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 threedimensional 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 cancer 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
Control
SACE
The calpain inhibitor CP1B  MMP-mRNA
expression in the leukemic THP-1 cells (Popp
et. al., Biol Chem 384)
AC(-)
MMP-2
Actin
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)
AC(-)
Galectin-1
AC(+)
Eukaryotic translation initiation factor 5A (eIF5A)
 Lysine residue
hypusine
 Proliferation and transformation of eukaryotic
cells
 Highly expressed in tumor cells.
(Prostate,ovarian, lung adenocarcinomas )
Chen et. al. Proteomics 2003
Eukaryotic translation initiation factor 5A (eIF-
5A)
 down-regulation of hypusine synthesis
Carraglia et. al., Adv Exp Med Biol. 472
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 )