Entity

Time filter

Source Type


Matsuda A.,University of California at San Francisco | Matsuda A.,National Institute of Communication Technology | Shao L.,University of California at San Francisco | Shao L.,Howard Hughes Medical Institute | And 8 more authors.
PLoS ONE | Year: 2010

Photoactivated localization microscopy (PALM) and related fluorescent biological imaging methods are capable of providing very high spatial resolutions (up to 20 nm). Two major demands limit its widespread use on biological samples: requirements for photoactivatable/photoconvertible fluorescent molecules, which are sometimes difficult to incorporate, and high background signals from autofluorescence or fluorophores in adjacent focal planes in three-dimensional imaging which reduces PALM resolution significantly. We present here a high-resolution PALM method utilizing conventional EGFP as the photoconvertible fluorophore, improved algorithms to deal with high levels of biological background noise, and apply this to imaging higher order chromatin structure. We found that the emission wavelength of EGFP is efficiently converted from green to red when exposed to blue light in the presence of reduced riboflavin. The photon yield of redconverted EGFP using riboflavin is comparable to other bright photoconvertible fluorescent proteins that allow < 20 nm resolution. We further found that image pre-processing using a combination of denoising and deconvolution of the raw PALM images substantially improved the spatial resolution of the reconstruction from noisy images. Performing PALM on Drosophila mitotic chromosomes labeled with H2AvD-EGFP, a histone H2A variant, revealed filamentous components of ~70 nm. This is the first observation of fine chromatin filaments specific for one histone variant at a resolution approximating that of conventional electron microscope images (10-30 nm). As demonstrated by modeling and experiments on a challenging specimen, the techniques described here facilitate super-resolution fluorescent imaging with common biological samples. © 2010 Matsuda et al.


Matsuda A.,Purdue University | Shieh A.W.-Y.,Washington University in St. Louis | Shieh A.W.-Y.,National Institute of Communication Technology | Chalker D.L.,Washington University in St. Louis | Forney J.D.,Purdue University
Eukaryotic Cell | Year: 2010

Development in ciliated protozoa involves extensive genome reorganization within differentiating macronuclei, which shapes the somatic genome of the next vegetative generation. Major events of macronuclear differentiation include excision of internal eliminated sequences (IESs), chromosome fragmentation, and genome amplification. Proteins required for these events include those with homology throughout eukaryotes as well as proteins apparently unique to ciliates. In this study, we identified the ciliate-specific Defective in IES Excision 5 (DIE5) genes of Paramecium tetraurelia (PtDIE5) and Tetrahymena thermophila (TtDIE5) as orthologs that encode nuclear proteins expressed exclusively during development. Abrogation of PtDie5 protein (PtDie5p) function by RNA interference (RNAi)-mediated silencing or TtDie5p by gene disruption resulted in the failure of developing macronuclei to differentiate into new somatic nuclei. Tetrahymena ΔDIE5 cells arrested late in development and failed to complete genome amplification, whereas RNAi-treated Paramecium cells highly amplified new macronuclear DNA before the failure in differentiation, findings that highlight clear differences in the biology of these distantly related species. Nevertheless, IES excision and chromosome fragmentation failed to occur in either ciliate, which strongly supports that Die5p is a critical player in these processes. In Tetrahymena, loss of zygotic expression during development was sufficient to block nuclear differentiation. This observation, together with the finding that knockdown of Die5p in Paramecium still allows genome amplification, indicates that this protein acts late in macronuclear development. Even though DNA rearrangements in these two ciliates look to be quite distinct, analysis of DIE5 establishes the action of a conserved mechanism within the genome reorganization pathway. © 2010, American Society for Microbiology.


Yaginuma N.,Ibaraki University | Umehira M.,Ibaraki University | Harada H.,National Institute of Communication Technology
IEICE Transactions on Communications | Year: 2014

In cognitive radio systems using TV white space, it is desirable to secure a control channel to exchange the wireless network control information and to secure minimum frequency resource for secondary user communications if TV white space is unavailable. In order to satisfy these requirements, this paper proposes guard band utilization, which aggregates the multiple guard bands between digital TV signals and uses them for a control channel and/or a communication channel. To investigate the feasibility of the proposed scheme, this paper evaluates the performance degradation of the digital TV signals when the guard band is used. Furthermore, it discusses the permissible transmitting power and occupied bandwidth of the guard band signals to avoid the harmful interference to the digital TV signals. Copyright © 2014 The Institute of Electronics, Information and Communication Engineers.


Song W.,Canon Inc. | Finch A.,National Institute of Communication Technology | Tanaka-Ishii K.,Kyushu University | Yasuda K.,National Institute of Communication Technology | Sumita E.,National Institute of Communication Technology
Transactions on Interactive Intelligent Systems | Year: 2013

picoTrans is a prototype system that introduces a novel icon-based paradigm for cross-lingual communication on mobile devices. Our approach marries a machine translation system with the popular picture book. Users interact with picoTrans by pointing at pictures as if it were a picture book; the system generates natural language from these icons and the user is able to interact with the icon sequence to refine the meaning of the words that are generated. When users are satisfied that the sentence generated represents what they wish to express, they tap a translate button and picoTrans displays the translation. Structuring the process of communication in this way has many advantages. First, tapping icons is a very natural method of user input on mobile devices; typing is cumbersome and speech input errorful. Second, the sequence of icons which is annotated both with pictures and bilingually with words is meaningful to both users, and it opens up a second channel of communication between them that conveys the gist of what is being expressed. We performed a number of evaluations of picoTrans to determine: its coverage of a corpus of in-domain sentences; the input efficiency in terms of the number of key presses required relative to text entry; and users' overall impressions of using the system compared to using a picture book. Our results show that we are able to cover 74% of the expressions in our test corpus using a 2000-icon set; we believe that this icon set size is realistic for a mobile device. We also found that picoTrans requires fewer key presses than typing the input and that the system is able to predict the correct, intended natural language sentence from the icon sequence most of the time, making user interaction with the icon sequence often unnecessary. In the user evaluation, we found that in general users prefer using picoTrans and are able to communicate more rapidly and expressively. Furthermore, users had more confidence that they were able to communicate effectively using picoTrans. © 2013 ACM.


Inoue F.,Kansai University | Yokoyama T.,Kansai University | Miyake H.,Kansai University | Tanaka S.,National Institute of Communication Technology | And 2 more authors.
2010 IEEE International Interconnect Technology Conference, IITC 2010 | Year: 2010

Low cost and low temperature fabrication process is required for TSV. In this study, we propose a low temperature deposition of barrier and copper seed layers by wet process only using electroless plating. Moreover, we use AuNPs as a catalyst which is densely adsorbed on SiO2 sidewall of TSV with SAM. We succeeded in conformal deposition of barrier and seed layers, and this method is effective for realizing a low resistance Cu-filled TSV. ©2010 IEEE.

Discover hidden collaborations