bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid Monte Carlo with multidimensional replica exchanges: Conformational equilibria of the hypervariable regions of a llama VHH antibody domain
Authors: Fenwick Michael K. , Escobedo Fernando A. 
Published: January 2003

AbstractSince the structural repertoire of the hypervariable regions of human antibodies is known to be more restricted than what is implied by sequence variability, a common approach to structural prediction is to use a knowledge‐based (KB) method, such as the canonical structure model (C. Chothia and A. M. Lesk, Journal of Molecular Biology, 1987, Vol. 196, pp. 901–917). However, this model is less successful when applied to camelid heavy chain antibodies. In this study, molecular simulations were used to examine the conformational equilibria of the hypervariable regions (H1, H2, and H3) of a llama heavy chain variable domain, for which KB predictions are poor. Simulations were carried out using both conventional molecular dynamics (MD) and hybrid Monte Carlo with multidimensional replica exchanges (HYMREX). The advantage of the latter method is its ability to selectively target parts of the Hamiltonian that can most readily improve sampling. A novel variant of HYMREX was implemented in which, besides the temperature, torsional interactions and the range of nonbonded interactions were varied. To compare the sampling abilities of MD and this HYMREX scheme, simulations were started from a misfolded conformational state. Overall, MD yielded final conformations more similar to the initial state, implying quasi‐ergodic sampling. In contrast, HYMREX achieved more ergodic sampling, and the majority of conformations that it sampled agreed well with the known crystal structure. The HYMREX simulation results were used to help identify the chief interactions governing the conformational equilibria and to reexamine the key assumptions underlying the KB predictions. The data show that the H1 region exhibited significant conformational freedom, in support of the hypothesis that main‐chain structural variability in this region could play a greater role in antigen binding in camelid antibodies than it does in normal antibodies. Key H1 residues and associated inter‐loop interactions are conjectured to account for the poor KB predictions. © 2002 Wiley Periodicals, Inc. Biopolymers 68:160–177, 2003
Bioprocess considerations for expanded‐bed chromatography of crude canola extract: Sample preparation and adsorbent reuse
Authors: Bai Yun , Glatz Charles E. 
Published: January 2003

AbstractCompared to the conventional microbial and mammalian systems, transgenic plants produce proteins in a different matrix. This provides opportunities and challenges for downstream processing. In the context of the plant host Brassica napus (canola), this work addresses the bioprocessing challenges of solid fractionation, resin fouling by native plant components (e.g., oil, phenolics, etc.), hydrodynamic stability, and resin reuse for expanded bed adsorption for product capture. Plant tissue processing and subsequent protein extraction typically result in an extract with a high content of solids containing a wide particle‐size distribution. Without removal of larger particles, the column inlet distributor plugged. The larger particles (> 50 μm) were easily removed through centrifugal settling comparable to that attainable with a scroll decanter. The remaining solids did not affect the column performance. Less than 4% of the lipids and phenolics in the fed extract bound to STREAMLINE™ DEAE resin, and this small proportion could be satisfactorily removed using recommended clean‐in‐place (CIP) procedures. Hydrodynamic expansion and adsorption kinetics of the STREAMLINE™ DEAE resin were maintained throughout 10 cycles of reuse, as was the structural integrity of the resin beads. No significant accumulation of N‐rich (e.g., proteins) and C/O‐rich components (e.g., oil and phenolics) occurred over the same period. © 2003 Wiley Periodicals Inc. Biotechnol Bioeng 81: 775–782, 2003.
Modeling of yeast metabolism and process dynamics in batch fermentation
Authors: Sainz Javier , Pizarro Francisco , Pérez‐Correa J. Ricardo , Agosin Eduardo 
Published: January 2003

AbstractMuch is known about yeast metabolism and the kinetics of industrial batch fermentation processes. In this study, however, we provide the first tool to evaluate the dynamic interaction that exists between them. A stoichiometric model, using wine fermentation as a case study, was constructed to simulate batch cultures of Saccharomyces cerevisiae. Five differential equations describe the evolution of the main metabolites and biomass in the fermentation tank, while a set of underdetermined linear algebraic equations models the pseudo‐steady‐state microbial metabolism. Specific links between process variables and the reaction rates of metabolic pathways represent microorganism adaptation to environmental changes in the culture. Adaptation requirements to changes in the environment, optimal growth, and homeostasis were set as the physiological objectives. A linear programming routine was used to define optimal metabolic mass flux distribution at each instant throughout the process. The kinetics of the process arise from the dynamic interaction between the environment and metabolic flux distribution. The model assessed the effect of nitrogen starvation and ethanol toxicity in wine fermentation and it was able to simulate fermentation profiles qualitatively, while experimental fermentation yields were reproduced successfully as well. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 81: 818–828, 2003.
Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture
Authors: Yoon Sung Ho , Han Mee‐Jung , Lee Sang Yup , Jeong Ki Jun , Yoo Jong‐Shin 
Published: January 2003

AbstractCombined transcriptome and proteome analysis was carried out to understand metabolic and physiological changes of Escherichia coli during the high cell density cultivation (HCDC). The expression of genes of TCA cycle enzymes, NADH dehydrogenase and ATPase, was up‐regulated during the exponential fed‐batch period and was down‐regulated afterward. However, expression of most of the genes involved in glycolysis and pentose phosphate pathway was up‐regulated at the stationary phase. The expression of most of amino acid biosynthesis genes was down‐regulated as cell density increased, which seems to be the major reason for the reduced specific productivity of recombinant proteins during HCDC. The expression of chaperone genes increased with cell density, suggesting that the high cell density condition itself can be stressful to the cells. Severe competition for oxygen at high cell density seemed to make cells use cytochrome bd, which is less efficient but has a high oxygen affinity than cytochrome bo3. Population cell density itself strongly affected the expression of porin protein genes, especially ompF, and hence the permeability of the outer membrane. Expression of phosphate starvation genes was most strongly up‐regulated toward the end of cultivation. It was also found that σE (rpoE) plays a more important role than σS (rpoS) at the stationary phase of HCDC. These findings should be invaluable in designing metabolic engineering and fermentation strategies for the production of recombinant proteins and metabolites by HCDC of E. coli. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 81: 753–767, 2003.
Expression of melanocortin 4 receptor mRNA in the central nervous system of the rat
Authors: Kishi Toshiro , Aschkenasi Carl J. , Lee Charlotte E. , Mountjoy Kathleen G. , Saper Clifford B. , Elmquist Joel K. 
Published: January 2003

AbstractThe melanocortin 4 receptor (MC4‐R) plays a pivotal role in maintaining energy homeostasis in rodents and humans. For example, MC4‐R deletion or mutation results in obesity, hyperphagia, and insulin resistance. Additionally, subsets of leptin‐induced autonomic responses can be blocked by melanocortin receptor antagonism, suggesting that MC4‐R–expressing neurons are downstream targets of leptin. However, the critical autonomic control sites expressing MC4‐Rs are still unclear. In the present study, we systematically examined the distribution of MC4‐R mRNA in the adult rat central nervous system, including the spinal cord, by using in situ hybridization histochemistry (ISHH) with a novel cRNA probe. Autonomic control sites expressing MC4‐R mRNA in the hypothalamus included the anteroventral periventricular, ventromedial preoptic, median preoptic, paraventricular, dorsomedial, and arcuate nuclei. The subfornical organ, dorsal hypothalamic, perifornical, and posterior hypothalamic areas were also observed to express MC4‐R mRNA. Within extrahypothalamic autonomic control sites, MC4‐R–specific hybridization was evident in the infralimbic and insular cortices, bed nucleus of the stria terminalis, central nucleus of the amygdala, periaqueductal gray, lateral parabrachial nucleus, nucleus of the solitary tract, dorsal motor nucleus of the vagus (DMV), and intermediolateral nucleus of the spinal cord (IML). By using dual‐label ISHH, we confirmed that the cells expressing MC4‐R mRNA in the IML and DMV were autonomic preganglionic neurons as cells in both sites coexpressed choline acetyltransferase mRNA. The distribution of MC4‐R mRNA is consistent with the proposed roles of central melanocortin systems in feeding and autonomic regulation. J. Comp. Neurol. 457:213–235, 2003. © 2003 Wiley‐Liss, Inc.
Epidermal reinnervation after intracutaneous axotomy in man
Authors: Rajan Bindu , Polydefkis Michael , Hauer Peter , Griffin John W. , McArthur Justin C. 
Published: January 2003

AbstractTwo distinct patterns of reinnervation occur after injury to the cutaneous nerves: regenerative growth of the injured nerve and “collateral sprouting” of neighboring intact nerves. We describe two complementary models of regrowth of transected small sensory fibers in human skin. The “incision” model uses a circular incision that transects the subepidermal plexus, resulting in Wallerian degeneration of the nerve fibers that enter the incised cylinder, leaving a defined zone of denervated dermis and epidermis. The “excision” model utilizes an identical incision, followed by removal of the incised cylinder of skin, leaving a denervated area in which Schwann cells are absent. In the incision model, the earliest reinervation of denervated epidermis occurred by collateral sprouting from the terminals of epidermal axons from just outside the incision line. These axon terminals extended horizontally across the incision line and through the superficial layers of the epidermis, beneath the stratum corneum. By 13 days, numerous regenerating axons appeared in the deeper dermis derived from transected axons. These regenerating axons grew toward and ultimately into the epidermis, so that epidermal axonal density had normalized by 30–75 days. The invasion of these axons was associated with regression of the horizontally growing collateral sprouts. In the excision model, new fibers arose by terminal elongation of the epidermal axons outside the incision line, as in the incision model, and especially by collateral branching of epidermal fibers at the incision margins. These collaterals reached the epidermal surface of the basal lamina at the dermal–epidermal junction and then grew slowly toward the center of the denervated circle. In contrast to the incision model, however, complete reinnervation was not achieved even after 23 months. These models can be used to study reinnervation of denervated skin in man in different injury models and have relevance for exploring the stimuli for axonal growth and remodeling. J. Comp. Neurol. 457:24–36, 2003. © 2003 Wiley‐Liss, Inc.
Tectothalamic visual projections in turtles: Their cells of origin revealed by tracing methods
Authors: Belekhova Margarita , Kenigfest Natalia , Rio Jean‐Paul , Repérant Jacques , Ward Roger , Vesselkin Nikolai , Karamian Olga 
Published: January 2003

AbstractIn two species of turtle (Emys orbicularis and Testudo horsfieldi), retrograde and anterograde tracer techniques were used to study projections from the optic tectum to the nucleus rotundus (Rot) and to the dorsal lateral geniculate nucleus (GLd). The ipsilateral Rot received the most massive tectal projections, stemming from numerous neurons located in the stratum griseum centrale (SGC). These neurons varied in size and shape, many of them having a wide zone of dendritic arborization within both the (SGC) and the stratum griseum et fibrosum superficiale (SGFS). Projections from the tectum to the GLd were ipsilateral, were extremely scarce, and arose from a small number of neurons of various shapes situated in the SGFS; these cells were, as a rule, smaller than those projecting to the Rot. For the most part, these neurons were radially oriented, with rather restricted dendritic arborizations in the most superficial sublayers of the SGFS; smaller numbers of projection neurons were horizontally oriented, with long dendrites branching throughout the layer. Some neurons located in the stratum griseum periventriculare (SGP) projected to both the Rot and the GLd. Most of these neurons had dendritic arborizations within the retinorecipient zone of the SGFS. We were unable to rule out the possibility that some cells projecting to the GLd were situated in the SGC. Both the GLd and the main body of the Rot did not contain neurons projecting to the optic tectum. Thalamic neurons projecting to the tectum were observed in the ventral lateral geniculate nucleus, the intergeniculate leaflet and the interstitial nuclei of the tectothalamic tract, and the nucleus of the decussatio supraoptica ventralis. The question of whether variation in the laminar organization of the tectorotundal and tectogeniculate projection neurons in reptiles, birds, and mammals may be related to different degrees of differentiation of the tectal layers is discussed. J. Comp. Neurol. 457:37–56, 2003. © 2003 Wiley‐Liss, Inc.
Changes in mouse barrel synapses consequent to sensory deprivation from birth
Authors: Sadaka Yair , Weinfeld Elizabeth , Lev Dmitri L. , White Edward L. 
Published: January 2003

AbstractNeonatal sensory deprivation induced by whisker trimming affects significantly the functional organization of receptive fields in adult barrel cortex. In this study, the effects of deprivation on thalamocortical synapses and on asymmetrical and symmetrical synapses not of thalamic origin were examined. Thalamocortical synapses were labeled by lesion‐induced degeneration in adult (postnatal day 60) mice subjected to whisker trimming from birth, other synaptic types were unlabeled. Brains were processed for electron microscopy, and numerical densities of synapses were evaluated by using stereologic approaches for whisker trimmed vs. control animals. Results demonstrated no change in nonthalamic, asymmetrical synapses; however, a decrease of 52% in the numerical density of symmetrical synapses (46.3 vs. 88.5 million per mm3; Z = −2.121; P < 0.05) and a decrease of 43% in the numerical density of thalamocortical synapses (57.5 vs. 102.33 million per mm3; Z = −2.121; P < 0.05) were observed after deprivation. Thus, experience‐dependent plasticity of receptive fields in barrel cortex involves directly axons of both extrinsic and intracortical origin. The proportion of thalamocortical axospinous to axodendritic synapses was the same in control vs. deprived animals: in each instance, 80% of the synapses were axospinous (Z = 0.85; P = 0.2). These results suggest that neither excitatory neurons, whose thalamocortical synapses are primarily axospinous, nor inhibitory neurons, whose thalamocortical synapses are mainly axodendritic (White [1989] Cortical Circuits. Synaptic Organization of the Cerebral Cortex; Structure, Function, and Theory. 1989; Boston: Birkhauser), are affected preferentially by the deprivation‐associated decrease in thalamocortical synapses. J. Comp. Neurol. 457:75–86, 2003. © 2003 Wiley‐Liss, Inc.
The relationship between hodological and cytoarchitectonic organization in the vestibular complex of the 11‐day chicken embryo
Authors: Díaz Carmen , Glover Joel C. , Puelles Luis , Bjaalie Jan G. 
Published: January 2003

AbstractTo understand the relationship between structure and function in specific brain regions, it is necessary to ascertain which anatomical features are physiologically relevant. Physiological studies of brain function traditionally have been set in the context of anatomical features based on cytoarchitectonics and myeloarchitectonics, but the relationship between structure and function in this context can be complex. Alternative schemes of anatomical organization, such as that based on hodology (the mapping of projections) may provide greater insight. Here, we make a direct comparison of the hodological and the cytoarchitectonic organization of the vestibular complex in the mid‐term chicken embryo, using retrograde tracing and three‐dimensional reconstruction. In one set of experiments, vestibulospinal and vestibulo‐ocular neuron groups were selectively labeled with biotin dextran‐amines and aligned with the cytoarchitectonically defined vestibular nuclei in alternating sections that were then combined into intercalated three‐dimensional models. This allowed a semiquantitative analysis of the apportionment of individual hodological groups among cytoarchitectonic nuclei. In another set of experiments, vestibulospinal and vestibulo‐ocular neuron groups were labeled differentially with fluorescent dextran‐amines, three‐dimensionally reconstructed, and subjected to a quantitative analysis of spatial overlap. Our results provide the first three‐dimensional representation and quantitative analysis of the hodological compartmentalization of the vestibular complex (the “hodological mosaic”). They also show directly how each hodologically defined neuron group relates to the conventional vestibular nuclei, underscoring the fact that the units of the hodological mosaic do not bear a one‐to‐one correspondence to the cytoarchitectonic nuclear divisions. Some hodologically defined groups are localized to restricted portions of a nucleus, whereas others overlap multiple nuclei. Thus, hodology and cytoarchitectonic features appear to be separately regulated in the vestibular complex of the chicken embryo, possibly through different sets of positional specification mechanisms. The three‐dimensional representations we present here provide a foundation for integrating anatomical, physiological, developmental, and evolutionary studies of the vestibular system. J. Comp. Neurol. 457:87–105, 2003. © 2003 Wiley‐Liss, Inc.
Progressive recovery of learning during regeneration of a single synapse in the medicinal leech
Authors: Burrell Brian D. , Sahley Christie L. , Muller Kenneth J. 
Published: January 2003

AbstractThe leech escape reflex—shortening of the body—can change with nonassociative conditioning, including sensitization, habituation, and dishabituation. Capacity for sensitization, which is an enhancement of the reflex, is lost when a single S‐interneuron is ablated, but the reflex response itself remains. In the present experiments, the S‐interneuron's axon in the living leech was filled with 6‐carboxyfluorescein (6‐CF) dye and cut with an argon laser microbeam (λ = 488 nm). In contrast to sham‐operated animals, axotomized preparations did not sensitize, reflecting the key role of the S‐cell. By 2 weeks or more, S‐cell axons had regenerated and reestablished synapses at their usual locations with neighboring S‐cells. By 4 weeks, this restored the ability to sensitize to a level indistinguishable from that of controls, but an intermediate state of recovery was seen from 2–3 weeks after injury—a period not previously examined. The small capacity for sensitization among newly regenerated preparations was significantly lower than in sham controls but appeared higher than in animals whose cut S‐cell axon had not regenerated its synapse. The results confirm the crucial role of the S‐cell in sensitization. Moreover, full sensitization does not occur immediately upon synapse regeneration. J. Comp. Neurol. 457:67–74, 2003. © 2003 Wiley‐Liss, Inc.
Reevaluation of the primary motor cortex connections with the thalamus in primates
Authors: Kultas‐Ilinsky Kristy , Sivan‐Loukianova Elena , Ilinsky Igor A. 
Published: January 2003

AbstractSix injections (∼1 mm in diameter) of biotinylated dextran amine (BDA) were placed in different locations of the primary motor cortex of the rhesus monkey. Anterograde and retrograde labeling patterns in the thalamus were charted and individual labeled axons traced in continuous serial sections. Both anterograde and retrograde labeling in the thalamus was extensive, spanning several millimeters mediolaterally and including ventral lateral, ventral anterior, centromedian, and centrolateral nuclei. Paracentral, mediodorsal, lateral posterior, and medial pulvinar nuclei were also labeled. Two basic types of corticothalamic axons were identified: small to medium‐width, type 1 axons that formed large terminal fields with small boutons, and thick, type 2 axons that formed small terminal fields with large boutons. Within each group, subtypes were identified based on specific features of the axons and terminals: two subtypes of type 1 axons and four subtypes of type 2 axons. The results revealed multiple modes of corticothalamic connectivity: sparsely distributed type 1 axons, dense plexuses of type 1 axons, type 2 axon terminal fields either singly or in clusters, and mixed plexuses of type 1 and type 2 axons. Only some cells in the plexuses were retrogradely labeled; some plexuses did not contain any labeled neurons, and many retrogradely labeled neurons were in the regions devoid of anterograde labeling. These connectivity patterns differed between thalamic nuclei. The results revealed much more complex relationships between M1 and thalamus than were previously thought to exist. It is suggested that this connectivity is neither of exclusively a feedback nature nor perfectly reciprocal but is subserved by a multitude of channels, most likely originating from different populations of cortical neurons, and feeding into a variety of functionally different neuronal networks, with each processing specific information. J. Comp. Neurol. 457:133–158, 2003. © 2003 Wiley‐Liss, Inc.