The Earth Microbiome Project

The Earth Microbiome Project (EMP) is a proposed massively multidisciplinary effort to analyze microbial communities across the globe from many environments.  The first EMP Conference is scheduled for June 2011 in Shenzhen, China.  The goal is to understand microbes (Bacterial, Archaeal, Eukaryal and Viral) in terms of whom they are and what they do; it is the grand challenge of microbial ecology.  Read more at the Earth Microbiome Project website.

How Pathogenic Bacteria Hide Inside Host Cells

A new study into Staphylococcus aureus, the bacterium which is responsible for severe chronic infections worldwide, reveals how the bacteria have developed a strategy of hiding within host cells to escape the immune system as well as many antibacterial treatments. The research, published by EMBO Molecular Medicine, demonstrates how ‘phenotype switching’ enables bacteria to adapt to their environmental conditions, lie dormant inside host cells and become a reservoir for relapsing infections.

Scientists Reconstruct a Bacterial Transport Channel in a Test Tube

ScienceDaily (June 14, 2010) — For a successful infection, bacteria must outwit the immune system of the host. To this aim, they deliver so-called virulence factors through a transport channel located in the bacterial membrane. In some bacteria this transport channel is formed like a syringe, enabling them to inject virulence factors directly into the host cell. Scientists from the Max Planck Society and the Federal Institute for Materials Research and Testing have now succeeded for the first time in elucidating basic principles of the assembly of this transport channel. This is an important starting point for the development of new drugs that might interfere considerably earlier than antibiotics in the course of infection. The research is published in Nature Structural & Molecular Biology.

Recommended Readings: Howard Hang, Ph.D. May 17, 2010

Monday Seminar Series

Discovery of Bacterial Virulence Inhibitors

From Plant Extracts

Howard Hang, Ph.D.,


Laboratory of Chemical Biology and Microbial Pathogenesis

May 17, 2010

3:45 p.m.-5:00 p.m.  Welch Hall Level two

Recommended Articles:

 Aiello D;  Williams JD; Majgier-Baranowska H, et al.   2010.  Discovery and Characterization of Inhibitors of Pseudomonas aeruginosa Type III Secretion ANTIMICROBIAL AGENTS AND CHEMOTHERAPY   54(5): 1988-1999   

Rasko DA; Sperandio V.   2010.  Anti-virulence strategies to combat bacteria-mediated disease .  NATURE REVIEWS DRUG DISCOVERY    9 (2): 117-128   

 Veenendaal AKJ;  Sundin C;  Blocker AJ.  2010.  Small-Molecule Type III Secretion System Inhibitors Block Assembly of the Shigella Type III Secreton .    JOURNAL OF BACTERIOLOGY     191(2):563-570   

 Pan NJ, Brady MJ, Leong JM, et al.   2009.  Targeting Type III Secretion in Yersinia pestis.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY     53(2): 385-392  

Raghavan AS, Hang HC .  2009  Seeing small molecules in action with bioorthogonal chemistry .  2009.
 DRUG DISCOVERY TODAY    14(3-4): 178-184    Request from Markus Library.

 Doring O;  Luthje S.   2001.  Inhibition of trans-membrane hexacyanoferrate III reductase activity and proton secretion of maize (Zea mays L.) roots by thenoyltrifluoroacetone .    PROTOPLASMA   217(1-3): 3-8      Request  from Markus Library.

Recommended Readings: Sean F. Brady Ph.D. May 10, 2010

Monday Seminar Series

Culture Independent Approaches for the

Discvoery of New Bacterial Metabolites

Sean F. Bady  Ph.D.,

Laboratory of Geneticall Encoded Small Molecules

Howard Hughes Medical Institute, The Rockefeller University

May 10, 2010

3:45 p.m.-5:00 p.m.  Welch Hall Level two


Recommended Articles:

 Simon, C;  Daniel, R.   2009.  Achievements and new knowledge unraveled by metagenomic approaches.  APPLIED MICROBIOLOGY AND BIOTECHNOLOGY    85(2): 265-276     Request from Markus Library.

 McAlpine, J. B.    2009.  Advances in the Understanding and Use of the Genomic Base of Microbial Secondary Metabolite Biosynthesis for the Discovery of New Natural Products.   JOURNAL OF NATURAL PRODUCTS,   72(3, Sp. Iss. SI): 566-572      Request from Markus Library.   

 Brady S.F; Simmons L;  Kim J.H. et al.   2009.  Metagenomic approaches to natural products from free-living and symbiotic organisms .   NATURAL PRODUCT REPORTS.    26(11): 1488-1503    Request from Markus Library.

 King, R. W.; Bauer, J. D.; Brady, S.F.    2009.  An Environmental DNA-Derived Type II Polyketide Biosynthetic Pathway Encodes the Biosynthesis of the Pentacyclic Polyketide ErdacinANGEWANDTE CHEMIE-INTERNATIONAL EDITION     48( 34): 6257-6261    

 Banik, J J; Brady, S. F.    2008.  Cloning and characterization of new glycopeptide gene clusters found in an environmental DNA megalibrary .  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.     105(45):17273-17277    

 Sharma P;  Kumari, H;  Kumar, M; Verna, M;  KUmariu K;  Malhotra, S;  Kurana, J; Lal, R.  2008.   From bacterial genomics to metagenomics: concept, tools and recent advances.   Indian Journal of Microbiology.  48(2);173-194.  Requesst from Markus Library.

  Brady SF, Bauer JD, Clarke-Pearson MF, et al.   2007. Natural products from isnA-containing biosynthetic gene clusters recovered from the genomes of cultured and uncultured bacteria.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.   129( 40): 12102-+    





Recommended Readings: David Levy, Ph.D

Friday Lecture Series

Non-canonical Functions of STAT3

David Levy, Ph.D., D.Ch.

Dr. Louis A. Schneider Professor of Molecular Pathology, New York University

March 26, 2010

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Gough DJ,* Corlett A,* Schlessinger K, Wegrezyn J, Larner AC, Levy DE. Mitochondrial Stat3 Supports Ras-Dependent Oncogenic Transformation. Science. 2009 Jun 26; 324(5935): 1713-16

Chou WC, Levy DE, Lee CK. STAT3 positively regulates an early step in B-cell development. Blood. 2006; 108: 3005–11

Chiarle R, Simmons WJ, Cai H, Dhall G, Zamo A, Raz R, Karras J, Levy DE, Inghirami G. Stat3 is required for ALK-mediated lymphomagenesis and provides a viable therapeutic target. Nature Med. 2005; 11: 623–9

Schlessinger K, Levy DE. Malignant transformation but not normal cell growth depend on STAT3. Cancer Res. 2005; 65: 5828–34

Gimeno R, Lee CK, Schindler C, Levy DE. Stat1 and Stat2 but not Stat3 Arbitrate Contradictory Growth Signals Elicited by alpha/beta Interferon in T Lymphocytes. Mol. Cell. Biol. 2005; 25: 5456–65

Changes in Gut Microbiota Linked to Obesity and Metabolic Syndrome

A study published online March 4, 2010 in Science Express reports the discovery that gut microbes may alter behavior and promote obesity and metabolic syndrome.  HHMI investigator Rob Knight at the University of Colorado did the analysis that led to this conclusion.  His study also showed that these bacteria may be transmissible between people.

Recommended Readings: Nicole Clay, Ph.D. Feb 8, 2010

Monday Lecture Series

MAMP-Activated Innate Immunity in Arabidopsis:

The Pathogen Recognition and Chemical Defense Systems

Nicole Clay, Ph.D.,

Post Doctoral Fellow, Department of Genetics, Harvard Medical School

Department of Molecular Biology, Massachusetts General Hospital

February 8, 2010

Welch Hall,  Level Two

4:00 p.m.-5:00 p.m

Recommended Review:

Chisholm ST; Coaker G; Day B; Staskawicz BJ.   2006.  Host-microbe interactions: Shaping the evolution of the plant immune response. CELL 124(4): 803-814

Recommended Articles:

Tsuda K;  Sato M; Stoddard T; Glazebrook J; Katagiri F.   2009.   Network Properties of Robust Immunity in Plants. PLOS GENETICS 5(12):article Number: e1000772

Saijo Y ;Tintor N; Lu XL; Rauf P; Pajerowska-Mukhtar K; Haweker H; Dong XN ; Robatzek S; Schulze-Lefert P.   2009.  Receptor quality control in the endoplasmic reticulum for plant innate immunity. EMBO JOURNAL 28(21):3439- 3449

Boller T, Felix G .  2009.  A Renaissance of Elicitors: Perception of Microbe-Associated Molecular Patterns and Danger Signals by Pattern-Recognition Receptors. ANNUAL REVIEW OF PLANT BIOLOGY 60: 379-406

Aslam SN, Erbs G, Morrissey KL, et al.  2009.  Microbe-associated molecular pattern (MAMP) signatures, synergy, size and charge: influences on perception or mobility and host defence responsesMOLECULAR PLANT PATHOLOGY 10(3):375-387

Miyashita M, Miyagawa H.  2008.  Plant pathogen recognition as a natural, original and simple model for chemogenomics: A brief overview of cell-based assays to screen for peptides acting as plant defense activators.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING 11(8): 647-652    Request from Markus Library

Chinchilla D; Bauer Z; Regenass M; Boller T; Felix G.  2006.   The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception. PLANT CELL 18(2): 465-476

Asai T.; Tena G; Plotnikova J; Wilmann MR; Chiu WL; Gomez-Gomez L: Boller T; Ausubel FM; Sheen j.  2002.  MAP kinase signaling cascade in Arabidopsis innate immunity. NATURE 415(6875):977-983

Recommended Readings: George A. M. Cross Ph.D. Monday Dec. 14, 2009

Monday Lecture


Daring to be Different: Unusual Aspects of Gene

Transcription in Trypanosomes

George A. M. Cross Ph.D

André and Bella Meyer Professor
Laboratory of Molecular Parasitology

The Rockefeller University

Dec. 14, 2009

Welch Hall, Level Two  4 p.m.

Recommended Articles:

Figueiredo LM, Cross GAM, Janzen CJ .  2009.  Epigenetic regulation in African trypanosomes: a new kid on the block. NATURE REVIEWS. Microbiology.    7(7): 504-513    

Siegel TN, Hekstra DR, Kemp LE, et al.   2009.  Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei .   GENES & DEVELOPMENT.   23(9): 1063-1076    

Talbert PB, Henikoff S. 2009.  Chromatin-based transcriptional punctuation . GENES & DEVELOPMENT    23(9): 1037-1041   

Ibrahim, B. Syed;  Kanneganti, Nalini;  Rieckhof, Gabrielle E.; Das, Anish;  Laurents, Douglas V.; Palenchar, Jennifer B.;  Bellofatto, Vivian;  Wah, David A.   2009.   Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei. 2009.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA .   106 (32): 13242-13247   

Haenni S, Studer E, Burkard GS, et al. 2009.  Bidirectional silencing of RNA polymerase I transcription by a strand switch region in Trypanosoma bruceiNUCLEIC ACIDS RESEARCH   37(15): 5007-5018   

Koumandou VL, Natesan SKA, Sergeenko T, et al.  2008.  The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages.   BMC GENOMICS    9: Article Number 298    

Das, A; Banday, M; Bellofatto, V.    2008.  RNA polymerase transcription machinery in trypanosomes Eukaryotic Cell.   7:429-434

Siegel, TN; Tan, KS; Cross, GAM.  2005.  Systematic study of sequence motifs for RNA trasn-splicing in Trypanosoma brucei.  Molecular and Cellular Biology.  25:9586-9594

Recommended Readings: Jean-Laurent Casanova, M.D., Ph.D.

Friday Lecture Series:

M.D.-Ph.D. Recruitment Lecture

Two Kindreds with X-linked Recessive Mycobacterial Disease: Toward a Genetic Theory of Infectious Diseases

Jean-Laurent Casanova, M.D.,  Ph.D.

professor and head, Laboratory of Human Genetics of Infectious Diseases, Rockefeller University

November 20, 2009

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Articles:

Bustamante, J., S. Boisson-Dupuis, E. Jouanguy, C. Picard, A. Puel, L. Abel, and J. -L Casanova. 2008. Novel primary immunodeficiencies revealed by the investigation of paediatric infectious diseases. Current opinion in immunology 20, (1): 39-48

Casanova, J. -L, and L. Abel. 2007. Primary immunodeficiencies: A field in its infancy. Science 317, (5838): 617-619

Maródi, L., and J. -L Casanova. 2009. Primary immunodeficiency diseases: The J project. The Lancet 373, (9682): 2179-2181

Quintana-Murci, L., A. Alcaïs, L. Abel, and J. -L Casanova. 2007. Immunology in natura: Clinical, epidemiological and evolutionary genetics of infectious diseases. Nature immunology 8, (11): 1165-1171

Von Bernuth, H., C. Picard, Z. Jin, R. Pankla, H. Xiao, C. -L Ku, M. Chrabieh, et al. 2008. Pyogenic bacterial infections in humans with MyD88 deficiency. Science 321, (5889): 691-696