Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.
Genome ; Indonesia ; Pliability ; Sequence Alignment

The retinal vein occlusion is one of the most common retinal diseases, and the establishment of animal model in rats will be a great help for further study. We occluded branch retinal veins with rose bengal dye injection followed by argon-green laser photocoagulation in albino rats. Retinal vein occlusion was maintained over 1 day in 35 eyes out of 47, maximally over 5 days. Retinal tissue damage was confined to the photocoagulated areas in most eyes and the loss of ganglion cells began when the occlusion persisted over 1 day. If the reproducibility is further increased, this will be a good animal model of retinal vein occlusion in albino rats.
Animals ; Ganglion Cysts ; Light Coagulation ; Models, Animal ; Rats* ; Retinal Diseases ; Retinal Vein Occlusion* ; Retinal Vein* ; Retinaldehyde* ; Rose Bengal

The retinal vein occlusion is one of the most common vision-threatening retinal diseases, and both the hemi-central and central retinal vein occlusion might induce severe visual loss. There have been many studies on the role of abnormally produced oxygen free radicals and excitatory amino acids in the mechanism of ischemic retinal injury. Many free radical scavengers, such as superoxide dismutase (SOD), catalase, and EGB 761 were reported to reduce the extent of ischemic retinal injury in animal experiments. Ascorbic acid is also a well-known free radical scavenger, but its in vivo therapeutic effects on retinal ischemia has not been studied, yet. We induced experimental retinal vein occlusion in 48 albino rat eyes; half of major veins in 24 eyes (group A) and total veins in 24 eyes (group B), with rose bengal dye injection followed by argon-green laser photocoagulation. The occlusion of veins was confirmed with fluorescein angiography. We injected ascorbic acid intraperitoneally just after venous occlusion in 12 eyes for each group. Rats were sacrificed after I week (group A) or 2 weeks (group B) following experiment and histological examination was done. In both groups, inner retina was less damaged than outer retina. The density of retinal ganglion cells was reduced to a less degree in eyes of rats treated with ascorbic acid in group A(P=0.0318). These data support the idea that the reactive free adicals are involved in the mechanism of ischemic retinal injury and thus the ascorbic acid may attenuate the ischemic retinal damage.
Animal Experimentation ; Animals ; Ascorbic Acid* ; Catalase ; Excitatory Amino Acids ; Fluorescein Angiography ; Free Radical Scavengers ; Free Radicals ; Ischemia ; Light Coagulation ; Models, Animal ; Oxygen ; Rats ; Retina ; Retinal Diseases ; Retinal Ganglion Cells ; Retinal Vein Occlusion* ; Retinal Vein* ; Retinaldehyde* ; Rose Bengal ; Superoxide Dismutase ; Veins

The retinal vein occlusion is one of the most common, vision-threatening retinal diseases, and the establishment of animal model in rats will be of great help for further study. We occluded retinal veins with rose bengal dye injection followed by argon green laser photocoagulation in albino rats and confirmed the occlusion of veins with fluorescein angiography one hour after photocoagulation. We occluded half of an all of major retinal veins in 12 eyes, respectively. After 1-2 weeks of follow-up, histologic examinations were done. Eyes which underwent occlusion of all major retinal veins showed severe retinal atrophy and preretinal neovas-cularization developed in two eyes. Eyes which underwent occlusion of half of retinal veins showed relatively less damage and the number of retinal ganglion cells was significantly reduced in occluded area than that in control area (P=0.0033), which might represent the ischemic damage of inner retina. We expect that it will be possible to establish an animal model of retinal vein occlusion in albino rats using this method.
Animals ; Argon ; Atrophy ; Fluorescein Angiography ; Follow-Up Studies ; Light Coagulation ; Models, Animal ; Rats* ; Retina ; Retinal Diseases ; Retinal Ganglion Cells ; Retinal Vein ; Retinal Vein Occlusion ; Retinaldehyde ; Rose Bengal ; Veins*

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
Computational Biology ; Databases, Protein ; Indonesia ; Proteins ; Software

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
Computational Biology ; Databases, Protein ; Indonesia ; Proteins ; Software

To establish animal model of exudative retinal detachment in Sprague Dawley albino rats and to elucidate the possible role of retinal vein in the induction of exudative retinal detachments, rose bengal photosensitive dye was injected intravenously and argon laser was applied. In group A(10 eyes), laser was applied on intervascular retinal areas linearly. In group B (12 eyes), laser was applied on major retinal veins. In group C(4 eyes), laser was applied on major retinal arteris. In group D(3 eyes), laser was applied on major retinal veins without rose bengal dye and in group E(26 eyes), only the rose bengal dye was perfused. And in group F(3 eyes), normal eyes were fixed for negative controls. Exudative bullous retinal detachment occurred only in group B and these resutls were confirmed in histological examinations. In control groups (D and E), tissue injuries were not found. In conclusion, exudative retinal detachment could be induced by occlusion of retinal veins in albino rats and the abnormalities of retinal venous blood flow were required for the induction of exudative retinal detachment.
Animals ; Argon ; Models, Animal ; Rats* ; Retinal Detachment* ; Retinal Vein ; Retinaldehyde* ; Rose Bengal

The frequencies of multiple synchronous carcinomas of the colon and the rectum have been reported to range from 2.1 to 6.3%. Currently, the frequency is higher in colorectal cancer patients, and the diagnosis is better due to the many diagnostic tools that have been developed. There are a few reported cases of five cancers in a patient at the same time. We report here on the case of five synchronous cancers arising from the colon and the rectum in a patient without a familial history of colon cancer or of genetic predisposing factor. The patient was a 62-yr-old woman who presented with frequently loose stool for six months and intermittent abdominal pain for two months. Colonoscopic examination revealed two adenocarcinomas, one each at the sigmoid colon and the rectum; the cancer in the sigmoid colon was obstructed at nearly 40 cm above the anal verge. Computed tomographic colonoscopy revealed many other polyps and masses in the colon and a metastatic mass at segment 8 in the liver. A total proctocolectomy and ileostomy were performed. Histologic evaluation revealed the five lesions to be adenocarcinomas invading the pericolic fat; 1 out of 30 lymph nodes was invaded by the cancer cells.
Abdominal Pain ; Adenocarcinoma ; Colon ; Colon, Sigmoid ; Colonic Neoplasms ; Colonoscopy ; Colorectal Neoplasms ; Female ; Humans ; Ileostomy ; Liver ; Lymph Nodes ; Polyps ; Rectum

PURPOSE: Fitz-Hugh-Curtis (FHC) syndrome has been described as perihepatitis associated with pelvic inflammatory disease during surgery. Recently, on computerized tomography a linear enhancement of the liver capsule was detected in a patient with FHC syndrome. We studied to evaluate the clinical course of the disease. METHODS: Sixteen patients diagnosed with FHC syndrome from CT findings were retrospectively studied from April, 2006 to June, 2008. RESULTS: The mean age of the patients was 25.9 (19~35) years and mean duration of abdominal pain was 3.9 (1~14) days. The most common complaint was right upper quadrant area pain (11 cases, 68.8%). 12 patients showed leukocytosis and all the patients had elevated serum C-reative protein levels. All the patients had normal liver function. Among the 9 patients which had polymerase chain reaction test for sexually transmitted disease (Chlamydia trachomatis, Ureaplasma urealyticum, Neisseria gonorrheae, Mycoplasma hominis), all showed more than one positive results (Chlamydia trachomatis 6 cases, Ureaplasma urealyticum 6 cases, Mycoplasma hominis 2 cases). On simple abdomen X-ray, 7 cases (43.8%) showed paralytic ileus. 14 cases received only antibiotic treatment, but 1 case had to take operation (laparoscopic-assisted adhesiolysis) due to constant abdominal pain and prolonged ileus. CONCLUSION: It is important to rule out FHC syndrome by using CT findings, especially young women with right upper abdominal pain and PID. Usually, FHC syndrome can be treated easily with proper antibiotics.
Abdomen ; Abdominal Pain ; Anti-Bacterial Agents ; Chlamydia Infections ; Female ; Gonorrhea ; Hepatitis ; Humans ; Ileus ; Intestinal Pseudo-Obstruction ; Leukocytosis ; Liver ; Mycoplasma ; Mycoplasma hominis ; Neisseria ; Pelvic Inflammatory Disease ; Peritonitis ; Polymerase Chain Reaction ; Retrospective Studies ; Sexually Transmitted Diseases ; Ureaplasma urealyticum

The static approach of representing metabolic pathway diagrams offers no flexibility. Thus, many systems adopt automatic graph layout techniques to visualize the topological architecture of pathways. There are weaknesses, however, because automatically drawn figures are generally difficult to understand. The problem becomes even more serious when we attempt to visualize all of the information in a single, big picture, which usually results in a confusing diagram. To provide a partial solution to this thorny issue, we propose J2dpathway, a metabolic pathway atlas viewer that has node-abstracting features.
Metabolic Networks and Pathways ; Pliability