Journal Club Announcements

This website serves as the homepage for #gplusmicrojc, a microbiology journal club hosted by Karen Lo and Laura Williams. We schedule journal clubs as interesting papers pop up (and we have the time to coordinate). Our past journal clubs have involved scientists of different fields from across the globe (one of the great strengths of online journal clubs!).

We host journal club using Google+ Hangouts, which allows 10 people in a video chat. Contact Karen (@kareynlo) or Laura (@MicroWavesSci) for an invite to join the Hangout or watch the journal club live at our YouTube page.

Friday, May 5 at 2 pm ET: Processes shaping microbiome of bromeliad plants

In microbiome studies, researchers often consider both taxonomic composition (what bacterial taxa are there?) and functional capacity (what can these bacteria do?). In this paper, researchers looked at the microbial communities in the “tanks” of bromeliad plants. These “tanks” are central cavities that collect rainwater and organic material. The researchers used 16S rRNA gene data to detect different types of bacteria and classified these bacteria into one of nine metabolic functional groups. They then examined the taxonomic composition within each of these groups. What processes, such as environmental filtering, random demographic drift or biotic interactions, affect the composition of these functional groups? Join us Friday May 5 to discuss!

Link to paper: https://www.nature.com/articles/s41559-016-0015

Link to join Hangout: https://hangouts.google.com/hangouts/_/dxrz43wldbeutbn2faynfr7uzme

Thursday, March 23 at 3 pm ET: Ancient genes in modern times

What happens when a time-traveling gene is plunked down into a modern bacterial genome? How does the ancient gene sequence evolve? What adaptations occur across the modern genome? In this week’s #microjc, we’ll discuss a paper in which the authors used phylogenetic inference to go back ~700 million years and reconstruct the gene sequence of a protein important for bacterial translation (EF-Tu). They then replaced the modern gene sequence in an E. coli genome with this ancient sequence and grew the hybrid over thousands of generations in the lab. Just like Sean Astin and Pauly Shore thawing out Brendan Fraser, we’ll discuss what happens when ancient and modern collide (yes, that was an Encino Man reference). Join us!

Link to paper (open access): http://link.springer.com/article/10.1007/s00239-017-9781-0

Link to join Hangout: https://hangouts.google.com/hangouts/_/lajut3szxfg7blnizwiivjr4iye

Thursday, February 23 at 2 pm ET: Modeling biotic interactions in soil biogeochemistry

In this edition of #microjc, we’ll discuss a recent review and synthesis paper exploring models of soil biogeochemistry. These models are valuable for understanding and predicting the outcomes of climate change and environmental disturbances. However, the authors of this paper argue that current models don’t adequately consider biotic interactions, such as predation and competition. What exactly is missing from these models, and how can we improve them? We’ll tackle this topic, and I will brush up on my Michaelis-Menten equations. Join us!

Link to paper: http://onlinelibrary.wiley.com/doi/10.1111/ele.12712/epdf

Link to join Hangout: https://hangouts.google.com/call/767gzerhvzcytj3qliggrh3lhae

Friday Feb 3rd at 3pm ET: Microbial metabolites modify fly manners

MicroJC is back from winter holiday! We’re kicking off with a bang, with what could be a landmark paper in host-microbe community interactions. Within a host’s microbiome, each constituent can produce a multitude of metabolites. These metabolites create a chemical mosaic that interacts with other members of the microbiome and the host, which ultimately affects host fitness in a positive, neutral, or negative manner.

If microbiome composition can have a large impact on host fitness, wouldn’t it make sense for the host to shape its own microbiome to maximize fitness? So any animal may change its behavior to acquire certain microbes, much like you or I may choose to eat fermented food or probiotic yogurt. How then specifically do interactions between microbes affect animal fitness? In Elife this month, a group of researchers examine these critical questions by looking at metabolite exchange between microbial species and fruit fly feeding/egg-laying behavior. Join us on Friday, February 3rd at 3PM ET as we look at the first paper to connect these dots.

Link to join our Hangout:
https://hangouts.google.com/call/nzrwwyxl7ff3tpzdpu6sgn2j4ee

Elife paper (open access):

https://elifesciences.org/content/6/e18855/article-data

Wednesday, Dec 21 at 1 pm ET: How bacteria affect multicellular development

How did multicellular life evolve? This is a fundamental question in biology. One way to investigate this question is to probe the developmental programs of organisms like choanoflagellates, protists that are considered the closest living relatives of animals. Some species of choanoflagellates alternate between a single-celled and a multicellular form, called a rosette. The formation of this colonial assemblage of individual choanoflagellates is prompted by cues from environmental bacteria. This system provides a fascinating glimpse into how our own microbial partners may have impacted our evolution as multicellular animals.

In this paper published earlier this year, Nicole King and her colleagues looked at one particular species of bacteria and analyzed how its lipids affect the development of rosettes. Join us on Wednesday 12/21 at 1 pm ET as we talk choanos, bacteria and multicellular life! (You know, just your typical holiday party topics.)

Link to paper (open access): http://www.pnas.org/content/113/28/7894.full

Link to join Hangout is here: https://hangouts.google.com/call/5n3nwj3tubbmnjud3putwlmoqee

Oct 27 @ 1pm ET: Bacteria Spearguns

Bacteria have unusual problems. Everything they create is in their cytosol compartmentalized within by their barrier membranes. They have to resolve how to deliver these components outside of the cell. If they had all the time in the world, diffusion would work. But what if delivery had to be really fast, like handing someone some thing traveling by at top speed in a split second?

Bacteria resolve this issue through power ranger megazord-like protein nanomachines called secretion systems. These massive multi-component protein complexes assemble to deliver proteins, DNA, and small molecules across membranes. One type of secretion system, the speargun resembling Type 6 secretion system (T6SS, creatively named by the order of discovery), has starred in many unusual bacterial findings. This month, we’ll discuss a brand new paper on bacteria cooperating by sharing and recycling T6SS components between neighboring cells. How do they do this? Join us on Oct 27th to find out!

Join us for the hangout!
https://hangouts.google.com/call/dzpmzje6mnauxd2bkjab7kyimue

Or (lurk) watch on YouTube Live! link:

Paper Abstract:

http://dx.doi.org/10.1016/j.cell.2016.08.023

Link to the paper:

Type VI Secretion System Substrates Are Transferred and Reused among Sister Cells

Supplemental Information

May 18 at 3 pm ET: a minimal genome for cellular life

What are the essential components for cellular life? Which pathways and gene products are required, and which are dispensable or redundant? Of course, “essential” and “dispensable” are context-dependent terms, but it can be a useful exercise to break a cellular organism down to the minimal blueprint needed for viability. In March of this year, a team of scientists from multiple institutions tinkered with a synthetic Mycoplasma genome to construct a severely reduced genome capable of supporting a viable cell. This 531 kb genome had 473 genes, including 149 genes of unknown function. On Wednesday, May 18, we’ll talk about the construction of this minimal bacterial genome, the concept of “quasi-essential” genes, and genes of unknown function. The big question, as my students are fond of saying, is “What is life?!”

All are welcome to join us! We are always glad for new people to hop in to the discussion. Click the following link to join the Hangout: https://hangouts.google.com/call/xlbyxxzdgrdghbhhxunnfazrkue

Because this paper relies heavily on a 2010 paper describing the construction of the synthetic genome, I’ll include links to both papers.

2016 minimal bacterial genome: http://science.sciencemag.org/content/351/6280/aad6253.full

2010 synthetic genome: http://science.sciencemag.org/content/329/5987/52.full