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  • 1
    Publication Date: 2016-03-03
    Description: Fungi interact with plants in various ways, with each interaction giving rise to different alterations in both partners. While fungal pathogens have detrimental effects on plant physiology, mutualistic fungi augment host defence responses to pathogens and/or improve plant nutrient uptake. Tropic growth towards plant roots or stomata, mediated by chemical and topographical signals, has been described for several fungi, with evidence of species-specific signals and sensing mechanisms. Fungal partners secrete bioactive molecules such as small peptide effectors, enzymes and secondary metabolites which facilitate colonization and contribute to both symbiotic and pathogenic relationships. There has been tremendous advancement in fungal molecular biology, omics sciences and microscopy in recent years, opening up new possibilities for the identification of key molecular mechanisms in plant–fungal interactions, the power of which is often borne out in their combination. Our fragmentary knowledge on the interactions between plants and fungi must be made whole to understand the potential of fungi in preventing plant diseases, improving plant productivity and understanding ecosystem stability. Here, we review innovative methods and the associated new insights into plant–fungal interactions.
    Print ISSN: 0168-6445
    Electronic ISSN: 1574-6976
    Topics: Biology
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  • 2
    Publication Date: 2013-12-10
    Description: In this brief paper, an extension of the result of Fujisaki & Befekadu (2009, Reliable decentralized stabilization of multi-channel systems: a design method via dilated Linear Matrix Inequalities (LIMs) and unknown disturbance observers. Int. J. Contr. , 82 , 2040–2050.) concerning the problem of reliable stabilization for generalized multi-channel systems is given. Specifically, we use a rectangular dilated LMIs framework to provide a relaxed sufficient condition for the reliable stabilization of a multi-channel system both when all of the controllers work together and when one of the controllers ceases to function due to a failure.
    Print ISSN: 0265-0754
    Electronic ISSN: 1471-6887
    Topics: Mathematics
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  • 3
    Publication Date: 2014-10-09
    Description: Dystroglycan is a transmembrane glycoprotein whose interactions with the extracellular matrix (ECM) are necessary for normal muscle and brain development, and disruptions of its function lead to dystroglycanopathies, a group of congenital muscular dystrophies showing extreme genetic and clinical heterogeneity. Specific glycans bound to the extracellular portion of dystroglycan, α-dystroglycan, mediate ECM interactions and most known dystroglycanopathy genes encode glycosyltransferases involved in glycan synthesis. POMK , which was found mutated in two dystroglycanopathy cases, is instead involved in a glycan phosphorylation reaction critical for ECM binding, but little is known about the clinical presentation of POMK mutations or of the function of this protein in the muscle. Here, we describe two families carrying different truncating alleles, both removing the kinase domain in POMK, with different clinical manifestations ranging from Walker–Warburg syndrome, the most severe form of dystroglycanopathy, to limb-girdle muscular dystrophy with cognitive defects. We explored POMK expression in fetal and adult human muscle and identified widespread expression primarily during fetal development in myocytes and interstitial cells suggesting a role for this protein during early muscle differentiation. Analysis of loss of function in the zebrafish embryo and larva showed that pomk function is necessary for normal muscle development, leading to locomotor dysfuction in the embryo and signs of muscular dystrophy in the larva. In summary, we defined diverse clinical presentations following POMK mutations and showed that this gene is necessary for early muscle development.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 4
    Publication Date: 2014-11-21
    Description: Lethal congenital contracture syndrome (LCCS) is a lethal autosomal recessive form of arthrogryposis multiplex congenita (AMC). LCCS is genetically heterogeneous with mutations in five genes identified to date, all with a role in the innervation or contractile apparatus of skeletal muscles. In a consanguineous Saudi family with multiple stillbirths presenting with LCCS, we excluded linkage to all known LCCS loci and combined autozygome analysis and whole-exome sequencing to identify a novel homozygous variant in ZBTB42 , which had been shown to be enriched in skeletal muscles, especially at the neuromuscular junction. Knockdown experiments of zbtb42 in zebrafish consistently resulted in grossly abnormal skeletal muscle development and myofibrillar disorganization at the microscopic level. This severe muscular phenotype is successfully rescued with overexpression of the human wild-type ZBTB42 gene, but not with the mutant form of ZBTB42 that models the human missense change. Our data assign a novel muscular developmental phenotype to ZBTB42 in vertebrates and establish a new LCCS6 type caused by ZBTB42 mutation.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 5
    Publication Date: 2014-06-10
    Description: Autosomal recessive centronuclear myopathy (CNM2), caused by mutations in bridging integrator 1 ( BIN1 ), is a mildly progressive neuromuscular disorder characterized by abnormally centralized myonuclei and muscle weakness. BIN1 is important for membrane sensing and remodeling in vitro in different cell types. However, to fully understand the biological roles of BIN1 in vivo and to answer critical questions concerning the muscle-specific function of BIN1 in vertebrates, robust small animal models are required. In this study, we create and characterize a novel zebrafish model of CNM2 using antisense morpholinos. Immunofluorescence and histopathological analyses of Bin1-deficient zebrafish skeletal muscle reveal structural defects commonly reported in human CNM2 biopsies. Live imaging of zebrafish embryos shows defective calcium release in bin1 morphants, linking the presence of abnormal triads to impairments in intracellular signaling. RNA-mediated rescue assays demonstrate that knockdown of zebrafish bin1 can reliably examine the pathogenicity of novel BIN1 mutations in vivo . Finally, our results strongly suggest that the phosphoinositide-binding domain of BIN1, present only in skeletal muscle isoforms, may be more critical for muscle maturation and maintenance than for early muscle development. Overall, our data support that BIN1 plays an important role in membrane tubulation and may promote skeletal muscle weakness in CNM2 by disrupting machinery necessary for excitation–contraction coupling in vertebrate organisms. The reproducible phenotype of Bin1-deficient zebrafish, together with the generalized advantages of the teleost system, makes this model readily adaptable to high-throughput screening strategies and may be used to identify therapies for CNM2 and related neuromuscular diseases.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 6
    Publication Date: 2014-06-21
    Description: We describe a ribonucleic acid (RNA) reporter system for live-cell imaging of gene expression to detect changes in polymerase II activity on individual promoters in individual cells. The reporters use strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags) that can be expressed from a promoter of choice. For imaging, the cells are incubated with their ligands that are separately conjugated with one of the FRET pair, Cy3 and Cy5. The IMAGEtags were expressed in yeast from the GAL1, ADH1 or ACT1 promoters. Transcription from all three promoters was imaged in live cells and transcriptional increases from the GAL1 promoter were observed with time after adding galactose. Expression of the IMAGEtags did not affect cell proliferation or endogenous gene expression. Advantages of this method are that no foreign proteins are produced in the cells that could be toxic or otherwise influence the cellular response as they accumulate, the IMAGEtags are short lived and oxygen is not required to generate their signals. The IMAGEtag RNA reporter system provides a means of tracking changes in transcriptional activity in live cells and in real time.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2012-10-11
    Description: : High-throughput sequencing currently generates a wealth of small RNA (sRNA) data, making data mining a topical issue. Processing of these large data sets is inherently multidimensional as length, abundance, sequence composition, and genomic location all hold clues to sRNA function. Analysis can be challenging because the formulation and testing of complex hypotheses requires combined use of visualization, annotation and abundance profiling. To allow flexible generation and querying of these disparate types of information, we have developed the shortran pipeline for analysis of plant or animal short RNA sequencing data. It comprises nine modules and produces both graphical and MySQL format output. Availability: shortran is freely available and can be downloaded from http://users-mb.au.dk/pmgrp/shortran/ Contact: vgupta@cs.au.dk or sua@mb.au.dk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2020-08-21
    Description: XTE J1810−197 (J1810) was the first magnetar identified to emit radio pulses, and has been extensively studied during a radio-bright phase in 2003–2008. It is estimated to be relatively nearby compared to other Galactic magnetars, and provides a useful prototype for the physics of high magnetic fields, magnetar velocities, and the plausible connection to extragalactic fast radio bursts. Upon the rebrightening of the magnetar at radio wavelengths in late 2018, we resumed an astrometric campaign on J1810 with the Very Long Baseline Array, and sampled 14 new positions of J1810 over 1.3 yr. The phase calibration for the new observations was performed with two-phase calibrators that are quasi-colinear on the sky with J1810, enabling substantial improvement of the resultant astrometric precision. Combining our new observations with two archival observations from 2006, we have refined the proper motion and reference position of the magnetar and have measured its annual geometric parallax, the first such measurement for a magnetar. The parallax of 0.40 ± 0.05 mas corresponds to a most probable distance $2.5^{, +0.4}_{, -0.3}$ kpc for J1810. Our new astrometric results confirm an unremarkable transverse peculiar velocity of ≈200 $ m km~s^{-1}$ for J1810, which is only at the average level among the pulsar population. The magnetar proper motion vector points back to the central region of a supernova remnant (SNR) at a compatible distance at ≈70 kyr ago, but a direct association is disfavoured by the estimated SNR age of ∼3 kyr.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    Publication Date: 2000-08-01
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
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