Evidence for rolling circle replication of tandem genes in Drosophila

Extrachromosomal circular DNA (eccDNA) is one characteristic of the plasticity of the eukaryotic genome. It is found in various organisms and contains sequences derived primarily from repetitive chromosomal DNA. Using 2D gel electrophoresis, we have previously detected eccDNA composed of chromosomal tandem repeats throughout the life cycle of Drosophila. Here, we report for the first time evidence suggesting the occurrence of rolling circle replication of eccDNA in Drosophila. We show, on 2D gels, specific structures that can be enriched by benzoylated naphthoylated DEAE-cellulose chromatography and were identified in other systems as rolling circle intermediates (RCIs). These RCIs are homologous to histone genes, Stellate and Suppressor of Stellate, which are all organized in the chromosomes as tandem repeats. RCIs are detected throughout the life cycle of Drosophila and in cultured fly cells. These structures are found regardless of the expression of the replicated gene or of its chromosomal copy number.     

Application of expert networks for predicting proteins secondary structure

The present study utilizes expert neural networks for the prediction of proteins secondary structure. We use three independent networks, one for each structure (alpha, beta and coil) as the first-level processing unit; decision upon the chosen structure for each residue is carried out by a second-level, post-processing unit, which utilizes the Chou and Fasman frequency values Falpha and Fbeta in order to strengthen and/or deplete the probability of the specific structure under investigation. The highest prediction case was 76%. Our method requires primitive computational means and a relatively small training set, while still been comparable to previous work. It is not meant to be an alternative to the determination of secondary structure by means of free energy minimization, integration of dynamic equations of motion or crystallography, which are expensive, time-consuming and complicated, but to provide additional constrains, which might be considered and incorporated into larger computing setups in order to reduce the initial search space for the above methods.     

Numerical simulation of a fully baffled biological reactor: the differential circumferential averaging mixing plane approach

A modified mixing plane approach for steady state simulation of flow field in fully baffled biological reactor is presented and discussed. Without requiring any experimental input, this approach of dividing the vessel into suitable number of connected and disconnected zones; solving steady state equation separately in each zone and then transferring information between them, provides a computationally less intensive alternative for simulating the flow in the whole vessel. Impeller used is the standard Rushton Turbine positioned at mid-height of the reactor and simulations are carried out using standard k-epsilon turbulence model implemented in CFD code FLUENT. Meshing is done using tetrahedral elements such that mesh size gradually increases from the center to the periphery. Most of the previous simulation works present only a few aspects of the flow field with scant importance to the energy balance in the tank and near tip turbulence. In this work, complete model prediction for velocity field and turbulence parameters (near tip and in the bulk region) are validated by comparison with experimental data. As compared to previous simulation works, the results predicted by this "Differential circumferential averaging mixing plane approach" show a better qualitative and quantitative agreement with the published experimental data. A distribution of energy dissipation in various zones of vessel is presented. Also a qualitative picture of flow field and stagnant zones inside the reactor is presented and discussed. Comparison of flow characteristics for different number of baffles shows that for the present dimension of the vessel, five baffles gives maximum enhanced mixing.     

Innexin genes and gap junction proteins in the locust frontal ganglion

Gap junctions (GJs) belong to one of the most conserved cellular structures in multicellular organisms. They probably serve similar functions in all Metazoa, providing one of the most common forms of intercellular communication. GJs are widely distributed in embryonic cells and tissues and have been attributed an important role in development, modulating cell growth and differentiation. These channels have been also implicated in mediating electrical synaptic signaling; Coupling through GJs is now accepted as a major pathway that supports network behavior and contributes to physiological rhythms. Here we focus on the physiology and molecular biology of GJs in a recently established model for the study of rhythm-generating networks and their role in behavior: the frontal ganglion (FG) of the desert locust, Schistocerca gregaria. Four novel genes of the invertebrate GJs (innexin) gene family were found to be expressed in the FG: Sg-inx1, Sg-inx2, Sg-inx3 and Sg-inx4. Immunohistochemistry revealed that some of the neurons in the FG express at least one innexin protein, INX1. We also established the presence of functional gap junction proteins in the FG and demonstrated functional electrical coupling between the neurons in the FG. This study forms the basis for further investigation of the role of GJs in network development and behavior.     

The Regulative Role of Neurite Mechanical Tension in Network Development

A bewildering series of dynamical processes take part in the development of the nervous system. Neuron branching dynamics, the continuous formation and elimination of neural interconnections, are instrumental in constructing distinct neuronal networks, which are the functional building blocks of the nervous system. In this study, we investigate and validate the important regulative role of mechanical tension in determining the final morphology of neuronal networks. To single out the mechanical effect, we cultured relatively large invertebrate neurons on clean quartz surfaces. Applied to these surfaces were isolated anchoring sites consisting of carbon nanotube islands to which the cells and the neurites could mechanically attach. Inspection of branching dynamics and network wiring upon development revealed an innate selection mechanism in which one axon branch wins over another. The apparent mechanism entails the build-up of mechanical tension in developing axons. The tension is maintained by the attachment of the growth cone to the substrate or, alternatively, to the neurites of a target neuron. The induced tension promotes the stabilization of one set of axon branches while causing retraction or elimination of axon collaterals. We suggest that these findings represent a crucial, early step that precedes the formation of synapses and regulates neuronal interconnections. Mechanical tension serves as a signal for survival of the axonal branch and perhaps for the subsequent formation of synapses.     

Beclin 1 self‐association is independent of autophagy induction by amino acid deprivation and rapamycin treatment

Autophagy, a process of self‐digestion of cellular constituents, regulates the balance between protein synthesis and protein degradation. Beclin 1 represents an important component of the autophagic machinery. It interacts with proteins that positively regulate autophagy, such as Vps34, UVRAG, and Ambra1, as well as with anti‐apoptotic proteins such as Bcl‐2 via its BH3‐like domain to negatively regulate autophagy. Thus, Beclin 1 interactions with several proteins may regulate autophagy. To identify novel Beclin 1 interacting proteins, we utilized a GST‐Beclin 1 fusion protein. Using mass spectroscopic analysis, we identified Beclin 1 as a protein that interacts with GST‐Beclin 1. Further examination by cross linking and co‐immunoprecipitation experiments confirmed that Beclin 1 self‐interacts and that the coiled coil and the N‐terminal region of Beclin 1 contribute to its oligomerization. Importantly, overexpression of vps34, UVRAG, or Bcl‐x_L, had no effect on Beclin 1 self‐interaction. Moreover, this self‐interaction was independent of autophagy induction by amino acid deprivation or rapamycin treatment. These results suggest that full‐length Beclin 1 is a stable oligomer under various conditions. Such an oligomer may provide a platform for further protein–protein interactions. J. Cell. Biochem. 110: 1262–1271, 2010. Published 2010 Wiley‐Liss, Inc.     

A semianalytical model to study the effect of cortical tension on cell rolling

Cell rolling on the vascular endothelium plays an important role in trafficking of leukocytes, stem cells, and cancer cells. We describe a semianalytical model of cell rolling that focuses on the microvillus as the unit of cell-substrate interaction and integrates microvillus mechanics, receptor clustering, force-dependent receptor-ligand kinetics, and cortical tension that enables incorporation of cell body deformation. Using parameters obtained from independent experiments, the model showed excellent agreement with experimental studies of neutrophil rolling on P-selectin and predicted different regimes of cell rolling, including spreading of the cells on the substrate under high shear. The cortical tension affected the cell-surface contact area and influenced the rolling velocity, and modulated the dependence of rolling velocity on microvillus stiffness. Moreover, at the same shear stress, microvilli of cells with higher cortical tension carried a greater load compared to those with lower cortical tension. We also used the model to obtain a scaling dependence of the contact radius and cell rolling velocity under different conditions of shear stress, cortical tension, and ligand density. This model advances theoretical understanding of cell rolling by incorporating cortical tension and microvillus extension into a versatile, semianalytical framework.     

Extensive apoptotic death of rat colonic cells deprived of crypt habitat

Apoptosis in cells of different lineages is restrained by survival signals which depend upon cell-to-cell communication. The aim of this study was to determine whether colonic cells deprived of crypt ambient are doomed to die prior to their normal chronological demise. Apoptosis was studied in rat whole colonic tissue, in isolated intact crypts, and in colonic cell populations collected from the crypt axis at different stages of proliferation and differentiation. In a number of experiments, cell harvest was performed in the presence of either a tetrapeptide (YVAD-CMK) inhibitor of interleukin-1β-converting enzyme (ICE), or tyrphostin A25, a protein tyrosine kinase inhibitor, or sodium-orthovanadate, a phosphatase inhibitor. DNA fragmentation was assessed by electrophoretic and nonisotopic-labeling procedures. The ultrastructure of colonic tissue specimens and isolated cells was examined by transmission electron microscopy. Apoptosis in whole colonic tissue and in isolated crypts was confined predominantly to cells resident in the upper crypt regions. In contrast, extensive apoptotic death was observed in isolated colonic cells, irrespective of their developmental stage and positional hierarchy within the crypt continuum at harvest time. An apoptotic gradient, however, was evident. Exposure to YVAD-CMK resulted in a marked decrease in the number of apoptotic cells. Treatment with tyrphostin A25 caused a sharp rise in the apoptotic index; conversely, vanadate significantly impeded apoptosis. Cumulatively, these results indicate that disordered intercellular communication provokes unscheduled ICE-mediated apoptosis of colonocytes, and that local signals along the crypt continuum control both the reprieve from death and the timely demise of distinct colonic cell populations. Attenuation of tyrosine phosphorylation may be a contributory event in the acquisition of the apoptotic phenotype. J. Cell. Physiol. 177:377–386, 1998. © 1998 Wiley-Liss, Inc.     

ARTS, the unusual septin: structural and functional aspects

The human Septin 4 gene (Sept4) encodes two major protein isoforms; Sept4_i1 (H5/PNUTL2) and Sept4_i2/ARTS. Septins have been traditionally studied for their role in cytokinesis and their filament-forming abilities, but subsequently have been implicated in diverse functions, including membrane dynamics, cytoskeletal reorganization, vesicle trafficking, and tumorigenesis. ARTS is localized at mitochondria and promotes programmed cell death (apoptosis). These features distinguish ARTS from any other known human septin family member. This review compares the structural and functional properties of ARTS with other septins. In addition, it describes how a combination of two distinct promoters, differential splicing, and intron retention leads to the generation of two different Sept4 variants with diverse biological activity.