Biomedical subjects

Takuma Ishida

Publications and source records attributed to Takuma Ishida.

3 recordsLinked to original sources

PubMed2005

Motion-JPEG2000 codec compensated for interlaced scanning videos.

This paper presents an implementation scheme of Motion-JPEG2000 (MJP2) integrated with invertible deinterlacing. In previous work, we developed an invertible deinterlacing technique that suppresses the comb-tooth artifacts which are caused by field interleaving for interlaced scanning videos, and affect the quality of scalable frame-based codecs, such as MJP2. Our technique has two features, where sampling density is preserved and image quality is recovered by an inverse process. When no codec is placed between the deinterlacer and inverse process, the original video is perfectly reconstructed. Otherwise, it is almost completely recovered. We suggest an application scenario of this invertible deinterlacer for enhancing the sophisticated signal-to-noise ratio scalability in the frame-based MJP2 coding. The proposed system suppresses the comb-tooth artifacts at low bitrates, while enabling the quality recovery through its inverse process at high bitrates within the standard bitstream format. The main purpose of this paper is to present a system that yields high quality recovery for an MJP2 codec. We demonstrate that our invertible deinterlacer can be embedded into the discrete.wavelet transform employed in MJP2. As a result, the energy gain factor to control rate-distortion characteristics can be compensated for optimal compression. Simulation results show that the recovery of quality is improved by, for example, more than 2.0 dB in peak signal-to-noise ratio by applying our proposed gain compensation when decoding 8-bit grayscale Football sequence at 2.0 bpp.

Algorithms↗

PubMed2004

Protein associations in DnaA-ATP hydrolysis mediated by the Hda-replicase clamp complex.

In Escherichia coli, the activity of ATP-bound DnaA protein in initiating chromosomal replication is negatively controlled in a replication-coordinated manner. The RIDA (regulatory inactivation of DnaA) system promotes DnaA-ATP hydrolysis to produce the inactivated form DnaA-ADP in a manner depending on the Hda protein and the DNA-loaded form of the beta-sliding clamp, a subunit of the replicase holoenzyme. A highly functional form of Hda was purified and shown to form a homodimer in solution, and two Hda dimers were found to associate with a single clamp molecule. Purified mutant Hda proteins were used in a staged in vitro RIDA system followed by a pull-down assay to show that Hda-clamp binding is a prerequisite for DnaA-ATP hydrolysis and that binding is mediated by an Hda N-terminal motif. Arg(168) in the AAA(+) Box VII motif of Hda plays a role in stable homodimer formation and in DnaA-ATP hydrolysis, but not in clamp binding. Furthermore, the DnaA N-terminal domain is required for the functional interaction of DnaA with the Hda-clamp complex. Single cells contain approximately 50 Hda dimers, consistent with the results of in vitro experiments. These findings and the features of AAA(+) proteins, including DnaA, suggest the following model. DnaA-ATP is hydrolyzed at a binding interface between the AAA(+) domains of DnaA and Hda; the DnaA N-terminal domain supports this interaction; and the interaction of DnaA-ATP with the Hda-clamp complex occurs in a catalytic mode.

Adenosine Triphosphatases↗

PubMed2004

DiaA, a novel DnaA-binding protein, ensures the timely initiation of Escherichia coli chromosome replication.

The DnaA protein is the initiator of Escherichia coli chromosomal replication. In this study, we identify a novel DnaA-associating protein, DiaA, that is required for the timely initiation of replication during the cell cycle. DiaA promotes the growth of specific temperature-sensitive dnaA mutants and ensures stable minichromosome maintenance, whereas DiaA does not decrease the cellular DnaA content. A diaA::Tn5 mutation suppresses the cold-sensitive growth of an overinitiation type dnaA mutant independently of SeqA, a negative modulator of initiation. Flow cytometry analyses revealed that the timing of replication initiation is disrupted in the diaA mutant cells as well as wild-type cells with pBR322 expressing the diaA gene. Gel filtration and chemical cross-linking experiments showed that purified DiaA forms a stable homodimer. Immunoblotting analysis indicated that a single cell contains about 280 DiaA dimers. DiaA stimulates minichromosome replication in an in vitro system especially when the level of DnaA included is limited. Moreover, specific and direct binding between DnaA and DiaA was observed, which requires a DnaA N-terminal region. DiaA binds to both ATP- and ADP-bound forms of DnaA with a similar affinity. Thus, we conclude that DiaA is a novel DnaA-associating factor that is crucial to ensure the timely initiation of chromosomal replication.

Bacterial Outer Membrane Proteins↗