Segments Of Different Lengths Research Articles

Promoter Analysis of a Powdery Mildew Induced Vitis vinifera NAC Transcription Factor Gene

Grapevine is an economically important crop throughout the world. However commonly cultivated species Vitis vinifera is susceptible to powdery mildew fungi. The objective of this study was to analyze the promoter of VvNAC36 transcription factor gene, which was induced by powdery mildew infection, as it was shown by previous microarray results. Analysis of VvNAC36 transcription factor promoter allows identifying the important cis-elements, which are responsible for gene regulation during infection. Knowing that the responsible cis-element of the gene is crucial for further study, the role of this gene is in powdery mildew infected grapevine. The study was performed using circumspect methodology. To confirm the presence of transgene in transgenic plants the PCR and glufosinate total herbicide application was used. The transplanted transgenic seedlings were infected with Golovinomyces orontii. To detect the GUS reporter gene expression, histochemical GUS staining and spectrophotometric assays were applied in each deletion variant. Finally the promoter sequence was analyzed by the PLACE (a database for PLAntCisacting Elements) program for identifying cis-elements. The results of the study showed significant difference in mock treated and induced expression in transgenic plants transformed with VvNAC36 promoter segments of different lengths, fused to GUS reporter gene. In basal expression level, the deletion variants 1178 bp and 257 bp differed significantly. Powdery mildew infection significantly increased the expression in all promoter variants, except the two shortest fragments. Based on the promoter motif analysis, it can be concluded, that the GT1-box (GAAAAA) supposed to have crucial role in regulating of VvNAC36 transcription factor gene during powdery mildew infection.

Structural studies of influenza virus RNPs by electron microscopy indicate molecular contortions within NP supra-structures

Ribonucleoprotein (RNP) complexes of influenza viruses are composed of multiple copies of the viral nucleoprotein (NP) that can form filamentous supra-structures. RNPs package distinct viral genomic RNA segments of different lengths into pleomorphic influenza virions. RNPs also function in viral RNA transcription and replication. Different RNP segments have varying lengths, but all must be incorporated into virions during assembly and then released during viral entry for productive infection cycles. RNP structures serve varied functions in the viral replication cycle, therefore understanding their molecular organization and flexibility is essential to understanding these functions. Here, we show using electron tomography and image analyses that isolated RNP filaments are not rigid helical structures, but instead display variations in lengths, curvatures, and even tolerated kinks and local unwinding. Additionally, we observed NP rings within RNP preparations, which were commonly composed of 5, 6, or 7 NP molecules and were of similar widths to filaments, suggesting plasticity in NP-NP interactions mediate RNP structural polymorphism. To demonstrate that NP alone could generate rings of variable oligomeric state, we performed 2D single particle image analysis on recombinant NP and found that rings of 4 and 5 protomers dominated, but rings of all compositions up to 7 were directly observed with variable frequency. This structural flexibility may be needed as RNPs carry out the interactions and conformational changes required for RNP assembly and genome packaging as well as virus uncoating.

Non-canonical ribosomal DNA segments in the human genome, and nucleoli functioning

Ribosomal DNA (rDNA) in the human genome is represented by tandem repeats of 43kb nucleotide sequences that form nucleoli organizers (NORs) on each of five pairs of acrocentric chromosomes. RDNA-similar segments of different lengths are also present on (NOR)− chromosomes. Many of these segments contain nucleotide substitutions, supplementary microsatellite clusters, and extended deletions. Recently, it was shown that, in addition to ribosome biogenesis, nucleoli exhibit additional functions, such as cell-cycle regulation and response to stresses. In particular, several stress-inducible loci located in the ribosomal intergenic spacer (rIGS) produce stimuli-specific noncoding nucleolus RNAs. By mapping the 5′/3′ ends of the rIGS segments scattered throughout (NOR)− chromosomes, we discovered that the bonds in the rIGS that were most often susceptible to disruption in the rIGS were adjacent to, or overlapped with stimuli-specific inducible loci. This suggests the interconnection of the two phenomena — nucleoli functioning and the scattering of rDNA-like sequences on (NOR)− chromosomes.

GENLIB: an R package for the analysis of genealogical data.

BackgroundFounder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for researchers in evolutionary and population genetics, demography and genetic epidemiology. However, analyzing large genealogical datasets requires specialized methods and software. The GENLIB software was developed to study the large genealogies of the French Canadian population of Quebec, Canada. These genealogies are accessible through the BALSAC database, which contains over 3 million records covering the whole province of Quebec over four centuries. Using this resource, extended pedigrees of up to 17 generations can be constructed from a sample of present-day individuals.ResultsWe have extended and implemented GENLIB as a package in the R environment for statistical computing and graphics, thus allowing optimal flexibility for users. The GENLIB package includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations.The goal of this paper is to present the full functionalities of GENLIB. We used a sample of 140 individuals from the province of Quebec (Canada) to demonstrate GENLIB’s functions. Ascending genealogies for these individuals were reconstructed using BALSAC, yielding a large pedigree of 41,523 individuals. Using GENLIB’s functions, we provide a detailed description of these genealogical data in terms of completeness, genetic contribution of founders, relatedness, inbreeding and the overall complexity of the genealogical tree. We also present gene-dropping simulations based on the whole genealogy to investigate identical-by-descent sharing of alleles and chromosomal segments of different lengths and estimate probabilities of identical-by-descent sharing.ConclusionsThe R package GENLIB provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0581-5) contains supplementary material, which is available to authorized users.

Performance Evaluation of DS-CDMA System Using Chaotic Binary Sequences

In this paper generation of binary sequences derived from chaotic sequences defined over Z 4 is proposed. The six chaotic map equations considered in this paper are Logistic map, Tent Map, Cubic Map, Quadratic Map and Bernoulli Map. Using these chaotic map equations, sequences over Z 4 are generated which are converted to binary sequences using polynomial mapping. Segments of sequences of different lengths are tested for cross correlation and linear complexity properties. It is found that some segments of different length of these sequences have good cross correlation and linear complexity properties. The Bit Error Rate performance in DS-CDMA communication systems using these binary sequences is found to be better than Gold sequences and Kasami sequences.

Implementing stationary-phase optimized selectivity in supercritical fluid chromatography.

The performance of stationary-phase optimized selectivity liquid chromatography (SOS-LC) for improved separation of complex mixtures has been demonstrated before. A dedicated kit containing column segments of different lengths and packed with different stationary phases is commercially available together with algorithms capable of predicting and ranking isocratic and gradient separations over vast amounts of possible column combinations. Implementation in chromatographic separations involving compressible fluids, as is the case in supercritical fluid chromatography, had thus far not been attempted. The challenge of this approach is the dependency of solute retention with the mobile-phase density, complicating linear extrapolation of retention over longer or shorter columns segments, as is the case in conventional SOS-LC. In this study, the possibilities of performing stationary-phase optimized selectivity supercritical fluid chromatography (SOS-SFC) are demonstrated with typical low density mobile phases (94% CO2). The procedure is optimized with the commercially available column kit and with the classical isocratic SOS-LC algorithm. SOS-SFC appears possible without any density correction, although optimal correspondence between prediction and experiment is obtained when isopycnic conditions are maintained. As also the influence of the segment order appears significantly less relevant than expected, the use of the approach in SFC appears as promising as is the case in HPLC. Next to the classical use of SOS for faster baseline separation of all solutes in a mixture, the benefits of the approach for predicting as wide as possible separation windows around to-be-purified solutes in semipreparative SFC are illustrated, leading to significant production rate improvements in (semi)preparative SFC.

Hierarchical String Cuts: A Translation, Rotation, Scale and Mirror Invariant Descriptor for Fast Shape Retrieval.

This paper presents a novel approach for both fast and accurately retrieving similar shapes. A hierarchical string cuts (HSC) method is proposed to partition a shape into multiple level curve segments of different lengths from a point moving around the contour to describe the shape gradually and completely from the global information to the finest details. At each hierarchical level, the curve segments are cut by strings to extract features that characterize the geometric and distribution properties in that particular level of details. The translation, rotation, scale and mirror invariant HSC descriptor enables a fast metric based matching to achieve the desired high accuracy. Encouraging experimental results on four databases demonstrated that the proposed method can consistently achieve higher (or similar) retrieval accuracies than the state-of-the-art benchmarks with a more than 120 times faster speed. This may suggest a new way of developing shape retrieval techniques in which a high accuracy can be achieved by a fast metric matching algorithm without using the time-consuming correspondence optimisation strategy.

Galileo and Aristotle's Wheel

At the beginning of his last major work, Galileo tackles an old paradox, Aristotle’s Wheel, in order to produce a model of the continuum that explains (at least to him) how line segments of different length could be put into a one-to-one correspondence. His argument seems like a playful digression. However, it is precisely this type of a one-to-one correspondence that he needs to support his work on free fall. In this article, we investigate how Galileo’s model for the wheel paradox informs his work on free fall. We also examine some of the reasons his results on free fall—results that were grounded in his notion of the continuum— were not readily accepted in his time.

Modeling Reliability in Freeway Networks

The stochastic nature of freeway capacity typically has been analyzed at specific points that are considered bottlenecks. The stochastic relationship between the adjacent bottlenecks has not been taken into account. This paper introduces a concept for the stochastic interpretation of capacity and breakdown probability within a larger freeway network consisting of several combined bottlenecks. The presented stochastic methodology delivers a theoretical average capacity and the probability of breakdown for freeway segments of different lengths. The methodology can also be used to identify the effects of consecutive freeway segments and bottlenecks such as on-ramps, off-ramps, and weaving areas having different characteristics. The proposed method makes it possible to determine the breakdown probability as a function of the average volume or density. Hence, the risk of traffic flow disturbance along a freeway segment or within a freeway network can be analyzed.

Bar piezoelectric ceramic transformers.

Bar-shaped piezoelectric ceramic transformers (PTs) working in the longitudinal vibration mode (k31 mode) were studied. Two types of the transformer were designed--one with the electrode divided into two segments of different length, and one with the electrodes divided into three symmetrical segments. Parameters of studied transformers such as efficiency, transformation ratio, and input and output impedances were measured. An analytical model was developed for PT parameter calculation for both two- and three-segment PTs. Neither type of bar PT exhibited very high efficiency (maximum 72% for three-segment PT design) at a relatively high transformation ratio (it is 4 for two-segment PT and 2 for three-segment PT at the fundamental resonance mode). The optimum resistive loads were 20 and 10 kΩ for two- and three-segment PT designs for the fundamental resonance, respectively, and about one order of magnitude smaller for the higher overtone (i.e., 2 kΩ and 500 Ω, respectively). The no-load transformation ratio was less than 27 (maximum for two-segment electrode PT design). The optimum input electrode aspect ratios (0.48 for three-segment PT and 0.63 for two-segment PT) were calculated numerically under no-load conditions.

Controlled wurtzite inclusions in self-catalyzed zinc blende III–V semiconductor nanowires

The control of the Ga droplet during the MBE growth and its impact on the crystal structure of self-catalyzed GaAs nanowires (NWs) were investigated. The consumption of the droplet proceeds in two steps. First, the contact angle decreases to 90° keeping the NW diameter constant. The crystal structure changes from zinc blende (ZB) to wurtzite (WZ). Then, the contact angle keeps constant while the top radius of the NW decreases and the NW grows again in ZB configuration. During the last step, {110}, {211}B and {100} facets develop at the top. Calculations show that the Ga desorption from the droplet has to be taken into account during its consumption. With this information, several WZ segments of different lengths were placed into ZB GaAs NWs via partial droplet consumption. For this purpose, we supplied As and Ga separately, in order to partially consume and refill the Ga droplet. The same mechanism was applied to self-catalyzed InAs NWs resulting in short WZ segments inserted in a ZB twinning superlattice.

Optical properties of collective excitations for an atomic chain with vacancies

Resonant dipole-dipole interaction modifies the energy and decay rate of electronic excitations for a collection of ultracold atoms. Collective excitations of a finite linear atomic chain can be divided into dark and bright modes. Typically the superradiant mode with maximum effective collective dipole dominates resonant light scattering. The generic case of two chain segments of different length and position exhibits an interaction blockade and spatially structured light emission. Ultimately, an extended system of several interfering segments models a long chain with randomly distributed defects of vacant sites. The corresponding emission pattern provides a sensitive tool to study structural and dynamical properties of the system.

Gauge Factor Tuning, Long-Term Stability, and Miniaturization of Nanoelectromechanical Carbon-Nanotube Sensors

Integrated piezoresitive strain gauges are established transducers for measuring displacements in microelectromechanical systems (MEMS). Due to large gauge factors (GFs) and low power operation and nanometer dimensions, carbon nanotubes (CNTs) are ideal candidates for further downscaling strain-gauge-based MEMS devices. Here, we present zero-level packaged strain gauges based on individual single-walled CNTs in a field-effect transistor configuration, which can be utilized as long-term stable and tunable transducers for measuring membrane deflections in ultraminiaturized pressure sensors. The gate electrode allows adjusting GFs of nanotube strain gauges by almost a factor of 10. Studies on nanotube segments of different lengths show highly reproducible GFs along the same CNT. The zero-level packaged pressure sensors show stable GFs over a period of at least 14 months. This paper is an important step toward reliable nanoscaled strain gauges with many potential applications, such as ultraminiaturized pressure-sensitive membranes or cantilever-based transducers.

In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions.

Nascent transmembrane (TM) polypeptide segments are recognized and inserted into the lipid bilayer by the cellular translocon machinery. The recognition rules, described by a biological hydrophobicity scale, correlate strongly with physical hydrophobicity scales that describe the free energy of insertion of TM helices from water. However, the exact relationship between the physical and biological scales is unknown, because solubility problems limit our ability to measure experimentally the direct partitioning of hydrophobic peptides across lipid membranes. Here we use microsecond molecular dynamics (MD) simulations in which monomeric polyleucine segments of different lengths are allowed to partition spontaneously into and out of lipid bilayers. This approach directly reveals all states populated at equilibrium. For the hydrophobic peptides studied here, only surface-bound and transmembrane-inserted helices are found. The free energy of insertion is directly obtained from the relative occupancy of these states. A water-soluble state was not observed, consistent with the general insolubility of hydrophobic peptides. The approach further allows determination of the partitioning pathways and kinetics. Surprisingly, the transfer free energy appears to be independent of temperature, which implies that surface-to-bilayer peptide insertion is a zero-entropy process. We find that the partitioning free energy of the polyleucine segments correlates strongly with values from translocon experiments but reveals a systematic shift favoring shorter peptides, suggesting that translocon-to-bilayer partitioning is not equivalent but related to spontaneous surface-to-bilayer partitioning.

Determining the width of the optimal space needed to accommodate the drivers of passenger vehicles using the analogy of anthropometric measurement dynamics and mechanical mechanisms

This paper discusses a new way of modelling the width of the space that accommodates the drivers of passenger vehicles. The fact that there is a more or less fixed zero point, which is the origin of the coordinates of the man-vehicle system makes it possible to determine the mechanical–mathematical co-dependence in this system more accurately. The space is determined by taking extreme pairs of the dimensions and a series of anthropometric measurements to which the vehicle needs to be adjusted as the measurement limits. These were determined by analysis which includes both the theory of mechanisms and vehicle mechanics. In this way the method of adapting the vehicle to accommodate a range from the 5th-percentile woman to the 95th-percentile man has finally been surpassed. The paper demonstrates a methodology for designing the interior space of a passenger vehicle based on the fact that, in a range of anthropometric measurements of equal total lengths, each measurement has segments of different lengths, because people with the same leg lengths have different upper-and lower-leg lengths. Therefore the interior space of the vehicle is designed to accommodate extreme measurements and to allow for limitations caused by movement and the physical laws derived from seeing the anthropometric measurement mechanism as a mechanical mechanism. The paper offers a design for the space behind the windscreen, the position of the steering wheel, and the position of the foot controls together with the total space which the driver occupies, primarily from the aspect of anthropometric limitations, concluding that the maximum width for accommodation of the driver at the lowest level of a seat along the x axis is 169 mm, and along the y axis is 1013 mm.

Topological Quantum Hashing with the Icosahedral Group

We study an efficient algorithm to hash any single-qubit gate into a braid of Fibonacci anyons represented by a product of icosahedral group elements. By representing the group elements by braid segments of different lengths, we introduce a series of pseudogroups. Joining these braid segments in a renormalization group fashion, we obtain a Gaussian unitary ensemble of random-matrix representations of braids. With braids of length O(log2(1/epsilon)), we can approximate all SU(2) matrices to an average error epsilon with a cost of O(log(1/epsilon)) in time. The algorithm is applicable to generic quantum compiling.

The coupling among electron transfer, deformation, screening and binding in electrochemically active macromolecules

Experimental data are presented demonstrating that electrochemically active macromolecules show a coupling among electron transfer, deformation, screening and binding. The work includes dependence of the redox potential of synthetic and natural electrochemically active polymers on the electrolyte pH (electron transfer-binding coupling), the changes in volume during the redox switching of synthetic electrochemically active polymers (deformation-electron transfer coupling) and the changes in the macromolecular conformation during the acid-base titration of polyelectrolytes and proteins (deformation-binding coupling). A simple equilibrium statistical thermodynamic model is presented that allows explaining these couplings effects. The model is based on the assumption that a macromolecule is composed of segments of different length that may bind species present in the external solution and that also contain redox centers that may be oxidized and reduced. The partition function of the system is obtained, and from it the expressions for the redox potentials, the total length and the chemical potential of the bound species are obtained. Simple calculations shows that the model satisfactorily explains the qualitative behavior of the experimental results.

Effect of Linker Length and Dockerin Position on Conversion of a Thermobifida fusca Endoglucanase to the Cellulosomal Mode

We have been developing the cellulases of Thermobifida fusca as a model to explore the conversion from a free cellulase system to the cellulosomal mode. Three of the six T. fusca cellulases (endoglucanase Cel6A and exoglucanases Cel6B and Cel48A) have been converted in previous work by replacing their cellulose-binding modules (CBMs) with a dockerin, and the resultant recombinant "cellulosomized" enzymes were incorporated into chimeric scaffolding proteins that contained cohesin(s) together with a CBM. The activities of the resultant designer cellulosomes were compared with an equivalent mixture of wild-type enzymes. In the present work, a fourth T. fusca cellulase, Cel5A, was equipped with a dockerin and intervening linker segments of different lengths to assess their contribution to the overall activity of simple one- and two-enzyme designer cellulosome complexes. The results demonstrated that cellulose binding played a major role in the degradation of crystalline cellulosic substrates. The combination of the converted Cel5A endoglucanase with the converted Cel48A exoglucanase also exhibited a measurable proximity effect for the most recalcitrant cellulosic substrate (Avicel). The length of the linker between the catalytic module and the dockerin had little, if any, effect on the activity. However, positioning of the dockerin on the opposite (C-terminal) side of the enzyme, consistent with the usual position of dockerins on most cellulosomal enzymes, resulted in an enhanced synergistic response. These results promote the development of more complex multienzyme designer cellulosomes, which may eventually be applied for improved degradation of plant cell wall biomass.

Intermodular Linker Flexibility Revealed from Crystal Structures of Adjacent Cellulosomal Cohesins of Acetivibrio cellulolyticus

Cellulosome complexes comprise an intercalated set of multimodular dockerin-containing enzymatic subunits connected to cohesin-containing nonenzymatic subunits called scaffoldins. The adjoining modules in each cellulosomal subunit are interconnected by a variety of linker segments of different lengths and composition. The exact role of the cellulosomal linkers has yet to be described, although it is assumed that they contribute to the architecture and action of the cellulosome by providing the protein subunits with flexibility and by providing spacers between the enzymatic modules that could enhance interactions with the cellulose substrate. Here we present four crystal structures of Acetivibrio cellulolyticus cellulosomal type II cohesins with linker extensions. Two of the structures represent two different crystal forms (trigonal and orthorhombic) of the same N-terminal cohesin module (CohB1) together with its full (6-residue) native C-terminal linker, derived from scaffoldin B. The other two structures belong to the adjacent (second) cohesin module (CohB2), each of which was crystallized with the same 6-residue linker segment, but now positioned at the N-terminus and with either a truncated (5-residue) or a full-length (45-residue) C-terminal linker, respectively. Comparison between the two CohB1 structures revealed significant differences in the conformation of their equivalent C-terminal linker segment. In one crystal form a helical conformation was observed, as opposed to an extended conformation in the other. The CohB2 structures also displayed diverse conformations in their linker segments. In these structures, different linker conformations were observed in the individual molecules within the asymmetric unit of each structure. This conformational diversity implies that the linkers may adopt alternative conformations in their natural environment, consistent with varying environmental conditions. The findings suggest that linkers can play an important role in the assembly, dynamics and function of the cellulosomal components.

An algorithm for the two-dimensional cutting problem of punched strips with blade length constraint

This paper presents an algorithm for generating optimal T-shaped cutting patterns of punched strips. A strip contains only items of the same type. The stock plate is divided into items in two stages. First a guillotine machine cuts the plate into strips, then a stamping press punches out the items from the strips. The blade length of the guillotine machine may be shorter than the plate length. The algorithm divides the plate into two segments. Each segment contains strips of the same direction. The strip directions of the two segments are perpendicular to each other. The algorithm uses dynamic programming techniques to determine the optimal strip layouts on segments of different lengths not longer than the blade length, considers all possible combinations of two segments, and selects the best pair as the optimal solution. The computational results indicate that the new algorithm is much more efficient than the existing algorithm.