Cabinet

Protocols

Rag2 genotyping PCR protocol (link)
Commassie Staining Protocol (January 2008)
Retroviral Transduction of B cells (January 2008)
Western Blot (link)
Purification of antibodies (January 2008)
Elispot
Immunization
Immunostaining
Recovery of plasmids from yeast
Sorting of single cells
Sorting of single cells
Preparation of competent cells using CaCl2 (link)
CaCl2 Competent cell stock protocol
Transform plasmid to competent cells
Transformation of bacteria (link)
Tissue Culture Methods (link)
Centrifuge RCF/RPM calculator (link1)
Centrifuge RCF/RPM calculator (link2)
10X PBS solution preparation (link)
RBC lysis Buffer preparation (link)
Stock Solutions
Primer Design (link1)
Primer Design (link2)
Sequence Extractor (link)
The Sequence Manipulation Suite (link)
DNA extraction Protocol (link)
Oligos to order
PHA Clones DB SNP recommended alphabetical symbolism
addgene (link)
Heat Inactivation of Serum
Glycerol Bacterial Stocks
Infection of in vitro stimulated mouse B cells
DNA extraction from blood cells
Isolating DNA from Mouse Tail Clips + Lysis Buffer
TAE Buffer 50 X
Analysis of Real-time Q PCR data by the 2^-DDct method
AID cytidine deaminse activity assay
WHOLE BLOOD FACS STAINING FROM TAIL BLOOD (link)

Constants, tables and conversions

Link (for details)

Molarity Calculator

Convert between times gravity (× g) and centrifuge rotor speed (RPM)

JOURNAL CLUB

25.02.2010 8:30AM (Clara):
to announce...

23.02.2010 8:30AM (Vasco):
L1 retrotransposition in human neural progenitor cells (Nature 2009)Download file

11.02.2010 8:30AM (Thiago):
to announce...

09.02.2010 8:30AM (Catarina):
to announce...

28.01.2010 8:30AM (Daniel):
to announce...

26.01.2010 8:30AM (Thiago):
to announce...

14.01.2010 8:30AM (Clara):

12.01.2010 8:30AM (Vasco):
Reprogramming towards pluripotency requires AID-dependent DNA demethylation (Nature 2009) )Download file

(...)

27.08.2009 8:30AM (Nadine):
To be announced...

25.08.2009 8:30AM (Clara):
To be announced...

13.08.2009 8:30AM (Vasco):
To be announced...

11.08.2009 8:30AM (Nadine):
To be announced...

30.07.2009 8:30AM (Catarina):
Another look on: "Alternative Splicing Regulates Activation-Induced Cytidine Deaminase (AID): Implications for Suppression of AID Mutagenic Activity in Normal and Malignant B-Cells" ( link )

"Active nuclear import and cytoplasmic retention of activation-induced deaminase" Patenaude, Noia et al (2009) NATURE STRUCTURAL & MOLECULAR BIOLOGY ( link ) (Postponed)

28.07.2009 8:30AM (Daniel):
"AID upmutants isolated using a high-throughput screen highlight the immunity/cancer balance limiting DNA deaminase activity" Download file

----PAST----

16.07.2009 8:30AM (Thiago):
--

14.07.2009 8:30AM (Catarina):
--

02.07.2009 8:30AM (Vasco):
--

30.06.2009 8:30AM (Clara):
"RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci" Hewitt, Skok et al. (2009) Nature Immunology Download file

18.06.2009 8:30AM (Thiago):
"Control of Stochasticity in Eukaryotic Gene Expression" Raser & O'Shea (2004) Science Download file

16.06.2009 8:30AM (Daniel):
...

04.06.2009 8:30AM (Nadine):
"Haploinsufficiency of Activation-Induced Deaminase for Antibody Diversification and Chromosome Translocations both In Vitro and In Vivo" Sernández IV, de Yébenes VG, Dorsett Y, Ramiro AR, (2008) PLoS ONE 3(12): e3927 ( link )

02.06.2009 8:30AM (Clara):
"Locus ‘decontraction’ and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene" Roldán and Skok, Nat Immunol. 2005 January; 6(1): 31–41. ( link )

21.05.2009 8:30AM (Vasco):
"Human Chromosomal Translocations at CpG Sites and a Theoretical Basis for Their Lineage and Stage Specificity" Cell (2008) 135, 1130–1142 link to PubMed

19.05.2009 8:30AM (Thiago):
"Stochastic Gene Expression in a Single Cell" Science (2002) 297, 1183 Elowitz et al. 2002

07.05.2009 8:30AM (Catarina):
Announced By e-mail...

05.05.2009 8:30AM (Daniel):
"Organ-specific profiles of genetic changes in cancers caused by activation-induced cytidine deaminase expression" Int J Cancer (2008) 123(12):2735-40 link to PubMed

23.04.2009 8:30AM (Nadine):
"Tissue-specific sensitivity to AID expression in transgenic mouse models" Gene. (2006) 377:150-8 link to PubMed

21.04.2009 8:30AM (Clara):
"Targeted inhibition of V(D)J recombination by a histone methyltransferase." Osipovich, O., R. Milley, et al. (2004). Nat Immunol 5(3): 309-16. Link to pdf

09.04.2009 8:30AM (Vasco):
"Differences between homologous alleles of olfactory receptor genes require the Polycomb Group protein Eed."Alexander, M. K., S. Mlynarczyk-Evans, et al. (2007). J Cell Biol 179(2): 269-76. link to PubMed
and: "X chromosome choice occurs independently of asynchronous replication timing." Gribnau, J., S. Luikenhuis, et al. (2005). J Cell Biol 168(3): 365-73. link to PubMed
and: "Asynchronous replication of imprinted genes is established in the gametes and maintained during development." Simon, I., T. Tenzen, et al. (1999). Nature 401(6756): 929-32.
Link to pdf

07.04.2009 8:30AM (Catarina):
"Specific recruitment of protein kinase A to the immunoglobulin locus regulates class-switch recombination"Vuong, 2009

26.03.2009 8:30AM (Daniel):
Part II

24.03.2009 8:30AM (Daniel):
Part I of: Nonaka, T., T. Doi, et al. (2009). "Carboxy-terminal domain of AID required for its mRNA complex formation in vivo." Proc Natl Acad Sci U S A 106(8): 2747-51. PubMed link

19.03.2009 8:30AM (Nadine):
"Activation-Induced Cytidine Deaminase Links Between Inflammation and
the Development of Colitis-Associated Colorectal Cancers" Endo et al, Gastroenterology (2008)

10.03.2009 8:30AM (Clara):
"A role for the IgH intronic enhancer Emu in enforcing allelic exclusion" (Li and Eckhardt, JEM2008)

05.03.2009 8:30AM (Vasco):
"AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity."
MacDuff, 2009 (link)
and: "Specific recruitment of protein kinase A to the immunoglobulin locus regulates class-switch recombination"Vuong, 2009

19.02.2009 8:30AM (Catarina, 2nd part):
"Rate of Increase in Circulating IL-7 and Loss of IL-7R Expression Differ in HIV-1 and HIV-2 Infections: Two Lymphopenic Diseases with Similar Hyperimmune Activation but Distinct Outcomes"
Albuquerque 2007
and: "Efficient Thymopoiesis Contributes to the Maintenance of Peripheral CD4 T Cells during Chronic Human Immunodeficiency Virus Type 2 Infection" Gautier 2007

12.02.2009 8:30AM (Daniel):
Arakawa, 2007

15.01.2009 8:30AM (Daniel):
Muto, 2006

13.01.2009 8:30AM (Nadine):
Takai, 2008

08.01.2009 8:30AM (Clara):
Liang, 2004

--2008--

04.11.2008 8:30AM (Clara):
Nguyen, 2007 (PMID: 18045541) Comment to Nguyen, 2007

15.10.2008 8:30AM (Clara):
Calado, 2007

06.10.2008 8:30AM
Nepal, 2008 Complementary Honjo, 2007(Nadine)

02.10.2008 8:30AM
Yoo, 2007 (Daniel)

25.09.2008 8:30AM
Virgina, 2006 (Daniel)

23.09.2008, 8:30AM
Voss, 2006 Commented by: Borst and Genest, 2006(Clara)

18.09.2008, 8:30AM
Fagarasan, 2001(Clara)

16.09.08, 8:30AM
Activation-induced cytidine deaminase deficiency causes organ-specific autoimmune disease. PLoS ONE. 2008 Aug 21;3(8)(Vasco)

11.09.08
Alternative Splicing Regulates Activation-Induced Cytidine Deaminase (AID): Implications for Suppression of AID Mutagenic Activity in Normal and Malignant B-Cells Blood First Edition Paper, prepublished online August 5, 2008; DOI 10.1182/blood-2008-03-145995(Vasco)

17.07.2008
They are all about miRNA-155 that acts on AID (Sorry for being chosen on such short notice,no worries about reading, I'm not shure I'll read myself*ok ok, just joking*)Nussenzweig et al. Complementary: Desiderio STeng et al.

08.07.2008
Ferwerda, 2007Directed Evolution 1Directed Evoltution 2(Vasco)

03.07.08
Immortal Strand - review 1Immortal strand - review 2(Vasco)

8:30, 26.06.08
Nature. 2007 Sep 13;449(7159):238-42.Linkand Haematopoietic stem cells do not asymmetrically segregate chromosomes or retain BrdU. Kiel MJ, He S, Ashkenazi R, Gentry SN, Teta M, Kushner JA, Jackson TL, Morrison SJ.Schlimgen, 2008 (Vasco)

8:30 AM, 19.06.08
Gimerlbrant, 2007(Clara - postponed)

8:30 AM, 19.06.08
Pereira, 2003, 20.05.08 (Vasco)Casellas, 1998, 5.06.08 (Vasco) Pancer, 2004 9 AM, 12.06.08 (Vasco)

Lab Members

Get experienced!

Current

Past

Schedule Week 23-27 Mar 2009

Tentative schedule (30/03-04/04/2009)

Immunology Journal Club

THE IMMUNOLOGY JOURNAL CLUB AT IGC MEETS EVERY OTHER FRIDAY, AT 5 PM (IONIANS).
IF YOU WANT TO PRESENT A PAPER, PLEASE WRITE TO vbarreto arroba igc.gulbenkian.pt

Participants: Vasco Barreto, Lisa Bergman, Íris Caramalho, Nadine Caratão, Margarida Carneiro, Joana Côrte Real, Daniel Espadinha, Constantin Fesel, Andreia Lino, Cláudia Oliveira, Clara Pereira, Miguel Soares, Carlos Tadokoro, Nuno Costa, João Duarte, Ricardo Paiva, Leonor Sarmento, Jocelyne, Inês Trancoso, Ana martins, Constantin.

NEXT DISCUSSION - Mon, 30th Mar 2009 at 10a.m.

By Vasco Barreto and Andreia Lino

and

PAST DISCUSSIONS

16-01-2009 By João Duarte

LINK TO PDF

19-12-2008 By C. Tadokoro.
Maternal Alloantigens and Fetal Tregs Science2008

16-10 (THURSDAY, EXCEPTIONALLY) by Iris Caramalho

by Iris Caramalho (pdf)

and Pedro Garaldes


by *Pedro Geraldes himself, a prospective postdoc.(link to pdf)

26-10-09 (Vasco)

Teaching (IGC) -October 30 2008

VRL-lamprey
Lamprey-commentary
Dscam-innate immunity (pdf)
Dscam-commentary