Sample records for v583 reveals adaptive

  1. The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood.

    PubMed

    Vebø, Heidi C; Snipen, Lars; Nes, Ingolf F; Brede, Dag A

    2009-11-04

    Enterococcus faecalis plays a dual role in human ecology, predominantly existing as a commensal in the alimentary canal, but also as an opportunistic pathogen that frequently causes nosocomial infections like bacteremia. A number of virulence factors that contribute to the pathogenic potential of E. faecalis have been established. However, the process in which E. faecalis gains access to the bloodstream and establishes a persistent infection is not well understood. To enhance our understanding of how this commensal bacterium adapts during a bloodstream infection and to examine the interplay between genes we designed an in vitro experiment using genome-wide microarrays to investigate what effects the presence of and growth in blood have on the transcriptome of E. faecalis strain V583. We showed that growth in both 2xYT supplemented with 10% blood and in 100% blood had a great impact on the transcription of many genes in the V583 genome. We identified several immediate changes signifying cellular processes that might contribute to adaptation and growth in blood. These include modulation of membrane fatty acid composition, oxidative and lytic stress protection, acquisition of new available substrates, transport functions including heme/iron transporters and genes associated with virulence in E. faecalis. The results presented here reveal that cultivation of E. faecalis in blood in vitro has a profound impact on its transcriptome, which includes a number of virulence traits. Observed regulation of genes and pathways revealed new insight into physiological features and metabolic capacities which enable E. faecalis to adapt and grow in blood. A number of the regulated genes might potentially be useful candidates for development of new therapeutic approaches for treatment of E. faecalis infections.

  2. Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine.

    PubMed

    Arntzen, Magnus Øverlie; Karlskås, Ingrid Lea; Skaugen, Morten; Eijsink, Vincent G H; Mathiesen, Geir

    2015-01-01

    Enterococcus faecalis is a robust bacterium, which is able to survive in and adapt to hostile environments such as the urinary tract and bladder. In this label-free quantitative proteomic study based on MaxQuant LFQ algorithms, we identified 127 proteins present in the secretome of the clinical vancomycin-resistant isolate E. faecalis V583 and we compared proteins secreted in the initial phase of cultivation in urine with the secretome during cultivation in standard laboratory medium, 2xYT. Of the 54 identified proteins predicted to be secreted, six were exclusively found after cultivation in urine including the virulence factor EfaA ("endocarditis specific antigen") and its homologue EF0577 ("adhesion lipoprotein"). These two proteins are both involved in manganese transport, known to be an important determinant of colonization and infection, and may additionally function as adhesins. Other detected urine-specific proteins are involved in peptide transport (EF0063 and EF3106) and protease inhibition (EF3054). In addition, we found an uncharacterized protein (EF0764), which had not previously been linked to the adaptation of V583 to a urine environment, and which is unique to E. faecalis. Proteins found in both environments included a histone-like protein, EF1550, that was up-regulated during cultivation in urine and that has a homologue in streptococci (HlpA) known to be involved in bacterial adhesion to host cells. Up-regulated secreted proteins included autolysins. These results from secretome analyses are largely compatible with previously published data from transcriptomics studies. All in all, the present data indicate that transport, in particular metal transport, adhesion, cell wall remodelling and the unknown function carried out by the unique EF0764 are important for enterococcal adaptation to the urine environment. These results provide a basis for a more targeted exploration of novel proteins involved in the adaptability and pathogenicity of E. faecalis.

  3. Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine

    PubMed Central

    Arntzen, Magnus Øverlie; Karlskås, Ingrid Lea; Skaugen, Morten; Eijsink, Vincent G. H.; Mathiesen, Geir

    2015-01-01

    Enterococcus faecalis is a robust bacterium, which is able to survive in and adapt to hostile environments such as the urinary tract and bladder. In this label-free quantitative proteomic study based on MaxQuant LFQ algorithms, we identified 127 proteins present in the secretome of the clinical vancomycin-resistant isolate E. faecalis V583 and we compared proteins secreted in the initial phase of cultivation in urine with the secretome during cultivation in standard laboratory medium, 2xYT. Of the 54 identified proteins predicted to be secreted, six were exclusively found after cultivation in urine including the virulence factor EfaA (“endocarditis specific antigen”) and its homologue EF0577 (“adhesion lipoprotein”). These two proteins are both involved in manganese transport, known to be an important determinant of colonization and infection, and may additionally function as adhesins. Other detected urine-specific proteins are involved in peptide transport (EF0063 and EF3106) and protease inhibition (EF3054). In addition, we found an uncharacterized protein (EF0764), which had not previously been linked to the adaptation of V583 to a urine environment, and which is unique to E. faecalis. Proteins found in both environments included a histone-like protein, EF1550, that was up-regulated during cultivation in urine and that has a homologue in streptococci (HlpA) known to be involved in bacterial adhesion to host cells. Up-regulated secreted proteins included autolysins. These results from secretome analyses are largely compatible with previously published data from transcriptomics studies. All in all, the present data indicate that transport, in particular metal transport, adhesion, cell wall remodelling and the unknown function carried out by the unique EF0764 are important for enterococcal adaptation to the urine environment. These results provide a basis for a more targeted exploration of novel proteins involved in the adaptability and pathogenicity of E

  4. 12 CFR 583.8 - Corporation.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 6 2013-01-01 2012-01-01 true Corporation. 583.8 Section 583.8 Banks and... SAVINGS AND LOAN HOLDING COMPANIES § 583.8 Corporation. The term Corporation means the Federal Deposit Insurance Corporation. ...

  5. 12 CFR 583.8 - Corporation.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 6 2012-01-01 2012-01-01 false Corporation. 583.8 Section 583.8 Banks and... SAVINGS AND LOAN HOLDING COMPANIES § 583.8 Corporation. The term Corporation means the Federal Deposit Insurance Corporation. ...

  6. 12 CFR 583.8 - Corporation.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Corporation. 583.8 Section 583.8 Banks and... SAVINGS AND LOAN HOLDING COMPANIES § 583.8 Corporation. The term Corporation means the Federal Deposit Insurance Corporation. ...

  7. 12 CFR 583.8 - Corporation.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Corporation. 583.8 Section 583.8 Banks and... SAVINGS AND LOAN HOLDING COMPANIES § 583.8 Corporation. The term Corporation means the Federal Deposit Insurance Corporation. ...

  8. 12 CFR 583.8 - Corporation.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 6 2014-01-01 2012-01-01 true Corporation. 583.8 Section 583.8 Banks and... SAVINGS AND LOAN HOLDING COMPANIES § 583.8 Corporation. The term Corporation means the Federal Deposit Insurance Corporation. ...

  9. 49 CFR 583.1 - Scope.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Scope. 583.1 Section 583.1 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.1 Scope. This part establishes...

  10. 49 CFR 583.1 - Scope.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Scope. 583.1 Section 583.1 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.1 Scope. This part establishes...

  11. 49 CFR 583.3 - Applicability.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Applicability. 583.3 Section 583.3 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.3 Applicability. This part...

  12. 49 CFR 583.17 - Reporting.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Reporting. 583.17 Section 583.17 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.17 Reporting. For each model...

  13. 49 CFR 583.17 - Reporting.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Reporting. 583.17 Section 583.17 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.17 Reporting. For each model...

  14. 49 CFR 583.3 - Applicability.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Applicability. 583.3 Section 583.3 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.3 Applicability. This part...

  15. 49 CFR 583.17 - Reporting.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Reporting. 583.17 Section 583.17 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.17 Reporting. For each model...

  16. 49 CFR 583.3 - Applicability.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Applicability. 583.3 Section 583.3 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.3 Applicability. This part...

  17. 49 CFR 583.3 - Applicability.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Applicability. 583.3 Section 583.3 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.3 Applicability. This part...

  18. 49 CFR 583.17 - Reporting.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Reporting. 583.17 Section 583.17 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.17 Reporting. For each model...

  19. 49 CFR 583.3 - Applicability.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Applicability. 583.3 Section 583.3 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.3 Applicability. This part...

  20. 49 CFR 583.1 - Scope.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Scope. 583.1 Section 583.1 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.1 Scope. This part establishes...

  1. 49 CFR 583.1 - Scope.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Scope. 583.1 Section 583.1 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.1 Scope. This part establishes...

  2. 49 CFR 583.1 - Scope.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Scope. 583.1 Section 583.1 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.1 Scope. This part establishes...

  3. 12 CFR 583.5 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false [Reserved] 583.5 Section 583.5 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.5 [Reserved] ...

  4. 12 CFR 583.19 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false [Reserved] 583.19 Section 583.19 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.19 [Reserved] ...

  5. 40 CFR 58.3 - Applicability.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Applicability. 58.3 Section 58.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) AMBIENT AIR QUALITY SURVEILLANCE General Provisions § 58.3 Applicability. This part applies to: (a) State air...

  6. 49 CFR 583.2 - Purpose.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Purpose. 583.2 Section 583.2 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.2 Purpose. The purpose of this...

  7. 49 CFR 583.2 - Purpose.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Purpose. 583.2 Section 583.2 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.2 Purpose. The purpose of this...

  8. 49 CFR 583.2 - Purpose.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Purpose. 583.2 Section 583.2 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.2 Purpose. The purpose of this...

  9. 49 CFR 583.2 - Purpose.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Purpose. 583.2 Section 583.2 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.2 Purpose. The purpose of this...

  10. 49 CFR 583.2 - Purpose.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Purpose. 583.2 Section 583.2 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.2 Purpose. The purpose of this...

  11. 7 CFR 58.3 - Authority.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Authority. 58.3 Section 58.3 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections... Inspection and Grading Services of Manufactured or Processed Dairy Products Administration § 58.3 Authority...

  12. 24 CFR 583.5 - Definitions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM General § 583.5 Definitions. As used in this part: Applicant... definition, governmental entities include those that have general governmental powers (such as a city or... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Definitions. 583.5 Section 583.5...

  13. 12 CFR 583.13 - Office.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Office. 583.13 Section 583.13 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.13 Office. The term Office means the Office of Thrift Supervision. ...

  14. 12 CFR 583.18 - Registrant.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Registrant. 583.18 Section 583.18 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.18 Registrant. The term registrant means a savings and loan...

  15. 12 CFR 583.16 - Person.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Person. 583.16 Section 583.16 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.16 Person. The term person means an individual or company. ...

  16. 12 CFR 583.1 - Acquire.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Acquire. 583.1 Section 583.1 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.1 Acquire. The term acquire means to acquire, directly or indirectly...

  17. 12 CFR 583.9 - Director.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Director. 583.9 Section 583.9 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.9 Director. The term director as used in any document specified in...

  18. 12 CFR 583.14 - Officer.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Officer. 583.14 Section 583.14 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.14 Officer. The term officer as used in any document specified in...

  19. 12 CFR 583.22 - State.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false State. 583.22 Section 583.22 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.22 State. The term State includes the District of Columbia and the...

  20. 12 CFR 583.3 - Bank.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Bank. 583.3 Section 583.3 Banks and Banking... AND LOAN HOLDING COMPANIES § 583.3 Bank. The term bank means any national bank, state bank, state-chartered savings bank, cooperative bank, or industrial bank, the deposits of which are insured by the...

  1. 12 CFR 583.7 - Control.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Control. 583.7 Section 583.7 Banks and Banking... AND LOAN HOLDING COMPANIES § 583.7 Control. For purposes of this chapter, a person shall be deemed to have control of: (a) A savings association if the person directly or indirectly or acting in concert...

  2. 12 CFR 583.7 - Control.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 6 2014-01-01 2012-01-01 true Control. 583.7 Section 583.7 Banks and Banking... AND LOAN HOLDING COMPANIES § 583.7 Control. For purposes of this chapter, a person shall be deemed to have control of: (a) A savings association if the person directly or indirectly or acting in concert...

  3. 12 CFR 583.7 - Control.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 6 2012-01-01 2012-01-01 false Control. 583.7 Section 583.7 Banks and Banking... AND LOAN HOLDING COMPANIES § 583.7 Control. For purposes of this chapter, a person shall be deemed to have control of: (a) A savings association if the person directly or indirectly or acting in concert...

  4. 12 CFR 583.7 - Control.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Control. 583.7 Section 583.7 Banks and Banking... AND LOAN HOLDING COMPANIES § 583.7 Control. For purposes of this chapter, a person shall be deemed to have control of: (a) A savings association if the person directly or indirectly or acting in concert...

  5. 12 CFR 583.7 - Control.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 6 2013-01-01 2012-01-01 true Control. 583.7 Section 583.7 Banks and Banking... AND LOAN HOLDING COMPANIES § 583.7 Control. For purposes of this chapter, a person shall be deemed to have control of: (a) A savings association if the person directly or indirectly or acting in concert...

  6. 49 CFR 583.15 - Joint ownership.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Joint ownership. 583.15 Section 583.15 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.15 Joint...

  7. 49 CFR 583.5 - Label requirements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Label requirements. 583.5 Section 583.5 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.5 Label...

  8. 49 CFR 583.5 - Label requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Label requirements. 583.5 Section 583.5 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.5 Label...

  9. 49 CFR 583.5 - Label requirements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Label requirements. 583.5 Section 583.5 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.5 Label...

  10. 49 CFR 583.5 - Label requirements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Label requirements. 583.5 Section 583.5 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.5 Label...

  11. 49 CFR 583.5 - Label requirements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Label requirements. 583.5 Section 583.5 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.5 Label...

  12. 49 CFR 583.15 - Joint ownership.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Joint ownership. 583.15 Section 583.15 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.15 Joint...

  13. 49 CFR 583.15 - Joint ownership.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Joint ownership. 583.15 Section 583.15 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.15 Joint...

  14. 49 CFR 583.15 - Joint ownership.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Joint ownership. 583.15 Section 583.15 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.15 Joint...

  15. 24 CFR 583.400 - Grant agreement.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 3 2014-04-01 2013-04-01 true Grant agreement. 583.400 Section 583... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Administration § 583.400 Grant agreement. (a... of this part will be incorporated in a grant agreement executed by HUD and the recipient. (b...

  16. 12 CFR 583.24 - Uninsured institution.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Uninsured institution. 583.24 Section 583.24 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.24 Uninsured institution. The term uninsured institution...

  17. 24 CFR 583.320 - Site control.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Site control. 583.320 Section 583... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.320 Site control. (a) Site control. (1) Where grant funds will be used for acquisition, rehabilitation, or new construction...

  18. 24 CFR 583.320 - Site control.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 3 2013-04-01 2013-04-01 false Site control. 583.320 Section 583... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.320 Site control. (a) Site control. (1) Where grant funds will be used for acquisition, rehabilitation, or new construction...

  19. 24 CFR 583.320 - Site control.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 3 2014-04-01 2013-04-01 true Site control. 583.320 Section 583... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.320 Site control. (a) Site control. (1) Where grant funds will be used for acquisition, rehabilitation, or new construction...

  20. 24 CFR 583.320 - Site control.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 3 2011-04-01 2010-04-01 true Site control. 583.320 Section 583... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.320 Site control. (a) Site control. (1) Where grant funds will be used for acquisition, rehabilitation, or new construction...

  1. 24 CFR 583.320 - Site control.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 3 2012-04-01 2012-04-01 false Site control. 583.320 Section 583... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.320 Site control. (a) Site control. (1) Where grant funds will be used for acquisition, rehabilitation, or new construction...

  2. 12 CFR 583.15 - Parent company.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Parent company. 583.15 Section 583.15 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.15 Parent company. The term parent company means any company...

  3. 49 CFR 583.16 - Maintenance of records.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Maintenance of records. 583.16 Section 583.16 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.16 Maintenance...

  4. 49 CFR 583.14 - Currency conversion rate.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Currency conversion rate. 583.14 Section 583.14 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.14 Currency...

  5. 49 CFR 583.16 - Maintenance of records.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Maintenance of records. 583.16 Section 583.16 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.16 Maintenance...

  6. 49 CFR 583.16 - Maintenance of records.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Maintenance of records. 583.16 Section 583.16 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.16 Maintenance...

  7. 49 CFR 583.14 - Currency conversion rate.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Currency conversion rate. 583.14 Section 583.14 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.14 Currency...

  8. 49 CFR 583.14 - Currency conversion rate.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Currency conversion rate. 583.14 Section 583.14 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.14 Currency...

  9. 49 CFR 583.14 - Currency conversion rate.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Currency conversion rate. 583.14 Section 583.14 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.14 Currency...

  10. 49 CFR 583.16 - Maintenance of records.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Maintenance of records. 583.16 Section 583.16 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.16 Maintenance...

  11. 49 CFR 583.14 - Currency conversion rate.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Currency conversion rate. 583.14 Section 583.14 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.14 Currency...

  12. 12 CFR 583.23 - Subsidiary.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Subsidiary. 583.23 Section 583.23 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING... owned or controlled directly or indirectly by a person, and includes any service corporation owned in...

  13. 7 CFR 51.583 - Reasonably well developed.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Reasonably well developed. 51.583 Section 51.583... STANDARDS) United States Standards for Celery Definitions § 51.583 Reasonably well developed. Reasonably well developed means that the branches are of reasonable width and thickness in relation to the length...

  14. 7 CFR 51.583 - Reasonably well developed.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Reasonably well developed. 51.583 Section 51.583... STANDARDS) United States Standards for Celery Definitions § 51.583 Reasonably well developed. Reasonably well developed means that the branches are of reasonable width and thickness in relation to the length...

  15. 7 CFR 51.583 - Reasonably well developed.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Reasonably well developed. 51.583 Section 51.583... STANDARDS) United States Standards for Celery Definitions § 51.583 Reasonably well developed. Reasonably well developed means that the branches are of reasonable width and thickness in relation to the length...

  16. 12 CFR 583.6 - Company.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Corporation, (b) The Resolution Trust Corporation, (c) Any Federal Home Loan Bank, (d) The Office of Thrift... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Company. 583.6 Section 583.6 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS...

  17. Impact of Manganese, Copper and Zinc Ions on the Transcriptome of the Nosocomial Pathogen Enterococcus faecalis V583

    PubMed Central

    Coelho Abrantes, Marta; Lopes, Maria de Fátima; Kok, Jan

    2011-01-01

    Mechanisms that enable Enterococcus to cope with different environmental stresses and their contribution to the switch from commensalism to pathogenicity of this organism are still poorly understood. Maintenance of intracellular homeostasis of metal ions is crucial for survival of these bacteria. In particular Zn2+, Mn2+ and Cu2+ are very important metal ions as they are co-factors of many enzymes, are involved in oxidative stress defense and have a role in the immune system of the host. Their concentrations inside the human body vary hugely, which makes it imperative for Enterococcus to fine-tune metal ion homeostasis in order to survive inside the host and colonize it. Little is known about metal regulation in Enterococcus faecalis. Here we present the first genome-wide description of gene expression of E. faecalis V583 growing in the presence of high concentrations of zinc, manganese or copper ions. The DNA microarray experiments revealed that mostly transporters are involved in the responses of E. faecalis to prolonged exposure to high metal concentrations although genes involved in cellular processes, in energy and amino acid metabolisms and genes related to the cell envelope also seem to play important roles. PMID:22053193

  18. 12 CFR 583.17 - Qualified thrift lender.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Qualified thrift lender. 583.17 Section 583.17 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.17 Qualified thrift lender. The term qualified thrift...

  19. 12 CFR 583.4 - Bank holding company.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Bank holding company. 583.4 Section 583.4 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.4 Bank holding company. The term bank holding company...

  20. 21 CFR 58.3 - Definitions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 109 and 509. (9) [Reserved] (10) A Notice of Claimed Investigational Exemption for a New Animal Drug, described in part 511. (11) A new animal drug application, described in part 514. (12) [Reserved] (13) An... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Definitions. 58.3 Section 58.3 Food and Drugs FOOD...

  1. 21 CFR 58.3 - Definitions.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 109 and 509. (9) [Reserved] (10) A Notice of Claimed Investigational Exemption for a New Animal Drug, described in part 511. (11) A new animal drug application, described in part 514. (12) [Reserved] (13) An... 21 Food and Drugs 1 2014-04-01 2014-04-01 false Definitions. 58.3 Section 58.3 Food and Drugs FOOD...

  2. 21 CFR 58.3 - Definitions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 109 and 509. (9) [Reserved] (10) A Notice of Claimed Investigational Exemption for a New Animal Drug, described in part 511. (11) A new animal drug application, described in part 514. (12) [Reserved] (13) An... 21 Food and Drugs 1 2011-04-01 2011-04-01 false Definitions. 58.3 Section 58.3 Food and Drugs FOOD...

  3. 21 CFR 58.3 - Definitions.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 109 and 509. (9) [Reserved] (10) A Notice of Claimed Investigational Exemption for a New Animal Drug, described in part 511. (11) A new animal drug application, described in part 514. (12) [Reserved] (13) An... 21 Food and Drugs 1 2012-04-01 2012-04-01 false Definitions. 58.3 Section 58.3 Food and Drugs FOOD...

  4. 21 CFR 58.3 - Definitions.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 109 and 509. (9) [Reserved] (10) A Notice of Claimed Investigational Exemption for a New Animal Drug, described in part 511. (11) A new animal drug application, described in part 514. (12) [Reserved] (13) An... 21 Food and Drugs 1 2013-04-01 2013-04-01 false Definitions. 58.3 Section 58.3 Food and Drugs FOOD...

  5. 12 CFR 583.4 - Bank holding company.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Bank holding company. 583.4 Section 583.4 Banks... AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.4 Bank holding company. The term bank holding company means any company which has control over any bank or over any company that is or becomes a bank holding...

  6. 24 CFR 583.300 - General operation.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 3 2011-04-01 2010-04-01 true General operation. 583.300 Section... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.300 General operation... condition of the structure and the operation of the housing or services. (b) Habitability standards. Except...

  7. 24 CFR 583.300 - General operation.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 3 2012-04-01 2012-04-01 false General operation. 583.300 Section... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.300 General operation... condition of the structure and the operation of the housing or services. (b) Habitability standards. Except...

  8. 24 CFR 583.300 - General operation.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 3 2013-04-01 2013-04-01 false General operation. 583.300 Section... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.300 General operation... condition of the structure and the operation of the housing or services. (b) Habitability standards. Except...

  9. 24 CFR 583.300 - General operation.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 3 2014-04-01 2013-04-01 true General operation. 583.300 Section... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583.300 General operation... condition of the structure and the operation of the housing or services. (b) Habitability standards. Except...

  10. 20 CFR 410.583 - Responsibility of representative payee.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Responsibility of representative payee. 410.583 Section 410.583 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL COAL MINE HEALTH AND SAFETY ACT OF 1969, TITLE IV-BLACK LUNG BENEFITS (1969- ) Payment of Benefits § 410.583 Responsibility of...

  11. 20 CFR 410.583 - Responsibility of representative payee.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 20 Employees' Benefits 2 2011-04-01 2011-04-01 false Responsibility of representative payee. 410.583 Section 410.583 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL COAL MINE HEALTH AND SAFETY ACT OF 1969, TITLE IV-BLACK LUNG BENEFITS (1969- ) Payment of Benefits § 410.583 Responsibility of...

  12. 24 CFR 583.405 - Program changes.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Program changes. 583.405 Section... DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Administration § 583.405 Program changes. (a) HUD approval. (1) A recipient may not make any significant changes to an approved program without prior HUD...

  13. 24 CFR 583.230 - Environmental review.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Environmental review. 583.230... § 583.230 Environmental review. (a) Activities under this part are subject to HUD environmental regulations in part 58 of this title, except that HUD will perform an environmental review in accordance with...

  14. 24 CFR 583.230 - Environmental review.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 3 2011-04-01 2010-04-01 true Environmental review. 583.230... § 583.230 Environmental review. (a) Activities under this part are subject to HUD environmental regulations in part 58 of this title, except that HUD will perform an environmental review in accordance with...

  15. 49 CFR 583.9 - Attachment and maintenance of label.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Attachment and maintenance of label. 583.9 Section 583.9 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.9...

  16. 49 CFR 583.9 - Attachment and maintenance of label.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Attachment and maintenance of label. 583.9 Section 583.9 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.9...

  17. 49 CFR 583.9 - Attachment and maintenance of label.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Attachment and maintenance of label. 583.9 Section 583.9 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.9...

  18. 49 CFR 583.9 - Attachment and maintenance of label.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Attachment and maintenance of label. 583.9 Section 583.9 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.9...

  19. 49 CFR 583.9 - Attachment and maintenance of label.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Attachment and maintenance of label. 583.9 Section 583.9 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.9...

  20. 7 CFR 51.583 - Reasonably well developed.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Reasonably well developed. 51.583 Section 51.583 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... well developed. Reasonably well developed means that the branches are of reasonable width and thickness...

  1. 7 CFR 51.583 - Reasonably well developed.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Reasonably well developed. 51.583 Section 51.583 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... well developed. Reasonably well developed means that the branches are of reasonable width and thickness...

  2. 34 CFR 5.83 - Contents of request for review.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PURSUANT TO PUB. L. 90-23 (Eff. until 7-14-10) Administrative Review § 5.83 Contents of request for review. The request for review shall include a copy of the written request and the denial. ... 34 Education 1 2010-07-01 2010-07-01 false Contents of request for review. 5.83 Section 5.83...

  3. Enterococcus faecalis Prophage Dynamics and Contributions to Pathogenic Traits

    PubMed Central

    Matos, Renata C.; Lapaque, Nicolas; Rigottier-Gois, Lionel; Debarbieux, Laurent; Meylheuc, Thierry; Gonzalez-Zorn, Bruno; Repoila, Francis; Lopes, Maria de Fatima; Serror, Pascale

    2013-01-01

    Polylysogeny is frequently considered to be the result of an adaptive evolutionary process in which prophages confer fitness and/or virulence factors, thus making them important for evolution of both bacterial populations and infectious diseases. The Enterococcus faecalis V583 isolate belongs to the high-risk clonal complex 2 that is particularly well adapted to the hospital environment. Its genome carries 7 prophage-like elements (V583-pp1 to -pp7), one of which is ubiquitous in the species. In this study, we investigated the activity of the V583 prophages and their contribution to E. faecalis biological traits. We systematically analyzed the ability of each prophage to excise from the bacterial chromosome, to replicate and to package its DNA. We also created a set of E. faecalis isogenic strains that lack from one to all six non-ubiquitous prophages by mimicking natural excision. Our work reveals that prophages of E. faecalis V583 excise from the bacterial chromosome in the presence of a fluoroquinolone, and are able to produce active phage progeny. Intricate interactions between V583 prophages were also unveiled: i) pp7, coined EfCIV583 for E. faecalis chromosomal island of V583, hijacks capsids from helper phage 1, leading to the formation of distinct virions, and ii) pp1, pp3 and pp5 inhibit excision of pp4 and pp6. The hijacking exerted by EfCIV583 on helper phage 1 capsids is the first example of molecular piracy in Gram positive bacteria other than staphylococci. Furthermore, prophages encoding platelet-binding-like proteins were found to be involved in adhesion to human platelets, considered as a first step towards the development of infective endocarditis. Our findings reveal not only a role of E. faecalis V583 prophages in pathogenicity, but also provide an explanation for the correlation between antibiotic usage and E. faecalis success as a nosocomial pathogen, as fluoriquinolone may provoke release of prophages and promote gene dissemination among

  4. 49 CFR 583.13 - Supplier certification and certificates.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Supplier certification and certificates. 583.13 Section 583.13 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  5. 49 CFR 583.13 - Supplier certification and certificates.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Supplier certification and certificates. 583.13 Section 583.13 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  6. 49 CFR 583.13 - Supplier certification and certificates.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Supplier certification and certificates. 583.13 Section 583.13 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  7. 49 CFR 583.13 - Supplier certification and certificates.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Supplier certification and certificates. 583.13 Section 583.13 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  8. 49 CFR 583.13 - Supplier certification and certificates.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Supplier certification and certificates. 583.13 Section 583.13 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  9. An Approach to V&V of Embedded Adaptive Systems

    NASA Technical Reports Server (NTRS)

    Liu, Yan; Yerramalla, Sampath; Fuller, Edgar; Cukic, Bojan; Gururajan, Srikaruth

    2004-01-01

    Rigorous Verification and Validation (V&V) techniques are essential for high assurance systems. Lately, the performance of some of these systems is enhanced by embedded adaptive components in order to cope with environmental changes. Although the ability of adapting is appealing, it actually poses a problem in terms of V&V. Since uncertainties induced by environmental changes have a significant impact on system behavior, the applicability of conventional V&V techniques is limited. In safety-critical applications such as flight control system, the mechanisms of change must be observed, diagnosed, accommodated and well understood prior to deployment. In this paper, we propose a non-conventional V&V approach suitable for online adaptive systems. We apply our approach to an intelligent flight control system that employs a particular type of Neural Networks (NN) as the adaptive learning paradigm. Presented methodology consists of a novelty detection technique and online stability monitoring tools. The novelty detection technique is based on Support Vector Data Description that detects novel (abnormal) data patterns. The Online Stability Monitoring tools based on Lyapunov's Stability Theory detect unstable learning behavior in neural networks. Cases studies based on a high fidelity simulator of NASA's Intelligent Flight Control System demonstrate a successful application of the presented V&V methodology. ,

  10. 12 CFR 583.12 - Multiple savings and loan holding company.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Multiple savings and loan holding company. 583.12 Section 583.12 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.12 Multiple savings and loan...

  11. 49 CFR 583.4 - Definitions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.4 Definitions. (a) Statutory... automobile are included with such vehicle whether or not such component parts are permanently installed in or...

  12. 49 CFR 583.4 - Definitions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.4 Definitions. (a) Statutory... automobile are included with such vehicle whether or not such component parts are permanently installed in or...

  13. 49 CFR 583.4 - Definitions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.4 Definitions. (a) Statutory... automobile are included with such vehicle whether or not such component parts are permanently installed in or...

  14. 49 CFR 583.4 - Definitions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.4 Definitions. (a) Statutory... automobile are included with such vehicle whether or not such component parts are permanently installed in or...

  15. 49 CFR 583.4 - Definitions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING § 583.4 Definitions. (a) Statutory... automobile are included with such vehicle whether or not such component parts are permanently installed in or...

  16. 27 CFR 19.583 - Spirits for industrial use.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Spirits for industrial use. 19.583 Section 19.583 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU... container is not exposed; (2) Required marks are applied to an exterior surface of the case; (3) The case is...

  17. 24 CFR 583.125 - Grants for operating costs.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    .... Operating costs are those associated with the day-to-day operation of the supportive housing. They also... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Grants for operating costs. 583.125... for operating costs. (a) General. HUD will provide grants to pay a portion (as described in § 583.130...

  18. 49 CFR 583.12 - Suppliers of engines and transmissions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Suppliers of engines and transmissions. 583.12 Section 583.12 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  19. 49 CFR 583.12 - Suppliers of engines and transmissions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Suppliers of engines and transmissions. 583.12 Section 583.12 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  20. 49 CFR 583.12 - Suppliers of engines and transmissions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Suppliers of engines and transmissions. 583.12 Section 583.12 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  1. 49 CFR 583.12 - Suppliers of engines and transmissions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Suppliers of engines and transmissions. 583.12 Section 583.12 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  2. 49 CFR 583.12 - Suppliers of engines and transmissions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Suppliers of engines and transmissions. 583.12 Section 583.12 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS CONTENT LABELING...

  3. 12 CFR 583.20 - Savings and loan holding company.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Savings and loan holding company. 583.20... REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.20 Savings and loan holding company. The term savings and loan holding company means any company that directly or indirectly controls a savings...

  4. 12 CFR 583.2 - Affiliate.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.2 Affiliate. The term affiliate of a specified savings association means any person or company which controls, is controlled by, or is under common control with...

  5. 12 CFR 583.3 - Bank.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.3 Bank. The term bank means any national bank, state bank, state-chartered savings bank, cooperative bank, or industrial bank, the deposits of which are insured by the...

  6. Adjacent Vehicle Number-Triggered Adaptive Transmission for V2V Communications.

    PubMed

    Wei, Yiqiao; Chen, Jingjun; Hwang, Seung-Hoon

    2018-03-02

    For vehicle-to-vehicle (V2V) communication, such issues as continuity and reliability still have to be solved. Specifically, it is necessary to consider a more scalable physical layer due to the high-speed mobility of vehicles and the complex channel environment. Adaptive transmission has been adapted in channel-dependent scheduling. However, it has been neglected with regards to the physical topology changes in the vehicle network. In this paper, we propose a physical topology-triggered adaptive transmission scheme which adjusts the data rate between vehicles according to the number of connectable vehicles nearby. Also, we investigate the performance of the proposed method using computer simulations and compare it with the conventional methods. The numerical results show that the proposed method can provide more continuous and reliable data transmission for V2V communications.

  7. 40 CFR 35.583 - Eligible recipients.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Clean Water Act (see 40 CFR 130.6(d)). ... STATE AND LOCAL ASSISTANCE Environmental Program Grants for Tribes Water Pollution Control (sections 106 and 518) § 35.583 Eligible recipients. A Tribe, including an Intertribal Consortium, is eligible to...

  8. 40 CFR 35.583 - Eligible recipients.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Clean Water Act (see 40 CFR 130.6(d)). ... STATE AND LOCAL ASSISTANCE Environmental Program Grants for Tribes Water Pollution Control (sections 106 and 518) § 35.583 Eligible recipients. A Tribe, including an Intertribal Consortium, is eligible to...

  9. 40 CFR 35.583 - Eligible recipients.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Clean Water Act (see 40 CFR 130.6(d)). ... STATE AND LOCAL ASSISTANCE Environmental Program Grants for Tribes Water Pollution Control (sections 106 and 518) § 35.583 Eligible recipients. A Tribe, including an Intertribal Consortium, is eligible to...

  10. 40 CFR 35.583 - Eligible recipients.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Clean Water Act (see 40 CFR 130.6(d)). ... STATE AND LOCAL ASSISTANCE Environmental Program Grants for Tribes Water Pollution Control (sections 106 and 518) § 35.583 Eligible recipients. A Tribe, including an Intertribal Consortium, is eligible to...

  11. 40 CFR 35.583 - Eligible recipients.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Clean Water Act (see 40 CFR 130.6(d)). ... STATE AND LOCAL ASSISTANCE Environmental Program Grants for Tribes Water Pollution Control (sections 106 and 518) § 35.583 Eligible recipients. A Tribe, including an Intertribal Consortium, is eligible to...

  12. 49 CFR 583.10 - Outside suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Outside suppliers of passenger motor vehicle equipment. 583.10 Section 583.10 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  13. 49 CFR 583.11 - Allied suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Allied suppliers of passenger motor vehicle equipment. 583.11 Section 583.11 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  14. 49 CFR 583.10 - Outside suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Outside suppliers of passenger motor vehicle equipment. 583.10 Section 583.10 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  15. 49 CFR 583.11 - Allied suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Allied suppliers of passenger motor vehicle equipment. 583.11 Section 583.11 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  16. 49 CFR 583.11 - Allied suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Allied suppliers of passenger motor vehicle equipment. 583.11 Section 583.11 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  17. 49 CFR 583.11 - Allied suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Allied suppliers of passenger motor vehicle equipment. 583.11 Section 583.11 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  18. 49 CFR 583.10 - Outside suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Outside suppliers of passenger motor vehicle equipment. 583.10 Section 583.10 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  19. 49 CFR 583.10 - Outside suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Outside suppliers of passenger motor vehicle equipment. 583.10 Section 583.10 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  20. 49 CFR 583.10 - Outside suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Outside suppliers of passenger motor vehicle equipment. 583.10 Section 583.10 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  1. 49 CFR 583.11 - Allied suppliers of passenger motor vehicle equipment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Allied suppliers of passenger motor vehicle equipment. 583.11 Section 583.11 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  2. Adjacent Vehicle Number-Triggered Adaptive Transmission for V2V Communications

    PubMed Central

    Wei, Yiqiao; Chen, Jingjun

    2018-01-01

    For vehicle-to-vehicle (V2V) communication, such issues as continuity and reliability still have to be solved. Specifically, it is necessary to consider a more scalable physical layer due to the high-speed mobility of vehicles and the complex channel environment. Adaptive transmission has been adapted in channel-dependent scheduling. However, it has been neglected with regards to the physical topology changes in the vehicle network. In this paper, we propose a physical topology-triggered adaptive transmission scheme which adjusts the data rate between vehicles according to the number of connectable vehicles nearby. Also, we investigate the performance of the proposed method using computer simulations and compare it with the conventional methods. The numerical results show that the proposed method can provide more continuous and reliable data transmission for V2V communications. PMID:29498646

  3. 24 CFR 583.140 - Technical assistance.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Technical assistance. 583.140... Technical assistance. (a) General. HUD may set aside funds annually to provide technical assistance, either... technical assistance is for the purpose of promoting the development of supportive housing and supportive...

  4. 49 CFR 583.6 - Procedure for determining U.S./Canadian parts content.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Procedure for determining U.S./Canadian parts content. 583.6 Section 583.6 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  5. 49 CFR 583.6 - Procedure for determining U.S./Canadian parts content.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Procedure for determining U.S./Canadian parts content. 583.6 Section 583.6 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  6. 49 CFR 583.6 - Procedure for determining U.S./Canadian parts content.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Procedure for determining U.S./Canadian parts content. 583.6 Section 583.6 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  7. 49 CFR 583.6 - Procedure for determining U.S./Canadian parts content.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Procedure for determining U.S./Canadian parts content. 583.6 Section 583.6 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  8. 49 CFR 583.6 - Procedure for determining U.S./Canadian parts content.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Procedure for determining U.S./Canadian parts content. 583.6 Section 583.6 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AUTOMOBILE PARTS...

  9. 12 CFR 583.21 - Savings association.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.21 Savings association. The term savings association means a Federal savings and loan association or a Federal savings bank chartered under section 5 of the Home Owners' Loan Act, a building and loan, savings and loan or homestead association or a cooperative...

  10. 76 FR 34689 - Commission Information Collection Activities [FERC-583], Comment Request; Extension

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-14

    ... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. IC11-583-000] Commission Information Collection Activities [FERC-583], Comment Request; Extension AGENCY: Federal Energy Regulatory.... 3506(c)(2)(A) (2006), (Pub. L. 104-13), the Federal Energy Regulatory Commission (Commission or FERC...

  11. 49 CFR 583.7 - Procedure for determining major foreign sources of passenger motor vehicle equipment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... passenger motor vehicle equipment. 583.7 Section 583.7 Transportation Other Regulations Relating to... passenger motor vehicle equipment. (a) Each manufacturer, except as specified in § 583.5(f) and (g), shall determine the countries, if any, which are major foreign sources of passenger motor vehicle equipment and...

  12. Camelid genomes reveal evolution and adaptation to desert environments.

    PubMed

    Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

    2014-10-21

    Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

  13. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

    PubMed Central

    Das, Anupam; Espinosa-Cantú, Adriana; De Maeyer, Dries; Arslan, Ahmed; Van Pee, Michiel; van der Zande, Elisa; Meert, Wim; Yang, Yudi; Zhu, Bo; Marchal, Kathleen; DeLuna, Alexander; Van Noort, Vera; Jelier, Rob; Verstrepen, Kevin J.

    2015-01-01

    Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts. PMID:26545090

  14. 28 CFR 58.3 - Qualification for membership on panels of private trustees.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... private trustees. 58.3 Section 58.3 Judicial Administration DEPARTMENT OF JUSTICE (CONTINUED) REGULATIONS... private trustees. (a) To be eligible for appointment to the panel and to retain eligibility therefor, an... the private panel. However, each person who, in the opinion of the U.S. Trustee or of the Director...

  15. 49 CFR 583.8 - Procedure for determining country of origin for engines and transmissions (for purposes of...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Procedure for determining country of origin for engines and transmissions (for purposes of determining the information specified by §§ 583.5(a)(4) and 583.5(a)(5) only). 583.8 Section 583.8 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY...

  16. 19 CFR 10.583 - Filing of claim for preferential tariff treatment upon importation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... RATE, ETC. Dominican Republic-Central America-United States Free Trade Agreement Import Requirements... upon importation. 10.583 Section 10.583 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT... prepared by the importer, exporter, or producer of the good; or (2) The importer's knowledge that the good...

  17. Perceptual suppression revealed by adaptive multi-scale entropy analysis of local field potential in monkey visual cortex.

    PubMed

    Hu, Meng; Liang, Hualou

    2013-04-01

    Generalized flash suppression (GFS), in which a salient visual stimulus can be rendered invisible despite continuous retinal input, provides a rare opportunity to directly study the neural mechanism of visual perception. Previous work based on linear methods, such as spectral analysis, on local field potential (LFP) during GFS has shown that the LFP power at distinctive frequency bands are differentially modulated by perceptual suppression. Yet, the linear method alone may be insufficient for the full assessment of neural dynamic due to the fundamentally nonlinear nature of neural signals. In this study, we set forth to analyze the LFP data collected from multiple visual areas in V1, V2 and V4 of macaque monkeys while performing the GFS task using a nonlinear method - adaptive multi-scale entropy (AME) - to reveal the neural dynamic of perceptual suppression. In addition, we propose a new cross-entropy measure at multiple scales, namely adaptive multi-scale cross-entropy (AMCE), to assess the nonlinear functional connectivity between two cortical areas. We show that: (1) multi-scale entropy exhibits percept-related changes in all three areas, with higher entropy observed during perceptual suppression; (2) the magnitude of the perception-related entropy changes increases systematically over successive hierarchical stages (i.e. from lower areas V1 to V2, up to higher area V4); and (3) cross-entropy between any two cortical areas reveals higher degree of asynchrony or dissimilarity during perceptual suppression, indicating a decreased functional connectivity between cortical areas. These results, taken together, suggest that perceptual suppression is related to a reduced functional connectivity and increased uncertainty of neural responses, and the modulation of perceptual suppression is more effective at higher visual cortical areas. AME is demonstrated to be a useful technique in revealing the underlying dynamic of nonlinear/nonstationary neural signal.

  18. 25 CFR 162.583 - What are the consent requirements for a leasehold mortgage of a WSR lease?

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false What are the consent requirements for a leasehold mortgage of a WSR lease? 162.583 Section 162.583 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER LEASES AND PERMITS Wind and Solar Resource Leases Wsr Leasehold Mortgages § 162.583...

  19. 25 CFR 162.583 - What are the consent requirements for a leasehold mortgage of a WSR lease?

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 1 2014-04-01 2014-04-01 false What are the consent requirements for a leasehold mortgage of a WSR lease? 162.583 Section 162.583 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER LEASES AND PERMITS Wind and Solar Resource Leases Wsr Leasehold Mortgages § 162.583...

  20. 24 CFR 583.330 - Applicability of other Federal requirements.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Development (Continued) OFFICE OF ASSISTANT SECRETARY FOR COMMUNITY PLANNING AND DEVELOPMENT, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT COMMUNITY FACILITIES SUPPORTIVE HOUSING PROGRAM Program Requirements § 583... the approval of applications for assistance for acquisition or construction (including rehabilitation...

  1. 44 CFR 5.83 - Authority to accept service of subpoenas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... production of records held by FEMA Regional offices or for the oral or written testimony of FEMA Regional... AGENCY, DEPARTMENT OF HOMELAND SECURITY GENERAL PRODUCTION OR DISCLOSURE OF INFORMATION Subpoenas or Other Legal Demands for Testimony or the Production or Disclosure of Records or Other Information § 5.83...

  2. 12 CFR 583.11 - Diversified savings and loan holding company.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Diversified savings and loan holding company... DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.11 Diversified savings and loan holding company. The term diversified savings and loan holding company means any savings and loan holding...

  3. 49 CFR 583.8 - Procedure for determining country of origin for engines and transmissions (for purposes of...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...) AUTOMOBILE PARTS CONTENT LABELING § 583.8 Procedure for determining country of origin for engines and... engines and transmissions (for purposes of determining the information specified by §§ 583.5(a)(4) and...) Each supplier of an engine or transmission shall determine the country of origin once a year for each...

  4. 49 CFR 583.8 - Procedure for determining country of origin for engines and transmissions (for purposes of...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...) AUTOMOBILE PARTS CONTENT LABELING § 583.8 Procedure for determining country of origin for engines and... engines and transmissions (for purposes of determining the information specified by §§ 583.5(a)(4) and...) Each supplier of an engine or transmission shall determine the country of origin once a year for each...

  5. 49 CFR 583.8 - Procedure for determining country of origin for engines and transmissions (for purposes of...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...) AUTOMOBILE PARTS CONTENT LABELING § 583.8 Procedure for determining country of origin for engines and... engines and transmissions (for purposes of determining the information specified by §§ 583.5(a)(4) and...) Each supplier of an engine or transmission shall determine the country of origin once a year for each...

  6. 49 CFR 583.8 - Procedure for determining country of origin for engines and transmissions (for purposes of...

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...) AUTOMOBILE PARTS CONTENT LABELING § 583.8 Procedure for determining country of origin for engines and... engines and transmissions (for purposes of determining the information specified by §§ 583.5(a)(4) and...) Each supplier of an engine or transmission shall determine the country of origin once a year for each...

  7. Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L.)

    PubMed Central

    Abebe, Tiegist D.; Naz, Ali A.; Léon, Jens

    2015-01-01

    Land plants are sessile organisms that cannot escape the adverse climatic conditions of a given environment. Hence, adaptation is one of the solutions to surviving in a challenging environment. This study was aimed at detecting adaptive loci in barley landraces that are affected by selection. To that end, a diverse population of barley landraces was analyzed using the genotyping by sequencing approach. Climatic data for altitude, rainfall and temperature were collected from 61 weather sites near the origin of selected landraces across Ethiopia. Population structure analysis revealed three groups whereas spatial analysis accounted significant similarities at shorter geographic distances (< 40 Km) among barley landraces. Partitioning the variance between climate variables and geographic distances indicated that climate variables accounted for most of the explainable genetic variation. Markers by climatic variables association analysis resulted in altogether 18 and 62 putative adaptive loci using Bayenv and latent factor mixed model (LFMM), respectively. Subsequent analysis of the associated SNPs revealed putative candidate genes for plant adaptation. This study highlights the presence of putative adaptive loci among barley landraces representing original gene pool of the farming communities. PMID:26483825

  8. Adaptive Statistical Iterative Reconstruction-V Versus Adaptive Statistical Iterative Reconstruction: Impact on Dose Reduction and Image Quality in Body Computed Tomography.

    PubMed

    Gatti, Marco; Marchisio, Filippo; Fronda, Marco; Rampado, Osvaldo; Faletti, Riccardo; Bergamasco, Laura; Ropolo, Roberto; Fonio, Paolo

    The aim of this study was to evaluate the impact on dose reduction and image quality of the new iterative reconstruction technique: adaptive statistical iterative reconstruction (ASIR-V). Fifty consecutive oncologic patients acted as case controls undergoing during their follow-up a computed tomography scan both with ASIR and ASIR-V. Each study was analyzed in a double-blinded fashion by 2 radiologists. Both quantitative and qualitative analyses of image quality were conducted. Computed tomography scanner radiation output was 38% (29%-45%) lower (P < 0.0001) for the ASIR-V examinations than for the ASIR ones. The quantitative image noise was significantly lower (P < 0.0001) for ASIR-V. Adaptive statistical iterative reconstruction-V had a higher performance for the subjective image noise (P = 0.01 for 5 mm and P = 0.009 for 1.25 mm), the other parameters (image sharpness, diagnostic acceptability, and overall image quality) being similar (P > 0.05). Adaptive statistical iterative reconstruction-V is a new iterative reconstruction technique that has the potential to provide image quality equal to or greater than ASIR, with a dose reduction around 40%.

  9. CFRP strengthening of KY 583 over the Bluegrass Parkway Bridge in Hardin County.

    DOT National Transportation Integrated Search

    2017-09-01

    The report details the planning, design, and construction of the retrofit measure on the KY 583 Bridge (047B00072N), which traverses the Bluegrass Parkway in Hardin County, Kentucky. Reinforced concrete girders within the span over the eastbound Blue...

  10. Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture.

    PubMed

    Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

    2012-03-01

    Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure-function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing-loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (k(cat)/K(M)) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing-loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.

  11. 49 CFR 195.583 - What must I do to monitor atmospheric corrosion control?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 3 2011-10-01 2011-10-01 false What must I do to monitor atmospheric corrosion... SAFETY TRANSPORTATION OF HAZARDOUS LIQUIDS BY PIPELINE Corrosion Control § 195.583 What must I do to monitor atmospheric corrosion control? (a) You must inspect each pipeline or portion of pipeline that is...

  12. Influence of artificial aging in marginal adaptation of mixed class V cavities.

    PubMed

    Tonetto, Mateus Rodrigues; Bandéca, Matheus Coelho; Barud, Hélida Gomes de Oliveira; Pinto, Shelon Cristina Souza; Lima, Darlon Martins; Borges, Alvaro Henrique; de Campos, Edson Alves; de Andrade, Marcelo Ferrarezi

    2013-03-01

    The aim of this study was to investigate whether the artificial aging by thermal cycling had influenced the marginal adaptation of class V restorations with/without chlorhexidine application in the bond process. Twelve intact human third molars were used. Class V cavity preparations were performed on the buccal surface and the teeth received 35% phosphoric acid-etching procedure (Ultradent Products Inc., South Jordan, Utah, USA). Subsequently, the samples were divided in two groups: Untreated acid-etched dentin and chlorhexidine application as an adjunct in the bond process. The adhesive Single Bond 2 (3M ESPE, St. Paul, MN, USA) was used after 2% chlorhexidine application, and the restorations were performed with Filtek™ Z350 XT (3M ESPE) composite resin. The specimens were submitted to artificial aging by thermal cycling with 3,000 cycles. Analyzes were performed on scanning electron microscopy using replicas of marginal adaptation in percentage of continuous margin before and after the artificial aging. The data were analyzed by paired test and the results showed statistically significant differences in the percentage of continuous margin with/without chlorhexidine treatment before and after thermal cycling. This study concluded that the artificial aging by thermal cycling influenced the marginal adaptation of mixed class V composite restorations.

  13. Adaptive evolution influences the infectious dose of MERS-CoV necessary to achieve severe respiratory disease.

    PubMed

    Douglas, Madeline G; Kocher, Jacob F; Scobey, Trevor; Baric, Ralph S; Cockrell, Adam S

    2018-04-01

    We recently established a mouse model (288-330 +/+ ) that developed acute respiratory disease resembling human pathology following infection with a high dose (5 × 10 6 PFU) of mouse-adapted MERS-CoV (icMERSma1). Although this high dose conferred fatal respiratory disease in mice, achieving similar pathology at lower viral doses may more closely reflect naturally acquired infections. Through continued adaptive evolution of icMERSma1 we generated a novel mouse-adapted MERS-CoV (maM35c4) capable of achieving severe respiratory disease at doses between 10 3 and 10 5 PFU. Novel mutations were identified in the maM35c4 genome that may be responsible for eliciting etiologies of acute respiratory distress syndrome at 10-1000 fold lower viral doses. Importantly, comparative genetics of the two mouse-adapted MERS strains allowed us to identify specific mutations that remained fixed through an additional 20 cycles of adaptive evolution. Our data indicate that the extent of MERS-CoV adaptation determines the minimal infectious dose required to achieve severe respiratory disease. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Erratum: ``Stellar Halo Parameters from 4588 Subdwarfs'' (ApJ, 583, 765 [2003])

    NASA Astrophysics Data System (ADS)

    Gould, Andrew

    2004-06-01

    An error has been discovered in the computer program that determined the stellar halo parameters using ~4500 halo stars drawn from the revised New Luyten Two-Tenths catalog. None of the major scientific conclusions of that paper are qualitatively altered. In particular, five of the nine velocity-ellipsoid parameters remain consistent with zero within their small errors. However, many individual parameters have changed their values by 1 or 2 σ and a few by more. I explain the nature of the error and give corrected values for the parameters. The ~4500 halo stars analyzed were selected from the revised New Luyten Two-Tenths catalog (A. Gould & S. Salim, ApJ, 583, 765 [2003]; S. Salim & A. Gould, ApJ, 583, 765 [2003]) by demanding that the reduced proper motion (RPM) discriminator,η≡V-5log(μ)-3.1(V-J)-1.47|sinb|-2.73,(1)lie within the secure halo range, 1<=η<=4.15. Here μ is the proper motion in arcsec per year and b is the Galactic latitude. A programming error inadvertently multiplied b by a factor 10, thereby scattering about 10% of the halo sample out of the selection interval and also scattering a roughly equal number of stars in the other direction, i.e., into the selection range (see Fig. 1). The error affected only the selection process and did not affect the analysis of the selected stars. After correcting this error, I find that the total sample is very slightly reduced to 4564 stars. The revised fit parameters typically differ from those in the original paper by 1 to 2 σ. Because the sample size does not significantly change, the error estimates also do not change. The new estimates of the parameters are as follows. The luminosity function (LF) in 1 mag intervals MV=3,4,...,15 is given by Φ(MV)=(0.03, 0.17, 0.49, 0.61, 0.64, 0.86, 2.24, 4.66, 4.50, 2.57, 2.07, 1.66, 1.53)×10-5 pc-3 (see Fig. 2). The bulk motion of the halo relative to the Sun is U1=8.5+/-2.2kms-1 and U3=-7.5+/-2.4kms-1 in the radial (outward) and vertical (upward) directions

  15. Adaptive feature selection using v-shaped binary particle swarm optimization.

    PubMed

    Teng, Xuyang; Dong, Hongbin; Zhou, Xiurong

    2017-01-01

    Feature selection is an important preprocessing method in machine learning and data mining. This process can be used not only to reduce the amount of data to be analyzed but also to build models with stronger interpretability based on fewer features. Traditional feature selection methods evaluate the dependency and redundancy of features separately, which leads to a lack of measurement of their combined effect. Moreover, a greedy search considers only the optimization of the current round and thus cannot be a global search. To evaluate the combined effect of different subsets in the entire feature space, an adaptive feature selection method based on V-shaped binary particle swarm optimization is proposed. In this method, the fitness function is constructed using the correlation information entropy. Feature subsets are regarded as individuals in a population, and the feature space is searched using V-shaped binary particle swarm optimization. The above procedure overcomes the hard constraint on the number of features, enables the combined evaluation of each subset as a whole, and improves the search ability of conventional binary particle swarm optimization. The proposed algorithm is an adaptive method with respect to the number of feature subsets. The experimental results show the advantages of optimizing the feature subsets using the V-shaped transfer function and confirm the effectiveness and efficiency of the feature subsets obtained under different classifiers.

  16. Adaptive feature selection using v-shaped binary particle swarm optimization

    PubMed Central

    Dong, Hongbin; Zhou, Xiurong

    2017-01-01

    Feature selection is an important preprocessing method in machine learning and data mining. This process can be used not only to reduce the amount of data to be analyzed but also to build models with stronger interpretability based on fewer features. Traditional feature selection methods evaluate the dependency and redundancy of features separately, which leads to a lack of measurement of their combined effect. Moreover, a greedy search considers only the optimization of the current round and thus cannot be a global search. To evaluate the combined effect of different subsets in the entire feature space, an adaptive feature selection method based on V-shaped binary particle swarm optimization is proposed. In this method, the fitness function is constructed using the correlation information entropy. Feature subsets are regarded as individuals in a population, and the feature space is searched using V-shaped binary particle swarm optimization. The above procedure overcomes the hard constraint on the number of features, enables the combined evaluation of each subset as a whole, and improves the search ability of conventional binary particle swarm optimization. The proposed algorithm is an adaptive method with respect to the number of feature subsets. The experimental results show the advantages of optimizing the feature subsets using the V-shaped transfer function and confirm the effectiveness and efficiency of the feature subsets obtained under different classifiers. PMID:28358850

  17. Revealing Adaptive Management of Environmental Flows.

    PubMed

    Allan, Catherine; Watts, Robyn J

    2018-03-01

    Managers of land, water, and biodiversity are working with increasingly complex social ecological systems with high uncertainty. Adaptive management (learning from doing) is an ideal approach for working with this complexity. The competing social and environmental demands for water have prompted interest in freshwater adaptive management, but its success and uptake appear to be slow. Some of the perceived "failure" of adaptive management may reflect the way success is conceived and measured; learning, rarely used as an indicator of success, is narrowly defined when it is. In this paper, we document the process of adaptive flow management in the Edward-Wakool system in the southern Murray-Darling Basin, Australia. Data are from interviews with environmental water managers, document review, and the authors' structured reflection on their experiences of adaptive management and environmental flows. Substantial learning occurred in relation to the management of environmental flows in the Edward-Wakool system, with evidence found in planning documents, water-use reports, technical reports, stakeholder committee minutes, and refereed papers, while other evidence was anecdotal. Based on this case, we suggest it may be difficult for external observers to perceive the success of large adaptive management projects because evidence of learning is dispersed across multiple documents, and learning is not necessarily considered a measure of success. We suggest that documentation and sharing of new insights, and of the processes of learning, should be resourced to facilitate social learning within the water management sector, and to help demonstrate the successes of adaptive management.

  18. Revealing Adaptive Management of Environmental Flows

    NASA Astrophysics Data System (ADS)

    Allan, Catherine; Watts, Robyn J.

    2018-03-01

    Managers of land, water, and biodiversity are working with increasingly complex social ecological systems with high uncertainty. Adaptive management (learning from doing) is an ideal approach for working with this complexity. The competing social and environmental demands for water have prompted interest in freshwater adaptive management, but its success and uptake appear to be slow. Some of the perceived "failure" of adaptive management may reflect the way success is conceived and measured; learning, rarely used as an indicator of success, is narrowly defined when it is. In this paper, we document the process of adaptive flow management in the Edward-Wakool system in the southern Murray-Darling Basin, Australia. Data are from interviews with environmental water managers, document review, and the authors' structured reflection on their experiences of adaptive management and environmental flows. Substantial learning occurred in relation to the management of environmental flows in the Edward-Wakool system, with evidence found in planning documents, water-use reports, technical reports, stakeholder committee minutes, and refereed papers, while other evidence was anecdotal. Based on this case, we suggest it may be difficult for external observers to perceive the success of large adaptive management projects because evidence of learning is dispersed across multiple documents, and learning is not necessarily considered a measure of success. We suggest that documentation and sharing of new insights, and of the processes of learning, should be resourced to facilitate social learning within the water management sector, and to help demonstrate the successes of adaptive management.

  19. The adaptive statistical iterative reconstruction-V technique for radiation dose reduction in abdominal CT: comparison with the adaptive statistical iterative reconstruction technique.

    PubMed

    Kwon, Heejin; Cho, Jinhan; Oh, Jongyeong; Kim, Dongwon; Cho, Junghyun; Kim, Sanghyun; Lee, Sangyun; Lee, Jihyun

    2015-10-01

    To investigate whether reduced radiation dose abdominal CT images reconstructed with adaptive statistical iterative reconstruction V (ASIR-V) compromise the depiction of clinically competent features when compared with the currently used routine radiation dose CT images reconstructed with ASIR. 27 consecutive patients (mean body mass index: 23.55 kg m(-2) underwent CT of the abdomen at two time points. At the first time point, abdominal CT was scanned at 21.45 noise index levels of automatic current modulation at 120 kV. Images were reconstructed with 40% ASIR, the routine protocol of Dong-A University Hospital. At the second time point, follow-up scans were performed at 30 noise index levels. Images were reconstructed with filtered back projection (FBP), 40% ASIR, 30% ASIR-V, 50% ASIR-V and 70% ASIR-V for the reduced radiation dose. Both quantitative and qualitative analyses of image quality were conducted. The CT dose index was also recorded. At the follow-up study, the mean dose reduction relative to the currently used common radiation dose was 35.37% (range: 19-49%). The overall subjective image quality and diagnostic acceptability of the 50% ASIR-V scores at the reduced radiation dose were nearly identical to those recorded when using the initial routine-dose CT with 40% ASIR. Subjective ratings of the qualitative analysis revealed that of all reduced radiation dose CT series reconstructed, 30% ASIR-V and 50% ASIR-V were associated with higher image quality with lower noise and artefacts as well as good sharpness when compared with 40% ASIR and FBP. However, the sharpness score at 70% ASIR-V was considered to be worse than that at 40% ASIR. Objective image noise for 50% ASIR-V was 34.24% and 46.34% which was lower than 40% ASIR and FBP. Abdominal CT images reconstructed with ASIR-V facilitate radiation dose reductions of to 35% when compared with the ASIR. This study represents the first clinical research experiment to use ASIR-V, the newest version of

  20. Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit

    PubMed Central

    Baerenfaller, Katja; Massonnet, Catherine; Walsh, Sean; Baginsky, Sacha; Bühlmann, Peter; Hennig, Lars; Hirsch-Hoffmann, Matthias; Howell, Katharine A; Kahlau, Sabine; Radziejwoski, Amandine; Russenberger, Doris; Rutishauser, Dorothea; Small, Ian; Stekhoven, Daniel; Sulpice, Ronan; Svozil, Julia; Wuyts, Nathalie; Stitt, Mark; Hilson, Pierre; Granier, Christine; Gruissem, Wilhelm

    2012-01-01

    Leaves have a central role in plant energy capture and carbon conversion and therefore must continuously adapt their development to prevailing environmental conditions. To reveal the dynamic systems behaviour of leaf development, we profiled Arabidopsis leaf number six in depth at four different growth stages, at both the end-of-day and end-of-night, in plants growing in two controlled experimental conditions: short-day conditions with optimal soil water content and constant reduced soil water conditions. We found that the lower soil water potential led to reduced, but prolonged, growth and an adaptation at the molecular level without a drought stress response. Clustering of the protein and transcript data using a decision tree revealed different patterns in abundance changes across the growth stages and between end-of-day and end-of-night that are linked to specific biological functions. Correlations between protein and transcript levels depend on the time-of-day and also on protein localisation and function. Surprisingly, only very few of >1700 quantified proteins showed diurnal abundance fluctuations, despite strong fluctuations at the transcript level. PMID:22929616

  1. The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods

    PubMed Central

    Cao, Zhijian; Yu, Yao; Wu, Yingliang; Hao, Pei; Di, Zhiyong; He, Yawen; Chen, Zongyun; Yang, Weishan; Shen, Zhiyong; He, Xiaohua; Sheng, Jia; Xu, Xiaobo; Pan, Bohu; Feng, Jing; Yang, Xiaojuan; Hong, Wei; Zhao, Wenjuan; Li, Zhongjie; Huang, Kai; Li, Tian; Kong, Yimeng; Liu, Hui; Jiang, Dahe; Zhang, Binyan; Hu, Jun; Hu, Youtian; Wang, Bin; Dai, Jianliang; Yuan, Bifeng; Feng, Yuqi; Huang, Wei; Xing, Xiaojing; Zhao, Guoping; Li, Xuan; Li, Yixue; Li, Wenxin

    2013-01-01

    Representing a basal branch of arachnids, scorpions are known as ‘living fossils’ that maintain an ancient anatomy and are adapted to have survived extreme climate changes. Here we report the genome sequence of Mesobuthus martensii, containing 32,016 protein-coding genes, the most among sequenced arthropods. Although M. martensii appears to evolve conservatively, it has a greater gene family turnover than the insects that have undergone diverse morphological and physiological changes, suggesting the decoupling of the molecular and morphological evolution in scorpions. Underlying the long-term adaptation of scorpions is the expansion of the gene families enriched in basic metabolic pathways, signalling pathways, neurotoxins and cytochrome P450, and the different dynamics of expansion between the shared and the scorpion lineage-specific gene families. Genomic and transcriptomic analyses further illustrate the important genetic features associated with prey, nocturnal behaviour, feeding and detoxification. The M. martensii genome reveals a unique adaptation model of arthropods, offering new insights into the genetic bases of the living fossils. PMID:24129506

  2. The adaptive statistical iterative reconstruction-V technique for radiation dose reduction in abdominal CT: comparison with the adaptive statistical iterative reconstruction technique

    PubMed Central

    Cho, Jinhan; Oh, Jongyeong; Kim, Dongwon; Cho, Junghyun; Kim, Sanghyun; Lee, Sangyun; Lee, Jihyun

    2015-01-01

    Objective: To investigate whether reduced radiation dose abdominal CT images reconstructed with adaptive statistical iterative reconstruction V (ASIR-V) compromise the depiction of clinically competent features when compared with the currently used routine radiation dose CT images reconstructed with ASIR. Methods: 27 consecutive patients (mean body mass index: 23.55 kg m−2 underwent CT of the abdomen at two time points. At the first time point, abdominal CT was scanned at 21.45 noise index levels of automatic current modulation at 120 kV. Images were reconstructed with 40% ASIR, the routine protocol of Dong-A University Hospital. At the second time point, follow-up scans were performed at 30 noise index levels. Images were reconstructed with filtered back projection (FBP), 40% ASIR, 30% ASIR-V, 50% ASIR-V and 70% ASIR-V for the reduced radiation dose. Both quantitative and qualitative analyses of image quality were conducted. The CT dose index was also recorded. Results: At the follow-up study, the mean dose reduction relative to the currently used common radiation dose was 35.37% (range: 19–49%). The overall subjective image quality and diagnostic acceptability of the 50% ASIR-V scores at the reduced radiation dose were nearly identical to those recorded when using the initial routine-dose CT with 40% ASIR. Subjective ratings of the qualitative analysis revealed that of all reduced radiation dose CT series reconstructed, 30% ASIR-V and 50% ASIR-V were associated with higher image quality with lower noise and artefacts as well as good sharpness when compared with 40% ASIR and FBP. However, the sharpness score at 70% ASIR-V was considered to be worse than that at 40% ASIR. Objective image noise for 50% ASIR-V was 34.24% and 46.34% which was lower than 40% ASIR and FBP. Conclusion: Abdominal CT images reconstructed with ASIR-V facilitate radiation dose reductions of to 35% when compared with the ASIR. Advances in knowledge: This study represents the first

  3. Long adaptation reveals mostly attractive shifts of orientation tuning in cat primary visual cortex.

    PubMed

    Ghisovan, N; Nemri, A; Shumikhina, S; Molotchnikoff, S

    2009-12-15

    In the adult brain, sensory cortical neurons undergo transient changes of their response properties following prolonged exposure to an appropriate stimulus (adaptation). In cat V1, orientation-selective cells shift their preferred orientation after being adapted to a non-preferred orientation. There are conflicting reports as to the direction of those shifts, towards (attractive) or away (repulsive) from the adapter. Moreover, the mechanisms underlying attractive shifts remain unexplained. In the present investigation we show that attractive shifts are the most frequent outcome of a 12 min adaptation. Overall, cells displaying selectivity for oblique orientations exhibit significantly larger shifts than cells tuned to cardinal orientations. In addition, cells selective to cardinal orientations had larger shift amplitudes when the absolute difference between the original preferred orientation and the adapting orientation increased. Conversely, cells tuned to oblique orientations exhibited larger shift amplitudes when this absolute orientation difference was narrower. Hence, neurons tuned to oblique contours appear to show more plasticity in response to small perturbations. Two different mechanisms appear to produce attractive and repulsive orientation shifts. Attractive shifts result from concurrent response depression on the non-adapted flank and selective response facilitation on the adapted flank of the orientation tuning curve. In contrast, repulsive shifts are caused solely by response depression on the adapted flank. We suggest that an early mechanism leads to repulsive shifts while attractive shifts engage a subsequent late facilitation. A potential role for attractive shifts may be improved stimulus discrimination around the adapting orientation.

  4. Validation of the Spanish adaptation of the Consensus Auditory-Perceptual Evaluation of Voice (CAPE-V).

    PubMed

    Núñez-Batalla, Faustino; Morato-Galán, Marta; García-López, Isabel; Ávila-Menéndez, Arántzazu

    2015-01-01

    The Consensus Auditory-Perceptual Evaluation of Voice (CAPE-V) was developed.to promote a standardised approach to evaluating and documenting auditory perceptual judgments of vocal quality. This tool was originally developed in English language and its Spanish version is still inexistent. The aim of this study was to develop a Spanish adaptation of CAPE-V and to examine the reliability and empirical validity of this Spanish version. To adapt the CAPE-V protocol to the Spanish language, we proposed 6 phrases phonetically designed according to the CAPE-V requirements. Prospective instrument validation was performed. The validity of the Spanish version of the CAPE-V was examined in 4 ways: intra-rater reliability, inter-rater reliability and CAPE-V versus GRABS judgments. Inter-rater reliability coefficients for the CAPE-V ranged from 0.93 for overall severity to 0.54 for intensity; intra-rater reliability ranged from 0.98 for overall severity to 0.85 for intensity. The comparison of judgments between GRABS and CAPE-V ranged from 0.86 for overall severity to 0.61 for breathiness. The present study supports the use of the Spanish version of CAPE-V because of its validity and reliability. Copyright © 2014 Elsevier España, S.L.U. and Sociedad Española de Otorrinolaringología y Patología Cérvico-Facial. All rights reserved.

  5. Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

    PubMed Central

    Förster, Frank; Beisser, Daniela; Grohme, Markus A.; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C.; Shkumatov, Alexander V.; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O.; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. PMID:22563243

  6. Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations.

    PubMed

    Förster, Frank; Beisser, Daniela; Grohme, Markus A; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C; Shkumatov, Alexander V; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.

  7. Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens.

    PubMed

    Wang, Ming-Shan; Li, Yan; Peng, Min-Sheng; Zhong, Li; Wang, Zong-Ji; Li, Qi-Ye; Tu, Xiao-Long; Dong, Yang; Zhu, Chun-Ling; Wang, Lu; Yang, Min-Min; Wu, Shi-Fang; Miao, Yong-Wang; Liu, Jian-Ping; Irwin, David M; Wang, Wen; Wu, Dong-Dong; Zhang, Ya-Ping

    2015-07-01

    Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200-4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome of a Tibetan chicken and resequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups. Further analyses revealed that several candidate genes in the calcium-signaling pathway are possibly involved in adaptation to the hypoxia experienced by these chickens, as these genes appear to have experienced directional selection in the two Tibetan chicken populations, suggesting a potential genetic mechanism underlying high altitude adaptation in Tibetan chickens. The candidate selected genes identified in this study, and their variants, may be useful targets for clarifying our understanding of the domestication of chickens in Tibet, and might be useful in current breeding efforts to develop improved breeds for the highlands. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation

    DOE PAGES

    Kurczy, Michael E.; Forsberg, Erica M.; Thorgersen, Michael P.; ...

    2016-04-05

    Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using 15NO 3 as a nitrogen source. In contrast to a control ( Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee ( Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2more » strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. In conclusion, the use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.« less

  9. Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kurczy, Michael E.; Forsberg, Erica M.; Thorgersen, Michael P.

    Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using 15NO 3 as a nitrogen source. In contrast to a control ( Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee ( Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2more » strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. In conclusion, the use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.« less

  10. 40 CFR 80.583 - What alternative sampling and testing requirements apply to importers who transport motor vehicle...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... requirements apply to importers who transport motor vehicle diesel fuel, NRLM diesel fuel, or ECA marine fuel... (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Motor Vehicle Diesel Fuel; Nonroad, Locomotive, and Marine Diesel Fuel; and ECA Marine Fuel Sampling and Testing § 80.583 What...

  11. Initial phantom study comparing image quality in computed tomography using adaptive statistical iterative reconstruction and new adaptive statistical iterative reconstruction v.

    PubMed

    Lim, Kyungjae; Kwon, Heejin; Cho, Jinhan; Oh, Jongyoung; Yoon, Seongkuk; Kang, Myungjin; Ha, Dongho; Lee, Jinhwa; Kang, Eunju

    2015-01-01

    The purpose of this study was to assess the image quality of a novel advanced iterative reconstruction (IR) method called as "adaptive statistical IR V" (ASIR-V) by comparing the image noise, contrast-to-noise ratio (CNR), and spatial resolution from those of filtered back projection (FBP) and adaptive statistical IR (ASIR) on computed tomography (CT) phantom image. We performed CT scans at 5 different tube currents (50, 70, 100, 150, and 200 mA) using 3 types of CT phantoms. Scanned images were subsequently reconstructed in 7 different scan settings, such as FBP, and 3 levels of ASIR and ASIR-V (30%, 50%, and 70%). The image noise was measured in the first study using body phantom. The CNR was measured in the second study using contrast phantom and the spatial resolutions were measured in the third study using a high-resolution phantom. We compared the image noise, CNR, and spatial resolution among the 7 reconstructed image scan settings to determine whether noise reduction, high CNR, and high spatial resolution could be achieved at ASIR-V. At quantitative analysis of the first and second studies, it showed that the images reconstructed using ASIR-V had reduced image noise and improved CNR compared with those of FBP and ASIR (P < 0.001). At qualitative analysis of the third study, it also showed that the images reconstructed using ASIR-V had significantly improved spatial resolution than those of FBP and ASIR (P < 0.001). Our phantom studies showed that ASIR-V provides a significant reduction in image noise and a significant improvement in CNR as well as spatial resolution. Therefore, this technique has the potential to reduce the radiation dose further without compromising image quality.

  12. Comparative Genomic Analysis MERS CoV Isolated from Humans and Camels with Special Reference to Virus Encoded Helicase.

    PubMed

    Alnazawi, Mohamed; Altaher, Abdallah; Kandeel, Mahmoud

    2017-01-01

    Middle East Respiratory Syndrome Coronavirus (MERS CoV) is a new emerging viral disease characterized by high fatality rate. Understanding MERS CoV genetic aspects and codon usage pattern is important to understand MERS CoV survival, adaptation, evolution, resistance to innate immunity, and help in finding the unique aspects of the virus for future drug discovery experiments. In this work, we provide comprehensive analysis of 238 MERS CoV full genomes comprised of human (hMERS) and camel (cMERS) isolates of the virus. MERS CoV genome shaping seems to be under compositional and mutational bias, as revealed by preference of A/T over G/C nucleotides, preferred codons, nucleotides at the third position of codons (NT3s), relative synonymous codon usage, hydropathicity (Gravy), and aromaticity (Aromo) indices. Effective number of codons (ENc) analysis reveals a general slight codon usage bias. Codon adaptation index reveals incomplete adaptation to host environment. MERS CoV showed high ability to resist the innate immune response by showing lower CpG frequencies. Neutrality evolution analysis revealed a more significant role of mutation pressure in cMERS over hMERS. Correspondence analysis revealed that MERS CoV genomes have three genetic clusters, which were distinct in their codon usage, host, and geographic distribution. Additionally, virtual screening and binding experiments were able to identify three new virus-encoded helicase binding compounds. These compounds can be used for further optimization of inhibitors.

  13. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species.

    PubMed

    Ronkin, Dana; Seroussi, Eyal; Nitzan, Tali; Doron-Faigenboim, Adi; Cnaani, Avner

    2015-03-01

    Tilapias are a group of freshwater species, which vary in their ability to adapt to high salinity water. Osmotic regulation in fish is conducted mainly in the gills, kidney, and gastrointestinal tract (GIT). The mechanisms involved in ion and water transport through the GIT is not well-characterized, with only a few described complexes. Comparing the transcriptome of the anterior and posterior intestinal sections of a freshwater and saltwater adapted fish by deep-sequencing, we examined the salinity adaptation of two tilapia species: the high salinity-tolerant Oreochromis mossambicus (Mozambique tilapia), and the less salinity-tolerant Oreochromis niloticus (Nile tilapia). This comparative analysis revealed high similarity in gene expression response to salinity change between species in the posterior intestine and large differences in the anterior intestine. Furthermore, in the anterior intestine 68 genes were saltwater up-regulated in one species and down-regulated in the other species (47 genes up-regulated in O. niloticus and down-regulated in O. mossambicus, with 21 genes showing the reverse pattern). Gene ontology (GO) analysis showed a high proportion of transporter and ion channel function among these genes. The results of this study point to a group of genes that differed in their salinity-dependent regulation pattern in the anterior intestine as potentially having a role in the differential salinity tolerance of these two closely related species. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Cone and Rod Loss in Stargardt Disease Revealed by Adaptive Optics Scanning Light Ophthalmoscopy

    PubMed Central

    Song, Hongxin; Rossi, Ethan A.; Latchney, Lisa; Bessette, Angela; Stone, Edwin; Hunter, Jennifer J.; Williams, David R.; Chung, Mina

    2015-01-01

    Importance Stargardt disease (STGD1) is characterized by macular atrophy and flecks in the retinal pigment epithelium. The causative ABCA4 gene encodes a protein localizing to photoreceptor outer segments. The pathologic steps by which ABCA4 mutations lead to clinically detectable retinal pigment epithelium changes remain unclear. We investigated early STGD1 using adaptive optics scanning light ophthalmoscopy. Observations Adaptive optics scanning light ophthalmoscopy imaging of 2 brothers with early STGD1 and their unaffected parents was compared with conventional imaging. Cone and rod spacing were increased in both patients (P <.001) with a dark cone appearance. No foveal cones were detected in the older brother. In the younger brother, foveal cones were enlarged with low density (peak cone density, 48.3 × 103 cones/mm2). The ratio of cone to rod spacing was increased in both patients, with greater divergence from normal approaching the foveal center, indicating that cone loss predominates centrally and rod loss increases peripherally. Both parents had normal photoreceptor mosaics. Genetic testing revealed 3 disease-causing mutations. Conclusions and Relevance This study provides in vivo images of rods and cones in STGD1. Although the primary clinical features of STGD1 are retinal pigment epithelial lesions, adaptive optics scanning light ophthalmoscopy reveals increased cone and rod spacing in areas that appear normal in conventional images, suggesting that photoreceptor loss precedes clinically detectable retinal pigment epithelial disease in STGD1. PMID:26247787

  15. Comparative genomics reveals insights into avian genome evolution and adaptation

    PubMed Central

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  16. Computed Tomography Image Quality Evaluation of a New Iterative Reconstruction Algorithm in the Abdomen (Adaptive Statistical Iterative Reconstruction-V) a Comparison With Model-Based Iterative Reconstruction, Adaptive Statistical Iterative Reconstruction, and Filtered Back Projection Reconstructions.

    PubMed

    Goodenberger, Martin H; Wagner-Bartak, Nicolaus A; Gupta, Shiva; Liu, Xinming; Yap, Ramon Q; Sun, Jia; Tamm, Eric P; Jensen, Corey T

    The purpose of this study was to compare abdominopelvic computed tomography images reconstructed with adaptive statistical iterative reconstruction-V (ASIR-V) with model-based iterative reconstruction (Veo 3.0), ASIR, and filtered back projection (FBP). Abdominopelvic computed tomography scans for 36 patients (26 males and 10 females) were reconstructed using FBP, ASIR (80%), Veo 3.0, and ASIR-V (30%, 60%, 90%). Mean ± SD patient age was 32 ± 10 years with mean ± SD body mass index of 26.9 ± 4.4 kg/m. Images were reviewed by 2 independent readers in a blinded, randomized fashion. Hounsfield unit, noise, and contrast-to-noise ratio (CNR) values were calculated for each reconstruction algorithm for further comparison. Phantom evaluation of low-contrast detectability (LCD) and high-contrast resolution was performed. Adaptive statistical iterative reconstruction-V 30%, ASIR-V 60%, and ASIR 80% were generally superior qualitatively compared with ASIR-V 90%, Veo 3.0, and FBP (P < 0.05). Adaptive statistical iterative reconstruction-V 90% showed superior LCD and had the highest CNR in the liver, aorta, and, pancreas, measuring 7.32 ± 3.22, 11.60 ± 4.25, and 4.60 ± 2.31, respectively, compared with the next best series of ASIR-V 60% with respective CNR values of 5.54 ± 2.39, 8.78 ± 3.15, and 3.49 ± 1.77 (P <0.0001). Veo 3.0 and ASIR 80% had the best and worst spatial resolution, respectively. Adaptive statistical iterative reconstruction-V 30% and ASIR-V 60% provided the best combination of qualitative and quantitative performance. Adaptive statistical iterative reconstruction 80% was equivalent qualitatively, but demonstrated inferior spatial resolution and LCD.

  17. Transcriptomic Analysis Reveals Selective Metabolic Adaptation of Streptococcus suis to Porcine Blood and Cerebrospinal Fluid

    PubMed Central

    Koczula, Anna; Jarek, Michael; Visscher, Christian; Valentin-Weigand, Peter; Goethe, Ralph; Willenborg, Jörg

    2017-01-01

    Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF) revealed conserved activities of central carbon metabolism in both body fluids. On the other hand, they suggested differences in the de novo amino acid biosynthesis. This prompted us to further dissect S. suis adaptation to porcine blood and CSF by RNA deep sequencing (RNA-seq). In blood, the majority of differentially expressed genes were associated with transport of alternative carbohydrate sources and the carbohydrate metabolism (pentose phosphate pathway, glycogen metabolism). In CSF, predominantly genes involved in the biosynthesis of branched-chain and aromatic amino acids were differentially expressed. Especially, isoleucine biosynthesis seems to be of major importance for S. suis in CSF because several related biosynthetic genes were more highly expressed. In conclusion, our data revealed niche-specific metabolic gene activity which emphasizes a selective adaptation of S. suis to host environments. PMID:28212285

  18. Transcriptomic Analysis Reveals Selective Metabolic Adaptation of Streptococcus suis to Porcine Blood and Cerebrospinal Fluid.

    PubMed

    Koczula, Anna; Jarek, Michael; Visscher, Christian; Valentin-Weigand, Peter; Goethe, Ralph; Willenborg, Jörg

    2017-02-15

    Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF) revealed conserved activities of central carbon metabolism in both body fluids. On the other hand, they suggested differences in the de novo amino acid biosynthesis. This prompted us to further dissect S. suis adaptation to porcine blood and CSF by RNA deep sequencing (RNA-seq). In blood, the majority of differentially expressed genes were associated with transport of alternative carbohydrate sources and the carbohydrate metabolism (pentose phosphate pathway, glycogen metabolism). In CSF, predominantly genes involved in the biosynthesis of branched-chain and aromatic amino acids were differentially expressed. Especially, isoleucine biosynthesis seems to be of major importance for S. suis in CSF because several related biosynthetic genes were more highly expressed. In conclusion, our data revealed niche-specific metabolic gene activity which emphasizes a selective adaptation of S. suis to host environments.

  19. The Detection of Focal Liver Lesions Using Abdominal CT: A Comparison of Image Quality Between Adaptive Statistical Iterative Reconstruction V and Adaptive Statistical Iterative Reconstruction.

    PubMed

    Lee, Sangyun; Kwon, Heejin; Cho, Jihan

    2016-12-01

    To investigate image quality characteristics of abdominal computed tomography (CT) scans reconstructed with adaptive statistical iterative reconstruction V (ASIR-V) vs currently using applied adaptive statistical iterative reconstruction (ASIR). This institutional review board-approved study included 35 consecutive patients who underwent CT of the abdomen. Among these 35 patients, 27 with focal liver lesions underwent abdomen CT with a 128-slice multidetector unit using the following parameters: fixed noise index of 30, 1.25 mm slice thickness, 120 kVp, and a gantry rotation time of 0.5 seconds. CT images were analyzed depending on the method of reconstruction: ASIR (30%, 50%, and 70%) vs ASIR-V (30%, 50%, and 70%). Three radiologists independently assessed randomized images in a blinded manner. Imaging sets were compared to focal lesion detection numbers, overall image quality, and objective noise with a paired sample t test. Interobserver agreement was assessed with the intraclass correlation coefficient. The detection of small focal liver lesions (<10 mm) was significantly higher when ASIR-V was used when compared to ASIR (P <0.001). Subjective image noise, artifact, and objective image noise in liver were generally significantly better for ASIR-V compared to ASIR, especially in 50% ASIR-V. Image sharpness and diagnostic acceptability were significantly worse in 70% ASIR-V compared to various levels of ASIR. Images analyzed using 50% ASIR-V were significantly better than three different series of ASIR or other ASIR-V conditions at providing diagnostically acceptable CT scans without compromising image quality and in the detection of focal liver lesions. Copyright © 2016 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

  20. Infusing and selecting V&V activities

    NASA Technical Reports Server (NTRS)

    Feather, M. S.

    2002-01-01

    The evolving nature of software development poses a continuing series of challenges for V&V. In response, the V&V community selectively adapts the use of existing V&V activities, and introduces new and improved ones.

  1. Comparative genomics reveals insights into avian genome evolution and adaptation.

    PubMed

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S; Gatesy, John; Hoffmann, Federico G; Opazo, Juan C; Håstad, Olle; Sawyer, Roger H; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A; Green, Richard E; O'Brien, Stephen J; Griffin, Darren; Johnson, Warren E; Haussler, David; Ryder, Oliver A; Willerslev, Eske; Graves, Gary R; Alström, Per; Fjeldså, Jon; Mindell, David P; Edwards, Scott V; Braun, Edward L; Rahbek, Carsten; Burt, David W; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D; Gilbert, M Thomas P; Wang, Jun

    2014-12-12

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. Copyright © 2014, American Association for the Advancement of Science.

  2. Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance.

    PubMed

    Miller, Corwin; Kong, Jiayi; Tran, Truc T; Arias, Cesar A; Saxer, Gerda; Shamoo, Yousif

    2013-11-01

    With increasing numbers of hospital-acquired antibiotic resistant infections each year and staggering health care costs, there is a clear need for new antimicrobial agents, as well as novel strategies to extend their clinical efficacy. While genomic studies have provided a wealth of information about the alleles associated with adaptation to antibiotics, they do not provide essential information about the relative importance of genomic changes, their order of appearance, or potential epistatic relationships between adaptive changes. Here we used quantitative experimental evolution of a single polymorphic population in continuous culture with whole-genome sequencing and allelic frequency measurements to study daptomycin (DAP) resistance in the vancomycin-resistant clinical pathogen Enterococcus faecalis S613. Importantly, we sustained both planktonic and nonplanktonic (i.e., biofilm) populations in coculture as the concentration of antibiotic was raised, facilitating the development of more ecological complexity than is typically observed in laboratory evolution. Quantitative experimental evolution revealed a clear order and hierarchy of genetic changes leading to resistance, the signaling and metabolic pathways responsible, and the relative importance of these mutations to the evolution of DAP resistance. Despite the relative simplicity of this ex vivo approach compared to the ecological complexity of the human body, we showed that experimental evolution allows for rapid identification of clinically relevant adaptive molecular pathways and new targets for drug design in pathogens.

  3. AFLPs and Mitochondrial Haplotypes Reveal Local Adaptation to Extreme Thermal Environments in a Freshwater Gastropod

    PubMed Central

    Quintela, María; Johansson, Magnus P.; Kristjánsson, Bjarni K.; Barreiro, Rodolfo; Laurila, Anssi

    2014-01-01

    The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher FST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence. PMID:25007329

  4. Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.

    PubMed

    Yuan, Yuan; Cao, Duanfang; Zhang, Yanfang; Ma, Jun; Qi, Jianxun; Wang, Qihui; Lu, Guangwen; Wu, Ying; Yan, Jinghua; Shi, Yi; Zhang, Xinzheng; Gao, George F

    2017-04-10

    The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.

  5. The replication of a mouse adapted SARS-CoV in a mouse cell line stably expressing the murine SARS-CoV receptor mACE2 efficiently induces the expression of proinflammatory cytokines

    PubMed Central

    Regla-Nava, Jose A.; Jimenez-Guardeño, Jose M.; Nieto-Torres, Jose L.; Gallagher, Thomas M.; Enjuanes, Luis; DeDiego, Marta L.

    2013-01-01

    Infection of conventional mice with a mouse adapted (MA15) severe acute respiratory syndrome (SARS) coronavirus (CoV) reproduces many aspects of human SARS such as pathological changes in lung, viremia, neutrophilia, and lethality. However, established mouse cell lines highly susceptible to mouse-adapted SARS-CoV infection are not available. In this work, efficiently transfectable mouse cell lines stably expressing the murine SARS-CoV receptor angiotensin converting enzyme 2 (ACE2) have been generated. These cells yielded high SARS-CoV-MA15 titers and also served as excellent tools for plaque assays. In addition, in these cell lines, SARS-CoV-MA15 induced the expression of proinflammatory cytokines and IFN-β, mimicking what has been observed in experimental animal models infected with SARS-CoV and SARS patients. These cell lines are valuable tools to perform in vitro studies in a mouse cell system that reflects the species used for in vivo studies of SARS-CoV-MA15 pathogenesis. PMID:23911968

  6. Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease

    NASA Astrophysics Data System (ADS)

    Nawaz, Meh Sameen; Vik, Erik Sebastian; Ronander, Mia Elise; Solvoll, Anne Marthe; Blicher, Pernille; Bjørås, Magnar; Alseth, Ingrun; Dalhus, Bjørn

    2016-04-01

    Endonuclease V (EndoV) is an enzyme with specificity for deaminated adenosine (inosine) in nucleic acids. EndoV from Escherichia coli (EcEndoV) acts both on inosines in DNA and RNA, whereas the human homolog cleaves only at inosines in RNA. Inosines in DNA are mutagenic and the role of EndoV in DNA repair is well established. In contrast, the biological function of EndoV in RNA processing is largely unexplored. Here we have characterized a second mammalian EndoV homolog, mouse EndoV (mEndoV), and show that mEndoV shares the same RNA selectivity as human EndoV (hEndoV). Mouse EndoV cleaves the same inosine-containing substrates as hEndoV, but with reduced efficiencies. The crystal structure of mEndoV reveals a conformation different from the hEndoV and prokaryotic EndoV structures, particularly for the conserved tyrosine in the wedge motif, suggesting that this strand separating element has some flexibility. Molecular dynamics simulations of mouse and human EndoV reveal alternative conformations for the invariant tyrosine. The configuration of the active site, on the other hand, is very similar between the prokaryotic and mammalian versions of EndoV.

  7. β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

    PubMed Central

    Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

    2015-01-01

    Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix. PMID:25550503

  8. β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR.

    PubMed

    Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

    2015-01-13

    Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix.

  9. Adaptation of influenza A(H1N1)pdm09 virus in experimental mouse models.

    PubMed

    Prokopyeva, E A; Sobolev, I A; Prokopyev, M V; Shestopalov, A M

    2016-04-01

    In the present study, three mouse-adapted variants of influenza A(H1N1)pdm09 virus were obtained by lung-to-lung passages of BALB/c, C57BL/6z and CD1 mice. The significantly increased virulence and pathogenicity of all of the mouse-adapted variants induced 100% mortality in the adapted mice. Genetic analysis indicated that the increased virulence of all of the mouse-adapted variants reflected the incremental acquisition of several mutations in PB2, PB1, HA, NP, NA, and NS2 proteins. Identical amino acid substitutions were also detected in all of the mouse-adapted variants of A(H1N1)pdm09 virus, including PB2 (K251R), PB1 (V652A), NP (I353V), NA (I106V, N248D) and NS1 (G159E). Apparently, influenza A(H1N1)pdm09 virus easily adapted to the host after serial passages in the lungs, inducing 100% lethality in the last experimental group. However, cross-challenge revealed that not all adapted variants are pathogenic for different laboratory mice. Such important results should be considered when using the influenza mice model. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Multiple adaptable mechanisms early in the primate visual pathway

    PubMed Central

    Dhruv, Neel T.; Tailby, Chris; Sokol, Sach H.; Lennie, Peter

    2011-01-01

    We describe experiments that isolate and characterize multiple adaptable mechanisms that influence responses of orientation-selective neurons in primary visual cortex (V1) of anesthetized macaque (Macaca fascicularis). The results suggest that three adaptable stages of machinery shape neural responses in V1: a broadly-tuned early stage and a spatio-temporally tuned later stage, both of which provide excitatory input, and a normalization pool that is also broadly tuned. The early stage and the normalization pool are revealed by adapting gratings that themselves fail to evoke a response from the neuron: either low temporal frequency gratings at the null orientation or gratings of any orientation drifting at high temporal frequencies. When effective, adapting stimuli that altered the sensitivity of these two mechanisms caused reductions of contrast gain and often brought about a paradoxical increase in response gain due to a relatively greater desensitization of the normalization pool. The tuned mechanism is desensitized only by stimuli well-matched to a neuron’s receptive field. We could thus infer desensitization of the tuned mechanism by comparing effects obtained with adapting gratings of preferred and null orientation modulated at low temporal frequencies. PMID:22016535

  11. The replication of a mouse adapted SARS-CoV in a mouse cell line stably expressing the murine SARS-CoV receptor mACE2 efficiently induces the expression of proinflammatory cytokines.

    PubMed

    Regla-Nava, Jose A; Jimenez-Guardeño, Jose M; Nieto-Torres, Jose L; Gallagher, Thomas M; Enjuanes, Luis; DeDiego, Marta L

    2013-11-01

    Infection of conventional mice with a mouse adapted (MA15) severe acute respiratory syndrome (SARS) coronavirus (CoV) reproduces many aspects of human SARS such as pathological changes in lung, viremia, neutrophilia, and lethality. However, established mouse cell lines highly susceptible to mouse-adapted SARS-CoV infection are not available. In this work, efficiently transfectable mouse cell lines stably expressing the murine SARS-CoV receptor angiotensin converting enzyme 2 (ACE2) have been generated. These cells yielded high SARS-CoV-MA15 titers and also served as excellent tools for plaque assays. In addition, in these cell lines, SARS-CoV-MA15 induced the expression of proinflammatory cytokines and IFN-β, mimicking what has been observed in experimental animal models infected with SARS-CoV and SARS patients. These cell lines are valuable tools to perform in vitro studies in a mouse cell system that reflects the species used for in vivo studies of SARS-CoV-MA15 pathogenesis. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. In vitro adaptation of Plasmodium falciparum reveal variations in cultivability.

    PubMed

    White, John; Mascarenhas, Anjali; Pereira, Ligia; Dash, Rashmi; Walke, Jayashri T; Gawas, Pooja; Sharma, Ambika; Manoharan, Suresh Kumar; Guler, Jennifer L; Maki, Jennifer N; Kumar, Ashwani; Mahanta, Jagadish; Valecha, Neena; Dubhashi, Nagesh; Vaz, Marina; Gomes, Edwin; Chery, Laura; Rathod, Pradipsinh K

    2016-01-22

    Culture-adapted Plasmodium falciparum parasites can offer deeper understanding of geographic variations in drug resistance, pathogenesis and immune evasion. To help ground population-based calculations and inferences from culture-adapted parasites, the complete range of parasites from a study area must be well represented in any collection. To this end, standardized adaptation methods and determinants of successful in vitro adaption were sought. Venous blood was collected from 33 P. falciparum-infected individuals at Goa Medical College and Hospital (Bambolim, Goa, India). Culture variables such as whole blood versus washed blood, heat-inactivated plasma versus Albumax, and different starting haematocrit levels were tested on fresh blood samples from patients. In vitro adaptation was considered successful when two four-fold or greater increases in parasitaemia were observed within, at most, 33 days of attempted culture. Subsequently, parasites from the same patients, which were originally cryopreserved following blood draw, were retested for adaptability for 45 days using identical host red blood cells (RBCs) and culture media. At a new endemic area research site, ~65% of tested patient samples, with varied patient history and clinical presentation, were successfully culture-adapted immediately after blood collection. Cultures set up at 1% haematocrit and 0.5% Albumax adapted most rapidly, but no single test condition was uniformly fatal to culture adaptation. Success was not limited by low patient parasitaemia nor by patient age. Some parasites emerged even after significant delays in sample processing and even after initiation of treatment with anti-malarials. When 'day 0' cryopreserved samples were retested in parallel many months later using identical host RBCs and media, speed to adaptation appeared to be an intrinsic property of the parasites collected from individual patients. Culture adaptation of P. falciparum in a field setting is formally shown to be

  13. Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability

    PubMed Central

    Li, Jia; Liu, Fei; Wang, Qi; Ge, Pupu; Woo, Patrick C. Y.; Yan, Jinghua; Zhao, Yanlin; Gao, George F.; Liu, Cui Hua; Liu, Changting

    2014-01-01

    The emergence and rapid spread of New Delhi Metallo-beta-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae strains has caused a great concern worldwide. To better understand the mechanisms underlying environmental adaptation of those highly drug-resistant K. pneumoniae strains, we took advantage of the China's Shenzhou 10 spacecraft mission to conduct comparative genomic and transcriptomic analysis of a NDM-1 K. pneumoniae strain (ATCC BAA-2146) being cultivated under different conditions. The samples were recovered from semisolid medium placed on the ground (D strain), in simulated space condition (M strain), or in Shenzhou 10 spacecraft (T strain) for analysis. Our data revealed multiple variations underlying pathogen adaptation into different environments in terms of changes in morphology, H2O2 tolerance and biofilm formation ability, genomic stability and regulation of metabolic pathways. Additionally, we found a few non-coding RNAs to be differentially regulated. The results are helpful for better understanding the adaptive mechanisms of drug-resistant bacterial pathogens. PMID:25163721

  14. Population variation revealed high-altitude adaptation of Tibetan mastiffs.

    PubMed

    Li, Yan; Wu, Dong-Dong; Boyko, Adam R; Wang, Guo-Dong; Wu, Shi-Fang; Irwin, David M; Zhang, Ya-Ping

    2014-05-01

    With the assistance of their human companions, dogs have dispersed into new environments during the expansion of human civilization. Tibetan Mastiff (TM), a native of the Tibetan Plateau, was derived from the domesticated Chinese native dog and, like Tibetans, has adapted to the extreme environment of high altitude. Here, we genotyped genome-wide single-nucleotide polymorphisms (SNPs) from 32 TMs and compared them with SNPs from 20 Chinese native dogs and 14 gray wolves (Canis lupus). We identified 16 genes with signals of positive selection in the TM, with 12 of these candidate genes associated with functions that have roles in adaptation to high-altitude adaptation, such as EPAS1, SIRT7, PLXNA4, and MAFG that have roles in responses to hypoxia. This study provides important information on the genetic diversity of the TM and potential mechanisms for adaptation to hypoxia.

  15. Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity

    NASA Astrophysics Data System (ADS)

    Corcoran, Martin M.; Phad, Ganesh E.; Bernat, Néstor Vázquez; Stahl-Hennig, Christiane; Sumida, Noriyuki; Persson, Mats A. A.; Martin, Marcel; Hedestam, Gunilla B. Karlsson

    2016-12-01

    Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool.

  16. Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity

    PubMed Central

    Corcoran, Martin M.; Phad, Ganesh E.; Bernat, Néstor Vázquez; Stahl-Hennig, Christiane; Sumida, Noriyuki; Persson, Mats A.A.; Martin, Marcel; Hedestam, Gunilla B. Karlsson

    2016-01-01

    Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool. PMID:27995928

  17. Adaptation Shifts Preferred Orientation of Tuning Curve in the Mouse Visual Cortex

    PubMed Central

    Jeyabalaratnam, Jeyadarshan; Bharmauria, Vishal; Bachatene, Lyes; Cattan, Sarah; Angers, Annie; Molotchnikoff, Stéphane

    2013-01-01

    In frontalized mammals it has been demonstrated that adaptation produces shift of the peak of the orientation tuning curve of neuron following frequent or lengthier presentation of a non-preferred stimulus. Depending on the duration of adaptation the shift is attractive (toward the adapter) or repulsive (away from the adapter). Mouse exhibits a salt-and-pepper cortical organization of orientation maps, hence this species may respond differently to adaptation. To examine this question, we determined the effect of twelve minutes of adaptation to one particular orientation on neuronal orientation tuning curves in V1 of anesthetized mice. Multi-unit activity of neurons in V1 was recorded in a conventional fashion. Cells were stimulated with sine-wave drifting gratings whose orientation tilted in steps. Results revealed that similarly to cats and monkeys, majority of cells shifted their optimal orientation in the direction of the adapter while a small proportion exhibited a repulsive shift. Moreover, initially untuned cells showing poor tuning curves reacted to adaptation by displaying sharp orientation selectivity. It seems that modification of the cellular property following adaptation is a general phenomenon observed in all mammals in spite of the different organization pattern of the visual cortex. This study is of pertinence to comprehend the mechanistic pathways of brain plasticity. PMID:23717586

  18. Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds

    PubMed Central

    Yang, Xukai; Wang, Dehe; Zhu, Feng; Yang, Ning; Hou, Zhuocheng; Ning, Zhonghua

    2018-01-01

    Selection for cold tolerance in chickens is important for improving production performance and animal welfare. The identification of chicken breeds with higher cold tolerance and production performance will help to target candidates for the selection. The thyroid gland plays important roles in thermal adaptation, and its function is influenced by breed differences and transcriptional plasticity, both of which remain largely unknown in the chicken thyroid transcriptome. In this study, we subjected Bashang Long-tail (BS) and Rhode Island Red (RIR) chickens to either cold or warm environments for 21 weeks and investigated egg production performance, body weight changes, serum thyroid hormone concentrations, and thyroid gland transcriptome profiles. RIR chickens had higher egg production than BS chickens under warm conditions, but BS chickens produced more eggs than RIRs under cold conditions. Furthermore, BS chickens showed stable body weight gain under cold conditions while RIRs did not. These results suggested that BS breed is a preferable candidate for cold-tolerance selection and that the cold adaptability of RIRs should be improved in the future. BS chickens had higher serum thyroid hormone concentrations than RIRs under both environments. RNA-Seq generated 344.3 million paired-end reads from 16 sequencing libraries, and about 90% of the processed reads were concordantly mapped to the chicken reference genome. Differential expression analysis identified 46–1,211 genes in the respective comparisons. With regard to breed differences in the thyroid transcriptome, BS chickens showed higher cell replication and development, and immune response-related activity, while RIR chickens showed higher carbohydrate and protein metabolism activity. The cold environment reduced breed differences in the thyroid transcriptome compared with the warm environment. Transcriptional plasticity analysis revealed different adaptive responses in BS and RIR chickens to cope with the cold

  19. Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds.

    PubMed

    Xie, Shanshan; Yang, Xukai; Wang, Dehe; Zhu, Feng; Yang, Ning; Hou, Zhuocheng; Ning, Zhonghua

    2018-01-01

    Selection for cold tolerance in chickens is important for improving production performance and animal welfare. The identification of chicken breeds with higher cold tolerance and production performance will help to target candidates for the selection. The thyroid gland plays important roles in thermal adaptation, and its function is influenced by breed differences and transcriptional plasticity, both of which remain largely unknown in the chicken thyroid transcriptome. In this study, we subjected Bashang Long-tail (BS) and Rhode Island Red (RIR) chickens to either cold or warm environments for 21 weeks and investigated egg production performance, body weight changes, serum thyroid hormone concentrations, and thyroid gland transcriptome profiles. RIR chickens had higher egg production than BS chickens under warm conditions, but BS chickens produced more eggs than RIRs under cold conditions. Furthermore, BS chickens showed stable body weight gain under cold conditions while RIRs did not. These results suggested that BS breed is a preferable candidate for cold-tolerance selection and that the cold adaptability of RIRs should be improved in the future. BS chickens had higher serum thyroid hormone concentrations than RIRs under both environments. RNA-Seq generated 344.3 million paired-end reads from 16 sequencing libraries, and about 90% of the processed reads were concordantly mapped to the chicken reference genome. Differential expression analysis identified 46-1,211 genes in the respective comparisons. With regard to breed differences in the thyroid transcriptome, BS chickens showed higher cell replication and development, and immune response-related activity, while RIR chickens showed higher carbohydrate and protein metabolism activity. The cold environment reduced breed differences in the thyroid transcriptome compared with the warm environment. Transcriptional plasticity analysis revealed different adaptive responses in BS and RIR chickens to cope with the cold

  20. The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal

    PubMed Central

    Seim, Inge; Ma, Siming; Zhou, Xuming; Gerashchenko, Maxim V.; Lee, Sang-Goo; Suydam, Robert; George, John C.; Bickham, John W.; Gladyshev, Vadim N.

    2014-01-01

    Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt's bat. The bowhead whale transcriptome is a valuable resource for the study of this remarkable animal, including the evolution of longevity and its important correlates such as resistance to cancer and other diseases. PMID:25411232

  1. Adaptive Q–V Scheme for the Voltage Control of a DFIG-Based Wind Power Plant

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, Jinho; Seok, Jul-Ki; Muljadi, Eduard

    Wind generators within a wind power plant (WPP) will produce different amounts of active power because of the wake effect, and therefore, they have different reactive power capabilities. This paper proposes an adaptive reactive power to the voltage (Q-V) scheme for the voltage control of a doubly fed induction generator (DFIG)-based WPP. In the proposed scheme, the WPP controller uses a voltage control mode and sends a voltage error signal to each DFIG. The DFIG controller also employs a voltage control mode utilizing the adaptive Q-V characteristics depending on the reactive power capability such that a DFIG with a largermore » reactive power capability will inject more reactive power to ensure fast voltage recovery. Test results indicate that the proposed scheme can recover the voltage within a short time, even for a grid fault with a small short-circuit ratio, by making use of the available reactive power of a WPP and differentiating the reactive power injection in proportion to the reactive power capability. This will, therefore, help to reduce the additional reactive power and ensure fast voltage recovery.« less

  2. Metabolomic profiling of the heart during acute ischemic preconditioning reveals a role for SIRT1 in rapid cardioprotective metabolic adaptation.

    PubMed

    Nadtochiy, Sergiy M; Urciuoli, William; Zhang, Jimmy; Schafer, Xenia; Munger, Joshua; Brookes, Paul S

    2015-11-01

    Ischemic preconditioning (IPC) protects tissues such as the heart from prolonged ischemia-reperfusion (IR) injury. We previously showed that the lysine deacetylase SIRT1 is required for acute IPC, and has numerous metabolic targets. While it is known that metabolism is altered during IPC, the underlying metabolic regulatory mechanisms are unknown, including the relative importance of SIRT1. Thus, we sought to test the hypothesis that some of the metabolic adaptations that occur in IPC may require SIRT1 as a regulatory mediator. Using both ex-vivo-perfused and in-vivo mouse hearts, LC-MS/MS based metabolomics and (13)C-labeled substrate tracing, we found that acute IPC altered several metabolic pathways including: (i) stimulation of glycolysis, (ii) increased synthesis of glycogen and several amino acids, (iii) increased reduced glutathione levels, (iv) elevation in the oncometabolite 2-hydroxyglutarate, and (v) inhibition of fatty-acid dependent respiration. The majority (83%) of metabolic alterations induced by IPC were ablated when SIRT1 was acutely inhibited with splitomicin, and a principal component analysis revealed that metabolic changes in response to IPC were fundamentally different in nature when SIRT1 was inhibited. Furthermore, the protective benefit of IPC was abrogated by eliminating glucose from perfusion media while sustaining normal cardiac function by burning fat, thus indicating that glucose dependency is required for acute IPC. Together, these data suggest that SIRT1 signaling is required for rapid cardioprotective metabolic adaptation in acute IPC. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Adaptive reconfigurable V-BLAST type equalizer for cognitive MIMO-OFDM radios

    NASA Astrophysics Data System (ADS)

    Ozden, Mehmet Tahir

    2015-12-01

    An adaptive channel shortening equalizer design for multiple input multiple output-orthogonal frequency division multiplexing (MIMO-OFDM) radio receivers is considered in this presentation. The proposed receiver has desirable features for cognitive and software defined radio implementations. It consists of two sections: MIMO decision feedback equalizer (MIMO-DFE) and adaptive multiple Viterbi detection. In MIMO-DFE section, a complete modified Gram-Schmidt orthogonalization of multichannel input data is accomplished using sequential processing multichannel Givens lattice stages, so that a Vertical Bell Laboratories Layered Space Time (V-BLAST) type MIMO-DFE is realized at the front-end section of the channel shortening equalizer. Matrix operations, a major bottleneck for receiver operations, are accordingly avoided, and only scalar operations are used. A highly modular and regular radio receiver architecture that has a suitable structure for digital signal processing (DSP) chip and field programable gate array (FPGA) implementations, which are important for software defined radio realizations, is achieved. The MIMO-DFE section of the proposed receiver can also be reconfigured for spectrum sensing and positioning functions, which are important tasks for cognitive radio applications. In connection with adaptive multiple Viterbi detection section, a systolic array implementation for each channel is performed so that a receiver architecture with high computational concurrency is attained. The total computational complexity is given in terms of equalizer and desired response filter lengths, alphabet size, and number of antennas. The performance of the proposed receiver is presented for two-channel case by means of mean squared error (MSE) and probability of error evaluations, which are conducted for time-invariant and time-variant channel conditions, orthogonal and nonorthogonal transmissions, and two different modulation schemes.

  4. Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles* #

    PubMed Central

    Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen

    2016-01-01

    Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802

  5. Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles.

    PubMed

    Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-Yu; Zhang, Xiao-Mei; Song, Da-Feng; Zhang, Chen

    2016-08-01

    In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.

  6. Adaptive Statistical Iterative Reconstruction-V: Impact on Image Quality in Ultralow-Dose Coronary Computed Tomography Angiography.

    PubMed

    Benz, Dominik C; Gräni, Christoph; Mikulicic, Fran; Vontobel, Jan; Fuchs, Tobias A; Possner, Mathias; Clerc, Olivier F; Stehli, Julia; Gaemperli, Oliver; Pazhenkottil, Aju P; Buechel, Ronny R; Kaufmann, Philipp A

    The clinical utility of a latest generation iterative reconstruction algorithm (adaptive statistical iterative reconstruction [ASiR-V]) has yet to be elucidated for coronary computed tomography angiography (CCTA). This study evaluates the impact of ASiR-V on signal, noise and image quality in CCTA. Sixty-five patients underwent clinically indicated CCTA on a 256-slice CT scanner using an ultralow-dose protocol. Data sets from each patient were reconstructed at 6 different levels of ASiR-V. Signal intensity was measured by placing a region of interest in the aortic root, LMA, and RCA. Similarly, noise was measured in the aortic root. Image quality was visually assessed by 2 readers. Median radiation dose was 0.49 mSv. Image noise decreased with increasing levels of ASiR-V resulting in a significant increase in signal-to-noise ratio in the RCA and LMA (P < 0.001). Correspondingly, image quality significantly increased with higher levels of ASiR-V (P < 0.001). ASiR-V yields substantial noise reduction and improved image quality enabling introduction of ultralow-dose CCTA.

  7. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    PubMed Central

    2013-01-01

    Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

  8. The influence of surround suppression on adaptation effects in primary visual cortex

    PubMed Central

    Wissig, Stephanie C.

    2012-01-01

    Adaptation, the prolonged presentation of stimuli, has been used to probe mechanisms of visual processing in physiological, imaging, and perceptual studies. Previous neurophysiological studies have measured adaptation effects by using stimuli tailored to evoke robust responses in individual neurons. This approach provides an incomplete view of how an adapter alters the representation of sensory stimuli by a population of neurons with diverse functional properties. We implanted microelectrode arrays in primary visual cortex (V1) of macaque monkeys and measured orientation tuning and contrast sensitivity in populations of neurons before and after prolonged adaptation. Whereas previous studies in V1 have reported that adaptation causes stimulus-specific suppression of responsivity and repulsive shifts in tuning preference, we have found that adaptation can also lead to response facilitation and shifts in tuning toward the adapter. To explain this range of effects, we have proposed and tested a simple model that employs stimulus-specific suppression in both the receptive field and the spatial surround. The predicted effects on tuning depend on the relative drive provided by the adapter to these two receptive field components. Our data reveal that adaptation can have a much richer repertoire of effects on neuronal responsivity and tuning than previously considered and suggest an intimate mechanistic relationship between spatial and temporal contextual effects. PMID:22423001

  9. Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast

    PubMed Central

    Hope, Elyse A.; Amorosi, Clara J.; Miller, Aaron W.; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J.

    2017-01-01

    Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. PMID:28450459

  10. Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast.

    PubMed

    Hope, Elyse A; Amorosi, Clara J; Miller, Aaron W; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J

    2017-06-01

    Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1 , and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1 , which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. Copyright © 2017 Hope et al.

  11. An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes

    PubMed Central

    Shafqat-Abbasi, Hamdah; Kowalewski, Jacob M; Kiss, Alexa; Gong, Xiaowei; Hernandez-Varas, Pablo; Berge, Ulrich; Jafari-Mamaghani, Mehrdad; Lock, John G; Strömblad, Staffan

    2016-01-01

    Mesenchymal (lamellipodial) migration is heterogeneous, although whether this reflects progressive variability or discrete, 'switchable' migration modalities, remains unclear. We present an analytical toolbox, based on quantitative single-cell imaging data, to interrogate this heterogeneity. Integrating supervised behavioral classification with multivariate analyses of cell motion, membrane dynamics, cell-matrix adhesion status and F-actin organization, this toolbox here enables the detection and characterization of two quantitatively distinct mesenchymal migration modes, termed 'Continuous' and 'Discontinuous'. Quantitative mode comparisons reveal differences in cell motion, spatiotemporal coordination of membrane protrusion/retraction, and how cells within each mode reorganize with changed cell speed. These modes thus represent distinctive migratory strategies. Additional analyses illuminate the macromolecular- and cellular-scale effects of molecular targeting (fibronectin, talin, ROCK), including 'adaptive switching' between Continuous (favored at high adhesion/full contraction) and Discontinuous (low adhesion/inhibited contraction) modes. Overall, this analytical toolbox now facilitates the exploration of both spontaneous and adaptive heterogeneity in mesenchymal migration. DOI: http://dx.doi.org/10.7554/eLife.11384.001 PMID:26821527

  12. Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes.

    PubMed

    Kumar, Vikas; Kutschera, Verena E; Nilsson, Maria A; Janke, Axel

    2015-08-07

    The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic

  13. The selectivity of responses to red-green colour and achromatic contrast in the human visual cortex: an fMRI adaptation study.

    PubMed

    Mullen, Kathy T; Chang, Dorita H F; Hess, Robert F

    2015-12-01

    There is controversy as to how responses to colour in the human brain are organized within the visual pathways. A key issue is whether there are modular pathways that respond selectively to colour or whether there are common neural substrates for both colour and achromatic (Ach) contrast. We used functional magnetic resonance imaging (fMRI) adaptation to investigate the responses of early and extrastriate visual areas to colour and Ach contrast. High-contrast red-green (RG) and Ach sinewave rings (0.5 cycles/degree, 2 Hz) were used as both adapting stimuli and test stimuli in a block design. We found robust adaptation to RG or Ach contrast in all visual areas. Cross-adaptation between RG and Ach contrast occurred in all areas indicating the presence of integrated, colour and Ach responses. Notably, we revealed contrasting trends for the two test stimuli. For the RG test, unselective processing (robust adaptation to both RG and Ach contrast) was most evident in the early visual areas (V1 and V2), but selective responses, revealed as greater adaptation between the same stimuli than cross-adaptation between different stimuli, emerged in the ventral cortex, in V4 and VO in particular. For the Ach test, unselective responses were again most evident in early visual areas but Ach selectivity emerged in the dorsal cortex (V3a and hMT+). Our findings support a strong presence of integrated mechanisms for colour and Ach contrast across the visual hierarchy, with a progression towards selective processing in extrastriate visual areas. © 2015 The Authors. European Journal of Neuroscience published by Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  14. Adaptive Circuits for the 0.5-V Nanoscale CMOS Era

    NASA Astrophysics Data System (ADS)

    Itoh, Kiyoo; Yamaoka, Masanao; Oshima, Takashi

    The minimum operating voltage, Vmin, of nanoscale CMOS LSIs is investigated to breach the 1-V wall that we are facing in the 65-nm device generation, and open the door to the below 0.5-V era. A new method using speed variation is proposed to evaluate Vmin. It shows that Vmin is very sensitive to the lowest necessary threshold voltage, Vt0, of MOSFETs and to threshold-voltage variations, ΔVt, which become more significant with device scaling. There is thus a need for low-Vt0 circuits and ΔVt-immune MOSFETs to reduce Vmin. For memory-rich LSIs, the SRAM block is particularly problematic because it has the highest Vmin. Various techniques are thus proposed to reduce the Vmin: using RAM repair, shortening the data line, up-sizing, and using more relaxed MOSFET scaling. To effectively reduce Vmin of other circuit blocks, dual-Vt0 and dual-VDD circuits using gate-source reverse biasing, temporary activation, and series connection of another small low-Vt0 MOSFET are proposed. They are dynamic logic circuits enabling the power-delay product of the conventional static CMOS inverter to be reduced to 0.09 at a 0.2-V supply, and a DRAM dynamic sense amplifier and power switches operable at below 0.5V. In addition, a fully-depleted structure (FD-SOI) and fin-type structure (FinFET) for Vt-immune MOSFETs are discussed in terms of their low-voltage potential and challenges. As a result, the height up-scalable FinFETs turns out to be quite effective to reduce Vmin to less than 0.5V, if combined with the low-Vt0 circuits. For mixed-signal LSIs, investigation of low-voltage potential of analog circuits, especially for comparators and operational amplifiers, reveals that simple inverter op-amps, in which the low gain and nonlinearity are compensated for by digitally assisted analog designs, are crucial to 0.5-V operations. Finally, it is emphasized that the development of relevant devices and fabrication processes is the key to the achievement of 0.5-V nanoscale LSIs.

  15. Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation

    PubMed Central

    2013-01-01

    Background To cope with environmental challenges bacteria possess sophisticated defense mechanisms that involve stress-induced adaptive responses. The canonical stress regulators CtsR and HrcA play a central role in the adaptations to a plethora of stresses in a variety of organisms. Here, we determined the CtsR and HrcA regulons of the lactic acid bacterium Lactobacillus plantarum WCFS1 grown under reference (28°C) and elevated (40°C) temperatures, using ctsR, hrcA, and ctsR-hrcA deletion mutants. Results While the maximum specific growth rates of the mutants and the parental strain were similar at both temperatures (0.33 ± 0.02 h-1 and 0.34 ± 0.03 h-1, respectively), DNA microarray analyses revealed that the CtsR or HrcA deficient strains displayed altered transcription patterns of genes encoding functions involved in transport and binding of sugars and other compounds, primary metabolism, transcription regulation, capsular polysaccharide biosynthesis, as well as fatty acid metabolism. These transcriptional signatures enabled the refinement of the gene repertoire that is directly or indirectly controlled by CtsR and HrcA of L. plantarum. Deletion of both regulators, elicited transcriptional changes of a large variety of additional genes in a temperature-dependent manner, including genes encoding functions involved in cell-envelope remodeling. Moreover, phenotypic assays revealed that both transcription regulators contribute to regulation of resistance to hydrogen peroxide stress. The integration of these results allowed the reconstruction of CtsR and HrcA regulatory networks in L. plantarum, highlighting the significant intertwinement of class I and III stress regulons. Conclusions Taken together, our results enabled the refinement of the CtsR and HrcA regulatory networks in L. plantarum, illustrating the complex nature of adaptive stress responses in this bacterium. PMID:24238744

  16. The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution.

    PubMed

    Reznick, D N; Ghalambor, C K

    2001-01-01

    Under what conditions might organisms be capable of rapid adaptive evolution? We reviewed published studies documenting contemporary adaptations in natural populations and looked for general patterns in the population ecological causes. We found that studies of contemporary adaptation fall into two general settings: (1) colonization of new environments that established newly adapted populations, and (2) local adaptations within the context of a heterogeneous environments and metapopulation structure. Local ecological processes associated with colonizations and introductions included exposure to: (1) a novel host or food resource; (2) a new biophysical environment; (3) a new predator community; and (4) a new coexisting competitor. The new environments that were colonized often had depauperate communities, sometimes because of anthropogenic disturbance. Local adaptation in heterogeneous environments was also often associated with recent anthropogenic changes, such as insecticide and herbicide resistance, or industrial melanism. A common feature of many examples is the combination of directional selection with at least a short-term opportunity for population growth. We suggest that such opportunities for population growth may be a key factor that promotes rapid evolution, since directional selection might otherwise be expected to cause population decline and create the potential for local extinction, which is an ever-present alternative to local adaptation. We also address the large discrepancy between the rate of evolution observed in contemporary studies and the apparent rate of evolution seen in the fossil record.

  17. Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep.

    PubMed

    Rochus, Christina Marie; Tortereau, Flavie; Plisson-Petit, Florence; Restoux, Gwendal; Moreno-Romieux, Carole; Tosser-Klopp, Gwenola; Servin, Bertrand

    2018-01-23

    One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs. Population structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species ("selection hotspots") including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds. Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.

  18. Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization*

    PubMed Central

    Müller, Daniel B.; Schubert, Olga T.; Röst, Hannes; Aebersold, Ruedi; Vorholt, Julia A.

    2016-01-01

    Plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. Niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. To gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upon Arabidopsis phyllosphere colonization. The highly quantitative mass spectrometric technique SWATH MS was used and allowed for the analysis of over two thousand proteins spanning more than three orders of magnitude in abundance for each of the model strains. The data suggest that Sphingomonas melonis utilizes amino acids and hydrocarbon compounds during colonization of leaves whereas Methylobacterium extorquens relies on methanol metabolism in addition to oxalate metabolism, aerobic anoxygenic photosynthesis and alkanesulfonate utilization. Comparative genomic analyses indicates that utilization of oxalate and alkanesulfonates is widespread among leaf microbiota members whereas, aerobic anoxygenic photosynthesis is almost exclusively found in Methylobacteria. Despite the apparent niche separation between these two strains we also found a relatively small subset of proteins to be coregulated, indicating common mechanisms, underlying successful leaf colonization. Overall, our results reveal for two ubiquitous phyllosphere commensals species-specific adaptations to the host environment and provide evidence for niche separation within the plant microbiota. PMID:27457762

  19. Characterisation of the Transcriptomes of Genetically Diverse Listeria monocytogenes Exposed to Hyperosmotic and Low Temperature Conditions Reveal Global Stress-Adaptation Mechanisms

    PubMed Central

    Durack, Juliana; Ross, Tom; Bowman, John P.

    2013-01-01

    The ability of Listeria monocytogenes to adapt to various food and food- processing environments has been attributed to its robustness, persistence and prevalence in the food supply chain. To improve the present understanding of molecular mechanisms involved in hyperosmotic and low-temperature stress adaptation of L. monocytogenes, we undertook transcriptomics analysis on three strains adapted to sub-lethal levels of these stress stimuli and assessed functional gene response. Adaptation to hyperosmotic and cold-temperature stress has revealed many parallels in terms of gene expression profiles in strains possessing different levels of stress tolerance. Gene sets associated with ribosomes and translation, transcription, cell division as well as fatty acid biosynthesis and peptide transport showed activation in cells adapted to either cold or hyperosmotic stress. Repression of genes associated with carbohydrate metabolism and transport as well as flagella was evident in stressed cells, likely linked to activation of CodY regulon and consequential cellular energy conservation. PMID:24023890

  20. Fishing in troubled waters: Revealing genomic signatures of local adaptation in response to freshwater pollutants in two macroinvertebrates.

    PubMed

    Weigand, Hannah; Weiss, Martina; Cai, Huimin; Li, Yongping; Yu, Lili; Zhang, Christine; Leese, Florian

    2018-08-15

    Local adaptation is of fundamental importance for populations to cope with fast, human-mediated environmental changes. In the past, analyses of local adaptation were restricted to few model species. Nowadays, due to the increased affordability of high-throughput sequencing, local adaptation can be studied much easier by searching for patterns of positive selection using genomic data. In the present study, we analysed effects of wastewater treatment plant and ore mining effluents on stream invertebrate populations. The two different anthropogenic stressors have impacted on stream ecosystems over different time scales and with different potencies. As target organisms we selected two macroinvertebrate species with different life histories and dispersal capacities: the caddisfly Glossosoma conformis and the flatworm Dugesia gonocephala. We applied a genome-wide genetic marker technique, termed ddRAD (double digest restriction site associated DNA) sequencing, to identify local adaptation. Ten and 18% of all loci were identified as candidate loci for local adaptation in D. gonocephala and G. conformis, respectively. However, after stringent re-evaluation of the genomic data, strong evidence for local adaptation remained only for one population of the flatworm D. gonocephala affected by high copper concentration from ore mining. One of the corresponding candidate loci is arnt, a gene associated with the response to xenobiotics and potentially involved in metal detoxification. Our results support the hypotheses that local adaptation is more likely to play a central role in environments impacted by a stronger stressor for a longer time and that it is more likely to occur in species with lower migration rates. However, these findings have to be interpreted cautiously, as several confounding factors may have limited the possibility to detect local adaptation. Our study highlights how genomic tools can be used to study the adaptability and thus resistance of natural

  1. Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.

    PubMed

    Fletcher, Eugene; Feizi, Amir; Bisschops, Markus M M; Hallström, Björn M; Khoomrung, Sakda; Siewers, Verena; Nielsen, Jens

    2017-01-01

    Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions. Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether these mechanisms will be similar for tolerance to both organic and inorganic acids is yet to be explored. We therefore evolved Saccharomyces cerevisiae to acquire tolerance to HCl (inorganic acid) and to 0.3M L-lactic acid (organic acid) at pH 2.8 and then isolated several low pH tolerant strains. Whole genome sequencing and RNA-seq analysis of the evolved strains revealed different sets of genome alterations suggesting a divergence in adaptation to these two acids. An altered sterol composition and impaired iron uptake contributed to HCl tolerance whereas the formation of a multicellular morphology and rapid lactate degradation was crucial for tolerance to high concentrations of lactic acid. Our findings highlight the contribution of both the selection pressure and nature of the acid as a driver for directing the evolutionary path towards tolerance to low pH. The choice of carbon source was also an important factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending on the acid of interest. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  2. PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses

    PubMed Central

    Xiao, Chencheng; Ma, Wenjun; Sun, Na; Huang, Lihong; Li, Yaling; Zeng, Zhaoyong; Wen, Yijun; Zhang, Zaoyue; Li, Huanan; Li, Qian; Yu, Yuandi; Zheng, Yi; Liu, Shukai; Hu, Pingsheng; Zhang, Xu; Ning, Zhangyong; Qi, Wenbao; Liao, Ming

    2016-01-01

    Human infections with avian influenza H7N9 or H10N8 viruses have been reported in China, raising concerns that they might cause human epidemics and pandemics. However, how these viruses adapt to mammalian hosts is unclear. Here we show that besides the commonly recognized viral polymerase subunit PB2 residue 627 K, other residues including 87E, 292 V, 340 K, 588 V, 648 V, and 676 M in PB2 also play critical roles in mammalian adaptation of the H10N8 virus. The avian-origin H10N8, H7N9, and H9N2 viruses harboring PB2-588 V exhibited higher polymerase activity, more efficient replication in mammalian and avian cells, and higher virulence in mice when compared to viruses with PB2-588 A. Analyses of available PB2 sequences showed that the proportion of avian H9N2 or human H7N9 influenza isolates bearing PB2-588 V has increased significantly since 2013. Taken together, our results suggest that the substitution PB2-A588V may be a new strategy for an avian influenza virus to adapt mammalian hosts. PMID:26782141

  3. Exercise-induced adaptations to white and brown adipose tissue.

    PubMed

    Lehnig, Adam C; Stanford, Kristin I

    2018-03-07

    The beneficial effects of exercise on skeletal muscle and the cardiovascular system have long been known. Recent studies have focused on investigating the effects of exercise on adipose tissue and the effects that these exercise-induced adaptations have on overall metabolic health. Examination of exercise-induced adaptations in both white adipose tissue (WAT) and brown adipose tissue (BAT) has revealed marked differences in each tissue with exercise. In WAT, there are changes to both subcutaneous WAT (scWAT) and visceral WAT (vWAT), including decreased adipocyte size and lipid content, increased expression of metabolic genes, altered secretion of adipokines and increased mitochondrial activity. Adaptations specific to scWAT include lipidomic remodeling of phospholipids and, in rodents, the beiging of scWAT. The changes to BAT are less clear: studies evaluating the effect of exercise on the BAT of humans and rodents have revealed contradictory data, making this an important area of current investigation. In this Review, we discuss the exercise-induced changes to WAT and BAT that have been reported by different studies and highlight the current questions in this field. © 2018. Published by The Company of Biologists Ltd.

  4. Repeated exposure to immobilization or two different footshock intensities reveals differential adaptation of the hypothalamic-pituitary-adrenal axis.

    PubMed

    Rabasa, Cristina; Muñoz-Abellán, Cristina; Daviu, Núria; Nadal, Roser; Armario, Antonio

    2011-05-03

    Factors involved in adaptation to repeated stress are not well-characterized. For instance, acute footshock (FS) of high intensity appears to be less severe than immobilization (IMO) in light of the speed of post-stress recovery of the hypothalamic-pituitary-adrenal (HPA) axis and other physiological variables. However, repeated exposure to IMO consistently resulted in reduction of the HPA response to the same stressor (adaptation), whereas failure to adapt has been usually reported after FS. Thus, in the present work we directly compared the activation of HPA axis and other physiological changes in response to both acute and repeated exposure to IMO and two intensities of FS (medium and high) in adult male rats. Control rats were exposed to the FS boxes but they did not receive shocks. Daily repeated exposure to IMO resulted in significant adaptation of the overall ACTH and corticosterone responses to the stressor. Such a reduction was also observed with repeated exposure to FS boxes and FS-medium, whereas repeated exposure to FS-high only resulted in a small reduction of the corticosterone response during the post-stress period. This suggests that some properties of FS-high make adaptation to it difficult. Interestingly, overall changes in food intake and body weight gain throughout the week of exposure to the stressors reveal a greater impact of IMO than FS-high, indicating that factors other than the intensity of a stressor, at least when evaluated in function of the above physiological variables, can influence HPA adaptation. Since FS exposure is likely to cause more pain than IMO, activation of nociceptive signals above a certain level may negatively affect HPA adaptation to repeated stressors. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization.

    PubMed

    Müller, Daniel B; Schubert, Olga T; Röst, Hannes; Aebersold, Ruedi; Vorholt, Julia A

    2016-10-01

    Plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. Niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. To gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upon Arabidopsis phyllosphere colonization. The highly quantitative mass spectrometric technique SWATH MS was used and allowed for the analysis of over two thousand proteins spanning more than three orders of magnitude in abundance for each of the model strains. The data suggest that Sphingomonas melonis utilizes amino acids and hydrocarbon compounds during colonization of leaves whereas Methylobacterium extorquens relies on methanol metabolism in addition to oxalate metabolism, aerobic anoxygenic photosynthesis and alkanesulfonate utilization. Comparative genomic analyses indicates that utilization of oxalate and alkanesulfonates is widespread among leaf microbiota members whereas, aerobic anoxygenic photosynthesis is almost exclusively found in Methylobacteria. Despite the apparent niche separation between these two strains we also found a relatively small subset of proteins to be coregulated, indicating common mechanisms, underlying successful leaf colonization. Overall, our results reveal for two ubiquitous phyllosphere commensals species-specific adaptations to the host environment and provide evidence for niche separation within the plant microbiota. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Mental Rotation Meets the Motion Aftereffect: The Role of hV5/MT+ in Visual Mental Imagery

    ERIC Educational Resources Information Center

    Seurinck, Ruth; de Lange, Floris P.; Achten, Erik; Vingerhoets, Guy

    2011-01-01

    A growing number of studies show that visual mental imagery recruits the same brain areas as visual perception. Although the necessity of hV5/MT+ for motion perception has been revealed by means of TMS, its relevance for motion imagery remains unclear. We induced a direction-selective adaptation in hV5/MT+ by means of an MAE while subjects…

  7. Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas

    PubMed Central

    Roller, Devin G.; Capaldo, Brian; Bekiranov, Stefan; Mackey, Aaron J.; Conaway, Mark R.; Petricoin, Emanuel F.; Gioeli, Daniel; Weber, Michael J.

    2016-01-01

    Over half of BRAFV600E melanomas display intrinsic resistance to BRAF inhibitors, in part due to adaptive signaling responses. In this communication we ask whether BRAFV600E melanomas share common adaptive responses to BRAF inhibition that can provide clinically relevant targets for drug combinations. We screened a panel of 12 treatment-naïve BRAFV600E melanoma cell lines with MAP Kinase pathway inhibitors in pairwise combination with 58 signaling inhibitors, assaying for synergistic cytotoxicity. We found enormous diversity in the drug combinations that showed synergy, with no two cell lines having an identical profile. Although the 6 lines most resistant to BRAF inhibition showed synergistic benefit from combination with lapatinib, the signaling mechanisms by which this combination generated synergistic cytotoxicity differed between the cell lines. We conclude that adaptive responses to inhibition of the primary oncogenic driver (BRAFV600E) are determined not only by the primary oncogenic driver but also by diverse secondary genetic and epigenetic changes (“back-seat drivers”) and hence optimal drug combinations will be variable. Because upregulation of receptor tyrosine kinases is a major source of drug resistance arising from diverse adaptive responses, we propose that inhibitors of these receptors may have substantial clinical utility in combination with inhibitors of the MAP Kinase pathway. PMID:26673621

  8. Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas.

    PubMed

    Roller, Devin G; Capaldo, Brian; Bekiranov, Stefan; Mackey, Aaron J; Conaway, Mark R; Petricoin, Emanuel F; Gioeli, Daniel; Weber, Michael J

    2016-01-19

    Over half of BRAFV600E melanomas display intrinsic resistance to BRAF inhibitors, in part due to adaptive signaling responses. In this communication we ask whether BRAFV600E melanomas share common adaptive responses to BRAF inhibition that can provide clinically relevant targets for drug combinations. We screened a panel of 12 treatment-naïve BRAFV600E melanoma cell lines with MAP Kinase pathway inhibitors in pairwise combination with 58 signaling inhibitors, assaying for synergistic cytotoxicity. We found enormous diversity in the drug combinations that showed synergy, with no two cell lines having an identical profile. Although the 6 lines most resistant to BRAF inhibition showed synergistic benefit from combination with lapatinib, the signaling mechanisms by which this combination generated synergistic cytotoxicity differed between the cell lines. We conclude that adaptive responses to inhibition of the primary oncogenic driver (BRAFV600E) are determined not only by the primary oncogenic driver but also by diverse secondary genetic and epigenetic changes ("back-seat drivers") and hence optimal drug combinations will be variable. Because upregulation of receptor tyrosine kinases is a major source of drug resistance arising from diverse adaptive responses, we propose that inhibitors of these receptors may have substantial clinical utility in combination with inhibitors of the MAP Kinase pathway.

  9. Redefining diagnostic symptoms of depression using Rasch analysis: testing an item bank suitable for DSM-V and computer adaptive testing.

    PubMed

    Mitchell, Alex J; Smith, Adam B; Al-salihy, Zerak; Rahim, Twana A; Mahmud, Mahmud Q; Muhyaldin, Asma S

    2011-10-01

    We aimed to redefine the optimal self-report symptoms of depression suitable for creation of an item bank that could be used in computer adaptive testing or to develop a simplified screening tool for DSM-V. Four hundred subjects (200 patients with primary depression and 200 non-depressed subjects), living in Iraqi Kurdistan were interviewed. The Mini International Neuropsychiatric Interview (MINI) was used to define the presence of major depression (DSM-IV criteria). We examined symptoms of depression using four well-known scales delivered in Kurdish. The Partial Credit Model was applied to each instrument. Common-item equating was subsequently used to create an item bank and differential item functioning (DIF) explored for known subgroups. A symptom level Rasch analysis reduced the original 45 items to 24 items of the original after the exclusion of 21 misfitting items. A further six items (CESD13 and CESD17, HADS-D4, HADS-D5 and HADS-D7, and CDSS3 and CDSS4) were removed due to misfit as the items were added together to form the item bank, and two items were subsequently removed following the DIF analysis by diagnosis (CESD20 and CDSS9, both of which were harder to endorse for women). Therefore the remaining optimal item bank consisted of 17 items and produced an area under the curve (AUC) of 0.987. Using a bank restricted to the optimal nine items revealed only minor loss of accuracy (AUC = 0.989, sensitivity 96%, specificity 95%). Finally, when restricted to only four items accuracy was still high (AUC was still 0.976; sensitivity 93%, specificity 96%). An item bank of 17 items may be useful in computer adaptive testing and nine or even four items may be used to develop a simplified screening tool for DSM-V major depressive disorder (MDD). Further examination of this item bank should be conducted in different cultural settings.

  10. The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation

    PubMed Central

    Arkin, Adam

    2006-01-01

    Two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. To understand how these systems adapt to allow organisms to detect niche-specific signals, we analyzed the phylogenetic distribution of nearly 5,000 histidine protein kinases from 207 sequenced prokaryotic genomes. We found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environmental conditions. Both lineage-specific gene family expansion and horizontal gene transfer play major roles in the introduction of new histidine kinases into genomes; however, there are differences in how these two evolutionary forces act. Genes imported via horizontal transfer are more likely to retain their original functionality as inferred from a similar complement of signaling domains, while gene family expansion accompanied by domain shuffling appears to be a major source of novel genetic diversity. Family expansion is the dominant source of new histidine kinase genes in the genomes most enriched in signaling proteins, and detailed analysis reveals that divergence in domain structure and changes in expression patterns are hallmarks of recent expansions. Finally, while these two modes of gene acquisition are widespread across bacterial taxa, there are clear species-specific preferences for which mode is used. PMID:17083272

  11. ASIS v1.0: an adaptive solver for the simulation of atmospheric chemistry

    NASA Astrophysics Data System (ADS)

    Cariolle, Daniel; Moinat, Philippe; Teyssèdre, Hubert; Giraud, Luc; Josse, Béatrice; Lefèvre, Franck

    2017-04-01

    This article reports on the development and tests of the adaptive semi-implicit scheme (ASIS) solver for the simulation of atmospheric chemistry. To solve the ordinary differential equation systems associated with the time evolution of the species concentrations, ASIS adopts a one-step linearized implicit scheme with specific treatments of the Jacobian of the chemical fluxes. It conserves mass and has a time-stepping module to control the accuracy of the numerical solution. In idealized box-model simulations, ASIS gives results similar to the higher-order implicit schemes derived from the Rosenbrock's and Gear's methods and requires less computation and run time at the moderate precision required for atmospheric applications. When implemented in the MOCAGE chemical transport model and the Laboratoire de Météorologie Dynamique Mars general circulation model, the ASIS solver performs well and reveals weaknesses and limitations of the original semi-implicit solvers used by these two models. ASIS can be easily adapted to various chemical schemes and further developments are foreseen to increase its computational efficiency, and to include the computation of the concentrations of the species in aqueous-phase in addition to gas-phase chemistry.

  12. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

    PubMed Central

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea’s genetic data sources. PMID:27446038

  13. In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells

    PubMed Central

    Yokoyama, Masaru; Nomaguchi, Masako; Doi, Naoya; Kanda, Tadahito; Adachi, Akio; Sato, Hironori

    2016-01-01

    Variable V1/V2 and V3 loops on human immunodeficiency virus type 1 (HIV-1) envelope-gp120 core play key roles in modulating viral competence to recognize two infection receptors, CD4 and chemokine-receptors. However, molecular bases for the modulation largely remain unclear. To address these issues, we constructed structural models for a full-length gp120 in CD4-free and -bound states. The models showed topologies of gp120 surface loop that agree with those in reported structural data. Molecular dynamics simulation showed that in the unliganded state, V1/V2 loop settled into a thermodynamically stable arrangement near V3 loop for conformational masking of V3 tip, a potent neutralization epitope. In the CD4-bound state, however, V1/V2 loop was rearranged near the bound CD4 to support CD4 binding. In parallel, cell-based adaptation in the absence of anti-viral antibody pressures led to the identification of amino acid substitutions that individually enhance viral entry and growth efficiencies in association with reduced sensitivity to CCR5 antagonist TAK-779. Notably, all these substitutions were positioned on the receptors binding surfaces in V1/V2 or V3 loop. In silico structural studies predicted some physical changes of gp120 by substitutions with alterations in viral replication phenotypes. These data suggest that V1/V2 loop is critical for creating a gp120 structure that masks co-receptor binding site compatible with maintenance of viral infectivity, and for tuning a functional balance of gp120 between immune escape ability and infectivity to optimize HIV-1 replication fitness. PMID:26903989

  14. DHA-fluorescent probe is sensitive to membrane order and reveals molecular adaptation of DHA in ordered lipid microdomains☆

    PubMed Central

    Teague, Heather; Ross, Ron; Harris, Mitchel; Mitchell, Drake C.; Shaikh, Saame Raza

    2012-01-01

    Docosahexaenoic acid (DHA) disrupts the size and order of plasma membrane lipid microdomains in vitro and in vivo. However, it is unknown how the highly disordered structure of DHA mechanistically adapts to increase the order of tightly packed lipid microdomains. Therefore, we studied a novel DHA-Bodipy fluorescent probe to address this issue. We first determined if the DHA-Bodipy probe localized to the plasma membrane of primary B and immortal EL4 cells. Image analysis revealed that DHA-Bodipy localized into the plasma membrane of primary B cells more efficiently than EL4 cells. We then determined if the probe detected changes in plasma membrane order. Quantitative analysis of time-lapse movies established that DHA-Bodipy was sensitive to membrane molecular order. This allowed us to investigate how DHA-Bodipy physically adapted to ordered lipid microdomains. To accomplish this, we employed steady-state and time-resolved fluorescence anisotropy measurements in lipid vesicles of varying composition. Similar to cell culture studies, the probe was highly sensitive to membrane order in lipid vesicles. Moreover, these experiments revealed, relative to controls, that upon incorporation into highly ordered microdomains, DHA-Bodipy underwent an increase in its fluorescence lifetime and molecular order. In addition, the probe displayed a significant reduction in its rotational diffusion compared to controls. Altogether, DHA-Bodipy was highly sensitive to membrane order and revealed for the first time that DHA, despite its flexibility, could become ordered with less rotational motion inside ordered lipid microdomains. Mechanistically, this explains how DHA acyl chains can increase order upon formation of lipid microdomains in vivo. PMID:22841541

  15. Comparison of Models for Bubonic Plague Reveals Unique Pathogen Adaptations to the Dermis.

    PubMed

    Gonzalez, Rodrigo J; Weening, Eric H; Lane, M Chelsea; Miller, Virginia L

    2015-07-01

    Vector-borne pathogens are inoculated in the skin of mammals, most likely in the dermis. Despite this, subcutaneous (s.c.) models of infection are broadly used in many fields, including Yersinia pestis pathogenesis. We expand on a previous report where we implemented intradermal (i.d.) inoculations to study bacterial dissemination during bubonic plague and compare this model with an s.c. We found that i.d. inoculations result in faster kinetics of infection and that bacterial dose influenced mouse survival after i.d. but not s.c. inoculation. Moreover, a deletion mutant of rovA, previously shown to be moderately attenuated in the s.c. model, was severely attenuated in the i.d. Lastly, based on previous observations where a population bottleneck from the skin to lymph nodes was observed after i.d., but not after s.c., inoculations, we used the latter model as a strategy to identify an additional bottleneck in bacterial dissemination from lymph nodes to the bloodstream. Our data indicate that the more biologically relevant i.d. model of bubonic plague differs significantly from the s.c. model in multiple aspects of infection. These findings reveal adaptations of Y. pestis to the dermis and how these adaptations can define the progression of disease. They also emphasize the importance of using a relevant route of infection when addressing host-pathogen interactions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  16. Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities

    PubMed Central

    Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M.; Valenzuela, Alejandra; Schmidt, Rebeccah A.; Goodwin, Lynne A.; Woyke, Tanja; Currie, Cameron R.; Suen, Garret

    2013-01-01

    Sphingomonads comprise a physiologically versatile group within the Alphaproteobacteria that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling. PMID:23563954

  17. Adaptive Flight Control for Aircraft Safety Enhancements

    NASA Technical Reports Server (NTRS)

    Nguyen, Nhan T.; Gregory, Irene M.; Joshi, Suresh M.

    2008-01-01

    This poster presents the current adaptive control research being conducted at NASA ARC and LaRC in support of the Integrated Resilient Aircraft Control (IRAC) project. The technique "Approximate Stability Margin Analysis of Hybrid Direct-Indirect Adaptive Control" has been developed at NASA ARC to address the needs for stability margin metrics for adaptive control that potentially enables future V&V of adaptive systems. The technique "Direct Adaptive Control With Unknown Actuator Failures" is developed at NASA LaRC to deal with unknown actuator failures. The technique "Adaptive Control with Adaptive Pilot Element" is being researched at NASA LaRC to investigate the effects of pilot interactions with adaptive flight control that can have implications of stability and performance.

  18. SU-E-T-301: Dosimetric Comparison Between Adaptive and Rectilinear Template-Based Prostate Seed Implants

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sugar, E Neubauer; Buzurovic, I; O’Farrell, D

    2015-06-15

    Purpose: To compare the dosimetry of a standard rectilinear and an adaptive technique used in I125 prostate seed implants. Methods: To achieve favorable dosimetry in prostate implants we used adaptive needle updates to match actual positions in real-time. The seed locations were optimized based on actual needle locations. The seeds were delivered automatically with a robotic device seedSelectron™ (Elekta Brachytherapy). In this study, we evaluated the former approach against the standard rectilinear technique in which the needles have a parallel distribution. The treatment plans for 10 patients were analyzed. For comparison, the actual treatment plans were revised so each needlemore » was repositioned to its original parallel location through the template. The analysis was performed by comparing the target coverage and dose to the organs at risk. The comparison was done using the following planning goals: the target D90> 90%, V100% > 90%, V50% <70% and V200% <30%; the urethra V125% < 1cm3 and V150%= 0cm3; and the Rectum V100%<1cm3 and V69% < 8cm3. The prescription dose to the target was 145Gy. Results: The average target volume and number of seeds were 44.39cm3(SD=11.14) and 74(SD=12), respectively. The D90 for adaptive and rectilinear plans was 159.9Gy(SD=2.99) and 155.53Gy(SD=4.04) resulting in a 2.74% difference for the average target coverage. A similar difference (1.75%) was noticed in the target V100[%]. No significant difference was noticed in the dose to the urethra and rectum. All planning goals were met with both the adaptive and rectilinear approach for each plan. Conclusion: The study reveals enhanced coverage of the target when using the adaptive needle adjustments as compared to the rectilinear approach for the analyzed cases. However, the differences in dosimetry did not translate to meaningful clinical outcomes.« less

  19. Differential effect of visual motion adaption upon visual cortical excitability.

    PubMed

    Lubeck, Astrid J A; Van Ombergen, Angelique; Ahmad, Hena; Bos, Jelte E; Wuyts, Floris L; Bronstein, Adolfo M; Arshad, Qadeer

    2017-03-01

    The objectives of this study were 1 ) to probe the effects of visual motion adaptation on early visual and V5/MT cortical excitability and 2 ) to investigate whether changes in cortical excitability following visual motion adaptation are related to the degree of visual dependency, i.e., an overreliance on visual cues compared with vestibular or proprioceptive cues. Participants were exposed to a roll motion visual stimulus before, during, and after visual motion adaptation. At these stages, 20 transcranial magnetic stimulation (TMS) pulses at phosphene threshold values were applied over early visual and V5/MT cortical areas from which the probability of eliciting a phosphene was calculated. Before and after adaptation, participants aligned the subjective visual vertical in front of the roll motion stimulus as a marker of visual dependency. During adaptation, early visual cortex excitability decreased whereas V5/MT excitability increased. After adaptation, both early visual and V5/MT excitability were increased. The roll motion-induced tilt of the subjective visual vertical (visual dependence) was not influenced by visual motion adaptation and did not correlate with phosphene threshold or visual cortex excitability. We conclude that early visual and V5/MT cortical excitability is differentially affected by visual motion adaptation. Furthermore, excitability in the early or late visual cortex is not associated with an increase in visual reliance during spatial orientation. Our findings complement earlier studies that have probed visual cortical excitability following motion adaptation and highlight the differential role of the early visual cortex and V5/MT in visual motion processing. NEW & NOTEWORTHY We examined the influence of visual motion adaptation on visual cortex excitability and found a differential effect in V1/V2 compared with V5/MT. Changes in visual excitability following motion adaptation were not related to the degree of an individual's visual

  20. Sequence and Secondary Structure of the Mitochondrial Small-Subunit rRNA V4, V6, and V9 Domains Reveal Highly Species-Specific Variations within the Genus Agrocybe

    PubMed Central

    Gonzalez, Patrice; Labarère, Jacques

    1998-01-01

    A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The

  1. Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6, and V9 domains reveal highly species-specific variations within the genus Agrocybe.

    PubMed

    Gonzalez, P; Labarère, J

    1998-11-01

    A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The

  2. Mechanism of Cell Culture Adaptation of an Enteric Calicivirus, the Porcine Sapovirus Cowden Strain.

    PubMed

    Lu, Zhongyan; Yokoyama, Masaru; Chen, Ning; Oka, Tomoichiro; Jung, Kwonil; Chang, Kyeong-Ok; Annamalai, Thavamathi; Wang, Qiuhong; Saif, Linda J

    2016-02-01

    The porcine sapovirus (SaV) (PoSaV) Cowden strain is one of only a few culturable enteric caliciviruses. Compared to the wild-type (WT) PoSaV Cowden strain, tissue culture-adapted (TC) PoSaV has two conserved amino acid substitutions in the RNA-dependent RNA polymerase (RdRp) and six in the capsid protein (VP1). By using the reverse-genetics system, we identified that 4 amino acid substitutions in VP1 (residues 178, 289, 324, and 328), but not the substitutions in the RdRp region, were critical for the cell culture adaptation of the PoSaV Cowden strain. The other two substitutions in VP1 (residues 291 and 295) reduced virus replication in vitro. Three-dimensional (3D) structural analysis of VP1 showed that residue 178 was located near the dimer-dimer interface, which may affect VP1 assembly and oligomerization; residues 289, 291, 324, and 328 were located at protruding subdomain 2 (P2) of VP1, which may influence virus binding to cellular receptors; and residue 295 was located at the interface of two monomeric VP1 proteins, which may influence VP1 dimerization. Although reversion of the mutation at residue 291 or 295 from that of the TC strain to that of the WT reduced virus replication in vitro, it enhanced virus replication in vivo, and the revertants induced higher-level serum and mucosal antibody responses than those induced by the TC PoSaV Cowden strain. Our findings reveal the molecular basis for PoSaV adaptation to cell culture. These findings may provide new, critical information for the cell culture adaptation of other PoSaV strains and human SaVs or noroviruses. The tissue culture-adapted porcine sapovirus Cowden strain is one of only a few culturable enteric caliciviruses. We discovered that 4 amino acid substitutions in VP1 (residues 178, 289, 324, and 328) were critical for its adaptation to LLC-PK cells. Two substitutions in VP1 (residues 291 and 295) reduced virus replication in vitro but enhanced virus replication and induced higher-level serum and

  3. Visuomotor adaptability in older adults with mild cognitive decline.

    PubMed

    Schaffert, Jeffrey; Lee, Chi-Mei; Neill, Rebecca; Bo, Jin

    2017-02-01

    The current study examined the augmentation of error feedback on visuomotor adaptability in older adults with varying degrees of cognitive decline (assessed by the Montreal Cognitive Assessment; MoCA). Twenty-three participants performed a center-out computerized visuomotor adaptation task when the visual feedback of their hand movement error was presented in a regular (ratio=1:1) or enhanced (ratio=1:2) error feedback schedule. Results showed that older adults with lower scores on the MoCA had less adaptability than those with higher MoCA scores during the regular feedback schedule. However, participants demonstrated similar adaptability during the enhanced feedback schedule, regardless of their cognitive ability. Furthermore, individuals with lower MoCA scores showed larger after-effects in spatial control during the enhanced schedule compared to the regular schedule, whereas individuals with higher MoCA scores displayed the opposite pattern. Additional neuro-cognitive assessments revealed that spatial working memory and processing speed were positively related to motor adaptability during the regular scheduled but negatively related to adaptability during the enhanced schedule. We argue that individuals with mild cognitive decline employed different adaptation strategies when encountering enhanced visual feedback, suggesting older adults with mild cognitive impairment (MCI) may benefit from enhanced visual error feedback during sensorimotor adaptation. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. An adaptive, conservative 0D-2V multispecies Rosenbluth–Fokker–Planck solver for arbitrarily disparate mass and temperature regimes

    DOE PAGES

    Taitano, William; Chacon, Luis; Simakov, Andrei Nikolaevich

    2016-04-25

    In this paper, we propose an adaptive velocity-space discretization scheme for the multi-species, multidimensional Rosenbluth–Fokker–Planck (RFP) equation, which is exactly mass-, momentum-, and energy-conserving. Unlike most earlier studies, our approach normalizes the velocity-space coordinate to the temporally varying individual plasma species' local thermal velocity, v th (t), and explicitly considers the resulting inertial terms in the Fokker–Planck equation. Our conservation strategy employs nonlinear constraints to enforce discretely the conservation properties of these inertial terms and the Fokker–Planck collision operator. To deal with situations of extreme thermal velocity disparities among different species, we employ an asymptotic v th -ratio-based expansion ofmore » the Rosenbluth potentials that only requires the computation of several velocity-space integrals. Numerical examples demonstrate the favorable efficiency and accuracy properties of the scheme. Specifically, we show that the combined use of the velocity-grid adaptivity and asymptotic expansions delivers many orders-of-magnitude savings in mesh resolution requirements compared to a single, static uniform mesh.« less

  5. Adaptive responses reveal contemporary and future ecotypes in a desert shrub

    USGS Publications Warehouse

    Richardson, Bryce A.; Kitchen, Stanley G.; Pendleton, Rosemary L.; Pendleton, Burton K.; Germino, Matthew J.; Rehfeldt, Gerald E.; Meyer, Susan E.

    2014-01-01

    Interacting threats to ecosystem function, including climate change, wildfire, and invasive species necessitate native plant restoration in desert ecosystems. However, native plant restoration efforts often remain unguided by ecological genetic information. Given that many ecosystems are in flux from climate change, restoration plans need to account for both contemporary and future climates when choosing seed sources. In this study we analyze vegetative responses, including mortality, growth, and carbon isotope ratios in two blackbrush (Coleogyne ramosissima) common gardens that included 26 populations from a range-wide collection. This shrub occupies ecotones between the warm and cold deserts of Mojave and Colorado Plateau ecoregions in western North America. The variation observed in the vegetative responses of blackbrush populations was principally explained by grouping populations by ecoregions and by regression with site-specific climate variables. Aridity weighted by winter minimum temperatures best explained vegetative responses; Colorado Plateau sites were usually colder and drier than Mojave sites. The relationship between climate and vegetative response was mapped within the boundaries of the species–climate space projected for the contemporary climate and for the decade surrounding 2060. The mapped ecological genetic pattern showed that genetic variation could be classified into cool-adapted and warm-adapted ecotypes, with populations often separated by steep clines. These transitions are predicted to occur in both the Mojave Desert and Colorado Plateau ecoregions. While under contemporary conditions the warm-adapted ecotype occupies the majority of climate space, climate projections predict that the cool-adapted ecotype could prevail as the dominant ecotype as the climate space of blackbrush expands into higher elevations and latitudes. This study provides the framework for delineating climate change-responsive seed transfer guidelines, which are

  6. Adaptive responses reveal contemporary and future ecotypes in a desert shrub.

    PubMed

    Richardson, Bryce A; Kitchen, Stanley G; Pendleton, Rosemary L; Pendleton, Burton K; Germino, Matthew J; Rehfeldt, Gerald E; Meyer, Susan E

    2014-03-01

    Interacting threats to ecosystem function, including climate change, wildfire, and invasive species necessitate native plant restoration in desert ecosystems. However, native plant restoration efforts often remain unguided by ecological genetic information. Given that many ecosystems are in flux from climate change, restoration plans need to account for both contemporary and future climates when choosing seed sources. In this study we analyze vegetative responses, including mortality, growth, and carbon isotope ratios in two blackbrush (Coleogyne ramosissima) common gardens that included 26 populations from a range-wide collection. This shrub occupies ecotones between the warm and cold deserts of Mojave and Colorado Plateau ecoregions in western North America. The variation observed in the vegetative responses of blackbrush populations was principally explained by grouping populations by ecoregions and by regression with site-specific climate variables. Aridity weighted by winter minimum temperatures best explained vegetative responses; Colorado Plateau sites were usually colder and drier than Mojave sites. The relationship between climate and vegetative response was mapped within the boundaries of the species-climate space projected for the contemporary climate and for the decade surrounding 2060. The mapped ecological genetic pattern showed that genetic variation could be classified into cool-adapted and warm-adapted ecotypes, with populations often separated by steep dines. These transitions are predicted to occur in both the Mojave Desert and Colorado Plateau ecoregions. While under contemporary conditions the warm-adapted ecotype occupies the majority of climate space, climate projections predict that the cool-adapted ecotype could prevail as the dominant ecotype as the climate space of blackbrush expands into higher elevations and latitudes. This study provides the framework for delineating climate change-responsive seed transfer guidelines, which are needed

  7. Orion FSW V and V and Kedalion Engineering Lab Insight

    NASA Technical Reports Server (NTRS)

    Mangieri, Mark L.

    2010-01-01

    NASA, along with its prime Orion contractor and its subcontractor s are adapting an avionics system paradigm borrowed from the manned commercial aircraft industry for use in manned space flight systems. Integrated Modular Avionics (IMA) techniques have been proven as a robust avionics solution for manned commercial aircraft (B737/777/787, MD 10/90). This presentation will outline current approaches to adapt IMA, along with its heritage FSW V&V paradigms, into NASA's manned space flight program for Orion. NASA's Kedalion engineering analysis lab is on the forefront of validating many of these contemporary IMA based techniques. Kedalion has already validated many of the proposed Orion FSW V&V paradigms using Orion's precursory Flight Test Article (FTA) Pad Abort 1 (PA-1) program. The Kedalion lab will evolve its architectures, tools, and techniques in parallel with the evolving Orion program.

  8. Functional photoreceptor loss revealed with adaptive optics: an alternate cause of color blindness.

    PubMed

    Carroll, Joseph; Neitz, Maureen; Hofer, Heidi; Neitz, Jay; Williams, David R

    2004-06-01

    There is enormous variation in the X-linked L/M (long/middle wavelength sensitive) gene array underlying "normal" color vision in humans. This variability has been shown to underlie individual variation in color matching behavior. Recently, red-green color blindness has also been shown to be associated with distinctly different genotypes. This has opened the possibility that there may be important phenotypic differences within classically defined groups of color blind individuals. Here, adaptive optics retinal imaging has revealed a mechanism for producing dichromatic color vision in which the expression of a mutant cone photopigment gene leads to the loss of the entire corresponding class of cone photoreceptor cells. Previously, the theory that common forms of inherited color blindness could be caused by the loss of photoreceptor cells had been discounted. We confirm that remarkably, this loss of one-third of the cones does not impair any aspect of vision other than color.

  9. The first structure of a cold-active catalase from Vibrio salmonicida at 1.96 A reveals structural aspects of cold adaptation.

    PubMed

    Riise, Ellen Kristin; Lorentzen, Marit Sjo; Helland, Ronny; Smalås, Arne O; Leiros, Hanna-Kirsti S; Willassen, Nils Peder

    2007-02-01

    The cold-adapted catalase from the fish-pathogenic bacterium Vibrio salmonicida (VSC) has recently been characterized and shown to be two times more catalytically efficient compared with catalase from the mesophilic human pathogen Proteus mirabilis [PMC; Lorentzen et al. (2006), Extremophiles, 10, 427-440]. VSC is also less temperature-stable, with a half-life of 5 min at 333 K compared with 50 min for PMC. This was the background for solving the crystal structure of the cold-adapted VSC to 1.96 A and performing an extensive structural comparison of VSC and PMC. The comparison revealed that the entrance (the major channel) leading to the catalytically essential haem group, is locally more flexible and slightly wider in VSC. This might explain the enhanced catalytic efficiency of the nearly diffusion-controlled degradation of hydrogen peroxide into water and molecular oxygen in VSC. The reduced thermal stability of the cold-adapted VSC may be explained by a reduced number of ion-pair networks. The four C-terminal alpha-helices are displaced in the structures, probably owing to missing ionic interactions in VSC compared with PMC, and this is postulated as an initiation site for unfolding the cold-adapted enzyme. VSC is the first crystal structure reported of a cold-adapted monofunctional haem-containing catalase.

  10. Dosimetric advantages of a clinical daily adaptive plan selection strategy compared with a non-adaptive strategy in cervical cancer radiation therapy.

    PubMed

    van de Schoot, Agustinus J A J; de Boer, Peter; Visser, Jorrit; Stalpers, Lukas J A; Rasch, Coen R N; Bel, Arjan

    2017-05-01

    Radiation therapy (RT) using a daily plan selection adaptive strategy can be applied to account for interfraction organ motion while limiting organ at risk dose. The aim of this study was to quantify the dosimetric consequences of daily plan selection compared with non-adaptive RT in cervical cancer. Ten consecutive patients who received pelvic irradiation, planning CTs (full and empty bladder), weekly post-fraction CTs and pre-fraction CBCTs were included. Non-adaptive plans were generated based on the PTV defined using the full bladder planning CT. For the adaptive strategy, multiple PTVs were created based on both planning CTs by ITVs of the primary CTVs (i.e., GTV, cervix, corpus-uterus and upper part of the vagina) and corresponding library plans were generated. Daily CBCTs were rigidly aligned to the full bladder planning CT for plan selection. For daily plan recalculation, selected CTs based on initial similarity were deformably registered to CBCTs. Differences in daily target coverage (D 98%  > 95%) and in V 0.5Gy , V 1.5Gy , V 2Gy , D 50% and D 2% for rectum, bladder and bowel were assessed. Non-adaptive RT showed inadequate primary CTV coverage in 17% of the daily fractions. Plan selection compensated for anatomical changes and improved primary CTV coverage significantly (p < 0.01) to 98%. Compared with non-adaptive RT, plan selection decreased the fraction dose to rectum and bowel indicated by significant (p < 0.01) improvements for daily V 0.5Gy , V 1.5Gy , V 2Gy , D 50% and D 2% . However, daily plan selection significantly increased the bladder V 1.5Gy , V 2Gy , D 50% and D 2% . In cervical cancer RT, a non-adaptive strategy led to inadequate target coverage for individual patients. Daily plan selection corrected for day-to-day anatomical variations and resulted in adequate target coverage in all fractions. The dose to bowel and rectum was decreased significantly when applying adaptive RT.

  11. Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences.

    PubMed

    Chen, Sunlu; Zheng, Huizhen; Kishima, Yuji

    2017-06-01

    The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.

  12. Face adaptation aftereffects reveal anterior medial temporal cortex role in high level category representation.

    PubMed

    Furl, N; van Rijsbergen, N J; Treves, A; Dolan, R J

    2007-08-01

    Previous studies have shown reductions of the functional magnetic resonance imaging (fMRI) signal in response to repetition of specific visual stimuli. We examined how adaptation affects the neural responses associated with categorization behavior, using face adaptation aftereffects. Adaptation to a given facial category biases categorization towards non-adapted facial categories in response to presentation of ambiguous morphs. We explored a hypothesis, posed by recent psychophysical studies, that these adaptation-induced categorizations are mediated by activity in relatively advanced stages within the occipitotemporal visual processing stream. Replicating these studies, we find that adaptation to a facial expression heightens perception of non-adapted expressions. Using comparable behavioral methods, we also show that adaptation to a specific identity heightens perception of a second identity in morph faces. We show both expression and identity effects to be associated with heightened anterior medial temporal lobe activity, specifically when perceiving the non-adapted category. These regions, incorporating bilateral anterior ventral rhinal cortices, perirhinal cortex and left anterior hippocampus are regions previously implicated in high-level visual perception. These categorization effects were not evident in fusiform or occipital gyri, although activity in these regions was reduced to repeated faces. The findings suggest that adaptation-induced perception is mediated by activity in regions downstream to those showing reductions due to stimulus repetition.

  13. Comparative system identification of flower tracking performance in three hawkmoth species reveals adaptations for dim light vision.

    PubMed

    Stöckl, Anna L; Kihlström, Klara; Chandler, Steven; Sponberg, Simon

    2017-04-05

    Flight control in insects is heavily dependent on vision. Thus, in dim light, the decreased reliability of visual signal detection also prompts consequences for insect flight. We have an emerging understanding of the neural mechanisms that different species employ to adapt the visual system to low light. However, much less explored are comparative analyses of how low light affects the flight behaviour of insect species, and the corresponding links between physiological adaptations and behaviour. We investigated whether the flower tracking behaviour of three hawkmoth species with different diel activity patterns revealed luminance-dependent adaptations, using a system identification approach. We found clear luminance-dependent differences in flower tracking in all three species, which were explained by a simple luminance-dependent delay model, which generalized across species. We discuss physiological and anatomical explanations for the variance in tracking responses, which could not be explained by such simple models. Differences between species could not be explained by the simple delay model. However, in several cases, they could be explained through the addition on a second model parameter, a simple scaling term, that captures the responsiveness of each species to flower movements. Thus, we demonstrate here that much of the variance in the luminance-dependent flower tracking responses of hawkmoths with different diel activity patterns can be captured by simple models of neural processing.This article is part of the themed issue 'Vision in dim light'. © 2017 The Author(s).

  14. The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.

    PubMed

    Woo, Patrick C Y; Lau, Susanna K P; Tse, Herman; Teng, Jade L L; Curreem, Shirly O T; Tsang, Alan K L; Fan, Rachel Y Y; Wong, Gilman K M; Huang, Yi; Loman, Nicholas J; Snyder, Lori A S; Cai, James J; Huang, Jian-Dong; Mak, William; Pallen, Mark J; Lok, Si; Yuen, Kwok-Yung

    2009-03-01

    Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish intestines and freshwater environments. The gene contents support its phenotypic properties and suggest that amino acids and fatty acids can be used as carbon sources. The extensive variety of transporters, including multidrug efflux and heavy metal transporters as well as genes involved in chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase, superoxide dismutase, and other putative virulence factors-such as hemolysins, RTX toxins, patatin-like proteins, phospholipase A1, and collagenases-are present. Proteomes of L. hongkongensis HLHK9 cultured at 37 degrees C (human body temperature) and 20 degrees C (freshwater habitat temperature) showed differential gene expression, including two homologous copies of argB, argB-20, and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)-NAGK-20 and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37 degrees C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similar duplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that similar mechanisms for temperature adaptation may be employed by other

  15. Proteomic and comparative genomic analysis reveals adaptability of Brassica napus to phosphorus-deficient stress.

    PubMed

    Chen, Shuisen; Ding, Guangda; Wang, Zhenhua; Cai, Hongmei; Xu, Fangsen

    2015-03-18

    proteome alteration of the roots and leaves in two B. napus genotypes, with different P-deficient tolerances, in response to long-term low P stress and short-term P-free starvation by 2-DE. And comparative genomic was conducted to map the DAPs to the linkage map of B. napus by sequence alignment. The present study offers new insights into adaptability mechanism of B. napus to P deficiency and provides novel information in map-based cloning to isolate the genes in B. napus and scientific improvement of P-efficient in practice. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Visceral and somatic pain modalities reveal NaV1.7‐independent visceral nociceptive pathways

    PubMed Central

    Hockley, James R. F.; González‐Cano, Rafael; McMurray, Sheridan; Tejada‐Giraldez, Miguel A.; McGuire, Cian; Torres, Antonio; Wilbrey, Anna L.; Cibert‐Goton, Vincent; Nieto, Francisco R.; Pitcher, Thomas; Knowles, Charles H.; Baeyens, José Manuel; Wood, John N.; Winchester, Wendy J.; Bulmer, David C.; Cendán, Cruz Miguel

    2017-01-01

    Key points Voltage‐gated sodium channels play a fundamental role in determining neuronal excitability.Specifically, voltage‐gated sodium channel subtype NaV1.7 is required for sensing acute and inflammatory somatic pain in mice and humans but its significance in pain originating from the viscera is unknown.Using comparative behavioural models evoking somatic and visceral pain pathways, we identify the requirement for NaV1.7 in regulating somatic (noxious heat pain threshold) but not in visceral pain signalling.These results enable us to better understand the mechanisms underlying the transduction of noxious stimuli from the viscera, suggest that the investigation of pain pathways should be undertaken in a modality‐specific manner and help to direct drug discovery efforts towards novel visceral analgesics. Abstract Voltage‐gated sodium channel NaV1.7 is required for acute and inflammatory pain in mice and humans but its significance for visceral pain is unknown. Here we examine the role of NaV1.7 in visceral pain processing and the development of referred hyperalgesia using a conditional nociceptor‐specific NaV1.7 knockout mouse (NaV1.7Nav1.8) and selective small‐molecule NaV1.7 antagonist PF‐5198007. NaV1.7Nav1.8 mice showed normal nociceptive behaviours in response to intracolonic application of either capsaicin or mustard oil, stimuli known to evoke sustained nociceptor activity and sensitization following tissue damage, respectively. Normal responses following induction of cystitis by cyclophosphamide were also observed in both NaV1.7Nav1.8 and littermate controls. Loss, or blockade, of NaV1.7 did not affect afferent responses to noxious mechanical and chemical stimuli in nerve–gut preparations in mouse, or following antagonism of NaV1.7 in resected human appendix stimulated by noxious distending pressures. However, expression analysis of voltage‐gated sodium channel α subunits revealed NaV1.7 mRNA transcripts in nearly all retrogradely

  17. Adaptive track scheduling to optimize concurrency and vectorization in GeantV

    DOE PAGES

    Apostolakis, J.; Bandieramonte, M.; Bitzes, G.; ...

    2015-05-22

    The GeantV project is focused on the R&D of new particle transport techniques to maximize parallelism on multiple levels, profiting from the use of both SIMD instructions and co-processors for the CPU-intensive calculations specific to this type of applications. In our approach, vectors of tracks belonging to multiple events and matching different locality criteria must be gathered and dispatched to algorithms having vector signatures. While the transport propagates tracks and changes their individual states, data locality becomes harder to maintain. The scheduling policy has to be changed to maintain efficient vectors while keeping an optimal level of concurrency. The modelmore » has complex dynamics requiring tuning the thresholds to switch between the normal regime and special modes, i.e. prioritizing events to allow flushing memory, adding new events in the transport pipeline to boost locality, dynamically adjusting the particle vector size or switching between vector to single track mode when vectorization causes only overhead. Lastly, this work requires a comprehensive study for optimizing these parameters to make the behaviour of the scheduler self-adapting, presenting here its initial results.« less

  18. Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies.

    PubMed

    Willing, Eva-Maria; Bentzen, Paul; van Oosterhout, Cock; Hoffmann, Margarete; Cable, Joanne; Breden, Felix; Weigel, Detlef; Dreyer, Christine

    2010-03-01

    Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise F(ST) values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. F(ST) outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations.

  19. Monitoring the Performance of a Neuro-Adaptive Controller

    NASA Technical Reports Server (NTRS)

    Schumann, Johann; Gupta, Pramod

    2004-01-01

    Traditional control has proven to be ineffective to deal with catastrophic changes or slow degradation of complex, highly nonlinear systems like aircraft or spacecraft, robotics, or flexible manufacturing systems. Control systems which can adapt toward changes in the plant have been proposed as they offer many advantages (e.g., better performance, controllability of aircraft despite of a damaged wing). In the last few years, use of neural networks in adaptive controllers (neuro-adaptive control) has been studied actively. Neural networks of various architectures have been used successfully for online learning adaptive controllers. In such a typical control architecture, the neural network receives as an input the current deviation between desired and actual plant behavior and, by on-line training, tries to minimize this discrepancy (e.g.; by producing a control augmentation signal). Even though neuro-adaptive controllers offer many advantages, they have not been used in mission- or safety-critical applications, because performance and safety guarantees cannot b e provided at development time-a major prerequisite for safety certification (e.g., by the FAA or NASA). Verification and Validation (V&V) of an adaptive controller requires the development of new analysis techniques which can demonstrate that the control system behaves safely under all operating conditions. Because of the requirement to adapt toward unforeseen changes during operation, i.e., in real time, design-time V&V is not sufficient.

  20. Characterization of photosynthetic ferredoxin from the Antarctic alga Chlamydomonas sp. UWO241 reveals novel features of cold adaptation.

    PubMed

    Cvetkovska, Marina; Szyszka-Mroz, Beth; Possmayer, Marc; Pittock, Paula; Lajoie, Gilles; Smith, David R; Hüner, Norman P A

    2018-05-08

    The objective of this work was to characterize photosynthetic ferredoxin from the Antarctic green alga Chlamydomonas sp. UWO241, a key enzyme involved in distributing photosynthetic reducing power. We hypothesize that ferredoxin possesses characteristics typical of cold-adapted enzymes, namely increased structural flexibility and high activity at low temperatures, accompanied by low stability at moderate temperatures. To address this objective, we purified ferredoxin from UWO241 and characterized the temperature dependence of its enzymatic activity and protein conformation. The UWO241 ferredoxin protein, RNA, and DNA sequences were compared with homologous sequences from related organisms. We provide evidence for the duplication of the main ferredoxin gene in the UWO241 nuclear genome and the presence of two highly similar proteins. Ferredoxin from UWO241 has both high activity at low temperatures and high stability at moderate temperatures, representing a novel class of cold-adapted enzymes. Our study reveals novel insights into how photosynthesis functions in the cold. The presence of two distinct ferredoxin proteins in UWO241 could provide an adaptive advantage for survival at cold temperatures. The primary amino acid sequence of ferredoxin is highly conserved among photosynthetic species, and we suggest that subtle differences in sequence can lead to significant changes in activity at low temperatures. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

  1. New adaptive statistical iterative reconstruction ASiR-V: Assessment of noise performance in comparison to ASiR.

    PubMed

    De Marco, Paolo; Origgi, Daniela

    2018-03-01

    To assess the noise characteristics of the new adaptive statistical iterative reconstruction (ASiR-V) in comparison to ASiR. A water phantom was acquired with common clinical scanning parameters, at five different levels of CTDI vol . Images were reconstructed with different kernels (STD, SOFT, and BONE), different IR levels (40%, 60%, and 100%) and different slice thickness (ST) (0.625 and 2.5 mm), both for ASiR-V and ASiR. Noise properties were investigated and noise power spectrum (NPS) was evaluated. ASiR-V significantly reduced noise relative to FBP: noise reduction was in the range 23%-60% for a 0.625 mm ST and 12%-64% for the 2.5 mm ST. Above 2 mGy, noise reduction for ASiR-V had no dependence on dose. Noise reduction for ASIR-V has dependence on ST, being greater for STD and SOFT kernels at 2.5 mm. For the STD kernel ASiR-V has greater noise reduction for both ST, if compared to ASiR. For the SOFT kernel, results varies according to dose and ST, while for BONE kernel ASIR-V shows less noise reduction. NPS for CT Revolution has dose dependent behavior at lower doses. NPS for ASIR-V and ASiR is similar, showing a shift toward lower frequencies as the IR level increases for STD and SOFT kernels. The NPS is different between ASiR-V and ASIR with BONE kernel. NPS for ASiR-V appears to be ST dependent, having a shift toward lower frequencies for 2.5 mm ST. ASiR-V showed greater noise reduction than ASiR for STD and SOFT kernels, while keeping the same NPS. For the BONE kernel, ASiR-V presents a completely different behavior, with less noise reduction and modified NPS. Noise properties of the ASiR-V are dependent on reconstruction slice thickness. The noise properties of ASiR-V suggest the need for further measurements and efforts to establish new CT protocols to optimize clinical imaging. © 2018 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

  2. Impact of a New Adaptive Statistical Iterative Reconstruction (ASIR)-V Algorithm on Image Quality in Coronary Computed Tomography Angiography.

    PubMed

    Pontone, Gianluca; Muscogiuri, Giuseppe; Andreini, Daniele; Guaricci, Andrea I; Guglielmo, Marco; Baggiano, Andrea; Fazzari, Fabio; Mushtaq, Saima; Conte, Edoardo; Annoni, Andrea; Formenti, Alberto; Mancini, Elisabetta; Verdecchia, Massimo; Campari, Alessandro; Martini, Chiara; Gatti, Marco; Fusini, Laura; Bonfanti, Lorenzo; Consiglio, Elisa; Rabbat, Mark G; Bartorelli, Antonio L; Pepi, Mauro

    2018-03-27

    A new postprocessing algorithm named adaptive statistical iterative reconstruction (ASIR)-V has been recently introduced. The aim of this article was to analyze the impact of ASIR-V algorithm on signal, noise, and image quality of coronary computed tomography angiography. Fifty consecutive patients underwent clinically indicated coronary computed tomography angiography (Revolution CT; GE Healthcare, Milwaukee, WI). Images were reconstructed using filtered back projection and ASIR-V 0%, and a combination of filtered back projection and ASIR-V 20%-80% and ASIR-V 100%. Image noise, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) were calculated for left main coronary artery (LM), left anterior descending artery (LAD), left circumflex artery (LCX), and right coronary artery (RCA) and were compared between the different postprocessing algorithms used. Similarly a four-point Likert image quality score of coronary segments was graded for each dataset and compared. A cutoff value of P < .05 was considered statistically significant. Compared to ASIR-V 0%, ASIR-V 100% demonstrated a significant reduction of image noise in all coronaries (P < .01). Compared to ASIR-V 0%, SNR was significantly higher with ASIR-V 60% in LM (P < .01), LAD (P < .05), LCX (P < .05), and RCA (P < .01). Compared to ASIR-V 0%, CNR for ASIR-V ≥60% was significantly improved in LM (P < .01), LAD (P < .05), and RCA (P < .01), whereas LCX demonstrated a significant improvement with ASIR-V ≥80%. ASIR-V 60% had significantly better Likert image quality scores compared to ASIR-V 0% in segment-, vessel-, and patient-based analyses (P < .01). Reconstruction with ASIR-V 60% provides the optimal balance between image noise, SNR, CNR, and image quality. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

  3. Physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine Bacillus subtilis C01 to alumina nanoparticles.

    PubMed

    Mu, Dashuai; Yu, Xiuxia; Xu, Zhenxing; Du, Zongjun; Chen, Guanjun

    2016-07-21

    An increasing number of studies have investigated the effects of nanoparticles (NPs) on microbial systems; however, few existing reports have focused on the defense mechanisms of bacteria against NPs. Whether secondary metabolism biosynthesis is a response to NP stress and contributes to the adaption of bacteria to NPs is unclear. Here, a significant induction in the surfactin production and biofilm formation were detected by adding Al2O3 NPs to the B. subtilis fermentation broth. Physiological analysis showed that Al2O3 NP stress could also affect the cell and colony morphogenesis and inhibit the motility and sporulation. Exogenously adding commercial surfactin restored the swarming motility. Additionally, a suite of toxicity assays analyzing membrane damage, cellular ROS generation, electron transport activity and membrane potential was used to determine the molecular mechanisms of toxicity of Al2O3 NPs. Furthermore, whole transcriptomic analysis was used to elucidate the mechanisms of B. subtilis adaption to Al2O3 NPs. These results revealed several mechanisms by which marine B. subtilis C01 adapt to Al2O3 NPs. Additionally, this study broadens the applications of nanomaterials and describes the important effects on secondary metabolism and multicellularity regulation by using Al2O3 NPs or other nano-products.

  4. Rapid thermal adaptation in a marine diatom reveals constraints and tradeoffs.

    PubMed

    O'Donnell, Daniel R; Hamman, Carolyn R; Johnson, Evan C; Kremer, Colin T; Klausmeier, Christopher A; Litchman, Elena

    2018-06-25

    Rapid evolution in response to environmental change will likely be a driving force determining the distribution of species across the biosphere in coming decades. This is especially true of microorganisms, many of which may evolve in step with warming, including phytoplankton, the diverse photosynthetic microbes forming the foundation of most aquatic food webs. Here we tested the capacity of a globally important, model marine diatom Thalassiosira pseudonana, for rapid evolution in response to temperature. Selection at 16 and 31°C for 350 generations led to significant divergence in several temperature response traits, demonstrating local adaptation and the existence of tradeoffs associated with adaptation to different temperatures. In contrast, competitive ability for nitrogen (commonly limiting in marine systems), measured after 450 generations of temperature selection, did not diverge in a systematic way between temperatures. This study shows how rapid thermal adaptation affects key temperature and nutrient traits and, thus, a population's long-term physiological, ecological, and biogeographic response to climate change. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  5. Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations.

    PubMed

    Sandberg, Troy E; Pedersen, Margit; LaCroix, Ryan A; Ebrahim, Ali; Bonde, Mads; Herrgard, Markus J; Palsson, Bernhard O; Sommer, Morten; Feist, Adam M

    2014-10-01

    Adaptive laboratory evolution (ALE) has emerged as a valuable method by which to investigate microbial adaptation to a desired environment. Here, we performed ALE to 42 °C of ten parallel populations of Escherichia coli K-12 MG1655 grown in glucose minimal media. Tightly controlled experimental conditions allowed selection based on exponential-phase growth rate, yielding strains that uniformly converged toward a similar phenotype along distinct genetic paths. Adapted strains possessed as few as 6 and as many as 55 mutations, and of the 144 genes that mutated in total, 14 arose independently across two or more strains. This mutational recurrence pointed to the key genetic targets underlying the evolved fitness increase. Genome engineering was used to introduce the novel ALE-acquired alleles in random combinations into the ancestral strain, and competition between these engineered strains reaffirmed the impact of the key mutations on the growth rate at 42 °C. Interestingly, most of the identified key gene targets differed significantly from those found in similar temperature adaptation studies, highlighting the sensitivity of genetic evolution to experimental conditions and ancestral genotype. Additionally, transcriptomic analysis of the ancestral and evolved strains revealed a general trend for restoration of the global expression state back toward preheat stressed levels. This restorative effect was previously documented following evolution to metabolic perturbations, and thus may represent a general feature of ALE experiments. The widespread evolved expression shifts were enabled by a comparatively scant number of regulatory mutations, providing a net fitness benefit but causing suboptimal expression levels for certain genes, such as those governing flagellar formation, which then became targets for additional ameliorating mutations. Overall, the results of this study provide insight into the adaptation process and yield lessons important for the future

  6. Transfer of adaptation reveals shared mechanism in grasping and manual estimation.

    PubMed

    Cesanek, Evan; Domini, Fulvio

    2018-06-19

    An influential idea in cognitive neuroscience is that perception and action are highly separable brain functions, implemented in distinct neural systems. In particular, this theory predicts that the functional distinction between grasping, a skilled action, and manual estimation, a type of perceptual report, should be mirrored by a split between their respective control systems. This idea has received support from a variety of dissociations, yet many of these findings have been criticized for failing to pinpoint the source of the dissociation. In this study, we devised a novel approach to this question, first targeting specific grasp control mechanisms through visuomotor adaptation, then testing whether adapted mechanisms were also involved in manual estimation - a response widely characterized as perceptual in function. Participants grasped objects in virtual reality that could appear larger or smaller than the actual physical sizes felt at the end of each grasp. After brief exposure to a size perturbation, manual estimates were biased in the same direction as the maximum grip apertures of grasping movements, indicating that the adapted mechanism is active in both tasks, regardless of the perception-action distinction. Additional experiments showed that the transfer effect generalizes broadly over space (Exp. 1B) and does not appear to arise from a change in visual perception (Exp. 2). We discuss two adaptable mechanisms that could have mediated the observed effect: (a) an afferent proprioceptive mechanism for sensing grip shape; and (b) an efferent visuomotor transformation of size information into a grip-shaping motor command. Copyright © 2018. Published by Elsevier Ltd.

  7. Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage.

    PubMed

    Peng, Tangjian; Ma, Liyuan; Feng, Xue; Tao, Jiemeng; Nan, Meihua; Liu, Yuandong; Li, Jiaokun; Shen, Li; Wu, Xueling; Yu, Runlan; Liu, Xueduan; Qiu, Guanzhou; Zeng, Weimin

    2017-01-01

    Acidithiobacillus ferrivorans is an acidophile that often occurs in low temperature acid mine drainage, e.g., that located at high altitude. Being able to inhabit the extreme environment, the bacterium must possess strategies to copy with the survival stress. Nonetheless, information on the strategies is in demand. Here, genomic and transcriptomic assays were performed to illuminate the adaptation mechanisms of an A. ferrivorans strain YL15, to the alpine acid mine drainage environment in Yulong copper mine in southwest China. Genomic analysis revealed that strain has a gene repertoire for metal-resistance, e.g., genes coding for the mer operon and a variety of transporters/efflux proteins, and for low pH adaptation, such as genes for hopanoid-synthesis and the sodium:proton antiporter. Genes for various DNA repair enzymes and synthesis of UV-absorbing mycosporine-like amino acids precursor indicated hypothetical UV radiation-resistance mechanisms in strain YL15. In addition, it has two types of the acquired immune system-type III-B and type I-F CRISPR/Cas modules against invasion of foreign genetic elements. RNA-seq based analysis uncovered that strain YL15 uses a set of mechanisms to adapt to low temperature. Genes involved in protein synthesis, transmembrane transport, energy metabolism and chemotaxis showed increased levels of RNA transcripts. Furthermore, a bacterioferritin Dps gene had higher RNA transcript counts at 6°C, possibly implicated in protecting DNA against oxidative stress at low temperature. The study represents the first to comprehensively unveil the adaptation mechanisms of an acidophilic bacterium to the acid mine drainage in alpine regions.

  8. Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage

    PubMed Central

    Ma, Liyuan; Feng, Xue; Tao, Jiemeng; Nan, Meihua; Liu, Yuandong; Li, Jiaokun; Shen, Li; Wu, Xueling; Yu, Runlan; Liu, Xueduan; Qiu, Guanzhou; Zeng, Weimin

    2017-01-01

    Acidithiobacillus ferrivorans is an acidophile that often occurs in low temperature acid mine drainage, e.g., that located at high altitude. Being able to inhabit the extreme environment, the bacterium must possess strategies to copy with the survival stress. Nonetheless, information on the strategies is in demand. Here, genomic and transcriptomic assays were performed to illuminate the adaptation mechanisms of an A. ferrivorans strain YL15, to the alpine acid mine drainage environment in Yulong copper mine in southwest China. Genomic analysis revealed that strain has a gene repertoire for metal-resistance, e.g., genes coding for the mer operon and a variety of transporters/efflux proteins, and for low pH adaptation, such as genes for hopanoid-synthesis and the sodium:proton antiporter. Genes for various DNA repair enzymes and synthesis of UV-absorbing mycosporine-like amino acids precursor indicated hypothetical UV radiation—resistance mechanisms in strain YL15. In addition, it has two types of the acquired immune system–type III-B and type I-F CRISPR/Cas modules against invasion of foreign genetic elements. RNA-seq based analysis uncovered that strain YL15 uses a set of mechanisms to adapt to low temperature. Genes involved in protein synthesis, transmembrane transport, energy metabolism and chemotaxis showed increased levels of RNA transcripts. Furthermore, a bacterioferritin Dps gene had higher RNA transcript counts at 6°C, possibly implicated in protecting DNA against oxidative stress at low temperature. The study represents the first to comprehensively unveil the adaptation mechanisms of an acidophilic bacterium to the acid mine drainage in alpine regions. PMID:28542527

  9. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.

    PubMed

    Eoche-Bosy, D; Gautier, M; Esquibet, M; Legeai, F; Bretaudeau, A; Bouchez, O; Fournet, S; Grenier, E; Montarry, J

    2017-09-01

    Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaV vrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability. © 2017 John Wiley & Sons Ltd.

  10. Crystal structure of a shark single-domain antibody V region in complex with lysozyme.

    PubMed

    Stanfield, Robyn L; Dooley, Helen; Flajnik, Martin F; Wilson, Ian A

    2004-09-17

    Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), in which the variable (V) domains recognize antigens with only a single immunoglobulin domain, akin to camelid heavy-chain V domains. The 1.45 angstrom resolution crystal structure of the type I IgNAR V domain in complex with hen egg-white lysozyme (HEL) reveals a minimal antigen-binding domain that contains only two of the three conventional complementarity-determining regions but still binds HEL with nanomolar affinity by means of a binding interface comparable in size to conventional antibodies.

  11. Fast and robust online adaptive planning in stereotactic MR-guided adaptive radiation therapy (SMART) for pancreatic cancer.

    PubMed

    Bohoudi, O; Bruynzeel, A M E; Senan, S; Cuijpers, J P; Slotman, B J; Lagerwaard, F J; Palacios, M A

    2017-12-01

    To implement a robust and fast stereotactic MR-guided adaptive radiation therapy (SMART) online strategy in locally advanced pancreatic cancer (LAPC). SMART strategy for plan adaptation was implemented with the MRIdian system (ViewRay Inc.). At each fraction, OAR (re-)contouring is done within a distance of 3cm from the PTV surface. Online plan re-optimization is based on robust prediction of OAR dose and optimization objectives, obtained by building an artificial neural network (ANN). Proposed limited re-contouring strategy for plan adaptation (SMART 3CM ) is evaluated by comparing 50 previously delivered fractions against a standard (re-)planning method using full-scale OAR (re-)contouring (FULLOAR). Plan quality was assessed using PTV coverage (V 95% , D mean , D 1cc ) and institutional OAR constraints (e.g. V 33Gy ). SMART 3CM required a significant lower number of optimizations than FULLOAR (4 vs 18 on average) to generate a plan meeting all objectives and institutional OAR constraints. PTV coverage with both strategies was identical (mean V 95% =89%). Adaptive plans with SMART 3CM exhibited significant lower intermediate and high doses to all OARs than FULLOAR, which also failed in 36% of the cases to adhere to the V 33Gy dose constraint. SMART 3CM approach for LAPC allows good OAR sparing and adequate target coverage while requiring only limited online (re-)contouring from clinicians. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Adapting the SpaceCube v2.0 Data Processing System for Mission-Unique Application Requirements

    NASA Technical Reports Server (NTRS)

    Petrick, David; Gill, Nat; Hasouneh, Munther; Stone, Robert; Winternitz, Luke; Thomas, Luke; Davis, Milton; Sparacino, Pietro; Flatley, Thomas

    2015-01-01

    The SpaceCube (sup TM) v2.0 system is a superior high performance, reconfigurable, hybrid data processing system that can be used in a multitude of applications including those that require a radiation hardened and reliable solution. This paper provides an overview of the design architecture, flexibility, and the advantages of the modular SpaceCube v2.0 high performance data processing system for space applications. The current state of the proven SpaceCube technology is based on nine years of engineering and operations. Five systems have been successfully operated in space starting in 2008 with four more to be delivered for launch vehicle integration in 2015. The SpaceCube v2.0 system is also baselined as the avionics solution for five additional flight projects and is always a top consideration as the core avionics for new instruments or spacecraft control. This paper will highlight how this multipurpose system is currently being used to solve design challenges of three independent applications. The SpaceCube hardware adapts to new system requirements by allowing for application-unique interface cards that are utilized by reconfiguring the underlying programmable elements on the core processor card. We will show how this system is being used to improve on a heritage NASA GPS technology, enable a cutting-edge LiDAR instrument, and serve as a typical command and data handling (C&DH) computer for a space robotics technology demonstration.

  13. Adapting the SpaceCube v2.0 Data Processing System for Mission-Unique Application Requirements

    NASA Technical Reports Server (NTRS)

    Petrick, David

    2015-01-01

    The SpaceCubeTM v2.0 system is a superior high performance, reconfigurable, hybrid data processing system that can be used in a multitude of applications including those that require a radiation hardened and reliable solution. This paper provides an overview of the design architecture, flexibility, and the advantages of the modular SpaceCube v2.0 high performance data processing system for space applications. The current state of the proven SpaceCube technology is based on nine years of engineering and operations. Five systems have been successfully operated in space starting in 2008 with four more to be delivered for launch vehicle integration in 2015. The SpaceCube v2.0 system is also baselined as the avionics solution for five additional flight projects and is always a top consideration as the core avionics for new instruments or spacecraft control. This paper will highlight how this multipurpose system is currently being used to solve design challenges of three independent applications. The SpaceCube hardware adapts to new system requirements by allowing for application-unique interface cards that are utilized by reconfiguring the underlying programmable elements on the core processor card. We will show how this system is being used to improve on a heritage NASA GPS technology, enable a cutting-edge LiDAR instrument, and serve as a typical command and data handling (CDH) computer for a space robotics technology demonstration.

  14. Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant.

    PubMed

    Lee, Chien-Yueh; Hsieh, Ping-Han; Chiang, Li-Mei; Chattopadhyay, Amrita; Li, Kuan-Yi; Lee, Yi-Fang; Lu, Tzu-Pin; Lai, Liang-Chuan; Lin, En-Chung; Lee, Hsinyu; Ding, Shih-Torng; Tsai, Mong-Hsun; Chen, Chien-Yu; Chuang, Eric Y

    2018-05-01

    The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear. We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago. This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.

  15. Revealing strategies of quorum sensing in Azospirillum brasilense strains Ab-V5 and Ab-V6.

    PubMed

    Fukami, Josiane; Abrantes, Julia Laura Fernandes; Del Cerro, Pablo; Nogueira, Marco Antonio; Ollero, Francisco Javier; Megías, Manuel; Hungria, Mariangela

    2018-01-01

    Azospirillum brasilense is an important plant-growth promoting bacterium (PGPB) that requires several critical steps for root colonization, including biofilm and exopolysaccharide (EPS) synthesis and cell motility. In several bacteria these mechanisms are mediated by quorum sensing (QS) systems that regulate the expression of specific genes mediated by the autoinducers N-acyl-homoserine lactones (AHLs). We investigated QS mechanisms in strains Ab-V5 and Ab-V6 of A. brasilense, which are broadly used in commercial inoculants in Brazil. Neither of these strains carries a luxI gene, but there are several luxR solos that might perceive AHL molecules. By adding external AHLs we verified that biofilm and EPS production and cell motility (swimming and swarming) were regulated via QS in Ab-V5, but not in Ab-V6. Differences were observed not only between strains, but also in the specificity of LuxR-type receptors to AHL molecules. However, Ab-V6 was outstanding in indole acetic acid (IAA) synthesis and this molecule might mimic AHL signals. We also applied the quorum quenching (QQ) strategy, obtaining transconjugants of Ab-V5 and Ab-V6 carrying a plasmid with acyl-homoserine lactonase. When maize (Zea mays L.) was inoculated with the wild-type and transconjugant strains, plant growth was decreased with the transconjugant of Ab-V5-confirming the importance of an AHL-mediated QS system-but did not affect plant growth promotion by Ab-V6.

  16. Genomic signatures reveal geographic adaption and human selection in cattle

    USDA-ARS?s Scientific Manuscript database

    We investigated geographic adaptation and human selection using high-density SNP data of five diverse cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-k...

  17. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America.

    PubMed

    Swarts, Kelly; Gutaker, Rafal M; Benz, Bruce; Blake, Michael; Bukowski, Robert; Holland, James; Kruse-Peeples, Melissa; Lepak, Nicholas; Prim, Lynda; Romay, M Cinta; Ross-Ibarra, Jeffrey; Sanchez-Gonzalez, Jose de Jesus; Schmidt, Chris; Schuenemann, Verena J; Krause, Johannes; Matson, R G; Weigel, Detlef; Buckler, Edward S; Burbano, Hernán A

    2017-08-04

    By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  18. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

    PubMed Central

    Castoe, Todd A.; de Koning, A. P. Jason; Hall, Kathryn T.; Card, Daren C.; Schield, Drew R.; Fujita, Matthew K.; Ruggiero, Robert P.; Degner, Jack F.; Daza, Juan M.; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J.; Castoe, Jill M.; Fox, Samuel E.; Poole, Alex W.; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W.; Li, Qing; Schott, Ryan K.; Kapusta, Aurélie; Minx, Patrick; Feschotte, Cédric; Uetz, Peter; Ray, David A.; Hoffmann, Federico G.; Bogden, Robert; Smith, Eric N.; Chang, Belinda S. W.; Vonk, Freek J.; Casewell, Nicholas R.; Henkel, Christiaan V.; Richardson, Michael K.; Mackessy, Stephen P.; Bronikowski, Anne M.; Yandell, Mark; Warren, Wesley C.; Secor, Stephen M.; Pollock, David D.

    2013-01-01

    Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome. PMID:24297902

  19. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

    PubMed

    Castoe, Todd A; de Koning, A P Jason; Hall, Kathryn T; Card, Daren C; Schield, Drew R; Fujita, Matthew K; Ruggiero, Robert P; Degner, Jack F; Daza, Juan M; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J; Castoe, Jill M; Fox, Samuel E; Poole, Alex W; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W; Li, Qing; Schott, Ryan K; Kapusta, Aurélie; Minx, Patrick; Feschotte, Cédric; Uetz, Peter; Ray, David A; Hoffmann, Federico G; Bogden, Robert; Smith, Eric N; Chang, Belinda S W; Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Richardson, Michael K; Mackessy, Stephen P; Bronikowski, Anne M; Bronikowsi, Anne M; Yandell, Mark; Warren, Wesley C; Secor, Stephen M; Pollock, David D

    2013-12-17

    Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

  20. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.

    Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the button mushroom forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose,more » pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.« less

  1. Revealing Risks in Adaptation Planning: expanding Uncertainty Treatment and dealing with Large Projection Ensembles during Planning Scenario development

    NASA Astrophysics Data System (ADS)

    Brekke, L. D.; Clark, M. P.; Gutmann, E. D.; Wood, A.; Mizukami, N.; Mendoza, P. A.; Rasmussen, R.; Ikeda, K.; Pruitt, T.; Arnold, J. R.; Rajagopalan, B.

    2015-12-01

    Adaptation planning assessments often rely on single methods for climate projection downscaling and hydrologic analysis, do not reveal uncertainties from associated method choices, and thus likely produce overly confident decision-support information. Recent work by the authors has highlighted this issue by identifying strengths and weaknesses of widely applied methods for downscaling climate projections and assessing hydrologic impacts. This work has shown that many of the methodological choices made can alter the magnitude, and even the sign of the climate change signal. Such results motivate consideration of both sources of method uncertainty within an impacts assessment. Consequently, the authors have pursued development of improved downscaling techniques spanning a range of method classes (quasi-dynamical and circulation-based statistical methods) and developed approaches to better account for hydrologic analysis uncertainty (multi-model; regional parameter estimation under forcing uncertainty). This presentation summarizes progress in the development of these methods, as well as implications of pursuing these developments. First, having access to these methods creates an opportunity to better reveal impacts uncertainty through multi-method ensembles, expanding on present-practice ensembles which are often based only on emissions scenarios and GCM choices. Second, such expansion of uncertainty treatment combined with an ever-expanding wealth of global climate projection information creates a challenge of how to use such a large ensemble for local adaptation planning. To address this challenge, the authors are evaluating methods for ensemble selection (considering the principles of fidelity, diversity and sensitivity) that is compatible with present-practice approaches for abstracting change scenarios from any "ensemble of opportunity". Early examples from this development will also be presented.

  2. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

    PubMed Central

    Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.; Foulongne-Oriol, Marie; Lombard, Vincent; Nagye, Laszlo G.; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L.; Bailey, Andrew M.; Billette, Christophe; Coutinho, Pedro M.; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hildén, Kristiina; Kües, Ursula; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Murat, Claude; Riley, Robert W.; Salamov, Asaf A.; Schmutz, Jeremy; Subramanian, Venkataramanan; Wösten, Han A. B.; Xu, Jianping; Eastwood, Daniel C.; Foster, Gary D.; Sonnenberg, Anton S. M.; Cullen, Dan; de Vries, Ronald P.; Lundell, Taina; Hibbett, David S.; Henrissat, Bernard; Burton, Kerry S.; Kerrigan, Richard W.; Challen, Michael P.; Grigoriev, Igor V.; Martin, Francis

    2012-01-01

    Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics. PMID:23045686

  3. Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection.

    PubMed

    Moreira, Leandro M; Soares, Márcia R; Facincani, Agda P; Ferreira, Cristiano B; Ferreira, Rafael M; Ferro, Maria I T; Gozzo, Fábio C; Felestrino, Érica B; Assis, Renata A B; Garcia, Camila Carrião M; Setubal, João C; Ferro, Jesus A; de Oliveira, Julio C F

    2017-07-11

    Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. A proteomic analysis under in planta infectious and non-infectious conditions was conducted in order to increase our knowledge about the adaptive process of Xac during infection. For that, a 2D-based proteomic analysis of Xac at 1, 3 and 5 days after inoculation, in comparison to Xac growth in NB media was carried out and followed by MALDI-TOF-TOF identification of 124 unique differentially abundant proteins. Among them, 79 correspond to up-regulated proteins in at least one of the three stages of infection. Our results indicate an important role of proteins related to biofilm synthesis, lipopolysaccharides biosynthesis, and iron uptake and metabolism as possible modulators of plant innate immunity, and revealed an intricate network of proteins involved in reactive oxygen species adaptation during Plants` Oxidative Burst response. We also identified proteins previously unknown to be involved in Xac-Citrus interaction, including the hypothetical protein XAC3981. A mutant strain for this gene has proved to be non-pathogenic in respect to classical symptoms of citrus canker induced in compatible plants. This is the first time that a protein repertoire is shown to be active and working in an integrated manner during the infection process in a compatible host, pointing to an elaborate mechanism for adaptation of Xac once inside the plant.

  4. ISAARE: Information System for Adaptive, Assistive, and Recreational Equipment: Volume I: Existence; Volume II, Communication; Volume V, Adaptation.

    ERIC Educational Resources Information Center

    Melichar, Joseph F.

    Described as part of the Information System for Adaptive, Assistive and Recreational Equipment are equipment items for physically handicapped pupils in the functional areas of existence, equipment and adaptation. Reviewed in the existence section are such items as assistive food containers and container stabilizers, feeder accessories, bowel and…

  5. Embedded pitch adapters: A high-yield interconnection solution for strip sensors

    NASA Astrophysics Data System (ADS)

    Ullán, M.; Allport, P. P.; Baca, M.; Broughton, J.; Chisholm, A.; Nikolopoulos, K.; Pyatt, S.; Thomas, J. P.; Wilson, J. A.; Kierstead, J.; Kuczewski, P.; Lynn, D.; Hommels, L. B. A.; Fleta, C.; Fernandez-Tejero, J.; Quirion, D.; Bloch, I.; Díez, S.; Gregor, I. M.; Lohwasser, K.; Poley, L.; Tackmann, K.; Hauser, M.; Jakobs, K.; Kuehn, S.; Mahboubi, K.; Mori, R.; Parzefall, U.; Clark, A.; Ferrere, D.; Gonzalez Sevilla, S.; Ashby, J.; Blue, A.; Bates, R.; Buttar, C.; Doherty, F.; McMullen, T.; McEwan, F.; O'Shea, V.; Kamada, S.; Yamamura, K.; Ikegami, Y.; Nakamura, K.; Takubo, Y.; Unno, Y.; Takashima, R.; Chilingarov, A.; Fox, H.; Affolder, A. A.; Casse, G.; Dervan, P.; Forshaw, D.; Greenall, A.; Wonsak, S.; Wormald, M.; Cindro, V.; Kramberger, G.; Mandić, I.; Mikuž, M.; Gorelov, I.; Hoeferkamp, M.; Palni, P.; Seidel, S.; Taylor, A.; Toms, K.; Wang, R.; Hessey, N. P.; Valencic, N.; Hanagaki, K.; Dolezal, Z.; Kodys, P.; Bohm, J.; Mikestikova, M.; Bevan, A.; Beck, G.; Milke, C.; Domingo, M.; Fadeyev, V.; Galloway, Z.; Hibbard-Lubow, D.; Liang, Z.; Sadrozinski, H. F.-W.; Seiden, A.; To, K.; French, R.; Hodgson, P.; Marin-Reyes, H.; Parker, K.; Jinnouchi, O.; Hara, K.; Bernabeu, J.; Civera, J. V.; Garcia, C.; Lacasta, C.; Marti i Garcia, S.; Rodriguez, D.; Santoyo, D.; Solaz, C.; Soldevila, U.

    2016-09-01

    A proposal to fabricate large area strip sensors with integrated, or embedded, pitch adapters is presented for the End-cap part of the Inner Tracker in the ATLAS experiment. To implement the embedded pitch adapters, a second metal layer is used in the sensor fabrication, for signal routing to the ASICs. Sensors with different embedded pitch adapters have been fabricated in order to optimize the design and technology. Inter-strip capacitance, noise, pick-up, cross-talk, signal efficiency, and fabrication yield have been taken into account in their design and fabrication. Inter-strip capacitance tests taking into account all channel neighbors reveal the important differences between the various designs considered. These tests have been correlated with noise figures obtained in full assembled modules, showing that the tests performed on the bare sensors are a valid tool to estimate the final noise in the full module. The full modules have been subjected to test beam experiments in order to evaluate the incidence of cross-talk, pick-up, and signal loss. The detailed analysis shows no indication of cross-talk or pick-up as no additional hits can be observed in any channel not being hit by the beam above 170 mV threshold, and the signal in those channels is always below 1% of the signal recorded in the channel being hit, above 100 mV threshold. First results on irradiated mini-sensors with embedded pitch adapters do not show any change in the interstrip capacitance measurements with only the first neighbors connected.

  6. Positron Emission Tomography Imaging Reveals Auditory and Frontal Cortical Regions Involved with Speech Perception and Loudness Adaptation.

    PubMed

    Berding, Georg; Wilke, Florian; Rode, Thilo; Haense, Cathleen; Joseph, Gert; Meyer, Geerd J; Mamach, Martin; Lenarz, Minoo; Geworski, Lilli; Bengel, Frank M; Lenarz, Thomas; Lim, Hubert H

    2015-01-01

    Considerable progress has been made in the treatment of hearing loss with auditory implants. However, there are still many implanted patients that experience hearing deficiencies, such as limited speech understanding or vanishing perception with continuous stimulation (i.e., abnormal loudness adaptation). The present study aims to identify specific patterns of cerebral cortex activity involved with such deficiencies. We performed O-15-water positron emission tomography (PET) in patients implanted with electrodes within the cochlea, brainstem, or midbrain to investigate the pattern of cortical activation in response to speech or continuous multi-tone stimuli directly inputted into the implant processor that then delivered electrical patterns through those electrodes. Statistical parametric mapping was performed on a single subject basis. Better speech understanding was correlated with a larger extent of bilateral auditory cortex activation. In contrast to speech, the continuous multi-tone stimulus elicited mainly unilateral auditory cortical activity in which greater loudness adaptation corresponded to weaker activation and even deactivation. Interestingly, greater loudness adaptation was correlated with stronger activity within the ventral prefrontal cortex, which could be up-regulated to suppress the irrelevant or aberrant signals into the auditory cortex. The ability to detect these specific cortical patterns and differences across patients and stimuli demonstrates the potential for using PET to diagnose auditory function or dysfunction in implant patients, which in turn could guide the development of appropriate stimulation strategies for improving hearing rehabilitation. Beyond hearing restoration, our study also reveals a potential role of the frontal cortex in suppressing irrelevant or aberrant activity within the auditory cortex, and thus may be relevant for understanding and treating tinnitus.

  7. Positron Emission Tomography Imaging Reveals Auditory and Frontal Cortical Regions Involved with Speech Perception and Loudness Adaptation

    PubMed Central

    Berding, Georg; Wilke, Florian; Rode, Thilo; Haense, Cathleen; Joseph, Gert; Meyer, Geerd J.; Mamach, Martin; Lenarz, Minoo; Geworski, Lilli; Bengel, Frank M.; Lenarz, Thomas; Lim, Hubert H.

    2015-01-01

    Considerable progress has been made in the treatment of hearing loss with auditory implants. However, there are still many implanted patients that experience hearing deficiencies, such as limited speech understanding or vanishing perception with continuous stimulation (i.e., abnormal loudness adaptation). The present study aims to identify specific patterns of cerebral cortex activity involved with such deficiencies. We performed O-15-water positron emission tomography (PET) in patients implanted with electrodes within the cochlea, brainstem, or midbrain to investigate the pattern of cortical activation in response to speech or continuous multi-tone stimuli directly inputted into the implant processor that then delivered electrical patterns through those electrodes. Statistical parametric mapping was performed on a single subject basis. Better speech understanding was correlated with a larger extent of bilateral auditory cortex activation. In contrast to speech, the continuous multi-tone stimulus elicited mainly unilateral auditory cortical activity in which greater loudness adaptation corresponded to weaker activation and even deactivation. Interestingly, greater loudness adaptation was correlated with stronger activity within the ventral prefrontal cortex, which could be up-regulated to suppress the irrelevant or aberrant signals into the auditory cortex. The ability to detect these specific cortical patterns and differences across patients and stimuli demonstrates the potential for using PET to diagnose auditory function or dysfunction in implant patients, which in turn could guide the development of appropriate stimulation strategies for improving hearing rehabilitation. Beyond hearing restoration, our study also reveals a potential role of the frontal cortex in suppressing irrelevant or aberrant activity within the auditory cortex, and thus may be relevant for understanding and treating tinnitus. PMID:26046763

  8. Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bird, Jordan T.; Baker, Brett J.; Probst, Alexander J.

    The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, USA, we sequenced a single cell amplified genome (SAG), WOR_SM1_SCG, and used it to identify and refine two high-quality genomes from metagenomes, WOR_SM1_79 and WOR_SM1_86-2, from the same site.more » These three genomic reconstructions form a monophyletic group, which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, caused the protein to be encoded as two subunits at non-adjacent loci. Consistent with the terrestrial spring clades, our estuarine genomes contained a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H)-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identified two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which was more widespread, diverse, and not associated with visible mats. The core Alti-1 genome suggested Alti-1 is adapted for the stream environment with lipopolysaccharide production capacity and extracellular hami structures. The core Alti-2 genome suggested members of this clade are free-living with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These

  9. Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales

    PubMed Central

    Baker, Brett J.; Probst, Alexander J.; Podar, Mircea; Lloyd, Karen G.

    2016-01-01

    The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, USA, we sequenced a single cell amplified genome (SAG), WOR_SM1_SCG, and used it to identify and refine two high-quality genomes from metagenomes, WOR_SM1_79 and WOR_SM1_86-2, from the same site. These three genomic reconstructions form a monophyletic group, which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, caused the protein to be encoded as two subunits at non-adjacent loci. Consistent with the terrestrial spring clades, our estuarine genomes contained a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H)-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identified two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which was more widespread, diverse, and not associated with visible mats. The core Alti-1 genome suggested Alti-1 is adapted for the stream environment with lipopolysaccharide production capacity and extracellular hami structures. The core Alti-2 genome suggested members of this clade are free-living with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These data

  10. Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales

    DOE PAGES

    Bird, Jordan T.; Baker, Brett J.; Probst, Alexander J.; ...

    2016-08-05

    The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, USA, we sequenced a single cell amplified genome (SAG), WOR_SM1_SCG, and used it to identify and refine two high-quality genomes from metagenomes, WOR_SM1_79 and WOR_SM1_86-2, from the same site.more » These three genomic reconstructions form a monophyletic group, which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, caused the protein to be encoded as two subunits at non-adjacent loci. Consistent with the terrestrial spring clades, our estuarine genomes contained a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H)-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identified two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which was more widespread, diverse, and not associated with visible mats. The core Alti-1 genome suggested Alti-1 is adapted for the stream environment with lipopolysaccharide production capacity and extracellular hami structures. The core Alti-2 genome suggested members of this clade are free-living with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These

  11. Adaptive Evolution of the Venom-Targeted vWF Protein in Opossums that Eat Pitvipers

    PubMed Central

    Jansa, Sharon A.; Voss, Robert S.

    2011-01-01

    The rapid evolution of venom toxin genes is often explained as the result of a biochemical arms race between venomous animals and their prey. However, it is not clear that an arms race analogy is appropriate in this context because there is no published evidence for rapid evolution in genes that might confer toxin resistance among routinely envenomed species. Here we report such evidence from an unusual predator-prey relationship between opossums (Marsupialia: Didelphidae) and pitvipers (Serpentes: Crotalinae). In particular, we found high ratios of replacement to silent substitutions in the gene encoding von Willebrand Factor (vWF), a venom-targeted hemostatic blood protein, in a clade of opossums known to eat pitvipers and to be resistant to their hemorrhagic venom. Observed amino-acid substitutions in venom-resistant opossums include changes in net charge and hydrophobicity that are hypothesized to weaken the bond between vWF and one of its toxic snake-venom ligands, the C-type lectin-like protein botrocetin. Our results provide the first example of rapid adaptive evolution in any venom-targeted molecule, and they support the notion that an evolutionary arms race might be driving the rapid evolution of snake venoms. However, in the arms race implied by our results, venomous snakes are prey, and their venom has a correspondingly defensive function in addition to its usual trophic role. PMID:21731638

  12. Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

    PubMed

    Herrera, Carlos M; Bazaga, Pilar

    2010-08-01

    *In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

  13. A model of anuran auditory periphery reveals frequency-dependent adaptation to be a contributing mechanism for two-tone suppression and amplitude modulation coding.

    PubMed

    Wotton, J M; Ferragamo, M J

    2011-10-01

    Anuran auditory nerve fibers (ANF) tuned to low frequencies display unusual frequency-dependent adaptation which results in a more phasic response to signals above best frequency (BF) and a more tonic response to signals below. A network model of the first two layers of the anuran auditory system was used to test the contribution of this dynamic peripheral adaptation on two-tone suppression and amplitude modulation (AM) tuning. The model included a peripheral sandwich component, leaky-integrate-and-fire cells and adaptation was implemented by means of a non-linear increase in threshold weighted by the signal frequency. The results of simulations showed that frequency-dependent adaptation was both necessary and sufficient to produce high-frequency-side two-tone suppression for the ANF and cells of the dorsal medullary nucleus (DMN). It seems likely that both suppression and this dynamic adaptation share a common mechanism. The response of ANFs to AM signals was influenced by adaptation and carrier frequency. Vector strength synchronization to an AM signal improved with increased adaptation. The spike rate response to a carrier at BF was the expected flat function with AM rate. However, for non-BF carrier frequencies the response showed a weak band-pass pattern due to the influence of signal sidebands and adaptation. The DMN received inputs from three ANFs and when the frequency tuning of inputs was near the carrier, then the rate response was a low-pass or all-pass shape. When most of the inputs were biased above or below the carrier, then band-pass responses were observed. Frequency-dependent adaptation enhanced the band-pass tuning for AM rate, particularly when the response of the inputs was predominantly phasic for a given carrier. Different combinations of inputs can therefore bias a DMN cell to be especially well suited to detect specific ranges of AM rates for a particular carrier frequency. Such selection of inputs would clearly be advantageous to the frog

  14. Statistical Inference for Data Adaptive Target Parameters.

    PubMed

    Hubbard, Alan E; Kherad-Pajouh, Sara; van der Laan, Mark J

    2016-05-01

    Consider one observes n i.i.d. copies of a random variable with a probability distribution that is known to be an element of a particular statistical model. In order to define our statistical target we partition the sample in V equal size sub-samples, and use this partitioning to define V splits in an estimation sample (one of the V subsamples) and corresponding complementary parameter-generating sample. For each of the V parameter-generating samples, we apply an algorithm that maps the sample to a statistical target parameter. We define our sample-split data adaptive statistical target parameter as the average of these V-sample specific target parameters. We present an estimator (and corresponding central limit theorem) of this type of data adaptive target parameter. This general methodology for generating data adaptive target parameters is demonstrated with a number of practical examples that highlight new opportunities for statistical learning from data. This new framework provides a rigorous statistical methodology for both exploratory and confirmatory analysis within the same data. Given that more research is becoming "data-driven", the theory developed within this paper provides a new impetus for a greater involvement of statistical inference into problems that are being increasingly addressed by clever, yet ad hoc pattern finding methods. To suggest such potential, and to verify the predictions of the theory, extensive simulation studies, along with a data analysis based on adaptively determined intervention rules are shown and give insight into how to structure such an approach. The results show that the data adaptive target parameter approach provides a general framework and resulting methodology for data-driven science.

  15. Search for heavy Majorana neutrinos in $$\\mu^\\pm \\mu^\\pm+$$ jets events in proton-proton collisions at $$\\sqrt{s}$$ = 8 TeV

    DOE PAGES

    Khachatryan, Vardan

    2015-07-02

    Our search is performed for heavy Majorana neutrinos (N) using an event signature defined by two muons of the same charge and two jets (μ ±μ ±jj). The data correspond to an integrated luminosity of 19.7 fb -1 of proton–proton collisions at a center-of-mass energy of 8 TeV, collected with the CMS detector at the CERN LHC. We did not observe an excess of events beyond the expected standard model background and upper limits are set on |V μN| 2 as a function of Majorana neutrino mass mN for masses in the range of 40–500 GeV, where V μN ismore » the mixing element of the heavy neutrino with the standard model muon neutrino. The limits obtained are |V μN| 2 < 0.00470 for m N = 90 GeV, |V μN| 2 < 0.0123 for m N = 200 GeV, and |V μN| 2 < 0.583 for mN = 500 GeV. These results extend considerably the regions excluded by previous direct searches.« less

  16. Population resequencing reveals candidate genes associated with salinity adaptation of the Pacific oyster Crassostrea gigas.

    PubMed

    She, Zhicai; Li, Li; Meng, Jie; Jia, Zhen; Que, Huayong; Zhang, Guofan

    2018-06-06

    The Pacific oyster Crassostrea gigas is an important cultivated shellfish. As a euryhaline species, it has evolved adaptive mechanisms responding to the complex and changeable intertidal environment that it inhabits. To investigate the genetic basis of this salinity adaptation mechanism, we conducted a genome-wide association study using phenotypically differentiated populations (hyposalinity and hypersalinity adaptation populations, and control population), and confirmed our results using an independent population, high-resolution melting, and mRNA expression analysis. For the hyposalinity adaptation, we determined 24 genes, including Cg_CLCN7 (chloride channel protein 7) and Cg_AP1 (apoptosis 1 inhibitor), involved in the ion/water channel and transporter mechanisms, free amino acid and reactive oxygen species metabolism, immune responses, and chemical defence. Three SNPs located on these two genes were significantly differentiated between groups, as was Cg_CLCN7. For the hypersalinity adaptation, the biological process for positive regulating the developmental process was enriched. Enriched gene functions were focused on transcriptional regulation, signal transduction, and cell growth and differentiation, including calmodulin (Cg_CaM) and ficolin-2 (Cg_FCN2). These genes and polymorphisms possibly play an important role in oyster hyposalinity and hypersalinity adaptation. They not only further our understanding of salinity adaptation mechanisms but also provide markers for highly adaptable oyster strains suitable for breeding.

  17. Preparation of γ-LiV2O5 from polyoxovanadate cluster Li7[V15O36(CO3)] as a high-performance cathode material and its reaction mechanism revealed by operando XAFS

    NASA Astrophysics Data System (ADS)

    Wang, Heng; Isobe, Jin; Shimizu, Takeshi; Matsumura, Daiju; Ina, Toshiaki; Yoshikawa, Hirofumi

    2017-08-01

    γ-phase LiV2O5, which shows superior electrochemical performance as cathode material in Li-ion batteries, was prepared by annealing the polyoxovanadate cluster Li7 [V15O36(CO3)]. The reaction mechanism was studied using operando X-ray absorption fine structure (XAFS), powder X-ray diffraction (PXRD), and X-ray photoelectron spectroscopy (XPS) analyses. The X-ray absorption near edge structure (XANES) and XPS results reveal that γ-LiV2O5 undergoes two-electron redox reaction per V2O5 pyramid unit, resulting in a large reversible capacity of 260 Ah/kg. The extended X-ray absorption fine structure (EXAFS) and PXRD analyses also suggest that the V-V distance slightly increases, due to the reduction of V5+ to V4+ during Li ion intercalation as the material structure is maintained. As a result, γ-LixV2O5 shows highly reversible electrochemical reaction with x = 0.1-1.9.

  18. Complex adaptive behavior and dexterous action

    PubMed Central

    Harrison, Steven J.; Stergiou, Nicholas

    2016-01-01

    Dexterous action, as conceptualized by Bernstein in his influential ecological analysis of human behavior, is revealed in the ability to flexibly generate behaviors that are adaptively tailored to the demands of the context in which they are embedded. Conceived as complex adaptive behavior, dexterity depends upon the qualities of robustness and degeneracy, and is supported by the functional complexity of the agent-environment system. Using Bernstein’s and Gibson’s ecological analyses of behavior situated in natural environments as conceptual touchstones, we consider the hypothesis that complex adaptive behavior capitalizes upon general principles of self-organization. Here, we outline a perspective in which the complex interactivity of nervous-system, body, and environment is revealed as an essential resource for adaptive behavior. From this perspective, we consider the implications for interpreting the functionality and dysfunctionality of human behavior. This paper demonstrates that, optimal variability, the topic of this special issue, is a logical consequence of interpreting the functionality of human behavior as complex adaptive behavior. PMID:26375932

  19. Development of ultra-short PCR assay to reveal BRAF V600 mutation status in Thai colorectal cancer tissues.

    PubMed

    Chat-Uthai, Nunthawut; Vejvisithsakul, Pichpisith; Udommethaporn, Sutthirat; Meesiri, Puttarakun; Danthanawanit, Chetiya; Wongchai, Yannawan; Teerapakpinyo, Chinachote; Shuangshoti, Shanop; Poungvarin, Naravat

    2018-01-01

    The protein kinase BRAF is one of the key players in regulating cellular responses to extracellular signals. Somatic mutations of the BRAF gene, causing constitutive activation of BRAF, have been found in various types of human cancers such as malignant melanoma, and colorectal cancer. BRAF V600E and V600K, most commonly observed mutations in these cancers, may predict response to targeted therapies. Many techniques suffer from a lack of diagnostic sensitivity in mutation analysis in clinical samples with a low cancer cell percentage or poor-quality fragmented DNA. Here we present allele-specific real-time PCR assay for amplifying 35- to 45-base target sequences in BRAF gene. Forward primer designed for BRAF V600E detection is capable of recognizing both types of BRAF V600E mutation, i.e. V600E1 (c.1799T>A) and V600E2 (c.1799_1800delTGinsAA), as well as complex tandem mutation caused by nucleotide changes in codons 600 and 601. We utilized this assay to analyze Thai formalin-fixed paraffin-embedded tissues. Forty-eight percent of 178 Thai colorectal cancer tissues has KRAS mutation detected by highly sensitive commercial assays. Although these DNA samples contain low overall yield of amplifiable DNA, our newly-developed assay successfully revealed BRAF V600 mutations in 6 of 93 formalin-fixed paraffin-embedded colorectal cancer tissues which KRAS mutation was not detected. Ultra-short PCR assay with forward mutation-specific primers is potentially useful to detect BRAF V600 mutations in highly fragmented DNA specimens from cancer patients.

  20. Adaptive Immunity Restricts Replication of Novel Murine Astroviruses

    PubMed Central

    Yokoyama, Christine C.; Loh, Joy; Zhao, Guoyan; Stappenbeck, Thaddeus S.; Wang, David; Huang, Henry V.

    2012-01-01

    The mechanisms of astrovirus pathogenesis are largely unknown, in part due to a lack of a small-animal model of disease. Using shotgun sequencing and a custom analysis pipeline, we identified two novel astroviruses capable of infecting research mice, murine astrovirus (MuAstV) STL1 and STL2. Subsequent analysis revealed the presence of at least two additional viruses (MuAstV STL3 and STL4), suggestive of a diverse population of murine astroviruses in research mice. Complete genomic characterization and subsequent phylogenetic analysis showed that MuAstV STL1 to STL4 are members of the mamastrovirus genus and are likely members of a new mamastrovirus genogroup. Using Rag1−/− mice deficient in B and T cells, we demonstrate that adaptive immunity is required to control MuAstV infection. Furthermore, using Stat1−/− mice deficient in innate signaling, we demonstrate a role for the innate immune response in the control of MuAstV replication. Our results demonstrate that MuAstV STL permits the study of the mechanisms of astrovirus infection and host-pathogen interactions in a genetically manipulable small-animal model. Finally, we detected MuAstV in commercially available mice, suggesting that these viruses may be present in academic and commercial research mouse facilities, with possible implications for interpretation of data generated in current mouse models of disease. PMID:22951832

  1. Reliability and Validity of the Vietnamese Vineland Adaptive Behavior Scales with Preschool-Age Children

    ERIC Educational Resources Information Center

    Goldberg, Michael R.; Dill, Charles A.; Shin, Jin Y.; Nhan, Nguyen Viet

    2009-01-01

    This study was conducted to examine an adaptation of the Vineland Adaptive Behavior Scale (VABS) [Sparrow, S. S., Balla, D. A., & Cicchetti, D. V. (1984). "The Vineland Adaptive Behavior Scales." Circle Pines, MN: America Guidance Service; Sparrow, S. S., Balla, D. A., & Cicchetti, D. V. (2005). "Vineland Adaptive Behavior…

  2. Multiple adaptive amino acid substitutions increase the virulence of a wild waterfowl-origin reassortant H5N8 avian influenza virus in mice.

    PubMed

    Yu, Zhijun; Cheng, Kaihui; Sun, Weiyang; Zhang, Xinghai; Xia, Xianzhu; Gao, Yuwei

    2018-01-15

    A novel H5N8 highly pathogenic avian influenza virus (HPAIV) caused poultry outbreaks in the Republic of Korea in 2014. The novel H5N8 HPAIV has spread to Asia, Europe, and North America and caused great public concern from then on. Here, we generated mouse-adapted variants of a wild waterfowl-origin H5N8 HPAIV to identify adaptive mutants that confer enhanced pathogenicity in mammals. The mouse lethal doses (MLD 50 ) of the mouse-adapted variants were reduced 31623-fold compared to the wild-type (WT) virus. Mouse-adapted variants displayed enhanced replication in vitro and in vivo, and expanded tissue tropism in mice. Sequence analysis revealed four amino acid substitutions in the PB2 (E627K), PA (F35S), HA (R227H), and NA (I462V) proteins. These data suggest that multiple amino acid substitutions collaboratively increase the virulence of a wild bird-origin reassortant H5N8 HPAIV and cause severe disease in mice. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Face adaptation improves gender discrimination.

    PubMed

    Yang, Hua; Shen, Jianhong; Chen, Juan; Fang, Fang

    2011-01-01

    Adaptation to a visual pattern can alter the sensitivities of neuronal populations encoding the pattern. However, the functional roles of adaptation, especially in high-level vision, are still equivocal. In the present study, we performed three experiments to investigate if face gender adaptation could affect gender discrimination. Experiments 1 and 2 revealed that adapting to a male/female face could selectively enhance discrimination for male/female faces. Experiment 3 showed that the discrimination enhancement induced by face adaptation could transfer across a substantial change in three-dimensional face viewpoint. These results provide further evidence suggesting that, similar to low-level vision, adaptation in high-level vision could calibrate the visual system to current inputs of complex shapes (i.e. face) and improve discrimination at the adapted characteristic. Copyright © 2010 Elsevier Ltd. All rights reserved.

  4. Horizontal vestibuloocular reflex evoked by high-acceleration rotations in the squirrel monkey. IV. Responses after spectacle-induced adaptation

    NASA Technical Reports Server (NTRS)

    Clendaniel, R. A.; Lasker, D. M.; Minor, L. B.; Shelhamer, M. J. (Principal Investigator)

    2001-01-01

    The horizontal angular vestibuloocular reflex (VOR) evoked by sinusoidal rotations from 0.5 to 15 Hz and acceleration steps up to 3,000 degrees /s(2) to 150 degrees /s was studied in six squirrel monkeys following adaptation with x2.2 magnifying and x0.45 minimizing spectacles. For sinusoidal rotations with peak velocities of 20 degrees /s, there were significant changes in gain at all frequencies; however, the greatest gain changes occurred at the lower frequencies. The frequency- and velocity-dependent gain enhancement seen in normal monkeys was accentuated following adaptation to magnifying spectacles and diminished with adaptation to minimizing spectacles. A differential increase in gain for the steps of acceleration was noted after adaptation to the magnifying spectacles. The gain during the acceleration portion, G(A), of a step of acceleration (3,000 degrees /s(2) to 150 degrees /s) increased from preadaptation values of 1.05 +/- 0.08 to 1.96 +/- 0.16, while the gain during the velocity plateau, G(V), only increased from 0.93 +/- 0.04 to 1.36 +/- 0.08. Polynomial fits to the trajectory of the response during the acceleration step revealed a greater increase in the cubic than the linear term following adaptation with the magnifying lenses. Following adaptation to the minimizing lenses, the value of G(A) decreased to 0.61 +/- 0.08, and the value of G(V) decreased to 0.59 +/- 0.09 for the 3,000 degrees /s(2) steps of acceleration. Polynomial fits to the trajectory of the response during the acceleration step revealed that there was a significantly greater reduction in the cubic term than in the linear term following adaptation with the minimizing lenses. These findings indicate that there is greater modification of the nonlinear as compared with the linear component of the VOR with spectacle-induced adaptation. In addition, the latency to the onset of the adapted response varied with the dynamics of the stimulus. The findings were modeled with a bilateral model

  5. Rapid Motion Adaptation Reveals the Temporal Dynamics of Spatiotemporal Correlation between ON and OFF Pathways

    PubMed Central

    Oluk, Can; Pavan, Andrea; Kafaligonul, Hulusi

    2016-01-01

    At the early stages of visual processing, information is processed by two major thalamic pathways encoding brightness increments (ON) and decrements (OFF). Accumulating evidence suggests that these pathways interact and merge as early as in primary visual cortex. Using regular and reverse-phi motion in a rapid adaptation paradigm, we investigated the temporal dynamics of within and across pathway mechanisms for motion processing. When the adaptation duration was short (188 ms), reverse-phi and regular motion led to similar adaptation effects, suggesting that the information from the two pathways are combined efficiently at early-stages of motion processing. However, as the adaption duration was increased to 752 ms, reverse-phi and regular motion showed distinct adaptation effects depending on the test pattern used, either engaging spatiotemporal correlation between the same or opposite contrast polarities. Overall, these findings indicate that spatiotemporal correlation within and across ON-OFF pathways for motion processing can be selectively adapted, and support those models that integrate within and across pathway mechanisms for motion processing. PMID:27667401

  6. Matched rabbit monoclonal antibodies against αv-series integrins reveal a novel αvβ3-LIBS epitope, and permit routine staining of archival paraffin samples of human tumors

    PubMed Central

    Goodman, Simon L.; Grote, Hans Juergen; Wilm, Claudia

    2012-01-01

    Summary The relationship between integrin expression and function in pathologies is often contentious as comparisons between human pathological expression and expression in cell lines is difficult. In addition, the expression of even integrins αvβ6 and αvβ8 in tumor cell lines is not comprehensively documented. Here, we describe rabbit monoclonal antibodies (RabMabs) against the extracellular domains of αv integrins that react with both native integrins and formalin fixed, paraffin embedded (FFPE) human tissues. These RabMabs, against αvβ3 (EM22703), αvβ5 (EM09902), αvβ6 (EM05201), αvβ8 (EM13309), and pan-αv (EM01309), recognize individual integrin chains in Western blots and in flow cytometry. EM22703 detected a ligand-induced binding site (LIBS), reporting an epitope enhanced by the binding of an RGD-peptide to αvβ3. αvβ8 was rarely expressed in human tumor specimens, and weakly expressed in non-small-cell lung carcinoma (NSCLC). However, ovarian carcinoma cell lines expressed αvβ8, as did some melanoma cells, whereas U87MG glioma lacked αvβ8 expression. We observed an unexpected strong expression of αvβ6 in tumor samples of invasive ductal breast adenoma, colorectal carcinoma (CRC), and NSCLC. αvβ3 was strongly expressed in some invasive NSCLC cohorts. Interestingly, PC3 prostate cell and human prostate tumors did not express αvβ3. The RabMabs stained plasma membranes in FFPE-immunohistochemistry (IHC) samples of tumor cell lines from lung, ovary, colon, prostate, squamous cell carcinoma of head and neck (SCCHN), breast, and pancreas carcinomas. The RabMabs are unique tools for probing αv integrin biology, and suggest that especially αvβ6 and αvβ8 biologies still have much to reveal. PMID:23213423

  7. Coherent Optical Adaptive Techniques (COAT)

    DTIC Science & Technology

    1975-01-01

    8217 neceeemry and Identity by block number) Laser Phased Array Adaptive Optics Atmospheric-Turbulence and Thermal Blooming Compensation 20...characteristics of an experimental, visible wavelength, eighteen-element, self-adaptive optical phased array. Measurements on a well-characterized...V LOCAL PHASING ■ LOOP OPTICAL DETECTOR’ LOCAL LOCK / ROOF TOP "^/PROPAGATION’ ^ GLINT ■lm FOCAL LENGTH LENS DETECTOR DMWI rh

  8. Intrinsic, Narrow N V Absorption Reveals a Clumpy Outflow in z < 0.4 Radio-Loud Quasars

    NASA Astrophysics Data System (ADS)

    DeMarcy, Bryan; Serra, Viktoriah; Culliton, Chris; Ganguly, Rajib; Runnoe, Jessie; Charlton, Jane; Eracleous, Michael; Misawa, Toru; Narayanan, Anand

    2018-01-01

    Quasar outflows are often invoked in models for galaxy evolution to inject energy and momentum into the gas in the host galaxy and influence its star formation history. Thus, the study of quasar outflows is essential for understanding galaxy evolution. N V absorption systems within the associated region (|Δv| ≤ 5000 km s-1) of the quasar are thought to be intrinsic since many show evidence for partial covering of the quasar. A recent archival study of quasar spectra taken with COS/G130M or G160M found 39/181 radio-quiet quasars show intrinsic N V absorption, while none of the 31 radio-loud quasars have N V absorption detected (Culliton et al. 2017). Further investigation of these radio-loud quasars showed a clear bias towards compact morphologies as revealed by FIRST 1.4 GHz imaging and comparatively flat radio spectra. This suggests we are viewing more face-on orientations which prevent us from seeing absorption outflows. The cause for such bias within the HST archive is still unknown; however, it could explain the lack of radio-loud intrinsic N V absorption seen by Culliton et al. (2017). Alternatively, the quasar wind structure may be fundamentally different between radio-loud and radio-quiet objects. We used COS/G130M or G160M to obtain rest-frame UV spectra (1195 Å - 1250 Å) of 14 low-redshift SDSS radio-loud quasars which show lobe-dominated FIRST morphologies to distinguish between these possibilities. Intrinsic N V absorption was detected in 6 of our 14 quasars. This suggests the lack of detections in the archival study was a result of an orientation effect/sampling bias rather than to differences in wind structure between radio-loud and radio-quiet quasars. Interestingly, we find significant overlap in radio core fractions between quasars with and without N V detection. Quasars in our sample with N V detection span a range of core fractions from < 0.01 up to 0.89 while those without detected N V range from 0.04 up to 0.93. A laminar outflow with a

  9. Structures of Ca(V) Ca**2+/CaM-IQ Domain Complexes Reveal Binding Modes That Underlie Calcium-Dependent Inactivation And Facilitation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, E.Y.; Rumpf, C.H.; Fujiwara, Y.

    2009-05-20

    Calcium influx drives two opposing voltage-activated calcium channel (Ca{sub V}) self-modulatory processes: calcium-dependent inactivation (CDI) and calcium-dependent facilitation (CDF). Specific Ca{sup 2+}/calmodulin (Ca{sup 2+}/CaM) lobes produce CDI and CDF through interactions with the Ca{sub V}{alpha}{sub 1} subunit IQ domain. Curiously, Ca{sup 2+}/CaM lobe modulation polarity appears inverted between Ca{sub V}1s and Ca{sub V}2s. Here, we present crystal structures of Ca{sub V}2.1, Ca{sub V}2.2, and Ca{sub V}2.3 Ca{sup 2+}/CaM-IQ domain complexes. All display binding orientations opposite to Ca{sub V}1.2 with a physical reversal of the CaM lobe positions relative to the IQ {alpha}-helix. Titration calorimetry reveals lobe competition for a high-affinitymore » site common to Ca{sub V}1 and Ca{sub V}2 IQ domains that is occupied by the CDI lobe in the structures. Electrophysiological experiments demonstrate that the N-terminal Ca{sub V}2 Ca{sup 2+}/C-lobe anchors affect CDF. Together, the data unveil the remarkable structural plasticity at the heart of Ca{sub V} feedback modulation and indicate that Ca{sub V}1 and Ca{sub V}2 IQ domains bear a dedicated CDF site that exchanges Ca{sup 2+}/CaM lobe occupants.« less

  10. Contextual modulation revealed by optical imaging exhibits figural asymmetry in macaque V1 and V2.

    PubMed

    Zarella, Mark D; Ts'o, Daniel Y

    2017-01-01

    Neurons in early visual cortical areas are influenced by stimuli presented well beyond the confines of their classical receptive fields, endowing them with the ability to encode fine-scale features while also having access to the global context of the visual scene. This property can potentially define a role for the early visual cortex to contribute to a number of important visual functions, such as surface segmentation and figure-ground segregation. It is unknown how extraclassical response properties conform to the functional architecture of the visual cortex, given the high degree of functional specialization in areas V1 and V2. We examined the spatial relationships of contextual activations in macaque V1 and V2 with intrinsic signal optical imaging. Using figure-ground stimulus configurations defined by orientation or motion, we found that extraclassical modulation is restricted to the cortical representations of the figural component of the stimulus. These modulations were positive in sign, suggesting a relative enhancement in neuronal activity that may reflect an excitatory influence. Orientation and motion cues produced similar patterns of activation that traversed the functional subdivisions of V2. The asymmetrical nature of the enhancement demonstrated the capacity for visual cortical areas as early as V1 to contribute to figure-ground segregation, and the results suggest that this information can be extracted from the population activity constrained only by retinotopy, and not the underlying functional organization.

  11. Contextual modulation revealed by optical imaging exhibits figural asymmetry in macaque V1 and V2

    PubMed Central

    Zarella, Mark D; Ts’o, Daniel Y

    2017-01-01

    Neurons in early visual cortical areas are influenced by stimuli presented well beyond the confines of their classical receptive fields, endowing them with the ability to encode fine-scale features while also having access to the global context of the visual scene. This property can potentially define a role for the early visual cortex to contribute to a number of important visual functions, such as surface segmentation and figure–ground segregation. It is unknown how extraclassical response properties conform to the functional architecture of the visual cortex, given the high degree of functional specialization in areas V1 and V2. We examined the spatial relationships of contextual activations in macaque V1 and V2 with intrinsic signal optical imaging. Using figure–ground stimulus configurations defined by orientation or motion, we found that extraclassical modulation is restricted to the cortical representations of the figural component of the stimulus. These modulations were positive in sign, suggesting a relative enhancement in neuronal activity that may reflect an excitatory influence. Orientation and motion cues produced similar patterns of activation that traversed the functional subdivisions of V2. The asymmetrical nature of the enhancement demonstrated the capacity for visual cortical areas as early as V1 to contribute to figure–ground segregation, and the results suggest that this information can be extracted from the population activity constrained only by retinotopy, and not the underlying functional organization. PMID:28761385

  12. Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication.

    PubMed

    Legras, Jean-Luc; Galeote, Virginie; Bigey, Frédéric; Camarasa, Carole; Marsit, Souhir; Nidelet, Thibault; Sanchez, Isabelle; Couloux, Arnaud; Guy, Julie; Franco-Duarte, Ricardo; Marcet-Houben, Marina; Gabaldon, Toni; Schuller, Dorit; Sampaio, José Paulo; Dequin, Sylvie

    2018-07-01

    The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries, and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups. Most of these strains, compared with the reference genome, possessed additional genetic elements acquired by introgression or horizontal transfer, several of which were population-specific. In addition, several genomic regions in each population showed evidence of nonneutral evolution, as shown by high differentiation, or of selective sweeps including genes with key functions in these environments (e.g., amino acid transport for wine yeast). Linking genetics to lifestyle differences and metabolite traits has enabled us to elucidate the genetic basis of several niche-specific population traits, such as growth on galactose for cheese strains. These data indicate that yeast has been subjected to various divergent selective pressures depending on its niche, requiring the development of customized genomes for better survival in these environments. These striking genome dynamics associated with local adaptation and domestication reveal the remarkable plasticity of the S. cerevisiae genome, revealing this species to be an amazing complex of specialized populations.

  13. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel

    2012-02-07

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diversemore » isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.« less

  14. Effect of acid adaptation on the environmental stress tolerance of three strains of Vibrio parahaemolyticus.

    PubMed

    Chiang, Ming-Lun; Chen, Hsi-Chia; Wu, Chieh; Chen, Ming-Ju

    2014-04-01

    Three strains of Vibrio parahaemolyticus (690, BCRC 13023, and BCRC 13025), involved in foodborne outbreaks in Taiwan, were subjected to acid adaptation at pH 5.5 for 90 min. The effects of acid adaptation on the tolerance of V. parahaemolyticus to various environmental stresses, including heat (47°C), cold (4°C and -20°C), ethanol (8%), high salt (20% NaCl), and hydrogen peroxide (20 ppm) were examined. Results showed that acid adaptation increased the thermal tolerance of the three test strains of V. parahaemolyticus, while it did not affect their cold tolerance. Acid adaptation also increased the ethanol tolerance in V. parahaemolyticus 690 and BCRC 13025, but not in BCRC 13023. Differences in the tolerance to high salts were noted among the three strains after prior acid adaptation. However, these acid-adapted V. parahaemolyticus strains were more susceptible to hydrogen peroxide than their nonadapted controls. These findings demonstrated that acid adaption responses of V. parahaemolyticus varied among strains and types of stress challenge.

  15. Differential photosynthetic and morphological adaptations to low light affect depth distribution of two submersed macrophytes in lakes.

    PubMed

    Chen, Jianfeng; Cao, Te; Zhang, Xiaolin; Xi, Yilong; Ni, Leyi; Jeppesen, Erik

    2016-10-03

    To evaluate the relative importance of photosynthetic versus morphological adaptations of submersed macrophytes to low light intensity in lakes, rapid light curves (RLCs), morphological parameters, relative growth rate (RGR), clonal reproduction and abundance of two submersed macrophytes (Potamogeton maackianus and Vallisneria natans) were examined under 2.8%, 7.1%, 17.1% and 39.5% ambient light in a field and outdoor experimental study. The plants increased their initial slope of RLCs (α) and decreased their minimum saturating irradiance (E k ) and maximum relative electron transport rate (ETRm) of RLCs under low light stress, but V. natans was more sensitive in RLCs than P. maackianus. Accordingly, the RGR, plant height and abundance of P. maackianus were higher in the high light regimes (shallow water) but lower in the low light regimes than those of V. natans. At the 2.8% ambient light, V. natans produced ramets and thus fulfilled its population expansion, in contrast to P. maackianus. The results revealed that P. maackianus as a canopy-former mainly elongated its shoot length towards the water surface to compensate for the low light conditions, however, it became limited in severe low light stress conditions. V. natans as a rosette adapted to low light stress mainly through photosynthetic adjustments and superior to severely low light than shoot elongation.

  16. Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts.

    PubMed

    Alex, Anoop; Antunes, Agostinho

    2018-01-01

    Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.

  17. Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts

    PubMed Central

    Alex, Anoop

    2018-01-01

    Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts. PMID:29775460

  18. Linear hypergeneralization of learned dynamics across movement speeds reveals anisotropic, gain-encoding primitives for motor adaptation.

    PubMed

    Joiner, Wilsaan M; Ajayi, Obafunso; Sing, Gary C; Smith, Maurice A

    2011-01-01

    The ability to generalize learned motor actions to new contexts is a key feature of the motor system. For example, the ability to ride a bicycle or swing a racket is often first developed at lower speeds and later applied to faster velocities. A number of previous studies have examined the generalization of motor adaptation across movement directions and found that the learned adaptation decays in a pattern consistent with the existence of motor primitives that display narrow Gaussian tuning. However, few studies have examined the generalization of motor adaptation across movement speeds. Following adaptation to linear velocity-dependent dynamics during point-to-point reaching arm movements at one speed, we tested the ability of subjects to transfer this adaptation to short-duration higher-speed movements aimed at the same target. We found near-perfect linear extrapolation of the trained adaptation with respect to both the magnitude and the time course of the velocity profiles associated with the high-speed movements: a 69% increase in movement speed corresponded to a 74% extrapolation of the trained adaptation. The close match between the increase in movement speed and the corresponding increase in adaptation beyond what was trained indicates linear hypergeneralization. Computational modeling shows that this pattern of linear hypergeneralization across movement speeds is not compatible with previous models of adaptation in which motor primitives display isotropic Gaussian tuning of motor output around their preferred velocities. Instead, we show that this generalization pattern indicates that the primitives involved in the adaptation to viscous dynamics display anisotropic tuning in velocity space and encode the gain between motor output and motion state rather than motor output itself.

  19. Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait.

    PubMed

    Olofsson, Jill K; Bianconi, Matheus; Besnard, Guillaume; Dunning, Luke T; Lundgren, Marjorie R; Holota, Helene; Vorontsova, Maria S; Hidalgo, Oriane; Leitch, Ilia J; Nosil, Patrik; Osborne, Colin P; Christin, Pascal-Antoine

    2016-12-01

    Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C 4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C 4 and non-C 4 genotypes, with some populations using laterally acquired C 4 -adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C 4 and non-C 4 A. semialata individuals spanning the species' range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C 4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C 4 functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C 4 -related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  20. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

    PubMed

    Sammond, Deanne W; Kastelowitz, Noah; Himmel, Michael E; Yin, Hang; Crowley, Michael F; Bomble, Yannick J

    2016-01-01

    Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

  1. Panel V: Adaptive Health Behaviors Among Ethnic Minorities

    PubMed Central

    Bagley, Shirley P.; Angel, Ronald; Dilworth-Anderson, Peggye; Liu, William; Schinke, Steven

    2006-01-01

    Race, ethnicity, and cultural attitudes and practices are among the variables that influence health behaviors, including adaptive health behaviors. The following discussions highlight the important role of social conditions in shaping health behaviors and the central role of family in promoting health across the Asian, Hispanic, Native American, and African American ethnic groups. Factors that may lead to health-damaging behaviors are also discussed. The need for additional research that identifies correlations among physiological, social, and behavioral factors and health behaviors, as well as underlying mechanisms, is called for. PMID:8654341

  2. QCD compositeness as revealed in exclusive vector boson reactions through double-photon annihilation: e +e - →γγ* → γV 0 and e +e - γ*γ* V$$0\\atop{a}$$V$$0\\atop{b}$$

    DOE PAGES

    Brodsky, Stanley J.; Lebed, Richard F.; Lyubovitskij, Valery E.

    2017-01-01

    We study the exclusive double-photon annihilation processes, e +e - →γγ* → γV 0 and e +e - γ*γ* Vmore » $$0\\atop{a}$$V$$0\\atop{b}$$, where the V$$0\\atop{i}$$ is a neutral vector meson produced in the forward kinematical region: s>> -t and -t >> Λ$$2\\atop{QCD}$$. We show how the differential cross sections $$dσ\\atop{dt}$$, as predicted by QCD, have additional falloff in the momentum transfer squared t due to the QCD compositeness of the hadrons, consistent with the leading-twist fixed-θ CM scaling laws, both in terms of conventional Feynman diagrams and by using the AdS/QCD holographic model to obtain the results more transparently. However, even though they are exclusive channels and not associated with the conventional electron–positron annihilation process e +e -→γ*→ $$q\\bar{q}$$, these total cross sections σ(e +e -→γV 0)and σ(e +e -→V$$0\\atop{a}$$V$$0\\atop{b}$$), integrated over the dominant forward-and backward-θ CM angular domains, scale as 1/s, and thus contribute to the leading-twist scaling behavior of the ratio R e+e-. We generalize these results to exclusive double-electroweak vector-boson annihilation processes accompanied by the forward production of hadrons, such as e +e -→Z 0V 0and e +e -→W -ρ +. These results can also be applied to the exclusive production of exotic hadrons such as tetraquarks, where the cross-section scaling behavior can reveal their multiquark nature.« less

  3. QCD compositeness as revealed in exclusive vector boson reactions through double-photon annihilation: e +e - →γγ* → γV 0 and e +e - γ*γ* V$$0\\atop{a}$$V$$0\\atop{b}$$

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Brodsky, Stanley J.; Lebed, Richard F.; Lyubovitskij, Valery E.

    We study the exclusive double-photon annihilation processes, e +e - →γγ* → γV 0 and e +e - γ*γ* Vmore » $$0\\atop{a}$$V$$0\\atop{b}$$, where the V$$0\\atop{i}$$ is a neutral vector meson produced in the forward kinematical region: s>> -t and -t >> Λ$$2\\atop{QCD}$$. We show how the differential cross sections $$dσ\\atop{dt}$$, as predicted by QCD, have additional falloff in the momentum transfer squared t due to the QCD compositeness of the hadrons, consistent with the leading-twist fixed-θ CM scaling laws, both in terms of conventional Feynman diagrams and by using the AdS/QCD holographic model to obtain the results more transparently. However, even though they are exclusive channels and not associated with the conventional electron–positron annihilation process e +e -→γ*→ $$q\\bar{q}$$, these total cross sections σ(e +e -→γV 0)and σ(e +e -→V$$0\\atop{a}$$V$$0\\atop{b}$$), integrated over the dominant forward-and backward-θ CM angular domains, scale as 1/s, and thus contribute to the leading-twist scaling behavior of the ratio R e+e-. We generalize these results to exclusive double-electroweak vector-boson annihilation processes accompanied by the forward production of hadrons, such as e +e -→Z 0V 0and e +e -→W -ρ +. These results can also be applied to the exclusive production of exotic hadrons such as tetraquarks, where the cross-section scaling behavior can reveal their multiquark nature.« less

  4. Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Oda, Yasuhiro; Larimer, Frank W; Chain, Patrick S. G.

    The bacterial genus Rhodopseudomonas is comprised of photosynthetic bacteria found widely distributed in aquatic sediments. Members of the genus catalyze hydrogen gas production, carbon dioxide sequestration, and biomass turnover. The genome sequence of Rhodopseudomonas palustris CGA009 revealed a surprising richness of metabolic versatility that would seem to explain its ability to live in a heterogeneous environment like sediment. However, there is considerable genotypic diversity among Rhodopseudomonas isolates. Here we report the complete genome sequences of four additional members of the genus isolated from a restricted geographical area. The sequences confirm that the isolates belong to a coherent taxonomic unit, butmore » they also have significant differences. Whole genome alignments show that the circular chromosomes of the isolates consist of a collinear backbone with a moderate number of genomic rearrangements that impact local gene order and orientation. There are 3,319 genes, 70% of the genes in each genome, shared by four or more strains. Between 10% and 18% of the genes in each genome are strain specific. Some of these genes suggest specialized physiological traits, which we verified experimentally, that include expanded light harvesting, oxygen respiration, and nitrogen fixation capabilities, as well as anaerobic fermentation. Strain-specific adaptations include traits that may be useful in bioenergy applications. This work suggests that against a backdrop of metabolic versatility that is a defining characteristic of Rhodopseudomonas, different ecotypes have evolved to take advantage of physical and chemical conditions in sediment microenvironments that are too small for human observation.« less

  5. Canine distemper virus in the Serengeti ecosystem: molecular adaptation to different carnivore species.

    PubMed

    Nikolin, Veljko M; Olarte-Castillo, Ximena A; Osterrieder, Nikolaus; Hofer, Heribert; Dubovi, Edward; Mazzoni, Camila J; Brunner, Edgar; Goller, Katja V; Fyumagwa, Robert D; Moehlman, Patricia D; Thierer, Dagmar; East, Marion L

    2017-04-01

    Was the 1993/1994 fatal canine distemper virus (CDV) epidemic in lions and spotted hyaenas in the Serengeti ecosystem caused by the recent spillover of a virulent domestic dog strain or one well adapted to these noncanids? We examine this question using sequence data from 13 'Serengeti' strains including five complete genomes obtained between 1993 and 2011. Phylogenetic and haplotype network analyses reveal that strains from noncanids during the epidemic were more closely related to each other than to those from domestic or wild canids. All noncanid 'Serengeti' strains during the epidemic encoded: (1) one novel substitution G134S in the CDV-V protein; and (2) the rare amino acid combination 519I/549H at two sites under positive selection in the region of the CDV-H protein that binds to SLAM (CD 150) host cell receptors. Worldwide, only a few noncanid strains in the America II lineage encode CDV-H 519I/549H. All canid 'Serengeti' strains during the epidemic coded CDV-V 134G, and CDV-H 519R/549Y, or 519R/549H. A functional assay of cell entry revealed the highest performance by CDV-H proteins encoding 519I/549H in cells expressing lion SLAM receptors, and the highest performance by proteins encoding 519R/549Y, typical of dog strains worldwide, in cells expressing dog SLAM receptors. Our findings are consistent with an epidemic in lions and hyaenas caused by CDV variants better adapted to noncanids than canids, but not with the recent spillover of a dog strain. Our study reveals a greater complexity of CDV molecular epidemiology in multihost environments than previously thought. © 2016 John Wiley & Sons Ltd.

  6. Adaptive Hybrid Picture Coding. Volume 2.

    DTIC Science & Technology

    1985-02-01

    ooo5 V.a Measurement Vector ..eho..............57 V.b Size Variable o .entroi* Vector .......... .- 59 V * c Shape Vector .Ř 0-60o oe 6 I V~d...the Program for the Adaptive Line of Sight Method .i.. 18.. o ... .... .... 1 B Details of the Feature Vector FormationProgram .. o ...oo..-....- .122 C ...shape recognition is analogous to recognition of curves in space. Therefore, well known concepts and theorems from differential geometry can be 34 . o

  7. Adaptation and learning: characteristic time scales of performance dynamics.

    PubMed

    Newell, Karl M; Mayer-Kress, Gottfried; Hong, S Lee; Liu, Yeou-Teh

    2009-12-01

    A multiple time scales landscape model is presented that reveals structures of performance dynamics that were not resolved in the traditional power law analysis of motor learning. It shows the co-existence of separate processes during and between practice sessions that evolve in two independent dimensions characterized by time scales that differ by about an order of magnitude. Performance along the slow persistent dimension of learning improves often as much and sometimes more during rest (memory consolidation and/or insight generation processes) than during a practice session itself. In contrast, the process characterized by the fast, transient dimension of adaptation reverses direction between practice sessions, thereby significantly degrading performance at the beginning of the next practice session (warm-up decrement). The theoretical model fits qualitatively and quantitatively the data from Snoddy's [Snoddy, G. S. (1926). Learning and stability. Journal of Applied Psychology, 10, 1-36] classic learning study of mirror tracing and other averaged and individual data sets, and provides a new account of the processes of change in adaptation and learning. 2009 Elsevier B.V. All rights reserved.

  8. IgV peptide mapping of native Ro60 autoantibody proteomes in primary Sjögren's syndrome reveals molecular markers of Ro/La diversification.

    PubMed

    Wang, Jing J; Al Kindi, Mahmood A; Colella, Alex D; Dykes, Lukah; Jackson, Michael W; Chataway, Tim K; Reed, Joanne H; Gordon, Tom P

    2016-12-01

    We have used high-resolution mass spectrometry to sequence precipitating anti-Ro60 proteomes from sera of patients with primary Sjögren's syndrome and compare immunoglobulin variable-region (IgV) peptide signatures in Ro/La autoantibody subsets. Anti-Ro60 were purified by elution from native Ro60-coated ELISA plates and subjected to combined de novo amino acid sequencing and database matching. Monospecific anti-Ro60 Igs comprised dominant public and minor private sets of IgG1 kappa and lambda restricted heavy and light chains. Specific IgV amino acid substitutions stratified anti-Ro60 from anti-Ro60/La responses, providing a molecular fingerprint of Ro60/La determinant spreading and suggesting that different forms of Ro60 antigen drive these responses. Sequencing of linked anti-Ro52 proteomes from individual patients and comparison with their anti-Ro60 partners revealed sharing of a dominant IGHV3-23/IGKV3-20 paired clonotype but with divergent IgV mutational signatures. In summary, anti-Ro60 IgV peptide mapping provides insights into Ro/La autoantibody diversification and reveals serum-based molecular markers of humoral Ro60 autoimmunity. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. MEG adaptation reveals action representations in posterior occipitotemporal regions.

    PubMed

    Hauswald, Anne; Tucciarelli, Raffaele; Lingnau, Angelika

    2018-06-01

    When we observe other people's actions, a number of parietal and precentral regions known to be involved in the planning and execution of actions are recruited for example seen as power decreases in alpha and beta frequencies indicative of increased activation. It has been argued that this recruitment reflects the process of simulating the observed action, thereby providing access to the meaning of the action. Alternatively, it has been suggested that rather than providing access to the meaning of an action, parietal and precentral regions might be recruited as a consequence of action understanding. A way to distinguish between these alternatives is to examine where in the brain and at which time point it is possible to discriminate between different types of actions (e.g., pointing or grasping) irrespective of the way these are performed. To this aim, we presented participants with videos of simple hand actions performed with the left or right hand towards a target on the left or the right side while recording magnetoencephalography (MEG) data. In each trial, participants were presented with two subsequent videos (S1, S2) depicting either the same (repeat trials) or different (non-repeat trials) actions. We predicted that areas that are sensitive to the type of action should show stronger adaptation (i.e., a smaller decrease in alpha and beta power) in repeat in comparison to non-repeat trials. Indeed, we observed less alpha and beta power decreases during the presentation of S2 when the action was repeated compared to when two different actions were presented indicating adaptation of neuronal populations that are selective for the type of action. Sources were obtained exclusively in posterior occipitotemporal regions, supporting the notion that an early differentiation of actions occurs outside the motor system. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Genes Activated by Vibrio cholerae upon Exposure to Caenorhabditis elegans Reveal the Mannose-Sensitive Hemagglutinin To Be Essential for Colonization.

    PubMed

    List, Cornelia; Grutsch, Andreas; Radler, Claudia; Cakar, Fatih; Zingl, Franz G; Schild-Prüfert, Kristina; Schild, Stefan

    2018-01-01

    successfully adapted a genetic reporter technology and identified more than 100 genes activated by V. cholerae upon exposure to the bacterium-grazing nematode Caenorhabditis elegans This screen provides a first glimpse into responses and adaptational strategies of the bacterial pathogen against such natural predators. Subsequent phenotypic characterization revealed the mannose-sensitive hemagglutinin to be crucial for colonization of the worm, which causes developmental delay and growth retardation. Copyright © 2018 List et al.

  11. Modeled Sea Level Rise Impacts on Coastal Ecosystems at Six Major Estuaries on Florida's Gulf Coast: Implications for Adaptation Planning.

    PubMed

    Geselbracht, Laura L; Freeman, Kathleen; Birch, Anne P; Brenner, Jorge; Gordon, Doria R

    2015-01-01

    The Sea Level Affecting Marshes Model (SLAMM) was applied at six major estuaries along Florida's Gulf Coast (Pensacola Bay, St. Andrews/Choctawhatchee Bays, Apalachicola Bay, Southern Big Bend, Tampa Bay and Charlotte Harbor) to provide quantitative and spatial information on how coastal ecosystems may change with sea level rise (SLR) and to identify how this information can be used to inform adaption planning. High resolution LiDAR-derived elevation data was utilized under three SLR scenarios: 0.7 m, 1 m and 2 m through the year 2100 and uncertainty analyses were conducted on selected input parameters at three sites. Results indicate that the extent, spatial orientation and relative composition of coastal ecosystems at the study areas may substantially change with SLR. Under the 1 m SLR scenario, total predicted impacts for all study areas indicate that coastal forest (-69,308 ha; -18%), undeveloped dry land (-28,444 ha; -2%) and tidal flat (-25,556 ha; -47%) will likely face the greatest loss in cover by the year 2100. The largest potential gains in cover were predicted for saltmarsh (+32,922 ha; +88%), transitional saltmarsh (+23,645 ha; na) and mangrove forest (+12,583 ha; +40%). The Charlotte Harbor and Tampa Bay study areas were predicted to experience the greatest net loss in coastal wetlands The uncertainty analyses revealed low to moderate changes in results when some numerical SLAMM input parameters were varied highlighting the value of collecting long-term sedimentation, accretion and erosion data to improve SLAMM precision. The changes predicted by SLAMM will affect exposure of adjacent human communities to coastal hazards and ecosystem functions potentially resulting in impacts to property values, infrastructure investment and insurance rates. The results and process presented here can be used as a guide for communities vulnerable to SLR to identify and prioritize adaptation strategies that slow and/or accommodate the changes underway.

  12. Arbuscular mycorrhiza fungi facilitate rapid adaptation of Elsholtzia splendens to copper.

    PubMed

    Li, Junmin; Liang, Huijuan; Yan, Ming; Chen, Luxi; Zhang, Huating; Liu, Jie; Wang, Suizi; Jin, Zexin

    2017-12-01

    Closely associated microbes have been shown to drive local adaptation of plants. However, few studies provide direct evidence, disclosing the role of arbuscular mycorrhiza fungi (AMF) in their rapid adaptation of plants toward heavy metal tolerance. Elsholtzia splendens is a Cu-tolerant plant that was used as a model plant to study seed morphological traits as well as traits related to seed germination and seedling growth. This was achieved after acclimation for two generations with 1000mg/kg CuSO 4 in either absence or presence of AMF. In the absence of AMF, acclimation to Cu for two generations significantly decreased surface area, perimeter length, and perimeter width of E. splendens seeds, as well as seedling survival rate and fresh weight of the radicle of seedlings. However, in the presence of AMF, both the germination rate and the germination index of E. splendens seeds as well as the fresh weights of hypocotyl and radicle significantly increased. These results revealed that after Cu acclimation treatment, seeds and seedlings that had been inoculated with AMF outperformed those without AMF inoculation under Cu addition, indicating that AMF can facilitate rapid adaptation of E. splendens to Cu stress. In addition, two generations of Cu acclimation under AMF absence significantly increased radicle length, while amplitude increased under AMF presence, indicating that the direct adaptive plasticity response of radicle length to Cu stress helps with the Cu stress adaptation of E. splendens. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.

    Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research.more » Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. As a result, the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.« less

  14. Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

    DOE PAGES

    Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; ...

    2016-01-07

    Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research.more » Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. As a result, the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.« less

  15. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms

    PubMed Central

    Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; Yin, Hang; Crowley, Michael F.; Bomble, Yannick J.

    2016-01-01

    Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions. PMID:26741367

  16. HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G

    PubMed Central

    Ikeda, Terumasa; Albin, John S.; Li, Ming; Thali, Markus

    2018-01-01

    HIV-1 replication normally requires Vif-mediated neutralization of APOBEC3 antiviral enzymes. Viruses lacking Vif succumb to deamination-dependent and -independent restriction processes. Here, HIV-1 adaptation studies were leveraged to ask whether viruses with an irreparable vif deletion could develop resistance to restrictive levels of APOBEC3G. Several resistant viruses were recovered with multiple amino acid substitutions in Env, and these changes alone are sufficient to protect Vif-null viruses from APOBEC3G-dependent restriction in T cell lines. Env adaptations cause decreased fusogenicity, which results in higher levels of Gag-Pol packaging. Increased concentrations of packaged Pol in turn enable faster virus DNA replication and protection from APOBEC3G-mediated hypermutation of viral replication intermediates. Taken together, these studies reveal that a moderate decrease in one essential viral activity, namely Env-mediated fusogenicity, enables the virus to change other activities, here, Gag-Pol packaging during particle production, and thereby escape restriction by the antiviral factor APOBEC3G. We propose a new paradigm in which alterations in viral homeostasis, through compensatory small changes, constitute a general mechanism used by HIV-1 and other viral pathogens to escape innate antiviral responses and other inhibitions including antiviral drugs. PMID:29677220

  17. The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet

    PubMed Central

    Liu, Han; Chen, Chunhai; Gao, Zexia; Min, Jiumeng; Gu, Yongming; Jian, Jianbo; Jiang, Xiewu; Cai, Huimin; Ebersberger, Ingo; Xu, Meng; Zhang, Xinhui; Chen, Jianwei; Luo, Wei; Chen, Boxiang; Chen, Junhui; Liu, Hong; Li, Jiang; Lai, Ruifang; Bai, Mingzhou; Wei, Jin; Yi, Shaokui; Wang, Huanling; Cao, Xiaojuan; Zhou, Xiaoyun; Zhao, Yuhua; Wei, Kaijian; Yang, Ruibin; Liu, Bingnan; Zhao, Shancen; Fang, Xiaodong

    2017-01-01

    Abstract The blunt snout bream Megalobrama amblycephala is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption. As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala, with 779.54 Mb anchored on 24 linkage groups. Integrating spatiotemporal transcriptome analyses, we show that intermuscular bone is formed in the more basal teleosts by intramembranous ossification and may be involved in muscle contractibility and coordinating cellular events. Comparative analysis revealed that olfactory receptor genes, especially of the beta type, underwent an extensive expansion in herbivorous cyprinids, whereas the gene for the umami receptor T1R1 was specifically lost in M. amblycephala. The composition of gut microflora, which contributes to the herbivorous adaptation of M. amblycephala, was found to be similar to that of other herbivores. As a valuable resource for the improvement of M. amblycephala livestock, the draft genome sequence offers new insights into the development of intermuscular bone and herbivorous adaptation. PMID:28535200

  18. Development of Methodologies for IV and V of Neural Networks

    NASA Technical Reports Server (NTRS)

    Taylor, Brian; Darrah, Marjorie

    2003-01-01

    Non-deterministic systems often rely upon neural network (NN) technology to "lean" to manage flight systems under controlled conditions using carefully chosen training sets. How can these adaptive systems be certified to ensure that they will become increasingly efficient and behave appropriately in real-time situations? The bulk of Independent Verification and Validation (IV&V) research of non-deterministic software control systems such as Adaptive Flight Controllers (AFC's) addresses NNs in well-behaved and constrained environments such as simulations and strict process control. However, neither substantive research, nor effective IV&V techniques have been found to address AFC's learning in real-time and adapting to live flight conditions. Adaptive flight control systems offer good extensibility into commercial aviation as well as military aviation and transportation. Consequently, this area of IV&V represents an area of growing interest and urgency. ISR proposes to further the current body of knowledge to meet two objectives: Research the current IV&V methods and assess where these methods may be applied toward a methodology for the V&V of Neural Network; and identify effective methods for IV&V of NNs that learn in real-time, including developing a prototype test bed for IV&V of AFC's. Currently. no practical method exists. lSR will meet these objectives through the tasks identified and described below. First, ISR will conduct a literature review of current IV&V technology. TO do this, ISR will collect the existing body of research on IV&V of non-deterministic systems and neural network. ISR will also develop the framework for disseminating this information through specialized training. This effort will focus on developing NASA's capability to conduct IV&V of neural network systems and to provide training to meet the increasing need for IV&V expertise in such systems.

  19. What is adaptive about adaptive decision making? A parallel constraint satisfaction account.

    PubMed

    Glöckner, Andreas; Hilbig, Benjamin E; Jekel, Marc

    2014-12-01

    There is broad consensus that human cognition is adaptive. However, the vital question of how exactly this adaptivity is achieved has remained largely open. Herein, we contrast two frameworks which account for adaptive decision making, namely broad and general single-mechanism accounts vs. multi-strategy accounts. We propose and fully specify a single-mechanism model for decision making based on parallel constraint satisfaction processes (PCS-DM) and contrast it theoretically and empirically against a multi-strategy account. To achieve sufficiently sensitive tests, we rely on a multiple-measure methodology including choice, reaction time, and confidence data as well as eye-tracking. Results show that manipulating the environmental structure produces clear adaptive shifts in choice patterns - as both frameworks would predict. However, results on the process level (reaction time, confidence), in information acquisition (eye-tracking), and from cross-predicting choice consistently corroborate single-mechanisms accounts in general, and the proposed parallel constraint satisfaction model for decision making in particular. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Imagining sex and adapting to it: different aftereffects after perceiving versus imagining faces.

    PubMed

    D'Ascenzo, Stefania; Tommasi, Luca; Laeng, Bruno

    2014-03-01

    A prolonged exposure (i.e., perceptual adaptation) to a male or a female face can produce changes (i.e., aftereffects) in the subsequent gender attribution of a neutral or average face, so that it appears respectively more female or more male. Studies using imagery adaptation and its aftereffects have yielded conflicting results. In the present study we used an adaptation paradigm with both imagined and perceived faces as adaptors, and assessed the aftereffects in judged masculinity/femininity when viewing an androgynous test face. We monitored eye movements and pupillary responses as a way to confirm whether participants did actively engage in visual imagery. The results indicated that both perceptual and imagery adaptation produce aftereffects, but that they run in opposite directions: a contrast effect with perception (e.g., after visual exposure to a female face, the androgynous appears as more male) and an assimilation effect with imagery (e.g., after imaginative exposure to a female face, the androgynous face appears as more female). The pupillary responses revealed dilations consistent with increased cognitive effort during the imagery phase, suggesting that the assimilation aftereffect occurred in the presence of an active and effortful mental imagery process, as also witnessed by the pattern of eye movements recorded during the imagery adaptation phase. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1

    USDA-ARS?s Scientific Manuscript database

    In order to characterize the evolutionary adaptations of avian paramyxovirus 1 (APMV-1) genomes, we have compared codon usage and codon adaptation indexes among groups of Newcastle disease viruses that differ in biological, ecological, and genetic characteristics. We have used available GenBank com...

  2. Neutron scattering reveals the dynamic basis of protein adaptation to extreme temperature.

    PubMed

    Tehei, Moeava; Madern, Dominique; Franzetti, Bruno; Zaccai, Giuseppe

    2005-12-09

    To explore protein adaptation to extremely high temperatures, two parameters related to macromolecular dynamics, the mean square atomic fluctuation and structural resilience, expressed as a mean force constant, were measured by neutron scattering for hyperthermophilic malate dehydrogenase from Methanococcus jannaschii and a mesophilic homologue, lactate dehydrogenase from Oryctolagus cunniculus (rabbit) muscle. The root mean square fluctuations, defining flexibility, were found to be similar for both enzymes (1.5 A) at their optimal activity temperature. Resilience values, defining structural rigidity, are higher by an order of magnitude for the high temperature-adapted protein (0.15 Newtons/meter for O. cunniculus lactate dehydrogenase and 1.5 Newtons/meter for M. jannaschii malate dehydrogenase). Thermoadaptation appears to have been achieved by evolution through selection of appropriate structural rigidity in order to preserve specific protein structure while allowing the conformational flexibility required for activity.

  3. Questionnaire Adapting: Little Changes Mean a Lot.

    PubMed

    Sousa, Vanessa E C; Matson, Jeffrey; Dunn Lopez, Karen

    2017-09-01

    Questionnaire development involves rigorous testing to ensure reliability and validity. Due to time and cost constraints of developing new questionnaires, researchers often adapt existing questionnaires to better fit the purpose of their study. However, the effect of such adaptations is unclear. We conducted cognitive interviews as a method to evaluate the understanding of original and adapted questionnaire items to be applied in a future study. The findings revealed that all subjects (a) comprehended the original and adapted items differently, (b) changed their scores after comparing the original to the adapted items, and (c) were unanimous in stating that the adapted items were easier to understand. Cognitive interviewing allowed us to assess the interpretation of adapted items in a useful and efficient manner before use in data collection.

  4. Vehicle-to-infrastructure program cooperative adaptive cruise control.

    DOT National Transportation Integrated Search

    2015-03-01

    This report documents the work completed by the Crash Avoidance Metrics Partners LLC (CAMP) Vehicle to Infrastructure (V2I) Consortium during the project titled Cooperative Adaptive Cruise Control (CACC). Participating companies in the V2I Cons...

  5. Lysosomal metabolomics reveals V-ATPase- and mTOR-dependent regulation of amino acid efflux from lysosomes.

    PubMed

    Abu-Remaileh, Monther; Wyant, Gregory A; Kim, Choah; Laqtom, Nouf N; Abbasi, Maria; Chan, Sze Ham; Freinkman, Elizaveta; Sabatini, David M

    2017-11-10

    The lysosome degrades and recycles macromolecules, signals to the cytosol and nucleus, and is implicated in many diseases. Here, we describe a method for the rapid isolation of mammalian lysosomes and use it to quantitatively profile lysosomal metabolites under various cell states. Under nutrient-replete conditions, many lysosomal amino acids are in rapid exchange with those in the cytosol. Loss of lysosomal acidification through inhibition of the vacuolar H + -adenosine triphosphatase (V-ATPase) increased the luminal concentrations of most metabolites but had no effect on those of the majority of essential amino acids. Instead, nutrient starvation regulates the lysosomal concentrations of these amino acids, an effect we traced to regulation of the mechanistic target of rapamycin (mTOR) pathway. Inhibition of mTOR strongly reduced the lysosomal efflux of most essential amino acids, converting the lysosome into a cellular depot for them. These results reveal the dynamic nature of lysosomal metabolites and that V-ATPase- and mTOR-dependent mechanisms exist for controlling lysosomal amino acid efflux. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  6. A Modified Active Appearance Model Based on an Adaptive Artificial Bee Colony

    PubMed Central

    Othman, Zulaiha Ali

    2014-01-01

    Active appearance model (AAM) is one of the most popular model-based approaches that have been extensively used to extract features by highly accurate modeling of human faces under various physical and environmental circumstances. However, in such active appearance model, fitting the model with original image is a challenging task. State of the art shows that optimization method is applicable to resolve this problem. However, another common problem is applying optimization. Hence, in this paper we propose an AAM based face recognition technique, which is capable of resolving the fitting problem of AAM by introducing a new adaptive ABC algorithm. The adaptation increases the efficiency of fitting as against the conventional ABC algorithm. We have used three datasets: CASIA dataset, property 2.5D face dataset, and UBIRIS v1 images dataset in our experiments. The results have revealed that the proposed face recognition technique has performed effectively, in terms of accuracy of face recognition. PMID:25165748

  7. A modified active appearance model based on an adaptive artificial bee colony.

    PubMed

    Abdulameer, Mohammed Hasan; Sheikh Abdullah, Siti Norul Huda; Othman, Zulaiha Ali

    2014-01-01

    Active appearance model (AAM) is one of the most popular model-based approaches that have been extensively used to extract features by highly accurate modeling of human faces under various physical and environmental circumstances. However, in such active appearance model, fitting the model with original image is a challenging task. State of the art shows that optimization method is applicable to resolve this problem. However, another common problem is applying optimization. Hence, in this paper we propose an AAM based face recognition technique, which is capable of resolving the fitting problem of AAM by introducing a new adaptive ABC algorithm. The adaptation increases the efficiency of fitting as against the conventional ABC algorithm. We have used three datasets: CASIA dataset, property 2.5D face dataset, and UBIRIS v1 images dataset in our experiments. The results have revealed that the proposed face recognition technique has performed effectively, in terms of accuracy of face recognition.

  8. [Problems in the individual adaptation of working women].

    PubMed

    Grebeneva, O V; Balaeva, E A

    2008-01-01

    The mechanisms of development of dysadaptive changes were revealed in factory workers in relation to congenital personality traits and the schemes of individual adaptation strategies were defined. At the same time increased anxiety leading to the accelerated rates of aging preceded impaired adaptive processes. The differences in the female adaptive patterns were determined by both the degree of emotional stability and the baseline energy capacities of the cardiorespiratory system and the involvement of a mental component in adaptation.

  9. Melon chlorotic leaf curl virus: characterization and differential reassortment with closest relatives reveal adaptive virulence in the squash leaf curl virus clade and host shifting by the host-restricted bean calico mosaic virus.

    PubMed

    Idris, A M; Mills-Lujan, K; Martin, K; Brown, J K

    2008-02-01

    The genome components of the Melon chlorotic leaf curl virus (MCLCuV) were cloned from symptomatic cantaloupe leaves collected in Guatemala during 2002. The MCLCuV DNA-A and DNA-B components shared their closest nucleotide identities among begomoviruses, at approximately 90 and 81%, respectively, with a papaya isolate of MCLCuV from Costa Rica. The closest relatives at the species level were other members of the Squash leaf curl virus (SLCV) clade, which is endemic in the southwestern United States and Mexico. Biolistic inoculation of cantaloupe seedlings with the MCLCuV DNA-A and -B components resulted in the development of characteristic disease symptoms, providing definitive evidence of causality. MCLCuV experimentally infected species within the Cucurbitaceae, Fabaceae, and Solanaceae. The potential for interspecific reassortment was examined for MCLCuV and its closest relatives, including the bean-restricted Bean calico mosaic virus (BCaMV), and three other cucurbit-infecting species, Cucurbit leaf crumple virus (CuLCrV), SLCV, and SMLCV. The cucurbit viruses have distinct but overlapping host ranges. All possible reassortants were established using heterologous combinations of the DNA-A or DNA-B components. Surprisingly, only certain reassortants arising from MCLCuV and BCaMV, or MCLCuV and CuLCrV, were viable in bean, even though it is a host of all of the "wild-type" (parent) viruses. The bean-restricted BCaMV was differentially assisted in systemically infecting the cucurbit test species by the components of the four cucurbit-adapted begomoviruses. In certain heterologous combinations, the BCaMV DNA-A or -B component was able to infect one or more cucurbit species. Generally, the reassortants were less virulent in the test hosts than the respective wild-type (parent) viruses, strongly implicating adaptive modulation of virulence. This is the first illustration of reassortment resulting in the host range expansion of a host-restricted begomovirus.

  10. Comparative genome analysis reveals genetic adaptation to versatile environmental conditions and importance of biofilm lifestyle in Comamonas testosteroni.

    PubMed

    Wu, Yichao; Arumugam, Krithika; Tay, Martin Qi Xiang; Seshan, Hari; Mohanty, Anee; Cao, Bin

    2015-04-01

    Comamonas testosteroni is an important environmental bacterium capable of degrading a variety of toxic aromatic pollutants and has been demonstrated to be a promising biocatalyst for environmental decontamination. This organism is often found to be among the primary surface colonizers in various natural and engineered ecosystems, suggesting an extraordinary capability of this organism in environmental adaptation and biofilm formation. The goal of this study was to gain genetic insights into the adaption of C. testosteroni to versatile environments and the importance of a biofilm lifestyle. Specifically, a draft genome of C. testosteroni I2 was obtained. The draft genome is 5,778,710 bp in length and comprises 110 contigs. The average G+C content was 61.88 %. A total of 5365 genes with 5263 protein-coding genes were predicted, whereas 4324 (80.60 % of total genes) protein-encoding genes were associated with predicted functions. The catabolic genes responsible for biodegradation of steroid and other aromatic compounds on draft genome were identified. Plasmid pI2 was found to encode a complete pathway for aniline degradation and a partial catabolic pathway for chloroaniline. This organism was found to be equipped with a sophisticated signaling system which helps it find ideal niches and switch between planktonic and biofilm lifestyles. A large number of putative multi-drug-resistant genes coding for abundant outer membrane transporters, chaperones, and heat shock proteins for the protection of cellular function were identified in the genome of strain I2. In addition, the genome of strain I2 was predicted to encode several proteins involved in producing, secreting, and uptaking siderophores under iron-limiting conditions. The genome of strain I2 contains a number of genes responsible for the synthesis and secretion of exopolysaccharides, an extracellular component essential for biofilm formation. Overall, our results reveal the genomic features underlying the adaption

  11. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

    PubMed Central

    Kerou, Melina; Offre, Pierre; Valledor, Luis; Abby, Sophie S.; Melcher, Michael; Nagler, Matthias; Weckwerth, Wolfram; Schleper, Christa

    2016-01-01

    Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile “Ca. Nitrosotalea devanaterra” revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and “Ca. Nitrosopelagicus brevis” proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs. PMID:27864514

  12. The Adaptive Edge: Introducing Adaptive Skills Techniques to Army Special Forces

    DTIC Science & Technology

    2010-12-01

    Submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE IN DEFENSE ANALYSIS from the NAVAL...Brian Greenshields Second Reader Gordon McCormick Chairman, Department of Defense Analysis iv THIS PAGE INTENTIONALLY LEFT BLANK v...Cultural Adaptability as: Taking action to learn about and understand the climate , orientation, needs, values of other groups, organizations, and

  13. An adaptive human response mechanism controlling the V/STOL aircraft. Appendix 3: The adaptive control model of a pilot in V/STOL aircraft control loops. M.S. Thesis. Final Report

    NASA Technical Reports Server (NTRS)

    Kucuk, Senol

    1988-01-01

    Importance of the role of human operator in control systems has led to the particular area of manual control theory. Human describing functions were developed to model human behavior for manual control studies to take advantage of the successful and safe human operations. A single variable approach is presented that can be extended for multi-variable tasks where a low order human response model is used together with its rules, to adapt the model on-line, being capable of responding to the changes in the controlled element dynamics. Basic control theory concepts are used to combine the model, constrained with the physical observations, particularly, for the case of aircraft control. Pilot experience is represented as the initial model parameters. An adaptive root-locus method is presented as the adaptation law of the model where the closed loop bandwidth of the system is to be preserved in a stable manner with the adjustments of the pilot handling qualities which relate the latter to the closed loop bandwidth and damping of the closed loop pilot aircraft combination. A Kalman filter parameter estimator is presented as the controlled element identifier of the adaptive model where any discrepancies of the open loop dynamics from the presented one, are sensed to be compensated.

  14. Genome-Wide DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and Freshwater Conditions.

    PubMed

    Artemov, Artem V; Mugue, Nikolai S; Rastorguev, Sergey M; Zhenilo, Svetlana; Mazur, Alexander M; Tsygankova, Svetlana V; Boulygina, Eugenia S; Kaplun, Daria; Nedoluzhko, Artem V; Medvedeva, Yulia A; Prokhortchouk, Egor B

    2017-09-01

    The three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution-adaptation to a freshwater environment. Although genetic adaptations to freshwater environments are well-studied, epigenetic adaptations have attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of the marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into a freshwater environment and freshwater sticklebacks placed into seawater. We showed that the DNA methylation profile after placing a marine stickleback into fresh water partially converged to that of a freshwater stickleback. For six genes including ATP4A ion pump and NELL1, believed to be involved in skeletal ossification, we demonstrated similar changes in DNA methylation in both evolutionary and short-term adaptation. This suggested that an immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. For the first time, we demonstrated that genes encoding ion channels KCND3, CACNA1FB, and ATP4A were differentially methylated between the marine and the freshwater populations. Other genes encoding ion channels were previously reported to be under selection in freshwater populations. Nevertheless, the genes that harbor genetic and epigenetic changes were not the same, suggesting that epigenetic adaptation is a complementary mechanism to selection of genetic variants favorable for freshwater environment. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Adaptation of the membrane in Archaea.

    PubMed

    Oger, Philippe M; Cario, Anaïs

    2013-12-15

    Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. This is achieved in bacteria and eucarya by a modification of the membrane lipid compositions, a strategy termed homeoviscous adaptation. We review here evidence for homeoviscous adaptation in Archaea, and discuss the limits of this strategy and our knowledge in this very peculiar domain of life. © 2013 Elsevier B.V. All rights reserved.

  16. [Combined use of wide-detector and adaptive statistical iterative reconstruction-V technique in abdominal CT with low radiation dose].

    PubMed

    Wang, H X; Lü, P J; Yue, S W; Chang, L Y; Li, Y; Zhao, H P; Li, W R; Gao, J B

    2017-12-05

    Objective: To investigate the image quality and radiation dose with wide-detector(80 mm) and adaptive statistical iterative reconstruction-V (ASIR-V) technique at abdominal contrast enhanced CT scan. Methods: In the first phantom experiment part, the percentage of ASIR-V for half dose of combined wide detector with ASIR-V technique as compared with standard-detector (40 mm) technique was determined. The human experiment was performed based on the phantom study, 160 patients underwent contrast-enhanced abdominal CT scan were prospectively collected and divided into the control group ( n =40) with image reconstruction using 40% ASIR (group A) and the study group ( n =120) with random number table. According to pre-ASIR-V percentage, the study group was assigned into three groups[40 cases in each group, group B: 0 pre-ASIR-V scan with image reconstruction of 0-100% post-ASIR-V (interval 10%, subgroups B0-B10); group C: 20% pre-ASIR-V with 20%, 40% and 60% post-ASIR-V (subgroups C1-C3); group D: 40%pre-ASIR-V with 40% and 60% post-ASIR-V (subgroups D1-D2)]. Image noise, CT attenuation values and CNR of the liver, pancreas, aorta and portal vein were compared by using two sample t test and One-way ANOVA. Qualitative visual parameters (overall image quality as graded on a 5-point scale) was compared by Mann-Whitney U test and Kruskal-Wallis H test. Results: The phantom experiment showed that the percentage of pre-ASIR-V for half dose was 40%. With the 40% pre-ASIR-V, radiation dose in the study group was reduced by 35.5% as compared with the control group. Image noise in the subgroups of B2-B10, C2-C3 and D1-D2 were lower ( t =-14.681--3.046, all P <0.05) while CNR in the subgroups of B4-B10, C2-3 and D1-D2 were higher( t =2.048-9.248, all P <0.05)than those in group A, except the CNR of liver in the arterial phase (AP) in C2, D1 and D2 and the CNR of pancreas in AP in D1 ( t =0.574-1.327, all P >0.05). The subjective image quality scores increased gradually in the range

  17. Kinetic solvers with adaptive mesh in phase space.

    PubMed

    Arslanbekov, Robert R; Kolobov, Vladimir I; Frolova, Anna A

    2013-12-01

    An adaptive mesh in phase space (AMPS) methodology has been developed for solving multidimensional kinetic equations by the discrete velocity method. A Cartesian mesh for both configuration (r) and velocity (v) spaces is produced using a "tree of trees" (ToT) data structure. The r mesh is automatically generated around embedded boundaries, and is dynamically adapted to local solution properties. The v mesh is created on-the-fly in each r cell. Mappings between neighboring v-space trees is implemented for the advection operator in r space. We have developed algorithms for solving the full Boltzmann and linear Boltzmann equations with AMPS. Several recent innovations were used to calculate the discrete Boltzmann collision integral with dynamically adaptive v mesh: the importance sampling, multipoint projection, and variance reduction methods. We have developed an efficient algorithm for calculating the linear Boltzmann collision integral for elastic and inelastic collisions of hot light particles in a Lorentz gas. Our AMPS technique has been demonstrated for simulations of hypersonic rarefied gas flows, ion and electron kinetics in weakly ionized plasma, radiation and light-particle transport through thin films, and electron streaming in semiconductors. We have shown that AMPS allows minimizing the number of cells in phase space to reduce the computational cost and memory usage for solving challenging kinetic problems.

  18. Photoreceptor perturbation around subretinal drusenoid deposits revealed by adaptive optics scanning laser ophthalmoscopy

    PubMed Central

    Zhang, Yuhua; Wang, Xiaolin; Rivero, Ernesto Blanco; Clark, Mark E; Witherspoon, Clark Douglas; Spaide, Richard F; Girkin, Christopher A.; Owsley, Cynthia; Curcio, Christine A.

    2014-01-01

    Purpose To describe the microscopic structure of photoreceptors impacted by subretinal drusenoid deposits, also called pseudodrusen, an extracellular lesion associated with age-related macular degeneration (AMD), using adaptive optics scanning laser ophthalmoscopy (AOSLO). Design Observational case series. Methods Fifty-three patients with AMD and 10 age-similar subjects in normal retinal health were recruited. All subjects underwent color fundus photography, infrared reflectance, red-free reflectance, autofluorescence, and spectral-domain optical coherence tomography (SD-OCT). Subretinal drusenoid deposits were classified with a 3-stage OCT-based grading system. Lesions and surrounding photoreceptors were examined with AOSLO. Results Subretinal drusenoid deposits were found in 26 eyes of 13 patients with AMD and imaged by AOSLO and SD-OCT in 18 eyes (n=342 lesions). SD-OCT showed subretinal drusenoid deposits as highly reflective material accumulated internal to the retinal pigment epithelium. AOSLO revealed that photoreceptor reflectivity was qualitatively reduced by stage 1 subretinal drusenoid deposits and greatly reduced by stage 2. AOSLO presented a distinct structure in stage 3, a hyporeflective annulus consisting of deflected, degenerated or absent photoreceptors. A central core with a reflectivity superficially resembling photoreceptors is formed by the lesion material itself. A hyporeflective gap in the photoreceptor ellipsoid zone on either side of this core shown in SD-OCT corresponded to the hyporeflective annulus seen by AOSLO. Conclusions AOSLO and multimodal imaging of subretinal drusenoid deposits indicate solid, space filling lesions in the subretinal space. Associated retinal reflectivity changes are related to lesion stages and are consistent with perturbations to photoreceptors, as suggested by histology. PMID:24907433

  19. Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans).

    PubMed

    Dudaniec, Rachael Y; Yong, Chuan Ji; Lancaster, Lesley T; Svensson, Erik I; Hansson, Bengt

    2018-06-01

    Insect distributions are shifting rapidly in response to climate change and are undergoing rapid evolutionary change. We investigate the molecular signatures underlying local adaptation in the range-expanding damselfly, Ischnura elegans. Using a landscape genomic approach combined with generalized dissimilarity modelling (GDM), we detect selection signatures on loci via allelic frequency change along environmental gradients. We analyse 13,612 single nucleotide polymorphisms (SNPs), derived from restriction site-associated DNA sequencing (RADseq), in 426 individuals from 25 sites spanning the I. elegans distribution in Sweden, including its expanding northern range edge. Environmental association analysis (EAA) and the magnitude of allele frequency change along the range expansion gradient revealed significant signatures of selection in relation to high maximum summer temperature, high mean annual precipitation and low wind speeds at the range edge. SNP annotations with significant signatures of selection revealed gene functions associated with ongoing range expansion, including heat shock proteins (HSP40 and HSP70), ion transport (V-ATPase) and visual processes (long-wavelength-sensitive opsin), which have implications for thermal stress response, salinity tolerance and mate discrimination, respectively. We also identified environmental thresholds where climate-mediated selection is likely to be strong, and indicate that I. elegans is rapidly adapting to the climatic environment during its ongoing range expansion. Our findings empirically validate an integrative approach for detecting spatially explicit signatures of local adaptation along environmental gradients. © 2018 John Wiley & Sons Ltd.

  20. The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Blanc, Guillaume; Agarkova, Irina; Grimwood, Jane

    2012-02-13

    Background Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced. Results The 48.8 Mb genome contained in 20 chromosomes exhibits significant synteny conservation with the chromosomes of its relatives Chlorella variabilis and Chlamydomonas reinhardtii. The order of the genes is highly reshuffled within synteny blocks, suggesting that intra-chromosomal rearrangementsmore » were more prevalent than inter-chromosomal rearrangements. Remarkably, Zepp retrotransposons occur in clusters of nested elements with strictly one cluster per chromosome probably residing at the centromere. Several protein families overrepresented in C. subellipsoidae include proteins involved in lipid metabolism, transporters, cellulose synthases and short alcohol dehydrogenases. Conversely, C-169 lacks proteins that exist in all other sequenced chlorophytes, including components of the glycosyl phosphatidyl inositol anchoring system, pyruvate phosphate dikinase and the photosystem 1 reaction center subunit N (PsaN). Conclusions We suggest that some of these gene losses and gains could have contributed to adaptation to low temperatures. Comparison of these genomic features with the adaptive strategies of psychrophilic microbes suggests that prokaryotes and eukaryotes followed comparable evolutionary routes to adapt to cold environments.« less

  1. Prevalence and genotypic characterization of Human Parvovirus B19 in children with measles- and rubella-like illness in Iran.

    PubMed

    Rezaei, Farhad; Sarshari, Behrang; Ghavami, Nastaran; Meysami, Parisa; Shadab, Azadeh; Salimi, Hamid; Mokhtari-Azad, Talat

    2016-06-01

    Human Parvovirus B19 (B19V) is a prototype of the Erythroparvovirus genus in Parvoviridae family. B19V infections are often associated with fever and rash, and can be mistakenly reported as measles or rubella. Differential diagnosis of B19V illness is necessary for case management and also for public health control activities, particularly in outbreak situations in which measles or rubella is suspected. To investigate the causative role of B19V infection in children with measles- and rubella-like illness, a total of 583 sera from children with exanthema were tested for presence of B19V by determining anti-B19V IgG and IgM antibodies by ELISA as well as B19V DNA detection by nested PCR. DNA positive samples were assessed further for determination of viral load and sequence analysis by Real-Time PCR and Sanger sequencing method, respectively. Out of 583 patients, 112 (19.21%) patients were positive for B19V-IgM antibody, 110 (18.87%) were positive for B19V-IgG antibody, and 63 (10.81%) were positive for B19V viral DNA. The frequency of B19V-IgG antibodies were increased with age; that is children under 6 year old showed 7.11% seroprevalence for B19V-IgG as compared to 18.39% and 28.91% for age groups 6 to >11 and 11-14 years old, respectively. Phylogenetic analysis of the NS1-VPu1 overlapping region revealed that all sequenced B19V-DNA belonged to genotype 1. The results of this study may aid the surveillance programs aiming at eradicating measles/rubella virus in Iran, as infections with B19V can be mistakenly reported as measles or rubella if laboratory testing is not conducted. © 2015 Wiley Periodicals, Inc.

  2. Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Oyama, Takuji; Toyota, Kenji; Waku, Tsuyoshi

    2009-08-01

    The structures of the ligand-binding domains (LBDs) of human peroxisome proliferator-activated receptors (PPARα, PPARγ and PPARδ) in complexes with a pan agonist, an α/δ dual agonist and a PPARδ-specific agonist were determined. The results explain how each ligand is recognized by the PPAR LBDs at an atomic level. Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone receptor family, which is defined as transcriptional factors that are activated by the binding of ligands to their ligand-binding domains (LBDs). Although the three PPAR subtypes display different tissue distribution patterns and distinct pharmacological profiles, they all are essentially related to fatty-acid andmore » glucose metabolism. Since the PPARs share similar three-dimensional structures within the LBDs, synthetic ligands which simultaneously activate two or all of the PPARs could be potent candidates in terms of drugs for the treatment of abnormal metabolic homeostasis. The structures of several PPAR LBDs were determined in complex with synthetic ligands, derivatives of 3-(4-alkoxyphenyl)propanoic acid, which exhibit unique agonistic activities. The PPARα and PPARγ LBDs were complexed with the same pan agonist, TIPP-703, which activates all three PPARs and their crystal structures were determined. The two LBD–ligand complex structures revealed how the pan agonist is adapted to the similar, but significantly different, ligand-binding pockets of the PPARs. The structures of the PPARδ LBD in complex with an α/δ-selective ligand, TIPP-401, and with a related δ-specific ligand, TIPP-204, were also determined. The comparison between the two PPARδ complexes revealed how each ligand exhibits either a ‘dual selective’ or ‘single specific’ binding mode.« less

  3. MERS-CoV infection: Mind the public knowledge gap.

    PubMed

    Bawazir, Amen; Al-Mazroo, Eman; Jradi, Hoda; Ahmed, Anwar; Badri, Motasim

    In August 2015, the Corona outbreak caused by Middle East respiratory syndrome coronavirus (MERS-CoV) was the 9th episode since June 2012 in Saudi Arabia. Little is known about the public awareness toward the nature or prevention of the disease. The aim of this work was to assess the knowledge of the adult population in Riyadh toward the MERS-CoV. In this cross-sectional survey, a self-administrated questionnaire was distributed to randomly selected participants visiting malls in Riyadh. The questionnaire contained measurable epidemiological and clinical MERS-CoV knowledge level variables and relevant source of information. The study included 676 participants. Mean age was 32.5 (±SD 8.6) years and 353 (47.8%) were males. Almost all participants heard about the corona disease and causative agent. The study showed a fair overall knowledge (66.0%), less knowledge on epidemiological features of the disease (58.3%), and good knowledge (90.7%) on the clinical manifestation of the MERS-CoV. Internet was the major (89.0%) source of disease information, and other sources including health care providers, SMS, television, magazines and books were low rated (all <25%). In a multivariate logistic regression analysis age ≤30 years (Odds Ratio (OR)=1.647, 95%CI 1.048-2.584, P=0.030), male gender (OR=1.536, 95%CI 1.105-2.134, P=0.01), and no tertiary education (OR=1.957, 95%CI 1.264-3.030, P=0.003) were independent significant predictors of poor epidemiological knowledge. This study concludes that there was inadequate epidemiological knowledge received by the public and the reliance mostly on the clinical manifestations to recognizing the MERS-CoV disease. Comprehensive public health education programs is important to increase awareness of simple epidemiological determinants of the disease is warranted. Copyright © 2017. Published by Elsevier Ltd.

  4. Effects of practice schedule and task specificity on the adaptive process of motor learning.

    PubMed

    Barros, João Augusto de Camargo; Tani, Go; Corrêa, Umberto Cesar

    2017-10-01

    This study investigated the effects of practice schedule and task specificity based on the perspective of adaptive process of motor learning. For this purpose, tasks with temporal and force control learning requirements were manipulated in experiments 1 and 2, respectively. Specifically, the task consisted of touching with the dominant hand the three sequential targets with specific movement time or force for each touch. Participants were children (N=120), both boys and girls, with an average age of 11.2years (SD=1.0). The design in both experiments involved four practice groups (constant, random, constant-random, and random-constant) and two phases (stabilisation and adaptation). The dependent variables included measures related to the task goal (accuracy and variability of error of the overall movement and force patterns) and movement pattern (macro- and microstructures). Results revealed a similar error of the overall patterns for all groups in both experiments and that they adapted themselves differently in terms of the macro- and microstructures of movement patterns. The study concludes that the effects of practice schedules on the adaptive process of motor learning were both general and specific to the task. That is, they were general to the task goal performance and specific regarding the movement pattern. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Attention modulates visual size adaptation.

    PubMed

    Kreutzer, Sylvia; Fink, Gereon R; Weidner, Ralph

    2015-01-01

    The current study determined in healthy subjects (n = 16) whether size adaptation occurs at early, i.e., preattentive, levels of processing or whether higher cognitive processes such as attention can modulate the illusion. To investigate this issue, bottom-up stimulation was kept constant across conditions by using a single adaptation display containing both small and large adapter stimuli. Subjects' attention was directed to either the large or small adapter stimulus by means of a luminance detection task. When attention was directed toward the small as compared to the large adapter, the perceived size of the subsequent target was significantly increased. Data suggest that different size adaptation effects can be induced by one and the same stimulus depending on the current allocation of attention. This indicates that size adaptation is subject to attentional modulation. These findings are in line with previous research showing that transient as well as sustained attention modulates visual features, such as contrast sensitivity and spatial frequency, and influences adaptation in other contexts, such as motion adaptation (Alais & Blake, 1999; Lankheet & Verstraten, 1995). Based on a recently suggested model (Pooresmaeili, Arrighi, Biagi, & Morrone, 2013), according to which perceptual adaptation is based on local excitation and inhibition in V1, we conclude that guiding attention can boost these local processes in one or the other direction by increasing the weight of the attended adapter. In sum, perceptual adaptation, although reflected in changes of neural activity at early levels (as shown in the aforementioned study), is nevertheless subject to higher-order modulation.

  6. Functional connectivity patterns reflect individual differences in conflict adaptation.

    PubMed

    Wang, Xiangpeng; Wang, Ting; Chen, Zhencai; Hitchman, Glenn; Liu, Yijun; Chen, Antao

    2015-04-01

    Individuals differ in the ability to utilize previous conflict information to optimize current conflict resolution, which is termed the conflict adaptation effect. Previous studies have linked individual differences in conflict adaptation to distinct brain regions. However, the network-based neural mechanisms subserving the individual differences of the conflict adaptation effect have not been studied. The present study employed a psychophysiological interaction (PPI) analysis with a color-naming Stroop task to examine this issue. The main results were as follows: (1) the anterior cingulate cortex (ACC)-seeded PPI revealed the involvement of the salience network (SN) in conflict adaptation, while the posterior parietal cortex (PPC)-seeded PPI revealed the engagement of the central executive network (CEN). (2) Participants with high conflict adaptation effect showed higher intra-CEN connectivity and lower intra-SN connectivity; while those with low conflict adaptation effect showed higher intra-SN connectivity and lower intra-CEN connectivity. (3) The PPC-centered intra-CEN connectivity positively predicted the conflict adaptation effect; while the ACC-centered intra-SN connectivity had a negative correlation with this effect. In conclusion, our data demonstrated that conflict adaptation is likely supported by the CEN and the SN, providing a new perspective on studying individual differences in conflict adaptation on the basis of large-scale networks. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. The neural oscillations of conflict adaptation in the human frontal region.

    PubMed

    Tang, Dandan; Hu, Li; Chen, Antao

    2013-07-01

    Incongruency between print color and the semantic meaning of a word in a classical Stroop task activates the human conflict monitoring system and triggers a behavioral conflict. Conflict adaptation has been suggested to mediate the cortical processing of neural oscillations in such a conflict situation. However, the basic mechanisms that underlie the influence of conflict adaptation on the changes of neural oscillations are not clear. In the present study, electroencephalography (EEG) data were recorded from sixteen healthy human participants while they were performing a color-word Stroop task within a novel look-to-do transition design that included two response modalities. In the 'look' condition, participants were informed to look at the color of presented words but no responses were required; in the 'do' condition, they were informed to make arranged responses to the color of presented words. Behaviorally, a reliable conflict adaptation was observed. Time-frequency analysis revealed that (1) in the 'look' condition, theta-band activity in the left- and right-frontal regions reflected a conflict-related process at a response inhibition level; and (2) in the 'do' condition, both theta-band activity in the left-frontal region and alpha-band activity in the left-, right-, and centro-frontal regions reflected a process of conflict control, which triggered neural and behavioral adaptation. Taken together, these results suggest that there are frontal mechanisms involving neural oscillations that can mediate response inhibition processes and control behavioral conflict. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide.

    PubMed

    Young, J N; Rickaby, R E M; Kapralov, M V; Filatov, D A

    2012-02-19

    Rubisco, the most abundant enzyme on the Earth and responsible for all photosynthetic carbon fixation, is often thought of as a highly conserved and sluggish enzyme. Yet, different algal Rubiscos demonstrate a range of kinetic properties hinting at a history of evolution and adaptation. Here, we show that algal Rubisco has indeed evolved adaptively during ancient and distinct geological periods. Using DNA sequences of extant marine algae of the red and Chromista lineage, we define positive selection within the large subunit of Rubisco, encoded by rbcL, to occur basal to the radiation of modern marine groups. This signal of positive selection appears to be responding to changing intracellular concentrations of carbon dioxide (CO(2)) triggered by physiological adaptations to declining atmospheric CO(2). Within the ecologically important Haptophyta (including coccolithophores) and Bacillariophyta (diatoms), positive selection occurred consistently during periods of falling Phanerozoic CO(2) and suggests emergence of carbon-concentrating mechanisms. During the Proterozoic, a strong signal of positive selection after secondary endosymbiosis occurs at the origin of the Chromista lineage (approx. 1.1 Ga), with further positive selection events until 0.41 Ga, implying a significant and continuous decrease in atmospheric CO(2) encompassing the Cryogenian Snowball Earth events. We surmise that positive selection in Rubisco has been caused by declines in atmospheric CO(2) and hence acts as a proxy for ancient atmospheric CO(2).

  9. Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide

    PubMed Central

    Young, J. N.; Rickaby, R. E. M.; Kapralov, M. V.; Filatov, D. A.

    2012-01-01

    Rubisco, the most abundant enzyme on the Earth and responsible for all photosynthetic carbon fixation, is often thought of as a highly conserved and sluggish enzyme. Yet, different algal Rubiscos demonstrate a range of kinetic properties hinting at a history of evolution and adaptation. Here, we show that algal Rubisco has indeed evolved adaptively during ancient and distinct geological periods. Using DNA sequences of extant marine algae of the red and Chromista lineage, we define positive selection within the large subunit of Rubisco, encoded by rbcL, to occur basal to the radiation of modern marine groups. This signal of positive selection appears to be responding to changing intracellular concentrations of carbon dioxide (CO2) triggered by physiological adaptations to declining atmospheric CO2. Within the ecologically important Haptophyta (including coccolithophores) and Bacillariophyta (diatoms), positive selection occurred consistently during periods of falling Phanerozoic CO2 and suggests emergence of carbon-concentrating mechanisms. During the Proterozoic, a strong signal of positive selection after secondary endosymbiosis occurs at the origin of the Chromista lineage (approx. 1.1 Ga), with further positive selection events until 0.41 Ga, implying a significant and continuous decrease in atmospheric CO2 encompassing the Cryogenian Snowball Earth events. We surmise that positive selection in Rubisco has been caused by declines in atmospheric CO2 and hence acts as a proxy for ancient atmospheric CO2. PMID:22232761

  10. T Cell Adaptive Immunity Proceeds through Environment-Induced Adaptation from the Exposure of Cryptic Genetic Variation

    PubMed Central

    Whitacre, James M.; Lin, Joseph; Harding, Angus

    2011-01-01

    Evolution is often characterized as a process involving incremental genetic changes that are slowly discovered and fixed in a population through genetic drift and selection. However, a growing body of evidence is finding that changes in the environment frequently induce adaptations that are much too rapid to occur by an incremental genetic search process. Rapid evolution is hypothesized to be facilitated by mutations present within the population that are silent or “cryptic” within the first environment but are co-opted or “exapted” to the new environment, providing a selective advantage once revealed. Although cryptic mutations have recently been shown to facilitate evolution in RNA enzymes, their role in the evolution of complex phenotypes has not been proven. In support of this wider role, this paper describes an unambiguous relationship between cryptic genetic variation and complex phenotypic responses within the immune system. By reviewing the biology of the adaptive immune system through the lens of evolution, we show that T cell adaptive immunity constitutes an exemplary model system where cryptic alleles drive rapid adaptation of complex traits. In naive T cells, normally cryptic differences in T cell receptor reveal diversity in activation responses when the cellular population is presented with a novel environment during infection. We summarize how the adaptive immune response presents a well studied and appropriate experimental system that can be used to confirm and expand upon theoretical evolutionary models describing how seemingly small and innocuous mutations can drive rapid cellular evolution. PMID:22363338

  11. Genomic, transcriptomic and phenomic variation reveals the complex adaptation to stress response of modern maize breeding

    USDA-ARS?s Scientific Manuscript database

    Early maize adaptation to different agricultural environments was an important process associated with the creation of a stable food supply that allowed the evolution of human civilization in the Americas. To explore the mechanisms of maize adaptation, genomic, transcriptomic and phenomic data were ...

  12. Assessing Adaptive Functioning in Death Penalty Cases after Hall and DSM-5.

    PubMed

    Hagan, Leigh D; Drogin, Eric Y; Guilmette, Thomas J

    2016-03-01

    DSM-5 and Hall v. Florida (2014) have dramatically refocused attention on the assessment of adaptive functioning in death penalty cases. In this article, we address strategies for assessing the adaptive functioning of defendants who seek exemption from capital punishment pursuant to Atkins v. Virginia (2002). In particular, we assert that evaluations of adaptive functioning should address assets as well as deficits; seek to identify credible and reliable evidence concerning the developmental period and across the lifespan; distinguish incapacity from the mere absence of adaptive behavior; adhere faithfully to test manual instructions for using standardized measures of adaptive functioning; and account for potential bias on the part of informants. We conclude with brief caveats regarding the standard error of measurement (SEM) in light of Hall, with reference to examples of ordinary life activities that directly illuminate adaptive functioning relevant to capital cases. © 2016 American Academy of Psychiatry and the Law.

  13. Whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic Leptospira

    PubMed Central

    Xu, Yinghua; Zhu, Yongzhang; Wang, Yuezhu; Chang, Yung-Fu; Zhang, Ying; Jiang, Xiugao; Zhuang, Xuran; Zhu, Yongqiang; Zhang, Jinlong; Zeng, Lingbing; Yang, Minjun; Li, Shijun; Wang, Shengyue; Ye, Qiang; Xin, Xiaofang; Zhao, Guoping; Zheng, Huajun; Guo, Xiaokui; Wang, Junzhi

    2016-01-01

    Leptospirosis, caused by pathogenic Leptospira spp., has recently been recognized as an emerging infectious disease worldwide. Despite its severity and global importance, knowledge about the molecular pathogenesis and virulence evolution of Leptospira spp. remains limited. Here we sequenced and analyzed 102 isolates representing global sources. A high genomic variability were observed among different Leptospira species, which was attributed to massive gene gain and loss events allowing for adaptation to specific niche conditions and changing host environments. Horizontal gene transfer and gene duplication allowed the stepwise acquisition of virulence factors in pathogenic Leptospira evolved from a recent common ancestor. More importantly, the abundant expansion of specific virulence-related protein families, such as metalloproteases-associated paralogs, were exclusively identified in pathogenic species, reflecting the importance of these protein families in the pathogenesis of leptospirosis. Our observations also indicated that positive selection played a crucial role on this bacteria adaptation to hosts. These novel findings may lead to greater understanding of the global diversity and virulence evolution of Leptospira spp. PMID:26833181

  14. Image quality comparison of two adaptive statistical iterative reconstruction (ASiR, ASiR-V) algorithms and filtered back projection in routine liver CT.

    PubMed

    Chen, Li-Hong; Jin, Chao; Li, Jian-Ying; Wang, Ge-Liang; Jia, Yong-Jun; Duan, Hai-Feng; Pan, Ning; Guo, Jianxin

    2018-06-06

    To compare image quality of two adaptive statistical iterative reconstruction (ASiR and ASiR-V) algorithms using objective and subjective metrics for routine liver CT, with the conventional filtered back projection (FBP) reconstructions as reference standards. This institutional review board-approved study included 52 patients with clinically suspected hepatic metastases. Patients were divided equally into ASiR and ASiR-V groups with same scan parameters. Images were reconstructed with ASiR and ASiR-V from 0 (FBP) to 100% blending percentages at 10% interval in its respective group. Mean and standard deviation of CT numbers for liver parenchyma were recorded. Two experienced radiologists reviewed all images for image quality blindly and independently. Data were statistically analyzed. There was no difference in CT dose index between ASiR and ASiR-V groups. As the percentage of ASiR and ASiR-V increased from 10 to 100% , image noise reduced by 8.6 -57.9% and 8.9-81.6%, respectively, compared with FBP. There was substantial interobserver agreement in image quality assessment for ASiR and ASiR-V images. Compared with FBP reconstruction, subjective image quality scores of ASiR and ASiR-V improved significantly as percentage increased from 10 to 80% for ASiR (peaked at 50% with 32.2% noise reduction) and from 10 to 90% (peaked at 60% with 51.5% noise reduction) for ASiR-V. Both ASiR and ASiR-V improved the objective and subjective image quality for routine liver CT compared with FBP. ASiR-V provided further image quality improvement with higher acceptable percentage than ASiR, and ASiR-V60% had the highest image quality score. Advances in knowledge: (1) Both ASiR and ASiR-V significantly reduce image noise compared with conventional FBP reconstruction. (2) ASiR-V with 60 blending percentage provides the highest image quality score in routine liver CT.

  15. Positively Charged Residues at the Five-Fold Symmetry Axis of Cell Culture-Adapted Foot-and-Mouth Disease Virus Permit Novel Receptor Interactions

    PubMed Central

    Berryman, Stephen; Clark, Stuart; Kakker, Naresh K.; Silk, Rhiannon; Seago, Julian; Wadsworth, Jemma; Chamberlain, Kyle; Knowles, Nick J.

    2013-01-01

    Field isolates of foot-and-mouth disease virus (FMDV) have a restricted cell tropism which is limited by the need for certain RGD-dependent integrin receptors. In contrast, cell culture-adapted viruses use heparan sulfate (HS) or other unidentified molecules as receptors to initiate infection. Here, we report several novel findings resulting from cell culture adaptation of FMDV. In cell culture, a virus with the capsid of the A/Turkey/2/2006 field isolate gained the ability to infect CHO and HS-deficient CHO cells as a result of a single glutamine (Q)-to-lysine (K) substitution at VP1-110 (VP1-Q110K). Using site-directed mutagenesis, the introduction of lysine at this same site also resulted in an acquired ability to infect CHO cells by type O and Asia-1 FMDV. However, this ability appeared to require a second positively charged residue at VP1-109. CHO cells express two RGD-binding integrins (α5β1 and αvβ5) that, although not used by FMDV, have the potential to be used as receptors; however, viruses with the VP1-Q110K substitution did not use these integrins. In contrast, the VP1-Q110K substitution appeared to result in enhanced interactions with αvβ6, which allowed a virus with KGE in place of the normal RGD integrin-binding motif to use αvβ6 as a receptor. Thus, our results confirmed the existence of nonintegrin, non-HS receptors for FMDV on CHO cells and revealed a novel, non-RGD-dependent use of αvβ6 as a receptor. The introduction of lysine at VP1-110 may allow for cell culture adaptation of FMDV by design, which may prove useful for vaccine manufacture when cell culture adaptation proves intractable. PMID:23740982

  16. Criticality of Adaptive Control Dynamics

    NASA Astrophysics Data System (ADS)

    Patzelt, Felix; Pawelzik, Klaus

    2011-12-01

    We show, that stabilization of a dynamical system can annihilate observable information about its structure. This mechanism induces critical points as attractors in locally adaptive control. It also reveals, that previously reported criticality in simple controllers is caused by adaptation and not by other controller details. We apply these results to a real-system example: human balancing behavior. A model of predictive adaptive closed-loop control subject to some realistic constraints is introduced and shown to reproduce experimental observations in unprecedented detail. Our results suggests, that observed error distributions in between the Lévy and Gaussian regimes may reflect a nearly optimal compromise between the elimination of random local trends and rare large errors.

  17. Adaptive cyber-attack modeling system

    NASA Astrophysics Data System (ADS)

    Gonsalves, Paul G.; Dougherty, Edward T.

    2006-05-01

    The pervasiveness of software and networked information systems is evident across a broad spectrum of business and government sectors. Such reliance provides an ample opportunity not only for the nefarious exploits of lone wolf computer hackers, but for more systematic software attacks from organized entities. Much effort and focus has been placed on preventing and ameliorating network and OS attacks, a concomitant emphasis is required to address protection of mission critical software. Typical software protection technique and methodology evaluation and verification and validation (V&V) involves the use of a team of subject matter experts (SMEs) to mimic potential attackers or hackers. This manpower intensive, time-consuming, and potentially cost-prohibitive approach is not amenable to performing the necessary multiple non-subjective analyses required to support quantifying software protection levels. To facilitate the evaluation and V&V of software protection solutions, we have designed and developed a prototype adaptive cyber attack modeling system. Our approach integrates an off-line mechanism for rapid construction of Bayesian belief network (BN) attack models with an on-line model instantiation, adaptation and knowledge acquisition scheme. Off-line model construction is supported via a knowledge elicitation approach for identifying key domain requirements and a process for translating these requirements into a library of BN-based cyber-attack models. On-line attack modeling and knowledge acquisition is supported via BN evidence propagation and model parameter learning.

  18. Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in Arabidopsis lyrata.

    PubMed

    Turner, Thomas L; von Wettberg, Eric J; Nuzhdin, Sergey V

    2008-09-11

    Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low CaratioMg ratio in A. lyrata.

  19. Kinetic solvers with adaptive mesh in phase space

    NASA Astrophysics Data System (ADS)

    Arslanbekov, Robert R.; Kolobov, Vladimir I.; Frolova, Anna A.

    2013-12-01

    An adaptive mesh in phase space (AMPS) methodology has been developed for solving multidimensional kinetic equations by the discrete velocity method. A Cartesian mesh for both configuration (r) and velocity (v) spaces is produced using a “tree of trees” (ToT) data structure. The r mesh is automatically generated around embedded boundaries, and is dynamically adapted to local solution properties. The v mesh is created on-the-fly in each r cell. Mappings between neighboring v-space trees is implemented for the advection operator in r space. We have developed algorithms for solving the full Boltzmann and linear Boltzmann equations with AMPS. Several recent innovations were used to calculate the discrete Boltzmann collision integral with dynamically adaptive v mesh: the importance sampling, multipoint projection, and variance reduction methods. We have developed an efficient algorithm for calculating the linear Boltzmann collision integral for elastic and inelastic collisions of hot light particles in a Lorentz gas. Our AMPS technique has been demonstrated for simulations of hypersonic rarefied gas flows, ion and electron kinetics in weakly ionized plasma, radiation and light-particle transport through thin films, and electron streaming in semiconductors. We have shown that AMPS allows minimizing the number of cells in phase space to reduce the computational cost and memory usage for solving challenging kinetic problems.

  20. Phenotypic divergence along geographic gradients reveals potential for rapid adaptation of the White-nose Syndrome pathogen, Pseudogymnoascus destructans, in North America.

    PubMed

    Forsythe, Adrian; Giglio, Victoria; Asa, Jonathan; Xu, Jianping

    2018-06-18

    White-nose Syndrome (WNS) is an ongoing epizootic affecting multiple species of North American bats, caused by epidermal infections of the psychrophilic filamentous fungus, Pseudogymnoascus destructans Since its introduction from Europe, WNS has spread rapidly across eastern North America and resulted in high mortality rates in bats. At present, the mechanisms behind its spread and the extent of its adaptation to different geographic and ecological niches remain unknown. The objective of this study was to examine the geographic patterns of phenotypic variation and the potential evidence for adaptation among strains representing broad geographic locations in eastern North America. The morphological features of these strains were evaluated on artificial medium, and the viability of asexual arthroconidia of representative strains were investigated after storage at high (23°C), moderate (14°C), and low (4°C) temperatures at different lengths of times. Our analyses identified evidence for a geographic pattern of colony morphology changes among the clonal descendants of the fungus, with trait values correlated with increased distance from the epicenter of WNS. Our genomic comparisons of three representative isolates revealed novel genetic polymorphisms and suggested potential candidate mutations that might be related to some of the phenotypic changes. These results show that even though this pathogen arrived in North America only recently and reproduces asexually, there has been substantial evolution and phenotypic diversification during its rapid clonal expansion. Importance The causal agent of White-nose Syndrome in bats is Pseudogymnoascus destructans , a filamentous fungus recently introduced from its native range in Europe. Infections caused by P. destructans have progressed across the eastern parts of Canada and the United States over the last ten years. It is not clear how the disease is spread as the pathogen is unable to grow above 23°C and ambient

  1. Delivering organisational adaptation through legislative mechanisms: Evidence from the Adaptation Reporting Power (Climate Change Act 2008).

    PubMed

    Jude, S R; Drew, G H; Pollard, S J T; Rocks, S A; Jenkinson, K; Lamb, R

    2017-01-01

    There is increasing recognition that organisations, particularly in key infrastructure sectors, are potentially vulnerable to climate change and extreme weather events, and require organisational responses to ensure they are resilient and adaptive. However, detailed evidence of how adaptation is facilitated, implemented and reported, particularly through legislative mechanisms is lacking. The United Kingdom Climate Change Act (2008), introduced the Adaptation Reporting Power, enabling the Government to direct so-called reporting authorities to report their climate change risks and adaptation plans. We describe the authors' unique role and experience supporting the Department for Environment, Food and Rural Affairs (Defra) during the Adaptation Reporting Power's first round. An evaluation framework, used to review the adaptation reports, is presented alongside evidence on how the process provides new insights into adaptation activities and triggered organisational change in 78% of reporting authorities, including the embedding of climate risk and adaptation issues. The role of legislative mechanisms and risk-based approaches in driving and delivering adaptation is discussed alongside future research needs, including the development of organisational maturity models to determine resilient and well adapting organisations. The Adaptation Reporting Power process provides a basis for similar initiatives in other countries, although a clear engagement strategy to ensure buy-in to the process and research on its long-term legacy, including the potential merits of voluntary approaches, is required. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  2. Verification and Validation Methodology of Real-Time Adaptive Neural Networks for Aerospace Applications

    NASA Technical Reports Server (NTRS)

    Gupta, Pramod; Loparo, Kenneth; Mackall, Dale; Schumann, Johann; Soares, Fola

    2004-01-01

    Recent research has shown that adaptive neural based control systems are very effective in restoring stability and control of an aircraft in the presence of damage or failures. The application of an adaptive neural network with a flight critical control system requires a thorough and proven process to ensure safe and proper flight operation. Unique testing tools have been developed as part of a process to perform verification and validation (V&V) of real time adaptive neural networks used in recent adaptive flight control system, to evaluate the performance of the on line trained neural networks. The tools will help in certification from FAA and will help in the successful deployment of neural network based adaptive controllers in safety-critical applications. The process to perform verification and validation is evaluated against a typical neural adaptive controller and the results are discussed.

  3. Adaptation and resiliency in Swedish families.

    PubMed

    Kiehl, Ermalynn M; Carson, David K; Dykes, Anna-Karin

    2007-09-01

    A longitudinal research project began in 1993 of Norwegian, Swedish and American mothers' perception of her family's dynamics and adaptation during childbearing and childrearing. Results indicated that Swedish mothers adapted better than other mothers. In 2003, a mixed design study was conducted with original Swedish mothers that aimed to describe the experience of motherhood, the meaning mothers attached to events in their lives that made adaptation necessary, and ways in which they achieved adaptation. Fourteen mothers completed quantitative instruments and 13 of those mothers were interviewed. Audiotaped interviews were transcribed and analysed for themes using a protocol based on a model of family resiliency. Quantitative findings revealed statistically significant findings in areas of children, mother's work outside the home and families in which a major illness had occurred. Qualitative findings revealed that protective factors far outweighed vulnerability and risk factors. Mothers' satisfaction with life manifested itself in love of home, contentment with employment, fulfillment from an active and healthy life and support from a society that provides a wide range of social benefits for the family. Vulnerability occurred primarily when mothers were tired, lacked personal time or someone in the family was experiencing a serious illness. Results of this study enhance the scholarly scientific knowledge about the uniqueness of Swedish mothers, and increased understanding of family dynamics and adaptation. Many of the findings relate in some way to overall social benefits and supports available for families.

  4. Interactions between concentric form-from-structure and face perception revealed by visual masking but not adaptation

    PubMed Central

    Feczko, Eric; Shulman, Gordon L.; Petersen, Steven E.; Pruett, John R.

    2014-01-01

    Findings from diverse subfields of vision research suggest a potential link between high-level aspects of face perception and concentric form-from-structure perception. To explore this relationship, typical adults performed two adaptation experiments and two masking experiments to test whether concentric, but not nonconcentric, Glass patterns (a type of form-from-structure stimulus) utilize a processing mechanism shared by face perception. For the adaptation experiments, subjects were presented with an adaptor for 5 or 20 s, prior to discriminating a target. In the masking experiments, subjects saw a mask, then a target, and then a second mask. Measures of discriminability and bias were derived and repeated measures analysis of variance tested for pattern-specific masking and adaptation effects. Results from Experiment 1 show no Glass pattern-specific effect of adaptation to faces; results from Experiment 2 show concentric Glass pattern masking, but not adaptation, may impair upright/inverted face discrimination; results from Experiment 3 show concentric and radial Glass pattern masking impaired subsequent upright/inverted face discrimination more than translational Glass pattern masking; and results from Experiment 4 show concentric and radial Glass pattern masking impaired subsequent face gender discrimination more than translational Glass pattern masking. Taken together, these findings demonstrate interactions between concentric form-from-structure and face processing, suggesting a possible common processing pathway. PMID:24563526

  5. Laboratory tests for assessing adaptability and stickiness of dental composites.

    PubMed

    Rosentritt, Martin; Buczovsky, Sebastian; Behr, Michael; Preis, Verena

    2014-09-01

    Handling (stickiness, adaptability) of a dental composite does strongly influence quality and success of a dental restoration. The purpose was to develop an in vitro test, which allows for evaluating adaptability and stickiness. 15 dentists were asked for providing individual assessment (school scores 1-6) of five dental composites addressing adaptability and stickiness. Composites were applied with a dental plugger (d=1.8 mm) in a class I cavity (human tooth 17). The tooth was fixed on a force gauge for simultaneous determination of application forces with varying storage (6/25°C) and application temperatures (6/25°C). On basis of these data tensile tests were performed with a dental plugger (application force 1N/2N; v=35 mm/min) on PMMA- or human tooth plates. Composite was dosed onto the tip of the plugger and applied. Application and unplugging was performed once and unplugging forces (UF) and length of the adhesive flags (LAF) were determined at different storage (6/25°C) and application temperatures (25/37°C). Unplugging work (UW) was calculated from area of UF and LAF data. The individual assessment revealed significantly different temperature-dependent application forces between 0.58 N and 2.23 N. Adaptability was assessed between 2.1 and 2.8 school scores. Stickiness varied significantly between the materials (scores: 2-3.2). UW differed significantly between the materials with values between 3.20 N mm and 37.83 N mm. Between PMMA substrate or tooth slides and between 1N or 2N application force only small UW differences were found. The presented in vitro unplugging work allows for an in vitro estimation of the handling parameters adaptability and stickiness. Copyright © 2014 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  6. Genetic analysis of Aedes albopictus (Diptera, Culicidae) reveals a deep divergence in the original regions.

    PubMed

    Ruiling, Zhang; Tongkai, Liu; Zhendong, Huang; Guifen, Zhuang; Dezhen, Ma; Zhong, Zhang

    2018-05-02

    Aedes albopictus has been described as one of the 100 worst invasive species in the world. This mosquito originated from southeastern Asia and currently has a widespread presence in every continent except Antarctica. The rapid global expansion of Ae. albopictus has increased public health concerns about arbovirus-related disease threats. Adaptation, adaption to novel areas is a biological challenge for invasive species, and the underlying processes can be studied at the molecular level. In this study, genetic analysis was performed using mitochondrial gene NADH dehydrogenase subunit 5 (ND5), based on both native and invasive populations. Altogether, 38 haplotypes were detected with H1 being the dominant and widely distributed in 21 countries. Both phylogenetic and network analyses supported the existence of five clades, with only clade I being involved in the subsequent global spread of Asian tiger mosquito. The other four clades (II, III, IV and V) were restricted to their original regions, which could be ancestral populations that had diverged from clade I in the early stages of evolution. Neutrality tests suggested that most of the populations had experienced recent expansion. Analysis of molecular variance and the population-pair statistic F ST revealed that most populations lacked genetic structure, while high variability was detected within populations. Multiple and independent human-mediated introductions may explain the present results. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Structural changes in plasma membranes prepared from irradiated Chinese hamster V79 cells as revealed by Raman spectroscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Verma, S.P.; Sonwalkar, N.

    1991-04-01

    The effect of gamma irradiation on the integrity of plasma membranes isolated from Chinese hamster V79 cells was investigated by Raman spectroscopy. Plasma membranes of control V79 cells show transitions between {minus}10 and 5{degree}C (low-temperature transition), 10 and 22{degree}C (middle-temperature transition), and 32 and 40{degree}C (high-temperature transition). Irradiation (5 Gy) alters these transitions markedly. First, the low-temperature transition shifts to higher temperature (onset and completion temperatures 4 and 14{degree}C). Second, the middle-temperature transition shifts up to the range of about 20-32{degree}C, but the width remains unchanged. Third, the higher temperature transition broadens markedly and shifts to the range of aboutmore » 15-40{degree}C. Protein secondary structure as determined by least-squares analysis of the amide I bands shows 36% total helix, 55% total beta-strand, and 9% turn plus undefined for control plasma membrane proteins. Plasma membrane proteins of irradiated V79 cells show an increase in total helix (40 and 45% at 5 and 10 Gy, respectively) and a decrease in the total beta-strand (48 and 44% at 5 and 10 Gy, respectively) structures. The qualitative analysis of the Raman features of plasma membranes and model compounds in the 1600 cm-1 region, assigned to tyrosine groups, revealed that irradiation alters the microenvironment of these groups. We conclude that the radiation dose used in the survival range of Chinese hamster V79 cells can cause damage to plasma membrane proteins without detectable lipid peroxidation, and that the altered proteins react differently with lipids, yielding a shift in the thermal transition properties.« less

  8. H.E.S.S. reveals a lack of TeV emission from the supernova remnant Puppis A

    NASA Astrophysics Data System (ADS)

    H. E. S. S. Collaboration; Abramowski, A.; Aharonian, F.; Ait Benkhali, F.; Akhperjanian, A. G.; Angüner, E. O.; Backes, M.; Balenderan, S.; Balzer, A.; Barnacka, A.; Becherini, Y.; Becker Tjus, J.; Berge, D.; Bernhard, S.; Bernlöhr, K.; Birsin, E.; Biteau, J.; Böttcher, M.; Boisson, C.; Bolmont, J.; Bordas, P.; Bregeon, J.; Brun, F.; Brun, P.; Bryan, M.; Bulik, T.; Carrigan, S.; Casanova, S.; Chadwick, P. M.; Chakraborty, N.; Chalme-Calvet, R.; Chaves, R. C. G.; Chrétien, M.; Colafrancesco, S.; Cologna, G.; Conrad, J.; Couturier, C.; Cui, Y.; Davids, I. D.; Degrange, B.; Deil, C.; deWilt, P.; Djannati-Ataï, A.; Domainko, W.; Donath, A.; O'C. Drury, L.; Dubus, G.; Dutson, K.; Dyks, J.; Dyrda, M.; Edwards, T.; Egberts, K.; Eger, P.; Espigat, P.; Farnier, C.; Fegan, S.; Feinstein, F.; Fernandes, M. V.; Fernandez, D.; Fiasson, A.; Fontaine, G.; Förster, A.; Füßling, M.; Gabici, S.; Gajdus, M.; Gallant, Y. A.; Garrigoux, T.; Giavitto, G.; Giebels, B.; Glicenstein, J. F.; Gottschall, D.; Grondin, M.-H.; Grudzińska, M.; Hadasch, D.; Häffner, S.; Hahn, J.; Harris, J.; Heinzelmann, G.; Henri, G.; Hermann, G.; Hervet, O.; Hillert, A.; Hinton, J. A.; Hofmann, W.; Hofverberg, P.; Holler, M.; Horns, D.; Ivascenko, A.; Jacholkowska, A.; Jahn, C.; Jamrozy, M.; Janiak, M.; Jankowsky, F.; Jung-Richardt, I.; Kastendieck, M. A.; Katarzyński, K.; Katz, U.; Kaufmann, S.; Khélifi, B.; Kieffer, M.; Klepser, S.; Klochkov, D.; Kluźniak, W.; Kolitzus, D.; Komin, Nu.; Kosack, K.; Krakau, S.; Krayzel, F.; Krüger, P. P.; Laffon, H.; Lamanna, G.; Lefaucheur, J.; Lefranc, V.; Lemière, A.; Lemoine-Goumard, M.; Lenain, J.-P.; Lohse, T.; Lopatin, A.; Lu, C.-C.; Marandon, V.; Marcowith, A.; Marx, R.; Maurin, G.; Maxted, N.; Mayer, M.; McComb, T. J. L.; Méhault, J.; Meintjes, P. J.; Menzler, U.; Meyer, M.; Mitchell, A. M. W.; Moderski, R.; Mohamed, M.; Morå, K.; Moulin, E.; Murach, T.; de Naurois, M.; Niemiec, J.; Nolan, S. J.; Oakes, L.; Odaka, H.; Ohm, S.; Opitz, B.; Ostrowski, M.; Oya, I.; Panter, M.; Parsons, R. D.; Arribas, M. Paz; Pekeur, N. W.; Pelletier, G.; Petrucci, P.-O.; Peyaud, B.; Pita, S.; Poon, H.; Pühlhofer, G.; Punch, M.; Quirrenbach, A.; Raab, S.; Reichardt, I.; Reimer, A.; Reimer, O.; Renaud, M.; de los Reyes, R.; Rieger, F.; Romoli, C.; Rosier-Lees, S.; Rowell, G.; Rudak, B.; Rulten, C. B.; Sahakian, V.; Salek, D.; Sanchez, D. A.; Santangelo, A.; Schlickeiser, R.; Schüssler, F.; Schulz, A.; Schwanke, U.; Schwarzburg, S.; Schwemmer, S.; Sol, H.; Spanier, F.; Spengler, G.; Spies, F.; Stawarz, Ł.; Steenkamp, R.; Stegmann, C.; Stinzing, F.; Stycz, K.; Sushch, I.; Tavernet, J.-P.; Tavernier, T.; Taylor, A. M.; Terrier, R.; Tluczykont, M.; Trichard, C.; Valerius, K.; van Eldik, C.; van Soelen, B.; Vasileiadis, G.; Veh, J.; Venter, C.; Viana, A.; Vincent, P.; Vink, J.; Völk, H. J.; Volpe, F.; Vorster, M.; Vuillaume, T.; Wagner, S. J.; Wagner, P.; Wagner, R. M.; Ward, M.; Weidinger, M.; Weitzel, Q.; White, R.; Wierzcholska, A.; Willmann, P.; Wörnlein, A.; Wouters, D.; Yang, R.; Zabalza, V.; Zaborov, D.; Zacharias, M.; Zdziarski, A. A.; Zech, A.; Zechlin, H.-S.

    2015-02-01

    Context. Puppis A is an interesting ~4 kyr-old supernova remnant (SNR) that shows strong evidence of interaction between the forward shock and a molecular cloud. It has been studied in detail from radio frequencies to high-energy (HE, 0.1-100 GeV) γ-rays. An analysis of the Fermi-LAT data has shown extended HE γ-ray emission with a 0.2-100 GeV spectrum exhibiting no significant deviation from a power law, unlike most of the GeV-emitting SNRs known to be interacting with molecular clouds. This makes it a promising target for imaging atmospheric Cherenkov telescopes (IACTs) to probe the γ-ray emission above 100 GeV. Aims: Very-high-energy (VHE, E ≥ 0.1 TeV) γ-ray emission from Puppis A has been, for the first time, searched for with the High Energy Stereoscopic System (H.E.S.S.). Methods: Stereoscopic imaging of Cherenkov radiation from extensive air showers is used to reconstruct the direction and energy of the incident γ-rays in order to produce sky images and source spectra. The profile likelihood method is applied to find constraints on the existence of a potential break or cutoff in the photon spectrum. Results: The analysis of the H.E.S.S. data does not reveal any significant emission towards Puppis A. The derived upper limits on the differential photon flux imply that its broadband γ-ray spectrum must exhibit a spectral break or cutoff. By combining Fermi-LAT and H.E.S.S. measurements, the 99% confidence-level upper limits on such a cutoff are found to be 450 and 280 GeV, assuming a power law with a simple exponential and a sub-exponential cutoff, respectively. It is concluded that none of the standard limitations (age, size, radiative losses) on the particle acceleration mechanism, assumed to be continuing at present, can explain the lack of VHE signal. The scenario in which particle acceleration has ceased some time ago is considered as an alternative explanation. The HE/VHE spectrum of Puppis A could then exhibit a break of non-radiative origin (as

  9. Dysfunction of Rapid Neural Adaptation in Dyslexia.

    PubMed

    Perrachione, Tyler K; Del Tufo, Stephanie N; Winter, Rebecca; Murtagh, Jack; Cyr, Abigail; Chang, Patricia; Halverson, Kelly; Ghosh, Satrajit S; Christodoulou, Joanna A; Gabrieli, John D E

    2016-12-21

    Identification of specific neurophysiological dysfunctions resulting in selective reading difficulty (dyslexia) has remained elusive. In addition to impaired reading development, individuals with dyslexia frequently exhibit behavioral deficits in perceptual adaptation. Here, we assessed neurophysiological adaptation to stimulus repetition in adults and children with dyslexia for a wide variety of stimuli, spoken words, written words, visual objects, and faces. For every stimulus type, individuals with dyslexia exhibited significantly diminished neural adaptation compared to controls in stimulus-specific cortical areas. Better reading skills in adults and children with dyslexia were associated with greater repetition-induced neural adaptation. These results highlight a dysfunction of rapid neural adaptation as a core neurophysiological difference in dyslexia that may underlie impaired reading development. Reduced neurophysiological adaptation may relate to prior reports of reduced behavioral adaptation in dyslexia and may reveal a difference in brain functions that ultimately results in a specific reading impairment. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Genomic Analysis of Differentiation between Soil Types Reveals Candidate Genes for Local Adaptation in Arabidopsis lyrata

    PubMed Central

    Turner, Thomas L.; von Wettberg, Eric J.; Nuzhdin, Sergey V.

    2008-01-01

    Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low Ca∶Mg ratio in A. lyrata. PMID:18784841

  11. Proteomic Profiling Reveals Adaptive Responses to Surgical Myocardial Ischemia Reperfusion in Hibernating Arctic Ground Squirrels Compared to Rats

    PubMed Central

    Quinones, Quintin J.; Zhang, Zhiquan; Ma, Qing; Smith, Michael P.; Soderblom, Erik; Moseley, M. Arthur; Bain, James; Newgard, Christopher B.; Muehlbauer, Michael J.; Hirschey, Matthew; Drew, Kelly L.; Barnes, Brian M.; Podgoreanu, Mihai V.

    2016-01-01

    Background Hibernation is an adaptation to extreme environments known to provide organ protection against ischemia-reperfusion (I/R) injury. An unbiased systems approach was utilized to investigate hibernation-induced changes characteristic of the hibernator cardioprotective phenotype, by comparing the myocardial proteome of winter hibernating arctic ground squirrels (HIB AGS), summer active (SA) AGS, and rats subjected to I/R, and further correlating with targeted metabolic changes. Methods In a well-defined rodent model of I/R by deep hypothermic circulatory arrest followed by 3h or 24h of reperfusion or sham, myocardial protein abundance in AGS (HIB, SA) and rats (n=4-5/group) was quantified by label-free proteomics (n=4-5/group), and correlated with metabolic changes. Results Compared to rats, HIB AGS displayed markedly reduced plasma levels of Troponin I, myocardial apoptosis, and left ventricular contractile dysfunction. Of the 1,320 rat and 1,478 AGS proteins identified, 545 were differentially expressed between HIB AGS and rat hearts (47% upregulated, 53% downregulated). Gene ontology analysis revealed downregulation in HIB AGS hearts of most proteins involved in mitochondrial energy transduction, including electron transport chain complexes, acetyl CoA biosynthesis, Krebs cycle, glycolysis and ketogenesis. Conversely, fatty acid oxidation enzymes and Sirtuin-3 were upregulated in HIB AGS, with preserved peroxisome proliferator activated receptor-α activity and reduced tissue levels of acylcarnitines and ceramides following I/R. Conclusions Natural cardioprotective adaptations in hibernators involve extensive metabolic remodeling, featuring increased expression of fatty acid metabolic proteins and reduced levels of toxic lipid metabolites. Robust upregulation of Sirtuin-3 suggests that post-translational modifications may underlie organ protection in hibernating mammals. PMID:27187119

  12. Symmetry Breaking Analysis of Prism Adaptation's Latent Aftereffect

    ERIC Educational Resources Information Center

    Frank, Till D.; Blau, Julia J. C.; Turvey, Michael T.

    2012-01-01

    The effect of prism adaptation on movement is typically reduced when the movement at test (prisms off) differs on some dimension from the movement at training (prisms on). Some adaptation is latent, however, and only revealed through further testing in which the movement at training is fully reinstated. Applying a nonlinear attractor dynamic model…

  13. Complex Adaptive Schools: Educational Leadership and School Change

    ERIC Educational Resources Information Center

    Kershner, Brad; McQuillan, Patrick

    2016-01-01

    This paper utilizes the theoretical framework of complexity theory to compare and contrast leadership and educational change in two urban schools. Drawing on the notion of a complex adaptive system--an interdependent network of interacting elements that learns and evolves in adapting to an ever-shifting context--our case studies seek to reveal the…

  14. Psychosocial Adaptation to Chronic Illness and Disability: A Virtue Based Model.

    PubMed

    Kim, Jeong Han; McMahon, Brian T; Hawley, Carolyn; Brickham, Dana; Gonzalez, Rene; Lee, Dong-Hun

    2016-03-01

    Psychosocial adaptation to chronic illness and disability (CID) is an area of study where a positive psychology perspective, especially the study of virtues and character strengths, can be implemented within the rehabilitation framework. A carefully developed theory to guide future interdisciplinary research is now timely. A traditional literature review between philosophy and rehabilitation psychology was conducted in order to develop a virtue-based psychosocial adaptation theory, merging important perspectives from the fields of rehabilitation and positive psychology. The virtue-based psychosocial adaptation model (V-PAM) to CID is proposed in the present study. The model involves five qualities or constructs: courage, practical wisdom, commitment to action, integrity and emotional transcendence. Each of these components of virtue contributes to an understanding of psychosocial adaptation. The present study addresses the implications and applications of V-PAM that will advance this understanding.

  15. Pattern Adaptation and Normalization Reweighting.

    PubMed

    Westrick, Zachary M; Heeger, David J; Landy, Michael S

    2016-09-21

    Adaptation to an oriented stimulus changes both the gain and preferred orientation of neural responses in V1. Neurons tuned near the adapted orientation are suppressed, and their preferred orientations shift away from the adapter. We propose a model in which weights of divisive normalization are dynamically adjusted to homeostatically maintain response products between pairs of neurons. We demonstrate that this adjustment can be performed by a very simple learning rule. Simulations of this model closely match existing data from visual adaptation experiments. We consider several alternative models, including variants based on homeostatic maintenance of response correlations or covariance, as well as feedforward gain-control models with multiple layers, and we demonstrate that homeostatic maintenance of response products provides the best account of the physiological data. Adaptation is a phenomenon throughout the nervous system in which neural tuning properties change in response to changes in environmental statistics. We developed a model of adaptation that combines normalization (in which a neuron's gain is reduced by the summed responses of its neighbors) and Hebbian learning (in which synaptic strength, in this case divisive normalization, is increased by correlated firing). The model is shown to account for several properties of adaptation in primary visual cortex in response to changes in the statistics of contour orientation. Copyright © 2016 the authors 0270-6474/16/369805-12$15.00/0.

  16. Mechanisms of Host Receptor Adaptation by Severe Acute Respiratory Syndrome Coronavirus

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wu, Kailang; Peng, Guiqing; Wilken, Matthew

    The severe acute respiratory syndrome coronavirus (SARS-CoV) from palm civets has twice evolved the capacity to infect humans by gaining binding affinity for human receptor angiotensin-converting enzyme 2 (ACE2). Numerous mutations have been identified in the receptor-binding domain (RBD) of different SARS-CoV strains isolated from humans or civets. Why these mutations were naturally selected or how SARS-CoV evolved to adapt to different host receptors has been poorly understood, presenting evolutionary and epidemic conundrums. In this study, we investigated the impact of these mutations on receptor recognition, an important determinant of SARS-CoV infection and pathogenesis. Using a combination of biochemical, functional,more » and crystallographic approaches, we elucidated the molecular and structural mechanisms of each of these naturally selected RBD mutations. These mutations either strengthen favorable interactions or reduce unfavorable interactions with two virus-binding hot spots on ACE2, and by doing so, they enhance viral interactions with either human (hACE2) or civet (cACE2) ACE2. Therefore, these mutations were viral adaptations to either hACE2 or cACE2. To corroborate the above analysis, we designed and characterized two optimized RBDs. The human-optimized RBD contains all of the hACE2-adapted residues (Phe-442, Phe-472, Asn-479, Asp-480, and Thr-487) and possesses exceptionally high affinity for hACE2 but relative low affinity for cACE2. The civet-optimized RBD contains all of the cACE2-adapted residues (Tyr-442, Pro-472, Arg-479, Gly-480, and Thr-487) and possesses exceptionally high affinity for cACE2 and also substantial affinity for hACE2. These results not only illustrate the detailed mechanisms of host receptor adaptation by SARS-CoV but also provide a molecular and structural basis for tracking future SARS-CoV evolution in animals.« less

  17. Mechanisms of Host Receptor Adaptation by Severe Acute Respiratory Syndrome Coronavirus*

    PubMed Central

    Wu, Kailang; Peng, Guiqing; Wilken, Matthew; Geraghty, Robert J.; Li, Fang

    2012-01-01

    The severe acute respiratory syndrome coronavirus (SARS-CoV) from palm civets has twice evolved the capacity to infect humans by gaining binding affinity for human receptor angiotensin-converting enzyme 2 (ACE2). Numerous mutations have been identified in the receptor-binding domain (RBD) of different SARS-CoV strains isolated from humans or civets. Why these mutations were naturally selected or how SARS-CoV evolved to adapt to different host receptors has been poorly understood, presenting evolutionary and epidemic conundrums. In this study, we investigated the impact of these mutations on receptor recognition, an important determinant of SARS-CoV infection and pathogenesis. Using a combination of biochemical, functional, and crystallographic approaches, we elucidated the molecular and structural mechanisms of each of these naturally selected RBD mutations. These mutations either strengthen favorable interactions or reduce unfavorable interactions with two virus-binding hot spots on ACE2, and by doing so, they enhance viral interactions with either human (hACE2) or civet (cACE2) ACE2. Therefore, these mutations were viral adaptations to either hACE2 or cACE2. To corroborate the above analysis, we designed and characterized two optimized RBDs. The human-optimized RBD contains all of the hACE2-adapted residues (Phe-442, Phe-472, Asn-479, Asp-480, and Thr-487) and possesses exceptionally high affinity for hACE2 but relative low affinity for cACE2. The civet-optimized RBD contains all of the cACE2-adapted residues (Tyr-442, Pro-472, Arg-479, Gly-480, and Thr-487) and possesses exceptionally high affinity for cACE2 and also substantial affinity for hACE2. These results not only illustrate the detailed mechanisms of host receptor adaptation by SARS-CoV but also provide a molecular and structural basis for tracking future SARS-CoV evolution in animals. PMID:22291007

  18. RIACS Workshop on the Verification and Validation of Autonomous and Adaptive Systems

    NASA Technical Reports Server (NTRS)

    Pecheur, Charles; Visser, Willem; Simmons, Reid

    2001-01-01

    The long-term future of space exploration at NASA is dependent on the full exploitation of autonomous and adaptive systems: careful monitoring of missions from earth, as is the norm now, will be infeasible due to the sheer number of proposed missions and the communication lag for deep-space missions. Mission managers are however worried about the reliability of these more intelligent systems. The main focus of the workshop was to address these worries and hence we invited NASA engineers working on autonomous and adaptive systems and researchers interested in the verification and validation (V&V) of software systems. The dual purpose of the meeting was to: (1) make NASA engineers aware of the V&V techniques they could be using; and (2) make the V&V community aware of the complexity of the systems NASA is developing.

  19. Genomic characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation.

    PubMed

    Maeno, Shintaro; Tanizawa, Yasuhiro; Kanesaki, Yu; Kubota, Eri; Kumar, Himanshu; Dicks, Leon; Salminen, Seppo; Nakagawa, Junichi; Arita, Masanori; Endo, Akihito

    2016-12-01

    Lactobacillus kunkeei is classified as a sole obligate fructophilic lactic acid bacterium that is found in fructose-rich niches, including the guts of honeybees. The species is differentiated from other lactobacilli based on its poor growth with glucose, enhanced growth in the presence of oxygen and other electron acceptors, and production of high concentrations of acetate from the metabolism of glucose. These characteristics are similar to phylogenetically distant Fructobacillus spp. In the present study, the genomic structure of L. kunkeei was characterized by using 16 different strains, and it had significantly less genes and smaller genomes when compared with other lactobacilli. Functional gene classification revealed that L. kunkeei had lost genes specifically involved in carbohydrate transport and metabolism. The species also lacked most of the genes for respiration, although growth was enhanced in the presence of oxygen. The adhE gene of L. kunkeei, encoding a bifunctional alcohol dehydrogenase (ADH)/aldehyde dehydrogenase (ALDH) protein, lacked the part encoding the ADH domain, which is reported here for the first time in lactic acid bacteria. The deletion resulted in the lack of ADH activity, implying a requirement for electron acceptors in glucose assimilation. These results clearly indicated that L. kunkeei had undergone a specific reductive evolution in order to adapt to fructose-rich environments. The reduction characteristics were similar to those of Fructobacillus spp., but distinct from other lactobacilli with small genomes, such as Lactobacillus gasseri and Lactobacillus vaginalis. Fructose-richness thus induced an environment-specific gene reduction in phylogenetically distant microorganisms. Copyright © 2016 Elsevier GmbH. All rights reserved.

  20. Assessment of noise reduction potential and image quality improvement of a new generation adaptive statistical iterative reconstruction (ASIR-V) in chest CT.

    PubMed

    Tang, Hui; Yu, Nan; Jia, Yongjun; Yu, Yong; Duan, Haifeng; Han, Dong; Ma, Guangming; Ren, Chenglong; He, Taiping

    2018-01-01

    To evaluate the image quality improvement and noise reduction in routine dose, non-enhanced chest CT imaging by using a new generation adaptive statistical iterative reconstruction (ASIR-V) in comparison with ASIR algorithm. 30 patients who underwent routine dose, non-enhanced chest CT using GE Discovery CT750HU (GE Healthcare, Waukesha, WI) were included. The scan parameters included tube voltage of 120 kVp, automatic tube current modulation to obtain a noise index of 14HU, rotation speed of 0.6 s, pitch of 1.375:1 and slice thickness of 5 mm. After scanning, all scans were reconstructed with the recommended level of 40%ASIR for comparison purpose and different percentages of ASIR-V from 10% to 100% in a 10% increment. The CT attenuation values and SD of the subcutaneous fat, back muscle and descending aorta were measured at the level of tracheal carina of all reconstructed images. The signal-to-noise ratio (SNR) was calculated with SD representing image noise. The subjective image quality was independently evaluated by two experienced radiologists. For all ASIR-V images, the objective image noise (SD) of fat, muscle and aorta decreased and SNR increased along with increasing ASIR-V percentage. The SD of 30% ASIR-V to 100% ASIR-V was significantly lower than that of 40% ASIR (p < 0.05). In terms of subjective image evaluation, all ASIR-V reconstructions had good diagnostic acceptability. However, the 50% ASIR-V to 70% ASIR-V series showed significantly superior visibility of small structures when compared with the 40% ASIR and ASIR-V of other percentages (p < 0.05), and 60% ASIR-V was the best series of all ASIR-V images, with a highest subjective image quality. The image sharpness was significantly decreased in images reconstructed by 80% ASIR-V and higher. In routine dose, non-enhanced chest CT, ASIR-V shows greater potential in reducing image noise and artefacts and maintaining image sharpness when compared to the recommended level of 40%ASIR algorithm

  1. Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs

    PubMed Central

    Li, Hu; Leavengood, John M.; Chapman, Eric G.; Burkhardt, Daniel; Song, Fan; Jiang, Pei; Liu, Jinpeng; Cai, Wanzhi

    2017-01-01

    Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character state reconstruction and divergence time estimation suggest that the success of true bugs (Heteroptera) is probably due to angiosperm coevolution, but key adaptive innovations (e.g. prognathous mouthpart, predatory behaviour, and haemelytron) facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats. PMID:28878063

  2. Neural Specificity for Grammatical Operations is Revealed by Content-Independent fMR Adaptation

    PubMed Central

    Shapiro, Kevin A.; Moo, Lauren R.; Caramazza, Alfonso

    2012-01-01

    The ability to generate novel sentences depends on cognitive operations that specify the syntactic function of nouns, verbs, and other words retrieved from the mental lexicon. Although neuropsychological studies suggest that such operations rely on neural circuits distinct from those encoding word form and meaning, it has not been possible to characterize this distinction definitively with neuroimaging. We used functional magnetic resonance imaging (fMRI) to show that a brain area engaged in a given grammatical operation can be identified uniquely by a monotonic decrease in activation as that operation is repeated. We applied this methodology to identify areas involved selectively in the operation of inflection of nouns or verbs. By contrast, areas involved in processing word meaning do not show this monotonic adaptation across stimuli. These results are the first to demonstrate adaptation in the fMR signal evoked not by specific stimuli, but by well-defined cognitive linguistic operations. PMID:22347206

  3. Physicochemical properties and interfacial adaptation of root canal sealers.

    PubMed

    Cañadas, Piedad S; Berástegui, Ester; Gaton-Hernández, Patrícia; Silva, Léa A B; Leite, Giselle A; Silva, Roberto S

    2014-01-01

    This study compared the physicochemical properties and interfacial adaptation to canal walls of Endo-CPM-Sealer, Sealapex and Activ GP with the well-established AH Plus sealer. The following analyses were performed: radiopacity, pH variation and solubility using samples of each material and scanning electron microscopy of root-filled bovine incisors to evaluate the interfacial adaptation. Data were analyzed by the parametric and no-parametric tests (α=0.05). All materials were in accordance with the ANSI/ADA requirements for radiopacity. Endo-CPM-Sealer presented the lowest radiopacity values and AH Plus was the most radiopaque sealer (p=0.0001). Except for ActiV GP, which was acidic, all other sealers had basic chemical nature and released hydroxyl ions. Regarding solubility, all materials met the ANSI/ADA recommendations, with no statistically significant difference between the sealers (p=0.0834). AH Plus presented the best adaptation to canal walls in the middle (p=0.0023) and apical (p=0.0012) thirds, while the sealers Activ GP and Endo-CPM-Sealer had poor adaptation to the canal walls. All sealers, except for ActiV GP, were alkaline and all of them fulfilled the ANSI/ADA requirements for radiopacity and solubility. Regarding the interfacial adaptation, AH Plus was superior to the others considering the adaptation to the bovine root canal walls.

  4. Influence of incorrect application of a water-based adhesive system on the marginal adaptation of Class V restorations.

    PubMed

    Peschke, A; Blunck, U; Roulet, J F

    2000-10-01

    To determine the influence of incorrectly performed steps during the application of the water-based adhesive system OptiBond FL on the marginal adaptation of Class V composite restorations. In 96 extracted human teeth Class V cavities were prepared. Half of the margin length was situated in dentin. The teeth were randomly divided into 12 groups. The cavities were filled with Prodigy resin-based composite in combination with OptiBond FL according to the manufacturer's instructions (Group O) and including several incorrect application steps: Group A: prolonged etching (60 s); Group B: no etching of dentin; Group C: excessive drying after etching; Group D: short rewetting after excessive drying; Group E: air drying and rewetting; Group F: blot drying; Group G: saliva contamination; Group H: application of primer and immediate drying; group I: application of only primer; group J: application of only adhesive; Group K: no light curing of the adhesive before the application of composite. After thermocycling, replicas were taken and the margins were quantitatively analyzed in the SEM. Statistical analysis of the results was performed using non-parametric procedures. With exception of the "rewetting groups" (D and E) and the group with saliva contamination (G), all other application procedures showed a significantly higher amount of marginal openings in dentin compared to the control group (O). Margin quality in enamel was only affected when the primer was not applied.

  5. Automated tube voltage adaptation in head and neck computed tomography between 120 and 100 kV: effects on image quality and radiation dose.

    PubMed

    May, Matthias S; Kramer, Manuel R; Eller, Achim; Wuest, Wolfgang; Scharf, Michael; Brand, Michael; Saake, Marc; Schmidt, Bernhard; Uder, Michael; Lell, Michael M

    2014-09-01

    Low tube voltage allows for computed tomography (CT) imaging with increased iodine contrast at reduced radiation dose. We sought to evaluate the image quality and potential dose reduction using a combination of attenuation based tube current modulation (TCM) and automated tube voltage adaptation (TVA) between 100 and 120 kV in CT of the head and neck. One hundred thirty consecutive patients with indication for head and neck CT were examined with a 128-slice system capable of TCM and TVA. Reference protocol was set at 120 kV. Tube voltage was reduced to 100 kV whenever proposed by automated analysis of the localizer. An additional small scan aligned to the jaw was performed at a fixed 120 kV setting. Image quality was assessed by two radiologists on a standardized Likert-scale and measurements of signal- (SNR) and contrast-to-noise ratio (CNR). Radiation dose was assessed as CTDIvol. Diagnostic image quality was excellent in both groups and did not differ significantly (p = 0.34). Image noise in the 100 kV data was increased and SNR decreased (17.8/9.6) in the jugular veins and the sternocleidomastoid muscle when compared to 120 kV (SNR 24.4/10.3), but not in fatty tissue and air. However, CNR did not differ statistically significant between 100 (23.5/14.4/9.4) and 120 kV data (24.2/15.3/8.6) while radiation dose was decreased by 7-8%. TVA between 100 and 120 kV in combination with TCM led to a radiation dose reduction compared to TCM alone, while keeping CNR constant though maintaining diagnostic image quality.

  6. Reflections on the Adaptive Designs Accelerating Promising Trials Into Treatments (ADAPT-IT) Process—Findings from a Qualitative Study

    PubMed Central

    Guetterman, Timothy C.; Fetters, Michael D.; Legocki, Laurie J.; Mawocha, Samkeliso; Barsan, William G.; Lewis, Roger J.; Berry, Donald A.; Meurer, William J.

    2015-01-01

    Context The context for this study was the Adaptive Designs Advancing Promising Treatments Into Trials (ADAPT-IT) project, which aimed to incorporate flexible adaptive designs into pivotal clinical trials and to conduct an assessment of the trial development process. Little research provides guidance to academic institutions in planning adaptive trials. Objectives The purpose of this qualitative study was to explore the perspectives and experiences of stakeholders as they reflected back about the interactive ADAPT-IT adaptive design development process, and to understand their perspectives regarding lessons learned about the design of the trials and trial development. Materials and methods We conducted semi-structured interviews with ten key stakeholders and observations of the process. We employed qualitative thematic text data analysis to reduce the data into themes about the ADAPT-IT project and adaptive clinical trials. Results The qualitative analysis revealed four themes: education of the project participants, how the process evolved with participant feedback, procedures that could enhance the development of other trials, and education of the broader research community. Discussion and conclusions While participants became more likely to consider flexible adaptive designs, additional education is needed to both understand the adaptive methodology and articulate it when planning trials. PMID:26622163

  7. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

    USDA-ARS?s Scientific Manuscript database

    By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern te...

  8. Evaluation of delivered dose for a clinical daily adaptive plan selection strategy for bladder cancer radiotherapy.

    PubMed

    Lutkenhaus, Lotte J; Visser, Jorrit; de Jong, Rianne; Hulshof, Maarten C C M; Bel, Arjan

    2015-07-01

    To account for variable bladder size during bladder cancer radiotherapy, a daily plan selection strategy was implemented. The aim of this study was to calculate the actually delivered dose using an adaptive strategy, compared to a non-adaptive approach. Ten patients were treated to the bladder and lymph nodes with an adaptive full bladder strategy. Interpolated delineations of bladder and tumor on a full and empty bladder CT scan resulted in five PTVs for which VMAT plans were created. Daily cone beam CT (CBCT) scans were used for plan selection. Bowel, rectum and target volumes were delineated on these CBCTs, and delivered dose for these was calculated using both the adaptive plan, and a non-adaptive plan. Target coverage for lymph nodes improved using an adaptive strategy. The full bladder strategy spared the healthy part of the bladder from a high dose. Average bowel cavity V30Gy and V40Gy significantly reduced with 60 and 69ml, respectively (p<0.01). Other parameters for bowel and rectum remained unchanged. Daily plan selection compared to a non-adaptive strategy yielded similar bladder coverage and improved coverage for lymph nodes, with a significant reduction in bowel cavity V30Gy and V40Gy only, while other sparing was limited. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  9. 16S metagenomic analysis reveals adaptability of a mixed-PAH-degrading consortium isolated from crude oil-contaminated seawater to changing environmental conditions.

    PubMed

    Muangchinda, Chanokporn; Rungsihiranrut, Adisan; Prombutara, Pinidphon; Soonglerdsongpha, Suwat; Pinyakong, Onruthai

    2018-05-29

    A bacterial consortium, named SWO, was enriched from crude oil-contaminated seawater from Phrao Bay in Rayong Province, Thailand, after a large oil spill in 2013. The bacterial consortium degraded a polycyclic aromatic hydrocarbon (PAH) mixture consisting of phenanthrene, anthracene, fluoranthene, and pyrene (50 mg L -1 each) by approximately 73%, 69%, 52%, and 48%, respectively, within 21 days. This consortium exhibited excellent adaptation to a wide range of environmental conditions. It could degrade a mixture of four PAHs under a range of pH values (4.0-9.0), temperatures (25 °C-37 °C), and salinities (0-10 g L -1 with NaCl). In addition, this consortium degraded 20-30% of benzo[a]pyrene and perylene (10 mg L -1 each), high molecular weight PAHs, in the presence of other PAHs within 35 days, and degraded 40% of 2% (v/v) crude oil within 20 days. The 16S rRNA gene amplicon sequencing analysis demonstrated that Pseudomonas and Methylophaga were the dominant genera of consortium SWO in almost all treatments, while Pseudidiomarina, Thalassospira and Alcanivorax were predominant under higher salt concentrations. Moreover, Pseudomonas and Alcanivorax were dominant in the crude oil-degradation treatment. Our results suggest that the consortium SWO maintained its biodegradation ability by altering the bacterial community profile upon encountering changes in the environmental conditions. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. The adaptive pattern of the auditory N1 peak revealed by standardized low-resolution brain electromagnetic tomography.

    PubMed

    Zhang, Fawen; Deshpande, Aniruddha; Benson, Chelsea; Smith, Mathew; Eliassen, James; Fu, Qian-Jie

    2011-07-11

    The N1 peak in the late auditory evoked potential (LAEP) decreases in amplitude following stimulus repetition, displaying an adaptive pattern. The present study explored the functional neural substrates that may underlie the N1 adaptive pattern using standardized Low Resolution Electromagnetic Tomography (sLORETA). Fourteen young normal hearing (NH) listeners participated in the study. Tone bursts (80 dB SPL) were binaurally presented via insert earphones in trains of 10; the inter-stimulus interval was 0.7s and the inter-train interval was 15s. Current source density analysis was performed for the N1 evoked by the 1st, 2nd and 10th stimuli (S(1), S(2) and S(10)) at 3 different timeframes that corresponded to the latency ranges of the N1 waveform subcomponents (70-100, 100-130 and 130-160 ms). The data showed that S(1) activated broad regions in different cortical lobes and the activation was much smaller for S(2) and S(10). Response differences in the LAEP waveform and sLORETA were observed between S(1) and S(2), but not between the S(2) and S(10). The sLORETA comparison map between S(1) and S(2) responses showed that the activation was located in the parietal lobe for the 70-100 ms timeframe, the frontal and limbic lobes for the 100-130 ms timeframe, and the frontal lobe for the 130-160 ms timeframe. These sLORETA comparison results suggest a parieto-frontal network that might help to sensitize the brain to novel stimuli by filtering out repetitive and irrelevant stimuli. This study demonstrates that sLORETA may be useful for identifying generators of scalp-recorded event related potentials and for examining the physiological features of these generators. This technique could be especially useful for cortical source localization in individuals who cannot be examined with functional magnetic resonance imaging or magnetoencephalography (e.g., cochlear implant users). Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Adaptable interaction between aquaporin-1 and band 3 reveals a potential role of water channel in blood CO2 transport.

    PubMed

    Hsu, Kate; Lee, Ting-Ying; Periasamy, Ammasi; Kao, Fu-Jen; Li, Li-Tzu; Lin, Chuang-Yu; Lin, Hui-Ju; Lin, Marie

    2017-10-01

    Human CO 2 respiration requires rapid conversion between CO 2 and HCO 3 - Carbonic anhydrase II facilitates this reversible reaction inside red blood cells, and band 3 [anion exchanger 1 (AE1)] provides a passage for HCO 3 - flux across the cell membrane. These 2 proteins are core components of the CO 2 transport metabolon. Intracellular H 2 O is necessary for CO 2 /HCO 3 - conversion. However, abundantly expressed aquaporin 1 (AQP1) in erythrocytes is thought not to be part of band 3 complexes or the CO 2 transport metabolon. To solve this conundrum, we used Förster resonance energy transfer (FRET) measured by fluorescence lifetime imaging (FLIM-FRET) and identified interaction between aquaporin-1 and band 3 at a distance of 8 nm, within the range of dipole-dipole interaction. Notably, their interaction was adaptable to membrane tonicity changes. This suggests that the function of AQP1 in tonicity response could be coupled or correlated to its function in band 3-mediated CO 2 /HCO 3 - exchange. By demonstrating AQP1 as a mobile component of the CO 2 transport metabolon, our results uncover a potential role of water channel in blood CO 2 transport and respiration.-Hsu, K., Lee, T.-Y., Periasamy, A., Kao, F.-J., Li, L.-T., Lin, C.-Y., Lin, H.-J., Lin, M. Adaptable interaction between aquaporin-1 and band 3 reveals a potential role of water channel in blood CO 2 transport. © FASEB.

  12. Chimeras of Bet v 1 and Api g 1 reveal heterogeneous IgE responses in patients with birch pollen allergy

    PubMed Central

    Gepp, Barbara; Lengger, Nina; Bublin, Merima; Hemmer, Wolfgang; Breiteneder, Heimo; Radauer, Christian

    2014-01-01

    Background Characterization of IgE-binding epitopes of allergens and determination of their patient-specific relevance is crucial for the diagnosis and treatment of allergy. Objective We sought to assess the contribution of specific surface areas of the major birch pollen allergen Bet v 1.0101 to binding IgE of individual patients. Methods Four distinct areas of Bet v 1 representing in total 81% of its surface were grafted onto the scaffold of its homolog, Api g 1.0101, to yield the chimeras Api-Bet-1 to Api-Bet-4. The chimeras were expressed in Escherichia coli and purified. IgE binding of 64 sera from Bet v 1–sensitized subjects with birch pollen allergy was determined by using direct ELISA. Specificity was assessed by means of inhibition ELISA. Results rApi g 1.0101, Api-Bet-1, Api-Bet-2, Api-Bet-3, and Api-Bet-4 bound IgE from 44%, 89%, 80%, 78%, and 48% of the patients, respectively. By comparing the amount of IgE binding to the chimeras and to rApi g 1.0101, 81%, 70%, 75%, and 45% of the patients showed significantly enhanced IgE binding to Api-Bet-1, Api-Bet-2, Api-Bet-3, and Api-Bet-4, respectively. The minority (8%) of the sera revealed enhanced IgE binding exclusively to a single chimera, whereas 31% showed increased IgE binding to all 4 chimeras compared with rApi g 1.0101. The chimeras inhibited up to 70% of IgE binding to rBet v 1.0101, confirming the specific IgE recognition of the grafted regions. Conclusion The Bet v 1–specific IgE response is polyclonal, and epitopes are spread across the entire Bet v 1 surface. Furthermore, the IgE recognition profile of Bet v 1 is highly patient specific. PMID:24529686

  13. Chimeras of Bet v 1 and Api g 1 reveal heterogeneous IgE responses in patients with birch pollen allergy.

    PubMed

    Gepp, Barbara; Lengger, Nina; Bublin, Merima; Hemmer, Wolfgang; Breiteneder, Heimo; Radauer, Christian

    2014-07-01

    Characterization of IgE-binding epitopes of allergens and determination of their patient-specific relevance is crucial for the diagnosis and treatment of allergy. We sought to assess the contribution of specific surface areas of the major birch pollen allergen Bet v 1.0101 to binding IgE of individual patients. Four distinct areas of Bet v 1 representing in total 81% of its surface were grafted onto the scaffold of its homolog, Api g 1.0101, to yield the chimeras Api-Bet-1 to Api-Bet-4. The chimeras were expressed in Escherichia coli and purified. IgE binding of 64 sera from Bet v 1-sensitized subjects with birch pollen allergy was determined by using direct ELISA. Specificity was assessed by means of inhibition ELISA. rApi g 1.0101, Api-Bet-1, Api-Bet-2, Api-Bet-3, and Api-Bet-4 bound IgE from 44%, 89%, 80%, 78%, and 48% of the patients, respectively. By comparing the amount of IgE binding to the chimeras and to rApi g 1.0101, 81%, 70%, 75%, and 45% of the patients showed significantly enhanced IgE binding to Api-Bet-1, Api-Bet-2, Api-Bet-3, and Api-Bet-4, respectively. The minority (8%) of the sera revealed enhanced IgE binding exclusively to a single chimera, whereas 31% showed increased IgE binding to all 4 chimeras compared with rApi g 1.0101. The chimeras inhibited up to 70% of IgE binding to rBet v 1.0101, confirming the specific IgE recognition of the grafted regions. The Bet v 1-specific IgE response is polyclonal, and epitopes are spread across the entire Bet v 1 surface. Furthermore, the IgE recognition profile of Bet v 1 is highly patient specific. Copyright © 2014 The Authors. Published by Mosby, Inc. All rights reserved.

  14. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation

    PubMed Central

    Hori, Koichi; Maruyama, Fumito; Fujisawa, Takatomo; Togashi, Tomoaki; Yamamoto, Nozomi; Seo, Mitsunori; Sato, Syusei; Yamada, Takuji; Mori, Hiroshi; Tajima, Naoyuki; Moriyama, Takashi; Ikeuchi, Masahiko; Watanabe, Mai; Wada, Hajime; Kobayashi, Koichi; Saito, Masakazu; Masuda, Tatsuru; Sasaki-Sekimoto, Yuko; Mashiguchi, Kiyoshi; Awai, Koichiro; Shimojima, Mie; Masuda, Shinji; Iwai, Masako; Nobusawa, Takashi; Narise, Takafumi; Kondo, Satoshi; Saito, Hikaru; Sato, Ryoichi; Murakawa, Masato; Ihara, Yuta; Oshima-Yamada, Yui; Ohtaka, Kinuka; Satoh, Masanori; Sonobe, Kohei; Ishii, Midori; Ohtani, Ryosuke; Kanamori-Sato, Miyu; Honoki, Rina; Miyazaki, Daichi; Mochizuki, Hitoshi; Umetsu, Jumpei; Higashi, Kouichi; Shibata, Daisuke; Kamiya, Yuji; Sato, Naoki; Nakamura, Yasukazu; Tabata, Satoshi; Ida, Shigeru; Kurokawa, Ken; Ohta, Hiroyuki

    2014-01-01

    The colonization of land by plants was a key event in the evolution of life. Here we report the draft genome sequence of the filamentous terrestrial alga Klebsormidium flaccidum (Division Charophyta, Order Klebsormidiales) to elucidate the early transition step from aquatic algae to land plants. Comparison of the genome sequence with that of other algae and land plants demonstrate that K. flaccidum acquired many genes specific to land plants. We demonstrate that K. flaccidum indeed produces several plant hormones and homologues of some of the signalling intermediates required for hormone actions in higher plants. The K. flaccidum genome also encodes a primitive system to protect against the harmful effects of high-intensity light. The presence of these plant-related systems in K. flaccidum suggests that, during evolution, this alga acquired the fundamental machinery required for adaptation to terrestrial environments. PMID:24865297

  15. Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats

    PubMed Central

    Chen, Ling-Yun; Zhao, Shu-Ying; Wang, Qing-Feng; Moody, Michael L.

    2015-01-01

    Adaptation to aquatic habitats is a formidable challenge for terrestrial angiosperms that has long intrigued scientists. As part of a suite of work to explore the molecular mechanism of adaptation to aquatic habitats, we here sequenced the transcriptome of the submerged aquatic plant Ranunculus bungei, and two terrestrial relatives R. cantoniensis and R. brotherusii, followed by comparative evolutionary analyses to determine candidate genes for adaption to aquatic habitats. We obtained 126,037, 140,218 and 114,753 contigs for R. bungei, R. cantoniensis and R. brotherusii respectively. Bidirectional Best Hit method and OrthoMCL method identified 11,362 and 8,174 1:1:1 orthologous genes (one ortholog is represented in each of the three species) respectively. Non-synonymous/synonymous (dN/dS) analyses were performed with a maximum likelihood method and an approximate method for the three species-pairs. In total, 14 genes of R. bungei potentially involved in the adaptive transition from terrestrial to aquatic habitats were identified. Some of the homologs to these genes in model plants are involved in vacuole protein formation, regulating ‘water transport process’ and ‘microtubule cytoskeleton organization’. Our study opens the door to understand the molecular mechanism of plant adaptation from terrestrial to aquatic habitats. PMID:25993393

  16. Inactivation of Heat Adapted and Chlorine Adapted Listeria Monocytogenes ATCC 7644 on Tomatoes Using Sodium Dodecyl Sulphate, Levulinic Acid and Sodium Hypochlorite Solution.

    PubMed

    Ijabadeniyi, Oluwatosin Ademola; Mnyandu, Elizabeth

    2017-04-13

    The effectiveness of sodium dodecyl sulphate (SDS), sodium hypochlorite solution and levulinic acid in reducing the survival of heat adapted and chlorine adapted Listeria monocytogenes ATCC 7644 was evaluated. The results against heat adapted L. monocytognes revealed that sodium hypochlorite solution was the least effective, achieving log reduction of 2.75, 2.94 and 3.97 log colony forming unit (CFU)/mL for 1, 3 and 5 minutes, respectively. SDS was able to achieve 8 log reduction for both heat adapted and chlorine adapted bacteria. When used against chlorine adapted L. monocytogenes sodium hypochlorite solution achieved log reduction of 2.76, 2.93 and 3.65 log CFU/mL for 1, 3 and 5 minutes, respectively. Using levulinic acid on heat adapted bacteria achieved log reduction of 3.07, 2.78 and 4.97 log CFU/mL for 1, 3, 5 minutes, respectively. On chlorine adapted bacteria levulinic acid achieved log reduction of 2.77, 3.07 and 5.21 log CFU/mL for 1, 3 and 5 minutes, respectively. Using a mixture of 0.05% SDS and 0.5% levulinic acid on heat adapted bacteria achieved log reduction of 3.13, 3.32 and 4.79 log CFU/mL for 1, 3 and 5 minutes while on chlorine adapted bacteria it achieved 3.20, 3.33 and 5.66 log CFU/mL, respectively. Increasing contact time also increased log reduction for both test pathogens. A storage period of up to 72 hours resulted in progressive log reduction for both test pathogens. Results also revealed that there was a significant difference (P≤0.05) among contact times, storage times and sanitizers. Findings from this study can be used to select suitable sanitizers and contact times for heat and chlorine adapted L. monocytogenes in the fresh produce industry.

  17. Development of Mission Adaptive Digital Composite Aerostructure Technologies (MADCAT)

    NASA Technical Reports Server (NTRS)

    Cheung, Kenneth; Cellucci, Daniel; Copplestone, Grace; Cramer, Nick; Fusco, Jesse; Jenett, Benjamin; Kim, Joseph; Mazhari, Alex; Trinh, Greenfield; Swei, Sean

    2017-01-01

    This paper reviews the development of the Mission Adaptive Digital Composite Aerostructures Technologies (MADCAT) v0 demonstrator aircraft, utilizing a novel aerostructure concept that combines advanced composite materials manufacturing and fabrication technologies with a discrete construction approach to achieve high stiffness-to-density ratio ultra-light aerostructures that provide versatility and adaptability. This revolutionary aerostructure concept has the potential to change how future air vehicles are designed, built, and flown, with dramatic reductions in weight and manufacturing complexity the number of types of structural components needed to build air vehicles while enabling new mission objectives. We utilize the innovative digital composite materials and discrete construction technologies to demonstrate the feasibility of the proposed aerostructure concept, by building and testing a scaled prototype UAV, MADCAT v0. This paper presents an overview of the design and development of the MADCAT v0 flight demonstrator.

  18. Verification and Validation Challenges for Adaptive Flight Control of Complex Autonomous Systems

    NASA Technical Reports Server (NTRS)

    Nguyen, Nhan T.

    2018-01-01

    Autonomy of aerospace systems requires the ability for flight control systems to be able to adapt to complex uncertain dynamic environment. In spite of the five decades of research in adaptive control, the fact still remains that currently no adaptive control system has ever been deployed on any safety-critical or human-rated production systems such as passenger transport aircraft. The problem lies in the difficulty with the certification of adaptive control systems since existing certification methods cannot readily be used for nonlinear adaptive control systems. Research to address the notion of metrics for adaptive control began to appear in the recent years. These metrics, if accepted, could pave a path towards certification that would potentially lead to the adoption of adaptive control as a future control technology for safety-critical and human-rated production systems. Development of certifiable adaptive control systems represents a major challenge to overcome. Adaptive control systems with learning algorithms will never become part of the future unless it can be proven that they are highly safe and reliable. Rigorous methods for adaptive control software verification and validation must therefore be developed to ensure that adaptive control system software failures will not occur, to verify that the adaptive control system functions as required, to eliminate unintended functionality, and to demonstrate that certification requirements imposed by regulatory bodies such as the Federal Aviation Administration (FAA) can be satisfied. This presentation will discuss some of the technical issues with adaptive flight control and related V&V challenges.

  19. Clonal expansion of environmentally-adapted Escherichia coli contributes to propagation of antibiotic resistance genes in beef cattle feedlots.

    PubMed

    Tymensen, Lisa; Zaheer, Rahat; Cook, Shaun R; Amoako, Kingsley K; Goji, Noriko; Read, Ron; Booker, Calvin W; Hannon, Sherry J; Neumann, Norman; McAllister, Tim A

    2018-05-11

    Livestock wastewater lagoons represent important environmental reservoirs of antibiotic resistance genes (ARGs), although factors contributing to their proliferation within these reservoirs remain poorly understood. Here, we characterized Escherichia coli from feedlot cattle feces and associated wastewater lagoons using CRISPR1 subtyping, and demonstrated that while generic E. coli were genetically diverse, populations were dominated by several 'feedlot-adapted' CRISPR types (CTs) that were widely distributed throughout the feedlot. Moreover, E. coli bearing beta-lactamase genes, which confer reduced susceptibility to third-generation cephalosporin's, predominantly belonged to these feedlot-adapted CTs. Remarkably, the genomic region containing the CRISPR1 allele was more frequently subject to genetic exchange among wastewater isolates compared to fecal isolates, implicating this region in environmental adaptation. This allele is proximal to the mutS-rpoS-nlpD region, which is involved in regulating recombination barriers and adaptive stress responses. There were no loss-of-function mutS or rpoS mutations or beneficial accessory genes present within the mutS-rpoS-nlpD region that would account for increased environmental fitness among feedlot-adapted isolates. However, comparative sequence analysis revealed that protein sequences within this region were conserved among most feedlot-adapted CTs, but not transient fecal CTs, and did not reflect phylogenetic relatedness, implying that adaptation to wastewater environments may be associated with genetic variation related to stress resistance. Collectively, our findings suggest adaptation of E. coli to feedlot environments may contribute to propagation of ARGs in wastewater lagoons. Copyright © 2018. Published by Elsevier B.V.

  20. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

    PubMed

    Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Heimberg, Alysha M; Jansen, Hans J; McCleary, Ryan J R; Kerkkamp, Harald M E; Vos, Rutger A; Guerreiro, Isabel; Calvete, Juan J; Wüster, Wolfgang; Woods, Anthony E; Logan, Jessica M; Harrison, Robert A; Castoe, Todd A; de Koning, A P Jason; Pollock, David D; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S; Ribeiro, José M C; Arntzen, Jan W; van den Thillart, Guido E E J M; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P; Spaink, Herman P; Duboule, Denis; McGlinn, Edwina; Kini, R Manjunatha; Richardson, Michael K

    2013-12-17

    Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection.

  1. Comparison of a brain-based adaptive system and a manual adaptable system for invoking automation.

    PubMed

    Bailey, Nathan R; Scerbo, Mark W; Freeman, Frederick G; Mikulka, Peter J; Scott, Lorissa A

    2006-01-01

    Two experiments are presented examining adaptive and adaptable methods for invoking automation. Empirical investigations of adaptive automation have focused on methods used to invoke automation or on automation-related performance implications. However, no research has addressed whether performance benefits associated with brain-based systems exceed those in which users have control over task allocations. Participants performed monitoring and resource management tasks as well as a tracking task that shifted between automatic and manual modes. In the first experiment, participants worked with an adaptive system that used their electroencephalographic signals to switch the tracking task between automatic and manual modes. Participants were also divided between high- and low-reliability conditions for the system-monitoring task as well as high- and low-complacency potential. For the second experiment, participants operated an adaptable system that gave them manual control over task allocations. Results indicated increased situation awareness (SA) of gauge instrument settings for individuals high in complacency potential using the adaptive system. In addition, participants who had control over automation performed more poorly on the resource management task and reported higher levels of workload. A comparison between systems also revealed enhanced SA of gauge instrument settings and decreased workload in the adaptive condition. The present results suggest that brain-based adaptive automation systems may enhance perceptual level SA while reducing mental workload relative to systems requiring user-initiated control. Potential applications include automated systems for which operator monitoring performance and high-workload conditions are of concern.

  2. CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis.

    PubMed

    Price, Valerie J; Huo, Wenwen; Sharifi, Ardalan; Palmer, Kelli L

    2016-01-01

    Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis. IMPORTANCE

  3. Methodology: Adapting the 'Training and Visit' System to Population Programmes.

    ERIC Educational Resources Information Center

    Asian-Pacific Population Programme News, 1985

    1985-01-01

    Provides suggestions for adapting the "training and visit" (T&V) system to population programs. Summarizes six main elements of a T&V system for population, health, and nutrition programs and describes four principles of agricultural extension programs. Implications of this process are also reviewed. (ML)

  4. Adaptive Control Allocation for Fault Tolerant Overactuated Autonomous Vehicles

    DTIC Science & Technology

    2007-11-01

    Tolerant Overactuated Autonomous Vehicles Casavola, A.; Garone, E. (2007) Adaptive Control Allocation for Fault Tolerant Overactuated Autonomous ...Adaptive Control Allocation for Fault Tolerant Overactuated Autonomous Vehicles 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...Tolerant Overactuated Autonomous Vehicles 3.2 - 2 RTO-MP-AVT-145 UNCLASSIFIED/UNLIMITED Control allocation problem (CAP) - Given a virtual input v(t

  5. Mistranslation: from adaptations to applications.

    PubMed

    Hoffman, Kyle S; O'Donoghue, Patrick; Brandl, Christopher J

    2017-11-01

    The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Conflict adaptation in patients diagnosed with schizophrenia.

    PubMed

    Abrahamse, Elger; Ruitenberg, Marit; Boddewyn, Sarah; Oreel, Edith; de Schryver, Maarten; Morrens, Manuel; van Dijck, Jean-Philippe

    2017-11-01

    Cognitive control impairments may contribute strongly to the overall cognitive deficits observed in patients diagnosed with schizophrenia. In the current study we explore a specific cognitive control function referred to as conflict adaptation. Previous studies on conflict adaptation in schizophrenia showed equivocal results, and, moreover, were plagued by confounded research designs. Here we assessed for the first time conflict adaptation in schizophrenia with a design that avoided the major confounds of feature integration and stimulus-response contingency learning. Sixteen patients diagnosed with schizophrenia and sixteen healthy, matched controls performed a vocal Stroop task to determine the congruency sequence effect - a marker of conflict adaptation. A reliable congruency sequence effect was observed for both healthy controls and patients diagnosed with schizophrenia. These findings indicate that schizophrenia is not necessarily accompanied by impaired conflict adaptation. As schizophrenia has been related to abnormal functioning in core conflict adaptation areas such as anterior cingulate and dorsolateral prefrontal cortex, further research is required to better understand the precise impact of such abnormal brain functioning at the behavioral level. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. ADAPTATION TO POVERTY IN LONG-RUN PANEL DATA

    PubMed Central

    Clark, Andrew E.; D’Ambrosio, Conchita; Ghislandi, Simone

    2017-01-01

    We consider the link between poverty and subjective well-being and focus in particular on potential adaptation to poverty. We use panel data on almost 54,000 individuals living in Germany from 1985 to 2012 to show, first, that life satisfaction falls with both the incidence and intensity of contemporaneous poverty. We then reveal that there is little evidence of adaptation within a poverty spell: poverty starts bad and stays bad in terms of subjective well-being. We cannot identify any cause of poverty entry that explains the overall lack of poverty adaptation. PMID:28690342

  8. Integrated 'omics analysis reveals new drug-induced mitochondrial perturbations in human hepatocytes.

    PubMed

    Wolters, Jarno E J; van Breda, Simone G J; Grossmann, Jonas; Fortes, Claudia; Caiment, Florian; Kleinjans, Jos C S

    2018-06-01

    We performed a multiple 'omics study by integrating data on epigenomic, transcriptomic, and proteomic perturbations associated with mitochondrial dysfunction in primary human hepatocytes caused by the liver toxicant valproic acid (VPA), to deeper understand downstream events following epigenetic alterations in the mitochondrial genome. Furthermore, we investigated persistence of cross-omics changes after terminating drug treatment. Upon transient methylation changes of mitochondrial genes during VPA-treatment, increasing complexities of gene-interaction networks across time were demonstrated, which normalized during washout. Furthermore, co-expression between genes and their corresponding proteins increased across time. Additionally, in relation to persistently decreased ATP production, we observed decreased expression of mitochondrial complex I and III-V genes. Persistent transcripts and proteins were related to citric acid cycle and β-oxidation. In particular, we identified a potential novel mitochondrial-nuclear signaling axis, MT-CO2-FN1-MYC-CPT1. In summary, this cross-omics study revealed dynamic responses of the mitochondrial epigenome to an impulse toxicant challenge resulting in persistent mitochondrial dysfunctioning. Moreover, this approach allowed for discriminating between the toxic effect of VPA and adaptation. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Cultural adaptation of the Latin American version of the World Health Organization Composite International Diagnostic Interview (WHO-CIDI) (v 3.0) for use in Spain.

    PubMed

    Navarro-Mateu, Fernando; Morán-Sánchez, Inés; Alonso, Jordi; Tormo, Ma José; Pujalte, Ma Luisa; Garriga, Ascensión; Aguilar-Gaxiola, Sergio; Navarro, Carmen

    2013-01-01

    To develop a Spanish version of the WHO-Composite International Diagnostic Interview (WHO-CIDI) applicable to Spain, through cultural adaptation of its most recent Latin American (LA v 20.0) version. A 1-week training course on the WHO-CIDI was provided by certified trainers. An expert panel reviewed the LA version, identified words or expressions that needed to be adapted to the cultural or linguistic norms for Spain, and proposed alternative expressions that were agreed on through consensus. The entire process was supervised and approved by a member of the WHO-CIDI Editorial Committee. The changes were incorporated into a Computer Assisted Personal Interview (CAPI) format and the feasibility and administration time were pilot tested in a convenience sample of 32 volunteers. A total of 372 questions were slightly modified (almost 7% of approximately 5000 questions in the survey) and incorporated into the CAPI version of the WHO-CIDI. Most of the changes were minor - but important - linguistic adaptations, and others were related to specific Spanish institutions and currency. In the pilot study, the instrument's mean completion administration time was 2h and 10min, with an interquartile range from 1.5 to nearly 3h. All the changes made were tested and officially approved. The Latin American version of the WHO-CIDI was successfully adapted and pilot-tested in its computerized format and is now ready for use in Spain. Copyright © 2012 SESPAS. Published by Elsevier Espana. All rights reserved.

  10. Genome Sequence of African Swine Fever Virus BA71, the Virulent Parental Strain of the Nonpathogenic and Tissue-Culture Adapted BA71V.

    PubMed

    Rodríguez, Javier M; Moreno, Leticia Tais; Alejo, Alí; Lacasta, Anna; Rodríguez, Fernando; Salas, María L

    2015-01-01

    The strain BA71V has played a key role in African swine fever virus (ASFV) research. It was the first genome sequenced, and remains the only genome completely determined. A large part of the studies on the function of ASFV genes, viral transcription, replication, DNA repair and morphogenesis, has been performed using this model. This avirulent strain was obtained by adaptation to grow in Vero cells of the highly virulent BA71 strain. We report here the analysis of the genome sequence of BA71 in comparison with that of BA71V. They possess the smallest genomes for a virulent or an attenuated ASFV, and are essentially identical except for a relatively small number of changes. We discuss the possible contribution of these changes to virulence. Analysis of the BA71 sequence allowed us to identify new similarities among ASFV proteins, and with database proteins including two ASFV proteins that could function as a two-component signaling network.

  11. Genome Sequence of African Swine Fever Virus BA71, the Virulent Parental Strain of the Nonpathogenic and Tissue-Culture Adapted BA71V

    PubMed Central

    Rodríguez, Javier M.; Moreno, Leticia Tais; Alejo, Alí; Lacasta, Anna; Rodríguez, Fernando; Salas, María L.

    2015-01-01

    The strain BA71V has played a key role in African swine fever virus (ASFV) research. It was the first genome sequenced, and remains the only genome completely determined. A large part of the studies on the function of ASFV genes, viral transcription, replication, DNA repair and morphogenesis, has been performed using this model. This avirulent strain was obtained by adaptation to grow in Vero cells of the highly virulent BA71 strain. We report here the analysis of the genome sequence of BA71 in comparison with that of BA71V. They possess the smallest genomes for a virulent or an attenuated ASFV, and are essentially identical except for a relatively small number of changes. We discuss the possible contribution of these changes to virulence. Analysis of the BA71 sequence allowed us to identify new similarities among ASFV proteins, and with database proteins including two ASFV proteins that could function as a two-component signaling network. PMID:26618713

  12. Cortical and subcortical connections of V1 and V2 in early postnatal macaque monkeys.

    PubMed

    Baldwin, Mary K L; Kaskan, Peter M; Zhang, Bin; Chino, Yuzo M; Kaas, Jon H

    2012-02-15

    Connections of primary (V1) and secondary (V2) visual areas were revealed in macaque monkeys ranging in age from 2 to 16 weeks by injecting small amounts of cholera toxin subunit B (CTB). Cortex was flattened and cut parallel to the surface to reveal injection sites, patterns of labeled cells, and patterns of cytochrome oxidase (CO) staining. Projections from the lateral geniculate nucleus and pulvinar to V1 were present at 4 weeks of age, as were pulvinar projections to thin and thick CO stripes in V2. Injections into V1 in 4- and 8-week-old monkeys labeled neurons in V2, V3, middle temporal area (MT), and dorsolateral area (DL)/V4. Within V1 and V2, labeled neurons were densely distributed around the injection sites, but formed patches at distances away from injection sites. Injections into V2 labeled neurons in V1, V3, DL/V4, and MT of monkeys 2-, 4-, and 8-weeks of age. Injections in thin stripes of V2 preferentially labeled neurons in other V2 thin stripes and neurons in the CO blob regions of V1. A likely thick stripe injection in V2 at 4 weeks of age labeled neurons around blobs. Most labeled neurons in V1 were in superficial cortical layers after V2 injections, and in deep layers of other areas. Although these features of adult V1 and V2 connectivity were in place as early as 2 postnatal weeks, labeled cells in V1 and V2 became more restricted to preferred CO compartments after 2 weeks of age. Copyright © 2011 Wiley-Liss, Inc.

  13. Adaptive optics plug-and-play setup for high-resolution microscopes with multi-actuator adaptive lens

    NASA Astrophysics Data System (ADS)

    Quintavalla, M.; Pozzi, P.; Verhaegen, Michelle; Bijlsma, Hielke; Verstraete, Hans; Bonora, S.

    2018-02-01

    Adaptive Optics (AO) has revealed as a very promising technique for high-resolution microscopy, where the presence of optical aberrations can easily compromise the image quality. Typical AO systems however, are almost impossible to implement on commercial microscopes. We propose a simple approach by using a Multi-actuator Adaptive Lens (MAL) that can be inserted right after the objective and works in conjunction with an image optimization software allowing for a wavefront sensorless correction. We presented the results obtained on several commercial microscopes among which a confocal microscope, a fluorescence microscope, a light sheet microscope and a multiphoton microscope.

  14. Importance of the cutoff value in the quadratic adaptive integrate-and-fire model.

    PubMed

    Touboul, Jonathan

    2009-08-01

    The quadratic adaptive integrate-and-fire model (Izhikevich, 2003 , 2007 ) is able to reproduce various firing patterns of cortical neurons and is widely used in large-scale simulations of neural networks. This model describes the dynamics of the membrane potential by a differential equation that is quadratic in the voltage, coupled to a second equation for adaptation. Integration is stopped during the rise phase of a spike at a voltage cutoff value V(c) or when it blows up. Subsequently the membrane potential is reset, and the adaptation variable is increased by a fixed amount. We show in this note that in the absence of a cutoff value, not only the voltage but also the adaptation variable diverges in finite time during spike generation in the quadratic model. The divergence of the adaptation variable makes the system very sensitive to the cutoff: changing V(c) can dramatically alter the spike patterns. Furthermore, from a computational viewpoint, the divergence of the adaptation variable implies that the time steps for numerical simulation need to be small and adaptive. However, divergence of the adaptation variable does not occur for the quartic model (Touboul, 2008 ) and the adaptive exponential integrate-and-fire model (Brette & Gerstner, 2005 ). Hence, these models are robust to changes in the cutoff value.

  15. Modeled Sea Level Rise Impacts on Coastal Ecosystems at Six Major Estuaries on Florida’s Gulf Coast: Implications for Adaptation Planning

    PubMed Central

    Birch, Anne P.; Brenner, Jorge; Gordon, Doria R.

    2015-01-01

    The Sea Level Affecting Marshes Model (SLAMM) was applied at six major estuaries along Florida’s Gulf Coast (Pensacola Bay, St. Andrews/Choctawhatchee Bays, Apalachicola Bay, Southern Big Bend, Tampa Bay and Charlotte Harbor) to provide quantitative and spatial information on how coastal ecosystems may change with sea level rise (SLR) and to identify how this information can be used to inform adaption planning. High resolution LiDAR-derived elevation data was utilized under three SLR scenarios: 0.7 m, 1 m and 2 m through the year 2100 and uncertainty analyses were conducted on selected input parameters at three sites. Results indicate that the extent, spatial orientation and relative composition of coastal ecosystems at the study areas may substantially change with SLR. Under the 1 m SLR scenario, total predicted impacts for all study areas indicate that coastal forest (-69,308 ha; -18%), undeveloped dry land (-28,444 ha; -2%) and tidal flat (-25,556 ha; -47%) will likely face the greatest loss in cover by the year 2100. The largest potential gains in cover were predicted for saltmarsh (+32,922 ha; +88%), transitional saltmarsh (+23,645 ha; na) and mangrove forest (+12,583 ha; +40%). The Charlotte Harbor and Tampa Bay study areas were predicted to experience the greatest net loss in coastal wetlands The uncertainty analyses revealed low to moderate changes in results when some numerical SLAMM input parameters were varied highlighting the value of collecting long-term sedimentation, accretion and erosion data to improve SLAMM precision. The changes predicted by SLAMM will affect exposure of adjacent human communities to coastal hazards and ecosystem functions potentially resulting in impacts to property values, infrastructure investment and insurance rates. The results and process presented here can be used as a guide for communities vulnerable to SLR to identify and prioritize adaptation strategies that slow and/or accommodate the changes underway. PMID:26207914

  16. Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory.

    PubMed

    Wünsche, Andrea; Dinh, Duy M; Satterwhite, Rebecca S; Arenas, Carolina Diaz; Stoebel, Daniel M; Cooper, Tim F

    2017-03-01

    Populations evolving in constant environments exhibit declining adaptability. Understanding the basis of this pattern could reveal underlying processes determining the repeatability of evolutionary outcomes. In principle, declining adaptability can be due to a decrease in the effect size of beneficial mutations, a decrease in the rate at which they occur, or some combination of both. By evolving Escherichia coli populations started from different steps along a single evolutionary trajectory, we show that declining adaptability is best explained by a decrease in the size of available beneficial mutations. This pattern reflected the dominant influence of negative genetic interactions that caused new beneficial mutations to confer smaller benefits in fitter genotypes. Genome sequencing revealed that starting genotypes that were more similar to one another did not exhibit greater similarity in terms of new beneficial mutations, supporting the view that epistasis acts globally, having a greater influence on the effect than on the identity of available mutations along an adaptive trajectory. Our findings provide support for a general mechanism that leads to predictable phenotypic evolutionary trajectories.

  17. Climate change vulnerability, adaptation and risk perceptions at farm level in Punjab, Pakistan.

    PubMed

    Abid, Muhammad; Schilling, Janpeter; Scheffran, Jürgen; Zulfiqar, Farhad

    2016-03-15

    Pakistan is among the countries highly exposed and vulnerable to climate change. The country has experienced many severe floods, droughts and storms over the last decades. However, little research has focused on the investigation of vulnerability and adaptation to climate-related risks in Pakistan. Against this backdrop, this article investigates the farm level risk perceptions and different aspects of vulnerability to climate change including sensitivity and adaptive capacity at farm level in Pakistan. We interviewed a total of 450 farming households through structured questionnaires in three districts of Punjab province of Pakistan. This study identified a number of climate-related risks perceived by farm households such as extreme temperature events, insect attacks, animal diseases and crop pests. Limited water availability, high levels of poverty and a weak role of local government in providing proper infrastructure were the factors that make farmers more sensitive to climate-related risks. Uncertainty or reduction in crop and livestock yields; changed cropping calendars and water shortage were the major adverse impacts of climate-related risks reported by farmers in the study districts. Better crop production was reported as the only positive effect. Further, this study identified a number of farm level adaptation methods employed by farm households that include changes in crop variety, crop types, planting dates and input mix, depending upon the nature of the climate-related risks. Lack of resources, limited information, lack of finances and institutional support were some constraints that limit the adaptive capacity of farm households. This study also reveals a positive role of cooperation and negative role of conflict in the adaptation process. The study suggests to address the constraints to adaptation and to improve farm level cooperation through extended outreach and distribution of institutional services, particularly climate-specific farm advisory

  18. Do stressful conditions make adaptation difficult? Guppies in the oil-polluted environments of southern Trinidad

    PubMed Central

    Rolshausen, Gregor; Phillip, Dawn A T; Beckles, Denise M; Akbari, Ali; Ghoshal, Subhasis; Hamilton, Patrick B; Tyler, Charles R; Scarlett, Alan G; Ramnarine, Indar; Bentzen, Paul; Hendry, Andrew P

    2015-01-01

    The ability of populations to rapidly adapt to new environments will determine their future in an increasingly human-modified world. Although meta-analyses do frequently uncover signatures of local adaptation, they also reveal many exceptions. We suggest that particular constraints on local adaptation might arise when organisms are exposed to novel stressors, such as anthropogenic pollution. To inform this possibility, we studied the extent to which guppies (Poecilia reticulata) show local adaptation to oil pollution in southern Trinidad. Neutral genetic markers revealed that paired populations in oil-polluted versus not-polluted habitats diverged independently in two different watersheds. Morphometrics revealed some divergence (particularly in head shape) between these environments, some of which was parallel between rivers. Reciprocal transplant experiments in nature, however, found little evidence of local adaptation based on survival and growth. Moreover, subsequent laboratory experiments showed that the two populations from oil-polluted sites showed only weak local adaptation even when compared to guppies from oil-free northern Trinidad. We conclude that guppies show little local adaptation to oil pollution, which might result from the challenges associated with adaptation to particularly stressful environments. It might also reflect genetic drift owing to small population sizes and/or high gene flow between environments. PMID:26495039

  19. Revealing the supernova-gamma-ray burst connection with TeV neutrinos.

    PubMed

    Ando, Shin'ichiro; Beacom, John F

    2005-08-05

    Gamma-ray bursts (GRBs) are rare, powerful explosions displaying highly relativistic jets. It has been suggested that a significant fraction of the much more frequent core-collapse supernovae are accompanied by comparably energetic but mildly relativistic jets, which would indicate an underlying supernova-GRB connection. We calculate the neutrino spectra from the decays of pions and kaons produced in jets in supernovae, and show that the kaon contribution is dominant and provides a sharp break near 20 TeV, which is a sensitive probe of the conditions inside the jet. For a supernova at 10 Mpc, 30 events above 100 GeV are expected in a 10 s burst in the IceCube detector.

  20. The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.

    PubMed Central

    Housset, D; Mazza, G; Grégoire, C; Piras, C; Malissen, B; Fontecilla-Camps, J C

    1997-01-01

    The crystal structure of a mouse T-cell antigen receptor (TCR) Fv fragment complexed to the Fab fragment of a specific anti-clonotypic antibody has been determined to 2.6 A resolution. The polypeptide backbone of the TCR V alpha domain is very similar to those of other crystallographically determined V alphas, whereas the V beta structure is so far unique among TCR V beta domains in that it displays a switch of the c" strand from the inner to the outer beta-sheet. The beta chain variable region of this TCR antigen-binding site is characterized by a rather elongated third complementarity-determining region (CDR3beta) that packs tightly against the CDR3 loop of the alpha chain, without leaving any intervening hydrophobic pocket. Thus, the conformation of the CDR loops with the highest potential diversity distinguishes the structure of this TCR antigen-binding site from those for which crystallographic data are available. On the basis of all these results, we infer that a significant conformational change of the CDR3beta loop found in our TCR is required for binding to its cognate peptide-MHC ligand. PMID:9250664

  1. Evolutionary history of a complex adaptation: Tetrodotoxin resistance in salamanders

    PubMed Central

    Hanifin, Charles T.; Gilly, William F.

    2017-01-01

    Understanding the processes that generate novel adaptive phenotypes is central to evolutionary biology. We used comparative analyses to reveal the history of tetrodotoxin (TTX) resistance in TTX-bearing salamanders. Resistance to TTX is a critical component of the ability to use TTX defensively but the origin of the TTX-bearing phenotype is unclear. Skeletal muscle of TTX-bearing salamanders (modern newts, family: Salamandridae) is unaffected by TTX at doses far in excess of those that block action potentials in muscle and nerve of other vertebrates. Skeletal muscle of non-TTX-bearing salamandrids is also resistant to TTX but at lower levels. Skeletal muscle TTX resistance in the Salamandridae results from the expression of TTX-resistant variants of the voltage-gated sodium channel NaV 1.4 (SCN4a). We identified four substitutions in the coding region of salSCN4a that are likely responsible for the TTX resistance measured in TTX-bearing salamanders and variation at one of these sites likely explains variation in TTX resistance among other lineages. Our results suggest that exaptation has played a role in the evolution of the TTX-bearing phenotype and provide empirical evidence that complex physiological adaptations can arise through the accumulation of beneficial mutations in the coding region of conserved proteins. PMID:25346116

  2. Complex Patterns of Local Adaptation in Teosinte

    PubMed Central

    Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

    2013-01-01

    Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

  3. The Relations of Employability Skills to Career Adaptability among Technical School Students

    ERIC Educational Resources Information Center

    de Guzman, Allan B.; Choi, Kyoung Ok

    2013-01-01

    This two pronged study reports the initial validation of the psychometric properties and factor structure of the Career Adapt-Abilities Scale (CAAS) in the context of Papua New Guinea (PNG) and the investigation of the relationship between employability skills and career adaptability. Results of the study revealed that CAAS can be a valid and…

  4. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

    PubMed Central

    Dasmahapatra, Kanchon K; Walters, James R.; Briscoe, Adriana D.; Davey, John W.; Whibley, Annabel; Nadeau, Nicola J.; Zimin, Aleksey V.; Hughes, Daniel S. T.; Ferguson, Laura C.; Martin, Simon H.; Salazar, Camilo; Lewis, James J.; Adler, Sebastian; Ahn, Seung-Joon; Baker, Dean A.; Baxter, Simon W.; Chamberlain, Nicola L.; Chauhan, Ritika; Counterman, Brian A.; Dalmay, Tamas; Gilbert, Lawrence E.; Gordon, Karl; Heckel, David G.; Hines, Heather M.; Hoff, Katharina J.; Holland, Peter W.H.; Jacquin-Joly, Emmanuelle; Jiggins, Francis M.; Jones, Robert T.; Kapan, Durrell D.; Kersey, Paul; Lamas, Gerardo; Lawson, Daniel; Mapleson, Daniel; Maroja, Luana S.; Martin, Arnaud; Moxon, Simon; Palmer, William J.; Papa, Riccardo; Papanicolaou, Alexie; Pauchet, Yannick; Ray, David A.; Rosser, Neil; Salzberg, Steven L.; Supple, Megan A.; Surridge, Alison; Tenger-Trolander, Ayse; Vogel, Heiko; Wilkinson, Paul A.; Wilson, Derek; Yorke, James A.; Yuan, Furong; Balmuth, Alexi L.; Eland, Cathlene; Gharbi, Karim; Thomson, Marian; Gibbs, Richard A.; Han, Yi; Jayaseelan, Joy C.; Kovar, Christie; Mathew, Tittu; Muzny, Donna M.; Ongeri, Fiona; Pu, Ling-Ling; Qu, Jiaxin; Thornton, Rebecca L.; Worley, Kim C.; Wu, Yuan-Qing; Linares, Mauricio; Blaxter, Mark L.; Constant, Richard H. ffrench; Joron, Mathieu; Kronforst, Marcus R.; Mullen, Sean P.; Reed, Robert D.; Scherer, Steven E.; Richards, Stephen; Mallet, James; McMillan, W. Owen; Jiggins, Chris D.

    2012-01-01

    The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation. PMID:22722851

  5. Adaptive evolution of the STRA6 genes in mammalian.

    PubMed

    Wu, Jianghong; Xiang, Hui; Qi, Yunxia; Yang, Ding; Wang, Xiaojuan; Sun, Hailian; Wang, Feng; Liu, Bin

    2014-01-01

    Stimulated by retinoic acid 6 (STRA6) is the receptor for retinol binding protein and is relevant for the transport of retinol to specific sites such as the eye. The adaptive evolution mechanism that vertebrates have occupied nearly every habitat available on earth and adopted various lifestyles associated with different light conditions and visual challenges, as well as their role in development and adaptation is thus far unknown. In this work, we have investigated different aspects of vertebrate STRA6 evolution and used molecular evolutionary analyses to detect evidence of vertebrate adaptation to the lightless habitat. Free-ratio model revealed significant rate shifts immediately after the species divergence. The amino acid sites detected to be under positive selection are within the extracellular loops of STRA6 protein. Branch-site model A test revealed that STRA6 has undergone positive selection in the different phyla of mammalian except for the branch of rodent. The results suggest that interactions between different light environments and host may be driving adaptive change in STRA6 by competition between species. In support of this, we found that altered functional constraints may take place at some amino acid residues after speciation. We suggest that STRA6 has undergone adaptive evolution in different branch of vertebrate relation to habitat environment.

  6. Genetic adaptation to historical pathogen burdens.

    PubMed

    Fedderke, Johannes W; Klitgaard, Robert E; Napolioni, Valerio

    2017-10-01

    Historical pathogen burdens are examined as possible triggers for genetic adaptation. Evidence of adaptation emerges for the acid phosphatase locus 1 (ACP1), interleukin-6 (IL6), interleukin-10 (IL10 ), human leukocyte antigen (HLA) polymorphisms, along with a measure of heterozygosity over 783 alleles. Results are robust to controlling for the physical and historical environment humans faced, and to endogeneity of the historical pathogen burden measure. The present study represents a proof-of-concept which may pave the way to the analysis of future aggregate measures coming from whole-genome sequencing/genotyping data. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.

    PubMed

    Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

    2013-07-01

    Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

  8. HIV-1 Env C2-V4 Diversification in a Slow-Progressor Infant Reveals a Flat but Rugged Fitness Landscape

    PubMed Central

    Smith, S. Abigail; Wood, Charles; West, John T.

    2013-01-01

    Human immunodeficiency virus type-1 (HIV-1) fitness has been associated with virus entry, a process mediated by the envelope glycoprotein (Env). We previously described Env genetic diversification in a Zambian, subtype C infected, slow-progressor child (1157i) in parallel with an evolving neutralizing antibody response. Because of the role the Variable-3 loop (V3) plays in transmission, cell tropism, neutralization sensitivity, and fitness, longitudinally isolated 1157i C2-V4 alleles were cloned into HIV-1NL4-3-eGFP and -DsRed2 infectious molecular clones. The fluorescent reporters allowed for dual-infection competitions between all patient-derived C2-V4 chimeras to quantify the effect of V3 diversification and selection on fitness. ‘Winners’ and ‘losers’ were readily discriminated among the C2-V4 alleles. Exceptional sensitivity for detection of subtle fitness differences was revealed through analysis of two alleles differing in a single synonymous amino acid. However, when the outcomes of N = 33 competitions were averaged for each chimera, the aggregate analysis showed that despite increasing diversification and divergence with time, natural selection of C2-V4 sequences in this individual did not appear to be producing a ‘survival of the fittest’ evolutionary pattern. Rather, we detected a relatively flat fitness landscape consistent with mutational robustness. Fitness outcomes were then correlated with individual components of the entry process. Env incorporation into particles correlated best with fitness, suggesting a role for Env avidity, as opposed to receptor/coreceptor affinity, in defining fitness. Nevertheless, biochemical analyses did not identify any step in HIV-1 entry as a dominant determinant of fitness. Our results lead us to conclude that multiple aspects of entry contribute to maintaining adequate HIV-1 fitness, and there is no surrogate analysis for determining fitness. The capacity for subtle polymorphisms in Env to nevertheless

  9. Comparative population genomics of Fusarium graminearum reveals adaptive divergence among cereal head blight pathogens

    USDA-ARS?s Scientific Manuscript database

    In this study we sequenced the genomes of 60 Fusarium graminearum, the major fungal pathogen responsible for Fusarium head blight (FHB) in cereal crops world-wide. To investigate adaptive evolution of FHB pathogens, we performed population-level analyses to characterize genomic structure, signatures...

  10. Estrogen receptor quantitation and staging as complementary prognostic indicators in breast cancer: a study of 583 patients.

    PubMed

    Godolphin, W; Elwood, J M; Spinelli, J J

    1981-12-01

    Estrogen receptor (ER) quantity was measured at the time of primary diagnosis on 583 patients with breast cancer seen at the major treatment centre in British Columbia between 1975 and 1979. Survival rates (overall, recurrence-free and post-recurrence) were assessed relative to ER concentration, staging, menopausal status, age, differentiation, and therapy. A linear trend in increased survival was demonstrable through variations in ER concentration from less than 1 to greater than 260 fmoles/mg cytosol protein. This trend was highly significant and remained after adjustment for stage, menopausal status, and age, and was seen for all groups of patients except those with metastatic disease. The association of high ER concentration with increased recurrence-free survival was not due to differing responses to adjuvant therapy, but the trend in post-recurrence survival was only significant in patients who had received hormonal therapy. Survival was as strongly associated with receptor concentration as with staging, and these two factors were almost completely independent. A proportional hazards model was fitted to produce predictions of survival, and showed that TNM stage III patients with high ER concentrations have a better survival than stage I or II patients with lower ER concentrations. This suggests that quantitative assessment of ER status is essential to definition of risk in breast cancer patients and that stratification in clinical trials and consideration for adjuvant therapy ought to be guided, in part, by a standardized ER-quantitative determination performed on the primary tumor.

  11. The Joint Adaptive Kalman Filter (JAKF) for Vehicle Motion State Estimation.

    PubMed

    Gao, Siwei; Liu, Yanheng; Wang, Jian; Deng, Weiwen; Oh, Heekuck

    2016-07-16

    This paper proposes a multi-sensory Joint Adaptive Kalman Filter (JAKF) through extending innovation-based adaptive estimation (IAE) to estimate the motion state of the moving vehicles ahead. JAKF views Lidar and Radar data as the source of the local filters, which aims to adaptively adjust the measurement noise variance-covariance (V-C) matrix 'R' and the system noise V-C matrix 'Q'. Then, the global filter uses R to calculate the information allocation factor 'β' for data fusion. Finally, the global filter completes optimal data fusion and feeds back to the local filters to improve the measurement accuracy of the local filters. Extensive simulation and experimental results show that the JAKF has better adaptive ability and fault tolerance. JAKF enables one to bridge the gap of the accuracy difference of various sensors to improve the integral filtering effectivity. If any sensor breaks down, the filtered results of JAKF still can maintain a stable convergence rate. Moreover, the JAKF outperforms the conventional Kalman filter (CKF) and the innovation-based adaptive Kalman filter (IAKF) with respect to the accuracy of displacement, velocity, and acceleration, respectively.

  12. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

    PubMed Central

    Vonk, Freek J.; Casewell, Nicholas R.; Henkel, Christiaan V.; Heimberg, Alysha M.; Jansen, Hans J.; McCleary, Ryan J. R.; Kerkkamp, Harald M. E.; Vos, Rutger A.; Guerreiro, Isabel; Calvete, Juan J.; Wüster, Wolfgang; Woods, Anthony E.; Logan, Jessica M.; Harrison, Robert A.; Castoe, Todd A.; de Koning, A. P. Jason; Pollock, David D.; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B.; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S.; Ribeiro, José M. C.; Arntzen, Jan W.; van den Thillart, Guido E. E. J. M.; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P.; Spaink, Herman P.; Duboule, Denis; McGlinn, Edwina; Kini, R. Manjunatha; Richardson, Michael K.

    2013-01-01

    Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection. PMID:24297900

  13. SU-E-J-73: Extension of a Clinical OIS/EMR/R&V System to Deliver Safe and Efficient Adaptive Plan-Of-The-Day Treatments Using a Fully Customizable Plan-Library-Based Workflow

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Akhiat, A.; Elekta, Sunnyvale, CA; Kanis, A.P.

    Purpose: To extend a clinical Record and Verify (R&V) system to enable a safe and fast workflow for Plan-of-the-Day (PotD) adaptive treatments based on patient-specific plan libraries. Methods: Plan libraries for PotD adaptive treatments contain for each patient several pre-treatment generated treatment plans. They may be generated for various patient anatomies or CTV-PTV margins. For each fraction, a Cone Beam CT scan is acquired to support the selection of the plan that best fits the patient’s anatomy-of-the-day. To date, there are no commercial R&V systems that support PotD delivery strategies. Consequently, the clinical workflow requires many manual interventions. Moreover, multiplemore » scheduled plans have a high risk of excessive dose delivery. In this work we extended a commercial R&V system (MOSAIQ) to support PotD workflows using IQ-scripting. The PotD workflow was designed after extensive risk analysis of the manual procedure, and all identified risks were incorporated as logical checks. Results: All manual PotD activities were automated. The workflow first identifies if the patient is scheduled for PotD, then performs safety checks, and continues to treatment plan selection only if no issues were found. The user selects the plan to deliver from a list of candidate plans. After plan selection, the workflow makes the treatment fields of the selected plan available for delivery by adding them to the treatment calendar. Finally, control is returned to the R&V system to commence treatment. Additional logic was added to incorporate off-line changes such as updating the plan library. After extensive testing including treatment fraction interrupts and plan-library updates during the treatment course, the workflow is running successfully in a clinical pilot, in which 35 patients have been treated since October 2014. Conclusion: We have extended a commercial R&V system for improved safety and efficiency in library-based adaptive strategies enabling a wide

  14. Adaptive Optics for Industry and Medicine

    NASA Astrophysics Data System (ADS)

    Dainty, Christopher

    2008-01-01

    Monteiro ... [et al.]. Adaptive optics system to compensate complex-shaped wavefronts (oral paper) / Miguel Ares, and Santiago Royo. A kind of novel linear phase retrieval wavefront sensor and its application in close-loop adaptive optics system (oral paper) / Xinyang Li ... [et al.]. Ophthalmic Shack-Hatmann wavefront sensor applications (oral paper) / Daniel R. Neal. Wave front sensing of an optical vortex and its correction with the help of bimorph mirror (poster paper) / F. A. Starikov ... [et al.]. Recent advances in laser metrology and correction of high numerical aperture laser beams using quadri-wave lateral shearing-interferometry (poster paper) / Benoit Wattellier, Ivan Doudet and William Boucher. Thin film optical metrology using principles of wavefront sensing and interference (poster paper) / D. M. Faichnie, A. H. Greenaway and I. Bain. Direct diffractive image simulation (poster paper) / A. P. Maryasov, N. P. Maryasov, A. P. Layko. High speed smart CMOS sensor for adaptive optics (poster paper) / T. D. Raymond ... [et al.]. Traceable astigmatism measurements for wavefront sensors (poster paper) / S. R. G. Hall, S. D. Knox, R. F. Stevens -- pt. 3. Adaptive optics in vision science. Dual-conjugate adaptive optics instrument for wide-field retinal imaging (oral paper) / Jörgen Thaung, Mette-Owner Petersen and Zoran Popovic. Visual simulation using electromagnetic adaptive-optics (oral paper) / Laurent Vabre ... [et al.]. High-resolution field-of-view widening in human eye retina imaging (oral paper) / Alexander V. Dubinin, Tatyana Yu. Cherezova, Alexis V. Kudryashov. Psychophysical experiments on visual performance with an ocular adaptive optics system (oral paper) / E. Dalimier, J. C. Dainty and J. Barbur. Does the accommodative mechanism of the eye calibrate itself using aberration dynamics? (oral paper) / K. M. Hampson, S. S. Chin and E. A. H. Mallen. A study of field aberrations in the human eye (oral paper) / Alexander V. Goncharov ... [et al.]. Dual

  15. Alertness function of thalamus in conflict adaptation.

    PubMed

    Wang, Xiangpeng; Zhao, Xiaoyue; Xue, Gui; Chen, Antao

    2016-05-15

    Conflict adaptation reflects the ability to improve current conflict resolution based on previously experienced conflict, which is crucial for our goal-directed behaviors. In recent years, the roles of alertness are attracting increasing attention when discussing the generation of conflict adaptation. However, due to the difficulty of manipulating alertness, very limited progress has been made in this line. Inspired by that color may affect alertness, we manipulated background color of experimental task and found that conflict adaptation significantly presented in gray and red backgrounds but did not in blue background. Furthermore, behavioral and functional magnetic resonance imaging results revealed that the modulation of color on conflict adaptation was implemented through changing alertness level. In particular, blue background eliminated conflict adaptation by damping the alertness regulating function of thalamus and the functional connectivity between thalamus and inferior frontal gyrus (IFG). In contrast, in gray and red backgrounds where alertness levels are typically high, the thalamus and the right IFG functioned normally and conflict adaptations were significant. Therefore, the alertness function of thalamus is determinant to conflict adaptation, and thalamus and right IFG are crucial nodes of the neural circuit subserving this ability. Present findings provide new insights into the neural mechanisms of conflict adaptation. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

    USDA-ARS?s Scientific Manuscript database

    Modulating days to flowering is a key mechanism in plants for adapting to new environments, and variation in days to flowering drives population structure by limiting mating. To elucidate the genetic architecture of flowering across maize, a quantitative trait, we mapped flowering in five global pop...

  17. Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis.

    PubMed

    Kujala, S T; Knürr, T; Kärkkäinen, K; Neale, D B; Sillanpää, M J; Savolainen, O

    2017-05-01

    Local adaptation is a common feature of plant and animal populations. Adaptive phenotypic traits are genetically differentiated along environmental gradients, but the genetic basis of such adaptation is still poorly known. Genetic association studies of local adaptation combine data over populations. Correcting for population structure in these studies can be problematic since both selection and neutral demographic events can create similar allele frequency differences between populations. Correcting for demography with traditional methods may lead to eliminating some true associations. We developed a new Bayesian approach for identifying the loci underlying an adaptive trait in a multipopulation situation in the presence of possible double confounding due to population stratification and adaptation. With this method we studied the genetic basis of timing of bud set, a surrogate trait for timing of yearly growth cessation that confers local adaptation to the populations of Scots pine (Pinus sylvestris). Population means of timing of bud set were highly correlated with latitude. Most effects at individual loci were small. Interestingly, we found genetic heterogeneity (that is, different sets of loci associated with the trait) between the northern and central European parts of the cline. We also found indications of stronger stabilizing selection toward the northern part of the range. The harsh northern conditions may impose greater selective pressure on timing of growth cessation, and the relative importance of different environmental cues used for tracking the seasons might differ depending on latitude of origin.

  18. Infected colonic mass revealing a lung adenocarcinoma.

    PubMed

    Doussot, Alexandre; Chalumeau, Claire; Combier, Christophe; Cheynel, Nicolas; Facy, Olivier

    2013-12-01

    We report the case of lung adenocarcinoma revealed by infected colonic tumor in a 62-year-old man. An en bloc surgical resection was performed with uneventful recovery. The pathologic report concluded in a right mesocolic lymph node metastases from a mildly differentiated adenocarcinoma from pulmonary origin. GI metastases of lung cancer are described in the literature and are frequently asymptomatic in patient with a known primary cancer. In this patient, the complication of the metastases revealed the primary and immunochemistry permitted to adapt the systemic chemotherapy. Copyright © 2012. Published by Elsevier Masson SAS.

  19. Adaptation and diversity along an altitudinal gradient in Ethiopian barley (Hordeum vulgare L.) landraces revealed by molecular analysis

    PubMed Central

    2010-01-01

    Background Among the cereal crops, barley is the species with the greatest adaptability to a wide range of environments. To determine the level and structure of genetic diversity in barley (Hordeum vulgare L.) landraces from the central highlands of Ethiopia, we have examined the molecular variation at seven nuclear microsatellite loci. Results A total of 106 landrace populations were sampled in the two growing seasons (Meher and Belg; the long and short rainy seasons, respectively), across three districts (Ankober, Mojanawadera and Tarmaber), and within each district along an altitudinal gradient (from 1,798 to 3,324 m a.s.l). Overall, although significant, the divergence (e.g. FST) is very low between seasons and geographical districts, while it is high between different classes of altitude. Selection for adaptation to different altitudes appears to be the main factor that has determined the observed clinal variation, along with population-size effects. Conclusions Our data show that barley landraces from Ethiopia are constituted by highly variable local populations (farmer's fields) that have large within-population diversity. These landraces are also shown to be locally adapted, with the major driving force that has shaped their population structure being consistent with selection for adaptation along an altitudinal gradient. Overall, our study highlights the potential of such landraces as a source of useful alleles. Furthermore, these landraces also represent an ideal system to study the processes of adaptation and for the identification of genes and genomic regions that have adaptive roles in crop species. PMID:20565982

  20. Genetics of climate change adaptation.

    PubMed

    Franks, Steven J; Hoffmann, Ary A

    2012-01-01

    The rapid rate of current global climate change is having strong effects on many species and, at least in some cases, is driving evolution, particularly when changes in conditions alter patterns of selection. Climate change thus provides an opportunity for the study of the genetic basis of adaptation. Such studies include a variety of observational and experimental approaches, such as sampling across clines, artificial evolution experiments, and resurrection studies. These approaches can be combined with a number of techniques in genetics and genomics, including association and mapping analyses, genome scans, and transcription profiling. Recent research has revealed a number of candidate genes potentially involved in climate change adaptation and has also illustrated that genetic regulatory networks and epigenetic effects may be particularly relevant for evolution driven by climate change. Although genetic and genomic data are rapidly accumulating, we still have much to learn about the genetic architecture of climate change adaptation.

  1. Faith-adapted psychological therapies for depression and anxiety: Systematic review and meta-analysis.

    PubMed

    Anderson, Naomi; Heywood-Everett, Suzanne; Siddiqi, Najma; Wright, Judy; Meredith, Jodi; McMillan, Dean

    2015-05-01

    Incorporating faith (religious or spiritual) perspectives into psychological treatments has attracted significant interest in recent years. However, previous suggestion that good psychiatric care should include spiritual components has provoked controversy. To try to address ongoing uncertainty in this field we present a systematic review and meta-analysis to assess the efficacy of faith-based adaptations of bona fide psychological therapies for depression or anxiety. A systematic review and meta-analysis of randomised controlled trials were performed. The literature search yielded 2274 citations of which 16 studies were eligible for inclusion. All studies used cognitive or cognitive behavioural models as the basis for their faith-adapted treatment (F-CBT). We identified statistically significant benefits of using F-CBT. However, quality assessment using the Cochrane risk of bias tool revealed methodological limitations that reduce the apparent strength of these findings. Whilst the effect sizes identified here were statistically significant, there were relatively a few relevant RCTs available, and those included were typically small and susceptible to significant biases. Biases associated with researcher or therapist allegiance were identified as a particular concern. Despite some suggestion that faith-adapted CBT may out-perform both standard CBT and control conditions (waiting list or "treatment as usual"), the effect sizes identified in this meta-analysis must be considered in the light of the substantial methodological limitations that affect the primary research data. Before firm recommendations about the value of faith-adapted treatments can be made, further large-scale, rigorously performed trials are required. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Patterns of Transfer of Adaptation Among Body Segments

    NASA Technical Reports Server (NTRS)

    Seidler, R. D.; Bloomberg, J. J.; Stelmach, George E.

    2000-01-01

    Two experiments were conducted in order to determine the patterns of transfer of visuomotor adaptation between arm and head pointing. An altered gain of display of pointing movements was used to induce a conflict between visual and somatosensory representations. Two subject groups participated in Experiment One: group 1 adapted shoulder pointing movements, and group 2 adapted wrist pointing movements to a 0.5 gain of display. Following the adaptation regimen, subjects performed a transfer test in which the shoulder group performed wrist movements and the wrist group performed shoulder movements. The results demonstrated that both groups displayed typical adaptation curves, initially undershooting the target followed by a return to baseline performance. Transfer tests revealed that both groups had high transfer of the acquired adaptation to the other joint. Experiment Two followed a similar design except that group 1 adapted head pointing movements and group 2 adapted arm pointing movements. The arm adaptation had high transfer to head pointing while the head adaptation had very little transfer to arm pointing. These results imply that, while the arm segments may share a common target representation for goal-directed actions, individual but functionally dependent target representations may exist for the control of head and arm movements.

  3. Multi‐omic profiling ­of EPO‐producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    PubMed Central

    Ley, Daniel; Seresht, Ali Kazemi; Engmark, Mikael; Magdenoska, Olivera; Nielsen, Kristian Fog; Kildegaard, Helene Faustrup

    2015-01-01

    ABSTRACT Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi‐omics approach was applied to study the production of erythropoietin (EPO) in a panel of CHO‐K1 cells under growth‐limited and unlimited conditions in batch and chemostat cultures. Physiological characterization of the EPO‐producing cells included global transcriptome analysis, targeted metabolome analysis, including intracellular pools of glycolytic intermediates, NAD(P)H/NAD(P)+, adenine nucleotide phosphates (ANP), and extracellular concentrations of sugars, organic acids, and amino acids. Potential impact of EPO expression on the protein secretory pathway was assessed at multiple stages using quantitative PCR (qPCR), reverse transcription PCR (qRT‐PCR), Western blots (WB), and global gene expression analysis to assess EPO gene copy numbers, EPO gene expression, intracellular EPO retention, and differentially expressed genes functionally related to secretory protein processing, respectively. We found no evidence supporting the existence of production bottlenecks in energy metabolism (i.e., glycolytic metabolites, NAD(P)H/NAD(P)+ and ANPs) in batch culture or in the secretory protein production pathway (i.e., gene dosage, transcription and post‐translational processing of EPO) in chemostat culture at specific productivities up to 5 pg/cell/day. Time‐course analysis of high‐ and low‐producing clones in chemostat culture revealed rapid adaptation of transcription levels of amino acid catabolic genes in favor of EPO production within nine generations. Interestingly, the adaptation was followed by an increase in specific EPO productivity. Biotechnol. Bioeng. 2015;112: 2373–2387. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. PMID

  4. Key issues review: evolution on rugged adaptive landscapes

    NASA Astrophysics Data System (ADS)

    Obolski, Uri; Ram, Yoav; Hadany, Lilach

    2018-01-01

    Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors in the genetic space. How do populations evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930s by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes. The development of landscape models led to numerous theoretical studies analyzing evolution on rugged landscapes under different biological conditions. The large body of theoretical work suggests that adaptive landscapes are major determinants of the progress and outcome of evolutionary processes. Recent technological advances in molecular biology and microbiology allow experimenters to measure adaptive values of large sets of allele combinations and construct empirical adaptive landscapes for the first time. Such empirical landscapes have already been generated in bacteria, yeast, viruses, and fungi, and are contributing to new insights about evolution on adaptive landscapes. In this Key Issues Review we will: (i) introduce the concept of adaptive landscapes; (ii) review the major theoretical studies of evolution on rugged landscapes; (iii) review some of the recently obtained empirical adaptive landscapes; (iv) discuss recent mathematical and statistical analyses motivated by empirical adaptive landscapes, as well as provide the reader with instructions and source code to implement simulations of evolution on adaptive landscapes; and (v) discuss possible future directions for this exciting field.

  5. Admixture facilitates genetic adaptations to high altitude in Tibet

    PubMed Central

    Jeong, Choongwon; Alkorta-Aranburu, Gorka; Basnyat, Buddha; Neupane, Maniraj; Witonsky, David B.; Pritchard, Jonathan K.; Beall, Cynthia M.; Di Rienzo, Anna

    2015-01-01

    Admixture is recognized as a widespread feature of human populations, renewing interest in the possibility that genetic exchange can facilitate adaptations to new environments. Studies of Tibetans revealed candidates for high-altitude adaptations in the EGLN1 and EPAS1 genes, associated with lower hemoglobin concentration. However, the history of these variants or that of Tibetans remains poorly understood. Here, we analyze genotype data for the Nepalese Sherpa, and find that Tibetans are a mixture of ancestral populations related to the Sherpa and Han Chinese. EGLN1 and EPAS1 genes show a striking enrichment of high-altitude ancestry in the Tibetan genome, indicating that migrants from low altitude acquired adaptive alleles from the highlanders. Accordingly, the Sherpa and Tibetans share adaptive hemoglobin traits. This admixture-mediated adaptation shares important features with adaptive introgression. Therefore, we identify a novel mechanism, beyond selection on new mutations or on standing variation, through which populations can adapt to local environments. PMID:24513612

  6. Factor V Leiden mutation in pregnancy.

    PubMed

    Cohen, Susan Murphy

    2004-01-01

    Normal maternal adaptation to pregnancy significantly increases the risk for thrombus formation. Inherited thrombophilias further increase risk for deep venous thrombosis and adverse outcome in pregnancy. Factor V Leiden mutation is the most common inherited thrombophilia, occurring in approximately 5% of the White and 1% of the Black populations. Nurses should be knowledgeable about screening for and diagnosis of factor V Leiden mutation, risk reduction counseling, recommended care of the affected patient, and implications of anticoagulant therapy during the perinatal period.

  7. Error Argumentation Enhance Adaptability in Adults With Low Motor Ability.

    PubMed

    Lee, Chi-Mei; Bo, Jin

    2016-01-01

    The authors focused on young adults with varying degrees of motor difficulties and examined their adaptability in a visuomotor adaptation task where the visual feedback of participants' movement error was presented with either 1:1 ratio (i.e., regular feedback schedule) or 1:2 ratio (i.e., enhanced feedback schedule). Within-subject design was used with two feedback schedules counter-balanced and separated for 10 days. Results revealed that participants with greater motor difficulties showed less adaptability than those with normal motor abilities in the regular feedback schedule; however, all participants demonstrated similar level of adaptability in the enhanced feedback schedule. The results suggest that error argumentation enhances adaptability in adults with low motor ability.

  8. A framework to investigate drivers of adaptation decisions in marine fishing: Evidence from urban, semi-urban and rural communities.

    PubMed

    Malakar, Krishna; Mishra, Trupti; Patwardhan, Anand

    2018-05-11

    Traditional fishing livelihoods need to adapt to changing fish catch/populations, led by numerous anthropogenic, environmental and climatic stressors. The decision to adapt can be influenced by a variety of socio-economic and perceptual factors. However, adaptation decision-making in fishing communities has rarely been studied. Based on previous literature and focus group discussions with community, this study identifies few prominent adaptation responses in marine fishing and proposes credible factors driving decisions to adopt them. Further, a household survey is conducted, and the association of these drivers with various adaptation strategies is examined among fisherfolk of Maharashtra (India). This statistical analysis is based on 601 responses collected across three regional fishing groups: urban, semi-urban and rural. Regional segregation is done to understand variability in decision-making among groups which might be having different socio-economic and perceptual attributes. The survey reveals that only few urban fishing households have been able to diversify into other livelihoods. While having economic capital increases the likelihood of adaptation among urban and semi-urban communities, rural fishermen are significantly driven by social capital. Perception of climate change affecting fish catch drives adoption of mechanized boats solely in urban region. But increasing number of extreme events affects decisions of semi-urban and rural fishermen. Further, rising pollution and trade competition is associated with adaptation responses in the urban and semi-urban community. Higher education might help fishermen choose convenient forms of adaptation. Also, cooperative membership and subsidies are critical in adaptation decisions. The framework and insights of the study suggest the importance of acknowledging differential decision-making of individuals and communities, for designing effective adaptation and capacity-building policies. Copyright © 2018 Elsevier

  9. Contributions of adaptation currents to dynamic spike threshold on slow timescales: Biophysical insights from conductance-based models

    NASA Astrophysics Data System (ADS)

    Yi, Guosheng; Wang, Jiang; Wei, Xile; Deng, Bin; Li, Huiyan; Che, Yanqiu

    2017-06-01

    Spike-frequency adaptation (SFA) mediated by various adaptation currents, such as voltage-gated K+ current (IM), Ca2+-gated K+ current (IAHP), or Na+-activated K+ current (IKNa), exists in many types of neurons, which has been shown to effectively shape their information transmission properties on slow timescales. Here we use conductance-based models to investigate how the activation of three adaptation currents regulates the threshold voltage for action potential (AP) initiation during the course of SFA. It is observed that the spike threshold gets depolarized and the rate of membrane depolarization (dV/dt) preceding AP is reduced as adaptation currents reduce firing rate. It is indicated that the presence of inhibitory adaptation currents enables the neuron to generate a dynamic threshold inversely correlated with preceding dV/dt on slower timescales than fast dynamics of AP generation. By analyzing the interactions of ionic currents at subthreshold potentials, we find that the activation of adaptation currents increase the outward level of net membrane current prior to AP initiation, which antagonizes inward Na+ to result in a depolarized threshold and lower dV/dt from one AP to the next. Our simulations demonstrate that the threshold dynamics on slow timescales is a secondary effect caused by the activation of adaptation currents. These findings have provided a biophysical interpretation of the relationship between adaptation currents and spike threshold.

  10. Role of protein kinase C in light adaptation of molluscan microvillar photoreceptors

    PubMed Central

    Piccoli, Giuseppe; del Pilar Gomez, Maria; Nasi, Enrico

    2002-01-01

    The mechanisms by which Ca2+ regulates light adaptation in microvillar photoreceptors remain poorly understood. Protein kinase C (PKC) is a likely candidate, both because some sub-types are activated by Ca2+ and because of its association with the macromolecular ‘light-transduction complex’ in Drosophila. We investigated the possible role of PKC in the modulation of the light response in molluscan photoreceptors. Western blot analysis with isoform-specific antibodies revealed the presence of PKCα in retinal homogenates. Immunocytochemistry in isolated cell preparations confirmed PKCα localization in microvillar photoreceptors, preferentially confined to the light-sensing lobe. Light stimulation induced translocation of PKCα immunofluorescence to the photosensitive membrane, an effect that provides independent evidence for PKC activation by illumination; a similar outcome was observed after incubation with the phorbol ester PMA. Several chemically distinct activators of PKC, such as phorbol-12-myristate-13-acetate (PMA), (-)indolactam V and 1,2,-dioctanoyl-sn-glycerol (DOG) inhibited the light response of voltage-clamped microvillar photoreceptors, but were ineffective in ciliary photoreceptors, in which light does not activate the Gq/PLC cascade, nor elevates intracellular Ca2+. Pharmacological inhibition of PKC antagonized the desensitization produced by adapting lights and also caused a small, but consistent enhancement of basal sensitivity. These results strongly support the involvement of PKC activation in the light-dependent regulation of response sensitivity. However, unlike adapting background light or elevation of [Ca2+]i, PKC activators did not speed up the photoresponse, nor did PKC inhibitors antagonize the accelerating effects of background adaptation, suggesting that modulation of photoresponse time course may involve a separate Ca2+-dependent signal. PMID:12205183

  11. HIGH-REDSHIFT DUST OBSCURED GALAXIES: A MORPHOLOGY-SPECTRAL ENERGY DISTRIBUTION CONNECTION REVEALED BY KECK ADAPTIVE OPTICS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Melbourne, J.; Matthews, K.; Soifer, B. T.

    A simple optical to mid-IR color selection, R - [24]>14, i.e., f {sub {nu}}(24 {mu}m)/f {sub {nu}}(R) {approx}> 1000, identifies highly dust obscured galaxies (DOGs) with typical redshifts of z {approx} 2 {+-} 0.5. Extreme mid-IR luminosities (L {sub IR} > 10{sup 12-14}) suggest that DOGs are powered by a combination of active galactic nuclei (AGNs) and star formation, possibly driven by mergers. In an effort to compare their photometric properties with their rest-frame optical morphologies, we obtained high-spatial resolution (0.''05-0.''1) Keck Adaptive Optics K'-band images of 15 DOGs. The images reveal a wide range of morphologies, including small exponentialmore » disks (eight of 15), small ellipticals (four of 15), and unresolved sources (two of 15). One particularly diffuse source could not be classified because of low signal-to-noise ratio. We find a statistically significant correlation between galaxy concentration and mid-IR luminosity, with the most luminous DOGs exhibiting higher concentration and smaller physical size. DOGs with high concentration also tend to have spectral energy distributions (SEDs) suggestive of AGN activity. Thus, central AGN light may be biasing the morphologies of the more luminous DOGs to higher concentration. Conversely, more diffuse DOGs tend to show an SED shape suggestive of star formation. Two of 15 in the sample show multiple resolved components with separations of {approx}1 kpc, circumstantial evidence for ongoing mergers.« less

  12. An adaptive, implicit, conservative, 1D-2V multi-species Vlasov-Fokker-Planck multi-scale solver in planar geometry

    NASA Astrophysics Data System (ADS)

    Taitano, W. T.; Chacón, L.; Simakov, A. N.

    2018-07-01

    We consider a 1D-2V Vlasov-Fokker-Planck multi-species ionic description coupled to fluid electrons. We address temporal stiffness with implicit time stepping, suitably preconditioned. To address temperature disparity in time and space, we extend the conservative adaptive velocity-space discretization scheme proposed in [Taitano et al., J. Comput. Phys., 318, 391-420, (2016)] to a spatially inhomogeneous system. In this approach, we normalize the velocity-space coordinate to a temporally and spatially varying local characteristic speed per species. We explicitly consider the resulting inertial terms in the Vlasov equation, and derive a discrete formulation that conserves mass, momentum, and energy up to a prescribed nonlinear tolerance upon convergence. Our conservation strategy employs nonlinear constraints to enforce these properties discretely for both the Vlasov operator and the Fokker-Planck collision operator. Numerical examples of varying degrees of complexity, including shock-wave propagation, demonstrate the favorable efficiency and accuracy properties of the scheme.

  13. A proteomic and ultrastructural characterization of Aspergillus fumigatus' conidia adaptation at different culture ages.

    PubMed

    Anjo, Sandra I; Figueiredo, Francisco; Fernandes, Rui; Manadas, Bruno; Oliveira, Manuela

    2017-05-24

    The airborne fungus Aspergillus fumigatus is one of the most common agents of human fungal infections with a remarkable impact on public health. However, A. fumigatus conidia atmospheric resistance and longevity mechanisms are still unknown. Therefore, in this work, the processes underlying conidial adaptation were studied by a time course evaluation of the proteomics and ultrastructural changes of A. fumigatus' conidia at three time-points selected according to relevant changes previously established in conidial survival rates. The proteomics characterization revealed that conidia change from a highly active metabolic to a dormant state, culminating in cell autolysis as revealed by the increased levels of hydrolytic enzymes. Structural characterization corroborates the proteomics data, with noticeable changes observed in mitochondria, nucleus and plasma membrane ultrastructure, accompanied by the formation of autophagic vacuoles. These changes are consistent with both apoptotic and autophagic processes, and indicate that the changes in protein levels may anticipate those in cell morphology. The findings presented in this work not only clarify the processes underlying conidial adaptation to nutrient limiting conditions but can also be exploited for improving infection control strategies and in the development of new therapeutical drugs. Additionally, the present study was deposited in a public database and thus, it may also be a valuable dataset to be used by the scientific community as a tool to understand and identified other potential targets associated with conidia resistance. Copyright © 2017. Published by Elsevier B.V.

  14. The Spectropolarimetric Evolution of V838 Mon

    NASA Technical Reports Server (NTRS)

    Wisniewski, John P.

    2007-01-01

    I review photo-polarimetric and spectropolarimetric observations of V838 Mon, which revealed that it had an asymmetrical inner circumstellar envelope following its 2nd photometric outburst. Electron scattering, modified by preor post-scattering H absorption, is the polarizing mechanism in V838 Mon's envelope. The simplest geometry implied by these observations is that of a spheroidal shell, flattened by at least 20% and having a projected position angle on the sky of approx. 37 degrees. Analysis of V838 Mon's polarized flux reveals that this electron scattering shell lies interior to the envelope region in which Halpha and Ca II triplet emission originates. To date, none of the theoretical models proposed for V838 Mon have demonstrated that they can reproduce the evolution of V838 Mon's inner circumstellar environment, as probed by spectropolarimetry.

  15. Promoting Reasoning through the Magic V Task

    ERIC Educational Resources Information Center

    Bragg, Leicha A.; Widjaja, Wanty; Loong, Esther Yook-Kin; Vale, Colleen; Herbert, Sandra

    2015-01-01

    Reasoning in mathematics plays a critical role in developing mathematical understandings. In this article, Bragg, Loong, Widjaja, Vale & Herbert explore an adaptation of the Magic V Task and how it was used in several classrooms to promote and develop reasoning skills.

  16. A review of plan library approaches in adaptive radiotherapy of bladder cancer.

    PubMed

    Collins, Shane D; Leech, Michelle M

    2018-05-01

    Large variations in the shape and size of the bladder volume are commonly observed in bladder cancer radiotherapy (RT). The clinical target volume (CTV) is therefore frequently inadequately treated and large isotropic margins are inappropriate in terms of dose to organs at risk (OAR); thereby making adaptive radiotherapy (ART) attractive for this tumour site. There are various methods of ART delivery, however, for bladder cancer, plan libraries are frequently used. A review of published studies on plan libraries for bladder cancer using four databases (Pubmed, Science Direct, Embase and Cochrane Library) was conducted. The endpoints selected were accuracy and feasibility of initiation of a plan library strategy into a RT department. Twenty-four articles were included in this review. The majority of studies reported improvement in accuracy with 10 studies showing an improvement in planning target volume (PTV) and CTV coverage with plan libraries, some by up to 24%. Seventeen studies showed a dose reduction to OARs, particularly the small bowel V45Gy, V40Gy, V30Gy and V10Gy, and the rectal V30Gy. However, the occurrence of no suitable plan was reported in six studies, with three studies showing no significant difference between adaptive and non-adaptive strategies in terms of target coverage. In addition, inter-observer variability in plan selection appears to remain problematic. The additional resources, education and technology required for the initiation of plan library selection for bladder cancer may hinder its routine clinical implementation, with eight studies illustrating increased treatment time required. While there is a growing body of evidence in support of plan libraries for bladder RT, many studies differed in their delivery approach. The advent of the clinical use of the MRI-linear accelerator will provide RT departments with the opportunity to consider daily online adaption for bladder cancer as an alternate to plan library approaches.

  17. A Comparison of a Brain-Based Adaptive System and a Manual Adaptable System for Invoking Automation

    NASA Technical Reports Server (NTRS)

    Bailey, Nathan R.; Scerbo, Mark W.; Freeman, Frederick G.; Mikulka, Peter J.; Scott, Lorissa A.

    2004-01-01

    Two experiments are presented that examine alternative methods for invoking automation. In each experiment, participants were asked to perform simultaneously a monitoring task and a resource management task as well as a tracking task that changed between automatic and manual modes. The monitoring task required participants to detect failures of an automated system to correct aberrant conditions under either high or low system reliability. Performance on each task was assessed as well as situation awareness and subjective workload. In the first experiment, half of the participants worked with a brain-based system that used their EEG signals to switch the tracking task between automatic and manual modes. The remaining participants were yoked to participants from the adaptive condition and received the same schedule of mode switches, but their EEG had no effect on the automation. Within each group, half of the participants were assigned to either the low or high reliability monitoring task. In addition, within each combination of automation invocation and system reliability, participants were separated into high and low complacency potential groups. The results revealed no significant effects of automation invocation on the performance measures; however, the high complacency individuals demonstrated better situation awareness when working with the adaptive automation system. The second experiment was the same as the first with one important exception. Automation was invoked manually. Thus, half of the participants pressed a button to invoke automation for 10 s. The remaining participants were yoked to participants from the adaptable condition and received the same schedule of mode switches, but they had no control over the automation. The results showed that participants who could invoke automation performed more poorly on the resource management task and reported higher levels of subjective workload. Further, those who invoked automation more frequently performed

  18. The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Blanc, Guillaume; Duncan, Garry A.; Agarakova, Irina

    Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might havemore » retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes.« less

  19. Advances in Rotor Performance and Turbulent Wake Simulation Using DES and Adaptive Mesh Refinement

    NASA Technical Reports Server (NTRS)

    Chaderjian, Neal M.

    2012-01-01

    Time-dependent Navier-Stokes simulations have been carried out for a rigid V22 rotor in hover, and a flexible UH-60A rotor in forward flight. Emphasis is placed on understanding and characterizing the effects of high-order spatial differencing, grid resolution, and Spalart-Allmaras (SA) detached eddy simulation (DES) in predicting the rotor figure of merit (FM) and resolving the turbulent rotor wake. The FM was accurately predicted within experimental error using SA-DES. Moreover, a new adaptive mesh refinement (AMR) procedure revealed a complex and more realistic turbulent rotor wake, including the formation of turbulent structures resembling vortical worms. Time-dependent flow visualization played a crucial role in understanding the physical mechanisms involved in these complex viscous flows. The predicted vortex core growth with wake age was in good agreement with experiment. High-resolution wakes for the UH-60A in forward flight exhibited complex turbulent interactions and turbulent worms, similar to the V22. The normal force and pitching moment coefficients were in good agreement with flight-test data.

  20. Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature fermentations.

    PubMed

    García-Ríos, Estéfani; López-Malo, María; Guillamón, José Manuel

    2014-12-03

    The wine industry needs better-adapted yeasts to grow at low temperature because it is interested in fermenting at low temperature to improve wine aroma. Elucidating the response to cold in Saccharomyces cerevisiae is of paramount importance for the selection or genetic improvement of wine strains. We followed a global approach by comparing transcriptomic, proteomic and genomic changes in two commercial wine strains, which showed clear differences in their growth and fermentation capacity at low temperature. These strains were selected according to the maximum growth rate in a synthetic grape must during miniaturized batch cultures at different temperatures. The fitness differences of the selected strains were corroborated by directly competing during fermentations at optimum and low temperatures. The up-regulation of the genes of the sulfur assimilation pathway and glutathione biosynthesis suggested a crucial role in better performance at low temperature. The presence of some metabolites of these pathways, such as S-Adenosilmethionine (SAM) and glutathione, counteracted the differences in growth rate at low temperature in both strains. Generally, the proteomic and genomic changes observed in both strains also supported the importance of these metabolic pathways in adaptation at low temperature. This work reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature. We propose that a greater activation of this metabolic route enhances the synthesis of key metabolites, such as glutathione, whose protective effects can contribute to improve the fermentation process.

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