Pre-Clinical Models of Diffuse Intrinsic Pontine Glioma.

Diffuse intrinsic pontine glioma (DIPG) is a rare and incurable brain tumor that arises in the brainstem of children predominantly between the ages of 6 and 8. Its intricate morphology and involvement of normal pons tissue precludes surgical resection, and the standard of care today remains fractionated radiation alone. In the past 30 years, there have been no significant advances made in the treatment of DIPG. This is largely because we lack good models of DIPG and therefore have little biological basis for treatment. In recent years, however, due to increased biopsy and acquisition of autopsy specimens, research is beginning to unravel the genetic and epigenetic drivers of DIPG. Insight gleaned from these studies has led to improvements in approaches to both model these tumors in the lab and to potentially treat them in the clinic. This review will detail the initial strides toward modeling DIPG in animals, which included allograft and xenograft rodent models using non-DIPG glioma cells. Important advances in the field came with the development of in vitro cell and in vivo xenograft models derived directly from autopsy material of DIPG patients or from human embryonic stem cells. Finally, we will summarize the progress made in the development of genetically engineered mouse models of DIPG. Cooperation of studies incorporating all of these modeling systems to both investigate the unique mechanisms of gliomagenesis in the brainstem and to test potential novel therapeutic agents in a preclinical setting will result in improvement in treatments for DIPG patients.

Predicting Transcript Production Rates in Yeast With Sparse Linear Models

To provide biological insights into transcriptional regulation, a couple of groups have recently presented models relating the promoter DNA-bound transcription factors (TFs) to downstream gene’s mean transcript level or transcript production rates over time. However, transcript production is dynamic in response to changes of TF concentrations over time. Also, TFs are not the only factors binding to promoters; other DNA binding factors (DBFs) bind as well, especially nucleosomes, resulting in competition between DBFs for binding at same genomic location. Additionally, not only TFs, but also some other elements regulate transcription. Within core promoter, various regulatory elements influence RNAPII recruitment, PIC formation, RNAPII searching for TSS, and RNAPII initiating transcription. Moreover, it is proposed that downstream from TSS, nucleosomes resist RNAPII elongation.

Here, we provide a machine learning framework to predict transcript production rates from DNA sequences. We applied this framework in the S. cerevisiae yeast for two scenarios: a) to predict the dynamic transcript production rate during the cell cycle for native promoters; b) to predict the mean transcript production rate over time for synthetic promoters. As far as we know, our framework is the first successful attempt to have a model that can predict dynamic transcript production rates from DNA sequences only: with cell cycle data set, we got Pearson correlation coefficient Cp = 0.751 and coefficient of determination r2 = 0.564 on test set for predicting dynamic transcript production rate over time. Also, for DREAM6 Gene Promoter Expression Prediction challenge, our fitted model outperformed all participant teams, best of all teams, and a model combining best team’s k-mer based sequence features and another paper’s biologically mechanistic features, in terms of all scoring metrics.

Moreover, our framework shows its capability of identifying generalizable fea- tures by interpreting the highly predictive models, and thereby provide support for associated hypothesized mechanisms about transcriptional regulation. With the learned sparse linear models, we got results supporting the following biological insights: a) TFs govern the probability of RNAPII recruitment and initiation possibly through interactions with PIC components and transcription cofactors; b) the core promoter amplifies the transcript production probably by influencing PIC formation, RNAPII recruitment, DNA melting, RNAPII searching for and selecting TSS, releasing RNAPII from general transcription factors, and thereby initiation; c) there is strong transcriptional synergy between TFs and core promoter elements; d) the regulatory elements within core promoter region are more than TATA box and nucleosome free region, suggesting the existence of still unidentified TAF-dependent and cofactor-dependent core promoter elements in yeast S. cerevisiae; e) nucleosome occupancy is helpful for representing +1 and -1 nucleosomes’ regulatory roles on transcription.

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

Insight into Biological Small-Molecule Activation from Enzymes, Model Complexes, and X-ray Spectroscopy

Thesis (Ph.D.)--University of Washington, 2016-08

Small bowel obstruction caused by mesh migration. Case report

Introduction. Endoscopic hernia repair methods have become increasingly popular over the past 15 years. Nonetheless, there is no consensus regarding an optimal fixation method. Transabdominal sutures and titanium tacks or staples are the most traditional ones. Case report. We present a case of mechanic small bowel obstruction due to mesh migration occurring one year and a half after incisional hernia repair with polytetrafluoroethylene mesh fixed by spiral tacks. Discussion. Titanium spiral tacks are dangerous because of their sharp components, which can damage organs such as the small intestine, by causing microperforations. The type of prosthesis used has also contributed to the intraluminal migration, since polytetrafluoroethylene mesh is very flexible and poorly integrates in the abdominal wall. Conclusion. A prosthesis of a different material combined with a different fixation system such as absorbable tacks, biological glue, or mechanical tacks without sharp components, would have obviated mesh migration. .

Sparse Signal Representation in Digital and Biological Systems

Theories of sparse signal representation, wherein a signal is decomposed as the sum of a small number of constituent elements, play increasing roles in both mathematical signal processing and neuroscience. This happens despite the differences between signal models in the two domains. After reviewing preliminary material on sparse signal models, I use work on compressed sensing for the electron tomography of biological structures as a target for exploring the efficacy of sparse signal reconstruction in a challenging application domain. My research in this area addresses a topic of keen interest to the biological microscopy community, and has resulted in the development of tomographic reconstruction software which is competitive with the state of the art in its field. Moving from the linear signal domain into the nonlinear dynamics of neural encoding, I explain the sparse coding hypothesis in neuroscience and its relationship with olfaction in locusts. I implement a numerical ODE model of the activity of neural populations responsible for sparse odor coding in locusts as part of a project involving offset spiking in the Kenyon cells. I also explain the validation procedures we have devised to help assess the model's similarity to the biology. The thesis concludes with the development of a new, simplified model of locust olfactory network activity, which seeks with some success to explain statistical properties of the sparse coding processes carried out in the network.

Biological Inspiration for Artificial Immune Systems

Artificial immune systems (AISs) to date have generally been inspired by naive biological metaphors. This has limited the effectiveness of these systems. In this position paper two ways in which AISs could be made more biologically realistic are discussed. We propose that AISs should draw their inspiration from organisms which possess only innate immune systems, and that AISs should employ systemic models of the immune system to structure their overall design. An outline of plant and invertebrate immune systems is presented, and a number of contemporary systemic models are reviewed. The implications for interdisciplinary research that more biologically-realistic AISs could have is also discussed.

Relating bisimulations with attractors in boolean network models

When studying a biological regulatory network, it is usual to use boolean network models. In these models, boolean variables represent the behavior of each component of the biological system. Taking in account that the size of these state transition models grows exponentially along with the number of components considered, it becomes important to have tools to minimize such models. In this paper, we relate bisimulations, which are relations used in the study of automata (general state transition models) with attractors, which are an important feature of biological boolean models. Hence, we support the idea that bisimulations can be important tools in the study some main features of boolean network models.We also discuss the differences between using this approach and other well-known methodologies to study this kind of systems and we illustrate it with some examples.

TRIB2 in human AML: a biological and clinical investigation

Acute myeloid leukemia (AML) involves the proliferation, abnormal survival and arrest of cells at a very early stage of myeloid cell differentiation. The biological and clinical heterogeneity of this disease complicates treatment and highlights the significance of understanding the underlying causes of AML, which may constitute potential therapeutic targets, as well as offer prognostic information. Tribbles homolog 2 (Trib2) is a potent murine oncogene capable of inducing transplantable AML with complete penetrance. The pathogenicity of Trib2 is attributed to its ability to induce proteasomal degradation of the full length isoform of the transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα p42). The role of TRIB2 in human AML cells, however, has not been systematically investigated or targeted. Across human cancers, TRIB2 oncogenic activity was found to be associated with its elevated expression. In the context of AML, TRIB2 overexpression was suggested to be associated with the large and heterogeneous subset of cytogenetically normal AML patients. Based upon the observation that overexpression of TRIB2 has a role in cellular transformation, the effect of modulating its expression in human AML was examined in a human AML cell line that expresses high levels of TRIB2, U937 cells. Specific suppression of TRIB2 led to impaired cell growth, as a consequence of both an increase in apoptosis and a decrease in cell proliferation. Consistent with these in vitro results, TRIB2 silencing strongly reduced progression of the U937 in vivo xenografts, accompanied by detection of a lower spleen weight when compared with mice transplanted with TRIB2- expressing control cells. Gene expression analysis suggested that TRIB2 modulates apoptosis and cell-cycle sensitivity by influencing the expression of a subset of genes known to have implications on these phenotypes. Furthermore, TRIB2 was found to be expressed in a significant subset of AML patient samples analysed. To investigate whether increased expression of this gene could be afforded prognostic significance, primary AML cells with dichotomized levels of TRIB2 transcripts were evaluated in terms of their xenoengraftment potential, an assay reported to correlate with disease aggressiveness observed in humans. A small cohort of analysed samples with higher TRIB2 expression did not associate with preferential leukaemic cell engraftment in highly immune-deficient mice, hence, not predicting for an adverse prognosis. However, further experiments including a larger cohort of well characterized AML patients would be needed to clarify TRIB2 significance in the diagnostic setting. Collectively, these data support a functional role for TRIB2 in the maintenance of the oncogenic properties of human AML cells and suggest TRIB2 can be considered a rational therapeutic target. Proteasome inhibition has emerged as an attractive target for the development of novel anti-cancer therapies and results from translational research and clinical trials support the idea that proteasome inhibitors should be considered in the treatment of AML. The present study argued that proteasome inhibition would effectively inhibit the function of TRIB2 by abrogating C/EBPα p42 protein degradation and that it would be an effective pharmacological targeting strategy in TRIB2-positive AMLs. Here, a number of cell models expressing high levels of TRIB2 were successfully targeted by treatment with proteasome inhibitors, as demonstrated by multiple measurements that included increased cytotoxicity, inhibition of clonogenic growth and anti-AML activity in vivo. Mechanistically, it was shown that block of the TRIB2 degradative function led to an increase of C/EBPα p42 and that response was specific to the TRIB2-C/EBPα axis. Specificity was addressed by a panel of experiments showing that U937 cells (express detectable levels of endogenous TRIB2 and C/EBPα) treated with the proteasome inhibitor bortezomib (Brtz) displayed a higher cytotoxic response upon TRIB2 overexpression and that ectopic expression of C/EBPα rescued cell death. Additionally, in C/EBPα-negative leukaemia cells, K562 and Kasumi 1, Brtz-induced toxicity was not increased following TRIB2 overexpression supporting the specificity of the compound on the TRIB2-C/EBPα axis. Together these findings provide pre-clinical evidence that TRIB2- expressing AML cells can be pharmacologically targeted with proteasome inhibition due, in part, to blockage of the TRIB2 proteolytic function on C/EBPα p42. A large body of evidence indicates that AML arises through the stepwise acquisition of genetic and epigenetic changes. Mass spectrometry data has identified an interaction between TRIB2 and the epigenetic regulator Protein Arginine Methyltransferase 5 (PRMT5). Following assessment of TRIB2‟s role in AML cell survival and effective targeting of the TRIB2-C/EBPα degradation pathway, a putative TRIB2/PRMT5 cooperation was investigated in order to gain a deeper understanding of the molecular network in which TRIB2 acts as a potent myeloid oncogene. First, a microarray data set was interrogated for PRMT5 expression levels and the primary enzyme responsible for symmetric dimethylation was found to be transcribed at significantly higher levels in AML patients when compared to healthy controls. Next, depletion of PRMT5 in the U937 cell line was shown to reduce the transformative phenotype in the high expressing TRIB2 AML cells, which suggests that PRMT5 and TRIB2 may cooperate to maintain the leukaemogenic potential. Importantly, PRMT5 was identified as a TRIB2-interacting protein by means of a protein tagging approach to purify TRIB2 complexes from 293T cells. These findings trigger further research aimed at understanding the underlying mechanism and the functional significance of this interplay. In summary, the present study provides experimental evidence that TRIB2 has an important oncogenic role in human AML maintenance and, importantly in such a molecularly heterogeneous disease, provides the rational basis to consider proteasome inhibition as an effective targeting strategy for AML patients with high TRIB2 expression. Finally, the identification of PRMT5 as a TRIB2-interacting protein opens a new level of regulation to consider in AML. This work may contribute to our further understanding and therapeutic strategies in acute leukaemias.

Inverse identification of the bending stiffness of a braided polyethylene twine subject to large deformation: application to the identification of the mesh opening rigidity of fishing nets.

The evaluation of the mesh opening stiffness of fishing nets is an important issue in assessing the selectivity of trawls. It appeared that a larger bending rigidity of twines decreases the mesh opening and could reduce the escapement of fish. Nevertheless, netting structure is complex. A netting is made up of braided twines made of polyethylene or polyamide. These twines are tied with non-symmetrical knots. Thus, these assemblies develop contact-friction interactions. Moreover, the netting can be subject to large deformation. In this study, we investigate the responses of netting samples to different types of solicitations. Samples are loaded and unloaded with creep and relaxation stages, with different boundary conditions. Then, two models have been developed: an analytical model and a finite element model. The last one was used to assess, with an inverse identification algorithm, the bending stiffness of twines. In this paper, experimental results and a model for netting structures made up of braided twines are presented. During dry forming of a composite, for example, the matrix is not present or not active, and relative sliding can occur between constitutive fibres. So an accurate modelling of the mechanical behaviour of fibrous material is necessary. This study offers experimental data which could permit to improve current models of contact-friction interactions [4], to validate models for large deformation analysis of fibrous materials [1] on a new experimental case, then to improve the evaluation of the mesh opening stiffness of a fishing net

Mesh Adaption for Tracking Vortex Structures in OVERTURNS Simulation of the S-76 Rotor in Hover

The constant need to improve helicopter performance requires the optimization of existing and future rotor designs. A crucial indicator of rotor capability is hover performance, which depends on the near-body flow as well as the structure and strength of the tip vortices formed at the trailing edge of the blades. Computational Fluid Dynamics (CFD) solvers must balance computational expenses with preservation of the flow, and to limit computational expenses the mesh is often coarsened in the outer regions of the computational domain. This can lead to degradation of the vortex structures which compose the rotor wake. The current work conducts three-dimensional simulations using OVERTURNS, a three-dimensional structured grid solver that models the flow field using the Reynolds-Averaged Navier-Stokes equations. The S-76 rotor in hover was chosen as the test case for evaluating the OVERTURNS solver, focusing on methods to better preserve the rotor wake. Using the hover condition, various computational domains, spatial schemes, and boundary conditions were tested. Furthermore, a mesh adaption routine was implemented, allowing for the increased refinement of the mesh in areas of turbulent flow without the need to add points to the mesh. The adapted mesh was employed to conduct a sweep of collective pitch angles, comparing the resolved wake and integrated forces to existing computational and experimental results. The integrated thrust values saw very close agreement across all tested pitch angles, while the power was slightly over predicted, resulting in under prediction of the Figure of Merit. Meanwhile, the tip vortices have been preserved for multiple blade passages, indicating an improvement in vortex preservation when compared with previous work. Finally, further results from a single collective pitch case were presented to provide a more complete picture of the solver results.

Biological activity of Pyrrole-Imidazole polyamides in vivo

This thesis focuses on biological activity of pyrrole-imidazole polyamides in vivo. The work presented includes experiments underlining sequence selectivity of these compounds in living cells and potential methods to improve it. A large fraction of this thesis is devoted to activity of Py-Im in murine models of cancer. We investigated the pharmacokinetics and biodistribution of two compounds – targeted to 5'-WGGWCW-3' and 5'-WTWCGW-3' sequences – and characterized their activity by measuring their effects on tumor growth, gene expression in vivo and in tissue culture, and their effects on physiology of tumors. The initial theoretical studies suggested that a large fraction of genomic sites are bound by Py-Im polyamides non-specifically and experimental data shows that the programmed binding sequence is not a sole determinant of the patterns of gene regulation. Despite the likely presence of non-specific effects of Py-Im polyamides in living cells, in vivo administration of Py-Im polyamides resulted in tolerable host toxicity and anti-tumor activity. Py-Im polyamide targeted to Estrogen Receptor Response Element showed downregulation of ER-driven gene expression in tumor cells, while the compound targeted to hypoxia response element reduced vascularization of tumors and their growth rate, induced apoptosis of cells in hypoxic areas and reduced expression of proangiogenic and prometastatic factors. Further studies, showed that polyamides distributed to many of the tested tissues and their FITC-conjugates showed nuclear uptake. The gene expression effects were also present in murine tissues, such as liver and kidneys, indicating a potential for use for Py-Im polyamides in non-cancerous diseases.

Conceptos y prácticas de la actividad física que se reproducen en las clases sociales: aproximación desde el enfoque determinantes/ determinación social de la salud

El concepto de actividad física es concebido de diferentes formas. Mostrando que existen varios factores que afectan de manera directa e indirecta la percepción que los sujetos construyen entorno a él, generando así una aproximación a diferentes definiciones de la actividad física desde varias perspectivas y dimensiones, donde predomina una noción netamente biológica. Este estudio pretende analizar, como desde las clases sociales se concibe la actividad física en sus conceptos y prácticas considerando los modelos de determinantes y determinación social para la salud. Con fin de comprender como los autores de la literatura científica conciben la actividad física y la relación con las clases sociales, desde una perspectiva teórica de los determinantes sociales de la salud y la teoría de la determinación social, se realizó una revisión documental y análisis de contenido de los conceptos y prácticas de la actividad física que se han considerado en los últimos 10 años. Para ello se seleccionaron las bases de datos PubMed y BVS (Biblioteca Virtual de Salud) por sus énfasis en publicaciones de salud mundialmente. Mostrando que la actividad física es concebida dominantemente desde una perspectiva biológica que ejerce una mirada reduccionista. Las relaciones entre actividad física y las clases sociales están claramente establecidas, sin embargo, estas relaciones pueden discrepar teniendo en cuenta el concepto de clase social, el contexto y la orientación de los autores y las poblaciones objetos de estudio. Obteniendo como resultado que los estudios documentados, revisados y analizados muestran una clara tendencia al modelo de determinantes; no obstante, algunos estudios en sus análisis se orientan hacia el modelo de determinación social. En cuanto al concepto de clases sociales los autores consideran una combinación de factores culturales y económicos sin atreverse a adoptar un concepto específico.

How to enhance Geobotany in the frame of the renewed Biological Sciences?

In recent decades the importance of structuring sciences such as botany or phytosociology faced a declining attention from the scientific community. This was accompanied by a growing interest in theoretical ecology. For such scenario greatly contributed an hypothetical exhaustion of research topics in these areas, but especially the introduction of new technologies that have provided powerful tools for data analysis. This allowed, for example, to make predictions about the impacts of climate change on species and plant communities and the consequent recognition of theoretical ecology, as one of the most prestigious pieces of current biological sciences. However, theoretical ecology has been facing serious knoledge gaps that greatly compromise their results, putting again the spotligth on structuring sciences. For example there are enourmous gaps in knowledge and data on dispersal, species and communities chorology and abundace, as well as in biological interactions. These data is essential, since they will determine ecological behavior of species. Its omission always limits the understanding and proper execution of the models generated by theoretical ecology. In this conference we will present a review on the gaps in knowledge and data in flora and vegetation fields in order to identify situations where geobotanical knowledge can make their major contribution. Furthermore, we will emphasize the need to reformulate objectives in geobotanical sciences in order to give it the deserved scientific recognition, considering the relationship between different scientific knowledges.