MORGAN was running still the trial period remote desktop, which took some effort to get set up on Windows 2012 in the first place and was behaving a bit differently than on CAJAL. On CAJAL I had entered the license info on the original configuration run but it promptly forgot this info when the trial period expired (it thought it was still running on trial licenses) and I had to renter this info to get it to run. So on Morgan I just let the trial expire first before trying to install the licenses I bought.
It’s really hard to find out where to enter the RD licenses. You might think this big licenses icon in the server manager would be the place…
but you’d be wrong. This doesn’t even have the option to enter yet.
So I first readded server roles, remote desktop (I think this was already working, see previous configure of remote desktop Morgan post). I don’t think this was necessary, but it went through a whole round of install and reboot. (during which time the monitor was disconnected and refused to reconnect).
What I really want is here: Select the RD icon at the bottom left of the tool panel in Server Manager, and then select Collections. We first need to create a new Session. I created a MorganSession here.
Then select Servers and right click on the Morgan Server and select RD License Manager. Here you will be able to enter the Agreement number and specify the number (5) and type (per User CAL). I actually did this before adding the Morgan Session and it didn’t work (even after a system reboot). Then I added the session and then in started working.
You can also test if the licenses are working here:
- now the server works again and accepts remote connections.
- only another hour+ of troubleshooting just to enter two stupid numbers in the right place.
(7:00 pm – 9:15 pm, 3/4/15)
- Adam Fagen, Exec. director GS
- 1600 registrants, 36% faculty, 16% postdoc
- 30 countries, 46 states
- Next Fly meeting is in July 2016. Joint sessions with other genetics (including Denis Duboule and Francis Collins)
- Wangler … Bellen 2015 Fruit Flies in Biomedical Research: The value of Fly research
Fprmer Levine lab members here
- Angelike Stathopolous
- Jessica Cande
- Dave Hendrix
- Christine Rushlow
- John Reinitz
- David Arnosti
- Tony Ip
- Alistair Boettiger
- Scott Barolo
- Matthias Mannervik
- Michelle Markstein
- Haini Cai
- Albert Erives
Larry Sandler Award Speaker
- Zhao Zhang
- PI at Carnegie Institute (as Spradling)
- Genome faces challenges from outside
- High number of transposons.
- piRNAs inhibit transpsons to maintain genome stability.
- 23 – 30 nt.
- associate with Piwi and Ago3
- mainly function in germline
- come from large pi RNA clusters (142 clusters in genome).
- how to sort piRNA precursors into piRNAs and not translate.
- mutant named as they make single dorsal appendage
- rhi ChIP-seq (didn’t work for months)
- Very strong correlation between rhi ChIP-seq and PiRNA production across the genome.
- 131 of 142 clusters correlate reduction in piRNA in rhino mutant and amount of rhino binding (peak height)
- Rhi binding surpresses splicing
- spliced transcripts lose piRNA production
- Rhino binding can convert coding gene Sox2F into a piRNA precursor.
- mutate Rhino, all transcripts are spliced
- Rhi LacI fusion represses gene expression
- anti-sense transcription also necessary for piRNA generation?
- cap-binding protein (required for splicing) recruited to 5′ end of protein coding genes
- rhino associates 5′, blocks cap-binding protein (homologous but enzyamtically inactive).
- Rhino has chromodomain and chromo-shadow, bot doesn’t bind heterochromatin. How is it targeted?
- what happens if you tether HP1 to LacI? Also silencing?
- Why need to block splicing for piRNA generation?
- similar to other otrganisms use piRNAs
- Allan Spradling
- BA in physics at Chicago
- Went to Carnegie after his post doc and has been there since.
- HHMI for 27 years
- 168 publications. 1982 paper with Rubin: transformation based on transposable elements (pElement transgenesis)
Title: Drosophila: asuming the mantle of leadership in Biology
- An era of unprecedented progress in genetics.
- no cloned genes, no sequencing of DNA (let alone genomes)
- expanded scope of and awareness of genetics
How did this growth happen?
- Vannevar Bush and James Shannon
- Even the 50s NIH had a multimillion dollar budget, most given to doctors. These guys decided to support Ph.D.s
- NIGMS lead to an explosion of basic biology
- Spradling, first grant at 30, (claims given for accomplishment not writing).
why don’t we feel better about the future?
- gov is seriously considering a return to the earlier form of NIH
- logical continuation: continue with model organisms
- new human / mammalian-cell centric vision.
How much conservation really is there?
- Mouse ovary (superficially) looks very different than fly ovary in structure and behavior
- Drosophila: 16 cell cyst -> become 15 NCs and 1 OC.
- motors fire up and a lot of things start moving from all those nurse cells into the oocyte (mitochondria, RNPs and others)
- Ring canals in 16 cell mouse oocyte follow the same steps of transport. Single germ cell labeling and lineage tracing in the mouse.
- Mouse cyst are unstable, don’t remain connected. Could make multiple follicle cells
- find more cells get multiple centrosomes (get downstream stuff pumped into them).
- Cells lacking Balbiani body golgi (follicle precursor) apoptose.
- Mouse oocytes may start life unequal. (Early eggs come from big cysts and are of higher quality?)
- No germline stem cells in mice.
- despite ‘quack stem cell treatments’ that offer to proliferate stem cells in coordination with IVF.
- 32 mature eggs on each ovary, only 1 can be released at a time. One is always protruding more and is uniquely expressing high levels of metalloprotease
- Drosophila ‘corpus lutium’, steroid produced from remaining follicle cells. Only one remains at a time.
- homolog of fallopian tube
- oocytes like to load up on lipids. Leads to problems in humans generating infirtility
- Fly produces proteins and substantial amount of lipid (stage 10) into oocyte. This requires substantial amount of the flies metabolic resources
- controlled by an ectodysin pulse.
- Corresponding pathway is used in mammalian liver. Is it also use in mammalian reproduction / oogenesis?
- Drosophila females increase substantially in fat once the ovaries are sexually mature (as in humans).
- this change is driven by the brain. presence of ovaries leads to higher ectodysin release.
- Could never have anticipated this level of conservation. Built ever since the Hox genes — tissue and physiology conservation.
- existence of this unexpected conservation is also pretty cool science.
- every college graduate should be aware of this remarkable conservation.
- Best thing to do is discover something new.
Mammals and polyploid cells
- get new polyploid cells in heart attack.
- wounded flies cells around the wound become polyploid — EdU replication up, but no cell division.
- scales with wound size. replaces the number of genomes that were lost in the wound.
- cells persist for life time. Process contributes to wound healing — healing is worse if you knock out this response.
- Hippo pathway required
- overexpresion of hippo get more than normal polyploidy.
- polyploid cells in aging and wounding might be a general stress response?
- hypothesize that this restores mechanical stability.
- Polyploid cells different levels of genes due to under-replication. Proposed nested forks, factors of 2
- salivary gland under-replication
- arrested forks are not actually stable — cells repair these by break and religation. Test this by sequencing. Confirmed. creates deletions in low replicating regions. These sum deletions are what create the low read count of under-replication.
- All these breaks create extensive genomic novelity. generates diversity in IgG regions and others (?)
Superior tools in flies
- MIMICs make GFP lines.
- swapped in Hsp70 promoter into lots of sites (heterochromatic and non heterochromatic) Under heat shock, some cell types turn on GFP and some don’t. chromatin state mapping in cell type specific way.
- ‘not going to understand biology better until we get better understanding of gene regulation and genomics’
- tissue culture cell models for multicellular interactions has not played through
- tissue culture models wouldn’t need to be cut by a large fraction to increase model organism work by a large fraction.
- should do more cross-system research
- convincing society will require great leadership, but alternative will be disasterous.
- billions of dollars spent on GWAS (mammalian centered technology). Follow which genes segregate and relate to populations. Should have talked to Drosophila pop bio first. 100 million dollar study in height explains less than 1% of variation with a BMP receptor link (could have guessed?)
- lots of stuff maps to non-regulatory regions (which we don’t know very much about in human / mammals)
- ENCODE – no biological questions.
- human genetics wants to go from genome to disease. Need to look at development — tried this already in model organism, a useful model will need to look at the genes in their tissue context.
- least favorite nucleomics. 3C, 5C ‘after all the aggregation artifacts’. Project is “limited to mammalian cells”.
- come on, we’ve learned the best about this stuff from model organisms. If you are going to do this, at least do it in a model organism.
- education about evolution. First, its surprising, don’t make people feel bad or negative. We just need to spread the idea better.
- First mission statement of NIH is to understand what underlies the biology. No statement about health in that mission statement, only the second statement is health relevant.
- we need to step up the efforts. Tell them more of the science.
- Model organism people need to work together and talk together more. Our community is not so visible.
- GSA medal: Heinikoff (last 15 years) and before.
- Education award: (chair at U. Minnasota)
- Thomas Hunt Morgan Career award: Brian Charlesworth — origin of sex chromosomes, sex chromosome evolution. advanced concept of genetic load of deleterious mutations. pioneer in studying aging and the evolution of aging.