Tuesday, May 27, 2014


Tuesday May 27th
NRT LG 503/504  (across the lobby from Aresty) - Health Sciences Campus

1:45-2  meet and greet
2-5 presentations
5:15-6 mingling and questions

2:00   Jim Knowles   “Single Cell RNA Sequencing of Neurons”

2:25  Charles Nicolet  “Overview of the Next Gen Sequencing Core”

2:40  Lora Barsky  “Overview of the Flow Cytometry Core”

3:10  Fluidigm  “Defy the law of averages:  Fluidigm’s Biomark* and C1 single cell auto prep systems”

2:55 Daniel Campo “Single Cell Sequencing Experiences at UPC”

3:45 Clontech, Rachel Fish “V3 SMARTer for Single Cell RNA Seq”

4:00 NuGen “Target Enrichment and sequencing of captured circulating tumor cells”

4:15 Qiagen

4:30 Nanostring*

4:45  Fluidigm CyTOF

*Technologies currently available in the Molecular Genomics Core

Refreshments Generously Provided by Fluidigm

Note that there are a few minutes before and more time afterwards to ask questions, gather materials and speak to the vendors and application scientists, and snack.

To all MEB, GeoBio and Earth Sci

When: 1100 am Monday 2 June 2014
Where: Torrey Webb Room/ AHF


Microbialite genetic diversity and N cycling
Luisa I Falcón
Bacterial Ecology Lab., Institute of Ecology, UNAM

Microbialites have played an important role in the early history of life on Earth with fossilized forms representing the oldest evidence of life on our planet dating back to 3500 Ma. Extant microbialites have been suggested to be highly productive and diverse communities with an evident role in the cycling of major elements, and in contributing to carbonate precipitation. We have analyzed microbial genetic diversity of microbialites living in different types of environments throughout Mexico, including desert ponds, coastal lagoons and crater-lakes. Microbialite communities are very diverse (H = 6–7) and show geographic variation in composition, as well as an environmental effect related to pH and conductivity, which together explain 33% of the genetic variation. N cycle pathways including N2 fixation, nitrification, denitrification and anammox are evident in the potential community, but only N2 fixation by heterocyst-forming Cyanobacteria within Nostocales are actively transcribed. Our studies suggest that N limitation in the environment strongly favors autotrophy and diazotrophy and restricts remineralization pathways via denitrification and anammox. Cyanobacteria that form heterocysts and are actively transcribing for N2 fixation, are fundamental players in microbialites since they are responsible for providing reduced N –amides, C in lipids and carbohydrates, and host in their external cell membranes the main sites of carbonate mineral precipitation.

5th International Course in Microbial Ecology, Venice (Italy)

Dear Microbial Ecologist,

We are proud to announce the 5th International Course in Microbial Ecology, this year entitled “Deciphering microbial diversity and function in the environment through Next Generation Sequencing” (October 6-10, 2014), which will take place at the Institute of Marine Science, National Research Council in the old town centre of Venice, Italy.

The course builds on the successes of the four previous courses (former “SItEmicro Course in Microbial Ecology”) and is dedicated to advanced master students, PhD students, post-docs and young researchers interested in aquatic and terrestrial microbial ecology, and in bioinformatics. The course will focus on the use of next generation sequencing datasets for the study of microbial communities, under the guide of experienced international researchers. Participation is limited to 30 applicants.

The course will train microbial ecologists in the analysis of the structure and function of environmental microbial communities by using molecular tools. The techniques covered include sample collection and processing, DNA extraction, PCR of ribosomal genes, quanti­fication/analysis of environmental DNA, amplicon (marker gene) data generation and analysis using different tools (QIIME, Mothur) and metagenomics.

Detailed information is provided in the flyer attached to this email, and at the official webpage of the course: www.microbeco.org. Updates on the registration procedures, the selection of the successful applications, the final program and preliminary materials for the course will be periodically published on the website and on the next numbers of the SM Newsletter.

We look forward in seeing you in Venice.


The Organizing Committee
Gian Marco Luna
Stefano Amalfitano
Manuela Coci
Gianluca Corno