CIDD Graduate Students: What do we do?

Many of us including graduate students, post docs, and faculty, gathered together on Monday to discuss who we are as CIDD, what we expect of ourselves, and what the faculty expect of us. Additionally, we discussed and proposed multiple venues in which students and post docs would have the opportunity to discuss their ideas, research/data, job opportunities, and life in general. So for those of you who are curious about grad life at CIDD or are hopelessly wishing for more scientific opportunities to land at your feet…pay attention.

Continue reading

Posted in Academics, Club Business, Journal Club, Outreach, Professional Training, Social | Leave a comment

CIDD GSA Journal Club 2-9-16

Just a reminder that we will be having our third journal club of the semester this coming Tuesday, February 9th from 9-10 am in W-201 of MSC. This week’s paper is from Britt Glausinger‘s lab and can be found here.

In the future, the schedule and papers chosen for each journal club can be found as PDFs in this box.com folder (open to anyone).

Hope to see you all there!

Posted in News | Leave a comment

CGSA Journal Club 2/2/16

Just a reminder that we will be having our second journal club of the semester this coming Tuesday, February 2nd from 9-10 am in W-201 of MSC. This week’s paper is from David Pride‘s group and can be found here.

In the future, the schedule and papers chosen for each journal club can be found as PDFs in this box.com folder (open to anyone).

Hope to see you all there!

 

 

Posted in News | Leave a comment

CIDD Lunch 2-4-16

CIDD grads and post-docs,

Please join us for lunch with Dr. Nels Elde, Assistant Professor of  Human Genetics at The University of Utah following his seminar titled “The generosity of selfish genes.”

When: Thursday, February 4th, 11:00 am – 12:00 pm

Where: W-203 Millennium Science Complex

Please RSVP by Wednesday, Feb. 3rd using the poll below.

 

Posted in News | Leave a comment

CGSA Journal Club this Semester

Hey all,

Before the summer symposium on “Living with our Viromes” (May 24-25), you are invited to join in a semester-long journal club on papers by each of the invited symposium speakers. This will be Tuesdays 9:00-10:00 am, in W201 MSC. This is journal club is being run in conjunction w/ the CGSA & is open to anyone interested in learning more about the viruses around us. As with all CGSA journal clubs, we’re aiming to foster open conversation & make the topics accessible to all. Since everyone’s got plenty to balance, we’ll also aim to keep each journal club to 1 hour. See the schedule below for specific dates & details. The papers for each journal club can be found as PDFs in this box.com folder (open to anyone).

We are starting THIS TUESDAY 1/19 with a paper by Rich Condit for any and all of you who are interested in attending. If you have any questions, you can contact myself (mms426@psu.edu) or Moriah Szpara (moriah@psu.edu).

 

Posted in News | Leave a comment

Interesting upcoming disease networks talk Feb 2 at 3:30 PM

Petter Holme from Sungkyunkwan University is giving a networks talk at 3:30 PM in 339 Davey Laboratory.  The title of his talk is “Temporal networks: A physics perspective“, and the description is:

Networks are all around us—from power-grids to the nervous system, from polymer interactions to friendship networks, from protein interactions to chains of historical events. Network theory is a framework that seeks to explain how such networks function, evolve and can be controlled. Like (or, perhaps, as a branch of) statistical physics, it is way to explain how system-wide properties emerges from the microscopic interactions between nodes in the networks. Moreover, network theory gives methods to extract useful information from large-scale data sets of complex systems, thus forming a connection between physics and data science. Sometimes, one has information not only about which nodes that interact, but also when the interaction happens. This information can be crucial for understanding how dynamical systems (like diseases spreading over human contact networks) behave. I will discuss the theory of temporal networks—integrating information about time and network topology. This theory, it turns out, becomes rather different from static network theory (partly because temporal networks are not transitive, in the algebraic sense). I will use disease spreading on temporal networks as my main example, but also discuss the state of the field in general, and its future challenges.

Posted in Seminars | Leave a comment

CIDD Lunch 1-21-16

CIDD grads and post-docs,

Please join us for lunch with Dr. Janis Antonovics, Lewis and Clarke Professor of Biology, University of Virginia directly after his seminar titled “Vector-based disease transmission across host density gradients; from field studies to theory.”

When: Thursday, January 21, 11:00 am – 12:00 pm

Where: W-203 Millennium Science Complex

Please RSVP by Wednesday, Jan. 20th using the poll below.

Posted in News | Leave a comment

CIDD Lunch with Dr. Aaron King 12-10-15

CIDD grads and post-docs,

Please join us for lunch with Dr. Aaron King,  Associate Professor of Ecology and Evolutionary Biology and Mathematics at University of Michigan immediately following his CIDD seminar: “Process from pattern in diseases with complex ecologies”

When: Thursday, December 10, 11:00 am – 12:00 pm

Where: W-203 Millennium Science Complex

Please RSVP by Wednesday, Dec. 9th using the poll below.

Posted in News | 1 Comment

CIDD Lunch with Dr. Troy Day

CIDD grads and post-docs,

I hope you all had a nice holiday break!

Please join us for lunch with Dr. Troy Day immediately following his CIDD seminar: “Can we design evolution-proof antimicrobial drugs?”.

When: Thursday, December 3, 11:00 am – 12:00 pm

Where: W-203 Millennium Science Complex

Please RSVP by Wednesday, Dec. 2nd using the poll below.

Posted in News | Leave a comment

Ten cross-scale disease questions I wish I could answer

CIDD has the personnel to do some amazing work on cross-scale disease dynamics, but it’s not always clear how to relate within- and between-host processes. People researching within-host processes may not understand the sorts of questions that researchers working between hosts will hone in on as important, and vice-versa. In this post, I ask ten questions whose answers would really improve how I think about the interface between immunology and epidemiology. I’d love to see other people’s lists; these are just my off-the-cuff, post-CIDD-lunch (highly-hyphenated) initial attempts.

Before I begin, here’s my basic premise. I think there are three links relating what happens within the host to what happens between hosts. These are

1. How (and how long, and at what intensity) does the pathogen persist in the host?

2. How does pathogen load (+ other load-related within-host processes) map to transmission between hosts?

3. How does pathogen load (+ other load-related within-host processes) map to disease-induced mortality?

Since I work on wildlife, I don’t have the luxury of actually studying any given system in great detail (read: my animals don’t survive in pens). As a consequence, I’m on an on-going quest for general motifs within the host that I could apply to different systems, to think what’s driving population-level epidemiology.

These motifs are hard to identify (especially for the immunological illiterati such as myself)! But I’m an optimist, so I’m putting these out there as a wish-list for public consumption. The wording is intentionally simplistic, an admittedly serious transgression; I hope you’ll forgive.

Lots of people are working on these questions already. Some are stolen from other places, and some probably even have clear, published answers. My point isn’t so much that these specific questions are the “right” ones, but rather that they’re the sort of questions on the research horizon that we at CIDD are uniquely equipped to tackle.

So, without further ado:

1. When (both epidemiologically and immunologically) can we treat a host as a well-mixed unit, and in what situations should we be particularly concerned about spatial structure within the host? When do we expect immune-privileged sites to have major implications on epidemiological processes?

2. Should we think about population-level epidemiology of pathogens with primarily mucosal vs. primarily humoral immune responses in fundamentally different ways?

3a. Are there general motifs of pathogen dynamics within the host, and how those motifs map to transmission and disease-induced mortality rates? Do classic predator-prey functional response models within the host (e.g., host immune defenses “prey on” pathogen load) actually make sense, or are they just stand-ins until we know better?

3b. Under what conditions will our epidemiological understanding benefit from incorporating these general motifs into population-level models? What motifs do we actually know well-enough to incorporate?

4. How do we map from the ecological definition of “tolerance” (e.g. – loosely – host fitness is independent of pathogen load) to the immunological one (e.g. – again, loosely – host does not mount an immune response to the pathogen)? What’s going on in systems where we see ecological tolerance, but not immunological tolerance? Would considering high- and low-zone tolerance improve some population-level epidemiological models? For what systems?

5. Are there general mechanisms underlying chronic carriage, and can we build any systematic expectations about when chronic carriage maps to chronic shedding (e.g., when do carriers transmit)? Also, are there cases when we can predict who’s carrying, and how accurate are those predictions?

6. What is the relative importance of host behavior and within-host dynamics in determining who’s a super-spreader? Does this vary systematically between systems?

7. I hear that sometimes I should think about other within-host processes besides just immune response relating to transmission. Are there particular kinds of pathogens where that’s likely to be true? What other within-host systems should I worry about? How does the function of those systems relate to pathogen persistence and transmission, and disease-induced mortality? Are there general themes here??

8. How do we best use existing immunology to think about co-infection? Do we have a basis for moving past a world-view focused on Th1/Th2 trade-offs?

9. Also, do we expect that Th17 and Tregs have major epidemiological implications in some cases? Which cases, and how?

10. What epidemiological inferences can we back out of serology data, and could we learn a lot more? When is it worthwhile to parse IgG from IgA from IgM? How much additional information would that give us to estimate force of infection? (inspired by the RAPIDD serology workshop, Jan 2015).

Obviously, I’m overlooking a lot here (maternal immunity, environmental effects, etc.), simplifying a ton, and asking for knowledge that may not yet exist. What have I ruthlessly overlooked, or horrifically oversimplified? Where are the other big gaps? What should I REALLY be writing my dissertation about?

Most importantly, what is the complementary set of questions from someone with a within-host perspective?

— kez

Posted in News | 1 Comment