
Authors: Joh Lawrence D. , Wroblewski Tadeusz , Ewing Nicholas N. , VanderGheynst Jean S. 
Published: June 2005

AbstractTransient expression following agroinfiltration of plant tissue was investigated as a system for producing recombinant protein. As a model system, Agrobacterium tumefaciens containing the β‐glucuronidase (GUS) gene was vacuum infiltrated into lettuce leaf disks. Infiltration with a suspension of 109 colony forming units/mL followed by incubation for 72 h at 22°C in continuous darkness produced a maximum of 0.16% GUS protein based on dry tissue or 1.1% GUS protein based on total soluble protein. This compares favorably to expression levels for commercially manufactured GUS protein from transgenic corn seeds. A. tumefaciens culture medium pH between 5.6 and 7.0 and surfactant concentrations ≤100 ppm in the vacuum infiltration did not affect GUS expression, while infiltration with an A. tumefaciens density of 107 and 108 colony forming units/mL, incubation at 29°C, and a surfactant concentration of 1,000 ppm significantly reduced expression. Incubation in continuous light caused lettuce to produce GUS protein more rapidly, but final levels did not exceed the GUS production in leaves incubated in continuous darkness after 72 h at 22°C. The kinetics of GUS expression during incubation in continuous light and dark were represented well using a logistic model, with rate constants of 0.30 and 0.29/h, respectively. To semi‐quantitatively measure the GUS expression in large numbers of leaf disks, a photometric enhancement of the standard histochemical staining method was developed. A linear relationship with an R 2 value of 0.90 was determined between log10 (% leaf darkness) versus log10 (GUS activity). Although variability in expression level was observed, agroinfiltration appears to be a promising technology that could potentially be scaled up to produce high‐value recombinant proteins in planta. © 2005 Wiley Periodicals, Inc.
Automated in situ measurement of cell‐specific antibody secretion and laser‐mediated purification for rapid cloning of highly‐secreting producers
Authors: Hanania Elie G. , Fieck Annabeth , Stevens Janine , Bodzin Leon J. , Palsson Bernhard Ø. , Koller Manfred R. 
Published: June 2005

AbstractCloning of highly‐secreting recombinant cells is critical for biopharmaceutical manufacturing, but faces numerous challenges including the fact that secreted protein does not remain associated with the producing cell. A fundamentally new approach was developed combining in situ capture and measurement of individual cell protein secretion followed by laser‐mediated elimination of all non‐ and poorly‐secreting cells, leaving only the highest‐secreting cell in a well. Recombinant cells producing humanized antibody were cultured serum‐free on a capture matrix, followed by staining with fluorescently‐labeled anti‐human antibody fragment. A novel, automated, high‐throughput instrument (called LEAP™) was used to image and locate every cell, quantify the cell‐associated and secreted antibody (surrounding each cell), eliminate all undesired cells from a well via targeted laser irradiation, and then track clone outgrowth and stability. Temporarily sparing an island of helper cells around the clone of interest improved cloning efficiency (particularly when using serum‐free medium), and helper cells were easily eliminated with the laser after several days. The in situ nature of this process allowed several serial sub‐cloning steps to be performed within days of one another, resulting in rapid generation of clonal populations with significantly increased and more stable, homogeneous antibody secretion. Cell lines with specific antibody secretion rates of > 50 pg/cell per day (in static batch culture) were routinely obtained as a result of this cloning approach, often times representing up to 20% of the clones screened. © 2005 Wiley Periodicals, Inc.
In silico mutagenesis of RNA splicing in HIV‐1
Authors: Kim Hwijin , Yin John 
Published: June 2005

AbstractHuman immunodeficiency virus type‐1 (HIV‐1) relies on both partial and complete splicing of its full‐length RNA transcripts to generate a distribution of essential spliced mRNA products. The complexity of the splicing process, which can employ multiple alternative splice sites, challenges our ability to understand how mutations in splice sites may influence the composition of the resulting mRNA pool and, more broadly, the development of viral progeny. Here, we begin to systematically address these issues by developing a mechanistic mathematical model for the splicing process. We identify as key parameters the probabilities that the cellular splice machinery selects specific splice acceptors, and we show how the splicing process depends on these probabilities. Further, by incorporating this splicing model into a detailed kinetic model for HIV‐1 intracellular development we find that an increase in the fraction of either rev or tat mRNA in the HIV‐1 mRNA pool is generally beneficial for HIV‐1 growth. However, a splice site mutation that excessively increases the fraction of either mRNA can be detrimental due to the corresponding reduction in the other mRNA, suggesting that a balance of Rev and Tat is needed in order for HIV‐1 to optimize its growth. Although our model is based on still very limited quantitative data on RNA splicing, Rev‐mediated splicing regulation and nuclear export, and the effects of associated mutations, it serves as a starting point for better understanding how variations in essential post‐transcriptional functions can impact the intracellular development of HIV‐1. © 2005 Wiley Periodicals, Inc.
The RNA‐Bound Conformation of Neamine as Determined by Transferred NOE Experiments
Authors: Szilaghi Richard , Shahzad‐ul‐Hussan Syed , Weimar Thomas 
Published: June 2005

AbstractThe tRNAPhe‐bound conformation of the aminoglycoside neamine, a member of the neomycin B family, has been investigated by transferred NOE experiments in aqueous solution. This is the first time that the bioactive conformation of an RNA‐bound aminoglycoside has been determined by this method. In buffers without divalent Mg2+ ions, a high degree of electrostatically driven unspecific binding of aminoglycosides to the RNA was observed. Careful optimization of experimental conditions yielded buffer conditions optimized for cryo‐probe NMR experiments. In particular, addition of Mg2+ ions to the solutions was necessary to reduce the amount of unspecific binding as monitored by one‐dimensional NMR and surface plasmon resonance experiments. CD spectroscopy was used to probe the effect of aminoglycosides and buffer conditions on the double helical content of tRNAPhe. Finally the tRNAPhe‐bound conformation of neamine was determined by trNOE build‐up curves and compared with the previously reported crystal structure of neomycin B complexed to this RNA. Although the aminoglycoside in the crystal structure contains several configurational errors, the overall shape of the crystallographically determined RNA‐bound structure is identical to the RNA‐bound conformation defined by the NMR experiments. Therefore, the crystal structure has been refined by trNOE data. This is particularly important in the context of aminoglycosides being discussed as lead structures for the development of new anti‐RNA drugs.
Synthesis and Application of Integrin Targeting Lipopeptides in Targeted Gene Delivery
Authors: Waterhouse Jodie E. , Harbottle Richard P. , Keller Michael , Kostarelos Kostas , Coutelle Charles , Jorgensen Michael R. , Miller Andrew D. 
Published: June 2005

AbstractOne of the main problems facing gene therapy is the ability to target the delivery of DNA to specific cells of choice. Recently, we developed a synthetic nonviral vector platform system known as LMD (liposome:mu:DNA) that was designed for further modular upgrading with tool‐kits of chemical components. First‐generation LMD systems were prepared from DC‐Chol/DOPE cationic liposomes (DC‐Chol=3β‐[N‐(N′,N′‐dimethylaminoethane)carbamoyl] cholesterol, DOPE=dioleoyl‐L‐α‐phosphatidylethanolamine), μ peptide from the adenovirus core and plasmid DNA (pDNA). Here we report attempts to realise peptide‐targeted gene delivery that build upon the LMD platform. Our strategy was to prepare novel lipopeptides with a lipid moiety designed to insert into the outer lipid bilayer of LMD particles whilst simultaneously presenting a peptide moiety for cell‐surface receptor binding. One main functional peptide sequence was selected (PLAEIDGIELA; tenascin peptide sequence) known to target α9β1‐integrin proteins predominant on upper‐airway epithelial cells. This sequence was investigated along with a corresponding control sequence. The syntheses of two classes (A and B) of lipopeptides are reported; the syntheses of class A lipopeptides requires a modification of Mitsunobu chemistry that could be of general utility to facilitate Mitsunobu reactions in other diverse systems. “Targeted” LMD and LD transfections with class A or B lipopeptides exhibit nonspecific peptide enhancements (up to one order of magnitude) over nonlipopeptide control transfections but few specific effects. Specific targeting effects can be seen if the overall LMD or LD particle cationic charge is lowered, but nonspecific effects are never eliminated. Whilst promising, these data now highlight the need for in vivo data and even a new modular, aqueous chemistry for the controlled adaptation of LMD particles in buffer in order for successful peptide‐targeted, synthetic, nonviral gene delivery to be realised.
Enantioselective Hydrogenation of β‐Ketoesters with Monodentate Ligands.
Authors: Junge Kathrin , Hagemann Bernhard , Enthaler Stephan , Oehme Guenther , Michalik Manfred , Monsees Axel , Riermeier Thomas , Dingerdissen Uwe , Beller Matthias 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
Calcium Phosphate—Vanadate Apatite (CPVAP)‐Catalyzed Aerobic Oxidation of Propargylic Alcohols with Molecular Oxygen.
Authors: Maeda Yasunari , Washitake Yosuke , Nishimura Takahiro , Iwai Keisuke , Yamauchi Takayoshi , Uemura Sakae 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
A New Class of Acyclic 2‐Alkyl‐1,2‐diaryl (E)‐Olefins as Selective Cyclooxygenase‐2 (COX‐2) Inhibitors.
Authors: Uddin Md. Jashim , Rao P. N. Praveen , Rahim Md. Abdur , McDonald Robert , Knaus Edward E. 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
Direct Organocatalytic Asymmetric Heterodomino Reactions: The Knoevenagel/Diels—Alder/Epimerization Sequence for the Highly Diastereoselective Synthesis of Symmetrical and Nonsymmetrical Synthons of Benzoanellated Centropolyquinanes.
Authors: Ramachary D. B. , Anebouselvy K. , Chowdari Naidu S. , Barbas Carlos F. III 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
Rearrangement of 4‐(1‐Haloalkyl)‐ and 4‐(2‐Haloalkyl)‐2‐azetidinones into Methyl ω‐Alkylaminopentenoates via Transient Aziridines and Azetidines.
Authors: Dejaegher Yves , De Kimpe Norbert 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
β‐Acylvinyl Anion and Dianion Equivalents: Lithiation of 1‐[(2EZ)‐3‐Chloroprop‐2‐enyl]‐1H‐1,2,3‐benzotriazole: Preparation and Elaboration of 1‐(2‐Oxiranylvinyl)‐1H‐benzotriazoles.
Authors: Katritzky Alan R. , Manju Kavita , Gromova Anna V. , Steel Peter J. 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
General One‐Pot, Three‐Step Methodology Leading to an Extended Class of N‐Heterocyclic Cations: Spontaneous Nucleophilic Addition, Cyclization, and Hydride Loss.
Authors: Parenty Alexis D. C. , Smith Louise V. , Pickering Alexandra L. , Long De‐Liang , Cronin Leroy 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
Reactions with Methylamine of Pyrilo‐2‐cyanines Containing Polyfluorophenyl Substituents.
Authors: Kargapolova I. Yu. , Orlova N. A. , Shakirov M. M. , Gerasimova T. N. , Shelkovnikov V. V. 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
Fabrication of Nano‐Precision PDMS Replica Using Two‐Photon Photopolymerization and Vacuum Pressure Difference Technique.
Authors: Park Sang Hu , Lim Tae Woo , Yang Dong‐Yol , Kong Hong Jin , Kim Ran‐Hee , Kim Kyoung‐Soo , Lee Kwang‐Sup 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
Stereodivergent Construction of Cyclic Ethers by a Regioselective and Enantiospecific Rhodium‐Catalyzed Allylic Etherification: Total Synthesis of Gaur Acid.
Authors: Evans P. Andrew , Leahy David K. , Andrews William J. , Uraguchi Daisuke 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
Antiferroelectric Liquid Crystal from Bent‐Core Molecule with Vinyl End Group.
Authors: Lee Chong‐Kwang , Kwon Soon‐Sik , Kim Tae‐Sung , Shin Sung‐Tae , Choi Hong , Choi E‐Joon , Kim Sea‐Yun , Zin Wang‐Choel , Kim Dae‐Choel , Chien Liang‐Chy 
Published: June 2005

AbstractFor Abstract see ChemInform Abstract in Full Text.
GFP as a tool for the analysis of proteins in the flagellar basal apparatus of Chlamydomonas
Authors: Schoppmeier Jutta , Mages Wolfgang , Lechtreck Karl‐Ferdinand 
Published: June 2005

AbstractGreen fluorescent protein (GFP) was used to analyse three proteins in the flagellar basal apparatus of C. reinhardtii: (1) Striated fiber assemblin (SFA), the major component of the striated microtubule‐associated fibers; (2) Centrin, present in the nucleus basal body connectors (NBBCs) and the distal connecting fiber (dCF) between the two basal bodies; and (3) DIP13, the Chlamydomonas homologue of human autoantigen NA14. The fusions co‐localized with the wild‐type proteins when expressed moderately. Overexpression of centrin‐GFP and DIP13‐GFP resulted in the formation of large aggregates and disturbed the distribution of the respective wild‐type proteins. The amount of wild‐type DIP13 was significantly reduced in cells overexpressing DIP13‐GFP. Moreover, the cells frequently failed to assemble full‐length flagella and flagellar regeneration was delayed, indicating a role of DIP13 during flagellar assembly. In contrast, overexpression of GFP‐SFA, which retained more wild‐type properties than SFA‐GFP, increased the size of the striated fibers without altering the cross‐shaped pattern. Abnormal patterns were observed in centrin‐deficient cells, suggesting that centrin is required for proper localization of SFA. Photobleaching of GFP‐SFA fibers indicated that GFP‐SFA in the fibers is turned over slowly. Conditionally expressed centrin‐GFP was incorporated into NBBCs in regions close to the basal bodies, but underrepresented in the dCF, indicative of a different dynamic of these two centrin fibers. Bending of the NBBCs was observed in vivo during flagellar motion, indicating that the filaments are flexible. In conclusion, in Chlamydomonas GFP‐tagging is a useful tool for yielding new insights into the function and properties of the analyzed proteins. Cell Motil. Cytoskeleton 61:189–200, 2005. © 2005 Wiley‐Liss, Inc.
Adaptive multi‐resolution triangulations based on physical compression
Authors: Marroquim Ricardo , Cavalcanti Paulo Roma , Esperança Claudio , Velho Luiz 
Published: June 2005

AbstractThis paper presents a method for generating multi‐resolution adaptive triangulations of non‐manifold 3D objects composed of several regions with arbitrary geometry. The process first immerses the input boundary elements inside a semi‐regular adaptive tetrahedral mesh known as a BMT triangulation. The mesh elements are then pushed towards the boundary by means of a physically based compression scheme, more specifically, a mass‐spring system. The final triangulation has no degenerated tetrahedra and provides an approximation of the boundary based on a chosen resolution. Copyright © 2005 John Wiley & Sons, Ltd.
Relative absorption model of color vision
Authors: Yoder Lane 
Published: June 2005

AbstractOpponent processing is widely accepted as providing a general framework for the standard model of human color vision. After the cones' responses are transmitted to second stage neurons, however, there is no consensus on exactly how synaptic connections are organized. The Relative Absorption Model introduced here is an explicit neural network that generates neural correlates of color vision. The model makes detailed predictions of known color and neural phenomena, including familiar aspects of color perception. Until now these phenomena have not had an explicit neural explanation. The model's simplicity shows that color does not require complex processing of spectral information. The network receives excitatory and inhibitory input from three classes of spatially proximate photoreceptors with different spectral sensitivities. Four second stage neurons provide symmetric input to four third stage neurons, whose outputs are correlates of red, green, blue, and yellow. These color cells identify which receptor type has the greatest absorption of photons and which has the least. Their response intensities correspond to the differences between those absorptions and the middle absorption. A single second stage neuron computes violet and purple information that is then transmitted through the red and blue channels, the only channels in the network capable of conveying the information. Five additional neurons produce correlates of black and white. The white cell's response intensity measures the smallest of the three absorptions, and the black response measures how far the largest absorption is from full saturation. © 2005 Wiley Periodicals, Inc. Col Res Appl, 30, 252–264, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.20121
Evaluation of image similarity by histogram intersection
Authors: Lee S. M. , Xin J. H. , Westland S. 
Published: June 2005

AbstractColour is the most widely used attribute in image retrieval and object recognition. A technique known as histogram intersection has been widely studied and is considered to be effective for color‐image indexing. The key issue of this algorithm is the selection of an appropriate color space and optimal quantization of the selected color space. The goal of this article is to measure the model performance in predicting human judgment in similarity measurement for various images, to explore the capability of the model with a wide set of color spaces, and to find the optimal quantization of the selected color spaces. Six color spaces and twelve quantization levels are involved in evaluating the performance of histogram intersection. The categorical judgment and rank order experiments were conducted to measure image similarity. The CIELAB color space was found to perform at least as good as or better than the other color spaces tested, and the ability to predict image similarity increased with the number of bins used in the histograms, for up to 512 bins (8 per channel). With more than 512 bins, further improvement was negligible for the image datasets used in this study. © 2005 Wiley Periodicals, Inc. Col Res Appl, 30, 265–274, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.20122