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 )