bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water resource hazard management system: assessing sustainable practices at the farm and catchment scales
Authors: Ochola W. O. , Kerkides P. , Argyrokastritis I. 
Published: October 2002

AbstractWater quality is a pivotal environmental indicator of sustainable land management and environmental ‘health’. Hazards to water resource use at the farm and catchment scales have far‐reaching physical, biological, environmental and socio‐economic impacts. These impacts are exacerbated by on‐site and off‐site agricultural and non‐agricultural activities. A prototype water hazard management decision support system that uses an integrated framework to identify, by origin, hazards and related best water management practices guidelines is proposed. The system recommends best management guidelines with respect to the inherent water resource use mitigations. The system has been calibrated by and applied to expert knowledge and experimental and survey data from Kiumbu Catchment in central Kenya. Suggestions are made for the inclusion of GIS capabilities for the production of water resource assessment maps and other spatial water quality indicators. Copyright © 2002 John Wiley & Sons, Ltd.
Approaches to the assessment of toxicity data with endpoints related to endocrine disruption
Authors: Harvey Philip W. , Johnson Ian 
Published: October 2002

AbstractThere has been a substantial proliferation in the number of studies reporting endocrine effects as an endpoint. The vast majority have focused on oestrogenicity in vitro but, with recent recommendations by the USEPA Endocrine Disrupter Screening and Testing Advisory Committee, tests are now being developed for (anti)‐androgenicity and effects on the thyroid, largely because of the potential for altering reproduction or development via these mechanisms. Despite being a vital organ and involved in reproduction and development, there is currently no provision for assessing adrenocortical function. Similarly, the entire process of steroidogenesis poses multiple molecular targets for toxic disruption that are not included in current test strategies and at present there is no clear position on the significance of the data being generated. This review provides a framework for approaching endocrine data: that all the glands, tissues, receptors, transporter proteins and enzymes that comprise the endocrine system are targets for toxicity. They should be considered in much the same way as other target organs, with appropriate provision for the special cases of carcinogenesis and teratogenesis, and a pragmatic weight of evidence approach should be adopted considering all available data and recognizing its limitations. In this approach, structure–activity relationships and in vitro and targeted in vivo screens provide useful data but repeat‐dose regulatory studies with defined endpoints provide the most powerful tools for hazard assessment. Pragmatic consideration should be given to exposure issues (which may highlight the practical irrelevance, for example, of very low potency oestrogens) and subsequently whether endocrine disruption is the critical or most sensitive endpoint for a compound. Finally, endocrine disruption may be considered a mechanism and, as with other toxic endpoints, knowledge of effect and no‐observable‐effect levels and reversibility is as important as identifying the target tissue or any inherent hormone‐like property. Copyright © 2002 John Wiley & Sons, Ltd.
Analysis of the energetic state of heart cells after adenovirus‐mediated expression of hALC‐1
Authors: Zacharzowsky Udo B. , Wolff Gerhard , Kott Monika , Haase Hannelore , Bartsch Holger , Nuessler Andreas K. , Baltas Leonidas G. , Karawajew Leonid , Morano Ingo 
Published: October 2002

AbstractExpression of the human atrial myosin light chain 1 (hALC‐1) in the cardiac ventricle in vivo as well as in primary cultivated adult cardiomyocytes caused a pronounced positive inotropic effect. Therefore, it is one of the most promising candidate gene to treat congestive heart failure (CHF). In this work, we investigated, whether hALC‐1 expression also modifies the energetic state of cardiomyocytes. Primary cultivated neonatal rat hearts cells (NRHC) were infected with adenoviral vectors (Ad vectors) containing a hALC‐1 cDNA (AdCMV.hALC‐1) or a control Ad vector. Infection efficiency of NRHC reached 100% at 50 multiplicity of infection (MOI). Interestingly and in contrast to primary cultures of liver cells, there were no cytotoxic side effects or induction of apoptosis up to MOI 50 in Ad vector infected NRHC. NRHC expressed large amounts of hALC‐1 upon infection with AdCMV.hALC‐1 which could easily been detected by protein staining and Western blot analysis. Analysis of intracellular hALC‐1 localization by double‐labeling immunofluorescence of AdCMV.hALC‐1 infected cardiomyocytes revealed the typical myofibrillar striation pattern, as well as co‐localization of hALC‐1 with myosin heavy chains. There was no difference in the oxygen consumption between controls and AdCMV.hALC‐1 infected NRHC. These data suggest that first: adenoviral vectors could be used as a safe and effective tool for gene transfer to cardiomyocytes, and second: that a positive inotropic effect of hALC‐1 is not associated with enhanced oxygen consumption. © 2002 Wiley‐Liss, Inc.
Differential effects of iron deficiency on the expression of CD80 and CD86 co‐stimulatory receptors in mitogen‐treated and untreated murine spleen cells
Authors: Kuvibidila Solo R. , Porretta Connie 
Published: October 2002

AbstractThe interaction of CD28 and its ligands (CD80, CD86) on antigen presenting cells and that of TCR/CD3‐MHC are required for T lymphocyte activation. To determine whether impaired lymphocyte proliferation associated with iron deficiency is due to reduced expression of these ligands, spleen cells obtained from eight to nine C57BL/6 mice/group of iron deficient (ID), iron replete (R), control (C), pair‐fed (PF), and high iron (HI) mice were labeled with anti‐CD80‐fluorescein isothiocyante (FITC) and anti‐CD86‐FITC. Diets differed only in iron concentration: 5, 50, and 125 mg/kg for the ID, C, and HI, respectively. Mean levels of hemoglobin and liver iron stores of ID and R mice were less than 50% those of C mice (P < 0.005). In non‐activated and concanavalin A‐treated cultures, significant differences were observed among groups in the percentage of CD80 + cells: ID>R > C = PF = HI (P < 0.05). The same trend was observed for CD86 + cells (P > 0.05). Fluorescence intensity (FI) of either marker did not significantly change by iron status. In vitro iron chelation by deferoxamine (20, 200 μg/ml) for 1, 2, and 24 h increased FI of both markers on unactivated B and T cells (P < 0.05). However, it had no effect on FI of either marker of mitogen‐treated cells presumably because the maximum levels are achieved by the mitogen. Lymphocyte proliferative responses to mitogens positively and significantly correlated with CD80 and CD86 FI (r = 0.41−0.59) but negatively correlated with the percentages of CD80 + cells (r = −0.48) (P < 0.05). Data suggest that impaired lymphocyte proliferation associated with iron deficiency is not due to reduced CD80 and CD86 expression. J. Cell. Biochem. 86: 571–582, 2002. © 2002 Wiley‐Liss, Inc.
Differential involvement of protein kinase C in basal versus acetylcholine‐regulated prolactin secretion in rat anterior pituitary cells during aging
Authors: Pu Hsiao‐Fung , Liu Tsuei‐Chu 
Published: October 2002

AbstractAlthough it is well known that plasma concentration of prolactin (PRL) increases during aging in rats, how the anterior pituitary (AP) aging per se affects PRL secretion remains obscure. The objectives of this study were to determine if changes in the pituitary PRL responsiveness to acetylcholine (ACh; a paracrine factor in the AP), as compared with that to other PRL stimulators or inhibitors, contribute to the known age‐related increase in PRL secretion, and if protein kinase C (PKC) is involved. We also determined if replenishment with aging‐declined hormones such as estrogen/thyroid hormone influences the aging‐caused effects on pituitary PRL responses. AP cells were prepared from old (23–24‐month‐old) as well as young (2–3‐month‐old) ovariectomized rats. Cells were pretreated for 5 days with diluent or 17β‐estradiol (E2; 0.6 nM) in combination with or without triiodothyronine (T3; 10 nM). Then, cells were incubated for 20 min with thyrotropin‐releasing hormone (TRH; 100 nM), angiotensin II (AII; 0.2–20 nM), vasoactive intestinal peptide (VIP; 10−9–10−5 M), dopamine (DA; 10−9–10−5 M), or ACh (10−7–10−3 M). Cells were also challenged with ACh, TRH, or phorbol 12‐myristate 13‐acetate (PMA; 10−6 M) following PKC depletion by prolonged PMA (10−6 M for 24 h) pretreatment. We found that estrogen priming of AP cells could reverse the aging‐caused effects on pituitary PRL responses to AII and DA. In hormone‐replenished cells aging enhanced the stimulation of PRL secretion by TRH and PMA, but not by AII and VIP. Aging also reduced the responsiveness of cells to ACh and DA in suppressing basal PRL secretion, and attenuated ACh inhibition of TRH‐induced PRL secretion. Furthermore, ACh suppressed TRH‐induced PRL secretion mainly via the PMA‐sensitive PKC in the old AP cells, but via additional mechanisms in young AP cells. On the contrary, basal PRL secretion was PKC (PMA‐sensitive)‐independent in the old AP cells, but dependent in the young AP cells. Taken together, these results suggest differential roles of PMA‐sensitive PKC in regulating basal and ACh‐regulated PRL responses in old versus young AP cells. The persistent aging‐induced differences in AP cell responsiveness to ACh, DA, TRH, and PMA following hormone (E2/T3) replenishment suggest an intrinsic pituitary change that may contribute, in part, to the elevated in vivo PRL secretion observed in aged rats. J. Cell. Biochem. 86: 268–276, 2002. © 2002 Wiley‐Liss, Inc.
Effects of cell swelling on intracellular calcium and membrane currents in bovine articular chondrocytes
Authors: Yellowley Clare E. , Hancox Jules C. , Donahue Henry J. 
Published: October 2002

AbstractChondrocytes experience a dynamic extracellular osmotic environment during normal joint loading when fluid is forced from the matrix, increasing the local proteoglycan concentration and therefore the ionic strength and osmolarity. To exist in such a challenging environment, chondrocytes must possess mechanisms by which cell volume can be regulated. In this study, we investigated the ability of bovine articular chondrocytes (BAC) to regulate cell volume during a hypo‐osmotic challenge. We also examined the effect of hypo‐osmotic stress on early signaling events including [Ca2+]i and membrane currents. Changes in cell volume were measured by monitoring the fluorescence of calcein‐loaded cells. [Ca2+]i was quantified using fura‐2, and membrane currents were recorded using patch clamp. BAC exhibited regulated volume decrease (RVD) when exposed to hypo‐osmotic saline which was inhibited by Gd3+. Swelling stimulated [Ca2+]i transients in BAC which were dependent on swelling magnitude. Gd3+, zero [Ca2+]o, and thapsigargin all attenuated the [Ca2+]i response, suggesting roles for Ca2+ influx through stretch activated channels, and Ca2+ release from intracellular stores. Inward and outward membrane currents significantly increased during cell swelling and were inhibited by Gd3+. These results indicate that RVD in BAC may involve [Ca2+]i and ion channel activation, both of which play pivotal roles in RVD in other cell types. These signaling pathways are also similar to those activated in chondrocytes subjected to other biophysical signals. It is possible, then, that these signaling events may also be involved in a mechanism by which mechanical loads are transduced into appropriate cellular responses by chondrocytes. J. Cell. Biochem. 86: 290–301, 2002. © 2002 Wiley‐Liss, Inc.
Identification of PSF as a protein kinase Cα‐binding protein in the cell nucleus
Authors: Rosenberger Uwe , Lehmann Ingo , Weise Christoph , Franke Peter , Hucho Ferdinand , Buchner Klaus 
Published: October 2002

AbstractProtein kinase C (PKC) isoforms are present in the cell nucleus in diverse cell lines and tissues. Since little is known about proteins interacting with PKC inside the cell nucleus, we used Neuro‐2a neuroblastoma cells, in which PKCα is present in the nucleus, to screen for nuclear binding partners for PKC. Applying overlay assays, we detected several nuclear proteins which bind to PKCα. Specificity of binding was shown by its dependence on PKC activation by phorbol ester, calcium, and phosphatidylserine. The PKC‐binding proteins were partially purified and analyzed by microsequencing and mass spectrometry. Four proteins could be identified: PTB‐associated splicing factor (PSF), p68 RNA helicase, and the heterogeneous nuclear ribonucleoprotein (hnRNP) proteins A3 and L. In the case of PSF, binding to PKC could also be demonstrated in a GST‐pull‐down assay using GST‐PKCα, expressed in insect cells. Phosphorylation experiments revealed that PSF is a weak in vitro substrate for PKCα. J. Cell. Biochem. 86: 394–402, 2002. © 2002 Wiley‐Liss, Inc.
ATP and UTP at low concentrations strongly inhibit bone formation by osteoblasts: A novel role for the P2Y2 receptor in bone remodeling
Authors: Hoebertz Astrid , Mahendran Siva , Burnstock Geoffrey , Arnett Timothy R. 
Published: October 2002

AbstractThere is increasing evidence that extracellular nucleotides act on bone cells via multiple P2 receptors. The naturally‐occurring ligand ATP is a potent agonist at all receptor subtypes, whereas ADP and UTP only act at specific receptor subtypes. We have reported that the formation and resorptive activity of rodent osteoclasts are stimulated powerfully by both extracellular ATP and its first degradation product, ADP, the latter acting at nanomolar concentrations, probably via the P2Y1 receptor subtype. In the present study, we investigated the actions of ATP, ADP, adenosine, and UTP on osteoblastic function. In 16–21 day cultures of primary rat calvarial osteoblasts, ADP and the selective P2Y1 agonist 2‐methylthioADP were without effect on bone nodule formation at concentrations between 1 and 125 μM, as was adenosine. However, UTP, a P2Y2 and P2Y4 receptor agonist, known to be without effect on osteoclast function, strongly inhibited bone nodule formation at concentrations ≥ 1 μM. ATP was inhibitory at ≥ 10 μM. Rat osteoblasts express P2Y2, but not P2Y4 receptor mRNA, as determined by in situ hybridization. Thus, the low‐dose effects of extracellular nucleotides on bone formation and bone resorption appear to be mediated via different P2Y receptor subtypes: ADP, signalling through the P2Y1 receptor on both osteoclasts and osteoblasts, is a powerful stimulator of osteoclast formation and activity, whereas UTP, signalling via the P2Y2 receptor on osteoblasts, blocks bone formation by osteoblasts. ATP, the ‘universal’ agonist, can simultaneously stimulate resorption and inhibit bone formation. These findings suggest that extracellular nucleotides could function locally as important negative modulators of bone metabolism, perhaps contributing to bone loss in a number of pathological states. J. Cell. Biochem. 86: 413–419, 2002. © 2002 Wiley‐Liss, Inc.
Improved semiempirical heats of formation through the use of bond and group equivalents
Authors: Repasky Matthew P. , Chandrasekhar Jayaraman , Jorgensen William L. 
Published: October 2002

AbstractDeficiencies in energetics obtained using the common semiempirical methods, AM1, PM3, and MNDO, may partly be traced to the use of pseudoatomic equivalents for conversion of molecular energies to heats of formation at 298 K. We present an alternative scheme based on the use of bond and group equivalents. Values for the 61 bond and group equivalents necessary for treatment of molecules containing the common organic elements, hydrogen, carbon, nitrogen, and oxygen have been derived. For a set of 583 neutral, closed‐shell molecules mean absolute errors in AM1, PM3, and MNDO heats of formation are reduced from 6.6, 4.2, and 8.2 kcal/mol to 2.3, 2.2, and 3.0 kcal/mol, respectively. Several systematic problems are overcome in the present scheme including relative stabilities of branched hydrocarbons, energetics of conjugated systems, heats of formation of long chain hydrocarbons, and enthalpies of molecules containing multiple heteroatoms. Although the approach is restricted to molecules with well‐defined functional groups, the equivalents are easy to incorporate and are chemically relevant. This revised procedure allows semiempirical methods to be used for far more reliable evaluations of heats of reactions. Estimates are made of the errors inherent in these semiempirical formalisms, arising from integral approximations and the neglect of explicit treatment of electron correlation effects, while excluding those from inadequate parameterization. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 498–510, 2002; DOI 10.1002/jcc.2002;10023
Monte Carlo sampling algorithm for searching a scale‐transformed energy space of polypeptides
Authors: Nakamura Hideaki 
Published: October 2002

AbstractA Monte Carlo sampling algorithm for searching a scale‐transformed conformational energy space of polypeptides is presented. This algorithm is based on the assumption that energy barriers can be overcome by a uniform sampling of the logarithmically transformed energy space. This algorithm is tested with Met‐enkephalin. For comparison, the entropy sampling Monte Carlo (ESMC) simulation is performed. First, the global minimum is easily found by the optimization of a scale‐transformed energy space. With a new Monte Carlo sampling, energy barriers of 3000 kcal/mol are frequently overcome, and low‐energy conformations are sampled more efficiently than with ESMC simulations. Several thermodynamic quantities are calculated with good accuracy. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 511–516, 2002; DOI 10.1002/jcc.10034
New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates
Authors: Nakamura Shugo , Kyono Daisuke , Ikeguchi Mitsunori , Shimizu Kentaro 
Published: October 2002

AbstractA new algorithm for parallel calculation of the second derivatives (Hessian) of the conformational energy function of biomolecules in internal coordinates is proposed. The basic scheme of this algorithm is the division of the entire calculation of the Hessian matrix (called “task”) into subtasks and the optimization of the assignment of processors to each subtask by considering both the load balancing and reduction of the communication cost. A genetic algorithm is used for this optimization considering the dependencies between subtasks. We applied this method to a glutaminyl transfer RNA (Gln‐tRNA) molecule for which the scalability of our previously developed parallel algorithm was significantly decreased when the large number of processors was used. The speedup for the calculation was 32.6 times with 60 processors, which is considerably better than the speedup for our previously reported parallel algorithm. The elapsed time for the calculation of subtasks, data sending, and data receiving was analyzed, and the effect of the optimization using the genetic algorithm is discussed. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 463–469, 2002; DOI 10.1002/jcc.10039
Quantum chemical geometry optimizations in proteins using crystallographic raw data
Authors: Ryde Ulf , Olsen Lars , Nilsson Kristina 
Published: October 2002

AbstractA method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM‐X)is used to study the binding of the inhibitor N‐methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4–6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal‐bound water molecules) and even to locally improve them. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1058–1070, 2002
A comparison of predicted and experimental vibrational spectra in some small fluorocarbons
Authors: Jiang He , Appadoo Dominic , Robertson Evan , McNaughton Don 
Published: October 2002

AbstractThe vibrational assignments of difluoromethane, cis and trans 1,2‐difluoroethylene, trifluoroethylene, 2‐fluoropropene, 1,1‐difluoroethylene, and tetrafluoroethylene have been reassessed in the light of recent theoretical work. Inconsistent experimental wave number values and assignments have been clarified, and some changes to the experimental assignments are proposed. The assignments compare favorably with recent scaled density functional theory calculations using the hybrid three‐parameter B3‐PW91 density functional. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1220–1225, 2002
Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations
Authors: Kuttel Michelle , Brady J. W. , Naidoo Kevin J. 
Published: October 2002

AbstractWe present a CHARMM Carbohydrate Solution Force Field (CSFF) suitable for nanosecond molecular dynamics computer simulations. The force field was derived from a recently published sugar parameter set.1 Dihedral angle parameters for the primary alcohol as well as the secondary hydroxyl groups were adjusted. Free energy profiles of the hydroxymethyl group for two monosaccharides (β‐D‐glucose and β‐D‐galactose) were calculated using the new parameter set and compared with similar force fields. Equilibrium rotamer populations obtained from the CSFF are in excellent agreement with NMR data (glucose gg:gt:tg ≈ 66:33:1 and galactose gg:gt:tg ≈ 4:75:21). In addition, the primary alcohol rotational frequency is on the nanosecond time scale, which conforms to experimental observations. Equilibrium population distributions of the primary alcohol conformers for glucose and galactose are reached within 10 nanoseconds of molecular dynamics simulations. In addition, gas phase vibrational frequencies computed for β‐D‐glucose using this force field compare well with experimental frequencies. Carbohydrate parameter sets that produce both conformational energies and rotational frequencies for the pyranose primary alcohol group that are consistent with experimental observations should allow for increased accuracy in modeling the flexibility of biologically important (1‐6)‐linked saccharides in solution. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1236–1243, 2002