Give Yourself the ABRF 2015 Annual Meeting For the Holidays

By: Kevin Knudtson

Chair, ABRF 2015 Program Committee

As the holidays near ABRFer’s have two things on their minds: choosing what new instrument their institution will place in their lab for Christmas and the ABRF Annual Meeting.  While I cannot tell you what new toy to place in your lab, I can tell you why you should not miss the ABRF 2015 Annual Meeting (!

Enrich your career with this year’s theme, “Integrative Technologies for Advancing Scientific Cores”.  The ABRF 2015 Annual Meeting will be held on March 28th-31st at the America’s Convention Center in the heart of downtown St. Louis.  The Renaissance Grand Hotel, located just across the street from the convention center, is the official conference hotel.  Its central location will place you near the many downtown attractions, restaurants and shops. St. Louis is filled with exciting networking opportunities for those who may consider arriving early or staying late, such as:

  • Celebrate the St. Louis Gateway Arch 50th anniversary with friends
  • Meet old and new collaborators for frozen custard or gooey cakes
  • Enjoy a St. Louis style pizza and beer with your colleagues

The program starts with three fantastic satellite workshops on Saturday, March 28th. Continue reading

The New ABRF’s Metagenomic Research Group (MGRG) and the Extreme Microbiome Project

By Scott Tighe, MGRG ChairMicrobiome Project

Metagenomics and microbiome studies seem to be popping up everywhere. In response to this rapidly growing field, the ABRF has organized a new research group called the Metagenomics Research Group, or MGRG, for short. The group is chaired by Scott Tighe from the University of Vermont who previously served as Chair of the NARG, FCRG, and coordinator for the ongoing NGS study. The current membership of the MGRG is impressive to say the least, with backgrounds in microbiology, genetics, bioinformatics, oceanography, climate research, and more.   ”With such a dynamic multidisciplinary field, I decided to go for the gusto and get the best members I could find; in fact a large percentage of the membership have been involved with microbiome studies for up to two decades.”  Said Scott.  The current  members include  Scott Tighe (Univ of Vermont), Kelley Thomas (UNH), Matt Settles (Univ of Idaho), Ken McGrath (AGRF-Brisbane Australia), Shawn Levy (Hudson Alpha), Nathan Biven (Univ of Missouri), Chris Mason (Weill Cornell), Darryl Reeves (Weill Cornell), Stefan Green (UIC), Natalia Reyero (Mississippi St.), Russ Carmical (BCM), Don Baldwin (Pathonomics), Samantha Joye (Univ of Georgia), Nadim Ajami (BCM), Ebrahim Afshinnekoo (Weill Cornell), Jodie Lee (ATCC) and Tim Hunter (Univ of Vermont),  is the executive board liaison.

Two projects are presently underway by the new MGRG.  The first is an effort to create a cellular-based bacterial standard and the second is the Extreme Microbiome Project (XMP). The development of the bacterial standard builds off of previous work by the nucleic acids research group (NARG) in 2013 which assembled an ethanol-fixed intact microbial community standard with known numbers and types of bacteria used for DNA extraction efficiency studies. Although the MGRG is assembling a similar standard, it will be more refined and include fewer microbial species of varying GC content and Class I genomes. Standards with Class II and Class III genomes will be developed at a later time. The development of the bacterial standard was encouraged by our collaborator Marc Salit from NIST, with input from Jodie Lee at the American Type Culture collection (ATCC).Metagenomics Blog Nov 2014 Continue reading

The ABRF Flow Cytometry Research Group (FCRG)

By:  Peter Lopez, ABRF FCRG

The ABRF Flow Cytometry Research Group was formed in 2012 as a result of the constant encouragement of Michelle Detwiler (then at Roswell Park) with input from Scott Tighe (Vermont Cancer Center). Peter Lopez (NYU Langone Medical Center), following up on his work while at Cytomation (manufacturer of the MoFlo cell sorter), was prompted by a poster at the ISAC’s “CYTO” international flow cytometry congress  by Monica DeLay (Cincinnati Children’s Hospital Medical Center), to come up with the idea for the multi-center study that seeks to answer the question—does cell sorting produce cells that are perturbed in any way? Monica had shown in her poster that dendritic cells purified by cell sorting may have compromised antigen presentation capabilities, depending on cell sorting conditions. With Scott’s help to craft the genomics side of the group’s study, the FCRG study was started. While Scott initially co-chaired the group with Peter, Monica is the co-chair at this time, and the group currently has 10 members, with many others in the flow cytometry community looking to join.

Surprisingly, in the long history of mainstream flow cytometry and cell sorting , vanishingly few papers have addressed the condition of cells after cell sorting. Investigators were just happy to get viable cells out of the process (which is most often the case), and then followed up with downstream applications using these sorted cells. Cell sorting condition tailoring or guidelines do exist, but are rarely published. Word-of-mouth best-practice scenarios exist that most core labs follow, such as if more than half the cells are dead before sorting, the resulting sorted cells often had a lower overall viability, even when  viability markers are used to ensure only sorting viable cells. Continue reading