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  • 1
    Publication Date: 2016-07-08
    Description: The RNA binding protein HuR determines the differential translation of autism-associated FoxP subfamily members in the developing neocortex Scientific Reports, Published online: 7 July 2016; doi:10.1038/srep28998
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 2
    Publication Date: 2011-12-14
    Description: Although genetic imprinting was discovered in maize 40 years ago, its exact extent in the triploid endosperm remains unknown. Here, we have analyzed global patterns of allelic gene expression in developing maize endosperms from reciprocal crosses between inbreds B73 and Mo17. We have defined an imprinted gene as one in which the relative expression of the maternal and paternal alleles differ at least fivefold in both hybrids of the reciprocal crosses. We found that at least 179 genes (1.6% of protein-coding genes) expressed in the endosperm are imprinted, with 68 of them showing maternal preferential expression and 111 paternal preferential expression. Additionally, 38 long noncoding RNAs were imprinted. The latter are transcribed in either sense or antisense orientation from intronic regions of normal protein-coding genes or from intergenic regions. Imprinted genes show a clear pattern of clustering around the genome, with a number of imprinted genes being adjacent to each other. Analysis of allele-specific methylation patterns of imprinted loci in the hybrid endosperm identified 21 differentially methylated regions (DMRs) of several hundred base pairs in length, corresponding to both imprinted genes and noncoding transcripts. All DMRs identified are uniformly hypomethylated in maternal alleles and hypermethylated in paternal alleles, regardless of the imprinting direction of their corresponding loci. Our study indicates highly extensive and complex regulation of genetic imprinting in maize endosperm, a mechanism that can potentially function in the balancing of the gene dosage of this triploid tissue.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 3
    Publication Date: 2010-08-31
    Description: The 7-methylguanosine cap structure at the 5' end of eukaryotic messenger RNAs is a critical determinant of their stability and translational efficiency. It is generally believed that 5'-end capping is a constitutive process that occurs during mRNA maturation and lacks the need for a quality-control mechanism to ensure its fidelity. We recently reported that the yeast Rai1 protein has pyrophosphohydrolase activity towards mRNAs lacking a 5'-end cap. Here we show that, in vitro as well as in yeast cells, Rai1 possesses a novel decapping endonuclease activity that can also remove the entire cap structure dinucleotide from an mRNA. This activity is targeted preferentially towards mRNAs with unmethylated caps in contrast to the canonical decapping enzyme, Dcp2, which targets mRNAs with a methylated cap. Capped but unmethylated mRNAs generated in yeast cells with a defect in the methyltransferase gene are more stable in a rai1-gene-disrupted background. Moreover, rai1Delta yeast cells with wild-type capping enzymes show significant accumulation of mRNAs with 5'-end capping defects under nutritional stress conditions of glucose starvation or amino acid starvation. These findings provide evidence that 5'-end capping is not a constitutive process that necessarily always proceeds to completion and demonstrates that Rai1 has an essential role in clearing mRNAs with aberrant 5'-end caps. We propose that Rai1 is involved in an as yet uncharacterized quality control process that ensures mRNA 5'-end integrity by an aberrant-cap-mediated mRNA decay mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948066/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948066/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiao, Xinfu -- Xiang, Song -- Oh, Chanseok -- Martin, Charles E -- Tong, Liang -- Kiledjian, Megerditch -- GM077175/GM/NIGMS NIH HHS/ -- GM67005/GM/NIGMS NIH HHS/ -- R01 GM077175/GM/NIGMS NIH HHS/ -- R01 GM077175-04/GM/NIGMS NIH HHS/ -- R01 GM090059/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Sep 30;467(7315):608-11. doi: 10.1038/nature09338. Epub 2010 Aug 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20802481" target="_blank"〉PubMed〈/a〉
    Keywords: *5' Untranslated Regions/genetics ; Amino Acids/deficiency/metabolism ; Endoribonucleases/metabolism ; Exoribonucleases/metabolism ; Glucose/deficiency/metabolism ; Guanosine/*analogs & derivatives/metabolism ; Hydrolysis ; Methylation ; Nuclear Proteins/genetics/*metabolism ; RNA Caps/genetics/*metabolism ; RNA Stability ; RNA, Fungal/genetics/*metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Stress, Physiological/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2010-01-22
    Description: In extremely acidic environments, enteric bacteria such as Escherichia coli rely on the amino acid antiporter AdiC to expel protons by exchanging intracellular agmatine (Agm(2+)) for extracellular arginine (Arg(+)). AdiC is a representative member of the amino acid-polyamine-organocation (APC) superfamily of membrane transporters. The structure of substrate-free AdiC revealed a homodimeric assembly, with each protomer containing 12 transmembrane segments and existing in an outward-open conformation. The overall folding of AdiC is similar to that of the Na(+)-coupled symporters. Despite these advances, it remains unclear how the substrate (arginine or agmatine) is recognized and transported by AdiC. Here we report the crystal structure of an E. coli AdiC variant bound to Arg at 3.0 A resolution. The positively charged Arg is enclosed in an acidic binding chamber, with the head groups of Arg hydrogen-bonded to main chain atoms of AdiC and the aliphatic portion of Arg stacked by hydrophobic side chains of highly conserved residues. Arg binding induces pronounced structural rearrangement in transmembrane helix 6 (TM6) and, to a lesser extent, TM2 and TM10, resulting in an occluded conformation. Structural analysis identified three potential gates, involving four aromatic residues and Glu 208, which may work in concert to differentially regulate the upload and release of Arg and Agm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gao, Xiang -- Zhou, Lijun -- Jiao, Xuyao -- Lu, Feiran -- Yan, Chuangye -- Zeng, Xin -- Wang, Jiawei -- Shi, Yigong -- England -- Nature. 2010 Feb 11;463(7282):828-32. doi: 10.1038/nature08741. Epub 2010 Jan 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ministry of Education Protein Science Laboratory, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090677" target="_blank"〉PubMed〈/a〉
    Keywords: Agmatine/metabolism ; Amino Acid Transport Systems/*chemistry/*metabolism ; Antiporters/*chemistry/*metabolism ; Arginine/chemistry/*metabolism ; Biological Transport ; Conserved Sequence ; Crystallography, X-Ray ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Protein Conformation ; Protein Folding ; Protein Multimerization ; Protons ; Static Electricity ; Structure-Activity Relationship ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2009-02-06
    Description: The 5'--〉3' exoribonucleases (XRNs) comprise a large family of conserved enzymes in eukaryotes with crucial functions in RNA metabolism and RNA interference. XRN2, or Rat1 in yeast, functions primarily in the nucleus and also has an important role in transcription termination by RNA polymerase II (refs 7-14). Rat1 exoribonuclease activity is stimulated by the protein Rai1 (refs 15, 16). Here we report the crystal structure at 2.2 A resolution of Schizosaccharomyces pombe Rat1 in complex with Rai1, as well as the structures of Rai1 and its murine homologue Dom3Z alone at 2.0 A resolution. The structures reveal the molecular mechanism for the activation of Rat1 by Rai1 and for the exclusive exoribonuclease activity of Rat1. Biochemical studies confirm these observations, and show that Rai1 allows Rat1 to degrade RNAs with stable secondary structure more effectively. There are large differences in the active site landscape of Rat1 compared to related and PIN (PilT N terminus) domain-containing nucleases. Unexpectedly, we identified a large pocket in Rai1 and Dom3Z that contains highly conserved residues, including three acidic side chains that coordinate a divalent cation. Mutagenesis and biochemical studies demonstrate that Rai1 possesses pyrophosphohydrolase activity towards 5' triphosphorylated RNA. Such an activity is important for messenger RNA degradation in bacteria, but this is, to our knowledge, the first demonstration of this activity in eukaryotes and suggests that Rai1/Dom3Z may have additional important functions in RNA metabolism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739979/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739979/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiang, Song -- Cooper-Morgan, Amalene -- Jiao, Xinfu -- Kiledjian, Megerditch -- Manley, James L -- Tong, Liang -- GM077175/GM/NIGMS NIH HHS/ -- GM28983/GM/NIGMS NIH HHS/ -- GM67005/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM067005/GM/NIGMS NIH HHS/ -- R01 GM067005-01A2/GM/NIGMS NIH HHS/ -- R01 GM077175/GM/NIGMS NIH HHS/ -- R01 GM077175-02/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Apr 9;458(7239):784-8. doi: 10.1038/nature07731. Epub 2009 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, New York 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194460" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Exoribonucleases/*chemistry/genetics/*metabolism ; Mice ; *Models, Molecular ; Mutation ; *Nuclear Proteins/chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; *Schizosaccharomyces/chemistry/enzymology/genetics ; Schizosaccharomyces pombe Proteins/*chemistry/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2016-01-08
    Description: Electroreduction of CO2 into useful fuels, especially if driven by renewable energy, represents a potentially 'clean' strategy for replacing fossil feedstocks and dealing with increasing CO2 emissions and their adverse effects on climate. The critical bottleneck lies in activating CO2 into the CO2(*-) radical anion or other intermediates that can be converted further, as the activation usually requires impractically high overpotentials. Recently, electrocatalysts based on oxide-derived metal nanostructures have been shown to enable CO2 reduction at low overpotentials. However, it remains unclear how the electrocatalytic activity of these metals is influenced by their native oxides, mainly because microstructural features such as interfaces and defects influence CO2 reduction activity yet are difficult to control. To evaluate the role of the two different catalytic sites, here we fabricate two kinds of four-atom-thick layers: pure cobalt metal, and co-existing domains of cobalt metal and cobalt oxide. Cobalt mainly produces formate (HCOO(-)) during CO2 electroreduction; we find that surface cobalt atoms of the atomically thin layers have higher intrinsic activity and selectivity towards formate production, at lower overpotentials, than do surface cobalt atoms on bulk samples. Partial oxidation of the atomic layers further increases their intrinsic activity, allowing us to realize stable current densities of about 10 milliamperes per square centimetre over 40 hours, with approximately 90 per cent formate selectivity at an overpotential of only 0.24 volts, which outperforms previously reported metal or metal oxide electrodes evaluated under comparable conditions. The correct morphology and oxidation state can thus transform a material from one considered nearly non-catalytic for the CO2 electroreduction reaction into an active catalyst. These findings point to new opportunities for manipulating and improving the CO2 electroreduction properties of metal systems, especially once the influence of both the atomic-scale structure and the presence of oxide are mechanistically better understood.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gao, Shan -- Lin, Yue -- Jiao, Xingchen -- Sun, Yongfu -- Luo, Qiquan -- Zhang, Wenhua -- Li, Dianqi -- Yang, Jinlong -- Xie, Yi -- England -- Nature. 2016 Jan 7;529(7584):68-71. doi: 10.1038/nature16455.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hefei National Laboratory for Physical Sciences at Microscale, Collaborative Innovation Center of Chemistry for Energy Materials, University of Science and Technology of China, Hefei, Anhui 230026, China. ; Hefei Science Center of CAS, Hefei, Anhui 230061, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26738592" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2018-05-05
    Description: The fat-1 gene from Caenorhabditis elegans encodes a fatty acid desaturase which was widely studied due to its beneficial function of converting n-6 polyunsaturated fatty acids (n-6PUFAs) to n-3 polyunsaturated fatty acids (n-3PUFAs). To date, many fat-1 transgenic animals have been generated to study disease pathogenesis or improve meat quality. However, all of them were generated using a random integration method with variable transgene expression levels and the introduction of selectable marker genes often raise biosafety concern. To this end, we aimed to generate marker-free fat-1 transgenic pigs in a site-specific manner. The Rosa26 locus, first found in mouse embryonic stem cells, has become one of the most common sites for inserting transgenes due to its safe and ubiquitous expression. In our study, the fat-1 gene was inserted into porcine Rosa 26 (pRosa26) locus via Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) system. The Southern blot analysis of our knock-in pigs indicated a single copy of the fat-1 gene at the pRosa26 locus. Furthermore, this single-copy fat-1 gene supported satisfactory expression in a variety of tissues in F1 generation pigs. Importantly, the gas chromatography analysis indicated that these fat-1 knock-in pigs exhibited a significant increase in the level of n-3PUFAs, leading to an obvious decrease in the n-6PUFAs/n-3PUFAs ratio from 9.36 to 2.12 (*** P 〈 0.0001). Altogether, our fat-1 knock-in pigs hold great promise for improving the nutritional value of pork and serving as an animal model to investigate therapeutic effects of n-3PUFAs on various diseases.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 8
    Publication Date: 2016-10-15
    Description: IEEE 802.11, as the standard protocol for wireless local area networks, has achieved substantial developments during recent years and has been widely used in industry and in our daily life. The fundamental access method of the protocol is the distributed coordinated function (DCF), in which the carrier sense multiple access with collision avoidance is used to enable the automatic medium sharing among wireless stations. In this article, a coloured Petri net model for IEEE 802.11 DCF is developed aiming at analysing its performance by simulation. The model is carefully built to capture almost all aspects of the protocol precisely, including the physical and virtual carrier sense functions, traffic generation, backoff procedure, transmission, reception, retransmission, request-to-send/clear-to-send, etc. The topology and ratio ranges are specified so as to address the hidden node problem. The model is organized in a hierarchical and modularized manner, and the symmetries existed in the protocol are exploited to build a compact and scalable model. The model is simulated to compute some performance metrics for each node and for all nodes, including throughput, delivery ratio and delay. The results are compared with NS-2 to validate the model.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 9
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Tetrahedron Letters 35 (1994), S. 1103-1104 
    ISSN: 0040-4039
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    International journal of infrared and millimeter waves 10 (1989), S. 519-528 
    ISSN: 1572-9559
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract This paper proposes a new type of high permittivity whispering gallery mode cylindrical dielectric resonators with a geometry which is very suitable for use in microstrip type integrated circuits. These “oversized” resonators, together with high Q factors and ease of fabrication, are potentially interesting for millimeter wave integrated filters and oscillators. In this paper, we report an experimental investigation of such resonators carried out in Ka band (26.5–40 GHz). Measured results including resonant frequencies and loaded quality factors will be presented. Application to millimeter wave filters will also be demonstrated.
    Type of Medium: Electronic Resource
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