APPENDICES - digital.library.adelaide.edu.au · 233 Table A1.2. The degenerate genetic code used to...

232

APPENDICES

Appendix 1: The genetic code and degenerate primer design

Table A1.1. Standard genetic triplet codes with their accompanying amino acids (Alberts

et al., 1994). Methionine (in red) is the start codon, which is encoded by only one triplet

(ATG). The stop codons are in blue.

T C A G

T

TTT

TTC

TTA

TTG

Phe (F)

“

Leu (L)

“

TCT

TCC

TCA

TCG

Ser (S)

“

“

“

TAT

TAC

TAA

TAG

Tyr (Y)

“

Stop

Stop

TGT

TGC

TGA

TGG

Cys (C)

“

Stop

Trp (W)

C

CTT

CTC

CTA

CTG

Leu (L)

“

“

“

CCT

CCC

CCA

CCG

Pro (P)

“

“

“

CAT

CAC

CAA

CAG

His (H)

“

Gln (Q)

“

CGT

CGC

CGA

CGG

Arg (R)

“

“

“

A

ATT

ATC

ATA

ATG

Ile (I)

“

“

Met (M)

ACT

ACC

ACA

ACG

Thr (T)

“

“

“

AAT

AAC

AAA

AAG

Asn (N)

“

Lys (K)

“

AGT

AGC

AGA

AGG

Ser (S)

“

Arg (R)

“

G

GTT

GTC

GTA

GTG

Val (V)

“

“

“

GCT

GCC

GCA

GCG

Ala (A)

“

“

“

GAT

GAC

GAA

GAG

Asp (D)

“

Glu (E)

“

GGT

GGC

GGA

GGG

Gly (G)

“

“

“

233

Table A1.2. The degenerate genetic code used to design primers.

Abbreviation letter Nucleotide represented

A A

C C

G G

T T

R AG

Y CT

M AC

K GT

W AT

S CG

B CGT

D AGT

H ACT

V ACG

N ACGT

234

Appendix 2: Phylogenetic Analysis by Maximum Likelihood (PAML)

seqfile = cterminal.txt * sequence data filename treefile = wholetree.txt * tree structure file name outfile = surfactantout * main result file name

noisy = 3 * 0,1,2,3,9: how much rubbish on the screen verbose = 1 * 0: concise; 1: detailed, 2: too much runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs CodonFreq = 3 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F) * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

model = 2 * models for codons: * 0:one, 1:b, 2:2 or more dN/dS ratios for branches * models for AAs or codon-translated AAs: * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

NSsites = 3 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; * 13:3normal>0

icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below Mgene = 0 * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff * AA: 0:rates, 1:separate

fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated kappa = 2 * initial or fixed kappa fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate omega = 1 * initial or fixed omega, for codons or codon-based AAs

fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha alpha = 0. * initial or fixed alpha, 0:infinity (constant rate) Malpha = 0 * different alphas for genes ncatG = 4 * # of categories in dG of NSsites models

clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis getSE = 1 * 0: don't want them, 1: want S.E.s of estimates RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

Small_Diff = .5e-6* cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?* ndata = 10* fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed method = 0 * 0: simultaneous; 1: one branch at a time

* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., * 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., * 10: blepharisma nu.* These codes correspond to transl_table 1 to 11 of GENEBANK.

Fig. A2.1. CODEML menu options given in the PAML program.

235

Table A2.1. Chi square distribution table used to determine whether the models used in chapter 3 provided a significantly better fit to the data than

the comparative model.

df p=0.25 0.2 0.15 0.1 0.05 0.025 0.02 0.01 0.005 0.0025 0.001 0.0005

1 1.32 1.64 2.07 2.71 3.84 5.02 5.41 6.63 7.88 9.14 10.83 12.12

2 2.77 3.22 3.79 4.61 5.99 7.38 7.82 9.21 10.6 11.98 13.82 15.2

3 4.11 4.64 5.32 6.25 7.81 9.35 9.84 11.34 12.84 14.32 16.27 17.73

4 5.39 5.59 6.74 7.78 9.49 11.14 11.67 13.23 14.86 16.42 18.47 20

5 6.63 7.29 8.12 9.24 11.07 12.83 13.33 15.09 16.75 18.39 20.51 22.11

6 7.84 8.56 9.45 10.64 12.53 14.45 15.03 16.81 13.55 20.25 22.46 24.1

7 9.04 5.8 10.75 12.02 14.07 16.01 16.62 18.48 20.28 22.04 24.32 26.02

8 10.22 11.03 12.03 13.36 15.51 17.53 18.17 20.09 21.95 23.77 26.12 27.87

9 11.39 12.24 13.29 14.68 16.92 19.02 19.63 21.67 23.59 25.46 27.83 29.67

10 12.55 13.44 14.53 15.99 18.31 20.48 21.16 23.21 25.19 27.11 29.59 31.42

11 13.7 14.63 15.77 17.29 19.68 21.92 22.62 24.72 26.76 28.73 31.26 33.14

12 14.85 15.81 16.99 18.55 21.03 23.34 24.05 26.22 28.3 30.32 32.91 34.82

13 15.93 15.58 18.9 19.81 22.36 24.74 25.47 27.69 29.82 31.88 34.53 36.48

14 17.12 18.15 19.4 21.06 23.68 26.12 26.87 29.14 31.32 33.43 36.12 38.11

15 18.25 19.31 20.6 22.31 25 27.49 28.26 30.58 32.8 34.95 37.7 39.72

16 19.37 20.47 21.79 23.54 26.3 28.85 29.63 32 34.27 36.46 39.25 41.31

17 20.49 21.61 22.98 24.77 27.59 30.19 31 33.41 35.72 37.95 40.79 42.88

18 21.6 22.76 24.16 25.99 28.87 31.53 32.35 34.81 37.16 39.42 42.31 44.43

236

df p=0.25 0.2 0.15 0.1 0.05 0.025 0.02 0.01 0.005 0.0025 0.001 0.0005

19 22.72 23.9 25.33 27.2 30.14 32.85 33.69 36.19 38.58 40.88 43.82 45.97

20 23.83 25.04 26.5 28.41 31.41 34.17 35.02 37.57 40 42.34 45.31 47.5

21 24.93 26.17 27.66 29.62 39.67 35.48 36.34 38.93 41.4 43.78 46.8 49.01

22 26.04 27.3 28.82 30.81 33.92 36.78 37.66 40.29 42.8 45.2 48.27 50.51

23 27.14 28.43 29.98 32.01 35.17 38.08 38.97 41.64 44.18 46.62 49.73 52

24 28.24 29.55 31.13 33.2 36.42 39.36 40.27 42.98 45.56 48.03 51.18 53.48

25 29.34 30.68 32.28 34.38 37.65 40.65 41.57 44.31 46.93 49.44 52.62 54.95

26 30.43 31.79 33.43 35.56 38.89 41.92 42.86 45.64 48.29 50.83 54.05 56.41

27 31.53 32.91 34.57 36.74 40.11 43.19 44.14 46.96 49.64 52.22 55.48 57.86

28 32.62 34.03 35.71 37.92 41.34 44.46 45.42 48.28 50.99 53.59 56.89 59.3

29 33.71 35.14 36.85 39.09 42.56 45.72 46.69 49.59 52.34 54.97 58.3 60.73

30 34.8 36.25 37.99 40.26 43.77 46.98 47.96 50.89 53.67 56.33 59.7 62.16

40 45.62 47.27 49.24 51.81 55.76 59.34 60.44 63.69 66.77 69.7 73.4 76.09

50 56.33 53.16 60.35 63.17 67.5 71.42 72.61 76.15 79.49 82.66 86.66 89.56

237

6.35.3 15.3 1 00.7 7 6 65.3 1 0 0 65.3 1 0 0 6 02.2 4.1 3.1 3.1 2.9 3.1 3.15 1.3 0.3 0.3 5.7 0.3 0.3 2.8

2.7 9 8 8 2 8 8 4.9 7.72 8.3 7.3 7.3 1.3 7.3 7.3 4.2 7 0.7

5.7 0.6 0.4 0.4 6.4 0.4 0.4 3.5 0.7 8.4 7.70.1 6.4 5.4 5.4 0.6 5.4 5.4 2.3 5.1 2.6 1.9 5.81 7.3 6.3 6.3 0.3 6.3 6.3 3.2 6 1.7 1 6.7 0.9

3.4 2.9 1.9 1.9 4.1 1.9 1.9 1.2 1.6 6.1 5.4 2.3 3.5 4.42.6 3.7 2.7 2.7 3.3 2.7 2.7 0.4 2.4 5.3 4.6 3.1 2.7 3.6 0.82.5 3.8 2.8 2.8 3.2 2.8 2.8 0.3 2.5 5.2 4.5 3.2 2.6 3.5 0.9 0.12.7 3.6 2.6 2.6 3.4 2.6 2.6 0.5 2.3 5.4 4.7 3 2.8 3.7 0.7 0.1 0.23.1 3.2 2.2 2.2 3.8 2.2 2.2 0.9 1.9 5.8 5.1 2.6 3.2 4.1 0.3 0.5 0.6 0.42.4 8.7 7.7 7.7 1.7 7.7 7.7 4.6 7.4 0.3 0.4 8.1 2.3 1.4 5.8 5 4.9 5.1 5.5

A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5 3.8 -3.9 1.9 2.8 -1.6 -0.8 -0.7 -0.9 -1.3 4.2

Fig. A2.2. Distance matrix composed for hydrophobicity using values from Haig and Hurst (1991), originally taken from Kyte and Doolittle (1982).

The distances are calculated as the absolute value of the difference between one amino acid value and another.

238

2.16 3.93 0.9 3

2.2 4.3 8.2 5.25.5 3.4 0.5 2.5 7.71.6 0.5 4.4 1.4 3.8 3.90.9 1.2 5.1 2.1 3.1 4.6 0.71.4 0.7 4.6 1.6 3.6 4.1 0.2 0.52.1 4.2 8.1 5.1 0.1 7.6 3.7 3 3.52.1 4.2 8.1 5.1 0.1 7.6 3.7 3 3.5 03.1 1 2.9 0.1 5.3 2.4 1.5 2.2 1.7 5.2 5.21.7 3.8 7.7 4.7 0.5 7.2 3.3 2.6 3.1 0.4 0.4 4.82 4.1 8 5 0.2 7.5 3.6 2.9 3.4 0.1 0.1 5.1 0.3

0.4 2.5 6.4 3.4 1.8 5.9 2 1.3 1.8 1.7 1.7 3.5 1.3 1.60.5 1.6 5.5 2.5 2.7 5 1.1 0.4 0.9 2.6 2.6 2.6 2.2 2.5 0.90.4 2.5 6.4 3.4 1.8 5.9 2 1.3 1.8 1.7 1.7 3.5 1.3 1.6 0 0.91.8 3.9 7.8 4.8 0.4 7.3 3.4 2.7 3.2 0.3 0.3 4.9 0.1 0.2 1.4 2.3 1.41.6 3.7 7.6 4.6 0.6 7.1 3.2 2.5 3 0.5 0.5 4.7 0.1 0.4 1.2 2.1 1.2 0.21.4 3.5 7.4 4.4 0.8 6.9 3 2.3 2.8 0.7 0.7 4.5 0.3 0.6 1 1.9 1 0.4 0.2

A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val7 9.1 13 10 4.8 12.5 8.6 7.9 8.4 4.9 4.9 10.1 5.3 5 6.6 7.5 6.6 5.2 5.4 5.6

Fig. A2.3. Distance matrix composed for polar requirement using values from Haig and Hurst (1991), originally taken from Woese et al. (1966).

The distances are calculated in the same way as for Fig. A2.2.

239

4.763.23 7.990.59 5.35 2.640.93 5.69 2.3 0.342.78 7.54 0.45 2.19 1.850.35 5.11 2.88 0.24 0.58 2.430.03 4.79 3.2 0.56 0.9 2.75 0.321.59 3.17 4.82 2.18 2.52 4.37 1.94 1.620.02 4.74 3.25 0.61 0.95 2.8 0.37 0.05 1.570.02 4.78 3.21 0.57 0.91 2.76 0.33 0.01 1.61 0.043.74 1.02 6.97 4.33 4.67 6.52 4.09 3.77 2.15 3.72 3.760.26 5.02 2.97 0.33 0.67 2.52 0.09 0.23 1.85 0.28 0.24 40.52 5.28 2.71 0.07 0.41 2.26 0.17 0.49 2.11 0.54 0.5 4.26 0.260.3 4.46 3.53 0.89 1.23 3.08 0.65 0.33 1.29 0.28 0.32 3.44 0.56 0.82

0.32 5.08 2.91 0.27 0.61 2.46 0.03 0.29 1.91 0.34 0.3 4.06 0.06 0.2 0.620.16 4.6 3.39 0.75 1.09 2.94 0.51 0.19 1.43 0.14 0.18 3.58 0.42 0.68 0.14 0.480.11 4.87 3.12 0.48 0.82 2.67 0.24 0.08 1.7 0.13 0.09 3.85 0.15 0.41 0.41 0.21 0.270.34 5.1 2.89 0.25 0.59 2.44 0.01 0.31 1.93 0.36 0.32 4.08 0.08 0.18 0.64 0.02 0.5 0.230.04 4.8 3.19 0.55 0.89 2.74 0.31 0.01 1.63 0.06 0.02 3.78 0.22 0.48 0.34 0.28 0.2 0.07 0.3

A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val6 10.76 2.77 5.41 5.07 3.22 5.65 5.97 7.59 6.02 5.98 9.74 5.74 5.48 6.3 5.68 6.16 5.89 5.66 5.96

Fig. A2.4. Distance matrix composed for isoelectric point using values from Haig and Hurst (1991), originally taken from Alff-Steinberger (1969).

The distances are calculated in the same way as for Fig. A2.2.

240

0.190.03 0.220.18 0.36 0.150.07 0.26 0.05 0.100.04 0.15 0.07 0.22 0.120.14 0.33 0.11 0.04 0.06 0.180.04 0.15 0.06 0.21 0.11 0.01 0.170.43 0.24 0.46 0.61 0.50 0.39 0.57 0.390.11 0.08 0.14 0.29 0.19 0.07 0.25 0.07 0.320.10 0.09 0.13 0.28 0.18 0.06 0.24 0.07 0.33 0.010.16 0.03 0.19 0.33 0.23 0.12 0.30 0.12 0.27 0.05 0.060.07 0.12 0.10 0.24 0.14 0.03 0.21 0.03 0.36 0.04 0.03 0.090.55 0.36 0.57 0.72 0.62 0.51 0.68 0.51 0.12 0.44 0.45 0.39 0.480.09 0.10 0.12 0.27 0.17 0.05 0.23 0.06 0.34 0.02 0.01 0.07 0.03 0.450.04 0.23 0.02 0.13 0.03 0.09 0.09 0.08 0.47 0.15 0.15 0.20 0.11 0.59 0.140.10 0.29 0.07 0.08 0.02 0.14 0.04 0.14 0.53 0.21 0.20 0.26 0.17 0.65 0.19 0.060.60 0.41 0.63 0.78 0.68 0.56 0.74 0.57 0.17 0.49 0.50 0.44 0.53 0.06 0.51 0.65 0.700.49 0.30 0.52 0.67 0.57 0.45 0.63 0.45 0.06 0.38 0.39 0.33 0.42 0.06 0.40 0.53 0.59 0.110.05 0.23 0.02 0.13 0.03 0.09 0.09 0.08 0.48 0.16 0.15 0.20 0.11 0.59 0.14 0.00 0.05 0.65 0.54

A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val

-0.11 0.08 -0.14 -0.29 -0.18 -0.07 -0.25 -0.07 0.32 0.00 -0.01 0.05 -0.04 0.44 -0.02 -0.15 -0.21 0.49 0.38 -0.16

Fig. A2.5. Distance matrix composed for aromaticity using values from Xia (2000). The distances are calculated in the same way as for Fig. A2.2.

241

9325 6823 70 224 69 1 154 39 29 31 3052 41 27 29 28 228 121 53 51 52 82 8065 28 40 42 41 11 13 9380 13 55 57 56 26 28 108 1580 13 55 57 56 26 28 108 15 088 5 63 65 64 34 36 116 23 8 874 19 49 51 50 20 22 102 9 6 6 14

101 8 76 78 77 47 49 129 36 21 21 13 271.5 91.5 23.5 21.5 22.5 52.5 50.5 29.5 63.5 78.5 78.5 86.5 72.5 99.51 92 24 22 23 53 51 29 64 79 79 87 73 100 0.5

30 63 5 7 6 24 22 58 35 50 50 58 44 71 28.5 29139 46 114 116 115 85 87 167 74 59 59 51 65 38 138 138 109105 12 80 82 81 51 53 133 40 25 25 17 31 4 104 104 75 3453 40 28 30 29 1 1 81 12 27 27 35 21 48 51.5 52 23 86 52

A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val31 124 56 54 55 85 83 3 96 111 111 119 105 132 33 32 61 170 136 84

Fig. A2.6. Distance matrix composed for volume using values from Grantham (1974). The distances are calculated in the same way as for Fig.

A2.2.

242

0.651.33 0.681.38 0.73 0.052.75 2.1 1.42 1.370.89 0.24 0.44 0.49 1.860.82 0.17 0.51 0.56 1.93 0.070.74 0.09 0.59 0.64 2.01 0.15 0.080.58 0.07 0.75 0.8 2.17 0.31 0.24 0.16

0 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.580 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0

0.33 0.32 1 1.05 2.42 0.56 0.49 0.41 0.25 0.33 0.330 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0 0 0.330 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0 0 0.33 0

0.39 0.26 0.94 0.99 2.36 0.5 0.43 0.35 0.19 0.39 0.39 0.06 0.39 0.391.42 0.77 0.09 0.04 1.33 0.53 0.6 0.68 0.84 1.42 1.42 1.09 1.42 1.42 1.030.71 0.06 0.62 0.67 2.04 0.18 0.11 0.03 0.13 0.71 0.71 0.38 0.71 0.71 0.32 0.710.13 0.52 1.2 1.25 2.62 0.76 0.69 0.61 0.45 0.13 0.13 0.2 0.13 0.13 0.26 1.29 0.580.2 0.45 1.13 1.18 2.55 0.69 0.62 0.54 0.38 0.2 0.2 0.13 0.2 0.2 0.19 1.22 0.51 0.070 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0 0 0.33 0 0 0.39 1.42 0.71 0.13 0.2

A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val0.00 0.65 1.33 1.38 2.75 0.89 0.82 0.74 0.58 0.00 0.00 0.33 0.00 0.00 0.39 1.42 0.71 0.13 0.20 0.00

Fig. A2.7. Distance matrix composed for chemical composition of the side chain using values from Grantham (1974). The distances are calculated

in the same way as for Fig. A2.2.

243

2.43.5 1.14.9 2.5 1.42.6 5 6.1 7.52.4 0 1.1 2.5 54.2 1.8 0.7 0.7 6.8 1.80.9 1.5 2.6 4 3.5 1.5 3.32.3 0.1 1.2 2.6 4.9 0.1 1.9 1.42.9 5.3 6.4 7.8 0.3 5.3 7.1 3.8 5.23.2 5.6 6.7 8.1 0.6 5.6 7.4 4.1 5.5 0.33.2 0.8 0.3 1.7 5.8 0.8 1 2.3 0.9 6.1 6.42.4 4.8 5.9 7.3 0.2 4.8 6.6 3.3 4.7 0.5 0.8 5.62.9 5.3 6.4 7.8 0.3 5.3 7.1 3.8 5.2 0 0.3 6.1 0.50.1 2.5 3.6 5 2.5 2.5 4.3 1 2.4 2.8 3.1 3.3 2.3 2.81.1 1.3 2.4 3.8 3.7 1.3 3.1 0.2 1.2 4 4.3 2.1 3.5 4 1.20.5 1.9 3 4.4 3.1 1.9 3.7 0.4 1.8 3.4 3.7 2.7 2.9 3.4 0.6 0.62.7 5.1 6.2 7.6 0.1 5.1 6.9 3.6 5 0.2 0.5 5.9 0.3 0.2 2.6 3.8 3.21.9 4.3 5.4 6.8 0.7 4.3 6.1 2.8 4.2 1 1.3 5.1 0.5 1 1.8 3 2.4 0.82.2 4.6 5.7 7.1 0.4 4.6 6.4 3.1 4.5 0.7 1 5.4 0.2 0.7 2.1 3.3 2.7 0.5 0.3

A R N D C Q E G H I L K M F P S T W Y VAla Arg Asp Asn Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2 4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9

Fig. A2.8. Distance matrix composed for polarity using values from Grantham (1974). The distances are calculated in the same way as for Fig.

A2.2.

244

Table A2.2. Log likelihood values for each species group analysed using the free

parameter branch model (BM1).

Group SP-C§ lnL Group SP-C§ lnLAll W -878.490 Mustelidae3 W -210.761

C -406.099 C -94.568N -374.959 N -118.701

Castor W -163.201 Otariidae W -179.104C -96.947 C -93.066N -45.762 N -59.883

Cavia W -181.431 Otariidae2 W -173.886C -103.772 C -89.142N -51.733 N -58.984

Cetacea W -189.991 Phocidae W -199.476C -95.154 C -89.142N -59.156 N -85.085

Cetacea2 W -171.960 Pinnipedia W -209.717C -88.117 C -93.722N -52.011 N -92.606

Condylura W -200.931 Primate W -133.496C -174.720 C -75.934N -86.903 N -39.776

Hydrochaerus W -146.248 Sirenia W -159.649C -79.241 C -69.434N -44.392 N -87.509

Hydromys W -139.184 Tapirus W -182.591C -117.551 C -83.521N -63.047 N -62.640

Mustelidae W -221.646 Ursus W -205.896C -98.727 C -94.264N -122.953 N -107.755

Mustelidae2 W -215.756C -98.587N -142.173

§Region of protein analysed: W = whole protein, C = C-terminal, N = N-terminal.

245

Table A2.3. Estimates of ω under the two ratios branch model (BM2).

Group SP-C§ lnL ω1 Group SP-C§ lnL ω1

All W -920.142 ωt=0.245ωd=0.382 Mustelidae3 W -214.516 ωt=0.557

ωd=0.000

C -422.518 ωt=0.062ωd=0.553 C -95.943 ωt=0.108

ωd=1.008

N -374.959 ωt=0.104ωd=0.103 N -100.037 ωt=0.349

ωd=0.000

Castor W -163.749 ωt=0.003ωd=999.00 Otariidae W -181.319 ωt=0.767

ωd=0.000

C -96.947 ωt=0.000ωd=0.694 C -95.091 ωt=0.229

ωd=0.000

N -45.785 ωt=0.042ωd=0.000 N -59.883 ωt=999.00

ωd=0.000

Cavia W -182.023 ωt=0.005ωd=999.00 Otariidae2 W -176.099 ωt=0.777

ωd=1.000

C -103.772 ωt=0.000ωd=0.306 C -91.128 ωt=0.252

ωd=999.00

N -51.826 ωt=0.048ωd=0.000 N -58.983 ωt=825.142

ωd=0.000

Cetacea W -194.044 ωt=0.473ωd=0.000 Phocidae W -199.684 ωt=0.687

ωd=999.00

C -96.065 ωt=0.093ωd=0.000 C -91.128 ωt=0.252

ωd=999.00

N -59.676 ωt=0.003ωd=0.000 N -87.131 ωt=704.302

ωd=0.328

Cetacea2 W -174.699 ωt=0.997ωd=0.000 Pinnipedia W -214.969 ωt=0.662

ωd=1.925

C -88.682 ωt=0.104ωd=0.000 C -95.749 ωt=0.228

ωd=0.000

246


N -52.121 ωt=0.000ωd=0.834 N -96.233 ωt=999.00

ωd=0.030

Condylura W -200.931 ωt=0.027ωd=0.489 Primate W -133.496 ωt=0.000

ωd=998.990

C -178.138 ωt=0.003ωd=0.703 C -75.935 ωt=0.000

ωd=50.320

N -89.675 ωt=0.284ωd=0.163 N -39.776 ωt=0.000

ωd=1.000

Hydrochaerus W -146.416 ωt=0.017ωd=0.000 Sirenia W -159.649 ωt=1.707

ωd=1.210

C -79.241 ωt=0.000ωd=0.000 C -69.434 ωt=0.000

ωd=0.946

N -44.421 ωt=0.047ωd=0.000 N -75.674 ωt=0.605

ωd=998.990

Hydromys W -139.825 ωt=0.090ωd=0.000 Tapirus W -183.397 ωt=0.281

ωd=0.362

C -119.713 ωt=0.312ωd=0.000 C -83.521 ωt=0.000

ωd=0.000

N -64.692 ωt=0.000ωd=0.000 N -63.010 ωt=0.004

ωd=0.051

Mustelidae W -225.366 ωt=0.510ωd=0.000 Ursus W -207.057 ωt=0.538

ωd=1.000

C -100.823 ωt=0.088ωd=0.000 C -95.640 ωt=0.109

ωd=1.000

N -102.815 ωt=0.377ωd=0.000 N -92.549 ωt=0.224

ωd=0.000

Mustelidae2 W -216.918 ωt=0.494ωd=0.000

C -100.684 ωt=0.088ωd=0.000

247


N -101.715 ωt=0.168ωd=1.456

§Region of protein analysed: W = whole protein, C = C-terminal, N = N-terminal. 1ω is estimated for terrestrial (ωt) and diving (ωd) lineages

separately.

248

REFERENCES

Abdellatif, M.M. and Hollingsworth, M. (1980). Effect of oxotremorine and epinephrine on

lung surfactant secretion in neonatal rabbits. Pediatric Research 14(8):916-920.

Adachi, H., Hayashi, H., Sato, H., Dempo, K. and Akino, T. (1989). Characterization of

phospholipids accumulated in pulmonary-surfactant compartments of rats

intratracheally exposed to silica. Biochemical Journal 262:781-786.

Adams, F.H., Fujiwara, T., Emmanouilides, G.C. and Räihä, N. (1970). Lung

phospholipids of human fetuses and infants with and without hyaline membrane

disease. Journal of Pediatrics 77:833-841.

Adamson, I.Y., Young, L. and King, G.M. (1991). Reciprocal epithelial: fibroblast

interactions in the control of fetal and adult rat lung cells in culture. Experimental

Lung Research 17(4):821-835.

Aita, T., Urata, S. and Husimi, Y. (2000). From amino acid landscape to protein

landscape: Analysis of genetic codes in terms of fitness landscape. Journal of

Molecular Evolution 50:313-323.

Alberts, B., Bray, B., Lewis, J., Raff, M., Roberts, K. and Watson, J.D. (1994). "Molecular

biology of the cell". Garland Publishing Inc., London.

Alff-Steinberger, C. (1969). The genetic code and error transmission. Proceedings of the

National Academy of Sciences U.S.A. 64(2):584-591.

Allegra, L., Bossi, R. and Braga, P. (1985). Influence of surfactant on mucociliary

transport. European Journal of Respiratory Disease 142:71-76.

Amirkhanian, J.D. and Merritt, T.A. (1995). The influence of pH on surface properties of

lung surfactants. Lung 173:243-254.

Amrein, M., von Nahmen, A. and Sieber, M. (1997). A scanning force- and fluorescence

light microscopy study of the structure and function of a model pulmonary

surfactant. European Biophysical Journal 26(5):349-357.

Andrews, R.D., Costa, D.P., Le Boeuf, B.J. and Jones, D.R. (2000). Breathing frequencies

of northern elephant seals at sea and on land revealed by heart rate spectral

analysis. Respiration Physiology 123:71-85.

Arnason, U. (1977). The relationship between the four principal pinniped karyotypes.

Hereditas 87:227-242.

Arnason, U., Bodin, K., Gullberg, A., Ledje, C. and Mouchaty, S. (1995). A molecular view

of pinniped relationships with particular emphasis on the true seals. Journal of

Molecular Evolution 40(1):78-85.

249

Arnason, U. and Gullberg, A. (1996). Cytochrome b nucleotide sequences and the

identification of five primary lineages of extant cetaceans. Molecular and Biological

Evolution 13(2):407-417.

Arnason, U. and Widegren, B. (1986). Pinniped phylogeny enlightened by molecular

hybridizations using highly repetitive DNA. Molecular and Biological Evolution

3:356-365.

Ashton, M.R., Postle, A.D., Hall, M.A., Smith, S.L., Kelly, F.J. and Normand, I.C. (1992).

Phosphatidylcholine composition of endotracheal tube aspirates of neonates and

subsequent respiratory disease. Archives of Disease in Childhood 67:378-382.

Augustin-Voss, H.G., Schoon, H.A., Stockhofe, N. and Ueberschär, S. (1989). Isolation of

bovine type II pneumocytes in high yield and purity. Lung 167:1-10.

Babu, K.S., Woodcock, D.A., Smith, S.E., Staniforth, J.N., Holgate, S.T. and Conway, J.H.

(2003). Inhaled synthetic surfactant abolished the early allergen-induced response

in asthma. European Respiratory Journal 21(6):1046-1049.

Bachofen, H., Ammann, A., Wangensteen, D. and Weibel , E.R. (1982). Perfusion fixation

of lungs for structure-function analysis: Credits and limitations. Journal of Applied

Physiology 53:528-533.

Bachofen, H., Hildebrandt, J. and Bachofen, M. (1970). Pressure-volume curves of air-

and liquid-filled excised lungs - surface tension in situ. Journal of Applied


Bachofen, H., Schürch, S., Urbinelli, M. and Weibel, E.R. (1987). Relations among

alveolar surface tension, surface area, volume and recoil pressure. Journal of

Applied Physiology 62:1878-1887.

Baker, M.L., Wares, J.P., Harrison, G.A. and Miller, R.D. (2004). Relationships among the

families and orders of marsupials and the major mammalian lineages based on

recombinant activating gene-1. Journal of Mammalian Evolution 11(1):1-16.

Ballard, P.L. (1989). Hormonal regulation of pulmonary surfactant. Endocrine Review

10(2):165-181.

Ballard, P.L., Hovey, M.L. and Gonzales, L.K. (1984). Thyroid hormone stimulation of

phosphatidylcholine synthesis in cultured fetal rabbit lung. Journal of Clinical

Investigation 74:898-905.

Banes, A.J., Tsuzaki, M., Yamamoto, J., Fischer, T., Brigman, B., Brown, T. and Miller, L.

(1995). Mechanoreception at the cellular level: the detection, interpretation, and

diversity of responses to mechanical signals. Biochemistry and Cell Biology 73(7-

250

8):349-365.

Bangham, A.D., Morley, C.J. and Phillips, M.C. (1979). The physical properties of an

effective lung surfactant. Biochimica et Biophysica Acta 573:552-556.

Baritussio, A., Bellina, L., Carraro, R., Rossi, A., Enzi, G., Magoon, M.W. and Mussini, I.

(1984). Heterogeneity of alveolar surfactant in the rabbit: Composition,

morphology, and labelling of subfractions isolated by centrifugation of lung lavage.

European Journal of Clinical Investigation 14:24-29.

Barkai, G., Mashiach, S., Goldman, B., Kalina, M. and Shinitzky, M. (1985). The effect of

pressure on the lipid microviscosity and phase transition of lung surfactant.

Biochimica et Biophysica Acta 834:103-109.

Barnes, L.G., Domning, D.P. and Ray, C.E. (1985). Status of studies on fossil marine

mammals. Marine Mammal Science 1(1):15-53.

Barshtein, G., Bergelson, L., Dagan, A., Gratton, E. and Yedgar, S. (1997). Membrane

lipid order of human red blood cells is altered by physiological levels of hydrostatic

pressure. American Journal of Physiology Heart and Circulatory Physiology

272(41):H538-H543.

Bartlett, G.R. (1959). Phosphorus assay in column chromatography. Journal of Biological

Chemistry 234:466-468.

Bastacky, J., Lee, C.Y.C., Goerke, J., Koushafar, H., Yager, D., Kenaga, L., Speed, T.P.,

Chen, Y. and Clements, J.A. (1995). Alveolar lining layer is thin and continuous:

Low temperature scanning electron microscopy of rat lung. Journal of Applied


Beck, D.C., Ikegami, M., Na, C.L., Zaltash, S., Johansson, J., Whitsett, J.A. and Weaver,

T.E. (2000). The role of homodimers in surfactant protein B function in vivo.

Journal of Biological Chemistry 275(5):3365-3370.

Beers, M.F. and Fisher, A.B. (1992). Surfactant protein C: A review of its unique

properties and metabolism. American Journal of Physiology 263:L151-L160.

Beers, M.F., Hamvas, A., Moxley, M.A., Gonzales, L.W., Guttentag, S.H., Solarin, K.O.,

Longmore, W.J., Nogee, L.M. and Ballard, P.L. (2000). Pulmonary surfactant

metabolism in infants lacking surfactant protein B. American Journal of Respiratory

Cell and Molecular Biology 22(3):380-391.

Beers, M.F., Kim, C.Y., Dodia, C. and Fisher, A.B. (1994). Localization, synthesis, and

processing of surfactant protein SP-C in rat lung analyzed by epitope-specific

antipeptide anitbodies. Journal of Biological Chemistry 269(32):20318-20328.

251

Benson, B.J., Kitterman, J.A., Clements, J.A., Mescher, E.J. and Tooley, W.H. (1983).

Changes in phospholipid composition of lung surfactant during development in the

fetal lamb. Biochimica et Biophysica Acta 753:83-88.

Bergendahl, M., Vance, M.L., Iranmanesh, A., Thorner, M.O. and Veldhuis, J.D. (1996).

Fasting as a metabolic stress paradigm selectively amplifies cortisol secretory

burst mass and delays the time of maximal nyctohemeral cortisol concentrations in

healthy men. Journal of Clinical Endocrinology and Metabolism 81:692-699.

Bernal, A.L. and Phizacherley, P.J. (2000). Fetal surfactant as a source of arachidonate in

human amniotic fluid. Prostaglandins and Other Lipid Mediators 60:59-70.

Bernhard, W., Gebert, A., Vieten, G., Rau, G.A., Hohlfeld, J.M., Postle, A.D. and Freihorst,

J. (2001a). Pulmonary surfactant in birds: Coping with surface tension in a tubular

lung. American Journal of Physiology Regulatory and Integrative Comparative

Physiology 281(1):R327-R337.

Bernhard, W., Haagsman, H.P., Tschernig, T., Poets, C.F., Postle, A.D., van Eijk, M.E.

and von der Hardt, H. (1997). Conductive airway surfactant: surface-tension

function, biochemical composition, and possible alveolar origin. American Journal

of Respiratory Cell and Molecular Biology 17(1):41-50.

Bernhard, W., Haslam, P.L. and Floros, J. (2004). From birds to humans: New concepts

on airways relative to alveolar surfactant. American Journal of Respiratory Cell and

Molecular Biology 30:6-11.

Bernhard, W., Hoffmann, S., Dombrowsky, H., Rau, G.A., Kamlage, A., Kappler, M.,

Haitsma, J.J., Freihorst, J., von der Hardt, H. and Poets, C.F. (2001b).

Phosphatidylcholine molecular species in lung surfactant: Composition in relation

to respiratory rate and lung development. American Journal of Respiratory Cell

and Molecular Biology 25(6):725-731.

Bernhard, W., Postle, A.D., Rau, G.A. and Freihorst, J. (2001c). Pulmonary and gastric

surfactants. A comparison of the effect of surface requirements on function and

phospholipid composition. Comparative Biochemistry and Physiology A Molecular

and Integrative Physiology 129(1):173-182.

Berta, A. and Sumich, J.L. (1999). "Marine Mammals: Evolutionary Biology". Academic

Press, San Diego.

Berta, A. and Wyss, A.R. (1994). Pinniped phylogeny. Proceedings of the San Diego

Society of Natural History 29:33-56.

Bijaoui, E.L., Champagne, V., Baconnier, P.F., Kimoff, R.J. and Bates, J.H.T. (2002).

Mechanical properties of the lung and upper airways in patients with sleep-

252

disordered breathing. American Journal of Respiratory and Critical Care Medicine

165(8):1055-1061.

Bininda-Emonds, O.R.P., Gittleman, J.L. and Purvis, A. (1999). Building large trees by

combining phylogenetic information: a complete phylogeny of the extant Carnivora

(Mammalia). Biological Reviews 74(2):143-175.

Bishop, I.R. and Foxon, G.E.H. (1968). The mechanism of breathing in the South

American lungfish, Lepidosiren paradoxa; A radiological study. Journal of Zoology

154:263-271.

Bishop, J.G., Dean, A.M. and Mitchell-Olds, T. (2000). Rapid evolution in plant chitinases:

Molecular targets of selection in plant-pathogen coevolution. Proceedings of the

National Academy of Science U.S.A. 97:5322-5327.

Blanco, O. and Catalá, A. (2001). Surfactant protein A inhibits the non-enzymatic lipid

peroxidation of porcine lung surfactant. Prostaglandins, Leukotrienes and

Essential Fatty Acids 66(4):185-190.

Bligh, E.G. and Dyer, W.J. (1959). A rapid method of total lipid extraction and purification.

Canadian Journal of Biochemistry and Physiology 37:911-917.

Bodmer, R.E. (1990). Responses of ungulates to seasonal inundations in the Amazon

floodplain. Journal of Tropical Ecology 6(2):191-201.

Boshier, D.P. and Hill, P. (1972). Structural aspects of ventilation and diffusion in the

Weddell seal (Leptonychotes weddelli). In "Functional anatomy of marine

mammals". (R.J. Harrison, Ed.). pp. Academic Press, London.

Boutilier, R.G., Reed, J.Z. and Fedak, M.A. (2001). Unsteady-state gas exchange and

storage in diving marine mammals: the harbor porpoise and gray seal. American

Journal of Physiology Regulatory and Integrative Comparative Physiology

281:R490-R494.

Boyd, R.B. (1975). A gross and microscopic study of the respiratory anatomy of the

antarctic Weddell seal, Leptonychotes weddelli. Journal of Anatomy 147:309-336.

Bridges, J.P., Wert, S.E., Nogee, L.M. and Weaver, T.E. (2003). Expression of a human

SP-C mutation associated with interstitial lung disease disrupts lung development

in transgenic mice. Journal of Biological Chemistry 278(52):52739-52746.

Bringezu, F., Pinkerton, K.E. and Zasadzinski, J.A. (2003). Environmental tobacco smoke

effects on the primary lipids of lung surfactant. Langmuir 19:2900-2907.

Brooks, R.E. (1970). Ultrastructure of the physostomatous swimbladder of rainbow trout

(Salmo gairdneri). Zeitschrift fur Zellforschung 106:473-483.

253

Brown, L.S. and Longmore, W.J. (1981). Adrenergic and cholinergic regulation of lung

surfactant secretion in the isolated perfused rat lung and in the alveolar type II cell

in culture. Journal of Biological Chemistry 256(1):66-72.

Bünger, H. and Pison, U. (1995). Quantitative analysis of pulmonary surfactant

phospholipids by high-performance liquid chromatography and light-scattering

detection. Journal of Chromatography B 672:25-31.

Burdge, G.C., Kelly, F.J. and Postle, A.D. (1993). Synthesis of phosphatidylcholine in

guinea-pig fetal lung involves acyl remodelling and differential turnover of

individual molecular species. Biochimica et Biophysica Acta 1166:251-257.

Butler, P.J., Woakes, A.J., Smale, K., Roberts, C.A., Hillidge, C.J., Snow, D.H. and Marlin,

D.J. (1993). Respiration ad cardiovascular adjustments during exercise of

increasing intensity and during recovery in thoroughbred racehorses. Journal of

Experimental Biology 179:159-180.

Campbell, N.A. (1987). "Biology". The Benjamin/Cummings Publishing Company, Inc.,

Redwood City.

Casadei, M.A., Manas, P., Niven, G., Needs, E. and Mackey, B.M. (2002). Role of

membrane fluidity in pressure resistance of Escherichia coli NCTC 8164. Applied

Environmental Microbiology 68(12):5965-5972.

Castellini, M.A., Castellini, J.M. and Rivera, P.M. (2001). Adaptations to pressure in the

RBC metabolism of diving mammals. Comparative Biochemistry and Physiology

Part A 129:751-757.

Chailley-Heu, B., Rubio, S., Rougier, J.P., Ducroc, R., Barlier-Mur, A.M., Ronco, P. and

Bourbon, J.R. (1997). Expression of hydrophilic surfactant proteins by mesentery

cells in rat and man. Biochemical Journal 328:251-256.

Champagne, C.D., Houser, D.S. and Crocker, D.E. (2005). Glucose production and

substrate cycle activity in a fasting adapted animal, the northern elephant seal.

Journal of Experimental Biology 208(5):859-868.

Chelly, N., Mouhieddine-Gueddiche, O.B., Barlier-Mur, A.M., Chailley-Heu, B. and

Bourbon, J.R. (1999). Keratinocyte growth factor enhances maturation of fetal rat

lung type II cells. American Journal of Respiratory Cell and Molecular Biology

20:423-432.

Chen, M. and Brown, L.A.S. (1990). Histamine stimulation of surfactant secretion from rat

type II pneumocytes. American Journal of Physiology 258:L195-L200.

254

Chen, S.S. and Kou, A.Y. (1982). Improved procedure for the separation of phospholipids

by high-performance liquid chormatography. Journal of Chromatography 227:25-

31.

Cheng, G., Ueda, T., Sugiyama, K., Toda, M. and Fukuda, T. (2001). Compositional and

functional changes of pulmonary surfactant in a guinea-pig model of chronic

asthma. Respiration Medicine 95(3):180-186.

Clements, J.A., Hustead, R.F., Johnson, R.P. and Gribetz, I. (1961). Pulmonary surface

tension and alveolar stability. Journal of Applied Physiology 16(3):444-450.

Cockshutt, A.M. and Possmayer, F. (1991). Lysophosphatidylcholine sensitizes lipid

extracts of pulmonary surfactant to inhibition by serum proteins. Biochimica et

Biophysica Acta 1086:63-71.

Codd, J.R., Orgeig, S., Daniels, C.B. and Schurch, S. (2003). Alterations in surface

activity of pulmonary surfactant in Gould's wattled bat during rapid arousal from

torpor. Biochemical and Biophysical Research Communications 308(3):463-468.

Codd, J.R., Schürch, S., Daniels, C.B. and Orgeig, S. (2002). Torpor-associated

fluctuations in surfactant activity in Gould's Wattled Bat. Biochimica et Biophysica

Acta 1580:57-66.

Codd, J.R., Slocombe, N.C., Daniels, C.B., Wood, P.G. and Orgeig, S. (2000). Periodic

fluctuations in the pulmonary surfactant system in Gould's wattled bat

(Chalinolobus gouldii). Physiological and Biochemical Zoology 73(5):605-612.

Cole, F.S., Hamvas, A. and Nogee, L.M. (2001). Genetic disorders of neonatal respiratory

function. Pediatric Research 50(2):157-162.

Costa, D.P., Gales, N.J. and Goebel, M.E. (2001). Aerobic dive limit: how often does it

occur in nature? Comparative Biochemistry and Physiology A Molecular and

Integrative Physiology Molecular and Integrative Physiology 129(4):771-783.

Cotes, J.E. (1993). "Lung Function: Assessment and Application in Medicine". Blackwell

Scientific Publications, Oxford.

Craig, A.B. and Påsche, A. (1980). Respiratory physiology of freely diving harbor seals

(Phoca vitulina). Physiological Zoology 53(4):419-432.

Crapo, J.D. (1993). New concepts in the formation of pulmonary edema. American

Review of Respiratory Disease 147:790-792.

Creuwels, L.A.J.M., Van Golde, L.M.G. and Haagsman, H.P. (1997). The pulmonary

surfactant system: Biochemical and clinical aspects. Lung 175(1):1-39.

255

Crouch, E., Parghi, D., Kuan, S.F. and Persson, A. (1992). Surfactant protein D:

subcellular localization in nonciliated bronchiolar epithelial cells. American Journal

of Physiology Lung Cellular and Molecular Physiology 263:L60-L66.

Crouch, E., Persson, A., Chang, D. and Heuser, J. (1994). Molecular structure of

pulmonary surfactant protein D (SP-D). Journal of Biological Chemistry

269(25):17311-17319.

Crouch, E. and Wright, J. (2001a). Surfactant proteins A and D and pulmonary host

defense. Annual Review of Physiology 63:521-554.

Crouch, E.C. (1998a). Collectins and pulmonary host disease. American Journal of

Respiratory Cell and Molecular Biology 19:177-201.

Crouch, E.C. (1998b). Structure, biologic properties, and expression of surfactant protein

D (SP-D). Biochimica et Biophysica Acta 1408(2-3):278-289.

Crouch, E.C. and Wright, J. (2001b). Surfactant proteins A and D and pulmonary host

defense. Annual Review of Physiology 63:521-554.

Currie, W.D., van Schaik, S.M., Vargas, I. and Enhorning, G. (1998). Ozone affects

breathing and pulmonary surfactant function in mice. Toxicology 125(1):21-30.

Curstedt, T., Johansson, J., Persson, P., Eklund, A., Robertson, B., Löwenadler, B. and

Jörnvall, H. (1990). Hydrophobic surfactant-associated polypeptides: SP-C is a

lipopeptide with two palmitoylated cysteine residues, whereas SP-B lacks

covalently linked fatty acyl groups. Proceedings of the National Academy of

Sciences U.S.A. 87:2985-2989.

Curstedt, T., Jornvall, H., Robertson, B., Bergman, T. and Berggren, P. (1987). Two

hydrophobic low-molecular-mass protein fractions of pulmonary surfactant.

Characterization and biophysical activity. European Journal of Biochemistry

168(2):255-262.

Dainiak, N., Hoffman, R., Maffei, L.A. and Forget, B.G. (1978). Potentiation of human

erythropoiesis in vitro by thyroid homrone. Nature 272:260-262.

Daniels, C.B., Barr, H.A. and Nicholas, T.E. (1989). A comparison of the surfactant

associated lipids derived from reptilian and mammalian lungs. Respiration


Daniels, C.B., Lopatko, O.V. and Orgeig, S. (1998a). Evolution of surface activity related

functions of vertebrate pulmonary surfactant. Clinical and Experimental

Pharmacology and Physiology 25:716-721.

256

Daniels, C.B., McGregor, L.K. and Nicholas, T.E. (1994a). The dragon's breath: A model

for the dynamics of breathing and faveolar ventilation in agamid lizards.

Herpetologica 50:251-261.

Daniels, C.B. and Orgeig, S. (2001). The comparative biology of pulmonary surfactant:

past, present and future. Comparative Biochemistry and Physiology A Molecular


Daniels, C.B. and Orgeig, S. (2003). Pulmonary surfactant: the key to the evolution of air

breathing. News in Physiological Sciences 18:151-157.

Daniels, C.B., Orgeig, S. and Smits, A.W. (1995a). Invited Perspective: The evolution of

the vertebrate pulmonary surfactant system. Physiological Zoology 68(4):539-566.

Daniels, C.B., Orgeig, S., Smits, A.W. and Miller, J.D. (1996). The influence of

temperature, phylogeny, and lung structure on the lipid composition of reptilian

pulmonary surfactant. Experimental Lung Research 22:267-281.

Daniels, C.B., Orgeig, S., Sullivan, L.C., Ling, N., Bennett, M.B., Schurch, S., Val, A.L.

and Brauner, C.J. (2004). The origin and evolution of the surfactant system in fish:

insights into the evolution of lungs and swim bladders. Physiological and

Biochemical Zoology 77(5):732-749.

Daniels, C.B., Orgeig, S., Wilsen, J. and Nicholas, T.E. (1994b). Pulmonary-type

surfactants in the lungs of terrestrial and aquatic amphibians. Respiration


Daniels, C.B., Orgeig, S., Wood, P.G., Sullivan, L.C., Lopatko, O.V. and Smits, A.W.

(1998b). The changing state of surfactant lipids: New insights from ancient

animals. American Zoologist 38:305-320.

Daniels, C.B. and Skinner, C.H. (1994). The composition and function of surface active

lipids in the goldfish swim bladder. Physiological Zoology 67(5):1230-1256.

Daniels, C.B., Smits, A.W. and Orgeig, S. (1995b). Pulmonary surfactant lipids in the

faveolar and saccular lung regions of snakes. Physiological Zoology 68(5):812-

830.

Daniels, C.B., Wood, P.G., Lopatko, O.V., Codd, J.R., Johnston, S.D. and Orgeig, S.

(1999). Surfactant in the gas mantle of the snail Helix aspersa. Physiological and

Biochemical Zoolology 72(6):691-698.

Danlois, F., Zaltash, S., Johansson, J., Robertson, B., Haagsman, H.P., Rollin, F.,

Ruysschaert, J.M. and Vandenbussche, G. (2003a). Pulmonary surfactant from

healthy Belgian White and Blue and Holstein Friesian calves: biochemical and

biophysical comparison. Veterinary Journal 165(1):65-72.

257

Danlois, F., Zaltash, S., Johansson, J., Robertson, B., Haagsman, H.P., Rollin, F.,

Ruysschaert, J.-M. and Vandenbussche, G. (2003b). Pulmonary surfactant from

healthy Belgian White and Blue and Holstein Fresian calves: Biochemical and

biophysical comparison. The Veterinary Journal 165:65-72.

Danlois, F., Zaltash, S., Johansson, J., Robertson, B., Haagsman, H.P., van Eijk, M.,

Beers, M.F., Rollin, F., Ruysschaert, J.M. and Vandenbussche, G. (2000). Very

low surfactant protein C contents in newborn Belgian White and Blue calves with

respiratory distress syndrome. Biochemical Journal 351:779-787.

Das, D.K., Ayromlooi, J., Bandyopadhyay, D., Bandyopadhyay, S., Neogi, A. and

Steinberg, H. (1984). Potentiation of surfactant release in fetal lung by thyroid

hormone action. Journal of Applied Physiology 56:1621-1626.

Davidson, K.G., Acton, S.M., Barr, H.A. and Nicholas, T.E. (1997). Effect of lowering

serum cholesterol on the composition of surfactant in adult rat lung. American

Journal of Physiology Lung Cellular and Molecular Physiology 272(16):L106-L114.

Davies, P., Reid, L., Lister, G. and Pitt, B. (1988). Postnatal growth of the sheep lung: A

morphometric study. Anatomical Record 220:281-286.

Davis, R.W., Fuiman, L.A., Williams, T.M. and Le Boeuf, B.J. (2001). Three-dimensional

movements and swimming activity of a northern elephant seal. Comparative

Biochemistry and Physiology Part A 129:759-770.

Dayhoff, M.R., Schwartz, R.M. and Orcutt, B.C. (1978). A model of evolutionary change in

proteins. In "Atlas of protein sequence and structure"). pp. 345-352. National

Biomedical Research Foundation, Washington, D.C.

DeLong, E.F. and Yayanos, A.A. (1986). Biochemical function and ecological significance

of novel bacterial lipids in deep-sea prokaryotes. Applied and Environmental

Microbiology 51:730-737.

DeLong, R.L. and Stewart, B.S. (1991). Diving patterns of northern elephant seal bulls.

Marine Mammal Science 7(4):369-384.

Denison, D.M. and Kooyman, G.L. (1973). The structure and function of the small airways

in pinniped and sea otter lungs. Respiration Physiology 17(1):1-10.

Denison, D.M., Warrell, D.A. and West, J.B. (1971). Airway structure and alveolar

emptying in the lungs of sea lions and dogs. Respiration Physiology 13(3):253-

260.

Diemel, R.V., Snel, M.M., Van Golde, L.M., Putz, G., Haagsman, H.P. and Batenburg, J.J.

(2002). Effects of cholesterol on surface activity and surface topography of spread

surfactant films. Biochemistry 41(50):15007-15016.

258

Djurhuus, R., Svardal, A.M. and Thorsen, E. (1998). Toxicity of hyperoxia and high

pressure on C3H/10T1/2 cells and effects on cellular glutathione. Undersea

Hyperbaric Medicine 25(1):33-41.

Dobbs, L.G. and Mason, R.J. (1979). Pulmonary alveolar type II cells isolated from rats.

Journal of Clinical Investigation 63:378-387.

Dobbs, L.G., Wright, J.R., Hawgood, S., Gonzalez, R., Venstrom, K. and Nellenbogen, J.

(1987). Pulmonary surfactant and its components inhibit secretion of

phosphatidylcholine from cultured rat alveolar type II cells. Proceedings of the

National Academy of Sciences U.S.A. 84:1010-1014.

Dorris, M., Viney, M.E. and Blaxter, M.L. (2002). Molecular phylogenetic analysis of the

genus Strongyloides and related nematodes. International Journal of Parasitology

32(12):1507-1517.

Dos Santos, C.C. and Slutsky, A.S. (2000). Mechanotransduction, ventilator-induced lung

injury and multiple organ dysfunction syndrome. Intensive Care Medicine 26:638-

642.

Dreyfuss, D. and Saumon, G. (1993). Role of tidal volume, FRC, and end inspiratory

volume in the development of pulmonary edema following mechanical ventilation.

American Review of Respiratory Disease 148:1194-1203.

Dreyfuss, D. and Saumon, G. (1998). Ventilator-induced lung injury: Lessons from

experimental studies. American Journal of Respiratory and Critical Care Medicine

157:294-323.

Duck-Chong, C.G. (1978). The isolation of lamellar bodies and their membranous content

from rat lung, lamb tracheal fluid and human amniotic fluid. Life Sciences 22:2025-

2030.

Edwards, Y.S. (2001). Stretch stimulation: its effects on alveolar type II cell function in the

lung. Comparative Biochemistry and Physiology A Molecular and Integrative

Physiology Molecular and Integrative Physiology 129(1):245-260.

Edwards, Y.S., Sutherland, L.M., Power, J.H., Nicholas, T.E. and Murray, A.W. (1999).

Cyclic stretch induces both apoptosis and secretion in rat alveolar type II cells.

FEBS letters 448(1):127-130.

Egberts, J., Beintema-Dubbeldam, A. and de Boers, A. (1987). Phosphatidylinositol and

not phosphatidylglycerol is the important minor phospholipid in rhesus-monkey

surfactant. Biochimica et Biophysica Acta 919:90-92.

259

Egberts, J., Fontijne, P. and Van Der Weijen, G.C. (1981). Premature changes in surface

activity in lung fluid of fetal lambs. European Journal of Obstetrics, Gynecology,

and Reproductive Biology 12:59-67.

Eliakim, R., Becich, K.M.J., Green, M.J. and Alpers, D.H. (1991). Developmental

expression of intestinal surfactant like particles in rats. American Journal of

Physiology 261:G269-G279.

Elson-Riggins, J.G., Al-Banna, L., Platzer, E.G. and Kaloshian, I. (2001). Characterization

of Otostrongylus circumlitus from Pacific harbor and northern elephant seals.

Journal of Parasitology 87(1):73-78.

Engelhardt, F.R. and Ferguson, J.M. (1980). Adaptive hormone changes in harp seals,

Phoca groenlandica, and gray seals, Halichoerus grypus, during the postnatal

period. General and Comparative Endocrinology 40:434-445.

Enhörning, G. (1977). Pulsating bubble technique for evaluating pulmonary surfactant.

Journal of Applied Physiology 43:198-203.

Enhörning, G. (2001). Pulmonary surfactant function studied with the pulsating bubble

surfactometer (PBS) and the capillary surfactometer (CS). Comparative

Biochemistry and Physiology A Molecular and Integrative Physiology 129(1):221-

226.

Enhörning, G. and Holm, B.A. (1993). Disruption of pulmonary surfactant's ability to

maintain openness of a narrow tube. Journal of Applied Physiology 74:2922-2927.

Epstein, C.J. (1967). Non-randomness of amino-acid changes in the evolution of

homologous proteins. Nature 215:355-359.

Escamilla, R., Prevost, M.-C., Cariven, C., Hermant, C., Krempf, M. and Chap, H. (1993).

Bronchoalveolar lavage phospholipid abnormalities in HIV-infected patients.

European Respiratory Journal 6:1301-1307.

Evans, H.E. (1993). "Miller's Anatomy of the Dog". W.B. Saunders Company,

Philadelphia.

Falabella, V., Lewis, M. and Campagna, C. (1999). Development of cardiorespiratory

patterns associated with terrestrial apneas in free-ranging southern elephant seals.

Physiological and Biochemical Zoology 72(1):64-70.

Fanning, J.C. and Harrison, R.J. (1972). The structure of the trachea and lungs of the

South Australian Bottle-nosed dolphin. In "Functional Anatomy of Marine

Mammals". (R.J. Harrison, Ed.). pp. 231-252. Academic Press, London.

Fares, M.A., Moya, A., Escarmis, C., Braranowski, E., Domingo, E. and Barrio, E. (2001).

Evidence for positive selection in the capsid protein-coding region of the foot-and-

260

mouth disease virus (FMDV) subjected to experimental passage regimens.

Molecular and Biological Evolution 18:10-21.

Farrell, P.M., Bourbon, J.R., Notter, R.H., Marin, L., Nogee, L.M. and Whitsett, J.A.

(1990). Relationships among surfactant fraction lipids, proteins and biophysical

properties in the developing rat lung. Biochimica et Biophysica Acta 1044(1):84-

90.

Feldkamp, S.D., DeLong, R.L. and Antonelis, G.A. (1989). Diving patterns of California

sea lions, Zalophus californianus. Canadian Journal of Zoology 67:872-883.

Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F. and Whitehouse, C.M. (1989). Electrospray

ionization for mass spectrometry of large biomolecules. Science 246:64-71.

Fish, F.E. (2000). Biomechanics and energetics in aquatic and semiaquatic mammals:

Platypus to whale. Physiological and Biochemical Zoology 73(6):683-698.

Fisher, J.H., Emrie, P.A., Drabkin, H.A., Kushnik, T., Gerber, M., Hofmann, T. and Jones,

C. (1988). The gene encoding the hydrophobic surfactant protein SP-C is located

on 8p and identifies an EcoRI RFLP. American Journal of Human Genetics

43:436-441.

Fleming, B.D. and Keough, K.M.W. (1988). Surface respreading after collapse of

monolayers containing major lipids of pulmonary surfactant. Chemistry and

Physics of Lipids 49:81-86.

Fletouris, D.J., Botsoglou, N.A., Psomas, I.E. and Mantis, A.I. (1998). Rapid determination

of cholesterol in milk and milk products by direct saponification and capillary gas

chromatography. Journal of Dairy Science 81:2833-2840.

Flynn, J.J. and Nedbal, M.A. (1998). Phylogeny of the Carnivora (Mammalia): Congruence

vs. incompatibility among multiple data sets. Molecular and Phylogenetic Evolution

9(3):414-426.

Fordyce, R.E. (1980). Whale evolution and Oligocene southern ocean environment.

Palaeogeography, Palaeoclimatology and Palaeoecology 31:319-336.

Frappell, P.B. and Daniels, C.B. (1991a). Temperature effects on ventilation and

metabolism in the lizard, Ctenophorus nuchalis. Respiration Physiology 86:257-

270.

Frappell, P.B. and Daniels, C.B. (1991b). Ventilation and oxygen consumption in agamid

lizards. Physiological Zoology 64:985-1001.

Frappell, P.B., Hinds, D.S. and Boggs, D.F. (2001). Scaling of respiratory variables and

the bathing pattern in birds: An allometric and phylogenetic approach.

Physiological and Biochemical Zoology 74(1):75-89.

261

Frerking, I., Günther, A., Seeger, W. and Pison, U. (2001). Pulmonary surfactant:

functions, abnormalities and therapeutic options. Intensive Care Medicine

27:1699-1717.

Fujiwara, T., Adams, F.H., Nozaki, M. and Dermer, G.B. (1970). Pulmonary surfactant

phospholipids from turkey lung: Comparison with rabbit lung. American Journal of


Galindo-Leal, C. and Zuleta, G. (1997). The distribution, habitat, and conservation status

of the Pacific water shrew, Sorex bendirii, in British Columbia. Canadian Field

Naturalist 111(3):422-428.

Garland Jr, T. and Ives, A.R. (2000). Using the Past to Predict the Present: Confidence

Intervals for Regression Equations in Phylogenetic Comparative Methods. The

American Naturalist 155(3):346-364.

Garland Jr, T., P.E., M. and Ives, A.R. (1999). An introduction to phylogenetically based

statistical methods, with a new method for confidence intervals on ancestral

values. American Zoology 39:374-388.

Gatesy, J. (1997). More DNA support for a Ceatcea/Hipopotamidae clade: the blood-

clotting protein gene γ-fibrinogen. Molecular and Biological Evolution 14(5):537-

543.

Gatesy, J., Hayashi, C., Cronin, M.A. and Arctander, P. (1996). Evidence from milk casein

genes that cetaceans are close relatives of hippopotamid artiodactyls. Molecular

and Biological Evolution 13(7):954-963.

Gehr, P., Mwangi, D.K., Ammann, A., Maloiy, G.M.O., Taylor, C.R. and Weibel, E.R.

(1981). Design of the mammalian respiratory system. V. Scaling morphometric

pulmonary diffusing capacity to body mass: Wild and domestic mammals.

Respiration Physiology 44:61-86.

Ghosh, D., Bal, B., Kashyap, V.K. and Pal, S. (2003). Molecular phylogenetic exploration

of bacterial diversity in a Bakreshwar (India) hot spring and culture of Shewanella-

related thermophiles. Applied Environmental Microbiology 69(7):4332-4336.

Gibson, R.A. and McMurchie, E.J. (1986). Changes in lung surfactant lipids associated

with the sudden infant death syndrome. Australian Paediatric Journal 22 Suppl.1:77-80.

Gibson, R.A. and McMurchie, E.J. (1988). Decreased lung surfactant disaturated

phosphatidylcholine in sudden infant death syndrome. Early Human Development

17:145-155.

Gilder, H. and McSherry, C.K. (1974). Mechanisms of oxygen inhibition of pulmonary

surfactant synthesis. Surgery 76(1):72-79.

262

Gilder, H. and McSherry, C.K. (1976). Phosphatidylcholine synthesis and pulmonary

oxygen toxicity. Biochimica et Biophysica Acta 441(1):48-56.

Gilfillan, A.M. and Rooney, S.A. (1986). Leukotrienes stimulate phosphatidylcholine

secretion in cultured type II pneumocytes. Biochimica et Biophysica Acta 876:22-

27.

Gjertz, I., Kovacs, K.M., Lydersen, C. and Wiig, Ø. (2000). Movements and diving of adult

ringed seals (Phoca hispida) in Svalbard. Polar Biology 23:651-656.

Glantschnig, H., Varga, F., Rumpler, M. and Klaushofer, K. (1996). Prostacyclin (PGI2): a

potential mediator of c-fos expression induced by hydrostatic pressure in

osteoblastic cells. European Journal of Clinical Investigation 26:544-548.

Glasser, S.W., Detmer, E.A., Ikegami, M., Na, C.L., Stahlman, M.T. and Whitsett, J.A.

(2003). Pneumonitis and emphysema in sp-C gene targeted mice. The Journal of

Biological Chemistry 278(16):14291-14298.

Glasser, S.W., Korfhagen, T.R., Perme, C.M., Pilot-Matias, T.J., Kister, S.E. and Whitsett,

J.A. (1988). Two SP-C genes encoding human pulmonary surfactant proteolipid.

Journal of Biological Chemistry 263(21):10326-10331.

Gluck, L., Landowne, R.A. and Kulovich, M.V. (1970). Biochemical development of

surface activity in mammalian lung. Pediatric Research 4:352-364.

Goerke, J. and Clements, J.A. (1985). Alveolar surface tension and lung surfactant. In

"Handbook of Physiology, Section 3: The Respiratory System. Vol III: Mechanics

of Breathing, Part I". (P.T. Macklem and J. Mead, Eds.). pp. 247-260. American

Physiological Society, Washington D.C.

Goerke, J. and Gonzales, J. (1981). Temperature dependence of dipalmitol

phosphatidylcholine monolayer stability. Journal of Applied Physiology 51:1108-

1114.

Goniakowska-Witalinska, L. (1984). Tubular myelin structure in the lungs of amphibia. The

mode of formation. European Journal of Cell Biology 33:127-133.

Goniakowska-Witalinska, L. (1986). Lung of the tree frog, Hyla arborea L. Anatomy and

Embryology 174:379-389.

Gonzales, L.W., Ballard, P.L., Ertsey, R. and Williams, M.C. (1986). Glucocorticoids and

thyroid hormones stimulate biochemical and morphological differentiation of

human fetal lung in organ culture. Journal of Clinical Endocrinology and

Metabolism 62:678-691.

263

Goodman, R.E., Brown, S.E.S. and Crandall, E.D. (1984). Regulation of transport across

pulmonary alveolar epithelial cell monolayers. Journal of Applied Physiology

57:703-710.

Gould, V.E., Tosco, R., Wheelis, R.F., Gould, N.S. and Kapanci, Y. (1972). Oxygen

pneumonitis in man. Ultrastructural observations on the development of alveolar

lesions. Laboratory Investigation 26:499-508.

Grantham, R. (1974). Amino acid difference formula to help explain protein evolution.

Science 185(4754):862-864.

Gregory, T., Steinberg, K.P., Spragg, R., Gadek, J.E., Hyers, T.M., Longmore, W.J.,

Moxley, M.A., Cai, G.Z., Hite, R.D., Smith, R.M., Hudson, L.D., Crim, C., Newton,

P., Mitchell, B.R. and Gold, A.J. (1997). Bovine surfactant therapy for patients with

acute respiratory distress syndrome. American Journal of Respiratory and Critical

Care Medicine 155:1309-1315.

Gregory, T.J., Longmore, W.J., Moxley, M.A., Whitsett, J.A., Reed, C.R., Fowler, A.A.,

3rd, Hudson, L.D., Maunder, R.J., Crim, C. and Hyers, T.M. (1991). Surfactant

chemical composition and biophysical activity in acute respiratory distress

syndrome. Journal of Clinical Investigation 88(6):1976-1981.

Griese, M., Gobran, L.I. and Rooney, S.A. (1992). Ontogeny of surfactant secretion in

type II pneumocytes from fetal, newborn and adult rats. American Journal of

Physiology 262:L337-L343.

Gross, I. (1990). Regulation of fetal lung maturation. American Journal of Physiology

259(6 Pt 1):L337-344.

Gross, I., Ballard, P.L., Ballard, R.A., Jones, C.T. and Wilson, C.M. (1983). Corticosteroid

stimulation of phosphatidylcholine synthesis in cultured fetal rabbit lung: Evidence

for de novo protein synthesis mediated by glucocorticoid receptors. Endocrinology

112:829-837.

Gross, I., Wilson, C.M., Ingleson, L.D., Brehier, A. and Rooney, S.A. (1979). The influence

of hormones on the biochemical development of fetal rat lung in organ culture. I.

Estrogen. Biochimica et Biophysica Acta 575(3):375-383.

Gross, I., Wilson, C.M., Ingleson, L.D., Brehier, A. and Rooney, S.A. (1980). Fetal lung in

organ culture. III. Comparison of dexamethasone, thyroxine, and methylxanthines.

American Journal of Physiology 48(5):872 - 877.

Gugerli, F., Sperisen, C., Buchler, U., Brunner, I., Brodbeck, S., Palmer, J.D. and Qiu, Y.L.

(2001). The evolutionary split of Pinaceae from other conifers: evidence from an

http://phylogeny.arizona.edu/macclade/macclade.html

264

intron loss and a multigene phylogeny. Molecular Phylogenetics and Evolution

21(2):167-175.

Guimond, R.W. and Hutchison, V.H. (1976). Gas exchange of the giant salamanders of

North America. In "Respiration of Amphibious Vertebrates". (G.M. Hughes, Ed.).

pp. 313-338. Academic Press, London.

Gunther, A., Siebert, C., Schmidt, R., Ziegler, S., Grimminger, F., Yabut, M., Temmesfeld,

B., Walmrath, D., Morr, H. and Seeger, W. (1996). Surfactant alterations in severe

pneumonia, acute respiratory distress syndrome, and cardiogenic lung edema.

American Journal of Respiratory and Critical Care Medicine 153(1):176-184.

Gustafsson, M., Palmblad, M., Curstedt, T., Johansson, J. and Schurch, S. (2000).

Palmitoylation of a pulmonary surfactant protein C analogue affects the surface

associated lipid reservoir and film stability. Biochimica et Biophysica Acta 1466(1-2):169-178.

Guthmann, F., Haupt, R., Schlame, M., Stevens, P.A. and Rüstow, B. (1995). Alveolar

surfactant subfractions differ in their lipid composition. International Journal of

Biochemical Cellular Biology 27:1021-1026.

Guyton, A.C., Moffat, D.S. and Adair, T.H. (1984). Role of alveolar surface tension in

transepithelial movement of fluid. In "Pulmonary Surfactant". (B. Robertson, L.M.G.

Van Golde and J.J. Batenburg, Eds.). pp. 171-185. Elsevier Science Publishers,

Amsterdam.

Haagsman, H.P. and Diemel, R.V. (2001). Surfactant-associated proteins: functions and

structural variation. Comparative Biochemistry and Physiology A Molecular and

Integrative Physiology 129(1):91-108.

Haagsman, H.P. and Van Golde, L.M.G. (1991). Synthesis and assembly of lung

surfactant. Annual Review of Physiology 53:441-464.

Haig, D. and Hurst, L.D. (1991). A quantitative measure of error minimization in the

genetic code. Journal of Molecular Evolution 33:412-417.

Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and

analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41:95-

98.

Halle, D. and Yedgar, S. (1988). Mild pressure induces resistance of erythrocytes to

hemolysis by snake venom phospholipase A2. Biophysical Journal 54:393-396.

265

Haller, T., Ortmayr, J., Friedrich, F., Volkl, H. and Dietl, P. (1998). Dynamics of surfactant

release in alveolar type II cells. Proceedings of the National Academy of Sciences

U.S.A. 95:1579-1584.

Hallman, M., Enhorning, G. and Possmayer, F. (1985). Composition and surface activity

of normal and phoshpatidylglycerol-deficient lung surfactant. Pediatric Research

19(3):286-292.

Hallman, M., Feldman, B.H., Kirkpatrick, E. and Gluck, L. (1977). Absence of

phosphatidylglycerol (PG) in respiratory distress syndrome in the newborn.

Pediatric Research 11:714-720.

Hallman, M. and Gluck, L. (1975). Phosphatidylglycerol in lung surfactant II. Subcellular

distribution and mechanism of biosynthesis in vitro. Biochimica et Biophysica Acta

409:172-191.

Hallman, M., Glumoff, V. and Ramet, M. (2001). Surfactant in respiratory distress

syndrome and lung injury. Comparative Biochemistry and Physiology A Molecular


Hallman, M., Spragg, R., Harrell, J.H., Moser, K.M. and Gluck, L. (1982a). Evidence of

lung surfactant abnormality in respiratory failure. Study of bronchoalveolar lavage

phospholipids, surface activity, phospholipase activity, and plasma myoinositol.

Journal of Clinical Investigation 70(3):673-683.

Hallman, M., Wermer, D., Epstein, B.L. and Gluck, L. (1982b). Effects of maternal insulin

or glucose infusion on the fetus: Study on lung surfactant phospholipids, plasma

myoinositol, and fetal growth in the rabbit. American Journal of Obstetrics and

Gynecology 142(7):877-882.

Hamosh, M. and Hamosh, P. (1977). The effect of prolactin on the lecithin content of fetal

rabbit lung. Journal of Clinical Investigation 59(5):1002-1005.

Hamrahian, A.H., Oseni, T.S. and Arafah, B.M. (2004). Measurements of serum free

cortisol in critically ill patients. New England Journal of Medicine 350(16):1629-

1638.

Hamrick, M.W. (2001). Morphological diversity in digital skin microstructure of didelphid

marsupials. Journal of Anatomy 198(6):683-688.

Hance, A.J., Robin, E.D., Halter, J.B., Lewiston, N., Robin, D.A., Cornell, L., Caligiuri, M.

and Theodore, J. (1982). Hormonal changes and enforced diving in the harbor

seal Phoca vitulina. II. Plasma catecholamines. American Journal of Physiology

Regulatory and Integrative Comparative Physiology 242(5):R528-R532.

Haney, P.J., Badger, J.H., Buldak, G.L., Reich, C.I., Woese, C.R. and Olsen, G.J. (1999).

Thermal adaptation analyzed by comparison of protein sequences from mesophilic

266

and extremely thermophilic Methanococcus species. Proceedings of the National

Academy of Science U.S.A. 96:3578-3583.

Harlan, W.R., Margraf, J.H. and Said, S.I. (1966). Pulmonary lipid composition of species

with and without surfactant. American Journal of Physiology 211:855-861.

Harper, R.M. (1986). State-related physiological changes and risk for the Sudden Infant

Death Syndrome. Australian Paediatric Journal 22(Suppl. 1):55-58.

Harrison, R.J. and Kooyman, G.L. (1968). General physiology of the pinnipedia. In "The

Behaviour and Physiology of Pinnipeds". (R.J. Harrison, R.C. Hubbard, R.S.

Peterson, C.E. Rice and R.J. Schusterman, Eds.). pp. 211-296. Appleton-Century-

Crofts, New York.

Hartshorn, K., Chang, D., Rust, K., White, M., Heuser, J. and Crouch, E. (1996a).

Interactions of recombinant human pulmonary SP-D and SP-D multimers with

influenza A. American Journal of Physiology Lung Cellular and Molecular


Hartshorn, K., Reid, K.B., White, M.R., Jensenius, J.C., Morris, S.M., Tauber, A.I. and

Crouch, E. (1996b). Neutrophil deactivation by influenza A viruses: Mechanisms of

protection after viral opsonization with collectins and hemagglutination-inhibiting

antibodies. Blood 87(8):3450-3461.

Hartshorn, K., White, M., Shepherd, V., Reid, K., Jensenius, J. and Crouch, E. (1997).

Mechanisms of anti-influenza activity of surfactant proteins A and D: Comparison

with serum collectins. American Journal of Physiology Lung Cellular and Molecular


Hartshorn, K.L., Crouch, E.C., White, M.R., Eggleton, P., Tauber, A.I., Chang, D. and

Sastry, K. (1994). Evidence for a protective role of pulmonary surfactant protein D

(SP-D) against influenza A viruses. Journal of Clinical Investigation 94(1):311-319.

Harvey, P.H. and Pagel, M.D. (1991). "The Comparative Method in Evolutionary Biology".

Oxford University Press, New York.

Harwood, J.L., Desai, R., Hext, P., Tetley, T. and Richards, R. (1975). Characterization of

pulmonary surfactant from ox, rabbit, rat and sheep. Biochemical Journal 151:707-

714.

Haslett, J.N., Sanoudou, D., Kho, A.T., Han, M., Bennett, R.R., Kohane, I.S., Beggs, A.H.

and Kunkel, L.M. (2003). Gene expression profiling of Duchenne muscular

dystrophy skeletal muscle. Neurogenetics 4(4):163-171.

Hawgood, S. (1992). The hydrophilic surfactant protein SP-A: Molecular biology, structure

and function. In "Pulmonary Surfactant: from Molecular Biology to Clinical

267

Practice". (B. Robertson, L.M.G. Van Golde and J.J. Batenbrug, Eds.). pp. 33-54.

Elsevier Science Publishing, Amsterdam.

Hawgood, S., Benson, B.J. and Hamilton, R.L. (1985). Effects of a surfactant-associated

protein and calcium ions on the structure and surface activity of lung surfactant

lipids. Biochemistry 24:184-190.

Hawgood, S., Benson, B.J., Schilling, J., Damm , D. and Clements, J.A. (1987).

Nucleotide and amino acid sequences of pulmonary surfactant protein SP 18 and

evidence for cooperation between SP 18 and SP 28-36 in surfactant lipid

adsorption. Proceedings of the National Academy of Sciences U.S.A. 84:66-70.

Hawgood, S. and Poulain, F.R. (2001). The pulmonary collectins and surfactant

metabolism. Annual Review of Physiology 63:495-519.

Haydon, D.T., Easteal, S., Southey, M.C., Tesoriero, A., Giles, G.G., McCredie, M.R.E.,

Hopper, J.L. and Venter, D.J. (2001). Evidence for positive selection in foot-and-

mouth disease virus capsid genes from field isolates. Genetics 157:7-15.

Heeley, E.L., Hohlfeld, J.M., Krug, N. and Postle, A.D. (2000). Phospholipid molecular

species of bronchoalveolar lavage fluid after local allergen challenge in asthma.

American Journal of Physiology Lung Cellular and Molecular Physiology

278(2):L305-L311.

Henk, W.G. and Haldiman, J.T. (1990). Microanatomy of the lung of the bowhead whale

Balaena mysticetus. The Anatomical Record 226:187-197.

Hill, C.M., Brown, B.D., Morley, C.J., Davis, J.A. and Barson, A.J. (1988). Pulmonary

surfactant. II. In sudden infant death syndrome. Early Human Development

16:153-162.

Hochachka, P.W. and Somero, G.N. (1984). "Biochemical Adaptation". Princeton

University Press, Princeton.

Hoffman, D.R., Hoffman, L.H. and Snyder, F. (1986). Cytotoxicity and metabolism of alkyl

phospholipid analogues in neoplastic cells. Cancer Research 46(11):5803-5809.

Hohlfeld, J., Fabel, H. and Hamm, H. (1997). The role of pulmonary surfactant in

obstructive airways disease. European Respiratory Journal 10(2):482-491.

Holm, B.A., Enhorning, G. and Notter, R.H. (1988). A biophysical mechanism by which

plasma proteins inhibit lung surfactant activity. Chemistry and Physics of Lipids

49:49-55.

Homan, R. and Anderson, M.K. (1998). Rapid separation and quantitation of combined

neutral and polar lipid classes by high-performance liquid chromatography and

evaporative light-scattering detection. Journal of Chromatography B 708:21-26.

268

Honda, Y., Tsunematsu, K., Suzuki, A. and Akino, T. (1988). Changes in phospholipids in

bronchoalveolar lavage fluid of patients with interstitial lung diseases. Lung

166:293-301.

Hoppe, H.J. and Reid, K.B. (1994). Collectins - soluble proteins containing collagenous

regions and lectin domains - and their roles in innate immunity. Protein Science

3:1143-1158.

Hughes, A.L., Ota, T. and Nei, M. (1990). Positive Darwinian selection promotes charge

profile diversity in the antigen-binding cleft of class I major-histocompatibility-

complex molecules. Molecular Biology and Evolution 7(6):515-524.

Hughes, G.M., Ryan, J.W. and Ryan, U. (1973). Freeze-fractured lamellate bodies of

Protopterus lung: A comparative study. Journal of Physiology 236:15-16.

Ikegami, M. and Jobe, A. (1983). Surfactant function in respiratory distress syndrome.

Journal of Pediatrics 102:443-447.

Ingenito, E.P., Mora, R. and Mark, L. (2000). Pivotal role of anionic phospholipids in

determining dynamic behavior of lung surfactant. American Journal of Respiratory

and Critical Care Medicine 161(3 Pt 1):831-838.

Ingold, K.U., Webb, A.C., Witter, D., Burton, G.W., Metcalfe, T.A. and Muller, D.P. (1987).

Vitamin E remains the major lipid-soluble, chain-breaking antioxidant in human

plasma even in individuals suffering severe vitamin E deficiency. Archives of

Biochemistry and Biophysics 259:224-225.

Inoue, H., Inoue, C. and Hildebrandt, J. (1981). Temperature and surface forces in

excised rabbit lungs. Journal of Applied Physiology 51:823-829.

Jackson, J.C., Palmer, S., Wilson, C.B., Standaert, T.A., Truog, W.E., Murphy, J.H. and

Hodson, W.A. (1988). Postnatal changes in lung phospholipids and alveolar

macrophages in term newborn monkeys. Respiration Physiology 73:289-300.

Janssens, P.A., Grigg, J.A., Dove, H. and Hulbert, A.J. (1990). Thyroid hormones during

development of a marsupial, the tammar wallaby, Macropus eugenii. Journal of

Endocrinology 127(3):427-436.

Jeong, S.C., Ritchie, N.J. and Myrold, D.D. (1999). Molecular phylogenies of plants and

Frankia support multiple origins of actinorhizal symbioses. Molecular

Phylogenetics and Evolution 13(3):493-503.

Johansson, J. (1998). Structure and properties of surfactant protein C. Biochimica et


Johansson, J. and Curstedt, T. (1997). Molecular structures and interactions of pulmonary

surfactant components. European Journal of Biochemistry 244:675-693.

269

John, T.M., Ronald, K. and George, J.C. (1987). Blood levels of thyroid hormones and

certain metabolites in relation to moult in the harp seal (Phoca groenlandica).

Comparative Biochemistry and Physiology A Molecular and Integrative Physiology

88(4):655-657.

Johnston, S.D., Orgeig, S., Lopatko, O.V. and Daniels, C.B. (2000). Development of the

pulmonary surfactant system in two oviparous vertebrates. American Journal of

Physiology Regulatory and Integrative Comparative Physiology 278(2):R486-493.

Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992). The rapid generation of mutation

data matrices from protein sequences. Computational and Applied Bioscience

8:275-282.

Kahn, M.C., Anderson, G.J., Anyan, W.R. and Hall, S.B. (1995). Phosphatidylcholine

molecular species of calf lung surfactant. American Journal of Physiology

269:L567-L573.

Kakuta, Y., Sasaki, H. and Takishima, T. (1991). Effect of artificial surfactant on ciliary

beat frequency in guinea pig trachea. Respiration Physiology 83:313-322.

Kalin, N., Claass, A., Sommer, M., Puchelle, E. and Tummler, B. (1999). DeltaF508 CFTR

protein expression in tissues from patients with cystic fibrosis. Journal of Clinical

Investigation 103(10):1379-1389.

Kaneshiro, S.M. and Clark, D.S. (1995). Pressure effects on the composition and thermal

behavior of lipids from the deep-sea thermophile Methanococcus jannaschii.

Journal of Bacteriology 177(13):3668-3672.

Kankavi, O. (2003). Immunodetection of surfactant proteins in human organ of Corti,

Eustachian tube and kidney. Acta Biochimica Polonica 50(4):1057-1064.

Kasper, M., Albrecht, S., Grossmann, H., Grosser, M., Schuh, D. and Muller, M. (1995).

Monoclonal antibodies to surfactant protein D: evaluation of immunoreactivity in

normal rat lung and in a radiation-induced fibrosis model. Experimental Lung

Research 21(4):577-588.

Katsanidis, E. and Addis, P.B. (1999). Novel HPLC analysis of tocopherols, tocotrienols,

and cholesterol in tissue. Free Radical Biology and Medicine 27(11-12):1137-

1140.

Katyal, S.L., Estes, L.W. and Lombardi, B. (1977). Method for the isolation of surfactant

from homogenates and lavages of lung of adult, newborn, and fetal rats.

Laboratory Investigation 36(6):585-592.

Kawano, T., Mori, S., Cybulsky, M., Burger, R., Ballin, A., Cutz, E. and Bryan, A.C. (1987).

Effects of granulocyte depletion in a ventilated surfactant-depleted lung. Journal of


270

Kazzi, S.N., Schürch, S., McLaughlin, K.L., Romero, R. and Janisse, J. (2000). Surfactant

phospholipids and surface activity among preterm infants with respiratory distress

syndrome who develop bronchopulmonary dysplasia. Acta Paediatrica

89(10):1218-1225.

Keith, K.A., Wan, W.B., Ciesla, S.L., Beadle, J.R., Hostetler, K.Y. and Kern, E.R. (2004).

Inhibitory activity of alkoxylalkyl and alkyl esters of Cidofovir and cyclic Cidofovir

against orthopoxvirus replication in vitro. Antimicrobial Agents and Chemotherapy

48(5):1869-1871.

Kelley, L.A., MacCallum, R.M. and Sternberg, M.J.E. (2000). Enhanced genome

annotation using structural profiles in the program 3D-PSSM. Journal of Molecular

Biology 299(2):501-522.

Kelly, B.P. and Wartzok, D. (1996). Ringed seal diving behavior in the breeding season.

Canadian Journal of Zoology 74:1547-1555.

Kenny, D.E., O'Hara, T.M., Chen, T.C., Lu, Z., Tian, X. and Holick, M.F. (2004). Vitamin D

content in Alaskan Arctic zooplankton, fishes, and marine mammals. Zoo Biology

31(1):33-43.

Keough, K.M.W. (1998). Surfactant composition and extracellular transformations. In

"Lung Surfactant: Cellular and Molecular Processing". (S.A. Rooney, Ed.). pp. 1-

27. R.G. Landes Company, Austin, TX.

Kerem, D.H., Kylstra, J.A. and Saltzman, H.A. (1975). Respiratory flow rates in the sea

lion. Undersea Biomedical Research 2(1):20-27.

Khan, A.Q., Sikpi, M.O. and Das, S.K. (1985). Phospholipid composition of guinea pig

lung lavage. Lipids 20:7-10.

Kikkawa, Y. and Yoneda, K. (1974). The type II epithelial cell of the lung: I. Method of

isolation. Laboratory Investigation 30:76-84.

Kilburn, K.H. (1969). Alveolar clearance of particles. A bullfrog lung model. Archives of

Environmental Health 18:556-563.

King, J.E. (1964). "Seals of the world". British Museum (Natural History), London.

Kolleck, I., Sinha, P. and Rüstow, B. (2002). Vitamin E as an antioxidant of the lung:

Mechanisms of vitamin E delivery to alveolar type II cells. American Journal of

Respiratory and Critical Care Medicine 166:S62-S66.

Kooyman, G.L. (1973). Respiratory adaptations in marine mammals. American Zoologist

13:457-468.

Kooyman, G.L. (1989). Diving Physiology: Marine Mammals. In "Comparative Pulmonary

Physiology: Current Concepts". (S.C. Wood, Ed.). pp. 721-734. Marcel Dekker,

Inc., New York.

http://evolve.zoo.ox.ac.uk/

271

Kooyman, G.L., Hammond, D.D. and Schroeder, J.P. (1970). Bronchograms and

tracheograms of seals under pressure. Science 169(940):82-84.

Kunnasranta, M. (2001). Behavioural biology of two ringed seal (Phoca hispida)

subspecies in the large European lakes Saimaa and Ladoga. PhD thesis, Biology,

University of Joensuu.

Kuroki, Y. and Akino, T. (1991). Pulmonary surfactant protein A (SP-A) specifically binds

dipalmitoylphosphatidylcholine. Journal of Biological Chemistry 266:3068-3073.

Kuroki, Y., Mason, R.J. and Voelker, D.R. (1988). Alveolar type II cells express a high-

affinity receptor for pulmonary surfactant protein A. Proceedings of the National

Academy of Sciences U.S.A. 85:5566-5570.

Kyte, J. and Doolittle, R.F. (1982). A simple method for displaying the hydropathic

character of a protein. Journal of Molecular Biology 157:105-132.

Lachmann, B., Eijking, E.P., So, K.L. and Gomers, D. (1994). In vivo evaluation of the

inhibitory capacity of human plasma on exogenous surfactant function. Intensive

Care Medicine 20:6-11.

Lambson, R.O. and Cohn, J.E. (1968). Ultrastructure of the lung of the goose and its lining

of surface material. Journal of Anatomy 122:631-650.

Langman, C., Orgeig, S. and Daniels, C.B. (1996). Alterations in composition and function

of surfactant associated with torpor in Sminthopsis crassicaudata. American

Journal of Physiology 271:R437-R445.

Langworthy, T.A. and Pond, J.L. (1986). Membrane and lipids of thermophiles. In

"Thermophiles: General, Molecular, and Applied Microbiology". (T.D. Brock, Ed.).

pp. 107-135. John Wiley and Sons, New York.

Le Boeuf, B.J., Costa, D.P., Huntley, A.C. and Feldkamp, S.D. (1988). Continuous, deep

diving in female Northern elephant seals, Mirounga angustirostris. Canadian

Journal of Zoology 66:446-458.

Le Boeuf, B.J., Crocker, D.E., Grayson, J., Gedamke, J., Webb, P.M., Blackwell, S.B. and

Costa, D.P. (2000). Respiration and heart rate at the surface between dives in

northern elephant seals. Journal of Experimental Biology 203:3265-3274.

Ledje, C. and Arnason, U. (1996). Phylogenetic relationships within caniform carnivores

based on analyses of the mitochondrial 12S rRNA gene. Journal of Molecular

Evolution 43(6):641-649.

Lee, K.Y.C., Gopal, A., von Nahmen, A., Zasadzinski, J.A., Majewski, J., Smith, G.S.,

Howes, P.B. and Kjaer, K. (2002). Influence of palmitic acid and hexadecanol on

the phase transition temperature and molecular placing of dipalmitoylphosphatidyl-

272

choline monolayers at the air-water interface. Journal of Chemical Physics

116(2):774-783.

Lee, M.M., Green, F.H.Y., Schürch, S., Cheng, S., Bjarnason, S.G., Leonard, S., Wallace,

W., Possmayer, F. and Vallyathan, V. (2004). Comparison of inhibitory effects of

oxygen radicals and calf serum protein on surfactant activity. Molecular and

Cellular Biochemistry 259:15-22.

Lempert, J. and Macklem, P.T. (1971). Effect of temperature on rabbit lung surfactant and

pressure-volume hysteresis. Journal of Applied Physiology 31:380-385.

Lento, G.M., Hickson, R.E., Chambers, G.K. and Penny, D. (1995). Use of spectral

analysis to test hypotheses on the origin of pinnipeds. Molecular and Biological

Evolution 12(1):28-52.

Lewis, J.F., Ikegami, M. and Jobe, A.H. (1990). Altered surfactant function and

metabolism in rabbits with acute lung injury. Journal of Applied Physiology

69(6):2303-2310.

Lewis, J.F. and Veldhuizen, R. (2003). The role of exogenous surfactant in the treatment

of acute lung injury. Annual Review of Physiology 65:613-642.

Li, W.H. (1997). "Molecular Evolution". Sinauer Associates, Sunderland, MA.

Liau, D.F., Barrett, C.R., Bell, A.L. and Ryan, S.F. (1987). Functional abnormalities of lung

surfactant in experimental acute alveolar injury in the dog. American Review of

Respiratory Disease 136(2):395-401.

Liggins, G.C. (1976). Adrenocortical-related maturational events in the foetus. American

Journal of Obstetrics and Gynecology 126:931-941.

Little, G.J. (1991). Thyroid morphology and function and its role in thermoregulation in the

newborn southern elephant seal (Mirounga leonina) at Macquarie Island. Journal

of Anatomy 176:55-69.

Liu, M., Tanswell, A.K. and Post, M. (1999). Mechanical force-induced signal transduction

in lung cells. American Journal of Physiology Lung Cellular and Molecular

Physiology 277(4 Pt 1):L667-L683.

Liu, M., Wang, L., Li, E. and Enhorning, G. (1996). Pulmonary surfactant given

prophylactically alleviates an asthma attack in guinea pigs. Clinical and

Experimental Allergy 26:270-275.

Lopatko, O.V., Orgeig, S., Daniels, C.B. and Palmer, D. (1998). Alterations in the surface

properties of lung surfactant in the torpid marsupial Sminthopsis crassicaudata.

Journal of Applied Physiology 84(1):146-156.

273

Lopatko, O.V., Orgeig, S., Palmer, D., Schürch, S. and Daniels, C.B. (1999). Alterations in

pulmonary surfactant after rapid arousal from torpor in the marsupial Sminthopsis

crassicaudata. Journal of Applied Physiology 86(6):1959-1970.

Lopez, C.J., Sesma, C.P. and Vazquez, C.J.J. (1984). The development of the osmophillic

inclusion bodies within the granular pneumocyte of chicken lung. Anatomical

Record 210:597-602.

López-Hernández, J., González-Castro, M.J. and Piñeiro-Sotelo, M. (1999). Determination

of sterols in sea urchin gonads by high-performance liquid chromatography with

ultraviolet detection. Journal of Chromatographic Science 37(7):237-239.

Madan, T., Kishore, U., Shah, A., Eggleton, P., Strong, P., Wang, J.Y., Aggrawal, S.S.,

Sarma, P.U. and Reid, K.B. (1997). Lung surfactant proteins A and D can inhibit

specific IgE binding to the allergens of Aspergillus fumigatus and block allergen-

induced histamine release from human basophils. Clinical and Experimental

Immunology 110(2):241-249.

Maddison, W.P. and Maddison, D.R. (1992). MacClade: Analysis of phylogeny and

character evolution. Available at

http://phylogeny.arizona.edu/macclade/macclade.html

Madsen, J., Kliem, A., Tornoe, I., Skjodt, K. and Holmskov, U. (2000). Localization of lung

surfactant protein D on mucosal surfaces in human tissues. Journal of Immunology

164:5866-5870.

Magoon, M.W., Wright, J.R., Baritussio, A.G., Williams, M.C., Goerke, J., Benson, B.J.,

Hamilton, R.L. and Clements, J.A. (1983). Subfractionation of lung surfactant.

Implications for metabolism and surface activity. Biochimica et Biophysica Acta

750(1):18-31.

Mallampalli, R.K., Mathur, S.N., Warnock, L.J., Salome, R.G., Hunninghake, G.W. and

Field, F.J. (1996). Betamethasone modulation of sphingomyelin hydrolysis up-

regulates CTP:cholinephosphate cytidylyltransferase activity in adult rat lung.

Biochemical Journal 318:333-341.

Marino, P.A. and Rooney, S.A. (1980). Surfactant secretion in a newborn rabbit lung slice

model. Biochimica et Biophysica Acta 620:509-519.

Martin, K.M. and Hutchison, V.H. (1979). Ventilatory activity in Amphiuma tridactylum and

Siren lacertina (Amphibia, Caudata). Journal of Herpetology 13:427-434.

Martinez, P. and Morros, A. (1996). Membrane lipid dynamics during human sperm

capacitation. Frontiers in Biosciences 1:103-117.

274

Massaro, D., Clerch, L. and Massaro, G.D. (1982). Surfactant secretion: Evidence that

cholinergic stimulation of secretion is indirect. American Journal of Physiology

243:C39-C45.

Matalon, S., Lazrak, A., Jain, L. and Eaton, D.C. (2002). Invited Review: Biophysical

properties of sodium channels in lung alveolar epithelial cells. Journal of Applied

Physiology 93(5):1852-1859.

McGregor, L.K., Daniels, C.B. and Nicholas, T.E. (1993). Lung ultrastructure and the

surfactant-like system of the central netted dragon, Ctenophorus nuchalis. Copeia

1993(2):326-333.

McIntyre, I.W., Campbell, K.L. and MacArthur, R.A. (2002). Body oxygen stores, aerobic

dive limits and diving behaviour of the star-nosed mole (Condylura cristata) and

comparisons with non-aquatic talpids. Journal of Experimental Biology 205(Pt1):45-54.

McMahan, M.J., Mimouni, F., Miodovnik, M., Hull, W.M. and Whitsett, J.A. (1987).

Surfactant associated protein (SAP-35) in amniotic fluid from diabetic and

nondiabetic pregnancies. Obstetrics and Gynecology 70:94-98.

McSherry, C.K., Panossian, A., Jaeger, V.J. and Veith, F.J. (1967). Effects of hyperbaric

oxygen, the hyperbaric state, and rapid decompression on pulmonary surfactant.

Journal of Surgical Research 8(7):334-340.

Meban, C. (1978). Influence of pH and temperature on behaviour of surfactant from

human neonatal lungs. Biology of the Neonate 33:106-111.

Meban, C. (1980). Physical properties of surfactant from the lungs of the tortoise Testudo

hermanni. Comparative Biochemistry and Physiology 67(2):253-257.

Meban, C. (1981). Effect of lipids and other substances on the adsorption of dipalmityol

phosphatidyl choline. Pediatric Research 15:1029-1031.

Melin, S.R., DeLong, R.L. and Thomason, J.R. (2000). Attendance patterns of California

sea lion (Zalophus californianus) females and pups during the non-breeding

season at San Miguel island. Marine Mammal Science 16(1):169-185.

Mendelson, C.R. and Boggaram, V. (1991). Hormonal control of the surfactant system in

fetal lung. Annual Review of Physiology 53:415-440.

Mendelson, C.R., Johnston, J.M., MacDonald, P.C. and Snyder, J.M. (1981).

Multihormonal regulation of surfactant synthesis by human fetal lung in vitro.

Journal of Clinical Endocrinology and Metabolism 53(2):307-317.

Merrill, J.D. and Ballard, R.A. (2003). Pulmonary surfactant for neonatal respiratory

disorders. Current Opinion in Pediatrics 15:149-154.

275

Miles, P.R., Bowman, L., Rao, K.M.K., Baatz, J.E. and Huffman, L. (1999). Pulmonary

surfactant inhibits LPS-induced nitric oxide production by alveolar macrophages.

American Journal of Physiology Lung Cellular and Molecular Physiology

276(20):L186-L196.

Miles, P.R., Wright, J.R., Bowman, L. and Castranova, V. (1983). Incorporation of

[3H]palmitate into disaturated phosphatidylcholines in alveolar type II cells isolated

by centrifugal elutriation. Biochimica et Biophysica Acta 753(1):107-118.

Miller, L.D., Wert, S.E. and Whitsett, J.A. (2001a). Surfactant proteins and cell markers in

the respiratory epithelium of the amphibian, Ambystoma mexicanum. Comparative


149.

Miller, N.J., Orgeig, S., Daniels, C.B. and Baudinette, R.V. (2001b). Postnatal

development and control of the pulmonary surfactant system in the tammar

wallaby, Macropus eugenii. Journal of Experimental Biology 204(23):4031-4042.

Miyamura, K., Leigh, L.E.A., Lu, J., Hopkin, J., López-Bernal, A. and Reid, K.B.M. (1994).

Surfactant protein D binding to alveolar macrophages. Biochemistry Journal

300:237-242.

Miyata, T., Miyazawa, S. and Yasunaga, T. (1979). Two types of amino acid substitutions

in protein evolution. Journal of Molecular Evolution 12:219-236.

Montgelard, C., Catzeflis, F.M. and Douzery, E. (1997). Phylogenetic relationships of

artiodactyls and cetaceans as deduced from the comparison of cytochrome b and

12S rRNA mitochondrial sequences. Molecular and Biological Evolution 14(5):550-

559.

Munford, R.S., Sheppard, P.O. and O'Hara, P.J. (1995). Saposin-like proteins (SAPLIP)

carry out diverse functions on a common backbone structure. Journal of Lipid

Research 36:1653-1663.

Murata, Y., Kuroki, Y. and Akino, T. (1993). Role of C-terminal domain of pulmonary

surfactant protein A in binding to alveolar type II cells and regulation of

phospholipid secretion. Biochemistry Journal 291:71-76.

Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A. and O'Brien, S.J.

(2001). Molecular phylogenetics and the origins of placental mammals. Nature

409:614-618.

Nachtman, J.P., Hajratwala, B.R., Moon, H.L., Gross, K.B. and Wright, E.S. (1986).

Surface-tension measurements of pulmonary lavage from ozone-exposed rats.

Journal of Toxicology and Environmental Health 19(1):127-136.

276

Nakos, G., Kitsiouli, E.I. and Lekka, M.E. (1998). Bronchoalveolar lavage alterations in

pulmonary embolism. American Journal of Respiratory and Critical Care Medicine

158:1504-1510.

Nicholas, T.E., Power, J.H.T. and Barr, H.A. (1982). The pulmonary consequences of a

deep breath. Respiration Physiology 49:315-324.

Nielsen, R. and Yang, Z. (1998). Likelihood models for detecting positively selected amino

acid sites and applications to the HIV-1 envelope gene. Genetics 148(3):929-936.

Nikaido, M., Rooney, A.P. and Okada, N. (1999). Phylogenetic relationships among

cetartiodactyls based on insertions of short and long interpersed elements:

Hippopotamuses are the closest extant relatives of whales. Proceedings of the

National Academy of Science U.S.A. 96:10261-10266.

Nogee, L.M. (1998). Genetics of the hydrophobic surfactant proteins. Biochimica et


Nogee, L.M., Demello, D.E. and Colton, H.R. (1993). Deficiency of pulmonary surfactant

protein B in congenital alveolar proteinosis. New England Journal of Medicine

328:406-410.

Notter, R.H., Holcomb, S. and Mavis, R.D. (1980a). Dynamic surface properties of

phosphatidylglycerol-dipalmitoylphosphatidylcholine mixed films. Chemistry and

Physics of Lipids 27:305-319.

Notter, R.H., Tabak, S.A. and Mavis, R.D. (1980b). Surface properties of binary mixtures

of some pulmonary surfactant components. Journal of Lipid Research 21:10-22.

Notter, R.H. and Wang, Z. (1997). Pulmonary surfactant: physical chemistry, physiology,

and replacement. Reviews in Chemical Engineering 13(4):1-118.

Onderka, D.K. (1989). Prevalence and pathology of nematode infections in the lungs of

ringed seals (Phoca hispida) of the western arctic of Canada. Journal of Wildlife

Disease 25(2):218-224.

Oosterlaken-Dijksterhuis, M.A., Haagsman, H.P., van Golde, L.M.G. and Demel, R.A.

(1991). Interaction of lipid vesicles with monomolecular layers containing lung

surfactant proteins SP-B or SP-C. Biochemistry 30(33):8276-8281.

Orgeig, S. and Daniels, C.B. (1995). The evolutionary significance of pulmonary surfactant

in lungfish (Dipnoi). American Journal of Respiratory Cell and Molecular Biology

13:161-166.

Orgeig, S. and Daniels, C.B. (2001). The roles of cholesterol in pulmonary surfactant:

insights from comparative and evolutionary studies. Comparative Biochemistry and

Physiology A Molecular and Integrative Physiology 129(1):75-89.

277

Orgeig, S., Daniels, C.B., Johnston, S.D. and Sullivan, L.C. (2003). The pattern of

surfactant cholesterol during vertebrate evolution and development: does

ontogeny recapitulate phylogeny? Reproduction, Fertility and Development

15(1):55-73.

Orgeig, S., Daniels, C.B. and Smits, A.W. (1994). The composition and function of the

pulmonary surfactant system during metamorphosis in the tiger salamander

Ambystoma tigrinum. Journal of Comparative Physiology B 164:337-342.

Orgeig, S., Daniels, C.B. and Sullivan, L.C. (2004). Development of the pulmonary

surfactant system. In "The Lung: Development, Aging and the Environment". (R.

Harding, K. Pinkerton and C. Plopper, Eds.). pp. 149-167. Academic Press,

London.

Ormond, C.J. (2004). Coping with the cold: Heterothermic mammals provide a new

paradigm for surfactant composition and function. Ph.D. thesis, School of Earth &

Environmental Sciences, University of Adelaide.

Ormond, C.J., Daniels, C.B. and Orgeig, S. (2001). Neurochemical and thermal control of

surfactant secretion by alveolar type II cells isolated from the marsupial,

Sminthopsis crassicaudata. Journal of Comparative Physiology B 171(3):223-230.

Ormond, C.J., Postle, A.D., Orgeig, S., Possmayer, F., Bernhard, W., Panda, A.K.,

Jurgens, K.D., Milsom, W.K., Nag, K. and Daniels, C.B. (2005).

Dipalmitoylphosphatidylcholine is not the major surfactant phospholipid species in

all mammals. American Journal of Physiology Regulatory and Integrative

Comparative Physiology submitted.

Ortiz, R.M., Wade, C.E. and Ortiz, C.L. (2001). Effects of prolongued fasting on plasma

cortisol and TH in postweaned northern elephant seal pups. American Journal of

Physiology Regulatory and Integrative Comparative Physiology 280:R790-R795.

Oulton, M., MacDonald, J., Janigan, D.T. and Faulkner, G.T. (1993). Mouse alveolar

surfactant: characterization of subtypes prepared by differential centrifugation.

Lipids 28:715-720.

Oyarzun, M.J. and Clements, J.A. (1977). Ventilatory and cholinergic control of pulmonary

surfactant in the rabbit. Journal of Applied Physiology 43(1):39-45.

Oyarzun, M.J. and Clements, J.A. (1978). Control of lung surfactant by ventilation,

adrenergic mediators, and prostaglandins in the rabbit. American Review of

Respiratory Disease 117:879-891.

Paananen, R., Glumoff, V. and Hallman, M. (1999). Surfactant protein A and D expression

in the porcine Eustachian tube. FEBS letters 452:141-144.

278

Paananen, R., Glumoff, V., Sormunen, R., Voorhout, W. and Hallman, M. (2001a).

Expression and localization of lung surfactant protein B in Eustachian tube

epithelium. American Journal of Physiology Lung Cellular and Molecular


Paananen, R., Sormunen, R., Glumoff, V., van Eijk, M. and Hallman, M. (2001b).

Surfactant proteins A and D in eustachian tube epithelium. American Journal of

Physiology Lung Cellular and Molecular Physiology 281:L660-L667.

Page, R.D.M. (1996). TREEVIEW: An application to display phylogenetic trees on

personal computers. Computer Applications in the Biosciences 12:357-358.

Page, R.D.M. and Holmes, E.C. (1998). "Molecular Evolution: A Phylogenetic Approach".

Blackwell Science Ltd, Oxford.

Parker, J.C., Hernandez, L.A., Longenecker, G.L., Peevy, K. and Johnson, W. (1990).

Lung edema caused by high peak inspiratory pressure in dogs. American Review

of Respiratory Disease 142:321-328.

Paterson, J.F., Hammond, M.D., Montgomery, M.R., Sharp, J.T., Farrier, S.E. and Balis,

J.U. (1992). Acute ozone-induced lung injury in rats: Structural-functional

relationships of developing alveolar edema. Toxicology and Applied Pharmacology

117:37-45.

Pattle, R.E. (1958). Properties, function, and origin of the alveolar lining layer.

Proc.Roy.Soc.Lond. 148:217-240.

Persson, A., Chang, D. and Crouch, E.C. (1990). Surfactant protein D is a divalent cation-

dependent carbohydrate-binding protein. The Journal of Biological Chemistry

256(10):5755-5760.

Persson, A.V., Gibbons, B.J., Shoemaker, J.D., Moxley, M.A. and Longmore, W.J. (1992).

The major glycolipid recognized by SP-D in surfactant is phosphatidylinositol.

Biochemistry 31:12183-12189.

Pfleger, R.C. and Thomas, H.G. (1971). Beagle dog pulmonary surfactant lipids. Archives

of Internal Medicine 127:863-872.

Phillips, H.J. (1973). Dye exclusion test for cell viability. In "Tissue Culture - Methods and

Application". (P.F. Kruse and M.K. Patterson, Eds.). pp. 406. Academic Press,

New York.

Phleger, C.F., Smith, D.G., MacIntyre, D.H. and Saunders, B.S. (1978). Alveolar and

saccular lung phospholipids of the anaconda Eunectes murinus. Canadian Journal

of Zoology 56:1009-1013.

279

Piknova, B., Schief, W.R., Vogel, V., Discher, B.M. and Hall, S.B. (2001). Discrepancy

between phase behavior of lung surfactant phospholipids and the classical model

of surfactant function. Biophysical Journal 81(4):2172-2180.

Pison, U., Seeger, W., Buchhorn, R., Joka, T., Brand, M., Obertacke, U., Neuhof, H. and

Schmit-Neuerburg, K.P. (1989). Surfactant abnormalities in patients with

respiratory failure after multiple trauma. American Review of Respiratory Disease

140(4):1033-1039.

Pison, U., Wright, J.R. and Hawgood, S. (1992). Specific binding of surfactant apoprotein

SP-A to rat alveolar macrophages. American Journal of Physiology Lung Cellular

and Molecular Physiology 262:L412-L417.

Plasencia, I., Rivas, L., Casals, C., Keough, K.M. and Perez-Gil, J. (2001). Intrinsic

structural differences in the N-terminal segment of pulmonary surfactant protein

SP-C from different species. Comparative Biochemistry and Physiology A

Molecular and Integrative Physiology 129(1):129-139.

Plasencia, I., Rivas, L., Keough, K.M., Marsh, D. and Perez-Gil, J. (2004). The N-terminal

segment of pulmonary surfactant lipopeptide SP-C has intrinsic propensity to

interact with and perturb phospholipid bilayers. Biochemistry Journal 377(Pt1):183-193.

Platzker, A.C.G., Kitterman, J.A., Mescher, E.J., Clements, J.A. and Tooley, W.H. (1975).

Surfactant in the lung and tracheal fluid of the fetal lamb and acceleration of its

appearance by dexamethasone. Pediatrics 56:544-561.

Podar, M., Haddock, S.H., Sogin, M.L. and Harbison, G.R. (2001). A molecular

phylogenetic framework for the phylum Ctenophora using 18S rRNA genes.

Molecular Phylogenetics and Evolution 21(2):218-230.

Podkowa, D. and Goniakowska-Witalinska, L. (2003). Morphology of the air-breathing

stomach of the catfish Hypostomus plecostomus. Journal of Morphology 257:147-

163.

Pogson, G.H. and Mesa, K.A. (2004). Positive Darwinian selection at the pantophysin

(Pan I) locus in marine gadid fishes. Molecular and Biological Evolution 21(1):65-

75.

Ponganis, P.J., Gentry, R.L., Ponganis, E.P. and Ponganis, K.V. (1992). Analysis of swim

velocities during deep and shallow dives of two northern fur seals, Callorhinus

ursinus. Marine Mammal Science 8(1):69-75.

280

Possmayer, F. (2004). Physicochemical aspects of pulmonary surfactant. In "Fetal and

Neonatal Physiology". (R.A. Polin, W.W. Fox and S.H. Abman, Eds.). pp. 1014-

1034. W. B. Saunders Company, Philadelphia.

Possmayer, F., Nag, K., Rodriguez, K., Qanbar, R. and Schurch, S. (2001). Surface

activity in vitro: role of surfactant proteins. Comparative Biochemistry and

Physiology A Molecular and Integrative Physiology 129(1):209-220.

Post, M., Barsoumian, A. and Smith, B.T. (1986). The cellular mechanism of

glucocorticoid acceleration of fetal lung maturation: Fibroblast-pneumocyte factor

stimulates choline-phosphate cytidylyltransferase activity. Journal of Biological

Chemistry 261(5):2179-2184.

Post, M., Floros, J. and Smith, B.T. (1984). Inhibition of lung maturation by monoclonal

antibodies against fibroblast-pneumonocyte factor. Nature 308(5956):284-286.

Post, M. and Smith, B.T. (1992). Hormonal control of surfactant metabolism. In

"Pulmonary Surfactant: From Molecular Biology to Clinical Practice". (B.

Robertson, L.M.G. Van Golde and J.J. Batenburg, Eds.). pp. 379-424. Elsevier

Science Publishers B.V., Amsterdam.

Postle, A.D., Heeley, E.L. and Wilton, D.C. (2001). A comparison of the molecular species

compositions of mammalian lung surfactant phospholipids. Comparative


73.

Poulain, F.R., Akiyama, J., Allen, L., Brown, C., Chang, R., Goerke, J., Dobbs, L. and

Hawgood, S. (1999). Ultrastructure of phospholipid mixtures reconsituted with

surfactant proteins B and D. American Journal of Respiratory Cell and Molecular

Biology 20:1049-1058.

Poulain, F.R., Allen, L., Williams, C., Hamilton, R.L. and Hawgood, S. (1992). Effects of

surfactant apolipoproteins on liposome structure: Implications for tubular myelin

formation. American Journal of Physiology Lung Cellular and Molecular Physiology

262:L730-L7739.

Prem, C. and Pelster, B. (2001). Swimbladder gas gland cells cultured on permeable

supports regain their characteristic polarity. Journal of Experimental Biology

204(Pt 23):4023-4029.

Prem, C., Salvenmoser, W., Würtz, J. and Pelster, B. (2000). Swimbladder gas gland cells

produce surfactant: In vivo and in culture. American Journal of Physiology

Regulatory and Integrative Comparative Physiology 279:R2336-R2343.

Przybylski, R., Zambiazi, R. and Li, W. (1999). Kinetics of sterols changes during storage

and frying of canola oils. Proceedings of the 10th International Rapeseed

281

Congress, Canberra, Australia, The Regional Institute, Ltd.

Putman, E., Creuwels, L.A.J.M., van Golde , L.M.G. and Haagsman, H.P. (1996). Surface

properties, morphology and protein composition of pulmonary surfactant subtypes.

Biochemical Journal 320:599-605.

Putman, E., Liese, W., Voorhout, W.F., van Bree, L., van Golde, L.M.G. and Haagsman,

H.P. (1997). Short-term ozone exposure affects the surface activity of pulmonary

surfactant. Toxicology and Applied Pharmacology 142:288-296.

Pysher, T.J., Konrad, K.D. and Reed, G.B. (1977). Effects of hydrocortisone and

pilocarpine on fetal rat lung explants. Laboratory Investigation 37:588-594.

Ramadurai, S.M., Nielsen, H.C., Chen, Y., Hatzis, D. and Sosenko, I.R. (1998).

Differential effect in vivo of thyroid hormone on the expression of surfactant

phospholipid, surfactant protein mRNA and antioxidant enzyme mRNA in fetal rat

lung. Experimental Lung Research 24:641-657.

Rambaut, A. (1996). Se-Al: Sequence Alignment Editor. Available at

http://evolve.zoo.ox.ac.uk/

Randall, D.J., Burggren, W.W., Farrell, A.P. and Haswell, M.S. (1981). "The Evolution of

Air Breathing in Vertebrates". Cambridge University Press, London.

Rau, G.A., Vieten, G., Haitsma, J.J., Freihorst, J., Poets, C.F., Ure, B.M. and Bernhard,

W. (2004). Surfactant in newborn compared to adolescent pigs: adaptation to

neonatal respiration. American Journal of Respiratory Cell and Molecular Biology

30(5):694-701.

Reading, P., Holmskov, U. and Anders, E. (1998). Antiviral activity of bovine collectins

against rotaviruses. Journal of Genetic Virology 79:2255-2263.

Redding, R.A., Douglas, W.H. and Stein, M. (1972). Thyroid hormone influence upon lung

surfactant metabolism. Science 175(25):994-996.

Reed, J.Z., Chambers, C., Fedak, M.A. and Butler, P.J. (1994). Gas exchange of captive

freely diving grey seals (Halichoerus grypus). Journal of Experimental Biology

191:1-18.

Revak, S.D., Merritt, T.A., Degryse, E., Stefani, L., Courtney, M., Hallman, M. and

Cochrane, C.G. (1988). Use of human surfactant low molecular weight apoproteins

in the reconstitution of surfactant biological activity. Journal of Clinical Investigation

81:826-833.

Ribbons, K.A., Baudinette, R.V. and McMurchie, E.J. (1989). The development of

pulmonary surfactant lipids in a neonatal marsupial and the rat. Respiration

282

Physiology 75:1-10.

Rice, W.R., Ross, G.F., Singleton, F.M., Dingle, S. and Whitsett, J.A. (1987). Surfactant-

associated protein inhibits phospholipid secretion from type II cells. Journal of


Rice, W.R., Sarin, V.K., Fox, J.L., Baatz, J.E., Wert, S.E. and Whitsett, J.A. (1989).

Surfactant peptides stimulate uptake of phosphatidylcholine by isolated cells.


Richman, P.S., Batcher, S. and Catanzaro, A. (1990). Pulmonary surfactant suppresses

the immune lung injury response inhaled antigen in guinea pigs. Journal of

Laboratory and Clinical Medicine 116:18-26.

Ridgway, S.H., Bowers, C.A., Miller, D., Schultz, M.L., Jacobs, C.A. and Dooley, C.A.

(1984). Diving and blood oxygen in the white whale. Canadian Journal of Zoology

62:2349-2351.

Ridgway, S.H. and Howard, R. (1979). Dolphin lung collapse and intramuscular circulation

during free diving: Evidence from nitrogen washout. Science 206:1182-1183.

Riley, D.J., Rannels, D.E., Low, R.B., Jensen, L. and Jacobs, T.P. (1990). Effect of

physical forces on lung structure, function, and metabolism. American Review of

Respiratory Disease 142:910-914.

Riviere, J.E., Engelhardt, F.R. and Solomon, J. (1977). The relationship of thyroxine and

cortisol to the moult of the harbor seal Phoca vitulina. General and Comparative

Endocrinology 31:398-401.

Robinson, P.C., Voelker, D.R. and Mason, R.J. (1984). Isolation and culture of human

alveolar type II epithelial cells. Characterization of their phospholipid secretion.

American Review of Respiratory Disease 130(6):1156-1160.

Rodriguez Capote, K., McCormack, F.X. and Possmayer, F. (2003). Pulmonary surfactant

protein-A (SP-A) restores the surface properties of surfactant after oxidation by a

mechanism that requires the Cys6 interchain disulfide bond and the phospholipid

binding domain. Journal of Biological Chemistry 278(23):20461-20474.

Rooney, S.A., Gobran, L.I., Marino, P.A., Maniscalco, W.M. and Gross, I. (1979). Effects

of betamethasone on phospholipid content, composition and biosynthesis in the

fetal rabbit lung. Biochimica et Biophysica Acta 572:64-76.

Rose, F., Zwick, K., Ghofrani, H.A., Sibelius, U., Seeger, W., Walmrath, D. and

Grimminger, F. (1999). Prostacyclin enhances stretch-induced surfactant secretion

in alveolar epithelial type II cells. American Journal of Respiratory and Critical Care

Medicine 160:846-851.

283

Rotenberg, Y., Boruvka, L. and Neumann, A.W. (1983). Determination of surface tension

and contact angle from the shapes of axisymmetric fluid interfaces. Journal of

Colloid and Interface Science 93:169-183.

Rubin, L.P., Kifor, O., Hua, J., Brown, E.M. and Torday, J.S. (1994). Parathyroid hormone

(PTH) and PTH-related protein stimulate surfactant phospholipid synthesis in rat

fetal lung, apparently by a mesenchymal-epithelial mechanism. Biochimica et


Rubio, S., Chailley-Heu, B., Ducroc, R. and Bourbon, J.R. (1996). Antibody against

pulmonary surfactant protein A recognizes proteins in intestine and swim bladder

of the freshwater fish, Carp. Biochemical and Biophysical Research

Communications 225:901-906.

Rubio, S., Lacaze-Masmonteil, T., Chailley-Heu, B., Kahn, A., Bourbon, J.R. and Ducroc,

R. (1995). Pulmonary surfactant protein A (SP-A) is expressed by epithelial cells of

small and large intestine. Journal of Biological Chemistry 270:12162-12169.

Rustow, B., Haupt, R., Stevens, P.A. and Kunze, D. (1993). Type II pneumocytes secrete

vitamin E together with surfactant lipids. American Journal of Physiology 265(2 Pt1):L133-139.

Rüstow, B., Kolleck, I., Guthmann, F., Haupt, R., Kunze, D. and Stevens, P. (1994).

Synthesis and secretion of plasmalogens by type-II pneumocytes. Biochemical

Journal 302:665-668.

Sadana, T., Dhall, K., Sanyal, S.N., Wali, A., Minocha, R. and Majumdar, S. (1988).

Isolation and chemical composition of surface-active material from human lung

lavage. Lipids 23:551-558.

Sanchez-Esteban, J., Tsai, S., Sang, J., Qin, J., Torday, J.S. and Rubin, L.P. (1998).

Effects of mechanical forces on lung-specific gene expression. American Journal

of Medical Science 316(3):200-204.

Sanders, R.L. and Longmore, W.J. (1975). Phosphatidylglycerol in rat lung. II.

Comparison of occurrence, composition, and metabolism in surfactant and

residual lung fractions. Biochemistry 14:835-840.

Sanderson, M.J. and Driskell, A.C. (2003). The challenge of constructing large

phylogenetic trees. Trends in Plant Science 8(8):374-379.

Sanderson, R.J., Paul, G.W., Vatter, A.E. and Filley, G.F. (1976). Morphological and

physical basis for lung surfactant action. Respiration Physiology 27(3):379-392.

284

Savov, J., Silbajoris, R. and Young, S.L. (1999). Mechanical ventilation of rat lung: Effect

on surfactant forms. American Journal of Physiology Lung Cellular and Molecular

Physiology 277(21):L320-L326.

Scheffer, V.B. (1958). "Seals, sea lions and walruses: A review of the pinnipedia".

Stanford University Press, Stanford, California.

Schellenberg, J.C., Liggins, G.C., Manzi, M., Kitterman, J.A. and Lee, C.G. (1988).

Synergistic hormonal effects on lung maturation in fetal sheep. Journal of Applied


Schmidt, R., Meier, U., Markart, P., Grimminger, F., Velcovsky, H.G., Morr, H., Seeger, W.

and Gunther, A. (2002). Altered fatty acid composition of lung surfactant

phospholipids in interstitial lung disease. American Journal of Physiology Lung

Cellular and Molecular Physiology 283(5):L1079-1085.

Schmidt, R., Meier, U., Yabut-Perez, M., Walmrath, D., Grimminger, F., Seeger, W. and

Günther, A. (2001). Alteration of fatty acid profile in different surfactant

phospholipids in acute respiratory distress syndrome and severe pneumonia.

American Journal of Respiratory and Critical Care Medicine 163:95-100.

Schoel, W.M., Schürch, S. and Goerke, J. (1994). The captive bubble method for the

evaluation of pulmonary surfactant: Surface tension, area, and volume

calculations. Biochimica et Biophysica Acta 1200:281-290.

Schreer, J.F. and Kovacs, K.M. (1997). Allometry of diving capacity in air-breathing

vertebrates. Canadian Journal of Zoology 75:339-358.

Schroter, R.C. (1980). Quantitative comparisons of mammalian lung pressure volume

curves. Respiration Physiology 42(2):101-107.

Schürch, S. (1982). Surface tension at low lung volumes: dependence on time and

alveolar size. Respiration Physiology 48:339-355.

Schürch, S. and Bachofen, H. (1995). Biophysical aspects in the design of a therapeutic

surfactant. In "Surfactant Therapy for Lung Disease". (B. Robertson and H.W.

Teausch, Eds.). pp. 3-32. Marcel Dekker,

Schürch, S., Bachofen, H., Goerke, J. and Green, F. (1992). Surface properties of rat

pulmonary surfactant studied with the captive bubble method: Adsorption,

hysteresis, stability. Biochimica et Biophysica Acta 1103:127-136.

Schürch, S., Bachofen, H., Goerke, J. and Possmayer, F. (1989). A captive bubble

method reproduces the in situ behaviour of lung surfactant monolayers. Journal of


285

Schürch, S., Bachofen, H. and Possmayer, F. (2001). Surface activity in situ, in vivo, and

in the captive bubble surfactometer. Comparative Biochemistry and Physiology A

Molecular and Integrative Physiology 129(1):195-207.

Schürch, S., Bachofen, H. and Weibel, E.R. (1985). Alveolar surface tensions in excised

rabbit lungs: effect of temperature. Respiration Physiology 62:31-45.

Schürch, S., Green, F.H.Y. and Bachofen, H. (1998). Formation and structure of surface

films: Captive bubble surfactometry. Biochimica et Biophysica Acta 1408:180-202.

Schürch, S., Qanbar, R., Bachofen, H. and Possmayer, F. (1995). The surface-associated

surfactant reservoir in the alveolar lining. Biology of the Neonate 67(suppl):61-76.

Seeger, W., Grube, C., Gunther, A. and Schmidt, R. (1993). Surfactant inhibition by

plasma proteins: differential sensitivity of various surfactant preparations.

European Respiratory Journal 6:971-977.

Shaffer, S.A., Costa, D.P., Williams, T.M. and Ridgway, S.H. (1997). Diving and swimming

performance of white whales, Delphinapterus leucas: An assessment of plasma

lactate and blood gas levels and respiratory rates. Journal of Experimental Biology

200:3091-3099.

Sharma, A., Gonzales, L.W. and Ballard, P.L. (1993). Hormonal regulation of

cholinephosphate cytidylyltransferase in human fetal lung. Biochimica et


Shawer, M., Greenspan, P., Øie, S. and Lu, R.D. (2002). VLDL-resembling phospholipid-

submicron emulsion for cholesterol-based drug targeting. Journal of

Pharmaceutical Sciences 91(6):1405-1413.

Shelley, S.A., Paciga, J.E. and Balis, J.U. (1977). Purification of surfactant from lung

washings and washings contaminated with blood constituents. Lipids 12:505-510.

Shelley, S.A., Paciga, J.E. and Balis, J.U. (1984). Lung surfactant phospholipids in

different animal species. Lipids 19:857-862.

Sherwood, L. (1997). "Human Physiology: From Cells to Systems". Wadsworth Publishing

Company, Belmont.

Shiffer, K., Hawgood, S., Düzgünes, N. and Goerke, J. (1988). Interactions of the low

molecular weight group of surfactant-associated proteins (SP 5-18) with pulmonary

surfactant lipids. Biochemistry 27:2689-2695.

Siegwart, B., Gehr, P., Gil, J. and Weibel, E.R. (1971). Morphometric estimation of

pulmonary diffusion capacity. IV. The normal dog lung. Respiration Physiology

13(2):141-159.

286

Simonson, S.G., Huang, Y.C., Fracica, P.J., Welty-Wolf, K.E., Moon, R.E., Young, S.L.

and Piantadosi, C.A. (1997). Changes in the lung after prolonged positive pressure

ventilation in normal baboons. Journal of Critical Care 12:72-82.

Slip, D.J., Hindel, M.A. and Burton, H.R. (1994). Diving behaviour of southern elephant

seals from Macquarie Island. In "Elephant Seals". (B.J. Le Boeuf and R.M. Laws,

Eds.). pp. 253-270. University of California Press, Berkeley.

Slocombe, N.C., Codd, J.R., Wood, P.G., Orgeig, S. and Daniels, C.B. (2000). The effect

of alterations in activity and body temperature on the pulmonary surfactant system

in the lesser long-eared bat Nyctophilus geoffroyi. Journal of Experimental Biology

203(16):2429-2435.

Smith, B.T. and Sabry, K. (1983). Glucocorticoid-thyroid synergism in lung maturation: A

mechanism involving epithelial-mesenchymal interaction. Proceedings of the

National Academy of Science U.S.A. 80(7):1951-1954.

Smith, R.A. and Zapol, W.M. (1989). Modification of high pressure nervous syndrome in

mice by corticosteroids. In "High pressure nervous syndrome - 20 years later".

(J.C. Rostain, E. Martinez and C. Lemaire, Eds.). pp. 155-162. ARAS-SHNP,

Marseilles.

Sneath, P.H.A. (1966). Relations between chemical structure and biological activity in

peptides. Journal of Theoretical Biology 12:157-195.

Soltis, D.E. and Soltis, P.S. (2003). The role of phylogenetics in comparative genetics.

Plant Physiology 132(4):1790-1800.

Somero, G.N. (1992). Adaptations to high hydrostatic pressure. Annual Review of


Somero, G.N. (2003). Protein adaptations to temperature and pressure: Complementary

roles of adaptive changes in amino acid sequence and internal milieu.

Comparative Biochemistry and Physiology Part B 136:577-591.

Southall, D.P., Johnson, P., Salmons, S., Talbert, D.G., Morley, C.J. and Miller, J. (1985).

Prolonged expiratory apnoea: a disorder resulting in episodes of severe arterial

hypoxaemia in infants and young children. The Lancet 2:571-577.

Spragg, R.G., Gilliard, N., Richman, P., Smith, R.M., Hite, R.D., Pappert, D., Robertson,

B., Curstedt, T. and Strayer, D. (1994). Acute effects of a single dose of porcine

surfactant on patients with the adult respiratory distress syndrome. Chest 105:195-

202.

Spragg, R.G., Ponganis, P.J., Marsh, J.J., Rau, G.A. and Bernhard, W. (2004). Surfactant

from diving aquatic mammals. Journal of Applied Physiology 96(5):1626-1632.

287

Stark-Vancs, V., Bell, P.B. and Hutchison, V.H. (1984). Morphological and

pharmacological basis for pulmonary ventilation in Amphiuma tridactylum. Cell and

Tissue Research 238:1-12.

Steinschneider, A. (1972). Prolonged apnea and the sudden infant death syndrome:

clinical and laboratory observations. Pediatrics 50:646-654.

Stevens, P.A., Wright, J. and Clements, J.A. (1987). Changes in quantity, composition,

and surface activity of alveolar surfactant at birth. Journal of Applied Physiology

63:1049-1057.

Stewardson, C.L., Hemsley, S., Meyer, M.A., Canfield, P.J. and Maindonald, J.H. (1999).

Gross and microscopic visceral anatomy of the male Cape fur seal, Arctocephalus

pusillus pusillus (Pinnipedia: Otariidae), with reference to organ size and growth.

Journal of Anatomy 195:235-255.

Stewart, B.S. and DeLong, R.L. (1995). Double migrations of the northern elephant seal,

Mirounga angustirostris. Journal of Mammalogy 76:196-205.

Stone, K.C., Mercer, R.R., Gehr, P., Stockstill, B. and Crapo, J.D. (1992). Allometric

relationships of cell numbers and size in the mammalian lung. American Journal of

Respiratory Cell and Molecular Biology 6(2):235-243.

Strang, L.B. (1989). Solute and water transport across the pulmonary epithelium: a new

chapter in lung physiology inaugurated by Alfred Jost. Biology of the Neonate

55(6):355-365.

Subramaniam, S., Whitsett, J.A., Hull, W. and Gairola, C.G. (1996). Alteration of

pulmonary surfactant proteins in rats chronically exposed to cigarette smoke.

Toxicology and Applied Pharmacology 140(2):274-280.

Sukarova-Stefanovska, E., Zisovski, N., Muratovska, O., Kostova, S. and Efremov, G.D.

(2002). Three novel point mutations causing haemophilia A. Haemophilia 8(5):715-

718.

Sullivan, L.C. (2002). The control of pulmonary surfactant development in oviparous

amniotes. Ph.D. thesis, Environmental Biology, University of Adelaide.

Sullivan, L.C., Daniels, C.B., Phillips, I.D., Orgeig, S. and Whitsett, J.A. (1998).

Conservation of surfactant protein A: evidence for a single origin for vertebrate

pulmonary surfactant. Journal of Molecular Evolution 46(2):131-138.

Sullivan, L.C. and Orgeig, S. (2001). Dexamethasone and epinephrine stimulate

surfactant secretion in type II cells of embryonic chickens. American Journal of

Physiology Regulatory and Integrative Comparative Physiology 281(3):R770-777.

288

Sullivan, L.C., Orgeig, S. and Daniels, C.B. (2002a). Control of the development of the

pulmonary surfactant system in the saltwater crocodile, Crocodylus porosus.

American Journal of Physiology Regulatory and Integrative Comparative

Physiology 283(5):R1164-R1176.

Sullivan, L.C., Orgeig, S. and Daniels, C.B. (2002b). Regulation of pulmonary surfactant

secretion in the developing lizard, Pogona vitticeps. Comparative Biochemistry and

Physiology A Molecular and Integrative Physiology Molecular and Integrative

Physiology 133(3):539-546.

Sullivan, L.C., Orgeig, S., Wood, P.G. and Daniels, C.B. (2001). The ontogeny of

pulmonary surfactant secretion in the embryonic green sea turtle (Chelonia

mydas). Physiological and Biochemical Zoology 74(4):493-501.

Suzuki, Y. (1982). Effect of protein, cholesterol, and phosphatidylglycerol on the surface

activity of the lipid-protein complex reconstituted from pig pulmonary surfactant.

Journal of Lipid Research 23:62-69.

Suzuki, Y., Fujita, Y. and Kogishi, K. (1989). Reconstitution of tubular myelin from

synthetic lipids and proteins associated with pig pulmonary surfactant. American

Review of Respiratory Disease 140:75-81.

Swanson, W.J., Yang, Z., Wolfner, M.F. and Aquadro, C.F. (2001). Positive Darwinian

selection in the evolution of mammalian female reproductive proteins. Proceedings

of the National Academy of Science U.S.A. 98:2509-2514.

Swendsen, C.L., Skita, V. and Thrall, R.S. (1996). Alterations in surfactant neutral lipid

composition during the development of bleomycin-induced pulmonary fibrosis.


Szalay, F. (1969). The Hapalodectinae and a phylogeny of the Mesonychidae (Mammalia,

Condylarthra). American Museum Novitates 2361:1-26.

Takamoto, D.Y., Lipp, M.M., von Nahmen, A., Lee, K.Y., Waring, A.J. and Zasadzinski,

J.A. (2001). Interaction of lung surfactant proteins with anionic phospholipids.

Biophysical Journal 81(1):153-169.

Tanaka, Y. and Takei, T. (1983). Lung surfactants. I. Comparison of surfactants prepared

from lungs of calf, ox, dog and rabbit. Chemical and Pharmaceutical Bulletin

31(11):4091-4099.

Taneva, S. and Keough, K.M.W. (1997). Cholesterol modifies the properties of surface

films of dipalmitoylphosphatidylcholine plus pulmonary surfactant-associated

protein B or C spread or adsorbed at the air-water interface. Biochemistry

36(4):912-922.

289

Taneva, S.G. and Keough, K.M.W. (1994). Dynamic surface properties of pulmonary

surfactant proteins SP-B and SP-C and their mixtures with

dipalmitoylphosphatidylcholine. Biochemistry 33(49):14660-14670.

Taylor, A.E., Rehder, K., Hyatt, R.E. and Parker, J.C. (1989). Pulmonary fluid exchange.

In "Clinical Respiration Physiology". (M. Wonsiewicz, Ed.). pp. 169-191. Saunders,

Philadelphia.

Taylor, C.G., McCutchon, T.L., Boermans, H.J., DiSilvestro, R.A. and Bray, T.M. (1997).

Comparison of Zn and vitamin E for protection against hyperoxia-induced lung

damage. Free Radical Biology and Medicine 22:543-550.

Tedford, R.H. (1976). Relationship of pinnipeds to other carnivores (Mammalia).

Systematic Zoology 25:363-374.

ten Brinke, A., van Golde, L.M. and Batenburg, J.J. (2002). Palmitoylation and processing

of the lipopeptide surfactant protein C. Biochimica et Biophysica Acta 1583(3):253-

265.

Tenner, A.J., Robinson, S.L., Borchelt, J. and Wright, J.R. (1989). Human pulmonary

surfactant protein (SP-A), a protein structurally homologous to C1q, can enhance

FcR- and CR1-mediated phagocytosis. Journal of Biological Chemistry 264:13923-

13928.

Thewissen, J.G.M. (1994). Phylogenetic aspects of cetacean origins: a morphological

perspective. Journal of Mammal Evolution 2:157-183.

Thomas, A.Q., Lane, K., Phillips, J., 3rd, Prince, M., Markin, C., Speer, M., Schwartz,

D.A., Gaddipati, R., Marney, A., Johnson, J., Roberts, R., Haines, J., Stahlman, M.

and Loyd, J.E. (2002). Heterozygosity for a surfactant protein C gene mutation

associated with usual interstitial pneumonitis and cellular nonspecific interstitial

pneumonitis in one kindred. American Journal of Respiratory and Critical Care

Medicine 165(9):1322-1328.

Tino, M.J. and Wright, J.R. (1999). Surfactant proteins A and D specifically stimulate

directed actin-based responses in alveolar macrophages. American Journal of

Physiology Lung Cellular and Molecular Physiology 276:L164-L174.

Touchstone, J.C., Chen, J.C. and Beaver, K.M. (1980). Improved separation of

phospholipids in thin layer chromatography. Lipids 15:61-62.

Tsuno, K., Prato, P. and Kolobow, T. (1990). Acute lung injury from mechanical ventilation

at moderately high airway pressures. Journal of Applied Physiology 69:956-961.

Tyler, W.S. and Pangborn, J. (1964). Laminated membrane surface and osmiophilic

inclusions in avian lung epithelium. Journal of Cell Biology 20:157-164.

290

Uhlson, C., Harrison, K., Allen, C.B., Ahmad, S., White, C.W. and Murphy, R.C. (2002).

Oxidized phospholipids derived from ozone-treated lung surfactant extract reduce

macrophage and epithelial cell viability. Chemical Research Toxicology 15:896-

906.

van Daal, G.J., Bos, J.A., Eijking, E.P., Gommers, D., Hannappel, E. and Lachmann, B.

(1992). Surfactant replacement therapy improves pulmonary mechanics in end-

stage influenza A pneumonia in mice. American Review of Respiratory Disease

145:859-863.

van Iwwaarden, J.F., Van Strijp, J.A.G., Visser, H., Haagsman, H.P., Verhoef, J. and van

Golde , L.M.G. (1992). Binding of surfactant protein A (SP-A) to herpes simplex

virus type I-infected cells is mediated by the carbohydrate moiety of SP-A. Journal

of Biological Chemistry 267:25039-25043.

Veldhuizen, E.J. and Haagsman, H.P. (2000). Role of pulmonary surfactant components

in surface film formation and dynamics. Biochimica et Biophysica Acta

1467(2):255-270.

Veldhuizen, E.J.A., Batenbrug, J.J., van Golde , L.M.G. and Haagsman, H.P. (2000a).

The role of surfactant proteins in DPPC enrichment of surface films. Biophysical

Journal 79:3164-3171.

Veldhuizen, R.A.W., Nag, K., Orgeig, S. and Possmayer, F. (1998). The role of lipids in

pulmonary surfactant. Biochimica et Biophysica Acta 1408:90-108.

Veldhuizen, R.A.W., Tremblay, L.N., Govindarajan, A., van Rozendaal, B.A.W.M.,

Haagsman, H.P. and Slutsky, A.S. (2000b). Pulmonary surfactant is altered during

mechanical ventilation of isolated rat lung. Critical Care Medicine 28(7):2545-2551.

Veldhuizen, R.A.W., Welk, B., Harbottle, R., Hearn, S., Nag, K., Peterson, N. and

Possmayer, F. (2002). Mechanical ventilation of isolated rat lungs changes the

structure and biophysical properties of surfactant. Journal of Applied Physiology

92:1169-1175.

Veldhuizen, R.A.W., Yao, L.-J., Hearn, S.A., Possmayer, F. and Lewis, J.F. (1996).

Surfactant associated protein A is important for maintaining surfactant large-

aggregate forms during surface-area cycling. Journal of Biochemistry 313:835-

840.

Viscardi, R.M., Strauss, K. and Hasday, J.D. (1997). Oleic acid stimulates rapid

translocation of cholinephosphate cytidylyltransferase in type II cells. Biochimica et

Biophysica Acta 1349(2):157-170.

von Nahmen, A., Schenk, M., Sieber, M. and Amrein, M. (1997). The structure of a model

pulmonary surfactant as revealed by scanning force microscopy. Biophysical

291

Journal 72(1):463-469.

von Neergaard, K.V. (1929). New notions on a fundamental principle of respiratory

mechanics: the retractile force of the lung, dependent on the surface tension in the

alveoli. Zeitschrift für Gesundheit und Experimentelle Medizin 66:373-394.

Vrana, P.B., Milinkovitch, M.C., Powell, J.R. and Wheeler, W.C. (1994). Higher level

relationships of the arctoid Carnivora based on sequence data and "total

evidence". Molecular and Phylogenetic Evolution 3(1):47-58.

Wali, A., Dhall, K., Sanyal, S.N., Juneja, R. and Majumdar, S. (1990). Sequential isolation

and biochemical analysis of pulmonary surfactant from human lung homogenate.

Biochemistry International 20(5):869-877.

Walmrath, D., Günther, A., Ghofrani, H.A., Schermuly, R., Schneider, T., Grimminger, F.

and Seeger, W. (1996). Bronchoscopic surfactant administration in patients with

severe adult respiratory distress syndrome and sepsis. American Journal of

Respiratory and Critical Care Medicine 154:57-62.

Walters, R.W., Jenq, R.R. and Hall, S.B. (2000). Distinct steps in the adsorption of

pulmonary surfactant to an air-liquid interface. Biophysical Journal 78(1):257-266.

Walther, F.J., Gordon, L.M., Zasadzinski, J.A., Sherman, M.A. and Waring, A.J. (2000).

Surfactant protein B and C analogues. Molecular Genetics and Metabolism 71(1-2):342-351.

Wang, W.J., Mulugeta, S., Russo, S.J. and Beers, M.F. (2003). Deletion of exon 4 from

human surfactant protein C results in aggresome formation and generation of a

dominant negative. Journal of Cell Science 116(4):683-692.

Wang, Z., Gurel, O., Baatz, J.E. and Notter, R.H. (1996). Acylation of pulmonary

surfactant protein C is required for its optimal surface active interactions with

phospholipids. Journal of Biological Chemistry. 271:19104-19109.

Wang, Z.M., Yasui, M. and Celsi, G. (1994). Glucocorticoids regulate the transcription of

Na+-K+-ATPase genes in the infant rat kidney. American Journal of Physiology Cell

Physiology 267:C450-C455.

Warburton, D., Buckley, S., Cosico, L. and Forman, H.J. (1989). Sublethal oxidant injury

inhibits signal transduction in rat type II pneumocytes. American Journal of


Weaver, T.E. and Conkright, J.J. (2001). Functions of surfactant proteins B and C. Annual

Review of Physiology 63:555-578.

Webb, H.H. and Tierney, D.F. (1974). Experimental pulmonary edema due to intermittent

positive pressure ventilation with high inflation pressures: Protection by positive

292

end-expiratory pressure. American Review of Respiratory Disease 110:556-565.

Webb, W.R., Lanius, J.W., Aslami, A. and Reynolds, R.C. (1966). The effects of

hyperbaric-oxygen tensions on pulmonary surfactant in guinea pigs and rats. Jama

195(4):279-280.

Wert, S.E., Yoshida, M., LeVine, A.M., Ikegami, M., Jones, T., Ross, G.F., Fisher, J.H.,

Korfhagen, T.R. and Whitsett, J.A. (2000). Increased metalloproteinase activity,

oxidant production, and emphysema in surfactant protein D gene-inactivated mice.

Proceedings of the National Academy of Sciences of the United States of America

97(11):5972-5977.

West, J.B. (1985). "Respiratory Physiology - the Essentials". Williams and Wilkins,

Baltimore, MD.

Wetzstein, H.Y., Stratton, C.J. and Olson, N. (1980). The stereoscanning electron

microscopy and ultrastructural histochemistry of the avian and reptilian surfactant

systems: indian dove, desert spiny and taiwan golden skink lizards. Anatomical

Record 197:63-73.

Whelan, S. and Goldman, N. (2001). A general empirical model of protein evolution

derived from multiple protein families using a maximum-likelihood approach.

Molecular and Biological Evolution 18(5):691-699.

Whitmore, F.C. and Sanders, A.E. (1976). Review of the Oligocene Cetacea. Systematic

Zoology 25:304-320.

Whitsett, J.A. and Baatz, J.E. (1992). Hydrophobic surfactant proteins SP-B and SP-C:

Molecular biology, structure and function. In "Pulmonary Surfactant: From

Molecular Biology to Clinical Practise". (B. Robertson, L.M.G. Van Golde and J.J.

Batenburg, Eds.). pp. 55-75. Elsevier Science Publishers, Amsterdam.

Whitsett, J.A., Nogee, L.M., Weaver, T.E. and Horowitz, A.D. (1995). Human surfactant

protein B: structure, function, regulation, and genetic disease. Physiological

Review 75(4):749-757.

Wickham, L.L., Elsner, R., White, F.C. and Cornell, L.H. (1989). Blood viscosity in phocid

seals: Possible adaptations to diving. Journal of Comparative Physiology B

159(2):153-158.

Williams, E.E., Stewart, B.S., Beuchat, C.A., Somero, G.N. and Hazel, J.R. (2001).

Hydrostatic-pressure and temperature affects the molecular order of erythrocyte

membranes from deep-, shallow-, and non-diving mammals. Canadian Journal of

Zoology 79:888-894.

293

Williams, M.C. and Benson, B.J. (1981). Immunocytochemical localization and

identification of the major surfactant protein in adult rat lung. Journal of

Histochemistry and Cytochemistry 29(2):291-305.

Wilson, J.L. and Farber, S. (1933). Pathogenesis of atelectasis of the new-born. American

Journal of Diseases of Children 46:590-603.

Wirsen, C.O., Jannasch, H.W., Wakeham, S.G. and Canuel, E.A. (1987). Membrane lipids

of a psychrophilic and barophilic deep-sea bacterium. Current Microbiology

14:319-322.

Wirtz, H. and Schmidt, M. (1992). Ventilation and secretion of pulmonary surfactant.

Clinical Investigation 70:3-13.

Wirtz, H.R.W. and Dobbs, L.G. (1990). Calcium mobilization and exocytosis after one

mechanical stretch of lung epithelial cells. Science 250:1266-1269.

Woakes, A.J., Butler, P.J. and Snow, D.H. (1987). The measurement of respiratory airflow

in exercising horses. In "Equine Exercise Physiology". (J.R. Gillespie and N.E.

Robinson, Eds.). pp. 194-205. ICEEP Publications, Davis, CA.

Woese, C.R., Dugre, D.H., Dugre, S.A., Kondo, M. and Saxinger, W.C. (1966). On the

fundamental nature and evolution of the genetic code. Cold Spring Harbor

Symposia on Quantitative Biology 31:723-736.

Woldstad, S. and Jenssen, B.M. (1999). Thyroid hormones in grey seal pups (Halichoerus

grypus). Comparative Biochemistry and Physiology A Molecular and Integrative


Wong, C.J., Akiyama, J., Allen, L. and Hawgood, S. (1996). Localization and

developmental expression of surfactant proteins A and D in the respiratory tract of

the mouse. Pediatric Research 39:930-937.

Wood, P.G., Andrew, L.K., Daniels, C.B., Orgeig, S. and Roberts, C.T. (1997). Autonomic

control of the pulmonary surfactant system and lung compliance in the lizard.

Physiological Zoology 70(4):444-455.

Wood, P.G. and Daniels, C.B. (1996). Factors affecting opening and filling pressures in

the lungs of the lizard Pogona vitticeps. Respiration Physiology 103:203-210.

Wood, P.G., Daniels, C.B. and Orgeig, S. (1995). Functional significance and control of

release of pulmonary surfactant in the lizard lung. American Journal of Physiology

269(4 Pt 2):R838-847.

Wood, P.G., Lopatko, O.V., Orgeig, S., Codd, J.R. and Daniels, C.B. (1999). Control of

pulmonary surfactant secretion from type II pneumocytes isolated from the lizard

Pogona vitticeps. American Journal of Physiology 277(6 Pt 2):R1705-1711.

294

Wood, P.G., Lopatko, O.V., Orgeig, S., Joss, J.M., Smits, A.W. and Daniels, C.B. (2000a).

Control of pulmonary surfactant secretion: an evolutionary perspective. American

Journal of Physiology Regulatory and Integrative Comparative Physiology

278(3):R611-619.

Wood, P.G., Ponganis, P.J., Spragg, R.G. and Daniels, C.B. (2000b). The composition of

pulmonary surfactant in the northern elephant seal (Mirounga angustirotris).

Comparative Biochemistry and Physiology B 126(Suppl. 1):S108.

Wozencraft, W.C. (1989). The phylogeny of the recent carnivora. In "Carnivore behavior,

ecology, and evolution". (J.L. Gittleman, Ed.). pp. 495-535. Chapman and Hall,

London.

Wright, J.R. (1990). Clearance and recycling of pulmonary surfactant. American Journal of


Wright, J.R., Benson, B.J., Williams, M.C., Goerke, J. and Clements, J.A. (1984). Protein

composition of rabbit alveolar surfactant subfractions. Biochimica et Biophysica

Acta 791:320-332.

Wu, G., Hua, L., Zhu, J., Mo, Q.H. and Xu, X.M. (2003). Rapid, accurate genotyping of

beta-thalassaemia mutations using a novel multiplex primer extension/denaturing

high-performance liquid chromatography assay. British Journal of Haematology

122(2):311-316.

Wyss, A.R. (1988). Evidence from flipper structure for a single origin of pinnipeds. Nature

334:427-428.

Wyss, A.R. and Flynn, J. (1993). A phylogenetic analysis and definition of the Carnivora.

In "Mammal Phylogeny: Placentals". (F.S. Szalay, M.J. Novacek and M.C.

McKenna, Eds.). pp. 32-52. Springer-Verlag, New York.

Xia, X. (2000). "Data analysis in molecular biology and evolution". Kluwer Academic

Publishers, Boston.

Xia, X. and Li, W.H. (1998). What amino acid properties affect protein evolution? Journal

of Molecular Evolution 47:557-564.

Yang, Z. (1997). PAML: a program package for phylogenetic analysis by maximum

likelihood. Computational Applied Bioscience 13(5):555-556.

Yang, Z. and Bielawski, J.P. (2000). Statistical methods for detecting molecular

adaptation. Trends in Ecology and Evolution 15(12):496-503.

Yang, Z. and Nielsen, R. (2002). Codon-substitution models for detecting molecular

adaptation at individual sites along specific lineages. Molecular and Biological

Evolution 19(6):908-917.

295

Yang, Z., Nielsen, R., Goldman, N. and Krabbe-Pedersen, A.M. (2000a). Codon-

substitution models for heterogeneous selection pressures at amino acid sites.

Genetics 155:431-449.

Yang, Z., Nielsen, R. and Hasegawa, M. (1998). Models of amino acid substitution and

applications to mitochondrial protein evolution. Molecular and Biological Evolution

15(12):1600-1611.

Yang, Z., Swanson, W.J. and Vacquier, V.D. (2000b). Maximum-likelihood analysis of

molecular adaptation in abalone sperm lysin reveals variable selective pressures

among lineages and sites. Molecular and Biological Evolution 17(10):1446-1455.

Yano, T., Mason, R.J., Pan, T., Deterding, R.R., Nielsen, L.D. and Shannon, J.M. (2000).

KGF regulates pulmonary epithelial proliferation and surfactant protein gene

expression in adult rat lung. American Journal of Physiology Lung Cellular and

Molecular Physiology 279:L1146-L1158.

Young, S.L. and Silbajoris, R. (1986). Dexamethasone increases adult rat lung surfactant

lipids. Journal of Applied Physiology 60:1665-1672.

Yu, S., Harding, P.G.R., Smith, N. and Possmayer, F. (1983). Bovine pulmonary

surfactant: Chemical composition and physical properties. Lipids 18:522-529.

Yu, S. and Possmayer, F. (1994). Effect of pulmonary surfactant protein A (SP-A) and

calcium on the adsorption of cholesterol and film stability. Biochimica et Biophysica

Acta 1211:350-358.

Yu, S.H. and Possmayer, F. (1996). Effect of pulmonary surfactant protein A and neutral

lipid on accretion and organization of dipalmitoylphosphatidylcholine in surface

films. Journal of Lipid Research 37:1278-1288.

Yu, S.H. and Possmayer, F. (1998). Interaction of pulmonary surfactant protein A with

dipalmitoylphosphatidylcholine and cholesterol at the air/water interface. Journal of

Lipid Research 39:555-568.

Zanotto, P.M., Kallas, E.G., Souza, R.F. and Holmes, E.C. (1999). Genealogical evidence

for positive selection in the nef gene of HIV-1. Genetics 153:1077-1089.

Zasadzinski, J.A., Ding, J., Warriner, H.E., Bringezu, F. and Waring, A.J. (2001). The

physics and physiology of lung surfactants. Current Opinion in Colloid and

Interface Science 6(5-6):506-513.

Zhang, J. (2000). Rates of conservative and radical nonsynonymous nucleotide

substitutions in mammalian nuclear genes. Journal of Molecular Evolution 50:56-

68.

296

Zlateva, K.T., Lemey, P., Vandamme, A.M. and Van Ranst, M. (2004). Molecular evolution

and circulation patterns of human respiratory syncytial virus subgroup A: Positively

selected sites in the attachment G glycoprotein. Journal of Virology 78(9):4675-

4683.

APPENDICES - digital.library.adelaide.edu.au · 233 Table A1.2. The degenerate genetic code used to...

Documents

Transcript of APPENDICES - digital.library.adelaide.edu.au · 233 Table A1.2. The degenerate genetic code used to...