diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index 8d7a4c1f95b..00000000000 Binary files a/.DS_Store and /dev/null differ diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml new file mode 100644 index 00000000000..cc879427924 --- /dev/null +++ b/.github/workflows/jekyll.yml @@ -0,0 +1,16 @@ +name: Jekyll site CI + +on: [push] + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v1 + - name: Build the site in the jekyll/builder container + run: | + docker run \ + -v ${{ github.workspace }}:/srv/jekyll -v ${{ github.workspace }}/_site:/srv/jekyll/_site \ + jekyll/builder:latest /bin/bash -c "chmod 777 /srv/jekyll && jekyll build --future" diff --git a/CNAME b/CNAME deleted file mode 100644 index 588576342d0..00000000000 --- a/CNAME +++ /dev/null @@ -1 +0,0 @@ -www.allanlab.org \ No newline at end of file diff --git a/README.md b/README.md index 0651ae5cf7e..593cb722fe0 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,5 @@ -# Allan Lab Website +# Roychoudhuri Lab Website -This is the website of our academic research group at Leiden University. - -This website is powered by Jekyll and some Bootstrap, Bootwatch. We tried to make it simple yet adaptable, so that it is easy for you to use it as a template. Plese feel free to copy and modify for your own purposes. You don't have to link to us or mention us (but of course we appreciate it). - -Go to *aboutwebsite.md* to learn how to copy and modidy this page for your purpose. - - -Copyright Allan Lab. Code released under the MIT License. +This is the website of our academic research group at the Department of Pathology at Cambridge University. +Go to *about.md* to learn how to copy and modidy this page for your purpose. diff --git a/_config.yml b/_config.yml_inactivated similarity index 51% rename from _config.yml rename to _config.yml_inactivated index d28d0b61a13..763124cf35d 100644 --- a/_config.yml +++ b/_config.yml_inactivated @@ -6,14 +6,12 @@ # 'jekyll serve'. If you change this file, please restart the server process. # Site settings -title: The Allan Lab -email: your-email@domain.com +title: Roychoudhuri Lab - Immune regulation in inflammation and cancer +email: rr257@cam.ac.uk description: > # this means to ignore newlines until "baseurl:" - Write an awesome description for your new site here. You can edit this - line in _config.yml. It will appear in your document head meta (for - Google search results) and in your feed.xml site description. + Immune regulation in inflammation and cancer. We are located at the Department of Pathology at the University of Cambridge, Cambridge, UK. We study the immunoregulatory mechanisms that suppress immune activation under homeostasis and cancer immunosuppression. We are interested in the differentiation and function of CD4+ T cells, including Foxp3+ regulatory T cells, and CD8+ T cells with cytotoxic function. We are interested in the mechanisms that restrict T cell activation and CD8+ T cell memory in the context of adoptive immunotherapy and immune checkpoint blockade therapy. baseurl: "" -url: "" +url: "http://roychoudhurilab.org" include: - .htaccess @@ -29,8 +27,14 @@ lsi: false excerpt_separator: "\n\n" incremental: false - - +#Collections +collections: + members: + output: true + permalink: member/:name + sort_by: tier + + # Markdown Processing kramdown: input: GFM @@ -43,3 +47,5 @@ kramdown: enable_coderay: false parse_block_html: true # default for kramdown is false. This will enable using Markdown links + +theme: jekyll-theme-slate diff --git a/_data/.DS_Store b/_data/.DS_Store deleted file mode 100644 index 5008ddfcf53..00000000000 Binary files a/_data/.DS_Store and /dev/null differ diff --git a/_data/affiliations.yml b/_data/affiliations.yml new file mode 100644 index 00000000000..883795da8d8 --- /dev/null +++ b/_data/affiliations.yml @@ -0,0 +1,8 @@ +- title: Department of Pathology (Cambridge) + link: https://www.path.cam.ac.uk/ + +- title: CRUK Cambridge Centre (Cambridge) + link: https://crukcambridgecentre.org.uk/ + +- title: Babraham Institute (Cambridge) + link: https://www.babraham.ac.uk \ No newline at end of file diff --git a/_data/alumni_bsc.yml b/_data/alumni_bsc.yml deleted file mode 100644 index 2f487973bbf..00000000000 --- a/_data/alumni_bsc.yml +++ /dev/null @@ -1,15 +0,0 @@ -- name: Vishnu Saj, Spring 2017 - -- name: Arjo Andringa, Spring 2016 - -- name: Joey Braspenning, Spring 2017 - -- name: Tjerk Benschop, Summer 2017 - -- name: Margot Leemker, Spring 2017 - -- name: Sietske Lensen, Spring 2017 - -- name: Daniëlle van Klink, Spring 2016 - -- name: Amber Vervloet, Spring 2019 diff --git a/_data/alumni_members.yml b/_data/alumni_members.yml deleted file mode 100644 index 8bf7671b141..00000000000 --- a/_data/alumni_members.yml +++ /dev/null @@ -1,31 +0,0 @@ -- name: Gijsbert Verdoes - photo: verdoes.jpg - duration: In the Allan Lab 2015 - 2018, now Project manager at the FMD - info: Fine mechanical engineer associated with the FMD working in our group - email: verdoes@fmd.physics.leidenuniv.nl - number_educ: 1 - education1: Leidse instrumentmakers School - education2: - education3: - education4: - -- name: Irene Battisti - photo: irene.jpg - info: PhD student - duration: In the Allan Lab Jan 2015 to June 2019, now R&D scientist at Nearfield Instruments - email: Battisti@Physics.LeidenUniv.nl - number_educ: 3 - education1: Master Padova University - education2: Master thesis at Leiden University with Jan van Ruitenbeek - education3: PhD Leiden University! - -- name: Doohee Cho - photo: Doohee2.jpg - info: Postdoc - duration: In the Allan Lab May 2017 to June 2019, now assistant professor at Yonsei University - email: cho@physics.leidenuniv.nl - number_educ: 4 - education1: B.S. Yonsei University, Korea - education2: PhD Yonsei University, Korea with In-Whan Lyo - education3: Postdoc POSTECH with Han Woong Yeom - education4: Postdoc Rutgers with Sang-Wook Cheong diff --git a/_data/alumni_msc.yml b/_data/alumni_msc.yml deleted file mode 100644 index fe0b4c85213..00000000000 --- a/_data/alumni_msc.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: Maarten Leeuwenhoek, Spring 2015 - -- name: Koen M Bastiaans, Spring 2015 - -- name: Farshaad Hoeseni, Fall 2015 - -- name: Oliver Ostojic, Spring 2016 - -- name: Tjerk Benschop, Spring 2016 - -- name: Bert Visscher, Fall 2017 - -- name: Ahmad Jamalzada, Fall 2017 - -- name: Corne Koks, Fall 2018 - -- name: Damian Bouwmeester, Summer 2019 diff --git a/_data/alumni_visitors.yml b/_data/alumni_visitors.yml deleted file mode 100644 index 2d18cf43f64..00000000000 --- a/_data/alumni_visitors.yml +++ /dev/null @@ -1,11 +0,0 @@ -- name: Nikolaos Iliopoulos, Spring 2016 - -- name: Vitaly Fedoseev, all of 2016 - -- name: Alexander Vanstone, Spring 2016 - -- name: Ramakrishna Aluru, Summer 2018 - -- name: Changwei Zou, Spring 2018 - -- name: Kemal Demir, Summer 2019 diff --git a/_data/collaborations.yml b/_data/collaborations.yml new file mode 100644 index 00000000000..9a89aa03f57 --- /dev/null +++ b/_data/collaborations.yml @@ -0,0 +1,16 @@ +- title: Klaus Okkenhaug (Pathology) + link: https://www.path.cam.ac.uk/directory/klaus-okkenhaug + +- title: David Adams (Sanger) + link: https://www.sanger.ac.uk/person/adams-david/ + +- title: Nicholas Restifo (NIH, US) + +- title: Gosia Trynka (Sanger) + +- title: Enrico Lugli (Humanitas, Milan) + link: https://www.humanitas-research.org/researcher/dr-enrico-lugli/ + +- title: Tim Halim (CRUK CI) + +- title: Luca Gattinoni (NIH, US) diff --git a/_data/facilities.yml b/_data/facilities.yml new file mode 100644 index 00000000000..40d6a87d18a --- /dev/null +++ b/_data/facilities.yml @@ -0,0 +1,19 @@ +- title: University Biomedical Services (Cambridge) + link: https://www.ubs.admin.cam.ac.uk/ + +- title: High-throughput sequencing (Pathology) + link: https://www.cgs.path.cam.ac.uk/ + +- title: Genomics core facility (CRUK CI) + link: https://www.cruk.cam.ac.uk/core-facilities/genomics-core + +- title: Flow cytometry (Pathology) + link: https://www.bio.cam.ac.uk/facilities/flow + +- title: NIHR cell phenotyping hub (Cambridge) + link: https://www.med.cam.ac.uk/nihr-cambridge-brc-cell-phenotyping-hub/ + +- title: High-throughput sequencing (Pathology) + link: https://www.cgs.path.cam.ac.uk/ + + \ No newline at end of file diff --git a/_data/news.yml b/_data/news.yml index 5fa3eb50451..01c29f99f3c 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -1,129 +1,9 @@ -- date: 10. December 2019 - headline: "Koen defends his PhD with a cum laude (top 5%)!" - -- date: 5. September 2019 - headline: "The noise doubling paper is published in Phys. Rev. B!" - -- date: 25. August 2019 - headline: "Doohee got an assistant professor job at Yonsei University!" - -- date: 25. July 2019 - headline: "The inhomogeneous superfluid paper is published in Nature!" - -- date: 15. July 2019 - headline: "We imaged the doubling of shot noise due to Andreev reflections in a STM, posted on arXiv." - -- date: 24. May 2019 - headline: "The smart tip paper is finally published ! A collaboration with the Gröblacher Lab at TU Delft." - -- date: 08. May 2019 - headline: "Irene defends her PhD!" - -- date: 08. May 2019 - headline: "Dome makes it on the University website. " - -- date: 13. December 2018 - headline: "Our paper about how to construct an STM is in Review of Scientific Instruments. " - -- date: 08. October 2018 - headline: "We discovered charge trapping in a high-Tc superconductor! Publication in Nature Physics. " - -- date: 27. September 2018 - headline: "Our MHz amplifier for STM is published in Review of Scientific Instruments. " - -- date: 16. May 2018 - headline: "Milan, Koen and Irene talk about superconductivity in Made in Leiden." - -- date: 4. May 2018 - headline: "Welcome Ram!" - -- date: 5.-9. March 2018 - headline: "Irene and Milan are at the March Meeting (Talk Tue 10am, session E45)" - -- date: 13. November 2017 - headline: " New paper published in collaboration with the group of Jan van Ruitenbeek" - -- date: 10. November 2017 - headline: "Doohee makes the third place at the LION Image Award. " - -- date: 9. October 2017 - headline: "We contributed to Miguel and Jan's new paper. " - -- date: 12. August 2017 - headline: "We got an ERC starting grant." - -- date: 10. August 2017 - headline: "Our paper is published in SciPost Physics." - -- date: 17. - 21. July 2017 - headline: "Milan wins the Bryan R. Coles prize at SCES 2017, Prague. Koen received the best poster presentation award. " - -- date: 17. - 21. July 2017 - headline: "Koen, Maarten and Milan will be at SCES 2017, Prague. Come check out our posters on Tuesday&Thursday and talk on Thursday!" - -- date: 18. June 2017 - headline: "Paper on poor electronic screening published in PRB as Editors' selection! " - -- date: 15. May 2017 - headline: Welcome Doohee! - -- date: 13. - 17. March 2017 - headline: Koen & Irene give talks at the APS March Meeting in New Orleans. - -- date: 27. January - 3. March 2017 - headline: "We are looking forward to co-hosting the workshop on unconventional superconductivity at the Lorentz center. " - -- date: 17-18. January 2017 - headline: Irene, Koen, Maarten and Milan will be at Physics@Veldhoven 2017. (Talk at PT6.1 and poster at P9.022). - -- date: 25. November 2016 - headline: "We are part of a newly granted Vrije Programma on strange metals, together with the groups of Hussey, Golden, vHeumen, Zaanen, Schalm, Stoof and Vandoren, see press release. We also got a Projectruimte." - -- date: 19. September 2016 - headline: " Our first paper from Leiden is online at Nature Physics! " - -- date: 12. September 2016 - headline: Koen is at Correl16, Julich. - -- date: 01. July 2016 - headline: Milan is at the strongly correlated electron GRC 2016. - -- date: 24. June 2016 - headline: Felix Baumberger is visiting. - -- date: 17. June 2016 - headline: Irene is at SNS2016. - -- date: 28. April 2016 - headline: Our results on the Mott & pseudo gap physics posted on arXiv ! - -- date: 14. May 2016 - headline: Ivan Bozovic is visiting. - -- date: 17. March 2016 - headline: Koen, Irene & Vitaly present a poster at Sun Sailing Science. - -- date: 17. Jan 2016 - headline: "We discover electronic order and pseudogap in a non-cuprate materal! " - -- date: 01. Jan 2016 - headline: Welcome Vitaly! - -- date: 17. June 2015 - headline: Welcome Kees! - -- date: 17. June 2015 - headline: "Maarten wins the LION image award! Check out his submission." - -- date: 17. June 2015 - headline: " We win a Vidi grant: 800kEUR to invest in science! (Leiden news, FOM news item) " - -- date: 01. Sept 2015 - headline: "Welcome Koen and Maarten: from Master- to PhD-students" - -- date: 17. June 2015 - headline: "We got our commercial STM from Unisoku, and we are already busy modifying." - -- date: 01. Jan 2015 - headline: Welcome Irene, Gijsbert & Milan — our lab is officially starting! +- date: 9th September 2019 + headline: "Francis Grant defends his doctrate" + +- date: 5th September 2019 + headline: "Firas publishes in Current Protocols in Immunology" + +- date: 1st April 2019 + headline: "Dr Paula Kuo joins the lab!" diff --git a/_data/pictures_Leiden.yml b/_data/pictures_Leiden.yml deleted file mode 100644 index a86e9249844..00000000000 --- a/_data/pictures_Leiden.yml +++ /dev/null @@ -1,34 +0,0 @@ -- title: pic1_description - image: DSC_0366.JPG -- title: pic1_description - image: DSC_0368.JPG -- title: pic_description - image: 20150918_145800.jpg -- title: pic1_description - image: DSC_0030.jpg -- title: pic1_description - image: DSC_0051.jpg -- title: pic1_description - image: DSC_0116.jpg -- title: pic1_description - image: DSC_0119.jpg -- title: pic1_description - image: DSC_0128.jpg -- title: pic1_description - image: DSC_0139.jpg -- title: pic1_description - image: DSC_0636.jpg -- title: pic1_description - image: DSC_0683.jpg -- title: pic1_description - image: DSC_0696.jpg -- title: pic1_description - image: DSC_0757.jpg -- title: pic1_description - image: IMG_4334.jpg -- title: pic1_description - image: IMG_4376.jpg -- title: pic1_description - image: tamagochi.jpg -- title: pic1_description - image: tmp2-2.jpg diff --git a/_data/publist.yml b/_data/publist.yml index 0eca1766750..4e7bb272042 100644 --- a/_data/publist.yml +++ b/_data/publist.yml @@ -1,253 +1,121 @@ -- title: "A strongly inhomogeneous superfluid in an iron-based superconductor" - image: STS_news.png - description: We succeeded in measuring the superfluid density with atomic resolution on an unconventional superconductor! In contrast to expectations for conventional superconductors, we find that the superfluid densisty is strongly inhomogeneous in FeTe0.55Se0.45. - authors: D Cho* & KM Bastiaans* & D Chatzopoulos*, GD Gu, MP Allan - link: - url: https://www.nature.com/articles/s41586-019-1408-8 - display: Nature 571, 541 (2019) - highlight: 1 - news2: -- title: "Imaging doubled shot noise in a Josephson scanning tunneling microscope" - image: PbSpub.png - description: We have imaged the doubling of the current noise due to Andreev reflections in a Josephson scanning tunneling microscope. - authors: KM Bastiaans, D Cho, D Chatzopoulos, M Leeuwenhoek, C Koks, MP Allan +- title: "CCR8 marks highly suppressive Treg cells within tumours but is dispensable for their accumulation and suppressive function" + image: Whiteside_immunology_ccr8_2021.png + description: Treg cells within tumours contribute powerfully to cancer immunosupression and express high levels of CCR8. The findings suggest that depletion of CCR8-expressing Treg cells, rather than blocking CCR8 function, will enable therapeutic disruption of tumour-associated Treg cells. + authors: Whiteside S, et al. link: - url: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.104506 - display: Phys. Rev. B 100, 104506 (2019) + url: 33838058.pdf + display: Immunology (2021) highlight: 1 news2: - -- title: "Definition of design guidelines, construction and performance of an ultra-stable scanning tunneling microscope for spectroscopic imaging" - image: DomePub.png - description: Our first completely home-built STM is alive! And it has the world’s highest resonance frequency. - authors: I Battisti, G Verdoes, K van Oosten, KM Bastiaans, and MP Allan - link: - url: https://aip.scitation.org/doi/10.1063/1.5064442 - display: Rev. Sci. Instrum. 89, 123705 (2018) + +- title: "A cell-based bioluminescence assay reveals dose-dependent and contextual repression of AP-1-driven gene expression by BACH2" + image: Vardaka_Scirep_2020.png + description: Dose-dependent repression of AP-1 driven gene expression by BACH2. Activation of IFNG expression by the +18k enhancer is modelled by a cell-based bioluminescence assay permitting high-throughput drug screening for agonists and antagonists of BACH2 function. + authors: Vardaka P, et al. + link: + url: 33144667.pdf + display: Sci Rep (2020) highlight: 1 news2: - -- title: "Charge trapping and super-Poissonian noise centres in a cuprate superconductor" - image: Pub_BCl.png - description: Using our newly developed noise-spectroscopy technique we discover charge trapping in a cuprate high-temperature superconductor. - authors: KM Bastiaans* & D Cho*, T Benschop, I Battisti, Y Huang, MS Golden, Q Dong, Y Jin, J Zaanen, MP Allan - link: - url: https://www.nature.com/articles/s41567-018-0300-z - display: Nature Physics 14, 1183 (2018) + +- title: "A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells" + image: Nasrallah_Imianowski_Lrrc32_Nature.png + description: CRISPR-based mutagenesis of disease-associated distal enhancer homologs in mice reveals a regulatory switch for signal-driven GARP expression by Treg cells. The function of the enhancer is required for Treg cells to control gut inflammation. + authors: Nasrallah R, Imianowski C, et al. + link: + url: nasrallah_imianowski_nature_2020.pdf + display: Nature (2020) highlight: 1 - news1: Instrument details in Rev. Sci. Instrum. 89, 093709 (2018) - news2: See also quantum universe (in dutch), Phys.org , Leiden University news, UvA news. - -- title: "Amplifier for scanning tunneling microscopy at MHz frequencies" - image: Fano.png - description: We develop, build and test a novel amplifier circuit capable of measuring the tunneling current in the MHz regime while simultaneously performing conventional STM measurements. We are looking forward to performing scanning noise spectroscopy on quantum materials! - authors: KM Bastiaans, T Benschop, D Chatzopoulos, D Cho, Q Dong, Y Jin, MP Allan - link: - url: https://aip.scitation.org/doi/10.1063/1.5043267 - display: Rev. Sci. Instrum. 89, 093709 (2018) - highlight: 0 news2: -- title: "Nanofabricated tips as a platform for double-tip and device based scanning tunneling microscopy" - image: SmartPub.png - description: We introduce a platform for bringing new, device-based functionality to STM, with the goal of utilizing decades of progress in device engineering for the field of scanning probe. - authors: M Leeuwenhoek, RA Norte, KM Bastiaans, Doohee Cho, I Battisti, YaM Blanter, S Gröblacher, MP Allan +- title: "BACH2 promotes the functional quiescence and maintenance of resting Treg cells" + image: Grant_Yang_Bach2_JEM.png + description: The transcription factor BACH2 is repurposed following Treg lineage specification and its high expression in resting Treg cells is required for their quiescence and durable maintenance. Durable maintenance of resting Treg cell responses is required for immune homeostasis and cancer immunosuppression. + authors: Grant FM, Yang J, et al. link: - url: https://iopscience.iop.org/article/10.1088/1361-6528/ab1c7f/pdf - display: Nanotechnology 30, 335702 (2019) + url: Grant_Yang_JEM.pdf + display: J Exp Med (2020) highlight: 1 news2: - -- title: "Revisiting quasiparticle scattering interference in high-temperature superconductors: the problem of narrow peaks" - image: dummy.png - description: "" - authors: MA Sulangi, MP Allan, J Zaanen - link: - url: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.134507 - display: PRB 96, 134507 (2017) - highlight: 0 - news2: Coverd in Superconductor Week, November 30, 2017 Vol. 31, No. 10 - -- title: Robust procedure for creating and characterizing the atomic structure of scanning tunneling microscope tips - image: dummy.png - description: "" - authors: S Tewari, KM Bastiaans, MP Allan, JM van Ruitenbeek - link: - url: http://www.beilstein-journals.org/bjnano/content/pdf/2190-4286-8-238.pdf - display: Beilstein J. Nanotechnol. 8, 2389 (2017) - highlight: 0 - news2: - -- title: Creating better superconductors by periodic nanopatterning - image: SCAUweb.jpg - description: - We propose an approach to transform a ‘pristine’ material into a better (meta-) superconductor by making use of modern fabrication techniques -- designing and engineering the electronic properties of thin films via periodic patterning on the nanoscale. - authors: - MP Allan, MH Fischer, O Ostojic, A Andringa - link: - url: https://scipost.org/SciPostPhys.3.2.010/pdf - display: SciPost Phys. 3, 010 (2017) + +- title: "Protocols for integrative genome-wide analysis of transcription factor binding and chromatin accessibility in lymphocytes" + image: sadiyah_CPI_2019_a.png + description: Experimental and computational protocols to enable integrative analysis of TF binding and chromatin accessibility in lymphocytes. + authors: Sadiyah MF, Roychoudhuri R. + link: + url: sadiyah2019.pdf + display: Curr Protoc Immunol (2019) 126:e84. highlight: 1 + news2: -- title: Poor electronic screening in lightly doped Mott insulators observed with scanning tunneling microscopy - image: TIBB.png - description: - We develop a simple model to interpret STM results on lightly doped Mott insulators, and find that the effective Mott gap measured by STM correspons to the one measured with other techniques when taking into account the poor electronic screeing. - authors: - I Battisti, V Fedoseev, KM Bastiaans, A de la Torre, RS Perry, F Baumberger, MP Allan - link: - url: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.95.235141 - display: Phys. Rev. B 95, 235141, Editors' suggestion (2017) - highlight: 0 - -- title: Universality of pseudo gap and emergent order in lightly doped Mott insulators - image: Mott_phase_sep.jpg - description: - We discover of electronic order, pseudo gap phase separation and an impurity-band Mott transition in an iridate compound, cuprate-style. Along the way, we gained unique knowledge on how a Mott state collapses. +- title: "A human monogenic inflammatory disease caused by loss-of-function mutations in BACH2" + image: afzali_NI_2017_b.png + description: The discovery of a human monogenic disease resulting from inactivating mutations of BACH2, termed BACH2-related Immunodeficiency and Autoimmunity (BRIDA). The work, resulted from an international collaboration with clinicians and scientists in the UK and the US. authors: - I. Battisti* & K.M. Bastiaans*, V. Fedoseev, A. de la Torre, N. Iliopoulos, A. Tamai, E.C. Hunter, R.S. Perry, J. Zaanen, F. Baumberger, M.P. Allan link: - url: http://www.nature.com/nphys/journal/vaop/ncurrent/full/nphys3894.html - display: Nature Physics 13, 21 (2017) + url: Afzali NI 2017.pdf + display: Nat Immunol (2017) 18:813-823. highlight: 1 - news2: See also Leiden University news by Erik Arends, Phys.org - -- title: Identifying the fingerprint of antiferromagnetic spin fluctuations in iron pnictide superconductors - image: Pub_FP.png - description: - Both the density of states and the QPI dispersion of LiFeAs shows signatures of electron-boson coupling. Comparing these with fingerprints of different boson couplings to conclude that these signatures stem from AF spin fluctuations. - authors: - MP Allan* & Kyungmin Lee* & AW Rost*, MH Fischer, F Massee, K Kihou, C-H Lee, A Iyo, H Eisaki, T-M Chuang, AP Mackenzie, JC Davis, DJ Scalapino, E-A Kim - link: - url: http://www.nature.com/nphys/journal/v11/n2/full/nphys3187.html - display: Nature Physics 11, 177 (2015) + news2: + +- title: "BACH transcription factors in innate and adaptive immunity" + image: igarashi_nri_2017_b.png + description: A review on BACH family transcriptional repressors in innate and adaptive immunity. We highlight similarities at a molecular level in the cell-type-specific activities of the BACH factors, proposing that competitive interactions of BACH proteins with transcriptional activators of the bZIP family form a common mechanistic theme underlying their diverse actions. + authors: Igarashi K, Kurosaki T and Roychoudhuri R + link: + url: Igarashi NRI 2017.pdf + display: Nat Rev Immunol (2017) 17:437-450. highlight: 1 - news1: - news2: See also Cornell Chronicle by Anne Ju, Phys.org - -- title: Direct evidence for a magnetic f-electron mediated Cooper pairing mechanism of heavy fermion superconductivity in CeCoIn5 - image: dummy.png - description: "" - authors: - J Van Dyke, F Massee, MP Allan, JC Davis, C Petrovic, and DK Morr - link: - url: http://www.pnas.org/content/111/32/11663 - display: PNAS 111, 11663 (2014) - highlight: 0 - news1: News item in Science - news2: + news2: -- title: Imaging Cooper pairing of heavy fermions in CeCoIn5 - image: Pub_CeCoIn5.png - description: - The heavy Fermion superconductor CeCoIn5 has a d-wave gap with nodes along the (1,1) direction, as we find using QPI. +- title: "High levels of extracellular potassium in tumours suppress T cell activation" + image: eil_nature_2016_b.png + description: Cell death within tumours releases intracellular potassium into the extracellular space causing profound suppression of T cell activation and anti-tumour immunity. Engineering CD8+ T cells to be resistant to high extracellular potassium levels in tumours improves adoptive immunotherapy. authors: - MP Allan* & F Massee*, DK Morr, J van Dyke, AW Rost, AP Mackenzie, C Petrovic, JC Davis link: - url: http://www.nature.com/nphys/journal/vaop/ncurrent/abs/nphys2671.html - display: Nature Physics 9, 468 (2013) + url: Eil Nature 2016.pdf + display: Nature (2016) 537:539-543. highlight: 1 - news1: Featured in 'News and Views' by L Taillefer - news2: See also Phys.org, DoE headliner + news2: -- title: Formation of heavy d-electron quasiparticles in Sr3Ru2O7 - image: Pub_327.png - description: - Using APRES, we find that the bands in Sr3Ru2O7 look more like in heavy fermion material than in a normal metal. We present a detailed investigation into the formation of this particular electronic structure. +- title: "Oxygen-sensing by T cells promotes cancer metastasis to the lung" + image: clever_cell_2016_a.png + description: The HIF prolyl hydroxylases PHD1, PHD2 and PHD3 mediate sensitivity of T cells to environmental local oxygen concentrations within tissues, promoting Treg cell differentiation and permissivity of the lung to cancer metastasis. authors: - MP Allan, A Tamai, E Rozbicki, MH Fischer, J Voss, PDC King, W Meevasana, S Thirupathaiah, E Rienks, J Fink, A Tennant, RS Perry, JF Mercure, MA Wang, J Lee, CJ Fennie, E-A Kim, MJ Lawler, KM Shen, AP Mackenzie, Z-X Shen, F Baumberger link: - url: http://iopscience.iop.org/1367-2630/15/6/063029 - display: New Journal of Physics 15, 063029 (2013) + url: Clever Cell 2016.pdf + display: Cell (2016) 166:1117-1131 highlight: 1 - news: Video abstract available + news2: -- title: Anisotropic impurity states, quasiparticle scattering and nematic transport in underdoped Ca(Fe1−xCox)2As2 - image: Pub_nemat2b.png - description: - We elucidate on the formation of the electronic nematic state in Co-CaFe2As2, finding that the Cobalt dopant atoms play a key role. +- title: "BACH2 functions as an AP-1 repressor in lymphocytes to promote CD8+ T cell memory" + image: roychoudhuri_ni_2016_a.png + description: The transcription factor BACH2 functions as a steric repressor of AP-1 transcription factors in CD8+ T cells, restraining TCR-driven terminal effector differentiation to preserve long-lived memory CD8+ T cell responses authors: - MP Allan, T-M Chuang, F Massee, Y Xie, N Ni, SL Bud’ko, GS Boebinger, Q Wang, DS Dessau, PC Canfield, MS Golden, JC Davis - highlight: 1 link: - url: http://www.nature.com/nphys/journal/v9/n4/full/nphys2544.html - display: Nature Physics 9, 220 (2013) - news2: See also Tech Connect by Jennifer Rocha, Phys.org by Bill Steele - -- title: Anisotropic energy gaps of iron-based superconductivity from intraband quasiparticle interference in LiFeAs - image: Pub_LiFeAs.png - description: - In contrast to earlier photoemission reports, we show that the gaps in iron based superconductors are not isotropic but modulated with angle. - authors: - MP Allan⋆ & AW Rost⋆, AP Mackenzie, Y Xie, JC Davis, K Kihou, CH Lee, A Iyo, H Eisaki, T-M Chuang - link: - url: http://www.sciencemag.org/content/336/6081/563 - display: Science 336, 563 (2012) + url: Roychoudhuri NI 2016.pdf + display: Nat Immunol (2016) 17:851-860. highlight: 1 - news2: See also Cornell Cornincle by Bill Steele, Eureka Alert + news2: Commentary by Sidwell and Kallies (Nat Immunol 17:744-5. -- title: How Kondo-holes create intense nanoscale heavy-fermion hybridization disorder - image: dummy.png - description: "" - authors: MH Hamidian, AR Schmidt, IA Firmo, MP Allan, P Bradley, JD Garrett, TJ Williams, GM Luke, Y Dubi, AV Balatsky, JC Davis - link: - url: http://www.pnas.org/content/108/45/18233 - display: PNAS 108, 18233 (2011) - highlight: 0 - news2: -- title: Nematic electronic structure in the “parent” state of the iron-based superconductor Ca(Fe1−xCox)2As2 - image: Pub_nemat1.png - description: - We discovered an electronic nematic in the iron based superconductor Co-CaFe2As2! This state is by now confirmed and quite well characterized by transport, photoemission, and more SI-STM experiments. - authors: - T-M Chuang* & MP Allan*, J Lee, Y Xie, N Ni, SL Bud’ko, GS Boebinger PC Canfield, JC Davis +- title: "The transcription factor BACH2 promotes tumour immunosuppression through its function in Treg cell development" + image: roychoudhuri_jci_2016_a.png + description: BACH2 promotes tumour immunosuppression through its role in Foxp3+ Treg cell differentiation. These results are consistent with the results of a recent large in vivo screen of host immunosuppressive factors published by the Adams lab. + authors: link: - url: http://www.sciencemag.org/content/327/5962/181 - display: Science 327, 181 (2010) + url: Roychoudhuri JCI 2016.pdf + display: J Clin Invest (2016) 126:599-604. highlight: 1 - news1: Featured in a ‘Perspective’ by E Fradkin & SA Kivelson - news2: See also Article on NewScientist by Colin Barras - -- title: Heavy d-electron quasiparticle interference and real-space electronic structure of Sr3Ru2O7 - image: Pub_hBN.png - description: - QPI in Sr327. - authors: Jinho Lee* & M. P. Allan*, M. A.Wang, J. Farrell, S. A. Grigera, F. Baumberger, J. C. Davis and A. P. Mackenzie - link: - url: https://www.nature.com/nphys/journal/v5/n11/full/nphys1397.html - display: Nature Physics 5, 800 (2009) - highlight: 0 + news2: -- title: Fermi surface and van Hove singularities in the itinerant metamagnet Sr3Ru2O7 - image: Pub_hBN.png - description: - We determine the Fermi surface of Sr327. - authors: - A Tamai, MP Allan, JF Mercure, W Meevasana, R Dunkel, DH Lu, RS Perry, AP Mackenzie, David J Singh, Z-X Shen, F Baumberger +- title: "The transcriptional repressor BACH2 is required for Treg cell development and suppression of lethal inflammation" + image: Roychoudhuri_nature_2013_a.png + description: The transcription factor BACH2 plays a critical role in Treg cell development, required for immunological tolerance and suppression of lethal inflammation.
Commentary by Kallies and Vasanthakumar (Immunol Cell Biol. 91:491-2. + authors: link: - url: http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.101.026407 - display: Phys. Rev. Lett. 101, 026407 (2008) - highlight: 0 - -- title: Tunable self-assembly of one-dimensional nanostructures with orthogonal directions - image: Pub_hBN.png - description: - Hexagonal boron nitride shows fancy superstructures on the Mo(111) surface. - authors: - MP Allan, S Berner, M Corso, T Greber, J Osterwalder - link: - url: http://www.nanoscalereslett.com/content/2/2/94 - display: Nanoscale Research Letters 2, 94 (2007) + url: Roychoudhuri Nature 2013.pdf + display: Nature (2013) 498:506-10. highlight: 1 - -- title: Photoelectron Diffraction for a Look inside Nanostructures - image: dummy.png - description: "" - authors: - J Osterwalder, A Tamai, W Auwärter; MP Allan, T Greber - link: - url: hhttp://www.ingentaconnect.com/content/scs/chimia/2006/00000060/00000011/art00013 - display: CHIMIA 11, 759 (2006) - highlight: 0 + news2: Recommended by F1000 diff --git a/_data/students.yml b/_data/students.yml deleted file mode 100644 index 90023111051..00000000000 --- a/_data/students.yml +++ /dev/null @@ -1,16 +0,0 @@ -#- name: -# photo: rock.jpg -# info: -# email: -# number_educ: -# education1: -# education2: -# education3: -# education4: - -- name: Rosanne Wijgman - photo: rock.jpg - info: Master student - email: rosanne.wijgman@student.ru.nl - number_educ: 0 - education1: diff --git a/_includes/.DS_Store b/_includes/.DS_Store deleted file mode 100644 index 5008ddfcf53..00000000000 Binary files a/_includes/.DS_Store and /dev/null differ diff --git a/_includes/analytics.html b/_includes/analytics.html index 833e7a8d40e..6da404171aa 100644 --- a/_includes/analytics.html +++ b/_includes/analytics.html @@ -1,10 +1,9 @@ + + \ No newline at end of file + gtag('config', 'UA-155138764-1'); + diff --git a/_includes/carousel.html b/_includes/carousel.html new file mode 100644 index 00000000000..11d7e7a1bd5 --- /dev/null +++ b/_includes/carousel.html @@ -0,0 +1,44 @@ + \ No newline at end of file diff --git a/_includes/footer.html b/_includes/footer.html index 83c32077761..c6231a07c4a 100644 --- a/_includes/footer.html +++ b/_includes/footer.html @@ -1,32 +1,34 @@ + diff --git a/_layouts/piclay.html b/_layouts/piclay.html index 3a7ddcaa493..77188ead2c3 100644 --- a/_layouts/piclay.html +++ b/_layouts/piclay.html @@ -1,7 +1,7 @@ --- layout: default --- - +
{{ content }}
diff --git a/_layouts/publications.html b/_layouts/publications.html index ac4e92cde37..16a6fbe55ab 100644 --- a/_layouts/publications.html +++ b/_layouts/publications.html @@ -1,6 +1,7 @@ --- layout: default --- +
{{ content }}
diff --git a/_layouts/research.html b/_layouts/research.html index 1fb65e77360..491090915ac 100644 --- a/_layouts/research.html +++ b/_layouts/research.html @@ -1,6 +1,7 @@ --- layout: default --- +
{{ content }}
diff --git a/_layouts/researchlay.html b/_layouts/researchlay.html new file mode 100644 index 00000000000..faf32cb0351 --- /dev/null +++ b/_layouts/researchlay.html @@ -0,0 +1,44 @@ +--- +layout: default +--- + +
+ {{ content }} +
+
+

Research Group

+ +{% include research_team_list.html %} + [Team]  +[Join us]
+ +

Collaborators:

+ + + + +

Environment:

+ + + +

Facilities and resources:

+ + + + +
diff --git a/_layouts/team.html b/_layouts/team.html index c17f2cea8b9..3f838571ccf 100644 --- a/_layouts/team.html +++ b/_layouts/team.html @@ -1,6 +1,7 @@ --- layout: default --- +
{{ content }}
diff --git a/_layouts/textlay.html b/_layouts/textlay.html index a2bbf5e3f9a..9d3ef57ac3e 100644 --- a/_layouts/textlay.html +++ b/_layouts/textlay.html @@ -1,6 +1,7 @@ --- layout: default --- +
{{ content }}
diff --git a/_members/alberto.md b/_members/alberto.md new file mode 100644 index 00000000000..db0196f0c7a --- /dev/null +++ b/_members/alberto.md @@ -0,0 +1,13 @@ +--- +fullname: Alberto Conti +layout: members +position: Doctoral scientist +tier: d +picture: alberto.jpg +email: agc53@cam.ac.uk +pubmed_searchterm: conti ag [author] +--- + +Alberto graduated in 2020 from the University of York, completing an undergraduate degree in Biochemistry with a Year in Industry. As part of his degree, he worked at the Adaptive Immunity Research Unit within GSK, where he characterised a tolerogenic sub-population of dendritic cells. + +After graduating, Alberto joined the Roychoudhuri team in the Department of Pathology as part of the MRes/PhD CRUK Cambridge Centre training programme. His research focuses on better understanding the interface between the immune system and tumours to improve the efficacy of immunotherapy. \ No newline at end of file diff --git a/_members/alexander.md b/_members/alexander.md new file mode 100644 index 00000000000..98786e29e7c --- /dev/null +++ b/_members/alexander.md @@ -0,0 +1,13 @@ +--- +fullname: Alexander Wesolowski +layout: members +position: Doctoral Scientist +tier: d +picture: alexander.jpg +email: ajw299@cam.ac.uk +pubmed_searchterm: wesolowski alexander [author] +--- + +Xan graduated from University College London in 2019 with a BSc degree in Biochemistry. His undergraduate research project involved metagenomic sequencing of the human microbiome and has an interest in the application of Omic technologies in research. Alongside his studies, Xan completed internships both in industry, at Kadmon Inc. in New York, and a research-charity, the Wellcome Trust in London. Subsequently, he worked as a research assistant in Professor Ed Bullmore lab at Cambridge University, where he was involved in research on immune function and dysregulation in various psychiatric disorders. + +Xan is now undertaking his PhD in Rahul Roychoudhuri’s group, studying the host-encoded factors that render CD8+ T cells susceptible to suppression within the tumour microenvironment. \ No newline at end of file diff --git a/_members/charlotte.md b/_members/charlotte.md new file mode 100644 index 00000000000..bbe06b66ebd --- /dev/null +++ b/_members/charlotte.md @@ -0,0 +1,15 @@ +--- +fullname: Charlotte Imianowski +layout: members +position: Doctoral Scientist +tier: d +picture: charlotte.jpg +email: cji27@cam.ac.uk +pubmed_searchterm: imianowski cj [author] +--- + +Charlotte graduated in 2016 with a BA in Cell and Systems Biology from the University of Oxford. Her research involved interrogating the function of a tumour suppressor gene in colorectal cancer. + +Subsequently, she worked as a Research Assistant in Professor Bass Hassan’s group at the Sir William Dunn School of Pathology, University of Oxford. Her projects have included validating a CRISPR-Cas9 approach to target a gene of interest in Ewing’s Sarcoma, and developing a method for diagnosing Ewing’s Sarcoma using liquid biopsies. + +Charlotte is now undertaking a PhD in Rahul Roychoudhuri’s lab, studying inhibitory mechanisms that restrict NK cell function within tumours. diff --git a/_members/jie.md b/_members/jie.md new file mode 100644 index 00000000000..f2b8cd9b934 --- /dev/null +++ b/_members/jie.md @@ -0,0 +1,15 @@ +--- +fullname: Jie Yang +layout: members +position: Postdoctoral Scientist +tier: b +picture: jie.jpg +email: jy437@cam.ac.uk +pubmed_searchterm: Yang J[Author] AND (Seddon B [Author] OR Morrison WI [Author] OR Roychoudhuri R [Author]) +--- + +Having originally trained in Veterinary Medicine, Jie undertook a PhD in Infection and Immunology with Professor Ivan Morrison at the Roslin Institute in Edinburgh. The research involved the molecular characterisation of the bovine Granzyme gene family and identified a critical role of granzyme B in CD8+ T cell-mediated killing of cells infected by Theileria. Parva. This study provided the knowledge and tools that have subsequently been used to refine and enhance the immunological evaluation of T cell responses induced in vaccine trials against East Coast fever in Africa. Following this, Jie joined the group of Professor Benedict Seddon in the Francis Crick Institute Mill Hill Laboratory. Among other findings, he identified a novel function of Interleukin (IL)-7 in innate lymphoid cell (ILC)-3-dependent lymphocyte migration into lymph nodes. + +To pursue his passion in lymphocyte migration and activation in cancer, Jie joined Dr. Rahul’s lab in 2018 and is currently a College Research Associate at Homerton College. Here his focus is on the earliest adaptive immune events that occur during cancer metastasis using mouse primary and metastatic tumour models in conjunction with cellular and molecular immunology techniques. This study will enable new insights into how adaptive immune responses primed by primary tumour deposits are recruited to metastases and provide an understanding of the influence of primary tumours on immunity to metastasis. + +Jie is also working on inhibitory mechanisms which restrict Treg cell activation under homeostatic conditions and during the immunosuppression responses to tumours. diff --git a/_members/rahul.md b/_members/rahul.md new file mode 100644 index 00000000000..2c1d07e762e --- /dev/null +++ b/_members/rahul.md @@ -0,0 +1,16 @@ +--- +fullname: Rahul Roychoudhuri +layout: members +position: Principal Investigator +tier: a +picture: Rahul Roychoudhuri photograph.jpg +email: rr257@cam.ac.uk +tel: +44 1223 496315 +pubmed_searchterm: roychoudhuri r [author] +--- + +Rahul Roychoudhuri is an Associate Professor at the [University of Cambridge](www.cam.ac.uk) [Department of Pathology](www.path.cam.ac.uk), and Director of Studies in Pathology at [St Catherine's College](https://www.caths.cam.ac.uk/). He is Theme Lead in Infection and Immunity at the [School of the Biological Sciences](https://www.bio.cam.ac.uk/) at the University of Cambridge. Rahul is also a Lister Institute Prize Fellow. + +Rahul studied Natural Sciences at the University of Cambridge and Clinical Medicine at King's College London. Rahul undertook his Ph.D. in Gary Nabel's laboratory at the US National Institutes of Health (NIH) and a postdoctoral fellowship at Nicholas Restifo's laboratory at the US National Cancer Institute (NCI). His research has made fundamental contributions to our understanding of immune regulation, tumour immunosuppression, immunological memory and gene regulation. A major contribution of his early research was the discovery of mechanisms underlying differentiation of a powerfully suppressive subset of T cells called regulatory T (Treg) cells. He discovered the critical function of the transcription factor BACH2 in Treg lineage specification (Roychoudhuri et al., Nature 2013; Vahedi et al., Nature 2015), and in suppression of immune responses against solid tumours (Roychoudhuri et al., J Clin Invest 2016). This work led to discovery of a new monogenic disease caused by BACH2 insufficiency (Nat Immunol 2017; reviewed in Nat Rev Immunol 2017). + +The group's work has established molecular mechanisms required for the quiescence and long-term survival of memory CD8+ T cells (Roychoudhuri et al., Nat Immunol, 2016) and Treg cells (Grant, Yang, et al., J Exp Med 2020), and shown that pharmacological AKT inhibition provides a means of expanding memory CD8+ T cells for adoptive immunotherapy of cancer (Cancer Res 2015). Rahul's work has shown that Treg differentiation in peripheral tissues is sensitive to local oxygen concentrations resulting in permissivity of the lung to cancer metastasis (Clever, Roychoudhuri, et al., Cell 2016). The laboratory has contributed to studies demonstrating that high potassium levels within the interstitial environment of tumours restricts CD8+ T cell activation (Nature 2016; Science 2019). Rahul’s research group is focussed on the biology of two cell types with critical functions in inflammation and tumour immunity: CD4+ T cells, including Treg cells, and cytotoxic CD8+ T cells. In 2015 Rahul was awarded a Sir Henry Dale Fellowship by the Wellcome Trust and The Royal Society. In 2017 Rahul was awarded a Lister Institute Research Prize. Rahul is a reviewer for a number of peer-reviewed scientific journals and grant agencies, and serves on the Editorial board of Immunology and the International Journal of Molecular Sciences. \ No newline at end of file diff --git a/_members/sarah.md b/_members/sarah.md new file mode 100644 index 00000000000..3ee98bc62ce --- /dev/null +++ b/_members/sarah.md @@ -0,0 +1,18 @@ +--- +fullname: Sarah Whiteside +layout: members +position: Postdoctoral Scientist +tier: c +picture: sarah.jpg +email: sw925@cam.ac.uk +pubmed_searchterm: whiteside sk [author] +--- + +Sarah grew up in Vermont and completed her undergraduate studies at Elon University in North Carolina. She obtained a Bachelor of Science in Biochemistry with minors in both Economics and Classical Studies. She earned her PhD in Microbiology and Immunology from the University of Utah in the Department of Pathology. Her graduate work focused on determining the role of T cells in Lyme disease in the laboratory of Professor Janis Weis. Her findings revealed a non-classical role for T cells driving Lyme arthritis dependent on T cell intrinsic expression of the microbial pattern recognition receptor TLR2. Sarah joined Rahul’s group in 2018 and is currently a College Research Associate at King’s College. + +Her postdoctoral research aims to identify new ways to exploit the immune system to treat cancer. Cancer immunotherapies, which work by activating the immune system to attack tumours, have revolutionized cancer treatment and fundamentally changed clinical outcomes for patients with a subset of cancer types. However, immunotherapy can also lead to immune-mediated damage of non-tumour tissues, which often resembles autoimmune disease. Sarah is currently working to understand the mechanisms by which T cell immunity is supressed in cancer. In doing so, she hopes to enable the development of new selective therapies targeting the manipulation of immune function in patients. + + + + + diff --git a/_members/tarrion.md b/_members/tarrion.md new file mode 100644 index 00000000000..23c37ae9c65 --- /dev/null +++ b/_members/tarrion.md @@ -0,0 +1,15 @@ +--- +fullname: Tarrion Baird +layout: members +position: Doctoral scientist +tier: d +picture: tarrion.jpg +email: temb2@cam.ac.uk +pubmed_searchterm: baird tem [author] +--- + +Tarrion graduated from the University of Leeds in 2019 with an undergraduate degree in Biochemistry. As a part of this degree she spent a year in the oncology molecular pathology group at AstraZeneca, developing IHC assays for novel predictive biomarkers. She completed her undergraduate research project in the Naseem Lab, researching platelet-immune cell interactions. + +Tarrion is studying for her PhD as a part of the University of Cambridge BBSRC DTP. As part of this programme, she completed two rotations, one in the Jackson lab developing a library of cyclic peptides in yeast, and one the Coleman lab, researching the role of miRNAs in germ cell cancer. Tarrion's research in the Roychoudhuri lab aims to exploit tumour evolution to understand how cancer evades immune attack. + + diff --git a/_pages/.DS_Store b/_pages/.DS_Store deleted file mode 100644 index 5008ddfcf53..00000000000 Binary files a/_pages/.DS_Store and /dev/null differ diff --git a/_pages/404.md b/_pages/404.md index 4dfa48449bd..06bef5b1107 100755 --- a/_pages/404.md +++ b/_pages/404.md @@ -5,6 +5,10 @@ excerpt: "Page not found. Your pixels are in another canvas." sitemap: false permalink: /404.html --- +
 : +
 : +
 : +
 : Sorry, but the page you were trying to view does not exist. diff --git a/_pages/Contact.md b/_pages/Contact.md new file mode 100644 index 00000000000..a4179abcf21 --- /dev/null +++ b/_pages/Contact.md @@ -0,0 +1,25 @@ +--- +title: "Roychoudhuri Lab - Contact us" +layout: contact +excerpt: "Contact" +sitemap: false +permalink: /contact +--- +### Contact + +The laboratory is located at the [Immunology Division](https://www.path.cam.ac.uk/directory/immunology-division) at the [Department of Pathology](https://www.path.cam.ac.uk/), [University of Cambridge](https://www.cam.ac.uk).

+ +**We are located at:**
+
+Roychoudhuri Lab,
+Division of Immunology,
+Department of Pathology,
+University of Cambridge,
+Tennis Court Road,
+Cambridge,
+CB2 1QP.
+
+**Tel:** +44 1223 496315
+**Email:** rr257@cam.ac.uk
+
  +
  \ No newline at end of file diff --git a/_pages/about.md b/_pages/about.md new file mode 100644 index 00000000000..9e6d1b36adc --- /dev/null +++ b/_pages/about.md @@ -0,0 +1,19 @@ +--- +title: "About the website" +layout: textlay +excerpt: "About the website." +sitemap: false +permalink: /about.html +--- + +# Site design + +This website is hosted on [Github.io](github.io) and powered by [Jekyll](https://jekyllrb.com). The website is based on a [template](https://github.com/mpa139/allanlab) by Milan Allan and uses [Bootstrap](http://www.getbootstrap.com) and [Bootswatch](http://www.bootswatch.com). All pages are written in [markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet). + +Lists of publications are generated in real-time based on a modified version of a great [script](http://www.alexhadik.com/blog/2014/6/12/create-pubmed-citations-automatically-using-pubmed-api) by Alex Hadik, modified to allow for links to full-text PDFs. + + + + + + diff --git a/_pages/aboutwebsite.md b/_pages/aboutwebsite.md deleted file mode 100644 index bd18ba1d937..00000000000 --- a/_pages/aboutwebsite.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: "About the website" -layout: textlay -excerpt: "About the website." -sitemap: false -permalink: /aboutwebsite.html ---- - -# Use this website as a template for your academic research group - -This website is powered by [Jekyll](https://jekyllrb.com) and uses some [Bootstrap](http://www.getbootstrap.com) and [Bootswatch](http://www.bootswatch.com). We tried to make it simple yet adaptable, so that it is easy for you to re-use it for your purpose. - -### Getting started -All pages are written in [markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) for easy editing, and [Jekyll](https://jekyllrb.com) uses Liquid for the data-driven pages. The publicaion list, news items, and group members are stored as `.yml` data sheets (plain text) in the `_data folder`, so that one can update the website easily. The pages are in the `_pages` folder. Updating and maintaining is easy using [Github](http://www.github.com) (not worldpress-easy, but there are other advantages (see e.g. [this](https://www.taniarascia.com/make-a-static-website-with-jekyll/), or [this](http://www.webdesignerdepot.com/2015/11/jekyll-against-the-rest-of-the-world/)). [Jekyll](https://jekyllrb.com) takes all the markdown and data files, and creates beautiful `html` files in the `_site` folder. - -If you never used [Jekyll](https://jekyllrb.com), read the [wikipedia article](https://en.wikipedia.org/wiki/Jekyll_(software)) article and check out [their website](https://jekyllrb.com). Same for [Github](http://www.github.com), which will host your first website draft. - -Create and open a github account, go to [our repository](https://github.com/allanlab/allanlab), and click 'fork'. This is now your copy of the website, and you can change and adapt it as you want. You don't have to link to us or mention us (but of course we appreciate it). Then change the name of the repository to "your_username" and the name of the branch to "gh-pages". Your website is now automatically published under *your_username.github.io/your_username/*. Except that it probably still looks like our website. - -To modify the webpage, you can either do everything on on github.com (go to a file, click "edit", then "commit", "push"), or install [Jekyll](https://jekyllrb.com) on your computer and play with your local copy that you sync with the branch on github.com. The former is much easier in the beginning, but a bit less convenient once you start rewriting everythint. To get it to work on your computer (and to learn a bit more about [Jekyll](https://jekyllrb.com)), [here](https://www.taniarascia.com/make-a-static-website-with-jekyll/) and [here](https://scotch.io/tutorials/getting-started-with-jekyll-plus-a-free-bootstrap-3-starter-theme) are tutorials on how to use it and how set it up locally. Also, consider using the [Github desktop app](http://www.desktop.github.com), I found it helpful. - -### Customization -Now let's make this *your* website. - -First, go to the `news.ylm`, `publist.ylm`, and `team.ylm` files in the `_data` folder and insert your own data into the data fields. Watch out: [Jekyll](https://jekyllrb.com) is quite strict about extra or missing spaces etc. Adhere to the format. In the beginning, test each change: commit, push, and check the published website. - -For publications, you can add a "1" in the highlight field, then it will be featured prominently. You can add important news items (red, "news1"), and less important news items (blue, "news2"). - -For the news items, just keep adding them. The first 10 will be displayed on the 'home' page. - -For the `team.ylm` file - -Next, change the content of all files in the `_pages` folder. To change the title in the homepage, go to `homelay.html` in the `_layout` folder. - -Lastly, change the footer and perhaps header appropriately (in `_include`). - -You might also want to change the style or theme. I imported style files (in sass) from Bootstrap/Bootwatch, you can replace them with your own (in the `_sass directory`). For small changes, just work on the override stuff in the `main.sass` file in the `CSS` folder. Or change some variables in the `_variables.sass` file, like the background color etc. - -As said, [Jekyll](https://jekyllrb.com) takes all the markdown and data files, and creates beautiful `html` files in the `_site` folder.In the end, either upload these files to your server, or buy yourself a domain and check the instructions on github on how to host it there. - -### Copyright / credit - -You can use this template as you please. You don't have to link to us or mention us (but of course we appreciate it). We also welcome it if you send us an email with a link to your website, perhaps we'll publish a list here at some point. - -Comments welcome. - -Code released under the MIT License. - - - diff --git a/_pages/home.md b/_pages/home.md index c30a245281e..c631529c378 100644 --- a/_pages/home.md +++ b/_pages/home.md @@ -1,76 +1,24 @@ --- -title: "Allan Lab - Home" +title: "Roychoudhuri Lab - Home" layout: homelay -excerpt: "Allan Lab at Leiden University." +excerpt: "Roychoudhuri Lab at the University of Cambridge." sitemap: false permalink: / --- -We are a dynamic research group at the [Leiden Institute of Physics](http://www.physics.leidenuniv.nl). Our aim is to explore and understand [quantum materials](http://condensedconcepts.blogspot.nl/2013/05/what-is-quantum-matter.html), including strange metals, high-temperature superconductors, and quantum critical electron matter. +

T cell immunity in inflammation and cancer

+**T cells** drive immune activation and promote clearance of infections and cancer. However, their function can provoke autoimmune and allergic inflammation. The immune system therefore employs a variety of suppressive mechanisms, known as **immunoregulatory mechanisms**, to restrain excessive T cell activation and prevent autoimmune and allergic inflammation. It is now known that such suppressive mechanisms inhibit anti-tumour immunity to drive deleterious **immunosuppression** in cancer. Immunoregulatory mechanisms therefore function as ‘brakes’ within the immune system and have important consequences in **infection, inflammation and cancer**. +Our research aims to uncover the molecular and cellular mechanisms underpinning immune regulation and cancer immunosuppression. Fundamental discovery in the field of immunoregulation will pave the way for new therapies aimed at manipulating immune function in patients with autoimmunity and cancer (see [Research](research)). We have a particular interest in the immunoregulatory mechanisms that control the differentiation and function of CD4+ and CD8+ conventional T cells and Foxp3+ regulatory T (Treg) cells. - -{% endif %} - -{% if even_odd == 2 %} - -{% endif %} - -{% if even_odd == 3 %} - -{% endif %} - -

 

- -First advertisement. -
- -
- - -## ETHZ -From the [group of Andreas Wallraff](http://www.qudev.ethz.ch/). -
- -
- -## Cornell -From the [group of Seamus JC Davis](http://davisgroup.lassp.cornell.edu). -
- -
- -## St Andrews -From the [group of Felix Baumberger](http://dqmp.unige.ch/baumberger/) (now at University of Geneva). -
- -
diff --git a/_pages/publications.md b/_pages/publications.md index afbfbd2f0d2..0a8d837ae74 100644 --- a/_pages/publications.md +++ b/_pages/publications.md @@ -1,63 +1,13 @@ --- -title: "Allan Lab - Publications" -layout: gridlay -excerpt: "Allan Lab -- Publications." +title: "Roychoudhuri Lab - Publications" +layout: researchlay +excerpt: "Roychoudhuri Lab -- Publications." sitemap: false +pubmed_searchterm: Roychoudhuri R [author] permalink: /publications/ --- - -# Publications - -## Highlights - -(For a full list see [below](#full-list) or go to [Google Scholar](https://scholar.google.ch/citations?user=TqxYWZsAAAAJ), [ResearcherID](https://www.researcherid.com/rid/D-7763-2012)) - -{% assign number_printed = 0 %} -{% for publi in site.data.publist %} - -{% assign even_odd = number_printed | modulo: 2 %} -{% if publi.highlight == 1 %} - -{% if even_odd == 0 %} -
-{% endif %} - -
-
- {{ publi.title }} - -

{{ publi.description }}

-

{{ publi.authors }}

-

{{ publi.link.display }}

-

{{ publi.news1 }}

-

{{ publi.news2 }}

-
-
- -{% assign number_printed = number_printed | plus: 1 %} - -{% if even_odd == 1 %} -
-{% endif %} - -{% endif %} -{% endfor %} - -{% assign even_odd = number_printed | modulo: 2 %} -{% if even_odd == 1 %} - -{% endif %} - -

 

- - -## Full List - -{% for publi in site.data.publist %} - - {{ publi.title }}
- {{ publi.authors }}
{{ publi.link.display }} - -{% endfor %} - +### Publications +
+{% include pubmed_gen_reflist.html pubmed_searchterm = page.pubmed_searchterm %} +
\ No newline at end of file diff --git a/_pages/research.md b/_pages/research.md index 3562827593f..47b2ae1e28f 100644 --- a/_pages/research.md +++ b/_pages/research.md @@ -1,25 +1,58 @@ --- -title: "Allan Lab - Research" -layout: textlay -excerpt: "Allan Lab -- Research" +title: "Roychoudhuri Lab - Research" +layout: researchlay +excerpt: "Roychoudhuri Lab -- Research" sitemap: false permalink: /research/ --- -# Research +
+

Immune regulation and cancer immunosuppression

+**T cells** drive immune activation and promote clearance of infections and cancer. However, their function can provoke autoimmune and allergic inflammation. The immune system therefore employs a variety of suppressive mechanisms, known as **immunoregulatory mechanisms**, to restrain excessive T cell activation and prevent autoimmune and allergic inflammation. It is now known that such suppressive mechanisms inhibit anti-tumour immunity to drive deleterious **immunosuppression** in cancer. Immunoregulatory mechanisms therefore function as ‘brakes’ within the immune system and are important therapeutic targets in **infection, inflammation and cancer**. This is exemplified by the clinical efficacy of cancer immunotherapies targeting the immune ‘checkpoints’ PD-1 and CTLA-4 in certain cancers. **We believe that fundamental discovery in the fields of immune regulation and cancer immunosuppression will enable development of new and more effective therapies for patients with presently incurable autoimmune and allergic diseases and cancer.** -Our overarching goal is to explore and understand new quantum states of electronic matter on the atomic scale. To do so, we use and develop novel spectroscopic-imaging scanning tunneling microscopy (SI-STM) tools to visualize the relevant quantum mechanical degrees of freedom. +### Major research areas +#### **Mechanisms of regulatory T (Treg) cell development and function** -Questions of interest include: (i), How does the Mott state collapse upon doping and how is this related to the complex phase diagram of high-temperature superconductors? (ii), What is the strange metal phase seen in correlated electron systems? Is this an exotic long-range entangled state? What is the mechanism of dissipation in that state? (iii), Why is the transition temperature in high-temperature superconductors so high? - -![]({{ site.url }}{{ site.baseurl }}/images/respic/layers_real.jpg){: style="width: 300px; float: right; border: 10px"} +**Regulatory T (Treg) cells** are rare immune cells with powerful suppressive functions. Loss of Treg cells results in lethal inflammation, while defects in their function are associated with autoimmunity and allergy. Treg cells also suppress immune responses in cancer. There is intense medical interest in exploiting the powerful biological functions of Treg cells to treat patients with inflammatory diseases, transplantation and cancer. However, most efforts have thusfar been disappointing. We aim to better define mechanisms of Treg development and function, to identify new ways of exploiting or blocking the suppressive function of Treg cells in individuals with inflammation and cancer (**Fig. 1**). +
+
![Immunoregulatory function within the T cell lineage.]({{ site.url }}{{ site.baseurl }}/images/respic/treg_development.png) +
Figure 1. Regulatory T cell development. CD4+ effector and regulatory T (Treg) cells arise from common precursor cells within the thymus and periphery by exert opposing functions. Treg-mediated restraint of +effector cell function is a critical immunoregulatory mechanism required to prevent lethal inflammation. Modified from Igarashi, Kurosaki and Roychoudhuri, Nat Rev Immunol 2017. +
+
-Currently, our instrument of choice is SI-STM. State-of-the-art SI-STM measures an array of tunneling spectra on a given sample, registered to the atomic sites with picometer precision. Each is proportional to the local density of states at a given location. Ideally, the recorded spectra are so tightly packed that the measurement yields a three-dimensional mapping of the local density of states as a function of locations and energy. This is shown on the image on the right-hand side (10x10 nm2), and its Fourier transform, below. +The immunoregulatory function of Treg cells is a major focus of the laboratory's research. We have demonstrated the non-redundant requirement for the transcription factor BACH2 in Treg development (Nature 2013). Our findings provided a model of early Treg lineage commitment and explained why genetic polymorphisms at the human BACH2 locus are associated with autoimmune and allergic diseases. We established a now widely-accepted molecular model of how BACH2 functions in lymphocytes (Nat Immunol 2016; reviewed in Igarashi, Kurosaki and Roychoudhuri, Nat Rev Immunol 2017). Our research contributed to the discovery of a new human disease called BACH2-related Immunodeficiency and Autoimmunity (Afzali et al., Nat Immunol 2017). This has led to identification and improved management of patients with BRIDA. We showed that BACH2 promotes Treg-mediated cancer immunosuppression (J Clin Invest 2015). We have subsequently developed cell-based reporter assays for BACH2 function (Scientific Reports 2020), enabling a drug discovery programme in collaboration with Cancer Research UK Therapeutic Discovery Laboratories. -The quantum materials which we will investigate encapsulate some of the great unsolved mysteries of physics. They include high-temperature superconductors, quantum-critical compounds, graphene, and topological electronic matter that can be used for error-resistant quantum computing. +Our group showed that a distal enhancer at the prominent human autoimmune/allergic disease risk locus at chromosome 11q13.5 restricts gut inflammation by promoting expression of the TGF-b docking receptor GARP on Treg cells, revealing a novel mechanism of immune regulation in the gut (Nature 2020). We have shown that Treg differentiation is sensitive to local oxygen concentration contributing to lung immune homeostasis but creating a permissive environment for pulmonary cancer metastasis (Cell 2016). We showed that CCR8 expression marks Treg cells with highly suppressive function in tumours but that it is dispensable for their accumulation and suppressive function (Immunology 2021). -![]({{ site.url }}{{ site.baseurl }}/images/respic/layers_fft.jpg){: style="width: 300px; float: left; border: 10px"} +#### **T cell maintenance and memory** +T cell responses are clonally expanded from small numbers of antigen-specific naive precursor cells which arose during thymic development. Upon priming, antigen-specific T cell responses must be maintained over long periods of time to enable T cell memory and durable responses to chronic antigens. Our laboratory is interested in the mechanisms that underpin long-lived T cell responses. -A main goal is to use modern technology to build the new instrumentation needed to understand these quantum materials. I learned my trade in [Seamus Davis’ SI-STM lab](http://davisgroup.lassp.cornell.edu/) and with [Felix Baumberger](http://dpmc.unige.ch/gr_baumberger/index.html), and later moved as an [ETH fellow](http://www.ethfellows.ethz.ch/) to [Andreas Wallraff’s qudev lab](http://www.qudev.ethz.ch/) where we investigated coupled cavity arrays in circuit QED. This allowed me to learn new techniques such as high frequency measurements, low temperature noise-free amplification, and quantum-limited measurements. The goal is to combine these with SI-STM. +**CD8+ T cell memory** has been the focus of our prior research. However, we have recently become interested in understanding how clonal Treg responses are maintained over time. To work properly, Treg responses need to be remarkably long-lived: Treg cells produced during a critical time-window in early life need to be maintained throughout life to prevent lethal inflammation. Treg populations are maintained despite reduced thymic output of T cells as we age, and in the definitive absence of thymic output. The transfer of mature Treg cells into Treg-deficient mice establishes a long-lived population that prevents lethal inflammation over the lifespan of the host. **Maintenance of Treg responses** is also critical to immunoregulatory memory, limiting harmful immune reactions upon re-exposure to allergens and infection, and to the efficacy of Treg cell therapies. Much is known about how Treg cells develop, but we have lacked a framework for understanding how Treg responses are maintained. Our recent work has begun to reshape our thinking about how long-lived Treg responses are organised. We have found that long-term maintenance of Treg populations is dependent upon the presence of a subset of functionally quiescent cells marked by high levels of Bach2 expression (**Fig. 2**; Grant, Yang et al., J Exp Med 2020). We are developing new tools to understand how long-lived immunoregulatory and immunosuppressive Treg responses are maintained and establishing clinical collaborations to determine the consequences of this for inflammatory and allergic diseases and cancer. +
+![Functions of Bach2 in Treg development and maintenance.]({{ site.url }}{{ site.baseurl }}/images/respic/Bach2_Treg_maintenance_cropped.png) +
+Figure 2. Long-term maintenance of Treg responses requires quiescent Bach2-expressing cells. +
+ +We have a long-standing interest in T cell memory. We conducted one of the earliest multiplexed single-cell gene expression analyses of immune cells revealing unappreciated heterogeneity in memory CD8+ T responses to vaccination (PNAS 2011). We defined transcriptional and epigenetic programmes of vaccine-induced memory T cells (Vaccine 2015, Cell Mol Immunol 2015). We defined molecular mechanisms by which long-lived memory CD8+ T cell responses to viral infection are maintained (Nat Immunol 2016). We showed that long-term maintenance of Treg populations is dependent upon the presence of a subset of functionally quiescent cells marked by high levels of Bach2 expression (J Exp Med 2020). We have contributed to work showing that inhibition of AKT signalling enables expansion of T cells with a long-lived memory phenotype which mediates superior **adoptive immunotherapy responses** upon transfer into tumour-bearing recipients (Cancer Res, 2015), and that memory T cell–driven differentiation of naive cells impairs adoptive immunotherapy (J Clin Invest, 2015). + +#### **Molecular and cellular mechanisms of tumour immunosuppression** + +Cancers adapt to their immune environment to evade attack. According to the **cancer immunoediting** hypothesis, tumour development is characterized by an initial ‘elimination’ phase, during which a majority of cancer cells are destroyed by components of innate and adaptive immunity (**Fig. 3**). This is followed by an ‘equilibrium’ phase, during which pressure from the immune system contributes to evolutionary selection of tumour escape variants that give rise to an ‘escape’ phase characterized by evasion from immune control and unrestrained tumour growth. + +
+
![How is the function of the immune system suppressed during tumour development?]({{ site.url }}{{ site.baseurl }}/images/respic/cancer_development.png) +
Figure 3. Phases of tumour development according to the cancer immunoediting hypothesis. Tumour development is characterized by an initial ‘elimination’ phase, during which a majority of cancer cells are destroyed by a variety of components of the innate and adaptive immune systems, including CD8+ T cells and NK cells. This process results, referred to as immunoediting, results in an ‘equilibrium’ phase, during which pressure from the immune system contributes to selection of tumour variants that do not express antigens targeted by the adaptive immune system or have developed mechanisms to suppress immune function. This gives rise to the ‘escape’ phase characterized by recruitment and support of the differentiation and proliferation of immunosuppressive cell types including Treg cells, tumour-associated macrophages and myeloid-derived suppressor cells, expression of inhibitory ligands and such as PD-L1 and production of immunosuppressive factors such as TGF-b resulting in evasion from immune control and unrestrained tumour growth. +
+While selection of antigen-loss variants represents a mechanism of tumour escape, growth of tumours containing immunogenic epitopes is better explained through an understanding of the critical role of immunosuppression in promoting tumour escape. To achieve this, cancer cells subvert the biochemical, metabolic and ionic environment of tumours to drive immune dysfunction. Using **directed tumour evolution** and **high-throughput CRISPR-based functional genetics**, this work aims to identify novel immunoregulatory mechanisms operating within the tumour microenvironment. + +We have made progress in understanding mechanisms of tumour immunosuppression. We uncovered mechanisms by which Treg cells contribute to cancer immunosuppression (J Clin Invest 2016). Our group showed that maintenance of durable immunosuppressive Treg responses to cancer require the Treg cells with a quiescent phenotype (J Exp Med 2020). We showed that high interstitial potassium concentrations within tumours limits CD8+ T cell function through suppression of the AKT/mTOR pathway (Nature 2016). We showed that CCR8 marks Treg cells with highly suppressive function within tumours, but is dispensable for their accumulation and function (Immunology 2021). Our research findings and tools form the basis for industrial collaborations with GSK, F-Star Biotechnology and CRUK Therapeutic Discovery Laboratories. +
+ +### Research Highlights +(For a full list of publications **see below**) +
+{% include publication_highlights.html %} +
-This will enable the instrumental capabilities to visualize the different quantum mechanical degrees of freedom needed to understand next-generation quantum materials. STM will be the main method, but we use different spectroscopic-imaging techniques to visualize not only the topography, but also the density of states, spins, and other degrees of freedom hidden below the surface. diff --git a/_pages/team.md b/_pages/team.md index d0822e4bee0..e0daab1054e 100644 --- a/_pages/team.md +++ b/_pages/team.md @@ -1,86 +1,20 @@ --- -title: "Allan Lab - Team" +title: "Roychoudhuri Lab - Team" layout: gridlay -excerpt: "Allan Lab: Team members" +excerpt: "Roychoudhuri Lab: Group members" sitemap: false permalink: /team/ --- +
+### Group Members -# Group Members + **We are looking for new PhD students, Postdocs, and Master students to join the team** [(see openings)]({{ site.url }}{{ site.baseurl }}/vacancies) **!** - **We are looking for new PhD students, Postdocs, and Master students to join the team** [(see openings)]({{ site.url }}{{ site.baseurl }}/vacancies) **!** -Jump to [staff](#staff), [master and bachelor students](#master-and-bachelor-students), [alumni](#alumni), [administrative support](#administrative-support), [lab visitors](#lab-visitors). - -## Staff -{% assign number_printed = 0 %} -{% for member in site.data.team_members %} - -{% assign even_odd = number_printed | modulo: 2 %} - -{% if even_odd == 0 %} -
-{% endif %} - -
- -

{{ member.name }}

- {{ member.info }}
email: <{{ member.email }}> -
    - - {% if member.number_educ == 1 %} -
  • {{ member.education1 }}
    • - {% endif %} - - {% if member.number_educ == 2 %} -
  • {{ member.education1 }}
    • -
  • {{ member.education2 }}
    • - {% endif %} - - {% if member.number_educ == 3 %} -
  • {{ member.education1 }}
    • -
  • {{ member.education2 }}
    • -
  • {{ member.education3 }}
    • - {% endif %} - - {% if member.number_educ == 4 %} -
  • {{ member.education1 }}
    • -
  • {{ member.education2 }}
    • -
  • {{ member.education3 }}
    • -
  • {{ member.education4 }}
    • - {% endif %} - - {% if member.number_educ == 5 %} -
  • {{ member.education1 }}
    • -
  • {{ member.education2 }}
    • -
  • {{ member.education3 }}
    • -
  • {{ member.education4 }}
    • -
  • {{ member.education5 }}
    • - {% endif %} - -
-
- -{% assign number_printed = number_printed | plus: 1 %} - -{% if even_odd == 1 %} -
-{% endif %} - -{% endfor %} - -{% assign even_odd = number_printed | modulo: 2 %} -{% if even_odd == 1 %} - -{% endif %} - - - - -## Master and Bachelor Students {% assign number_printed = 0 %} -{% for member in site.data.students %} +{% assign members_sorted = site.members | sort: 'tier' %} +{% for member in members_sorted %} {% assign even_odd = number_printed | modulo: 2 %} @@ -89,32 +23,14 @@ Jump to [staff](#staff), [master and bachelor students](#master-and-bachelor-stu {% endif %}
-

{{ member.name }}

- {{ member.info }}
email: <{{ member.email }}> + + +

{{ member.fullname }}

+ {{ member.position }}
+ email: {{ member.email }}
+ >> More information
@@ -131,66 +47,4 @@ Jump to [staff](#staff), [master and bachelor students](#master-and-bachelor-stu {% endif %} - -## Alumni - -{% assign number_printed = 0 %} -{% for member in site.data.alumni_members %} - -{% assign even_odd = number_printed | modulo: 2 %} - -{% if even_odd == 0 %} -
-{% endif %} - -
- -

{{ member.name }}

- {{ member.duration }}
Role: {{ member.info }} -
    - -
-
- -{% assign number_printed = number_printed | plus: 1 %} - -{% if even_odd == 1 %} -
-{% endif %} - -{% endfor %} - -{% assign even_odd = number_printed | modulo: 2 %} -{% if even_odd == 1 %} - -{% endif %} - -## Former visitors, BSc/ MSc students -
- -
-

Visitors

-{% for member in site.data.alumni_visitors %} -{{ member.name }} -{% endfor %} -
- -
-

Master students

-{% for member in site.data.alumni_msc %} -{{ member.name }} -{% endfor %} -
- -
-

Bachelor Students

-{% for member in site.data.alumni_bsc %} -{{ member.name }} -{% endfor %} -
- -
- - -## Administrative Support -Ellie van Rijsewijk is helping us (and other groups) with administration. +
diff --git a/_pages/vacancies.md b/_pages/vacancies.md new file mode 100644 index 00000000000..1924d0eb9a4 --- /dev/null +++ b/_pages/vacancies.md @@ -0,0 +1,25 @@ +--- +title: "Roychoudhuri Lab - Vacancies" +layout: textlay +excerpt: "Openings" +sitemap: false +permalink: /vacancies +--- + +### Open positions + +We are always looking for new group members with passion, talent, and grit! + +You will have the chance to work on grand challenges in the field immunoregulation and tumour immunity. You will be involved in determining the important and interesting questions, designing and performing measurements, making discoveries and publishing findings. + +#### Applications for Postdoctoral Fellowships +We are happy to consider postdoc applications if you are interested in bringing your work to the laboratory. Please send me an [email](mailto:rr257@cam.ac.uk) stating briefly why you are interested in joining the group and attaching a CV. + +We are well supported by a variety of external funding agencies, several of which provide support for postdoctoral fellowships. We are happy to support the most talented postdocotral researchers to apply for fellowships in the group. Please contact me if you'd like to discuss this route to joining the laboratory. + +#### Master's and Bachelor's internships +If you are looking for a Masters project in the laboratory, contact me by email with a copy of your CV, a start and end date of the internship, and a brief statement of why you'd be interested in joining the laboratory. + +
+ {% include carousel.html %} +
diff --git a/_plugins/roychoudhuri - Shortcut.lnk b/_plugins/roychoudhuri - Shortcut.lnk new file mode 100644 index 00000000000..b2a43e54fd7 Binary files /dev/null and b/_plugins/roychoudhuri - Shortcut.lnk differ diff --git a/_sass/.DS_Store b/_sass/.DS_Store deleted file mode 100644 index 45a2f880a66..00000000000 Binary files a/_sass/.DS_Store and /dev/null differ diff --git a/_sass/bootstrap/_variables.scss b/_sass/bootstrap/_variables.scss index 26e7e3beab8..2f961b51c30 100644 --- a/_sass/bootstrap/_variables.scss +++ b/_sass/bootstrap/_variables.scss @@ -28,6 +28,7 @@ $brand-danger: #FF4136 !default; //** Background color for ``. $body-bg: #fff !default; +$body-padding: 25px !default; //** Global text color on ``. $text-color: $gray !default; @@ -358,35 +359,35 @@ $container-lg: $container-large-desktop !default; //## // Basics of a navbar -$navbar-height: 50px !default; +$navbar-height: 58px !default; $navbar-margin-bottom: $line-height-computed !default; $navbar-border-radius: $border-radius-base !default; $navbar-padding-horizontal: floor(($grid-gutter-width / 2)) !default; $navbar-padding-vertical: (($navbar-height - $line-height-computed) / 2) !default; $navbar-collapse-max-height: 340px !default; -$navbar-default-color: $text-color !default; -$navbar-default-bg: #f8f8f8 !default; -$navbar-default-border: $input-border !default; +$navbar-default-color: #FFFFFF !default; +$navbar-default-bg: #002940 !default; +$navbar-default-border: #002940 !default; // Navbar links -$navbar-default-link-color: $gray-light !default; -$navbar-default-link-hover-color: $gray-dark !default; +$navbar-default-link-color: #FFFFFF !default; +$navbar-default-link-hover-color: #2E65CA !default; $navbar-default-link-hover-bg: transparent !default; -$navbar-default-link-active-color: $navbar-default-link-hover-color !default; +$navbar-default-link-active-color: #2E65CA !default; $navbar-default-link-active-bg: transparent !default; -$navbar-default-link-disabled-color: $gray-lighter !default; +$navbar-default-link-disabled-color: #FFFFFF !default; $navbar-default-link-disabled-bg: transparent !default; // Navbar brand label -$navbar-default-brand-color: $navbar-default-link-hover-color !default; -$navbar-default-brand-hover-color: $navbar-default-link-hover-color !default; +$navbar-default-brand-color: #2E65CA !default; +$navbar-default-brand-hover-color: #2E65CA !default; $navbar-default-brand-hover-bg: transparent !default; // Navbar toggle $navbar-default-toggle-hover-bg: #fff !default; -$navbar-default-toggle-icon-bar-bg: $gray-light !default; -$navbar-default-toggle-border-color: $gray-lighter !default; +$navbar-default-toggle-icon-bar-bg: #fff !default; +$navbar-default-toggle-border-color: #fff !default; //=== Inverted navbar diff --git a/_sass/bootstrap/_variables copy.scss b/_sass/bootstrap/_variables_recent_old.scss similarity index 80% rename from _sass/bootstrap/_variables copy.scss rename to _sass/bootstrap/_variables_recent_old.scss index e0496852917..abfc763d97c 100644 --- a/_sass/bootstrap/_variables copy.scss +++ b/_sass/bootstrap/_variables_recent_old.scss @@ -1,5 +1,5 @@ $bootstrap-sass-asset-helper: false !default; -// +// Lumen 3.3.7 // Variables // -------------------------------------------------- @@ -12,14 +12,14 @@ $gray-base: #000 !default; $gray-darker: lighten($gray-base, 13.5%) !default; // #222 $gray-dark: lighten($gray-base, 20%) !default; // #333 $gray: lighten($gray-base, 33.5%) !default; // #555 -$gray-light: lighten($gray-base, 46.7%) !default; // #777 +$gray-light: lighten($gray-base, 60%) !default; // #999 $gray-lighter: lighten($gray-base, 93.5%) !default; // #eee -$brand-primary: darken(#428bca, 6.5%) !default; // #337ab7 -$brand-success: #5cb85c !default; -$brand-info: #5bc0de !default; -$brand-warning: #f0ad4e !default; -$brand-danger: #d9534f !default; +$brand-primary: #158CBA !default; +$brand-success: #28B62C !default; +$brand-info: #75CAEB !default; +$brand-warning: #FF851B !default; +$brand-danger: #FF4136 !default; //== Scaffolding @@ -29,12 +29,12 @@ $brand-danger: #d9534f !default; //** Background color for ``. $body-bg: #fff !default; //** Global text color on ``. -$text-color: $gray-dark !default; +$text-color: $gray !default; //** Global textual link color. $link-color: $brand-primary !default; //** Link hover color set via `darken()` function. -$link-hover-color: darken($link-color, 15%) !default; +$link-hover-color: $link-color !default; //** Link hover decoration. $link-hover-decoration: underline !default; @@ -43,13 +43,13 @@ $link-hover-decoration: underline !default; // //## Font, line-height, and color for body text, headings, and more. -$font-family-sans-serif: "Helvetica Neue", Helvetica, Arial, sans-serif !default; +$font-family-sans-serif: 'Lato',Helvetica, Arial, sans-serif !default; $font-family-serif: Georgia, "Times New Roman", Times, serif !default; //** Default monospace fonts for ``, ``, and `
`.
 $font-family-monospace:   Menlo, Monaco, Consolas, "Courier New", monospace !default;
 $font-family-base:        $font-family-sans-serif !default;
 
-$font-size-base:          14px !default;
+$font-size-base:          16px !default;
 $font-size-large:         ceil(($font-size-base * 1.25)) !default; // ~18px
 $font-size-small:         ceil(($font-size-base * 0.85)) !default; // ~12px
 
@@ -67,9 +67,9 @@ $line-height-computed:    floor(($font-size-base * $line-height-base)) !default;
 
 //** By default, this inherits from the ``.
 $headings-font-family:    inherit !default;
-$headings-font-weight:    500 !default;
+$headings-font-weight:    400 !default;
 $headings-line-height:    1.1 !default;
-$headings-color:          inherit !default;
+$headings-color:          $gray-dark !default;
 
 
 //== Iconography
@@ -77,11 +77,7 @@ $headings-color:          inherit !default;
 //## Specify custom location and filename of the included Glyphicons icon font. Useful for those including Bootstrap via Bower.
 
 //** Load fonts from this directory.
-
-// [converter] If $bootstrap-sass-asset-helper if used, provide path relative to the assets load path.
-// [converter] This is because some asset helpers, such as Sprockets, do not work with file-relative paths.
-$icon-font-path: if($bootstrap-sass-asset-helper, "bootstrap/", "../fonts/bootstrap/") !default;
-
+$icon-font-path: if($bootstrap-sass-asset-helper, "bootstrap/", "../fonts/") !default;
 //** File name for all font files.
 $icon-font-name:          "glyphicons-halflings-regular" !default;
 //** Element ID within SVG icon file.
@@ -92,13 +88,13 @@ $icon-font-svg-id:        "glyphicons_halflingsregular" !default;
 //
 //## Define common padding and border radius sizes and more. Values based on 14px text and 1.428 line-height (~20px to start).
 
-$padding-base-vertical:     6px !default;
+$padding-base-vertical:     7px !default;
 $padding-base-horizontal:   12px !default;
 
-$padding-large-vertical:    10px !default;
+$padding-large-vertical:    13px !default;
 $padding-large-horizontal:  16px !default;
 
-$padding-small-vertical:    5px !default;
+$padding-small-vertical:    4px !default;
 $padding-small-horizontal:  10px !default;
 
 $padding-xs-vertical:       1px !default;
@@ -108,8 +104,8 @@ $line-height-large:         1.3333333 !default; // extra decimals for Win 8.1 Ch
 $line-height-small:         1.5 !default;
 
 $border-radius-base:        4px !default;
-$border-radius-large:       6px !default;
-$border-radius-small:       3px !default;
+$border-radius-large:       5px !default;
+$border-radius-small:       2px !default;
 
 //** Global color for active items (e.g., navs or dropdowns).
 $component-active-color:    #fff !default;
@@ -140,7 +136,7 @@ $table-bg-hover:                #f5f5f5 !default;
 $table-bg-active:               $table-bg-hover !default;
 
 //** Border color for table and cell borders.
-$table-border-color:            #ddd !default;
+$table-border-color:            $gray-lighter !default;
 
 
 //== Buttons
@@ -149,9 +145,9 @@ $table-border-color:            #ddd !default;
 
 $btn-font-weight:                normal !default;
 
-$btn-default-color:              #333 !default;
-$btn-default-bg:                 #fff !default;
-$btn-default-border:             #ccc !default;
+$btn-default-color:              $gray !default;
+$btn-default-bg:                 $gray-lighter !default;
+$btn-default-border:             darken($btn-default-bg, 5%) !default;
 
 $btn-primary-color:              #fff !default;
 $btn-primary-bg:                 $brand-primary !default;
@@ -193,7 +189,7 @@ $input-bg-disabled:              $gray-lighter !default;
 //** Text color for ``s
 $input-color:                    $gray !default;
 //** `` border color
-$input-border:                   #ccc !default;
+$input-border:                   darken(#f8f8f8, 6.5%) !default;
 
 // TODO: Rename `$input-border-radius` to `$input-border-radius-base` in v4
 //** Default `.form-control` border radius
@@ -208,10 +204,10 @@ $input-border-radius-small:      $border-radius-small !default;
 $input-border-focus:             #66afe9 !default;
 
 //** Placeholder text color
-$input-color-placeholder:        #999 !default;
+$input-color-placeholder:        $gray-light !default;
 
 //** Default `.form-control` height
-$input-height-base:              ($line-height-computed + ($padding-base-vertical * 2) + 2) !default;
+$input-height-base:              ($line-height-computed + ($padding-base-vertical * 2) + 4) !default;
 //** Large `.form-control` height
 $input-height-large:             (ceil($font-size-large * $line-height-large) + ($padding-large-vertical * 2) + 2) !default;
 //** Small `.form-control` height
@@ -239,18 +235,18 @@ $cursor-disabled:                not-allowed !default;
 //** Background for the dropdown menu.
 $dropdown-bg:                    #fff !default;
 //** Dropdown menu `border-color`.
-$dropdown-border:                rgba(0,0,0,.15) !default;
+$dropdown-border:                $input-border !default;
 //** Dropdown menu `border-color` **for IE8**.
 $dropdown-fallback-border:       #ccc !default;
 //** Divider color for between dropdown items.
-$dropdown-divider-bg:            #e5e5e5 !default;
+$dropdown-divider-bg:            $gray-lighter !default;
 
 //** Dropdown link text color.
-$dropdown-link-color:            $gray-dark !default;
+$dropdown-link-color:            $gray-light !default;
 //** Hover color for dropdown links.
-$dropdown-link-hover-color:      darken($gray-dark, 5%) !default;
+$dropdown-link-hover-color:      $gray-dark !default;
 //** Hover background for dropdown links.
-$dropdown-link-hover-bg:         #f5f5f5 !default;
+$dropdown-link-hover-bg:         transparent !default;
 
 //** Active dropdown menu item text color.
 $dropdown-link-active-color:     $component-active-color !default;
@@ -258,7 +254,7 @@ $dropdown-link-active-color:     $component-active-color !default;
 $dropdown-link-active-bg:        $component-active-bg !default;
 
 //** Disabled dropdown menu item background color.
-$dropdown-link-disabled-color:   $gray-light !default;
+$dropdown-link-disabled-color:   $gray-lighter !default;
 
 //** Text color for headers within dropdown menus.
 $dropdown-header-color:          $gray-light !default;
@@ -311,7 +307,7 @@ $screen-desktop:             $screen-md-min !default;
 
 // Large screen / wide desktop
 //** Deprecated `$screen-lg` as of v3.0.1
-$screen-lg:                  1200px !default;
+$screen-lg:                  200px !default;
 $screen-lg-min:              $screen-lg !default;
 //** Deprecated `$screen-lg-desktop` as of v3.0.1
 $screen-lg-desktop:          $screen-lg-min !default;
@@ -369,54 +365,54 @@ $navbar-padding-horizontal:        floor(($grid-gutter-width / 2)) !default;
 $navbar-padding-vertical:          (($navbar-height - $line-height-computed) / 2) !default;
 $navbar-collapse-max-height:       340px !default;
 
-$navbar-default-color:             #777 !default;
+$navbar-default-color:             $text-color !default;
 $navbar-default-bg:                #f8f8f8 !default;
-$navbar-default-border:            darken($navbar-default-bg, 6.5%) !default;
+$navbar-default-border:            $input-border !default;
 
 // Navbar links
-$navbar-default-link-color:                #777 !default;
-$navbar-default-link-hover-color:          #333 !default;
+$navbar-default-link-color:                $gray-light !default;
+$navbar-default-link-hover-color:          $gray-dark !default;
 $navbar-default-link-hover-bg:             transparent !default;
-$navbar-default-link-active-color:         #555 !default;
-$navbar-default-link-active-bg:            darken($navbar-default-bg, 6.5%) !default;
-$navbar-default-link-disabled-color:       #ccc !default;
+$navbar-default-link-active-color:         $navbar-default-link-hover-color !default;
+$navbar-default-link-active-bg:            transparent !default;
+$navbar-default-link-disabled-color:       $gray-lighter !default;
 $navbar-default-link-disabled-bg:          transparent !default;
 
 // Navbar brand label
-$navbar-default-brand-color:               $navbar-default-link-color !default;
-$navbar-default-brand-hover-color:         darken($navbar-default-brand-color, 10%) !default;
+$navbar-default-brand-color:               $navbar-default-link-hover-color !default;
+$navbar-default-brand-hover-color:         $navbar-default-link-hover-color !default;
 $navbar-default-brand-hover-bg:            transparent !default;
 
 // Navbar toggle
-$navbar-default-toggle-hover-bg:           #ddd !default;
-$navbar-default-toggle-icon-bar-bg:        #888 !default;
-$navbar-default-toggle-border-color:       #ddd !default;
+$navbar-default-toggle-hover-bg:           #fff !default;
+$navbar-default-toggle-icon-bar-bg:        $gray-light !default;
+$navbar-default-toggle-border-color:       $gray-lighter !default;
 
 
 //=== Inverted navbar
 // Reset inverted navbar basics
-$navbar-inverse-color:                      lighten($gray-light, 15%) !default;
-$navbar-inverse-bg:                         #222 !default;
+$navbar-inverse-color:                      $gray-light !default;
+$navbar-inverse-bg:                         #fff !default;
 $navbar-inverse-border:                     darken($navbar-inverse-bg, 10%) !default;
 
 // Inverted navbar links
-$navbar-inverse-link-color:                 lighten($gray-light, 15%) !default;
-$navbar-inverse-link-hover-color:           #fff !default;
+$navbar-inverse-link-color:                 $gray-light !default;
+$navbar-inverse-link-hover-color:           $gray-dark !default;
 $navbar-inverse-link-hover-bg:              transparent !default;
 $navbar-inverse-link-active-color:          $navbar-inverse-link-hover-color !default;
-$navbar-inverse-link-active-bg:             darken($navbar-inverse-bg, 10%) !default;
-$navbar-inverse-link-disabled-color:        #444 !default;
+$navbar-inverse-link-active-bg:             transparent !default;
+$navbar-inverse-link-disabled-color:        $gray-lighter !default;
 $navbar-inverse-link-disabled-bg:           transparent !default;
 
 // Inverted navbar brand label
 $navbar-inverse-brand-color:                $navbar-inverse-link-color !default;
-$navbar-inverse-brand-hover-color:          #fff !default;
+$navbar-inverse-brand-hover-color:          $navbar-inverse-link-hover-color !default;
 $navbar-inverse-brand-hover-bg:             transparent !default;
 
 // Inverted navbar toggle
-$navbar-inverse-toggle-hover-bg:            #333 !default;
-$navbar-inverse-toggle-icon-bar-bg:         #fff !default;
-$navbar-inverse-toggle-border-color:        #333 !default;
+$navbar-inverse-toggle-hover-bg:            $gray-lighter !default;
+$navbar-inverse-toggle-icon-bar-bg:         $gray-light !default;
+$navbar-inverse-toggle-border-color:        $gray-lighter !default;
 
 
 //== Navs
@@ -425,21 +421,21 @@ $navbar-inverse-toggle-border-color:        #333 !default;
 
 //=== Shared nav styles
 $nav-link-padding:                          10px 15px !default;
-$nav-link-hover-bg:                         $gray-lighter !default;
+$nav-link-hover-bg:                         #fff !default;
 
 $nav-disabled-link-color:                   $gray-light !default;
 $nav-disabled-link-hover-color:             $gray-light !default;
 
 //== Tabs
-$nav-tabs-border-color:                     #ddd !default;
+$nav-tabs-border-color:                     $navbar-default-border !default;
 
 $nav-tabs-link-hover-border-color:          $gray-lighter !default;
 
-$nav-tabs-active-link-hover-bg:             $body-bg !default;
+$nav-tabs-active-link-hover-bg:             #fff !default;
 $nav-tabs-active-link-hover-color:          $gray !default;
-$nav-tabs-active-link-hover-border-color:   #ddd !default;
+$nav-tabs-active-link-hover-border-color:   $nav-tabs-border-color !default;
 
-$nav-tabs-justified-link-border-color:            #ddd !default;
+$nav-tabs-justified-link-border-color:            $nav-tabs-border-color !default;
 $nav-tabs-justified-active-link-border-color:     $body-bg !default;
 
 //== Pills
@@ -452,21 +448,21 @@ $nav-pills-active-link-hover-color:         $component-active-color !default;
 //
 //##
 
-$pagination-color:                     $link-color !default;
-$pagination-bg:                        #fff !default;
-$pagination-border:                    #ddd !default;
+$pagination-color:                     $btn-default-color !default;
+$pagination-bg:                        $btn-default-bg !default;
+$pagination-border:                    $btn-default-border !default;
 
-$pagination-hover-color:               $link-hover-color !default;
-$pagination-hover-bg:                  $gray-lighter !default;
-$pagination-hover-border:              #ddd !default;
+$pagination-hover-color:               $pagination-color !default;
+$pagination-hover-bg:                  $pagination-bg !default;
+$pagination-hover-border:              $pagination-border !default;
 
 $pagination-active-color:              #fff !default;
 $pagination-active-bg:                 $brand-primary !default;
-$pagination-active-border:             $brand-primary !default;
+$pagination-active-border:             $btn-primary-border !default;
 
 $pagination-disabled-color:            $gray-light !default;
-$pagination-disabled-bg:               #fff !default;
-$pagination-disabled-border:           #ddd !default;
+$pagination-disabled-bg:               $pagination-bg !default;
+$pagination-disabled-border:           $pagination-border !default;
 
 
 //== Pager
@@ -491,7 +487,7 @@ $pager-disabled-color:                 $pagination-disabled-color !default;
 
 $jumbotron-padding:              30px !default;
 $jumbotron-color:                inherit !default;
-$jumbotron-bg:                   $gray-lighter !default;
+$jumbotron-bg:                   #fafafa !default;
 $jumbotron-heading-color:        inherit !default;
 $jumbotron-font-size:            ceil(($font-size-base * 1.5)) !default;
 $jumbotron-heading-font-size:    ceil(($font-size-base * 4.5)) !default;
@@ -501,21 +497,21 @@ $jumbotron-heading-font-size:    ceil(($font-size-base * 4.5)) !default;
 //
 //## Define colors for form feedback states and, by default, alerts.
 
-$state-success-text:             #3c763d !default;
-$state-success-bg:               #dff0d8 !default;
-$state-success-border:           darken(adjust-hue($state-success-bg, -10), 5%) !default;
+$state-success-text:             #fff !default;
+$state-success-bg:               $brand-success !default;
+$state-success-border:           darken($state-success-bg, 4%) !default;
 
-$state-info-text:                #31708f !default;
-$state-info-bg:                  #d9edf7 !default;
-$state-info-border:              darken(adjust-hue($state-info-bg, -10), 7%) !default;
+$state-info-text:                #fff !default;
+$state-info-bg:                  $brand-info !default;
+$state-info-border:              darken($state-info-bg, 12%) !default;
 
-$state-warning-text:             #8a6d3b !default;
-$state-warning-bg:               #fcf8e3 !default;
-$state-warning-border:           darken(adjust-hue($state-warning-bg, -10), 5%) !default;
+$state-warning-text:             #fff !default;
+$state-warning-bg:               $brand-warning !default;
+$state-warning-border:           darken($state-warning-bg, 5%) !default;
 
-$state-danger-text:              #a94442 !default;
-$state-danger-bg:                #f2dede !default;
-$state-danger-border:            darken(adjust-hue($state-danger-bg, -10), 5%) !default;
+$state-danger-text:              #fff !default;
+$state-danger-bg:                $brand-danger !default;
+$state-danger-border:            darken($state-danger-bg, 10%) !default;
 
 
 //== Tooltips
@@ -560,7 +556,7 @@ $popover-arrow-color:                 $popover-bg !default;
 //** Popover outer arrow width
 $popover-arrow-outer-width:           ($popover-arrow-width + 1) !default;
 //** Popover outer arrow color
-$popover-arrow-outer-color:           fade_in($popover-border-color, 0.05) !default;
+$popover-arrow-outer-color:           fadein($popover-border-color, 5%) !default;
 //** Popover outer arrow fallback color
 $popover-arrow-outer-fallback-color:  darken($popover-fallback-border-color, 20%) !default;
 
@@ -593,7 +589,7 @@ $label-link-hover-color:      #fff !default;
 //##
 
 //** Padding applied to the modal body
-$modal-inner-padding:         15px !default;
+$modal-inner-padding:         20px !default;
 
 //** Padding applied to the modal title
 $modal-title-padding:         15px !default;
@@ -603,9 +599,9 @@ $modal-title-line-height:     $line-height-base !default;
 //** Background color of modal content area
 $modal-content-bg:                             #fff !default;
 //** Modal content border color
-$modal-content-border-color:                   rgba(0,0,0,.2) !default;
+$modal-content-border-color:                   rgba(0,0,0,.05) !default;
 //** Modal content border color **for IE8**
-$modal-content-fallback-border-color:          #999 !default;
+$modal-content-fallback-border-color:          $gray-lighter !default;
 
 //** Modal backdrop background color
 $modal-backdrop-bg:           #000 !default;
@@ -651,7 +647,7 @@ $alert-danger-border:         $state-danger-border !default;
 //##
 
 //** Background color of the whole progress component
-$progress-bg:                 #f5f5f5 !default;
+$progress-bg:                 $jumbotron-bg !default;
 //** Progress bar text color
 $progress-bar-color:          #fff !default;
 //** Variable for setting rounded corners on progress bar.
@@ -676,7 +672,7 @@ $progress-bar-info-bg:        $brand-info !default;
 //** Background color on `.list-group-item`
 $list-group-bg:                 #fff !default;
 //** `.list-group-item` border color
-$list-group-border:             #ddd !default;
+$list-group-border:             $gray-lighter !default;
 //** List group border radius
 $list-group-border-radius:      $border-radius-base !default;
 
@@ -684,9 +680,9 @@ $list-group-border-radius:      $border-radius-base !default;
 $list-group-hover-bg:           #f5f5f5 !default;
 //** Text color of active list items
 $list-group-active-color:       $component-active-color !default;
-//** Background color of active list items
+//** Background color of active list elements
 $list-group-active-bg:          $component-active-bg !default;
-//** Border color of active list elements
+//** Background color of active list items
 $list-group-active-border:      $list-group-active-bg !default;
 //** Text color for content within active list items
 $list-group-active-text-color:  lighten($list-group-active-bg, 40%) !default;
@@ -714,31 +710,31 @@ $panel-footer-padding:        $panel-heading-padding !default;
 $panel-border-radius:         $border-radius-base !default;
 
 //** Border color for elements within panels
-$panel-inner-border:          #ddd !default;
+$panel-inner-border:          transparent !default;
 $panel-footer-bg:             #f5f5f5 !default;
 
 $panel-default-text:          $gray-dark !default;
-$panel-default-border:        #ddd !default;
+$panel-default-border:        transparent !default;
 $panel-default-heading-bg:    #f5f5f5 !default;
 
 $panel-primary-text:          #fff !default;
-$panel-primary-border:        $brand-primary !default;
+$panel-primary-border:        transparent !default;
 $panel-primary-heading-bg:    $brand-primary !default;
 
 $panel-success-text:          $state-success-text !default;
-$panel-success-border:        $state-success-border !default;
+$panel-success-border:        transparent !default;
 $panel-success-heading-bg:    $state-success-bg !default;
 
 $panel-info-text:             $state-info-text !default;
-$panel-info-border:           $state-info-border !default;
+$panel-info-border:           transparent !default;
 $panel-info-heading-bg:       $state-info-bg !default;
 
 $panel-warning-text:          $state-warning-text !default;
-$panel-warning-border:        $state-warning-border !default;
+$panel-warning-border:        transparent !default;
 $panel-warning-heading-bg:    $state-warning-bg !default;
 
 $panel-danger-text:           $state-danger-text !default;
-$panel-danger-border:         $state-danger-border !default;
+$panel-danger-border:         transparent !default;
 $panel-danger-heading-bg:     $state-danger-bg !default;
 
 
@@ -751,7 +747,7 @@ $thumbnail-padding:           4px !default;
 //** Thumbnail background color
 $thumbnail-bg:                $body-bg !default;
 //** Thumbnail border color
-$thumbnail-border:            #ddd !default;
+$thumbnail-border:            $gray-lighter !default;
 //** Thumbnail border radius
 $thumbnail-border-radius:     $border-radius-base !default;
 
@@ -765,7 +761,7 @@ $thumbnail-caption-padding:   9px !default;
 //
 //##
 
-$well-bg:                     #f5f5f5 !default;
+$well-bg:                     $jumbotron-bg !default;
 $well-border:                 darken($well-bg, 7%) !default;
 
 
@@ -776,14 +772,14 @@ $well-border:                 darken($well-bg, 7%) !default;
 $badge-color:                 #fff !default;
 //** Linked badge text color on hover
 $badge-link-hover-color:      #fff !default;
-$badge-bg:                    $gray-light !default;
+$badge-bg:                    $brand-primary !default;
 
 //** Badge text color in active nav link
 $badge-active-color:          $link-color !default;
 //** Badge background color in active nav link
 $badge-active-bg:             #fff !default;
 
-$badge-font-weight:           bold !default;
+$badge-font-weight:           normal !default;
 $badge-line-height:           1 !default;
 $badge-border-radius:         10px !default;
 
@@ -795,13 +791,13 @@ $badge-border-radius:         10px !default;
 $breadcrumb-padding-vertical:   8px !default;
 $breadcrumb-padding-horizontal: 15px !default;
 //** Breadcrumb background color
-$breadcrumb-bg:                 #f5f5f5 !default;
+$breadcrumb-bg:                 $well-bg !default;
 //** Breadcrumb text color
-$breadcrumb-color:              #ccc !default;
+$breadcrumb-color:              $gray-light !default;
 //** Text color of current page in the breadcrumb
 $breadcrumb-active-color:       $gray-light !default;
 //** Textual separator for between breadcrumb elements
-$breadcrumb-separator:          "/" !default;
+$breadcrumb-separator:          ">" !default;
 
 
 //== Carousel
@@ -812,7 +808,7 @@ $carousel-text-shadow:                        0 1px 2px rgba(0,0,0,.6) !default;
 
 $carousel-control-color:                      #fff !default;
 $carousel-control-width:                      15% !default;
-$carousel-control-opacity:                    .5 !default;
+$carousel-control-opacity:                    .7 !default;
 $carousel-control-font-size:                  20px !default;
 
 $carousel-indicator-active-bg:                #fff !default;
@@ -826,7 +822,7 @@ $carousel-caption-color:                      #fff !default;
 //##
 
 $close-font-weight:           bold !default;
-$close-color:                 #000 !default;
+$close-color:                 #fff !default;
 $close-text-shadow:           0 1px 0 #fff !default;
 
 
diff --git a/css/main.scss b/css/main.scss
index a0371ab7c68..335d391489f 100644
--- a/css/main.scss
+++ b/css/main.scss
@@ -9,20 +9,38 @@ img { margin-bottom: 24px;
 }
 
 
+h1, h2, h3, h4, h5, h6 {
+  color:#333333;
+}
+
+
+
 body {
 	padding-top: 70px;
+	color:#333333;
+}
+
+footer p {
+  color: #333333;
 }
 
+
 figcaption {
     text-align: right;
     margin-top: -20px;
     margin-bottom: 20px;
+	
 }
 
 
 
 /* Top navigation bar */
 
+.navbar-header > li{
+  margin-top:40px;
+  margin-bottom:20px;
+}
+
 
 p.byline {
 	text-align: center;
@@ -30,20 +48,24 @@ p.byline {
 	line-height: 36px;
 	margin-top: -24px;
 	margin-bottom: 48px;
+
 }
 
 
 pubtit {
 	font-weight: bold;
+
 }
 
 firstp {
 }
 
 .container-fluid {
+  margin-top: auto;
   margin-right: auto;
   margin-left: auto;
-  max-width: 1000px; /* or 950px */
+  max-width: 1200px; /* or 950px */
+
 }
 
 /* Home, News */
@@ -60,11 +82,33 @@ firstp {
 	margin-bottom: 6px;
 }
 
+#research_contentid figure {
+	display: block; 
+	float: right;
+	margin: 0.5em;
+	padding: 0.5em;
+}
+
+#research_contentid img {
+	width: 100%; 
+	float: center; 
+	border: 10px;
+}
+
+#research_contentid figcaption {
+	caption-side: bottom;
+	font-style: italic;
+	float: center;
+	width: 100%;
+	text-align: 
+	justify;text-indent: 0;
+}
+
 /* Team & Publications */
 #gridid img { margin: 16px 22px 6px 0; border-radius:10%; box-shadow: 2px 2px 5px #888888 }
 #homeid img { margin: 0 0 0 0; border-radius:5%; box-shadow: 0px 0px 0px #888888 }
 #picid img { margin: 6px 3px 60px 6px; border-radius:1%; box-shadow: 2px 2px 5px #888888 }
-#gridid .row { margin-bottom: 24px; }
+#gridid .row { margin-bottom: 8px; }
 
 
 /* Grid overrides */
@@ -81,13 +125,13 @@ firstp {
 }
 
 
-/* Carusel */
+/* Carousel */
 
 .carousel {
     border-radius: 3px 3px 3px 3px;
-    margin-bottom: 20px;
-    margin-top: 20px;
-    margin-left: 30px;
-    margin-right: 30px;
+    margin-bottom: 10px;
+    margin-top: 10px;
+    margin-left: 0px;
+    margin-right: 0px;
 }
 
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diff --git a/temp_members/charlotte.md b/temp_members/charlotte.md
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+++ b/temp_members/charlotte.md
@@ -0,0 +1,15 @@
+---
+fullname: Charlotte Imianowski
+layout: members
+position: Doctoral Scientist
+tier: d
+picture: charlotte.jpg 
+email: cji27@cam.ac.uk 
+pubmed_searchterm: imianowski cj [author] 
+---
+
+Charlotte graduated in 2016 with a BA in Cell and Systems Biology from the University of Oxford. Her research involved interrogating the function of a tumour suppressor gene in colorectal cancer.
+
+Subsequently, she worked as a Research Assistant in Professor Bass Hassan’s group at the Sir William Dunn School of Pathology, University of Oxford. Her projects have included validating a CRISPR-Cas9 approach to target a gene of interest in Ewing’s Sarcoma, and developing a method for diagnosing Ewing’s Sarcoma using liquid biopsies.
+
+Charlotte is now undertaking a PhD in Rahul Roychoudhuri’s lab, studying inhibitory mechanisms that restrict NK cell function within tumours.
diff --git a/temp_members/firas.md b/temp_members/firas.md
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index 00000000000..5e88e406cba
--- /dev/null
+++ b/temp_members/firas.md
@@ -0,0 +1,13 @@
+---
+fullname: Firas Sadiyah
+layout: members
+position: Doctoral Scientist
+tier: d
+picture: firas.jpg
+email: firas.sadiyah@babraham.ac.uk
+pubmed_searchterm: sadiyah mf [author]
+---
+
+Firas gained an MSc in Biotechnology from Hanover Medical School (MHH) where he studied the molecular regulation of haematopoietic stem cell differentiation. Firas moved to the USA to continue this work as a research scholar at University of California in San Francisco (UCSF). At UCSF, Firas' research elucidated lineage-specific roles of key oncogenic proteins in acute lymphoblastic leukaemia (ALL) and chronic myeloid leukaemia (CML).
+
+Firas is now in Rahul Roychoudhuri’s group at the Babraham Institute, investigating how long range enhancer-promoter interactions drive cell-fate decisions within the CD4+ T cell lineage to dictate the outcome of immune responses. 
\ No newline at end of file
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+++ b/temp_members/jingru.md
@@ -0,0 +1,11 @@
+---
+fullname: Jingru Xu
+layout: members
+position: Master's intern
+tier: f
+picture: placeholder-person.jpg
+email: jx292@cam.ac.uk 
+pubmed_searchterm: 
+---
+
+Incomplete
\ No newline at end of file