Genomics
• study of molecular organization of genomes, their information content, and gene products they encode
• divided into three areas– structural genomics
• physical nature of genomes
– functional genomics• how genome functions
– comparative genomics• compares genomes of different organisms
Functional Genomics
• determination of how genome works
• three common approaches– genome annotation – study of RNA-level gene expression– study of protein-level gene expression
Genome Annotation
Evaluation of Protein-Level Gene Expression
• proteome– entire collection of proteins that an organism
produces
• proteomics– study of the proteome
Types of proteomic analysis
• functional proteomics– study of function of cellular proteins, how they
interact, and ways they are regulated
• structural proteomics– using known protein structures to predict three-
dimensional structures of other proteins and protein complexes
Evaluation of Protein-Level Gene Expression…
• usual approach is two-dimensional gel electrophoresis
• can also couple two-dimensional gel electrophoresis with mass spectrometry
Two-dimensional gel electrophoresis• separation of a mixture of proteins
along two dimensions– first dimension – isoelectric focusing
• each protein moves through pH gradient until reaches pH that equals its isoelectric point
– second dimension – SDS gel electrophoresis
• proteins separated based on size
Two-dimensional gel electrophoresis• when coupled with mass spectrometry,
used to:– determine mass of each protein– determine amino acid composition or
sequence of each protein– identify protein
Pandey et.al., Nature 405 (2000)
Eukaryotic translation initiation factor5A(eIF-5A)
Stanley Fields, Science 291
Proteomic analysis of the impact of Antrodia camphorata extract on human lung can
cer A549 cell
樟芝– 別名「紅樟」、「紅樟芝」– 學名為（ Antrodia camphorata ）
使用樟芝最早的是原住民– 受驚、風寒、中暑、頭疼、跌打損傷、中毒等內臟任何疾病都使用樟芝，為原住民的「法寶」
樟芝子實體具有強烈沖鼻的樟樹香氣，它的外型呈板狀或鐘狀，面為橘紅 (黃 )色，整面全有菌孔
樟芝最早的研究文獻報告在1990年發表，歸類為靈芝屬。
1995年張東柱等人依樟芝子實體型態及真菌的培養基特性，將樟芝重新命名為 Antrodia cinnamomea
1997年吳聲華等人，依據前兩次文獻將樟芝命名 Antrodia camphorata 。
樟芝的生理活性物質以三帖類、固醇類、多醣體等化合物為主
抗菌研究•樟芝的甲醇萃取物可以有效抑制金黃葡萄球菌及鬚滄小芽癬生長，且對腸道弛緩運動、血小板凝集作用以及多種腸道菌有抑制效果
•樟芝菌絲多醣體具有抑制B型肝炎抗毒以及抑制B型肝炎病毒核心抗原(HBe)的活性
Lee et.al., FEMS Microbiology Letters 209 (2002)
保肝作用•Song 等人 (2002) 利用四氯化碳誘導大鼠急性肝損傷，來測試樟芝菌絲體深層培養之發酵濾液乾燥物 (DMF) –降低肝臟血清之發炎指標 -GOT 及 GPT 之生化值–在肝臟組織病理切片中發現，能降低 CCl4對大鼠引發之肝細胞發炎 (inflammation) 及壞死 (necrosis) 等肝損傷現象
對腫瘤細胞反應能力
•Hsue 等人 (2004) 可引發 HL-60 進行 apoptosis
Solid-state cultured Antrodia camphorata mycelia ( 薇得生化科技公司 )
Ethanol extract (SACE)
The influence of SACE on the survival of A549 cells
The influence of SACE on the survival of MRC5 cell
SACEControl
The calpain inhibitor CP1B MMP-mRNA
expression in the leukemic THP-1 cells (Popp
et. al., Biol Chem 384)
MMP-2
Actin
AC(-) AC(+)
Human Galectin-1
A beta-galactoside binding protein.
Cell adhesion, cell proliferation, and cell death.
Tumor-immune privilege .
(Rubinstein et. al., Cancer cell 5,2004)
Tumor Cell Proliferation
(Activated)
Galectin-1
AC(+)AC(-)
Eukaryotic translation initiation factor 5A
(eIF-5A) Lysine residue hypusine Proliferation and transformation of eukaryotic
cells Highly expressed in tumor cells. (Prostate,o
varian, lung adenocarcinomas )
Chen et. al. Proteomics 2003
down-regulation of hypusine synthesis Carraglia et. al., Adv Exp Med Biol. 472
Eukaryotic translation initiation factor 5A
(eIF-5A)
Human calcium-dependent protease (Calpain)
Cell progression to apotosis
v-src transformation (Carraglia et. al., Mol. Cell. Biol. 22)
Degradation of p53 (Kubbatut et. al., Mol. Cell. Biol. 17)
Calpain inhibitor 1 p53-dependent apotosis (Atencio et. al., Cell Growth Differ. 11)
Annexin V
A calcium-binding protein annexin V
As inhibitor of protein kinase C
Annexin V proteins are highly expressed in tumor cells, including breast tumor, bladder cancer)
(Celis et. al., Mol. Cell. Proteomics 1)
Rho-GDP dissociation inhibitor
Regulate the Rho family proteins
Down-regulation of Rho-GDP dissociation
inhibitor induce the apotosis of lung
cancer H157 cell (MacKeigan et. al., Cancer Res.
63 )
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