Mathematical modelling of phenotypic selection with solid tumours

We present a space- and phenotype-structured model of selection dynamics between cancer cells within a solid tumour. In the framework of this model, we combine formal analyses with numerical simulations to investigate in silico the role played by the spatial distribution of oxygen and therapeutic agents in mediating phenotypic selection of cancer cells. Numerical simulations are performed on the 3D geometry of an in vivo human hepatic tumour, which was imaged using computerised tomography. Our modelling extends our previous work in the area through the inclusion of multiple therapeutic agents, one that is cytostatic, whilst the other is cytotoxic. In agreement with our previous work, the results show that spatial inhomogeneities in oxygen and therapeutic agent concentrations, which emerge spontaneously in solid tumours, can promote the creation of distinct local niches and lead to the selection of different phenotypic variants within the same tumour. A novel conclusion we infer from the simulations and analysis is that, for the same total dose, therapeutic protocols based on a combination of cytotoxic and cytostatic agents can be more effective than therapeutic protocols relying solely on cytotoxic agents in reducing the number of viable cancer cells

Should MS be Treated by Escalation or Induction Therapy?

MS is a chronic, increasingly disabling disease whose long-term outcomes determine the key social, medical and economic impact of this disease. Disease-modifying therapies (DMTs) for multiple sclerosis (MS) are prescribed to delay disease progression and to protect a patient’s functional capability. The concepts of escalation and induction immunotherapy in MS represent different therapeutic strategies for the treatment of MS. Both strategies may be valuable options for patients starting on DMT, however, induction therapy mainly focuses on patients with very aggressive course of MS from the onset. Using a patient unique approach to selection of treatment, MS can be effectively control disease and may delay or even prevent the development of secondary progressive MS

Cohomology of the Lie Superalgebra of Contact Vector Fields on R1∣1\mathbb{R}^{1|1} and Deformations of the Superspace of Symbols

Following Feigin and Fuchs, we compute the first cohomology of the Lie superalgebra $\mathcal{K}(1)$ of contact vector fields on the (1,1)-dimensional real superspace with coefficients in the superspace of linear differential operators acting on the superspaces of weighted densities. We also compute the same, but $\mathfrak{osp}(1|2)$-relative, cohomology. We explicitly give 1-cocycles spanning these cohomology. We classify generic formal $\mathfrak{osp}(1|2)$-trivial deformations of the $\mathcal{K}(1)$-module structure on the superspaces of symbols of differential operators. We prove that any generic formal $\mathfrak{osp}(1|2)$-trivial deformation of this $\mathcal{K}(1)$-module is equivalent to a polynomial one of degree $\leq4$. This work is the simplest superization of a result by Bouarroudj [On $\mathfrak{sl}$(2)-relative cohomology of the Lie algebra of vector fields and differential operators, J. Nonlinear Math. Phys., no.1, (2007), 112--127]. Further superizations correspond to $\mathfrak{osp}(N|2)$-relative cohomology of the Lie superalgebras of contact vector fields on $1|N$-dimensional superspace

Process for Making Single-Domain Magnetite Crystals

A process for making chemically pure, single-domain magnetite crystals substantially free of structural defects has been invented as a byproduct of research into the origin of globules in a meteorite found in Antarctica and believed to have originated on Mars. The globules in the meteorite comprise layers of mixed (Mg, Fe, and Ca) carbonates, magnetite, and iron sulfides. Since the discovery of the meteorite was announced in August 1996, scientists have debated whether the globules are of biological origin or were formed from inorganic materials by processes that could have taken place on Mars. While the research that led to the present invention has not provided a definitive conclusion concerning the origin of the globules, it has shown that globules of a different but related chemically layered structure can be grown from inorganic ingredients in a multistep precipitation process. As described in more detail below, the present invention comprises the multistep precipitation process plus a subsequent heat treatment. The multistep precipitation process was demonstrated in a laboratory experiment on the growth of submicron ankerite crystals, overgrown by submicron siderite and pyrite crystals, overgrown by submicron magnesite crystals, overgrown by submicron siderite and pyrite. In each step, chloride salts of appropriate cations (Ca, Fe, and Mg) were dissolved in deoxygenated, CO2- saturated water. NaHCO3 was added as a pH buffer while CO2 was passed continuously through the solution. A 15-mL aliquot of the resulting solution was transferred into each of several 20 mL, poly(tetrafluoroethylene)-lined hydrothermal pressure vessels. The vessels were closed in a CO2 atmosphere, then transferred into an oven at a temperature of 150 C. After a predetermined time, the hydrothermal vessels were removed from the oven and quenched in a freezer. Supernatant solutions were decanted, and carbonate precipitates were washed free of soluble salts by repeated decantations with deionized water

Survey of variation in human transcription factors reveals prevalent DNA binding changes

Published in final edited form as: Science. 2016 Mar 25; 351(6280): 1450–1454. Published online 2016 Mar 24. doi: 10.1126/science.aad2257Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA binding activity and used universal protein-binding microarrays to assay sequence-specific DNA binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA binding activities, which may contribute to phenotypic variation.National Institutes of Health; NHGRI R01 HG003985; P50 HG004233; A*STAR National Science Scholarship; National Science Foundatio

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs

Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DNA sequence. It has previously been shown that, when scoring matches to known TFBS motifs, interdependencies between positions within a motif should be taken into account. However, this remains a challenging task owing to the fact that sequences similar to those of known TFBSs can occur by chance with a relatively high frequency. Here we present a new method for matching sequences to TFBS motifs based on intuitionistic fuzzy sets (IFS) theory, an approach that has been shown to be particularly appropriate for tackling problems that embody a high degree of uncertainty. Results: We propose SCintuit, a new scoring method for measuring sequence-motif affinity based on IFS theory. Unlike existing methods that consider dependencies between positions, SCintuit is designed to prevent overestimation of less conserved positions of TFBSs. For a given pair of bases, SCintuit is computed not only as a function of their combined probability of occurrence, but also taking into account the individual importance of each single base at its corresponding position. We used SCintuit to identify known TFBSs in DNA sequences. Our method provides excellent results when dealing with both synthetic and real data, outperforming the sensitivity and the specificity of two existing methods in all the experiments we performed. Conclusions: The results show that SCintuit improves the prediction quality for TFs of the existing approaches without compromising sensitivity. In addition, we show how SCintuit can be successfully applied to real research problems. In this study the reliability of the IFS theory for motif discovery tasks is proven

Hypoxia-inducible factor-2α regulates the expression of TRAIL receptor DR5 in renal cancer cells

To understand the role of hypoxia-inducible factor (HIF)-2α in regulating sensitivity of renal cancer cells to tumor necrosis factor-related apoptosis inducing ligand (TRAIL)-induced apoptosis, we transfected wild-type and mutant von Hippel Lindau (VHL) proteins into TRAIL-sensitive, VHL-negative A498 cells. We find that wild-type VHL, but not the VHL mutants S65W and C162F that do not degrade HIF proteins, cause TRAIL resistance. Knock down of the HIF-2α protein by RNA interference (short hairpin RNA) blocked TRAIL-induced apoptosis, decreased the level of TRAIL receptor (DR5) protein and inhibited the transcription of DR5 messenger RNA. By using luciferase constructs containing the upstream region of the DR5 promoter, we demonstrate that HIF-2α stimulates the transcription of the DR5 gene by activating the upstream region between −448 and −1188. Because HIF-2α is thought to exert its effect on gene transcription by interacting with the Max protein partner of Myc in the Myc/Max dimer, small interfering RNAs to Myc were used to lower the levels of this protein. In multiple renal cancer cell lines decreasing the levels of Myc blocked the ability of HIF-2α to stimulate DR5 transcription. PS-341 (VELCADE, bortezomib), a proteasome inhibitor used to treat human cancer, increases the levels of both HIF-2α and c-Myc and elevates the level of DR5 in renal cancer, sensitizing renal cancer cells to TRAIL therapy. Similarly, increasing HIF-2α in prostate and lung cancer cell lines increased the levels of DR5. Thus, in renal cancer cell lines expressing HIF-2α, this protein plays a role in regulating the levels of the TRAIL receptor DR5

Molecular Pathways Mediating Immunosuppression in Response to Prolonged Intensive Physical Training, Low-Energy Availability, and Intensive Weight Loss

Exercise and exercise-induced weight loss have a beneficial effect on overall health, including positive effects on molecular pathways associated with immune function, especially in overweight individuals. The main aim of our study was to assess how energy deprivation (i.e., "semi-starvation") leading to substantial fat mass loss affects the immune system and immunosuppression in previously normal weight individuals. Thus, to address this hypothesis, we applied a high-throughput systems biology approach to better characterize potential key pathways associated with immune system modulation during intensive weight loss and subsequent weight regain. We examined 42 healthy female physique athletes (age 27.5 +/- 4.0 years, body mass index 23.4 +/- 1.7 kg/m(2)) volunteered into either a diet group (n = 25) or a control group (n = 17). For the diet group, the energy intake was reduced and exercise levels were increased to induce loss of fat mass that was subsequently regained during a recovery period. The control group was instructed to maintain their typical lifestyle, exercise levels, and energy intake at a constant level. For quantification of systems biology markers, fasting blood samples were drawn at three time points: baseline (PRE), at the end of the weight loss period (MID 21.1 +/- 3.1 weeks after PRE), and at the end of the weight regain period (POST 18.4 +/- 2.9 weeks after MID). In contrast to the control group, the diet group showed significant (false discovery ratePeer reviewe