Sunday, March 18, 2018

Thursday, March 15, 2018

particle tracking algrithm

A Lee, K Tsekouras, C Calderon, C Bustamante, and S Press.. Unraveling the thousand word picture: An introduction to super-resolution data analysis. Chem. Rev., 117:7276, 2017.

KWelsher and H Yang. Multi-resolution 3D visualization of the early stages of cellular uptake of peptide-coated nanoparticles. Nat. Nanotechnol., 9:198, 2014.

MK Cheezum, WF Walker, and WH Guilford. Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys. J., 81:2378, 2001.

Monday, March 5, 2018

UAB, march aging newsletter

Headline vs Study
Contrary or Null Findings
Basic Biology
Ecology & Evolution
Novel Organisms/Comparative
Odds & Ends

Wednesday, February 28, 2018

meiofauna diversity

meiofauna diversity, good topic for image analysis

reference: "multispecies coalescent delineate structure, not species. "

cytochrome oxidase subunit 1, phylogeny study
"cryptic diversity"

haplotype network show population structures, ototyphlonemertes duplex

spatial-phylo plot, which tool?

oil spill effect on meiofauna, population genomics study

global genomics initiative,

genome initiative workfow,
library prep, WGS, quality check. contamination genome, genome assemble.

meta barcoding genes on 18S (nuclear) and COI (mitochondrial). however, 18S is not informative, COI lacks universal primers

Metagenomics, unknown pools of worms,
poor reference genomes

PALADIN: protein alignment for functional profiling whole metagenome shotgun data

assembled mitochondrial genomes from meta-genomes

signal strength in WGS: single cell organism versus multi cell organisms

Sunday, February 25, 2018

Synthetical lethals in cellmap genetic networks

Guo: I think this is explained in the paper, van Leeuwen et al.,  "Exploring genetic suppression interactions on a global scale", Science (2016), 354:aag0839.

This paper mentioned synthetic letality but did not explicitly define if it is a positive or negative interaction. However, I think genetic interactions derived by synthetic lethality should be negative effect. As the positive effect indicates that if mutation of gene A causes a reduced fitness, the double mutation of A and B restored the fitness, and hence gene B is a genetic suppressor of gene A.

I cannot find it on the CellMap website. However, from the NxN database and the fitness data I identified 2191 negative GI's , in which the double mutant fitness (DMF) is lower than 0.1. You may use different criterion, e.g., 159 interactions with DMF <= 0; or 193 with DMF <= 0.01, etc.
See the attached csv file (ranked by the DMF). 

Friday, February 23, 2018

Female meiotic drive, Mimulus



female gametogensis is asymmetric, only one egg but 3 poly bodies. So, there is advantage for genes to be meiotic drivers.

Malik & Hensoff 2001, centromeric drive model. Cost associated with meiotic drive.

Mimulus best case of centromere meiotic drive. Fishman et al 2005, 2008. 
strong hetero-specific drive. M nasutus vs M. guttatus

weak conspecific drive in M. guttatus

Do CenH3 and centromer co-evolve?
Most abundant repeats in WG tend to be centromeric repeats

Finseth found many codons with >2 omega.
Finseth look for GWS in F2 plants, 122 individuals, 1247 markers (14 linkage groups, 14 chromosomes)

Look for genetic suppresor of CenH3 meiotic drive using genewise linkage disequilibrum (r^2),
D in nonrecombining block, suggesting recent selective sweep (Q: how is genetic surfing excluded? )

CenH3A and CenH3B

plan for population

Mimulus does not grow in TN?

Silene in TN
dioecious species
gynodiecious species


Saturday, February 17, 2018

cell size and aging

In yeast, cell size is an indicator for cell's remaining replicative lifespan, based on Jo 2015. So, the limit of cell size could be aging itself.

Friday, February 16, 2018

Monday, February 5, 2018