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Search Results: 1 - 10 of 5732 matches for " Igor Kondrychyn "
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The role of vasculature and blood circulation in zebrafish swimbladder development
Cecilia Winata, Svetlana Korzh, Igor Kondrychyn, Vladimir Korzh, Zhiyuan Gong
BMC Developmental Biology , 2010, DOI: 10.1186/1471-213x-10-3
Abstract: To investigate the role of endothelial cells (ECs) and blood circulation during development of the swimbladder, phenotypes of swimbladder were analysed at three different stages (~2, 3 and 5 dpf [day postfertilization]) in cloche (clo) mutant and Tnnt2 morphants, in the background of transgenic lines Et(krt4:EGFP)sq33-2 and Et(krt4:EGFP)sqet3 which express EGFP in the swimbladder epithelium and outer mesothelium respectively. Analyses of the three tissue layers of the swimbladder were performed using molecular markers hb9, fgf10a, acta2, and anxa5 to distinguish epithelium, mesenchyme, and outer mesothelium. We showed that the budding stage was independent of ECs and blood flow, while early epithelial growth, mesenchymal organization and its differentiation into smooth muscle, as well as outer mesothelial organization, were dependent on ECs. Blood circulation contributed to later stage of epithelial growth, smooth muscle differentiation, and organization of the outer mesothelium. Inflation of the swimbladder was also affected as a result of absence of ECs and blood flow.Our data demonstrated that the vascular system, though not essential in swimbladder budding, plays an important role in the development of the swimbladder starting from the early growth stage, including mesenchyme organization and smooth muscle differentiation, and outer mesothelial organization, which in turn may be essential for the function of the swimbladder as reflected in its eventual inflation.A functional vasculature is important for the survival of vertebrates, as well as for proper embryonic development [1-6]. However, it is difficult to study this structure in most vertebrate models in vivo due to the opacity of the embryo as well as the in utero development in mammals. In this respect, the zebrafish model has two major advantages. First, due to the external development of its transparent embryos, it is convenient to observe internal structures and perform analysis of vascular development
Stretching Morphogenesis of the Roof Plate and Formation of the Central Canal
Igor Kondrychyn, Cathleen Teh, Melvin Sin, Vladimir Korzh
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056219
Abstract: Background Neurulation is driven by apical constriction of actomyosin cytoskeleton resulting in conversion of the primitive lumen into the central canal in a mechanism driven by F-actin constriction, cell overcrowding and buildup of axonal tracts. The roof plate of the neural tube acts as the dorsal morphogenetic center and boundary preventing midline crossing by neural cells and axons. Methodology/Principal Findings The roof plate zebrafish transgenics expressing cytosolic GFP were used to study and describe development of this structure in vivo for a first time ever. The conversion of the primitive lumen into the central canal causes significant morphogenetic changes of neuroepithelial cells in the dorsal neural tube. We demonstrated that the roof plate cells stretch along the D–V axis in parallel with conversion of the primitive lumen into central canal and its ventral displacement. Importantly, the stretching of the roof plate is well-coordinated along the whole spinal cord and the roof plate cells extend 3× in length to cover 2/3 of the neural tube diameter. This process involves the visco-elastic extension of the roof place cytoskeleton and depends on activity of Zic6 and the Rho-associated kinase (Rock). In contrast, stretching of the floor plate is much less extensive. Conclusions/Significance The extension of the roof plate requires its attachment to the apical complex of proteins at the surface of the central canal, which depends on activity of Zic6 and Rock. The D–V extension of the roof plate may change a range and distribution of morphogens it produces. The resistance of the roof plate cytoskeleton attenuates ventral displacement of the central canal in illustration of the novel mechanical role of the roof plate during development of the body axis.
In vivo Analysis of Choroid Plexus Morphogenesis in Zebrafish
Marta García-Lecea, Igor Kondrychyn, Steven H. Fong, Zhang-Rui Ye, Vladimir Korzh
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003090
Abstract: Background The choroid plexus (ChP), a component of the blood-brain barrier (BBB), produces the cerebrospinal fluid (CSF) and as a result plays a role in (i) protecting and nurturing the brain as well as (ii) in coordinating neuronal migration during neurodevelopment. Until now ChP development was not analyzed in living vertebrates due to technical problems. Methodology/Principal Findings We have analyzed the formation of the fourth ventricle ChP of zebrafish in the GFP-tagged enhancer trap transgenic line SqET33-E20 (Gateways) by a combination of in vivo imaging, histology and mutant analysis. This process includes the formation of the tela choroidea (TC), the recruitment of cells from rhombic lips and, finally, the coalescence of TC resulting in formation of ChP. In Notch-deficient mib mutants the first phase of this process is affected with premature GFP expression, deficient cell recruitment into TC and abnormal patterning of ChP. In Hedgehog-deficient smu mutants the second phase of the ChP morphogenesis lacks cell recruitment and TC cells undergo apoptosis. Conclusions/Significance This study is the first to demonstrate the formation of ChP in vivo revealing a role of Notch and Hedgehog signalling pathways during different developmental phases of this process.
Genome-wide analysis of Tol2 transposon reintegration in zebrafish
Igor Kondrychyn, Marta Garcia-Lecea, Alexander Emelyanov, Sergey Parinov, Vladimir Korzh
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-418
Abstract: We performed a large-scale enhancer trap (ET) screen and generated 338 insertions of the Tol2 transposon-based ET cassette into the zebrafish genome. These insertions were generated by remobilizing the transposon from two different donor sites in two transgenic lines. We found that 39% of Tol2 insertions occurred in transcription units, mostly into introns. Analysis of the transposon target sites revealed no strict specificity at the DNA sequence level. However, Tol2 was prone to target AT-rich regions with weak palindromic consensus sequences centered at the insertion site.Our systematic analysis of sequential remobilizations of the Tol2 transposon from two independent sites within a vertebrate genome has revealed properties such as a tendency to integrate into transcription units and into AT-rich palindrome-like sequences. This information will influence the development of various applications involving DNA transposons and Tol2 in particular.The transposable element Tol2 from medaka fish is the first functional transposon identified in vertebrates [1]. It belongs to the hAT family (named for hobo, Ac and Tam3) and integrates into host DNA through a "cut-and-paste" mechanism [2]. Recently, a non-autonomous Tol2-based system has been developed as a tool for genome analysis of vertebrates and for highly efficient transgenesis [3-11]. It has been used for both gene trap and enhancer trap (ET) screens [12-14] as well as insertional mutagenesis [15,16]. Some of these applications have recently been reviewed [17,18].One of the features of non-autonomous transposon-based systems, including Tol2, is that a transposon integrated into a genome can be remobilized if transposase mRNA is available. Previous applications of the transposon system have been based on random integration after co-injection of a plasmid DNA harboring Tol2 and transposase mRNA. Such random integration is attractive for a wide variety of applications ranging from gene discovery to gene therapy. However,
Collective Cell Migration Drives Morphogenesis of the Kidney Nephron
Aleksandr Vasilyev,Yan Liu,Sudha Mudumana,Steve Mangos,Pui-Ying Lam,Arindam Majumdar,Jinhua Zhao,Kar-Lai Poon,Igor Kondrychyn,Vladimir Korzh,Iain A. Drummond
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000009
Abstract: Tissue organization in epithelial organs is achieved during development by the combined processes of cell differentiation and morphogenetic cell movements. In the kidney, the nephron is the functional organ unit. Each nephron is an epithelial tubule that is subdivided into discrete segments with specific transport functions. Little is known about how nephron segments are defined or how segments acquire their distinctive morphology and cell shape. Using live, in vivo cell imaging of the forming zebrafish pronephric nephron, we found that the migration of fully differentiated epithelial cells accounts for both the final position of nephron segment boundaries and the characteristic convolution of the proximal tubule. Pronephric cells maintain adherens junctions and polarized apical brush border membranes while they migrate collectively. Individual tubule cells exhibit basal membrane protrusions in the direction of movement and appear to establish transient, phosphorylated Focal Adhesion Kinase–positive adhesions to the basement membrane. Cell migration continued in the presence of camptothecin, indicating that cell division does not drive migration. Lengthening of the nephron was, however, accompanied by an increase in tubule cell number, specifically in the most distal, ret1-positive nephron segment. The initiation of cell migration coincided with the onset of fluid flow in the pronephros. Complete blockade of pronephric fluid flow prevented cell migration and proximal nephron convolution. Selective blockade of proximal, filtration-driven fluid flow shifted the position of tubule convolution distally and revealed a role for cilia-driven fluid flow in persistent migration of distal nephron cells. We conclude that nephron morphogenesis is driven by fluid flow–dependent, collective epithelial cell migration within the confines of the tubule basement membrane. Our results establish intimate links between nephron function, fluid flow, and morphogenesis.
Genome Wide Analysis Reveals Zic3 Interaction with Distal Regulatory Elements of Stage Specific Developmental Genes in Zebrafish
Cecilia L. Winata equal contributor,Igor Kondrychyn equal contributor,Vibhor Kumar,Kandhadayar G. Srinivasan,Yuriy Orlov,Ashwini Ravishankar,Shyam Prabhakar,Lawrence W. Stanton,Vladimir Korzh ,Sinnakaruppan Mathavan
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003852
Abstract: Zic3 regulates early embryonic patterning in vertebrates. Loss of Zic3 function is known to disrupt gastrulation, left-right patterning, and neurogenesis. However, molecular events downstream of this transcription factor are poorly characterized. Here we use the zebrafish as a model to study the developmental role of Zic3 in vivo, by applying a combination of two powerful genomics approaches – ChIP-seq and microarray. Besides confirming direct regulation of previously implicated Zic3 targets of the Nodal and canonical Wnt pathways, analysis of gastrula stage embryos uncovered a number of novel candidate target genes, among which were members of the non-canonical Wnt pathway and the neural pre-pattern genes. A similar analysis in zic3-expressing cells obtained by FACS at segmentation stage revealed a dramatic shift in Zic3 binding site locations and identified an entirely distinct set of target genes associated with later developmental functions such as neural development. We demonstrate cis-regulation of several of these target genes by Zic3 using in vivo enhancer assay. Analysis of Zic3 binding sites revealed a distribution biased towards distal intergenic regions, indicative of a long distance regulatory mechanism; some of these binding sites are highly conserved during evolution and act as functional enhancers. This demonstrated that Zic3 regulation of developmental genes is achieved predominantly through long distance regulatory mechanism and revealed that developmental transitions could be accompanied by dramatic changes in regulatory landscape.
Collective Cell Migration Drives Morphogenesis of the Kidney Nephron
Aleksandr Vasilyev,Yan Liu,Sudha Mudumana,Steve Mangos,Pui-Ying Lam,Arindam Majumdar,Jinhua Zhao,Kar-Lai Poon,Igor Kondrychyn,Vladimir Korzh,Iain A Drummond
PLOS Biology , 2009, DOI: 10.1371/journal.pbio.1000009
Abstract: Tissue organization in epithelial organs is achieved during development by the combined processes of cell differentiation and morphogenetic cell movements. In the kidney, the nephron is the functional organ unit. Each nephron is an epithelial tubule that is subdivided into discrete segments with specific transport functions. Little is known about how nephron segments are defined or how segments acquire their distinctive morphology and cell shape. Using live, in vivo cell imaging of the forming zebrafish pronephric nephron, we found that the migration of fully differentiated epithelial cells accounts for both the final position of nephron segment boundaries and the characteristic convolution of the proximal tubule. Pronephric cells maintain adherens junctions and polarized apical brush border membranes while they migrate collectively. Individual tubule cells exhibit basal membrane protrusions in the direction of movement and appear to establish transient, phosphorylated Focal Adhesion Kinase–positive adhesions to the basement membrane. Cell migration continued in the presence of camptothecin, indicating that cell division does not drive migration. Lengthening of the nephron was, however, accompanied by an increase in tubule cell number, specifically in the most distal, ret1-positive nephron segment. The initiation of cell migration coincided with the onset of fluid flow in the pronephros. Complete blockade of pronephric fluid flow prevented cell migration and proximal nephron convolution. Selective blockade of proximal, filtration-driven fluid flow shifted the position of tubule convolution distally and revealed a role for cilia-driven fluid flow in persistent migration of distal nephron cells. We conclude that nephron morphogenesis is driven by fluid flow–dependent, collective epithelial cell migration within the confines of the tubule basement membrane. Our results establish intimate links between nephron function, fluid flow, and morphogenesis.
On the Chain Length and Rate of Ozone Depletion in the Main Stratospheric Cycles  [PDF]
Igor Larin
Atmospheric and Climate Sciences (ACS) , 2013, DOI: 10.4236/acs.2013.31016
Abstract: Algorithm for calculation of the chain length and rate of stratospheric ozone depletion in Ox, HOx, NOx, ClOx and BrOx cycles has been developed. The most important new element in the theory of stratospheric chain processes is the correct determination the propagation rate, taking into account all reactions involved rather than a single reaction, which has the lowest rate, as it was usually done before. The role of null chain processes in the cycles has been considered and shown that these processes play a decisive role in formation of families of the odd oxygen, nitrogen, chlorine and bromine in the daytime while at night they play no role. Using two-dimensional model Socrates, and algorithm developed correct rate of ozone depletion and chain length in the cycles above for model conditions of June 2020 at 50N have been calculated.

On the Relationship between Statistical and Phenomenological Models of the Thermodynamic Systems  [PDF]
Igor Samkhan
Journal of Modern Physics (JMP) , 2013, DOI: 10.4236/jmp.2013.47A2006
Abstract:

The paper deals with the performing of a critical analysis of the problems arising in matching the classical models of the statistical and phenomenological thermodynamics. The performed analysis shows that some concepts of the statistical and phenomenological methods of describing the classical systems do not quite correlate with each other. Particularly, in these methods various caloric ideal gas equations of state are employed, while the possibility existing in the thermodynamic cyclic processes to obtain the same distributions both due to a change of the particle concentration and owing to a change of temperature is not allowed for in the statistical methods. The above-mentioned difference of the equations of state is cleared away when using in the statistical functions corresponding to the canonical Gibbs equations instead of the Planck’s constant a new scale factor that depends on the parameters of a system and coincides with the Planck’s constant in going of the system to the degenerate state. Under such an approach, the statistical entropy is transformed into one of the forms of heat capacity. In its turn, the agreement of the methods under consideration in the question as to the dependence of the molecular distributions on the concentration of particles, apparently, will call for further refinement of the physical model of ideal gas and the techniques for its statistical description.

How Concerned, Afraid and Hopeful Are We? Effects of Egoism and Altruism on Climate Change Related Issues  [PDF]
Igor Knez
Psychology (PSYCH) , 2013, DOI: 10.4236/psych.2013.410106
Abstract:

The idea that concerns for and emotional reactions to climate change may be due to environment-related egoism and altruism was tested. Participants assessed as “high” on egoism were shown to be more concerned for myself-related issues and afraid of the climate change impact on their local environment, indicating a self-benefit goal motive. Participants assessed as “high” on altruism were those more concerned for issues related to others and nature and more afraid and less hopeful for the whole world, indicating a pro-social goal motive in this group of individuals. This indicates that environment-related value orientations of egoism and altruism may prompt concerns and convey feelings differently about the climate change issue. Accordingly, when encouraging sustainable development, policy and pro-environmental actions, we have to bear in mind people’s world views grounded in environment-related selfishness vs. unselfishness; indicating different goal-directed motives in climate change decision making.

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