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111.
Ina Bock Arunkumar Dhayalan Srikanth Kudithipudi Ole Brandt Philipp Rathert Albert Jeltsch 《Epigenetics》2011,6(2):256-263
Chromatin structure is greatly influenced by histone tail post-translational modifications (PTM), which also play a central role in epigenetic processes. Antibodies against modified histone tails are central research reagents in chromatin biology and molecular epigenetics. We applied Celluspots peptide arrays for the specificity analysis of 36 commercial antibodies from different suppliers, which are directed towards modified histone tails. The arrays contained 384 peptides from eight different regions of the N-terminal tails of histones, viz. H3 1–19, 7–26, 16–35 and 26–45, H4 1–19 and 11–30, H2A 1–19 and H2B 1–19, featuring 59 post-translational modifications in many different combinations. Using various controls we document the reliability of the method. Our analysis revealed previously undocumented details in the specificity profiles of the tested antibodies. Most of the antibodies bound well to the PTM they have been raised for, but some failed. In addition, some antibodies showed high cross-reactivity and most antibodies were inhibited by specific additional PTMs close to the primary one. Furthermore, specificity profiles for antibodies directed toward the same modification sometimes were very different. The specificity of antibodies used in epigenetic research is an important issue. We provide a catalog of antibody specificity profiles for 36 widely used commercial histone tail PTM antibodies. Better knowledge about the specificity profiles of antibodies will enable researchers to implement necessary control experiments in biological studies and allow more reliable interpretation of biological experiments using these antibodies.Key words: histone modification, histone methylation, histone acetylation, histone phosphorylation, chromatin, antibody, specificity, ChIP 相似文献
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Although remarkable progress in metagenomic sequencing of various environmental samples has been made, large numbers of fragment sequences have been registered in the international DNA databanks, primarily without information on gene function and phylotype, and thus with limited usefulness. Industrial useful biological activity is often carried out by a set of genes, such as those constituting an operon. In this connection, metagenomic approaches have a weakness because sets of the genes are usually split up, since the sequences obtained by metagenome analyses are fragmented into 1-kb or much shorter segments. Therefore, even when a set of genes responsible for an industrially useful function is found in one metagenome library, it is usually difficult to know whether a single genome harbors the entire gene set or whether different genomes have individual genes. By modifying Self-Organizing Map (SOM), we previously developed BLSOM for oligonucleotide composition, which allowed classification (self-organization) of sequence fragments according to genomes. Because BLSOM could reassociate genomic fragments according to genomes, BLSOM may ameliorate the abovementioned weakness of metagenome analyses. Here, we have developed a strategy for clustering of metagenomic sequences according to phylotypes and genomes, by testing a gene set contributing to environment preservation. 相似文献
115.
Chieko Ozaka Naoyuki Yamamoto Jørgen G. Nielsen Hiroaki Somiya 《Ichthyological Research》2011,58(4):297-301
We report the presence of an aglomerular kidney in the pelagic deep-sea fish Saccopharynx
ampullaceus (Saccopharyngiformes: Saccopharyngidae). The thin kidney is unpaired and ribbon-like rostrally, while it is thicker caudally
with a rod-like shape. Light microscopic observation of serial sections revealed no glomeruli at all. The kidney is composed
of renal tubules, sinusoids and capillaries of the renal portal system and extensive interstitial lymphoid tissues. Each renal
tubule is surrounded by well-developed renal portal sinusoids, and the tubules are well separated from each other. There is
a large space dorsal to the vertebrae, similar to the situation in the closely related Eurypharynx pelecanoides. We consider that S. ampullaceus possesses an aglomerular kidney to gain neutral buoyancy. The urinary bladder of S. ampullaceus is a distinct vesicular structure, unlike that of E. pelecanoides. 相似文献
116.
Matsumoto J Kako Y Morita Y Kabeya H Sakano C Nagai A Maruyama S Nogami S 《Parasitology international》2011,60(3):331-332
The ingestion of undercooked meat from wild animals can be a source of Toxoplasma gondii infection in humans and other animals. In this study, we determined the seroprevalence of T. gondii infection in 175 wild boars (Sus scrofa leucomystax) and 107 wild sika deer (Cervus nippon) hunted in 2004–2007 in Gunma Prefecture, Japan, by using a commercial latex agglutination test (LAT). Antibodies (LAT, 1:64 or higher) to T. gondii were found in 6.3% of wild boars and 1.9% of sika deer. This is the first record of T. gondii infection in wild deer in Japan, and deer and wild boar meat should be cooked well before human consumption. 相似文献
117.
The type III secretion system (T3SS) is a complex macromolecular machinery employed by a number of Gram-negative species to initiate infection. Toxins secreted through the system are synthesized in the bacterial cytoplasm and utilize the T3SS to pass through both bacterial membranes and the periplasm, thus being introduced directly into the eukaryotic cytoplasm. A key element of the T3SS of all bacterial pathogens is the translocon, which comprises a pore that is inserted into the membrane of the target cell, allowing toxin injection. Three macromolecular partners associate to form the translocon: two are hydrophobic and one is hydrophilic, and the latter also associates with the T3SS needle. In this review, we discuss recent advances on the biochemical and structural characterization of the proteins involved in translocon formation, as well as their participation in the modification of intracellular signalling pathways upon infection. Models of translocon assembly and regulation are also discussed. 相似文献
118.
Smith I Broos A de Jong C Zeddeman A Smith C Smith G Moore F Barr J Crameri G Marsh G Tachedjian M Yu M Kung YH Wang LF Field H 《PloS one》2011,6(9):e25275
Hendra virus (HeV) causes a zoonotic disease with high mortality that is transmitted to humans from bats of the genus Pteropus (flying foxes) via an intermediary equine host. Factors promoting spillover from bats to horses are uncertain at this time, but plausibly encompass host and/or agent and/or environmental factors. There is a lack of HeV sequence information derived from the natural bat host, as previously sequences have only been obtained from horses or humans following spillover events. In order to obtain an insight into possible variants of HeV circulating in flying foxes, collection of urine was undertaken in multiple flying fox roosts in Queensland, Australia. HeV was found to be geographically widespread in flying foxes with a number of HeV variants circulating at the one time at multiple locations, while at times the same variant was found circulating at disparate locations. Sequence diversity within variants allowed differentiation on the basis of nucleotide changes, and hypervariable regions in the genome were identified that could be used to differentiate circulating variants. Further, during the study, HeV was isolated from the urine of flying foxes on four occasions from three different locations. The data indicates that spillover events do not correlate with particular HeV isolates, suggesting that host and/or environmental factors are the primary determinants of bat-horse spillover. Thus future spillover events are likely to occur, and there is an on-going need for effective risk management strategies for both human and animal health. 相似文献
119.
Effect of hydrophobic mutations in the H2-H3 subdomain of prion protein on stability and conversion in vitro and in vivo 总被引:1,自引:0,他引:1
Prion diseases are fatal neurodegenerative diseases, which can be acquired, sporadic or genetic, the latter being linked to mutations in the gene encoding prion protein. We have recently described the importance of subdomain separation in the conversion of prion protein (PrP). The goal of the present study was to investigate the effect of increasing the hydrophobic interactions within the H2-H3 subdomain on PrP conversion. Three hydrophobic mutations were introduced into PrP. The mutation V209I associated with human prion disease did not alter protein stability or in vitro fibrillization propensity of PrP. The designed mutations V175I and T187I on the other hand increased protein thermal stability. V175I mutant fibrillized faster than wild-type PrP. Conversion delay of T187I was slightly longer, but fluorescence intensity of amyloid specific dye thioflavin T was significantly higher. Surprisingly, cells expressing V209I variant exhibited inefficient proteinase K resistant PrP formation upon infection with 22L strain, which is in contrast to cell lines expressing wild-type, V175I and T187I mPrPs. In agreement with increased ThT fluorescence at the plateau T187I expressing cell lines accumulated an increased amount of the proteinase K-resistant prion protein. We showed that T187I induces formation of thin fibrils, which are absent from other samples. We propose that larger solvent accessibility of I187 in comparison to wild-type and other mutants may interfere with lateral annealing of filaments and may be the underlying reason for increased conversion efficiency. 相似文献
120.