GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF SALVAGE PATHWAYS: REGULATION OF ADENINE PHOSPHORIBOSYLTRANSFERASE ACTIVITY BY STRUCTURALLY SIMILAR SUBSTRATES

SUMMARY Motivation: Development of an in silico cell, a computer resource for modeling and analysis of physiological processes is an urgent task of systems biology and computational biology. Mathematical modeling of the genetic regulation of cell metabolism pathways, in particular, salvage pathways, is an important problem to be solved as part of this line of work. Results: By using the GeneNet technology, we reproduced the gene network of the regulation of salvage pathways in the E. coli cell. Mathematical models were constructed by the method of generalized Hill functions to describe the efficiency of enzyme systems and regulation of expression of genes coding for these enzymes. Availability: The diagram of the gene network is available through the GeneNet viewer at http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/viewer/index.shtml. Models are available on request

Modelling of molecular genetic systems in bacterial cell 45 AROMATIC AMINO ACID BIOSYNTHESIS IN ESCHERICHIA COLI: GENERALIZED HILL FUNCTION MODEL OF THE TRYPTOPHAN- SENSITIVE 3-DEOXY-D-ARABINO- HEPTULOSONATE-7-PHOSPHATE SYNTHASE REACTION DEMONSTRATE COMPL

SUMMARY Motivation: Development of an in silico cell as a computer resource for simulation and analysis of processes within living cells is an urgent task of systems biology and computational biology. Results: By using the GeneNet technology, we reproduced the gene network of the regulation of aromatic amino acid biosynthesis in the E. coli cell. Mathematical models were constructed by the method of generalized Hill functions. The models describe the efficiency of enzymatic systems and regulation of expression of related genes. Mathematical model of the enzyme tryptophan-sensitive 3-deoxy-d-arabinoheptulosonate-7-phosphate synthase reaction demonstrate complicated mechanism. Availability: Models are available on request. The diagram of the gene network regulating aromatic amino acid biosynthesis in E. coli is available through the GeneNet viewer a

GeneNet in 2005

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using ORACLE9i; (ii) the capacities to describe the structure of the protein complexes and the interactions between the units are increased; (iii) two tables with kinetic constants and more detailed descriptions of certain reactions were added; and (iv) a module for kinetic modeling was supplemented. The current SRS release of the GeneNet database contains 37 graphical maps of gene networks, as well as descriptions of 1766 proteins, 1006 genes, 241 small molecules and 3254 relationships between gene network units, and 552 kinetic constants. Information distributed between 16 interlinked tables was obtained by annotating 1980 journal publications. SRS release of the GeneNet database, the graphical viewer and the modeling section are available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/

Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues

When living systems detect changes in their external environment their response must be measured to balance the need to react appropriately with the need to remain stable, ignoring insignificant signals. Because this is a fundamental challenge of all biological systems that execute programs in response to stimuli, we developed a generalized time-frequency analysis (TFA) framework to systematically explore the dynamical properties of biomolecular networks. Using TFA, we focused on two well-characterized yeast gene regulatory networks responsive to carbon-source shifts and a mammalian innate immune regulatory network responsive to lipopolysaccharides (LPS). The networks are comprised of two different basic architectures. Dual positive and negative feedback loops make up the yeast galactose network; whereas overlapping positive and negative feed-forward loops are common to the yeast fatty-acid response network and the LPS-induced network of macrophages. TFA revealed remarkably distinct network behaviors in terms of trade-offs in responsiveness and noise suppression that are appropriately tuned to each biological response. The wild type galactose network was found to be highly responsive while the oleate network has greater noise suppression ability. The LPS network appeared more balanced, exhibiting less bias toward noise suppression or responsiveness. Exploration of the network parameter space exposed dramatic differences in system behaviors for each network. These studies highlight fundamental structural and dynamical principles that underlie each network, reveal constrained parameters of positive and negative feedback and feed-forward strengths that tune the networks appropriately for their respective biological roles, and demonstrate the general utility of the TFA approach for systems and synthetic biology

A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma.

BACKGROUND: Mechanistic models, when combined with pertinent data, can improve our knowledge regarding important molecular and cellular mechanisms found in cancer. These models make the prediction of tissue-level response to drug treatment possible, which can lead to new therapies and improved patient outcomes. Here we present a data-driven multiscale modeling framework to study molecular interactions between cancer, stromal, and immune cells found in the tumor microenvironment. We also develop methods to use molecular data available in The Cancer Genome Atlas to generate sample-specific models of cancer. RESULTS: By combining published models of different cells relevant to pancreatic ductal adenocarcinoma (PDAC), we built an agent-based model of the multicellular pancreatic tumor microenvironment, formally describing cell type-specific molecular interactions and cytokine-mediated cell-cell communications. We used an ensemble-based modeling approach to systematically explore how variations in the tumor microenvironment affect the viability of cancer cells. The results suggest that the autocrine loop involving EGF signaling is a key interaction modulator between pancreatic cancer and stellate cells. EGF is also found to be associated with previously described subtypes of PDAC. Moreover, the model allows a systematic exploration of the effect of possible therapeutic perturbations; our simulations suggest that reducing bFGF secretion by stellate cells will have, on average, a positive impact on cancer apoptosis. CONCLUSIONS: The developed framework allows model-driven hypotheses to be generated regarding therapeutically relevant PDAC states with potential molecular and cellular drivers indicating specific intervention strategies

Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression

The nuclear lamina is a filamentous structure subtending the nuclear envelope and required for chromatin organization, transcriptional regulation and maintaining nuclear structure. The trypanosomatid coiled-coil NUP-1 protein is a lamina component functionally analogous to lamins, the major lamina proteins of metazoa. There is little evidence for shared ancestry, suggesting the presence of a distinct lamina system in trypanosomes. To find additional trypanosomatid lamina components we identified NUP-1 interacting proteins by affinity capture and mass-spectrometry. Multiple components of the nuclear pore complex (NPC) and a second coiled-coil protein, which we termed NUP-2, were found. NUP-2 has a punctate distribution at the nuclear periphery throughout the cell cycle and is in close proximity to NUP-1, the NPCs and telomeric chromosomal regions. RNAi-mediated silencing of NUP-2 leads to severe proliferation defects, gross alterations to nuclear structure, chromosomal organization and nuclear envelope architecture. Further, transcription is altered at telomere-proximal variant surface glycoprotein (VSG) expression sites (ESs), suggesting a role in controlling ES expression, although NUP-2 silencing does not increase VSG switching. Transcriptome analysis suggests specific alterations to Pol I-dependent transcription. NUP-1 is mislocalized in NUP-2 knockdown cells and vice versa, implying that NUP-1 and NUP-2 form a co-dependent network and identifying NUP-2 as a second trypanosomatid nuclear lamina component

СОВРЕМЕННЫЕ КРИТЕРИИ ОТБОРА ПАЦИЕНТОВ ДЛЯ РЕКОНСТРУКЦИИ ВИСЦЕРАЛЬНЫМИ АУТОТРАНСПЛАНТАТАМИ ВЕРХНИХ ОТДЕЛОВ АЭРОДИГЕСТИВНОГО ТРАКТА ПРИ ЛЕЧЕНИИ ЗЛОКАЧЕСТВЕННЫХ ОПУХОЛЕЙ ГОЛОВЫ И ШЕИ

Introduction. The high incidence of cancer of the upper aerodigestive tract, impairment of breathing, speech, and swallowing functions accompanied by prolonged and often persistent disability put the rehabilitation and the quality of life of patients among the most important social problems.Material and methods. We have gained experience in reconstructing the pharynx and esophagus with various fragments of the gastrointestinal tract in 121 cancer patients. Based on our own clinical experience, the most important criteria of selecting patients after laryngectomy for reconstruction of the upper aerodigestive tract with visceral flaps were identified. Visceral autografts formed from different parts of the patient’s gastrointestinal tract were full-layer fragments of the abdominal organs, which included the mucous membrane of the stomach, small intestine, or large intestine. In some patients, the choice of flap was limited by a large omentum.Results. In 9.9 % of cases, flap necrosis was observed. Oral nutrition was restored in 93.9 % of patients. In 90.5 % of cases, speech function was restored after the installation of avoice prosthesis. The method of autologous transplantation of the ileo-colonic flap made it possible not only to remove the organs affected by the tumor, but also to simultaneously restore the lost nutrition and vocal functions without resorting to artificial prostheses, but using only their own tissues. The 5-year survival rates were 36.4 % and 67.3 % in patients with simultaneous reconstruction and in patients with delayed reconstruction, respectively.Conclusion. The use of visceral flaps in the reconstruction of the upper aerodigestive tract allows patients to restore both the nutrition and voice functions after laryngectomy.Введение. Значительная распространенность опухолей верхних отделов аэродигестивного тракта, сложность и стойкость нарушения функций дыхания, речи, глотания, сопровождающиеся длительной и нередко стойкой утратой трудоспособности, ставят проблему реабилитации и качества жизни больных в ряд важнейших социальных задач.Материал и методы. нами накоплен опыт реконструкции глотки и пищевода различными фрагментами желудочно-кишечного тракта у 121 пациента со злокачественными опухолями. на основе собственного клинического опыта нами были сформированы основные критерии отбора пациентов после ларингэктомии для реконструкции верхних отделов аэродигестивного тракта висцеральными аутотрансплантатами. Это были полнослойные фрагменты органов брюшной полости, которые включали в себя слизистую оболочку желудка, тонкой или толстой кишки. У ряда больных выбор аутотрансплантата ограничивался большим сальником.Результаты. В 9,9 % наблюдений был отмечен некроз аутотрансплантата. Питание через рот было восстановлено у 93,9 % оперированных больных. В 90,5 % случаев после установки голосового протеза была восстановлена речевая функция. Способ аутотрансплантации подвздошно-толстокишечного лоскута позволил в один хирургический этап выполнить не только удаление пораженных опухолью органов, но и одномоментно восстановить утраченные пищепроводную и голосовую функции, не прибегая к помощи искусственных протезов, а используя только собственные ткани. Показатели 5-летней выживаемости в группе больных при одномоментной реконструкции составили 36,4 %, в группе с отсроченной реконструкцией – 67,3 %.Заключение. использование висцеральных аутотрансплантатов при реконструкции верхних отделов аэродигестивного тракта после ларингэктомии позволяет восстановить пациентам как пищепроводную, так и голосовую функции

Реконструкция гортаноглотки с использованием аутологичных тканеинженерных эпителизированных лоскутов

After removal of metastatic malignant tumors of the hypopharynx and larynx, hypopharyngeal defects are formed. To restore the hypopharynx, a mucosa and a muscular component are needed.The objective of this study is to develop a hypopharyngeal reconstruction technique using prelaminated pectoralis major flap with mucosal epithelium analogue from autologous epithelial layers.Materials and methods. Nine patients underwent reconstruction of the hypopharynx using bioengineered prelaminated pectoralis major flaps. The mucosa was restored by tissue-engineered autologous epithelial cell layers that were obtained by culturing in vitro cells isolated from skin biopsies that were previously obtained from patients.Results. Oral nutrition was restored in all cases. Pharyngeal stenosis was detected in one (11%) patient. A stratified squamous epithelium on the pectoral fascia was revealed in 67% of cases at week 2 after prelamination, in 89% of cases at week 4 after reconstruction and in 100% of cases at month 3, 6, 12 and 24 after reconstruction.Conclusion. Reconstruction using prelaminated bioengineered flaps allows recreating the anatomical integrity and function of the hypopharynx.После удаления распространенных злокачественных опухолей гортаноглотки и гортани образуются дефекты верхних пищеварительных путей, для устранения которых необходимы слизистая оболочка и мышечный компонент.Целью данного исследования является разработка методики реконструкции гортаноглотки с использованием преламинированных пекторальных лоскутов с аналогом эпителия слизистой оболочки из аутологичных эпителиальных пластов.Материалы и методы. Девяти пациентам выполнена реконструкция гортаноглотки биоинженерными преламинированными пекторальными лоскутами с восстановлением слизистой оболочки тканеинженерными аутологичными эпителиальными клеточными пластами, которые были получены путем культивирования in vitro клеток, выделенных из предварительно полученных у пациентов биоптатов кожи.Результаты. Во всех случаях было восстановлено пероральное питание. У одного (11%) пациента был выявлен стеноз глотки. Многослойный плоский эпителий на фасции пекторального лоскута выявлен в 67% случаев через 2 недели после преламинации, в 89% случаев – через 4 недели после реконструкции и в 100% случаев – через 3, 6, 12, 24 месяца после реконструкции.Заключение. Реконструкция с использованием преламинированных биоинженерных лоскутов позволяет воссоздать анатомическую целостность и функцию гортаноглотки

Genome-Wide Analysis of Effectors of Peroxisome Biogenesis

Peroxisomes are intracellular organelles that house a number of diverse metabolic processes, notably those required for β-oxidation of fatty acids. Peroxisomes biogenesis can be induced by the presence of peroxisome proliferators, including fatty acids, which activate complex cellular programs that underlie the induction process. Here, we used multi-parameter quantitative phenotype analyses of an arrayed mutant collection of yeast cells induced to proliferate peroxisomes, to establish a comprehensive inventory of genes required for peroxisome induction and function. The assays employed include growth in the presence of fatty acids, and confocal imaging and flow cytometry through the induction process. In addition to the classical phenotypes associated with loss of peroxisomal functions, these studies identified 169 genes required for robust signaling, transcription, normal peroxisomal development and morphologies, and transmission of peroxisomes to daughter cells. These gene products are localized throughout the cell, and many have indirect connections to peroxisome function. By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function