bluuebunny/crossref_metadata_2025_split huggingface dataset:
A splicing model‐based DNA‐computing approach on microfluidic chip
Authors: Xie Hua , Li Bowei , Qin Jianhua , Huang Zhende , Zhu Yisheng , Lin Bingcheng 
Published: October 2009

AbstractDNA computing is a new computation form based on DNA biochemical reactions, which is mainly composed of sticker and splicing computation models. In this work, a microfluidic chip‐based approach was established for splicing model‐based DNA computing. A finite automaton with two input symbols (a, b) and three states (S0, S1, and S2) was applied in the pattern recognition for isosceles triangles. The DNA computation processes of automaton were realized through DNA digestion, ligation, DNA separation, and detection on the microfluidic chip. The established approach is efficient, controllable, and easy to integrate, which paves the way for the building of complete biomolecular computers in the future.
Outage minimisation in wireless relay networks with delay constraints and causal channel feedback
Authors: Li James C. F. , Dey Subhrakanti 
Published: October 2009

AbstractMotivated by delay‐sensitive information transmission applications, we solve an optimal power allocation problem with aK‐block delay constraint on data transmission using a cooperative relay network assuming a block fading channel model. Channel information is fed back to the transmitter only in a causal fashion, so that the optimal power allocation strategy is only based on the current and past channel gains. We consider the two simplest schemes for information transmission using a three node (a source, a relay and a destination) relay network, namely the amplify and forward (AF) and decode and forward (DF) protocols. We use a dynamic programming (DP) based methodology to solve a (K‐block delay constrained) general expected cost optimisation problem with a short term (overKblocks) sum power (total transmission power of the source and the relay) constraint. By specialising the cost function appropriately, we solve the delay constrained outage minimisation problem in this paper. We also propose a simple but sub‐optimal power allocation scheme based on a high signal to noise ratio (SNR) approximation, which is computationally much less demanding than the DP‐based optimal method. Extensive numerical results are presented for Rayleigh and Rician fading channels, including results demonstrating the performance gain obtained by optimally allocating the (sum of source and relay) power to the different blocks as opposed to equally distributing the total power across all blocks. The accuracy of the high SNR approximation based power allocation scheme is also illustrated. Copyright © 2009 John Wiley & Sons, Ltd.
Friedhof der Fischsaurier
Authors: Stinnesbeck Wolfgang , Frey Eberhard , Leppe Cartes Marcelo 
Published: October 2009

AbstractVor 120 Millionen Jahren gingen am Rande des Tyndall‐Gletschers die Ichthyosaurier zugrunde. Nun ergründen Paläontologen, wie es zu dem Massensterben auf engstem Raum kam – eine Spurensuche im chilenischen Nationalpark Torres del Paine
Quercetin‐induced upregulation of human GCLC gene is mediated by cis‐regulatory element for early growth response protein‐1 (EGR1) in INS‐1 beta‐cells
Authors: Kang Jung‐Hoon , Chang Seo‐Yoon , Jang Hyun‐Jong , Cho Jae Min , Kim Dong‐Bin , Lee Seong Su , Ko Seung Hyun , Park Yong‐Moon , Needs Paul W. , Jo Yang‐Hyeok , Kim Myung‐Jun 
Published: October 2009

AbstractThe catalytic subunit of γ‐glutamylcysteine ligase (GCLC) catalyses the rate‐limiting step in the de novo synthesis of glutathione (GSH), which is involved in maintaining intracellular redox balance. GSH is especially important for antioxidant defense system since beta‐cells show intrinsically low expression of antioxidant enzymes. In the present study, we investigated the regulatory mechanisms by which quercetin, a flavonoid, induces the expression of the GCLC gene in rat pancreatic beta‐cell line INS‐1. Promoter study found that the proximal GC‐rich region (from −90 to −34) of the GCLC promoter contained the quercetin‐responsive cis‐element(s). The quercetin‐responsive region contains consensus DNA binding site for early growth response 1 (EGR1) at ‐67 (5′‐CGCCTCCGC‐3′) which overlaps with a putative Sp1 binding site. Electrophoretic mobility shift assay showed that an oligonucleotide containing the EGR1 site was bound to nuclear factors EGR1, Sp1, and Sp3. In the promoter analysis, mutation of EGR1 site significantly reduced the quercetin response, whereas mutation of Sp1 site decreased only the basal activity of the GCLC promoter. Additionally, the transient overexpression of EGR1 significantly increased basal activity of the GCLC promoter. Finally, we showed that quercetin potently induced both EGR1 mRNA and its protein levels without affecting the expression of Sp1 and Sp3 proteins. Therefore, we concluded that EGR1 was bound to GC‐rich region of the GCLC gene promoter, which was prerequisite for the transactivation of the GCLC gene by quercetin. J. Cell. Biochem. 108: 1346–1355, 2009. © 2009 Wiley‐Liss, Inc.
Proteomic analysis of differentially expressed proteins in human cholangiocarcinoma cells treated withClonorchis sinensisexcretory–secretory products
Authors: Pak Jhang Ho , Moon Ju Hyun , Hwang Seung‐Jun , Cho Shin‐Hyeong , Seo Sang‐Beom , Kim Tong‐Soo 
Published: October 2009

AbstractSevereClonorchis sinensisinfection is a significant risk factor for malignant changes in bile ducts and surrounding liver tissues occurring as a result of direct contact withC. sinensisworms and their excretory–secretory products (ESP). However, the intrinsic molecular mechanisms involved in these processes remain obscure. To determine the effects ofC. sinensisinfection on protein expression in host bile duct epithelium, we examined proteomic profile changes in the human cholangiocarcinoma cell line (HuCCT1) treated with ESP at 24 h. Using a combination of 2‐DE, quantitative image and MALDI‐TOF MS analysis, we identified 83 proteins that were translationally modulated in response to ESP, among which 49 were up‐regulated and 34 down‐regulated. These proteins were classified under various biological categories, including metabolism, cell structure and architecture, proteolysis, protein modification, transport, signal transduction, and reactive oxygen species (ROS) detoxification. In particular, ESP induced the expression of redox‐regulating proteins, including peroxiredoxins (Prdx 2, 3, and 6) and thioredoxin 1 (Trx 1), possibly via intracellular ROS generation. Application of the proteomic approach to identify ESP response proteins should be a prerequisite before further investigation to clarify the molecular pathways and mechanisms involved inC. sinensisinfection of host cells. J. Cell. Biochem. 108: 1376–1388, 2009. © 2009 Wiley‐Liss, Inc.
VASP phosphorylation at serine239 regulates the effects of NO on smooth muscle cell invasion and contraction of collagen
Authors: Defawe Olivier D. , Kim Sarah , Chen Lihua , Huang Daming , Kenagy Richard D. , Renné Thomas , Walter Ulrich , Daum Günter , Clowes Alexander W. 
Published: October 2009

AbstractNitric oxide triggers cGMP‐dependent kinase‐mediated phosphorylation of the actin regulator vasodilator‐stimulated phosphoprotein (VASP) at residue serine239. The function of this phosphorylation for smooth muscle cell (SMC) adhesion, spreading, matrix contraction, and invasion is not well understood. We reconstituted VASP deficient SMC with wild‐type VASP (wt‐VASP) or VASP mutants that mimic “locked” serine239 phosphorylation (S239D‐VASP) or “blocked” serine239 phosphorylation (S239A‐VASP). Collagen gel contraction was reduced in S239D‐VASP compared to S239A‐VASP and wt‐VASP expressing cells and nitric oxide (NO) stimulation decreased gel contraction of wt‐VASP reconstituted SMC. Invasion of collagen was enhanced in S239D‐VASP and NO‐stimulated wild‐type SMCs compared to S239A‐VASP expressing cells. Expression of S239D‐VASP impaired SMC attachment to collagen, reduced the number of membrane protrusions, and caused cell rounding compared to expression of S239A‐VASP. Treatment of wt‐VASP reconstituted SMCs with NO exerted similar effects as expression of S239D‐VASP. As unstimulated cells were spreading on collagen S239A‐VASP and wt‐VASP localized to actin fibers whereas S239D‐VASP was enriched in the cytosol. NO interferes with SMC invasion and contraction of collagen matrices. This requires phosphorylation of VASP on serine239, which reduces VASP binding to actin fibers. These findings support the conclusion that VASP phosphorylation at serine239 regulates cytoskeleton remodeling. J. Cell. Physiol. 222:230–237, 2010. © 2009 Wiley‐Liss, Inc.
GATA3 in development and cancer differentiation: Cells GATA have it!
Authors: Chou Jonathan , Provot Sylvain , Werb Zena 
Published: October 2009

AbstractThere is increasing evidence that the numerous mechanisms that regulate cell differentiation during normal development are also involved in tumorigenesis. In breast cancer, differentiation markers expressed by the primary tumor are routinely profiled to guide clinical decisions. Indeed, numerous studies have shown that the differentiation profile correlates with the metastatic potential of tumors. The transcription factor GATA3 has emerged recently as a strong predictor of clinical outcome in human luminal breast cancer. In the mammary gland, GATA3 is required for luminal epithelial cell differentiation and commitment, and its expression is progressively lost during luminal breast cancer progression as cancer cells acquire a stem cell‐like phenotype. Importantly, expression of GATA3 in GATA3‐negative, undifferentiated breast carcinoma cells is sufficient to induce tumor differentiation and inhibits tumor dissemination in a mouse model. These findings demonstrate the exquisite ability of a differentiation factor to affect malignant properties, and raise the possibility that GATA3 or its downstream genes could be used in treating luminal breast cancer. This review highlights our recent understanding of GATA3 in both normal mammary development and tumor differentiation. J. Cell. Physiol. 222:42–49, 2010. © 2009 Wiley‐Liss, Inc.
Inositol 1,4,5‐trisphosphate receptor 1 degradation in mouse eggs and impact on [Ca2+]i oscillations
Authors: Lee Bora , Yoon Sook‐Young , Malcuit Chris , Parys Jan B. , Fissore Rafael A. 
Published: October 2009

AbstractThe initiation of normal embryo development depends on the completion of all events of egg activation. In all species to date, egg activation requires an increase(s) in the intracellular concentration of calcium ([Ca2+]i), which is almost entirely mediated by inositol 1,4,5‐trisphosphate receptor 1 (IP3R1). In mammalian eggs, fertilization‐induced [Ca2+]i responses exhibit a periodic pattern that are called [Ca2+]i oscillations. These [Ca2+]i oscillations are robust at the beginning of fertilization, which occurs at the second metaphase of meiosis, but wane as zygotes approach the pronuclear stage, time after which in the mouse oscillations cease altogether. Underlying this change in frequency are cellular and biochemical changes associated with egg activation, including degradation of IP3R1, progression through the cell cycle, and reorganization of intracellular organelles. In this study, we investigated the system requirements for IP3R1 degradation and examined the impact of the IP3R1 levels on the pattern of [Ca2+]i oscillations. Using microinjection of IP3 and of its analogs and conditions that prevent the development of [Ca2+]i oscillations, we show that IP3R1 degradation requires uniform and persistently elevated levels of IP3. We also established that progressive degradation of the IP3R1 results in [Ca2+]i oscillations with diminished periodicity while a near complete depletion of IP3R1s precludes the initiation of [Ca2+]i oscillations. These results provide insights into the mechanism involved in the generation of [Ca2+]i oscillations in mouse eggs. J. Cell. Physiol. 222:238–247, 2010. © 2009 Wiley‐Liss, Inc.
Simultaneous wet ball milling and mild acid hydrolysis of rice hull
Authors: Zhou Jinxiang , Chen Ding , Zhu Yonghua , Liao Hongdong , Yuan Li , Chen Zhenhua , Liu Xuanming 
Published: October 2009

AbstractBACKGROUND: Rice hull, an abundant residue but a big issue for the rice processing industry, has the potential to serve as a feedstock for production of ethanol because of its lignocellulosic composition. Simultaneous wet ball milling and mild acid hydrolysis of rice hull was studied in this work.RESULTS: Ball milling with 150 small stainless steel beads and rotation speed of 600 rpm in citrate solvent of pH 4 was the optimal condition for hydrolysis, and the yield of sugar increased with increased milling time. Corresponding structure transformations before and after milling analyzed by X‐ray diffraction (XRD), environmental scanning electron microscopy (ESEM) and transmission fourier transform infrared spectroscopy (FT‐IR) clearly indicate that this hydrolysis could be attributed to the crystalline and chemical structure changes of cellulose in rice hull during ball milling in mild acid solvent.CONCLUSION: This combined treatment of ball milling and citrate solvent greatly changed the crystalline and chemical structure and continuously generated sites accessible to citrate solvent, thus enabling hydrolysis of the rice hull. Copyright © 2009 Society of Chemical Industry
Different combinations of salts affect the growth and bacteriocin production by Lactobacillus salivarius CRL 1328
Authors: Juárez Tomás María Silvina , Bru Elena , Nader‐Macías María Elena 
Published: October 2009

AbstractBACKGROUND: The culture medium for optimal growth of vaginal Lactobacillus salivarius CRL 1328 is different from that for optimal bacteriocin production. To simultaneously obtain high amount of biomass and bacteriocin of this microorganism, the effects of different basal culture media and salts on both responses were evaluated. The study was performed by using a complete factorial experimental design 26, with central points. Sixty‐four different growth media, which resulted from the combinations of two basal culture media and two concentrations of five salts (ammonium citrate, sodium acetate, MgSO4, MnSO4, and K2HPO4) were assayed.RESULTS: Only the addition of MnSO4 to each culture medium significantly stimulated the growth of L. salivarius. The presence of sodium acetate or MgSO4 stimulated the bacteriocin production, while MnSO4 and K2HPO4 exerted an inhibitory effect. However, the simultaneous addition of MnSO4 and sodium acetate to both basal culture media allowed high bacteriocin levels to be reached, attenuating the inhibitory effect of Mn2+.CONCLUSIONS: The application of a complete experimental design contributed to simultaneous optimization of the biomass and bacteriocin production of L. salivarius CRL 1328. The results obtained are potentially applicable to the technological production of probiotic bacteria and antagonistic substance to be included in a probiotic pharmaceutical product. Copyright © 2009 Society of Chemical Industry
Optimization of inulinase production by solid‐state fermentation in a packed‐bed bioreactor
Authors: Mazutti Marcio A. , Zabot Giovani , Boni Gabriela , Skovronski Aline , de Oliveira Débora , Di Luccio Marco , Rodrigues Maria Isabel , Treichel Helen , Maugeri Francisco 
Published: October 2009

AbstractBACKGROUND: This work is focused on inulinase production by solid‐sate fermentation (SSF) using sugarcane bagasse, corn steep liquor (CSL), pre‐treated cane molasses, and soybean bran as substrates in a 3‐kg (dry basis) packed‐bed bioreactor. SSF was carried out by the yeast Kluyveromyces marxianus NRRL Y‐7571 and response surface methodology was used to optimize the temperature, air flow rate and initial mass of cells.RESULTS: The optimum inulinase activity (436.7 ± 36.3 U g−1 dry substrate) was obtained at 24 h at an inlet air temperature of 30 °C, air flow rate 2.2 m3 h−1 and 22 g of cells for fermentation. Inulinase productivity at these conditions was 18.2 U gds−1 h−1. Kinetic evaluation at the optimized conditions showed that the maximum inulinase production was verified at 24 h of fermentation. The carbon dioxide and the metabolic heat generation are directly associated with the consumption of total reducing sugars present in the medium.CONCLUSION: The high productivity achieved in this work shows the technical viability of inulinase production by SSF in a packed‐bed bioreactor. Copyright © 2009 Society of Chemical Industry
Cranial architecture of tube‐snouted gasterosteiformes (Syngnathus rostellatus and Hippocampus capensis)
Authors: Leysen Heleen , Jouk Philippe , Brunain Marleen , Christiaens Joachim , Adriaens Dominique 
Published: October 2009

AbstractThe long snout of pipefishes and seahorses (Syngnathidae, Gasterosteiformes) is formed as an elongation of the ethmoid region. This is in contrast to many other teleosts with elongate snouts (e.g., butterflyfishes) in which the snout is formed as an extension of the jaws. Syngnathid fishes perform very fast suction feeding, accomplished by powerful neurocranial elevation and hyoid retraction. Clearly, suction through a long and narrow tube and its hydrodynamic implications can be expected to require certain adaptations in the cranium, especially in musculoskeletal elements of the feeding apparatus. Not much is known about which skeletal elements actually support the snout and what the effect of elongation is on related structures. Here, we give a detailed morphological description of the cartilaginous and bony feeding apparatus in both juvenile and adult Syngnathus rostellatus and Hippocampus capensis. Our results are compared with previous morphological studies of a generalized teleost, Gasterosteus aculeatus. We found that the ethmoid region is elongated early during development, with the ethmoid plate, the hyosymplectic, and the basihyal cartilage being extended in the chondrocranium. In the juveniles of both species almost all bones are forming, although only as a very thin layer. The elongation of the vomeral, mesethmoid, quadrate, metapterygoid, symplectic, and preopercular bones is already present. Probably, because of the long and specialized parental care which releases advanced developmental stages from the brooding pouch, morphology of the feeding apparatus of juveniles is already very similar to that of the adults. We describe morphological features related to snout elongation that may be considered adaptations for suction feeding; e.g. the peculiar shape of the interhyal bone and its saddle‐shaped articulation with the posterior ceratohyal bone might aid in explosive hyoid retraction by reducing the risk of hyoid dislocation. J. Morphol., 2010. © 2009 Wiley‐Liss, Inc.
Synergistic effect between proteasome and autophagosome in the clearance of polyubiquitinated TDP‐43
Authors: Urushitani Makoto , Sato Takashi , Bamba Hitoshi , Hisa Yasuo , Tooyama Ikuo 
Published: October 2009

AbstractCytoplasmic aggregates of ubiquitinated TAR DNA‐binding protein 43 (TDP‐43) are a pathological hallmark of amyotrophic lateral sclerosis (ALS). However, the mechanism of TDP‐43 polyubiquitination remains elusive. We investigated the effect of nuclear exclusion of TDP‐43 on aggregate formation and fragmentation, using TDP‐43 expression constructs for WT or mutant TDP‐43 with a modified nuclear localizing signal (LQ‐NLS). Overexpression of the LQ‐NLS mutant alone induced no detectable cytoplasmic aggregates during a 72‐hr period. Polyubiquitination of both WT TDP‐43 and the LQ‐NLS mutant was similar in total cell lysates exposed to the proteasome inhibitor lactacystin. However, analysis of subcellular fractions demonstrated a higher concentration of polyubiquitinated TDP‐43 in the nuclear fraction than in the cytosol for WT, and vice versa for the LQ‐NLS mutant. Polyubiquitin‐charged WT and mutant TDP‐43 were highly concentrated in the membrane/microsome fraction, which was also positive for the autophagosome marker LC3. In addition, the autophagy inhibitor 3‐methyladenine (3MA) blocked degradation of both TDP‐43 types, whereas lactacystin was minimally restorative. Furthermore, lactacystin plus 3MA induced prominent cytoplasmic aggregates. We also demonstrated mediation of TDP‐43 polyubiquitination by lysine 48 of ubiquitin, indicating a degradation signal in both TDP‐43 types. This is the first report delineating the distribution of polyubiquitinated TDP‐43 and the degradation pathway of TDP‐43 and clarifying the crucial role of autophagosomes in TDP‐43 clearance. We also demonstrate that nuclear exclusion itself is not an immediate trigger for ALS pathology. Further clarification of the mechanism of polyubiquitination of TDP‐43 and the role of autophagosomes may help in understanding and treating ALS. © 2009 Wiley‐Liss, Inc.
Calcium imaging in single neurons from brain slices using bioluminescent reporters
Authors: Drobac Estelle , Tricoire Ludovic , Chaffotte Alain‐François , Guiot Elvire , Lambolez Bertrand 
Published: October 2009

AbstractResponses of three bioluminescent Ca2+ sensors were studied in vitro and in neurons from brain slices. These sensors consisted of tandem fusions of green fluorescent protein (GFP) with the photoproteins aequorin, obelin, or a mutant aequorin with high Ca2+ sensitivity. Kinetics of GFP‐obelin responses to a saturating Ca2+ concentration were faster than those of GFP‐aequorin at all Mg2+ concentrations tested, whereas GFP‐mutant aequorin responses were the slowest. GFP‐photoproteins were efficiently expressed in pyramidal neurons following overnight incubation of acute neocortical slices with recombinant Sindbis viruses. Expression of GFP‐photoproteins did not result in conspicuous modification of morphological or electrophysiological properties of layer V pyramidal cells. The three sensors allowed the detection of Ca2+ transients associated with action potential discharge in single layer V pyramidal neurons. In these neurons, depolarizing steps of increasing amplitude elicited action potential discharge of increasing frequency. Bioluminescent responses of the three sensors were similar in several respects: detection thresholds, an exponential increase with stimulus intensity, photoprotein consumptions, and kinetic properties. These responses, which were markedly slower than kinetics measured in vitro, increased linearly during the action potential discharge and decayed exponentially at the end of the discharge. Onset slopes increased with stimulus intensity, whereas decay kinetics remained constant. Dendritic light emission contributed to whole‐field responses, but the spatial resolution of bioluminescence imaging was limited to the soma and proximal apical dendrite. Nonetheless, the high signal‐to‐background ratio of GFP‐photoproteins allowed the detection of Ca2+ transients associated with 5 action potentials in single neurons upon whole‐field bioluminescence recordings. © 2009 Wiley‐Liss, Inc.