CD27 mediates interleukin-2-independent clonal expansion of the CD8+ T cell without effector differentiation

The clonal expansion of antigen-specific CD8+ T cells in response to microbial infections is essential for adaptive immunity. Although IL-2 has been considered to be primarily responsible for this process, quantitatively normal expansion occurs in the absence of IL-2 receptor signaling. Here, we show that ligating CD27 on CD8+ T cells that have been stimulated through the T cell receptor causes their expansion in the absence of IL-2 by mediating two distinct cellular processes: enhancing cell cycling and promoting cell survival by maintaining the expression of IL-7 receptor alpha. This pathway for clonal expansion of the CD8+ T cell is not associated with the development of a capacity either for production of IFN-gamma or for cytotoxic T lymphocyte function and, therefore, is uncoupled from differentiation. Furthermore, ligating CD27 increases the threshold concentration at which IL-2 induces IFN-gamma-producing capability by the CD8+ T cell, suggesting that CD27 signaling may suppress effector differentiation. Finally, CD8+ T cells that have been stimulated by the TCR/CD27 pathway maintain their capacity for subsequent expansion and effector differentiation in response to a viral challenge in vivo. Thus, the TCR/CD27 pathway enables the CD8+ T cell to replicate by a process of self-renewal, which may contribute to the continuous generation of new effector CD8+ T cells in persistent viral infections.

Stereo and motion parallax cues in human 3D vision: can they vanish without a trace?

In an immersive virtual reality environment, subjects fail to notice when a scene expands or contracts around them, despite correct and consistent information from binocular stereopsis and motion parallax, resulting in gross failures of size constancy (A. Glennerster, L. Tcheang, S. J. Gilson, A. W. Fitzgibbon, & A. J. Parker, 2006). We determined whether the integration of stereopsis/motion parallax cues with texture-based cues could be modified through feedback. Subjects compared the size of two objects, each visible when the room was of a different size. As the subject walked, the room expanded or contracted, although subjects failed to notice any change. Subjects were given feedback about the accuracy of their size judgments, where the “correct” size setting was defined either by texture-based cues or (in a separate experiment) by stereo/motion parallax cues. Because of feedback, observers were able to adjust responses such that fewer errors were made. For texture-based feedback, the pattern of responses was consistent with observers weighting texture cues more heavily. However, for stereo/motion parallax feedback, performance in many conditions became worse such that, paradoxically, biases moved away from the point reinforced by the feedback. This can be explained by assuming that subjects remap the relationship between stereo/motion parallax cues and perceived size or that they develop strategies to change their criterion for a size match on different trials. In either case, subjects appear not to have direct access to stereo/motion parallax cues.

Effects of triazole and strobilurin fungicide programmes, with and without late-season nitrogen fertiliser, on the baking quality of Malacca winter wheat

Field experiments were conducted over 3 years to study the effect of applying triazole and strobilurin fungicides on the bread-making quality of Malacca winter wheat. Averaged over all years the application of a fungicide programme increased yields, particularly when strobilurin fungicides were applied. Reductions in protein concentration, sulphur concentration, Hageberg failing number and loaf volumes also occurred as the amount of fungicide applied increased. However, there were no deleterious effects of fungicide application on sodium dodecyl sulphate (SDS) sedimentation volumes, N:S ratios or dough theology. Effects of fungicide application on bread-making quality were not product specific. Therefore, it appears that new mechanisms to explain strobilurin effects on bread-making quality do not need to be invoked. Where reductions in protein concentration did occur they could be compensated for by a late-season application of nitrogen either as granular ammonium nitrate at flag leaf emergence or foliar urea at anthesis. These applications, however, sometimes increased the N:S ratio of the extracted flour and failed to improve loaf volume. Multiple regression analysis revealed that main effects of year, flour protein concentration and N:S ratio could explain 93% of the variance in loaf volume caused by season, fungicide and nitrogen treatments. However, an equally good fit was achieved by just including sulphur concentration with year. (C) 2004 Elsevier Ltd. All rights reserved.

Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments

MOTIVATION: The accurate prediction of the quality of 3D models is a key component of successful protein tertiary structure prediction methods. Currently, clustering or consensus based Model Quality Assessment Programs (MQAPs) are the most accurate methods for predicting 3D model quality; however they are often CPU intensive as they carry out multiple structural alignments in order to compare numerous models. In this study, we describe ModFOLDclustQ - a novel MQAP that compares 3D models of proteins without the need for CPU intensive structural alignments by utilising the Q measure for model comparisons. The ModFOLDclustQ method is benchmarked against the top established methods in terms of both accuracy and speed. In addition, the ModFOLDclustQ scores are combined with those from our older ModFOLDclust method to form a new method, ModFOLDclust2, that aims to provide increased prediction accuracy with negligible computational overhead. RESULTS: The ModFOLDclustQ method is competitive with leading clustering based MQAPs for the prediction of global model quality, yet it is up to 150 times faster than the previous version of the ModFOLDclust method at comparing models of small proteins (<60 residues) and over 5 times faster at comparing models of large proteins (>800 residues). Furthermore, a significant improvement in accuracy can be gained over the previous clustering based MQAPs by combining the scores from ModFOLDclustQ and ModFOLDclust to form the new ModFOLDclust2 method, with little impact on the overall time taken for each prediction. AVAILABILITY: The ModFOLDclustQ and ModFOLDclust2 methods are available to download from: http://www.reading.ac.uk/bioinf/downloads/ CONTACT: l.j.mcguffin@reading.ac.uk.

Aqueous peroxyl radical exposure to THP-1 cells causes glutathione loss followed by protein oxidation and cell death without increased caspase-3 activity

Protein oxidation within cells exposed to oxidative free radicals has been reported to occur in an uninhibited manner with both hydroxyl and peroxyl radicals. In contrast, THP-1 cells exposed to peroxyl radicals (ROO center dot) generated by thermo decomposition of the azo compound AAPH showed a distinct lag phase of at least 6 h, during which time no protein oxidation or cell death was observed. Glutathione appears to be the source of the lag phase as cellular levels were observed to rapidly decrease during this period. Removal of glutathione with buthionine sulfoxamine eliminated the lag phase. At the end of the lag phase there was a rapid loss of cellular MTT reducing activity and the appearance of large numbers of propidium iodide/annexin-V staining necrotic cells with only 10% of the cells appearing apoptotic (annexin-V staining only). Cytochrome c was released into the cytoplasm after 12 h of incubation but no increase in caspase-3 activity was found at any time points. We propose that the rapid loss of glutathione caused by the AAPH peroxyl radicals resulted in the loss of caspase activity and the initiation of protein oxidation. The lack of caspase-3 activity appears to have caused the cells to undergo necrosis in response to protein oxidation and other cellular damage. (c) 2007 Elsevier B.V. All rights reserved.

Liquid matrix deposition on conductive hydrophobic surfaces for tuning and quantitation in UV-MALDI mass spectrometry

With its highly fluctuating ion production matrix-assisted laser desorption/ionization (MALDI) poses many practical challenges for its application in mass spectrometry. Instrument tuning and quantitative ion abundance measurements using ion signal alone depend on a stable ion beam. Liquid MALDI matrices have been shown to be a promising alternative to the commonly used solid matrices. Their application in areas where a stable ion current is essential has been discussed but only limited data have been provided to demonstrate their practical use and advantages in the formation of stable MALDI ion beams. In this article we present experimental data showing high MALDI ion beam stability over more than two orders of magnitude at high analytical sensitivity (low femtomole amount prepared) for quantitative peptide abundance measurements and instrument tuning in a MALDI Q-TOF mass spectrometer. Samples were deposited on an inexpensive conductive hydrophobic surface and shrunk to droplets <10 nL in size. By using a sample droplet <10 nL it was possible to acquire data from a single irradiated spot for roughly 10,000 shots with little variation in ion signal intensity at a laser repetition rate of 5-20 Hz.

Adjusted jackknife for imputation under unequal probability sampling without replacement

Imputation is commonly used to compensate for item non-response in sample surveys. If we treat the imputed values as if they are true values, and then compute the variance estimates by using standard methods, such as the jackknife, we can seriously underestimate the true variances. We propose a modified jackknife variance estimator which is defined for any without-replacement unequal probability sampling design in the presence of imputation and non-negligible sampling fraction. Mean, ratio and random-imputation methods will be considered. The practical advantage of the method proposed is its breadth of applicability.

Tuning of redox potential and visible absorption band of ruthenium(II) complexes of (benzimidazolyl) derivatives: synthesis, characterization, spectroscopic and redox properties, X-ray structures and DFT calculations

Six ruthenium(II) complexes have been prepared using the tridentate ligands 2,6-bis(benzimidazolyl) pyridine and bis(2-benzimidazolyl methyl) amine and having 2,2'-bipyridine, 2,2':6',2 ''-terpyridine, PPh3, MeCN and chloride as coligands. The crystal structures of three of the complexes trans-[Ru(bbpH(2))(PPh3)(2)(CH3CN)I(ClO4)(2) center dot 2H(2)O (2), [Ru(bbpH(2))(bpy)Cl]ClO4 (3) and [Ru(bbpH(2))(terpy)](ClO4)(2) (4) are also reported. The complexes show visible region absorption at 402-517 nm, indicating that it is possible to tune the visible region absorption by varying the ancillary ligand. Luminescence behavior of the complexes has been studied both at RT and at liquid nitrogen temperature (LNT). Luminescence of the complexes is found to be insensitive to the presence of dioxygen. Two of the complexes [Ru(bbpH(2))(bpy)Cl]ClO4 (3) and [Ru(bbpH(2))(terpy]ClO4)(2) (4) show RT emission in the NIR region, having lifetime, quantum yield and radiative constant values suitable for their application as NIR emitter in the solid state devices. The DFT calculations on these two complexes indicate that the metal t(2g) electrons are appreciably delocalized over the ligand backbone. (C) 2006 Elsevier B.V. All rights reserved.

Facile strategies for the synthesis and crystallization of linear trinuclear nickel(II)-Schiff base, complexes with carboxylate bridges: Tuning of coordination geometry and magnetic properties

Three new linear trinuclear nickel(II) complexes, [Ni-3(salpen)(2)(OAc)(2)(H2O)(2)]center dot 4H(2)O (1) (OAc = acetate, CH3COO-), [Ni-3(salpen)(2)(OBz)(2)] (2) (OBz=benzoate, PhCOO-) and [Ni-3(salpen)(2)(OCn)(2)(CH3CN)(2)] (4) (OCn = cinnamate, PhCH=CHCOO-), H(2)salpen = tetradentate ligand, N,N'-bis(salicylidene)-1,3-pentanediamine have been synthesized and characterized structurally and magnetically. The choice of solvent for growing single crystal was made by inspecting the morphology of the initially obtained solids with the help of SEM study. The magnetic properties of a closely related complex, [Ni-3(salpen)(2)(OPh)(2)(EtOH)] (3) (OPh = phenyl acetate, PhCH2COO-) whose structure and solution properties have been reported recently, has also been studied here. The structural analyses reveal that both phenoxo and carboxylate bridging are present in all the complexes and the three Ni(II) atoms remain in linear disposition. Although the Schiff base ligand and the syn-syn bridging bidentate mode of the carboxylate group remain the same in complexes 1-4, the change of alkyl/aryl group of the carboxylates brings about systematic variations between six- and five-coordination in the geometry of the terminal Ni(II) centres of the trinuclear units. The steric demand as well as hydrophobic nature of the alkyl/aryl group of the carboxylate is found to play a crucial role in the tuning of the geometry. Variable-temperature (2-300 K) magnetic susceptibility measurements show that complexes 1-4 are antiferromagnetically coupled (J = -3.2(1), -4.6(1). -3.2(1) and -2.8(1) cm(-1) in 1-4, respectively). Calculations of the zero-field splitting parameter indicate that the values of D for complexes 1-4 are in the high range (D = +9.1(2), +14.2(2), +9.8(2) and +8.6(1) cm(-1) for 1-4, respectively). The highest D value of +14.2(2) and +9.8(2) cm(-1) for complexes 2 and 3, respectively, are consistent with the pentacoordinated geometry of the two terminal nickel(II) ions in 2 and one terminal nickel(II) ion in 3. (C) 2009 Elsevier Ltd. All rights reserved.

Tuning of intramolecular electron transfer between Ru(II) and the disulfide bond

Reaction of 2,2'-dithiodipyridine (DTDP) with cis-Ru(bpy)(2)Cl-2 (bpy = 2,2'-bipyridine) and cis-Ru(phen)(2)Cl-2 (phen = 1,10-phenanthroline) respectively yields the dicationic species [Ru(bpy) (2)(DTDP)](2+) and [Ru(phen)(2) (DTDP)](2+) in which the S-S bond of DTDP remains intact. The S-S bond undergoes a reductive cleavage when DTDP is reacted with cis-Ru(bisox)(2)Cl-2 (bisox = 4,4,4',4'-tetramethyl-2,2'-bisoxazoline) under identical conditions to generate the monocationic species [Ru(bisox)(2)(2-thiolatopyridine)]. The intramolecular electron transfer between the metal and the S-S bond is found to be subtly controlled by the crystal field strength of the ancillary bidentate N-donor ligands.

Effects of triazole and strobilurin fungicide programmes, with and without late-season nitrogen fertiliser, on the baking quality of Malacca winter wheat

Field experiments were conducted over 3 years to study the effect of applying triazole and strobilurin fungicides on the bread-making quality of Malacca winter wheat. Averaged over all years the application of a fungicide programme increased yields, particularly when strobilurin fungicides were applied. Reductions in protein concentration, sulphur concentration, Hageberg failing number and loaf volumes also occurred as the amount of fungicide applied increased. However, there were no deleterious effects of fungicide application on sodium dodecyl sulphate (SDS) sedimentation volumes, N:S ratios or dough theology. Effects of fungicide application on bread-making quality were not product specific. Therefore, it appears that new mechanisms to explain strobilurin effects on bread-making quality do not need to be invoked. Where reductions in protein concentration did occur they could be compensated for by a late-season application of nitrogen either as granular ammonium nitrate at flag leaf emergence or foliar urea at anthesis. These applications, however, sometimes increased the N:S ratio of the extracted flour and failed to improve loaf volume. Multiple regression analysis revealed that main effects of year, flour protein concentration and N:S ratio could explain 93% of the variance in loaf volume caused by season, fungicide and nitrogen treatments. However, an equally good fit was achieved by just including sulphur concentration with year. (C) 2004 Elsevier Ltd. All rights reserved.

Learning associations between places and visual cues without learning to navigate: neither fornix nor entorhinal cortex is required

Rats with fornix transection, or with cytotoxic retrohippocampal lesions that removed entorhinal cortex plus ventral subiculum, performed a task that permits incidental learning about either allocentric (Allo) or egocentric (Ego) spatial cues without the need to navigate by them. Rats learned eight visual discriminations among computer-displayed scenes in a Y-maze, using the constant-negative paradigm. Every discrimination problem included two familiar scenes (constants) and many less familiar scenes (variables). On each trial, the rats chose between a constant and a variable scene, with the choice of the variable rewarded. In six problems, the two constant scenes had correlated spatial properties, either Alto (each constant appeared always in the same maze arm) or Ego (each constant always appeared in a fixed direction from the start arm) or both (Allo + Ego). In two No-Cue (NC) problems, the two constants appeared in randomly determined arms and directions. Intact rats learn problems with an added Allo or Ego cue faster than NC problems; this facilitation provides indirect evidence that they learn the associations between scenes and spatial cues, even though that is not required for problem solution. Fornix and retrohippocampal-lesioned groups learned NC problems at a similar rate to sham-operated controls and showed as much facilitation of learning by added spatial cues as did the controls; therefore, both lesion groups must have encoded the spatial cues and have incidentally learned their associations with particular constant scenes. Similar facilitation was seen in subgroups that had short or long prior experience with the apparatus and task. Therefore, neither major hippocampal input-output system is crucial for learning about allocentric or egocentric cues in this paradigm, which does not require rats to control their choices or navigation directly by spatial cues.

Phonological similarity effects without a phonological store: an individual differences model

The feature model of immediate memory (Nairne, 1990) is applied to an experiment testing individual differences in phonological confusions amongst a group (N=100) of participants performing a verbal memory test. By simulating the performance of an equivalent number of “pseudo-participants” the model fits both the mean performance and the variability within the group. Experimental data show that high-performing individuals are significantly more likely to demonstrate phonological confusions than low performance individuals and this is also true of the model, despite the model’s lack of either an explicit phonological store or a performance-linked strategy shift away from phonological storage. It is concluded that a dedicated phonological store is not necessary to explain the basic phonological confusion effect, and the reduction in such an effect can also be explained without requiring a change in encoding or rehearsal strategy or the deployment of a different storage buffer.