Sunday, December 20, 2020

An unprecedented mink cull has been ordered in Denmark amid the outbreak of SARS-CoV-2 in these farmed animals. The plan was announced after scientists discovered a widespread Y453F mutation in the spike protein, that has been passed from animal to humans.

This mutation is of particular concern, because it occurs at a conservative domain of the receptor binding domain (RBD) directly involved in ACE2 binding. Results from some preliminary studies suggest the Y453F mutation affects the ability of the Spike protein to bind with ACE2, while others demonstrate that the mutated spike can escape from detection from a commercial anti-S antibody.

Although there is still no clear evidence indicating this mutation, or any other mutation like the popular D614G, has any clinical significance, the characteristics of the mutations need to be thoroughly investigated in the context of vaccine and antibody therapy.

Sino Biological has launched the recombinant Y453F RBD protein. This product is the newest addition to a large library of recombinant spike variants (full list here). These proteins can be used to evaluate the efficacy of the antibodies and vaccination.

Full List of SARS-CoV-2 Spike Mutants

P337S	F338L	V341I	F342L	A344S

A348S	N354D	A352S	S359N	V367F

N370S	A372T	A372S	F377L	K378N

K378R	P384L	T385A	T393P	V395I

E406Q	R408I	Q409E	Q414R	Q414E

K417N	A435S	W436R	N439K	N440K

K444R	V445F	G446V	G446S	L452R

Y453F	F456L	F456E	K458R	K458Q

E471Q	I472V	G476S	S477R	S477I

S477N	T478I	P479S	N481D	G482S

V483A	V483I	G485S	F486S	F490S

S494P	P499R	V503F	Y505C	Y508H

A520V	A520S	P521S	P521R	A522V

A522S	D614G	D405V, Q414A

Friday, December 11, 2020

biological clocks, Forger,

Biological Clocks, Rhythms, and Oscillations

The Theory of Biological Timekeeping

Daniel B. Forger.

https://www.ncbi.nlm.nih.gov/books/NBK544607/

https://www.ncbi.nlm.nih.gov/books/NBK544607/pdf/Bookshelf_NBK544607.pdf

Forger said that many bio clock use the same mathematic equations (models). convergent evolution. Forger said that Hoff bifurcation seems to be the common cause in all biological clocks.

J Tyson seems to have strong reservation on Forger's argument of evolution of the general math equation.

General structure of clocks.

not all bacteria has circadian clocks.

Dynamo: Mapping Vector Field of Single Cells

Inclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and potential landscape mapping.

https://github.com/aristoteleo/dynamo-release

linear dynamic systems, laplace transform

https://see.stanford.edu/Course/EE263

https://see.stanford.edu/materials/lsoeldsee263/13-lin-sys.pdf

Thursday, December 10, 2020

advantages of temporal network, continued

Li, ..., Barabasi, Science, 2017,

temporal network advantages.

Energy needed from state vector x0 to final state xf
E(x0, xf) = 1/2 d^T x W^01_eff x d

where Weff encode the energy structure of the network.

I did not follow S1.1 method.

After reading Laplace transformation, and watched YouTube movies on solving differential equations with Laplace transformation, it seems the Li17 presented a general solution.

Li17 cited a yeast dynamic protein network:

27. J. Wang, X. Peng, M. Li, Y. Pan, Construction and application of dynamic protein interaction

network based on time course gene expression data. Proteomics 13, 301–312 (2013).

doi:10.1002/pmic.201200277 Medline

In Figure S6, a digram is presented to describe the construct of a yeast dynamic PPI. An interaction is consider as active when both protein are active at that time point. based on X. Tang, J. Wang, B. Liu, M. Li, G. Chen, Y. Pan, A comparison of the functional modules identified from time course and static PPI network data. BMC Bioinformatics 12, 339

(2011). doi:10.1186/1471-2105-12-339 Medline

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-339#Sec17

In Fig 2. Protein networks used contain only 84, 74, and 85 nodes. So, it seems Li17 only used a small subset of PPI.

Li17 fixed the number of driver nodes to 20% of the nodes. Hong did not find the criteria on the reasons behind this choice.

draw a graph diagram on latex

https://www.baeldung.com/cs/latex-drawing-graphs

Tuesday, December 8, 2020

PH525x series - Biomedical Data Science

http://genomicsclass.github.io/book/

https://github.com/genomicsclass/labs

geometric multiplicity == algebraic multiplicity-for-a-symmetric-matrix

good post to prove that geometric and algebraic multiplicity are the same for a symmetric matrix.

https://math.stackexchange.com/questions/393149/geometric-multiplicity-algebraic-multiplicity-for-a-symmetric-matrix

yeast double strand breaks, γ-H2AX and γ-H2B

Dynamics of yeast histone H2A and H2B phosphorylation in response to a double-strand break

https://www.nature.com/articles/nsmb.2737

In budding yeast, a single double-strand break (DSB) triggers extensive Tel1 (ATM)- and Mec1 (ATR)-dependent phosphorylation of histone H2A around the DSB, to form γ-H2AX

In Saccharomyces cerevisiae, histone H2A comprises the great majority of H2A isoforms and is phosphorylated on S129; we will refer to this modification also as γ-H2AX. Both in yeast and in mammals, γ-H2AX rapidly spreads on large chromatin domain (on more than a megabase in mammals and about 50 kb in yeast)

Both γ-H2AX and γ-H2B are strongly diminished over highly transcribed regions.

coding theory

https://en.wikipedia.org/wiki/Coding_theory

this is related to encryption and error detection.

Is this related to how DNA use quaternary code and basepairing?