bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymmetric nuclear reprogramming in somatic cell nuclear transfer?
Authors: Loi Pasqualino , Beaujean Nathalie , Khochbin Saadi , Fulka Josef , Ptak Grazyna 
Published: December 2007

AbstractDespite the progress achieved over the last decade after the birth of the first cloned mammal, the efficiency of reproductive cloning remains invariably low. However, research aiming at the use of nuclear transfer for the production of patient‐tailored stem cells for cell/tissue therapy is progressing rapidly. Yet, reproductive cloning has many potential implications for animal breeding, transgenic research and the conservation of endangered species. In this article we suggest that the changes in the epi‐/genotype observed in cloned embryos arise from unbalanced nuclear reprogramming between parental chromosomes. It is probable that the oocyte reprogramming machinery, devised for resident chromosomes, cannot target the paternal alleles of somatic cells. We, therefore, suggest that a reasonable approach to balance this asymmetry in nuclear reprogramming might involve the transient expression in donor cells of chromatin remodelling proteins, which are physiologically expressed during spermatogenesis, in order to induce a male‐specific chromatin organisation in the somatic cells before nuclear transfer. BioEssays 30:66–74, 2008. © 2007 Wiley Periodicals, Inc.
Damage‐induced reactivation of cohesin in postreplicative DNA repair
Authors: Ball Alexander R. , Yokomori Kyoko 
Published: December 2007

AbstractCohesin establishes sister‐chromatid cohesion during S phase to ensure proper chromosome segregation in mitosis. It also facilitates postreplicative homologous recombination repair of DNA double‐strand breaks by promoting local pairing of damaged and intact sister chromatids. In G2 phase, cohesin that is not bound to chromatin is inactivated, but its reactivation can occur in response to DNA damage. Recent papers by Koshland's and Sjögren's groups describe the critical role of the known cohesin cofactor Eco1 (Ctf7) and ATR checkpoint kinase in damage‐induced reactivation of cohesin, revealing an intricate mechanism that regulates sister‐chromatid pairing to maintain genome integrity.1,2 BioEssays 30:5–9, 2008. © 2007 Wiley Periodicals, Inc.
Alternative splicing: current perspectives
Authors: Kim Eddo , Goren Amir , Ast Gil 
Published: December 2007

AbstractAlternative splicing is a well‐characterized mechanism by which multiple transcripts are generated from a single mRNA precursor. By allowing production of several protein isoforms from one pre‐mRNA, alternative splicing contributes to proteomic diversity. But what do we know about the origin of this mechanism? Do the same evolutionary forces apply to alternatively and constitutively splice exons? Do similar forces act on all types of alternative splicing? Are the products generated by alternative splicing functional? Why is “improper” recognition of exons and introns allowed by the splicing machinery? In this review, we summarize the current knowledge regarding these issues from an evolutionary perspective. BioEssays 30:38–47, 2008. © 2007 Wiley Periodicals, Inc.
From priming to plasticity: the changing fate of rhizodermic cells
Authors: Savage Natasha Saint , Schmidt Wolfgang 
Published: December 2007

AbstractThe fate of root epidermal cells is controlled by a complex interplay of transcriptional regulators, generating a genetically determined, position‐biased arrangement of root hair cells. This pattern is altered during postembryonic development and in response to environmental signals to confer developmental plasticity that acclimates the plant to the prevailing conditions. Based on the hypothesis that events downstream of this initial mechanism can modulate the pattern installed during embryogenesis, we have developed a reaction diffusion model that reproduces the root hair patterning previously observed experimentally. Under all growth conditions, an almost equal spacing between root hair forming cells was observed both in vitro and in silico, indicating that long‐range intercellular communication is crucial for the trichoblasts' decision to form a root hair. We assume that a hair growth promoter (HGP) is upregulated in root‐hair‐forming cells by a trichoblast‐specific component. Once established, HGP production is self‐enhancing. The autocatalytic regulation of HGP is antagonized by an HGP‐produced hair growth inhibitor (HGI). HGI is exported from trichoblasts and diffuses to neighboring cells, where it inhibits further HGP production and promotes the non‐hair cell fate. Under conditions of phosphate deficiency, we hypothesise that HGP production is increased and HGI diffusion rate is reduced, leading to a position‐independent formation of extra root hairs. BioEssays 30:75–81, 2008. © 2007 Wiley Periodicals, Inc.
Right or left turn? RecA family protein filaments promote homologous recombination through clockwise axial rotation
Authors: Wang Ting‐Fang , Chen Li‐Tzu , Wang Andrew H.‐J. 
Published: December 2007

AbstractThe RecA family proteins mediate homologous recombination, a ubiquitous mechanism for repairing DNA double‐strand breaks (DSBs) and stalled replication forks. Members of this family include bacterial RecA, archaeal RadA and Rad51, and eukaryotic Rad51 and Dmc1. These proteins bind to single‐stranded DNA at a DSB site to form a presynaptic nucleoprotein filament, align this presynaptic filament with homologous sequences in another double‐stranded DNA segment, promote DNA strand exchange and then dissociate. It was generally accepted that RecA family proteins function throughout their catalytic cycles as right‐handed helical filaments with six protomers per helical turn. However, we recently reported that archaeal RadA proteins can also form an extended right‐handed filament with three monomers per helical turn and a left‐handed protein filament with four monomers per helical turn. Subsequent structural and functional analyses suggest that RecA family protein filaments, similar to the F1‐ATPase rotary motor, perform ATP‐dependent clockwise axial rotation during their catalytic cycles. This new hypothesis has opened a new avenue for understanding the molecular mechanism of RecA family proteins in homologous recombination. BioEssays 30:48–56, 2008. © 2007 Wiley Periodicals, Inc.
“JIP”ing along the axon: the complex roles of JIPs in axonal transport
Authors: Koushika Sandhya P. 
Published: December 2007

AbstractJIPs are JNK interacting proteins and bind to JNK cascade kinases. JIP1 and JIP3 were known to be adaptors linking cargo to Kinesin‐I, a major molecular motor for axonal transport. Recent research sheds further light on JIPs' complex roles in axonal transport, namely in activation of Kinesin‐I and in cargo release. In Drosophila, APLIP1/JIP1 allows the Kinesin‐I complex to enable cargo release through activation of JNK signaling.1 In mammalian cell culture, JIP1 is necessary and, together with UNC‐76/FEZ1, sufficient for activating Kinesin‐I.2 I discuss and compare the many roles played by JIP1 and JIP3 through interactions with several distinct players, in retrograde as well as anterograde transport. BioEssays 30:10–14, 2008. © 2007 Wiley Periodicals, Inc.
Live cells‐based cytotoxic sensorchip fabricated in a microfluidic system
Authors: Wada Ken‐Ichi , Taniguchi Akiyoshi , Kobayashi Jun , Yamato Masayuki , Okano Teruo 
Published: December 2007

AbstractWe report here a live cells‐based sensorchip fabricated in microfluidic channels in which several laminar flows were achieved. In addition, we established a cytotoxic sensor cell line, which was transfected with a green fluorescence protein (GFP) plasmid derived from the heat shock protein 70B′ (HSP70B′) promoter, which is induced by cytotoxic reagents. The fluorescence in the sensor cells increased in a CdCl2 dose‐dependent manner in the microfluidic channels. In this system, cytotoxic reagents can be quantitatively detected in a quick, sensitive and high‐throughput manner. The combination of sensor cells and microfluidic systems will provide an important basis for the development of micro‐total analysis systems (µ‐TAS) technology, and can be applied to toxicology, environmental assessment and drug screening. Biotechnol. Bioeng. 2008;99: 1513–1517. © 2007 Wiley Periodicals, Inc.
Kinetic and stoichiometric parameters estimation in a nitrifying bubble column through “in‐situ” pulse respirometry
Authors: Ordaz Alberto , Oliveira Catarina S. , Aguilar Ricardo , Carrión Manuel , Ferreira Eugénio C. , Alves Madalena , Thalasso Frédéric 
Published: December 2007

AbstractThis article proposes a simple “in‐situ” pulse respirometric method for the estimation of four important kinetic and stoichiometric parameters. The method is validated in a suspended biomass nitrifying reactor for the determination of (i) maximum oxygen uptake rate (OURexmax), (ii) oxidation yield (fE), (iii) biomass growth yield (fS), and (iv) affinity constant (KS). OURexmax and fE were directly obtained from respirograms. In the presented case study, a minimum substrate pulse of 10 mgNH‐N L−1 was necessary to determine OURexmax which was 61.15 ± 4.09 mgO2 L−1 h−1 (5 repetitions). A linear correlation (r2 = 0.93) obtained between OURexmax and the biomass concentration in the reactor suggests that biomass concentration can be estimated from respirometric experiments. The substrate oxidation yield, fE, was determined along 60 days of continuous operation with an average error of 5.6%. The biomass growth yield was indirectly estimated from the substrate oxidation yield fE. The average obtained value (0.10 ± 0.04 mgCOD mg−1COD) was in accordance with the fS estimation by the traditional COD mass balance method under steady‐state conditions (0.09 ± 0.01). The affinity constant KS was indirectly estimated after fitting the ascending part of the respirogram to a theoretical model. An average value of 0.48 ± 0.08 mgNH‐N L−1 was obtained, which is in the range of affinity constants reported in the literature for the nitrification process (0.16–2 mgNH‐N L−1). Biotechnol. Bioeng. 2008;100: 94–102. © 2007 Wiley Periodicals, Inc.
Plasmid DNA transfection using magnetite cationic liposomes for construction of multilayered gene‐engineered cell sheet
Authors: Ino Kosuke , Kawasumi Tamayo , Ito Akira , Honda Hiroyuki 
Published: December 2007

AbstractModification of cellular functions by overexpression of genes is being increasingly practiced for tissue engineering. In the present study, we investigated whether transfection efficiency could be enhanced by magnetofection that involves the use of plasmid DNA (pDNA)/magnetite cationic liposomes (MCLs) complexes (pDNA/MCL) and magnetic force. The transfection efficiencies of the magnetofection technique by pDNA/MCL in fibroblasts and keratinocytes using reporter genes were 36‐ and 10‐fold higher, respectively, than those of a lipofection technique by cationic liposomes. Moreover, in vitro construction of three‐dimensional (3D) tissues is an important challenge. We recently proposed a novel technique termed “magnetic force‐based tissue engineering” (Mag‐TE) to produce 3D tissues. Since the fibroblasts after magnetofection incorporated both magnetite nanoparticles and pDNA, we investigated whether multilayered heterotypic cell sheets expressing transgene could be fabricated by Mag‐TE. First, the fibroblasts were seeded onto an ultra‐low attachment culture plate. When a magnet was placed under the plate, the cells accumulated at the bottom of the culture plate. After 24 h of culture, the transgene‐expressing cells formed a multilayered cell sheet‐like structure. These results indicated that MCLs are a potent biomanipulation tool for both gene transfer and 3D tissue construction, suggesting that these techniques are useful for tissue engineering. Biotechnol. Bioeng. 2008;100: 168–176. © 2007 Wiley Periodicals, Inc.
Functionalization of a poly(D,L)lactic acid surface with galactose to improve human keratinocyte behavior for artificial epidermis
Authors: Renò F. , Traina V. , Gatti S. , Battistella E. , Cannas M. 
Published: December 2007

AbstractThe production of artificial epidermis using reabsorbable polymeric matrices is one of possible goals; one of most used strategies in this field is the polymer substrate functionalitation using specific growth factors, in order to accelerate and improve keratinocyte adhesion and proliferation. In this study films of poly(D,L)lactide (P(D,L)LA), have been functionalized with various concentrations of galactose (GAL, 1–5–10%, w/v) conjugated with poly‐L‐lysine (PLL) using 1‐etil‐3‐(3‐diaminopropil) carbodiimide (EDC) as a coupling agent. GAL is a disaccharide present in the extracellular matrix (ECM) and it is bind by Galectines, a family of cell receptors whose activation regulate the cell–matrix interaction and cell growth and apoptosis. One of these receptors, Galectin‐7 (Gal‐7), is selectively expressed by human keratinocytes. Spontaneously immortalized human keratinocytes (HaCaT) that express high level of Gal‐7 were allowed to adhere for 4 h in serum free condition on control P(D,L)LA (PLA), and on PLA‐GAL and cell proliferation; the production of matrix metalloproteinases (MMP‐2, MMP‐9, and MMP‐28), involved in cellular migration and tissue homeostasis have been analyzed after 24 h. The presence of GAL onto the polymer surface increased both cell adhesion, spreading and proliferation along with MMP‐9 and MMP‐28 production, suggesting that polymer functionalization using GAL could be an useful tool for the production of an artificial epidermis. Biotechnol. Bioeng. 2008;100: 195–202. © 2007 Wiley Periodicals, Inc.
Biosilicification of dual‐fusion enzyme immobilized on magnetic nanoparticle
Authors: Chien Liang‐Jung , Lee Cheng‐Kang 
Published: December 2007

AbstractRapid recovery, immobilization, and silica encapsulation of a dual‐fusion enzyme was achieved by using iminodiacetic acid (IDA) modified magnetic nanoparticle as a carrier. D‐amino acid oxidase (DAAO) of Rhodosporidium toruloides was used as a model enzyme in which a silica‐precipitating peptide R5 and a metal ion complexing peptide (His)6 were fused to its N‐ and C‐terminal, respectively. After charging the magnetic particle with Cu2+, the dual‐fusion DAAO of 0.43 g could be directly recovered from the recombinant E. coli crude extract and immobilized on 1 g of the magnetic particle. Once in contact with hydrolyzed tetramethoxysilane (TMOS), the homogeneously dispersed immobilized dual‐fusion DAAO was biosilicificated to form aggregates with size about 50 µm. The silica‐encapsulated immobilized DAAO demonstrated a pyruvic acid production rate comparable with that of the naked immobilized DAAO in five repeated batch reactions when D‐alanine was used as substrate. Furthermore, 85% of its activity remained after incubation at 60°C for 1 h while the naked immobilized DAAO lost all its activity. This process provides the advantages that recombinant fusion enzyme can be directly recovered from crude extract, silica encapsulation protects the enzyme from leakage and denaturation, and the enzyme activity can be easily retrieved by applying a magnetic field. Biotechnol. Bioeng. 2008;100: 223–230. © 2007 Wiley Periodicals, Inc.
Spectrophotometric ferric ion biosensor from Pseudomonas fluorescens culture
Authors: Gupta Varun , Saharan Krishna , Kumar Lalit , Gupta Roohi , Sahai Vikram , Mittal Aditya 
Published: December 2007

AbstractPseudomonas fluorescens cultures produce fluorescent siderophores. By utilizing optimal conditions for maximizing siderophore production in shake flask cultures of P. fluorescens, we report successful characterization of the culture broth supernatant as a robust ferric ions biosensor. For characterizing the ferric ions biosensor, we tested the effects of pH, buffers, different ferric salts and possible interference by ferrous ions under different solution conditions. We find that the biosensor is very specific to ferric ions only with sensitivity to concentrations as low as 10 µM. Further, the response time of the biosensor is the shortest (∼5 min or smaller) for citrate as the accompanying anion with ferric ions. While the response time is longer than that expected of normal biosensors, it is well compensated by the simplicity and economics of the biosensor production. Extremely low standard deviations in several experimental repeats also highlight the robustness of the ferric ions biosensor. Most importantly, the biosensor is extremely easy to use due to its straightforward spectrophotometric applications. We also show the utility of the biosensor with the high resolution technique of fluorescence microscopy. Finally, we report a novel mechanistic finding that siderophores present in the culture broth supernatants have two distinct optically active sites on them, which can be monitored independently in presence or absence of ferric ions. Biotechnol. Bioeng. 2008;100: 284–296. © 2007 Wiley Periodicals, Inc.
Serum‐free transient protein production system based on adenoviral vector and PER.C6 technology: High yield and preserved bioactivity
Authors: Havenga M.J.E. , Holterman L. , Melis I. , Smits S. , Kaspers J. , Heemskerk E. , Vlugt R. van der , Koldijk M. , Schouten G.J. , Hateboer G. , Brouwer K. , Vogels R. , Goudsmit J. 
Published: December 2007

AbstractStable E1 transformed cells, like PER.C6, are able to grow at scale and to high cell densities. E1‐deleted adenoviruses replicate to high titer in PER.C6 cells whereas subsequent deletion of E2A from the vector results in absence of replication in PER.C6 cells and drastically lowers the expression of adenovirus proteins in such cells. We therefore considered the use of an ΔE1/ΔE2 type 5 vector (Ad5) to deliver genes to PER.C6 cells growing in suspension with the aim to achieve high protein yield. To evaluate the utility of this system we constructed ΔE1/ΔE2 vector carrying different classes of protein, that is, the gene coding for spike protein derived from the Coronavirus causing severe acute respiratory syndrome (SARS‐CoV), a gene coding for the SARS‐CoV receptor or the genes coding for an antibody shown to bind and neutralize SARS‐CoV (SARS‐AB). The ΔE1/ΔE2A‐vector backbones were rescued on a PER.C6 cell line engineered to constitutively over express the Ad5 E2A protein. Exposure of PER.C6 cells to low amounts (30 vp/cell) of ΔE1/ΔE2 vectors resulted in highly efficient (>80%) transduction of PER.C6 cells growing in suspension. The efficient cell transduction resulted in high protein yield (up to 60 picogram/cell/day) in a 4 day batch production protocol. FACS and ELISA assays demonstrated the biological activity of the transiently produced proteins. We therefore conclude that ΔE1/ΔE2 vectors in combination with the PER.C6 technology may provide a viable answer to the increasing demand for high quality, high yield recombinant protein. Biotechnol. Bioeng. 2008;100: 273–283. © 2007 Wiley Periodicals, Inc.
Case study and application of process analytical technology (PAT) towards bioprocessing: Use of on‐line high‐performance liquid chromatography (HPLC) for making real‐time pooling decisions for process chromatography
Authors: Rathore Anurag S. , Yu Marcella , Yeboah Samuel , Sharma Ashutosh 
Published: December 2007

AbstractProcess analytical technology (PAT) has been gaining a lot of momentum in the biopharmaceutical community due to the potential for continuous real time quality assurance resulting in improved operational control and compliance. This paper presents a PAT application for one of the most commonly used unit operation in bioprocessing, namely liquid chromatography. Feasibility of using a commercially available online‐high performance liquid chromatography (HPLC) system for real‐time pooling of process chromatography column is examined. Further, experimental data from the feasibility studies are modeled and predictions of the model are compared to actual experimental data. It is found that indeed for the application under consideration, the online‐HPLC offers a feasible approach for analysis that can facilitate real‐time decisions for column pooling based on product quality attributes. It is shown that implementing this analytical scheme allows us to meet two of the key goals that have been outlined for PAT, that is, “variability is managed by the process” and “product quality attributes can be accurately and reliably predicted over the design space established for materials used, process parameters, manufacturing, environmental, and other conditions.” Finally, the implications of implementing such a PAT application in a manufacturing environment are discussed. The application presented here can be extended to other modes of process chromatography and/or HPLC analysis. Biotechnol. Bioeng. 2008;100: 306–316. © 2007 Wiley Periodicals, Inc.
Effect of electric currents on bacterial detachment and inactivation
Authors: Hong Seok Hoon , Jeong Joonseon , Shim Soojin , Kang Heekyoung , Kwon Sunghoon , Ahn Kyung Hyun , Yoon Jeyong 
Published: December 2007

AbstractSince biofilms show strong resistance to conventional disinfectants and antimicrobials, control of initial bacterial adhesion is generally accepted as one of the most effective strategies for preventing biofilm formation. Although electrical methods have been widely studied, the specific properties of cathodic, anodic, and block currents that influence the bacterial detachment and inactivation remained largely unclear. This study investigated the specific role of electric currents in the detachment and inactivation of bacteria adhered to an electrode surface. A real‐time bacterial adhesion observation and control system was employed that consisted of Pseudomonas aeruginosa PAO1 (PAO1) with green fluorescent protein as the indicator microorganism and a flow cell reactor mounted on a fluorescent microscope. The results suggest that the bacteria that remained on the electrode surface after application of a cathodic current were alive, although the extent of detachment was significant. In contrast, when an anodic current was applied, the bacteria that remained on the surface became inactive with time, although bacterial detachment was not significant. Further, under these conditions, active bacterial motions were observed, which weakened the binding between the electrode surface and bacteria. This phenomenon of bacterial motion on the surface can be used to maximize bacterial detachment by manipulation of the shear rate. These findings specific for each application of a cathodic or anodic electric current could successfully explain the effectiveness of block current application in controlling bacterial adhesion. Biotechnol. Bioeng. 2008;100: 379–386. © 2007 Wiley Periodicals, Inc.