Thursday, July 23, 2020

Why humidity matters, covid19

From
https://medicalxpress.com/news/2020-06-humidity-linked-covid-.html

Why humidity matters
Professor Ward said there are biological reasons why humidity matters in transmission of airborne viruses.
"When the humidity is lower, the air is drier and it makes the aerosols smaller," he said. "When you sneeze and cough those smaller infectious aerosols can stay suspended in the air for longer. That increases the exposure for other people. When the air is humid and the aerosols are larger and heavier, they fall and hit surfaces quicker."


https://www.medicalnewstoday.com/articles/how-humidity-may-affect-covid-19-outcome
Specifically, differences in temperature and humidity affect how stable and transmissible viruses are. For instance, some data reviewed in the new paper suggest that cold, dry, unventilated air may contribute to the transmission of influenza in the winter.

transcription fidelity and yeast aging

reviewers asks for mutation in DNA as a model. This is not correct (No, this is relavent 2020Oct), because yeast aging is a single-cell event. Its chromosome DNA unlikely to be mutated.

Experimental verification
Single cell variation
Old cell variation, 

Test of some mutants ???. On transcription fidelity,
Candidate genes: 
Transcriptional noise regulators. 
Maybe histone methylation, K4 methyltransferase? Transcript inititiation? KO? Over-expression? 
K4-methy hot in human aging. Six paralogs in human, involved in leukemia. 
Only one copy gene in yeast. No clear phenotype on growth fitness and aging in yeast. ?!!!! 

*** SET1 maybe not a general transcription initiation??? Only in stress-response. 


Aging is a stress condition. 
TODO: SET1 expression during aging in eLife Data set. and Dang’s lab RNA and protein level data. 

Gene Ontology Term: maintenance of transcriptional fidelity during DNA-templated transcription elongation




**** RPB9-deletion shorten RLS by 44% with p=1E-9. -> expect to increase expression noise -> aging. 


General transcription elongation factor
DST1-deletion does change average RLS. (Need to check its distribution of RLS, gene expression). 














RPB9
https://www.yeastgenome.org/locus/S000003038
RNA polymerase II subunit B12.6; contacts DNA; mutations affect transcription start site selection and fidelity of transcription 


DST1 / YGL043W Overview


K4 methyltransferase yeast  cerevisiae is SET1


R write.csv versus write.csv2



write.csv uses "." for the decimal point and a comma for the separator.

write.csv2 uses a comma for the decimal point and a semicolon for the separator, the Excel convention for CSV files in some Western European locales.

2m dew point, ERA5

In Kelvin

Temperature to which the air, at 2 metres above the surface of the Earth, would have to be cooled for saturation to occur.It is a measure of the humidity of the air. Combined with temperature and pressure, it can be used to calculate the relative humidity. 2m dew point temperature is calculated by interpolating between the lowest model level and the Earth's surface, taking account of the atmospheric conditions. Temperature measured in kelvin can be converted to degrees Celsius (°C) by subtracting 273.15.

https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-land?tab=overview


Low dew point == low humidity according to wikipedia, because less vapor is need for condensation
https://en.wikipedia.org/wiki/Dew_point

Dew pointRelative humidity at 32 °C (90 °F)
Over 26 °COver 80 °F73% and higher
24–26 °C75–80 °F62–72%
21–24 °C70–74 °F52–61%
18–21 °C65–69 °F44–51%
16–18 °C60–64 °F37–43%
13–16 °C55–59 °F31–36%
10–12 °C50–54 °F26–30%
Under 10 °CUnder 50 °F25% and lower
This seems to explain that the condensation on leaves is often seen in the early morning, but not during the daytime. So, if a mutant strain has a lower dew point, it tend be in drier locations. If a strain has a higher dew point, it tends to be more humid locations


Saturday, July 18, 2020

mouse, protein noises



https://www.nature.com/articles/nature18270
Defining the consequences of genetic variation on a proteome-wide scale
volume
  • Abstract

Genetic variation modulates protein expression through both transcriptional and post-transcriptional mechanisms. To characterize the consequences of natural genetic diversity on the proteome, here we combine a multiplexed, mass spectrometry-based method for protein quantification with an emerging outbred mouse model containing extensive genetic variation from eight inbred founder strains. By measuring genome-wide transcript and protein expression in livers from 192 Diversity outbred mice, we identify 2,866 protein quantitative trait loci (pQTL) with twice as many local as distant genetic variants. These data support distinct transcriptional and post-transcriptional models underlying the observed pQTL effects. Using a sensitive approach to mediation analysis, we often identified a second protein or transcript as the causal mediator of distant pQTL. Our analysis reveals an extensive network of direct protein–protein interactions. Finally, we show that local genotype can provide accurate predictions of protein abundance in an independent cohort of collaborative cross mice.

mutations ~ dewpoint in spike region


There are 3 mutations in the Spike region.





msa_position p q ref_position ref_seq type gene start end protein_id feature_position feature_position_mod3 triplet_start triplet_end ref_triplet mut_triplet ref_position_inProtein ref_AA ref_AAPosition mut_AA ref_freq mut_freq mut_seq CHR
3654 36985 0.00453724672342917 0.0019392834243773 23730 C CDS S 21563 25384 YP_009724390.1 2169 0 23728 23730 ACC ACT 7910 T T723 T 40314 1381 T 1
3655 37185 0 0 23928 C CDS S 21563 25384 YP_009724390.1 2367 0 23926 23928 TAC TAT 7976 Y Y789 Y 41149 530 T 1
3653 36626 1.98774342659889E-68 4.81792614569765E-68 23402 A CDS S 21563 25384 YP_009724390.1 1841 2 23401 23403 GAT GGT 7801 D D614 G 11231 30413 G 1

ef_tripletmut_tripletref_position_inProteinref_AAref_AAPositionmut_AAref_freqmut_freq
GATGGT7801DD614G1123130413G
ACCACT7910TT723T403141381T
TACTAT7976YY789Y41149530

Are synonymous codon adaptation in play?
In bat, ACT > ACC, in human, ACC > ACT, so T723T from ACC -> ACT change from human major codon to human minor codon.

In human, TAT > TAC, so Y789Y change from human major codon to minor codon.
So, the answer seems to be NO.

Bat virus codon usage versus human codon bias usage

West Caucasian bat virus [gbvrl]: 4 CDS's (1478 codons)
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=249584

West Caucasian bat virus [gbvrl]: 4 CDS's (1478 codons)

fields: [triplet] [frequency: per thousand] ([number])

UUU 18.9(    28)  UCU 29.8(    44)  UAU 22.3(    33)  UGU 12.9(    19)
UUC 21.0(    31)  UCC 18.9(    28)  UAC 18.3(    27)  UGC  8.8(    13)
UUA 10.8(    16)  UCA 18.9(    28)  UAA  0.7(     1)  UGA  1.4(     2)
UUG 20.3(    30)  UCG  4.1(     6)  UAG  0.7(     1)  UGG 12.9(    19)

CUU 14.2(    21)  CCU 18.3(    27)  CAU 12.9(    19)  CGU  3.4(     5)
CUC 12.9(    19)  CCC 13.5(    20)  CAC 16.2(    24)  CGC  1.4(     2)
CUA  8.8(    13)  CCA 14.2(    21)  CAA 16.9(    25)  CGA  2.7(     4)
CUG 16.2(    24)  CCG  2.7(     4)  CAG 10.1(    15)  CGG  1.4(     2)

AUU 16.2(    24)  ACU 15.6(    23)  AAU 26.4(    39)  AGU 16.2(    24)
AUC 27.1(    40)  ACC 12.2(    18)  AAC 17.6(    26)  AGC  6.8(    10)
AUA 18.3(    27)  ACA 22.3(    33)  AAA 23.7(    35)  AGA 29.8(    44)
AUG 23.7(    35)  ACG  3.4(     5)  AAG 35.2(    52)  AGG 17.6(    26)

GUU 17.6(    26)  GCU 15.6(    23)  GAU 37.9(    56)  GGU 10.1(    15)
GUC 18.9(    28)  GCC 13.5(    20)  GAC 23.0(    34)  GGC  6.1(     9)
GUA  9.5(    14)  GCA 14.2(    21)  GAA 38.6(    57)  GGA 21.7(    32)
GUG 21.0(    31)  GCG  2.0(     3)  GAG 32.5(    48)  GGG 19.6(    29)

Coding GC 43.96% 1st letter GC 46.75% 2nd letter GC 39.17% 3rd letter GC 45.94%
homo sapiens
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606
Homo sapiens [gbpri]: 93487 CDS's (40662582 codons)

fields: [triplet] [frequency: per thousand] ([number])

UUU 17.6(714298)  UCU 15.2(618711)  UAU 12.2(495699)  UGU 10.6(430311)
UUC 20.3(824692)  UCC 17.7(718892)  UAC 15.3(622407)  UGC 12.6(513028)
UUA  7.7(311881)  UCA 12.2(496448)  UAA  1.0( 40285)  UGA  1.6( 63237)
UUG 12.9(525688)  UCG  4.4(179419)  UAG  0.8( 32109)  UGG 13.2(535595)

CUU 13.2(536515)  CCU 17.5(713233)  CAU 10.9(441711)  CGU  4.5(184609)
CUC 19.6(796638)  CCC 19.8(804620)  CAC 15.1(613713)  CGC 10.4(423516)
CUA  7.2(290751)  CCA 16.9(688038)  CAA 12.3(501911)  CGA  6.2(250760)
CUG 39.6(1611801)  CCG  6.9(281570)  CAG 34.2(1391973)  CGG 11.4(464485)

AUU 16.0(650473)  ACU 13.1(533609)  AAU 17.0(689701)  AGU 12.1(493429)
AUC 20.8(846466)  ACC 18.9(768147)  AAC 19.1(776603)  AGC 19.5(791383)
AUA  7.5(304565)  ACA 15.1(614523)  AAA 24.4(993621)  AGA 12.2(494682)
AUG 22.0(896005)  ACG  6.1(246105)  AAG 31.9(1295568)  AGG 12.0(486463)

GUU 11.0(448607)  GCU 18.4(750096)  GAU 21.8(885429)  GGU 10.8(437126)
GUC 14.5(588138)  GCC 27.7(1127679)  GAC 25.1(1020595)  GGC 22.2(903565)
GUA  7.1(287712)  GCA 15.8(643471)  GAA 29.0(1177632)  GGA 16.5(669873)
GUG 28.1(1143534)  GCG  7.4(299495)  GAG 39.6(1609975)  GGG 16.5(669768)

Coding GC 52.27% 1st letter GC 55.72% 2nd letter GC 42.54% 3rd letter GC 58.55%

Wednesday, July 15, 2020

SFS information


 78.   During the past 12 months, please indicate which Department level Federal agencies in which your SFS program partnered and describe the activity (e.g., worked on a "real world" project or research for publication or presentation, invited agency as guest speaker, gave presentation at agency, networked in an informal setting, placed SFS students for internships or permanent positions upon graduation). Listed below are the Department level Federal agencies.
Department of Agriculture
Department of Commerce – Bureau of Economic Analysis
Department of Commerce – Federal Trade Commission
Department of Commerce – National Institute of Standards & Technology
Department of Defense – Air Force/Air Force Material Command
Department of Defense – Air Force/Air Force Research Laboratory
Department of Defense – Army/Army CIO
Department of Defense – Army/Army Cyber Command and Second Army 
Department of Defense – Army/Army Knowledge Leaders Program
Department of Defense – Army/Army Research Laboratory
Department of Defense – Army/Communications-Electronics Research, Development, and Engineering Center (CERDEC)
Department of Defense – Army/Engineering Research and Development Center (ERDC)
Department of Defense – Army/Intelligence Security Command (INSCOM)
Department of Defense – Army/US Army Corps of Engineers
Department of Defense - Defense Information Systems Agency
Department of Defense - Defense Intelligence Agency
Department of Defense - National Geospatial-Intelligence Agency
Department of Defense - National Security Agency
Department of Defense – Navy/Naval Air Systems Command (NAVAIR)
Department of Defense – Navy/Naval Criminal Investigative Service (NCIS)
Department of Defense – Navy/Naval Oceanographic Office
Department of Defense – Navy/Naval Post Graduate School
Department of Defense – Navy/Naval Research Laboratory
Department of Defense – Navy/Naval Sea Systems Command (NAVSEA)
Department of Defense – Navy/Office of Naval Research
Department of Defense – Navy/Space and Naval Warfare Systems Command (SPAWAR)
Department of Defense - Other DoD sub-agency
Department of Education
Department of Energy (if you partnered with the FFRDC, please select the FFRDC in question #78 below)
Department of Health and Human Services
Department of Homeland Security - Customs & Border Protection
Department of Homeland Security - Cybersecurity and Infrastructure Security Agency
Department of Homeland Security - Other DHS sub-agency
Department of Housing and Urban Development
Department of Interior
Department of Justice - Federal Bureau of Investigations
Department of Justice - Office of the Chief Information Officer
Department of Justice - Other DOJ sub-agency
Department of Labor
Department of State
Department of Transportation
Department of Treasury
Department of Veterans Affairs
 (Enter up to 2000 characters)

79.   During the past 12 months, please indicate which independent agencies in which your SFS program partnered and describe the activity (e.g., worked on a "real world" project or research for publication or presentation, invited agency as guest speaker, gave presentation at agency, networked in an informal setting, placed SFS students for internships or permanent positions upon graduation). Listed below are the Independent Federal agencies.
Administrative Conference of the United States
African Development Foundation 
Central Intelligence Agency
Commission on Civil Rights
Commission on Presidential Scholars
Commission on Security and Cooperation in Europe
Consumer Financial Protection Bureau
Corporation for National and Community Service
Defense Nuclear Facilities Safety Board
Denali Commission
Environmental Protection Agency
Equal Employment Opportunity Commission
Export-Import Bank of the United States
Farm Credit Administration
Executive Office of the President
Federal Communications Commission
Federal Deposit Insurance Corporation 
Federal Election Commission
Federal Housing Finance Agency
Federal Labor Relations Authority
Federal Maritime Commission
Federal Mediation and Conciliation Service
Federal Mine Safety and Health Review Commission
Federal Reserve System
Federal Retirement Thrift Investment Board
Federal Trade Commission
General Accountability Office
General Services Administration 
Institute of Museum and Library Services
Inter-American Foundation
Merit Systems Protection Board
Millennium Challenge Corporation
National Aeronautics and Space Administration
National Archives and Records Administration
National Capital Planning Commission
National Credit Union Administration
National Endowment for the Humanities
National Labor Relations Board
National Mediation Board
National Railroad Passenger Corporation
National Science Foundation
National Transportation Safety Board
Nuclear Regulatory Commission
Occupational Safety and Health Review Commission
Office of Government Ethics
Office of Personnel Management
Office of Special Counsel
Office of the Director of National Intelligence
Overseas Private Investment Corporation
Peace Corps
Pension Benefit Guaranty Corporation
Postal Regulatory Commission
Privacy and Civil Liberties Oversight Board
Railroad Retirement Board
Securities and Exchange Commission
Selective Service System
Small Business Administration
Smithsonian Institution 
Social Security Administration
Surface Transportation Board
Tennessee Valley Authority
U.S. Agency for Global Media
U.S. Agency for International Development
U.S. Commodity Futures Trading Commission
U.S. International Trade Commission
U.S. Nuclear Regulatory Commission
U.S. Postal Service
U.S. Trade and Development Agency
U.S. Courts
U.S. Senate

80.   During the past 12 months, please indicate which Federally Funded Research Development Centers (FFRDC) in which your SFS program partnered and describe the activity (e.g., worked on a "real world" project or research for publication or presentation, invited FFRDC as guest speaker, gave presentation at FFRDC, networked in an informal setting, placed SFS students for internships or permanent positions upon graduation). Listed below are the FFRDCs.
Aerospace Corporation
Ames Laboratory
Argonne National Laboratory
Arroyo Center
Brookhaven National Laboratory
Center for Advanced Aviation System Development
Center for Communications and Computing
Center for Enterprise Modernization
Center for Naval Analyses
Center for Nuclear Waste Regulatory Analyses
CMS Alliance to Modernize Healthcare
Fermi National Accelerator Laboratory
Frederick National Laboratory for Cancer Research
Homeland Security Operational Analysis Center
Homeland Security Systems Engineering and Development Institute 
Idaho National Laboratory
Institute for Defense Analyses
Jet Propulsion Laboratory
Johns Hopkins Applied Physics Laboratory
Judiciary Engineering and Modernization Center
Lawrence Berkeley National Laboratory
Lawrence Livermore National Laboratory
Lincoln Laboratory
Los Alamos National Laboratory
MITRE Corporation
National Biodefense Analysis and Countermeasures Center
National Center for Atmospheric Research
National Cybersecurity Center of Excellence
National Defense Research Institute
National Optical Astronomy Observatory
National Radio Astronomy Observatory
National Renewable Energy Laboratory
National Security Engineering Center
National Solar Observatory
Oak Ridge National Laboratory
Pacific Northwest National Laboratory 
Princeton Plasma Physics Laboratory
Project Air Force
Sandia National Laboratories
Savannah River National Laboratory 
Science and Technology Policy Institute
SLAC National Accelerator Laboratory
Software Engineering Institute
Systems and Analyses Center
 (Enter up to 2000 characters)
 81.   During the past 12 months, please indicate which city, county, state, or tribal organizations in which your SFS program partnered and describe the activity (e.g., worked on a "real world" project or research for publication or presentation, invited organization as guest speaker, gave presentation at organization, networked in an informal setting, placed SFS students for internships or permanent positions upon graduation). (Enter up to 2000 characters)