Biomedical subjects

Jun'ichi Suzuki

Publications and source records attributed to Jun'ichi Suzuki.

5 recordsLinked to original sources

PubMed2006

Protein threading with profiles and distance constraints using clique based algorithms.

With the advent of experimental technologies like chemical cross-linking, it has become possible to obtain distances between specific residues of a newly sequenced protein. These types of experiments usually are less time consuming than X-ray crystallography or NMR. Consequently, it is highly desired to develop a method that incorporates this distance information to improve the performance of protein threading methods. However, protein threading with profiles in which constraints on distances between residues are given is known to be NP-hard. By using the notion of a maximum edge-weight clique finding algorithm, we introduce a more efficient method called FTHREAD for profile threading with distance constraints that is 18 times faster than its predecessor CLIQUETHREAD. Moreover, we also present a novel practical algorithm NTHREAD for profile threading with Non-strict constraints. The overall performance of FTHREAD on a data set shows that although our algorithm uses a simple threading function, our algorithm performs equally well as some of the existing methods. Particularly, when there are some unsatisfied constraints, NTHREAD (Non-strict constraints threading algorithm) performs better than threading with FTHREAD (Strict constraints threading algorithm). We have also analyzed the effects of using a number of distance constraints. This algorithm helps the enhancement of alignment quality between the query sequence and template structure, once the corresponding template structure is determined for the target sequence.

Algorithms↗

PubMed2005

A fatal case of ruptured giant coronary artery aneurysm.

A 5-year-old Japanese boy died because of a ruptured left coronary artery aneurysm (CAA). He was diagnosed as having Kawasaki disease (KD) on the 5th day from onset, with all of the principal signs. On the 7th day of illness, bilateral CAAs were already found via echocardiography, and he was treated with intravenous (IV) gamma globulin and oral ASA. However, the fever persisted and the CAA progressed rapidly. Echocardiography on the 12th illness day showed a giant (18-mm) left anterior descending (LAD) artery aneurysm. Oral propranolol and nifedipine were administered, in conjunction with warfarin/aspirin anti-coagulation therapy. On the 13th day of illness, cardiac arrest developed abruptly, and, despite cardiopulmonary resuscitation (CPR), the patient remained unresponsive and died one hour later. The final pathological diagnosis was a ruptured LAD artery aneurysm and cardiac tamponade. Microscopic investigation of the ruptured vascular wall revealed marked neutrophilic infiltration, with fewer macrophages and lymphocytes. CAA ruptures are a very rare, but fatal, complication of KD. Based on a review of previous reports on CAA ruptures, we consider it useful to distinguish aneurysms which rapidly dilate and continue to expand beyond a diameter of 10 mm with ongoing vasculitis (these CAAs can be termed "super-giant") from the more common giant CAAs limited to a diameter of 8 or 9 mm, because a decision must be made as to whether to start intensive care or to intervene surgically, in order to ensure the survival of patients with such a potentially critical complication.

Aneurysm, Ruptured↗

PubMed2005

Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach.

"Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique by applying an efficient clique finding algorithm developed by our co-authors. Since our approach is based on deterministic algorithms in contrast to the various existing algorithms based on heuristic approaches, our algorithm guarantees of finding an optimal solution. We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found that our results are favorably comparable or better than the results produced by the existing methods. As our test set contains a protein of 494 residues, we have obtained considerable improvement in terms of size of the proteins and in terms of the efficiency and the accuracy of prediction.

Algorithms↗

PubMed2003

Expression of proliferating cell nuclear antigen in rat hearts subjected to transient ischemia followed by reperfusion.

Early mechanisms involved in improving capillarity and oxygen transport to cardiac tissue exposed to transient coronary ischemia followed by reperfusion were studied in rats. Under ether anaesthesia, the left coronary artery was mechanically occluded for 3 min after which it was released, and the rats allowed to recover. After 2, 24 or 48 h the rats were sacrificed and the hearts frozen in liquid nitrogen. Frozen cross-sections were stained immunohistochemically for proliferating cell nuclear antigen (PCNA) and for the growth factors, VEGF and bFGF. No reaction for PCNA was seen in sections of sham-operated hearts but an inhomogeneous reaction occurred in annular structures in the occluded hearts at 48 h reperfusion. The stain appeared to be located in proliferating nuclei, and in the cytosol of endothelial cells. It is suggested that PCNA is stimulated by the increase in growth factors that is known to occur within 2 h after the end of the coronary occlusion. It is concluded that the increase in capillarity, indicated by the nuclear proliferation of endothelial cells, will improve the transport of oxygen to the cardiac tissues.

Animals↗

PubMed2002

Coronary ischemia/reperfusion increases proliferating cell nuclear antigen in vascular endothelial cells in rat hearts.

To elucidate the sequence of early events in the increase in capillarity caused by reperfusion following transient coronary occlusion, the time course of expression of proliferating cell nuclear antigen (PCNA) was studied immunohistochemically in rat hearts subjected to different periods of reperfusion after a 3 minute occlusion. Twenty-one male Wistar rats were killed after different periods of reperfusion following occlusion of the coronary artery for 3 minutes. The left ventricles were removed and paired serial sections were treated immunohistochemically for PCNA or stained to show the enzymes characteristic of the arteriolar, intermediate and venular portions of the capillary bed. The time course of PCNA expression, and its distribution in relation to the different portions, was examined. An increase in PCNA-expressing nuclei was found at 24 hours after the start of reperfusion; numbers reached a maximum between 72 and 96 hours, and at 168 hours had decreased again. The majority of PCNA-expressing elements were localized to the dipeptidylpeptidase IV-reactive (i.e. venular) capillary portions, with some in the intermediate and alkaline phosphatase-reactive (i.e. arteriolar) portions. The distribution of PCNA in the early reperfusion period suggests that angiogenesis after transient ischemia occurs mainly from the venular side of the capillary bed, with some contribution from intermediate and arteriolar capillary portions.

Animals↗