Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system

Background: A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we utilised the latest information on the mouse transcriptome as revealed by the RIKEN FANTOM2 project to identify novel human disease-related candidate genes. We define a new term patholog to mean a homolog of a human disease-related gene encoding a product ( transcript, anti-sense or protein) potentially relevant to disease. Rather than just focus on Mendelian inheritance, we applied the analysis to all potential pathologs regardless of their inheritance pattern. Results: Bioinformatic analysis and human curation of 60,770 RIKEN full-length mouse cDNA clones produced 2,578 sequences that showed similarity ( 70 - 85% identity) to known human-disease genes. Using a newly developed biological information extraction and annotation tool ( FACTS) in parallel with human expert analysis of 17,051 MEDLINE scientific abstracts we identified 182 novel potential pathologs. Of these, 36 were identified by computational tools only, 49 by human expert analysis only and 97 by both methods. These pathologs were related to neoplastic ( 53%), hereditary ( 24%), immunological ( 5%), cardio-vascular (4%), or other (14%), disorders. Conclusions: Large scale genome projects continue to produce a vast amount of data with potential application to the study of human disease. For this potential to be realised we need intelligent strategies for data categorisation and the ability to link sequence data with relevant literature. This paper demonstrates the power of combining human expert annotation with FACTS, a newly developed bioinformatics tool, to identify novel pathologs from within large-scale mouse transcript datasets.

Reproductive system of the male hermit crab Clibanarius sclopetarius: gonopore, spermatophore, and spermatozoal morphologies

In the present study, the morphology and biometry of the spermatophores of the western Atlantic hermit crab Clibanarius sclopetarius (Herbst, 1796) are described, and the results are placed in the context of the Paguroidea, in particular the Diogenidae. Individuals of C. sclopetarius were sampled from a human-impacted mangrove area of southern Brazil. The male reproductive system was removed, measured and analyzed using stereoscopic, light, transmission-electron and scanning-electron microscopy. This system is composed of lobular testes connected to the vas deferens, and gonopores with membranous coverage. The mature spermatophore consists of a spherical pack that stores sperm. These cells consist of a spherical acrosomal vesicle, an amorphous cytoplasm and a distal nucleus. The results revealed that the gonopores, testis and vas deferens have the expected characteristics of the family Diogenidae, while the non-tripartite morphology of the spermatophores and the sperm follow the patterns found only in the genus Clibanarius, and the presence of the dense perforatorial ring is, to date, unique in the species of the genus, being a possible apomorphic characteristic.

Reproductive biology of Echinodorus longipetalus (Alismataceae): Sexual morphs, breeding system and pollinators

The floral biology, pollinators and breeding system of Echinodorus longipetalus Micheli were studied in a marshy area of the district of Taquaritinga (State of Sao Paulo), southeastern Brazil. E. longipetalus is gynodioecious and as far as is known, this is the first record of unisexual flowers, besides perfect flowers, in Echinodorus. Proportion of female individuals in the studied population is 50% and produces 31% more flowers than hermaphrodites. Perfect and pistillate flowers of E. longipetalus are similar in appearance and are pollinated by several species of Hymenoptera (mainly by Xylocopa (Neoxylocopa) suspecta Moure & Camargo). Perfect flowers offer pollen as a reward. Pistillate flowers attract floral visitors by deceit with their staminodes that resemble the stamens of the perfect flowers. Visits to pistillate flowers are quick (1-2 s), while visits to perfect flowers last up to 120 s. The perfect flowers are self-compatible and produce fruits through spontaneous self-pollination (control flowers), whereas the pistillate ones only set fruits through cross-pollinations. Perfect and pistillate flowers set more fruits under natural conditions than in manual treatments, respectively. Although the pistillate and perfect flowers bear a strong similarity, the selective pollinator behavior seems to be responsible for the increase of fruit set in perfect flowers. (C) 2008 Elsevier B.V. All rights reserved.

Process development for a recombinant Chinese Hamster Ovary (CHO) cell line utilizing a metal induced and amplified metallothionein expression system

The suspension Chinese Hamster Ovary cell line, 13-10-302, utilizing the metallothionein (MT) expression system producing recombinant human growth hormone (hGH) was studied in a serum-free and cadmium-free medium at different fermentation scales and modes of operation. Initial experiments were carried out to optimize the concentration of metal addition to induce the MT promoter. Subsequently, the cultivation of the 13-10-302 cell line was scaled up from spinner flasks into bioreactors, and the cultivation duration was extended with fed-batch and perfusion strategies utilizing 180 muM zinc to induce the promoter controlling expression of recombinant hGH. It was shown that a fed-batch process could increase the maximum cell numbers twofold, from 3.3 to 6.3 x 10(6) cell/mL, over those obtained in normal batch fermentations, and this coupled with extended fermentation times resulted in a fourfold increase in final hGH titer, from 135 +/- 15 to 670 +/- 70 mg/L at a specific productivity q(hGH) value of 12 pg cell(-1)d(-1). The addition of sodium butyrate increased the specific productivity of hGH in cells to a value of approximately 48 pg cell(-1)d(-1), resulting in a final hGH titer of over a gram per liter during fed-batch runs. A BioSep acoustic cell recycler was used to retain the cells in the bioreactor during perfusion operation. It was necessary to maintain the specific feeding rates (SFR) above a value of 0.2 vvd/(10(6) cell/mL) to maintain the viability and productivity of the 13-10-302 cells; under these conditions the viable cell number increased to over 107 cell/mL and resulted in a volumetric productivity of over 120 mg(hGH) L(-1)d(-1). Process development described in this work demonstrates cultivation at various scales and sustained high levels of productivity under cadmium free condition in a CHO cell line utilizing an inducible metallothionein expression system. (C) 2004 Wiley Periodicals, Inc.

Highly integrated and automated high-speed grinding system for printer heads constructed by combination materials

The fabrication of heavy-duty printer heads involves a great deal of grinding work. Previously in the printer manufacturing industry, four grinding procedures were manually conducted in four grinding machines, respectively. The productivity of the whole grinding process was low due to the long loading time. Also, the machine floor space occupation was large because of the four separate grinding machines. The manual operation also caused inconsistent quality. This paper reports the system and process development of a highly integrated and automated high-speed grinding system for printer heads. The developed system, which is believed to be the first of its kind, not only produces printer heads of consistently good quality, but also significantly reduces the cycle time and machine floor space occupation.