Footprint Patterns Research Articles

The impact of chromatin remodelling on cellulase expression in Trichoderma reesei.

BackgroundTrichoderma reesei is used for industry-scale production of plant cell wall-degrading enzymes, in particular cellulases, but also xylanases. The expression of the encoding genes was so far primarily investigated on the level of transcriptional regulation by regulatory proteins. Otherwise, the impact of chromatin remodelling on gene expression received hardly any attention. In this study we aimed to learn if the chromatin status changes in context to the applied conditions (repressing/inducing), and if the presence or absence of the essential transactivator, the Xylanase regulator 1 (Xyr1), influences the chromatin packaging.ResultsComparing the results of chromatin accessibility real-time PCR analyses and gene expression studies of the two prominent cellulase-encoding genes, cbh1 and cbh2, we found that the chromatin opens during sophorose-mediated induction compared to D-glucose-conferred repression. In the strain bearing a xyr1 deletion the sophorose mediated induction of gene expression is lost and the chromatin opening is strongly reduced. In all conditions the chromatin got denser when Xyr1 is absent. In the case of the xylanase-encoding genes, xyn1 and xyn2, the result was similar concerning the condition-specific response of the chromatin compaction. However, the difference in chromatin status provoked by the absence of Xyr1 is less pronounced. A more detailed investigation of the DNA accessibility in the cbh1 promoter showed that the deletion of xyr1 changed the in vivo footprinting pattern. In particular, we detected increased hypersensitivity on Xyr1-sites and stronger protection of Cre1-sites. Looking for the players directly causing the observed chromatin remodelling, a whole transcriptome shotgun sequencing revealed that 15 genes encoding putative chromatin remodelers are differentially expressed in response to the applied condition and two amongst them are differentially expressed in the absence of Xyr1.ConclusionsThe regulation of xylanase and cellulase expression in T. reesei is not only restricted to the action of transcription factors but is clearly related to changes in the chromatin packaging. Both the applied condition and the presence of Xyr1 influence chromatin status.

Elevated mutant dynorphin A causes Purkinje cell loss and motor dysfunction in spinocerebellar ataxia type 23.

Spinocerebellar ataxia type 23 is caused by mutations in PDYN, which encodes the opioid neuropeptide precursor protein, prodynorphin. Prodynorphin is processed into the opioid peptides, α-neoendorphin, and dynorphins A and B, that normally exhibit opioid-receptor mediated actions in pain signalling and addiction. Dynorphin A is likely a mutational hotspot for spinocerebellar ataxia type 23 mutations, and in vitro data suggested that dynorphin A mutations lead to persistently elevated mutant peptide levels that are cytotoxic and may thus play a crucial role in the pathogenesis of spinocerebellar ataxia type 23. To further test this and study spinocerebellar ataxia type 23 in more detail, we generated a mouse carrying the spinocerebellar ataxia type 23 mutation R212W in PDYN. Analysis of peptide levels using a radioimmunoassay shows that these PDYN(R212W) mice display markedly elevated levels of mutant dynorphin A, which are associated with climber fibre retraction and Purkinje cell loss, visualized with immunohistochemical stainings. The PDYN(R212W) mice reproduced many of the clinical features of spinocerebellar ataxia type 23, with gait deficits starting at 3 months of age revealed by footprint pattern analysis, and progressive loss of motor coordination and balance at the age of 12 months demonstrated by declining performances on the accelerating Rotarod. The pathologically elevated mutant dynorphin A levels in the cerebellum coincided with transcriptionally dysregulated ionotropic and metabotropic glutamate receptors and glutamate transporters, and altered neuronal excitability. In conclusion, the PDYN(R212W) mouse is the first animal model of spinocerebellar ataxia type 23 and our work indicates that the elevated mutant dynorphin A peptide levels are likely responsible for the initiation and progression of the disease, affecting glutamatergic signalling, neuronal excitability, and motor performance. Our novel mouse model defines a critical role for opioid neuropeptides in spinocerebellar ataxia, and suggests that restoring the elevated mutant neuropeptide levels can be explored as a therapeutic intervention.

Bone marrow stromal cells transplantation combined with ultrashortwave therapy promotes functional recovery on spinal cord injury in rats.

This study investigated the effects of bone marrow stromal cells (BMSCs) transplantation combined with low dose ultrashortwave (USW) radiation on functional recovery from spinal cord injury (SCI) in rats. Female Sprague-Dawley rats (n = 64) were randomly divided into five groups: sham-operated, as well as control, USW, BMSCs, and BMSCs + USW that were subjected to spinal cord contusion. BMSCs were transplanted into rats in the BMSCs and BMSCs+USW groups, while those in the USW and BMSCs + USW were exposed to radiation; Basso-Beattie-Bresnahan (BBB) tests were performed before the operation and at 1-week intervals after SCI for 7 weeks. 7 weeks later, animals were assessed footprint pattern, motor evoked potential (MEP), histological features, and expression of the ED1 and glial fibrillary acidic protein (GFAP), markers of activated macrophages and astrocytes, respectively, in the lesion area. BBB scores were higher in the BMSCs + USW than in the BMSCs and control groups. The USW and BMSCs + USW groups had improved coordination compared to the BMSCs and control groups (P < 0.01 and P < 0.001, respectively, vs. control). BMSCs + USW rats had a lower ratio of lesion/cavity to spinal cord area than the other injured rats, and also had expression of GFAP in transplanted BMSCs. All treatment groups had lower ED1 expression and MEP latency than the controls (P < 0.01 and P < 0.001, respectively). The results indicate that BMSCs transplantation combined with USW radiation is more effective than either treatment alone in promoting functional recovery after SCI, possibly due to concomitant suppression of inflammation and spinal cord repair.

Estimation of Sex from Foot Print using Standard Footprint Length Formula, Heel Ball Index and Foot Index

The present study revealed the importance of footprints and estimation of sex from footprints. Like fingerprints no two humans have the same footprint pattern which makes them a unique source to find the identity of a person. Footprints found at a crime scene can help in solving crime. Footprints are used to find sex of the individual. The standard foot print length (obtained from the statistically derived standard foot print length formula) was used as a benchmark to estimate the sex of the individual. Heel ball index is also used to estimate sex in which foot width at ball and foot width at heel is used. Heel Ball index may be utilized in sex determination when a part of the foot is brought for medico-legal investigation. Foot index is derived to determine the sex of an individual. The study will be a valuable tool in Forensic investigation in various areas, most importantly in identification in mass disasters cases and comparison of bodies in accidents etc.

Footprint-Driven Locomotion Composition

One of the most efficient ways of generating goal-directed walking motions is synthesising the final motion based on footprints. Nevertheless, current implementations have not examined the generation of continuous motion based on footprints, where different behaviours can be generated automatically. Therefore, in this paper a flexible approach for footprint-driven locomotion composition is presented. The presented solution is based on the ability to generate footprint-driven locomotion, with flexible features like jumping, running, and stair stepping. In addition, the presented system examines the ability of generating the desired motion of the character based on predefined footprint patterns that determine which behaviour should be performed. Finally, it is examined the generation of transition patterns based on the velocity of the root and the number of footsteps required to achieve the target behaviour smoothly and naturally.

Active control of divertor heat and particle fluxes in EAST towards advanced steady state operations

Significant progress has been made in EAST towards advanced steady state operations by active control of divertor heat and particle fluxes. Many innovative techniques have been developed to mitigate transient ELM and stationary heat fluxes on the divertor target plates. It has been found that lower hybrid current drive (LHCD) can lead to edge plasma ergodization, striation of the stationary heat flux and lower ELM transient heat and particle fluxes. With multi-pulse supersonic molecular beam injection (SMBI) to quantitatively regulate the divertor particle flux, the divertor power footprint pattern can be actively modified. H-modes have been extended over 30s in EAST with the divertor peak heat flux and the target temperature being controlled well below 2MW/m2 and 250°C, respectively, by integrating these new methods, coupled with advanced lithium wall conditioning and internal divertor pumping, along with an edge coherent mode to provide continuous particle and power exhaust.

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

The transcriptional activation of one out of ?2800 olfactory receptor (OR) alleles is a poorly understood process. Here, we identify a plethora of putative OR enhancers and study their in vivo activity in olfactory neurons. Distinguished by an unusual epigenetic signature, candidate OR enhancers are characterized by extensive interchromosomal interactions associated with OR transcription and share a similar pattern of transcription factor footprints. In particular, we establish the role of the transcription factor Bptf as a facilitator of both enhancer interactions and OR transcription. Our observations agree with the model whereby OR transcription occurs in the context of multiple interacting enhancers. Disruption of these interchromosomal interactions results in weak and multigenic OR expression, suggesting that the rare coincidence of numerous enhancers over a stochastically chosen OR may account for the singularity and robustness in OR transcription.

Mollaret's meningitis

A 48-year-old man presented with a 2 day history of fever, headache, chills, neck stiff ness, and nausea and vomiting. He had a history of two episodes of viral meningitis, which occurred 30 and 13 years before this presentation. An examination confi rmed meningism without focal neurological defi cits. Results of CSF tests showed protein concentration of 120 mg/dL (normal 12–60 mg/dL), normal glucose concentration, red blood cells 26 cells/μL, and white blood cells 327 cells/μL (10% neutrophils, 84% lymphocytes, 6% monocytes). CSF Gram stain and cultures were negative. Diff -Quik stain of CSF showed many large activated monocytes with several deep nuclear clefts visible as so-called cloverleaf nucleus (green arrowhead, fi gure A), footprintshaped nucleus (white arrowhead, fi gure B), and beanshaped nucleus (green arrow, fi gure C), with a background of normal monocytes (black arrowheads, fi gure A, B) and lymphocytes (black arrows, fi gure A, B). The features of these activated monocytes were compatible with those of Mollaret’s cells, and CSF herpes simplex virus type 2 (HSV2) PCR assay was positive. Large degenerated monocytes were present as ghost cells (asterisks, fi gure B), observed in the slide background. A diagnosis of Mollaret’s meningitis was made. The patient was discharged without antimicrobial therapy and recovered completely. Mollaret’s meningitis was fi rst described by the French neurologist Pierre Mollaret in 1944. The disease is characterised by recurrent (at least three episodes), benign (no long-term sequelae) and brief (2–5 day) episodes of aseptic lymphocytic meningitis, alternating with symptom-free interval, mostly caused by HSV2 infection. The disease is usually self-limited, and antiviral therapy is routinely not recommended. It is therefore also known as recurrent benign lymphocytic meningitis. Typically, results of CSF studies show hypercellularity and predominantly lymphocytic pleocytosis with positive HSV2 DNA by PCR assay. Cellular cytomorphological features of CSF charac teristically show diagnostic Mollaret’s cells, which are multiple activated large monocytes with deep nuclear clefts giving rise to various convoluted, eye-catching shapes of nuclei, such as cloverleaf, bean, and footprint patterns. Usually degenerated monocytes known as ghost cells are present, scattered at the background of the slide. Recognition of these cells in the CSF is crucial for a timely and accurate diagnosis because it could prevent extensive and costly diagnostic studies and antimicrobial therapies.

Wild Saccharomyces cerevisiae strains display biofilm-like morphology in contact with polyphenols from grapes and wine

Polyphenols are a major component of wine grapes, and contribute to color and flavor, but their influence upon yeast growth forms has not been investigated. In this work we have studied the effect of polyphenols on the ability of natural isolates of wine-related Saccharomyces cerevisiae strains to form biofilms attaching to plastic surfaces, to grow as mat colonies, to invade media, and to display filamentous growth. The use of carbon- and nitrogen-rich or deficient media simulated grape juice fermentation conditions. The addition of wine polyphenols to these media affected biofilm formation, and cells exhibited a wide variety of invasiveness and mat formation ability with associated different growth and footprint patterns. Microscopic observation revealed that some strains switched to filamentous phenotypes which were able to invade media. The wide range of phenotypic expression observed could have a role in selection of strains suitable for inoculated wine fermentations and may explain the persistence of yeast strains in vineyard and winery environments.

Synthesis of hexagonal planar array using swarm-based optimization algorithms

Nature inspired optimization algorithms, namely artificial bee colony (ABC) optimization and firefly algorithm (FA), have been applied to synthesize beam patterns of a hexagonal planar array of isotropic elements. Two different cases, comprising two different beam patterns of a pencil beam and a square footprint pattern over a bounded region with lower peak sidelobe levels are presented. The pencil beam is generated by thinning the uniformly excited array and the square footprint pattern is generated by imposing optimum amplitudes, phases, and their corresponding states (“on”/“off”) to the array elements. The optimum values of the parameters for both the cases are computed using ABC and FA individually, and the superiority of FA over ABC for the proposed problem in terms of computing solutions for both the cases is established.

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide-encoding genes in vertebrates, providing an entry point to define their function in vivo.

Heat flux modeling using ion drift effects in DIII-D H-mode plasmas with resonant magnetic perturbations

The heat flux patterns measured in low-collisionality DIII-D H-mode plasmas strongly deviate from simultaneously measured CII emission patterns, used as indicator of particle flux, during applied resonant magnetic perturbations. While the CII emission clearly shows typical striations, which are similar to magnetic footprint patterns obtained from vacuum field line tracing, the heat flux is usually dominated by one large peak at the strike point position. The vacuum approximation, which only considers applied magnetic fields and neglects plasma response and plasma effects, cannot explain the shape of the observed heat flux pattern. One possible explanation is the effect of particle drifts. This is included in the field line equations and the results are discussed with reference to the measurement. Electrons and ions show different drift motions at thermal energy levels in a guiding center approximation. While electrons hardly deviate from the field lines, ions can drift several centimetres away from field line flux surfaces. A model is presented in which an ion heat flux, based on the ion drift motion from various kinetic energies as they contribute to a thermal Maxwellian distribution, is calculated. The simulated heat flux is directly compared to measurements with a varying edge safety factor q95. This analysis provides evidence for the dominate effect of high-energy ions in carrying heat from the plasma inside the separatrix to the target. High-energy ions are deposited close to the unperturbed strike line, while low-energy ions can travel into the striated magnetic topology.

Characterization of divertor footprints and the pedestal plasmas in the presence of applied n = 3 fields for the attached and detached conditions in NSTX

Recent progress in the study of 3D field effects on the divertor and pedestal plasmas is reported with the use of a new set of diagnostics. A wide angle visible camera provides 2D data of lower divertor surface covering almost the full range of radius (r) and toroidal angle (Φ), a significant advantage over the conventional 1D radial profile in examining non-axisymmetric effects of 3D fields on the divertor footprints. The spatial distribution of connection lengths (Lc) calculated by vacuum field line tracing in the presence of 3D fields (n = 3) agrees with the footprint pattern observed in the 2D wide angle camera images. The full (r, Φ) image data with high temporal resolution revealed that the spatial structure of modified divertor footprints is maintained even during the edge-localized modes (ELMs) triggered by applied n = 3 fields, when the ELM size is sufficiently small, i.e. the ELMs are ‘phase locked’ to the imposed perturbation field structure. This phase-lock is lost during the ELM rise time for ELMs with large energy loss, e.g. ΔWELM/WMHD > 4–5%. Divertor gas puff was used to create detached divertor condition and the effect of 3D fields on the detachment was investigated. The divertor remains partially detached with the 3D field application when a sufficient amount of gas is injected into the divertor region, which is accompanied by a noticeable drop of pedestal electron temperature (Te). However, with a lower gas puff, the divertor plasma re-attaches, when 3D fields were applied to the detached plasma, and the pedestal Te rises back up. There observed no other change in the pedestal profile associated with the re-attachment, indicating that this is likely to be dominated by a change in the electron thermal transport processes. A TRANSP analysis shows that the drop of pedestal electron heat diffusivity (χe) is responsible for this change but the source of this reduction is yet unclear.

A Hybrid ABC-DE Algorithm and Its Application for Time-Modulated Arrays Pattern Synthesis

In this paper, a novel hybrid algorithm based on artificial bee colony (ABC) algorithm and differential evolution (DE) algorithm called ABC-DE is proposed to inherit their advantages and overcome their drawbacks. In ABC-DE algorithm, employed bees employ the mutation and crossover strategies of DE to enforce their exploration ability while onlooker bees keep their original updating strategy to retain the exploitation ability. Classical test functions have been provided to testify the ABC-DE algorithm. Furthermore, ABC-DE is applied to different types of time-modulated arrays (TMAs) pattern synthesis problems, including the syntheses of low equal-ripple sidelobe level (SLL) pattern, deep null level pattern, multiple-beams patterns and satellite footprint pattern. Experiment results reveal that ABC-DE has a promising performance in the convergence rate and the exploration ability when compared with other improved evolutionary algorithms, which indicates that the proposed algorithm can be an effective approach for TMAs synthesis problems.

Synthesis of satellite footprint patterns from rectangular planar array antenna by using swarm‐based optimization algorithms

SUMMARYA pattern synthesis method based on Firefly Algorithm (FA) and Artificial Bee Colony (ABC) optimization has been presented to generate satellite footprint patterns from a rectangular planar array of isotropic antennas by modifying the amplitude, phase, and the state of the array elements. Three cases comprising three different footprints of rectangular, square, and circular boundary are generated from the same array by using two different swarm‐based optimization algorithms FA and ABC. Both the algorithms, following the proposed procedures are able to generate the three different footprint patterns while maintaining a satisfactory lower peak side lobe level and ripple. A comparative analysis has been carried out between FA, ABC, and Genetic Algorithm (GA) for the presented problem in terms of fitness value for the three different cases. The superiority of FA and ABC over GA has been established in terms of finding better solutions for all the three cases of the proposed problem. Copyright © 2013 John Wiley &amp; Sons, Ltd.

Combination of differential evolution algorithm and fast fourier transform for synthesis of footprint patterns from rectangular planar array

ABSTRACTAn FFT‐based footprint pattern synthesis from a rectangular planar array of isotropic antennas by modifying the amplitude, phase and the state (‘on’/‘off’) of the array elements using differential evolution algorithm has been presented. Three different footprints of rectangular, square and circular boundaries are generated from the array while maintaining a satisfactory lower peak sidelobe level and ripple. The method greatly reduces the computational time than the conventional method of calculating beam patterns. The dynamic range ratio of the excitation amplitudes are kept below a threshold level to reduce the design complexity of the attenuators at the feed network level and to minimize the effect of mutual coupling among the array elements. Copyright © 2013 John Wiley &amp; Sons, Ltd.

Calculation and Analysis of Water Footprint in Shunyi District of Beijing

The water footprint and consumption pattern is an effective tool for quantitifying the volume of water resources consumption in certain region [ ].Shunyi’s water footprint in the period 2006-2010 is calculated in this article from the view of virtual water. The general water footprint in Shunyi District at the year 2010 reached 790 million m3 and water footprint per capita was 536.48 cubic meters. Shunyi 's water resource quantity per capita was 501.27 m3 in the same year and the Water Scarcity Index was 1.98. The result of calculation shows that the water resource volume of exploitation in Shunyi District of Beijing has been beyond the water resources carrying capacity.

Silencing Mutant Ataxin-3 Rescues Motor Deficits and Neuropathology in Machado-Joseph Disease Transgenic Mice

Machado-Joseph disease (MJD) or spinocerebellar ataxia type 3 (SCA3) is an autosomal dominantly-inherited neurodegenerative disorder caused by the over-repetition of a CAG codon in the MJD1 gene. This expansion translates into a polyglutamine tract that confers a toxic gain-of-function to the mutant protein – ataxin-3, leading to neurodegeneration in specific brain regions, with particular severity in the cerebellum. No treatment able to modify the disease progression is available. However, gene silencing by RNA interference has shown promising results. Therefore, in this study we investigated whether lentiviral-mediated allele-specific silencing of the mutant ataxin-3 gene, after disease onset, would rescue the motor behavior deficits and neuropathological features in a severely impaired transgenic mouse model of MJD. For this purpose, we injected lentiviral vectors encoding allele-specific silencing-sequences (shAtx3) into the cerebellum of diseased transgenic mice expressing the targeted C-variant of mutant ataxin-3 present in 70% of MJD patients. This variation permits to discriminate between the wild-type and mutant forms, maintaining the normal function of the wild-type allele and silencing only the mutant form. Quantitative analysis of rotarod performance, footprint and activity patterns revealed significant and robust alleviation of gait, balance (average 3-fold increase of rotarod test time), locomotor and exploratory activity impairments in shAtx3-injected mice, as compared to control ones injected with shGFP. An important improvement of neuropathology was also observed, regarding the number of intranuclear inclusions, calbindin and DARPP-32 immunoreactivity, fluorojade B and Golgi staining and molecular and granular layers thickness. These data demonstrate for the first time the efficacy of gene silencing in blocking the MJD-associated motor-behavior and neuropathological abnormalities after the onset of the disease, supporting the use of this strategy for therapy of MJD.

Oligonucleotide Models of Telomeric DNA and RNA Form a Hybrid G-quadruplex Structure as a Potential Component of Telomeres

Telomeric repeat-containing RNA, a non-coding RNA molecule, has recently been found in mammalian cells. The detailed structural features and functions of the telomeric RNA at human chromosome ends remain unclear, although this RNA molecule may be a key component of the telomere machinery. In this study, using model human telomeric DNA and RNA sequences, we demonstrated that human telomeric RNA and DNA oligonucleotides form a DNA-RNA G-quadruplex. We next employed chemistry-based oligonucleotide probes to mimic the naturally formed telomeric DNA-RNA G-quadruplexes in living cells, suggesting that the process of DNA-RNA G-quadruplex formation with oligonucleotide models of telomeric DNA and RNA could occur in cells. Furthermore, we investigated the possible roles of this DNA-RNA G-quadruplex. The formation of the DNA-RNA G-quadruplex causes a significant increase in the clonogenic capacity of cells and has an effect on inhibition of cellular senescence. Here, we have used a model system to provide evidence about the formation of G-quadruplex structures involving telomeric DNA and RNA sequences that have the potential to provide a protective capping structure for telomere ends.

Binding by the Hepatitis C Virus NS3 Helicase Partially Melts Duplex DNA

Binding of NS3 helicase to DNA was investigated by footprinting with KMnO(4), which reacts preferentially with thymidine residues in single-stranded DNA (ssDNA) compared to those in double-stranded DNA (dsDNA). A distinct pattern of reactivity was observed on ssDNA, which repeated every 8 nucleotides (nt) and is consistent with the known binding site size of NS3. Binding to a DNA substrate containing a partial duplex was also investigated. The DNA contained a 15 nt overhang made entirely of thymidine residues adjacent to a 22 bp duplex that contained thymidine at every other position. Surprisingly, the KMnO(4) reactivity pattern extended from the ssDNA into the dsDNA region of the substrate. Lengthening the partial duplex to 30 bp revealed a similar pattern extending from the ssDNA into the dsDNA, indicating that NS3 binds within the duplex region. Increasing the length of the ssDNA portion of the partial duplex by 4 nt resulted in a shift in the footprinting pattern for the ssDNA by 4 nt, which is consistent with binding to the 3'-end of the ssDNA. However, the footprinting pattern in the dsDNA region was shifted by only 1-2 bp, indicating that binding to the ssDNA-dsDNA region was preferred. Footprinting performed as a function of time indicated that NS3 binds to the ssDNA rapidly, followed by slower binding to the duplex. Hence, multiple molecules of NS3 can bind along a ssDNA-dsDNA partial duplex by interacting with the ssDNA as well as the duplex DNA.