bluuebunny/crossref_metadata_2025 huggingface dataset:
Land water storage within the Congo Basin inferred from GRACE satellite gravity data
Authors: Crowley John W. , Mitrovica Jerry X. , Bailey Richard C. , Tamisiea Mark E. , Davis James L.
Published: October 2006

GRACE satellite gravity data is used to estimate terrestrial (surface plus ground) water storage within the Congo Basin in Africa for the period of April, 2002–May, 2006. These estimates exhibit significant seasonal (30 ± 6 mm of equivalent water thickness) and long‐term trends, the latter yielding a total loss of ∼280 km3 of water over the 50‐month span of data. We also combine GRACE and precipitation data sets (CMAP, TRMM) to explore the relative contributions of the source term to the seasonal hydrological balance within the Congo Basin. We find that the seasonal water storage tends to saturate for anomalies greater than 30–40 mm of equivalent water thickness. Furthermore, precipitation contributed roughly three times the peak water storage after anomalously rainy seasons, in early 2003 and 2005, implying a ∼60–70% loss from runoff and evapotranspiration. Finally, a comparison of residual land water storage (monthly estimates minus best‐fitting trends) in the Congo and Amazon Basins shows an anti‐correlation, in agreement with the “see‐saw” variability inferred by others from runoff data.
Sensitivity of global river discharges under Holocene and future climate conditions
Authors: Aerts J. C. J. H. , Renssen H. , Ward P. J. , de Moel H. , Odada E. , Bouwer L. M. , Goosse H.
Published: October 2006

A comparative analysis of global river basins shows that some river discharges are more sensitive to future climate change for the coming century than to natural climate variability over the last 9000 years. In these basins (Ganges, Mekong, Volta, Congo, Amazon, Murray‐Darling, Rhine, Oder, Yukon) future discharges increase by 6–61%. These changes are of similar magnitude to changes over the last 9000 years. Some rivers (Nile, Syr Darya) experienced strong reductions in discharge over the last 9000 years (17–56%), but show much smaller responses to future warming. The simulation results for the last 9000 years are validated with independent proxy data.
Modeling the nonlinear effect of wind on rectilinear tidal flow
Authors: Ruessink B. G. , Houwman K. T. , Grasmeijer B. T.
Published: October 2006

Observations of near‐bed alongshore flow in 4–10 m depth at Terschelling, Netherlands, show that strong alongshore winds (≈15–20 m/s) in the flood direction reduce the tide current range and alter the tidal flow curve by bringing maximum flood flow forward in time and delaying maximum ebb flow. These nonlinear effects, which are more pronounced in shallower water, are reproduced well by a single‐point model in the vertical driven by large‐scale (O(km)) sea surface gradients and wind stress, using a quadratic bottom stress formulation and a time‐dependent eddy viscosity derived from a k‐ε turbulence closure model. Subsequent idealized model simulations using a (Terschelling based) M2 sea‐surface gradient and wind speeds between 0 and 20 m/s show that the wind‐induced modifications of the tidal flow are consistent with the interaction of the wind‐induced flow with the tidal flow through the quadratic bed stress. The wind‐driven flow enhances friction during the flood phase more than it reduces friction during the ebb flow, thereby increasing friction over a tidal cycle and, as a consequence, reducing the tide current range. The predicted increase in asymmetry of bed friction during flood and ebb flow with increasing wind speed also increases (decreases) the M4 (M6) amplitude, consistent with the observations. The M4/M2 amplitude ratio is predicted to be largest when the flow has just become unidirectional (that is, when the wind‐driven flow equals the tidal current).
Heart Rate Variability as an Index of Regulated Emotional Responding
Authors: Appelhans Bradley M. , Luecken Linda J.
Published: October 2006

The study of individual differences in emotional responding can provide considerable insight into interpersonal dynamics and the etiology of psychopathology. Heart rate variability (HRV) analysis is emerging as an objective measure of regulated emotional responding (generating emotional responses of appropriate timing and magnitude). This review provides a theoretical and empirical rationale for the use of HRV as an index of individual differences in regulated emotional responding. Two major theoretical frameworks that articulate the role of HRV in emotional responding are presented, and relevant empirical literature is reviewed. The case is made that HRV is an accessible research tool that can increase the understanding of emotion in social and psychopathological processes.
Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implications for drug design
Authors: Omari Kamel EL , Bronckaers Annelies , Liekens Sandra , Pérez-Pérez Maria-Jésus , Balzarini Jan , Stammers David K.
Published: October 2006

HTP (human thymidine phosphorylase), also known as PD-ECGF (platelet-derived endothelial cell growth factor) or gliostatin, has an important role in nucleoside metabolism. HTP is implicated in angiogenesis and apoptosis and therefore is a prime target for drug design, including antitumour therapies. An HTP structure in a closed conformation complexed with an inhibitor has previously been solved. Earlier kinetic studies revealed an ordered release of thymine followed by ribose phosphate and product inhibition by both ligands. We have determined the structure of HTP from crystals grown in the presence of thymidine, which, surprisingly, resulted in bound thymine with HTP in a closed dead-end com-plex. Thus thymine appears to be able to reassociate with HTP after its initial ordered release before ribose phosphate and induces the closed conformation, hence explaining the mechanism of non-competitive product inhibition. In the active site in one of the four HTP molecules within the crystal asymmetric unit, additional electron density is present. This density has not been previously seen in any pyrimidine nucleoside phosphorylase and it defines a subsite that may be exploitable in drug design. Finally, because our crystals did not require proteolysed HTP to grow, the structure reveals a loop (residues 406–415), disordered in the previous HTP structure. This loop extends across the active-site cleft and appears to stabilize the dimer interface and the closed conformation by hydrogen-bonding. The present study will assist in the design of HTP inhibitors that could lead to drugs for anti-angiogenesis as well as for the potentiation of other nucleoside drugs.
Free-energy profiles for catalysis by dual-specificity phosphatases
Authors: Arantes Guilherme M.
Published: October 2006

PTPs (protein tyrosine phosphatases) are fundamental enzymes for cell signalling and have been linked to the pathogenesis of several diseases, including cancer. Hence, PTPs are potential drug targets and inhibitors have been designed as possible therapeutic agents for Type II diabetes and obesity. However, a complete understanding of the detailed catalytic mechanism in PTPs is still lacking. Free-energy profiles, obtained by computer simulations of catalysis by a dual-specificity PTP, are shown in the present study and are used to shed light on the catalytic mechanism. A highly accurate hybrid potential of quantum mechanics/molecular mechanics calibrated specifically for PTP reactions was used. Reactions of alkyl and aryl substrates, with different protonation states and PTP active-site mutations, were simulated. Calculated reaction barriers agree well with experimental rate measurements. Results show the PTP substrate reacts as a bi-anion, with an ionized nucleophile. This protonation state has been a matter of debate in the literature. The inactivity of Cys→Ser active-site mutants is also not fully understood. It is shown that mutants are inactive because the serine nucleophile is protonated. Results also clarify the interpretation of experimental data, particularly kinetic isotope effects. The simulated mechanisms presented here are better examples of the catalysis carried out by PTPs.
Transmembrane segment 7 of human P-glycoprotein forms part of the drug-binding pocket
Authors: Loo Tip W. , Bartlett M. Claire , Clarke David M.
Published: October 2006

P-gp (P-glycoprotein; ABCB1) protects us by transporting a broad range of structurally unrelated compounds out of the cell. Identifying the regions of P-gp that make up the drug-binding pocket is important for understanding the mechanism of transport. The common drug-binding pocket is at the interface between the transmembrane domains of the two homologous halves of P-gp. It has been shown in a previous study [Loo, Bartlett and Clarke (2006) Biochem. J. 396, 537–545] that the first transmembrane segment (TM1) contributed to the drug-binding pocket. In the present study, we used cysteine-scanning mutagenesis, reaction with an MTS (methanethiosulfonate) thiol-reactive analogue of verapamil (termed MTS–verapamil) and cross-linking analysis to test whether the equivalent transmembrane segment (TM7) in the C-terminal-half of P-gp also contributed to drug binding. Mutation of Phe728 to cysteine caused a 4-fold decrease in apparent affinity for the drug substrate verapamil. Mutant F728C also showed elevated ATPase activity (11.5-fold higher than untreated controls) after covalent modification with MTS–verapamil. The activity returned to basal levels after treatment with dithiothreitol. The substrates, verapamil and cyclosporin A, protected the mutant from labelling with MTS–verapamil. Mutant F728C could be cross-linked with a homobifunctional thiol-reactive cross-linker to cysteines I306C(TM5) and F343C(TM6) that are predicted to line the drug-binding pocket. Disulfide cross-linking was inhibited by some drug substrates such as Rhodamine B, calcein acetoxymethyl ester, cyclosporin, verapamil and vinblastine or by vanadate trapping of nucleotides. These results indicate that TM7 forms part of the drug-binding pocket of P-gp.
The fructosamine 3-kinase knockout mouse: a tool for testing the glycation hypothesis of intracellular protein damage in diabetes and aging
Authors: Monnier Vincent M.
Published: October 2006

Protein glycation and the formation of AGEs (advanced glycation end-products) and cross-links have been hypothesized to play a role in the pathogenesis of age- and diabetes-related complications. The discovery that FN3K (fructosamine 3-kinase) results in protein deglycation upon phosphorylation of glucose-derived Amadori products suggests that intracellular glycation could be deleterious under certain circumstances. In order to approach the question of the biological relevance of intracellular glycation, in this issue of the Biochemical Journal, Veiga-da-Cunha and colleagues generated an FN3K-knockout mouse. The mice grow normally and are apparently healthy, and levels of protein-bound and free fructoselysine are elevated in several tissues of importance to diabetic complications. This commentary discusses the clinical and evolutionary significance of FN3K, and proposes experimental approaches for revealing the existence of a biological phenotype.
Vibrationally mediated photodissociation of ethene isotopic variants preexcited to the fourth C–H stretch overtone
Authors: Bespechansky Evgeny , Portnov Alexander , Zwielly Amir , Rosenwaks Salman , Bar Ilana
Published: October 2006

H and D photofragments produced via vibrationally mediated photodissociation of jet-cooled normal ethene (C2H4), 1,2-trans-d2-ethene (HDCCDH), and 1,1-d2-ethene (CH2CD2), initially excited to the fourth C–H stretch overtone region, were studied for the first time. H and D vibrational action spectra and Doppler profiles were measured. The action spectra include partially resolved features due to rotational cooling, while the monitored room temperature photoacoustic spectra exhibit only a very broad feature in each species. Simulation of the spectral contours allowed determination of the band types and origins, limited precision rotational constants, and linewidths, providing time scales for energy redistribution. The H and D Doppler profiles correspond to low average translational energies and show slight preferential C–H over C–D bond cleavage in the deuterated variants. The propensities toward H photofragments emerge even though the energy flow out of the initially prepared C–H stretch is on a picosecond time scale and the photodissociation occurs following internal conversion, indicating a more effective release of the light H atoms.
Feel the Presence: Technologies of Touch and Distance
Authors: Paterson Mark
Published: October 2006

Haptic devices for computers and video-game consoles aim to reproduce touch and to engage the user with ‘force feedback’. Although physical touch is often associated with proximity and intimacy, technologies of touch can reproduce such sensations over a distance, allowing intricate and detailed operations to be conducted through a network such as the Internet. The ‘virtual handshake’ between Boston and London in 2002 is given as an example. This paper is therefore a critical investigation into some technologies of touch, leading to observations about the sociospatial framework in which this technological touching takes place. Haptic devices have now become routinely included with video-game consoles, and have started to be used in computer-aided design and manufacture, medical simulation, and even the cybersex industry. The implications of these new technologies are enormous, as they remould the human–computer interface from being primarily audiovisual to being more truly multisensory, and thereby enhance the sense of ‘presence’ or immersion. But the main thrust of this paper is the development of ideas of presence over a large distance, and how this is enhanced by the sense of touch. By using the results of empirical research, including interviews with key figures in haptics research and engineering and personal experience of some of the haptic technologies available, I build up a picture of how ‘presence’, ‘copresence’, and ‘immersion’, themselves paradoxically intangible properties, are guiding the design, marketing, and application of haptic devices, and the engendering and engineering of a set of feelings of interacting with virtual objects, across a range of distances.
Decentering Queer Globalization: Diffusion and the ‘Global Gay’
Authors: Oswin Natalie
Published: October 2006

Queer geographers have been surprisingly slow to engage with the global turn that has existed for some time in queer studies outside the discipline. This is beginning to change but the range of sites addressed is limited largely to Euro-American ones. This paper considers the ways in which queer geographers might contribute to already-existing debates over the relationship between the ‘West’ and the ‘non-West’ in global queer studies. The paper departs from Larry Knopp and Michael Brown's “Queer diffusions”, a paper that appeared in a special issue of Society and Space (2003, 21 461–477). Though they limit themselves to the national scale of the United States, their argument that we should destigmatize places and identities cast as ‘backward’ has obvious relevance at the global scale. Its consistencies and inconsistencies with various strands of argument within the global queer-studies literature reveal that geographers might also learn from the spatial nuance developed in these debates. Specifically, this literature review concludes that we must also destigmatize those places and identities that are cast as ‘forward’ if queer globalization is to truly be decentered.
Sphenoid sinus barotrauma with intracranial air in sella turcica after diving
Authors: Tryggvason G. , Briem B. , Guðmundsson Ó. , Einarsdóttir H.
Published: October 2006

We report the case of a diver who presented with air in the sella turcica after barotrauma to the sphenoid sinus during an ascent from a dive. To our knowledge, this is the first report of intracranial air after a barotrauma to the sphenoid sinus.
Gadolinium-enhanced magnetic resonance imaging after percutaneous vertebroplasty does not improve the short-term prediction of new compression fractures
Authors: Maehara M. , Tanigawa N. , Ikeda K. , Ohmura N. , Komemushi A. , Kojima H. , Kariya S. , Sawada S.
Published: October 2006

Purpose: To investigate the relationships between contrast-enhanced magnetic resonance imaging (MRI) findings and new compression fractures occurring after percutaneous vertebroplasty (PVP) in order to determine the necessity of contrast-enhanced MRI.

Material and Methods: The material comprised 13 consecutive patients (27 vertebrae) with compression fractures who underwent vertebroplasty. Twenty-nine adjacent vertebrae were monitored for new compression fractures. We performed contrast-enhanced MRI within the 5 days following PVP.

Results: The 29 adjacent vertebrae displayed 10 enhanced lesions and 19 vertebral bodies without enhancement–unenhanced lesions on MRI within the 5 days after PVP. In 4 out of 10 vertebrae, enhanced lesions were seen within the 5 days after PVP, but no abnormalities were seen on preoperative MRI. In these 4 vertebrae, new compression fractures were seen within the 1 month following PVP. In the other 6 vertebrae, enhanced lesions were seen within the 5 days after PVP, and these signal changes were detected by preoperative MRI in the same area. In 3 of these 6 vertebrae, new compression fractures occurred at 4, 8, and 9 months after PVP, respectively. However, all of the enhanced lesions were detectable on unenhanced MRI, which was conducted at the same time as enhanced MRI.

Conclusion: New compression fractures after PVP may be predicted with early postoperative MRI. Contrast-enhanced MRI does not improve detection of the new lesions.
Maintained pain reduction in five patients with multiple myeloma 12 months after treatment of the involved cervical vertebrae with vertebroplasty
Authors: Pflugmacher R. , Schleicher P. , Schröder R. J. , Melcher I. , Klostermann C. K.
Published: October 2006

Purpose: To evaluate in a prospective study the clinical and radiographic outcome of vertebroplasty in patients with osteolytic lesions of the cervical spine caused by multiple myeloma.

Material and Methods: Pathological vertebral fractures associated with multiple myeloma were treated in five patients. Vertebroplasty was performed in 12 vertebral bodies. Symptomatic levels were identified by correlating the clinical presentation with magnetic resonance imaging (MRI), conventional radiographs, and computed tomography (CT). During the 12-month follow-up, pain symptoms were measured on a self-reported visual analog scale (VAS), neck pain disability index (NPDI, range 0–100%), and cervical spine functional score (CSFS, range 0–100). Medical imaging was performed pre- and postoperatively and after 3, 6, and 12 months. The vertebral height was measured to assess the restoration of the sagittal alignment.

Results: The median pain scores (VAS) as well as the NPDI and CSFS decreased significantly after vertebroplasty ( P<0.05). Cement leakage occurred in two of 12 vertebral bodies (16.6%), without clinical relevance. The vertebral body height was stabilized during follow-up.

Conclusion: Vertebroplasty in the cervical spine is an effective open surgical procedure for the stabilization of pathological vertebral fractures caused by multiple myeloma leading to a statistically significant reduction of pain status. Vertebral body height is stabilized and further deformities are avoided.
Contrast-enhanced dynamic magnetic resonance imaging of finger joints in osteoarthritis and rheumatoid arthritis: an analysis based on pharmacokinetic modeling
Authors: Kirkhus E. , Bjørnerud A. , Thoen J. , Johnston V. , Dale K. , Smith H. -J.
Published: October 2006

Purpose: To investigate a two-compartment kinetic model applied to the dynamic time course of contrast enhancement as a method to differentiate between finger-joint synovitis in established osteoarthritis (OA) and rheumatoid arthritis (RA).

Material and Methods: Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) of one hand in 19 patients and six healthy volunteers was undertaken. Eight patients had OA of the hand and eleven patients had RA. From the signal intensity curves, the three parameters Kps (endothelial transfer constant), Kep (elimination rate constant from extracellular space back to plasma) and Kel (elimination rate constant from plasma by renal excretion) were calculated.

Results: The rate constant Kps showed the best separation between the groups with significantly higher values in the RA group compared to the OA group ( P<0.005) and in the OA group compared to the control group ( P<0.005). Significantly higher values of Kep were also found in the RA group compared with the OA group ( P<0.005).

Conclusion: DCE-MRI may provide useful information that can help differentiate synovitis in OA from synovitis in RA.
Diagnostic difficulties in the management of H-type tracheoesophageal fistula
Authors: Ng J. , Antao B. , Bartram J. , Raghavan A. , Shawis R.
Published: October 2006

Purpose: To evaluate the diagnostic difficulties and pitfalls in establishing the diagnosis of congenital H-type tracheoesophageal fistula.

Material and Methods: A retrospective review of all cases of H-type tracheoesophageal fistula that were diagnosed in a single unit over a 6-year period. The variables assessed were age at presentation, presenting symptoms, time to diagnosis, investigations, and time to surgical repair of H-type fistula. The investigations leading to a definitive diagnosis are assessed and discussed.

Results: Between 1998 and 2004, five cases of H-type tracheoesophageal fistula presented to our unit. All cases had an upper gastrointestinal contrast study/tube esophagogram. In addition, four cases had a chest radiograph, three cases had a bronchoscopy, and one case an esophagoscopy. The median delay from the time of first presentation to diagnosis of H-type tracheoesophageal fistula was 14 days (7–58 days). Median age at surgery was 15 days (8–60 days).

Conclusion: Although symptoms are usually present from birth, the diagnosis of H-type fistula is difficult and often delayed. The various diagnostic techniques are not entirely reliable and fistula identification can be elusive. The authors present recommendations for the diagnostic work-up, which may increase the diagnostic potential and avoid unnecessary delays in the diagnosis and management of H fistula.
Incidence of adjacent vertebral fractures in patients treated with balloon kyphoplasty: two years’ prospective follow-up
Authors: Pflugmacher R. , Schroeder R.-J. , Klostermann C. K.
Published: October 2006

Purpose: To evaluate the long-term outcomes of 37 patients with 60 osteoporotic vertebral fractures, located in the thoracic and lumbar spine, treated with balloon kyphoplasty.

Material and Methods: Fourty-two patients (15 males and 27 females) with 67 osteoporotic vertebral fractures were treated with balloon kyphoplasty. We were able to have 2-year follow-up of 37 patients with 60 treated vertebrae. Baseline fracture rate in these 37 patients was 1.9 (60 fresh fractures and 11 old fractures already healed). Symptomatic levels were identified by correlating the clinical presentation with conventional radiographs, computed tomography (CT), and/or magnetic resonance imaging (MRI). During the 2-year follow-up, reduction in pain was determined. The effects on pain symptoms were measured on a self-reported visual analog scale (VAS) and the Oswestry score was documented to assess disability. Radiographic scans were performed pre- and postoperatively, and after 3, 6, 12, and 24 months. The vertebral height and endplate angles were measured to assess the restoration of the sagittal alignment.

Results: The median pain scores (VAS) decreased significantly from pre- to post-treatment as did the Oswestry Disability Score ( P<0.05). This improvement was maintained at 2-year follow-up. In eight patients (21.6%) (five female, three male), an adjacent fracture occurred in 11 vertebrae (18.3%) within 3 weeks to 22 months of follow-up (after 22 months no adjacent fracture occurred). This makes an annualized refracture rate of 10% (18.3/22×12). In three patients the adjacent fractures were asymptomatic. Five patients with symptomatic adjacent fractures (eight vertebrae) wanted to be treated again with balloon kyphoplasty. Clinically asymptomatic cement leakage occurred in nine of 67 vertebral bodies (13.4%). During 2-year follow-up, this surgical technique demonstrated restoration and stabilization of the height of the vertebral body.

Conclusion: Balloon kyphoplasty is an effective, minimally invasive procedure for the stabilization of osteoporotic vertebral fractures, leading to a statistically significant reduction of pain status.
Retropharyngeal tendinitis: radiographic and magnetic resonance imaging findings
Authors: Gelineck J. , Salomonsen M. , Hviid C.
Published: October 2006

Purpose: To describe the magnetic resonance imaging (MRI) findings in retropharyngeal tendinitis.

Material and methods: Within 1 year, four patients presenting with symptoms of retropharyngeal tendinitis were examined by radiography and MRI.

Results: On MRI and radiographs, all patients had characteristic soft-tissue swellings and calcifications related to the tendon of the longus colli muscle situated inferior to the anterior arc of C1. MRI showed well-defined edema, with high signal in the retropharyngeal tissue anterior to C1–C5 on short T1 inversion recovery (STIR) sequences, low signal on T1-weighted sequences, and low signal in the calcification on both sequences. In addition, three patients had high signal intensity changes on STIR sequences in the atlantoaxial joint situated posterior to the anterior arc of C1.

Conclusion: MRI is a sensitive and accurate method in the diagnosis of retropharyngeal tendinitis. A new finding in this condition is an effusion or synovitis in the anterior atlantoaxial joint. MRI is a valuable tool in differentiating retropharyngeal tendinitis from other diagnoses such as retropharyngeal abscess, pyogenic spondylitis, and spondyloarthropathy.
Sox2 is required for development of taste bud sensory cells
Authors: Okubo Tadashi , Pevny Larysa H. , Hogan Brigid L.M.
Published: October 2006

Sox2 is expressed in basal epithelial cells of the tongue, with high levels in taste bud placodes, fungiform papillae, and mature taste cells, and low levels in filiform papillae. High Sox2 expression appears to lie downstream from canonical Wnt signaling. In hypomorphic Sox2EGFP/LP embryos, placodes form but no mature taste buds develop. In contrast, transgenic overexpression of Sox2 in the basal cells inhibits differentiation of filiform keratinocytes. Together, our loss-of-function and gain-of-function studies suggest that Sox2 functions in a dose-dependent manner to regulate the differentiation of endodermal progenitor cells of the tongue into taste bud sensory cells versus keratinocytes.
FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalis
Authors: Davidson Brad , Shi Weiyang , Beh Jeni , Christiaen Lionel , Levine Mike
Published: October 2006

Comprehensive gene networks in Ciona intestinalis embryos provide a foundation for characterizing complex developmental processes, such as the initial phases of chordate heart development. The basic helix–loop–helix regulatory gene Ci-Mesp is required for activation of cardiac transcription factors. Evidence is presented that Ci-Ets1/2, a transcriptional effector of receptor tyrosine kinase (RTK) signaling, acts downstream from Mesp to establish the heart field. Asymmetric activation of Ets1/2, possibly through localized expression of FGF9, drives heart specification within this field. During gastrulation, Ets1/2 is expressed in a group of four cells descended from two Mesp-expressing founder cells (the B7.5 cells). After gastrulation, these cells divide asymmetrically; the smaller rostral daughters exhibit RTK activation (phosphorylation of ERK) and form the heart lineage while the larger caudal daughters form the anterior tail muscle lineage. Inhibition of RTK signaling prevents heart specification. Targeted inhibition of Ets1/2 activity or FGF receptor function also blocks heart specification. Conversely, application of FGF or targeted expression of constitutively active Ets1/2 (EtsVp16) cause both rostral and caudal B7.5 lineages to form heart cells. This expansion produces an unexpected phenotype: transformation of a single-compartment heart into a functional multicompartment organ. We discuss these results with regard to the development and evolution of the multichambered vertebrate heart.
Retrograde amnesia in patients with hippocampal, medial temporal, temporal lobe, or frontal pathology
Authors: Bright Peter , Buckman Joseph , Fradera Alex , Yoshimasu Haruo , Colchester Alan C.F. , Kopelman Michael D.
Published: October 2006

There is considerable controversy concerning the theoretical basis of retrograde amnesia (R.A.). In the present paper, we compare medial temporal, medial plus lateral temporal, and frontal lesion patients on a new autobiographical memory task and measures of the more semantic aspects of memory (famous faces and news events). Only those patients with damage extending beyond the medial temporal cortex into the lateral temporal regions showed severe impairment on free recall remote memory tasks, and this held for both the autobiographical and the more semantic memory tests. However, ont-test analysis, the medial temporal group was impaired in retrieving recent autobiographical memories. Within the medial temporal group, those patients who had combined hippocampal and parahippocampal atrophy (H+) on quantified MRI performed somewhat worse on the semantic tasks than those with atrophy confined to the hippocampi (H−), but scores were very similar on autobiographical episodic recall. Correlational analyses with regional MRI volumes showed that lateral temporal volume was correlated significantly with performance on all three retrograde amnesia tests. The findings are discussed in terms of consolidation, reconsolidation, and multiple trace theory: We suggest that a widely distributed network of regions underlies the retrieval of past memories, and that the extent of lateral temporal damage appears to be critical to the emergence of a severe remote memory impairment.
Staining Membrane-Bound Proteins with Coomassie Blue R250
Authors: Stochaj Wayne R. , Berkelman Tom , Laird Nancy
Published: October 2006

INTRODUCTION

Coomassie Blue R250 permanently stains membrane-bound proteins and is compatible with PVDF and nitrocellulose membranes, but it is incompatible with nylon membranes. This technique is relatively insensitive, with a detection limit of ~1.5 μg of protein. One drawback of Coomassie Blue staining is that it produces a high background that can make interpretation of results difficult.
Purification of Large “Troublesome” Polypeptides by RP-HPLC
Authors: Keah Hooi Hong , Hearn Milton T.W.
Published: October 2006

INTRODUCTION

This protocol addresses the group of large polypeptides that have proved to be troublesome to handle because of their low solubility or the presence of secondary structural elements that favor supramolecular self-self assembly. Included in this group are polypeptides with amphipathic α-helical or β-sheet structures with extensive runs of nonpolar (hydrophobic) amino acid side chains or proline-rich sequences. RP-HPLC provides one avenue to purify such troublesome examples provided certain steps and precautions are taken. (Related procedures are equally germane to polypeptides that have been lipidated or subjected to chemical modifications with nonpolar moieties, as well as to some core cyanogen bromide fragments of large proteins.) RP-HPLC methods not only enable concomitant desalting, removal of additives that aid dissolution of the polypeptide or protein, but also permit resolution and maintenance of a reasonably high concentration of the solutes, due to the presence of the (often) low-pH, aquo-organic solvent conditions.
Modification of Lysyl Side Chains Using Succinic Anhydride: Figure 1.
Authors: Simpson Richard J.
Published: October 2006

INTRODUCTION

The sites of trypsin cleavage can be restricted when the ϵ-amino group of lysine is blocked, for example, by succinic anhydride. This can be useful for obtaining overlapping peptides during classical protein sequencing strategies. For example, in selective peptide cleavage with trypsin, it may be desirable to block the ϵ-amino groups of lysine so that the enzyme attacks only at arginine peptide bonds. Another advantage of succinylation is that the reagent places substantial negative charge on the protein because the positively charged lysine side chain is replaced by a negatively charged carboxyl group of the succinate half-amide. Hence, succinylation may be used to solubilize a protein while blocking its lysine groups (in general, succinylated proteins are soluble at pH >7). The attached succinyl moiety forms a stable linkage to most protein treatments, but may be cleaved off with 6 N HCl at 100ºC.
Preparative 2D Gel Electrophoresis with Immobilized pH Gradients: Isoelectric Focusing of Proteins in a Multipurpose Flatbed Electrophoresis Unit
Authors: Stochaj Wayne R. , Berkelman Tom , Laird Nancy
Published: October 2006

INTRODUCTION

This protocol describes a method for separating proteins based on their net charge using the technique of isoelectric focusing (IEF) on immobilized pH gradient (IPG) gels. This method serves as the first dimension of the 2D separation. The method described in this protocol utilizes a flatbed unit; however, self-contained instruments for IEF are also available.
Preparative 2D Gel Electrophoresis with Immobilized pH Gradients: IEF of Proteins in an IEF-Dedicated Electrophoresis Unit
Authors: Stochaj Wayne R. , Berkelman Tom , Laird Nancy
Published: October 2006

INTRODUCTION

This protocol describes a method for separating proteins based on their net charge using the technique of isoelectric focusing (IEF) on immobilized pH gradient (IPG) gels, providing the first dimension of the 2D separation. In this protocol, the IPG gels are focused using self-contained instruments for IEF. These high-voltage systems allow fewer manipulations of the IPG gels, resulting in less error, strip mix-up, contamination, air contact, or urea crystallization. Because rehydration and IEF can be performed consecutively within a single unit, these two steps can be performed unattended overnight. Finally, faster separations and sharper focusing are possible due to the higher voltage available in these instruments.
Concentrating Acrylamide Gel Spots: Figure 1.
Authors: Simpson Richard J.
Published: October 2006

INTRODUCTION

This protocol describes a method for concentrating gel bands or spots excised from 1D or 2D acrylamide gels. Several replicate protein bands (or spots) are often required to provide sufficient material for sequencing. In these situations, it is necessary to excise several stained protein bands or spots from the gels and pre-concentrate them prior to electroblotting for amino-terminal sequencing or internal sequence analysis following in-gel proteolytic (or chemical) fragmentation. In the method described below, concentration is done by re-electrophoresis of the gel pieces in a simple SDS-PAGE gel poured in a single conventional glass Pasteur pipette.
Screening DNA Pools for T-DNA Insertions in Arabidopsis Genes
Authors: Weigel Detlef , Glazebrook Jane
Published: October 2006

INTRODUCTION

Many investigators are interested in studying the functions of genes whose sequences or expression patterns suggest roles in particular biological processes. A powerful way to identify a mutation in the gene of interest and to test mutant plants for phenotypes that are predicted to result from loss of function of that gene is by PCR screening. Pools of insertion lines are screened using one primer corresponding to the gene of interest and one primer corresponding to the end of the insertion element. The synthesis of a product indicates the presence of an insertion in the gene of interest. The pool is then repeatedly subdivided until a single plant carrying the desired insertion is identified.
Setting Up Arabidopsis Crosses
Authors: Weigel Detlef , Glazebrook Jane
Published: October 2006

INTRODUCTION

The inheritance of mutant phenotypes is most often analyzed in the progeny resulting from crosses between different parents. Because Arabidopsis naturally self-pollinates, the generation of cross-progeny requires some intervention by the investigator. This protocol describes the generation and collection of seeds by crossing suitable Arabidopsis parent plants.
Effects of probiotic supplementation for the first 6 months of life on allergen‐ and vaccine‐specific immune responses
Authors: Taylor A. L. , Hale J. , Wiltschut J. , Lehmann H. , Dunstan J. A. , Prescott S. L.
Published: October 2006

Background
A reduction in microbial burden during infancy when allergen‐specific memory is evolving has become a prominent explanation for the allergy epidemic.

Objective
We sought to determine whether probiotic dietary supplementation in the first 6 months of life could modify allergen‐ and vaccine‐specific immune responses.

Methods
Two hundred and thirty‐one pregnant women with a history of allergic disease and positive allergen skin prick test (SPT) were recruited into a randomized‐controlled trial. The infants received either a probiotic (3 × 109Lactobacillus acidophilus LAVRI‐A1; Probiomics) or placebo (maltodextrin alone) daily for the first 6 months of life, given independent of feeding methods. One hundred and seventy‐eight children completed the study; blood samples were available from 60 children in the placebo group and 58 children in the probiotic group. Infant cytokine (IL‐5, IL‐6, IL‐10, IL‐13, TNF‐α or TGF‐β) responses to tetanus toxoid (TT), house dust mite (HDM), ovalbumin (OVA), β‐lactoglobulin (BLG), Staphylococcus enterotoxin B (SEB) and phytohaemaglutinin (PHA) were measured at 6 months of age.

Results
Children who received the probiotics showed reduced production of IL‐5 and TGF‐β in response to polyclonal (SEB) stimulation (P=0.044 and 0.015, respectively). They also demonstrated significantly lower IL‐10 responses to TT vaccine antigen compared with the placebo group (P=0.03), and this was not due to any differences in vaccination. However, there were no significant effects of probiotics on either Type 1 (Th1) or Type 2 (Th2) T helper cell responses to allergens or other stimuli. The only other effects observed were for reduced TNF‐α and IL‐10 responsiveness to HDM allergens in children receiving probiotics (P=0.046 and 0.014, respectively).

Conclusions
In summary, although we did not see any consistent effects on allergen‐specific responses, our study suggests that probiotics may have immunomodulatory effects on vaccine responses. The significance and clinical relevance of this need to be determined in further studies.
Gastro‐duodenal digestion products of the major peanut allergen Ara h 1 retain an allergenic potential
Authors: Eiwegger T. , Rigby N. , Mondoulet L. , Bernard H. , Krauth M.‐T. , Boehm A. , Dehlink E. , Valent P. , Wal J. M. , Mills E. N. C. , Szépfalusi Z.
Published: October 2006

Background
The process of gastro‐duodenal digestion may play a role in determining the allergenic properties of food proteins. The sensitizing and allergenic potential of digestion products of highly degraded allergens, such as the major peanut allergen Ara h 1, is currently under debate. We evaluated the effect of in vitro gastro‐duodenal digestion of Ara h 1 on T cell reactivity and basophil histamine release.

Methods
An in vitro model of gastro‐duodenal digestion was used to investigate changes in the allergenic properties of Ara h 1 using in vitro assays monitoring T cell reactivity (proliferation, cytokine production) and histamine release of basophils from peanut allergic individuals. The digestion process was monitored using an SDS‐PAGE gel.

Results
In vitro gastric digestion led to rapid degradation of Ara h 1 into small fragments Mr L5600. Gastric digestion did not affect the ability of Ara h 1 to stimulate cellular proliferation. Gastro‐duodenal digestion significantly reduced its ability to stimulate clonal expansion (P<0,05; Wilxocon's signed rank test). The Th‐2 type cytokine polarization of T cells from peanut allergic donors (IFN‐γ/IL‐13 ratio and IFN‐γ/IL‐4 ratio of CFSElow CD4+ T cells) remained unchanged regardless of the level of digestion. Histamine release of basophils from peanut allergic individuals was induced to the same extent by native Ara h 1 and its digestion products.

Conclusion
Gastro‐duodenal digestion fragments of Ara h 1 retain T cell stimulatory and IgE‐binding and cross‐linking properties of the intact protein.
Association of TNF‐α genetic polymorphism with HLA DPB1*0301
Authors: Kim S. ‐H. , Ye Y. ‐M. , Lee S. ‐K. , Choi J. ‐H. , Holloway J. W. , Park C. ‐S. , Park H. ‐S.
Published: October 2006

Background
We speculated TNF‐α can be one of candidate gene for aspirin‐intolerant asthma (AIA) because TNF‐α is pro‐inflammatory cytokine and known to be increased level in asthmatic airways. In addition, genetic interaction between TNF‐α and human antigen leucocyte (HLA) DPB1*0301, which is a strong genetic marker for AIA, was examined for its close location within chromosome 6.

Method
To investigate genetic association of TNF‐α with an AIA phenotype, three study groups (163 patients with AIA, 197 patients with aspirin‐tolerant asthma (ATA), 257 normal control subjects) were enrolled. Single nucleotide polymorphisms (SNPs) were genotyped using a single‐base extension method and HLA DPB1 genotyping was determined by high‐throughput sequencing method.

Results
All five SNPs of TNF‐α were tested; there were no significant differences in allele and genotype frequencies among the three groups. However, significant association between TNF‐α−308G>A polymorphism and atopy status was noted (P<0.05). Gene to gene interaction between TNF‐α−1031T>C (or −863C>A or −857C>A) and HLA DPB1*0301 could synergistically increase the susceptibility to AIA with odds ratio (OR) to 7.738 (or OR=8.184 for −863C>A, OR=7.500 for −857C>T, P<0.001, respectively).

Conclusion
TNF‐α promoter polymorphism may significantly increase susceptibility to AIA by gene‐to‐gene interaction with HLA DPB1*0301.
Herbivory, current velocity and algal regrowth: how does periphyton grow when the grazers have gone?
Authors: WELLNITZ TODD , LEROY POFF N.
Published: October 2006

1. An experiment conducted in streamside channels was used to document the regrowth of grazed periphyton. Our objective was to determine the relative importance of current velocity, grazing duration, and grazer type in shaping the trajectory of algal and periphytic regrowth.

2. The grazing mayflies Baetis bicaudatus and Epeorus longimanus were used alone and in combination to create three grazing treatments at slow, medium and fast current (2–5, 15–20 and 30–40 cm s−1, respectively). Duration treatments consisted of 2, 4, 6, 8, 10 days of grazing. Chlorophyll a and ash‐free dry mass (AFDM) accumulation on grazed tiles was measured (as periphytic AFDM and chlorophyll a, respectively) at 2, 4, 6, 8 and 10 days following the removal of grazers.

3. Chlorophyll a and AFDM was best predicted by interactions between current velocity, grazing duration and regrowth time.

4. The two grazer species did not differ in their effect on Chlorophyll a and AFDM during the period of periphytic regrowth that followed grazing.

5. Longer grazing duration reduced periphytic biomass, but also accelerated algal regrowth, and this growth enhancement was more pronounced at slower current velocities.

6. Data from this study suggest that herbivory can have important historical effects on periphytic accrual.
Brain and Pituitary Melatonin Receptors in Male Rat during Post‐Natal and Pubertal Development and the Effect of Pinealectomy and Testosterone Manipulation
Authors: Zitouni M. , Pévet P. , Masson‐Pévet M.
Published: October 2006

Using quantitative autoradiography, melatonin receptors have been studied during post‐natal and pubertal development of the rat in 2 brain and 2 pituitary structures. In the pars distalis of anterior pituitary, melatonin receptors decrease gradually in density after birth and disappear in 30 day‐old animals. In contrast melatonin binding is only expressed in the paraventricular nuclei of the thalamus at the age of 21–23 days and is always present in adult animals. In the suprachiasmatic nuclei and in the pars tuberalis of the pituitary, melatonin receptor density decreases after birth, remains stable for approximately 1 month and increases again at puberty to reach the birth values in the adult. This increase was absent in pinealectomized and in castrated animals but present in castrated animals receiving testosterone suggesting that it depends upon circulating testosterone and melatonin levels. These results show that melatonin receptors are differentially regulated during post‐natal development in each of the 4 structures studied, and that melatonin and testosterone are 2 factors which could be involved in the regulation of melatonin receptor density in the suprachiasmatic nuclei and pars tuberalis.
Changes in Pineal Indoleamines in Rats after Single Melatonin Injections: Evidence for a Diurnal Sensitivity to Melatonin
Authors: Míguez Jesús M. , Simonneaux Valérie , Pévet Paul
Published: October 2006

We recently determined that melatonin stimulated serotonin (5‐HT) secretion from rat pineal glands by increasing 5‐HT release from the pinealocytes (μM melatonin concentrations) and by inhibiting 5‐HT uptake in the pineal sympathetic nerve endings (mM melatonin concentrations). The present study investigated whether a single melatonin injection could alter the content of indoleamines in the rat pineal gland, as well as its possible dependence on the daytime of administration. Melatonin (150 μg/kg) was i.p. injected at 8 time points (11.00 h, 14.00 h, 17.00 h, 20.00 h, 23.00 h, 02.00 h, 05.00 h and 08.00 h) to rats kept in 12:12 h light:dark cycle (lights on at 07.00 h). Melatonin injections in the afternoon (17:00 h) and late in the nighttime (02.00 h and 05.00 h) decreased pineal 5‐HT content 90 min later. The levels of 5‐hydroxyindoleacetic acid (5‐HIAA) were also decreased 90 min after the melatonin treatment at 14.00 h, 17.00 h and 02.00 h. The effect of melatonin on 5‐HT content was a long‐lasting effect (still evident after 180 min) only when injected at 02.00 h, whereas 5‐HIAA levels were found to be decreased 180 min after melatonin treatment at 14.00 h and 23.00 h. No changes in these compounds were detected 240 min after melatonin treatment. Moreover, melatonin did not change 5‐hydroxytryptophan levels at any of the daytime points studied. By contrast, 90 min after the injection of melatonin at 20.00 h, an increased content of pineal N‐acetylserotonin was observed. This effect of melatonin could be mediated through a phase alteration of the pineal N‐acetyltransferase activity rhythm by acting on the suprachiasmatic clock, althought a direct melatonin effect on the pineal rhythmic function cannot be excluded. The effects of the hormone on 5‐HT and 5‐HIAA contents agree with previous findings on the inhibitory effect of pharmacological doses of melatonin on pineal 5‐HT uptake, which presumably would result in a decreased intraneuronal content of 5‐HT and its acid metabolite. These data point to an acute regulatory action of exogenous melatonin on the pineal melatonin synthesis pathway which seems to be limited to two daytime phases: the afternoon‐early evening period and the second half of the night.