DrDaddy

Based on my experience, I'm going to disagree some of these responses.
 
Last year when I applied to PhD programs, I had 2 years of research experience studying bacterial infection and mammalian innate immune responses, including a few solid publications in the field. I looked at a number of environmental microbiology programs which had labs that studied ecological systems of bacterial infection and immune responses in invertebrates, and since I'd done summer research internships in environmental science and ecology I figured this was a perfect integration of my 2 interests. I spoke with prospective advisors at each of my schools to see if they thought this was too much of a stretch, and they all gave me positive feedback about my research background serving as a good, unique viewpoint that they typically don't get from applicants who are usually trained as ecologists. 
 
I was rejected from every single environmental micro program I applied to, and it's not like my GPA, GRE, recommendations, or personal statements were prohibitively terrible. I figured that the jump from biomedical micro & immuno to environmental micro & immuno wouldn't be too drastic, but admissions committees at these programs did. After I received all of my rejections, I was informed that I'd been awarded an NSF-GRFP (apparently my profile was good enough for them), so I contacted schools and many of them were happy to re-evaluate my application. When I went to meet with department members at places that agreed to admit me given my fellowship, they all said the exact same thing: I had a strong applicant profile overall, but because I didn't have research experience in their specific field of study, they weren't fully convinced that I fit into their programs properly.
 
One big caveat to this is that I was trying to switch from a biomedical field to environmental programs, which are smaller, have less funding, etc. so they are typically pickier about finding applicants who will be directly admitted to specific labs. That's not exactly your case with switching from plant bio to immuno/pharmacology Biomedical programs allow for rotations, so there is some more flexibility there, which could help you out.
 
bak3rme - what have you done that makes you want to pursue pharmacology or immuno programs? Classes? Is there any way to relate your previous experiences to where you'd like to go? I think that if you have absolutely nothing relating to either of those disciplines in your background, you could have a difficult time making a case for why those programs are a proper fit for you, especially since your competing applicants will most likely have at least some exposure to those fields.
 
Anyways, that's just my two cents based on my story. Everyone's got their personal opinions based on what they've seen and experienced.

There are tons of programs which fit those really broad interests; I'm surprised you only found two! UCSF is going to be a stretch with that GPA. You will need stellar GRE scores and amazing recommendation letters. I'm not sure on if your research experience is going to be on the good side for UCSF or not. You're right that most students don't have publications going into their PhD. I had two in prep, but I was also almost done with a MS. I thought about applying to UCSF for a similar program, but they also required the subject GRE, and I decided my GPA and general GRE weren't going to cut it.
 
If I had your GPA, I would probably either do a MS (and work your tail off to get a better GPA and gain research experience) or a post-bacc to raise my GPA while working as a lab technician and show I can be a serious graduate student. I'm not international, but I entered my PhD program with a 3.68 UG GPA and a 3.7 MS GPA plus 6 years of research experience (all of UG and MS, these aren't short research projects). I was accepted into other top-20 institutions than the one I ultimately attended, but I likely would not have been accepted into UCSF as I fell below their cutoffs. There are a select few that make it in despite that, and, while you can still apply there, you should have other really viable options.
 
What I would do is look into tons of programs, particularly umbrella programs, to make your choices for application to about 6-10 of them. You can have a couple of schools you're not sure you will get into, but also pick several you like that you think you have a chance at. Your GPA may really kill you, though, if these schools have cutoffs they use. Look into that before deciding to apply. Also look for professors you're interested in... the best thing is to pick a school with several professors you think you might be interested in working under. University of Florida has a good umbrella program and lots of  microbiology people. Baylor College of Medicine has several professors working with different pathogens, as well as a giant microbiome research presence. They also have a Tropical Diseases department.
 
To apply THIS application cycle, you need to take your GRE as soon as possible, as well as the TOEFL if it is required, unless you're wanting to take a year off. If you take it in September, you have time to retake the computer-based test in early November, but you may miss some deadlines. You should probably look into who will write your letters of recommendation about now. Some deadlines are as early as November, and since you're international, you may have earlier deadlines than US students (for example, UCSD makes you submit a pre-application).
 
Feel free to message me if you have questions. Good luck!

First off the rest of your application sounds pretty decent except for your GPA.  So you need to do what you can to show that was an aberration, not the norm.  My suggestion due to your financial situation would be to try to take a class (maybe too late for this fall semester but I'd highly recommend doing one this spring AND summer) and show that you can excel in courses.  If you can take a related graduate course in a school you may even be interested in great, if not take some of the undergrad courses that are relevant and at the intermediate/advanced level.  DO WELL.  Use this as an example to show you can achieve well.  Having that plus a decent GRE someone will say, this person has the ability they just may not have done it during their undergrad.  go from there.  Don't apply to an unfunded masters to accomplish this, unless you feel you must.  I think the same effect can be had by working and being successful in some courses going forward.  If you are able to still add a class this fall even better, the more evidence you give them you can succeed the better.  Now with all of this, obviously I am recommending you do this as a way to prep for application season next fall.  Thereby starting school in two years.  You can still apply to a masters now as you prepare but I don't think it would hurt to take some courses.  Even one or two classes with good grades can show them you are ready for school.  I am in the field you are interested in, if you'd like any specific answers or whatnot please feel free to PM me.
Best of luck.

its ah-mazing. as long as you know how to ignore and distance yourself from bxtches and moochers. 

My qualifying exam is literally in about 10 hours (yikes!). We were given a total of two months to work on it: two weeks for the abstract, one month for the proposal, and two weeks for the presentation. My defense sounds like it will be very similar in style to yours. I have been in lab daily working on my presentation and practicing, but I only stopped doing experiments in the past week or so. I would say a maximum of two weeks halting experiments is acceptable so long as you're still in the laboratory and accessible by the professor to show your progress.
 
I agree with the above posters. We're in graduate school to be researchers. I could accomplish a lot of experiments in two months and it would be a great deal of lost work which would ultimately slow my progress and delay graduation. Two months is far too long. Had I not been in the lab, I would have lost authorship on two papers that I generated data for.
 
You really do just need to manage your time. When I was writing the proposal, I would do lab work in the mornings, then write in the afternoons until I got bored. I'd do a couple of lab chores, and then start up writing, again. Your organization of your time will be key.

Oh I do hope you do not intend to pursue an academic career. Life gets significantly more difficult after you graduate. There are fewer jobs than PhD graduates so getting that postdoc won't be easy, not to mention that first TT job. And once you're on the TT, it's publish or perish (and teaching and service) for 7 years until you're up for tenure. Maybe then you could start having a life, assuming you're not particularly rushed to get that Full Professor rank?  Assuming you're one of the truly lucky ones who gets the perfect job straight out of school and can fast-track the TT, we're looking at a minimum of 10 years of everything on hold. If you're one of us mere mortals, you're probably looking at closer to 15 years of school-postdoc-TT job celibacy. I don't know about you, but I value the rest of my life just as much as my career. Being successful but completely alone for over a decade does not sound appealing at all. You need to start learning how to have a full and balanced life now, because it will not get easier later. 

Please dont act like you are amazing. You didnt "compete" with anyone you were at bottom of the barrel. I hope you can survive the first quarter.

I do think that you will have to do something about the GPA so I dont think that a research position will be enough. A masters is a great way to go or you could simply take a class a semseter (grad would be great or retake some of your bad grade classes) while working in a research position. This would help you fund the additional classes without needing loans. If you are worried about financing a mastesr then this could be a great compromise between the two plans.

I never posted one of these, so now that I've made my decision I figured I might as well. Maybe it'll give some hope for those with sub-3.0 GPAs in the future!
Undergrad Institution: R1
Major(s): Biology
Overall GPA: 2.821
Type of Student: American, Female
GRE Scores (revised version)
Q: 160 (83%)
V: 163 (93%)
W:4.5 (72%)
Research Experience: 2.5 years as an undergraduate research assistant in a molecular biology/biochemistry lab (no thesis or publications, no LoR from this lab), 3 years in a mbio/biochem lab as a research assistant (one 2nd author publication, 2 LoR from PI and co-mentor)
Awards/Honors/Recognitions: Awarded funding as an undergraduate in form of a fellowship
Pertinent Activities or Jobs: 1.5 years as a TA in undergrad, 5.5 years total as a research assistant, 2 years as a mentor to high school students
Special Bonus Points: Publication, LoRs from well-known PIs in the field I want to remain in, already took a few graduate courses at Case Western while working as a research assistant
Applying to Where: I knew where I wanted to go (and where I had a likelihood of getting in based on my PI's connections) but I also applied to a handful of extreme reach schools just to see.
Case Western Reserve University (BSTP) - Interviewed, Accepted
University of Rochester (BMB) - Interviewed, Accepted
University of Massachusetts Medical School (GSBS/BBS) - Interviewed, Accepted, Will Be Attending
MIT (Biology) - Rejected
University of Washington (MCB) - Rejected
University of Wisconsin - Madison (CMB) - Rejected
UC - Berkeley (MCB) - Rejected
The Ohio State University (MCDB) - Never Heard From
Tips for Future Applicants: Do what you can early on to recognize problem areas and do what you can to rectify them or boost other areas to compensate. I knew coming out of undergrad that I wouldn't be a competitive applicant. I took time off, worked hard, got a publication, and saved enough money while doing so that I can now buy a home when I start grad school this fall. I also spent all of last summer studying for the GRE.
Also, when you're interviewing, know your own research really well. Practice talking about it with friends, so they can ask you the obvious questions that you should be prepared for, but don't sound too rehearsed. Don't spend hours reading papers by your interviewers - focus on abstracts or reviews, but most will assume you haven't anyhow.
And most importantly, a bad undergraduate GPA will not ruin you. Just be prepared to defend your past and explain how things will be different in the future!

Also, it makes a hell of a lot more sense to post a "what are my chances?" thread in the "officially grads" forum of newly accepted grad students. That way they can tell you their stats and then you can compare.

Asking what your chances are in the "applications" forum - among people in the very same boat as you wondering the exact same thing about their own stats - isn't going to help anybody since nobody has any real answers.

No.

HELLO TO ALL... PLZ SUGGEST ME A STRONG TOPIC RELATED TO MICROBIOLOGY FOR Ph.D. AS SOON AS POSSIBLE.I HAVE TO PREPARE OUTLINE FOR PROPOSED RESEARCH WORK FOR INTERVIEW. I AM INTERESTED IN MICROBIAL GENETICS AND INDUSTRIAL MICROBIOLOGY....

This is small and nitpicky, but --

I really hate it when they address me by my first name when I haven't given them the permission to do so. This also bothers me in follow-up emails with POI. I'm not sure why it irks me so mcuh.

I would focus on how enjoyable and fun the program will be. When I used to see ads for grad school, I'd imagine myself giving up everything and not having time to do all the fun things I want to do, which is exactly what's happened now that I'm in grad school. If a grad school emphasized that it was actually fun and not stressful and going to take over one's life, I'd actually consider it.