Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network

The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these `transcriptional regulatory networks' (TRNs) in bacteria have an inherently hierarchical architecture, although the design principles and the specific advantages offered by this type of organization have not yet been fully elucidated. In this study, we focussed on the hierarchical structure of the TRN of the gram-positive bacterium Bacillus subtilis and performed a comparative analysis with the TRN of the gram-negative bacterium Escherichia coli. Using a graph-theoretic approach, we organized the transcription factors (TFs) and sigma-factors in the TRNs of B. subtilis and E. coli into three hierarchical levels (Top, Middle and Bottom) and studied several structural and functional properties across them. In addition to many similarities, we found also specific differences, explaining the majority of them with variations in the distribution of s-factors across the hierarchical levels in the two organisms. We then investigated the control of target metabolic genes by transcriptional regulators to characterize the differential regulation of three distinct metabolic subsystems (catabolism, anabolism and central energy metabolism). These results suggest that the hierarchical architecture that we observed in B. subtilis represents an effective organization of its TRN to achieve flexibility in response to a wide range of diverse stimuli.

Pattern-Formation During Self-organization in Three-Phase Eutectic Solidification

Eutectic growth is an interesting example for exploring the topic of pattern-formation in multi-phase systems, where the growth of the phases is coupled with the diffusive transport of one or more components in the melt. While in the case of binary alloys, the number of possibilities are limited (lamellae, rods, labyrinth etc.), their number rapidly increases with the number of components and phases. In this paper, we will investigate pattern formation during three-phase eutectic solidification using a state-of-the art phase-field method based on the grand-canonical density formulation. The major aim of the study is to highlight the role of two properties, which are the volume fraction of the solid phases and the solid-liquid interfacial energies, in the self-organization of the solid phases during directional growth. Thereafter, we will show representative phase-field simulations of a micro-structure in a real alloy (Ag-Al-Cu) using an asymmetric phase diagram as well as interfacial properties.

An investigation of the organization of canoe fisheries in Nigeria: A case study of Ilaje/Esedo local government area of Ondo State

The effects of some socio-economic variables on the performance of artisanal fishermen were investigated. The variables include the age-structure of the fishermen, level of investment, educational background, membership of co-operative societies and marketing arrangements. All these variables were found to be crucial to productivity in the artisanal fishing sector

Organization and function of the phage Lambda chromosome

The process of prophage integration by phage λ and the function and structure of the chromosomal elements required for λ integration have been studied with the use of λ deletion mutants. Since att^φ, the substrate of the integration enzymes, is not essential for λ growth, and since att^φ resides in a portion of the λ chromosome which is not necessary for vegetative growth, viable λ deletion mutants were isolated and examined to dissect the structure of att^φ.

Deletion mutants were selected from wild type populations by treating the phage under conditions where phage are inactivated at a rate dependent on the DNA content of the particles. A number of deletion mutants were obtained in this way, and many of these mutants proved to have defects in integration. These defects were defined by analyzing the properties of Int-promoted recombination in these att mutants.

The types of mutants found and their properties indicated that att^φ has three components: a cross-over point which is bordered on either side by recognition elements whose sequence is specifically required for normal integration. The interactions of the recognition elements in Int-promoted recombination between att mutants was examined and proved to be quite complex. In general, however, it appears that the λ integration system can function with a diverse array of mutant att sites.

The structure of att^φ was examined by comparing the genetic properties of various att mutants with their location in the λ chromosome. To map these mutants, the techniques of heteroduplex DNA formation and electron microscopy were employed. It was found that integration cross-overs occur at only one point in att^φ and that the recognition sequences that direct the integration enzymes to their site of action are quite small, less than 2000 nucleotides each. Furthermore, no base pair homology was detected between att^φ and its bacterial analog, att^B. This result clearly demonstrates that λ integration can occur between chromosomes which have little, if any, homology. In this respect, λ integration is unique as a system of recombination since most forms of generalized recombination require extensive base pair homology.

An additional study on the genetic and physical distances in the left arm of the λ genome was described. Here, a large number of conditional lethal nonsense mutants were isolated and mapped, and a genetic map of the entire left arm, comprising a total of 18 genes, was constructed. Four of these genes were discovered in this study. A series of λdg transducing phages was mapped by heteroduplex electron microscopy and the relationship between physical and genetic distances in the left arm was determined. The results indicate that recombination frequency in the left arm is an accurate reflection of physical distances, and moreover, there do not appear to be any undiscovered genes in this segment of the genome.

A novel brain partition highlights the modular skeleton shared by structure and function

Elucidating the intricate relationship between brain structure and function, both in healthy and pathological conditions, is a key challenge for modern neuroscience. Recent progress in neuroimaging has helped advance our understanding of this important issue, with diffusion images providing information about structural connectivity (SC) and functional magnetic resonance imaging shedding light on resting state functional connectivity (rsFC). Here, we adopt a systems approach, relying on modular hierarchical clustering, to study together SC and rsFC datasets gathered independently from healthy human subjects. Our novel approach allows us to find a common skeleton shared by structure and function from which a new, optimal, brain partition can be extracted. We describe the emerging common structure-function modules (SFMs) in detail and compare them with commonly employed anatomical or functional parcellations. Our results underline the strong correspondence between brain structure and resting-state dynamics as well as the emerging coherent organization of the human brain.

East African Freshwater Fisheries Research Organization Annual Report 1972

Feeding habits of many animals have been used widely in animal classifications. This is so, because the type of diet an organism requires demands structural specialisation which will utilise the available resource. Many animals may however have many structural modifications to enable them to be described as omnivourous or generalised feeders such as H. empodisma and H. riponianus (GREENWOOD 1960) which may show varying degrees of structural and adaptational intermediacy between two trophic groups. Generally, however, the diet of many animals including fish changes as the animal grow larger. The change in structural modifications is usually correlated with changes in the diet. In fishes the change may involve change from tricuspid to biscuspid and finally to unicuspid type of teeth. The degree of modification in the structure depends on the diet, thus Haplochromis that feeds on soft tissues of snails only requires modifications in oral dentition while Haplochromis that feeds on both soft tissues and shells of snails require modification in the lower pharyngeal bone for grinding purposes. Other modifications connected with food utilisation may be located in the alimentary canal. (I) The fish species that are commercially exploited are Protopterus aethiopicus, Clarias mossambicus, Tilapia esculenta, Tilapia amphimelas and Tilapia hybrids. The other fish species present in the lake but not commercially exploited are: Gnathonemus sp. Alestes sp. Labeo sp., Barbus paludinoses, Barbus jacksoni, Barbus lineomaculatus, Barbus regersi, Leptogrlanis sp., Schilbe sp., Haplochromis spp. and Hemihaplochromis sp. (2) Protopterus sp. and Clarias sp. are mostly caught with hooks on long lines. There has been a steady increase in number of hooks on the lake. Since the stocks of Protopterus and C/arias in the lake have a limit, we should control the number of hooks used by each of the fishermen in order to avoid overharvesting. (3) All the previous studies on Lake Kitangiri fisheries suggested the use of gill nets with mesh size greater than 88.9 mm in order to avoid the capture of immature Ti/apia spp. But if the fishermen are to obtain economic gains from the fishery, the optimum mesh size for use is 88.9 -101.6 mm. (4) The gillnet is a passive gear with very beneficial selective characteristics. Unfortunately the drive-in fishery which exists on Lake Kitangiri more or less destroys the gillnet selectivity characteristics. It is therefore recommended that the beating of water with poles be discouraged and stopped. (5) There is need for provision of stable fishing canoes to replace the unstable bottle palm dug-out canoes which are currently being used and which are very risky to operate. (6) The fish processing facilities on Lake Kitangiri are still inadequate. Most of the fish is sun dried, Since sun drying is very difficult during the rainy season, most fishermen carry out intensive fishing during the dry season, Concentrating most of the fishing effort in anyone season instead of spreading evenly this effort over the whole year could damage the age structure of the exploitable stocks. (7) There are considerable fluctuations in the volume of water of the lake. The feasibility of regulating the water loss through the effluent Sibiti river should be investigated by the Water Development Department. (8) Damming the Sibiti river is an expensive undertaking and therefore, the Rural Development Bank of Tanzania should be asked to assess the economic feasibility of such a project.

Self-similar organization of arrays of individual carbon nanotubes and carbon nanotube micropillars

It is well-known that carbon nanotube (CNT) growth from a dense arrangement of catalyst nanoparticles creates a vertically aligned CNT forest. CNT forests offer attractive anisotropic mechanical, thermal, and electrical properties, and their anisotropic structure is enabled by the self-organization of a large number of CNTs. This process is governed by individual CNT diameter, spacing, and the CNT-to-CNT interaction. However, little information is known about the self-organization of CNTs within a forest. Insight into the self-organization is, however, essential for tailoring the properties of the CNT forests for applications such as electrical interconnects, thermal interfaces, dry adhesives and energy storage. We demonstrate that arrays of CNT micropillars having micron-scale diameters organize in a similar manner as individual CNTs within a forest. For example, as previously demonstrated for individual CNTs within a forest, entanglement of small-diameter CNT micropillars during the initial stage of growth creates a film of entwined pillars. This layer enables coordinated subsequent growth of the pillars in the vertical direction, in a case where isolated pillars would not grow in a self-supporting fashion. Finally, we provide a detailed overview of the self-organization as a function of the diameter, length and spacing of the CNT pillars. This study, which is applicable to many one-dimensional nanostructured films, demonstrates guidelines for tailoring the self-organization which can enable control of the collective mechanical, electrical and interfacial properties of the films. © 2009 Elsevier B.V. All rights reserved.

Gene structure and transcription of IRF-1 and IRF-7 in the mandarin fish Siniperca chuatsi

The genes of IRF-1 and IRF-7 have been cloned from the mandarin fish (Siniperca chuatsi). The IRF-1 gene has 4919 nucleotides (nt) and contains 10exons and 9introns, with an open reading frame (ORF) of 903 ntencoding301 aa. The IRF-7 gene has 6057 nt and also contains 10exons and 9introns, with an ORF of 1308 nt encoding 436 aa. The IRF-1 and IRF-7 genes have only one copy each in the genome. The transcription of IRF-1 and IRF-7 in different organs was analyzed by real-time PCR, and both molecules were constitutively expressed. The IRF-I and IRF-7 mRNAs were abundant in gill, spleen, kidney and pronephros. The temporal transcriptional changes for IRF-1, IRF-7 and Mx were investigated within 48 h after poly I: C stimulation in liver, gill, spleen and pronephros. An increased transcription was detected for IRF-1 and IRF-7 12 h post-stimulation, being earlier than the transcription of Mx protein; however, IRF-1 and IRF-7 transcription decreased while the Mx protein was stable at 48 h post-stimulation. (c) 2007 Published by Elsevier B.V.

Gene structure and transcription of IRF-2 in the mandarin fish Siniperca chuatsi with the finding of alternative transcripts and microsatellite in the coding region

The gene of interferon regulatory factor-2 (IRF-2) has been cloned from the mandarin fish (Siniperca chuatsi). The IRF-2 gene has 6,418 nucleotides (nt) and contains eight exons and seven introns, encoding two mRNAs. The two IRF-2 mRNAs each contained an open reading frame of 873 nt, which both translate into the same 291 amino acids but differed in their 5' untranslated region: one mRNA was transcribed initially from the exon 1 bypassing exon 2, while the other was transcribed from the exon 2. The microsatellites (CA repeats) could be found in the carboxyl terminal region of mandarin fish IRF-2, which result in the truncated form molecules. The microsatellites' polymorphism was investigated, and eight alleles were found in 16 individuals. The microsatellites were also examined in IRF-2 of several freshwater perciform fishes. The transcription of the IRF-2 in different tissues with or without poly inosine-cytidine stimulation was analyzed by real-time PCR, and the constitutive transcription of both molecules could be detected in all the tissues examined.

Gene structure of goose-type lysozyme in the mandarin fish Siniperca chuatsi with analysis on the lytic activity of its recombinant in Escherichia coli

A goose-type lysozyme (g-lysozyme) gene has been cloned from the mandarin fish (Siniperca chuatsi), with its recombinant protein expressed in Escherichia coli. From the first transcription initiation site, the mandarin fish g-lysozyme gene extends 1307 nucleotides to the end of the 3' untranslated region, and it contains 5 exons and 4 introns. The open reading frame of the glysozyme transcript has 582 nucleotides which encode a 194 amino acid peptide. The 5' flanking region of mandarin fish glysozyme gene shows several common transcriptional factor binding sites when compared with that from Japanese flounder (Paralichthys olivaceus). The recombinant mandarin fish g-lysozyme was expressed in E. coli by using pET-32a vector, and the purified recombinant g-lysozyme shows lytic activity against Micrococcus lysodeikticus. (c) 2005 Elsevier B.V All rights reserved.

Guided self-organization in a dynamic embodied system based on attractor selection mechanism

Guided self-organization can be regarded as a paradigm proposed to understand how to guide a self-organizing system towards desirable behaviors, while maintaining its non-deterministic dynamics with emergent features. It is, however, not a trivial problem to guide the self-organizing behavior of physically embodied systems like robots, as the behavioral dynamics are results of interactions among their controller, mechanical dynamics of the body, and the environment. This paper presents a guided self-organization approach for dynamic robots based on a coupling between the system mechanical dynamics with an internal control structure known as the attractor selection mechanism. The mechanism enables the robot to gracefully shift between random and deterministic behaviors, represented by a number of attractors, depending on internally generated stochastic perturbation and sensory input. The robot used in this paper is a simulated curved beam hopping robot: a system with a variety of mechanical dynamics which depends on its actuation frequencies. Despite the simplicity of the approach, it will be shown how the approach regulates the probability of the robot to reach a goal through the interplay among the sensory input, the level of inherent stochastic perturbation, i.e., noise, and the mechanical dynamics. © 2014 by the authors; licensee MDPI, Basel, Switzerland.

X-ray evidence for Ge/Si(001) island columns in multilayer structure

A Ge/Si(0 0 1) multilayer structure is investigated by cross-sectional transmission electron microscopy, atomic force microscopy and double crystal X-lay diffraction. We find that the multilayer-structure-related satellite peaks in the rocking curve exhibit a similar nonuniform broadening and rye fit the zero-order peak with two Lorentz lineshapes. The ratio of the integrated intensity of two peaks is approximately equal with the anal ratio of the top Ge layer deposited between the areas that are and are not occupied by islands. It proves the existence of vertical-aligned island columns from the viewpoint of macroscopic dimension. (C) 2001 Elsevier Science B.V. All rights reserved.

Optical characterization of the Ge/Si (001) islands in multilayer structure

We show that the observed temperature dependence of the photoluminescence (PL) features can be consistently explained in terms of thermally activated carrier transfer processes in a multilayer structure of the self-organized Ge/Si(001) islands. The type II (electron confinement in Si) behavior of the Ge/Si islands is verified. With elevated temperature, the thermally activated electrons and holes enter the Ge islands from the Si and from the wetting layer (WL), respectively. An involvement of the type I (spatially direct) into type II (spatially indirect) recombination transition takes place at a high temperature.

Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B

This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.

Square lamellar structure having phase-separated microdomain in H-shaped block copolymer thin film

The morphology of a H-shaped block copolymer (poly(ethylene glycol) backbone and polystyrene branches (PS)(2)PEG(PS)(2)) in a thin film has been investigated. A peculiar square lamella that has a phase-separated microdomain at its surface is obtained after spin coating. The experimental temperature plays a critical role in the lamellar formation. The copolymer first self-assembles into square lamellar micelles with an incomplete crystalline core due to the crystallizability of PEG.