Interactions Between Oral Pathogens and Vascular Cells

描述（申请人提供）：牙龈卟啉单胞菌是成人牙周炎的主要病原。虽然作为一种牙周病原体已经确立，但最近人们认识到牙龈假单胞菌可能在全身性疾病（包括心血管疾病、早产和低出生体重）中起重要作用。心血管疾病是一组异质性疾病，是发达国家的主要死亡原因。因此，这种病原体造成的经济损失和心理影响可能是巨大的。在过去的几年里，我们研究了牙龈卟啉单胞菌的致病特性，重点研究了它与人体组织（包括冠状动脉内皮细胞）的相互作用和侵袭。然而，只有一株牙龈卟啉单胞菌全基因组序列的可用性阻碍了我们的研究工作。许多因素表明，由于菌株在某些毒力因素（包括相对宿主细胞侵袭能力）方面具有表型和基因异质性，因此应该对其他牙龈假单胞菌菌株进行调查。因此，本申请申请资金作为我们最近资助的竞争性更新（DE13545）的补充，以测序和注释P. gingivalis菌株381、33277、A7436和AJW4的基因组，然后进行比较基因组分析。基因组序列将使用由454生命科学公司（Branford， CT）开发的一种新的、具有成本效益的、大规模并行的DMA测序技术来确定。基因组组装将补充高达1倍的基因组覆盖使用配对端Sanger DNA测序读数。FGENESB将预测基因的位置和结构。根据公共基因数据的同源性搜索，将为预测的基因结构分配基因功能和名称。将进行成对基因组比较和多基因组比较，以确定这五个基因组中保守的同源物以及独特的基因。这些基因组中缺失的基因也将被确定。BLAST搜索、MUMmer程序和VISTA工具将用于这些目的。对于所有预测的蛋白质，将进行HMMER PFAM搜索以检测功能域。公共数据库中另外四个牙龈卟啉单胞菌全基因组序列的可用性将促进基础研究，包括父母对这一补充申请的资助，以及更快地开发诊断测试、治疗和预防策略。

DESCRIPTION (provided by applicant): Porphyromonas gingivalis is the major etiological agent of adult periodontitis. Although well established as a periodontal pathogen, it has more recently been recognized that P. gingivalis may have an important role in systemic disease, including cardiovascular diseases, prematurity and low birth weight. Cardiovascular diseases are a heterogeneous group of conditions that are the leading cause of death in developed countries. The economic losses and psychological repercussions caused by this pathogen are thus potentially enormous. During the past several years, we have investigated the pathogenic properties of P. gingivalis, focusing on its interactions with and invasion of human tissues, including coronary artery endothelial cells. However, the availability of the whole genome sequence of only one strain of P. gingivalis has hampered our research effort. Many factors suggest that investigation of other P. gingivalis strains should be pursued since strains are phenotypically and genotypically heterogeneous with regards to certain virulence factors including relative host cell invasive abilities. Consequently, this submission is requesting funding as a supplement to our recently funded competitive renewal (DE13545) to sequence and annotate the genomes of P. gingivalis strains 381, 33277, A7436, and AJW4, followed by comparative genomic analysis. Genome sequences will be determined using a new, cost-efficient, and massively parallel DMA sequencing technology developed by 454 Life Sciences (Branford, CT). Genome assembly will be supplemented with up to 1x genome coverage using paired-end Sanger DNA sequencing reads. Gene location and structures will be predicted using FGENESB. Gene function and names will be assigned to predicted gene structures based on homology searches of public gene data. Pairwise genome comparisons and multiple genome comparisons will be performed to identify orthologs that are conserved among these five genomes as well as unique genes. Genes that are missing from these genomes will also be determined. BLAST searches, MUMmer programs and VISTA tools will be used for these purposes. For all predicted proteins, a HMMER PFAM search will be conducted to detect functional domains. The availability of four additional whole genome sequences of P. gingivalis in public databases would facilitate basic research, including that of the parent grant to this supplemental application, and more rapid development of diagnostic tests, and treatment, and prevention strategies.