bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of molecular variation on protein interactions
Authors: Ho Jason G. S. , Middelberg Anton P. J. 
Published: October 2003

AbstractWe investigated the influence of solvation forces on protein–protein interactions for two forms of lysozyme: hen egg white (HEWL) and turkey egg white (TEWL). Turkey egg white has more surface exposed hydrophobic residues than HEWL and the protein–protein interactions of TEWL are shown to be more attractive than those of HEWL, for the conditions studied. The importance of including a solvation term in the potential of mean force model, to account for molecular variation in protein surface characteristics, is highlighted. We also show that the magnitude of this solvation term can be estimated using readily available data. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 611–616, 2003.
Minimization of carbon losses in pilot‐scale outdoor photobioreactors by model‐based predictive control
Authors: García Sánchez J. L. , Berenguel M. , Rodríguez F. , Fernández Sevilla J. M. , Brindley Alias C. , Acién Fernández F. G. 
Published: October 2003

AbstractThe optimization of carbon use in pilot‐scale outdoor tubular photobioreactors is investigated in this study. The behavior of a 0.20‐m3 tubular photobioreactor was studied, with and without algae, by steady‐state and pulse dynamic‐response analysis experiments. A model of the system was obtained and implemented in a programmable control unit and was used to control the reactor under normal production conditions. Results showed that, using and on–off control, the mean daily CO2 flow in the reactor was 0.86 g min−1, 19.7% of this being lost. By using a predictive control algorithm the mean daily CO2 flow was reduced to 0.74 g min−1, with losses being reduced to 15.6%. In this case, pH tracking was not adequate, especially at the beginning and end of the daylight period, because the variation in solar irradiance was not considered. Taking solar irradiance into account resulted in better performance, with mean daily CO2 flow reduced to 0.70 g min−1, and carbon losses reduced to 5.5%. pH tracking was improved and valve actuation was reduced. Improvement of pH control reduced pH gradients in the culture, which increased the photosynthesis rate and biomass productivity of the system. Biomass productivity increased from 1.28 to 1.48 g L−1 day−1 when on–off control was replaced by model‐based predictive control plus solar irradiance effect mode. Implementation of this methodology in outdoor photobioreactors can increase productivity by 15% and reduce the cost of producing biomass by >6%. Clearly, application of effective control techniques, such as model‐based predictive control (MPC), must be considered when developing these processes. © 2004 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 533–543, 2004.
Organic tissues in rotating bioreactors: fluid‐mechanical aspects, dynamic growth models, and morphological evolution
Authors: Lappa Marcello 
Published: October 2003

AbstractThis analysis deals with advances in tissue‐engineering models and computational methods as well as with novel results on the relative importance of “controlling forces” in the growth of organic constructs. Specifically, attention is focused on the rotary culture system, because this technique has proven to be the most practical solution for providing a suitable culture environment supporting three‐dimensional tissue assemblies. From a numerical point of view, the growing biological specimen gives rise to a moving boundary problem. A “volume‐of‐fraction” method is specifically and carefully developed according to the complex properties and mechanisms of organic tissue growth and, in particular, taking into account the sensitivity of the construct/liquid interface to the effect of the fluid‐dynamic shear stress (it induces changes in tissue metabolism and function that elicit a physiological response from the biological cells). The present study uses available data to introduce a set of growth models. The surface conditions are coupled to the transfer of mass and momentum at the specimen/culture‐medium interface and lead to the introduction of a group of differential equations for the nutrient concentration around the sample and for the evolution of tissue mass displacement. The models are then used to show how the proposed surface kinetic laws can predict (through sophisticated numerical simulations) many of the known characteristics of biological tissues grown using rotating‐wall perfused vessel bioreactors. This procedure provides a validation of the models and associated numerical method and also gives insight into the mechanisms of the phenomena. The interplay between the increasing size of the tissue and the structure of the convective field is investigated. It is shown that this interaction is essential in determining the time evolution of the tissue shape. The size of the growing specimen plays a critical role with regard to the intensity of convection and the related shear stresses. Convective effects, in turn, are found to impact growth rates, tissue size, and morphology, as well as the mechanisms driving growth. The method exhibits novel capabilities to predict and elucidate experimental observations and to identify cause‐and‐effect relationships. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 518–532, 2003.
Efficient anaerobic whole cell stereoselective bioreduction with recombinant saccharomyces cerevisiae
Authors: Katz Michael , Frejd Torbjörn , Hahn‐Hägerdal Bärbel , Gorwa‐Grauslund Marie F. 
Published: October 2003

AbstractIn this study we investigate the NADPH‐dependent stereoselective reduction of the bicyclic diketone bicyclo[2.2.2]octane‐2,6‐dione (BCO2,6D) to the chiral ketoalcohol (1R,4S,6S)‐6‐hydroxybicyclo[2.2.2]octane‐2‐one (BCO2one6ol). Our aim was to develop a whole cell batch process for reduction of carbonyl substrates with (i) a high cosubstrate yield (formed product/consumed cosubstrate) and (ii) a high conversion rate under anaerobic conditions with Saccharomyces cerevisiae as biocatalyst and glucose as cosubstrate. Five open reading frames (ORFs), YMR226c, YDR368w, YOR120w, YGL157w, and YGL039w, encoding reductases involved in the conversion of BCO2,6D were identified using cell‐free extract from strains belonging to the ExClone collection (yeast ORF expression clones; ResGen, Invitrogen Corp., UK). We report the one‐step purification and characterization of three major BCO2,6D reductases, YMR226cp, YDR368wp (YPR1p), and YOR120wp (GCY1p). The reductases were overexpressed under a strong constitutive promoter and the impact on cosubstrate yield, conversion time, glucose consumption rate, and reduction rate was investigated when reductases were overexpressed either alone or in combination with low phosphoglucose isomerase activity (encoded by YBR196c). Combining overexpression of BCO2,6D reductase with reduced glycolytic rate (low phosphoglucose isomerase activity) offers a fast whole cell stereoselective bioreduction system useful for facilitated anaerobic batch conversions. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 573–582, 2003.
Use of complex DNA and antibody microarrays as tools in functional analyses
Authors: Bauer Andrea , Beckmann Boris , Busold Christian , Brandt Ole , Kusnezow Wlad , Pullat Janne , Aign Verena , Fellenberg Kurt , Fleischer Robert , Jacob Anette , Frohme Marcus , Hoheisel Jörg D. 
Published: October 2003

AbstractWhile the deciphering of basic sequence information on a genomic scale is yielding complete genomic sequences in ever‐shorter intervals, experimental procedures for elucidating the cellular effects and consequences of the DNA‐encoded information become critical for further analyses. In recent years, DNA microarray technology has emerged as a prime candidate for the performance of many such functional assays. Technically, array technology has come a long way since its conception some 15 years ago, initially designed as a means for large‐scale mapping and sequencing. The basic arrangement, however, could be adapted readily to serve eventually as an analytical tool in a large variety of applications. On their own or in combination with other methods, microarrays open up many new avenues of functional analysis. Copyright © 2003 John Wiley & Sons, Ltd.
Transient expression of doublecortin during adult neurogenesis
Authors: Brown Jason P. , Couillard‐Després Sébastien , Cooper‐Kuhn Christiana M. , Winkler Jürgen , Aigner Ludwig , Kuhn H. Georg 
Published: October 2003

AbstractDuring development of the central nervous system, expression of the microtubule binding protein doublecortin (DCX) is associated with migration of neuroblasts. In addition to this developmental role, expression of DCX remains high within certain areas of the adult mammalian brain. These areas, mainly the dentate gyrus and the lateral ventricle wall in conjunction with the rostral migratory stream and olfactory bulb, retain the capacity to generate new neurons into adulthood. Adult neurogenesis is typically detected by incorporation of bromodeoxyuridine (BrdU) into dividing cells and colabeling of BrdU‐positive cells with markers for mature neurons. To elucidate whether DCX could act as an alternative indicator for adult neurogenesis, we investigated the temporal expression pattern of DCX in neurogenic regions of the adult brain. Analysis of newly generated cells showed that DCX is transiently expressed in proliferating progenitor cells and newly generated neuroblasts. As the newly generated cells began expressing mature neuronal markers, DCX immunoreactivity decreased sharply below the level of detection and remained undetectable thereafter. The transient expression pattern of DCX in neuronal committed progenitor cells/neuroblasts indicates that DCX could be developed into a suitable marker for adult neurogenesis and may provide an alternative to BrdU labeling. This assumption is further supported by our observation that the number of DCX‐expressing cells in the dentate gyrus was decreased with age according to the reduction of neurogenesis in the aging dentate gyrus previously reported. J. Comp. Neurol. 467:1–10, 2003. © 2003 Wiley‐Liss, Inc.
Green fluorescent protein expression and colocalization with calretinin, parvalbumin, and somatostatin in the GAD67‐GFP knock‐in mouse
Authors: Tamamaki Nobuaki , Yanagawa Yuchio , Tomioka Ryohei , Miyazaki Jun‐Ichi , Obata Kunihiko , Kaneko Takeshi 
Published: October 2003

Abstractγ‐aminobutyric acid (GABA)ergic neurons in the central nervous system regulate the activity of other neurons and play a crucial role in information processing. To assist an advance in the research of GABAergic neurons, here we produced two lines of glutamic acid decarboxylase–green fluorescence protein (GAD67‐GFP) knock‐in mouse. The distribution pattern of GFP‐positive somata was the same as that of the GAD67 in situ hybridization signal in the central nervous system. We encountered neither any apparent ectopic GFP expression in GAD67‐negative cells nor any apparent lack of GFP expression in GAD67‐positive neurons in the two GAD67‐GFP knock‐in mouse lines. The timing of GFP expression also paralleled that of GAD67 expression. Hence, we constructed a map of GFP distribution in the knock‐in mouse brain. Moreover, we used the knock‐in mice to investigate the colocalization of GFP with NeuN, calretinin (CR), parvalbumin (PV), and somatostatin (SS) in the frontal motor cortex. The proportion of GFP‐positive cells among NeuN‐positive cells (neocortical neurons) was approximately 19.5%. All the CR‐, PV‐, and SS‐positive cells appeared positive for GFP. The CR‐, PV, and SS‐positive cells emitted GFP fluorescence at various intensities characteristics to them. The proportions of CR‐, PV‐, and SS‐positive cells among GFP‐positive cells were 13.9%, 40.1%, and 23.4%, respectively. Thus, the three subtypes of GABAergic neurons accounted for 77.4% of the GFP‐positive cells. They accounted for 6.5% in layer I. In accord with unidentified GFP‐positive cells, many medium‐sized spherical somata emitting intense GFP fluorescence were observed in layer I. J. Comp. Neurol. 467:60–79, 2003. © 2003 Wiley‐Liss, Inc.
Synapse replacement in the striatum of the adult rat following unilateral cortex ablation
Authors: McNeill Thomas H. , Brown Sally A. , Hogg Elizabeth , Cheng Heng‐Wei , Meshul Charles K. 
Published: October 2003

AbstractDefining the selective pattern of synapse replacement that occurs in different areas of the damaged brain is essential for predicting the limits of functional compensation that can be achieved after various types of brain injury. Here we describe the time course of dendritic reorganization, spine loss and recovery, and synapse replacement in the striatum following a unilateral cortex ablation. We found that the time course for the transient loss and recovery of dendritic spines on medium spiny I (MSI) neurons, the primary postsynaptic target for corticostriatal axons, paralleled the time course for the removal of degenerating axon terminals from the neuropil and the formation of new synapses on MSI neurons. Reinnervation of the deafferented striatum occurred chiefly by axon terminals that formed asymmetric synapses with dendritic spines of MSI neurons, and the mean density of asymmetric synapses recovered to 86% of the sham‐operated rat value by 30 days postlesion. In addition, the synaptic circuitry of the reconstructed striatum was characterized by an increase in the number of multiple synaptic boutons (MSBs), i.e., presynaptic axon terminals that make contact with more than one dendritic spine. Whether the postsynaptic contacts of MSBs are formed with the dendritic spines of the same or a different parent dendrite in the striatum is unknown. Nevertheless, these data suggest that the formation of MSBs is an essential part of the compensatory response to the loss of input from the ipsilateral cortex following the aspiration lesion and may serve to modulate activity‐dependent adaptive changes in the reconstructed striatum that can lead to functional recovery. J. Comp. Neurol. 467:32–43, 2003. © 2003 Wiley‐Liss, Inc.
Brain‐derived neurotrophic factor regulates expression of vasoactive intestinal polypeptide in retinal amacrine cells
Authors: Cellerino Alessandro , Arango‐González Blanca , Pinzón‐Duarte Germán , Kohler Konrad 
Published: October 2003

AbstractBrain‐derived neurotrophic‐factor (BDNF) is expressed in the retina and controls the development of subtypes of amacrine cells. In the present study we investigated the effects of BDNF on amacrine cells expressing vasoactive intestinal polypeptide (VIP). Rats received three intraocular injections of BDNF on postnatal days (P) 16, 18, and 20. The animals were sacrificed on P22, P40, P60, P80, and P120, and VIP expression in their retinas was detected by immunohistochemistry (P22, P40) and by radioimmunoassay (RIA; P22, P40, P60, P80, P120) to assess the time course of BDNF effects on VIP. A significant increase in the density of VIP‐positive amacrine cells was detected in BDNF‐treated retinas, and VIP concentration was up‐regulated by 150% both at P22 and at P40 with respect to untreated controls. VIP concentration then slowly declined in the treated retinas over a period of 3 months; however, a statistically significant increase of 50% was still detectable on P120. The impact of endogenous BDNF on the regulation of VIP expression in the retina was analyzed in mice homozygous for a targeted deletion of the BDNF gene locus (bdnf−/−). VIP immunohistochemistry revealed a marked reduction of VIP‐positive amacrine cells and of VIP‐immunopositive processes in the inner plexiform layer of the BDNF knockout mice. Mice lacking BDNF expressed only 5% of the VIP protein in their retinas compared with the retinas of wild‐type mice as measured by RIA. Our data show that BDNF is a major regulator of VIP expression in retinal amacrine cells and exerts long‐lasting effects on VIP content. J. Comp. Neurol. 467:97–104, 2003. © 2003 Wiley‐Liss, Inc.
Organization of somatosensory cortex in the laboratory rat (Rattus norvegicus): Evidence for two lateral areas joined at the representation of the teeth
Authors: Remple Michael S. , Henry Erin C. , Catania Kenneth C. 
Published: October 2003

AbstractLateral somatosensory areas have not been explored in detail in rats, and theories on the organization of this region are based largely on anatomical tracing experiments. We investigated the topography of this region by using microelectrode recordings, which were related to flattened cortical sections processed for cytochrome oxidase (CO). Two lateral somatosensory areas were identified, each containing a complete representation of the body. A larger, more medial representation formed a mirror image of S1 along the rostrocaudal axis of the head region corresponding to the previously identified secondary somatosensory area (S2). A smaller, more lateral representation formed a mirror image of S2 along the rostrocaudal axis of the forelimb and hindlimb regions and likely corresponds to the parietal ventral area (PV) identified in other mammals. We also investigated the representation of the dentition and identified regions of cortex responsive to tooth stimulation. The lower incisor representation was rostral to the lower lip region of S1, and the upper incisor representation was lateral to the buccal pad region of S1. The upper and lower incisors flanked the tongue representation. An additional large region of far lateral cortex responded to both incisors. Finally, five CO‐dense modules were consistently identified rostral and lateral to the S1 face representation, which we refer to as OM1, OM2, OM3, FM, and HM. These modules closely correspond to the physiologically identified areas representing the lower incisor (OM1) and tongue (OM2) regions of S1 and the mixed tooth (OM3), forelimb (FM1), and hindlimb (HM) representations of S2 and PV. J. Comp. Neurol. 467:105–118, 2003. © 2003 Wiley‐Liss, Inc.
Cell surface carbohydrates and glomerular targeting of olfactory sensory neuron axons in the mouse
Authors: Lipscomb Brian W. , Treloar Helen B. , Klenoff Jason , Greer Charles A. 
Published: October 2003

AbstractCell surface carbohydrates have been implicated in axon guidance and targeting throughout the nervous system. We have begun to test the hypothesis that, in the olfactory system, a differential distribution of cell surface carbohydrates may influence olfactory sensory neuron (OSN) axon targeting. Specifically, we have examined the spatial distribution of two different plant lectins, Ulex europaeus agglutinin (UEA) and Dolichos biflorus agglutinin (DBA), to determine whether they exhibit differential and reproducible projections onto the main olfactory bulb. Each lectin exhibited a unique spatial domain of glomerular labeling that was consistent across animals. UEA labeling was strongest in the ventral aspect of the olfactory bulb; DBA labeling was strongest in the dorsal aspect of the olfactory bulb. Some evidence for colocalization was present where these two borders intersected. Large areas of the glomerular layer were not labeled by either lectin. To determine whether patterns of lectin labeling were reproducible at the level of individual glomeruli, UEA labeling was assessed relative to M72‐IRES‐taulacZ‐ and P2‐IRES‐taulacZ‐labeled axons. Although glomeruli neighboring these two identified glomeruli were consistently labeled with UEA, none of the lacZ positive axons was lectin labeled. Labeling of vomeronasal sensory neuron axons in the accessory olfactory bulb was more uniform for the two lectins. These data are the first to show a differential distribution of UEA vs. DBA labeling in the main olfactory bulb and are consistent with the hypothesis that a differential distribution of cell surface carbohydrates, a glycocode, may contribute to the targeting of OSN axons. J. Comp. Neurol. 467:22–31, 2003. © 2003 Wiley‐Liss, Inc.
Development of a sexually dimorphic neuromuscular system in male rats after spinal transection: Morphologic changes and implications for estrogen sites of action
Authors: Hebbeler Sara L. , Sengelaub Dale R. 
Published: October 2003

AbstractThe lumbar spinal cord of rats contains the sexually dimorphic, steroid‐sensitive spinal nucleus of the bulbocavernosus (SNB). In male rats, SNB motoneurons exhibit a biphasic pattern of dendritic growth, having an initial period of exuberant growth followed by a period of retraction to mature lengths by 7 weeks of age. This growth is steroid dependent: dendrites fail to grow after castration, but growth is supported in castrates treated with estradiol. In this experiment, we examined whether supraspinal afferent input by means of descending spinal tracts to the SNB was involved in the normal postnatal development of SNB motoneurons, and whether the effect of estradiol on SNB dendritic growth could be explained by an indirect action of estradiol on supraspinal afferents. Motoneuron morphology was assessed in normal males, early‐ or late‐postnatally transected males, castrated males left untreated or treated with estradiol, and transected castrates treated with estradiol. SNB motoneurons were retrogradely labeled with cholera toxin–horseradish peroxidase during both the growth and retraction phases of dendritic development and reconstructed in three dimensions. The removal of supraspinal afferents resulted in extremely local effects within the developing SNB arbor, as well as transient alterations in somal growth. Furthermore, spinal transection did not block the trophic effect of estradiol on supporting SNB dendritic growth, indicating that estrogens do not act by means of supraspinal input to support SNB motoneuron development. J. Comp. Neurol. 467:80–96, 2003. © 2003 Wiley‐Liss, Inc.
Nicotinic acetylcholine receptor distribution in relation to spinal neurotransmission pathways
Authors: Khan Imran , Osaka Hitoshi , Stanislaus Shanaka , Calvo Rosa M. , Deerinck Tom , Yaksh Tony L. , Taylor Palmer 
Published: October 2003

AbstractNeuronal nicotinic receptors (nAChR) are pentameric assemblies of subunits of a gene family where specified combinations of α and β subunits form functional receptors. To extend our understanding of the role of spinal nAChR in the processing of sensory stimuli and regulation of autonomic and motor responses, we initiated investigations to localize nAChR subunit expression within discrete spinal regions and cell types. High‐affinity epibatidine binding was present in the superficial dorsal and ventral horns, the mediolateral and central canal regions. RT‐PCR identified transcripts for α3, α4, α5, β2, and β4 in both spinal cord parenchyma and dorsal root ganglia (DRG). Our affinity‐purified antibodies against α3, α4, α5, β2, and β4 subunits identified specific protein bands of appropriate molecular mass (preadsorbed with the respective antigens) in specific tissues and cells that express nicotinic receptors, including the spinal cord and DRG neurons. Having established the absence of crossreactivity with related subunits, specific fluorescence labeling of nerve terminals and cell bodies was achieved and correlated with the distribution of defined marker proteins and nicotinic receptor binding sites determined autoradiographically. Our findings indicate that α3, α4, α5, β2, and β4 subunits are all expressed on primary afferents (IB4‐positive terminals) in the spinal cord. The predominant presynaptic (synaptophysin colocalization) labeling is in the superficial layer of the dorsal horn. These receptor subunits, except for β4, are also present in postsynaptic autonomic (anti‐bNOS‐positive) and somatic motor neurons (anti‐VAChT‐positive). The α3, α5, and β2 subunits showed additional staining in glial (anti‐GFAP‐positive) cells. These studies reveal a dense and distinguishable distribution of nAChR subunits in the spinal cord and point toward future therapeutic targeting for specific spinal actions. J. Comp. Neurol. 467:44–59, 2003. © 2003 Wiley‐Liss, Inc.