bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonpoint Nitrate Contamination of Ground Water in Merrick County, Nebraskaa
Authors: Spalding R. F. , Gormly J. R. , Curtiss B. H. , Exner M. E.
Published: July 2006

The areal distribution of 293 samples from the ground water of Merrick County, Nebraska has definite patterns of high (>20 ppm), intermediate (10–20 ppm), and low (<10 ppm) nitrate‐nitrogen concentrations. Where contamination is present the nitrate‐nitrogen concentrations are relatively homogeneous indicating large diffuse nonpoint sources. SYMAP (gray‐scale mapping) indicates exceptionally good correlation between the irrigated coarse‐textured soils and the higher nitrate‐nitrogen levels. The obvious implication is that the nitrate‐nitrogen levels are directly dependent on the leaching of nitrogenous material dispersed in or on the coarser‐textured soils. The widespread use of commercial nitrogen fertilizer on irrigated corn acreages is suspected of being the major contributor of nitrate to the ground water.
Grout‐Induced Temperature Rise Surrounding Wells
Authors: Molz Fred J. , Kurt Carl E.
Published: July 2006

Cement grout surrounding a well casing generates heat, called heat of hydration, as it hardens. This heat can raise the temperature of the casing‐grout‐soil system significantly. Because the strengths of plastic casing materials decrease relatively rapidly with increasing temperature, it is important to have some idea of the temperature increase to be expected. Solution of the radial heat‐flow equation predicts temperature rises at the outer casing boundary of 9°C (16.2°F) to 55°C (99°F) as the grout envelope around a 6‐inch, water‐filled casing varies from 1.5 inches to 12 inches. The time required for the peak temperature to be reached varies from 7 to 22 hours. The temperature increase is relatively insensitive to casing diameter and thermal properties of the casing and soil. It is relatively sensitive to the type of cement used in the grout and the material filling the casing while the grout is curing. All types of plastic casing have been used successfully for years. This is due partly to the fact that in most grouting operations from the bottom up, forces on the casing are such that there is little or no tendency for collapse. However, if an air‐filled, plastic casing were grouted from the top down, heat‐induced collapse would be much more likely, particularly in zones where caving took place during well drilling.
Non‐coding RNAs in the nervous system
Authors: Mehler Mark F. , Mattick John S.
Published: June 2006

Increasing evidence suggests that the development and function of the nervous system is heavily dependent on RNA editing and the intricate spatiotemporal expression of a wide repertoire of non‐coding RNAs, including micro RNAs, small nucleolar RNAs and longer non‐coding RNAs. Non‐coding RNAs may provide the key to understanding the multi‐tiered links between neural development, nervous system function, and neurological diseases.
Strategies to unravel molecular codes essential for the development of meso‐diencephalic dopaminergic neurons
Authors: Jacobs F. M. J. , Smits S. M. , Hornman K. J. M. , Burbach J. P. H. , Smidt M. P.
Published: June 2006

Understanding the development of neuronal systems has become an important asset in the attempt to solve complex questions about neuropathology as found in Parkinson's disease, schizophrenia and other complex neuronal diseases. The development of anatomical and functional divergent structures in the brain is achieved by a combination of early anatomical patterning and highly coordinated neuronal migration and differentiation events. Fundamental to the existence of divergent structures in the brain is the early region‐specific molecular programming. Neuronal progenitors located along the neural tube can still adapt many different identities. Their exact position in the developing brain, however, determines early molecular specification by region‐specific signalling molecules. These signals determine time and region‐specific expression of early regulatory genes, leading to neuronal differentiation. Here, we focus on a well‐described neuronal group, the meso‐diencephalic dopaminergic neurons, of which heterogeneity based on anatomical position could account for the difference in vulnerability of specific subgroups as observed in Parkinson's disease. The knowledge of their molecular coding helps us to understand how the meso‐diencephalic dopaminergic system is built and could provide clues that unravel mechanisms associated with the neuropathology in complex diseases such as Parkinson's disease.
Different levels of Ih determine distinct temporal integration in bursting and regular‐spiking neurons in rat subiculum
Authors: Van Welie Ingrid , Remme Michiel W. H. , Van Hooft Johannes A. , Wadman Wytse J.
Published: June 2006

Pyramidal neurons in the subiculum typically display either bursting or regular‐spiking behaviour. Although this classification into two neuronal classes is well described, it is unknown how these two classes of neurons contribute to the integration of input to the subiculum. Here, we report that bursting neurons posses a hyperpolarization‐activated cation current (Ih) that is two‐fold larger (conductance, 5.3 ± 0.5 nS) than in regular‐spiking neurons (2.2 ± 0.6 nS), whereas Ih exhibits similar voltage‐dependent and kinetic properties in both classes of neurons. Bursting and regular‐spiking neurons display similar morphology. The difference in Ih between the two classes of neurons is not responsible for the distinct firing patterns, as neither pharmacological blockade of Ih nor enhancement of Ih using a dynamic clamp affects the qualitative firing patterns. Instead, the difference in Ih between bursting and regular‐spiking neurons determines the temporal integration of evoked synaptic input from the CA1 area. In response to stimulation at 50 Hz, bursting neurons, with a large Ih, show ∼50% less temporal summation than regular‐spiking neurons. The amount of temporal summation in both neuronal classes is equal after pharmacological blockade of Ih. A computer simulation model of a subicular neuron with the properties of either a bursting or a regular‐spiking neuron confirmed the pivotal role of Ih in temporal integration of synaptic input. These data suggest that in the subicular network, bursting neurons are better suited to discriminate the content of high‐frequency input, such as that occurring during gamma oscillations, than regular‐spiking neurons.
Laser Forming of Varying Thickness Plate—Part I: Process Analysis
Authors: Cheng Peng , Fan Yajun , Zhang Jie , Yao Y. Lawrence , Mika David P. , Zhang Wenwu , Graham Michael , Marte Jud , Jones Marshall
Published: July 2006

High-intensity laser beams can be used to heat and bend metal plates, but the mechanisms of the laser forming (LF) process are not well understood or precisely controllable. The objective of the National Institute of Standards and Technology sponsored project “Laser Forming of Complex Structures” is to develop technologies for a controllable, repeatable laser forming process that shapes and reshapes a wide range of complex structures such as compressor airfoils that are complex 3D geometries with large thickness variation. In order to apply laser forming to complex 3D geometries, the process analysis and process synthesis (design process parameters such as scanning paths and heating conditions for a desired shape) of LF of varying thickness plate are conducted in this paper. In this study, experimental, numerical, and analytical methods are used to investigate the bending mechanism and parametric effects on the deformation characteristics of varying thickness plates. A transition of the laser forming mechanism was found to occur along the scanning path when the thickness varies. The effect of scanning speed, beam spot size, and multiple scanning on the degree of bending was investigated. The proposed analytical model can predict the bending angle and angle variations for laser forming of varying thickness plate.
Material Flow in FSW of AA7075-T6 Butt Joints: Continuous Dynamic Recrystallization Phenomena
Authors: Fratini L. , Buffa G. , Palmeri D. , Hua J. , Shivpuri R.
Published: June 2006

In the paper the continuous dynamic recrystallization (CDRX) phenomena occurring in the FSW of AA7075-T6 butt joints is investigated at the varying of the most relevant technological and geometrical parameters. In particular, both experiments and numerical simulations obtained utilizing a 3D Lagrangian implicit, coupled, rigid-viscoplastic model have been developed on FSW butt joints. The resulting microstructure at the core of the weldings is correlated to the material flow occurring during the FSW process.
Mathematical Modeling of the Biomechanics of the Lamina Cribrosa
Under Elevated Intraocular Pressures
Authors: Newson Tim , El-Sheikh Ahmed
Published: June 2006

Comprehensive understanding of the biomechanical performance of the lamina cribrosa (LC) and the optic nerve head is central to understanding the role of elevated intraocular pressures (IOP) in chronic open angle glaucoma. In this paper, six closed-from mathematical models based on different idealizations of the LC are developed and compared. This approach is used to create further understanding of the biomechanical behavior by identifying the LC features and properties that have a significant effect on its performance under elevated IOP. The models developed are based on thin circular plate and membrane theories, and consider influences such as in-plane pretension caused by scleral expansion and large deflections. Comparing the results of the six models against a full ocular globe finite element model suggests the significance of the in-plane pretension and the importance of assuming that the sclera provides the LC with a clamped edge. The model that provided the most accurate representation of the finite element model was also used to predict the behavior of a number of LC experimental tests presented in the literature. In addition to the deflections under elevated IOP, the model predictions include the distributions of stress and strain, which are shown to be compatible with the progression of visual field loss experienced in glaucoma.
Blood Flow Dynamics in Saccular Aneurysm Models of the Basilar Artery
Authors: Valencia Alvaro A. , Guzmán Amador M. , Finol Ender A. , Amon Cristina H.
Published: June 2006

Blood flow dynamics under physiologically realistic pulsatile conditions plays an important role in the growth, rupture, and surgical treatment of intracranial aneurysms. The temporal and spatial variations of wall pressure and wall shear stress in the aneurysm are hypothesized to be correlated with its continuous expansion and eventual rupture. In addition, the assessment of the velocity field in the aneurysm dome and neck is important for the correct placement of endovascular coils. This paper describes the flow dynamics in two representative models of a terminal aneurysm of the basilar artery under Newtonian and non-Newtonian fluid assumptions, and compares their hemodynamics with that of a healthy basilar artery. Virtual aneurysm models are investigated numerically, with geometric features defined by β=0deg and β=23.2deg, where β is the tilt angle of the aneurysm dome with respect to the basilar artery. The intra-aneurysmal pulsatile flow shows complex ring vortex structures for β=0deg and single recirculation regions for β=23.2deg during both systole and diastole. The pressure and shear stress on the aneurysm wall exhibit large temporal and spatial variations for both models. When compared to a non-Newtonian fluid, the symmetric aneurysm model (β=0deg) exhibits a more unstable Newtonian flow dynamics, although with a lower peak wall shear stress than the asymmetric model (β=23.2deg). The non-Newtonian fluid assumption yields more stable flows than a Newtonian fluid, for the same inlet flow rate. Both fluid modeling assumptions, however, lead to asymmetric oscillatory flows inside the aneurysm dome.
An Optimized Image Matching Method for Determining In-Vivo TKA Kinematics with a Dual-Orthogonal Fluoroscopic Imaging System
Authors: Bingham Jeffrey , Li Guoan
Published: June 2006

This study presents an optimized matching algorithm for a dual-orthogonal fluoroscopic image system used to determine six degrees-of-freedom total knee arthroplasty (TKA) kinematics in-vivo. The algorithm was evaluated using controlled conditions and standard geometries. Results of the validation demonstrate the algorithm’s robustness and capability of realizing a pose from a variety of initial poses. Under idealized conditions, poses of a TKA system were recreated to within 0.02±0.01 mm and 0.02±0.03 deg for the femoral component and 0.07±0.09 mm and 0.16±0.18 deg for the tibial component. By employing a standardized geometry with spheres, the translational accuracy and repeatability under actual conditions was found to be 0.01±0.06 mm. Application of the optimized matching algorithm to a TKA patient showed that the pose of in-vivo TKA components can be repeatedly located, with standard deviations less than ±0.12 mm and ±0.12 deg for the femoral component and ±0.29 mm and ±0.25 deg for the tibial component. This methodology presents a useful tool that can be readily applied to the investigation of in-vivo motion of TKA kinematics.
Validation of a New Model-Based Tracking Technique for Measuring Three-Dimensional, In Vivo Glenohumeral Joint Kinematics
Authors: Bey Michael J. , Zauel Roger , Brock Stephanie K. , Tashman Scott
Published: June 2006

Shoulder motion is complex and significant research efforts have focused on measuring glenohumeral joint motion. Unfortunately, conventional motion measurement techniques are unable to measure glenohumeral joint kinematics during dynamic shoulder motion to clinically significant levels of accuracy. The purpose of this study was to validate the accuracy of a new model-based tracking technique for measuring three-dimensional, in vivo glenohumeral joint kinematics. We have developed a model-based tracking technique for accurately measuring in vivo joint motion from biplane radiographic images that tracks the position of bones based on their three-dimensional shape and texture. To validate this technique, we implanted tantalum beads into the humerus and scapula of both shoulders from three cadaver specimens and then recorded biplane radiographic images of the shoulder while manually moving each specimen’s arm. The position of the humerus and scapula were measured using the model-based tracking system and with a previously validated dynamic radiostereometric analysis (RSA) technique. Accuracy was reported in terms of measurement bias, measurement precision, and overall dynamic accuracy by comparing the model-based tracking results to the dynamic RSA results. The model-based tracking technique produced results that were in excellent agreement with the RSA technique. Measurement bias ranged from −0.126to0.199mm for the scapula and ranged from −0.022to0.079mm for the humerus. Dynamic measurement precision was better than 0.130mm for the scapula and 0.095mm for the humerus. Overall dynamic accuracy indicated that rms errors in any one direction were less than 0.385mm for the scapula and less than 0.374mm for the humerus. These errors correspond to rotational inaccuracies of approximately 0.25deg for the scapula and 0.47deg for the humerus. This new model-based tracking approach represents a non-invasive technique for accurately measuring dynamic glenohumeral joint motion under in vivo conditions. The model-based technique achieves accuracy levels that far surpass all previously reported non-invasive techniques for measuring in vivo glenohumeral joint motion. This technique is supported by a rigorous validation study that provides a realistic simulation of in vivo conditions and we fully expect to achieve these levels of accuracy with in vivo human testing. Future research will use this technique to analyze shoulder motion under a variety of testing conditions and to investigate the effects of conservative and surgical treatment of rotator cuff tears on dynamic joint stability.
Comparative In Vitro Study of Bileaflet and Tilting Disk Valve Behavior in the Pulmonary Position
Authors: Gohean Jeffrey , Figliola Richard , Camp Tiffany , McQuinn Tim
Published: June 2006

A study of mechanical heart valve behavior in the pulmonary position as a function of pulmonary vascular resistance is reported for the St. Jude Medical bileaflet (SJMB) valve and the MedicalCV Omnicarbon (OTD) tilting disk valve. Tests were conducted in a pulmonic mock circulatory system and impedance was varied in terms of system pulmonary vascular resistance (PVR). An impedance spectrum was found using instantaneous pulmonary artery pressure and flow rate curves. Both valves fully opened and closed at and above a nominal PVR of 3.0mmHg∕L∕min. The SJMB valve was prone to leaflet bounce at closure, but otherwise completely closed, at settings above and below this nominal setting. At PVR values at and below 2.0mmHg∕L∕min, the SJMB valve exhibited two types of leaflet aberrant behavior: single leaflet only closure while the other leaflet fluttered, and incomplete closure where both leaflets flutter but neither remain fully closed. The OTD valve fully opened and closed to a PVR value of 1.6mmHg∕L∕min. At lower values, the valve did not close. Valves designed for the left heart can show aberrant behavior under normal conditions as pulmonary valves.
Response to Comment on "Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites"
Authors: Burger Joachim , Gronenborn Detlef , Forster Peter , Matsumura Shuichi , Bramanti Barbara , Haak Wolfgang
Published: June 2006

The discovery of mitochondrial type N1a in Central European Neolithic skeletons at a high frequency enabled us to answer the question of whether the modern population is maternally descended from the early farmers instead of addressing the traditional question of the origin of early European farmers.
Bacterial Diversity in Tree Canopies of the Atlantic Forest
Authors: Lambais M. R. , Crowley D. E. , Cury J. C. , Büll R. C. , Rodrigues R. R.
Published: June 2006

We found an extraordinary level of bacterial biodiversity in the tree leaf canopy of a tropical Atlantic forest by using culture-independent molecular methods. Our survey suggests that each tree species selects for a distinct microbial community. Analysis of the bacterial 16S ribosomal RNA gene sequences revealed that about 97% of the bacteria were unknown species and that the phyllosphere of any one tree species carries at least 95 to 671 bacterial species. The tree canopies of tropical forests likely represent a large reservoir of unexplored microbial diversity.
Rapid Advance of Spring Arrival Dates in Long-Distance Migratory Birds
Authors: Jonzén Niclas , Lindén Andreas , Ergon Torbjørn , Knudsen Endre , Vik Jon Olav , Rubolini Diego , Piacentini Dario , Brinch Christian , Spina Fernando , Karlsson Lennart , Stervander Martin , Andersson Arne , Waldenström Jonas , Lehikoinen Aleksi , Edvardsen Erik , Solvang Rune , Stenseth Nils Chr.
Published: June 2006

Several bird species have advanced the timing of their spring migration in response to recent climate change. European short-distance migrants, wintering in temperate areas, have been assumed to be more affected by change in the European climate than long-distance migrants wintering in the tropics. However, we show that long-distance migrants have advanced their spring arrival in Scandinavia more than short-distance migrants. By analyzing a long-term data set from southern Italy, we show that long-distance migrants also pass through the Mediterranean region earlier. We argue that this may reflect a climate-driven evolutionary change in the timing of spring migration.
Frictional Afterslip Following the 2005 Nias-Simeulue Earthquake, Sumatra
Authors: Hsu Ya-Ju , Simons Mark , Avouac Jean-Philippe , Galetzka John , Sieh Kerry , Chlieh Mohamed , Natawidjaja Danny , Prawirodirdjo Linette , Bock Yehuda
Published: June 2006

Continuously recording Global Positioning System stations near the 28 March 2005 rupture of the Sunda megathrust [moment magnitude (
M
w
) 8.7] show that the earthquake triggered aseismic frictional afterslip on the subduction megathrust, with a major fraction of this slip in the up-dip direction from the main rupture. Eleven months after the main shock, afterslip continues at rates several times the average interseismic rate, resulting in deformation equivalent to at least a
M
w
8.2 earthquake. In general, along-strike variations in frictional behavior appear to persist over multiple earthquake cycles. Aftershocks cluster along the boundary between the region of coseismic slip and the up-dip creeping zone. We observe that the cumulative number of aftershocks increases linearly with postseismic displacements; this finding suggests that the temporal evolution of aftershocks is governed by afterslip.
Surface and Deep Ocean Interactions During the Cold Climate Event 8200 Years Ago
Authors: Ellison Christopher R. W. , Chapman Mark R. , Hall Ian R.
Published: June 2006

Evidence from a North Atlantic deep-sea sediment core reveals that the largest climatic perturbation in our present interglacial, the 8200-year event, is marked by two distinct cooling events in the subpolar North Atlantic at 8490 and 8290 years ago. An associated reduction in deep flow speed provides evidence of a significant change to a major downwelling limb of the Atlantic meridional overturning circulation. The existence of a distinct surface freshening signal during these events strongly suggests that the sequenced surface and deep ocean changes were forced by pulsed meltwater outbursts from a multistep final drainage of the proglacial lakes associated with the decaying Laurentide Ice Sheet margin.
Studying Adolescence
Authors: Richter Linda M.
Published: June 2006

Young people in their teens constitute the largest age group in the world, in a special stage recognized across the globe as the link in the life cycle between childhood and adulthood. Longitudinal studies in both developed and developing countries and better measurements of adolescent behavior are producing new insights. The physical and psychosocial changes that occur during puberty make manifest generational and early-childhood risks to development, in the form of individual differences in aspects such as growth, educational attainment, self-esteem, peer influences, and closeness to family. They also anticipate threats to adult health and well-being. Multidisciplinary approaches, especially links between the biological and the social sciences, as well as studies of socioeconomic and cultural diversity and determinants of positive outcomes, are needed to advance knowledge about this stage of development.
Politics and the Life Cycle
Authors: Kinder Donald R.
Published: June 2006

The study of politics and the life cycle began with a rather single-minded focus on childhood and the family—on the idea, as Tocqueville famously put it, that the entire person could be “seen in the cradle of the child.” Politics does begin in childhood, and parents do influence their offspring, but change takes place over the entire span of life. I take up the early emergence of partisanship and essentialism, the formation of generations, politically consequential transitions in adulthood, and the rising of politics and its final decline.
Social Modulation of Pain as Evidence for Empathy in Mice
Authors: Langford Dale J. , Crager Sara E. , Shehzad Zarrar , Smith Shad B. , Sotocinal Susana G. , Levenstadt Jeremy S. , Chanda Mona Lisa , Levitin Daniel J. , Mogil Jeffrey S.
Published: June 2006

Empathy is thought to be unique to higher primates, possibly to humans alone. We report the modulation of pain sensitivity in mice produced solely by exposure to their cagemates, but not to strangers, in pain. Mice tested in dyads and given an identical noxious stimulus displayed increased pain behaviors with statistically greater co-occurrence, effects dependent on visual observation. When familiar mice were given noxious stimuli of different intensities, their pain behavior was influenced by their neighbor's status bidirectionally. Finally, observation of a cagemate in pain altered pain sensitivity of an entirely different modality, suggesting that nociceptive mechanisms in general are sensitized.
Structural Basis of RNA-Dependent Recruitment of Glutamine to the Genetic Code
Authors: Oshikane Hiroyuki , Sheppard Kelly , Fukai Shuya , Nakamura Yuko , Ishitani Ryuichiro , Numata Tomoyuki , Sherrer R. Lynn , Feng Liang , Schmitt Emmanuelle , Panvert Michel , Blanquet Sylvain , Mechulam Yves , Söll Dieter , Nureki Osamu
Published: June 2006

Glutaminyl–transfer RNA (Gln-tRNA
Gln
) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA
Gln
by the heterodimeric Glu-tRNA
Gln
amidotransferase GatDE. Here we report the crystal structure of the
Methanothermobacter thermautotrophicus
GatDE complexed to tRNA
Gln
at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA
Gln
mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom–long channel for ammonia transport connects the active sites in GatD and GatE. tRNA
Gln
recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code.
Intron Removal Requires Proofreading of U2AF/3' Splice Site Recognition by DEK
Authors: Soares Luis Miguel Mendes , Zanier Katia , Mackereth Cameron , Sattler Michael , Valcárcel Juan
Published: June 2006

Discrimination between splice sites and similar, nonsplice sequences is essential for correct intron removal and messenger RNA formation in eukaryotes. The 65- and 35-kD subunits of the splicing factor U2AF, U2AF
65
and U2AF
35
, recognize, respectively, the pyrimidine-rich tract and the conserved terminal AG present at metazoan 3′ splice sites. We report that DEK, a chromatin- and RNA-associated protein mutated or overexpressed in certain cancers, enforces 3′ splice site discrimination by U2AF. DEK phosphorylated at serines 19 and 32 associates with U2AF
35
, facilitates the U2AF
35
-AG interaction and prevents binding of U2AF
65
to pyrimidine tracts not followed by AG. DEK and its phosphorylation are required for intron removal, but not for splicing complex assembly, which indicates that proofreading of early 3′ splice site recognition influences catalytic activation of the spliceosome.
Stoking the Voters' Passions
Authors: Druckman James N.
Published: June 2006

Campaigning for Hearts and Minds
. How Emotional Appeals in Political Ads Work.
By Ted Brader
. University of Chicago Press, Chicago, 2006. 296 pp. $60, £38. ISBN 0-226-06988-5. Paper, $24, £15.50. ISBN 0-226-06989-3. Studies in Communication, Media, and Public Opinion.

The author examines the emotional appeals of political advertising and the use of ads that stoke enthusiasm or fear.
Would You Be Happier If You Were Richer? A Focusing Illusion
Authors: Kahneman Daniel , Krueger Alan B. , Schkade David , Schwarz Norbert , Stone Arthur A.
Published: June 2006

The belief that high income is associated with good mood is widespread but mostly illusory. People with above-average income are relatively satisfied with their lives but are barely happier than others in moment-to-moment experience, tend to be more tense, and do not spend more time in particularly enjoyable activities. Moreover, the effect of income on life satisfaction seems to be transient. We argue that people exaggerate the contribution of income to happiness because they focus, in part, on conventional achievements when evaluating their life or the lives of others.
The SloR/Dlg Metalloregulator ModulatesStreptococcus mutansVirulence Gene Expression
Authors: Rolerson Elizabeth , Swick Adam , Newlon Lindsay , Palmer Cameron , Pan Yong , Keeshan Britton , Spatafora Grace
Published: June 2006

Metal ion availability in the human oral cavity plays a putative role inStreptococcus mutansvirulence gene expression and in appropriate formation of the plaque biofilm. In this report, we present evidence that supports such a role for the DtxR-like SloR metalloregulator (called Dlg in our previous publications) in this oral pathogen. Specifically, the results of gel mobility shift assays revealed thesloABC,sloR,comDE,ropA,sod, andspaPpromoters as targets of SloR binding. We confirmed differential expression of these genes in a GMS584 SloR-deficient mutant versus the UA159 wild-type progenitor by real-time semiquantitative reverse transcriptase PCR experiments. The results of additional expression studies support a role for SloR inS. mutanscontrol of glucosyltransferases, glucan binding proteins, and genes relevant to antibiotic resistance. Phenotypic analysis of GMS584 revealed that it forms aberrant biofilms on an abiotic surface, is compromised for genetic competence, and demonstrates heightened incorporation of iron and manganese as well as resistance to oxidative stress compared to the wild type. Taken together, these findings support a role for SloR inS. mutansadherence, biofilm formation, genetic competence, metal ion homeostasis, oxidative stress tolerance, and antibiotic gene regulation, all of which contribute toS. mutans-induced disease.
CYP153A6, a Soluble P450 Oxygenase Catalyzing Terminal-Alkane Hydroxylation
Authors: Funhoff Enrico G. , Bauer Ulrich , García-Rubio Inés , Witholt Bernard , van Beilen Jan B.
Published: June 2006

The first and key step in alkane metabolism is the terminal hydroxylation of alkanes to 1-alkanols, a reaction catalyzed by a family of integral-membrane diiron enzymes related to
Pseudomonas putida
GPo1 AlkB, by a diverse group of methane, propane, and butane monooxygenases and by some membrane-bound cytochrome P450s. Recently, a family of cytoplasmic P450 enzymes was identified in prokaryotes that allow their host to grow on aliphatic alkanes. One member of this family, CYP153A6 from
Mycobacterium
sp. HXN-1500, hydroxylates medium-chain-length alkanes (C
6
to C
11
) to 1-alkanols with a maximal turnover number of 70 min
−1
and has a regiospecificity of ≥95% for the terminal carbon atom position. Spectroscopic binding studies showed that C
6
-to-C
11
aliphatic alkanes bind in the active site with

K
d

values varying from ∼20 nM to 3.7 μM. Longer alkanes bind more strongly than shorter alkanes, while the introduction of sterically hindering groups reduces the affinity. This suggests that the substrate-binding pocket is shaped such that linear alkanes are preferred. Electron paramagnetic resonance spectroscopy in the presence of the substrate showed the formation of an enzyme-substrate complex, which confirmed the binding of substrates observed in optical titrations. To rationalize the experimental observations on a molecular scale, homology modeling of CYP153A6 and docking of substrates were used to provide the first insight into structural features required for terminal alkane hydroxylation.
Modulation of the ComA-Dependent Quorum Response in
Bacillus subtilis
by Multiple Rap Proteins and Phr Peptides
Authors: Auchtung Jennifer M. , Lee Catherine A. , Grossman Alan D.
Published: June 2006

In
Bacillus subtilis
, extracellular peptide signaling regulates several biological processes. Secreted Phr signaling peptides are imported into the cell and act intracellularly to antagonize the activity of regulators known as Rap proteins.
B. subtilis
encodes several Rap proteins and Phr peptides, and the processes regulated by many of these Rap proteins and Phr peptides are unknown. We used DNA microarrays to characterize the roles that several
rap
-
phr
signaling modules play in regulating gene expression. We found that
rapK-phrK
regulates the expression of a number of genes activated by the response regulator ComA. ComA activates expression of genes involved in competence development and the production of several secreted products. Two Phr peptides, PhrC and PhrF, were previously known to stimulate the activity of ComA. We assayed the roles that PhrC, PhrF, and PhrK play in regulating gene expression and found that these three peptides stimulate ComA-dependent gene expression to different levels and are all required for full expression of genes activated by ComA. The involvement of multiple Rap proteins and Phr peptides allows multiple physiological cues to be integrated into a regulatory network that modulates the timing and magnitude of the ComA response.
Regulation of the
Chlamydia trachomatis
Histone H1-Like Protein Hc2 Is IspE Dependent and IhtA Independent
Authors: Grieshaber Nicole A. , Sager Janet Burgess , Dooley Cheryl A. , Hayes Stanley F. , Hackstadt Ted
Published: June 2006

The chlamydial histone-like proteins, Hc1 and Hc2, function as global regulators of chromatin structure and gene expression. Hc1 and Hc2 expression and activity are developmentally regulated. A small metabolite that disrupts Hc1 interaction with DNA also disrupts Hc2 interactions; however, the small regulatory RNA that inhibits Hc1 translation is specific to Hc1.
Glycogen Phosphorylase, the Product of the
glgP
Gene, Catalyzes Glycogen Breakdown by Removing Glucose Units from the Nonreducing Ends in
Escherichia coli
Authors: Alonso-Casajús Nora , Dauvillée David , Viale Alejandro Miguel , Muñoz Francisco José , Baroja-Fernández Edurne , Morán-Zorzano María Teresa , Eydallin Gustavo , Ball Steven , Pozueta-Romero Javier
Published: June 2006

To understand the biological function of bacterial glycogen phosphorylase (GlgP), we have produced and characterized
Escherichia coli
cells with null or altered
glgP
expression.
glgP
deletion mutants (Δ
glgP
) totally lacked glycogen phosphorylase activity, indicating that all the enzymatic activity is dependent upon the
glgP
product. Moderate increases of glycogen phosphorylase activity were accompanied by marked reductions of the intracellular glycogen levels in cells cultured in the presence of glucose. In turn, both glycogen content and rates of glycogen accumulation in
ΔglgP
cells were severalfold higher than those of wild-type cells. These defects correlated with the presence of longer external chains in the polysaccharide accumulated by
ΔglgP
cells. The overall results thus show that GlgP catalyzes glycogen breakdown and affects glycogen structure by removing glucose units from the polysaccharide outer chains in
E. coli
.
Is it time to re-assess the role of gliclazide? Targeting insulin resistance in type 2 diabetes patients suboptimally controlled with insulin
Authors: Brown N
Published: July 2006

Background

Adult patients with type 2 diabetes controlled with insulin frequently require the addition of insulin sensitising drugs such as metformin and sometimes glitazones to achieve optimum glycaemic control. Five of a group of eight people with suboptimal diabetes control who were treated by the introduction of gliclazide are reported on. Three patients were excluded. One with type 1 diabetes and two others who had dietary or other therapeutic interventions coinciding with re-introduction gliclazide. Does the re-introduction of gliclazide effect a clinically significant improvement in glycaemic control in type 2 diabetes patients with suboptimal control taking combinations of short and long acting insulin plus metformin?

Method

Five adult patients with type 2 diabetes with suboptimal control using combinations of short and long acting insulin plus metformin who were adherent to their dietary regimen were treated by the addition of gliclazide at different doses. Two of the patients were taking pioglitazone in addition to metformin and insulin. Their glycaemic control was monitored over the following six months.

Results

All five showed significant improvement in glycaemic control after three months. Mean reduction in HbA1c was 1.4% (range 0.9% to 2.5%). Six months after the introduction of gliclazide four patients had HbA1c below base line figure and in two patients clinically significant improvement had been maintained.

Conclusion

A double blind randomised placebo control study is necessary to evaluate a possible role for gliclazide in type 2 diabetes patients who have suboptimal glycaemic control using combinations of short and long acting insulin plus metformin.
Gastric type H+,K+-ATPase in the cochlear lateral wall is critically involved in formation of the endocochlear potential
Authors: Shibata Toshiaki , Hibino Hiroshi , Doi Katsumi , Suzuki Toshihiro , Hisa Yasuo , Kurachi Yoshihisa
Published: July 2006

Cochlear endolymph has a highly positive potential of approximately +80 mV known as the endocochlear potential (EP). The EP is essential for hearing and is maintained by K+ circulation from perilymph to endolymph through the cochlear lateral wall. Various K+ transport apparatuses such as the Na+,K+-ATPase, the Na+-K+-2Cl− cotransporter, and the K+ channels Kir4.1 and KCNQ1/KCNE1 are expressed in the lateral wall and are known to play indispensable roles in cochlear K+ circulation. The gastric type of the H+,K+-ATPase was also shown to be expressed in the cochlear lateral wall (Lecain E, Robert JC, Thomas A, and Tran Ba Huy P. Hear Res 149: 147–154, 2000), but its functional role has not been well studied. In this study we examined the precise localization of H+,K+-ATPase in the cochlea and its involvement in formation of EP. RT-PCR analysis showed that the cochlea expressed mRNAs of gastric α1-, but not colonic α2-, and β-subunits of H+,K+-ATPase. Immunolabeling of an antibody specific to the α1 subunit was detected in type II, IV, and V fibrocytes distributed in the spiral ligament of the lateral wall and in the spiral limbus. Strong immunoreactivity was also found in the stria vascularis. Immunoelectron microscopic examination exhibited that the H+,K+-ATPase was localized exclusively at the basolateral site of strial marginal cells. Application of Sch-28080, a specific inhibitor of gastric H+,K+-ATPase, to the spiral ligament as well as to the stria vascularis caused prominent reduction of EP. These results may imply that the H+,K+-ATPase in the cochlear lateral wall is crucial for K+ circulation and thus plays a critical role in generation of EP.
An oxidized metabolite of linoleic acid increases intracellular calcium in rat adrenal glomerulosa cells
Authors: Payet Marcel D. , Goodfriend Theodore L. , Bilodeau Lyne , Mackendale Cherilu , Chouinard Lucie , Gallo-Payet Nicole
Published: July 2006

EKODE, an epoxy-keto derivative of linoleic acid, was previously shown to stimulate aldosterone secretion in rat adrenal glomerulosa cells ( 15 ). In the present study, we investigated the effect of exogenous EKODE on cytosolic [Ca2+] increase and aimed to elucidate the mechanism involved in this process. Through the use of the fluorescent Ca2+-sensitive dye Fluo-4, EKODE was shown to rapidly increase intracellular [Ca2+] ([Ca2+]i) along a bell-shaped dose-response relationship with a maximum peak at 5 μM. Experiments performed in the presence or absence of Ca2+revealed that this increase in [Ca2+]ioriginated exclusively from intracellular pools. EKODE-induced [Ca2+]iincrease was blunted by prior application of angiotensin II, Xestospongin C, and cyclopiazonic acid, indicating that inositol trisphosphate (InsP3)-sensitive Ca2+stores can be mobilized by EKODE despite the absence of InsP3production. Accordingly, EKODE response was not sensitive to the phospholipase C inhibitor U-73122. EKODE mobilized a Ca2+store included in the thapsigargin (TG)-sensitive stores, although the interaction between EKODE and TG appears complex, since EKODE added at the plateau response of TG induced a rapid drop in [Ca2+]i. 9-Oxo-octadecadienoic acid, another oxidized derivative of linoleic acid, also increases [Ca2+]i, with a dose-response curve similar to EKODE. However, arachidonic and linoleic acids at 10 μM failed to increase [Ca2+]ibut did reduce the amplitude of the response to EKODE. It is concluded that EKODE mobilizes Ca2+from an InsP3-sensitive store and that this [Ca2+]iincrease is responsible for aldosterone secretion by glomerulosa cells. Similar bell-shaped dose-response curves for aldosterone and [Ca2+]iincreases reinforce this hypothesis.
Roles of insulin-like growth factor II in cardiomyoblast apoptosis and in hypertensive rat heart with abdominal aorta ligation
Authors: Lee Shin-Da , Chu Chun-Hsien , Huang Erh-Jung , Lu Min-Chi , Liu Jer-Yuh , Liu Chung-Jung , Hsu Hsi-Hsien , Lin James A. , Kuo Wei-Wen , Huang Chih-Yang
Published: July 2006

Although IGF-II activating the IGF-II receptor signaling pathway has been found to stimulate cardiomyocyte hypertrophy, the role of IGF-II in cardiac cell apoptosis remains unclear. This study aimed to identify the roles of IGF-II and/or IGF-II receptors (IGF-II/IIR) in cardiomyoblast apoptosis and in hypertensive rat hearts with abdominal aorta ligation. Cultured rat heart-derived H9c2 cardiomyoblasts and excised hearts from Sprague-Dawley rats with 0- to 20-day complete abdominal aorta ligation, a model of ANG II elevation and hypertension, were used. IGF-II/IIR expression, caspase activity, DNA fragmentation, and apoptotic cells were measured by RT-PCR, Western blot, agarose gel electrophoresis, and TUNEL assay following various combinations of ANG II, IGF-II/IIR antibody, CsA (calcineurin inhibitor), SP-600125 (JNK inhibitor), SB-203580 (p38 inhibitor), U-0126 (MEK inhibitor), or Staurosporine (PKC inhibitor) in H9c2 cells. ANG II-induced DNA fragmentation and TUNEL-positive cells were blocked by IGF-II/IIR antibodies and antisense IGF-II, but not by IGF-II sense. IGF-II-induced apoptosis was blocked by IGF-IIR antibody and CsA. The increased gene expressions of IGF-II and -IIR induced by ANG II were reversed by U-0126 and Sp600125, respectively. Caspase 8 activities induced by ANG II were attenuated by U-0126, SP-600125, and CsA. DNA fragmentation induced by ANG II was totally blocked by SP-600125, and CsA and was attenuated by U-0126. In rats with 0- to 20-day complete abdominal aorta ligation, the increases in IGF-II/IIR levels in the left ventricle were accompanied by hypertension as well as increases in caspase 9 activities and TUNEL-positive cardiac myocytes. ANG II-induced apoptosis was reversed by IGF-II/IIR blockade and coexisted with increased transactivation of IGF-II and -IIR, which are mediated by ERK and JNK pathways, respectively, both of which further contributed to cardiomyoblast apoptosis via calcineurin signaling. The increased cardiac IGF-II, IGF-IIR, caspase 9, and cellular apoptosis were also found in hypertensive rats with abdominal aorta ligation.
All-trans-retinoic acid distribution and metabolism in vitamin A-marginal rats
Authors: Cifelli Christopher J. , Ross A. Catharine
Published: July 2006

Retinoids, including all- trans-retinoic acid (RA), are considered to have anti-inflammatory properties and are used therapeutically for diseases of the skin and certain cancers. However, few studies have addressed the effects of disease states on RA metabolism. The present study was conducted to better understand the effects of exogenous RA, both in the absence and presence of inflammation, on the distribution and metabolism of a dose of [3H]RA. Female Sprague-Dawley rats fed a low vitamin A diet were pretreated with RA (po), a low dose of lipopolysaccharide (LPS, ip), or their combination. Twelve hours later, albumin-bound [3H]RA was injected intravenously, and tissue organic- and aqueous-phase3H was determined after 10 and 30 min. In liver and plasma,3H-labeled organic metabolites (e.g., 4-oxo- and 4-hydroxy-RA) were isolated by solid-phase extraction. LPS-induced inflammation significantly reduced plasma retinol by 47%, increased total3H in plasma at 10 min, and reduced total3H in liver at both times. In contrast, RA pretreatment did not affect plasma retinol, significantly increased total3H in plasma at both times, and did not affect liver total3H. However, by 30 min, RA significantly increased [3H]RA metabolism in plasma, liver, lung, and small intestine, as indicated by greater3H-labeled aqueous-phase and3H-labeled organic-phase metabolites. The results presented here demonstrate that, although LPS-induced inflammation affects the organ distribution of RA, the ability of RA to induce its own catabolism is maintained during inflammation. Thus we conclude that RA and LPS act independently to alter RA metabolism in vitamin A-marginal rats.
Effects of sleep deprivation on the development of autoimmune disease in an experimental model of systemic lupus erythematosus
Authors: Palma Beatriz Duarte , Gabriel Alexandre , Colugnati Fernando A. B. , Tufik Sergio
Published: June 2006

Sleep is hypothesized to play a restorative role on immune system. In addition, disturbed sleep is thought to impair host defense mechanisms. Chronic sleep deprivation is a common occurrence in modern society and has been observed in a number of chronic inflammatory conditions, such as systemic lupus erythematosus (SLE). New Zealand Black/New Zealand White (NZB/NZW) F1mice develop an autoimmune disease that strongly resembles SLE in humans, exhibiting high titers of antinuclear antibodies associated with the development of rapidly progressive and lethal glomerulonephritis. On the basis of this evidence, the present study examined the onset and progress of lupus in as-yet healthy female mice submitted to sleep deprivation. Sleep deprivation was accomplished by two 96-h periods in the multiple-platform method when mice were 10 wk old, and they were observed until 28 wk of age. Blood samples were collected from the orbital plexus fortnightly to evaluate serum antinuclear antibodies and anti-double-stranded DNA. Proteinuria and longevity as well as body weight were also assessed. The results indicated that mice submitted to sleep deprivation exhibited an earlier onset of the disease, as reflected by the increased number of antinuclear antibodies. However, no statistical difference was found in the other parameters analyzed. According to these results, sleep deprivation could be considered as a risk factor for the onset but not for the evolution of the disease.
Oxyresveratrol dampens neuroimmune responses in vivo: a selective effect on TNF-α
Authors: Mouihate A. , Horn T. F. , Pittman Q. J.
Published: June 2006

Consumption of nutrients rich in hydroxystilbenes has been promoted because of their health benefits, including dampening of inflammatory responses. However, few studies have examined their effects in vivo. Here, we show that the hydroxystilbene oxyresveratrol (trans-2,3′,4,5′-tetrahydroxystilbene: o-RES) blocked hypothermia but caused no significant effect on the febrile response to the immune stimulus, bacterial LPS in rats. This was associated with a reduction in the LPS-induced plasma cytokine, tumor necrosis factor (TNF)-α, but not IL-6. Both IL-6-stimulated STAT-3 and LPS-induced cycoloxygenase-2 expression in the hypothalamus were not affected by o-RES. These data strongly suggest that the o-RES-induced dampening of neuroimmune responses is largely due to its inhibitory effect on TNF-α production. In contrast to in vitro experiments, o-RES has no direct effect on NF-κB signaling pathway in vivo. The specific inhibitory effect of o-RES on TNF-α opens new avenues for the clinical use of o-RES in pathological conditions where excessive production of TNF-α is deleterious.