The heat-shock response in higher plants: a biochemical model

Abstract A compilation of existing data on higher plant responses to heat-shock temperatures has been utilized to produce a biochemically based model of integrated cellular responses to elevated temperatures. This model describes a potential mechanism for the triggering of several biochemical responses to a thermally induced leakage of extracellular or vacuolar ions into the cytoplasm. It seems possible that many of the observed heat-shock responses are involved in the protection of (a) enzymes from inactivation and (b) nucleic acids from cleavage induced by the presence of elevated levels of specific metals.     

Ordering events of biochemical evolution

Metabolic pathways exhibit structures resulting from an evolutionary process. Pathways have been inherited through time with modification, from the earliest periods of life. It is possible to compare the structure of pathways as done in comparative anatomy, i.e. for inferring ancestral pathways or parts of it (ancestral enzymatic functions), using standard phylogenetic reconstruction. Thus a phylogenetic tree of pathways provides a relative ordering of the rise of enzymatic functions. It even becomes possible to order the birth of each complete pathway in time. This particular "DNA-free" conceptual approach to evolutionary biochemistry is reviewed, gathering all the justifications given for it. Then, the method of assigning a given pathway to a time span of biochemical development is revisited. The previous method used an implicit "clock" of metabolic development that is difficult to justify. We develop a new clock-free approach, using functional biochemical arguments. Results of the two methods are not significantly different; our method is just more precise. This suggests that the clock assumed in the first method does not provoke any important artefact in describing the development of biochemical evolution. It is just unnecessary to postulate it. As a result, most of the amino acid metabolic pathways develop forwards, confirming former models of amino acid catabolism evolution, but not those for amino acid anabolism. The order of appearance of sectors of universal cellular metabolism is: (1) amino acid catabolism, (2) amino acid anabolism and closure of the urea cycle, (3) glycolysis and glycogenesis, (4) closure of the pentose-phosphate cycle, (5) closure of the Krebs cycle and fatty acids metabolism, (6) closure of the Calvin cycle.     

Bayesian sequential inference for stochastic kinetic biochemical network models.

As postgenomic biology becomes more predictive, the ability to infer rate parameters of genetic and biochemical networks will become increasingly important. In this paper, we explore the Bayesian estimation of stochastic kinetic rate constants governing dynamic models of intracellular processes. The underlying model is replaced by a diffusion approximation where a noise term represents intrinsic stochastic behavior and the model is identified using discrete-time (and often incomplete) data that is subject to measurement error. Sequential MCMC methods are then used to sample the model parameters on-line in several data-poor contexts. The methodology is illustrated by applying it to the estimation of parameters in a simple prokaryotic auto-regulatory gene network.     

Bystander-induced differentiation: a major response to targeted irradiation of a urothelial explant model

A ureter primary explant technique, using porcine tissue sections was developed to study bystander effects under in vivo like conditions where dividing and differentiated cells are present. Targeted irradiations of ureter tissue fragments were performed with the Gray Cancer Institute charged particle microbeam at a single location (2 microm precision) with 10 3He2+ particles (5 MeV; LET 70 keV/microm). After irradiation the ureter tissue section was incubated for 7 days allowing explant outgrowth to be formed. Differentiation was estimated using antibodies to Uroplakin III, a specific marker of terminal urothelial differentiation. Even although only a single region of the tissue section was targeted, thousands of additional cells were found to undergo bystander-induced differentiation in the explant outgrowth. This resulted in an overall increase in the fraction of differentiated cells from 63.5+/-5.4% to 76.6+/-5.6%. These changes are much greater than that observed for the induction of damage in this model. One interpretation of these results is that in the tissue environment, differentiation is a much more significant response to targeted irradiation and potentially a protective mechanism.     

Experimental model of membranous nephropathy in mice: sequence of histological and biochemical events

An experimental model of membranous nephropathy (MN) has not been established fully in mice. We characterized the time course of MN in a murine MN model induced by cationic bovine serum albumin (cBSA). Preimmunized mice received cBSA intravenously for six weeks to induce MN and were then sacrificed at different times. Metabolic profiles, renal histopathology, lymphocyte subsets, serum anti-cBSA immunoglobulins (Igs), antibody subclasses and circulating immune complexes (CIC) were evaluated to study the severity and mechanisms of disease initiation and progression. Clinical symptoms of overt proteinuria, hypoalbuminaemia and hypercholesterolaemia were observed from week 4, and typical histological findings of diffuse thickening of the glomerular basement membrane and subepithelial deposition were identified after week 6. Granular fluorescent staining for IgG and complement C3 were observed as early as week 4. Total splenocyte number increased, but the percentages of CD4+ and CD8+ cells did not change as the disease progressed. The predominant isotype of anti-cBSA Igs was IgG1, suggesting a T-helper 2 cell-prone immune response in the development of MN. The strong positive immunofluorescent staining of the immune complex concomitant with higher concentrations of Igs in serum but no significant change in CIC levels before week 4 suggest the involvement of in situ deposition of immune complex in the process of MN. This murine model resembles the clinical and pathological features of human MN and may provide a tool for investigating MN; this model may also have potential applications in gene-knockout or transgenic mouse technologies.     

Unitary correlates of linguo-pharyngeal events in a dyskinetic rat model.

1. The hypoglossal nucleus unitary correlates of ketamine- and electrically induced tongue contractions and swallowing events were recorded and compared in stereotaxically mounted rats. 2. Very few of the units recorded could be identified as motoneurons by antidromic invasion through electrical stimulation of the hypoglossal nerve. 3. The sample consists of 109 units, 2/3 of which were located in the retrusor pool and 1/3 in the protrusor region. 4. Linguo-pharyngeal events were considered to be electrically induced if they followed consistently, and with a relatively fixed latency, a single electrical pulse delivered to the superior laryngeal nerve, and ketamine-induced if no such time-locked sequence existed or if they occurred in the absence of electrical stimulation. 5. No differences could be discovered between the two types of linguo-pharyngeal events whether they were compared at the polygraphic or the unitary level. 6. These findings suggest that pharmacologically (ketamine)-induced dyskinetic activity does not differ from comparable motor patterns induced by classical electrophysiological means.     

Correction for missed events based on a realistic model of a detector.

Quantitative patch-clamp analysis based on dwell-time histograms has to deal with the problem of missed events. The correction of the evaluated time constants has to take into account the characteristics of the detector used for the reconstruction of the time series. In previous approaches a simple model of the detector has been used, which is based on the assumption that all events shorter than the temporal resolution tres were missed, irrespective of the preceding events. Rather than the standard assumption of a fixed dead time, we introduce a more realistic model of a detector by a continuous-time version of the Hinkley detector. The combined state of the channel and the detector obeys a Markov model, which is governed by a Fokker-Planck-Kolmogorov partial differential equation. The steady-state solution leads to the determination of the apparent time constants tau o and tau c depending on the true rate constants koc and kco and the temporal resolution tres of the detector. Simulations with different kinds of detectors, including the Bessel filter with half-amplitude threshold detection, are performed. They show that our new equation predicts the dependence of tau c and tau o on koc, kco, and tres better than the standard equation used until now.     

The genetics of PLT response. II. HLA-DRw is a major PLT-stimulating determinant.

PLT response is restricted by the HLA-D region. The present study was undertaken to help define the role of HLA-DRw in PLT restimulation. Haplotype-primed intrafamily PLT cells were made against specificities HLA-DRw1, HLA-DRw3, and HLA-DRw7; each PLT was then restimulated with cells from a 35-member unrelated panel. Restimulation values for each PLT were subjected to bimodal clustering analysis. In addition, blocking experiments were performed with other intrafamily and homozygous typing cell PLT after preincubation with B cell alloantisera. The results show a high correlation (0.881 less than or equal to r less than or equal to 1.00) between the HLA-DRw specificity of the priming haplotype and the HLA-DRw specificity of unrelated panel cells that restimulate in PLT. When stimulating cells were absorbed with the corresponding DRw alloantisera or p29,34 heteroantiserum (against B cell specific antigens), PLT restimulation was significantly blocked. However, the PLT cells treated with antisera showed no effect. The results strongly suggest that HLA-DRw is the principal PLT-stimulating determinant.     

Two-dimensional infrared correlation spectroscopy as a probe of sequential events in the thermal unfolding of cytochromes c.

The sequential unfolding events of horse, cow, and tuna ferricytochromes c (cyt c) as a function of increasing temperature over the range 25-81 degrees C were investigated by resolution-enhanced two-dimensional infrared (2D IR) correlation spectroscopy. The 2D IR analysis revealed that in the thermal denaturation of the two mammalian cyts, the overall sequence of unfolding is similar, with denaturation of extended-chain and turn structures occurring prior to unfolding of alpha-helices, followed by denaturation of residual stable extended-chain structures. In tuna cyt c, denaturation of all extended-chain structures precedes the unfolding of alpha-helices. Moreover, in cow cyt c, unfolding of all helical components occurs as one cooperative unit, but in horse and tuna cyts c, the helical components behave as subdomains that unfold separately, as proposed recently by Englander and co-workers for horse cyt c [Bai et al. (1995) Science 269, 192-197; Milne et al. (1999) J. Mol. Biol. 290, 811-822]. At higher temperatures, following the loss of secondary structure, protein aggregation occurs in the three cyts c. The data presented here establish that variations in the thermal unfolding of cyts c can be associated with specific sites in the protein that influence local flexibility yet have little affect on global stability. This study demonstrates the power of resolution-enhanced 2D IR correlation spectroscopy in probing unfolding events in homologous proteins.     

Expectations of clumpy resources influence predictions of sequential events

When predicting the next outcome in a sequence of events, people often appear to expect streaky patterns, such as that sport players can develop a “hot hand,” even if the sequence is actually random. This expectation, referred to as positive recency, can be adaptive in environments characterized by resources that are clustered across space or time (e.g., expecting to find multiple berries on separate bushes). But how strong is this disposition towards positive recency? If people perceive random sequences as streaky, will there be situations in which they forego a payoff because they prefer an unpredictable random environment over an exploitable but alternating pattern? To find out, 238 participants repeatedly chose to bet on the next outcome of one of two sequences of (binary) events, presented next to each other. One sequence displayed events at random while the other sequence was either more streaky (positively autocorrelated) or more alternating (negatively autocorrelated) than chance. The degree of autocorrelation varied in a between-subject design. Most people preferred to predict purely random sequences over those with moderate negative autocorrelation and thus missed the opportunity for above-chance payoff. Positive recency persisted despite extensive feedback and the opportunity to learn more rewarding behavior over time. Further, most participants' choice strategies were best described by a win-stay/lose-shift strategy, adaptive in clumpy or streaky environments. We discuss the implications regarding an evolved human tendency to expect streaky patterns, even if the sequence is actually random.     

Effects of trace element supplementation on the inflammatory response in a rabbit model of major trauma

Patients with a severe trauma exhibit a strong oxidative stress, an intense inflammatory response, and long-lasting hypermetabolism, all of which are proportional to the severity of injury. In this study, we investigated the impact of trace element (TE) supplementation on the inflammatory response in an animal model of major trauma. New Zealand White rabbits were randomly assigned as a control group (n=5) and an experimental group (n=70) that, after receiving a major trauma, was subdivided into Trauma-Control (n=35) and Trauma-TE (n=35) groups. Systemic inflammatory response syndrome (SIRS) was observed in 40 out of 70 rabbits with a trauma, with a higher incidence in the Trauma-Control group (88.6%; 31/35) than the Trauma-TE group (28.6%; 10/35) (p<0.01). The mortality rate was significantly different between the Trauma-Control and the Trauma-TE groups; (34% vs. 8%; p<0.01).There were significant post-trauma alterations in the levels of (1) serum and spleen zinc (Zn), copper (Cu), selenium (Se), and manganese (Mn), (2) serum AST and ALT, (3) serum interleukin-6/10, and (4) nuclear factor kappa binding (NF-κB) activity and the expression. TE supplementation: (1) improved blood urea nitrogen (BUN), and creatinine (Cr) levels, (2) stabilized IL-6/10 production, (3) decreased NF-κB p⁶⁵ production. Appropriate TE supplementation can improve the TE status, mitigate SIRS, and reduce the mortality due to multiple organ dysfunction syndromes (MODS)/multiple organ failure (MOF) after major trauma.     

Relative spectral response as a function of sequential ligand binding

A unique method is presented for the determination of the critical number of ligands that must bind to a macromolecule to elicit a spectroscopic response. This method is based on analysis of ligand binding data. For example, four Ca2+ and two Mg2+ ions are necessary for mirroring the relative decrease in the intrinsic fluorescence of bovine prothrombin fragment 1. For application of the method, ligand loading and relative spectroscopic response data must be measured over a full range of concentrations.     

Synthesis and biochemical characterization of a phosphorylated analogue of the response regulator CheB.

CheB is a response regulator protein in the bacterial chemotaxis two-component signal transduction pathway. Methylesterase CheB functions together with methyltransferase CheR to modulate the level of glutamate methylation in transmembrane chemoreceptors in response to environmental stimuli. The level of glutamate methylation in turn indirectly controls the direction of flagellar rotation. Like most two-component response regulators, CheB is activated in vivo by phosphorylation of a single aspartate, Asp 56, in its regulatory domain. Extensive biochemical and crystallographic studies have been completed on the inactive, unphosphorylated form of CheB. Because of the inherent lability of aspartyl phosphate bonds and the intrinsic phosphatase activity of CheB, the activated, phosphorylated form of CheB cannot be isolated for further characterization. We present a synthetic scheme to prepare an analogue of phosphorylated CheB using site-specific mutagenesis and chemical modification strategies. Initially, the two native cysteines found in CheB were substituted by serines and a cysteine was substituted for Asp 56 to yield D56C/C207S/C309S CheB. The unique cysteine in the substituted form of CheB was modified by sodium thiophosphate, Na(3)SPO(3), using two sequential disulfide bond exchange reactions. The analogue, D56C/C207S/C309S CheB-SPO(3), contained a thiophosphate group covalently bonded to the protein through a disulfide linkage at residue 56. Mass spectrometry showed that the protein was singly modified. Reverse phase chromatography showed that greater than 95% of the protein was modified under optimized conditions and that the analogue had a half-life of 28 days. In in vitro methylesterase assays in the presence of Mg(2+), the analogue exhibited activity equivalent to that of fully phosphorylated C207S/C309S CheB. Thus, D56C/C207S/C309S CheB-SPO(3) is a stable analogue that may be useful for characterization of the active form of CheB.     

Criteria for categorizing early biochemical events occurring during sporulation of Bacillus subtilis.

Two criteria are suggested for assessing the relevance of biochemical events occurring early in sporulation. The first is thymidine starvation, a condition known to inhibit sporulation. This also inhibits the production of metalloprotease, serine protease, and ribonuclease; alpha-amylase production, however, is unaffected. The second is the effect of a regulator mutation which increases the production of the proteases. In the mutant, ribonuclease is produced in correspondingly large quantities whereas alpha-amylase production is unaffected. We conclude that, whereas the serine protease is part of the main sequence of events leading to formation of the spore, the metalloprotease is a side effect, i.e., connected with the main sequence but not part of it. Ribonuclease could, on present evidence, be either in the main sequence or a side effect associated with it. Amylase, however, seems to be separately regulated and neither directly nor indirectly connected with the sporulation sequence.