The Edinburgh human metabolic network reconstruction and its functional analysis

A better understanding of human metabolism and its relationship with diseases is an important task in human systems biology studies. In this paper, we present a high-quality human metabolic network manually reconstructed by integrating genome annotation information from different databases and metabolic reaction information from literature. The network contains nearly 3000 metabolic reactions, which were reorganized into about 70 human-specific metabolic pathways according to their functional relationships. By analysis of the functional connectivity of the metabolites in the network, the bow-tie structure, which was found previously by structure analysis, is reconfirmed. Furthermore, the distribution of the disease related genes in the network suggests that the IN (substrates) subset of the bow-tie structure has more flexibility than other parts

Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway

*Background*
It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. 

*Results*
We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different regions within the 3’ end of the last exon. We demonstrate that in murine brown adipose tissue two downstream 3’ probe sets experience circadian baseline oscillation in counter-phase to the upstream probe set. Such differences in expression patterns are a telltale sign of alternative splicing within the last exon of SOCS3. In contrast, all three probe sets oscillated in a common phase in murine liver and white adipose tissue. This suggests that the regulation of SOCS3 expression in brown fat is tissue specific. Another component of the signaling pathway, Janus kinase (JAK), is directly regulated by SOCS and has alternative transcript probe sets oscillating in counter-phase in a white adipose tissue specific manner.
 
*Conclusion*
We hypothesize that differential oscillation of alternative transcripts may provide a mechanism to maintain steady levels of expression in spite of circadian baseline variation

Network Landscape from a Brownian Particle's Perspective

Given a complex biological or social network, how many clusters should it be decomposed into? We define the distance $d_{i,j}$ from node $i$ to node $j$ as the average number of steps a Brownian particle takes to reach $j$ from $i$. Node $j$ is a global attractor of $i$ if $d_{i,j}\leq d_{i,k}$ for any $k$ of the graph; it is a local attractor of $i$, if $j\in E_i$ (the set of nearest-neighbors of $i$) and $d_{i,j}\leq d_{i,l}$ for any $l\in E_i$. Based on the intuition that each node should have a high probability to be in the same community as its global (local) attractor on the global (local) scale, we present a simple method to uncover a network's community structure. This method is applied to several real networks and some discussion on its possible extensions is made.Comment: 5 pages, 4 color-figures. REVTeX 4 format. To appear in PR

Natural killer cells: origin, phenotype, function

Natural killer cells (NK) are innate immune lymphocytes produced in the bone marrow. Isolation of NK cells as a separate population of lymphocytes is related to discovery of their ability to induce the death of tumor cells without prior sensitization. In this review, an attempt was made to systematize the numerous data on the biology of NK cells presented in the literature. The authors consider the stages of NK cells` differentiation from a common lymphoid progenitor (CLP) in the bone marrow, describe two functionally different populations of mature NK cells – CD56brightCDl6- and CD56dimCD16+. In addition, the role of cytokines and chemokines in the development of NK cells is discussed. The review includes data on the spectrum of molecules expressed by NK cells: adhesion molecules (LFA-1, LFA-2, LFA-3; αMβ2, αXβ2, L-selectin, VLA-4, VLA-5; PECAM-1; CEACAM-1), cytokine receptors (IL-1R, IL-2ra, IL-2Rb/IL-2Rc, IL-6Rα, IL-7Ra, IL-8R, IL-10R, IL-12Rβ1, IL-15ra, IL-18R, IL-21ra, IFNGR2, TGFBR, c-Kit, CXCR1, CXCR3, CXCR4, CCR4, CCR5, CCR6, CCR7, IChemR23, CX3CR1), as well as receptors that regulate the activity of NK cells (LILRB1, LILRB2, LILRB4; KIR2DL1-5; KIR2DS1-5; KIR3DL1-3; KIR3DS1; NKG2A, NKG2C, NKG2D; Siglec7, Siglec9; CD16; NKRP-1; TIGIT; TACTILE; NKp30, NKp44, NKp46, NKp80; LAIR-1; PD-1; TIM-3; 2B4; TLR1-9). The authors also examine the mechanisms of implementing cytotoxic activity by NK cells, including cytotoxicity, via expression of MHC-I-specific receptors, CD16 Fc receptors, receptors and ligands of apoptosis (Fas-FasL and TRAIL-TRAILR) as well as other receptors. The review describes in detail the structure of immunological synapse between the NK cell and target cell, receptor interactions, and the role of the cytoskeleton in its formation. The data are summarized on the variants of exocytosis of lytic granules by NK cells, including complete or partial fusion of vesicles with the plasma membrane, exocytosis of vesicles containing perforin and FasL, and the formation of microvesicles containing granzyme B. The review also describes data on ability of NK cells to maintain activated state for a long time, as well as to maintain contact with several targets at the same time. In addition to the functions inherent in natural killers as cells of innate immunity, the authors point out their ability to exhibit the features of cells of adaptive immunity. In general, a variety of mechanisms that regulate the activity of NK cells may complement the specific functions of lymphocytes, thus making the immune system more efficient

THE ROLE OF INTERACTIONS BETWEEN TROPHOBLASTDERIVED EXTRACELLULAR MICROVESICLES, IMMUNE CELLS AND ENDOTHELIUM IN PATHOGENESIS OF PRE-ECLAMPSIA

Pre-eclampsia is a multisystemic disease that occurs in the second half of pregnancy, being characterized by the development of hypertension and proteinuria. Pre-eclampsia is still one of the main causes of maternal and neonatal morbidity and mortality. Pre-eclampsia is believed to be a result of complex interactions between maternal and placental factors. However, the exact pathophysiology of this syndrome remains unclear. Intercellular interactions are the basis of fetoplacental development in physiological pregnancy. A special mechanism of intercellular interactions is associated with the release of membranebound extracellular microvesicles by cells. Concentration and molecular composition of extracellular vesicles in biological fluids depend on the producer cell types, as well as the stimuli that trigger their formation. The studies of extracellular vesicles in pre-eclampsia focus on the particles produced by the cells of maternal cardiovascular system (endothelium, smooth muscle cells of blood vessels), and blood (erythrocytes, leukocytes, and platelets), like as by the cells of syncytiotrophoblast. Changed concentrations and molecular composition of these extracellular vesicles can contribute to the pathophysiology of pre-eclampsia, due to increased proinflammatory and procoagulant state occurring during pregnancy. This review focuses, firstly, on characteristics of the extracellular vesicles produced by syncytiotrophoblast, and possible role of their interaction with maternal immune cells, endothelial cells and platelets in the course of developing pre-eclampsia. Understanding the role of extracellular vesicles of syncytiotrophoblast in pathogenesis of pre-eclampsia could suggest an opportunity of providing these results for early and non-invasive diagnostics of placental disorders, as well as for predicting development of this disease

Микровезикулы лейкоцитарного происхождения

Microvesicles are a new field of biological research. They are subcellular structures ranging in size from 100 to 1000 nm and found in practically all human biological fluids. Their sources are different cells. Microvesicles have a diverse internal composition and carry a wide spectrum of molecules on their surface, which determines their participation in physiological and pathological processes. Their assumed role of biological markers of diseases has aroused great interest. At the present time, there is a lot of data in the world literature about microvesicles of platelets and endothelial cells, and there is practically no data about microvesicles of leukocytes. In this regard, the purpose of the given review was to summarize the data about microvesicles of leukocytes. The review presents data about source cells, internal and superficial composition of leukocytes’ microvesicles, their interaction with various cells, and involvement in physiological and pathological processes. Further study of microvesicles will make it possible to clarify their role in normal and pathological conditions, the possibility of using them as vectors of diseases and carriers of various biologically active molecules.Микровезикулы ― новый объект биологических исследований. Они представляют собой субклеточные структуры размером от 100 до 1000 нм и обнаружены практически во всех биологических жидкостях человека. Их источниками являются различные клетки организма. Микровезикулы обладают разнообразным внутренним составом и несут широкий спектр молекул на своей поверхности, что определяет их участие в физиологических и патологических процессах. Предполагается их роль в качестве биологических маркеров заболеваний, чем и обусловлен интерес к ним. В настоящее время в мировой литературе достаточно много данных o микровезикулах тромбоцитов и эндотелиальных клеток, при этом данных o микровезикулах лейкоцитов практически нет. В связи c этим целью настоящего обзора было суммирование данных o микровезикулах лейкоцитов. В обзоре представлены данные o клетках-источниках, внутреннем и поверхностном составе микровезикул лейкоцитов, их взаимодействии с различными клетками организма, вовлеченности в физиологические и патологические процессы. Дальнейшее изучение микровезикул позволит уточнить их роль в норме и при патологиях, возможность использования в качестве маркеров заболеваний и переносчиков различных биологически активных молекул

Center or Limit Cycle: Renormalization Group as a Probe

Based on our studies done on two-dimensional autonomous systems, forced non-autonomous systems and time-delayed systems, we propose a unified methodology - that uses renormalization group theory - for finding out existence of periodic solutions in a plethora of nonlinear dynamical systems appearing across disciplines. The technique will be shown to have a non-trivial ability of classifying the solutions into limit cycles and periodic orbits surrounding a center. Moreover, the methodology has a definite advantage over linear stability analysis in analyzing centers

Platelet-leukocyte interactions: immunoregulatory role and pathophysiological relevance

Blood platelets are the central players in thrombosis and blood coagulation. Moreover, they also exhibit immunoregulatory properties and bridge hemostasis and immunity. Morphological and functional characteristics of the platelets ensure continuous surveillance for the vascular system, recognition of different hazards, development of appropriate response and recruitment of immune cells. Indirect platelet-leukocyte interactions are mediated by immunoregulatory molecules that are released, along with coagulation and thrombosis factors in the course of platelet activation and degranulation. Chemokines, cytokines, growth factors, some of which are synthesized de novo, are released from activated platelets and modulate cellular functions, thus modulating both innate and adaptive immune response. Activated platelets enter contacts with immune cells to form heterotypic aggregates, i.e., platelet-leukocyte complexes that reside in blood circulation along with other blood cells. The aggregate formation and stabilization is mediated by interaction between the molecules expressed on the surface of platelets and leukocytes, in particular, P-selectin (CD62P) and PSGL-1 (CD162). Platelet-monocyte and platelet-neutrophil complexes are most abundant, with platelet-monocyte aggregates being most stable. Moreover, the platelet-derived microvesicles also interact with leukocytes to form heterotypic aggregates, thus, probably, modulating the immune cell functions via transfer of non-coding RNA molecules. Formation of platelet-leukocyte complexes results into mutual activation of platelets and leukocytes. Platelets and platelet-derived microvesicles stimulate phagocytic activity, cytokine secretion, and generation of reactive oxygen species in monocytes and neutrophils, inducing formation of neutrophilic extracellular traps and procoagulant phenotype in monocytes. The blood platelets regulate monocyte differentiation, promote adhesion, as well as transmigration of lymphocytes and NK cells. At the sites of inflammation, platelets enhance extravasation and infiltration of leukocytes into the damaged tissue. Impaired interactions of platelets with endothelial layer and immune cells may underlie pathogenic conditions. Increased level of circulating plateletleukocyte complexes is observed in various disorders including cardiovascular diseases, acute ischemic stroke, respiratory disorders, renal pathologies, liver diseases, diabetes, reproductive disorders, bacterial and viral infections. Further studies of platelet-leukocyte interactions are warranted to unveil pathogenic mechanisms and to develop new therapeutic approaches

Parameter estimation in spatially extended systems: The Karhunen-Loeve and Galerkin multiple shooting approach

Parameter estimation for spatiotemporal dynamics for coupled map lattices and continuous time domain systems is shown using a combination of multiple shooting, Karhunen-Loeve decomposition and Galerkin's projection methodologies. The resulting advantages in estimating parameters have been studied and discussed for chaotic and turbulent dynamics using small amounts of data from subsystems, availability of only scalar and noisy time series data, effects of space-time parameter variations, and in the presence of multiple time-scales.Comment: 11 pages, 5 figures, 4 Tables Corresponding Author - V. Ravi Kumar, e-mail address: [email protected]