Phase computations and phase models for discrete molecular oscillators

Background

Biochemical oscillators perform crucial functions in cells, e.g., they set up circadian clocks. The dynamical behavior of oscillators is best described and analyzed in terms of the scalar quantity, phase. A rigorous and useful definition for phase is based on the so-called isochrons of oscillators. Phase computation techniques for continuous oscillators that are based on isochrons have been used for characterizing the behavior of various types of oscillators under the influence of perturbations such as noise.

Results

In this article, we extend the applicability of these phase computation methods to biochemical oscillators as discrete molecular systems, upon the information obtained from a continuous-state approximation of such oscillators. In particular, we describe techniques for computing the instantaneous phase of discrete, molecular oscillators for stochastic simulation algorithm generated sample paths. We comment on the accuracies and derive certain measures for assessing the feasibilities of the proposed phase computation methods. Phase computation experiments on the sample paths of well-known biological oscillators validate our analyses.

Conclusions

The impact of noise that arises from the discrete and random nature of the mechanisms that make up molecular oscillators can be characterized based on the phase computation techniques proposed in this article. The concept of isochrons is the natural choice upon which the phase notion of oscillators can be founded. The isochron-theoretic phase computation methods that we propose can be applied to discrete molecular oscillators of any dimension, provided that the oscillatory behavior observed in discrete-state does not vanish in a continuous-state approximation. Analysis of the full versatility of phase noise phenomena in molecular oscillators will be possible if a proper phase model theory is developed, without resorting to such approximations.     

Paraoxonase 1 192 and 55 polymorphisms in osteosarcoma

Paraoxonase is an HDL-associated enzyme that plays a preventive role against oxidative stres. Previous studies suggested that involved an amino acid substitution at position 192 gives rise to two alloenzymes with a low activity (Q allele) and a high activity (R allele) towards paraoxon. There also exists a second polymorphism of the human PON1 gene affecting amino acid 55, giving rise to a leucine (L-allele) substitution for methionine (M-allele). PON1 gene polymorphisms were studied in 50 patients with osteosarcoma and 50 healthy controls. Paraoxonase genotypes were determined by PCR–RFLP. We found a reduction in the frequency of PON1 192 R allele in patients (P = 0.015). Besides, PON1 192 wild type QQ genotype (P = 0.015) and PON1 55 wild type L allele (P = 0.001) were higher in patients compared to healthy controls. PON1 192 QQ genotype was associated with osteosarcoma in multivariate logistic regression analysis. Our findings have suggested that PON1 192 wild type genotypes may be associated with a risk of developing osteosarcoma.     

In vitro and in silico studies of nitrobenzamide derivatives as potential anti-neuroinflammatory agents

Communicated by Ramaswamy H. Sarma     

DNA immunization against tissue-restricted antigens enhances tumor immunity after allogeneic hemopoietic stem cell transplantation

Malignant relapse remains a major problem for recipients of allogeneic hemopoietic stem cell transplantation (HSCT). We hypothesized that immunization of allogeneic HSCT recipients against tissue-restricted Ags using DNA vaccines would decrease the risk of relapse without enhancing graft-vs-host disease (GVHD). Using the mouse B16 melanoma model, we found that post-HSCT DNA immunization against a single tumor Ag induces tumor rejection that is significantly greater than HSCT alone in a T cell-depleted MHC-matched minor Ag-mismatched allogeneic HSCT model (LP --> B6). In treatment models, post-HSCT DNA immunization provides significantly greater overall survival than the vaccine alone. Donor leukocyte infusion further enhances tumor-free survival, including in treatment models. There was no GVHD in HSCT recipients treated with DNA vaccination and donor leukocyte infusion. Further analysis demonstrated that these effects are dependent on CD8+ T cells of donor origin that recognize multiple epitopes. These results demonstrate that DNA immunization against tissue-restricted Ags after allogeneic T cell-depleted HSCT can induce potent antitumor effects without causing GVHD.     

Biepicondylar fracture presenting with elbow dislocation: a case report

ABSTRACT: INTRODUCTION: Biepicondylar fracture of the elbow is very rare, and to date there have only been three reports of this injury and its treatment in the English scientific literature. This case report evaluates the surgical internal fixation of a biepicondylar fracture of the elbow with an associated dislocation. CASE PRESENTATION: We report the case of a 15-year-old Turkish girl with a biepicondylar fracture dislocation of the left elbow. Open reduction and an internal fixation operation were applied. There were no complications. CONCLUSION: In these injuries, open reduction and internal fixation appear to be a good method to restore elbow stability and function.     

Construction of a reading frame-independent yeast two-hybrid vector system for site-specific recombinational cloning and protein interaction screening

The yeast two-hybrid (Y2H) system is a powerful method to identify protein-protein inter-actions (PPI) in vivo, requiring minimal prior information of the putative interactors. The time and effort required for each experiment can be significantly reduced if the "bait" and the "prey" proteins are cloned into specific recombination-amenable two-hybrid vectors. We describe the construction of a reading frame-independent vector system for Y2H PPI studies. The described vector system knits together the advantages of site-specific recombination cloning with the Y2H system. The produced plasmids enable recombination-based cloning of genes or gene fragments in all possible reading frames into Y2H library vectors. Thus, Y2H screening libraries can be rapidly constructed and will present more amino termini in the correct reading frame. Additionally, advantageous for small-scale Y2H studies, there is no need to know the natural reading frame of the genes of interest, because the bait and prey genes can be transferred into the vectors by a single reaction and are present in all possible reading frames. Since the Y2H system per se is a positive selection system, only pairs of bait and prey genes harboring the correct reading frames will emerge. We tested the new vectors within the Y2H system and demonstrated full functionality without any undesired effects on the Y2H system itself. Besides the vector construction, we investigated the utility of the system for Y2H analysis and demonstrated clearly its practicability in genome-wide Y2H screenings and the advantage of using additional reading-frame Y2H cDNA libraries. We performed a series of genome-wide Y2H library screenings with the human vitamin D receptor protein (VDR) as bait. We investigated: (i) whether more protein interactors are found by using three instead of one reading-frame destination vectors; (ii) how much overlap between the different reading-frame libraries exists; and (iii) the rate of possible additional autoactivators. We conclude that our vectors deliver significantly more interactors and outperform a single reading-frame library. This new system could enable simple and fast large-scale PPI studies and the construction of high-quality screening libraries.     

Cation effects on swelling of kappa-carrageenan: a photon transmission study

Swelling behavior of kappa-carrageenan gels in water and KCl solutions was investigated by photon transmission experiments following the preparation of gels in the presence and absence of externally added K+ ion as a gel promoting agent. Transmitted photon intensity, Itr, increased continuously during swelling depending on the carrageenan and ion content in the gel. This increase in Itr was modeled using the Li-Tanaka equation. Both the experimental work and the model showed that the swelling of low carrageenan and ion content gels took less time than that of high ion content gels. It is confirmed that double helices in a swollen gel move much faster in pure water than in KCl solution during swelling processes. Swelling time constants, tau1, and collective diffusion coefficients, Do, were measured for the gels swollen in water and KCl solutions.     

Strategies to enhance T-cell reconstitution in immunocompromised patients

Immune deficiency, together with its associated risks such as infections, is becoming an increasingly important clinical problem owing to the ageing of the general population and the increasing number of patients with HIV/AIDS, malignancies (especially those treated with intensive chemotherapy or radiotherapy) or transplants (of either solid organs or haematopoietic stem cells). Of all immune cells, T cells are the most often affected, leading to a prolonged deficiency of T cells, which has important clinical consequences. Accordingly, strategies to improve the recovery and function of T cells, as we discuss here, should have a direct impact on reducing the morbidity and mortality of many patients and should increase the efficacy of therapeutic and prophylactic vaccinations against microbial pathogens or tumours.     

Experience-dependent modulation of C. elegans behavior by ambient oxygen

BACKGROUND: Ambient oxygen (O2) influences the behavior of organisms from bacteria to man. In C. elegans, an atypical O2 binding soluble guanylate cyclase (sGC), GCY-35, regulates O2 responses. However, how acute and chronic changes in O2 modify behavior is poorly understood. RESULTS: Aggregating C. elegans strains can respond to a reduction in ambient O2 by a rapid, reversible, and graded inhibition of roaming behavior. This aerokinetic response is mediated by GCY-35 and GCY-36 sGCs, which appear to become activated as O2 levels drop and to depolarize the AQR, PQR, and URX neurons. Coexpression of GCY-35 and GCY-36 is sufficient to transform olfactory neurons into O2 sensors. Natural variation at the npr-1 neuropeptide receptor alters both food-sensing and O2-sensing circuits to reconfigure the salient features of the C. elegans environment. When cultivated in 1% O2 for a few hours, C. elegans reset their preferred ambient O2, seeking instead of avoiding 0%-5% O2. This plasticity involves reprogramming the AQR, PQR, and URX neurons. CONCLUSIONS: To navigate O2 gradients, C. elegans can modulate turning rates and speed of movement. Aerotaxis can be reprogrammed by experience or engineered artificially. We propose a model in which prolonged activation of the AQR, PQR, and URX neurons by low O2 switches on previously inactive O2 sensors. This enables aerotaxis to low O2 environments and may encode a "memory" of previous cultivation in low O2.