Topic
MaMF
About: MaMF is a research topic. Over the lifetime, 11 publications have been published within this topic receiving 164 citations.
Papers
TL;DR: The data demonstrate the use of GFP as a reporter for protein localization under magnetite-forming conditions and the utility of MamC as an anchor for magnetosome-specific display of heterologous gene fusions.
Abstract: The magnetosomes of magnetotactic bacteria are prokaryotic organelles consisting of a magnetite crystal bounded by a phospholipid bilayer that contains a distinct set of proteins with various functions. Because of their unique magnetic and crystalline properties, magnetosome particles are potentially useful as magnetic nanoparticles in a number of applications, which in many cases requires the coupling of functional moieties to the magnetosome membrane. In this work, we studied the use of green fluorescent protein (GFP) as a reporter for the magnetosomal localization and expression of fusion proteins in the microaerophilic Magnetospirillum gryphiswaldense by flow cytometry, fluorescence microscopy, and biochemical analysis. Although optimum conditions for high fluorescence and magnetite synthesis were mutually exclusive, we established oxygen-limited growth conditions, which supported growth, magnetite biomineralization, and GFP fluorophore formation at reasonable rates. Under these optimized conditions, we studied the subcellular localization and expression of the GFP-tagged magnetosome proteins MamC, MamF, and MamG by fluorescence microscopy and immunoblotting. While all fusions specifically localized at the magnetosome membrane, MamC-GFP displayed the strongest expression and fluorescence. MamC-GFP-tagged magnetosomes purified from cells displayed strong fluorescence, which was sensitive to detergents but stable under a wide range of temperature and salt concentrations. In summary, our data demonstrate the use of GFP as a reporter for protein localization under magnetite-forming conditions and the utility of MamC as an anchor for magnetosome-specific display of heterologous gene fusions.
111 citations
TL;DR: A novel algorithm, MaMF, for identifying transcription factor (TF) binding site motifs that is deterministic and depends on an indexing technique to optimize the search process, suitable for application to large numbers of interesting gene sets.
Abstract: Motivation: We present a novel algorithm, MaMF, for identifying transcription factor (TF) binding site motifs. The method is deterministic and depends on an indexing technique to optimize the search process. On common yeast datasets, MaMF performs competitively with other methods. We also present results on a challenging group of eight sets of human genes known to be responsive to a diverse group of TFs. In every case, MaMF finds the annotated motif among the top scoring putative motifs. We compared MaMF against other motif finders on a larger human group of 21 gene sets and found that MaMF performs better than other algorithms. We analyzed the remaining high scoring motifs and show that many correspond to other TFs that are known to co-occur with the annotated TF motifs. The significant and frequent presence of co-occurring transcription factor binding sites explains in part the difficulty of human motif finding. MaMF is a very fast algorithm, suitable for application to large numbers of interesting gene sets.
Availability: The software is available for academic research use free of charge by email request.
Contact: [email protected]
Supplemental information: Data comprising the benchmarks used in the paper may be downloaded from http://www.jainlab.org/downloads.html.
23 citations
TL;DR: The first comprehensive high-resolution crystal structure analyses of the inhibitor-free form and the eight types of inhibitor against the cytokine activity of mouse AMF, finding the inhibitory activities of the six-carbon sugar complexes were found to be significantly higher than those of the four or five-carbon sugars.
17 citations
Abstract: DNA motifs are short sequences varying from 6 to 25 bp and can be highly variable and degenerated. One major approach for predicting transcription factor (TF) binding is using position weight matrix (PWM) to represent information content of regulatory sites; however, when used as the sole means of identifying binding sites suffers from the limited amount of training data available and a high rate of false-positive predictions. ChIPMotifs program is a de novo motif finding tool developed for ChIP-based high-throughput data, and W-ChIPMotifs is a Web application tool for ChIPMotifs. It composes various ab initio motif discovery tools such as MEME, MaMF, Weeder and optimizes the significance of the detected motifs by using bootstrap re-sampling error estimation and a Fisher test. Using these techniques, we determined a PWM for OCT4 which is similar to canonical OCT4 consensus sequence. In a separate study, we also use de novo motif discovery to suggest that ZNF263 binds to a 24-nt site that differs from the motif predicted by the zinc finger code in several positions.
5 citations
9 Sep 2010
TL;DR: From the result, the MAMF method is superior to the conventional methods in the impulse noise, especially for the intermediate-density and high-density noise, providing a quite stable performance over a wide variety of density of noise.
Abstract: In this paper, basing on the statistical features of the image, we propose a modified adaptive median filter (MAMF) for removal of impulse noise, especially for the high-density impulse noises. To avoid the shortcoming of the adaptive median filter (AMF) and the adaptive threshold median filter (ATMF), this method has been designed by combining the AMF with the Decision-Based Algorithm (DBA). From the result, the MAMF method is superior to the conventional methods in the impulse noise, especially for the intermediate-density and high-density noise, providing a quite stable performance over a wide variety of density of noise. Meanwhile, the downward tendency of the PNSR value of MAMF is gentler, with the higher quality than the DBA and the AMF.
4 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2021 | 1 |
| 2019 | 1 |
| 2018 | 1 |
| 2014 | 1 |
| 2012 | 1 |
| 2010 | 2 |