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Figure 2S

43210

76543210

  • C
  • A

-

-

080125 CSCs
080418 CSCs

+ IFN-a 48 h + IFN-a 72 h

+ IFN-a 48 h + IFN-a 72 h

  • MHC I
  • MHC II
  • MICA
  • MICB
  • ULBP-1
  • ULBP-2
  • ULBP-3
  • ULBP-4

  • MHC I
  • MHC II
  • MICA
  • MICB
  • ULBP-1
  • ULBP-2
  • ULBP-3
  • ULBP-4

7

13 12 11 10
9

B

D

-

-+ IFN-a 48 h + IFN-a 72 h

080125 FBS
080125 FBS
080418 FBS

+ IFN-a 48 h + IFN-a 72 h
6

543210

876543210

  • MHC I
  • MHC II
  • MICA
  • MICB
  • ULBP-1
  • ULBP-2
  • ULBP-3
  • ULBP-4

  • MHC I
  • MHC II
  • MICA
  • MICB
  • ULBP-1
  • ULBP-2
  • ULBP-3
  • ULBP-4

Molecule
Molecule

Supplemental Results

Table 1S. Modulation by IFN-α of APM in GBM CSC and FBS tumor cell lines.

Molecule *

  • Cell line
  • IFN-α‡
  • HLA
  • β2-m# HLA
  • LMP
  • TAP1 TAP2

class II

  • A
  • A HC§
  • 2
  • 7
  • 10

080125 CSCs

080125 FBS
-+-

1∞ (1) 3 (65) 2 (91) 1 (2) 6 (47) 2 (61) 1 (3) 1 (2) 1 (3) 2 (81) 11 (80) 13 (99) 1 (3) 8 (88) 4 (91) 1 (2) 1 (3) 2 (68) 2 (81) 4 (63) 4 (83) 1 (3) 6 (80) 3 (67) 2 (86) 1 (3) 2 (75) 2 (99) 14 (90) 7 (97) 5 (75) 7 (100) 6 (98) 2 (90) 1 (4) 3 (87)

+
080418 CSCs
080418 FBS
-+-

  • 2 (51) 1 (1)
  • 1 (3) 2 (47) 2 (83) 2 (54) 1 (4) 1 (2) 1 (3)

2 (81) 3 (76) 5 (75) 2 (50) 2 (83) 3 (71) 1 (3) 2 (87) 1 (2)
1 (3) 3 (70) 2 (88) 1 (4) 3 (87) 2 (76) 1 (3) 1 (3) 1 (2)
2 (78) 7 (98) 5 (99) 2 (94) 5 (100) 3 (100) 1 (4) 2 (100) 1 (2)

+

  • 070104 CSCs
  • -

1 (2) 1 (3)

1 (3) 2 (78) 1 (3)

1 (2) 1 (3) 1 (3) 1 (2)

+

2 (98) 8 (100) 10 (88) 4 (89) 3 (98) 3 (94) 1 (4) 2 (86) 2 (79)

* expression of APM molecules was evaluated by intracellular staining and cytofluorimetric analysis; ‡ cells were treatead or not (+/-) for 72 h with 1000 IU/ml of IFN-α; # β-2 microglobulin; § β-2 microglobulin-free HLA-A heavy chain; ∞ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate

significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times; SD for each value ≥ 0.8

≤ 4.

Table 2S . Expression   of proteasome and APM-associated chaperon molecules in GBM CSC and FBS tumor cell lines.

  • Cell line
  • Molecule *

  • Delta MB1
  • Z
  • Calnexin Calreticulin ERp57 Tapasin

0627 CSCs 7 ‡ (100) 1 (3) 1 (5) 20 (100)

0627 FBS 1 (1) 1 (2) 1 (3) 3 (99)

  • 2 (92)
  • 2 (67) 2 (86)

  • 1 (3)
  • 1 (2)
  • 1 (2)

080125 CSCs 16 (85) 1 (2) 1 (2) 49 (99)

080125 FBS 1 (5) 1 (4) 1 (5) 28 (100)

2 (85)

1 (3) 1 (2)

2 (99)
3 (95)

1 (3)

  • 080418 CSCs 8 (100) 1 (5) 1 (4) 13 (100)
  • 2 (99)

1 (5) 1 (3)
1 (4) 1 (5)

  • 080418 FBS 7 (89) 1 (5) 1 (4) 16 (98)
  • 3 (98)

  • 080201 CSCs 36 (99) 3 (98) 3 (98) 55 (100)
  • 10 (98)
  • 3 (98) 7 (97)

  • 080201 FBS 16 (98) 3 (98) 6 (98) 80 (100)
  • 9 (98)
  • 2 (97) 5 (98)

  • 071011 CSCs 17 (98) 3 (87) 3 (75) 100 (100) 15 (98)
  • 3 (87) 7 (76)

071011 FBS 16 (100) 1 (4) 2 (87) 20 (100)

080325 CSCs 10 (98) 3 (98) 4 (98) 200 (100) 070104 CSCs 1 (3) 2 (93) 1 (4) 52 (100)
1869 EBV-B 2 (99) 3 (89) 2 (82) 100 (91)
4 (87) 5 (99) 2 (88) 2 (94)

1 (3)

2 (95) 5 (98)

1 (4) 1 (3)

2 (81) 2 (70)
2 (98)

* expression of APM molecules was evaluated by immunofluorescence on permeabilized cells and cytofluorimetric analysis;

‡ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate

significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times; SD for each value ≥ 1.2 ≤ 4.

Table 3S . Modulation by IFN-α of the expression of proteasome and APM-associated chaperon molecules in GBM CSC and FBS tumor cell lines.

Molecule *

  • Cell line
  • IFN-α ‡ Delta MB1
  • Z
  • Calnexin Calreticulin ERp57 Tapasin

  • 080125 CSCs
  • -

+-

16# (85) 1 (2) 1 (5) 49 (100) 22 (100) 1 (3) 1 (4) 73 (100)
1 (5) 1 (4) 1 (5) 28 (100)
10 (99) 1 (2) 2 (99) 30 (100)
2 (95)
2 (100)
3 (95) 3 (98)

1 (2) 2 (3) 1 (2) 2 (2) 1 (2) 1 (3)

2 (89) 1 (2)

080125 FBS
+

080418 CSCs
080418 FBS
-+-

8 (100) 1 (5) 1 (4) 13 (100) 8 (100) 1 (4) 1 (3) 13 (100)
7 (89) 1 (5) 1 (4) 16 (98)
9 (100) 1 (3) 1 (3) 26 (100)
2 (99)

1 (5) 1 (4)

3 (100) 8 (99) 1 (3)
3 (98)

1 (3) 1 (5) 1 (2) 1 (3)

+

3 (99)

  • 070104 CSCs
  • -

  • 1 (3) 2 (93) 1 (4) 52 (100)
  • 2 (88)

1 (4) 1 (3) 1 (3) 1 (3)

+

  • 13 (99) 1 (3) 1 (4) 27 (100)
  • 3 (98)

* expression of APM molecules was evaluated by immunofluorescence on permeabilized cells and cytofluorimetric analysis;

‡ cells were treatead or not (+/-) for 72 h with 1000 IU/ml of IFN-α; # values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate

significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times; SD for each value ≥ 1 ≤

4.

Table 4S. Modulation of MHC and APM molecules by 5-Aza CdR treatment of GBM and FBS tumor cell lines

  • Cell line
  • 5-Aza-CdR *
  • Molecule ‡

  • MHC II
  • MICA
  • MB1
  • LMP10
  • TAP1

080125 CSCs
080125 FBS
-+-

1# (2)

1 (2)

1 (2) 1 (3)
1 (4) 1 (3)
1 (2)

2 (98)

1 (3)
1 (3) 1 (3) 1 (4)

2 (80)

1 (2) 1 (3) 1 (2)

2 (88)
3 (95) 3 (98)

+

3 (90)

080418 CSCs
080418 FBS
-+-

1 (2) 1 (3) 1 (3) 1 (3)
1 (2) 1 (3)
1 (5) 1 (3)
1 (4) 1 (3)
1 (3) 1 (2) 1 (3)

6 (99)
3 (95) 4 (99)
3 (98)
6 (100)
4 (97)
6 (100)

+

  • 070104
  • -

2 (18)

1 (3) 1 (4)

2 (93)

1 (3) 1 (2)
1 (3) 1 (3)

+

  • 5 (87)
  • 2 (97)

  • 1869 EBV-B
  • -

12 (96)

1 (3) 1 (3)

  • 3 (89)
  • 3 (91)
  • 4 (95)

+

  • 20 (100)
  • 5 (100)
  • 4 (100)
  • 8 (100)

* 5-Aza-2'-deoxycytidine (5μM) was added to culture medium for 4 days; ‡ molecule expression was assessed by surface (MHC II and MICA) or intracellular staining (MIB, LMP10 and TAP1) of cells with specific antibodies (see Material and Methods) and cytofluorimetric analysis.

# values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate

significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times; SD for each value ≥ 1 ≤ 4.

Table 5S. Expression of immune response inhibitory molecules by GBM CSC or FBS tumor cell lines

  • Cell line
  • Molecule*

  • CTLA-4
  • PD-1
  • PD-L1
  • PD-L2

1 (4)

070104 CSC

2‡ (69)

  • 5 (95)
  • 12 (98)

080125 CSCs
080125 FBS

2 (81)

2 (94)

10 (99)

1 (3)

  • 2 (65)
  • 3 (96)
  • 19 (99)
  • 2 (70)

080418 CSCs
080418 FBS

  • 2 (55)
  • 2 (85)
  • 7 (99)

1 (2)

  • 1 (3)
  • 1 (5)
  • 1 (2)

9 (98)

080201 CSCs
080201 FBS

  • 2 (77)
  • 3 (95)
  • 11 (99)

1 (3)

  • 2 (95)
  • 2 (97)
  • 31 (98)
  • 2 (93)

071011 CSCs
071011 FBS

  • 2 (42)
  • 2 (59)
  • 4 (97)

1 (2)

  • 1 (3)
  • 1 (5)
  • 1 (4)

2 (50)

080325 CSCs SW480 col
1061 mel

2 (62) 2 (59) 2 (54)
2 (56) 2 (80)

1 (1)

4 (94) 6 (98) 6 (99)

1 (3) 1 (1) 1 (2)

1869 EBV-B

1 (1)

  • 2 (83)
  • 5 (97)

1 (2)

* expression of the indicated molecules was evaluated by immunofluorescence and cytofluorimetric analysis; ‡ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control (MRFI); bold values

indicate significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times with SD for each value ≥ 0.6 ≤ 4.

SW480 col and 1061 mel, that are a colorectal and a melanoma cell lines, respectively, were used in the experiment as not GBM tumor cells.

Table 6S. Genes differentially expressed between CSC and FBS, p<0.005. Genes are ranked according to fold change.

Fold-
Paramet

UG cluster ric p- value
Permutati change on p-value (CSC/FB
S)

  • Gene symbol
  • Description

oligodendrocyte transcription factor 1 (OLIG1), mRNA. ubiquitin specific peptidase 30 (USP30), mRNA. calsequestrin 2 (cardiac muscle) (CASQ2), mRNA.

OLIG1 USP30 CASQ2

  • Hs.56663 7.53E-05 1.00E-04
  • 2192

2077 1593

Hs.486434 45281 Hs.57975 4.00E-07

906 134
SPARC-like 1 (hevin) (SPARCL1), transcript variant 2, mRNA.

SPARCL1
CA10
Hs.62886

  • 46627
  • 114

84
996 828 carbonic anhydrase X (CA10), transcript variant 3, mRNA. ADAM metallopeptidase domain 19 (meltrin beta) (ADAM19), transcript variant 2, mRNA. 3-hydroxy-3-methylglutarylCoenzyme A synthase 1 (soluble) (HMGCS1), transcript variant 2, mRNA. SRY (sex determining region Y)- box 8 (SOX8), mRNA. ribosomal protein S6 kinase, 90kDa, polypeptide 2

Hs.463466 18432

  • Hs.483944 26136
  • ADAM19

  • 64
  • 750

HMGCS1 SOX8
Hs.397729

  • 2109
  • 25

53
691 684

Hs.243678 16431

(RPS6KA2), transcript variant 2, mRNA. dipeptidyl-peptidase 4 (DPP4), mRNA. periostin, osteoblast specific factor (POSTN), transcript variant 2, mRNA.

RPS6KA2
DPP4
Hs.719131

  • 1855
  • 11

8
655 583

Hs.368912 25174

  • Hs.136348 27286
  • POSTN

779
57
569

  • 553
  • KIAA1549 KIAA1549 (KIAA1549), mRNA. Hs.605380

CDNA FLJ32758 fis, clone
1857 hCG_1999814 TESTI2001792 collagen, type VIII, alpha 2 (COL8A2), mRNA.

Hs.666511 22226

  • 2
  • 544

538 506

COL8A2 EMP2
Hs.353001 43215

2117 epithelial membrane protein 2 (EMP2), mRNA.

Hs.531561

  • 2084
  • 1.00E-04

guanine nucleotide binding protein (G protein), gamma 7 (GNG7), mRNA.

GNG7

  • Hs.515544 1.94E-05 1.00E-04
  • 505

PREDICTED: misc_RNA
LOC346329 (LOC346329), miscRNA. arylsulfatase D (ARSD), transcript

  • 2.57E-05 5.00E-04
  • 484

473

ARSD

variant 1, mRNA.

Hs.528631 29984 Hs.567236 507

823 shroom family member 2
SHROOM2 (SHROOM2), mRNA. olfactory receptor, family 51, subfamily B, member 2

  • 3.00E-04
  • 416

410 410 381

OR51B2 ST3GAL6 SIPA1L2

(OR51B2), mRNA.

Hs.680163 44691

1307
9.00E-04
38
ST3 beta-galactoside alpha-2,3- sialyltransferase 6 (ST3GAL6), mRNA. signal-induced proliferationassociated 1 like 2 (SIPA1L2), mRNA.

Hs.148716 Hs.715656

7475 1074
CD164 molecule, sialomucin (CD164), transcript variant 5, mRNA. calumenin (CALU), transcript variant 1, mRNA.

CD164 CALU

Hs.520313 1.10E-06 1.00E-04

Hs.718425 7871 799

381 377 paroxysmal nonkinesigenic dyskinesia (PNKD), transcript variant 2, mRNA.

PNKD

  • Hs.98475 5.75E-05 5.00E-04
  • 375

369 kelch domain containing 8A
KLHDC8A (KLHDC8A), mRNA.

Hs.10414

  • 15658
  • 54

169
25
RAB11 family interacting protein
RAB11FIP4 4 (class II) (RAB11FIP4), mRNA. Hs.406788 43079 chromosome 11 open reading
352 348

C11orf66

frame 66 (C11orf66), mRNA. trinucleotide repeat containing 6B (TNRC6B), transcript variant 2, mRNA.

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  • Análise Integrativa De Perfis Transcricionais De Pacientes Com

    Análise Integrativa De Perfis Transcricionais De Pacientes Com

    UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas.
  • (A) Co-IP of HA Tagged ARMC9 with Flag Tagged Interactors

    (A) Co-IP of HA Tagged ARMC9 with Flag Tagged Interactors

    Supplemental Figures Supplemental Figure 1 Validation of ARMC9 interactome. (A) Co-IP of HA tagged ARMC9 with Flag tagged interactors. HA tagged ARMC9 was transfected alone or in conjunction with Flag tagged interactor constructs, HA beads were used to pull down the bait construct and blots were probed for the presence of the Flag tagged interactors. Experiment was performed in biological triplicates. Full blots are viewable in Plemental Figure 10. (B) Single transfection of PalmMyr-CFP-ARMC9 (green) and (C) single transfection of mRFP-TOGARAM1 (red) shows the localization in the absence of the respective interactor. (D) Co-expression of mRFP-TOGARAM1 and PalmMyr-CFP-ARMC9 shows microtubule colocalization. Scale bar indicates 20 μm. 1 Supplemental Figure 2 In silico modeling of the TOG2 variants. (A) Ribbon model of the wild type TOG2 domain structure of TOGARAM1 generated using HOPE. The protein is colored by the following elements: alpha-helices are show in blue, beta-strand is shown in red, turns are green, 3/10 helix is yellow, and random coil is cyan. (B) p. Arg368Trp missense variant in the TOG2 domain in ribbon-presentation generated using HOPE. TOG2 is shown in grey, the side chain of the mutated residue is shown in magenta. (C) A close up of the side chain of both wild type and mutated residue is shown in green and red respectively. (D) Inverted view of wild type TOG2 domain structure of TOGARAM1 as compared to (a). (E) p.Leu375Pro missense variant modeled in the TOG2 domain of TOGARAM1 in ribbon-presentation. TOG2 is shown in grey, the side chain of the mutated residue is shown in magenta.
  • Noelia Díaz Blanco

    Noelia Díaz Blanco

    Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr.
  • An Integrated Genomic Analysis of Gene-Function Correlation on Schizophrenia Susceptibility Genes

    An Integrated Genomic Analysis of Gene-Function Correlation on Schizophrenia Susceptibility Genes

    Journal of Human Genetics (2010) 55, 285–292 & 2010 The Japan Society of Human Genetics All rights reserved 1434-5161/10 $32.00 www.nature.com/jhg ORIGINAL ARTICLE An integrated genomic analysis of gene-function correlation on schizophrenia susceptibility genes Tearina T Chu and Ying Liu Schizophrenia is a highly complex inheritable disease characterized by numerous genetic susceptibility elements, each contributing a modest increase in risk for the disease. Although numerous linkage or association studies have identified a large set of schizophrenia-associated loci, many are controversial. In addition, only a small portion of these loci overlaps with the large cumulative pool of genes that have shown changes of expression in schizophrenia. Here, we applied a genomic gene-function approach to identify susceptibility loci that show direct effect on gene expression, leading to functional abnormalities in schizophrenia. We carried out an integrated analysis by cross-examination of the literature-based susceptibility loci with the schizophrenia-associated expression gene list obtained from our previous microarray study (Journal of Human Genetics (2009) 54: 665–75) using bioinformatic tools, followed by confirmation of gene expression changes using qPCR. We found nine genes (CHGB, SLC18A2, SLC25A27, ESD, C4A/C4B, TCP1, CHL1 and CTNNA2) demonstrate gene-function correlation involving: synapse and neurotransmission; energy metabolism and defense mechanisms; and molecular chaperone and cytoskeleton. Our findings further support the roles of these genes in genetic influence and functional consequences on the development of schizophrenia. It is interesting to note that four of the nine genes are located on chromosome 6, suggesting a special chromosomal vulnerability in schizophrenia.
  • Quantigene Flowrna Probe Sets Currently Available

    Quantigene Flowrna Probe Sets Currently Available

    QuantiGene FlowRNA Probe Sets Currently Available Accession No. Species Symbol Gene Name Catalog No. NM_003452 Human ZNF189 zinc finger protein 189 VA1-10009 NM_000057 Human BLM Bloom syndrome VA1-10010 NM_005269 Human GLI glioma-associated oncogene homolog (zinc finger protein) VA1-10011 NM_002614 Human PDZK1 PDZ domain containing 1 VA1-10015 NM_003225 Human TFF1 Trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in) VA1-10016 NM_002276 Human KRT19 keratin 19 VA1-10022 NM_002659 Human PLAUR plasminogen activator, urokinase receptor VA1-10025 NM_017669 Human ERCC6L excision repair cross-complementing rodent repair deficiency, complementation group 6-like VA1-10029 NM_017699 Human SIDT1 SID1 transmembrane family, member 1 VA1-10032 NM_000077 Human CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) VA1-10040 NM_003150 Human STAT3 signal transducer and activator of transcripton 3 (acute-phase response factor) VA1-10046 NM_004707 Human ATG12 ATG12 autophagy related 12 homolog (S. cerevisiae) VA1-10047 NM_000737 Human CGB chorionic gonadotropin, beta polypeptide VA1-10048 NM_001017420 Human ESCO2 establishment of cohesion 1 homolog 2 (S. cerevisiae) VA1-10050 NM_197978 Human HEMGN hemogen VA1-10051 NM_001738 Human CA1 Carbonic anhydrase I VA1-10052 NM_000184 Human HBG2 Hemoglobin, gamma G VA1-10053 NM_005330 Human HBE1 Hemoglobin, epsilon 1 VA1-10054 NR_003367 Human PVT1 Pvt1 oncogene homolog (mouse) VA1-10061 NM_000454 Human SOD1 Superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult))
  • Genomic Signatures of Recent Adaptive Divergence in the Swamp Sparrow (Melospiza Georgiana)

    Genomic Signatures of Recent Adaptive Divergence in the Swamp Sparrow (Melospiza Georgiana)

    GENOMIC SIGNATURES OF RECENT ADAPTIVE DIVERGENCE IN THE SWAMP SPARROW (MELOSPIZA GEORGIANA) A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Petra Elizabeth Deane December 2017 © 2017 Petra Elizabeth Deane GENOMIC SIGNATURES OF RECENT ADAPTIVE DIVERGENCE IN THE SWAMP SPARROW (MELOSPIZA GEORGIANA) Petra Elizabeth Deane, Ph. D. Cornell University 2017 Populations that have recently diverged across sharp environmental gradients provide an opportunity to study the mechanisms by which natural selection drives adaptive divergence. Inland and coastal populations of the North American swamp sparrow (Melospiza georgiana) have become an emerging model system for studies of natural selection because they are morphologically and behaviorally distinct despite a very recent divergence time (<15,000 years), yet common garden experiments have demonstrated a genetic basis for their differences. I characterized genomic patterns of variation within and between inland and coastal swamp sparrows via reduced representation sequencing and demonstrated that background genomic differentiation (FST=0.02) and divergence (ΦST=0.05) between these populations is very low, rendering signatures of natural selection highly detectable (max FST=0.8). I then sequenced and assembled a de novo reference genome for the species and conducted a scan for genes involved in coastal adaptation, particularly the evolution of a deeper bill, darker plumage, and tolerance for salinity. I recovered a multigenic snapshot of adaptation via robust signatures of selection at 31 genes. As in Darwin’s finches, bone morphogenetic protein (BMP) signaling appears responsible for changes in bill depth, a putative magic trait for ecological speciation.