45. Biochemistry And Cell Biology

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45. Biochemistry And Cell Biology

 

 

CATEGORY: Medical & Medicine – 500 Courses

COURSE NUMBER: 45

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BOOKS/ MANUALS: Pages

Syllabus

ABSTRACT…………………………………………………………………………………………………….iii
LIST OF ILLUSTRATIONS………………………………………………………………………………ix
LIST OF TABLES …………………………………………………………………………………………..xii
ACKNOWLEDGMENTS ………………………………………………………………………………..xiv
DEDICATION……………………………………………………………………………………………….xvi
Chapter
1. STRUCTURAL ANALYSES OF THE HEMOPEXIN PROTEIN AS A MEANS
TO INFER THE EVOLUTION OF FUNCTIONALITY BETWEEN THE PEX
DOMAIN CONTAINING PROTEINS
a). Introduction……………………………………………………………………………………………1
b). Methods………………………………………………………………………………………………..7
c). Results ………………………………………………………………………………………………….8
2. DISCOVERY AND CHARACTERIZATION OF THE JEN-14 EPITOPE AS A
MOLECULAR SYNAPOMORPHY IN HEMOPEXIN
a). Introduction…………………………………………………………………………………………. 14
b). Methods……………………………………………………………………………………………… 15
c). Results ……………………………………………………………………………………………….. 16
d). Discussion and Conclusions…………………………………………………………………… 18
3. PHYLOGENOMIC ANALYSES PROVIDE INSIGHTS INTO PATTERNS OF
FUNCTIONAL DIVERSITY BETWEEN PEX DOMAIN CONTAINING
PROTEINS
a). Introduction…………………………………………………………………………………………. 22
b). Methods……………………………………………………………………………………………… 32
c). Results ……………………………………………………………………………………………….. 33
4. DISCUSSION AND CONCLUSIONS OF RESULTS FROM CHAPTERS 1-4
a). Discussion…………………………………………………………………………………………… 39
b). Conclusions ………………………………………………………………………………………… 48

5. DETERMINATION OF THE TERTIARY STRUCTURE OF THE PEX
DOMAIN IN THE HUMAN PROTEOGLYCAN-4 (LUBRICIN) PROTEIN
a). Introduction…………………………………………………………………………………………. 54
b). Methods and Results…………………………………………………………………………….. 59
6. EVOLUTIONARY ANALYSES OF TARGET GENES IDENTIFIED AS
POTENTIAL GENETIC MARKERS OF COMPLICATIONS ASSOCIATED
WITH DIET-INDUCED OBESITY
a). Introduction…………………………………………………………………………………………. 92
b). Methods and Results…………………………………………………………………………….. 99
c). Discussion…………………………………………………………………………………………. 108
Appendix
A. SUPPLEMENTAL INFORMATION ON 4-BLADED β-PROPELLER DOMAIN
CONTAINING PROTEINS ……………………………………………………………………… 112
B. LIST OF THE HUMAN MMPs INCLUDED IN THE PHYLOGENIES ALONG
WITH A BRIEF DESCRIPTION OF KNOWN FUNCTIONALITY……………….. 114
C. PRIMARY SEQUENCE IDENTITY BETWEEN VARIOUS PEX DOMAINS:
HPX, MMPs PRG4, VTN…………………………………………………………………………. 117
D. PRIMARY SEQUENCE AND HOMOLOGY MODEL OF THE PROTEIN
LIMUNECTIN FROM HORSESHOE CRAB …………………………………………….. 118
E. PRG4 – PEX-DOMAIN DNA NUCLEOTIDE SEQUENCE (SHOWN AS
CODONS) USED FOR ORDERING OF THE GBLOCK FOR CLONING,
EXPRESSION AND PURIFICATION………………………………………………………. 119
F. pET-44a-c(+) VECTOR MAP……………………………………………………………………… 120
G. RETURN OF RESULTS FROM MU-DNA LIMS SEQUENCING FACILITY
SUBMISSION OF SAMPLE FROM COLONY 8 FROM PCR OF
TRANSFORMED LIGATION PRODUCTS OF THE PRG4 PEX DOMAIN
pET44 CONSTRUCT………………………………………………………………………………. 121
H. ANALYSES FROM MASS SPECTROMETRY ON PRG4 PEX-DOMAIN ………. 122
I. SEQUENCE ALIGNMENTS FOR THE Atp1a3 PROTEIN IN PRIMATES
ROOTED WITH MURINES ……………………………………………………………………. 126

J. ACCESSION NUMBERS FOR ALL PROTEINS USED IN PHYLOGENETIC
AND/OR STATISTICAL ANALYSES………………………………………………………… 129
REFERENCES……………………………………………………………………………………………… 132
VITA…………………………………………………………………………………………………………… 151

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