bluuebunny/crossref_metadata_2025_split huggingface dataset:
The tetracycline: Mg2+ complex: A molecular mechanics force field
Authors: Aleksandrov Alexey , Simonson Thomas 
Published: July 2006

AbstractTetracycline (Tc) is an important antibiotic, which binds specifically to the ribosome and several proteins, in the form of a Tc–:Mg2+ complex. To model Tc:protein and Tc:RNA interactions, we have developed a molecular mechanics force field model of Tc, which is consistent with the CHARMM force field for proteins and nucleic acids. We used structures from the Cambridge Crystallographic Data Base to identify the main Tc conformations that are likely to be present in solution and in biomolecular complexes. A conformational search was also done, using the MM3 force field to perform simulated annealing of Tc. Several resulting, low‐energy structures were optimized with an ab initio model and used in developing the new Tc force field. Atomic charges and Lennard‐Jones parameters were derived from a supermolecule ab initio approach. We considered the ab initio energies and geometries of a probe water molecule interacting with Tc at 36 different positions. We considered both a neutral and a zwitterionic Tc form, with and without bound Mg2+. The final rms deviation between the ab initio and force field energies, averaged over all forms, was just 0.35 kcal/mol. The model also reproduces the ab initio geometry and flexibility of Tc. As further tests, we did simulations of a Tc crystal, of Tc:Mg2+ and Tc:Ca2+ complexes in aqueous solution, and of a solvated complex between Tc:Mg2+ and the Tet repressor protein (TetR). With slight, ad hoc adjustments, the model can reproduce the experimental, relative, Tc binding affinities of Mg2+ and Ca2+. It performs well for the structure and fluctuations of the Tc:Mg2+:TetR complex. The model should therefore be suitable to investigate the interactions of Tc with proteins and RNA. It provides a starting point to parameterize other compounds in the large Tc family. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1517–1533, 2006
Origin of hyperactivity in the hamster dorsal cochlear nucleus following intense sound exposure
Authors: Zhang J.S. , Kaltenbach J.A. , Godfrey D.A. , Wang J. 
Published: July 2006

AbstractThis study sought to determine whether maintenance of noise‐induced dorsal cochlear nucleus (DCN) hyperactivity depends on descending projections. Twenty‐two hamsters were exposed under anesthesia to a 10‐kHz tone at 125–130 dB SPL for 4 hr, and another 21 unexposed animals served as controls. After approximately 4–6 weeks of recovery, surgical transections were made to isolate the DCN from its adjacent brainstem structures. Spontaneous multiunit activity was recorded from the DCN surface 30–40 min after the surgical manipulations. Spontaneous rates were derived from the recording sites of the DCN along its mediolateral axis for each animal, yielding average spontaneous rates for both control and exposed groups. Histology was performed to assess the degree of sectioning of descending fiber tract connections to the cochlear nucleus, via the acoustic striae route, subpeduncular route, trapezoid body route, and ventral route of the olivocochlear bundle connection. The results showed that complete or nearly complete transections of descending inputs did not affect significantly the magnitude of DCN hyperactivity. However, this manipulation triggered a lateral shift of the peak mean rate, suggesting that descending inputs may play a modulatory role on the profile of DCN hyperactivity. Indeed, exposed animals with transection of only the strial route of entry manifested a level of hyperactivity much higher than that observed in exposed animals in which no sections were performed. This enhancement of DCN hyperactivity was weakened by damage to the subpeduncular or trapezoid routes of input, suggesting that the dorsally located inputs may have an inhibitory effect on DCN hyperactivity. © 2006 Wiley‐Liss, Inc.
Gene expression for enzymes and transporters involved in regulating adenosine and inosine levels in rat forebrain neurons, astrocytes and C6 glioma cells
Authors: Parkinson Fiona E. , Ferguson Jennifer , Zamzow Christina R. , Xiong Wei 
Published: July 2006

AbstractIn brain, levels of adenosine increase up to 100‐fold during cerebral ischemia. Based on in vitro studies, both astrocytes and neurons contribute to this adenosine release. Neurons release adenosine per se whereas astrocytes release adenine nucleotides that are metabolized to adenosine extracellularly. In contrast, inosine is released from both cell types via a nucleoside transporter. C6 glioma cells, which are derived from astrocytes, release inosine but not adenosine. The present study investigated the relative expression of purine metabolizing enzymes and transporters in neurons, astrocytes and C6 glioma cells by real‐time PCR analysis. In agreement with the extracellular formation of adenosine and intracellular formation of inosine by astrocytes, the present study showed high expression of ecto 5′‐nucleotidase and AMP deaminase type 3 in astrocytes. The lack of adenosine release from C6 glioma cells was consistent with the absence of expression of the AMP‐preferring cytosolic 5′‐nucleotidase in these cells. The predominance of nitrobenzylthioinosine (NBMPR) insensitive equilibrative nucleoside transport (ENT2) in all three cell types was consistent with the greater activity of this isoform in comparison to NBMPR‐sensitive ENT1 in these rat cells. Thus, cell type differences in adenosine formation and release are primarily a function of differences in expression of purinergic enzymes and transporters. © 2006 Wiley‐Liss, Inc.
Overexpression of copper/zinc‐superoxide dismutase in transgenic mice markedly impairs regeneration and increases development of neuropathic pain after sciatic nerve injury
Authors: Kotulska Katarzyna , LePecheur Marie , Marcol Wiesław , Lewin‐Kowalik Joanna , Larysz‐Brysz Magdalena , Paly Evelyn , Matuszek Iwona , London Jacqueline 
Published: July 2006

AbstractDespite the general capacity of peripheral nervous system to regenerate, peripheral nerve injury is often followed by incomplete recovery of function, sometimes with the burden of neuropathic pain. The mechanisms of both regeneration and nociception have not been clarified, but it is known that inflammatory reactions are involved. Cu/Zn‐superoxide dismutase (SOD1) is an important scavenger protein that acts against oxidative stress. It has been shown to play an important role in apoptosis and inflammation. The aim of this study was to examine the role of SOD1 overexpression in peripheral nerve regeneration and neuropathic pain‐related behavior in mice. Sciatic nerves of SOD1‐overexpressing and FVB/N wild type‐mice were transected and immediately resutured. Evaluation of motor and sensory function and autotomy was carried out during 4 weeks of followup. We found markedly worse sciatic function index outcome as well as more significant atrophy of denervated muscles in SOD1‐overexpressing animals compared with wild type. Autotomy was markedly worse in SOD1 transgenic mice than in wild‐type animals. Histological evaluation revealed that the intensity of regeneration features, including numbers of GAP‐43‐positive growth cones, Schwann cells, and macrophages in the distal stump of the transected nerve, was also decreased in transgenic mice. Neuroma formation at the injury site was significantly more prominent in this group. Taken together, our findings suggest that SOD1 overexpression is deleterious for nerve regeneration processes and aggravates neuropathic pain‐like state in mice. This can be at least partially ascribed to disturbed inflammatory reactions at the injury site. © 2006 Wiley‐Liss, Inc.
Molecular mechanisms of pain in the anterior cingulate cortex
Authors: Zhuo Min 
Published: July 2006

AbstractIt is well known that peripheral sensory stimuli, including pain, trigger a series of neuronal activities along the somatosensory pathways as well as the neuronal network in the high brain structures. These neuronal activities not only produce appropriate physiological responses but also induce long‐term plastic changes in some of the central synapses. It is believed that long‐term synaptic changes help the brain to process and store new information. Such learning is critical for animals and humans to gain new knowledge of changing enviornment, generate appropriate emotional responses, and avoid dangerous stimuli in the future. In the case of permanent injury, however, the brain fails to distinguish the difference between “useful” and painful stimuli. Long‐term synaptic changes work against the system and at least in part contribute to chronic pain. In this short article, the possible molecular mechanisms for long‐term plasticity within the anterior cingulate cortex (ACC) will be discussed and reviewed, and it is hypothesized that potentiation of excitatory responses within the ACC contributes to chronic pain and pain‐related mental disorders. © 2006 Wiley‐Liss, Inc.
Assessment of textile dye remediation using biotic and abiotic agents
Authors: El‐Rahim Wafaa M. Abd 
Published: July 2006

AbstractThe aim of the current work was to assess the removal of direct and reactive dyes using biotic and abiotic agents. Removal of dyes and their derivatives from aqueous solutions was investigated using sugarcane bagasse, sawdust, rice straw, charcoal and fungal biomass as dye removing agents. Seven fungal strains known to have high capacity in removing textile dyes were used. Results of this study indicated that Penicillium commune, P. freii, and P. allii removed 96, 64 and 65%, respectively, of direct violet dye after two hours of incubation. In addition, the use of rice straw was shown to be more efficient in dye removal, than was bagasse or sawdust. Rice straw was effective in removing 72% of direct violet dye within 24 hours. However, with reactive dyes, removal activity was reduced to 27%. Similar trends were recorded with the other tested biotic agents, fast removal of reactive dye was not found after 48 hours of contact time. Results of this study indicate that low‐cost, renewable, bioadsorption agents are relatively effective in removing textile dyes from solution. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characterization of Staphylococcus aureus strains isolated from humans in Argentina
Authors: Reinoso Elina Beatriz , Ibañez Fernando , Raspanti Claudia , Odierno Liliana , Bogni Cristina Inés 
Published: July 2006

AbstractHumans are a natural reservoir of Staphylococcus aureus and asymptomatic colonization is far more common than infection. The aim of this work was to characterize genotypically 68 S. aureus strains isolated from nasal swabs of healthy people and from human clinical infections. A total of fourteen (20%) strains were susceptible to all the antimicrobials tested. The strains isolated from nasal swabs showed the lowest percentages of resistance. Resistance to one or more than one antibiotics tested was detected in 83% and 70% of the S. aureus strains isolated from clinical infections and nasal swabs, respectively. All of the 68 S. aureus strains were subject to RAPD‐PCR analysis. Cluster A‐I grouped 42 (87%) clinical infection strains and cluster A‐II grouped 13 (65%) strains isolated from nasal swabs suggesting a genetic relationship among S. aureus strains. Cluster A‐II grouped 65% of the S. aureus strains associated with the anterior nares, suggesting that these strains may be adapted to this site. Furthermore, five RAPD profiles isolated from nasal swabs, belonged to clusters B to F, were similar to strains isolated from clinical infection, suggesting that they might have a high propensity to cause disease. The results of the present study allow a characterization of S. aureus strains isolated from humans and shows that some S. aureus genotypes from nasal swabs are similar to the genotypes obtained from clinical infections, suggesting that clinical isolates may be originated from human normal flora. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Bacterial community changes in diesel‐oil‐contaminated soil microcosms biostimulated with Luria–Bertani medium or bioaugmented with a petroleum‐degrading bacterium, Pseudomonas aeruginosa strain WatG
Authors: Ueno Akio , Ito Yukiya , Yamamoto Yusuke , Yumoto Isao , Okuyama Hidetoshi 
Published: July 2006

AbstractThe microbial community structure of diesel‐oil‐contaminated soil microcosms biostimulated with Luria–Bertani medium (LB‐BS) or bioaugmented with a petroleum‐degrading bacterium, Pseudomonas aeruginosa strain WatG (WatG‐BA), was investigated by denaturing gradient gel electrophoresis (DGGE) and by monitoring diesel oil degradation. The degradation in WatG‐BA (64.0% ± 4.2%) was higher than that in LB‐BS (49.5% ± 12.0%) during the first two weeks. The microbial community in WatG‐BA, which was markedly dominated by strain WatG, was much simpler than that in LB‐BS, where hydrocarbon degraders occurred after a lag of 3–7 days after the addition of diesel oil. The clustering profiles of the DGGE banding patterns of the two soil microcosms were only 12% similar. This difference is probably due to antibacterial substances, such as rhamnolipids, secreted by strain WatG. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Northern Hemisphere freezing/thawing index variations over the twentieth century
Authors: Frauenfeld Oliver W. , Zhang Tingjun , Mccreight James L. 
Published: July 2006

AbstractChanges in the ground thermal regime in high‐latitude cold regions have important consequences for surface and subsurface hydrology, the surface energy and moisture balance, carbon exchange, as well as ecosystem diversity and productivity. However, assessing these changes, particularly in light of significant atmospheric and terrestrial changes in recent decades, remains a challenge owing to data sparseness and discontinuous observations. The annual freezing and thawing index can be useful in evaluating permafrost and seasonally frozen ground distribution, has important engineering applications, and is a useful indicator of high‐latitude climate change. The freezing/thawing index is generally defined based on daily observations, which are not readily available for many high‐latitude locations. We thus employ monthly air temperatures, and provide an assessment of the validity of this approach. On the basis of a comprehensive relative error (RE) evaluation we find that our methodology introduces errors of less than 5% for most high‐latitude land areas, and works well in many midlatitude regions as well. We evaluate a suite of gridded monthly temperature datasets and select the University of East Anglia's Climatic Research Unit (CRU) temperature product, available for 1901–2002. We are thus able to provide a continuous long‐term 25 km × 25 km gridded Northern Hemisphere freezing/thawing index. Long‐term climatologies of the freezing/thawing index delineate the cold regions of the Northern Hemisphere, as well as areas of seasonally frozen ground and permafrost. Objective trend analysis indicates that in recent decades, no significant changes have occurred in Russian permafrost regions; however, seasonally frozen ground areas are experiencing significant warming trends. Over North America, Canadian and Alaskan permafrost regions are experiencing a decrease in freezing index during the cold season, while coastal areas and eastern Canada are seeing significant increase in warm season thawing index. Copyright © 2006 Royal Meteorological Society.
A new quantitative method: non‐destructive study by Raman spectroscopy of dyes fixed on wool fibres
Authors: Salpin Frédérique , Trivier Francis , Lecomte Sophie , Coupry Claude 
Published: July 2006

AbstractRaman spectroscopy was employed for the quantitative analysis of mixtures of the three dyes used at the Manufacture Nationale des Gobelins (Paris, France), fixed on wool fibres. It is based on a laboratory‐written program that implements the decomposition of the combined Raman spectrum into the relative contributions of the spectra of each constituent.To perfect the method, it was first applied to fibres dyed at the laboratory and then extended to the dyeing baths, before and after the dyeing process. Binary and ternary mixtures, in which the quantities were known, were used. The percentages obtained by applying the quantitative analysis of the Raman spectra were similar to those introduced. The method therefore allows quantification of the dyes and gives information about the dyeing process. Fibres recently dyed at the workshop of the Manufacture Nationale des Gobelins with unknown proportions were analysed using this method. The results obtained are in conformity with the observed colour of the dyed hanks of wool. Copyright © 2006 John Wiley & Sons, Ltd.
The microstructure and tannin content of banana fruit and their likely influence on juice extraction
Authors: Kyamuhangire William , Krekling Trygve , Reed Elisabeth , Pehrson Robert 
Published: July 2006

AbstractExtraction of banana juice using the traditional physical method is limited to Mbidde banana cultivars. Most other banana cultivars (including Matooke cultivars) do not produce juice by this method. A study of the microstructure and tannin content of banana fruit (Mbidde and Matooke cultivars) was carried out in order to understand the underlying factors in the juice extraction process and develop a working hypothesis to explain the mechanism of juice separation. Microscopic examination of pulp sections of Mbidde bananas revealed that their microstructure contained many more intensely stained and larger laticifer cells than pulp tissues of Matooke cultivars. On ripening, the intensity of staining of laticifer cells in Mbidde fruit appeared to increase, while there was limited or no staining in fruit of Matooke cultivars. There was also higher tannin content in Mbidde than in Matooke bananas at both unripe and ripe stages. The high tannin concentration corresponding to the unique presence of high numbers of laticifer cells in fruit of Mbidde cultivars suggests that the ability of the bananas to release juice is linked to tannins. During juice extraction the physical working of the banana pulp ruptures the laticifer cells, resulting in the release of tannins that interact with celluloses, hemicelluloses, proteins and, most importantly, pectins to form insoluble complexes, thus facilitating juice release. Copyright © 2006 Society of Chemical Industry
Biocomposites: technology, environmental credentials and market forces
Authors: Fowler Paul A , Hughes J Mark , Elias Robert M 
Published: July 2006

AbstractBiocomposites offer a significant non‐food market for crop‐derived fibres and resins. Considerable growth has been seen in the use of biocomposites in the automotive and decking markets over the past decade or so, but application in other sectors has hitherto been limited. Nevertheless, with suitable development, the potential exists for biocomposites to enter new markets and thus stimulate an increase in demand for non‐food crops. This paper reviews some of the technological challenges being faced in bringing these materials to a wider market together with potential solutions, as well as discussing market forces influencing their commercial uptake. Copyright © 2006 Society of Chemical Industry
Variation in the carotenoid composition of acerola and its processed products
Authors: Porcu Ornella Maria , Rodriguez‐Amaya Delia B 
Published: July 2006

AbstractAcerola is now commercially produced and processed in Brazil. Known for its very high vitamin C content, this fruit is also a good source of β‐carotene. The present study was carried out to verify variation in the carotenoid composition along the food chain. Neoxanthin, violaxanthin, lutein, β‐cryptoxanthin, α‐carotene and β‐carotene were found in the acerola fruit. β‐Carotene predominated with mean concentrations of 12.4 and 38.1 µg g−1 in the ripe fruit, 8.8 and 30.1 µg g−1 in the peeled ripe fruit and 5.4 and 12.0 µg g−1 in the partially ripe fruit of an undefined variety taken from home gardens and the commercial cultivar Olivier, respectively. Aside from β‐carotene, β‐cryptoxanthin increased significantly in both garden and commercial fruits and violaxanthin in the latter fruits during ripening. Peeling reduced β‐carotene in both garden and commercial lots, violaxanthin decreased in the commercial fruits, and the other carotenoids remained virtually unchanged. Four brands of frozen pulp and three brands of processed juice had variable and markedly lower carotenoid levels than those of the fresh fruit, indicating that the processing should be improved. Copyright © 2006 Society of Chemical Industry
Extra‐virgin and refined olive oils decrease plasma triglyceride, moderately affect lipoprotein oxidation susceptibility and increase bone density in growing pigs
Authors: Ostrowska Ewa , Gabler Nicholas K , Ridley Dan , Suster Danny , Eagling David R , Dunshea Frank R 
Published: July 2006

AbstractThe objective of this study was to determine the health benefits of extra‐virgin and refined olive oils, which are high in mono‐unsaturated fatty acids (MUFAs) and polyphenolic compounds using the pig as a model. Thirty‐two cross‐bred pigs were individually penned, allocated to one of four dietary treatments and fedad libitumfor 28 days. Two of the experimental diets consisted of a basal diet containing 12% tallow and either 7% sunflower oil (TSO) or 7% extra‐virgin olive oil (TEVO) on a w/w basis. The remaining diets contained 19% extra‐virgin olive oil (EVO) or 19% of refined olive oil (RO). On days 7, 14 and 28 fasted and 3‐h post‐prandial blood samples were taken. Body composition was measured at the beginning and end of the study using dual energy X‐ray absorptiometry. Daily gain, feed intake and lean and fat deposition were not significantly different between the treatments. However, the daily increase in bone mineral density was higher in pigs fed diets containing olive oil (1.23 vs 2.54, 6.28, 5.20 mg cm−2per day for TSO, TEVO, EVO and RO, respectively,P= 0.050). Both fasting and non‐fasting plasma triglycerides were lower (P= 0.003) in pigs fed MUFA‐rich diets, while the cholesterol profile was not significantly different between the treatments. The results fromin vitrocopper‐induced lipid peroxidation, expressed in terms of conjugated dienes, showed that low density lipoprotein (LDL) particles in postprandial serum from pigs fed olive oil were moderately more resistant to oxidative modification. In conclusion, these data demonstrate that both extra‐virgin and refined olive oils attenuate postprandial hypertriglyceridaemia, moderately affect oxidation susceptibility and increase bone mineral density in growing pigs. Copyright © 2006 Society of Chemical Industry