Hou 2016 CellMetabolism, systems approach to reverse engineer lifespan extension by DR

Hou16 designed microarray experiment with ad libitum (free feeding), CR, and intermittent fasting (IF). Hou16 argued that comparison of AD and IF give more information, especially short-term and long-term changes temporal expression changes, which are good points.

Hou16 also Bayesian inference to compare gene expression between WT and deletion mutation (no time points).

Hou16 use cDNA array for gene expression analysis (much cheaper than NGS).

Hou16's simultaneous perturbation experiment seems to be a good idea.

Hou16 made a connection to systems biology using standard ODE based on Michael-mention and Hill equations, arguing different steady-type represent "young" and "old" zones. 

library(xlsx) rJava problem in Rstudio

follow instrucitons on:
http://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite

 sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib/.

Delaney 2013.

Dietary restriction and mitochondrial function link replicative and chronological aging in Saccharomyces cerevisiae
Joe R. Delaney a,b, Christopher Murakami a, Annie Chou a, Daniel Carr a, Jennifer Schleit a,
George L. Sutphin a,b, Elroy H. An a, Anthony S. Castanza a, Marissa Fletcher a, Sarani Goswami a,
Sean Higgins a, Mollie Holmberg a, Jessica Hui a, Monika Jelic a, Ki-Soo Jeong a, Jin R. Kim a, Shannon Klum a, Eric Liao a, Michael S. Lin a, Winston Lo a, Hillary Miller a, Richard Moller a, Zhao J. Peng a, Tom Pollard a, Prarthana Pradeep a, Dillon Pruett a, Dilreet Rai a, Vanessa Ros a, Alex Schuster a, Minnie Singh a,
Benjamin L. Spector a, Helen Vander Wende a, Adrienne M. Wang a, Brian M. Wasko a,
Brady Olsen a, Matt Kaeberlein a,c,⁎ 

Delaney2013 Aging Cell. Show RLS at different CLS time point. This data can be used for binomial aging model fitting. 

Eisenberg 2009 Nature

Eisenberg 2009 Nature

Survival determined by annexin V/7‑AAD co-staining (unstained cells

were considered as viable) of human immune cells (PBMC) cultured for

6 and 12 days in the absence (black bar) or presence (white bars) of various

spermidine concentrations (as indicated).

McFaline-Figueroa 2011, mitochondrial quality control during inheritance is associated with lifespan and mother-daughter asymmetry in budding yeast

McFaline-Figueroa 2011, aging cell, mitochondrial quality control during inheritance is associated with lifespan and mother-daughter asymmetry in budding yeast

mitochondria with lower ROS are preferentially inherited by duaghter cells, and mitochondria with higher ROS are retained in mother cells.

MB2014 mitochrondrial in ageing

[MB14]Michael Breitenbach2014, mitochondria in ageing

MB14 showed H2O2 can fragment mitochondrial network and this fragment is reversible. Fragmentation of mitochondrail network in aged yeast cells are irreversible.

MB14 cite Gottschling's paper, arguing that heterophasmic nature of mitochrondrail genotypes in mother cells. Daughters cells start with homoplasmic state of mitochondria genotype (only one mitochondria genotype).

MB14 show some metabolite are prone to oxidation, and form 'underground metabolism" to the ageing process.

Replicative ageing ~ gradual decline of inner mito membrane potential (Lai 2002). In non-plant cells, mitochondria is the only place where Fe-Sulure clusters are formed. Low mito membrane potential -> low Iron intake, and hence low Fe-Sulfur clusters.  DNA replication machinery contain protein with iron sulfur clusters. Hence, low mito membrane potential can lead to genomic instablity (Veatch 2009). We 2011 showed that mito genome mutation ~ decline of mito membrane potential.

Fe4-S4 cluster can be oxidized by superoxide anions to Fe2+, which can lead to more ROS through fenton reacion. (Gardner 2002)

Figure 2 presented a small gene network with different lifespan painted in colors. A good idea. 

Spermine and spermidine are ROS scavengers and decline during aging. Supplemetion of spermind/spemidine extends yeast RLS (Eisenberg 2009, Morselli 2009)

Fig 3 is a nice summary figure, compare mito poential change between health and old cells. 

5210 insertion sort

Ask studens to work on sorting poker card. Closed books, closed notebook, closed computers.

First write the procedure down in clear English.

Then rewrite in pseduo code. (Many students wrote bubble-sort algorithm, which is O(n^2).

One student write a insertion-sort, close the CLRS textbook version.

With 50 minutes to go, I showed the textbook insertion sorting algorithm, and demos with stylroform cups step-by-step. After 2 steps, I asked students to volunteer and explained them.

I then quickly go over powerpoint, and ask students to present the ppt in video as homework.

1110L lab 1,

=> went over lab safety
=> Roster check, through Blackboard grading.

announced, weekly quiz (4 from previous week, 1 from current week).

need to email announce syllabus

todo: turning data/science into music, painting

turning data into music

https://cran.r-project.org/web/packages/tuneR/index.html

https://www.theguardian.com/science/life-and-physics/2012/may/23/cern-lhc-sound

CESC beginning of the school memo

Dear CECS faculty,

Welcome back! Some beginning of semester reminders. Please read through the following carefully and let your department head know if you have any questions.

·         Prior to the first day of your class, visit your classroom or laboratory, check equipment/lab setups, and make any necessary classroom/laboratory preparation requests to your departmental assistant.  Classes start on August 22.

·         Before the 22^nd of August, course syllabi should be posted to UTC Learn and sent to your departmental administrative assistant. Template for syllabi can be found: https://www.utc.edu/walker-center-teaching-learning/information-services/syllabus-resources.php

·         Inform your departmental administrative assistant office hours for your course for posting before the first day of your class.

·         Review your course assessment plan (must support ABET and SACS accreditation efforts).

·         On the first day of the class, review the syllabus, course goals and objectives, and expectations.

·         An initial meeting between departmental faculty mentors and junior tenure-track faculty is encouraged.  A meeting of the mentors and mentees has been set for September 29^th at 3 p.m. in the Maytag Conference Room.  Additional information will be sent by the Department Heads.

·         The fall Faculty Forum is scheduled on  Thursday, September 8 at 3 p.m. in the Maytag Conference Room, EMCS 426.  Please plan to attend.  An agenda will follow prior to the meeting date.

If you are teaching a lab course:

·         You must attend a lab safety training, if you have not already done so. No exceptions. They are currently scheduled as follows:

Today, Aug. 17^th – 1 p.m. and 6 p.m.

Aug. 18 – 9 a.m.       

           Aug. 19^th – 9 a.m.

sessions will be held in the Maytag Conf. Room EMCS 426

·         Lab Course Syllabi must include the lab safety agreement. You will need to cover this policy with the students and have them sign the attached form. Your syllabus should also include a link to the following lab safety manual:

https://www.utc.edu/college-engineering-computer-science/pdfs/laboratorysafetymanualv1.3.pdf

·         Lab students must be shown the CECS lab training video on first day of lab. The video can be accessed via this link: https://youtu.be/n7FnntGLaVo  Students must take quiz and pass the test to gain access to your course laboratory.  A pass list must be sent to  your Department  Administrative Assistants by the end of first week of class.

No student swipe card access will be granted until this is complete. Lab quiz info can be found here. https://www.utc.edu/college-engineering-computer-science/research-centers/laboratories.php

At the bottom of the page, under the heading Lab Safety Quiz info for Faculty, there are two links. The first one is a zip file which contains everything you need in order to upload the safety quiz to UTC Learn. The second one is a power point with instructions on how to use the zip file.

·         The campus bookstore has arranged for a “lab packet” including goggles, earplugs, and dust masks. Purchase of the CECS Lab Pack will be required for all lab courses, so please include on your syllabus. The price is around ten dollars.

Install Eclipses on osX

Follow the instructions here to edit *.ini file and link to jkd 8 java

https://wiki.eclipse.org/Eclipse.ini#-vm_value:_Mac_OS_X_Example

automated self-administered 24hours asa24 dietary assessment tool

http://epi.grants.cancer.gov/asa24/

• Features of the ASA24 Respondent Website
• Features of the ASA24 Research Website

ASA24-2016 is the only version accessible from both desktop/laptop computers and mobile devices (e.g. tablets, smartphones). Adaptations of the ASA24 system have been developed for children and international versions are also available/under development. This website provides details on the ASA24 system and how to access and use it in your research.

UTC Biology shipping address

shipping using any carrier except USPS please use the following shipping address:

702 E 5th Street

215 Holt Hall

Chattanooga, TN 37403

If you are using USPS, then use this address:

615 McCallie Ave.

Dept 2653

Chattanooga, TN 37403

IAM UTC EDU

UTC Identity and Access Management Site!

https://iam.utc.edu/IDMProv/portal/cn/GuestContainerPage/Welcome

UTC syllabus

http://www.utc.edu/walker-center-teaching-learning/information-services/syllabus-resources.php

UTC ZOOM

ZOOM video capture
http://www.utc.edu/walker-center-teaching-learning/classroom-technology/zoom.php

UTC fact book

UTC fact book
https://www.utc.edu/planning-evaluation-institutional-research/factbook/

UTC summer schedule, 2016

May 18 - June 28, June 29 - August 9, 2016

*** UTC biology dept meeting, 2016-2017

11:30am - 1:30, noon, Grote 208

Fall 2016	Spring 2017
August 16	January 13
September 2	January 27
September 23	February 10
October 7	February 24
October 21	March 10
November 11	March 24
December 2	April 7

NIH systems biology on aging RFP

http://grants.nih.gov/grants/guide/rfa-files/RFA-AG-17-004.html

UTC blackboard, course schedules

http://utc.edu/learn 

*** network aging to do list (master)

=> Manuscript

=> Fitting
-> binomial fitting

=> Simulations
Theoretical networks, link4, link5 network simulation done on Gordon.

50% link4 + 50% link5 theoretic network. then fit with binomial aging model. "estimation of n"?

-> Essential-essential interaction in aging.

sir2D, wildtype, wild lifespans fittings, nested model test

Gompertz fitting
Binomial fitting

degree>=4 simulation done
degree>=5 ?
degree>=6


I could try rnorm(lambda), lambda ~ 1/degree, degree, degree^2, fitting with binomial model.
page 46, GG91's generalized bionomial mortality model:


label permutation


References:
http://hongqinlab.blogspot.com/search/label/Binomial%20Aging

http://hongqinlab.blogspot.com/2014/07/glucose-dose-effect-on-rls-in-by4742.html