A mathematical model of breast cancer development, local treatment and recurrence

Cancer development is a stepwise process through which normal somatic cells acquire mutations which enable them to escape their normal function in the tissue and become self-sufficient in survival. The number of mutations depends on the patient's age, genetic susceptibility and on the exposure of the patient to carcinogens throughout their life. It is believed that in every malignancy 4-6 crucial similar mutations have to occur on cancer-related genes. These genes are classified as oncogenes and tumour suppressor genes (TSGs) which gain or lose their function respectively, after they have received one mutative hit or both of their alleles have been knocked out. With the acquisition of each of the necessary mutations the transformed cell gains a selective advantage over normal cells, and the mutation will spread throughout the tissue via clonal expansion. We present a simplified model of this mutation and expansion process, in which we assume that the loss of two TSGs is sufficient to give rise to a cancer. Our mathematical model of the stepwise development of breast cancer verifies the idea that the normal mutation rate in genes is only sufficient to give rise to a tumour within a clinically observable time if a high number of breast stem cells and TSGs exist or genetic instability is involved as a driving force of the mutation pathway. Furthermore, our model shows that if a mutation occurred in stem cells pre-puberty, and formed a field of cells with this mutation through clonal formation of the breast, it is most likely that a tumour will arise from within this area. We then apply different treatment strategies, namely surgery and adjuvant external beam radiotherapy and targeted intraoperative radiotherapy (TARGIT) and use the model to identify different sources of local recurrence and analyse their prevention.     

Familial aggregation of nasal conditioning capacity.

In our previous studies on nasal conditioning, we observed a large variability among individuals to condition inspired air. Although we previously investigated various physiological parameters (age, sex, nasal mucosal temperature, heart rate, blood pressure, and nasal volume) that might underlie these differences, we have been unable to explain this variability. Many proteins and molecules, which are under genetic control and could affect nasal conditioning, are involved in water transport,. In this study, we hypothesized that familial factors may contribute to the differences in nasal conditioning capacity (NCC). We performed a prospective study of 47 sibling pairs. Cold dry air was delivered to the nose, and the total water gradient (TWG) was calculated to determine the NCC. We found a highly significant intraclass correlation of 0.53 (P < 0.0001) between sibling pairs for the TWG. These results suggest that there is a familial basis for nasal conditioning and a large enough genetic component to search for genes explaining the observed correlation.     

Optimization of bioreactor using metabolic control analysis approach

A new methodology based on a metabolic control analysis (MCA) approach is developed for the optimization of continuous cascade bioreactor system. A general framework for representation of a cascade bioreactor system consisting of a large number of reactors as a single network is proposed. The kinetic and transport processes occurring in the system are represented as a reaction network with appropriate stoichiometry. Such representation of the bioreactor systems makes it amenable to the direct application of the MCA approach. The process sensitivity information is extracted using MCA methodology in the form of flux and concentration control coefficients. The process sensitivity information is shown to be a useful guide for determining the choice of decision variables for the purpose of optimization. A generalized problem of optimization of the bioreactor is formulated in which the decision variables are the operating conditions and kinetic parameters. The gradient of the objective function to be maximized with respect to all decision variables is obtained in the form of response coefficients. This gradient information can be used in any gradient-based optimization algorithm. The efficiency of the proposed technique is demonstrated with two examples taken from literature: biotransformation of crotonobetaine and alcohol fermentation in cascade bioreactor system.     

Influence of operational variables on properties of piroxicam pellets prepared by extrusion-spheronization: A technical note

Summary and Conclusion  The processing conditions has a pronounced effect on the pellet properties. Drying conditions influenced the mean size and the drug release of the pellets. Because of the shrinking of the pellets upon drying at higher temperatures, the pellets also showed increased densities. Freeze drying almost prevented shrinking and thus led to the highest drug release. With an increase in the temperature of drying, the drug release rate decreased. Both spheronization time and spheronization speed affected the shapes of pellets, and the changes in shapes then affected the pellet flow properties. Within the studied range, the circularity of the pellets was affected more by the spheronization time than by the spheronization speed. Drying conditions influenced pellet friability, which decreased with an increase in drying temperature, indicating the formation of more dense structures at higher temperatures. The same result was obtained with spheronization time. With an increase in spheronization time, the friability decreased, because of the formation of more compact masses at higher spheronization time. Mean size was not affected by spheronization time or spheronization speed. Published: March 9, 2007     

Olfactory Thresholds of the U.S. Population of Home-Dwelling Older Adults: Development and Validation of a Short,Reliable Measure

Current methods of olfactory sensitivity testing are logistically challenging and therefore infeasible for use in in-home surveys and other field settings. We developed a fast, easy and reliable method of assessing olfactory thresholds, and used it in the first study of olfactory sensitivity in a nationally representative sample of U.S. home-dwelling older adults. We validated our method via computer simulation together with a model estimated from 590 normosmics. Simulated subjects were assigned n-butanol thresholds drawn from the estimated normosmic distribution and based on these and the model, we simulated administration of both the staircase and constant stimuli methods. Our results replicate both the correlation between the two methods and their reliability as previously reported by studies using human subjects. Further simulations evaluated the reliability of different constant stimuli protocols, varying both the range of dilutions and number of stimuli (6–16). Six appropriately chosen dilutions were sufficient for good reliability (0.67) in normosmic subjects. Finally, we applied our method to design a 5-minute, in-home assessment of older adults (National Social Life, Health and Aging Project, or NSHAP), which had comparable reliability (0.56), despite many subjects having estimated thresholds above the strongest dilution. Thus, testing with a fast, 6-item constant stimuli protocol is informative, and permits olfactory testing in previously inaccessible research settings.     

Characterization of deamidation of barstar using electrospray ionization quadrupole time-of-flight mass spectrometry, which stabilizes an equilibrium unfolding intermediate

Deamidation of asparaginyl residues is a common posttranslational modification in proteins and has been studied extensively because of its important biological effects, such as those on enzymatic activity, protein folding, and proteolytic degradation. However, characterization of the sites of deamidation of a protein has been a difficult analytical problem. In this study, mass spectrometry has been used as an analytical tool to characterize the deamidation of barstar, an RNAse inhibitor. Upon incubation of the protein at alkaline pH for 5 h, intact mass analysis of barstar, using electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QToF MS), indicated an increase in the mass of +2 Da, suggesting possible deamidation of the protein. The sites of deamidation have been identified using the conventional bottom-up approach using a capillary liquid chromatography connected on line to an ESI QToF mass spectrometer and top down approach by direct infusion of the intact protein and fragmenting inside MS. These chemical modifications are shown to lead to stabilization of an unfolding intermediate, which can be observed in equilibrium unfolding studies.     

Fused tricyclic indoles as S1P₁ agonists with robust efficacy in animal models of autoimmune disease

Two series of fused tricyclic indoles were identified as potent and selective S1P(1) agonists. In vivo these agonists produced a significant reduction in circulating lymphocytes which translated into robust efficacy in several rodent models of autoimmune disease. Importantly, these agonists were devoid of any activity at the S1P(3) receptor in vitro, and correspondingly did not produce S1P(3) mediated bradycardia in telemeterized rat.     

Four-state folding of a SH3 domain: salt-induced modulation of the stabilities of the intermediates and native state

Unstable intermediates on the folding pathways of proteins can be stabilized sufficiently so that they accumulate to detectable extents by the addition of a suitable cosolute. Here, the effect of sodium sulfate (Na(2)SO(4)) on the folding of the SH3 domain of PI3 kinase was investigated in the presence of guanidine hydrochloride (GdnHCl) using intrinsic tyrosine fluorescence and 1-anilinonaphthalene-8-sulfonate (ANS) binding. The free energy of unfolding in water of the native state (N) increases linearly with Na(2)SO(4) concentration, indicating stabilization via the Hofmeister effect. The addition of 0.5 M Na(2)SO(4) causes accumulation of an early intermediate L, which manifests itself as (1) a sub-millisecond change in tyrosine and ANS fluorescence and (2) a curvature in the chevron plot. It is shown that L is a specific structural component of the initially collapsed ensemble. An intermediate, M, also accumulates in unfolding studies conducted in the presence of 0.5 M Na(2)SO(4) and manifests itself by causing a curvature in the unfolding arm of the chevron. M is shown to be a wet molten globule that binds to ANS under unfolding conditions and is stabilized to the same extent as N in the presence of Na(2)SO(4). A four-state U ? L ? M ? N scheme satisfactorily modeled the kinetic data. Thus, the folding of the PI3K SH3 domain in the presence of salt commences via the formation of a structured intermediate ensemble L, which accumulates before the rate-limiting step of folding. L subsequently proceeds to N via the late intermediate M that forms after the rate-limiting transition of folding.     

Role of budding yeast Rad18 in repair of HO-induced double-strand breaks

The Rad6-Rad18 complex mono-ubiquitinates proliferating cell nuclear antigen (PCNA) at the lysine 164 residue after DNA damage and promotes DNA polymerase eta (Poleta)- and Polzeta/Rev1-dependent DNA synthesis. Double-strand breaks (DSBs) of DNA can be repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ), both of which require new DNA synthesis. HO endonuclease introduces DSBs into specific DNA sequences. We have shown that Polzeta and Rev1 localize to HO-induced DSBs in a Mec1-dependent manner and promote Ku-dependent DSB repair. However, Polzeta and Rev1 localize to DSBs independently of PCNA ubiquitination. Here we provide evidence indicating that Rad18-mediated PCNA ubiquitination stimulates DNA synthesis by Polzeta and Rev1 in repair of HO-induced DSBs. Ubiquitination defective PCNA mutation or rad18Delta mutation confers the same DSB repair defect as rev1Delta mutation. Consistent with a role in DSB repair, Rad18 localizes to HO-induced DSBs in a Rad6-dependent manner. Unlike Polzeta or Rev1, Poleta is dispensable for repair of HO-induced DSBs. Ku and DNA ligase IV constitute a central NHEJ pathway. We also show that Polzeta and Rev1 act in the same pathway as DNA ligase IV, suggesting that Polzeta and Rev1 are involved in DNA synthesis during NHEJ. Our results suggest that Polzeta-Rev1 accumulates at regions near DSBs independently of PCNA ubiquitination and then interacts with ubiquitinated PCNA to facilitate DNA synthesis.     

Attention Enhances the Retrieval and Stability of Visuospatial and Olfactory Representations in the Dorsal Hippocampus

A key question in the analysis of hippocampal memory relates to how attention modulates the encoding and long-term retrieval of spatial and nonspatial representations in this region. To address this question, we recorded from single cells over a period of 5 days in the CA1 region of the dorsal hippocampus while mice acquired one of two goal-oriented tasks. These tasks required the animals to find a hidden food reward by attending to either the visuospatial environment or a particular odor presented in shifting spatial locations. Attention to the visuospatial environment increased the stability of visuospatial representations and phase locking to gamma oscillations—a form of neuronal synchronization thought to underlie the attentional mechanism necessary for processing task-relevant information. Attention to a spatially shifting olfactory cue compromised the stability of place fields and increased the stability of reward-associated odor representations, which were most consistently retrieved during periods of sniffing and digging when animals were restricted to the cup locations. Together, these results suggest that attention selectively modulates the encoding and retrieval of hippocampal representations by enhancing physiological responses to task-relevant information.