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Sample records for acid cas reg

  1. 40 CFR 180.1023 - Propanoic acid; exemptions from the requirement of a tolerance.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... byproducts; milk, and egg when applied as a bactericide/fungicide to livestock drinking water, poultry litter... (CAS Reg. No. 79-09-4), propanioc acid, calcium salt (CAS Reg. No. 4075-81-4), and propanioc...

  2. 21 CFR 173.45 - Polymaleic acid and its sodium salt.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Polymaleic acid and its sodium salt. 173.45... Polymer Adjuvants for Food Treatment § 173.45 Polymaleic acid and its sodium salt. Polymaleic acid (CAS Reg. No. 26099-09-2) and its sodium salt (CAS Reg. No. 70247-90-4) may be safely used in food...

  3. 21 CFR 173.45 - Polymaleic acid and its sodium salt.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Polymaleic acid and its sodium salt. 173.45 Section 173.45 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... and its sodium salt. Polymaleic acid (CAS Reg. No. 26099-09-2) and its sodium salt (CAS Reg. No....

  4. 21 CFR 173.45 - Polymaleic acid and its sodium salt.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Polymaleic acid and its sodium salt. 173.45 Section 173.45 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED... sodium salt. Polymaleic acid (CAS Reg. No. 26099-09-2) and its sodium salt (CAS Reg. No. 70247-90-4)...

  5. 21 CFR 173.45 - Polymaleic acid and its sodium salt.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Polymaleic acid and its sodium salt. 173.45 Section 173.45 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... and its sodium salt. Polymaleic acid (CAS Reg. No. 26099-09-2) and its sodium salt (CAS Reg. No....

  6. 21 CFR 173.45 - Polymaleic acid and its sodium salt.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Polymaleic acid and its sodium salt. 173.45 Section 173.45 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... and its sodium salt. Polymaleic acid (CAS Reg. No. 26099-09-2) and its sodium salt (CAS Reg. No....

  7. 21 CFR 184.1069 - Malic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Malic acid. 184.1069 Section 184.1069 Food and....1069 Malic acid. (a) Malic acid (C4H6O5, CAS Reg. No. of L-form 97-67-6, CAS Reg. No. of DL-form 617-48-1) is the common name for 1-hydroxy-1, 2-ethanedicarboxylic acid. L (+) malic acid, referred to as...

  8. 21 CFR 184.1069 - Malic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Malic acid. 184.1069 Section 184.1069 Food and... Substances Affirmed as GRAS § 184.1069 Malic acid. (a) Malic acid (C4H6O5, CAS Reg. No. of L-form 97-67-6, CAS Reg. No. of DL-form 617-48-1) is the common name for 1-hydroxy-1, 2-ethanedicarboxylic acid....

  9. 21 CFR 184.1069 - Malic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Malic acid. 184.1069 Section 184.1069 Food and... Substances Affirmed as GRAS § 184.1069 Malic acid. (a) Malic acid (C4H6O5, CAS Reg. No. of L-form 97-67-6, CAS Reg. No. of DL-form 617-48-1) is the common name for 1-hydroxy-1, 2-ethanedicarboxylic acid....

  10. 21 CFR 184.1069 - Malic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Malic acid. 184.1069 Section 184.1069 Food and... Substances Affirmed as GRAS § 184.1069 Malic acid. (a) Malic acid (C4H6O5, CAS Reg. No. of L-form 97-67-6, CAS Reg. No. of DL-form 617-48-1) is the common name for 1-hydroxy-1, 2-ethanedicarboxylic acid....

  11. 21 CFR 184.1069 - Malic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Malic acid. 184.1069 Section 184.1069 Food and... Substances Affirmed as GRAS § 184.1069 Malic acid. (a) Malic acid (C4H6O5, CAS Reg. No. of L-form 97-67-6, CAS Reg. No. of DL-form 617-48-1) is the common name for 1-hydroxy-1, 2-ethanedicarboxylic acid....

  12. Chemical mechanical planarization of Ge2Sb2Te5 using IC1010 and Politex reg pads in acidic slurry

    NASA Astrophysics Data System (ADS)

    He, Ao-Dong; Liu, Bo; Song, Zhi-Tang; Wang, Liang-Yong; Liu, Wei-Li; Feng, Gao-Ming; Feng, Song-Lin

    2014-08-01

    In the paper, chemical mechanical planarization (CMP) of Ge2Sb2Te5 (GST) is investigated using IC1010 and Politex reg pads in acidic slurry. For the CMP with blank wafer, it is found that the removal rate (RR) of GST increases with the increase of pressure for both pads, but the RR of GST polished using IC1010 is far more than that of Politex reg. To check the surface defects, GST film is observed with an optical microscope (OM) and scanning electron microscope (SEM). For the CMP with Politex reg, many spots are observed on the surface of the blank wafer with OM, but no obvious spots are observed with SEM. With regard to the patterned wafer, a few stains are observed on the GST cell, but many residues are found on other area with OM. However, from SEM results, a few residues are observed on the GST cell, more dielectric loss is revealed about the trench structure. For the CMP with IC1010, the surface of the polished blank wafer suffers serious scratches found with both OM and SEM, which may result from a low hardness of GST, compared with those of IC1010 and abrasives. With regard to the patterned wafer, it can achieve a clean surface and almost no scratches are observed with OM, which may result from the high-hardness SiO2 film on the surface, not from the soft GST film across the whole wafer. From the SEM results, a clean interface and no residues are observed on the GST surface, and less dielectric loss is revealed. Compared with Politex reg, the patterned wafer can achieve a good performance after CMP using IC1010.

  13. 78 FR 20029 - Castor Oil, Polymer With Adipic Acid, Linoleic Acid, Oleic Acid and Ricinoleic Acid; Tolerance...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-03

    ... AGENCY 40 CFR Part 180 Castor Oil, Polymer With Adipic Acid, Linoleic Acid, Oleic Acid and Ricinoleic..., polymer with adipic acid, linoleic acid, oleic acid and ricinoleic acid (CAS Reg. No. 1357486-09- 9) when used as an inert ingredient in a pesticide formulation. Advance Polymer Technology submitted a...

  14. Safety assessment for octadecyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)-propionate (CAS Reg. No. 2082-79-3) from use in food contact applications.

    PubMed

    Neal-Kluever, April P; Bailey, Allan B; Hatwell, Karen R

    2015-12-01

    Octadecyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate (CAS Reg. No. 2082-79-3), currently marketed as Irganox 1076 (I-76), is a sterically hindered phenolic antioxidant used in a variety of organic substrates, including those used in the manufacture of food contact articles. In 2012, the US Food and Drug Administration (USFDA), Office of Food Additive Safety (OFAS), initiated a post-market re-evaluation of the food contact applications of I-76. This project aimed to ensure that current dietary exposures from the use of I-76 in food contact articles are accurately captured and the safety assessment considered all relevant and available toxicological information. To accomplish these aims, the USFDA reviewed the available toxicological studies and chemistry information on food contact applications of I-76. Based on this in-depth analysis, a NOAEL of 64 mg/kg-bw/d (female rats) from a chronic rat study and a cumulative estimated dietary intake (CEDI) of 4.5 mg/p/d, was used to calculate a margin of exposure (MOE) of ∼850. We concluded that the previous and current exposure levels provide an adequate margin of safety (MOS) and remain protective of human health for the regulated uses.

  15. 21 CFR 184.1007 - Aconitic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Aconitic acid. 184.1007 Section 184.1007 Food and....1007 Aconitic acid. (a) Aconitic acid (1,2,3-propenetricarboxylic acid (C6H6O6), CAS Reg. No. 000499-12... acid can be isolated during sugarcane processing, by precipitation as the calcium salt from cane...

  16. 21 CFR 184.1097 - Tannic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Tannic acid. 184.1097 Section 184.1097 Food and....1097 Tannic acid. (a) Tannic acid (CAS Reg. No. 1401-55-4), or hydrolyzable gallotannin, is a complex polyphenolic organic structure that yields gallic acid and either glucose or quinic acid as hydrolysis...

  17. 21 CFR 184.1097 - Tannic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Tannic acid. 184.1097 Section 184.1097 Food and... Substances Affirmed as GRAS § 184.1097 Tannic acid. (a) Tannic acid (CAS Reg. No. 1401-55-4), or hydrolyzable gallotannin, is a complex polyphenolic organic structure that yields gallic acid and either glucose or...

  18. 21 CFR 184.1097 - Tannic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Tannic acid. 184.1097 Section 184.1097 Food and... Substances Affirmed as GRAS § 184.1097 Tannic acid. (a) Tannic acid (CAS Reg. No. 1401-55-4), or hydrolyzable gallotannin, is a complex polyphenolic organic structure that yields gallic acid and either glucose or...

  19. 21 CFR 184.1097 - Tannic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Tannic acid. 184.1097 Section 184.1097 Food and... Substances Affirmed as GRAS § 184.1097 Tannic acid. (a) Tannic acid (CAS Reg. No. 1401-55-4), or hydrolyzable gallotannin, is a complex polyphenolic organic structure that yields gallic acid and either glucose or...

  20. 21 CFR 184.1097 - Tannic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Tannic acid. 184.1097 Section 184.1097 Food and... Substances Affirmed as GRAS § 184.1097 Tannic acid. (a) Tannic acid (CAS Reg. No. 1401-55-4), or hydrolyzable gallotannin, is a complex polyphenolic organic structure that yields gallic acid and either glucose or...

  1. 21 CFR 184.1005 - Acetic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Acetic acid. 184.1005 Section 184.1005 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DIRECT FOOD....1005 Acetic acid. (a) Acetic acid (C2H4O2, CAS Reg. No. 64-19-7) is known as ethanoic acid. It...

  2. 21 CFR 172.345 - Folic acid (folacin).

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Folic acid (folacin). 172.345 Section 172.345 Food... Special Dietary and Nutritional Additives § 172.345 Folic acid (folacin). Folic acid (CAS Reg. No. 59-30-3... following prescribed conditions: (a) Folic acid is the chemical N- amino]benzoyl]-L-glutamic acid. (b)...

  3. 21 CFR 172.345 - Folic acid (folacin).

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Folic acid (folacin). 172.345 Section 172.345 Food... Special Dietary and Nutritional Additives § 172.345 Folic acid (folacin). Folic acid (CAS Reg. No. 59-30-3... following prescribed conditions: (a) Folic acid is the chemical N- amino]benzoyl]-L-glutamic acid. (b)...

  4. 21 CFR 172.345 - Folic acid (folacin).

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Folic acid (folacin). 172.345 Section 172.345 Food... Special Dietary and Nutritional Additives § 172.345 Folic acid (folacin). Folic acid (CAS Reg. No. 59-30-3... following prescribed conditions: (a) Folic acid is the chemical N- amino]benzoyl]-L-glutamic acid. (b)...

  5. 21 CFR 184.1081 - Propionic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Propionic acid. 184.1081 Section 184.1081 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DIRECT FOOD....1081 Propionic acid. (a) Propionic acid (C3H6O2, CAS Reg. No. 79-09-4) is an oily liquid having...

  6. 21 CFR 184.1090 - Stearic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Stearic acid. 184.1090 Section 184.1090 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DIRECT FOOD....1090 Stearic acid. (a) Stearic acid (C18H36O2, CAS Reg. No. 57-11-4) is a white to yellowish...

  7. 21 CFR 184.1095 - Sulfuric acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Sulfuric acid. 184.1095 Section 184.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1095 Sulfuric acid. (a) Sulfuric acid (H2SO4, CAS Reg. No. 7664-93-9),...

  8. 21 CFR 184.1095 - Sulfuric acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Sulfuric acid. 184.1095 Section 184.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1095 Sulfuric acid. (a) Sulfuric acid (H2SO4, CAS Reg. No. 7664-93-9),...

  9. 21 CFR 184.1095 - Sulfuric acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Sulfuric acid. 184.1095 Section 184.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1095 Sulfuric acid. (a) Sulfuric acid (H2SO4, CAS Reg. No. 7664-93-9),...

  10. 21 CFR 184.1095 - Sulfuric acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Sulfuric acid. 184.1095 Section 184.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1095 Sulfuric acid. (a) Sulfuric acid (H2SO4, CAS Reg. No. 7664-93-9),...

  11. 21 CFR 184.1095 - Sulfuric acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Sulfuric acid. 184.1095 Section 184.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DIRECT FOOD....1095 Sulfuric acid. (a) Sulfuric acid (H2SO4, CAS Reg. No. 7664-93-9), also known as oil of vitriol,...

  12. 76 FR 7703 - 1,4-Benzenedicarboxylic Acid, Dimethyl Ester, Polymer With 1,4-Butanediol, Adipic Acid, and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-11

    ... AGENCY 40 CFR Part 180 1,4-Benzenedicarboxylic Acid, Dimethyl Ester, Polymer With 1,4- Butanediol, Adipic..., polymer with 1,4-butanediol, adipic acid, and hexamethylene diisocyanate (CAS Reg. No. 55231-08-8... residues of 1,4-benzenedicarboxylic acid, dimethyl ester, polymer with 1,4-butanediol, adipic acid,...

  13. Studies in Rheoencephalography (REG)

    DTIC Science & Technology

    2010-04-01

    In two series of experiments on anaesthetized rats (N = 40) (1) before and after 10 min, whole body exposures to 2.45 GHz CW microwaves, and (2...cardiovascular system by quantitative polygraphic measurement. In acute experi - ments on rats, EEG, REG, brain tissue DC impedance and temperature...measurements obtained with an experimental screening device (“Cerberus”); 3) to compare the results of REG measurements with results obtained

  14. 21 CFR 184.1091 - Succinic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Succinic acid. 184.1091 Section 184.1091 Food and... Substances Affirmed as GRAS § 184.1091 Succinic acid. (a) Succinic acid (C4H6O4, CAS Reg. No. 110-15-6), also referred to as amber acid and ethylenesuccinic acid, is the chemical 1,4-butanedioic acid. It...

  15. 21 CFR 184.1009 - Adipic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Adipic acid. 184.1009 Section 184.1009 Food and... Substances Affirmed as GRAS § 184.1009 Adipic acid. (a) Adipic acid (C6H10O4, CAS Reg. No. 00124-04-9) is also known as 1,4-butanedicarboxylic acid or hexane-dioic acid. It is prepared by nitric acid...

  16. 21 CFR 184.1091 - Succinic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Succinic acid. 184.1091 Section 184.1091 Food and... Substances Affirmed as GRAS § 184.1091 Succinic acid. (a) Succinic acid (C4H6O4, CAS Reg. No. 110-15-6), also referred to as amber acid and ethylenesuccinic acid, is the chemical 1,4-butanedioic acid. It...

  17. 21 CFR 184.1009 - Adipic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Adipic acid. 184.1009 Section 184.1009 Food and... Substances Affirmed as GRAS § 184.1009 Adipic acid. (a) Adipic acid (C6H10O4, CAS Reg. No. 00124-04-9) is also known as 1,4-butanedicarboxylic acid or hexane-dioic acid. It is prepared by nitric acid...

  18. 21 CFR 184.1009 - Adipic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Adipic acid. 184.1009 Section 184.1009 Food and... Substances Affirmed as GRAS § 184.1009 Adipic acid. (a) Adipic acid (C6H10O4, CAS Reg. No. 00124-04-9) is also known as 1,4-butanedicarboxylic acid or hexane-dioic acid. It is prepared by nitric acid...

  19. 21 CFR 184.1091 - Succinic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Succinic acid. 184.1091 Section 184.1091 Food and... Substances Affirmed as GRAS § 184.1091 Succinic acid. (a) Succinic acid (C4H6O4, CAS Reg. No. 110-15-6), also referred to as amber acid and ethylenesuccinic acid, is the chemical 1,4-butanedioic acid. It...

  20. 21 CFR 184.1091 - Succinic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Succinic acid. 184.1091 Section 184.1091 Food and....1091 Succinic acid. (a) Succinic acid (C4H6O4, CAS Reg. No. 110-15-6), also referred to as amber acid and ethylenesuccinic acid, is the chemical 1,4-butanedioic acid. It is commercially prepared...

  1. 21 CFR 184.1091 - Succinic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Succinic acid. 184.1091 Section 184.1091 Food and... Substances Affirmed as GRAS § 184.1091 Succinic acid. (a) Succinic acid (C4H6O4, CAS Reg. No. 110-15-6), also referred to as amber acid and ethylenesuccinic acid, is the chemical 1,4-butanedioic acid. It...

  2. 21 CFR 184.1009 - Adipic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Adipic acid. 184.1009 Section 184.1009 Food and....1009 Adipic acid. (a) Adipic acid (C6H10O4, CAS Reg. No. 00124-04-9) is also known as 1,4-butanedicarboxylic acid or hexane-dioic acid. It is prepared by nitric acid oxidation of cyclohexanol...

  3. 21 CFR 184.1009 - Adipic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Adipic acid. 184.1009 Section 184.1009 Food and... Substances Affirmed as GRAS § 184.1009 Adipic acid. (a) Adipic acid (C6H10O4, CAS Reg. No. 00124-04-9) is also known as 1,4-butanedicarboxylic acid or hexane-dioic acid. It is prepared by nitric acid...

  4. 75 FR 70236 - Hop Beta Acids; Receipt of Application for Emergency Exemption, Solicitation of Public Comment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-17

    ... AGENCY Hop Beta Acids; Receipt of Application for Emergency Exemption, Solicitation of Public Comment... Agriculture, and the Oregon Department of Agriculture to use hop beta acids (CAS Reg. No. none specified) to... exemption regional request for use of hop beta acids in honey bee hives to control varroa mites....

  5. 21 CFR 186.1316 - Formic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Formic acid. 186.1316 Section 186.1316 Food and... Substances Affirmed as GRAS § 186.1316 Formic acid. (a) Formic acid (CH2O2, CAS Reg. No. 64-18-6) is also referred to as methanoic acid or hydrogen carboxylic acid. It occurs naturally in some insects and...

  6. 21 CFR 184.1065 - Linoleic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Linoleic acid. 184.1065 Section 184.1065 Food and... Substances Affirmed as GRAS § 184.1065 Linoleic acid. (a) Linoleic acid ((Z, Z)-9, 12-octadecadienoic acid (C17H31COOH) (CAS Reg. No. 60-33-3)), a straight chain unsaturated fatty acid with a molecular weight of...

  7. 21 CFR 186.1316 - Formic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Formic acid. 186.1316 Section 186.1316 Food and... Substances Affirmed as GRAS § 186.1316 Formic acid. (a) Formic acid (CH2O2, CAS Reg. No. 64-18-6) is also referred to as methanoic acid or hydrogen carboxylic acid. It occurs naturally in some insects and...

  8. 21 CFR 184.1065 - Linoleic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Linoleic acid. 184.1065 Section 184.1065 Food and... Substances Affirmed as GRAS § 184.1065 Linoleic acid. (a) Linoleic acid ((Z, Z)-9, 12-octadecadienoic acid (C17H31COOH) (CAS Reg. No. 60-33-3)), a straight chain unsaturated fatty acid with a molecular weight of...

  9. 21 CFR 186.1316 - Formic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Formic acid. 186.1316 Section 186.1316 Food and... Substances Affirmed as GRAS § 186.1316 Formic acid. (a) Formic acid (CH2O2, CAS Reg. No. 64-18-6) is also referred to as methanoic acid or hydrogen carboxylic acid. It occurs naturally in some insects and...

  10. 21 CFR 186.1316 - Formic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Formic acid. 186.1316 Section 186.1316 Food and....1316 Formic acid. (a) Formic acid (CH2O2, CAS Reg. No. 64-18-6) is also referred to as methanoic acid or hydrogen carboxylic acid. It occurs naturally in some insects and is contained in the free...

  11. 21 CFR 186.1316 - Formic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Formic acid. 186.1316 Section 186.1316 Food and... Substances Affirmed as GRAS § 186.1316 Formic acid. (a) Formic acid (CH2O2, CAS Reg. No. 64-18-6) is also referred to as methanoic acid or hydrogen carboxylic acid. It occurs naturally in some insects and...

  12. 21 CFR 184.1065 - Linoleic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Linoleic acid. 184.1065 Section 184.1065 Food and... Substances Affirmed as GRAS § 184.1065 Linoleic acid. (a) Linoleic acid ((Z, Z)-9, 12-octadecadienoic acid (C17H31COOH) (CAS Reg. No. 60-33-3)), a straight chain unsaturated fatty acid with a molecular weight of...

  13. 76 FR 6347 - (S,S)-Ethylenediamine Disuccinic Acid Trisodium Salt; Exemption From the Requirement of a Tolerance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-04

    ... AGENCY 40 CFR Part 180 (S,S)-Ethylenediamine Disuccinic Acid Trisodium Salt; Exemption From the... disuccinic acid trisodium salt (CAS Reg. No. 178949-82-1) when used as an inert ingredient (sequestrant or...)-ethylenediamine disuccinic acid trisodium salt. DATES: This regulation is effective February 4, 2011....

  14. 21 CFR 172.345 - Folic acid (folacin).

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Folic acid (folacin). 172.345 Section 172.345 Food... Additives § 172.345 Folic acid (folacin). Folic acid (CAS Reg. No. 59-30-3), also known as folacin or folate...) Folic acid is the chemical N- amino]benzoyl]-L-glutamic acid. (b) Folic acid meets the specifications...

  15. 77 FR 68686 - Xylenesulfonic Acid, Sodium Salt; Exemption From the Requirement of a Tolerance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-16

    ... AGENCY 40 CFR Part 180 Xylenesulfonic Acid, Sodium Salt; Exemption From the Requirement of a Tolerance... an exemption from the requirement of a tolerance for residues of xylenesulfonic acid, sodium salt (also known as sodium xylene sulfonate) (CAS Reg. No. 1300-72-7) when used as an inert ingredient...

  16. 21 CFR 184.1033 - Citric acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Citric acid. 184.1033 Section 184.1033 Food and... Substances Affirmed as GRAS § 184.1033 Citric acid. (a) Citric acid (C6H8O7, CAS Reg. No. 77-92-9) is the compound 2-hydroxy-1,2,3-propanetricarboxylic acid. It is a naturally occurring constituent of plant...

  17. 21 CFR 184.1061 - Lactic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Lactic acid. 184.1061 Section 184.1061 Food and... Substances Affirmed as GRAS § 184.1061 Lactic acid. (a) Lactic acid (C3H6O3, CAS Reg. Nos.: dl mixture, 598-82-3; l-isomer, 79-33-4; d-isomer, 10326-41-7), the chemical 2-hydroxypropanoic acid,...

  18. 21 CFR 184.1005 - Acetic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Acetic acid. 184.1005 Section 184.1005 Food and... Substances Affirmed as GRAS § 184.1005 Acetic acid. (a) Acetic acid (C2H4O2, CAS Reg. No. 64-19-7) is known as ethanoic acid. It occurs naturally in plant and animal tissues. It is produced by fermentation...

  19. 21 CFR 184.1005 - Acetic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Acetic acid. 184.1005 Section 184.1005 Food and... Substances Affirmed as GRAS § 184.1005 Acetic acid. (a) Acetic acid (C2H4O2, CAS Reg. No. 64-19-7) is known as ethanoic acid. It occurs naturally in plant and animal tissues. It is produced by fermentation...

  20. 21 CFR 184.1061 - Lactic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Lactic acid. 184.1061 Section 184.1061 Food and... Substances Affirmed as GRAS § 184.1061 Lactic acid. (a) Lactic acid (C3H6O3, CAS Reg. Nos.: dl mixture, 598-82-3; l-isomer, 79-33-4; d-isomer, 10326-41-7), the chemical 2-hydroxypropanoic acid,...

  1. 21 CFR 184.1005 - Acetic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Acetic acid. 184.1005 Section 184.1005 Food and... Substances Affirmed as GRAS § 184.1005 Acetic acid. (a) Acetic acid (C2H4O2, CAS Reg. No. 64-19-7) is known as ethanoic acid. It occurs naturally in plant and animal tissues. It is produced by fermentation...

  2. 21 CFR 186.1093 - Sulfamic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Sulfamic acid. 186.1093 Section 186.1093 Food and... Substances Affirmed as GRAS § 186.1093 Sulfamic acid. (a) Sulfamic acid (H3NO3S, CAS Reg. No. 5329-14-6) is a white crystalline solid manufactured from urea, sulfur trioxide, and sulfuric acid. It is soluble...

  3. 21 CFR 184.1033 - Citric acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Citric acid. 184.1033 Section 184.1033 Food and... Substances Affirmed as GRAS § 184.1033 Citric acid. (a) Citric acid (C6H8O7, CAS Reg. No. 77-92-9) is the compound 2-hydroxy-1,2,3-propanetricarboxylic acid. It is a naturally occurring constituent of plant...

  4. 21 CFR 184.1033 - Citric acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Citric acid. 184.1033 Section 184.1033 Food and....1033 Citric acid. (a) Citric acid (C6H8O7, CAS Reg. No. 77-92-9) is the compound 2-hydroxy-1,2,3-propanetricarboxylic acid. It is a naturally occurring constituent of plant and animal tissues. It occurs as...

  5. 21 CFR 186.1093 - Sulfamic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Sulfamic acid. 186.1093 Section 186.1093 Food and....1093 Sulfamic acid. (a) Sulfamic acid (H3NO3S, CAS Reg. No. 5329-14-6) is a white crystalline solid manufactured from urea, sulfur trioxide, and sulfuric acid. It is soluble and highly ionized in water. (b)...

  6. 21 CFR 184.1061 - Lactic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Lactic acid. 184.1061 Section 184.1061 Food and... Substances Affirmed as GRAS § 184.1061 Lactic acid. (a) Lactic acid (C3H6O3, CAS Reg. Nos.: dl mixture, 598-82-3; l-isomer, 79-33-4; d-isomer, 10326-41-7), the chemical 2-hydroxypropanoic acid,...

  7. 21 CFR 184.1033 - Citric acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Citric acid. 184.1033 Section 184.1033 Food and... Substances Affirmed as GRAS § 184.1033 Citric acid. (a) Citric acid (C6H8O7, CAS Reg. No. 77-92-9) is the compound 2-hydroxy-1,2,3-propanetricarboxylic acid. It is a naturally occurring constituent of plant...

  8. 21 CFR 184.1099 - Tartaric acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Tartaric acid. 184.1099 Section 184.1099 Food and....1099 Tartaric acid. (a) Food grade tartaric acid (C4H6O6, CAS Reg. No. 87-69-4) has the l configuration. The l form of tartaric acid is dextrorotatory in solution and is also known as l−(+)−tartaric...

  9. 21 CFR 184.1061 - Lactic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Lactic acid. 184.1061 Section 184.1061 Food and....1061 Lactic acid. (a) Lactic acid (C3H6O3, CAS Reg. Nos.: dl mixture, 598-82-3; l-isomer, 79-33-4; d-isomer, 10326-41-7), the chemical 2-hydroxypropanoic acid, occurs naturally in several foods. It...

  10. 21 CFR 184.1099 - Tartaric acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Tartaric acid. 184.1099 Section 184.1099 Food and... Substances Affirmed as GRAS § 184.1099 Tartaric acid. (a) Food grade tartaric acid (C4H6O6, CAS Reg. No. 87-69-4) has the l configuration. The l form of tartaric acid is dextrorotatory in solution and is...

  11. 21 CFR 184.1099 - Tartaric acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Tartaric acid. 184.1099 Section 184.1099 Food and... Substances Affirmed as GRAS § 184.1099 Tartaric acid. (a) Food grade tartaric acid (C4H6O6, CAS Reg. No. 87-69-4) has the l configuration. The l form of tartaric acid is dextrorotatory in solution and is...

  12. 21 CFR 186.1093 - Sulfamic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Sulfamic acid. 186.1093 Section 186.1093 Food and... Substances Affirmed as GRAS § 186.1093 Sulfamic acid. (a) Sulfamic acid (H3NO3S, CAS Reg. No. 5329-14-6) is a white crystalline solid manufactured from urea, sulfur trioxide, and sulfuric acid. It is soluble...

  13. 21 CFR 184.1061 - Lactic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Lactic acid. 184.1061 Section 184.1061 Food and... Substances Affirmed as GRAS § 184.1061 Lactic acid. (a) Lactic acid (C3H6O3, CAS Reg. Nos.: dl mixture, 598-82-3; l-isomer, 79-33-4; d-isomer, 10326-41-7), the chemical 2-hydroxypropanoic acid,...

  14. 21 CFR 184.1033 - Citric acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Citric acid. 184.1033 Section 184.1033 Food and... Substances Affirmed as GRAS § 184.1033 Citric acid. (a) Citric acid (C6H8O7, CAS Reg. No. 77-92-9) is the compound 2-hydroxy-1,2,3-propanetricarboxylic acid. It is a naturally occurring constituent of plant...

  15. 21 CFR 186.1093 - Sulfamic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Sulfamic acid. 186.1093 Section 186.1093 Food and... Substances Affirmed as GRAS § 186.1093 Sulfamic acid. (a) Sulfamic acid (H3NO3S, CAS Reg. No. 5329-14-6) is a white crystalline solid manufactured from urea, sulfur trioxide, and sulfuric acid. It is soluble...

  16. 21 CFR 184.1099 - Tartaric acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Tartaric acid. 184.1099 Section 184.1099 Food and... Substances Affirmed as GRAS § 184.1099 Tartaric acid. (a) Food grade tartaric acid (C4H6O6, CAS Reg. No. 87-69-4) has the l configuration. The l form of tartaric acid is dextrorotatory in solution and is...

  17. 21 CFR 184.1005 - Acetic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Acetic acid. 184.1005 Section 184.1005 Food and... Substances Affirmed as GRAS § 184.1005 Acetic acid. (a) Acetic acid (C2H4O2, CAS Reg. No. 64-19-7) is known as ethanoic acid. It occurs naturally in plant and animal tissues. It is produced by fermentation...

  18. 21 CFR 184.1099 - Tartaric acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Tartaric acid. 184.1099 Section 184.1099 Food and... Substances Affirmed as GRAS § 184.1099 Tartaric acid. (a) Food grade tartaric acid (C4H6O6, CAS Reg. No. 87-69-4) has the l configuration. The l form of tartaric acid is dextrorotatory in solution and is...

  19. 21 CFR 186.1093 - Sulfamic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Sulfamic acid. 186.1093 Section 186.1093 Food and... Substances Affirmed as GRAS § 186.1093 Sulfamic acid. (a) Sulfamic acid (H3NO3S, CAS Reg. No. 5329-14-6) is a white crystalline solid manufactured from urea, sulfur trioxide, and sulfuric acid. It is soluble...

  20. 21 CFR 184.1077 - Potassium acid tartrate.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Potassium acid tartrate. 184.1077 Section 184.1077... Listing of Specific Substances Affirmed as GRAS § 184.1077 Potassium acid tartrate. (a) Potassium acid tartrate (C4H5KO6, CAS Reg. No. 868-14-4) is the potassium acid salt of l−(+)−tartaric acid and is...

  1. 21 CFR 184.1077 - Potassium acid tartrate.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Potassium acid tartrate. 184.1077 Section 184.1077... Listing of Specific Substances Affirmed as GRAS § 184.1077 Potassium acid tartrate. (a) Potassium acid tartrate (C4H5KO6, CAS Reg. No. 868-14-4) is the potassium acid salt of l−(+)−tartaric acid and is...

  2. 21 CFR 184.1077 - Potassium acid tartrate.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Potassium acid tartrate. 184.1077 Section 184.1077... GRAS § 184.1077 Potassium acid tartrate. (a) Potassium acid tartrate (C4H5KO6, CAS Reg. No. 868-14-4) is the potassium acid salt of l−(+)−tartaric acid and is also called potassium bitartrate or cream...

  3. 21 CFR 184.1077 - Potassium acid tartrate.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Potassium acid tartrate. 184.1077 Section 184.1077... Listing of Specific Substances Affirmed as GRAS § 184.1077 Potassium acid tartrate. (a) Potassium acid tartrate (C4H5KO6, CAS Reg. No. 868-14-4) is the potassium acid salt of l−(+)−tartaric acid and is...

  4. 21 CFR 184.1077 - Potassium acid tartrate.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Potassium acid tartrate. 184.1077 Section 184.1077... Listing of Specific Substances Affirmed as GRAS § 184.1077 Potassium acid tartrate. (a) Potassium acid tartrate (C4H5KO6, CAS Reg. No. 868-14-4) is the potassium acid salt of l−(+)−tartaric acid and is...

  5. 21 CFR 173.395 - Trifluoromethane sulfonic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... CF3SO3H (CAS Reg. No. 1493-13-6). The catalyst (Trifluoromethane sulfonic acid) may safely be used in the... chapter) in accordance with the following conditions: (a) The catalyst meets the following specifications... steam and water and the catalyst is removed with the aqueous phase. Final traces of catalyst are...

  6. 21 CFR 173.395 - Trifluoromethane sulfonic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... sulfonic acid has the empirical formula CF3SO3H (CAS Reg. No. 1493-13-6). The catalyst (Trifluoromethane... catalyst meets the following specifications: Appearance, Clear liquid. Color, Colorless to amber... esterification reaction is quenched with steam and water and the catalyst is removed with the aqueous...

  7. 21 CFR 173.395 - Trifluoromethane sulfonic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... sulfonic acid has the empirical formula CF3SO3H (CAS Reg. No. 1493-13-6). The catalyst (Trifluoromethane... catalyst meets the following specifications: Appearance, Clear liquid. Color, Colorless to amber... esterification reaction is quenched with steam and water and the catalyst is removed with the aqueous...

  8. 21 CFR 173.395 - Trifluoromethane sulfonic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... sulfonic acid has the empirical formula CF3SO3H (CAS Reg. No. 1493-13-6). The catalyst (Trifluoromethane... catalyst meets the following specifications: Appearance, Clear liquid. Color, Colorless to amber... esterification reaction is quenched with steam and water and the catalyst is removed with the aqueous...

  9. NUHOMS{reg_sign} update

    SciTech Connect

    Rich, N.

    1995-12-31

    NUHOMS{reg_sign} is the dry spent fuel storage and transportation technology selected to date by the majority of commercial nuclear utilities. The author first gives a system overview of the NUHOMS{reg_sign}. Next she discusses the project status and licensing status. She closes with an update of the multi-purpose canister.

  10. 21 CFR 184.1081 - Propionic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Propionic acid. 184.1081 Section 184.1081 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1081 Propionic acid. (a) Propionic acid (C3H6O2, CAS Reg. No. 79-09-4)...

  11. 21 CFR 184.1081 - Propionic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Propionic acid. 184.1081 Section 184.1081 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1081 Propionic acid. (a) Propionic acid (C3H6O2, CAS Reg. No. 79-09-4)...

  12. 21 CFR 184.1090 - Stearic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Stearic acid. 184.1090 Section 184.1090 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1090 Stearic acid. (a) Stearic acid (C18H36O2, CAS Reg. No. 57-11-4) is...

  13. 21 CFR 184.1081 - Propionic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Propionic acid. 184.1081 Section 184.1081 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1081 Propionic acid. (a) Propionic acid (C3H6O2, CAS Reg. No. 79-09-4)...

  14. 21 CFR 184.1090 - Stearic acid.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Stearic acid. 184.1090 Section 184.1090 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1090 Stearic acid. (a) Stearic acid (C18H36O2, CAS Reg. No. 57-11-4) is...

  15. 21 CFR 184.1090 - Stearic acid.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Stearic acid. 184.1090 Section 184.1090 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1090 Stearic acid. (a) Stearic acid (C18H36O2, CAS Reg. No. 57-11-4) is...

  16. 21 CFR 184.1081 - Propionic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Propionic acid. 184.1081 Section 184.1081 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1081 Propionic acid. (a) Propionic acid (C3H6O2, CAS Reg. No. 79-09-4)...

  17. 21 CFR 184.1090 - Stearic acid.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Stearic acid. 184.1090 Section 184.1090 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1090 Stearic acid. (a) Stearic acid (C18H36O2, CAS Reg. No. 57-11-4) is...

  18. Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing.

    PubMed

    Jiang, Wen Zhi; Henry, Isabelle M; Lynagh, Peter G; Comai, Luca; Cahoon, Edgar B; Weeks, Donald P

    2016-11-11

    The CRISPR/Cas9 nuclease system is a powerful and flexible tool for genome editing, and novel applications of this system are being developed rapidly. Here, we used CRISPR/Cas9 to target the FAD2 gene in Arabidopsis thaliana and in the closely related emerging oil seed plant, Camelina sativa, with the goal of improving seed oil composition. We successfully obtained Camelina seeds in which oleic acid content was increased from 16% to over 50% of the fatty acid composition. These increases were associated with significant decreases in the less desirable polyunsaturated fatty acids, linoleic acid (i.e. a decrease from ~16% to <4%) and linolenic acid (a decrease from ~35% to <10%). These changes result in oils that are superior on multiple levels: they are healthier, more oxidatively stable and better suited for production of certain commercial chemicals, including biofuels. As expected, A. thaliana T2 and T3 generation seeds exhibiting these types of altered fatty acid profiles were homozygous for disrupted FAD2 alleles. In the allohexaploid, Camelina, guide RNAs were designed that simultaneously targeted all three homoeologous FAD2 genes. This strategy that significantly enhanced oil composition in T3 and T4 generation Camelina seeds was associated with a combination of germ-line mutations and somatic cell mutations in FAD2 genes in each of the three Camelina subgenomes.

  19. Cas9 Functionally Opens Chromatin

    PubMed Central

    Barkal, Amira A.; Srinivasan, Sharanya; Hashimoto, Tatsunori; Gifford, David K.; Sherwood, Richard I.

    2016-01-01

    Using a nuclease-dead Cas9 mutant, we show that Cas9 reproducibly induces chromatin accessibility at previously inaccessible genomic loci. Cas9 chromatin opening is sufficient to enable adjacent binding and transcriptional activation by the settler transcription factor retinoic acid receptor at previously unbound motifs. Thus, we demonstrate a new use for Cas9 in increasing surrounding chromatin accessibility to alter local transcription factor binding. PMID:27031353

  20. CRISPR/Cas9-mediated gene manipulation to create single-amino-acid-substituted and floxed mice with a cloning-free method

    PubMed Central

    Ma, Xiaolong; Chen, Chao; Veevers, Jennifer; Zhou, XinMin; Ross, Robert S.; Feng, Wei; Chen, Ju

    2017-01-01

    Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology is a powerful tool to manipulate the genome with extraordinary simplicity and speed. To generate genetically modified animals, CRISPR/Cas9-mediated genome editing is typically accomplished by microinjection of a mixture of Cas9 DNA/mRNA and single-guide RNA (sgRNA) into zygotes. However, sgRNAs used for this approach require manipulation via molecular cloning as well as in vitro transcription. Beyond these complexities, most mutants obtained with this traditional approach are genetically mosaic, yielding several types of cells with different genetic mutations. Recently, a growing body of studies has utilized commercially available Cas9 protein together with sgRNA and a targeting construct to introduce desired mutations. Here, we report a cloning-free method to target the mouse genome by pronuclear injection of a commercial Cas9 protein:crRNA:tracrRNA:single-strand oligodeoxynucleotide (ssODN) complex into mouse zygotes. As illustration of this method, we report the successful generation of global gene-knockout, single-amino-acid-substituted, as well as floxed mice that can be used for conditional gene-targeting. These models were produced with high efficiency to generate non-mosaic mutant mice with a high germline transmission rate. PMID:28176880

  1. CRISPR/Cas9-mediated gene manipulation to create single-amino-acid-substituted and floxed mice with a cloning-free method.

    PubMed

    Ma, Xiaolong; Chen, Chao; Veevers, Jennifer; Zhou, XinMin; Ross, Robert S; Feng, Wei; Chen, Ju

    2017-02-08

    Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology is a powerful tool to manipulate the genome with extraordinary simplicity and speed. To generate genetically modified animals, CRISPR/Cas9-mediated genome editing is typically accomplished by microinjection of a mixture of Cas9 DNA/mRNA and single-guide RNA (sgRNA) into zygotes. However, sgRNAs used for this approach require manipulation via molecular cloning as well as in vitro transcription. Beyond these complexities, most mutants obtained with this traditional approach are genetically mosaic, yielding several types of cells with different genetic mutations. Recently, a growing body of studies has utilized commercially available Cas9 protein together with sgRNA and a targeting construct to introduce desired mutations. Here, we report a cloning-free method to target the mouse genome by pronuclear injection of a commercial Cas9 protein:crRNA:tracrRNA:single-strand oligodeoxynucleotide (ssODN) complex into mouse zygotes. As illustration of this method, we report the successful generation of global gene-knockout, single-amino-acid-substituted, as well as floxed mice that can be used for conditional gene-targeting. These models were produced with high efficiency to generate non-mosaic mutant mice with a high germline transmission rate.

  2. Amylase and chitinase genes in Streptomyces lividans are regulated by reg1, a pleiotropic regulatory gene.

    PubMed Central

    Nguyen, J; Francou, F; Virolle, M J; Guérineau, M

    1997-01-01

    A regulatory gene, reg1, was identified in Streptomyces lividans. It encodes a 345-amino-acid protein (Reg1) which contains a helix-turn-helix DNA-binding motif in the N-terminal region. Reg1 exhibits similarity with the LacI/GalR family members over the entire sequence. It displays 95% identity with MalR (the repressor of malE in S. coelicolor), 65% identity with ORF-Sl (a putative regulatory gene of alpha-amylase of S. limosus), and 31% identity with CcpA (the carbon catabolite repressor in Bacillus subtilis). In S. lividans, the chromosomal disruption of reg1 affected the expression of several genes. The production of alpha-amylases of S. lividans and that of the alpha-amylase of S. limosus in S. lividans were enhanced in the reg1 mutant strains and relieved of carbon catabolite repression. As a result, the transcription level of the alpha-amylase of S. limosus was noticeably increased in the reg1 mutant strain. Moreover, the induction of chitinase production in S. lividans was relieved of carbon catabolite repression by glucose in the reg1 mutant strain, while the induction by chitin was lost. Therefore, reg1 can be regarded as a pleiotropic regulatory gene in S. lividans. PMID:9335287

  3. Pickliq{reg_sign} Process Pilot Program. Quarterly report, 2nd quarter 1997

    SciTech Connect

    1997-07-22

    Work on the funded project was completed during this period. The final report will be issued within the next week. The Pickliq{reg_sign} Process has been found to be economically viable in the copper industry and is expected to be viable in steel-hydrochloric acid applications with the development of a new hydrochloric acid regeneration process associated with the Pickliq{reg_sign} Process.

  4. New CRISPR-Cas systems discovered.

    PubMed

    Yang, Hui; Patel, Dinshaw J

    2017-03-01

    In bacteria and archaea, CRISPR-Cas adaptive immune systems utilize RNA-guided endonucleases to defend against invasion by foreign nucleic acids of bacteriophage, virus and plasmid origin. In a recent paper published in Nature, Burstein et al. identified the first Cas9 protein in uncultivated archaea and two novel CRISPR-CasX and CRISPR-CasY systems in uncultivated bacteria by capitalizing on analysis of terabase-scale metagenomic datasets from natural uncultivated organisms.

  5. Ultra-superovulation for the CRISPR-Cas9-mediated production of gene-knockout, single-amino-acid-substituted, and floxed mice.

    PubMed

    Nakagawa, Yoshiko; Sakuma, Tetsushi; Nishimichi, Norihisa; Yokosaki, Yasuyuki; Yanaka, Noriyuki; Takeo, Toru; Nakagata, Naomi; Yamamoto, Takashi

    2016-08-15

    Current advances in producing genetically modified mice using genome-editing technologies have indicated the need for improvement of limiting factors including zygote collection for microinjection and their cryopreservation. Recently, we developed a novel superovulation technique using inhibin antiserum and equine chorionic gonadotropin to promote follicle growth. This method enabled the increased production of fertilized oocytes via in vitro fertilization compared with the conventional superovulation method. Here, we verify that the ultra-superovulation technique can be used for the efficient generation of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated knockout mice by microinjection of plasmid vector or ribonucleoprotein into zygotes. We also investigated whether single-amino-acid-substituted mice and conditional knockout mice could be generated. Founder mice bearing base substitutions were generated more efficiently by co-microinjection of Cas9 protein, a guide RNA and single-stranded oligodeoxynucleotide (ssODN) than by plasmid microinjection with ssODN. The conditional allele was successfully introduced by the one-step insertion of an ssODN designed to carry an exon flanked by two loxP sequences and homology arms using a double-cut CRISPR-Cas9 strategy. Our study presents a useful method for the CRISPR-Cas9-based generation of genetically modified mice from the viewpoints of animal welfare and work efficiency.

  6. Flemion {reg_sign}S and PEFC

    SciTech Connect

    Yoshitake, M.; Yoshida, N.; Ishisaki, T.

    1996-12-31

    Asahi Glass Co., Ltd. (AGC) had commercialized chloro-alkali electrolysis process using perfluorinated ion exchange membranes (Flemion{reg_sign}). AGC participated in the PEFC project of NEDO (New Energy and Industrial Technology Development Organization) which started in the fiscal year 1992. In this program, AGC selected Flemion{reg_sign}S as one of the candidate membranes for PEFC. The properties of Flemion{reg_sign}S and Nafion{reg_sign}117 such as thermal stability, mechanical strength in dry and wet state, water content, AC specific resistance and gas permeability in dry and wet state, were evaluated and a new method of the preparation of membrane-electrode composites was developed.

  7. REG3A — EDRN Public Portal

    Cancer.gov

    REG3 is a pancreatic secretory protein that may be involved in cell proliferation or differentiation. It has similarity to the C-type lectin superfamily. The enhanced expression of this gene is observed during pancreatic inflammation and liver carcinogenesis.

  8. The effects of RegM on stress responses in Brucella melitensis.

    PubMed

    Dong, Hao; Liu, Wenjuan; Peng, Xiaowei; Wu, Qingmin

    2015-05-01

    Brucella melitensis is a facultative intracellular pathogen. The regM gene encodes a sensory transduction protein kinase in B. melitensis 16M, and genes orthologous to regM have been found to exist in many bacterial species. However, little is known about the regulation function of this gene in Brucella. In order to characterize this gene, we constructed a marked deletion mutant of regM as well as its complemented strain. The mutant was less able to withstand acid and hyperosmotic conditions than wild-type strain but shown no significant difference with wild-type strain when challenged by elevated temperature and hypotonic conditions. In addition, inactivation of regM did not affect virulence in B. melitensis 16M in macrophage and mice infection models.

  9. Stage-specific hypermutability of the regA locus of Volvox, a gene regulating the germ-soma dichotomy

    SciTech Connect

    Kirk, D.L.; Baran, G.J.; Harper, J.F.; Huskey, R.J.; Huson, K.S.; Zagris, N.

    1987-01-16

    Mutation at the regA locus confers on somatic cells of Volvox (which otherwise undergo programmed death) ability to redifferentiate as reproductive cells. Stable mutations at the regA locus, but not at other loci, were induced at high frequency when embryos at one particular stage were exposed to either UV irradiation, novobiocin, nalidixic acid, bleomycin, 4-hydroxyaminoquinoline-1-oxide, 5-bromodeoxyuridine, or 5-fluorouracil. All treatments led to some mutations that were not expressed until the second generation after treatment. The sensitive period was after somatic and reproductive cells of the next generation had been set apart, but before they had undergone cytodifferentiation. Hypermutability occurs in presumptive reproductive cells (in which regA is normally not expressed) somewhat before regA normally acts in somatic cells. We postulate that hypermutability of regA in the reproductive cells at this time reflects a change of state that the locus undergoes as it is inactivated.

  10. Production of α1,3-galactosyltransferase and cytidine monophosphate-N-acetylneuraminic acid hydroxylase gene double-deficient pigs by CRISPR/Cas9 and handmade cloning

    PubMed Central

    GAO, Hanchao; ZHAO, Chengjiang; XIANG, Xi; LI, Yong; ZHAO, Yanli; LI, Zesong; PAN, Dengke; DAI, Yifan; HARA, Hidetaka; COOPER, David K.C.; CAI, Zhiming; MOU, Lisha

    2016-01-01

    Gene-knockout pigs hold great promise as a solution to the shortage of organs from donor animals for xenotransplantation. Several groups have generated gene-knockout pigs via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) and somatic cell nuclear transfer (SCNT). Herein, we adopted a simple and micromanipulator-free method, handmade cloning (HMC) instead of SCNT, to generate double gene-knockout pigs. First, we applied the CRISPR/Cas9 system to target α1,3-galactosyltransferase (GGTA1) and cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) genes simultaneously in porcine fetal fibroblast cells (PFFs), which were derived from wild-type Chinese domestic miniature Wuzhishan pigs. Cell colonies were obtained by screening and were identified by Surveyor assay and sequencing. Next, we chose the GGTA1/CMAH double-knockout (DKO) cells for HMC to produce piglets. As a result, we obtained 11 live bi-allelic GGTA1/CMAH DKO piglets with the identical phenotype. Compared to cells from GGTA1-knockout pigs, human antibody binding and antibody-mediated complement-dependent cytotoxicity were significantly reduced in cells from GGTA1/CMAH DKO pigs, which demonstrated that our pigs would exhibit reduced humoral rejection in xenotransplantation. These data suggested that the combination of CRISPR/Cas9 and HMC technology provided an efficient and new strategy for producing pigs with multiple genetic modifications. PMID:27725344

  11. Production of α1,3-galactosyltransferase and cytidine monophosphate-N-acetylneuraminic acid hydroxylase gene double-deficient pigs by CRISPR/Cas9 and handmade cloning.

    PubMed

    Gao, Hanchao; Zhao, Chengjiang; Xiang, Xi; Li, Yong; Zhao, Yanli; Li, Zesong; Pan, Dengke; Dai, Yifan; Hara, Hidetaka; Cooper, David K C; Cai, Zhiming; Mou, Lisha

    2017-02-16

    Gene-knockout pigs hold great promise as a solution to the shortage of organs from donor animals for xenotransplantation. Several groups have generated gene-knockout pigs via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) and somatic cell nuclear transfer (SCNT). Herein, we adopted a simple and micromanipulator-free method, handmade cloning (HMC) instead of SCNT, to generate double gene-knockout pigs. First, we applied the CRISPR/Cas9 system to target α1,3-galactosyltransferase (GGTA1) and cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) genes simultaneously in porcine fetal fibroblast cells (PFFs), which were derived from wild-type Chinese domestic miniature Wuzhishan pigs. Cell colonies were obtained by screening and were identified by Surveyor assay and sequencing. Next, we chose the GGTA1/CMAH double-knockout (DKO) cells for HMC to produce piglets. As a result, we obtained 11 live bi-allelic GGTA1/CMAH DKO piglets with the identical phenotype. Compared to cells from GGTA1-knockout pigs, human antibody binding and antibody-mediated complement-dependent cytotoxicity were significantly reduced in cells from GGTA1/CMAH DKO pigs, which demonstrated that our pigs would exhibit reduced humoral rejection in xenotransplantation. These data suggested that the combination of CRISPR/Cas9 and HMC technology provided an efficient and new strategy for producing pigs with multiple genetic modifications.

  12. Pilot test of Pickliq{reg_sign} process to determine energy and environmental benefits & economic feasibility

    SciTech Connect

    Olsen, D.R.

    1997-07-13

    Green Technology Group (GTG) was awarded Grant No. DE-FG01-96EE 15657 in the amount of $99,904 for a project to advance GTG`s Pickliq{reg_sign} Process in the Copper and Steel Industries. The use of the Pickliq{reg_sign} Process can significantly reduce the production of waste acids containing metal salts. The Pickliq{reg_sign} Process can save energy and eliminate hazardous waste in a typical copper rod or wire mill or a typical steel wire mill. The objective of this pilot project was to determine the magnitude of the economic, energy and environmental benefits of the Pickliq{reg_sign} Process in two applications within the metal processing industry. The effectiveness of the process has already been demonstrated at facilities cleaning iron and steel with sulfuric acid. 9207 companies are reported to use sulfuric and hydrochloric acid in the USA. The USEPA TRI statistics of acid not recycled in the US is 2.4 x 10{sup 9} lbs (net) for Hydrochloric Acid and 2.0 x 10{sup 9} lbs (net) for Sulfuric Acid. The energy cost of not reclaiming acid is 10.7 x 10{sup 6} BTU/ton for Hydrochloric Acid and 21.6 x 10{sup 6} BTU/Ton for Sulfuric Acid. This means that there is a very large market for the application of the Pickliq{reg_sign} Process and the widespread use of the process will bring significant world wide savings of energy to the environment.

  13. 12 CFR 742.4 - RegFlex relief.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 7 2012-01-01 2012-01-01 false RegFlex relief. 742.4 Section 742.4 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS REGULATORY FLEXIBILITY PROGRAM § 742.4 RegFlex relief. (a) Exemptions. RegFlex credit unions are exempt from the...

  14. 12 CFR 742.4 - RegFlex relief.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 6 2011-01-01 2011-01-01 false RegFlex relief. 742.4 Section 742.4 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS REGULATORY FLEXIBILITY PROGRAM § 742.4 RegFlex relief. (a) Exemptions. RegFlex credit unions are exempt from the...

  15. RegB/RegA, a Highly Conserved Redox-Responding Global Two-Component Regulatory System

    PubMed Central

    Elsen, Sylvie; Swem, Lee R.; Swem, Danielle L.; Bauer, Carl E.

    2004-01-01

    The Reg regulon from Rhodobacter capsulatus and Rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. The redox signal that is detected by the membrane-bound sensor kinase, RegB, appears to originate from the aerobic respiratory chain, given that mutations in cytochrome c oxidase result in constitutive RegB autophosphorylation. Regulation of RegB autophosphorylation also involves a redox-active cysteine that is present in the cytosolic region of RegB. Both phosphorylated and unphosphorylated forms of the cognate response regulator RegA are capable of activating or repressing a variety of genes in the regulon. Highly conserved homologues of RegB and RegA have been found in a wide number of photosynthetic and nonphotosynthetic bacteria, with evidence suggesting that RegB/RegA plays a fundamental role in the transcription of redox-regulated genes in many bacterial species. PMID:15187184

  16. CAS77 and CAS7276: A Review.

    ERIC Educational Resources Information Center

    Harrison, Isom, Jr.

    This paper describes the content, organization, specifications, and methods of use of the CAS77 and CAS7276 online files of worldwide chemical literature, databases produced by Chemical Abstracts Service and available from System Development Corporation (SDC). The scope of the databases, their unit record, their data elements, their modes of…

  17. Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system.

    PubMed

    Wilkinson, Max E; Nakatani, Yoshio; Staals, Raymond H J; Kieper, Sebastian N; Opel-Reading, Helen K; McKenzie, Rebecca E; Fineran, Peter C; Krause, Kurt L

    2016-04-15

    CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogen Pectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptation in vivo and requires a conserved aspartic acid residue. By X-ray crystallography, we show that although P. atrosepticum Cas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.

  18. xdamp: An IDL{reg_sign}-based Data Manipulation Program

    SciTech Connect

    Ballard, W.P.

    1995-04-01

    The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA{trademark} (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of UNIX{reg_sign}-based workstations, a replacement was needed. This package uses the IDL{reg_sign} software, available from Research Systems Incorporated in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP. IDL is currently supported on a wide variety of UNIX platforms such as IBM{reg_sign} workstations, Hewlett Packard workstations, SUN{reg_sign} workstations, Microsoft{reg_sign} Windows{trademark} computers, Macintosh{reg_sign} computers and Digital Equipment Corporation VMS{reg_sign} systems. Thus, this program should be portable across many platforms. We have verified operation, albeit with some IDL bugs, on IBM UNIX platforms, DEC Alpha systems, HP 9000/7OO series workstations, and Macintosh computers, both regular and PowerPC{trademark} versions.

  19. PP1 phosphatase-binding motif in Reg1 protein of Saccharomyces cerevisiae is required for interaction with both the PP1 phosphatase Glc7 and the Snf1 protein kinase

    PubMed Central

    Tabba, Shadi; Mangat, Simmanjeet; McCartney, Rhonda; Schmidt, Martin C.

    2010-01-01

    In Saccharomyces cerevisiae, Snf1 kinase, the ortholog of the mammalian AMP-activated protein kinase, is activated by an increase in the phosphorylation of the conserved threonine residue in its activation loop. The phosphorylation status of this key site is determined by changes in the rate of dephosphorylation catalyzed by the yeast PP1 phosphatase Glc7 in a complex with the Reg1 protein. Reg1 and many PP1 phosphatase regulatory subunits utilize some variation of the conserved RVxF motif for interaction with PP1. In the Snf1 pathway, the exact role of the Reg1 protein is uncertain since it binds to both the Glc7 phosphatase and to Snf1, the Glc7 substrate. In this study we sought to clarify the role of Reg1 by separating the Snf1- and Glc7-binding functions. We generated a series of Reg1 proteins, some with deletions of conserved domains and one with two amino acid changes in the RVxF motif. The ability of Reg1 to bind Snf1 and Glc7 required the same domains of Reg1. Further, the RVxF motif that is essential for Reg1 binding to Glc7 is also required for binding to Snf1. Our data suggest that the regulation of Snf1 dephosphorylation is imparted through a dynamic competition between the Glc7 phosphatase and the Snf1 kinase for binding to the PP1 regulatory subunit Reg1. PMID:20170726

  20. Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System.

    PubMed

    Ka, Donghyun; Lee, Hasup; Jung, Yi-Deun; Kim, Kyunggon; Seok, Chaok; Suh, Nayoung; Bae, Euiyoung

    2016-01-05

    CRISPRs and Cas proteins constitute an RNA-guided microbial immune system against invading nucleic acids. Cas1 is a universal Cas protein found in all three types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition during CRISPR-mediated adaptive immunity. Here, we report the crystal structure of Streptococcus pyogenes Cas1 (SpCas1) in a type II CRISPR-Cas system and characterize its interaction with S. pyogenes Csn2 (SpCsn2). The SpCas1 structure reveals a unique conformational state distinct from type I Cas1 structures, resulting in a more extensive dimerization interface, a more globular overall structure, and a disruption of potential metal-binding sites for catalysis. We demonstrate that SpCas1 directly interacts with SpCsn2, and identify the binding interface and key residues for Cas complex formation. These results provide structural information for a type II Cas1 protein, and lay a foundation for studying multiprotein Cas complexes functioning in type II CRISPR-Cas systems.

  1. [CAS General Standards 2012

    ERIC Educational Resources Information Center

    Council for the Advancement of Standards in Higher Education, 2011

    2011-01-01

    The mission of the Council for the Advancement of Standards in Higher Education (CAS) is to promote the improvement of programs and services to enhance the quality of student learning and development. CAS is a consortium of professional associations who work collaboratively to develop and promulgate standards and guidelines and to encourage…

  2. Protein engineering of Cas9 for enhanced function.

    PubMed

    Oakes, Benjamin L; Nadler, Dana C; Savage, David F

    2014-01-01

    CRISPR/Cas systems act to protect the cell from invading nucleic acids in many bacteria and archaea. The bacterial immune protein Cas9 is a component of one of these CRISPR/Cas systems and has recently been adapted as a tool for genome editing. Cas9 is easily targeted to bind and cleave a DNA sequence via a complementary RNA; this straightforward programmability has gained Cas9 rapid acceptance in the field of genetic engineering. While this technology has developed quickly, a number of challenges regarding Cas9 specificity, efficiency, fusion protein function, and spatiotemporal control within the cell remain. In this work, we develop a platform for constructing novel proteins to address these open questions. We demonstrate methods to either screen or select active Cas9 mutants and use the screening technique to isolate functional Cas9 variants with a heterologous PDZ domain inserted within the protein. As a proof of concept, these methods lay the groundwork for the future construction of diverse Cas9 proteins. Straightforward and accessible techniques for genetic editing are helping to elucidate biology in new and exciting ways; a platform to engineer new functionalities into Cas9 will help forge the next generation of genome-modifying tools.

  3. Harnessing CRISPR-Cas9 immunity for genetic engineering.

    PubMed

    Charpentier, Emmanuelle; Marraffini, Luciano A

    2014-06-01

    CRISPR-Cas encodes an adaptive immune system that defends prokaryotes against infectious viruses and plasmids. Immunity is mediated by Cas nucleases, which use small RNA guides (the crRNAs) to specify a cleavage site within the genome of invading nucleic acids. In type II CRISPR-Cas systems, the DNA-cleaving activity is performed by a single enzyme Cas9 guided by an RNA duplex. Using synthetic single RNA guides, Cas9 can be reprogrammed to create specific double-stranded DNA breaks in the genomes of a variety of organisms, ranging from human cells to bacteria, and thus constitutes a powerful tool for genetic engineering. Here we describe recent advancements in our understanding of type II CRISPR-Cas immunity and how these studies led to revolutionary genome editing applications.

  4. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.

    PubMed

    Nuñez, James K; Kranzusch, Philip J; Noeske, Jonas; Wright, Addison V; Davies, Christopher W; Doudna, Jennifer A

    2014-06-01

    The initial stage of CRISPR-Cas immunity involves the integration of foreign DNA spacer segments into the host genomic CRISPR locus. The nucleases Cas1 and Cas2 are the only proteins conserved among all CRISPR-Cas systems, yet the molecular functions of these proteins during immunity are unknown. Here we show that Cas1 and Cas2 from Escherichia coli form a stable complex that is essential for spacer acquisition and determine the 2.3-Å-resolution crystal structure of the Cas1-Cas2 complex. Mutations that perturb Cas1-Cas2 complex formation disrupt CRISPR DNA recognition and spacer acquisition in vivo. Active site mutants of Cas2, unlike those of Cas1, can still acquire new spacers, thus indicating a nonenzymatic role of Cas2 during immunity. These results reveal the universal roles of Cas1 and Cas2 and suggest a mechanism by which Cas1-Cas2 complexes specify sites of CRISPR spacer integration.

  5. Overview of CRISPR-Cas9 Biology.

    PubMed

    Ratner, Hannah K; Sampson, Timothy R; Weiss, David S

    2016-12-01

    Prokaryotes use diverse strategies to improve fitness in the face of different environmental threats and stresses, including those posed by mobile genetic elements (e.g., bacteriophages and plasmids). To defend against these elements, many bacteria and archaea use elegant, RNA-directed, nucleic acid-targeting adaptive restriction machineries called CRISPR -: Cas (CRISPR-associated) systems. While providing an effective defense against foreign genetic elements, these systems have also been observed to play critical roles in regulating bacterial physiology during environmental stress. Increasingly, CRISPR-Cas systems, in particular the Type II systems containing the Cas9 endonuclease, have been exploited for their ability to bind desired nucleic acid sequences, as well as direct sequence-specific cleavage of their targets. Cas9-mediated genome engineering is transcending biological research as a versatile and portable platform for manipulating genetic content in myriad systems. Here, we present a systematic overview of CRISPR-Cas history and biology, highlighting the revolutionary tools derived from these systems, which greatly expand the molecular biologists' toolkit.

  6. Cigarette advertising and children's smoking: why Reg was withdrawn.

    PubMed Central

    Hastings, G. B.; Ryan, H.; Teer, P.; MacKintosh, A. M.

    1994-01-01

    OBJECTIVE--To examine the appeal of the Embassy Regal "Reg" campaign to young people. DESIGN--Three quantitative surveys and one piece of qualitative research: (a) self completion questionnaire administered in classrooms, (b) questionnaire led interviews with children, (c) questionnaire led interviews with adults, and (d) group discussions with children and adults. SETTINGS--(a) Secondary and middle schools in England; (b) north of England, Scotland, and Wales; (c) north of England, Scotland, and Wales; and (d) Glasgow. SUBJECTS--(a) 5451 schoolchildren aged 11-15 recruited by stratified random sampling; (b) 437 children aged 5-10 recruited by quota sampling; (c) 814 adults aged 15-65 recruited by quota sampling; and (d) 12 groups of children aged 10-15, three groups of adults aged 18-24, and three groups of adults aged 35-55. RESULTS--Children were familiar with cigarette advertising and in particular the Reg campaign. Although younger children struggled to understand the creative content of the adverts, older and smoking children could understand and appreciate the humour. They considered Reg to be amusing and could relate to the type of joke used in the advert. In addition Reg's flippant attitude towards serious issues appealed to the children. While adults aged 18-24 understood the campaign they did not identify with it, and 35-55 year olds (the campaign's supposed target) were unappreciative of the campaign. CONCLUSIONS--The Reg campaign was getting through to children more effectively than it was to adults and held most appeal for teenagers, particularly 14-15 year old smokers. It clearly contravened the code governing tobacco advertising, which states that advertising must not appeal to children more than it does to adults, and it may have had a direct impact on teenage smoking. In view of these findings the Advertising Standards Authority's decision to withdraw the Reg campaign seems appropriate. Images p935-a PMID:7950668

  7. The role of Cas8 in type I CRISPR interference.

    PubMed

    Cass, Simon D B; Haas, Karina A; Stoll, Britta; Alkhnbashi, Omer S; Sharma, Kundan; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita; Bolt, Edward L

    2015-05-05

    CRISPR (clustered regularly interspaced short palindromic repeat) systems provide bacteria and archaea with adaptive immunity to repel invasive genetic elements. Type I systems use 'cascade' [CRISPR-associated (Cas) complex for antiviral defence] ribonucleoprotein complexes to target invader DNA, by base pairing CRISPR RNA (crRNA) to protospacers. Cascade identifies PAMs (protospacer adjacent motifs) on invader DNA, triggering R-loop formation and subsequent DNA degradation by Cas3. Cas8 is a candidate PAM recognition factor in some cascades. We analysed Cas8 homologues from type IB CRISPR systems in archaea Haloferax volcanii (Hvo) and Methanothermobacter thermautotrophicus (Mth). Cas8 was essential for CRISPR interference in Hvo and purified Mth Cas8 protein responded to PAM sequence when binding to nucleic acids. Cas8 interacted physically with Cas5-Cas7-crRNA complex, stimulating binding to PAM containing substrates. Mutation of conserved Cas8 amino acid residues abolished interference in vivo and altered catalytic activity of Cas8 protein in vitro. This is experimental evidence that Cas8 is important for targeting Cascade to invader DNA.

  8. Development of the IGT RENUGAS(reg sign) process

    NASA Astrophysics Data System (ADS)

    Lau, Francis S.; Carty, Ronald H.; Onischak, Michael; Bain, Richard L.

    The development of the IGT RENUGAS(reg sign) process from a concept in 1977 to the design of a 91 metric ton per day demonstration gasifier planned for Hawaii is described. The RENUGAS(reg sign) process was specifically developed for pressurized fluidized bed gasification of biomass to produce either an industrial fuel gas or a chemical synthesis gas depending on air- or oxygen-blown operation. The RENUGAS(reg sign) gasifier is a single-stage fluidized bed reactor with a deep bed of inert fluidization solids that provide stable fluidization behavior and needed heat capacity for efficient transfer of energy released by the combustion to the endothermic devolatilization and gasification reactions. The use of a deep single-stage bed of inert solids yields high carbon conversion and low production of oils and tars. The 10.9 metric ton per day RENUGAS(reg sign) process development unit built at IGT under a USDOE program, has been tested under various operating conditions, processing over 81 metric tons of biomass feedstocks in over 220 hours of steady-state tests. Initial parameter variation tests were conducted to determine the optimum gasification conditions of temperature, pressure, steam input, and feedstock moisture and different feedstocks. Currently, the PDU is being used to test hot gas cleanup for power turbines in support of the Hawaii demonstration gasifier.

  9. Cas9-mediated targeting of viral RNA in eukaryotic cells.

    PubMed

    Price, Aryn A; Sampson, Timothy R; Ratner, Hannah K; Grakoui, Arash; Weiss, David S

    2015-05-12

    Clustered, regularly interspaced, short palindromic repeats-CRISPR associated (CRISPR-Cas) systems are prokaryotic RNA-directed endonuclease machineries that act as an adaptive immune system against foreign genetic elements. Using small CRISPR RNAs that provide specificity, Cas proteins recognize and degrade nucleic acids. Our previous work demonstrated that the Cas9 endonuclease from Francisella novicida (FnCas9) is capable of targeting endogenous bacterial RNA. Here, we show that FnCas9 can be directed by an engineered RNA-targeting guide RNA to target and inhibit a human +ssRNA virus, hepatitis C virus, within eukaryotic cells. This work reveals a versatile and portable RNA-targeting system that can effectively function in eukaryotic cells and be programmed as an antiviral defense.

  10. Cas9-mediated targeting of viral RNA in eukaryotic cells

    PubMed Central

    Price, Aryn A.; Sampson, Timothy R.; Ratner, Hannah K.; Grakoui, Arash; Weiss, David S.

    2015-01-01

    Clustered, regularly interspaced, short palindromic repeats–CRISPR associated (CRISPR-Cas) systems are prokaryotic RNA-directed endonuclease machineries that act as an adaptive immune system against foreign genetic elements. Using small CRISPR RNAs that provide specificity, Cas proteins recognize and degrade nucleic acids. Our previous work demonstrated that the Cas9 endonuclease from Francisella novicida (FnCas9) is capable of targeting endogenous bacterial RNA. Here, we show that FnCas9 can be directed by an engineered RNA-targeting guide RNA to target and inhibit a human +ssRNA virus, hepatitis C virus, within eukaryotic cells. This work reveals a versatile and portable RNA-targeting system that can effectively function in eukaryotic cells and be programmed as an antiviral defense. PMID:25918406

  11. Sediment toxicity in the Duluth-Superior Harbor: Use of Microtox{reg_sign} and Mutatox{reg_sign} as screening assays

    SciTech Connect

    Schubauer-Berigan, M.; Hubbard, C.; Schubauer-Berigan, J.; Tesser, G.

    1995-12-31

    Sediment toxicity tests were conducted in the Duluth-Superior Harbor at 40 sites as part of an integrated sediment assessment during the fall of 1993. Two rapid assays conducted with Photobacterium phosphoreum (Microtox{reg_sign} and Mutatox{reg_sign}) were compared with three standard US EPA sediment toxicity tests: Hyalella azteca (acute tests) and Chironomus tentans (acute and sub-lethal tests). The response in the two microbial assays was also evaluated for sensitivity to various contaminants analyzed simultaneously in the Duluth-Superior Harbor sediments. Microtox{reg_sign} and Mutatox{reg_sign} were found to be sensitive to approximately one-third and one-half the sediments, respectively; Chironomus tentans was sensitive to 15% of the sediments (either acutely or sub-lethally), while Hyalella azteca was not sensitive to any of the sediments. In almost all cases, Microtox{reg_sign} and Mutatox{reg_sign} correctly identified samples that were toxic to the chironomid, making it useful as a screening tool for toxicity, to reduce the number of sites to be tested with the benthic organisms. The subsequent application of Microtox{reg_sign} as a screen for sediment toxicity in an EMAP survey in the St. Louis River (MN) estuary will be discussed. Correlation of Microtox{reg_sign} and Mutatox{reg_sign} toxicity to environmental contaminants found in the sediments will be presented.

  12. IMHEX{reg_sign} fuel cells progress toward commercialization

    SciTech Connect

    Laurens, R.M.; Petraglia, V.J.

    1995-08-01

    The overall goal of M-C Power is the development and subsequent commercialization of Molten Carbonate Fuel Cell (MCFC) stacks. More specifically, MCFC`s based upon the Internally Manifolded. Heat EXchange (IMHEX{reg_sign}) plate design created by the Institute of Technology. In order to achieve the aforementioned goal, M-C Power assembled a formidible team of industry leaders. This group, referred to as the IMHEX{reg_sign} Team, has developed a strategy to move decisively through the stages of Technology Development and Product Design and Improvement through commercialization. This paper is to review the status of the overall commercialization program and activities. It will also provide an overview of the market entry product. Furthermore, we will evaluate the opportunities and benefits this product brings to a competive power industry.

  13. FieldREG II: consciousness field effects: replications and explorations.

    PubMed

    Nelson, R D; Jahn, R G; Dunne, B J; Dobyns, Y H; Bradish, G J

    2007-01-01

    Based on formal analysis of 18 exploratory applications, 12 of which have been reported previously, a testable general hypothesis for FieldREG experiments has been postulated, namely that data taken in environments fostering relatively intense or profound subjective resonance will show larger deviations of the mean relative to chance expectation than those generated in more pragmatic assemblies. The 61 subsequent FieldREG applications reported here comprise 21 hypothesis-based formal replications, along with 40 further explorations designed to learn more about the circumstances that favor anomalous deviations. The results of the formal replications strongly confirm the general hypothesis, yielding a composite probability against chance for the resonant subset of 2.2 x 10(-6) compared to 0.91 for the mundane subset. The exploratory work suggests other venues in which anomalous effects of group consciousness can be expected, and also identifies a number of situations that do not appear to be conducive to such responses.

  14. Administration of Anti-Reg I and Anti-PAPII Antibodies Worsens Pancreatitis

    PubMed Central

    Viterbo, Domenico; Callender, Gordon E; DiMaio, Theresa; Mueller, Cathy M; Smith-Norowitz, Tamar; Zenilman, Michael E; Bluth, Martin H

    2009-01-01

    Context The regeneration protein family (Reg), which includes Reg I and PAPII, is expressed in pancreas acinar cells, and increases in acute pancreatitis. We have demonstrated that Reg gene knockdown worsens severity of acute pancreatitis in the rat and hypothesize that the proteins offer a protective effect in this disease. Objective We investigated the ability of anti-Reg and anti-PAP antibody to neutralize pancreatic Reg protein and affect pancreatitis severity. Intervention Pancreatitis was induced in rats by retrograde ductal injection of 4% sodium taurocholate. Animals Eighty-four rats: 48 with induced pancreatitis, 30 sham operated, and 6 normal animals. Setting Intraductal anti-Reg I and/or anti-PAPII antibody was administered at induced pancreatitis and sham operated subgroups of 6 rats each. Main outcome measure Serum and pancreata were harvested 24 and/or 48 hours later and assessed for pancreatitis severity by pancreatic wet weight, serum C-reactive protein (CRP), amylase, PAPII levels, and histopathology. Results Animals induced with pancreatitis with administration of anti-Reg/PAP antibodies had significantly higher wet weights compared with taurocholate and histopathological analysis revealed that anti-Reg/PAP treated animals had worse tissue inflammation and necrosis compared with controls. Serum CRP, amylase, and Reg levels did not significantly differ between experimental and sham control groups. Conclusions Administration of anti-Reg/PAP antibody worsened taurocholate-induced organ specific pancreatitis. These data suggest that the Reg family of proteins is protective in acute pancreatitis. PMID:19129610

  15. Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314T)

    SciTech Connect

    Goker, Markus; Saunders, Elizabeth H; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, K; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Chang, Yun-Juan; Jeffries, Cynthia; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2012-01-01

    Thermovirga lienii Dahle and Birkeland 2006 is a member to the genomically so far uncharacterized genus Thermovirga in the phylum 'Synergistetes'. Members of the only recently (2007) proposed phylum 'Synergistetes' are of interest because of their isolated phylogenetic position and their diverse habitats, e.g. from man to oil well. The genome of T. lienii Cas60314T is only the 5th genome sequence (3rd completed) from this phylum to be published. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,999,646 bp long genome (including one plasmid) with its 1,914 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Primary processing of CRISPR RNA by the endonuclease Cas6 in Staphylococcus epidermidis.

    PubMed

    Wakefield, Noelle; Rajan, Rakhi; Sontheimer, Erik J

    2015-10-07

    In many bacteria and archaea, an adaptive immune system (CRISPR-Cas) provides immunity against foreign genetic elements. This system uses CRISPR RNAs (crRNAs) derived from the CRISPR array, along with CRISPR-associated (Cas) proteins, to target foreign nucleic acids. In most CRISPR systems, endonucleolytic processing of crRNA precursors (pre-crRNAs) is essential for the pathway. Here we study the Cas6 endonuclease responsible for crRNA processing in the Type III-A CRISPR-Cas system from Staphylococcus epidermidis RP62a, a model for Type III-A CRISPR-Cas systems, and define substrate requirements for SeCas6 activity. We find that SeCas6 is necessary and sufficient for full-length crRNA biogenesis in vitro, and that it relies on both sequence and stem-loop structure in the 3' half of the CRISPR repeat for recognition and processing.

  17. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation.

    PubMed

    Jinek, Martin; Jiang, Fuguo; Taylor, David W; Sternberg, Samuel H; Kaya, Emine; Ma, Enbo; Anders, Carolin; Hauer, Michael; Zhou, Kaihong; Lin, Steven; Kaplan, Matias; Iavarone, Anthony T; Charpentier, Emmanuelle; Nogales, Eva; Doudna, Jennifer A

    2014-03-14

    Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.

  18. Sensitivity of simulated South America climate to the land surface schemes in RegCM4

    NASA Astrophysics Data System (ADS)

    Llopart, Marta; da Rocha, Rosmeri P.; Reboita, Michelle; Cuadra, Santiago

    2017-02-01

    This work evaluates the impact of two land surface parameterizations on the simulated climate and its variability over South America (SA). Two numerical experiments using RegCM4 coupled with the Biosphere-Atmosphere Transfer Scheme (RegBATS) and the Community Land Model version 3.5 (RegCLM) land surface schemes are compared. For the period 1979-2008, RegCM4 simulations used 50 km horizontal grid spacing and the ERA-Interim reanalysis as initial and boundary conditions. For the period studied, both simulations represent the main observed spatial patterns of rainfall, air temperature and low level circulation over SA. However, with regard to the precipitation intensity, RegCLM values are closer to the observations than RegBATS (it is wetter in general) over most of SA. RegCLM also produces smaller biases for air temperature. Over the Amazon basin, the amplitudes of the annual cycles of the soil moisture, evapotranspiration and sensible heat flux are higher in RegBATS than in RegCLM. This indicates that RegBATS provides large amounts of water vapor to the atmosphere and has more available energy to increase the boundary layer thickness and cause it to reach the level of free convection (higher sensible heat flux values) resulting in higher precipitation rates and a large wet bias. RegCLM is closer to the observations than RegBATS, presenting smaller wet and warm biases over the Amazon basin. On an interannual scale, the magnitudes of the anomalies of the precipitation and air temperature simulated by RegCLM are closer to the observations. In general, RegBATS simulates higher magnitude for the interannual variability signal.

  19. Molecular modeling of the pendant chain in Nafion{reg_sign}

    SciTech Connect

    Paddison, S.J.; Zawodzinski, T.A.

    1998-03-01

    Ion transport through perfluorosulfonic acid ionomers such as Nafion{reg_sign} is controlled by both the microstructure of the polymer and the charge and water distribution in the hydrated polymer. The authors present here the results of theoretical calculations on the side chain of Nafion{reg_sign}, establishing microscopic information for the modeling of water modeling of water modeling of water and proton transport in the membrane. Optimized geometries for the trifluoromethane sulfonic acid fragment (CF{sub 3}SO{sub 3}H), the di-trifluoromethane ether fragment (CF{sub 3}OCF{sub 3}), and the side chain (CF{sub 3}{single_bond}OCF{sub 2}CF(CF{sub 3})OCF{sub 2}CF{sub 2}SO{sub 3}H) were determined by means of both ab initio Hartree Fock theory with second order Moeller-Plesset electron correlation corrections, and density functional theory with Becke`s three parameter hybrid method. Several rotational potential energy surfaces were calculated to assess chain flexibility and proton accessibility. A probe water molecule was added to each of the fragments to characterize hydrophilic sites. These calculations confirmed that the sulfonic acid group is hydrophilic and the ethers are hydrophobic. Molecular dynamics simulations were then performed on the side chain to check the conditions required to stretch the pendant chain. Thermal averages of several structural parameters assessing the flexibility and stretch of the chain were computed from selected conformations produced in the simulation and these results indicate that although the sulfonate group is free to rotate, the chain stretches little. The construction of a potential energy surface for rotation about the second ether group suggests that the side chain exists in a folded or curled up conformation. A physical continuum dielectric solvent model was used to obtain free energies of electrostatic interaction of the fragments and the full chain with the solvent.

  20. The expression patterns of Reg IV gene in normal rat reproduction system.

    PubMed

    Du, Fang; Yao, Zhen-Wei

    2013-01-01

    Reg IV, the latest member of the regenerating gene family, has been documented in different tissues of human and rat, such as the colon, small intestine, stomach, and pancreas. Expression of Reg IV gene in distinct cell types has been correlated with its various functions in regeneration, cell growth and survival, proliferation and differentiation, cell adhesion, and resistance to apoptosis. However, there was no evidence to show whether the Reg IV protein is present in the reproductive system of normal rat. The aim of this study was to reveal the expression patterns of Reg IV in rat ovary and uterus. The expression of Reg IV was analyzed by reverse transcription-polymerase chain reaction (RT-PCR) and Western blot at mRNA and protein levels, respectively. The localization of Reg IV protein within rat ovary and uterus was investigated by immunohistochemistry (IHC). Our results showed that the expression of Reg IV in ovary was significantly higher than that in the uterus. The strong immunoreactive signals of Reg IV was observed in granulosa cells and oocytes of ovarian follicles, corpus luteum, and interstitial cells in rat ovary; only weak signals were detected in luminal and gland epithelium of rat endometrium. These findings first demonstrate the expression of Reg IV in ovary and uterus of the healthy rat at both mRNA and protein levels. It provides an evidence of Reg IV expression in rat reproductive system, which may help elucidate a potential role in cell growth and proliferation of reproductive system.

  1. The on-line removal of non-regenerable salts from amine solutions using the UCARSEP{reg_sign} Process

    SciTech Connect

    Burns, D.; Gregory, R.A.

    1995-11-01

    Amine unit contamination with non-regenerable salts, whether as a result of acid or inorganic salt incursion, or solvent degradation, is a common industry problem. In MEA systems this is usually addressed by the use of a reclaimer but this is not a practical solution for DEA, MDEA or formulated solvents. Similarly, the old approach of purging solvent is no longer economically or environmentally justifiable. Neutralization of amine salts with a strong base can significantly prolong the useful life of the amine solution but eventually some of the salt may have to be removed, especially if mechanical losses are low. Electrodialysis (ED) has recently been applied to this problem and has been found to overcome many of the disadvantages of vacuum distillation and ion exchange technologies, both of which have been used in recent years for solvent clean-up. Union Carbide adapted ED technology to the unique conditions encountered in an amine system and developed the UCARSEP{reg_sign} Process. A mobile UCARSEP{reg_sign} unit has been built to achieve on-line salt removal rates of 40 lbmol/day (about 3,300 lb/day). This has been successfully used to clean up UCARSOL{reg_sign} solvents as well as DEA. Case studies are presented and the relative merits of this and other clean-up options are discussed.

  2. Characterization and evolution of Salmonella CRISPR-Cas systems.

    PubMed

    Shariat, Nikki; Timme, Ruth E; Pettengill, James B; Barrangou, Rodolphe; Dudley, Edward G

    2015-02-01

    Prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes) systems provide adaptive immunity from invasive genetic elements and encompass three essential features: (i) cas genes, (ii) a CRISPR array composed of spacers and direct repeats and (iii) an AT-rich leader sequence upstream of the array. We performed in-depth sequence analysis of the CRISPR-Cas systems in >600 Salmonella, representing four clinically prevalent serovars. Each CRISPR-Cas feature is extremely conserved in the Salmonella, and the CRISPR1 locus is more highly conserved than CRISPR2. Array composition is serovar-specific, although no convincing evidence of recent spacer acquisition against exogenous nucleic acids exists. Only 12% of spacers match phage and plasmid sequences and self-targeting spacers are associated with direct repeat variants. High nucleotide identity (>99.9%) exists across the cas operon among isolates of a single serovar and in some cases this conservation extends across divergent serovars. These observations reflect historical CRISPR-Cas immune activity, showing that this locus has ceased undergoing adaptive events. Intriguingly, the high level of conservation across divergent serovars shows that the genetic integrity of these inactive loci is maintained over time, contrasting with the canonical view that inactive CRISPR loci degenerate over time. This thorough characterization of Salmonella CRISPR-Cas systems presents new insights into Salmonella CRISPR evolution, particularly with respect to cas gene conservation, leader sequences, organization of direct repeats and protospacer matches. Collectively, our data suggest that Salmonella CRISPR-Cas systems are no longer immunogenic; rather, their impressive conservation indicates they may have an alternative function in Salmonella.

  3. Characterization and evolution of Salmonella CRISPR-Cas systems.

    PubMed

    Shariat, Nikki; Timme, Ruth E; Pettengill, James B; Barrangou, Rodolphe; Dudley, Edward G

    2015-02-01

    Prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes) systems provide adaptive immunity from invasive genetic elements and encompass three essential features: (i) cas genes, (ii) a CRISPR array composed of spacers and direct repeats and (iii) an AT-rich leader sequence upstream of the array. We performed in-depth sequence analysis of the CRISPR-Cas systems in >600 Salmonella, representing four clinically prevalent serovars. Each CRISPR-Cas feature is extremely conserved in the Salmonella, and the CRISPR1 locus is more highly conserved than CRISPR2. Array composition is serovar-specific, although no convincing evidence of recent spacer acquisition against exogenous nucleic acids exists. Only 12 % of spacers match phage and plasmid sequences and self-targeting spacers are associated with direct repeat variants. High nucleotide identity (>99.9 %) exists across the cas operon among isolates of a single serovar and in some cases this conservation extends across divergent serovars. These observations reflect historical CRISPR-Cas immune activity, showing that this locus has ceased undergoing adaptive events. Intriguingly, the high level of conservation across divergent serovars shows that the genetic integrity of these inactive loci is maintained over time, contrasting with the canonical view that inactive CRISPR loci degenerate over time. This thorough characterization of Salmonella CRISPR-Cas systems presents new insights into Salmonella CRISPR evolution, particularly with respect to cas gene conservation, leader sequences, organization of direct repeats and protospacer matches. Collectively, our data suggest that Salmonella CRISPR-Cas systems are no longer immunogenic; rather, their impressive conservation indicates they may have an alternative function in Salmonella.

  4. The structural biology of CRISPR-Cas systems.

    PubMed

    Jiang, Fuguo; Doudna, Jennifer A

    2015-02-01

    Prokaryotic CRISPR-Cas genomic loci encode RNA-mediated adaptive immune systems that bear some functional similarities with eukaryotic RNA interference. Acquired and heritable immunity against bacteriophage and plasmids begins with integration of ∼30 base pair foreign DNA sequences into the host genome. CRISPR-derived transcripts assemble with CRISPR-associated (Cas) proteins to target complementary nucleic acids for degradation. Here we review recent advances in the structural biology of these targeting complexes, with a focus on structural studies of the multisubunit Type I CRISPR RNA-guided surveillance and the Cas9 DNA endonuclease found in Type II CRISPR-Cas systems. These complexes have distinct structures that are each capable of site-specific double-stranded DNA binding and local helix unwinding.

  5. Hyperglycaemia inhibits REG3A expression to exacerbate TLR3-mediated skin inflammation in diabetes

    PubMed Central

    Wu, Yelin; Quan, Yanchun; Liu, Yuanqi; Liu, Keiwei; Li, Hongquan; Jiang, Ziwei; Zhang, Tian; Lei, Hu; Radek, Katherine A.; Li, Dongqing; Wang, Zhenhua; Lu, Jilong; Wang, Wang; Ji, Shizhao; Xia, Zhaofan; Lai, Yuping

    2016-01-01

    Dysregulated inflammatory responses are known to impair wound healing in diabetes, but the underlying mechanisms are poorly understood. Here we show that the antimicrobial protein REG3A controls TLR3-mediated inflammation after skin injury. This control is mediated by REG3A-induced SHP-1 protein, and acts selectively on TLR3-activated JNK2. In diabetic mouse skin, hyperglycaemia inhibits the expression of IL-17-induced IL-33 via glucose glycation. The decrease in cutaneous IL-33 reduces REG3A expression in epidermal keratinocytes. The reduction in REG3A is associated with lower levels of SHP-1, which normally inhibits TLR3-induced JNK2 phosphorylation, thereby increasing inflammation in skin wounds. To our knowledge, these findings show for the first time that REG3A can modulate specific cutaneous inflammatory responses and that the decrease in cutaneous REG3A exacerbates inflammation in diabetic skin wounds. PMID:27830702

  6. Reg proteins promote acinar-to-ductal metaplasia and act as novel diagnostic and prognostic markers in pancreatic ductal adenocarcinoma

    PubMed Central

    Zogopoulos, George; Shao, Qin; Dong, Kun; Lv, Fudong; Nwilati, Karam; Gui, Xian-yong; Cuggia, Adeline; Liu, Jun-Li; Gao, Zu-hua

    2016-01-01

    Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignant tumor. Acinar-to-ductal metaplasia (ADM) and pancreatic intraepithelial neoplasia (PanIN) are both precursor lesions that lead to the development of PDAC. Reg family proteins (Reg1A, 1B, 3A/G, 4) are a group of calcium-dependent lectins that promote islet growth in response to inflammation and/or injuries. The aim of this study was to establish a role for Reg proteins in the development of PDAC and their clinical value as biomarkers. We found that Reg1A and Reg3A/G were highly expressed in the ADM tissues by immunohistochemistry. In the 3-dimensional culture of mouse acinar cells, Reg3A promoted ADM formation with concurrent activation of mitogen-acitvated protein kinase. Upregulation of Reg1A and Reg1B levels was observed as benign ductal epithelium progresses from PanIN to invasive PDAC. Patients with PDAC showed significantly higher serum levels of Reg1A and Reg1B than matching healthy subjects. These results were further validated by the quantification of Reg 1A and 1B mRNA levels in the microdissected tissues (22- and 6-fold increases vs. non-tumor tissues). Interestingly, patients with higher levels of Reg1A and 1B exhibited improved survival rate than those with lower levels. Furthermore, tissue expressions of Reg1A, Reg1B, and Reg4 could differentiate metastatic PDAC in the liver from intrahepatic cholangiocarcinoma with 92% sensitivity and 95% specificity. Overall, our results demonstrate the upregulation of Reg proteins during PDAC development. If validated in larger scale, Reg1A and Reg1B could become clinical markers for detecting early stages of PDAC, monitoring therapeutic response, and/or predicting patient's prognosis. PMID:27788482

  7. An update on operation experience and scale-up with CYMIC{reg_sign}

    SciTech Connect

    Kokko, A.; Alliston, M.G.

    1996-12-31

    This paper describes the operational experiences with the first full-scale CYMIC{reg_sign} demonstration plant, the scale-up principles of CYMIC{reg_sign}, and finally a large-scale CYMIC{reg_sign} case. Kvaerner Pulping`s new-generation circulating fluidized bed (CFB) boiler, CYMIC{reg_sign} offers a multi-fuel combustion solution with low emissions, high efficiency and high availability. With the cyclone built inside the boiler furnace, its space requirements are extremely small. Due to the watercooled construction, the refractories are thin, minimizing the need for maintenance. The pilot testing with CYMIC{reg_sign} was successfully completed and with positive results in 1992. The next step was a CYMIC{reg_sign} scale-up and a full-scale demonstration project. The 32 MW{sub th} demonstration plant owned by VAPO Oy in the town of Lieksa, eastern Finland, is now in continuous operation. The CYMIC{reg_sign} has been further scaled by developing six standard cyclone sizes. The CYMIC{reg_sign}`s square furnace size can be varied and can be multiplied, offering a stepless capacity range from small Lieksa size units to utility boilers. The design of the CYMIC{reg_sign} process, including operation of the cyclone and the gas lock, has been verified. In addition, tests have been run measuring flue gas emissions and combustion efficiency. The most interesting results from these tests are discussed. A 185 MW{sub th} CYMIC{reg_sign} unit is now operating at the Rauma paper mill of Unite Paper Mills, Finland. The project began in November 1994 and the boiler started up in the summer of 1996. The design and the performance of this CYMIC{reg_sign} unit are presented.

  8. RIFM fragrance ingredient safety assessment, linalyl benzoate, CAS Registry Number 126-64-7.

    PubMed

    Api, A M; Belsito, D; Bhatia, S; Bruze, M; Calow, P; Dagli, M L; Dkant, W; Fryer, A D; Kromidas, L; La Cava, S; Lalko, J F; Lapczynski, A; Liebler, D C; Penning, T M; Politano, V T; Ritacco, G; Salvito, D; Schultz, T W; Shen, J; Sipes, I G; Wall, B; Wilcox, D K

    2016-11-01

    The use of this material under current conditions is supported by existing information. This material was evaluated for genotoxicity, repeated dose toxicity, developmental and reproductive toxicity, local respiratory toxicity, phototoxicity/photoallergenicity, skin sensitization, as well as environmental safety. Data show that this material is not genotoxic. Data from the suitable read across analog linalyl phenylacetate (CAS # 7143-69-3) show that this material does not have skin sensitization potential. The repeated dose toxicity endpoint was completed using linalyl cinnamate (CAS # 78-37-5) as a suitable read across analog, which provided a MOE > 100. The developmental and reproductive toxicity endpoint was completed using linalool (CAS # 78-70-6), dehydrolinalool (CAS # 29171-20-8), benzoic acid (CAS # 65-85-0) and sodium benzoate (CAS # 532-32-1) as suitable read across analogs, which provided a MOE > 100. The local respiratory toxicity endpoint was completed using linalool (CAS # 78-70-6) and benzoic acid (CAS # 65-85-0) as suitable read across analogs, which provided a MOE > 100. The phototoxicity/photoallergenicity endpoint was completed based on suitable UV spectra. The environmental endpoint was completed as described in the RIFM Framework along with data from the suitable read across analog linalyl cinnamate (CAS # 78-375).

  9. In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas System.

    PubMed

    Richter, Corinna; Gristwood, Tamzin; Clulow, James S; Fineran, Peter C

    2012-01-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and their associated proteins (Cas; CRISPR associated) are a bacterial defense mechanism against extra-chromosomal elements. CRISPR/Cas systems are distinct from other known defense mechanisms insofar as they provide acquired and heritable immunity. Resistance is accomplished in multiple stages in which the Cas proteins provide the enzymatic machinery. Importantly, subtype-specific proteins have been shown to form complexes in combination with small RNAs, which enable sequence-specific targeting of foreign nucleic acids. We used Pectobacterium atrosepticum, a plant pathogen that causes soft-rot and blackleg disease in potato, to investigate protein-protein interactions and complex formation in the subtype I-F CRISPR/Cas system. The P. atrosepticum CRISPR/Cas system encodes six proteins: Cas1, Cas3, and the four subtype specific proteins Csy1, Csy2, Csy3 and Cas6f (Csy4). Using co-purification followed by mass spectrometry as well as directed co-immunoprecipitation we have demonstrated complex formation by the Csy1-3 and Cas6f proteins, and determined details about the architecture of that complex. Cas3 was also shown to co-purify all four subtype-specific proteins, consistent with its role in targeting. Furthermore, our results show that the subtype I-F Cas1 and Cas3 (a Cas2-Cas3 hybrid) proteins interact, suggesting a protein complex for adaptation and a role for subtype I-F Cas3 proteins in both the adaptation and interference steps of the CRISPR/Cas mechanism.

  10. Bacteriochlorophyll-dependent expression of genes for pigment-binding proteins in Rhodobacter capsulatus involves the RegB/RegA two-component system.

    PubMed

    Abada, E M; Balzer, A; Jäger, A; Klug, G

    2002-04-01

    Expression of the puf and puc operons, which encode proteins of the photosynthetic apparatus of Rhodobacter capsulatus, is regulated by oxygen. A drop in the oxygen tension in the environment leads to an increase in the levels of puf and puc mRNAs. In strains lacking bacteriochlorophyll (Bchl) due to mutations in bch genes, the rise in puf and puc mRNA levels observed on reduction of oxygen tension is much less pronounced than in wild-type cells, indicating co-regulation of the syntheses of pigments and pigment-binding proteins. Here we show that Bchl synthesis also affects the expression of the bchC gene, which codes for a subunit of bacteriochlorophyll synthase, suggesting an autoregulatory mechanism for the Bchl biosynthetic pathway. Furthermore, our data provide evidence that the RegB/RegA two-component system, which is known to play a central role in oxygen-controlled expression of photosynthesis genes, is also involved in the Bchl-dependent regulation. Mutant strains which do not synthesize RegB or RegA show similar oxygen-dependent puf and puc expression in the presence and absence of Bchl. Our results support the view that the RegB/RegA system can directly or indirectly sense whether Bchl synthesis takes place or not.

  11. Coupling a new turbulence parametrization to RegCM adds realistic stratocumulus clouds

    NASA Astrophysics Data System (ADS)

    O'Brien, T. A.; Chuang, P. Y.; Sloan, L. C.; Faloona, I. C.; Rossiter, D. L.

    2011-12-01

    To model stratocumulus clouds in the regional climate model, RegCM4.1, the University of Washington (UW) turbulence parametrization has been coupled to RegCM. We describe improvements in RegCM's coastal and near-coastal climatology, including improvements in the representation of stratiform clouds. By comparing output from a 27-yr (1982-2009) simulation of the climate of Western North America to a wide variety of observational data (station data, satellite data, and aircraft in situ data), we show the following: (1) RegCM-UW is appropriate for use in general regional climate studies, and (2) the UW model distinctly improves the representation of the marine boundary layer in RegCM. These model-data comparisons also show that RegCM-UW has slight cold bias, a (wet) precipitation bias, a systematic low bias in the vertically-integrated liquid water content near the coast, and a high bias in the fractional cloud coverage. The model represents well the diurnal, monthly, and interannual variability in low clouds. These results show RegCM-UW as a nascent mesoscale stratocumulus model that is appropriate for stratocumulus investigations at scales ranging from hourly to decadal. The source code for RegCM-UW is publicly available, under the GNU license, through the International Centre for Theoretical Physics.

  12. Coupling a new turbulence parametrization to RegCM adds realistic stratocumulus clouds

    NASA Astrophysics Data System (ADS)

    O'Brien, T. A.; Chuang, P. Y.; Sloan, L. C.; Faloona, I. C.; Rossiter, D. L.

    2012-08-01

    To model stratocumulus clouds in the regional climate model, RegCM4.1, the University of Washington (UW) turbulence parametrization has been coupled to RegCM. We describe improvements in RegCM's coastal and near-coastal climatology, including improvements in the representation of stratiform clouds. By comparing output from a 27-yr (1982-2009) simulation of the climate of western North America to a wide variety of observational data (station data, satellite data, and aircraft in situ data), we show the following: (1) RegCM-UW is appropriate for use in general regional climate studies, and (2) the UW model distinctly improves the representation of the marine boundary layer in RegCM. These model-data comparisons also show that RegCM-UW has a slight cold bias, a (wet) precipitation bias, a systematic low bias in the vertically-integrated liquid water content near the coast, and a high bias in the fractional cloud coverage. The model represents well the diurnal, monthly, and interannual variability in low clouds. These results show RegCM-UW as a nascent mesoscale stratocumulus model that is appropriate for stratocumulus investigations at scales ranging from hourly to decadal. The source code for RegCM-UW is publicly available, under the GNU license, through the International Centre for Theoretical Physics.

  13. 12 CFR 742.3 - Loss and revocation of RegFlex designation.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 7 2012-01-01 2012-01-01 false Loss and revocation of RegFlex designation. 742.3 Section 742.3 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS REGULATORY FLEXIBILITY PROGRAM § 742.3 Loss and revocation of RegFlex designation. (a) Loss...

  14. 12 CFR 742.3 - Loss and revocation of RegFlex designation.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 6 2011-01-01 2011-01-01 false Loss and revocation of RegFlex designation. 742.3 Section 742.3 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS REGULATORY FLEXIBILITY PROGRAM § 742.3 Loss and revocation of RegFlex designation. (a) Loss...

  15. 12 CFR 742.2 - Criteria to qualify for RegFlex designation.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 6 2011-01-01 2011-01-01 false Criteria to qualify for RegFlex designation. 742.2 Section 742.2 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS REGULATORY FLEXIBILITY PROGRAM § 742.2 Criteria to qualify for RegFlex designation....

  16. 12 CFR 742.2 - Criteria to qualify for RegFlex designation.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 7 2012-01-01 2012-01-01 false Criteria to qualify for RegFlex designation. 742.2 Section 742.2 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS REGULATORY FLEXIBILITY PROGRAM § 742.2 Criteria to qualify for RegFlex designation....

  17. 12 CFR 742.2 - Criteria to qualify for RegFlex designation.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 6 2010-01-01 2010-01-01 false Criteria to qualify for RegFlex designation. 742.2 Section 742.2 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS REGULATORY FLEXIBILITY PROGRAM § 742.2 Criteria to qualify for RegFlex designation....

  18. 12 CFR 742.3 - Loss and revocation of RegFlex designation.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 6 2010-01-01 2010-01-01 false Loss and revocation of RegFlex designation. 742.3 Section 742.3 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS REGULATORY FLEXIBILITY PROGRAM § 742.3 Loss and revocation of RegFlex designation. (a) Loss...

  19. Exogenous TNFR2 activation protects from acute GvHD via host T reg cell expansion

    PubMed Central

    Chopra, Martin; Brandl, Andreas; Amich, Jorge; Mottok, Anja; Jordán-Garrote, Ana-Laura; Bäuerlein, Carina A.; Brede, Christian; Ribechini, Eliana; Fick, Andrea; Polz, Johannes; Nishikii, Hidekazu; Mattenheimer, Katharina; Schwinn, Stefanie; Winter, Thorsten; Krappmann, Sven; Einsele, Hermann; Reddehase, Matthias J.; Lutz, Manfred B.

    2016-01-01

    Donor CD4+Foxp3+ regulatory T cells (T reg cells) suppress graft-versus-host disease (GvHD) after allogeneic hematopoietic stem cell transplantation (HCT [allo-HCT]). Current clinical study protocols rely on the ex vivo expansion of donor T reg cells and their infusion in high numbers. In this study, we present a novel strategy for inhibiting GvHD that is based on the in vivo expansion of recipient T reg cells before allo-HCT, exploiting the crucial role of tumor necrosis factor receptor 2 (TNFR2) in T reg cell biology. Expanding radiation-resistant host T reg cells in recipient mice using a mouse TNFR2-selective agonist before allo-HCT significantly prolonged survival and reduced GvHD severity in a TNFR2- and T reg cell–dependent manner. The beneficial effects of transplanted T cells against leukemia cells and infectious pathogens remained unaffected. A corresponding human TNFR2-specific agonist expanded human T reg cells in vitro. These observations indicate the potential of our strategy to protect allo-HCT patients from acute GvHD by expanding T reg cells via selective TNFR2 activation in vivo. PMID:27526711

  20. xdamp Version 3: An IDL{reg_sign}-based data and image manipulation program

    SciTech Connect

    Ballard, W.P.

    1998-05-01

    The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA{trademark} (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of Unix{reg_sign}-based workstations, a replacement was needed. This package uses the IDL{reg_sign} software, available from Research Systems Incorporated in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP and earlier versions of xdamp. IDL is currently supported on a wide variety of Unix platforms such as IBM{reg_sign} workstations, Hewlett Packard workstations, SUN{reg_sign} workstations, Microsoft{reg_sign} Windows{trademark} computers, Macintosh{reg_sign} computers and Digital Equipment Corporation VMS{reg_sign} and Alpha{reg_sign} systems. Thus, xdamp is portable across many platforms. The author has verified operation, albeit with some minor IDL bugs, on personal computers using Windows 95 and Windows NT; IBM Unix platforms; and DEC alpha and VMS systems; HP 9000/700 series workstations; and Macintosh computers, both regular and PowerPC{trademark} versions. Version 3 adds the capability to manipulate images to the original xdamp capabilities.

  1. HIsmelt{reg_sign} technology: the future of ironmaking

    SciTech Connect

    Leczo, T.

    2009-03-15

    The unique liquid ironmaking process of HIsmelt{reg_sign} technology produces LD-quality hot metal or pig iron using lower-quality iron ore and non-coking coal, and a variety of iron and carbon-bearing mill wastes, without blending or agglomeration. A HIsmelt facility can replace an obsolete blast furnace in a brownfield application or can be the iron-producing component of a greenfield state-of-the-art steelmaking plant. Two companies in China have signed license agreements to build HIsmelt facilities, but are waiting until the plant in Kwinana, Australia operates for 3 months without any shutdowns or delays before they start construction on their plants.

  2. FASTPLOT: An interface to Microsoft{reg_sign} FORTRAN graphics

    SciTech Connect

    Ward, R.C.

    1994-03-01

    Interface routines to the Microsoft{reg_sign} FORTRAN graphics library (GRAPHICS.LIB) are provided to facilitate development of graphics codes. These routines are collected into the FASTPLOT library (FASTPLOT.LIB). The FASTPLOT routines simplified the development of applications utilizing graphics and add capabilities not available in GRAPHICS.LIB such as plotting histograms, splines, symbols, and error bars. Specifically, these routines were utilized in the development of the mortality data viewing code, MORTVIEW, for the US Environmental Protection Agency. Routines for color imaging, developed for use with the X-ray Computer Tomography (XCT) imaging code, and examples are also provided in the FASTPLOT library. Many example uses of FASTPLOT.LIB are contained in this document to facilitate applications development. The FASTPLOT.LIB library, source, and applications programs are supplied on the accompanying FASTPLOT diskette.

  3. BagReg: Protein inference through machine learning.

    PubMed

    Zhao, Can; Liu, Dao; Teng, Ben; He, Zengyou

    2015-08-01

    Protein inference from the identified peptides is of primary importance in the shotgun proteomics. The target of protein inference is to identify whether each candidate protein is truly present in the sample. To date, many computational methods have been proposed to solve this problem. However, there is still no method that can fully utilize the information hidden in the input data. In this article, we propose a learning-based method named BagReg for protein inference. The method firstly artificially extracts five features from the input data, and then chooses each feature as the class feature to separately build models to predict the presence probabilities of proteins. Finally, the weak results from five prediction models are aggregated to obtain the final result. We test our method on six public available data sets. The experimental results show that our method is superior to the state-of-the-art protein inference algorithms.

  4. Dual nuclease activity of a Cas2 protein in CRISPR-Cas subtype I-B of Leptospira interrogans.

    PubMed

    Dixit, Bhuvan; Ghosh, Karukriti Kaushik; Fernandes, Gary; Kumar, Pankaj; Gogoi, Prerana; Kumar, Manish

    2016-04-01

    Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 carries a set of cas genes associated with CRISPR-Cas subtype I-B. Herein, we report for the first time active transcription of a set of cas genes (cas1 to cas8) of L. interrogans where cas4, cas1, cas2 and cas6, cas3, cas8, cas7, cas5 are clustered together in two independent operons. As an initial step toward comprehensive understanding of CRISPR-Cas system in spirochete, the biochemical study of one of the core Leptospira Cas2 proteins (Lep_Cas2) showed nuclease activity on both DNA and RNA in a nonspecific manner. Additionally, unlike other known Cas2 proteins, Lep_Cas2 showed metal-independent RNase activity and preferential activity on RNA over DNA. These results provide insight for understanding Cas2 diversity existing in the prokaryotic adaptive immune system.

  5. 21 CFR 173.395 - Trifluoromethane sulfonic acid.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... has the empirical formula CF3SO3H (CAS Reg. No. 1493-13-6). The catalyst (Trifluoromethane sulfonic... catalyst meets the following specifications: Appearance, Clear liquid. Color, Colorless to amber... esterification reaction is quenched with steam and water and the catalyst is removed with the aqueous...

  6. 75 FR 47893 - Proposed Collection; Comment Request for REG-111583-07, (T.D. 9405) (Final)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-09

    ... Internal Revenue Service Proposed Collection; Comment Request for REG-111583-07, (T.D. 9405) (Final) AGENCY... regulations (REG-111583-07) (T.D. 9405), Employment Tax Adjustments. DATES: Written comments should be...: 1545-2097. Form Number: REG-111583-07 (T.D. 9405) (final). Abstract: This document contains...

  7. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

    DOEpatents

    Church, George M.; Esvelt, Kevin; Mali, Prashant

    2017-03-07

    Methods of modulating expression of a target nucleic acid in a cell are provided including use of multiple orthogonal Cas9 proteins to simultaneously and independently regulate corresponding genes or simultaneously and independently edit corresponding genes.

  8. xdamp Version 2: An IDL{reg_sign}-based data manipulation program

    SciTech Connect

    Ballard, W.P.

    1996-12-01

    The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA{trademark} (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of UNIX{reg_sign}-based workstations, a replacement was needed. This package uses the IDL{reg_sign} software, available from Research Systems Incorporated in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP.IDL is currently supported on a wide variety of UNIX platforms such as IBM{reg_sign} workstations, Hewlett Packard workstations, SUN{reg_sign} workstations, Microsoft{reg_sign} Windows{trademark} computers, Macintosh{reg_sign} computers and Digital Equipment Corporation VMS{reg_sign} systems. Thus, xdamp is portable across many platforms. The authors have verified operation, albeit with some minor IDL bugs, on IBM PC computers using Windows, Windows 95 and Windows NT; IBM UNIX platforms; DEC Alpha and VMS systems; HP 9000/700 series workstations; and Macintosh computers, both regular and PowerPC{trademark} versions. Version 2 updates xdamp to require IDL version 4.0.1, adds many enhancements, and fixes a number of bugs.

  9. Thiazolidinediones inhibit REG I{alpha} gene transcription in gastrointestinal cancer cells

    SciTech Connect

    Yamauchi, Akiyo; Takahashi, Iwao; Takasawa, Shin; Nata, Koji; Noguchi, Naoya; Ikeda, Takayuki; Yoshikawa, Takeo; Shervani, Nausheen J.; Suzuki, Iwao; Uruno, Akira; Unno, Michiaki; Okamoto, Hiroshi Sugawara, Akira

    2009-02-13

    REG (Regenerating gene) I{alpha} protein functions as a growth factor for gastrointestinal cancer cells, and its mRNA expression is strongly associated with a poor prognosis in gastrointestinal cancer patients. We here demonstrated that PPAR{gamma}-agonist thiazolidinediones (TZDs) inhibited cell proliferation and REG I{alpha} protein/mRNA expression in gastrointestinal cancer cells. TZDs inhibited the REG I{alpha} gene promoter activity, via its cis-acting element which lacked PPAR response element and could not bind to PPAR{gamma}, in PPAR{gamma}-expressing gastrointestinal cancer cells. The inhibition was reversed by co-treatment with a specific PPAR{gamma}-antagonist GW9662. Although TZDs did not inhibit the REG I{alpha} gene promoter activity in PPAR{gamma}-non-expressing cells, PPAR{gamma} overexpression in the cells recovered their inhibitory effect. Taken together, TZDs inhibit REG I{alpha} gene transcription through a PPAR{gamma}-dependent pathway. The TZD-induced REG I{alpha} mRNA reduction was abolished by cycloheximide, indicating the necessity of novel protein(s) synthesis. TZDs may therefore be a candidate for novel anti-cancer drugs for patients with gastrointestinal cancer expressing both REG I{alpha} and PPAR{gamma}.

  10. Exploiting CRISPR/Cas: interference mechanisms and applications.

    PubMed

    Richter, Hagen; Randau, Lennart; Plagens, André

    2013-07-12

    The discovery of biological concepts can often provide a framework for the development of novel molecular tools, which can help us to further understand and manipulate life. One recent example is the elucidation of the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) that protects bacteria and archaea against viruses or conjugative plasmids. The immunity is based on small RNA molecules that are incorporated into versatile multi-domain proteins or protein complexes and specifically target viral nucleic acids via base complementarity. CRISPR/Cas interference machines are utilized to develop novel genome editing tools for different organisms. Here, we will review the latest progress in the elucidation and application of prokaryotic CRISPR/Cas systems and discuss possible future approaches to exploit the potential of these interference machineries.

  11. Up-regulated Reg proteins induced by Interleukin-22 treatment ameliorate acute liver injury in rat model

    PubMed Central

    Zhang, Hong-Bin; Luo, Hong-Chun; Xin, Xiao-Juan; Zeng, Ai-Zhong

    2015-01-01

    Background: The regenerating gene (Reg), encoding lectin-related protein, was originally isolated from a rat regenerating pancreatic islets. Interleukin-22 (IL-22), a recently identified cytokine, is produced by Th 17 cells and natural killer cells. Both of them have been shown to play an important role in controlling tissue repair. But, it is unclear whether the IL-22/Reg axis is involved in liver regeneration and the improvement of liver function in a rat model of acute liver injury. Aims: We investigated the expression levels of Reg proteins after IL-22 stimulation in a rat model of acute liver injury, and estimated the effects of Reg proteins ameliorating acute liver injury. Methods: Western blot was used to measure the expressions of Reg I, Reg III, Reg IV proteins after treatment with recombinant lentivirus IL-22. At the same time, the expression levels of TB, ALT, AST, endotoxin (ETM), superoxide dismutase (SOD), malondialdehyde (MDA) were detected by related reagents. Results: In a rat model of acute liver injury, the expression levels of Reg I, Reg III, Reg IV proteins were increased after treatment with IL-22 recombinant lentivirus compared with treatment with lentivirus-empty vector, especially, Reg IV protein expression. Meanwhile, treatment with IL-22 recombinant lentivirus reduced serum levels of TB, ALT, AST, ETM, and decreased MAD levels in rat liver tissues, but increased SOD levels in rat liver tissues. Conclusion: IL-22 stimulation enhanced the expressions of Reg proteins in liver cell, especially, Reg IV protein, and ameliorated liver injury in a rat model of acute liver injury. Reg protein, especially Reg IV protein, might act as a biological mediator of immune cell-derived IL-22 in the recovering mechanism of liver injury. PMID:25785121

  12. The radii of SU Cas and TU Cas

    NASA Technical Reports Server (NTRS)

    Niva, G. D.; Schmidt, E. G.

    1980-01-01

    It is possible to obtain the masses of Cepheid variables by several methods involving the pulsation theory. However, these masses are frequently smaller than those indicated by the theory of stellar evolution. The cause of this discrepancy is not fully understood. Since the pulsation theory indicates that there is a relation among the mass, the radius and the period, the discrepancy also manifests itself in the radii of these stars. With this in mind, radius determinations for two Cepheids, SU Cas and TU Cas, were undertaken. It is concluded that because of the agreement between the present radius and the beat radius of TU Cas, the pulsation theory is giving correct information about the radii of beat Cepheids. This implies that the luminosities of short period Cepheids have been overestimated. Thus, the solution to the mass discrepancy should perhaps be sought in the theory of stellar evolution or in the possibility of mass loss.

  13. ROTO PEEN Scalar and VAC-PAC{reg_sign} system

    SciTech Connect

    1998-02-01

    The Pentek, Inc., milling technology, comprising the ROTO PEEN Scaler and the VAC-PAC{reg_sign} waste collection system, is a fully developed and commercialized technology used to remove hazardous coatings from concrete and steel floors, walls, ceilings, and structural components. This report describes a demonstration of the Pentek, Inc., milling system to remove the paint coating from 650 ft{sup 2} of concrete flooring on the service floor of the Chicago Pile-5 (CP-5) Research Reactor. CP-5 is a heavy-water moderated and cooled, highly enriched, uranium-fueled thermal reactor designed to supply neutrons for research. The reactor had a thermal-power rating of 5 megawatts and was operated continuously for 25 years until its final shutdown in 1979. These 25 years of operation produced activation and contamination characteristics representative of other nuclear facilities within the Department of Energy (DOE) complex and the commercial nuclear sector. CP-5 contains many of the essential features of other DOE and commercial nuclear facilities and can be used safely as a demonstration facility for the evaluation of innovative technologies for the future D and D of much larger, more highly contaminated facilities.

  14. Topical safety analysis report for the transportation of the NUHOMS{reg_sign} dry shielded canister. Volume 2

    SciTech Connect

    1993-08-01

    A thermal analyses for the 10CFR71 normal conditions of . transport and hypothetical accident conditions is presented for the conceptual NUHOMS{reg_sign} Transportation Cask and NUHOMS{reg_sign}-24P DSC system. The purpose of the thermal analyses presented herein is to demonstrate that the conceptual NUHOMS{reg_sign} Transportation Cask with the NUHOMS{reg_sign}-24P DSC provides suitable heat dissipation to maintain the heat removal capacity of the loaded NUHOMS{reg_sign} Transportation Cask. The thermal analyses results show that the maximum temperatures and pressures of the NUHOMS{reg_sign} Transportation Cask and the NUHOMS{reg_sign}-24P DSC are within their allowable material temperature and pressure limits.

  15. Fitting CRISPR-associated Cas3 into the helicase family tree.

    PubMed

    Jackson, Ryan N; Lavin, Matthew; Carter, Joshua; Wiedenheft, Blake

    2014-02-01

    Helicases utilize NTPs to modulate their binding to nucleic acids and many of these enzymes also unwind DNA or RNA duplexes in an NTP-dependent fashion. These proteins are phylogenetically related but functionally diverse, with essential roles in virtually all aspects of nucleic acid metabolism. A new class of helicases associated with RNA-guided adaptive immune systems in bacteria and archaea has recently been identified. Prokaryotes acquire resistance to invading genetic parasites by integrating short fragments of foreign nucleic acids into repetitive loci in the host chromosome known as CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR-associated gene 3 (cas3) encodes a conserved helicase protein that is essential for phage defense. Here we review recent advances in Cas3 biology, and provide a new phylogenetic framework that positions Cas3 in the helicase family tree. We anticipate that this Cas3 phylogeny will guide future biochemical and structural studies.

  16. The RegA regulon exhibits variability in response to altered growth conditions and differs markedly between Rhodobacter species

    PubMed Central

    Schindel, Heidi S.

    2016-01-01

    The RegB/RegA two-component system from Rhodobacter capsulatus regulates global changes in gene expression in response to alterations in oxygen levels. Studies have shown that RegB/RegA controls many energy-generating and energy-utilizing systems such as photosynthesis, nitrogen fixation, carbon fixation, hydrogen utilization, respiration, electron transport and denitrification. In this report, we utilized RNA-seq and ChIP-seq to analyse the breadth of genes indirectly and directly regulated by RegA. A comparison of mRNA transcript levels in wild type cells relative to a RegA deletion strain shows that there are 257 differentially expressed genes under photosynthetic defined minimal growth medium conditions and 591 differentially expressed genes when grown photosynthetically in a complex rich medium. ChIP-seq analysis also identified 61 unique RegA binding sites with a well-conserved recognition sequence, 33 of which exhibit changes in neighbouring gene expression. These transcriptome results define new members of the RegA regulon including genes involved in iron transport and motility. These results also reveal that the set of genes that are regulated by RegA are growth medium specific. Similar analyses under dark aerobic conditions where RegA is thought not to be phosphorylated by RegB reveal 40 genes that are differentially expressed in minimal medium and 20 in rich medium. Finally, a comparison of the R. capsulatus RegA regulon with the orthologous PrrA regulon in Rhodobacter sphaeroides shows that the number of photosystem genes regulated by RegA and PrrA are similar but that the identity of genes regulated by RegA and PrrA beyond those involved in photosynthesis are quite distinct. PMID:28348828

  17. A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii.

    PubMed

    Brendel, Jutta; Stoll, Britta; Lange, Sita J; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita

    2014-03-07

    The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1-8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.

  18. Cas9-dependent endogenous gene regulation is required for bacterial virulence.

    PubMed

    Sampson, Timothy R; Weiss, David S

    2013-12-01

    CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems are known to mediate bacterial defence against foreign nucleic acids. We recently demonstrated a non-canonical role for a CRISPR-Cas system in controlling endogenous gene expression, which had not previously been appreciated. In the present article, we describe the studies that led to this discovery, beginning with an unbiased genome-wide screen to identify virulence genes in the intracellular pathogen Francisella novicida. A gene annotated as encoding a hypothetical protein, but which we now know encodes the Cas protein Cas9, was identified as one of the most critical to the ability of F. novicida to replicate and survive during murine infection. Subsequent studies revealed a role for this protein in evasion of the host innate immune response. Specifically, Cas9 represses the expression of a BLP (bacterial lipoprotein) that could otherwise be recognized by TLR2 (Toll-like receptor 2), a host protein involved in initiating an antibacterial pro-inflammatory response. By repressing BLP levels, Cas9 mediates evasion of TLR2, promoting bacterial virulence. Finally, we described the molecular mechanism by which Cas9 functions in complex with two small RNAs to target the mRNA encoding the BLP for degradation. This work greatly broadened the paradigm for CRISPR-Cas function, highlighting a role in gene regulation that could be conserved in numerous bacteria, and elucidating its integral contribution to bacterial pathogenesis.

  19. Structural plasticity of PAM recognition by engineered variants of the RNA-guided endonuclease Cas9

    PubMed Central

    Anders, Carolin; Bargsten, Katja; Jinek, Martin

    2016-01-01

    Summary The RNA-guided endonuclease Cas9 from Streptococcus pyogenes (SpCas9) forms the core of a powerful genome editing technology. DNA cleavage by SpCas9 is dependent on the presence of a 5’-NGG-3’ protospacer adjacent motif (PAM) in the target DNA, restricting the choice of targetable sequences. To address this limitation, artificial SpCas9 variants with altered PAM specificities have recently been developed. Here we report crystal structures of the VQR, EQR, and VRER SpCas9 variants bound to target DNAs containing their preferred PAM sequences. The structures reveal that the non-canonical PAMs are recognized by an induced fit mechanism. Besides mediating sequence-specific base recognition, the amino acid substitutions introduced in the SpCas9 variants facilitate conformational remodeling of the PAM region of the bound DNA. Guided by the structural data, we developed a SpCas9 variant that specifically recognizes NAAG PAMs. Taken together, these studies inform further development of Cas9-based genome editing tools. PMID:26990992

  20. RegA control of bacteriochlorophyll and carotenoid synthesis in Rhodobacter capsulatus.

    PubMed

    Willett, Jonathan; Smart, James L; Bauer, Carl E

    2007-11-01

    We provide in vivo genetic and in vitro biochemical evidence that RegA directly regulates bacteriochlorophyll and carotenoid biosynthesis in Rhodobacter capsulatus. beta-Galactosidase expression assays with a RegA-disrupted strain containing reporter plasmids for Mg-protoporphyrin IX monomethyl ester oxidative cyclase (bchE), Mg-protoporphyrin IX chelatase (bchD), and phytoene dehydrogenase (crtI) demonstrate RegA is responsible for fourfold anaerobic induction of bchE, threefold induction of bchD, and twofold induction of crtI. Promoter mapping studies, coupled with DNase I protection assays, map the region of RegA binding to three sites in the bchE promoter region. Similar studies at the crtA and crtI promoters indicate that RegA binds to a single region equidistant from these divergent promoters. These results demonstrate that RegA is directly responsible for anaerobic induction of bacteriochlorophyll biosynthesis genes bchE, bchD, bchJ, bchI, bchG, and bchP and carotenoid biosynthesis genes crtI, crtB, and crtA.

  1. Translational control of regA, a key gene controlling cell differentiation in Volvox carteri.

    PubMed

    Babinger, Karin; Hallmann, Armin; Schmitt, Rüdiger

    2006-10-01

    The complete division of labour between the reproductive and somatic cells of the green alga Volvox carteri is controlled by three types of genes. One of these is the regA gene, which controls terminal differentiation of the somatic cells. Here, we examined translational control elements located in the 5' UTR of regA, particularly the eight upstream start codons (AUGs) that have to be bypassed by the translation machinery before regA can be translated. The results of our systematic mutational, structural and functional analysis of the 5' UTR led us to conclude that a ribosome-shunting mechanism--rather than leaky scanning, ribosomal reinitiation, or internal ribosome entry site (IRES)-mediated initiation--controls the translation of regA mRNA. This mechanism, which involves dissociation of the 40S initiation complex from the message, followed by reattachment downstream, in order to bypass a secondary structure block in the mRNA, was validated by deleting the predicted ;landing site' (which prevented regA expression) and inserting a stable 64 nucleotide hairpin just upstream of this site (which did not prevent regA expression). We believe that this is the first report suggesting that translation of an mRNA in a green eukaryote is controlled by ribosome shunting.

  2. Requirements and tasks of cohorts and registers, the German KoRegIT project.

    PubMed

    Michalik, Claudia; Dress, Jochen; Ngouongo, Sylvie; Stäubert, Sebastian; Weber, Ulrike; Brockmeyer, Norbert; Paulus, Ursula; Stausberg, Jürgen

    2014-01-01

    Epidemiological cohorts and registers (KoReg) are long lasting and complex research projects, which need systematic and extensive planning and steering. The aim of the KoRegIT project was to develop a generic catalogue of requirements to support the organisational- and IT-structure of KoReg. The catalogue of requirements comprises the top level (TL) tasks of the core processes. All TL were classified into the following project phases: 1. Development, 2. Operation, 3. Completion. According to the defined TL tasks, the appropriate use cases (UC) were identified. The catalogue currently specifies 45 TL tasks and 207 UC. The UC were elaborated by a short and standardized description of the task, the involved actors (human or external systems), the preconditions, which have to be fulfilled in order to realize this task, the normal flow of the task and the post conditions. The developed catalogue was reviewed by representatives of different KoReg in Germany. The draft catalogue of requirements was revised according to the reviewer's feedback and discussion. The revised and complete catalogue with all elaborated UC was reviewed again by further experts. The developed KoRegIT catalogue of requirements offers a supporting tool to set-up the organisational structures and processes of KoReg as well as the definition of the needed IT-infrastructure. In addition it can be used to optimize or to expand these structures.

  3. Using the SAS reg sign system for an analysis and reporting system for effluent monitoring

    SciTech Connect

    Walker, T.

    1991-09-19

    A computerized analysis and reporting system was developed for personnel involved in effluent monitoring operations at the Oak Ridge Y-12 Plant managed by Martin Marietta Energy Systems, Inc. for the United States Department of Energy under contract DE-AC05-84OR21400. SAS/ACCESS{reg sign} interface to Rdb/VMS{reg sign}, SAS/BASE{reg sign}, SAS/GRAPH{reg sign}, SAS{reg sign} BATCH, the macro facility, and some aspects of Digital Command Language (DCL{trademark}) were utilized in the development of the reporting and analysis system. This system essentially contains three modules, each of which has its own function. The basic functions include the creation of monthly reports for easy perusal for excursions; run charts of the observational laboratory data; and a nonparametric trend analysis of monthly summary values, which involves the computation of the Mann-Kendall test for slope. Digital Control Language is utilized to pass user supplied parameters to individual SAS{reg sign} programs within each module and the SASBATCH command is used to regulate time consuming programs to a batch queue.

  4. Using Pro/ENGINEER`s{reg_sign} interface module

    SciTech Connect

    Schulze, J.

    1994-06-01

    When the ACCORD Process introduced Pro/ENGINEER to Sandians several years ago, a new process for design/definition was implemented. Prior to ACCORD, engineers and draftsmen worked in the 2-D mode with a program caned ANVIL{reg_sign}, which had limited capabilities. Although the transition from 2-D modeling to 3-D modeling met with some resistance, most engineers have embraced this new concept with enthusiasm They are now able to work in the 3-D mode and at increased levels of productivity with appropriate time savings never achieved before. One area that Pro/ENGINEER is noted for that this report will concentrate on, is the powerful interface module with its wide selection of transfer file configurations. This allows the engineer to create parts or assemblies and transfer them to many different second party software packages whose vendors can provide the capability for stress analysis, rapid prototypes, virtual reality environments, or many other forms of advanced manufacturing modes of communication. The ACCORD Program has at its core, the Pro/ENGINEER program from Parametric Technology Inc. Included in the ACCORD program, are several supporting programs from other vendors to make this cooperation between software packages a reality. It is possible to create parts in Pro/ENG transfer those parts to another package that has the capability to analyze the parts for deficiencies, then optimize those parts, and allow for changes to be made. Also included in this report, are other packages closely tied to Pro/ENGINEER, but not necessarily supported under the ACCORD program. Some of these packages allow you to create very impressive video productions, or allow you to meander through a virtual reality scenario. All of these new software packages will give you a new perspective on performance. This report will show how some of these interfaces work, and how you can improve your productivity if you utilize the ACCORD program as it is implemented here at Sandia.

  5. CAS-Induced Difficulties in Learning Mathematics?

    ERIC Educational Resources Information Center

    Jankvist, Uffe Thomas; Misfeldt, Morten

    2015-01-01

    In recent years computer algebra systems (CAS) have become an integrated part of the upper secondary school mathematics program. Despite the many positive possibilities of CAS, there also seems to be a flip side of the coin in relation to actual difficulties in learning mathematics, not least because a strong dependence on CAS for mathematical…

  6. 21 CFR 177.2910 - Ultra-filtration membranes.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... with zirconium oxide (CAS Reg. No. 1314-23-4) containing up to 12 percent yttrium oxide (CAS Reg. No... with zirconium oxide (CAS Reg. No. 1314-23-4) containing up to 5 percent yttrium oxide (CAS Reg....

  7. The Global Response Regulator RegR Controls Expression of Denitrification Genes in Bradyrhizobium japonicum

    PubMed Central

    Torres, Maria J.; Argandoña, Montserrat; Vargas, Carmen; Bedmar, Eulogio J.; Fischer, Hans-Martin; Mesa, Socorro; Delgado, María J.

    2014-01-01

    Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. Genes controlled by RegR included nor and nos structural genes encoding nitric oxide and nitrous oxide reductase, respectively, genes encoding electron transport proteins such as cycA (blr7544) or cy2 (bll2388), and genes involved in nitric oxide detoxification (blr2806-09) and copper homeostasis (copCAB), as well as two regulatory genes (bll3466, bll4130). Purified RegR interacted with the promoters of norC (blr3214), nosR (blr0314), a fixK-like gene (bll3466), and bll4130, which encodes a LysR-type regulator. By using fluorescently labeled oligonucleotide extension (FLOE), we were able to identify two transcriptional start sites located at about 35 (P1) and 22 (P2) bp upstream of the putative translational start codon of norC. P1 matched with the previously mapped 5′end of norC mRNA which we demonstrate in this work to be under FixK2 control. P2 is a start site modulated by RegR and specific for anoxic conditions. Moreover, qRT-PCR experiments, expression studies with a norC-lacZ fusion, and heme c-staining analyses revealed that anoxia and nitrate are required for RegR-dependent induction of nor genes, and that this control is independent of the sensor protein RegS. PMID:24949739

  8. The global response regulator RegR controls expression of denitrification genes in Bradyrhizobium japonicum.

    PubMed

    Torres, Maria J; Argandoña, Montserrat; Vargas, Carmen; Bedmar, Eulogio J; Fischer, Hans-Martin; Mesa, Socorro; Delgado, María J

    2014-01-01

    Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. Genes controlled by RegR included nor and nos structural genes encoding nitric oxide and nitrous oxide reductase, respectively, genes encoding electron transport proteins such as cycA (blr7544) or cy2 (bll2388), and genes involved in nitric oxide detoxification (blr2806-09) and copper homeostasis (copCAB), as well as two regulatory genes (bll3466, bll4130). Purified RegR interacted with the promoters of norC (blr3214), nosR (blr0314), a fixK-like gene (bll3466), and bll4130, which encodes a LysR-type regulator. By using fluorescently labeled oligonucleotide extension (FLOE), we were able to identify two transcriptional start sites located at about 35 (P1) and 22 (P2) bp upstream of the putative translational start codon of norC. P1 matched with the previously mapped 5'end of norC mRNA which we demonstrate in this work to be under FixK2 control. P2 is a start site modulated by RegR and specific for anoxic conditions. Moreover, qRT-PCR experiments, expression studies with a norC-lacZ fusion, and heme c-staining analyses revealed that anoxia and nitrate are required for RegR-dependent induction of nor genes, and that this control is independent of the sensor protein RegS.

  9. Breast Cancer Anti-estrogen Resistance 3 (BCAR3) Protein Augments Binding of the c-Src SH3 Domain to Crk-associated Substrate (p130cas)*

    PubMed Central

    Makkinje, Anthony; Vanden Borre, Pierre; Near, Richard I.; Patel, Prayag S.; Lerner, Adam

    2012-01-01

    The focal adhesion adapter protein p130cas regulates adhesion and growth factor-related signaling, in part through Src-mediated tyrosine phosphorylation of p130cas. AND-34/BCAR3, one of three NSP family members, binds the p130cas carboxyl terminus, adjacent to a bipartite p130cas Src-binding domain (SBD) and induces anti-estrogen resistance in breast cancer cell lines as well as phosphorylation of p130cas. Only a subset of the signaling properties of BCAR3, specifically augmented motility, are dependent upon formation of the BCAR3-p130cas complex. Using GST pull-down and immunoprecipitation studies, we show that among NSP family members, only BCAR3 augments the ability of p130cas to bind the Src SH3 domain through an RPLPSPP motif in the p130cas SBD. Although our prior work identified phosphorylation of the serine within the p130cas RPLPSPP motif, mutation of this residue to alanine or glutamic acid did not alter BCAR3-induced Src SH3 domain binding to p130cas. The ability of BCAR3 to augment Src SH3 binding requires formation of a BCAR3-p130cas complex because mutations that reduce association between these two proteins block augmentation of Src SH3 domain binding. Similarly, in MCF-7 cells, BCAR3-induced tyrosine phosphorylation of the p130cas substrate domain, previously shown to be Src-dependent, was reduced by an R743A mutation that blocks BCAR3 association with p130cas. Immunofluorescence studies demonstrate that BCAR3 expression alters the intracellular location of both p130cas and Src and that all three proteins co-localize. Our work suggests that BCAR3 expression may regulate Src signaling in a BCAR3-p130cas complex-dependent fashion by altering the ability of the Src SH3 domain to bind the p130cas SBD. PMID:22711540

  10. Relationship between drug resistance and the clustered, regularly interspaced, short, palindromic repeat-associated protein genes cas1 and cas2 in Shigella from giant panda dung

    PubMed Central

    Ren, Lu; Deng, Lin-Hua; Zhang, Ri-Peng; Wang, Cheng-Dong; Li, De-Sheng; Xi, Li-Xin; Chen, Zhen-rong; Yang, Rui; Huang, Jie; Zeng, Yang-ru; Wu, Hong-Lin; Cao, San-Jie; Wu, Rui; Huang, Yong; Yan, Qi-Gui

    2017-01-01

    Abstract Background: To detect drug resistance in Shigella obtained from the dung of the giant panda, explore the factors leading to drug resistance in Shigella, understand the characteristics of clustered, regularly interspaced, short, palindromic repeats (CRISPR), and assess the relationship between CRISPR and drug resistance. Methods: We collected fresh feces from 27 healthy giant pandas in the Giant Panda Conservation base (Wolong, China). We identified the strains of Shigella in the samples by using nucleotide sequence analysis. Further, the Kirby-Bauer paper method was used to determine drug sensitivity of the Shigella strains. CRISPR-associated protein genes cas1 and cas2 in Shigella were detected by polymerase chain reaction (PCR), and the PCR products were sequenced and compared. Results: We isolated and identified 17 strains of Shigella from 27 samples, including 14 strains of Shigella flexneri, 2 strains of Shigella sonnei, and 1 strain of Shigella dysenteriae. Further, drug resistance to cefazolin, imipenem, and amoxicillin–clavulanic acid was identified as a serious problem, as multidrug-resistant strains were detected. Further, cas1 and cas2 showed different degrees of point mutations. Conclusion: The CRISPR system widely exists in Shigella and shares homology with that in Escherichia coli. The cas1 and cas 2 mutations contribute to the different levels of resistance. Point mutations at sites 3176455, 3176590, and 3176465 in cas1 (a); sites 3176989, 3176992, and 3176995 in cas1 (b); sites 3176156 and 3176236 in cas2 may affect the resistance of bacteria, cause emergence of multidrug resistance, and increase the types of drug resistance. PMID:28207509

  11. 21 CFR 74.706 - FD&C Yellow No. 6.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... compound is coupled with 6-hydroxy-2-naphthalene-sulfonic acid. The dye is isolated as the sodium salt and...&C Yellow No. 6 is principally the disodium salt of 6-hydroxy-5- -2-naphthalenesulfonic acid (CAS Reg. No. 2783-94-0). The trisodium salt of 3-hydroxy-4- -2,7-naphthalenedisulfonic acid (CAS Reg....

  12. 21 CFR 74.706 - FD&C Yellow No. 6.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... compound is coupled with 6-hydroxy-2-naphthalene-sulfonic acid. The dye is isolated as the sodium salt and...&C Yellow No. 6 is principally the disodium salt of 6-hydroxy-5- -2-naphthalenesulfonic acid (CAS Reg. No. 2783-94-0). The trisodium salt of 3-hydroxy-4- -2,7-naphthalenedisulfonic acid (CAS Reg....

  13. 21 CFR 74.706 - FD&C Yellow No. 6.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... compound is coupled with 6-hydroxy-2-naphthalene-sulfonic acid. The dye is isolated as the sodium salt and...&C Yellow No. 6 is principally the disodium salt of 6-hydroxy-5- -2-naphthalenesulfonic acid (CAS Reg. No. 2783-94-0). The trisodium salt of 3-hydroxy-4- -2,7-naphthalenedisulfonic acid (CAS Reg....

  14. 21 CFR 74.706 - FD&C Yellow No. 6.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... compound is coupled with 6-hydroxy-2-naphthalene-sulfonic acid. The dye is isolated as the sodium salt and...&C Yellow No. 6 is principally the disodium salt of 6-hydroxy-5- -2-naphthalenesulfonic acid (CAS Reg. No. 2783-94-0). The trisodium salt of 3-hydroxy-4- -2,7-naphthalenedisulfonic acid (CAS Reg....

  15. 21 CFR 74.706 - FD&C Yellow No. 6.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... compound is coupled with 6-hydroxy-2-naphthalene-sulfonic acid. The dye is isolated as the sodium salt and...&C Yellow No. 6 is principally the disodium salt of 6-hydroxy-5- -2-naphthalenesulfonic acid (CAS Reg. No. 2783-94-0). The trisodium salt of 3-hydroxy-4- -2,7-naphthalenedisulfonic acid (CAS Reg....

  16. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

    SciTech Connect

    Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S.; Arkin, Adam P.; Mironov, Andrey A.; Dubchak, Inna

    2010-05-26

    RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.

  17. Prevention of Reg I-induced β-cell apoptosis by IL-6/dexamethasone through activation of HGF gene regulation.

    PubMed

    Nakagawa, Kei; Takasawa, Shin; Nata, Koji; Yamauchi, Akiyo; Itaya-Hironaka, Asako; Ota, Hiroyo; Yoshimoto, Kiyomi; Sakuramoto-Tsuchida, Sumiyo; Miyaoka, Tomoko; Takeda, Maiko; Unno, Michiaki; Okamoto, Hiroshi

    2013-12-01

    Reg (regenerating gene) product, Reg protein, is induced in pancreatic β-cells and acts as autocrine/paracrine growth factor for regeneration via the cell surface Reg receptor. However, high concentrations of Reg I protein induced β-cell apoptosis. In the present study, we found that hepatocyte growth factor (HGF) attenuated the β-cell apoptosis induced by the high concentrations of Reg I protein and that the combined stimulation of interleukin-6 (IL-6) and dexamethasone (Dx) induced the accumulation of HGF mRNA as well as Reg I mRNA in β-cells. The accumulation of the HGF mRNA was caused by the activation of the HGF promoter. Deletion analysis revealed that the region of -96 to -92 of the HGF gene was responsible for the promoter activation by IL-6+Dx. The promoters contain a consensus transcription factor binding sequence for signal transducer and activator of transcription (STAT). Site-directed mutations of STAT-binding motif in the region markedly attenuated the HGF promoter activity. Chromatin immunoprecipitation assay showed that STAT3 is located at the active HGF promoter in response to IL-6+Dx stimulation. These results strongly suggest that the combined stimulation of IL-6 and glucocorticoids induces the activation of both Reg and HGF genes and that the anti-apoptotic effects of HGF against the Reg I-induced apoptosis may help β-cell regeneration by Reg I protein.

  18. CRISPR/Cas9 Technologies.

    PubMed

    Williams, Bart O; Warman, Matthew L

    2017-02-23

    The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) pathway is revolutionizing biological research. Modifications to this primitive prokaryotic immune system now enable scientists to efficiently edit DNA or modulate gene expression in living eukaryotic cells and organisms. Thus, many laboratories can now perform important experiments that previously were considered scientifically risky or too costly. Here, we describe the components of the CRISPR/Cas system that have been engineered for use in eukaryotes. We also explain how this system can be used to genetically modify cell lines and model organisms, or regulate gene expression in order to search for new participants in biological pathways. © 2017 American Society for Bone and Mineral Research.

  19. Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri.

    PubMed

    Sanozky-Dawes, Rosemary; Selle, Kurt; O'Flaherty, Sarah; Klaenhammer, Todd; Barrangou, Rodolphe

    2015-09-01

    Bacteria encode clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated genes (cas), which collectively form an RNA-guided adaptive immune system against invasive genetic elements. In silico surveys have revealed that lactic acid bacteria harbour a prolific and diverse set of CRISPR-Cas systems. Thus, the natural evolutionary role of CRISPR-Cas systems may be investigated in these ecologically, industrially, scientifically and medically important microbes. In this study, 17 Lactobacillus gasseri strains were investigated and 6 harboured a type II-A CRISPR-Cas system, with considerable diversity in array size and spacer content. Several of the spacers showed similarity to phage and plasmid sequences, which are typical targets of CRISPR-Cas immune systems. Aligning the protospacers facilitated inference of the protospacer adjacent motif sequence, determined to be 5'-NTAA-3' flanking the 3' end of the protospacer. The system in L. gasseri JV-V03 and NCK 1342 interfered with transforming plasmids containing sequences matching the most recently acquired CRISPR spacers in each strain. We report the distribution and function of a native type II-A CRISPR-Cas system in the commensal species L. gasseri. Collectively, these results open avenues for applications for bacteriophage protection and genome modification in L. gasseri, and contribute to the fundamental understanding of CRISPR-Cas systems in bacteria.

  20. A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion.

    PubMed

    Sampson, Timothy R; Napier, Brooke A; Schroeder, Max R; Louwen, Rogier; Zhao, Jinshi; Chin, Chui-Yoke; Ratner, Hannah K; Llewellyn, Anna C; Jones, Crystal L; Laroui, Hamed; Merlin, Didier; Zhou, Pei; Endtz, Hubert P; Weiss, David S

    2014-07-29

    Clustered, regularly interspaced, short palindromic repeats-CRISPR associated (CRISPR-Cas) systems defend bacteria against foreign nucleic acids, such as during bacteriophage infection and transformation, processes which cause envelope stress. It is unclear if these machineries enhance membrane integrity to combat this stress. Here, we show that the Cas9-dependent CRISPR-Cas system of the intracellular bacterial pathogen Francisella novicida is involved in enhancing envelope integrity through the regulation of a bacterial lipoprotein. This action ultimately provides increased resistance to numerous membrane stressors, including antibiotics. We further find that this previously unappreciated function of Cas9 is critical during infection, as it promotes evasion of the host innate immune absent in melanoma 2/apoptosis associated speck-like protein containing a CARD (AIM2/ASC) inflammasome. Interestingly, the attenuation of the cas9 mutant is complemented only in mice lacking both the AIM2/ASC inflammasome and the bacterial lipoprotein sensor Toll-like receptor 2, but not in single knockout mice, demonstrating that Cas9 is essential for evasion of both pathways. These data represent a paradigm shift in our understanding of the function of CRISPR-Cas systems as regulators of bacterial physiology and provide a framework with which to investigate the roles of these systems in myriad bacteria, including pathogens and commensals.

  1. Assessment of cerebral blood flow autoregulation (CBF AR) with rheoencephalography (REG): studies in animals

    NASA Astrophysics Data System (ADS)

    Popovic, Djordje; Bodo, Michael; Pearce, Frederick; van Albert, Stephen; Garcia, Alison; Settle, Tim; Armonda, Rocco

    2013-04-01

    The ability of cerebral vasculature to regulate cerebral blood flow (CBF) in the face of changes in arterial blood pressure (SAP) or intracranial pressure (ICP) is an important guard against secondary ischemia in acute brain injuries, and official guidelines recommend that therapeutic decisions be guided by continuous monitoring of CBF autoregulation (AR). The common method for CBF AR monitoring, which rests on real-time derivation of the correlation coefficient (PRx) between slow oscillations in SAP and ICP is, however, rarely used in clinical practice because it requires invasive ICP measurements. This study investigated whether the correlation coefficient between SAP and the pulsatile component of the non-invasive transcranial bioimpedance signal (rheoencephalography, REG) could be used to assess the state and lower limit of CBF AR. The results from pigs and rhesus macaques affirm the utility of REG; however, additional animal and clinical studies are warranted to assess selectivity of automatic REG-based evaluation of CBF AR.

  2. Regulatory Interactions in ProKaryotes from RegTransBase

    DOE Data Explorer

    Dubchak, Inna; Gelfand, Mikhail

    RegTransBase, a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains various types of experimental data, in particular: the activation or repression of transcription by an identified direct regulator determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA mapping or prediction of binding sites for a regulatory protein characterization of regulatory mutations. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species. (Specialized Interface)

  3. Composite molding of SPECTRA{reg_sign} extended chain polyethylene fibers in a flexible rubber matrix

    SciTech Connect

    McKeehan, K.

    1997-08-01

    THETA Technologies, Inc. is a multidisciplinary research and development firm involved in the design and development of affordable, lightweight, high ballistic protection modular body armor ensemble for future military, law enforcement, and specialized commercial market applications. In the course of their research, THETA Technologies, Inc. identified that current state-of-the-art in ballistic protection and overall composite reinforcement is a high density extended chain polyethylene (HDECPE) fiber known as SPECTRA{reg_sign}, a product of AlliedSignal Fibers, Petersburg, VA. SPECTRA{reg_sign} is ten times stronger than steel of equal weight. As a non-aramid polyethylene, it offers highly desirable properties in areas of resistance to chemical degradation, virtual neutral buoyancy (0.97), and increased capacity for composite bonding over competing nylon-based fibers, such as KEVLAR{reg_sign}. SPECTRA Shield{trademark}, a woven ballistic-resistant fabric using the SPECTRA{reg_sign} fiber, is presently the most effective ballistic-resistant component for both flexible and hard plate composite armors. THETA Technologies, Inc. identified a market need for a boot sole design that would measurably increase protection to the wearer without significantly degrading performance in other areas, such as flexibility and overall weight. THETA Technologies, Inc. proposed a nitrile rubber and SPECTRA{reg_sign} fiber matrix to produce an optimal boot sole. The objective of this CRADA effort was to develop and test a process for combining the SPECTRA{reg_sign} fiber, in both chopped fiber and SPECTRA Shield{trademark} form, within a semiflexible nitrile composite having desirable and marketable properties in areas of resistance to penetration and mechanical stress.

  4. Genome modification by CRISPR/Cas9.

    PubMed

    Ma, Yuanwu; Zhang, Lianfeng; Huang, Xingxu

    2014-12-01

    Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas)9-mediated genome modification enables us to edit the genomes of a variety of organisms rapidly and efficiently. The advantages of the CRISPR-Cas9 system have made it an increasingly popular genetic engineering tool for biological and therapeutic applications. Moreover, CRISPR-Cas9 has been employed to recruit functional domains that repress/activate gene expression or label specific genomic loci in living cells or organisms, in order to explore developmental mechanisms, gene expression regulation, and animal behavior. One major concern about this system is its specificity; although CRISPR-Cas9-mediated off-target mutation has been broadly studied, more efforts are required to further improve the specificity of CRISPR-Cas9. We will also discuss the potential applications of CRISPR-Cas9.

  5. Expanding CRISPR/Cas9 Genome Editing Capacity in Zebrafish Using SaCas9

    PubMed Central

    Feng, Yan; Chen, Cheng; Han, Yuxiang; Chen, Zelin; Lu, Xiaochan; Liang, Fang; Li, Song; Qin, Wei; Lin, Shuo

    2016-01-01

    The type II CRISPR/Cas9 system has been used widely for genome editing in zebrafish. However, the requirement for the 5′-NGG-3′ protospacer-adjacent motif (PAM) of Cas9 from Streptococcus pyogenes (SpCas9) limits its targeting sequences. Here, we report that a Cas9 ortholog from Staphylococcus aureus (SaCas9), and its KKH variant, successfully induced targeted mutagenesis with high frequency in zebrafish. Confirming previous findings, the SpCas9 variant, VQR, can also induce targeted mutations in zebrafish. Bioinformatics analysis of these new Cas targets suggests that the number of available target sites in the zebrafish genome can be greatly expanded. Collectively, the expanded target repertoire of Cas9 in zebrafish should further facilitate the utility of this organism for genetic studies of vertebrate biology. PMID:27317783

  6. 77 FR 20314 - 2-Propenoic Acid, 2-Methyl-, 2-Ethylhexyl Ester, Telomer With 1-Dodecanethiol, Ethenylbenzene and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-04

    ...), Hydrogen 2- Sulfobutanedioate, Sodium Salt, 2, 2'-(1,2-Diazenediyl)Bis[2- Methylpropanenitrile]-Initiated..., sodium salt, 2, 2'-(1,2-diazenediyl)bis -initiated, CAS Reg. No. 1283712-50-4; when used as an inert...-sulfobutanedioate, sodium salt, 2, 2'-(1,2- diazenediyl)bis -initiated on food or feed commodities. DATES:...

  7. Using the CRISPR-Cas System to Positively Select Mutants in Genes Essential for Its Function.

    PubMed

    Yosef, Ido; Goren, Moran G; Edgar, Rotem; Qimron, Udi

    2015-01-01

    The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated proteins (Cas) comprise a prokaryotic adaptive defense system against foreign nucleic acids. This defense is mediated by Cas proteins, which are guided by sequences flanked by the repeats, called spacers, to target nucleic acids. Spacers designed against the prokaryotic self chromosome are lethal to the prokaryotic cell. This self-killing of the bacterium by its own CRISPR-Cas system can be used to positively select genes that participate in this killing, as their absence will result in viable cells. Here we describe a positive selection assay that uses this feature to identify E. coli mutants encoding an inactive CRISPR-Cas system. The procedure includes establishment of an assay that detects this self-killing, generation of transposon insertion mutants in random genes, and selection of viable mutants, suspected as required for this lethal activity. This procedure enabled us to identify a novel gene, htpG, that is required for the activity of the CRISPR-Cas system. The procedures described here can be adjusted to various organisms to identify genes required for their CRISPR-Cas activity.

  8. [Application Progress of CRISPR/Cas9 System for Gene Editing in Tumor Research].

    PubMed

    Liu, Chao; Li, Zhiwei; Zhang, Yanqiao

    2015-09-20

    TCRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated nuclease 9) gene editing system is a new type of gene editing technology developed based on the immune mechanism of archaea resisting the invasion of exogenous nucleic acid. Compared with traditional gene editing system, CRISPR/Cas9 system is more efficient, easier operating, and less cytotoxic. Currently, CRISPR/Cas9 gene editing technology has been applied to many aspects of cancer research, including research on cancer genes, constructing animal tumor models, screening tumor resistance-associated and phenotypic-related genes and cancer gene therapy. In this review, the application of the CRISPR/Cas9 system in tumor research were introduced.

  9. Orthologs and paralogs of regA, a master cell-type regulatory gene in Volvox carteri.

    PubMed

    Duncan, Leonard; Nishii, Ichiro; Howard, Alicia; Kirk, David; Miller, Stephen M

    2006-07-01

    The multicellular green alga Volvox carteri forma nagariensis has only two cell types: terminally differentiated somatic cells and reproductive cells. The regA gene maintains the terminally differentiated state of the somatic cells, apparently by repressing transcription of genes required for chloroplast biogenesis and thereby preventing cell growth. Because the RegA protein sequence bore no obvious motifs, we are attempting to identify regions of functional importance by searching for strongly conserved domains in RegA orthologs. Here we report the cloning and characterization of regA from the most closely related known taxon, V. carteri f. kawasakiensis. Given the closeness of the relationship between these two formas, their regA genes are surprisingly different: they differ in the number of introns and by several lengthy indels, and they encode proteins that are only 80% identical. We also serendipitously discovered a paralogous gene immediately upstream of each regA locus. The two regA genes, both upstream paralogs and several genes in Chlamydomonas (the closest unicellular relative of Volvox) encode a conserved region (the VARL domain) that contains what appears to be a DNA-binding SAND domain. This discovery has opened up a new avenue for exploring how regA and the terminally differentiated state that it controls evolved.

  10. 75 FR 10018 - Proposed Collection; Comment Request for Notice 98-1 and REG-108639-99

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-04

    ... (TD 9169). Abstract: Notice 98-1 and REG-108639-99 provides guidance for discrimination testing under..., Nondiscrimination Testing, and final regulation, REG-108639-99 (TD 1969), Retirement Plans; Cash or Deferred...: Title: Nondiscrimination Testing (Notice 98-1) and Retirement Plans; Cash or Deferred Arrangements...

  11. Therapeutic genome engineering via CRISPR-Cas systems.

    PubMed

    Moreno, Ana M; Mali, Prashant

    2017-02-15

    Differences in genomes underlie most organismal diversity, and aberrations in genomes underlie many disease states. With the growing knowledge of the genetic and pathogenic basis of human disease, development of safe and efficient platforms for genome and epigenome engineering will transform our ability to therapeutically target human diseases and also potentially engineer disease resistance. In this regard, the recent advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) RNA-guided nuclease systems have transformed our ability to target nucleic acids. Here we review therapeutic genome engineering applications with a specific focus on the CRISPR-Cas toolsets. We summarize past and current work, and also outline key challenges and future directions. For further resources related to this article, please visit the WIREs website.

  12. 75 FR 5850 - Proposed Collection; Comment Request for REG-166012-02

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-04

    ... Service (IRS), Treasury. ACTION: Notice and request for comments. SUMMARY: The Department of the Treasury...(c)(2)(A)). Currently, the IRS is soliciting comments concerning REG-166012-02, Notional Principal..., NW., Washington, DC 20224, or through the Internet at Allan.M.Hopkins@irs.gov ....

  13. The antimicrobial protein REG3A regulates keratinocyte proliferation and differentiation after skin injury.

    PubMed

    Lai, Yuping; Li, Dongqing; Li, Changwei; Muehleisen, Beda; Radek, Katherine A; Park, Hyun Jeong; Jiang, Ziwei; Li, Zhiheng; Lei, Hu; Quan, Yanchun; Zhang, Tian; Wu, Yelin; Kotol, Paul; Morizane, Shin; Hata, Tissa R; Iwatsuki, Keiji; Tang, Ce; Gallo, Richard L

    2012-07-27

    Epithelial keratinocyte proliferation is an essential element of wound repair, and abnormal epithelial proliferation is an intrinsic element in the skin disorder psoriasis. The factors that trigger epithelial proliferation in these inflammatory processes are incompletely understood. Here we have shown that regenerating islet-derived protein 3-alpha (REG3A) is highly expressed in keratinocytes during psoriasis and wound repair and in imiquimod-induced psoriatic skin lesions. The expression of REG3A by keratinocytes is induced by interleukin-17 (IL-17) via activation of keratinocyte-encoded IL-17 receptor A (IL-17RA) and feeds back on keratinocytes to inhibit terminal differentiation and increase cell proliferation by binding to exostosin-like 3 (EXTL3) followed by activation of phosphatidylinositol 3 kinase (PI3K) and the kinase AKT. These findings reveal that REG3A, a secreted intestinal antimicrobial protein, can promote skin keratinocyte proliferation and can be induced by IL-17. This observation suggests that REG3A may mediate the epidermal hyperproliferation observed in normal wound repair and in psoriasis.

  14. The proteasome activator 11 S REG (PA28) and class I antigen presentation.

    PubMed Central

    Rechsteiner, M; Realini, C; Ustrell, V

    2000-01-01

    There are two immune responses in vertebrates: humoral immunity is mediated by circulating antibodies, whereas cytotoxic T lymphocytes (CTL) confer cellular immunity. CTL lyse infected cells upon recognition of cell-surface MHC Class I molecules complexed with foreign peptides. The displayed peptides are produced in the cytosol by degradation of host proteins or proteins from intracellular pathogens that might be present. Proteasomes are cylindrical multisubunit proteases that generate many of the peptides eventually transferred to the cell surface for immune surveillance. In mammalian proteasomes, six active sites face a central chamber. As this chamber is sealed off from the enzyme's surface, there must be mechanisms to promote entry of substrates. Two protein complexes have been found to bind the ends of the proteasome and activate it. One of the activators is the 19 S regulatory complex of the 26 S proteasome; the other activator is '11 S REG' [Dubiel, Pratt, Ferrell and Rechsteiner (1992) J. Biol. Chem. 267, 22369-22377] or 'PA28' [Ma, Slaughter and DeMartino (1992) J. Biol. Chem. 267, 10515-10523]. During the past 7 years, our understanding of the structure of REG molecules has increased significantly, but much less is known about their biological functions. There are three REG subunits, namely alpha, beta and gamma. Recombinant REGalpha forms a ring-shaped heptamer of known crystal structure. 11 S REG is a heteroheptamer of alpha and beta subunits. REGgamma is also presumably a heptameric ring, and it is found in the nuclei of the nematode work Caenorhabditis elegans and higher organisms, where it may couple proteasomes to other nuclear components. REGalpha and REGbeta, which are abundant in vertebrate immune tissues, are located mostly in the cytoplasm. Synthesis of REG alpha and beta subunits is induced by interferon-gamma, and this has led to the prevalent hypothesis that REG alpha/beta hetero-oligomers play an important role in Class I antigen

  15. Cas6 specificity and CRISPR RNA loading in a complex CRISPR-Cas system.

    PubMed

    Sokolowski, Richard D; Graham, Shirley; White, Malcolm F

    2014-06-01

    CRISPR-Cas is an adaptive prokaryotic immune system, providing protection against viruses and other mobile genetic elements. In type I and type III CRISPR-Cas systems, CRISPR RNA (crRNA) is generated by cleavage of a primary transcript by the Cas6 endonuclease and loaded into multisubunit surveillance/effector complexes, allowing homology-directed detection and cleavage of invading elements. Highly studied CRISPR-Cas systems such as those in Escherichia coli and Pseudomonas aeruginosa have a single Cas6 enzyme that is an integral subunit of the surveillance complex. By contrast, Sulfolobus solfataricus has a complex CRISPR-Cas system with three types of surveillance complexes (Cascade/type I-A, CSM/type III-A and CMR/type III-B), five Cas6 paralogues and two different CRISPR-repeat families (AB and CD). Here, we investigate the kinetic properties of two different Cas6 paralogues from S. solfataricus. The Cas6-1 subtype is specific for CD-family CRISPR repeats, generating crRNA by multiple turnover catalysis whilst Cas6-3 has a broader specificity and also processes a non-coding RNA with a CRISPR repeat-related sequence. Deep sequencing of crRNA in surveillance complexes reveals a biased distribution of spacers derived from AB and CD loci, suggesting functional coupling between Cas6 paralogues and their downstream effector complexes.

  16. CAS as Environments for Implementing Mathematical Microworlds.

    ERIC Educational Resources Information Center

    Alpers, Burkhard

    2002-01-01

    Investigates whether computer algebra systems (CAS) are suitable environments for implementing mathematical microworlds. Recalls what constitutes a microworld and explores how CAS can be used for implementation, stating potentials as well as limitations. Provides as an example the microworld "Formula 1", implemented in Maple Software. (Author/KHR)

  17. New Development of the Online Integrated Climate-Chemistry model framwork (RegCM-CHEM4)

    NASA Astrophysics Data System (ADS)

    Zakey, A. S.; Shalaby, A. K.; Solmon, F.; Giorgi, F.; Tawfik, A. B.; Steiner, A. L.; Baklanov, A.

    2012-04-01

    The RegCM-CHEM4 is a new online integrated climate-chemistry model based on the regional climate model (RegCM4). The RegCM4 developed at the Abdus Salam International Centre for Theoretical Physics (ICTP), is a hydrostatic, sigma coordinate model. Tropospheric gas-phase chemistry is integrated into the climate model using the condensed version of the Carbon Bond Mechanism CBM-Z with lumped species that represent broad categories of organics based on carbon bond structure. The computationally rapid radical balance method RBM is coupled as a chemical solver to the gas-phase mechanism. Photolysis rates are determined as a function of meteorological and chemical inputs and interpolated from an array of pre-determined values based on the Tropospheric Ultraviolet-Visible Model (TUV) with cloud cover corrections. Cloud optical depths and cloud altitudes from RegCM-CHEM4 are used in the photolysis calculations, thereby directly coupling the photolysis rates and chemical reactions to meteorological conditions at each model time step. In this study, we evaluate the model over Europe for two different time scales: (1) an event-based analysis of the ozone episode associated with the heat wave of August 2003 and (2) a climatological analysis of a six-year simulation (2000-2005). For the episode analysis, model simulations show a good agreement with the European Monitoring and Evaluation Program (EMEP) observations of hourly ozone over different regions in Europe and capture ozone concentrations during and after the summer 2003 heat wave event. Analysis of the full six years of simulation indicates that the coupled chemistry-climate model can reproduce the seasonal cycle of ozone, with an overestimation of ozone in the non-event years of 5-15 ppb depending on the geographic region. Overall, the ozone and ozone precursor evaluation shows the feasibility of using RegCM-CHEM4 for decadal-length simulations of chemistry-climate interactions.

  18. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.

    PubMed

    Hochstrasser, Megan L; Taylor, David W; Bhat, Prashant; Guegler, Chantal K; Sternberg, Samuel H; Nogales, Eva; Doudna, Jennifer A

    2014-05-06

    In bacteria, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) DNA-targeting complex Cascade (CRISPR-associated complex for antiviral defense) uses CRISPR RNA (crRNA) guides to bind complementary DNA targets at sites adjacent to a trinucleotide signature sequence called the protospacer adjacent motif (PAM). The Cascade complex then recruits Cas3, a nuclease-helicase that catalyzes unwinding and cleavage of foreign double-stranded DNA (dsDNA) bearing a sequence matching that of the crRNA. Cascade comprises the CasA-E proteins and one crRNA, forming a structure that binds and unwinds dsDNA to form an R loop in which the target strand of the DNA base pairs with the 32-nt RNA guide sequence. Single-particle electron microscopy reconstructions of dsDNA-bound Cascade with and without Cas3 reveal that Cascade positions the PAM-proximal end of the DNA duplex at the CasA subunit and near the site of Cas3 association. The finding that the DNA target and Cas3 colocalize with CasA implicates this subunit in a key target-validation step during DNA interference. We show biochemically that base pairing of the PAM region is unnecessary for target binding but critical for Cas3-mediated degradation. In addition, the L1 loop of CasA, previously implicated in PAM recognition, is essential for Cas3 activation following target binding by Cascade. Together, these data show that the CasA subunit of Cascade functions as an essential partner of Cas3 by recognizing DNA target sites and positioning Cas3 adjacent to the PAM to ensure cleavage.

  19. In vitro enzymology of Cas9.

    PubMed

    Anders, Carolin; Jinek, Martin

    2014-01-01

    Cas9 is a bacterial RNA-guided endonuclease that uses base pairing to recognize and cleave target DNAs with complementarity to the guide RNA. The programmable sequence specificity of Cas9 has been harnessed for genome editing and gene expression control in many organisms. Here, we describe protocols for the heterologous expression and purification of recombinant Cas9 protein and for in vitro transcription of guide RNAs. We describe in vitro reconstitution of the Cas9-guide RNA ribonucleoprotein complex and its use in endonuclease activity assays. The methods outlined here enable mechanistic characterization of the RNA-guided DNA cleavage activity of Cas9 and may assist in further development of the enzyme for genetic engineering applications.

  20. CAS

    SciTech Connect

    Martinez, B.; Pomeroy, G. )

    1989-12-02

    The Security Alarm System is a data acquisition and control system which collects data from intrusion sensors and displays the information in a real-time environment for operators. The Access Control System monitors and controls the movement of personnel with the use of card readers and biometrics hand readers.

  1. Development with quasi-bipolar Horizon{reg_sign} technology

    SciTech Connect

    Craven, W.B.

    1997-12-01

    Electrosource Inc. (ELSI) is now in production with an Electric Vehicle (EV) battery based on fundamental advances in materials design, manufacturing processes and well understood lead-acid electrochemistry. The production 12V-85Ah module is rated at 45 Whr/kg, 223 W/kg and 400 C/3 cycles. Production test modules have achieved over 50 Whr/kg and 500 cycles. Chrysler has chosen the Electrosource Horizon Battery for their EV Minivan that will be in production next year. Design flexibility has led to a Hybrid electric vehicle battery as well as SLI, UPS and portable power.

  2. Homology-directed repair in rodent zygotes using Cas9 and TALEN engineered proteins.

    PubMed

    Ménoret, Séverine; De Cian, Anne; Tesson, Laurent; Remy, Séverine; Usal, Claire; Boulé, Jean-Baptiste; Boix, Charlotte; Fontanière, Sandra; Crénéguy, Alison; Nguyen, Tuan H; Brusselle, Lucas; Thinard, Reynald; Gauguier, Dominique; Concordet, Jean-Paul; Cherifi, Yacine; Fraichard, Alexandre; Giovannangeli, Carine; Anegon, Ignacio

    2015-10-07

    The generation of genetically-modified organisms has been revolutionized by the development of new genome editing technologies based on the use of gene-specific nucleases, such as meganucleases, ZFNs, TALENs and CRISPRs-Cas9 systems. The most rapid and cost-effective way to generate genetically-modified animals is by microinjection of the nucleic acids encoding gene-specific nucleases into zygotes. However, the efficiency of the procedure can still be improved. In this work we aim to increase the efficiency of CRISPRs-Cas9 and TALENs homology-directed repair by using TALENs and Cas9 proteins, instead of mRNA, microinjected into rat and mouse zygotes along with long or short donor DNAs. We observed that Cas9 protein was more efficient at homology-directed repair than mRNA, while TALEN protein was less efficient than mRNA at inducing homology-directed repair. Our results indicate that the use of Cas9 protein could represent a simple and practical methodological alternative to Cas9 mRNA in the generation of genetically-modified rats and mice as well as probably some other mammals.

  3. The Regional Earth System Model (RegESM) using RegCM4 coupled with the MITgcm ocean model: First assessments over the MED-CORDEX domain

    NASA Astrophysics Data System (ADS)

    Mariotti, Laura; Utku Turunçoǧlu, Ufuk; Farneti, Riccardo; Sannino, Gianmaria; Vittoria Struglia, Maria; Carillo, Adriana; Giorgi, Filippo

    2016-04-01

    In the framework of global climate studies, there is an increasingly growing concern about the vulnerability of the Mediterranean region, where high population density and intense exploitation activities pose severe questions on the sustainability of terrestrial water management, both for the present and the future. Ocean modeling studies suggest that the Mediterranean thermohaline circulation could be weakened in conditions of global greenhouse warming, an event which would undoubtedly affect regional climate, possibly triggering global feedback processes. Experiments with the atmosphere-ocean coupled system confirmed that a good comprehension of Mediterranean processes requires the explicit inclusion of the feedbacks between the atmospheric and the oceanic components, thus achieving a complete, fully coupled description of the Mediterranean hydrological cycle, at the same time gaining new insights in our current ability to reproduce the atmospheric hydrological processes and to close the hydrological balance. These issues are addressed by the upgraded PROTHEUS system which was jointly developed by ENEA and ICTP. Here we present a first evaluation of the performances of the new PROTHEUS system (called PROTHEUS 2.0) composed by the regional climate model RegCM4 (Giorgi et al. 2012) coupled with both the ocean model MITgcm (Marshall J. et al. 1997a,b) and the HD river model (Max-Planck's HD model; Hagemann and Dümenil, 1998) using RegESM (Regional Earth System Model) as a driver. The three-component (atmosphere, ocean and river routing) fully coupled model exchanges sea surface temperature (SST) from the ocean to the atmospheric model, surface wind stress, energy and freshwater fluxes from the atmosphere to the ocean model, surface and sub-surface runoff from the atmospheric component to the river routing model (Max-Planck's HD model; Hagemann and Dümenil, 1998). In order to have water conservation within the system, the river routing component sends the

  4. New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae.

    PubMed

    Laughery, Marian F; Hunter, Tierra; Brown, Alexander; Hoopes, James; Ostbye, Travis; Shumaker, Taven; Wyrick, John J

    2015-12-01

    Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is an important tool for genome editing because the Cas9 endonuclease can induce targeted DNA double-strand breaks. Targeting of the DNA break is typically controlled by a single-guide RNA (sgRNA), a chimeric RNA containing a structural segment important for Cas9 binding and a 20mer guide sequence that hybridizes to the genomic DNA target. Previous studies have demonstrated that CRISPR-Cas9 technology can be used for efficient, marker-free genome editing in Saccharomyces cerevisiae. However, introducing the 20mer guide sequence into yeast sgRNA expression vectors often requires cloning procedures that are complex, time-consuming and/or expensive. To simplify this process, we have developed a new sgRNA expression cassette with internal restriction enzyme sites that permit rapid, directional cloning of 20mer guide sequences. Here we describe a flexible set of vectors based on this design for cloning and expressing sgRNAs (and Cas9) in yeast using different selectable markers. We anticipate that the Cas9-sgRNA expression vector with the URA3 selectable marker (pML104) will be particularly useful for genome editing in yeast, since the Cas9 machinery can be easily removed by counter-selection using 5-fluoro-orotic acid (5-FOA) following successful genome editing. The availability of new vectors that simplify and streamline the technical steps required for guide sequence cloning should help accelerate the use of CRISPR-Cas9 technology in yeast genome editing.

  5. RXTE Observations of Cas A

    NASA Technical Reports Server (NTRS)

    Rothschild, R. E.; Lingenfelter, R. E.; Heindl, W. A.; Blanco, P. R.; Pelling, M. R.; Gruber, D. E.; Allen, G. E.; Jahoda, K.; Swank, J. H.; Woosley, S. E.; Nomoto, K.; Higdon, J. C.; Dermer, Charles D. (Editor); Strickman, Mark S. (Editor); Kurfess, James D. (Editor)

    1997-01-01

    The exciting detection by the COMPTEL instrument of the 1157 keV Ti-44 line from the supernova remnant Cas A sets important new constraints on supernova dynamics and nucleosynthesis. The Ti-44 decay also produces x-ray lines at 68 and 78 keV, whose flux should be essentially the same as that of the gamma ray line. The revised COMPTEL flux of 4 x l0(exp -5) cm(exp -2)s(exp -1) is very near the sensitivity limit for line detection by the HEXTE instrument on RXTE. We report on the results from two RXTE observations - 20 ks during In Orbit Checkout in January 1996 and 200 ks in April 1996. We also find a strong continuum emission suggesting cosmic ray electron acceleration in the remnant.

  6. Study on analysis of waste edible oil with deterioration and removal of acid value, carbonyl value, and free fatty acid by a food additive (calcium silicate).

    PubMed

    Ogata, Fumihiko; Tanaka, Yuko; Tominaga, Hisato; Kangawa, Moe; Inoue, Kenji; Ueda, Ayaka; Iwata, Yuka; Kawasaki, Naohito

    2013-01-01

    This study investigated the regeneration of waste edible oil using a food additive (calcium silicate, CAS). Waste edible oil was prepared by combined heat and aeration treatment. Moreover, the deterioration of edible oil by combined heat and aeration treatment was greater than that by heat treatment alone. The acid value (AV) and carbonyl value (CV) increased with increasing deterioration; conversely, the tocopherol concentration decreased with increasing deterioration. The specific surface area, pore volume, and mean pore diameter of the 3 CAS formulations used (CAS30, CAS60, and CAS90) were evaluated, and scanning electron microscopic images were taken. The specific surface area increased in the order of CAS30 (115.54 m(2)/g) < CAS60 (163.93 m(2)/g) < CAS90 (187.47 m(2)/g). The mean pore diameter increased in the order of CAS90 (170.59 Å) < CAS60 (211.60 Å) < CAS30 (249.70 Å). The regeneration of waste edible oil was possible with CAS treatment. The AV reduced by 15.2%, 10.8%, and 23.1% by CAS30, CAS60, and CAS90 treatment, respectively, and the CV was reduced by 35.6%, 29.8%, and 31.3% by these 3 treatments, respectively. Moreover, the concentrations of tocopherol and free fatty acids did not change with CAS treatment. The characteristics of CAS were not related to the degree of change of AV and CV. However, the adsorption mechanism of polar and non-polar compounds generated in waste edible oil by CAS was related with the presence of silica gel molecules in CAS. The findings indicated that CAS was useful for the regeneration of waste edible oil.

  7. Translational regulation: identification of the site on bacteriophage T4 rIIB mRNA recognized by the regA gene function.

    PubMed Central

    Karam, J; Gold, L; Singer, B S; Dawson, M

    1981-01-01

    The bacteriophage T4 gene regA encodes a protein that diminishes the expression of many unlinked early T4 genes. Previous work demonstrated that regA-mediated repression occurs after transcription. We report here on the identification of the target site on one regA-sensitive mRNA, the message encoding the phage T4 rIIB protein. The target for regA-mediated action overlaps the translational initiation domain of the rIIB messenger. The regA protein may be a repressor that operates translationally on a significant and interesting set of early phage T4 mRNAs. Images PMID:7029523

  8. Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro.

    PubMed

    Hinz, John M; Laughery, Marian F; Wyrick, John J

    2015-12-08

    During Cas9 genome editing in eukaryotic cells, the bacterial Cas9 enzyme cleaves DNA targets within chromatin. To understand how chromatin affects Cas9 targeting, we characterized Cas9 activity on nucleosome substrates in vitro. We find that Cas9 endonuclease activity is strongly inhibited when its target site is located within the nucleosome core. In contrast, the nucleosome structure does not affect Cas9 activity at a target site within the adjacent linker DNA. Analysis of target sites that partially overlap with the nucleosome edge indicates that the accessibility of the protospacer-adjacent motif (PAM) is the critical determinant of Cas9 activity on a nucleosome.

  9. Conformational Dynamics of Response Regulator RegX3 from Mycobacterium tuberculosis

    PubMed Central

    Ahmad, Ashfaq; Cai, Yongfei; Chen, Xingqiang; Shuai, Jianwei; Han, Aidong

    2015-01-01

    Two-component signal transduction systems (TCS) are vital for adaptive responses to various environmental stresses in bacteria, fungi and even plants. A TCS typically comprises of a sensor histidine kinase (SK) with its cognate response regulator (RR), which often has two domains—N terminal receiver domain (RD) and C terminal effector domain (ED). The histidine kinase phosphorylates the RD to activate the ED by promoting dimerization. However, despite significant progress on structural studies, how RR transmits activation signal from RD to ED remains elusive. Here we analyzed active to inactive transition process of OmpR/PhoB family using an active conformation of RegX3 from Mycobacterium tuberculosis as a model system by computational approaches. An inactive state of RegX3 generated from 150 ns molecular dynamic simulation has rotameric conformations of Thr79 and Tyr98 that are generally conserved in inactive RRs. Arg81 in loop β4α4 acts synergistically with loop β1α1 to change its interaction partners during active to inactive transition, potentially leading to the N-terminal movement of RegX3 helix α1. Global conformational dynamics of RegX3 is mainly dependent on α4β5 region, in particular seven ‘hot-spot’ residues (Tyr98 to Ser104), adjacent to which several coevolved residues at dimeric interface, including Ile76-Asp96, Asp97-Arg111 and Glu24-Arg113 pairs, are critical for signal transduction. Taken together, our computational analyses suggest a molecular linkage between Asp phosphorylation, proximal loops and α4β5α5 dimeric interface during RR active to inactive state transition, which is not often evidently defined from static crystal structures. PMID:26201027

  10. Rheoencephalography (REG) as a Non-Invasive Monitoring Alternative for the Assessment of Brain Blood Flow

    DTIC Science & Technology

    2004-09-01

    arterial pressure of 40 mmHg, and then held there until experimental intervention, resuscitation, decompensation or death occurred. The experiment was...regulations relating to animals and experiments involving animals and adheres to principles stated in the Guide for the Care and Use of Laboratory Animals...Rheoencephalography (REG) as a Non-Invasive Monitoring Alternative for the Assessment of Brain Blood Flow P3 - 12 RTO-MP-HFM-109 experiments we

  11. Applications of the 3-D Deterministic Transport Attila{reg_sign} for Core Safety Analysis

    SciTech Connect

    Lucas, D.S.; Gougar, D.; Roth, P.A.; Wareing, T.; Failla, G.; McGhee, J.; Barnett, A.

    2004-10-06

    An LDRD (Laboratory Directed Research and Development) project is ongoing at the Idaho National Engineering and Environmental Laboratory (INEEL) for applying the three-dimensional multi-group deterministic neutron transport code (Attila{reg_sign}) to criticality, flux and depletion calculations of the Advanced Test Reactor (ATR). This paper discusses the model development, capabilities of Attila, generation of the cross-section libraries, and comparisons to an ATR MCNP model and future.

  12. A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Cas9 endonuclease of the Type II-a clustered regularly interspersed short palindromic repeats (CRISPR), of Streptococcus pyogenes (SpCas9) has been adapted as a widely used tool for genome editing and genome engineering. Herein, we describe a gene encoding a novel Cas9 ortholog (BpsuCas9) and th...

  13. Cas9 specifies functional viral targets during CRISPR-Cas adaptation.

    PubMed

    Heler, Robert; Samai, Poulami; Modell, Joshua W; Weiner, Catherine; Goldberg, Gregory W; Bikard, David; Marraffini, Luciano A

    2015-03-12

    Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their associated (Cas) proteins provide adaptive immunity against viral infection in prokaryotes. Upon infection, short phage sequences known as spacers integrate between CRISPR repeats and are transcribed into small RNA molecules that guide the Cas9 nuclease to the viral targets (protospacers). Streptococcus pyogenes Cas9 cleavage of the viral genome requires the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) sequence immediately downstream of the viral target. It is not known whether and how viral sequences flanked by the correct PAM are chosen as new spacers. Here we show that Cas9 selects functional spacers by recognizing their PAM during spacer acquisition. The replacement of cas9 with alleles that lack the PAM recognition motif or recognize an NGGNG PAM eliminated or changed PAM specificity during spacer acquisition, respectively. Cas9 associates with other proteins of the acquisition machinery (Cas1, Cas2 and Csn2), presumably to provide PAM-specificity to this process. These results establish a new function for Cas9 in the genesis of prokaryotic immunological memory.

  14. Intelligent HIP processing of a Spraycast-X{reg_sign} superalloy for aerospace applications

    SciTech Connect

    Zahrah, T.F.; Dalal, R.; Kissinger, R.

    1996-12-31

    An eddy current sensor system has been developed to monitor densification during hot isostatic pressing (HIP) of Spraycast-X{reg_sign} superalloy components for aerospace applications. The sensor system was designed, implemented and demonstrated by MATSYS personnel at the Howmet Corporation HIP facility. The eddy current sensor was used to monitor densification of Spraycast-X{reg_sign} Rene`41 ring segments from 95 to 98 percent relative density to full density. The sensor data were verified and validated by metallographic examinations of HIPed specimens. The grain size of the Spraycast-X{reg_sign} Rene`41 was not affected by HIP at both 1,066 C (1,950 F) and 1,121 C (2,050 F). Tensile strengths and 0.2% creep rupture properties were not sensitive to changes in HIP processing conditions. However, tensile ductilities and low cycle properties showed a strong correlation to HIP time at 1,121 C/103 MPa (2,050 F/15 KSI). As hole time at maximum temperature and pressure was increased from 1 to 4 hours, tensile ductilities and low cycle fatigue lives increased. The sensor system can be integrated with an intelligent closed loop control system to monitor and control densification rate and shape distortion.

  15. Correcting image placement errors using registration control (RegC®) technology in the photomask periphery

    NASA Astrophysics Data System (ADS)

    Cohen, Avi; Lange, Falk; Ben-Zvi, Guy; Graitzer, Erez; Vladimir, Dmitriev

    2012-11-01

    The ITRS roadmap specifies wafer overlay control as one of the major tasks for the sub 40 nm nodes in addition to CD control and defect control. Wafer overlay is strongly dependent on mask image placement error (registration errors or Reg errors)1. The specifications for registration or mask placement accuracy are significantly tighter in some of the double patterning techniques (DPT). This puts a heavy challenge on mask manufacturers (mask shops) to comply with advanced node registration specifications. The conventional methods of feeding back the systematic registration error to the E-beam writer and re-writing the mask are becoming difficult, expensive and not sufficient for the advanced nodes especially for double pattering technologies. Six production masks were measured on a standard registration metrology tool and the registration errors were calculated and plotted. Specially developed algorithm along with the RegC Wizard (dedicated software) was used to compute a correction lateral strain field that would minimize the registration errors. This strain field was then implemented in the photomask bulk material using an ultra short pulse laser based system. Finally the post process registration error maps were measured and the resulting residual registration error field with and without scale and orthogonal errors removal was calculated. In this paper we present a robust process flow in the mask shop which leads up to 32% registration 3sigma improvement, bringing some out-of-spec masks into spec, utilizing the RegC® process in the photomask periphery while leaving the exposure field optically unaffected.

  16. Rosebud syncoal partnership SynCoal{sup {reg_sign}} demonstration technology development update

    SciTech Connect

    Sheldon, R.W.; Heintz, S.J.

    1995-12-01

    Rosebud SynCoal{reg_sign} Partnership`s Advanced Coal Conversion Process (ACCP) is an advanced thermal coal upgrading process coupled with physical cleaning techniques to upgrade high moisture, low-rank coals to produce a high-quality, low-sulfur fuel. The coal is processed through two vibrating fluidized bed reactors where oxygen functional groups are destroyed removing chemically bound water, carboxyl and carbonyl groups, and volatile sulfur compounds. After thermal upgrading, the SynCoal{reg_sign} is cleaned using a deep-bed stratifier process to effectively separate the pyrite rich ash. The SynCoal{reg_sign} process enhances low-rank western coals with moisture contents ranging from 2555%, sulfur contents between 0.5 and 1.5 %, and heating values between 5,500 and 9,000 Btu/lb. The upgraded stable coal product has moisture contents as low as 1 %, sulfur contents as low as 0.3%, and heating values up to 12,000 Btu/lb.

  17. Evaluation of the tool "Reg Refine" for user-guided deformable image registration.

    PubMed

    Johnson, Perry B; Padgett, Kyle R; Chen, Kuan L; Dogan, Nesrin

    2016-05-01

    "Reg Refine" is a tool available in the MIM Maestro v6.4.5 platform (www.mimsoftware.com) that allows the user to actively participate in the deformable image registration process. The purpose of this work was to evaluate the efficacy of this tool and investigate strategies for how to apply it effectively. This was done by performing DIR on two publicly available ground-truth models, the Pixel-based Breathing Thorax Model (POPI) for lung, and the Deformable Image Registration Evaluation Project (DIREP) for head and neck. Image noise matched in both magnitude and texture to clinical CBCT scans was also added to each model to simulate the use case of CBCT-CT alignment. For lung, the results showed Reg Refine effective at improving registration accuracy when controlled by an expert user within the context of large lung deformation. CBCT noise was also shown to have no effect on DIR performance while using the MIM algorithm for this site. For head and neck, the results showed CBCT noise to have a large effect on the accuracy of registration, specifically for low-contrast structures such as the brainstem and parotid glands. In these cases, the Reg Refine tool was able to improve the registration accuracy when controlled by an expert user. Several strategies for how to achieve these results have been outlined to assist other users and provide feedback for developers of similar tools. PACS number(s): 87.44.Qr, 87.57.nj, 87.57.c.

  18. Measurement of acute toxicity to Mysidopsis bahia using DaphniaQuant{reg_sign} instrument and protocol

    SciTech Connect

    Blankemeyer, J.T.; Nguyen, T.; Burks, S.L.

    1994-12-31

    DaphniaQuant{reg_sign} uses a fluorescent dye to permeate the cells of aquatic organisms. The technique has been used on frog embryos, fish embryos, and bovine erythrocytes. Two wavelengths of light are used to excite the fluorescent dye, Di-4-ANEPPS. The blue excitation wavelength measures the cell membrane potential while the yellow excitation wavelength measures the amount of dye loaded into the organisms. The authors applied the technique to the shrimp, Mysidopsis bahia, used in marine toxicity testing. The authors used from 1 to 10 shrimp, loaded into a 3 ml spectrofluorometry plastic cuvette. The fluorescent dye, Di-4-ANEPPS, was mixed with the 3 ml of ASW in the cuvette at a final Di-4ANEPPS concentration of 10{sub {minus}6} M. After a thirty minute incubation, the fluorescence of Di-4-ANEPPS was measured in the DaphniaQuant{reg_sign} instrument. A similar protocol was used to test various concentrations of standard assay chemicals and effluents. The test chemical was mixed with ASW and Di-4-ANEPPS and incubated with the shrimp for thirty minutes. After thirty minutes, the fluorescence was measured and compared to the fluorescence of the control shrimp. The authors found that the fluorescence from a single shrimp was detectable and gave similar toxicity data as did the replicates using 10 shrimp. They conclude that the DaphniaQuant{reg_sign} assay can be successfully adapted to marine organisms, particularly Mysidopsis bahia.

  19. Field evaluation of 69-kV outdoor Polysil reg sign insulators

    SciTech Connect

    Richenbacher, A.G. )

    1990-03-01

    This report, together with previous interim reports, documents and summarizes the field performance of 69 kV Polysil{reg sign} insulators during the field trial period from January, 1983 to December, 1988. These insulators were manufactured for the Electric Power Research Institute by Lindsey Industries in 1979. A description of the insulator development and manufacturing process is contained in the EPRI Final Report EL1281-1. Following their manufacture, the insulators were delivered, in the form of test racks of 17 Polysil{reg sign} insulators and one porcelain insulator, to twelve United States utilities and the Instituto de Investigaciones Electricas (IIE) in Mexico. These racks were subsequently installed and energized at twenty-five test sites during the latter half of 1979 and early 1980 by the project participants for the purpose of analyzing the outdoor field performance of these insulators and comparing the relative effect on performance of variations in composition, coating, electrical grading method, and shape represented by individual insulators within the test racks. This report documents the effects of the various Polysil{reg sign} insulator parameters on electrical performance in the field over a specific period of 6 years. However, the insulators had been energized for approximately 3 years prior to the initiation of this project and, although specific performance data is not available for that time period, the overall effects of field exposure for that additional time period (total of 9 years) are seen in the results of this report. 3 refs., 23 figs., 9 tabs.

  20. Dichloroacetic acid

    Integrated Risk Information System (IRIS)

    EPA 635 / R - 03 / 007 www.epa.gov / iris TOXICOLOGICAL REVIEW OF DICHLOROACETIC ACID ( CAS No . 79 - 43 - 6 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) August 2003 U.S . Environmental Protection Agency Washington , DC DISCLAIMER This document has been revi

  1. Trichloroacetic acid

    Integrated Risk Information System (IRIS)

    EPA / 635 / R - 09 / 003F www.epa.gov / iris TOXICOLOGICAL REVIEW OF TRICHLOROACETIC ACID ( CAS No . 76 - 03 - 9 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) September 2011 U.S . Environmental Protection Agency Washington , DC ii DISCLAIMER This document has

  2. Chemical and radiation stability of SuperLig{reg_sign}644, resorcinol-formaldehyde, and CS-100 cesium ion exchange materials

    SciTech Connect

    Brown, G.N.; Adami, S.R.; Bray, L.A.

    1995-09-01

    At the request of the Initial Pretreatment Module Project within Westinghouse Hanford Company, Pacific Northwest Laboratory (PNL) conducted this study for the Efficient Separations and Processing Crosscutting Program (ESP) under the task ``Develop and Test Sorbents.`` The purpose of the study was to assess and compare the chemical and radiolytic stability of several cesium-selective ion exchange materials in simulated alkaline Hanford tank waste matrices. Pretreatment of nuclear process wastes to remove of cesium and other radionuclides by ion exchange was proposed previously as one method of minimizing the amount of high-level radioactive waste at Hanford. In this study, PNL evaluated three cesium-selective materials SuperLig{reg_sign}644, resorcinol-formaldehyde (R-F), and CS-100 for chemical and radiation stability in 1 M NaOH and a simulated neutralized current acid waste (NCAW). The objective of the study is to investigate the stability of the newly produced SuperLig{reg_sign}644 under a variety of conditions in an attempt to simulate and predict the degradation process. The following specific conclusions and recommendations resulted from the study.

  3. Evaluation and analysis of RegCM3 simulated summer rainfall over the Huaihe River Basin of China

    NASA Astrophysics Data System (ADS)

    Zong, Peishu; Wang, Huijun

    2011-06-01

    This study evaluates the ability of the Abdus Salam International Center for Theoretical Physics (ICTP) version 3 Regional Climate Model (RegCM3) in simulating the summer rainfall amount and distribution and large-scale circulation over the Huaihe River basin of China. We conducted the simulation for the period of 1982-2001 and the wet year of 2003 to test the ensemble simulation capacity of RegCM3. First, by comparing the simulated rainfall amount and distribution against the observations, it is found that RegCM3 can reproduce the rainfall pattern and its annual variations. In addition, the simulated spatial patterns of 850-hPa wind and specific humidity fields are close to the observations, although the wind speed and humidity values are larger. Finally, the ensemble simulation of RegCM3 for summer 2003 failed to capture the spatial distribution and underestimated the magnitude of the precipitation anomalies, and the reasons are analyzed.

  4. Feasibility of integrating other federal information systems into the Global Network of Environment and Technology, GNET{reg_sign}

    SciTech Connect

    1998-05-01

    The Global Environment and Technology Enterprise (GETE) of the Global Environment and Technology Foundation (GETF) has been tasked by the US Department of Energy`s (DOE), Federal Energy Technology Center (FETC) to assist in reducing DOE`s cost for the Global Network of Environment and Technology (GNET{reg_sign}). As part of this task, GETE is seeking federal partners to invest in GNET{reg_sign}. The authors are also seeking FETC`s commitment to serve as GNET`s federal agency champion promoting the system to potential agency partners. This report assesses the benefits of partnering with GNET{reg_sign} and provides recommendations for identifying and integrating other federally funded (non-DOE) environmental information management systems into GNET{reg_sign}.

  5. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

    PubMed Central

    Fonfara, Ines; Le Rhun, Anaïs; Chylinski, Krzysztof; Makarova, Kira S.; Lécrivain, Anne-Laure; Bzdrenga, Janek; Koonin, Eugene V.; Charpentier, Emmanuelle

    2014-01-01

    The CRISPR-Cas-derived RNA-guided Cas9 endonuclease is the key element of an emerging promising technology for genome engineering in a broad range of cells and organisms. The DNA-targeting mechanism of the type II CRISPR-Cas system involves maturation of tracrRNA:crRNA duplex (dual-RNA), which directs Cas9 to cleave invading DNA in a sequence-specific manner, dependent on the presence of a Protospacer Adjacent Motif (PAM) on the target. We show that evolution of dual-RNA and Cas9 in bacteria produced remarkable sequence diversity. We selected eight representatives of phylogenetically defined type II CRISPR-Cas groups to analyze possible coevolution of Cas9 and dual-RNA. We demonstrate that these two components are interchangeable only between closely related type II systems when the PAM sequence is adjusted to the investigated Cas9 protein. Comparison of the taxonomy of bacterial species that harbor type II CRISPR-Cas systems with the Cas9 phylogeny corroborates horizontal transfer of the CRISPR-Cas loci. The reported collection of dual-RNA:Cas9 with associated PAMs expands the possibilities for multiplex genome editing and could provide means to improve the specificity of the RNA-programmable Cas9 tool. PMID:24270795

  6. Highly efficient Cas9-mediated transcriptional programming.

    PubMed

    Chavez, Alejandro; Scheiman, Jonathan; Vora, Suhani; Pruitt, Benjamin W; Tuttle, Marcelle; P R Iyer, Eswar; Lin, Shuailiang; Kiani, Samira; Guzman, Christopher D; Wiegand, Daniel J; Ter-Ovanesyan, Dmitry; Braff, Jonathan L; Davidsohn, Noah; Housden, Benjamin E; Perrimon, Norbert; Weiss, Ron; Aach, John; Collins, James J; Church, George M

    2015-04-01

    The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. We describe an improved transcriptional regulator obtained through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease-null Cas9. We demonstrate its utility in activating endogenous coding and noncoding genes, targeting several genes simultaneously and stimulating neuronal differentiation of human induced pluripotent stem cells (iPSCs).

  7. The Reg3α (HIP/PAP) Lectin Suppresses Extracellular Oxidative Stress in a Murine Model of Acute Liver Failure

    PubMed Central

    Moniaux, Nicolas; Darnaud, Marion; Garbin, Kévin; Dos Santos, Alexandre; Guettier, Catherine; Samuel, Didier; Amouyal, Gilles; Amouyal, Paul; Bréchot, Christian; Faivre, Jamila

    2015-01-01

    Background and Aims Acute liver failure (ALF) is a rapidly progressive heterogeneous illness with high mortality rate and no widely accessible cure. A promising drug candidate according to previous preclinical studies is the Reg3α (or HIP/PAP) lectin, which alleviates ALF through its free-radical scavenging activity. Here we study the therapeutic targets of Reg3α in order to gain information on the nature of the oxidative stress associated with ALF. Methods Primary hepatocytes stressed with the reactive oxygen species (ROS) inducers TNFα and H2O2 were incubated with a recombinant Reg3α protein. ALF was induced in C57BL/6J mice by an anti-CD95 antibody. Livers and primary hepatocytes were harvested for deoxycholate separation of cellular and extracellular fractions, immunostaining, immunoprecipitation and malondialdehyde assays. Fibrin deposition was studied by immunofluorescence in frozen liver explants from patients with ALF. Results Fibrin deposition occurs during experimental and clinical acute liver injuries. Reg3α bound the resulting transient fibrin network, accumulated in the inflammatory extracellular matrix (ECM), greatly reduced extracellular ROS levels, and improved cell viability. Hepatocyte treatment with ligands of death receptors, e.g. TNFα and Fas, resulted in a twofold increase of malondialdehyde (MDA) level in the deoxycholate-insoluble fractions. Reg3α treatment maintained MDA at a level similar to control cells and thereby increased hepatocyte survival by 35%. No antioxidant effect of Reg3α was noted in the deoxycholate-soluble fractions. Preventing fibrin network formation with heparin suppressed the prosurvival effect of Reg3α. Conclusions Reg3α is an ECM-targeted ROS scavenger that binds the fibrin scaffold resulting from hepatocyte death during ALF. ECM alteration is an important pathogenic factor of ALF and a relevant target for pharmacotherapy. PMID:25938566

  8. Reg3α Overexpression Protects Pancreatic β Cells from Cytokine-Induced Damage and Improves Islet Transplant Outcome

    PubMed Central

    Ding, Ying; Xu, Yuemei; Shuai, Xuanyu; Shi, Xuhui; Chen, Xiang; Huang, Wenbin; Liu, Yun; Liang, Xiubin; Zhang, Zhihong; Su, Dongming

    2014-01-01

    The process of islet transplantation for treating type 1 diabetes has been limited by the high level of graft failure. This may be overcome by locally delivering trophic factors to enhance engraftment. Regenerating islet-derived protein 3α (Reg3α) is a pancreatic secretory protein which functions as an antimicrobial peptide in control of inflammation and cell proliferation. In this study, to investigate whether Reg3α could improve islet engraftment, a marginal mass of syngeneic islets pretransduced with adenoviruses expressing Reg3α or control EGFP were transplanted under the renal capsule of streptozotocin-induced diabetic mice. Mice receiving islets with elevated Reg3α production exhibited significantly lower blood glucose levels (9.057 ± 0.59 mmol/L versus 13.48 ± 0.35 mmol/L, P < 0.05) and improved glucose-stimulated insulin secretion (1.80 ± 0.17 ng/mL versus 1.16 ± 0.16 ng/mL, P < 0.05) compared with the control group. The decline of apoptotic events (0.57% ± 0.15% versus 1.06% ± 0.07%, P < 0.05) and increased β-cell proliferation (0.70% ± 0.10% versus 0.36% ± 0.14%, P < 0.05) were confirmed in islet grafts overexpressing Reg3α by morphometric analysis. Further experiments showed that Reg3α production dramatically protected cultured islets and pancreatic β cells from cytokine-induced apoptosis and the impairment of glucose-stimulated insulin secretion. Moreover, exposure to cytokines led to the activation of MAPKs in pancreatic β cells, which was reversed by Reg3α overexpression in contrast to control group. These results strongly suggest that Reg3α could enhance islet engraftments through its cytoprotective effect and advance the therapeutic efficacy of islet transplantation. PMID:25826674

  9. CRISPR-Cas: biology, mechanisms and relevance

    PubMed Central

    Hille, Frank

    2016-01-01

    Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent. This article is part of the themed issue ‘The new bacteriology’. PMID:27672148

  10. Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28.

    PubMed

    Smargon, Aaron A; Cox, David B T; Pyzocha, Neena K; Zheng, Kaijie; Slaymaker, Ian M; Gootenberg, Jonathan S; Abudayyeh, Omar A; Essletzbichler, Patrick; Shmakov, Sergey; Makarova, Kira S; Koonin, Eugene V; Zhang, Feng

    2017-02-16

    CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity. Using an E. coli essential gene screen, we demonstrate that Cas13b has a double-sided protospacer-flanking sequence and elucidate RNA secondary structure requirements for targeting. We also find that Csx27 represses, whereas Csx28 enhances, Cas13b-mediated RNA interference. Characterization of these CRISPR systems creates opportunities to develop tools to manipulate and monitor cellular transcripts.

  11. I can see CRISPR now, even when phage are gone: a view on alternative CRISPR-Cas functions from the prokaryotic envelope

    PubMed Central

    Ratner, Hannah K.; Sampson, Timothy R.; Weiss, David S.

    2015-01-01

    Purpose CRISPR-Cas systems are prokaryotic immune systems against invading nucleic acids that adapt as new environmental threats arise. There are emerging examples of CRISPR-Cas functions in bacterial physiology beyond their role in adaptive immunity. This highlights the poorly understood, but potentially common, moonlighting functions of these abundant systems. We propose that these non-canonical CRISPR-Cas activities have evolved to respond to stresses at the cell envelope. Recent findings Here, we discuss recent literature describing the impact of the extracellular environment on the regulation of CRISPR-Cas systems, and the influence of CRISPR-Cas activity on bacterial physiology. The described non-canonical CRISPR-Cas functions allow the bacterial cell to respond to the extracellular environment, primarily through changes in envelope physiology. Summary This review discusses the expanding non-canonical functions of CRISPR-Cas systems, including their roles in virulence, focusing mainly on their relationship to the cell envelope. We first examine the effects of the extracellular environment on regulation of CRISPR-Cas components, and then discuss the impact of CRISPR-Cas systems on bacterial physiology, focusing on their roles in influencing interactions with the environment including host organisms. PMID:25887612

  12. Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3.

    PubMed

    Gong, Bei; Shin, Minsang; Sun, Jiali; Jung, Che-Hun; Bolt, Edward L; van der Oost, John; Kim, Jeong-Sun

    2014-11-18

    Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a "Cascade" ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called "interference." After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3' to 5' nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3' to 5' translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems.

  13. CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells

    PubMed Central

    Deng, Wulan; Shi, Xinghua; Tjian, Robert; Lionnet, Timothée; Singer, Robert H.

    2015-01-01

    Direct visualization of genomic loci in the 3D nucleus is important for understanding the spatial organization of the genome and its association with gene expression. Various DNA FISH methods have been developed in the past decades, all involving denaturing dsDNA and hybridizing fluorescent nucleic acid probes. Here we report a novel approach that uses in vitro constituted nuclease-deficient clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated caspase 9 (Cas9) complexes as probes to label sequence-specific genomic loci fluorescently without global DNA denaturation (Cas9-mediated fluorescence in situ hybridization, CASFISH). Using fluorescently labeled nuclease-deficient Cas9 (dCas9) protein assembled with various single-guide RNA (sgRNA), we demonstrated rapid and robust labeling of repetitive DNA elements in pericentromere, centromere, G-rich telomere, and coding gene loci. Assembling dCas9 with an array of sgRNAs tiling arbitrary target loci, we were able to visualize nonrepetitive genomic sequences. The dCas9/sgRNA binary complex is stable and binds its target DNA with high affinity, allowing sequential or simultaneous probing of multiple targets. CASFISH assays using differently colored dCas9/sgRNA complexes allow multicolor labeling of target loci in cells. In addition, the CASFISH assay is remarkably rapid under optimal conditions and is applicable for detection in primary tissue sections. This rapid, robust, less disruptive, and cost-effective technology adds a valuable tool for basic research and genetic diagnosis. PMID:26324940

  14. PowerChip{reg_sign} gypsum: A new commercial product from the combustion of high sulfur coals and Orimulsion{reg_sign}

    SciTech Connect

    Welliver, W.R.; Roth, T.J.; Brown, J.R.; Hudson, M.S.; Colijn, H.

    1996-12-31

    In order to meet with the SO{sub 2} reduction provisions of the 1990 Clean Air Act Amendments, US utilities are faced with several compliance options. One of these is the installation of flue gas desulfurization facilities which produce either a by-product calcium sulfite sludge which must be landfilled, or a forced oxidized industrial gypsum. This gypsum can be difficult and time consuming to unload from railcars or trucks due to the fact that it has poor flowability. After 5 years of development, a technology now exists and is being commercially demonstrated which agglomerates industrial FGD gypsum into a physical form which may be directly compatible with the currently installed equipment traditionally used to handle natural rock gypsums in wallboard and cement plants. This technology uses pressure roll forced compaction to agglomerate the wet finely divided powder gypsum into a durable chip form of industrial gypsum. This novel technology known as PowerChip{reg_sign} gypsum has been developed and patented by Pure Air of Allentown, Pennsylvania, US. A pilot commercialization and demonstration is ongoing at Pure Air`s Bailly Plant in Chesterton, Indiana. The results, data and performance of the product from this demonstration unit will be discussed. Flowability tests were undertaken to evaluate handling properties of the Powder-Chip gypsum and suggestions for handling equipment will be discussed and compared to the traditional powder form or wet filter cake gypsum and natural gypsum rock. In essence, current FGD technology enables continued burning of high sulfur coal, or Orimulsion{reg_sign} in compliance with environmental regulations, while producing an industrial gypsum product.

  15. Influence of maternal ingestion of Aroclor 1254[reg sign] (PCB) or FireMaster BP-6[reg sign] (PBB) on unstimulated and stimulated corticosterone levels in young rats

    SciTech Connect

    Meserve, L.A.; Murray, B.A.; Landis, J.A. )

    1992-05-01

    The organohalides polychlorinated biphenyl (PCB) and polybrominated biphenyl (PBB) remain troublesome environmental pollutants. For example, the percentage of the population in which PCB is detectable in adipose tissue remains high. These compounds are of particular interest to residents of the North Central United States, especially in regions surrounding the Great Lakes where contaminated fish may be a regular component of the diet. Additionally, PBB was mistakenly fed to cattle and chickens in Michigan during the early 1970s, products of which were ingested by humans. Among the physiological effects of ingestion of PCB or PBB is the depression of thyroid status, which has been reported in adult humans, in adult experimental animals, and in the offspring of these animals. In adult rats, circulating levels of thyroid hormones are inversely proportional to dose of PCB or PBB in the diet. On the other hand, reports of effects of these organohalides on adrenocortical function remain equivocal, describing both PCB- and PBB-induced depression, and absence of effect in rats and monkeys. Despite the possible consequences of maternal ingestion of PCB or PBB on future generations, little work has been done previously to determine whether consumption of these materials by pregnant and lactating animals confers hypothyroidism on their offspring, and/or influences other mechanisms of endocrine control in the young. Since early studies showed that hypothyroidism induced by feeding pregnant rats the goitrogen thiouracil altered the functional capabilities in their young of the hypothalamus-pituitary-adrenal (HPA) axis, as revealed by circulating corticosterone levels, the present study was done to determine whether ingestion of either PCB (Aroclor 1254[reg sign]) or PBB (FireMaster BP-6[reg sign]) by pregnant and lactating rats resulted in depressed thyroid status and/or modified HPA axis function in their 15 day old young. 19 refs., 1 fig., 1 tab.

  16. Investigation of brightness changes of MZ Cas and TZ Cas in B- and V-light

    NASA Technical Reports Server (NTRS)

    Lukatskaya, F. I.; Kheylo, E. S.

    1973-01-01

    The results are presented concerning statistical processing of two-color observations of MZ Cas and TZ Cas. Light histograms, dispersion and statistical amplitudes are given. Light variations of the variables are represented by normal stochastic processes. Observational data are tabulated.

  17. Putting the CAS Standards to Work. Training Manual for the CAS Self Assessment Guides.

    ERIC Educational Resources Information Center

    Yerian, Jean M.; Miller, Theodore K., Ed.

    These 18 self-assessment guides and training manual from the Council for the Advancement of Standards (CAS) for Student Services/Development Programs translate the CAS Standards and Guidelines of 1986 into a format for self-study purposes. These self-study guides allow an institution to assure compliance with minimally-acceptable practice, gain an…

  18. CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance.

    PubMed

    Dupuis, Marie-Ève; Villion, Manuela; Magadán, Alfonso H; Moineau, Sylvain

    2013-01-01

    Bacteria have developed a set of barriers to protect themselves against invaders such as phage and plasmid nucleic acids. Different prokaryotic defence systems exist and at least two of them directly target the incoming DNA: restriction-modification (R-M) and CRISPR-Cas systems. On their own, they are imperfect barriers to invasion by foreign DNA. Here, we show that R-M and CRISPR-Cas systems are compatible and act together to increase the overall phage resistance of a bacterial cell by cleaving their respective target sites. Furthermore, we show that the specific methylation of phage DNA does not impair CRISPR-Cas acquisition or interference activities. Taken altogether, both mechanisms can be leveraged to decrease phage contaminations in processes relying on bacterial growth and/or fermentation.

  19. Unravelling the structural and mechanistic basis of CRISPR-Cas systems.

    PubMed

    van der Oost, John; Westra, Edze R; Jackson, Ryan N; Wiedenheft, Blake

    2014-07-01

    Bacteria and archaea have evolved sophisticated adaptive immune systems, known as CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, which target and inactivate invading viruses and plasmids. Immunity is acquired by integrating short fragments of foreign DNA into CRISPR loci, and following transcription and processing of these loci, the CRISPR RNAs (crRNAs) guide the Cas proteins to complementary invading nucleic acid, which results in target interference. In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR-Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.

  20. Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria.

    PubMed

    Dy, Ron L; Pitman, Andrew R; Fineran, Peter C

    2013-09-01

    The clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins form adaptive immune systems in bacteria to combat phage and other foreign genetic elements. Typically, short spacer sequences are acquired from the invader DNA and incorporated into CRISPR arrays in the bacterial genome. Small RNAs are generated that contain these spacer sequences and enable sequence-specific destruction of the foreign nucleic acids. Occasionally, spacers are acquired from the chromosome, which instead leads to targeting of the host genome. Chromosomal targeting is highly toxic to the bacterium, providing a strong selective pressure for a variety of evolutionary routes that enable host cell survival. Mutations that inactivate the CRISPR-Cas functionality, such as within the cas genes, CRISPR repeat, protospacer adjacent motifs (PAM), and target sequence, mediate escape from toxicity. This self-targeting might provide some explanation for the incomplete distribution of CRISPR-Cas systems in less than half of sequenced bacterial genomes. More importantly, self-genome targeting can cause large-scale genomic alterations, including remodeling or deletion of pathogenicity islands and other non-mobile chromosomal regions. While control of horizontal gene transfer is perceived as their main function, our recent work illuminates an alternative role of CRISPR-Cas systems in causing host genomic changes and influencing bacterial evolution.

  1. Alanine scan of α-conotoxin RegIIA reveals a selective α3β4 nicotinic acetylcholine receptor antagonist.

    PubMed

    Kompella, Shiva N; Hung, Andrew; Clark, Richard J; Marí, Frank; Adams, David J

    2015-01-09

    Activation of the α3β4 nicotinic acetylcholine receptor (nAChR) subtype has recently been implicated in the pathophysiology of various conditions, including development and progression of lung cancer and in nicotine addiction. As selective α3β4 nAChR antagonists, α-conotoxins are valuable tools to evaluate the functional roles of this receptor subtype. We previously reported the discovery of a new α4/7-conotoxin, RegIIA. RegIIA was isolated from Conus regius and inhibits acetylcholine (ACh)-evoked currents mediated by α3β4, α3β2, and α7 nAChR subtypes. The current study used alanine scanning mutagenesis to understand the selectivity profile of RegIIA at the α3β4 nAChR subtype. [N11A] and [N12A] RegIIA analogs exhibited 3-fold more selectivity for the α3β4 than the α3β2 nAChR subtype. We also report synthesis of [N11A,N12A]RegIIA, a selective α3β4 nAChR antagonist (IC50 of 370 nM) that could potentially be used in the treatment of lung cancer and nicotine addiction. Molecular dynamics simulations of RegIIA and [N11A,N12A]RegIIA bound to α3β4 and α3β2 suggest that destabilization of toxin contacts with residues at the principal and complementary faces of α3β2 (α3-Tyr(92), Ser(149), Tyr(189), Cys(192), and Tyr(196); β2-Trp(57), Arg(81), and Phe(119)) may form the molecular basis for the selectivity shift.

  2. Two enhancers and one silencer located in the introns of regA control somatic cell differentiation in Volvox carteri

    PubMed Central

    Stark, Klaus; Kirk, David L.; Schmitt, Rüdiger

    2001-01-01

    The regA gene plays a central role in germ-soma differentiation of Volvox carteri by suppressing all reproductive functions in somatic cells. Here we show that the minimal promoter of regA consists of only 42 bp immediately upstream of the transcription start site, and that it contains no discernible regulatory elements. However, introns 3 and 5 are both required for regA expression in somatic cells, and intron 7 is essential for silencing regA in gonidia (asexual reproductive cells). A regA gene lacking intron 7 rescues the normal phenotype of mutant somatic cells, but also results in gonidia that reproduce only weakly and soon die out. The same phenotype is observed when a regA gene containing intron 7 is placed under control of a constitutive promoter, suggesting that the silencing activity of intron 7 is promoter specific. Intron 7 is unusual in that it contains a potential ORF that is in frame with exons 7 and 8, and some transcripts are produced in which intron 7 is retained. However, a regulatory role for the intron 7 translation product can be ruled out, because a construct in which intron 7 must be translated, and one in which it cannot be translated, both result in wild-type development of both cell types. Furthermore, intron 7 is unable to act in trans to silence regA, but is able to exert its normal effect when placed in a different location within the gene. Therefore, it appears that intron 7 functions in gonidia as a classical cell-type-specific and promoter-specific enhancer, of the inhibitory type that is often referred to as a silencer. PMID:11390364

  3. High resolution climate change simulation of the 21st century over East Asia by RegCM3

    NASA Astrophysics Data System (ADS)

    Gao, Xuejie

    2010-05-01

    To meet the increasing demands from the climate change impact assessment studies, a high resolution climate change simulation over East Asia region has being performed in the National Climate Center of the China Meteorological Administration. The model employed in the study is the Abdus Salam International Centre for Theoretical Physics (ICTP) Regional Climate Model (RegCM3). A global model of the CCSR/NIES/FRCGC MIROC3.2_hires is selected to drive RegCM3 because of its high resolution (T106) and its good performances in simulating the present day climate over the region. The simulation is conducted at 25-km grid spacing for the period of 1951-2100. Observed CO2 concentration are used for the present day simulation of 1951-2000 and the emission scenario of IPCC SRES A1B is used as the GHG (greenhouse gases) forcing. Simulations of present day climate over China by RegCM3 and MIROC3.2_hires are compared against observation to valid the model performances. Results show that both models reproduced the general pattern of surface air temperature and precipitation well over the region. Compared to the driving MIROC3.2_hires, RegCM3 provides with more spatial details of the surface fields. Differed from previous GCM-RegCM3 simulations, the RegCM3 did not improves the general pattern of the precipitation due to the good performances of MIROC3.2_hires. Preliminary analysis of the future changes simulated by the two models' show difference, in particular during June-July-August. For example while the MIROC3.2_hires projected a prevailing increase of precipitation in JJA over China, the RegCM3 projected extended areas of decreased precipitation. The data are available for those interested from the community of climate change impacts studies.

  4. Rosebud SynCoal Partnership, SynCoal{reg_sign} demonstration technology update

    SciTech Connect

    Sheldon, R.W.

    1997-12-31

    An Advanced Coal Conversion Process (ACCP) technology being demonstrated in eastern Montana (USA) at the heart of one of the world`s largest coal deposits is providing evidence that the molecular structure of low-rank coals can be altered successfully to produce a unique product for a variety of utility and industrial applications. The product is called SynCoal{reg_sign} and the process has been developed by the Rosebud SynCoal Partnership (RSCP) through the US Department of Energy`s multi-million dollar Clean Coal Technology Program. The ACCP demonstration process uses low-pressure, superheated gases to process coal in vibrating fluidized beds. Two vibratory fluidized processing stages are used to heat and convert the coal. This is followed by a water spray quench and a vibratory fluidized stage to cool the coal. Pneumatic separators remove the solid impurities from the dried coal. There are three major steps to the SynCoal{reg_sign} process: (1) thermal treatment of the coal in an inert atmosphere, (2) inert gas cooling of the hot coal, and (3) removal of ash minerals. When operated continuously, the demonstration plant produces over 1,000 tons per day (up to 300,000 tons per year) of SynCoal{reg_sign} with a 2% moisture content, approximately 11,800b Btu/lb and less than 1.0 pound of SO{sub 2} per million Btu. This product is obtained from Rosebud Mine sub-bituminous coal which starts with 25% moisture, 8,600 Btu/lb and approximately 1.6 pounds of SO{sub 2} per million Btu.

  5. The Phase I CORDEX RegCM hyper-MAtrix (CREMA) experiment (Invited)

    NASA Astrophysics Data System (ADS)

    Giorgi, F.

    2013-12-01

    An ensemble of regional climate model (RCM) projections was produced with the RegCM4 modeling system as a first contribution to the CORDEX framework by the RegCM modeling community, the Phase I CORDEX RegCM hyper-MAtrix (CREMA) experiment. A total of 34 regional projections were completed covering the period 1970-2100 over five different CORDEX domains, Africa, Central America, South America, South Asia and the Mediterranean. The projections use different combinations of three driving GCMs (HadGEM, MPI and GFDL), two greenhouse gas concentration pathways (RCP4.5 and RCP8.5) and different land surface and convection schemes, which allows a first exploration of different sources of uncertainty. The paper will describe the CREMA phase I experiment and discuss some basic results from a first analysis of these runs, with emphasis on extreme events (including tropical storms), variability and regional circulations of relevance for the different domains (e.g. the monsoon). The CREMA Phase I experiment was completed as a collaboration between the Abdus Salam ICTP and the U. San Paolo, CICESE, and the Indian Institute of Technology, and the results from this first analysis are being published in a special issue of Climatic Change. The data from these projections is freely available following the CORDEX data policy for eventual further analysis and use in impact assessment studies. We plan to incrementally populate the CREMA ensemble with further simulations employing more driving GCMs and model configurations and to compare our resultswith other models participating to the CORDEX effort.

  6. Improvement of surface albedo parameterization within a regional climate model (RegCM3)

    NASA Astrophysics Data System (ADS)

    Bao, Y.; Lü, S.

    2009-03-01

    A parameterization for calculating surface albedo of Solar Zenith Angel (SZA) dependence with coefficient for each vegetation type determined on the Moderate Resolution Imaging Spectro-radiometer (MODIS) reformed by the Bidirectional Reflectance Distribution Function (BRDF) is incorporated within the latest Abdus Salam International Centre for Theoretical Physics (ICTP) Regional Climate Model (RegCM3), and evaluated with a high resolution one-way nesting simulation in China using the Climate Research Unit (CRU) data and the observations from the Field Experiment on Interaction between Land and Atmosphere in Arid Region of Northwest China (NWC-ALIEX). The performance of the SZA method modeling surface characteristic is investigated.Results indicate, RegCM with SZA method (RCM_SZA) considerably improve the cold bias of original RegCM (RCM_ORI) in air surface temperature in East Asia with 1.2 degree increased in summer due to the lower albedo produced by SZA method which makes more solar radiation absorbed by the surface and used for heating the atmosphere near to the surface. The simulated diurnal cycle of ground temperature conforms fairly well to the observation in the nesting simulation in Northwest China, especially during the noon time when the SZA has the lowest value. However, the modification can not obviously affect the East Asia summer monsoon precipitation simulation although RCM_SZA produce more evapo-transpiration in surface with more than 2 Wm-2 increases in simulated latent heat fluxes both in East Asia and in Northwest China compared to RCM_ORI.

  7. Evaluation of Boulder, CO,SmartRegs Ordinance and Better Buildings Program

    SciTech Connect

    Arena, L.; Vijayakumar, G.

    2012-04-01

    Under the SmartRegs ordinance in the city of Boulder, Colorado, all rental properties in the city must achieve an energy efficiency level comparable to a HERS Index of approximately 120 points or lower by the year 2019. The City of Boulder received a $12 million grant from the DOE’s Better Buildings initiative to create and incentivize their EnergySmart Program. In this report, the Consortium for Advanced Residential Buildings (CARB) describes its work with the program, including energy audits of rental properties, developing training programs for insulators and inspectors, and conducting interviews with property owners.

  8. Evaluation of Boulder, CO, SmartRegs Ordinance and Better Buildings Program

    SciTech Connect

    Arena, L.; Vijayakumar, G.

    2012-04-01

    Under the SmartRegs ordinance in the city of Boulder, Colorado, all rental properties in the city must achieve an energy efficiency level comparable to a HERS Index of approximately 120 points or lower by the year 2019. The City of Boulder received a $12 million grant from the DOE's Better Buildings initiative to create and incentivize their EnergySmart Program. In this report, the Consortium for Advanced Residential Buildings (CARB) describes its work with the program, including energy audits of rental properties, developing training programs for insulators and inspectors, and conducting interviews with property owners.

  9. Effects of Aroclor 1254 reg sign on hydrocortisone levels in adult Rhesus monkeys (Macaca mulatta)

    SciTech Connect

    Loo, J.C.K.; Tryphonas, H.; Jordan, N.; Brien, R.; Karpinski, K.R.; Arnold, D.L. )

    1989-11-01

    Researchers, using female Sprague Dawley rats, reported the effects of chronic (5-7 months) oral dosing with Aroclor 1254{reg sign} (Polychlorinated biphenyls-PCB) on the serum levels of corticosterone, the principle glucocorticoid in rats. Their findings indicated that corticosterone levels were significantly depressed at dose levels of 479 {mu}g/kg bw/day and above. The objective of the present study was to determine the effects of PCB on the hydrocortisone levels in Rhesus monkey (Macaca mulatta) serum. In the monkey the controlling hormone is hydrocortisone which is identical to that of humans.

  10. On the transferability of RegCM4: Europe, Africa and Asia

    NASA Astrophysics Data System (ADS)

    Belda, Michal; Halenka, Tomas

    2013-04-01

    Simulations driven by ERA-interim reanalysis for CORDEX domains covering Europe, Africa and Asia have been performed using RegCM4 at 50 km resolution. The same settings are used in basic simulations and preliminary evaluation of model performance for individual regions will be presented. Several settings of different options is tested and sensitivity of selected ones will be shown in individual regions. Secant Mercator projection is introduced for Africa providing more efficient model geometry setting, the impact of proper emissivity inclusion is compared especially for Africa and Asia desserts. CRU data are used for the validation.

  11. Sacroillite tuberculeuse: à propos de deux cas

    PubMed Central

    Diallo, Ismaël; Zabsonré, Joëlle Tiendrébéogo; Kambou, Bénilde Marie Ange Tiemtoré; Sondo, Apoline Kongnimissom; Sagna, Yempabou; Ouédraogo, Dieu-Donné

    2016-01-01

    La sacroiliite tuberculeuse est rare et de diagnostic difficile. Les auteurs rapportent deux cas. Il s'agissait dans le premier cas d'une patiente de 40 ans ayant une infection à VIH ; le diagnostic a été histologique après une biopsie chirurgicale. Le second cas a concerné un patient de 25 ans vivant en milieu carcéral chez qui le diagnostic a été établi sur la base des arguments cliniques, biologiques, radiologiques et l'efficacité du traitement ; l'intradermoréaction à la tuberculine était phlycténulaire. Le scanner a été indispensable au diagnostic lésionnel en montrant une érosion des berges et des abcès des parties molles. Le traitement a été médical et a fait appel aux antituberculeux. PMID:28292032

  12. Sensitivity of the GCM driven summer monsoon simulations to cumulus parameterization schemes in nested RegCM3

    NASA Astrophysics Data System (ADS)

    Sinha, P.; Mohanty, U. C.; Kar, S. C.; Dash, S. K.; Kumari, S.

    2013-04-01

    The regional climate model (RegCM3) from the Abdus Salam International Centre for Theoretical Physics has been used to simulate the Indian summer monsoon for three different monsoon seasons such as deficit (1987), excess (1988) and normal (1989). Sensitivity to various cumulus parameterization and closure schemes of RegCM3 driven by the National Centre for Medium Range Weather Forecasting global spectral model products has been tested. The model integration of the nested RegCM3 is conducted using 90 and 30-km horizontal resolutions for outer and inner domains, respectively. The India Meteorological Department gridded rainfall (1° × 1°) and National Centre for Environment Prediction (NCEP)-Department of Energy (DOE) reanalysis-2 of 2.5° × 2.5° horizontal resolution data has been used for verification. The RegCM3 forced by NCEP-DOE reanalysis-2 data simulates monsoon seasons of 1987 and 1988 reasonably well, but the monsoon season of 1989 is not represented well in the model simulations. The RegCM3 runs driven by the global model are able to bring out seasonal mean rainfall and circulations well with the use of the Grell and Anthes-Kuo cumulus scheme at 90-km resolution. While the rainfall intensity and distribution is brought out well with the Anthes-Kuo scheme, upper air circulation features are brought out better by the Grell scheme. The simulated rainfall distribution is better with RegCM3 using the MIT-Emanuel cumulus scheme for 30-km resolution. Several statistical analyses, such as correlation coefficient, root mean square error, equitable threat score, confirm that the performance of MIT-Emanuel scheme at 30-km resolution is better in simulating all-India summer monsoon rainfall. The RegCM3 simulated rainfall amount is more and closer to observations than that from the global model. The RegCM3 has corrected its driven GCM in terms of rainfall distribution and magnitude over some parts of India during extreme years. This study brings out several

  13. Evolution and classification of the CRISPR-Cas systems

    PubMed Central

    S. Makarova, Kira; H. Haft, Daniel; Barrangou, Rodolphe; J. J. Brouns, Stan; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; J. M. Mojica, Francisco; I. Wolf, Yuri; Yakunin, Alexander F.; van der Oost, John; V. Koonin, Eugene

    2012-01-01

    The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a `polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci. PMID:21552286

  14. SnapShot: Class 1 CRISPR-Cas Systems.

    PubMed

    Makarova, Kira S; Zhang, Feng; Koonin, Eugene V

    2017-02-23

    Class 1 CRISPR-Cas systems are characterized by effector modules consisting of multiple subunits. Class 1 systems comprise about 90% of all CRISPR-Cas loci identified in bacteria and archaea and can target both DNA and RNA.

  15. Lurgi's MPG gasification plus Rectisol{reg_sign} gas purification - advanced process combination for reliable syngas production

    SciTech Connect

    2005-07-01

    Lurgi's Multi Purpose Gasification Process (MPG) is the reliable partial oxidation process to convert hydrocarbon liquids, slurries and natural gas into valuable syngas. The MPG burner has once again proven its capabilities in an ammonia plant based on asphalt gasification. Lurgi is operating the HP-POX demonstration plant together with the University of Freiberg, Germany. Gasification tests at pressures of up to 100 bar have shown that syngas for high pressure synthesis such as methanol and ammonia can be produced more economically. The Rectisol{reg_sign} gas purification process yields ultra clean synthesis gas which is required to avoid problems in the downstream synthesis. Pure carbon dioxide is produced as a separate stream and is readily available for sequestration, enhanced oil recovery or other uses. The reliability of the Rectisol{reg_sign} process and the confidence of plant operators in this process are acknowledged by the fact that more than 75% of the syngas produced world wide by coal, oil and waste gasification is purified in Rectisol{reg_sign} units. Virtually all coal gasification plants currently under construction rely on Rectisol{reg_sign}. The new, large GTL plants and hydrogen production facilities require effective CO{sub 2} removal. New developments make Rectisol{reg_sign} attractive for this task. 10 figs., 3 tabs., 2 photos.

  16. Identification of a Ubiquinone-binding Site That Affects Autophosphorylation of the Sensor Kinase RegB*S

    PubMed Central

    Swem, Lee R.; Gong, Xing; Yu, Chang-An; Bauer, Carl E.

    2009-01-01

    Rhodobacter capsulatus regulates many metabolic processes in response to the level of environmental oxygen and the energy state of the cell. One of the key global redox regulators of the cell’s metabolic physiology is the sensor kinase RegB that controls the synthesis of numerous energy generation and utilization processes. In this study, we have succeeded in purifying full-length RegB containing six transmembrane-spanning elements. Exogenous addition of excess oxidized coenzyme Q1 is capable of inhibiting RegB autophosphorylation ~6-fold. However, the addition of reduced coenzyme Q1 exhibits no inhibitory effect on kinase activity. A ubiquinone-binding site, as defined by azidoquinone photo affinity cross-linking, was determined to lie within a periplasmic loop between transmembrane helices 3 and 4 that contains a fully conserved heptapeptide sequence of GGXXNPF. Mutation of the phenylalanine in this heptapeptide renders RegB constitutively active in vivo, indicating that this domain is responsible for sensing the redox state of the ubiquinone pool and subsequently controlling RegB autophosphorylation. PMID:16407278

  17. Classical dendritic cells are required for dietary antigen-mediated induction of peripheral T(reg) cells and tolerance.

    PubMed

    Esterházy, Daria; Loschko, Jakob; London, Mariya; Jove, Veronica; Oliveira, Thiago Y; Mucida, Daniel

    2016-05-01

    Oral tolerance prevents pathological inflammatory responses to innocuous foreign antigens by peripheral regulatory T cells (pT(reg) cells). However, whether a particular subset of antigen-presenting cells (APCs) is required during dietary antigen exposure for the 'instruction' of naive CD4(+) T cells to differentiate into pT(reg) cells has not been defined. Using myeloid lineage-specific APC depletion in mice, we found that monocyte-derived APCs were dispensable, while classical dendritic cells (cDCs) were critical, for pT(reg) cell induction and oral tolerance. CD11b(-) cDCs from the gut-draining lymph nodes efficiently induced pT(reg) cells and, conversely, loss of transcription factor IRF8-dependent CD11b(-) cDCs impaired their polarization, although oral tolerance remained intact. These data reveal the hierarchy of cDC subsets in the induction of pT(reg) cells and their redundancy during the development of oral tolerance.

  18. RegTransBase - A Database Of Regulatory Sequences and Interactionsin a Wide Range of Prokaryotic Genomes

    SciTech Connect

    Kazakov, Alexei E.; Cipriano, Michael J.; Novichkov, Pavel S.; Minovitsky, Simon; Vinogradov, Dmitry V.; Arkin, Adam; Mironov, AndreyA.; Gelfand, Mikhail S.; Dubchak, Inna

    2006-07-01

    RegTransBase, a manually curated database of regulatoryinteractions in prokaryotes, captures the knowledge in publishedscientific literature using a controlled vocabulary. Although a number ofdatabases describing interactions between regulatory proteins and theirbinding sites are currently being maintained, they focus mostly on themodel organisms Escherichia coli and Bacillus subtilis, or are entirelycomputationally derived. RegTransBase describes a large number ofregulatory interactions reported in many organisms and contains varioustypes of experimental data, in particular: the activation or repressionof transcription by an identified direct regulator; determining thetranscriptional regulatory function of a protein (or RNA) directlybinding to DNA (RNA); mapping or prediction of binding site for aregulatory protein; characterization of regulatory mutations. Currently,the RegTransBase content is derived from about 3000 relevant articlesdescribing over 7000 experiments in relation to 128 microbes. It containsdata on the regulation of about 7500 genes and evidence for 6500interactions with 650 regulators. RegTransBase also contains manuallycreated position weight matrices (PWM) that can be used to identifycandidate regulatory sites in over 60 species. RegTransBase is availableat http://regtransbase.lbl.gov.

  19. CRISPR-Cas immunity in prokaryotes.

    PubMed

    Marraffini, Luciano A

    2015-10-01

    Prokaryotic organisms are threatened by a large array of viruses and have developed numerous defence strategies. Among these, only clustered, regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity against foreign elements. Upon viral injection, a small sequence of the viral genome, known as a spacer, is integrated into the CRISPR locus to immunize the host cell. Spacers are transcribed into small RNA guides that direct the cleavage of the viral DNA by Cas nucleases. Immunization through spacer acquisition enables a unique form of evolution whereby a population not only rapidly acquires resistance to its predators but also passes this resistance mechanism vertically to its progeny.

  20. Highly efficient Cas9-mediated transcriptional programming

    DOE PAGES

    Chavez, Alejandro; Scheiman, Jonathan; Vora, Suhani; ...

    2015-03-02

    The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. Here we describe an improved transcriptional regulator through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease-null Cas9. Here, we demonstrate its utility in activating endogenous coding and non-coding genes, targeting several genes simultaneously and stimulating neuronal differentiation of human induced pluripotent stem cells (iPSCs).

  1. Targeted delivery of CRISPR/Cas9 to prostate cancer by modified gRNA using a flexible aptamer-cationic liposome.

    PubMed

    Zhen, Shuai; Takahashi, Yoichiro; Narita, Shunichi; Yang, Yi-Chen; Li, Xu

    2017-02-07

    The potent ability of CRISPR/Cas9 system to inhibit the expression of targeted gene is being exploited as a new class of therapeutics for a variety of diseases. However, the efficient and safe delivery of CRISPR/Cas9 into specific cell populations is still the principal challenge in the clinical development of CRISPR/Cas9 therapeutics. In this study, a flexible aptamer-liposome-CRISPR/Cas9 chimera was designed to combine efficient delivery and increased flexibility. Our chimera incorporated an RNA aptamer that specifically binds prostate cancer cells expressing the prostate-specific membrane antigen as a ligand. Cationic liposomes were linked to aptamers by the post-insertion method and were used to deliver therapeutic CRISPR/Cas9 that target the survival gene, polo-like kinase 1, in tumor cells. We demonstrate that the aptamer-liposome-CRISPR/Cas9 chimeras had a significant cell-type binding specificity and a remarkable gene silencing effect in vitro. Furthermore, silencing promoted a conspicuous regression of prostate cancer in vivo. Importantly, the approach described here provides a universal means of cell type-specific CRISPR/Cas9 delivery, which is a critical goal for the widespread therapeutic applicability of CRISPR/Cas9 or other nucleic acid drugs.

  2. Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer.

    PubMed

    Richter, Corinna; Dy, Ron L; McKenzie, Rebecca E; Watson, Bridget N J; Taylor, Corinda; Chang, James T; McNeil, Matthew B; Staals, Raymond H J; Fineran, Peter C

    2014-07-01

    Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arrays as spacers. This adaptation process is the least characterized step in CRISPR-Cas immunity. Here, we used Pectobacterium atrosepticum to investigate adaptation in Type I-F CRISPR-Cas systems. Pre-existing spacers that matched plasmids stimulated hyperactive primed acquisition and resulted in the incorporation of up to nine new spacers across all three native CRISPR arrays. Endogenous expression of the cas genes was sufficient, yet required, for priming. The new spacers inhibited conjugation and transformation, and interference was enhanced with increasing numbers of new spacers. We analyzed ∼ 350 new spacers acquired in priming events and identified a 5'-protospacer-GG-3' protospacer adjacent motif. In contrast to priming in Type I-E systems, new spacers matched either plasmid strand and a biased distribution, including clustering near the primed protospacer, suggested a bi-directional translocation model for the Cas1:Cas2-3 adaptation machinery. Taken together these results indicate priming adaptation occurs in different CRISPR-Cas systems, that it can be highly active in wild-type strains and that the underlying mechanisms vary.

  3. Empa's New Clothes: The Untold Story of the Empa-Reg Outcome Trial.

    PubMed

    Alzaid, Aus

    2017-03-16

    It is no secret that the diabetes community has been yearning for good news for quite some time. One outstanding issue undermining effective diabetes management has been the lack of demonstrable effects of glycemic interventions on cardiovascular (CV) outcome in people with type 2 diabetes. This, however, seems to have changed recently after the publication of the Empa-Reg Outcome Trial. The study reported an impressive reduction in CV deaths that was observed within weeks of treatment with the diabetes agent, Empagliflozin. The results exceeded all expectations and was quickly embraced by a wide and receptive diabetes audience. Fans and admirers of the study have since set out to accommodate the new findings to reshape our diabetes practice guidelines. However, before everything becomes cast in stone, I believe there's another side to the story of the Empa-Reg Outcome trial that the diabetes community needs to hear. Here, I debate the merits of the study and present the case as to why I think we might be led down the garden path by accepting this study at mere face value.

  4. A new regional climate simulation using RegCM4 over the CORDEX South Asia domain

    NASA Astrophysics Data System (ADS)

    Mariotti, Laura; Bacer, Sara; Coppola, Erika; Giorgi, Filippo

    2014-05-01

    We present a new high-resolution regional climate simulation over the CORDEX South Asia made with the latest version of the Regional Climate Model RegCM4. The simulation has been performed at 25 km of resolution using the ERA-Interim boundary conditions. The simulated results are compared with the monthly mean surface observations for temperature and precipitation over the entire domain. The rainy season during the June-July-August-September (JJAS) over India shows a bigger improvement using a different parameterization of the MIT-Emanuel convection scheme for land and ocean. Another big improvement has been found with the UW PBL scheme (Bretherton and McCaa, 2004). The model shows in JJAS season a slight cold bias over the mountain compared with CRU dataset, instead in Indian land area the pattern of the temperature is well represented. The monsoon precipitation over the Indian continent is reasonably represented. A good agreement was found from the comparison between RegCM4 with the IMD dataset by studying the area weighted average values time series of monthly accumulated rainfall (cm) in Indian land area.

  5. Predicting relative toxicity of metal ions to bacteria (Microtox{reg_sign}) using ion characteristics

    SciTech Connect

    McCloskey, J.T.; Newman, M.C.; Clark, S.B.

    1995-12-31

    The use of predictive effects models with metals has received little attention in toxicology. The purpose of this study was to predict the relative toxicity of individual metal ions and metal mixtures using ion characteristics. The concentration of metal resulting in a 50% reduction in light output (EC50) in marine bacteria (Vibrio fischeri) was determined for several metals using the Microtox{reg_sign} Toxicity Analyzer. Trends in metal toxicity were predicted by combining metal speciation calculations with empirical models based on metal ion characteristics. These trends were consistent for nine divalent metals (Ca{prime} Cd, Cu, Hg, Mg, Mn, Ni, Pb and Zn) whether the media mimicked salt water (NaC, medium) or freshwater (NaNO{sub 3} medium). When expanding the study to include an additional 14 mono-, di-, and trivalent metal ions, ion characteristics were still useful for predicting the relative toxicity of metal ions to bacteria. The prediction of nonadditive toxic effects using metal mixtures was also possible based on ion characteristics. Overall, models based on ion characteristics show much promise for predicting the relative toxicity of metal ions using the Microtox{reg_sign} assay.

  6. DNA targeting by the type I-G and type I-A CRISPR–Cas systems of Pyrococcus furiosus

    PubMed Central

    Elmore, Joshua; Deighan, Trace; Westpheling, Jan; Terns, Rebecca M.; Terns, Michael P.

    2015-01-01

    CRISPR–Cas systems silence plasmids and viruses in prokaryotes. CRISPR–Cas effector complexes contain CRISPR RNAs (crRNAs) that include sequences captured from invaders and direct CRISPR-associated (Cas) proteins to destroy corresponding invader nucleic acids. Pyrococcus furiosus (Pfu) harbors three CRISPR–Cas immune systems: a Cst (Type I-G) system with an associated Cmr (Type III-B) module at one locus, and a partial Csa (Type I-A) module (lacking known invader sequence acquisition and crRNA processing genes) at another locus. The Pfu Cmr complex cleaves complementary target RNAs, and Csa systems have been shown to target DNA, while the mechanism by which Cst complexes silence invaders is unknown. In this study, we investigated the function of the Cst as well as Csa system in Pfu strains harboring a single CRISPR–Cas system. Plasmid transformation assays revealed that the Cst and Csa systems both function by DNA silencing and utilize similar flanking sequence information (PAMs) to identify invader DNA. Silencing by each system specifically requires its associated Cas3 nuclease. crRNAs from the 7 shared CRISPR loci in Pfu are processed for use by all 3 effector complexes, and Northern analysis revealed that individual effector complexes dictate the profile of mature crRNA species that is generated. PMID:26519471

  7. Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system

    PubMed Central

    Staals, Raymond H. J.; Jackson, Simon A.; Biswas, Ambarish; Brouns, Stan J. J.; Brown, Chris M.; Fineran, Peter C.

    2016-01-01

    CRISPR–Cas systems provide bacteria with adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, we use high-throughput sequencing to analyse millions of spacer acquisition events in wild-type populations of Pectobacterium atrosepticum. Plasmids not previously encountered, or plasmids that had escaped CRISPR–Cas targeting via point mutation, are used to provoke naive or primed spacer acquisition, respectively. The origin, location and order of spacer acquisition show that spacer selection through priming initiates near the site of CRISPR–Cas recognition (the protospacer), but on the displaced strand, and is consistent with 3′–5′ translocation of the Cas1:Cas2-3 acquisition machinery. Newly acquired spacers determine the location and strand specificity of subsequent spacers and demonstrate that interference-driven spacer acquisition (‘targeted acquisition') is a major contributor to adaptation in type I-F CRISPR–Cas systems. Finally, we show that acquisition of self-targeting spacers is occurring at a constant rate in wild-type cells and can be triggered by foreign DNA with similarity to the bacterial chromosome. PMID:27694798

  8. Reg-2, A Downstream Signaling Protein in the Ciliary Neurotrophic Factor Survival Pathway, Alleviates Experimental Autoimmune Encephalomyelitis

    PubMed Central

    Jiang, Hong; Tian, Ke-Wei; Zhang, Fan; Wang, Beibei; Han, Shu

    2016-01-01

    Ciliary neurotrophic factor (CNTF), originally described as a neurocytokine that could support the survival of neurons, has been recently found to alleviate demyelination, prevent axon loss, and improve functional recovery in a rat model of acute experimental autoimmune encephalomyelitis (EAE). However, poor penetration into the brain parenchyma and unfavorable side effects limit the utility of CNTF. Here, we evaluated the therapeutic potential of a protein downstream of CNTF, regeneration gene protein 2 (Reg-2). Using multiple morphological, molecular biology, and electrophysiological methods to assess neuroinflammation, axonal loss, demyelination, and functional impairment, we observed that Reg-2 and CNTF exert similar effects in the acute phase of EAE. Both treatments attenuated axonal loss and demyelination, improved neuronal survival, and produced functional improvement. With a smaller molecular weight and improved penetration into the brain parenchyma, Reg-2 may be a useful substitute for CNTF therapy in EAE and multiple sclerosis (MS). PMID:27242448

  9. Boosting plant immunity with CRISPR/Cas.

    PubMed

    Chaparro-Garcia, Angela; Kamoun, Sophien; Nekrasov, Vladimir

    2015-11-19

    CRISPR/Cas has recently been transferred to plants to make them resistant to geminiviruses, a damaging family of DNA viruses. We discuss the potential and the limitations of this method.See related Research: http://www.genomebiology.com/2015/16/1/238.

  10. Using the CAS Standards in Assessment Projects

    ERIC Educational Resources Information Center

    Dean, Laura A.

    2013-01-01

    This chapter provides an overview of the use of professional standards of practice in assessment and of the Council for the Advancement of Standards in Higher Education (CAS). It outlines a model for conducting program self-studies and discusses the importance of implementing change based on assessment results.

  11. Effects of Using a Computer Algebra System (CAS) on Junior College Students' Attitudes towards CAS and Achievement in Mathematics

    ERIC Educational Resources Information Center

    Leng, Ng Wee; Choo, Kwee Tiow; Soon, Lau Hock; Yi-Huak, Koh; Sun, Yap Yew

    2005-01-01

    This study examines the effects of using Texas Instruments' Voyage 200 calculator (V200), a graphing calculator with a built-in computer algebra system (CAS), on attitudes towards CAS and achievement in mathematics of junior college students (17 year olds). Students' attitudes towards CAS were examined using a 40-item Likert-type instrument…

  12. Dynamic behavior of XD{reg_sign} TiB{sub 2} reinforced Ti-48Al(at. %)

    SciTech Connect

    Chin, E.S.C.; Weerasooriya, T.; Woolsey, P.; Biederman, R.R.

    1995-12-31

    The ballistic performance and dynamic behavior of XD{reg_sign} titanium diboride (TiB{sub 2}) reinforced Ti-48Al(at.%) composites were evaluated. The XD{reg_sign} composites exhibited ballistic performance comparable to that of an alumina ceramic. Unlike a ceramic, the composite targets were neither shattered nor pulverized. Both high strain rate testing and ballistic testing showed material behaviors independent of reinforcement loading. In this paper, the influence of microstructure on ballistic performance and high strain rate behavior will be discussed. A phenomenological model describing target/penetrator interactions will be presented.

  13. Fatigue crack propagation parallel to fibers in unidirectionally reinforced SCS-6/Timetal{reg_sign}21S

    SciTech Connect

    John, R.; Lackey, A.F.; Ashbaugh, N.E.

    1996-09-15

    The primary weakness of a component made of unidirectionally reinforced SCS-6/Timetal{reg_sign}21S is its susceptibility to transverse loads. The strength of the component in the transverse direction is significantly lower than that in the longitudinal direction under monotonic, sustained and fatigue loading conditions. The previous investigations did not investigate the effect of applied stress ratio on the crack growth behavior of the composite. This paper describes extensive characterization of the fatigue crack growth parallel to fibers in unidirectional SCS-6/Timetal{reg_sign}21S using two geometries, three applied stress ratios and closure measurements.

  14. CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA

    PubMed Central

    Zhou, Jianting; Wu, Ronghai; Xue, Xiaoli; Qin, Zhongjun

    2016-01-01

    Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated ‘CasHRA (Cas9-facilitated Homologous Recombination Assembly)’ that directly uses large circular DNAs in a one-step in vivo assembly process. The large circular DNAs are co-introduced into Saccharomyces cerevisiae by protoplast fusion, and they are cleaved by RNA-guided Cas9 nuclease to release the linear DNA segments for subsequent assembly by the endogenous homologous recombination system. The CasHRA method allows efficient assembly of multiple large DNA segments in vivo; thus, this approach should be useful in the last stage of genome construction. As a proof of concept, we combined CasHRA with an upstream assembly method (Gibson procedure of genome assembly) and successfully constructed a 1.03 Mb MGE-syn1.0 (Minimal Genome of Escherichia coli) that contained 449 essential genes and 267 important growth genes. We expect that CasHRA will be widely used in megabase-sized genome constructions. PMID:27220470

  15. Controlling UCAVs by JTACs in CAS missions

    NASA Astrophysics Data System (ADS)

    Kumaş, A. E.

    2014-06-01

    By means of evolving technology, capabilities of UAVs (Unmanned Aerial Vehicle)s are increasing rapidly. This development provides UAVs to be used in many different areas. One of these areas is CAS (Close Air Support) mission. UAVs have several advantages compared to manned aircraft, however there are also some problematic areas. The remote controlling of these vehicles from thousands of nautical miles away via satellite may lead to various problems both ethical and tactical aspects. Therefore, CAS missions require a good level of ALI (Air-Land Integration), a high SA (situational awareness) and precision engagement. In fact, there is an aware friendly element in the target area in CAS missions, unlike the other UAV operations. This element is an Airman called JTAC (Joint Terminal Attack Controller). Unlike the JTAC, UAV operators are too far away from target area and use the limited FOV (Field of View) provided by camera and some other sensor data. In this study, target area situational awareness of a UAV operator and a JTAC, in a high-risk mission for friendly ground forces and civilians such as CAS, are compared. As a result of this comparison, answer to the question who should control the UCAV (Unmanned Combat Aerial Vehicle) in which circumstances is sought. A literature review is made in UAV and CAS fields and recent air operations are examined. The control of UCAV by the JTAC is assessed by SWOT analysis and as a result it is deduced that both control methods can be used in different situations within the framework of the ROE (Rules Of Engagement) is reached.

  16. Simulating land use changes in the Upper Narew catchment using the RegCM model

    NASA Astrophysics Data System (ADS)

    Liszewska, Malgorzata; Osuch, Marzena; Romanowicz, Renata

    2010-05-01

    Catchment hydrology is influenced by climate forcing in the form of precipitation, temperature, evapotranspiration and human interactions such as land use and water management practices. The difficulty in separating different causes of change in a hydrological regime results from the complexity of interactions between those three factors and catchment responses and the uncertainty and scarcity of available observations. This paper describes an application of a regional climate model to simulate the variability in precipitation, temperature, evaporation and discharge under different land use parameterizations, using the Upper Narew catchment (north-east Poland) as a case study. We use RegCM3 model, developed at the International Centre for Theoretical Physics, Trieste, Italy. The model's dynamic core is based on the hydrostatic version of the NCAR/PSU Mesoscale Model version 5 (primitive equations, hydrostatic, compressible, sigma-vertical coordinate). The physical input includes radiation transfer, large-scale and convective precipitation, Planetary Boundary Layer, biosphere. The RegCM3 model has options to interface with a variety of re-analyses and GCM boundary conditions, and can thus be used for scenario assessments. The variability of hydrological conditions in response to regional climate model projections is modeled using an integrated Data Based Mechanistic (DBM) rainfall-flow/flow-routing model of the Upper River Narew catchment. The modelling tool developed is formulated in the MATLAB-SIMULINK language. The basic system structure includes rainfall-flow and flow routing modules, based on a Stochastic Transfer Function (STF) approach combined with a nonlinear transformation of rainfall into effective rainfall. We analyse the signal resulting from modified land use in a given region. 10 month-long runs have been performed from February to November for the period of 1991-2000 based on the NCEP re-analyses. The land use data have been taken from the GLCC

  17. Simulated Evapotranspiration over South America by Different RegCM4.3 Parameterizations

    NASA Astrophysics Data System (ADS)

    Reboita, Michelle; da Rocha, Rosmeri; Fernandez, Julio Pablo

    2014-05-01

    This study evaluates the simulated evapotranspiration by Regional Climate Model version 4.3 (RegCM4.3) over South America (SA). Seven different RegCM4.3 configurations are compared: control simulation (S_CTRL) used the Biosphere-Atmosphere Transfer Scheme (BATS), Holtslag for planetary boundary layer (PBL) and Mixed1 (Grell scheme over the continent and MIT scheme over the ocean) for cumulus convection; S_MIT changed Mixed1 by MIT convective scheme; and S_Tiedtke changed Mixed1 by Tiedtke scheme; S_PBL and S_PBL_MIT used University of Washington PBL (UW-PBL) instead Holtslag PBL; S_CLM and S_CLM_MIT changed BATS by Common Land Model (CLM). These experiments were carried out from January 1989 to January 2000 in a domain recommended by CORDEX to SA. S_Tiedtke underestimates the evapotranspiration in almost SA producing a precipitation dry bias over the continent. Simulations using MIT convective scheme overestimate the evapotranspiration resulting in positive bias in the precipitation mainly over the central part of Brazil during the wet season. Another interesting result is that changing the PBL scheme from Hosltslag to UW-PBL, the precipitation bias remains dry for the experiment with Mixed1 scheme (S_PBL) and wet for that with MIT scheme (S_PBL_MIT). Therefore, the convective scheme has a higher control over the precipitation than PBL scheme. When CLM is coupled to the RegCM4.3 it contributes for a general decrease in the evapotranspiration. Thus, (a) a more intense dry bias occurs in the experiment S_CLM (Mixed1 with CLM) compared with S_CTRL (Mixed1 with BATS) and (b) there is a reduction of the wet bias decrease in the experiment S_CLM_MIT (MIT with CLM) in relation to the S_MIT (MIT with BATS). The combination of CLM and MIT schemes produces the more realistic precipitation rate over Amazon and of the air temperature over all continental SA.

  18. In vivo genome editing using Staphylococcus aureus Cas9

    PubMed Central

    Ran, F. Ann; Cong, Le; Yan, Winston X.; Scott, David A.; Gootenberg, Jonathan S.; Kriz, Andrea J.; Zetsche, Bernd; Shalem, Ophir; Wu, Xuebing; Makarova, Kira S.; Koonin, Eugene; Sharp, Phillip A.; Zhang, Feng

    2015-01-01

    The RNA-guided endonuclease Cas9 has emerged as a versatile genome-editing platform. However, the size of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for basic research and therapeutic applications that employ the highly versatile adeno-associated virus (AAV) delivery vehicle. Here, we characterize six smaller Cas9 orthologs and show that Cas9 from Staphylococcus aureus (SaCas9) can edit the genome with efficiencies similar to those of SpCas9, while being >1kb shorter. We packaged SaCas9 and its sgRNA expression cassette into a single AAV vector and targeted the cholesterol regulatory gene Pcsk9 in the mouse liver. Within one week of injection, we observed >40% gene modification, accompanied by significant reductions in serum Pcsk9 and total cholesterol levels. We further demonstrate the power of using BLESS to assess the genome-wide targeting specificity of SaCas9 and SpCas9, and show that SaCas9 can mediate genome editing in vivo with high specificity. PMID:25830891

  19. Structure and Engineering of Francisella novicida Cas9

    PubMed Central

    Hirano, Hisato; Gootenberg, Jonathan S.; Horii, Takuro; Abudayyeh, Omar O.; Kimura, Mika; Hsu, Patrick D.; Nakane, Takanori; Ishitani, Ryuichiro; Hatada, Izuho; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

    2016-01-01

    Summary The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets complementary to the guide RNA, and has been applied to programmable genome editing. Cas9-mediated cleavage requires a protospacer adjacent motif (PAM) juxtaposed with the DNA target sequence, thus constricting the range of targetable sites. Here, we report the 1.7 Å resolution crystal structures of Cas9 from Francisella novicida (FnCas9), one of the largest Cas9 orthologs, in complex with a guide RNA and its PAM-containing DNA targets. A structural comparison of FnCas9 with other Cas9 orthologs revealed striking conserved and divergent features among distantly related CRISPR-Cas9 systems. We found that FnCas9 recognizes the 5′-NGG-3′ PAM, and used the structural information to create a variant that can recognize the more relaxed 5′-YG-3′ PAM. Furthermore, we demonstrated that pre-assembled FnCas9 ribonucleoprotein complexes can be microinjected into mouse zygotes to edit endogenous sites with the 5′-YG-3′ PAMs, thus expanding the target space of the CRISPR-Cas9 toolbox. PMID:26875867

  20. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

    PubMed Central

    2016-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system recently emerged as a transformative genome-editing technology that is innovating basic bioscience and applied medicine and biotechnology. The endonuclease Cas9 associates with a guide RNA to match and cleave complementary sequences in double stranded DNA, forming an RNA:DNA hybrid and a displaced non-target DNA strand. Although extensive structural studies are ongoing, the conformational dynamics of Cas9 and its interplay with the nucleic acids during association and DNA cleavage are largely unclear. Here, by employing multi-microsecond time scale molecular dynamics, we reveal the conformational plasticity of Cas9 and identify key determinants that allow its large-scale conformational changes during nucleic acid binding and processing. We show how the “closure” of the protein, which accompanies nucleic acid binding, fundamentally relies on highly coupled and specific motions of the protein domains, collectively initiating the prominent conformational changes needed for nucleic acid association. We further reveal a key role of the non-target DNA during the process of activation of the nuclease HNH domain, showing how the nontarget DNA positioning triggers local conformational changes that favor the formation of a catalytically competent Cas9. Finally, a remarkable conformational plasticity is identified as an intrinsic property of the HNH domain, constituting a necessary element that allows for the HNH repositioning. These novel findings constitute a reference for future experimental studies aimed at a full characterization of the dynamic features of the CRISPR-Cas9 system, and—more importantly—call for novel structure engineering efforts that are of fundamental importance for the rational design of new genome-engineering applications. PMID:27800559

  1. A novel putative lipoprotein receptor (CasLpR) in the hemocytes of the blue crab, Callinectes sapidus: cloning and up-regulated expression after the injection of LPS and LTA.

    PubMed

    Tsutsui, Naoaki; Chung, J Sook

    2012-03-01

    The full-length cDNA encoding a putative lipoprotein receptor (CasLpR) was isolated from the hemocytes of Callinectes sapidus using 5' and 3' RACEs. The open reading frame for CasLpR contains a precursor of putative CasLpR consisting of 1710 amino acid residues including 22 amino acid residues of the signal peptide (22 amino acids). Mature CasLpR (1688 amino acids with 5.6% of phosphorylation sites) has multiple, putative functional domains: five low-density lipoprotein receptor domains in the N-terminus, and a G-protein-coupled receptor proteolysis site domain and a 7 transmembrane receptor (secretin family) domain in the C-terminus. To date, there are no proteins with a similar domain structure in the GenBank. The expression pattern of CasLpR was exclusive in hemocytes among all tested tissues obtained from a juvenile female at intermolt stage: brain, eyestalk ganglia, pericardial organs, and thoracic ganglia complex (nervous system); hepatopancreas (digestive system); heart, artery and hemocytes (circulatory system); gill and antennal gland (excretory system), hypodermis; and Y-organ (endocrine organ). There was no CasLpR expression in the ovary of an adult female. A putative function of CasLpR was examined after challenges of lipopolysaccharides (LPS) and lipoteichoic acid (LTA) in vivo using qRT-PCR assays. Animals at 24 h after injection of LPS or LTA up-regulated the expression of CasLpR in hemocytes by ∼3.5 and 1.4 folds, respectively, compared to the controls that received saline injection. LPS challenge also caused the greatest increment (∼55 folds) of heat shock protein 90 (Hsp90) expression in these samples. These data indicate that putative CasLpR and CasHsp90 may be involved in the defense system or the stress response of C. sapidus.

  2. Introduction to the TAC special issue: The RegCNET network

    NASA Astrophysics Data System (ADS)

    Giorgi, F.; Pal, J. S.; Bi, X.; Sloan, L.; Elguindi, N.; Solmon, F.

    2006-09-01

    Fostering climate research in economically developing nations (EDNs) is especially important because the welfare and economies of these nations are particularly dependent on climate and its variability. A critical factor that undermines the advancement of research in EDNs is that many EDN scientists are confronted with scientific isolation and lack of exposure to state-of-the-art research methodologies. One of the means to ameliorate this problem is to build “south south” (i.e. EDN EDN) and “north south” (i.e. EDN EAN, or economically advanced nations) research partnerships, which become more effective when they are based on collaborative projects where the participants share their respective expertise. This is the central paradigm underlying the formation of the REGional Climate research NETwork, or RegCNET.

  3. Vascular legacy: HOPE ADVANCEs to EMPA-REG and LEADER: A Surprising similarity

    PubMed Central

    Kalra, Sanjay; Sahay, Rakesh

    2017-01-01

    Recently reported cardiovascular outcome studies on empagliflozin (EMPA-REG) and liraglutide (LEADER) have spurred interest in this field of diabetology. This commentary compares and contrasts these studies with two equally important outcome trials conducted using blood pressure lowering agents. A comparison with MICROHOPE (using ramipril) and ADVANCE (using perindopril + indapamide) blood pressure arms throws up interesting facts. The degree of blood pressure lowering, dissociation between cardiovascular and cerebrovascular benefits, and discordance between renal and retinal outcomes are surprisingly similar in these trials, conducted using disparate molecules. The time taken to achieve such benefits is similar for all drugs except empagliflozin. Such discussion helps inform rational and evidence-based choice of therapy and forms the framework for future research. PMID:28217527

  4. Assessment of TEES reg sign applications for Wet Industrial Wastes: Energy benefit and economic analysis report

    SciTech Connect

    Elliott, D.C.; Scheer, T.H.

    1992-02-01

    Fundamental work is catalyzed biomass pyrolysis/gasification led to the Thermochemical Environmental Energy System (TEES{reg sign}) concept, a means of converting moist biomass feedstocks to high-value fuel gases such as methane. A low-temperature (350{degrees}C), pressurized (3100 psig) reaction environment and a nickel catalyst are used to reduce volumes of very high-moisture wastes such as food processing byproducts while producing useful quantities of energy. A study was conducted to assess the economic viability of a range of potential applications of the process. Cases examined included feedstocks of cheese whey, grape pomace, spent grain, and an organic chemical waste stream. The analysis indicated that only the organic chemical waste process is economically attractive in the existing energy/economic environment. However, food processing cases will become attractive as alternative disposal practices are curtailed and energy prices rise.

  5. EXpectation Propagation LOgistic REgRession (EXPLORER): Distributed Privacy-Preserving Online Model Learning

    PubMed Central

    Wang, Shuang; Jiang, Xiaoqian; Wu, Yuan; Cui, Lijuan; Cheng, Samuel; Ohno-Machado, Lucila

    2013-01-01

    We developed an EXpectation Propagation LOgistic REgRession (EXPLORER) model for distributed privacy-preserving online learning. The proposed framework provides a high level guarantee for protecting sensitive information, since the information exchanged between the server and the client is the encrypted posterior distribution of coefficients. Through experimental results, EXPLORER shows the same performance (e.g., discrimination, calibration, feature selection etc.) as the traditional frequentist Logistic Regression model, but provides more flexibility in model updating. That is, EXPLORER can be updated one point at a time rather than having to retrain the entire data set when new observations are recorded. The proposed EXPLORER supports asynchronized communication, which relieves the participants from coordinating with one another, and prevents service breakdown from the absence of participants or interrupted communications. PMID:23562651

  6. RegPhos: a system to explore the protein kinase–substrate phosphorylation network in humans

    PubMed Central

    Lee, Tzong-Yi; Bo-Kai Hsu, Justin; Chang, Wen-Chi; Huang, Hsien-Da

    2011-01-01

    Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of experimental phosphorylation sites that has been identified by mass spectrometry-based proteomics, the desire to explore the networks of protein kinases and substrates is motivated. Manning et al. have identified 518 human kinase genes, which provide a starting point for comprehensive analysis of protein phosphorylation networks. In this study, a knowledgebase is developed to integrate experimentally verified protein phosphorylation data and protein–protein interaction data for constructing the protein kinase–substrate phosphorylation networks in human. A total of 21 110 experimental verified phosphorylation sites within 5092 human proteins are collected. However, only 4138 phosphorylation sites (∼20%) have the annotation of catalytic kinases from public domain. In order to fully investigate how protein kinases regulate the intracellular processes, a published kinase-specific phosphorylation site prediction tool, named KinasePhos is incorporated for assigning the potential kinase. The web-based system, RegPhos, can let users input a group of human proteins; consequently, the phosphorylation network associated with the protein subcellular localization can be explored. Additionally, time-coursed microarray expression data is subsequently used to represent the degree of similarity in the expression profiles of network members. A case study demonstrates that the proposed scheme not only identify the correct network of insulin signaling but also detect a novel signaling pathway that may cross-talk with insulin signaling network. This effective system is now freely available at http://RegPhos.mbc.nctu.edu.tw. PMID:21037261

  7. Differentiation of ICOS+ and ICOS- recent thymic emigrant regulatory T cells (RTE T regs) during normal pregnancy, pre-eclampsia and HELLP syndrome.

    PubMed

    Wagner, M I; Jöst, M; Spratte, J; Schaier, M; Mahnke, K; Meuer, S; Zeier, M; Steinborn, A

    2016-01-01

    Two different subsets of naturally occurring regulatory T cells (nTregs), defined by their expression of the inducible co-stimulatory (ICOS) molecule, are produced by the human thymus. To examine the differentiation of ICOS(+) and ICOS(-) CD45RA(+) CD31(+) recent thymic emigrant (RTE) T regs during normal pregnancy and in the presence of pre-eclampsia or haemolysis elevated liver enzymes low platelet (HELLP)-syndrome, we used six-colour flow cytometric analysis to determine the changes in the composition of the ICOS(+) and ICOS(-) T reg pools with CD45RA(+) CD31(+) RTE T regs, CD45RA(+) CD31(-) mature naive (MN) T regs, CD45RA(-) CD31(+) and CD45RA(-) CD31(-) memory Tregs. With the beginning of pregnancy until term, we observed a strong differentiation of both ICOS(+) and ICOS(-) CD45RA(+) CD31(+) RTE, but not CD45RA(+) CD31(-) MN T regs, into CD45RA(-) CD31(-) memory T regs. At the end of pregnancy, the onset of spontaneous term labour was associated with a significant breakdown of ICOS(+) CD45RA(-) CD31(-) memory T regs. However, in the presence of pre-eclampsia, there was a significantly increased differentiation of ICOS(+) and ICOS(-) CD45RA(+) CD31(+) RTE T regs into CD45RA(-) CD31(+) memory T regs, wherein the lacking differentiation into CD45RA(-) CD31(-) memory T regs was partially replaced by the increased differentiation of ICOS(+) and ICOS(-) CD45RA(+) CD31(-) MN Tregs into CD45RA(-) CD31(-) memory T regs. In patients with HELLP syndrome, this alternatively increased differentiation of CD45RA(-) CD31(-) MN T regs seemed to be exaggerated, and presumably restored the suppressive activity of magnetically isolated ICOS(+) and ICOS(-) T regs, which were shown to be significantly less suppressive in pre-eclampsia patients, but not in HELLP syndrome patients. Hence, our findings propose that the regular differentiation of both ICOS(+) and ICOS(-) CD45RA(+) CD31(+) RTE T regs ensures a healthy pregnancy course, while their disturbed differentiation is

  8. The role of CRISPR-Cas systems in virulence of pathogenic bacteria.

    PubMed

    Louwen, Rogier; Staals, Raymond H J; Endtz, Hubert P; van Baarlen, Peter; van der Oost, John

    2014-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example concerns a pathogenic bacterium that possesses a CRISPR-associated ribonucleoprotein complex that may play a dual role in defense and/or virulence. In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular.

  9. Adapting to new threats: the generation of memory by CRISPR-Cas immune systems.

    PubMed

    Heler, Robert; Marraffini, Luciano A; Bikard, David

    2014-07-01

    Clustered, regularly interspaced, short palindromic repeats (CRISPR) loci and their associated genes (cas) confer bacteria and archaea with adaptive immunity against phages and other invading genetic elements. A fundamental requirement of any immune system is the ability to build a memory of past infections in order to deal more efficiently with recurrent infections. The adaptive feature of CRISPR-Cas immune systems relies on their ability to memorize DNA sequences of invading molecules and integrate them in between the repetitive sequences of the CRISPR array in the form of 'spacers'. The transcription of a spacer generates a small antisense RNA that is used by RNA-guided Cas nucleases to cleave the invading nucleic acid in order to protect the cell from infection. The acquisition of new spacers allows the CRISPR-Cas immune system to rapidly adapt against new threats and is therefore termed 'adaptation'. Recent studies have begun to elucidate the genetic requirements for adaptation and have demonstrated that rather than being a stochastic process, the selection of new spacers is influenced by several factors. We review here our current knowledge of the CRISPR adaptation mechanism.

  10. Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon

    PubMed Central

    Sasaki, Nobuo; Sachs, Norman; Wiebrands, Kay; Ellenbroek, Saskia I. J.; Fumagalli, Arianna; Lyubimova, Anna; Begthel, Harry; van den Born, Maaike; van Es, Johan H.; Karthaus, Wouter R.; Li, Vivian S. W.; López-Iglesias, Carmen; Peters, Peter J.; van Rheenen, Jacco; van Oudenaarden, Alexander; Clevers, Hans

    2016-01-01

    Leucine-rich repeat-containing G-protein coupled receptor 5-positive (Lgr5+) stem cells reside at crypt bottoms of the small and large intestine. Small intestinal Paneth cells supply Wnt3, EGF, and Notch signals to neighboring Lgr5+ stem cells. Whereas the colon lacks Paneth cells, deep crypt secretory (DCS) cells are intermingled with Lgr5+ stem cells at crypt bottoms. Here, we report regenerating islet-derived family member 4 (Reg4) as a marker of DCS cells. To investigate a niche function, we eliminated DCS cells by using the diphtheria-toxin receptor gene knocked into the murine Reg4 locus. Ablation of DCS cells results in loss of stem cells from colonic crypts and disrupts gut homeostasis and colon organoid growth. In agreement, sorted Reg4+ DCS cells promote organoid formation of single Lgr5+ colon stem cells. DCS cells can be massively produced from Lgr5+ colon stem cells in vitro by combined Notch inhibition and Wnt activation. We conclude that Reg4+ DCS cells serve as Paneth cell equivalents in the colon crypt niche. PMID:27573849

  11. Intestinal REG3 Lectins Protect Against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation

    PubMed Central

    Wang, Lirui; Fouts, Derrick E.; Stärkel, Peter; Hartmann, Phillipp; Chen, Peng; Llorente, Cristina; DePew, Jessica; Moncera, Kelvin; Ho, Samuel B.; Brenner, David A.; Hooper, Lora V.; Schnabl, Bernd

    2016-01-01

    Summary Approximately half of all deaths from liver cirrhosis, the 10th leading cause of mortality in the United States, are related to alcohol use. Chronic alcohol consumption is accompanied by intestinal dysbiosis and bacterial overgrowth, yet little is known about the factors that alter the microbial composition or their contribution to liver disease. We previously associated chronic alcohol consumption with lower intestinal levels of the antimicrobial-regenerating islet-derived (REG)-3 lectins. Here, we demonstrate that intestinal deficiency in REG3B or REG3G increases numbers of mucosa-associated bacteria and enhances bacterial translocation to the mesenteric lymph nodes and liver, promoting the progression of ethanol-induced fatty liver disease toward steatohepatitis. Overexpression of Reg3g in intestinal epithelial cells restricts bacterial colonization of mucosal surfaces, reduces bacterial translocation, and protects mice from alcohol-induced steatohepatitis. Thus, alcohol appears to impair control of the mucosa-associated microbiota, and subsequent breach of the mucosal barrier facilitates progression of alcoholic liver disease. PMID:26867181

  12. CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.

    PubMed

    Pauling, Josch; Röttger, Richard; Tauch, Andreas; Azevedo, Vasco; Baumbach, Jan

    2012-01-01

    Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. The latter are genetic mechanisms that control a cell's characteristics, for instance, pathogenicity as well as survival and reproduction strategies. CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. Furthermore, with release 6.0, we provide easy-to-use functions that allow the user to submit data for persistent storage with the CoryneRegNet database. Thus, it offers important options to its users in terms of community demands. CoryneRegNet is publicly available at http://www.coryneregnet.de.

  13. Sensitivity analysis of different parameterization schemes using RegCM4.3 for the Carpathian region

    NASA Astrophysics Data System (ADS)

    Pieczka, Ildikó; Pongrácz, Rita; Szabóné André, Karolina; Kelemen, Fanni Dóra; Bartholy, Judit

    2016-10-01

    In order to quantify the impact of the use of different parameterization schemes on regional climate model outputs, hindcast experiments have been completed applying the Regional Climate Model version 4.3 (RegCM4.3) for the Carpathian region and its surroundings at 10-km horizontal resolution with three different cumulus convection schemes. Besides, the sensitivity of outputs for subgrid-scale processes is also studied by activating the subgrid Biosphere-Atmosphere Transfer Scheme (BATS) model within other RegCM experiments. Among the analyzed factors, RegCM is most sensitive to the applied convection scheme. The impact of closure assumption related to the used convective parameterization is secondary, while the use of subgridding has less influence on the outputs. RegCM4.3 results show improved performance over our previous model simulations but still have larger amplitude for annual precipitation cycle than the measurement-based reference data. Our validation results for temperature and precipitation suggest that for the selected region, the overall best performance is achieved when using the mixed Grell-Emanuel scheme together with Fritsch and Chappell closure.

  14. Effects of GLC7 and REG1 deletion on maltose metabolism and leavening ability of baker's yeast in lean dough.

    PubMed

    Lin, Xue; Zhang, Cui-Ying; Bai, Xiao-Wen; Xiao, Dong-Guang

    2015-09-10

    Maltose metabolism and leavening ability of baker's yeast (Saccharomyces cerevisiae) in lean dough is negatively influenced by glucose repression. To improve maltose metabolism and leavening ability, it is necessary to alleviate glucose repression. In this study, we focus on the effects of regulators (GLC7 encoding the catalytic and REG1 encoding the regulatory subunits of protein phosphatase type 1) of glucose repression on maltose metabolism and leavening ability of baker's yeast in lean dough. To this end, GLC7 and/or REG1 deletions were constructed and characterized in terms of the growth characteristics, maltose metabolism, leavening ability, and enzyme activities. The results suggest that GLC7 and/or REG1 deletions increased maltose metabolism and leavening ability at different level with glucose derepression and increased enzymes (maltase and maltose permease) activities. In a medium containing glucose and maltose, at the point of glucose exhaustion the maltose metabolized and the leavening ability were increased 59.3% and 23.1%, respectively, in the case of a REG1 single gene deletion.

  15. Inhibition of CRISPR-Cas9 with Bacteriophage Proteins.

    PubMed

    Rauch, Benjamin J; Silvis, Melanie R; Hultquist, Judd F; Waters, Christopher S; McGregor, Michael J; Krogan, Nevan J; Bondy-Denomy, Joseph

    2017-01-12

    Bacterial CRISPR-Cas systems utilize sequence-specific RNA-guided nucleases to defend against bacteriophage infection. As a countermeasure, numerous phages are known that produce proteins to block the function of class 1 CRISPR-Cas systems. However, currently no proteins are known to inhibit the widely used class 2 CRISPR-Cas9 system. To find these inhibitors, we searched cas9-containing bacterial genomes for the co-existence of a CRISPR spacer and its target, a potential indicator for CRISPR inhibition. This analysis led to the discovery of four unique type II-A CRISPR-Cas9 inhibitor proteins encoded by Listeria monocytogenes prophages. More than half of L. monocytogenes strains with cas9 contain at least one prophage-encoded inhibitor, suggesting widespread CRISPR-Cas9 inactivation. Two of these inhibitors also blocked the widely used Streptococcus pyogenes Cas9 when assayed in Escherichia coli and human cells. These natural Cas9-specific "anti-CRISPRs" present tools that can be used to regulate the genome engineering activities of CRISPR-Cas9.

  16. Precision Targeted Mutagenesis via Cas9 Paired Nickases in Rice

    PubMed Central

    Mikami, Masafumi; Toki, Seiichi; Endo, Masaki

    2016-01-01

    Recent reports of CRISPR- (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) mediated heritable mutagenesis in plants highlight the need for accuracy of the mutagenesis directed by this system. Off-target mutations are an important issue when considering functional gene analysis, as well as the molecular breeding of crop plants with large genome size, i.e. with many duplicated genes, and where the whole-genome sequence is still lacking. In mammals, off-target mutations can be suppressed by using Cas9 paired nickases together with paired guide RNAs (gRNAs). However, the performance of Cas9 paired nickases has not yet been fully assessed in plants. Here, we analyzed on- and off-target mutation frequency in rice calli and regenerated plants using Cas9 nuclease or Cas9 nickase with paired gRNAs. When Cas9 paired nickases were used, off-target mutations were fully suppressed in rice calli and regenerated plants. However, on-target mutation frequency also decreased compared with that induced by the Cas9 paired nucleases system. Since the gRNA sequence determines specific binding of Cas9 protein–gRNA ribonucleoproteins at the targeted sequence, the on-target mutation frequency of Cas9 paired nickases depends on the design of paired gRNAs. Our results suggest that a combination of gRNAs that can induce mutations at high efficiency with Cas9 nuclease should be used together with Cas9 nickase. Furthermore, we confirmed that a combination of gRNAs containing a one nucleotide (1 nt) mismatch toward the target sequence could not induce mutations when expressed with Cas9 nickase. Our results clearly show the effectiveness of Cas9 paired nickases in delivering on-target specific mutations. PMID:26936792

  17. Annotation and Classification of CRISPR-Cas Systems.

    PubMed

    Makarova, Kira S; Koonin, Eugene V

    2015-01-01

    The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods.

  18. RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse.

    PubMed

    Liu, Zhi-Ping; Wu, Canglin; Miao, Hongyu; Wu, Hulin

    2015-01-01

    Transcriptional and post-transcriptional regulation of gene expression is of fundamental importance to numerous biological processes. Nowadays, an increasing amount of gene regulatory relationships have been documented in various databases and literature. However, to more efficiently exploit such knowledge for biomedical research and applications, it is necessary to construct a genome-wide regulatory network database to integrate the information on gene regulatory relationships that are widely scattered in many different places. Therefore, in this work, we build a knowledge-based database, named 'RegNetwork', of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among transcription factors (TFs), microRNAs (miRNAs) and target genes from 25 selected databases. Moreover, we also inferred and incorporated potential regulatory relationships based on transcription factor binding site (TFBS) motifs into RegNetwork. As a result, RegNetwork contains a comprehensive set of experimentally observed or predicted transcriptional and post-transcriptional regulatory relationships, and the database framework is flexibly designed for potential extensions to include gene regulatory networks for other organisms in the future. Based on RegNetwork, we characterized the statistical and topological properties of genome-wide regulatory networks for human and mouse, we also extracted and interpreted simple yet important network motifs that involve the interplays between TF-miRNA and their targets. In summary, RegNetwork provides an integrated resource on the prior information for gene regulatory relationships, and it enables us to further investigate context-specific transcriptional and post-transcriptional regulatory interactions based on domain-specific experimental data. Database URL: http://www.regnetworkweb.org.

  19. RegPhos 2.0: an updated resource to explore protein kinase–substrate phosphorylation networks in mammals

    PubMed Central

    Huang, Kai-Yao; Wu, Hsin-Yi; Chen, Yi-Ju; Lu, Cheng-Tsung; Su, Min-Gang; Hsieh, Yun-Chung; Tsai, Chih-Ming; Lin, Kuo-I; Huang, Hsien-Da; Lee, Tzong-Yi; Chen, Yu-Ju

    2014-01-01

    Protein phosphorylation catalyzed by kinases plays crucial roles in regulating a variety of intracellular processes. Owing to an increasing number of in vivo phosphorylation sites that have been identified by mass spectrometry (MS)-based proteomics, the RegPhos, available online at http://csb.cse.yzu.edu.tw/RegPhos2/, was developed to explore protein phosphorylation networks in human. In this update, we not only enhance the data content in human but also investigate kinase–substrate phosphorylation networks in mouse and rat. The experimentally validated phosphorylation sites as well as their catalytic kinases were extracted from public resources, and MS/MS phosphopeptides were manually curated from research articles. RegPhos 2.0 aims to provide a more comprehensive view of intracellular signaling networks by integrating the information of metabolic pathways and protein–protein interactions. A case study shows that analyzing the phosphoproteome profile of time-dependent cell activation obtained from Liquid chromatography-mass spectrometry (LC-MS/MS) analysis, the RegPhos deciphered not only the consistent scheme in B cell receptor (BCR) signaling pathway but also novel regulatory molecules that may involve in it. With an attempt to help users efficiently identify the candidate biomarkers in cancers, 30 microarray experiments, including 39 cancerous versus normal cells, were analyzed for detecting cancer-specific expressed genes coding for kinases and their substrates. Furthermore, this update features an improved web interface to facilitate convenient access to the exploration of phosphorylation networks for a group of genes/proteins. Database URL: http://csb.cse.yzu.edu.tw/RegPhos2/ PMID:24771658

  20. Pancreatic stone protein/regenerating protein (PSP/reg): a novel secreted protein up-regulated in type 2 diabetes mellitus.

    PubMed

    Yang, Jiayue; Li, Ling; Raptis, Dimitri; Li, Xiaoshan; Li, Fengfei; Chen, Bijun; He, Jiajia; Graf, Rolf; Sun, Zilin

    2015-04-01

    Type 2 diabetes mellitus (T2DM) has insulin resistance (IR) or reduced β-cell mass, partially due to an increased β-cell apoptosis rate. Pancreatic stone protein/regenerating protein (PSP/reg) is a secretory protein produced in the pancreas and up-regulated dramatically during pancreatic disease. Recent studies revealed that β-cells undergoing apoptosis induce PSP/reg expression in surviving neighboring cells. Further experiments demonstrated that PSP/reg was elevated during disease progression in type 1 diabetes mellitus (T1DM). However, the association between PSP/reg and T2DM patients is unknown. The aim of this pilot study was to investigate PSP/reg in different clinical stages of T2DM and evaluate its correlation with chronic complications of diabetes. A total of 1,121 participants (479 males, 642 females; age range 23-80 years) were enrolled in this study. PSP/reg serum values were measured by a newly developed enzyme-linked immunosorbent assay (ELISA). We analyzed its correlation with clinical and biochemical parameters in subjects with T2DM at different clinical phases. Statistical analyses were conducted using SPSS 17.0 software. Correlations of PSP/reg and clinical parameters were performed using Spearman's rank correlation coefficient. Differences between groups were determined by Nemenyi test. PSP/reg was elevated in high-risk and impaired glucose regulation (IGR) patients (p<0.05). PSP/reg was significantly up-regulated in newly diagnosed T2DM patients and long-term diabetes patients with complications (p<0.001). PSP/reg levels correlated with the duration of diabetes (p<0.001). The area under the curve (AUC) for presence of diabetes-onset and its chronic complications was 0.640 and 0.754, respectively. PSP/reg is significantly up-regulated in T2DM patients, and PSP/reg levels are related to the duration of diabetes. Therefore, PSP/reg might be useful as a predictor of T2DM and disease progression.

  1. CRISPR/Cas9-mediated gene editing in human zygotes using Cas9 protein.

    PubMed

    Tang, Lichun; Zeng, Yanting; Du, Hongzi; Gong, Mengmeng; Peng, Jin; Zhang, Buxi; Lei, Ming; Zhao, Fang; Wang, Weihua; Li, Xiaowei; Liu, Jianqiao

    2017-03-01

    Previous works using human tripronuclear zygotes suggested that the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system could be a tool in correcting disease-causing mutations. However, whether this system was applicable in normal human (dual pronuclear, 2PN) zygotes was unclear. Here we demonstrate that CRISPR/Cas9 is also effective as a gene-editing tool in human 2PN zygotes. By injection of Cas9 protein complexed with the appropriate sgRNAs and homology donors into one-cell human embryos, we demonstrated efficient homologous recombination-mediated correction of point mutations in HBB and G6PD. However, our results also reveal limitations of this correction procedure and highlight the need for further research.

  2. Development of a CRISPR-Cas9 Tool Kit for Comprehensive Engineering of Bacillus subtilis

    PubMed Central

    Westbrook, Adam W.; Moo-Young, Murray

    2016-01-01

    ABSTRACT The establishment of a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system for strain construction in Bacillus subtilis is essential for its progression toward industrial utility. Here we outline the development of a CRISPR-Cas9 tool kit for comprehensive genetic engineering in B. subtilis. In addition to site-specific mutation and gene insertion, our approach enables continuous genome editing and multiplexing and is extended to CRISPR interference (CRISPRi) for transcriptional modulation. Our tool kit employs chromosomal expression of Cas9 and chromosomal transcription of guide RNAs (gRNAs) using a gRNA transcription cassette and counterselectable gRNA delivery vectors. Our design obviates the need for multicopy plasmids, which can be unstable and impede cell viability. Efficiencies of up to 100% and 85% were obtained for single and double gene mutations, respectively. Also, a 2.9-kb hyaluronic acid (HA) biosynthetic operon was chromosomally inserted with an efficiency of 69%. Furthermore, repression of a heterologous reporter gene was achieved, demonstrating the versatility of the tool kit. The performance of our tool kit is comparable with those of systems developed for Escherichia coli and Saccharomyces cerevisiae, which rely on replicating vectors to implement CRISPR-Cas9 machinery. IMPORTANCE In this paper, as the first approach, we report implementation of the CRISPR-Cas9 system in Bacillus subtilis, which is recognized as a valuable host system for biomanufacturing. The study enables comprehensive engineering of B. subtilis strains with virtually any desired genotypes/phenotypes and biochemical properties for extensive industrial application. PMID:27260361

  3. Guide RNA functional modules direct Cas9 activity and orthogonality.

    PubMed

    Briner, Alexandra E; Donohoue, Paul D; Gomaa, Ahmed A; Selle, Kurt; Slorach, Euan M; Nye, Christopher H; Haurwitz, Rachel E; Beisel, Chase L; May, Andrew P; Barrangou, Rodolphe

    2014-10-23

    The RNA-guided Cas9 endonuclease specifically targets and cleaves DNA in a sequence-dependent manner and has been widely used for programmable genome editing. Cas9 activity is dependent on interactions with guide RNAs, and evolutionarily divergent Cas9 nucleases have been shown to work orthogonally. However, the molecular basis of selective Cas9:guide-RNA interactions is poorly understood. Here, we identify and characterize six conserved modules within native crRNA:tracrRNA duplexes and single guide RNAs (sgRNAs) that direct Cas9 endonuclease activity. We show the bulge and nexus are necessary for DNA cleavage and demonstrate that the nexus and hairpins are instrumental in defining orthogonality between systems. In contrast, the crRNA:tracrRNA complementary region can be modified or partially removed. Collectively, our results establish guide RNA features that drive DNA targeting by Cas9 and open new design and engineering avenues for CRISPR technologies.

  4. Advances in therapeutic CRISPR/Cas9 genome editing.

    PubMed

    Savić, Nataša; Schwank, Gerald

    2016-02-01

    Targeted nucleases are widely used as tools for genome editing. Two years ago the clustered regularly interspaced short palindromic repeat (CRISPR)-associated Cas9 nuclease was used for the first time, and since then has largely revolutionized the field. The tremendous success of the CRISPR/Cas9 genome editing tool is powered by the ease design principle of the guide RNA that targets Cas9 to the desired DNA locus, and by the high specificity and efficiency of CRISPR/Cas9-generated DNA breaks. Several studies recently used CRISPR/Cas9 to successfully modulate disease-causing alleles in vivo in animal models and ex vivo in somatic and induced pluripotent stem cells, raising hope for therapeutic genome editing in the clinics. In this review, we will summarize and discuss such preclinical CRISPR/Cas9 gene therapy reports.

  5. 21 CFR 184.1845 - Stannous chloride (anhydrous and dihydrated).

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... chlorine or gaseous tin tetrachloride. Dihydrated stannous chloride (SnCl2·2H2O, CAS Reg. No. 10025-69-1... granulated tin suspended in water and hydrochloric acid or chlorine. (b) Both forms of the ingredient...

  6. Characterization and Evolution of Salmonella CRISPR-Cas Systems

    DTIC Science & Technology

    2014-01-01

    SECURITY CLASSIFICATION OF: Prokaryotic CRISPR -Cas (clustered regularly interspaced short palindromic repeats and CRISPR -associated genes) systems provide...adaptive immunity from invasive genetic elements and encompass three essential features: (i) cas genes, (ii) a CRISPR array composed of spacers and...direct repeats and (iii) an AT-rich leader sequence upstream of the array. We performed in- depth sequence analysis of the CRISPR -Cas systems in .600

  7. Establishment of CRISPR/Cas9 in Alternaria alternata.

    PubMed

    Wenderoth, Maximilian; Pinecker, Christoph; Voß, Benjamin; Fischer, Reinhard

    2017-03-10

    The filamentous fungus Alternaria alternata is a potent producer of many secondary metabolites, some of which like alternariol or alternariol-methyl ether are toxic and/or cancerogenic. Many Alternaria species do not only cause post-harvest losses of food and feed, but are aggressive plant pathogens. Despite the great economic importance and the large number of research groups working with the fungus, the molecular toolbox is rather underdeveloped. Gene deletions often result in heterokaryotic strains and therefore, gene-function analyses are rather tedious. In addition, A. alternata lacks a sexual cycle and classical genetic approaches cannot be combined with molecular biological methods. Here, we show that CRISPR/Cas9 can be efficiently used for gene inactivation. Two genes of the melanin biosynthesis pathway, pksA and brm2, were chosen as targets. Several white mutants were obtained after several rounds of strain purification through protoplast regeneration or spore inoculation. Mutation of the genes was due to deletions from 1bp to 1.5kbp. The CRISPR/Cas9 system was also used to inactivate the orotidine-5-phosphate decarboxylase gene pyrG to create a uracil-auxotrophic strain. The strain was counter-selected with fluor-orotic acid and could be re-transformed with pyrG from Aspergillus fumigatus and pyr-4 from Neurospora crassa. In order to test the functioning of GFP, the fluorescent protein was fused to a nuclear localization signal derived from the StuA transcription factor of Aspergillus nidulans. After transformation bright nuclei were visible.

  8. Self-assembled DNA nanoclews for the efficient delivery of CRISPR-Cas9 for genome editing.

    PubMed

    Sun, Wujin; Ji, Wenyan; Hall, Jordan M; Hu, Quanyin; Wang, Chao; Beisel, Chase L; Gu, Zhen

    2015-10-05

    CRISPR-Cas9 represents a promising platform for genome editing, yet means for its safe and efficient delivery remain to be fully realized. A novel vehicle that simultaneously delivers the Cas9 protein and single guide RNA (sgRNA) is based on DNA nanoclews, yarn-like DNA nanoparticles that are synthesized by rolling circle amplification. The biologically inspired vehicles were efficiently loaded with Cas9/sgRNA complexes and delivered the complexes to the nuclei of human cells, thus enabling targeted gene disruption while maintaining cell viability. Editing was most efficient when the DNA nanoclew sequence and the sgRNA guide sequence were partially complementary, offering a design rule for enhancing delivery. Overall, this strategy provides a versatile method that could be adapted for delivering other DNA-binding proteins or functional nucleic acids.

  9. Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling.

    PubMed

    Zheng, Wenjun

    2017-02-01

    In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals

  10. Control of gene expression by CRISPR-Cas systems.

    PubMed

    Bikard, David; Marraffini, Luciano A

    2013-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) loci and their associated cas (CRISPR-associated) genes provide adaptive immunity against viruses (phages) and other mobile genetic elements in bacteria and archaea. While most of the early work has largely been dominated by examples of CRISPR-Cas systems directing the cleavage of phage or plasmid DNA, recent studies have revealed a more complex landscape where CRISPR-Cas loci might be involved in gene regulation. In this review, we summarize the role of these loci in the regulation of gene expression as well as the recent development of synthetic gene regulation using engineered CRISPR-Cas systems.

  11. Ectopia cordis thoracique sporadique: description clinique d'un cas

    PubMed Central

    Lubala, Toni Kasole; Mutombo, Augustin Mulangu; Katamea, Tina; Lubala, Nina; Munkana, Arthur Ndundula; Kabuya, Maguy Sangaji; Monga, Joséphine Kalenga; Luboya, Oscar Numbi

    2012-01-01

    Nous décrivons un cas d'ectopia cordis, une malformation cardiaque congénitale extrêmement rare dans laquelle le coeur est partiellement ou complètement situé en dehors des limites de la cage thoracique. Dans le cas que nous décrivons, elle est thoracique et isolée. Ce cas a été diagnostiqué en salle de naissance au Katanga, au sud de la République Démocratique du Congo. Il s'agit du premier cas documenté chez un nouveau-né Congolais. PMID:23346276

  12. CRISPR-Cas9-guided Genome Engineering in C. elegans

    PubMed Central

    Kim, Hyun-Min; Colaiácovo, Monica P.

    2016-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system is successfully being used for efficient and targeted genome editing in various organisms including the nematode C. elegans. Recent studies developed various CRISPR-Cas9 approaches to enhance genome engineering via two major DNA double-strand break repair pathways: non-homologous end joining and homologous recombination. Here we describe a protocol for Cas9-mediated C. elegans genome editing together with single guide RNA (sgRNA) and repair template cloning and injection methods required for delivering Cas9, sgRNAs and repair template DNA into the C. elegans germline. PMID:27366893

  13. Calibrated Ancillary System (CAS) user's guide, volume 1

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Calibrated Ancillary System (CAS) provides real-time calibrated parameters from the orbiter downlink (ancillary data) to the Goddard Space Flight Center (GSFC). This user's guide contains the introduction to the equipment, operation, general procedures, and specific procedures of the CAS. Volume 1 includes a general overview of the CAS relationships with other equipment, physical design, and hardware and software subsystems. In addition, a description of the user levels and tasks, an introduction to CAS operation, and an outline of general operating procedures are included.

  14. Foreign DNA capture during CRISPR–Cas adaptive immunity

    PubMed Central

    Nuñez, James K.; Harrington, Lucas B.; Kranzusch, Philip J.; Engelman, Alan N.; Doudna, Jennifer A.

    2015-01-01

    Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign DNA of specific 30–40 base pair (bp) lengths into clustered regularly interspaced short palindromic repeats (CRISPR) loci as spacer segments1–6. The universally conserved Cas1–Cas2 integrase complex catalyzes spacer acquisition using a direct nucleophilic integration mechanism similar to retroviral integrases and transposases7–13. How the Cas1–Cas2 complex selects foreign DNA substrates for integration remains unknown. Here we present X-ray crystal structures of the Escherichia coli Cas1–Cas2 complex bound to cognate 33 nucleotide (nt) protospacer DNA substrates. The protein complex creates a curved binding surface spanning the length of the DNA and splays the ends of the protospacer to allow each terminal nucleophilic 3′–OH to enter a channel leading into the Cas1 active sites. Phosphodiester backbone interactions between the protospacer and the proteins explain the sequence-nonspecific substrate selection observed in vivo2–4. Our results uncover the structural basis for foreign DNA capture and the mechanism by which Cas1–Cas2 functions as a molecular ruler to dictate the sequence architecture of CRISPR loci. PMID:26503043

  15. Foreign DNA capture during CRISPR-Cas adaptive immunity.

    PubMed

    Nuñez, James K; Harrington, Lucas B; Kranzusch, Philip J; Engelman, Alan N; Doudna, Jennifer A

    2015-11-26

    Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign DNA of specific 30-40-base-pair lengths into clustered regularly interspaced short palindromic repeat (CRISPR) loci as spacer segments. The universally conserved Cas1-Cas2 integrase complex catalyses spacer acquisition using a direct nucleophilic integration mechanism similar to retroviral integrases and transposases. How the Cas1-Cas2 complex selects foreign DNA substrates for integration remains unknown. Here we present X-ray crystal structures of the Escherichia coli Cas1-Cas2 complex bound to cognate 33-nucleotide protospacer DNA substrates. The protein complex creates a curved binding surface spanning the length of the DNA and splays the ends of the protospacer to allow each terminal nucleophilic 3'-OH to enter a channel leading into the Cas1 active sites. Phosphodiester backbone interactions between the protospacer and the proteins explain the sequence-nonspecific substrate selection observed in vivo. Our results uncover the structural basis for foreign DNA capture and the mechanism by which Cas1-Cas2 functions as a molecular ruler to dictate the sequence architecture of CRISPR loci.

  16. Validation of newly designed regional earth system model (RegESM) for Mediterranean Basin

    NASA Astrophysics Data System (ADS)

    Turuncoglu, Ufuk Utku; Sannino, Gianmaria

    2016-06-01

    We present a validation analysis of a regional earth system model system (RegESM) for the Mediterranean Basin. The used configuration of the modeling system includes two active components: a regional climate model (RegCM4) and an ocean modeling system (ROMS). To assess the performance of the coupled modeling system in representing the climate of the basin, the results of the coupled simulation (C50E) are compared to the results obtained by a standalone atmospheric simulation (R50E) as well as several observation datasets. Although there is persistent cold bias in fall and winter, which is also seen in previous studies, the model reproduces the inter-annual variability and the seasonal cycles of sea surface temperature (SST) in a general good agreement with the available observations. The analysis of the near-surface wind distribution and the main circulation of the sea indicates that the coupled model can reproduce the main characteristics of the Mediterranean Sea surface and intermediate layer circulation as well as the seasonal variability of wind speed and direction when it is compared with the available observational datasets. The results also reveal that the simulated near-surface wind speed and direction have poor performance in the Gulf of Lion and surrounding regions that also affects the large positive SST bias in the region due to the insufficient horizontal resolution of the atmospheric component of the coupled modeling system. The simulated seasonal climatologies of the surface heat flux components are also consistent with the CORE.2 and NOCS datasets along with the overestimation in net long-wave radiation and latent heat flux (or evaporation, E), although a large observational uncertainty is found in these variables. Also, the coupled model tends to improve the latent heat flux by providing a better representation of the air-sea interaction as well as total heat flux budget over the sea. Both models are also able to reproduce the temporal evolution of

  17. CCISS, Vascular and BP Reg: Canadian space life science research on ISS

    NASA Astrophysics Data System (ADS)

    Hughson, Richard L.; Shoemaker, J. Kevin; Arbeille, Philippe

    2014-11-01

    A comprehensive goal of the Canadian Space Agency studies (CCISS, Vascular and BP Reg) has been to investigate the efficacy of current exercise countermeasures to maintain cardiovascular and cerebrovascular health on return to Earth after up to 6-months in space. Results from the CCISS experiments revealed no significant change of in-flight heart rate during daily activities or sleep, and small, but variable between astronauts, post-flight elevation. The between astronaut differences were exaggerated during measurement of spontaneous baroreflex slope, which was reduced post-flight (P<0.05) during paced breathing with 3 astronauts having significant correlations between reduced baroreflex and reduced RR-interval (consistent with reduced fitness). Cerebrovascular autoregulation and CO2 response were mildly impaired after flight. Some loss of in-flight fitness of astronauts in Vascular was reflected by the increase in HR at a work rate of 161±46 W of 12.3±10.5 bpm, 10.4±5.9 bpm and 13.4±5.7 bpm for early-flight, late-flight and R+1, respectively. On return to gravity, changes in resting heart rate for supine (5.9±3.5 bpm), sit (8.1±3.3 bpm) and stand (10.3±10.0 bpm) were small but variable between individuals (from -5 bpm to +20 bpm in post-flight standing) and not related to the change in exercise heart rate. In Vascular astronauts, pulse wave transit time measured to the finger tended to be reduced post-flight and carotid artery distensibility was significantly reduced (P=0.03, and n=6). The heart rate and baroreflex data suggest that some astronauts return with cardiovascular deconditioning in spite of the exercise regimes. However, greater arterial stiffness is common among all astronauts studied to date. The new CSA project, BP Reg, will monitor inflight blood pressure in an attempt to identify astronauts in greater need for countermeasures. Future research should focus on whether Vascular changes in astronauts might make them an appropriate model to study

  18. Impact of dust size parameterizations on aerosol burden and radiative forcing in RegCM4

    NASA Astrophysics Data System (ADS)

    Tsikerdekis, Athanasios; Zanis, Prodromos; Steiner, Allison L.; Solmon, Fabien; Amiridis, Vassilis; Marinou, Eleni; Katragkou, Eleni; Karacostas, Theodoros; Foret, Gilles

    2017-01-01

    We investigate the sensitivity of aerosol representation in the regional climate model RegCM4 for two dust parameterizations for the period 2007-2014 over the Sahara and the Mediterranean. We apply two discretization methods of the dust size distribution keeping the total mass constant: (1) the default RegCM4 4-bin approach, where the size range of each bin is calculated using an equal, logarithmic separation of the total size range of dust, using the diameter of dust particles, and (2) a newly implemented 12-bin approach with each bin defined according to an isogradient method where the size ranges are dependent on the dry deposition velocity of dust particles. Increasing the number of transported dust size bins theoretically improves the representation of the physical properties of dust particles within the same size bin. Thus, more size bins improve the simulation of atmospheric processes. The radiative effects of dust over the area are discussed and evaluated with the CALIPSO dust optical depth (DOD). This study is among the first studies evaluating the vertical profile of simulated dust with a pure dust product. Reanalysis winds from ERA-Interim and the total precipitation flux from the Climate Research Unit (CRU) observational gridded database are used to evaluate and explain the discrepancies between model and observations. The new dust binning approach increases the dust column burden by 4 and 3 % for fine and coarse particles, respectively, which increases DOD by 10 % over the desert and the Mediterranean. Consequently, negative shortwave radiative forcing (RF) is enhanced by more than 10 % at the top of the atmosphere and by 1 to 5 % on the surface. Positive longwave RF locally increases by more than 0.1 W m-2 in a large portion of the Sahara, the northern part of the Arabian Peninsula and the Middle East. The four-bin isolog method is to some extent numerically efficient, nevertheless our work highlights that the simplified representation of the four

  19. 2-Ethylhexanoic Acid; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final test rule, under section 4 of the Toxic Substances Control Act (TSCA), requiring manufacturers and processors of 2-ethylhexanoic acid (EHA, CAS No. 149-57-5) to conduct testing.

  20. Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system.

    PubMed

    Arslan, Zihni; Hermanns, Veronica; Wurm, Reinhild; Wagner, Rolf; Pul, Ümit

    2014-07-01

    The adaptation against foreign nucleic acids by the CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) depends on the insertion of foreign nucleic acid-derived sequences into the CRISPR array as novel spacers by still unknown mechanism. We identified and characterized in Escherichia coli intermediate states of spacer integration and mapped the integration site at the chromosomal CRISPR array in vivo. The results show that the insertion of new spacers occurs by site-specific nicking at both strands of the leader proximal repeat in a staggered way and is accompanied by joining of the resulting 5'-ends of the repeat strands with the 3'-ends of the incoming spacer. This concerted cleavage-ligation reaction depends on the metal-binding center of Cas1 protein and requires the presence of Cas2. By acquisition assays using plasmid-located CRISPR array with mutated repeat sequences, we demonstrate that the primary sequence of the first repeat is crucial for cleavage of the CRISPR array and the ligation of new spacer DNA.

  1. Tenth anniversary of CAS ONLINE service : What CAS services should be in the new era of chemical information

    NASA Astrophysics Data System (ADS)

    Kostakos, Charles N.

    Chemical Abstracts Service celebrated 10th anniversary of CAS online information service in 1990. A speech given on the occasion reviewed history of the CAS ONLINE, in relation to its most important benefits for scientists and engineers. The development of STN international, the network through which CAS ONLINE is accessible around the world, was also discussed in the speech. The CAS ONLINE now contains a wide variety of files relating to chemical field including CA file, Registry file. CA previews,. CASREACT, CIN. MARPAT, etc for supplying chemical information worldwide.

  2. Springing into Action: Reg2 Negatively Regulates Snf1 Protein Kinase and Facilitates Recovery from Prolonged Glucose Starvation in Saccharomyces cerevisiae

    PubMed Central

    Maziarz, Marcin; Shevade, Aishwarya; Barrett, LaKisha

    2016-01-01

    ABSTRACT Glucose is the preferred carbon source for the yeast Saccharomyces cerevisiae. Glucose limitation activates Snf1 protein kinase, a key regulator of energy homeostasis that promotes utilization of alternative carbon sources and enforces energy conservation. Snf1 activation requires phosphorylation of its T-loop threonine (Thr210) by upstream kinases. When glucose is abundant, Snf1 is inhibited by Thr210 dephosphorylation. This involves the function of the type 1 protein phosphatase Glc7, which is targeted to Snf1 by a regulatory subunit, Reg1. The reg1 mutation causes increased Snf1 activity and mimics various aspects of glucose limitation, including slower growth. Reg2 is another Glc7 regulatory subunit encoded by a paralogous gene, REG2. Previous evidence indicated that the reg2 mutation exacerbates the Snf1-dependent slow-growth phenotype caused by reg1, suggesting a link between Reg2 and Snf1. Here, we explore this link in more detail and present evidence that Reg2 contributes to Snf1 Thr210 dephosphorylation. Consistent with this role, Reg2 interacts with wild-type Snf1 but not with nonphosphorylatable Snf1-T210A. Reg2 accumulation increases in a Snf1-dependent manner during prolonged glucose deprivation, and glucose-starved cells lacking Reg2 exhibit delayed Snf1 Thr210 dephosphorylation and slower growth recovery upon glucose replenishment. Accordingly, cells lacking Reg2 are outcompeted by wild-type cells in the course of several glucose starvation/replenishment cycles. Collectively, our results support a model in which Reg2-Glc7 contributes to the negative control of Snf1 in response to glucose refeeding after prolonged starvation. The competitive growth advantage provided by Reg2 underscores the evolutionary significance of this paralog for S. cerevisiae. IMPORTANCE The ability of microorganisms to respond to stress is essential for their survival. However, rapid recovery from stress could be equally crucial in competitive environments. Therefore

  3. Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli.

    PubMed

    Almendros, Cristóbal; Guzmán, Noemí M; Díez-Villaseñor, César; García-Martínez, Jesús; Mojica, Francisco J M

    2012-01-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (cas) genes conform the CRISPR-Cas systems of various bacteria and archaea and produce degradation of invading nucleic acids containing sequences (protospacers) that are complementary to repeat intervening spacers. It has been demonstrated that the base sequence identity of a protospacer with the cognate spacer and the presence of a protospacer adjacent motif (PAM) influence CRISPR-mediated interference efficiency. By using an original transformation assay with plasmids targeted by a resident spacer here we show that natural CRISPR-mediated immunity against invading DNA occurs in wild type Escherichia coli. Unexpectedly, the strongest activity is observed with protospacer adjoining nucleotides (interference motifs) that differ from the PAM both in sequence and location. Hence, our results document for the first time native CRISPR activity in E. coli and demonstrate that positions next to the PAM in invading DNA influence their recognition and degradation by these prokaryotic immune systems.

  4. Investigation of Flash Fill{reg_sign} as a thermal backfill material

    SciTech Connect

    Ayers, P.H.; Charlton, C.B.; Frishette, C.W.

    1995-09-01

    Flash Fill{reg_sign} was created as a fast-setting, flowable backfill material made entirely from coal combustion by-products and water. Its quick-setting, self-leveling, self-compacting characteristics makes trench road repairs faster, easier, and more economical. Other uses include building foundations, fill around pipes, gas lines, and manholes, and replacement of weak subgrade beneath rooters. Flash Fill can be hand-excavated without the use of power assisted tools or machinery. To enhance thermal resistivity, the original Flash Fill mix was modified to include concrete sand. This resulted in a new Flash Fill, designated FSAND, with all of the aforementioned desirable characteristics of Flash Fill and a thermal resistivity of approximately 50{degree} C-cm/watt. Thermal resistivity tests using conventional laboratory thermal probes, high-current thermal tests, and moisture migration tests have been performed to determine the properties of FSAND. As a result of these tests, FSAND has been approved for use as power cable thermal backfill on all AEP System distribution projects.

  5. Exposing the impact of opp(reg)ressive policies on teacher development and on student learning

    NASA Astrophysics Data System (ADS)

    Rodriguez, Alberto J.

    2010-12-01

    This case study draws attention to Pedro's story, a Grade 6 Latino teacher who, along with other grade 4-6 teachers, participated in a three-year professional development research project. By using data analyzed from multiple ethnographic interviews with teachers and students, and by drawing from the quantitative analyzes of concept map unit tests, we illustrate how Pedro's significant professional growth and his students' learning were truncated by top-down school district policies. These policies were implemented because of the punitive nature of the No Child Left Behind Act. Simply put, this case study exposes the impact of opp(reg)ressive policies on learning, that is, policies simultaneously oppressive and regressive. The critical perspective of the project, and its emphasis on assisting teachers to make their pedagogy and curriculum more culturally and socially relevant, was informed by sociotransformative constructivism (sTc). This is a theoretical framework that affords equal importance to cross-cultural education (learning about and acting on socially/culturally relevant issues) and social constructivism (learning to critically produce and consume knowledge). We hope that this case study will provide additional insights into the slow progress we continue to make in science teacher professional development and in closing the achievement gap.

  6. Predicting relative toxicity and interactions of divalent metal ions: Microtox{reg_sign} bioluminescence assay

    SciTech Connect

    Newman, M.C.; McCloskey, J.T.

    1996-03-01

    Both relative toxicity and interactions between paired metal ions were predicted with least-squares linear regression and various ion characteristics. Microtox{reg_sign} 15 min EC50s (expressed as free ion) for Ca(II), Cd(II), Cu(II), Hg(II), Mg(II), Mn(II), Ni(II), Pb(II), and Zn(II) were most effectively modeled with the constant for the first hydrolysis (K{sub H} for M{sup n+} + H{sub 2}O {yields} MOH{sup a{minus}1} + H{sup +}) although other ion characteristics were also significant in regression models. The {vert_bar}log K{sub H}{vert_bar} is correlated with metal ion affinity to intermediate ligands such as many biochemical functional groups with O donor atoms. Further, ordination of metals according to ion characteristics, e.g., {vert_bar}log K{sub H}{vert_bar} facilitated prediction of paired metal interactions. Pairing metals with strong tendencies to complex with intermediate or soft ligands such as those with O or S donor atoms resulted in strong interactions.

  7. Performance of RegCM4 over major river basins in China

    NASA Astrophysics Data System (ADS)

    Gao, Xuejie; Shi, Ying; Han, Zhenyu; Wang, Meili; Wu, Jia; Zhang, Dongfeng; Xu, Ying; Giorgi, Filippo

    2017-04-01

    A long-term simulation for the period 1990-2010 is conducted with the latest version of the International Centre for Theoretical Physics' Regional Climate Model (RegCM4), driven by ERA-Interim boundary conditions at a grid spacing of 25 km. The Community Land Model (CLM) is used to describe land surface processes, with updates in the surface parameters, including the land cover and surface emissivity. The simulation is compared against observations to evaluate the model performance in reproducing the present day climatology and interannual variability over the 10 main river basins in China, with focus on surface air temperature and precipitation. Temperature and precipitation from the ERA-Interim reanalysis are also considered in the model assessment. Results show that the model reproduces the present day climatology over China and its main river basins, with better performances in June-July-August compared to December-January-February (DJF). In DJF, we find a warm bias at high latitudes, underestimated precipitation in the south, and overestimated precipitation in the north. The model in general captures the observed interannual variability, with greater skill for temperature. We also find an underestimation of heavy precipitation events in eastern China, and an underestimation of consecutive dry days in northern China and the Tibetan Plateau. Similar biases for both mean climatology and extremes are found in the ERA-Interim reanalysis, indicating the difficulties for climate models in simulating extreme monsoon climate events over East Asia.

  8. Dust size parameterization in RegCM4: Impact on aerosol burden and radiative forcing

    NASA Astrophysics Data System (ADS)

    Tsikerdekis, A.; Zanis, P.; Steiner, A. L.; Solmon, F.; Amiridis, V.; Marinou, E.; Katragkou, E.; Karacostas, T.; Foret, G.

    2015-12-01

    We investigate the sensitivity of two dust parameterizations of the regional climate model RegCM4, for the period 2008-2012, over a large domain focused on the Sahara and the Mediterranean. We implement two size bin distributions: 1) a 4-bin approach, where each bin is delimited using an isolog approach and every size group has equal ranges in logarithmic scale according to the diameter of the dust particles, and 2) a 12-bin approach with each bin defined according to an isogradient method, where the size ranges are dependent on the dry deposition velocity of dust particles. Increasing the number of the transported dust size bin improves the representation of the physical properties of dust particles that belong on the same group. Thus, more size bins minimize the error and improve the simulation of atmospheric processes. The emission, deposition and transport of dust are evaluated combined for each experiment to determine the impact of dust size bin partition. The radiative effects of dust over the area are also discussed and evaluated with the CALIPSO Aerosol Optical Depth (AOD) pure dust product. Techniques for the discrimination of the dust component from other aerosol types have been recently developed in the framework of the LIVAS (LIdar climatology of Vertical Aerosol Structure for space-based lidar simulation studies- http://lidar.space.noa.gr:8080/livas/).

  9. 21 CFR 573.210 - Benzoic acid.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 6 2014-04-01 2014-04-01 false Benzoic acid. 573.210 Section 573.210 Food and... Listing § 573.210 Benzoic acid. The food additive, benzoic acid, may be safely used in the manufacture of... acid (CAS 65-85-0) by weight with the sum of 2-methylbiphenyl, 3-methylbiphenyl,...

  10. Cas9 Variants Expand the Target Repertoire in Caenorhabditis elegans.

    PubMed

    Bell, Ryan T; Fu, Becky X H; Fire, Andrew Z

    2016-02-01

    The proliferation of CRISPR/Cas9-based methods in Caenorhabditis elegans has enabled efficient genome editing and precise genomic tethering of Cas9 fusion proteins. Experimental designs using CRISPR/Cas9 are currently limited by the need for a protospacer adjacent motif (PAM) in the target with the sequence NGG. Here we report the characterization of two modified Cas9 proteins in C. elegans that recognize NGA and NGCG PAMs. We found that each variant could stimulate homologous recombination with a donor template at multiple loci and that PAM specificity was comparable to that of wild-type Cas9. To directly compare effectiveness, we used CRISPR/Cas9 genome editing to generate a set of assay strains with a common single-guide RNA (sgRNA) target sequence, but that differ in the juxtaposed PAM (NGG, NGA, or NGCG). In this controlled setting, we determined that the NGA PAM Cas9 variant can be as effective as wild-type Cas9. We similarly edited a genomic target to study the influence of the base following the NGA PAM. Using four strains with four NGAN PAMs differing only at the fourth position and adjacent to the same sgRNA target, we observed that efficient homologous replacement was attainable with any base in the fourth position, with an NGAG PAM being the most effective. In addition to demonstrating the utility of two Cas9 mutants in C. elegans and providing reagents that permit CRISPR/Cas9 experiments with fewer restrictions on potential targets, we established a means to benchmark the efficiency of different Cas9::PAM combinations that avoids variations owing to differences in the sgRNA sequence.

  11. New CRISPR-Cas systems from uncultivated microbes.

    PubMed

    Burstein, David; Harrington, Lucas B; Strutt, Steven C; Probst, Alexander J; Anantharaman, Karthik; Thomas, Brian C; Doudna, Jennifer A; Banfield, Jillian F

    2017-02-09

    CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

  12. New CRISPR–Cas systems from uncultivated microbes

    NASA Astrophysics Data System (ADS)

    Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

    2016-12-01

    CRISPR–Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR–Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR–Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR–Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR–Cas system. In bacteria, we discovered two previously unknown systems, CRISPR–CasX and CRISPR–CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

  13. Recent Advances in Genome Editing Using CRISPR/Cas9

    PubMed Central

    Ding, Yuduan; Li, Hong; Chen, Ling-Ling; Xie, Kabin

    2016-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is a versatile tool for genome engineering that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This simple RNA-guided genome-editing technology has become a revolutionary tool in biology and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing method, summarize the recent advances in CRISPR/Cas9 technology, and discuss their implications for plant research. To date, targeted gene knockout using the Cas9/gRNA system has been established in many plant species, and the targeting efficiency and capacity of Cas9 has been improved by optimizing its expression and that of its gRNA. The CRISPR/Cas9 system can also be used for sequence-specific mutagenesis/integration and transcriptional control of target genes. We also discuss off-target effects and the constraint that the protospacer-adjacent motif (PAM) puts on CRISPR/Cas9 genome engineering. To address these problems, a number of bioinformatic tools are available to help design specific gRNAs, and new Cas9 variants and orthologs with high fidelity and alternative PAM specificities have been engineered. Owing to these recent efforts, the CRISPR/Cas9 system is becoming a revolutionary and flexible tool for genome engineering. Adoption of the CRISPR/Cas9 technology in plant research would enable the investigation of plant biology at an unprecedented depth and create innovative applications in precise crop breeding. PMID:27252719

  14. Closing the knowledge gap on cardiovascular disease in type 2 diabetes: the EMPA-REG OUTCOME trial and beyond

    PubMed Central

    Oral, Elif A

    2016-01-01

    Type 2 diabetes mellitus (T2DM) is associated with marked cardiovascular (CV) morbidity and mortality, including heart failure (HF). Until recently, an oral glucose-lowering agent that improved hyperglycemia as well as provided CV benefits in patients with T2DM and cardiovascular disease (CVD) was lacking. The newest class of glucose-lowering agents, sodium glucose cotransporter 2 (SGLT2) inhibitors, includes canagliflozin, dapagliflozin, and empagliflozin. Prior to the release of the LEADER trial results, the recent EMPA-REG OUTCOME study was the only dedicated CV trial to demonstrate a reduction in major adverse cardiac events, CV mortality, and all-cause mortality and a reduction in hospitalization for HF with empagliflozin, given on top of standard-of-care therapy in patients with T2DM and CVD. This paper summarizes the results from EMPA-REG OUTCOME and discusses their significance and clinical implications. PMID:27648101

  15. Innovative remote monitoring of plant health for environmental applications: A joint effort between EPCOT{reg_sign} and the DOE

    SciTech Connect

    Robitaille, H.; Capelle, G.; Di Benedetto, J.

    1996-12-31

    In September of 1994, the US Department of Energy (DOE), Environmental Management, Office of Science and Technology for (OST) and Epcot{reg_sign} in the WALT DISNEY WORLD{reg_sign} Resort (Epcot) signed an agreement to cooperate on the research, development, and public communication and display of environmental technologies. Although Epcot and OST have distinctive missions, certain areas of their respective research and development efforts are common, including the integration of remote sensors with robotics platforms, airborne surveys for environmental characterization and monitoring, and ground based measurements of vegetation stress. The first area of cooperative R&D pursued under the agreement is the evaluation of laser-induced fluorescence imaging (LIFI), a technology developed by OST and proven effective for uranium detection. This paper describes the efforts being conducted under the Epcot-OST agreement and presents initial results. An appendix describing LIFI technology is also included.

  16. Removal of contaminants from equipment and debris and waste minimization using TechXtract{reg_sign} technology

    SciTech Connect

    Bonem, M.W.

    1997-10-01

    Under this Program Research and Development Agreement (PRDA), EET, Inc., is extending its proprietary TechXtract{reg_sign} chemical decontamination technology into an effective, economical, integrated contaminant removal system. This integrated system will consist of a series of decontamination baths using the TechXtract{reg_sign} chemical formulas, followed by a waste treatment process that will remove the contaminants from the spent chemicals. Sufficient decontamination will result so that materials can be released without restriction after they have been treated, even those materials that have traditionally been considered to be {open_quotes}undecontaminable.{close_quotes} The secondary liquid waste will then be treated to separate any hazardous and radioactive contaminants, so that the spent chemicals and wastewater can be discharged through conventional, permitted outlets. The TechXtract{reg_sign} technology is a unique process that chemically extracts hazardous contaminants from the surface and substrate of concrete, steel, and other solid materials. This technology has been used successfully to remove contaminants as varied as PCBs, radionuclides, heavy metals, and hazardous organics. The process` advantage over other alternatives is its effectiveness in safe and consistent extraction of subsurface contamination. TechXtract{reg_sign} is a proprietary process developed, owned, and provided by EET, Inc. The objective of the PRDA is to demonstrate on a full-scale basis an economical system for decontaminating equipment and debris, with further treatment of secondary waste streams to minimize waste volumes. Contaminants will be removed from the contaminated items to levels where they can be released for unrestricted use. The entire system will be designed with maximum flexibility and automation in mind.

  17. Topical safety analysis report for the transportation of the NUHOMS{reg_sign} dry shielded canister. Volume 1

    SciTech Connect

    1993-08-01

    This Topical Safety Analysis Report (SAR) describes the design and the generic transportation licensing basis for utilizing the NUTECH HORIZONTAL MODULAR STORAGE (NUHOMS{reg_sign}) system dry shielded canister (DSC) containing twenty-four pressurized water reactor (PWR) spent fuel assemblies (SFA) in conjunction with a conceptually designed Transportation Cask. This SAR documents the design qualification of the NUHOMS{reg_sign} DSC as an integral part of a 10CFR71 Fissile Material Class III, Type B(M) Transportation Package. The package consists of the canister and a conceptual transportation cask (NUHOMS{reg_sign} Transportation Cask) with impact limiters. Engineering analysis is performed for the canister to confirm that the existing canister design complies with 10CFR71 transportation requirements. Evaluations and/or analyses is performed for criticality safety, shielding, structural, and thermal performance. Detailed engineering analysis for the transportation cask will be submitted in a future SAR requesting 10CFR71 certification of the complete waste package. Transportation operational considerations describe various operational aspects of the canister/transportation cask system. operational sequences are developed for canister transfer from storage to the transportation cask and interfaces with the cask auxiliary equipment for on- and off-site transport.

  18. Implementation and evaluation of online gas-phase chemistry within a regional climate model (RegCM-CHEM4)

    SciTech Connect

    Shalaby, A. K.; Zakey, A. S.; Tawfik, A. B.; Solmon, F.; Giorgi, Filippo; Stordal, F.; Sillman, S.; Zaveri, Rahul A.; Steiner, A. L.

    2012-05-22

    The RegCM-CHEM4 is a new online climate-chemistry model based on the International Centre for Theoretical Physics (ICTP) regional climate model (RegCM4). Tropospheric gas-phase chemistry is integrated into the climate model using the condensed version of the Carbon Bond Mechanism (CBM-Z; Zaveri and Peters, 1999) with a fast solver based on radical balances. We evaluate the model over Continental Europe for two different time scales: (1) an event-based analysis of the ozone episode associated with the heat wave of August 2003 and (2) a climatological analysis of a sixyear simulation (2000-2005). For the episode analysis, model simulations show good agreement with European Monitoring and Evaluation Program (EMEP) observations of hourly ozone over different regions in Europe and capture ozone concentrations during and after the August 2003 heat wave event. For long-term climate simulations, the model captures the seasonal cycle of ozone concentrations with some over prediction of ozone concentrations in non-heat wave summers. Overall, the ozone and ozone precursor evaluation shows the feasibility of using RegCM-CHEM4 for decadal-length simulations of chemistry-climate interactions.

  19. Use of RegCM gridded dataset for thunderstorm favorable conditions analysis over Poland—climatological approach

    NASA Astrophysics Data System (ADS)

    Walawender, Ewelina; Kielar, Rafał; Ustrnul, Zbigniew

    2017-01-01

    The paper analyzes equivalent data for a low density meteorological station network (spatially discontinuous data) and poor temporal homogeneity of thunderstorm observational data. Due to that, a Regional Climate Model (RegCM) dataset was tested. The Most Unstable Convective Available Potential Energy index value (MUCAPE) above the 200 J kg-1 threshold was selected as a predictor describing favorable conditions for the occurrence of thunderstorms. The quality of the dataset was examined through a comparison between model results and soundings from several aerological stations in Central Europe. Good, statistically significant (0.05 significance level) results were obtained through correlation analysis; the value of Pearson's correlation coefficient was above 0.8 in every single case. Then, using methods associated with gridded climatology, data series for 44 weather stations were derived and an analysis of correlation between RegCM modeled data and in situ thunderstorm observations was conducted with coefficients in the range of 0.75-0.90. The possibility of employing the dataset in thunderstorm climatology analysis was checked via a few examples by mapping monthly, seasonal, and annual means. Moreover, long-term variability and trend analysis along with modeled MUCAPE data were tested. As a result, the RegCM modeled MUCAPE gridded dataset was proposed as an easily available, suitable, and valuable predictor for thunderstorm climatology analysis and mapping. Finally, some limitations are discussed and recommendations for further improvements are given.

  20. Sensitivity of simulated extreme precipitation and temperature to convective parameterization using RegCM3 in China

    NASA Astrophysics Data System (ADS)

    Hui, Pinhong; Tang, Jianping; Wang, Shuyu; Wu, Jian

    2015-10-01

    In this study, the regional climate model of RegCM3 is applied to investigate the sensitivity of regional climate over China using four cumulus parameterizations, the modified Anthes-Kuo (AK), the Grell with Arakawa-Schubert closure, the Grell with Fritsch-Chappell closure, and the MIT-Emanuel (EM). The model was integrated over the period of 1982 to 2001 using the NCEP Reanalysis data NNRP2 as boundary conditions. RegCM3 coupled with various cumulus parameterizations is evaluated firstly as for its ability to represent regional climatology and climate extreme indices, and the results show that simulated regional climate in China is sensitive to the option of cumulus parameterizations. All the cumulus schemes produce a northward expansion of heavy rain area and an underestimation of surface air temperature. For precipitation, the AK scheme simulates relatively better magnitude, while the EM scheme has more reliable performance on the spatial distribution. RegCM3 can represent the spatial distributions of extreme indices for both precipitation and temperature, as well as their decadal trends irrelevant to the cumulus parameterizations. However, the model underestimates the consecutive dry days and overestimates the three extreme wet indices, with the EM scheme giving the worst result. Slight underestimations of extreme temperature indices are detected in all cumulus parameterization scheme runs. The shapes of probability distribution functions for extreme indices are correctly produced, though the probabilities of extreme dry and warm events are underestimated.

  1. Expanding the CRISPR Toolbox: Targeting RNA with Cas13b.

    PubMed

    Barrangou, Rodolphe; Gersbach, Charles A

    2017-02-16

    In this issue of Molecular Cell, Smargon et al. (2017) unearth Cas13b from type VI-B CRISPR-Cas immune systems and characterize its RNA-guided, RNA-targeting activity, including regulation by the novel co-factors Csx27 and Csx28, as well as non-specific collateral RNA damage.

  2. Using CAS to Solve a Mathematics Task: A Deconstruction

    ERIC Educational Resources Information Center

    Berger, Margot

    2010-01-01

    I investigate how and whether a heterogeneous group of first-year university mathematics students in South Africa harness the potential power of a computer algebra system (CAS) when doing a specific mathematics task. In order to do this, I develop a framework for deconstructing a mathematics task requiring the use of CAS, into its primary…

  3. Calibrated Ancillary System (CAS) user's guide, volume 2

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Calibrated Ancillary System (CAS) provides real-time calibrated parameters from the orbiter downlink (ancillary data) to the Goddard Space Flight Center (GSFC). This user's guide contains the introduction to the equipment, operation, general procedures, and specific procedures of CAS. Volume 2 describes the central status and control (CSAC) procedures, supervisor procedures, and logging procedures.

  4. Calibrated Ancillary System (CAS) user's guide, volume 3

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Calibrated Ancillary System (CAS) provides real-time calibrated parameters from the orbiter downlink (ancillary data) to the Goddard Space Flight Center (GSFC). This user's guide contains the introduction to the equipment, operation, general procedures, and specific procedures of the CAS. Volume 3 describes logging and delogging procedures, real-time procedures, and error messages.

  5. Calibrated Ancillary System (CAS) user's guide, volume 8

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Calibrated Ancillary System (CAS) provides real-time calibrated parameters from the orbiter downlink (ancillary data) to the Goddard Space Flight Center (GSFC). This user's guide contains the introduction to the equipment, operation, general procedures, and specific procedures of CAS. Volume 8 describes procedures for invoking checkout software, file maintenance procedures, system manager procedures.

  6. Transformation of OODT CAS to Perform Larger Tasks

    NASA Technical Reports Server (NTRS)

    Mattmann, Chris; Freeborn, Dana; Crichton, Daniel; Hughes, John; Ramirez, Paul; Hardman, Sean; Woollard, David; Kelly, Sean

    2008-01-01

    A computer program denoted OODT CAS has been transformed to enable performance of larger tasks that involve greatly increased data volumes and increasingly intensive processing of data on heterogeneous, geographically dispersed computers. Prior to the transformation, OODT CAS (also alternatively denoted, simply, 'CAS') [wherein 'OODT' signifies 'Object-Oriented Data Technology' and 'CAS' signifies 'Catalog and Archive Service'] was a proven software component used to manage scientific data from spaceflight missions. In the transformation, CAS was split into two separate components representing its canonical capabilities: file management and workflow management. In addition, CAS was augmented by addition of a resource-management component. This third component enables CAS to manage heterogeneous computing by use of diverse resources, including high-performance clusters of computers, commodity computing hardware, and grid computing infrastructures. CAS is now more easily maintainable, evolvable, and reusable. These components can be used separately or, taking advantage of synergies, can be used together. Other elements of the transformation included addition of a separate Web presentation layer that supports distribution of data products via Really Simple Syndication (RSS) feeds, and provision for full Resource Description Framework (RDF) exports of metadata.

  7. Optimization of genome editing through CRISPR-Cas9 engineering.

    PubMed

    Zhang, Jian-Hua; Adikaram, Poorni; Pandey, Mritunjay; Genis, Allison; Simonds, William F

    2016-04-01

    CRISPR (Clustered Regularly-Interspaced Short Palindromic Repeats)-Cas9 (CRISPR associated protein 9) has rapidly become the most promising genome editing tool with great potential to revolutionize medicine. Through guidance of a 20 nucleotide RNA (gRNA), CRISPR-Cas9 finds and cuts target protospacer DNA precisely 3 base pairs upstream of a PAM (Protospacer Adjacent Motif). The broken DNA ends are repaired by either NHEJ (Non-Homologous End Joining) resulting in small indels, or by HDR (Homology Directed Repair) for precise gene or nucleotide replacement. Theoretically, CRISPR-Cas9 could be used to modify any genomic sequences, thereby providing a simple, easy, and cost effective means of genome wide gene editing. However, the off-target activity of CRISPR-Cas9 that cuts DNA sites with imperfect matches with gRNA have been of significant concern because clinical applications require 100% accuracy. Additionally, CRISPR-Cas9 has unpredictable efficiency among different DNA target sites and the PAM requirements greatly restrict its genome editing frequency. A large number of efforts have been made to address these impeding issues, but much more is needed to fully realize the medical potential of CRISPR-Cas9. In this article, we summarize the existing problems and current advances of the CRISPR-Cas9 technology and provide perspectives for the ultimate perfection of Cas9-mediated genome editing.

  8. Reaction to Indispensable Manual Calculation Skills in a CAS Environment.

    ERIC Educational Resources Information Center

    Monaghan, John

    2001-01-01

    Reacts to an article published in a previous issue of this journal on the effects of graphing calculators and computer algebra systems (CAS) on students' manual calculation and algebraic manipulation skills. Considers the contribution made by Jean-Baptiste Lagrange to thinking about the role of CAS in teaching algebra. (ASK)

  9. 48 CFR 9903.201-2 - Types of CAS coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...) Receive a single CAS-covered contract award of $50 million or more; or (2) Received $50 million or more in... business unit receives a single CAS-covered contract award of $50 million or more, that contract must be... institution that operate as independent organizational entities under the auspices of the parent...

  10. From Calculus to Dynamical Systems through DGS and CAS

    ERIC Educational Resources Information Center

    García, Jeanett López; Zamudio, Jorge Javier Jiménez

    2015-01-01

    Several factors have motivated the use of CAS or DGS in the teaching-learning process, such as: the development of new technologies, the availability of computers, and the widespread use of the Internet, among others. Even more, the trend to include CAS and DGS in the curricula of some undergraduate studies has resulted in the instruction of the…

  11. Teaching Undergraduate Mathematics Using CAS Technology: Issues and Prospects

    ERIC Educational Resources Information Center

    Tobin, Patrick C.; Weiss, Vida

    2016-01-01

    The use of handheld CAS technology in undergraduate mathematics courses in Australia is paradoxically shrinking under sustained disapproval or disdain from the professional mathematics community. Mathematics education specialists argue with their mathematics colleagues over a range of issues in course development and this use of CAS or even…

  12. regA, a Volvox gene that plays a central role in germ-soma differentiation, encodes a novel regulatory protein.

    PubMed

    Kirk, M M; Stark, K; Miller, S M; Müller, W; Taillon, B E; Gruber, H; Schmitt, R; Kirk, D L

    1999-02-01

    Volvox has two cell types: mortal somatic cells and immortal germ cells. Here we describe the transposon-tagging, cloning and characterization of regA, which plays a central role as a master regulatory gene in Volvox germ-soma differentiation by suppressing reproductive activities in somatic cells. The 12.5 kb regA transcription unit generates a 6,725 nucleotide mRNA that appears at the beginning of somatic cell differentiation, and that encodes a 111 kDa RegA protein that localizes to the nucleus, and has an unusual abundance of alanine, glutamine and proline. This is a compositional feature shared by functional domains of many 'active' repressors. These findings are consistent with the hypothesis that RegA acts in somatic cells to repress transcription of genes required for growth and reproduction, including 13 genes whose products are required for chloroplast biogenesis.

  13. Evaluation of the Brinecell{reg_sign} electrochemical oxidation unit for destruction of noncyanide strippers and other colored compounds in wastewaters

    SciTech Connect

    Wikoff, P.M.; Suciu, D.F.

    1994-08-01

    The noncyanide strippers used in the plating operations at Kelly Air Force Base, in San Antonio, Texas, develop an intense red color during use. Currently, the spent strippers cannot be treated in the Industrial Wastewater Treatment Plant because, even after biological treatment, the color remains too high for discharge. The Brinecell{reg_sign} process was evaluated for its application in treating the spent stripping solutions. The Brinecell{reg_sign} produces strong oxidizing agents that could treat the color causing compounds. The Brinecell{reg_sign} process was used to treat a 1 to 400 dilution of spent Clepo 204-T at 50 C and 60 g/L salt. After 8 hours of treatment, the color remaining was 8 units and the solution appeared colorless. Treatment of the Metalx B-9 reduced the color to 60 units. The effect of salt concentration, solution temperature, and solution pH was evaluated on the Brinecell{reg_sign} treatment process.

  14. Impact of boundary conditions on RegCM4 20-year-long precipitation simulations over CORDEX-East Asia domain

    NASA Astrophysics Data System (ADS)

    Park, J.-H.; Oh, S. G.; Suh, M. S.; Kang, H. S.

    2012-04-01

    National Institute of Meteorological Research (NIMR) of KMA organizes a domestic collaborative research project for contributing CORDEX-East Asia. Within the evaluation framework of CORDEX, the preliminary goal of the project is to produce 20-year-long regional climate and to analyse the simulation results from four RCMs including RegCM4 driven by two boundary conditions. The final goal of this project is to predict the future climate over this region using multiple RCMs based on the new scenario, RCPs. The number of grid points for north-south and east-west directions is 197 x 233 and horizontal resolution is 50 km. In this work, the simulation results of 20-year (1989-2008) regional climate over CORDEX-East Asia by RegCM4 will be presented with focus on the precipitation and impacts of lateral boundary conditions, the ERA-Interim (ERA) and NCEP/DOE (R2). For the validation of RegCM4 simulations, global dataset (GPCP) and climate stations data (precipitation) from KMA were used. The RegCM4 adequately captures the seasonal evolution of precipitation associated to the seasonal march of East Asia monsoon. The RegCM4 well simulates spatial and temporal (inter-annual, seasonal and diurnal) variations of precipitation over CORDEX-East Asia. In general, RegCM4 overestimates precipitation over western South Pacific Sea and southern area of China. On the other hand, summer precipitation over the Korean peninsula is significantly underestimated, especially when driven by R2. In spatial distribution, the RegCM4 driven by ERA simulated more precipitation than that by R2 especially over land. On the other hand, precipitation over the ocean is underestimated when driven by ERA compared to that by R2. Although the performance skill of RegCM4 for precipitation is clearly different with location and season, it well simulates seasonal variation of precipitation over East Asia. However, it fails to capture the inter-annual variation of precipitation. In addition, RegCM4 fails to

  15. CRISPR-Cas Technologies and Applications in Food Bacteria.

    PubMed

    Stout, Emily; Klaenhammer, Todd; Barrangou, Rodolphe

    2017-02-28

    Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.

  16. Diversity and evolution of class 2 CRISPR-Cas systems.

    PubMed

    Shmakov, Sergey; Smargon, Aaron; Scott, David; Cox, David; Pyzocha, Neena; Yan, Winston; Abudayyeh, Omar O; Gootenberg, Jonathan S; Makarova, Kira S; Wolf, Yuri I; Severinov, Konstantin; Zhang, Feng; Koonin, Eugene V

    2017-03-01

    Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas.

  17. Guide RNA engineering for versatile Cas9 functionality

    PubMed Central

    Nowak, Chance M.; Lawson, Seth; Zerez, Megan; Bleris, Leonidas

    2016-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats system allows a single guide RNA (sgRNA) to direct a protein with combined helicase and nuclease activity to the DNA. Streptococcus pyogenes Cas9 (SpCas9), a CRISPR-associated protein, has revolutionized our ability to probe and edit the human genome in vitro and in vivo. Arguably, the true modularity of the Cas9 platform is conferred through the ease of sgRNA programmability as well as the degree of modifications the sgRNA can tolerate without compromising its association with SpCas9 and function. In this review, we focus on the properties and recent engineering advances of the sgRNA component in Cas9-mediated genome targeting. PMID:27733506

  18. Intra-field on-product overlay improvement by application of RegC and TWINSCAN corrections

    NASA Astrophysics Data System (ADS)

    Sharoni, Ofir; Dmitriev, Vladimir; Graitzer, Erez; Perets, Yuval; Gorhad, Kujan; van Haren, Richard; Cekli, Hakki E.; Mulkens, Jan

    2015-03-01

    The on product overlay specification and Advanced Process Control (APC) is getting extremely challenging particularly after the introduction of multi-patterning applications like Spacer Assisted Double Patterning (SADP) and multipatterning techniques like N-repetitive Litho-Etch steps (LEN, N >= 2). When the latter is considered, most of the intrafield overlay contributors drop out of the overlay budget. This is a direct consequence of the fact that the scanner settings (like dose, illumination settings, etc.) as well as the subsequent processing steps can be made very similar for two consecutive Litho-Etch layers. The major overlay contributor that may require additional attention is the Image Placement Error (IPE). When the inter-layer overlay is considered, controlling the intra-field overlay contribution gets more complicated. In addition to the IPE contribution, the TWINSCANTM lens fingerprint in combination with the exposure settings is going to play a role as well. Generally speaking, two subsequent functional layers have different exposure settings. This results in a (non-reticle) additional overlay contribution. In this paper, we have studied the wafer overlay correction capability by RegC® in addition to the TWINSCANTM intrafield corrections to improve the on product overlay performance. RegC® is a reticle intra-volume laser writing technique that causes a predictable deformation element (RegC® deformation element) inside the quartz (Qz) material of a reticle. This technique enables to post-process an existing reticle to correct for instance for IPE. Alternatively, a pre-determined intra-field fingerprint can be added to the reticle such that it results in a straight field after exposure. This second application might be very powerful to correct for instance for (cold) lens fingerprints that cannot be corrected by the scanner itself. Another possible application is the intra-field processing fingerprint. One should realize that a RegC® treatment of a

  19. Implementing the CAS Standards: The Implementation of the CAS Standards in Student Affairs as a Comprehensive Assessment Approach

    ERIC Educational Resources Information Center

    Dorman, Jesse A.

    2012-01-01

    The increasing use of the CAS standards as a comprehensive assessment approach in divisions of student affairs necessitates a more in-depth understanding of how the CAS standards are being implemented in these settings. In response to increasing calls for improvement, accountability and professionalism in student affairs (Bresciani, 2006; Cooper…

  20. Parp1 deficient mice are protected from streptozotocin-induced diabetes but not caerulein-induced pancreatitis, independent of the induction of Reg family genes.

    PubMed

    Li, Bing; Luo, Chen; Chowdhury, Subrata; Gao, Zu-Hua; Liu, Jun-Li

    2013-09-10

    Poly(ADP-ribose) polymerase (Parp) 1 is a key regulator of cell death, its inhibition prevented streptozotocin-induced diabetes and attenuated caerulein-induced acute pancreatitis. Reg family proteins are significantly induced by Parp1 inhibitor, experimental diabetes and/or acute pancreatitis. We propose that Reg proteins are involved in the protection of pancreatic cells by Parp1 inhibition. To test this possibility, Parp1-/- and wild-type mice were injected with streptozotocin to induce diabetes. Separately, acute pancreatitis was induced with repeated injections of caerulein. Upon streptozotocin administration, Parp1-/- mice displayed much decreased hyperglycemia and preserved serum insulin level. The treatment induced similar levels of Reg1, -2, -3α and -3β genes in the pancreas of both wild-type and Parp1-/- mice, suggesting that the upregulation of Reg family genes during streptozotocin-induced diabetes was independent of Parp1 ablation. In caerulein-induced pancreatitis, unlike being reported, Parp1 knockout caused no relief on the severity of pancreatitis; the upregulation of pancreatic Reg1, -2, -3α and -3β genes upon caerulein was unaffected by Parp1 deletion. Our results reconfirmed the protective effect of Parp1 gene deletion on islet β-cells but questioned its effect on the acinar cells. In either case, the significant induction of Reg family genes seemed independent of Parp1-mediated cell death.

  1. Rheoencephalographic (REG) Assessment of Head and Neck Cooling for use with Multiple Sclerosis Patients

    NASA Technical Reports Server (NTRS)

    Montogomery, Leslie D.; Ku, Yu-Tsuan E.; Webbon, Bruce W. (Technical Monitor)

    1995-01-01

    We have prepared a computer program (RHEOSYS:RHEOencephalographic impedance trace scanning SyStem) that can be used to automate the analysis of segmental impedance blood flow waveforms. This program was developed to assist in the post test analysis of recorded impedance traces from multiple segments of the body. It incorporates many of the blood flow, segmental volume, and vascular state indices reported in the world literature. As it is currently programmed, seven points are selected from each blood flow pulse and associated ECG waveforrn: 1. peak of the first ECG QRS complex, 2. start of systolic slope on the blood flow trace, 3. maximum amplitude of the impedance pulse, 4. position of the dicrotic notch, 5. maximum amplitude of the postdicrotic segment, 6. peak of the second ECG QRS complex, and 7. start of the next blood flow pulse. These points we used to calculate various geometric, area, and time-related values associated with the impedance pulse morphology. RHEOSYS then calculates a series of 34 impedance and cardiac cycle parameters which include pulse amplitudes; areas; pulse propagation times; cardiac cycle times; and various measures of arterial and various tone, contractility, and pulse volume. We used this program to calculate the scalp and intracranial blood flow responses to head and neck cooling as it may be applied to lower the body temperatures of multiple sclerosis patients. Twelve women and twelve men were tested using a commercially available head and neck cooling system operated at its maximum cooling capacity for a period of 30 minutes. Head and neck cooling produced a transient change in scalp blood flow and a significant, (P<0.05) decrease of approx. 30% in intracranial blood flow. Results of this experiment will illustrate how REG and RHEOSYS can be used in biomedical applications.

  2. Combustion of fuel with high fines in Ahlstrom Pyroflow{reg_sign} CFB boilers

    SciTech Connect

    Chelian, P.K.; Gamble, R.

    1995-12-31

    Ahlstrom Pyroflow{reg_sign} boilers have demonstrated the ability of circulating fluidized bed (CFB) boilers to successfully burn unconventional fuels. These boilers have played a major role in the utilization of waste fuels, like bituminous gob and anthracite culm. Many of the waste fuels are processed prior to combustion to increase their heating value. As the technology for combustion of these fuels advanced, so has the desire of the owners to utilize more of the waste fuel and minimize the rejects. In the past, a majority of the fines content (less than 150 microns) was rejected and returned to the piles along with other rejects. In some cases, pond settlings were found to have a reasonably useful heat content, and were a preferred supplement to the anthracite culm. The use of these rejects had one result in common, i.e., to increase the fines content in the fuel feed to the CFB boilers. Pyropower was involved in tests conducted at two boilers, one burning bituminous gob and the other burning processed anthracite culm and silt. These tests were aimed at studying the effect of the high fuel fines content on the CFB boiler performance to determine the maximum practical fines limit. There were concerns of high unburned carbon loss, high CO and high cyclone temperatures. The actual test data confirmed that these boilers could fire a high percent of fines without major concerns. This paper discusses in detail the results of the testing with anthracite culm and silt, and references similar observations made during the testing with high fines bituminous gob.

  3. Customization of regional climate model (RegCM4) over Indian region

    NASA Astrophysics Data System (ADS)

    Nayak, S.; Mandal, M.; Maity, S.

    2017-01-01

    The regional climate model (RegCM4) is customized for 10-year climate simulation over Indian region through sensitivity studies on cumulus convection and land surface parameterization schemes. The model is configured over 30° E-120° E and 15° S-45° N at 30-km horizontal resolution with 23 vertical levels. Six 10-year (1991-2000) simulations are conducted with the combinations of two land surface schemes (BATS, CLM3.5) and three cumulus convection schemes (Kuo, Grell, MIT). The simulated annual and seasonal climatology of surface temperature and precipitation are compared with CRU observations. The interannual variability of these two parameters is also analyzed. The results indicate that the model simulated climatology is sensitive to the convection as well as land surface parameterization. The analysis of surface temperature (precipitation) climatology indicates that the model with CLM produces warmer (dryer) climatology, particularly over India. The warmer (dryer) climatology is due to the higher sensible heat flux (lower evapotranspiration) in CLM. The model with MIT convection scheme simulated wetter and warmer climatology (higher precipitation and temperature) with smaller Bowen ratio over southern India compared to that with the Grell and Kuo schemes. This indicates that a land surface scheme produces warmer but drier climatology with sensible heating contributing to warming where as a convection scheme warmer but wetter climatology with latent heat contributing to warming. The climatology of surface temperature over India is better simulated by the model with BATS land surface model in combination with MIT convection scheme while the precipitation climatology is better simulated with BATS land surface model in combination with Grell convection scheme. Overall, the modeling system with the combination of Grell convection and BATS land surface scheme provides better climate simulation over the Indian region.

  4. Predicting the relative toxicity of metal ions using ion characteristics: Microtox{reg_sign} bioluminescence assay

    SciTech Connect

    McCloskey, J.T.; Newman, M.C.; Clark, S.B.

    1996-10-01

    Quantitative structure-activity relationships have been used to predict the relative toxicity of organic compounds. Although not as common, ion characteristics have also proven useful for predicting the relative toxicity of metal ions. The purpose of this study was to determine if the relative toxicity of metal ions using the Microtox{reg_sign} bioassay was predictable using ion characteristics. Median effect concentrations (EC50s) were determined for 20 metals in a NaNO{sub 3} medium, which reflected freshwater speciation conditions, using the Microtox bacterial assay. The log of EC50 values was modeled using several ion characteristics, and Akaike`s Information Criterion was calculated to determine which ion characteristics provided the best fit. Whether modeling total ion or free ion EC50 values, the one variable which best modeled EC50s was the softness index, while a combination of {chi}{sub m}{sup 2}r ({chi}{sub m} = electronegativity, r = Pauling ionic radius) and {vert_bar}log K{sub OH}{vert_bar} was the best two-variable model. Other variables, including {Delta}E{sub 0} and {chi}{sub m}{sup 2}r (one-variable models) and (AN/{Delta}IP, {Delta}E{sub 0}) and ({chi}{sub m}{sup 2}r, Z{sup 2}/r) (two-variable models), also gave adequate fits. Modeling with speciated (free ion) versus unspeciated (total ion) EC50 values did not improve fits. Modeling mono-, di-, and trivalent metal ions separately improved the models. The authors conclude that ion characteristics can be used to predict the relative toxicity of metal ions whether in freshwater (NaNO{sub 3} medium) or saltwater (NaCl medium) speciation conditions and that this approach can be applied to metal ions varying widely in both valence and binding tendencies.

  5. Interference activity of a minimal Type I CRISPR–Cas system from Shewanella putrefaciens

    PubMed Central

    Dwarakanath, Srivatsa; Brenzinger, Susanne; Gleditzsch, Daniel; Plagens, André; Klingl, Andreas; Thormann, Kai; Randau, Lennart

    2015-01-01

    Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)–Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minimal variant of the Type I-F system was identified in proteobacterial species including Shewanella putrefaciens CN-32. This variant lacks a large subunit (Csy1), Csy2 and Csy3 and contains two unclassified cas genes. The genome of S. putrefaciens CN-32 contains only five Cas proteins (Cas1, Cas3, Cas6f, Cas1821 and Cas1822) and a single CRISPR array with 81 spacers. RNA-Seq analyses revealed the transcription of this array and the maturation of crRNAs (CRISPR RNAs). Interference assays based on plasmid conjugation demonstrated that this CRISPR-Cas system is active in vivo and that activity is dependent on the recognition of the dinucleotide GG PAM (Protospacer Adjacent Motif) sequence and crRNA abundance. The deletion of cas1821 and cas1822 reduced the cellular crRNA pool. Recombinant Cas1821 was shown to form helical filaments bound to RNA molecules, which suggests its role as the Cascade backbone protein. A Cascade complex was isolated which contained multiple Cas1821 copies, Cas1822, Cas6f and mature crRNAs. PMID:26350210

  6. CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli.

    PubMed

    Díez-Villaseñor, César; Guzmán, Noemí M; Almendros, Cristóbal; García-Martínez, Jesús; Mojica, Francisco J M

    2013-05-01

    Prokaryotes immunize themselves against transmissible genetic elements by the integration (acquisition) in clustered regularly interspaced short palindromic repeats (CRISPR) loci of spacers homologous to invader nucleic acids, defined as protospacers. Following acquisition, mono-spacer CRISPR RNAs (termed crRNAs) guide CRISPR-associated (Cas) proteins to degrade (interference) protospacers flanked by an adjacent motif in extrachomosomal DNA. During acquisition, selection of spacer-precursors adjoining the protospacer motif and proper orientation of the integrated fragment with respect to the leader (sequence leading transcription of the flanking CRISPR array) grant efficient interference by at least some CRISPR-Cas systems. This adaptive stage of the CRISPR action is poorly characterized, mainly due to the lack of appropriate genetic strategies to address its study and, at least in Escherichia coli, the need of Cas overproduction for insertion detection. In this work, we describe the development and application in Escherichia coli strains of an interference-independent assay based on engineered selectable CRISPR-spacer integration reporter plasmids. By using this tool without the constraint of interference or cas overexpression, we confirmed fundamental aspects of this process such as the critical requirement of Cas1 and Cas2 and the identity of the CTT protospacer motif for the E. coli K12 system. In addition, we defined the CWT motif for a non-K12 CRISPR-Cas variant, and obtained data supporting the implication of the leader in spacer orientation, the preferred acquisition from plasmids harboring cas genes and the occurrence of a sequential cleavage at the insertion site by a ruler mechanism.

  7. The genome editing revolution: A CRISPR-Cas TALE off-target story.

    PubMed

    Stella, Stefano; Montoya, Guillermo

    2016-07-01

    In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than the previously available DNA binding templates, zinc fingers and meganucleases. Recently, the area experimented a quantum leap because of the introduction of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system (clustered regularly interspaced short palindromic sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR-Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human pathways or to improve key organisms for biotechnological applications, such as plants, livestock genome as well as yeasts and bacterial strains.

  8. Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems.

    PubMed

    Richter, Corinna; Chang, James T; Fineran, Peter C

    2012-10-19

    Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous 'innate' mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR) systems provide acquired, yet heritable, sequence-specific 'adaptive' immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas) proteins, into short interfering RNAs (crRNAs), which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s) of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.

  9. RIFM fragrance ingredient safety assessment, linalyl cinnamate, CAS Registry Number 78-37-5.

    PubMed

    Api, A M; Belsito, D; Bhatia, S; Bruze, M; Calow, P; Dagli, M L; Dekant, W; Fryer, A D; Kromidas, L; La Cava, S; Lalko, J F; Lapczynski, A; Liebler, D C; Penning, T M; Politano, V T; Ritacco, G; Salvito, D; Schultz, T W; Shen, J; Sipes, I G; Wall, B; Wilcox, D K

    2016-11-01

    The use of this material under current conditions is supported by existing information. This material was evaluated for genotoxicity, repeated dose toxicity, developmental and reproductive toxicity, local respiratory toxicity, phototoxicity/photoallergenicity, skin sensitization, as well as environmental safety. Data show that this material is not genotoxic nor does it have skin sensitization potential. The reproductive and local respiratory toxicity endpoints were completed using the TTC (Threshold of Toxicological Concern) for a Cramer Class I material (0.03 and 1.4 mg/day, respectively). The developmental toxicity endpoint was completed using linalool (CAS # 78-70-6), dehydrolinalool (CAS # 29171-20-8) and cinnamic acid (CAS # 621-82-9) as suitable read across analogs, which provided a MOE > 100. The repeated dose toxicity endpoint was completed using data on the target material which provided a MOE > 100. The phototoxicity/photoallergenicity endpoint was completed based on suitable UV spectra. The environmental endpoint was completed as described in the RIFM Framework.

  10. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity.

    PubMed

    Seed, Kimberley D; Lazinski, David W; Calderwood, Stephen B; Camilli, Andrew

    2013-02-28

    Bacteriophages (or phages) are the most abundant biological entities on earth, and are estimated to outnumber their bacterial prey by tenfold. The constant threat of phage predation has led to the evolution of a broad range of bacterial immunity mechanisms that in turn result in the evolution of diverse phage immune evasion strategies, leading to a dynamic co-evolutionary arms race. Although bacterial innate immune mechanisms against phage abound, the only documented bacterial adaptive immune system is the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) system, which provides sequence-specific protection from invading nucleic acids, including phage. Here we show a remarkable turn of events, in which a phage-encoded CRISPR/Cas system is used to counteract a phage inhibitory chromosomal island of the bacterial host. A successful lytic infection by the phage is dependent on sequence identity between CRISPR spacers and the target chromosomal island. In the absence of such targeting, the phage-encoded CRISPR/Cas system can acquire new spacers to evolve rapidly and ensure effective targeting of the chromosomal island to restore phage replication.

  11. Pilomatricome: étude de 22 cas

    PubMed Central

    Nasreddine, Fatima Zahra; Hali, Fouzia; Chiheb, Soumiya

    2016-01-01

    Le pilomatricome est une tumeur cutanée fréquente et bénigne du follicule pileux chez l'enfant. C'est une tumeur annexielle souvent méconnue et confondue avec d'autres lésions cutanées. Les localisations habituelles sont la tête et le cou. Le but de ce travail est de rapporter une série de 22 cas comportant des formes inhabituelles colligées au service de dermatologie sur une période allant de Janvier 2006 jusqu'au Mai 2015. L’étude a concerné 16 femmes et 6 hommes. La moyenne d’âge était de 23,3 ans (4-80 ans). La localisation cervico faciale a été observée dans 12 cas, 2 patients avaient des localisations multiples, un garçon de 4ans avait une localisation au niveau fronto-temporal et une fillette de 14 ans avait une localisation au niveau du visage et de l'avant-bras, et un patient de 48 ans avait une localisation sous unguéale. L'aspect clinique était typique dans tous les cas avec des nodules sous cutanés de consistance pierreuse. Tous les patients ont bénéficié d'une exérèse des nodules sous anesthésie locale. L’étude histologique était en faveur d'un épithélioma momifié de Malherbe d'exérèse complète sans signes de malignité. Aucun patient n'a présenté de rechute. L'originalité de notre étude réside dans la présence de localisations exceptionnelles au niveau latéro-vertébral, des membres et sous-unguéale, l’âge de survenue inhabituel à 80 ans et la présence de localisations multiples signalées chez 2 enfants. PMID:27516819

  12. CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum.

    PubMed

    Pohl, C; Kiel, J A K W; Driessen, A J M; Bovenberg, R A L; Nygård, Y

    2016-07-15

    CRISPR/Cas9 based systems have emerged as versatile platforms for precision genome editing in a wide range of organisms. Here we have developed powerful CRISPR/Cas9 tools for marker-based and marker-free genome modifications in Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. The developed CRISPR/Cas9 toolbox is highly flexible and allows editing of new targets with minimal cloning efforts. The Cas9 protein and the sgRNA can be either delivered during transformation, as preassembled CRISPR-Cas9 ribonucleoproteins (RNPs) or expressed from an AMA1 based plasmid within the cell. The direct delivery of the Cas9 protein with in vitro synthesized sgRNA to the cells allows for a transient method for genome engineering that may rapidly be applicable for other filamentous fungi. The expression of Cas9 from an AMA1 based vector was shown to be highly efficient for marker-free gene deletions.

  13. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

    PubMed Central

    Isaac, R Stefan; Jiang, Fuguo; Doudna, Jennifer A; Lim, Wendell A; Narlikar, Geeta J; Almeida, Ricardo

    2016-01-01

    The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to Cas9 is variable over several orders of magnitude depending on dynamic properties of the DNA sequence and the distance of the PAM site from the nucleosome dyad. We further find that chromatin remodeling enzymes stimulate Cas9 activity on nucleosomal templates. Our findings imply that the spontaneous breathing of nucleosomal DNA together with the action of chromatin remodelers allow Cas9 to effectively act on chromatin in vivo. DOI: http://dx.doi.org/10.7554/eLife.13450.001 PMID:27130520

  14. HPCCP/CAS Workshop Proceedings 1998

    NASA Technical Reports Server (NTRS)

    Schulbach, Catherine; Mata, Ellen (Editor); Schulbach, Catherine (Editor)

    1999-01-01

    This publication is a collection of extended abstracts of presentations given at the HPCCP/CAS (High Performance Computing and Communications Program/Computational Aerosciences Project) Workshop held on August 24-26, 1998, at NASA Ames Research Center, Moffett Field, California. The objective of the Workshop was to bring together the aerospace high performance computing community, consisting of airframe and propulsion companies, independent software vendors, university researchers, and government scientists and engineers. The Workshop was sponsored by the HPCCP Office at NASA Ames Research Center. The Workshop consisted of over 40 presentations, including an overview of NASA's High Performance Computing and Communications Program and the Computational Aerosciences Project; ten sessions of papers representative of the high performance computing research conducted within the Program by the aerospace industry, academia, NASA, and other government laboratories; two panel sessions; and a special presentation by Mr. James Bailey.

  15. Adaptation in CRISPR-Cas Systems.

    PubMed

    Sternberg, Samuel H; Richter, Hagen; Charpentier, Emmanuelle; Qimron, Udi

    2016-03-17

    Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in prokaryotes. The system preserves memories of prior infections by integrating short segments of foreign DNA, termed spacers, into the CRISPR array in a process termed adaptation. During the past 3 years, significant progress has been made on the genetic requirements and molecular mechanisms of adaptation. Here we review these recent advances, with a focus on the experimental approaches that have been developed, the insights they generated, and a proposed mechanism for self- versus non-self-discrimination during the process of spacer selection. We further describe the regulation of adaptation and the protein players involved in this fascinating process that allows bacteria and archaea to harbor adaptive immunity.

  16. On the ability of RegCM4 regional climate model to simulate surface solar radiation patterns over Europe: an assessment using satellite-based observations

    NASA Astrophysics Data System (ADS)

    Alexandri, G.; Georgoulias, A. K.; Zanis, P.; Katragkou, E.; Tsikerdekis, A.; Kourtidis, K.; Meleti, C.

    2015-11-01

    In this work, we assess the ability of RegCM4 regional climate model to simulate surface solar radiation (SSR) patterns over Europe. A decadal RegCM4 run (2000-2009) was implemented and evaluated against satellite-based observations from the Satellite Application Facility on Climate Monitoring (CM SAF), showing that the model simulates adequately the SSR patterns over the region. The SSR bias between RegCM4 and CM SAF is +1.5 % for MFG (Meteosat First Generation) and +3.3 % for MSG (Meteosat Second Generation) observations. The relative contribution of parameters that determine the transmission of solar radiation within the atmosphere to the deviation appearing between RegCM4 and CM SAF SSR is also examined. Cloud macrophysical and microphysical properties such as cloud fractional cover (CFC), cloud optical thickness (COT) and cloud effective radius (Re) from RegCM4 are evaluated against data from CM SAF. Generally, RegCM4 underestimates CFC by 24.3 % and Re for liquid/ice clouds by 36.1 %/28.3 % and overestimates COT by 4.3 %. The same procedure is repeated for aerosol optical properties such as aerosol optical depth (AOD), asymmetry factor (ASY) and single-scattering albedo (SSA), as well as other parameters, including surface broadband albedo (ALB) and water vapor amount (WV), using data from MACv1 aerosol climatology, from CERES satellite sensors and from ERA-Interim reanalysis. It is shown here that the good agreement between RegCM4 and satellite-based SSR observations can be partially attributed to counteracting effects among the above mentioned parameters. The potential contribution of each parameter to the RegCM4-CM SAF SSR deviations is estimated with the combined use of the aforementioned data and a~radiative transfer model (SBDART). CFC, COT and AOD are the major determinants of these deviations on a monthly basis; however, the other parameters also play an important role for specific regions and seasons. Overall, for the European domain, CFC, COT and

  17. Tumeur de Frantz: deux nouveaux cas

    PubMed Central

    Bellarbi, Salma; Sina, Mohamed; Jahid, Ahmed; Zouaidia, Fouad; Bernoussi, Zakia; Mahassini, Najat

    2013-01-01

    A travers cet article, nous détaillons les caractéristiques clinico-pathologiques et discutons l'histogenèse de la tumeur de Frantz. Deux patients opérés pour tumeur de Frantz. Ils ont eu un traitement chirurgical seul. L'étude morphologique était couplée à un examen immuno-histochimique (IHC) utilisant les anticorps anti CD10, anti- vimentine, anti-énolase neuronale spécifique (NSE), anti-synaptophysine, anti-chromogranine A et anti-cytokératine. Un immuno-marquage à l'anti-oestrogène et l'anti-progestérone a été réalisé dans un cas. Il s'agissait d'une femme âgée de 45ans et d'un garçon de 12 ans. Les aspects échographiques et scannographiques étaient non spécifiques. Une exérèse chirurgicale complète a été réalisée dans les deux cas. L'analyse histologique évoquait une tumeur de Frantz. Le diagnostic a été retenu après étude immuno-histohimique. L'évolution était favorable sans récidive avec respectivement un recul de 18 et 16 mois. La tumeur de Frantz est une entité rare. Son diagnostic repose sur l'examen anatomopathologique complété par l'étude immuno-histochimique. Son pronostic est excellent après résection chirurgicale. PMID:23503717

  18. CRISPR-Cas9-Mediated Genome Editing in Leishmania donovani

    PubMed Central

    Zhang, Wen-Wei

    2015-01-01

    ABSTRACT The prokaryotic CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9, an RNA-guided endonuclease, has been shown to mediate efficient genome editing in a wide variety of organisms. In the present study, the CRISPR-Cas9 system has been adapted to Leishmania donovani, a protozoan parasite that causes fatal human visceral leishmaniasis. We introduced the Cas9 nuclease into L. donovani and generated guide RNA (gRNA) expression vectors by using the L. donovani rRNA promoter and the hepatitis delta virus (HDV) ribozyme. It is demonstrated within that L. donovani mainly used homology-directed repair (HDR) and microhomology-mediated end joining (MMEJ) to repair the Cas9 nuclease-created double-strand DNA break (DSB). The nonhomologous end-joining (NHEJ) pathway appears to be absent in L. donovani. With this CRISPR-Cas9 system, it was possible to generate knockouts without selection by insertion of an oligonucleotide donor with stop codons and 25-nucleotide homology arms into the Cas9 cleavage site. Likewise, we disrupted and precisely tagged endogenous genes by inserting a bleomycin drug selection marker and GFP gene into the Cas9 cleavage site. With the use of Hammerhead and HDV ribozymes, a double-gRNA expression vector that further improved gene-targeting efficiency was developed, and it was used to make precise deletion of the 3-kb miltefosine transporter gene (LdMT). In addition, this study identified a novel single point mutation caused by CRISPR-Cas9 in LdMT (M381T) that led to miltefosine resistance, a concern for the only available oral antileishmanial drug. Together, these results demonstrate that the CRISPR-Cas9 system represents an effective genome engineering tool for L. donovani. PMID:26199327

  19. 205 PRODUCTION OF Cas9-EXPRESSING CATTLE USING DNA TRANSPOSON.

    PubMed

    Hahn, S-E; Yum, S-Y; Lee, S-J; Lee, C-I; Kim, H-S; Kim, H-J; Choi, W-J; Lee, J-H; Jang, G

    2016-01-01

    A genome-editing technology, CRISPR/Cas9 system is proved to be a powerful tool for knockout and knock-in in various species. When 2 components [Cas9 and single guide (sg) RNA] are delivered into cells or embryos, the events of gene editing occur. Because Cas9 is essential for every gene editing based on the CRISPR/Cas9 system, some studies reported that efficiency of gene editing would be increased as Cas9 was integrated into cells or animals. Accordingly, if the Cas9-expressing cattle is born, it would be broadly used for gene editing in cattle. For this study, the Cas9 and RFP genes were cloned into the PiggyBac transposon system. PiggyBac-Cas9-RFP and transposase were microinjected into 1436 IVF embryos and 241 blastocysts were formed. Blastocysts with RFP expression accounted for 14.1% of total formed blastocysts. Five blastocysts were selected and transferred into 5 recipient cow (1 embryo per recipient). After gestation periods, 4 transgenic cattle were delivered without any veterinary assistance. From transgenic cattle, ear skin tissue was collected for primary culture. On those primary cells, sgRNA in DNA form for various genes such as PRNP, RB1, and BLG were transfected with 2μg of sgRNA per 5×10(5) cells using electroporation. As expected, every group of each sgRNA delivered was confirmed to be mutated by T7E1 assay. The data demonstrated that, for the first time, transgenic cattle with Cas9 expression were born, grown up to date (age=5 months) and will be a valuable resource for genome editing in cattle.

  20. Programmable RNA recognition and cleavage by CRISPR/Cas9.

    PubMed

    O'Connell, Mitchell R; Oakes, Benjamin L; Sternberg, Samuel H; East-Seletsky, Alexandra; Kaplan, Matias; Doudna, Jennifer A

    2014-12-11

    The CRISPR-associated protein Cas9 is an RNA-guided DNA endonuclease that uses RNA-DNA complementarity to identify target sites for sequence-specific double-stranded DNA (dsDNA) cleavage. In its native context, Cas9 acts on DNA substrates exclusively because both binding and catalysis require recognition of a short DNA sequence, known as the protospacer adjacent motif (PAM), next to and on the strand opposite the twenty-nucleotide target site in dsDNA. Cas9 has proven to be a versatile tool for genome engineering and gene regulation in a large range of prokaryotic and eukaryotic cell types, and in whole organisms, but it has been thought to be incapable of targeting RNA. Here we show that Cas9 binds with high affinity to single-stranded RNA (ssRNA) targets matching the Cas9-associated guide RNA sequence when the PAM is presented in trans as a separate DNA oligonucleotide. Furthermore, PAM-presenting oligonucleotides (PAMmers) stimulate site-specific endonucleolytic cleavage of ssRNA targets, similar to PAM-mediated stimulation of Cas9-catalysed DNA cleavage. Using specially designed PAMmers, Cas9 can be specifically directed to bind or cut RNA targets while avoiding corresponding DNA sequences, and we demonstrate that this strategy enables the isolation of a specific endogenous messenger RNA from cells. These results reveal a fundamental connection between PAM binding and substrate selection by Cas9, and highlight the utility of Cas9 for programmable transcript recognition without the need for tags.

  1. Genome editing in Clostridium saccharoperbutylacetonicum N1-4 using CRISPR-Cas9 system.

    PubMed

    Wang, Shaohua; Dong, Sheng; Wang, Pixiang; Tao, Yong; Wang, Yi

    2017-03-03

    Clostridium saccharoperbutylacetonicum N1-4 is well known as a hyper-butanol-producing strain. However, the lack of genetic engineering tools hinders further elucidation of its solvent production mechanism and development of more robust strains. In this study, we set out to develop an efficient genome engineering system for this microorganism based on the CRISPR-Cas9 system. First, the functionality of the CRISPR-Cas9 system previously customized for C. beijerinckii was evaluated in C. saccharoperbutylacetonicum by targeting on pta and buk, two essential genes for acetate and butyrate production, respectively. The pta, buk single deletion, and the pta and buk double deletion mutants were successfully obtained based on this system. However, the genome engineering efficiency was rather low (the mutation rate is < 20%). Therefore, the efficiency was further optimized by evaluating various promoters for the gRNA expression. With promoter P J23119 , we achieved a mutation rate of 75% for pta deletion without serial subculturing as suggested previously for C. beijerinckii Thus, this developed CRISPR-Cas9 system is highly desirable for efficient genome editing in C. saccharoperbutylacetonicum Batch fermentation results revealed that both the acid and solvent production profiles were altered due to the disruption of acid production pathways, however neither acetate nor butyrate production was eliminated with the deletion of the corresponding gene. The butanol production, yield and selectivity were improved in mutants dependent on the fermentation medium. In the pta-buk double deletion mutant, the butanol production reached 19.0 g/l in P2 medium, which is one of the highest among the ever reported from batch fermentations.IMPORTANCE An efficient CRISPR-Cas9 genome engineering system was developed for C. saccharoperbutylacetonicum N1-4. This paves the way for elucidating the solvent production mechanism in this hyper-butanol-producing microorganism and developing strains

  2. Cas9 gRNA engineering for genome editing, activation and repression.

    PubMed

    Kiani, Samira; Chavez, Alejandro; Tuttle, Marcelle; Hall, Richard N; Chari, Raj; Ter-Ovanesyan, Dmitry; Qian, Jason; Pruitt, Benjamin W; Beal, Jacob; Vora, Suhani; Buchthal, Joanna; Kowal, Emma J K; Ebrahimkhani, Mohammad R; Collins, James J; Weiss, Ron; Church, George

    2015-11-01

    We demonstrate that by altering the length of Cas9-associated guide RNA (gRNA) we were able to control Cas9 nuclease activity and simultaneously perform genome editing and transcriptional regulation with a single Cas9 protein. We exploited these principles to engineer mammalian synthetic circuits with combined transcriptional regulation and kill functions governed by a single multifunctional Cas9 protein.

  3. Cas9 gRNA engineering for genome editing, activation and repression

    SciTech Connect

    Kiani, Samira; Chavez, Alejandro; Tuttle, Marcelle; Hall, Richard N.; Chari, Raj; Ter-Ovanesyan, Dmitry; Qian, Jason; Pruitt, Benjamin W.; Beal, Jacob; Vora, Suhani; Buchthal, Joanna; Kowal, Emma J. K.; Ebrahimkhani, Mohammad R.; Collins, James J.; Weiss, Ron; Church, George

    2015-09-07

    Here we demonstrate that by altering the length of Cas9-associated guide RNA(gRNA) we were able to control Cas9 nuclease activity and simultaneously perform genome editing and transcriptional regulation with a single Cas9 protein. We exploited these principles to engineer mammalian synthetic circuits with combined transcriptional regulation and kill functions governed by a single multifunctional Cas9 protein.

  4. 21 CFR 184.1721 - Sodium acetate.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Sodium acetate. 184.1721 Section 184.1721 Food and....1721 Sodium acetate. (a) Sodium acetate (C2H3O2Na, CAS Reg. No. 127-09-3 or C2H3O2Na·3H2O, CAS Reg. No. 6131-90-4) is the sodium salt of acetic acid and occurs naturally in plant and animal tissues....

  5. Grossesse intra murale à propos d'un cas

    PubMed Central

    de Tové, Kofi-Mensa Savi; Salifou, Kabibou; Imorou, Rachidi Sidi; Biaou, Olivier; Boco, Vicentia

    2015-01-01

    La grossesse intra-murale est la variété la plus rare de grossesse extra-utérine. Il s'agit de la localisation de l’œuf dans l’épaisseur du myomètre. En cas de retard diagnostic, l’évolution peut être catastrophique avec rupture utérine et hémorragie cataclysmique. L’échographie permet dans certains cas un diagnostic pré opératoire. Les auteurs rapportent un cas survenu chez une patiente aux antécédents de curetage. PMID:26448812

  6. Orbital period determination in an eclipsing dwarf nova HT Cas

    NASA Astrophysics Data System (ADS)

    Bąkowska, Karolina; Olech, Arkadiusz

    2014-09-01

    HT Cassiopeiae was discovered over seventy years ago (Hoffmeister 1943). Unfortunately, for 35 years this object did not receive any attention, until the eclipses of HT Cas were observed by Bond. After a first analysis, Patterson (1981) called HT Cas "a Rosetta stone among dwarf novae". Since then, the literature on this star is still growing, reaching several dozens of publications. We present an orbital period determination of HT Cas during the November 2010 super-outburst, but also during a longer time span, to check its stability.

  7. Study of Eclipsing Binary and Multiple Systems in OB Associations IV: Cas OB6 Member DN Cas

    NASA Astrophysics Data System (ADS)

    Bakış, V.; Bakış, H.; Bilir, S.; Eker, Z.

    2016-09-01

    An early-type, massive, short-period (Porb=2d.310951) eclipsing spectroscopic binary DN Cas has been re-visited with new spectral and photometric data. The masses and radii of the components have been obtained as M1=19.04± 0.07 M⊙, M2=13.73± 0.05 M⊙ and R1=7.22± 0.06 R⊙, R2=5.79± 0.06 R⊙, respectively. Both components present synchronous rotation (Vrot1=160 km s-1, Vrot2=130 km s-1) with their orbit. Orbital period analysis yielded a physically bound additional component in the system with a minimum mass of M3=0.88 M⊙ orbiting in an eccentric orbit (e = 0.37 ± 0.2) with an orbital period of P 12 = 42 ± 9 yr. High precision absolute parameters of the system allowed us to derive a distance to DN Cas as 1.7 ± 0.2 kpc which locates the system within the borders of the Cas OB6 association (d = 1.8 kpc). The space velocities and the age of DN Cas are in agreement with those of Cas OB6. The age of DN Cas (τ = 3-5 Myr) is found to be 1-2 Myr older than the embedded clusters (IC 1795, IC 1805, and IC 1848) in the Cas OB6 association, which implies a sequential star formation in the association.

  8. Evaluation of the capability of RegCM4.0 in simulating East African climate

    NASA Astrophysics Data System (ADS)

    Ogwang, Bob Alex; Chen, Haishan; Li, Xing; Gao, Chujie

    2016-04-01

    The International Centre for Theoretical Physics (ICTP) regional climate model RegCM4.0 is used in this study to examine its ability to reproduce the climate of East Africa (EA) in regard to the annual cycle and June-to-August (JJA) seasonal climatology. Two domain sizes [large domain (LD) and small domain (SD)] and two cumulus convection schemes [Grell convection scheme with Fritsch-Chappell closure assumption (GRE scheme) and MIT scheme (EMA scheme)] are used. Simulations were done for the period 1989-2008 at a resolution of 50 km. The experiments were performed with the initial and lateral boundary conditions obtained from ERA-Interim-gridded reanalysis data at a 1.5° resolution. The variables investigated are precipitation, temperature, humidity, diurnal temperature range, and 850-hPa winds. Results show that the model realistically reproduces the East African climate, with a few discrepancies due to the different cumulus convection schemes and the domain sizes used. Grell with Fritsch-Chappell (Grell-FC) scheme captures well the observed climate in regard to the annual cycle and June-to-August seasonal climatology, with a tendency to underestimate rainfall over the JJA rainfall maximum region (RMR). This scheme performs better in LD than in SD. EMA scheme similarly captures well the observed climatology. It tends to overestimate rainfall over RMR. It however performs better in SD than in LD. The ensemble mean of simulations with GRE and EMA schemes (ENSM) tends to offer an improved representation of the observed climate, with a few discrepancies owing to the individual schemes used. In general, therefore, considering the performance of the model in both domains, the East African climate based on this study is better simulated by the Grell-FC scheme over LD. The observed biases in this study signify that the ability of the model in simulating climate over East Africa is still a significant challenge. Thus, future work must focus on improving the performance of

  9. Regional modeling of Saharan dust events using the RegCM model

    NASA Astrophysics Data System (ADS)

    Santese, M.; Perrone, M. R.; Zakey, A.

    2009-04-01

    As one of the major components of the atmospheric aerosol, mineral dust plays an important role in the Earth's climate system. Dust has been found to redistribute the radiative energy from the surface to the dust loaded atmospheric column by cooling the surface while heating the dust layer. The resulting stabilizing effect on the vertical structure of the atmosphere can affect cloud formation and the dust production itself. In addition, dust may change the size number of cloud condensation nuclei (CCN) and thus the optical and precipitation properties of clouds. All these impacts are difficult to quantify due to the highly variable spatio-temporal distribution of mineral dust and uncertainties determining its optical and physicochemical properties (IPCC 2001). The distribution of dust has been modeled in many studies using general circulation models (GCMs). However, because the aerosol effects are especially important at the regional scale, the recent development of high-resolution regional climate models (RCMs) offers useful tools to assess the regional impacts of aerosols. Compared to global climate models (GCMs), the relatively high-resolution and detailed physical parameterizations by RCMs are particularly suitable to describe the complexity of aerosol processes (Solmon et al., 2006). Furthermore, the results from regional models are well suited for comparisons with measurements of individual events. Dust radiative effects on climate are likely to be especially important at the regional scale, thus RCMs can be particularly useful tools to investigate the regional climate effects of dust outbreaks (Zakey et al., 2006). In this work, we will use the regional climate model RegCM (Version 3.1), developed at the Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, to investigate dust event impacts over Mediterranean sites. The Sahara desert is the largest dust source on Earth, providing at least half of the emitted dust (Washington et al., 2003

  10. Estimates of common ragweed pollen emission and dispersion over Europe using RegCM-pollen model

    NASA Astrophysics Data System (ADS)

    Liu, L.; Solmon, F.; Vautard, R.; Hamaoui-Laguel, L.; Torma, Cs. Zs.; Giorgi, F.

    2015-11-01

    Common ragweed (Ambrosia artemisiifolia L.) is a highly allergenic and invasive plant in Europe. Its pollen can be transported over large distances and has been recognized as a significant cause of hayfever and asthma (D'Amato et al., 2007; Burbach et al., 2009). To simulate production and dispersion of common ragweed pollen, we implement a pollen emission and transport module in the Regional Climate Model (RegCM) version 4 using the framework of the Community Land Model (CLM) version 4.5. In the online model environment where climate is integrated with dispersion and vegetation production, pollen emissions are calculated based on the modelling of plant distribution, pollen production, species-specific phenology, flowering probability, and flux response to meteorological conditions. A pollen tracer model is used to describe pollen advective transport, turbulent mixing, dry and wet deposition. The model is then applied and evaluated on a European domain for the period 2000-2010. To reduce the large uncertainties notably due to ragweed density distribution on pollen emission, a calibration based on airborne pollen observations is used. Resulting simulations show that the model captures the gross features of the pollen concentrations found in Europe, and reproduce reasonably both the spatial and temporal patterns of flowering season and associated pollen concentrations measured over Europe. The model can explain 68.6, 39.2, and 34.3 % of the observed variance in starting, central, and ending dates of the pollen season with associated root mean square error (RMSE) equal to 4.7, 3.9, and 7.0 days, respectively. The correlation between simulated and observed daily concentrations time series reaches 0.69. Statistical scores show that the model performs better over the central Europe source region where pollen loads are larger. From these simulations health risks associated common ragweed pollen spread are then evaluated through calculation of exposure time above health

  11. RegCM4-HadGEM2-ES simulated cyclone climatology (1979-2005) over the Southwestern South Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Porfírio da Rocha, Rosmeri; Simões Reboita, Michelle

    2015-04-01

    Cyclones over the Southwestern South Atlantic Ocean (SAO) are a subject of great interest once they modify the weather and control the climate near east coast of South America (SA). In this study we compare the cyclones climatology in the period 1979-2005 simulated by Regional Climate Model version 4 (RegCM4) with that from ERA-Interim reanalysis (ECMWF). RegCM4 was nested in HadGEM2-ES output and the simulation used the SA domain of CORDEX project, with a horizontal grid of 50 km and 18 sigma-pressure levels in the vertical. The RegCM4 simulation used the land surface Biosphere-Atmosphere Transfer Scheme (BATS) and the mixed convection Emanuel-Grell scheme configurations. This simulation is part of the CREMA (CORDEX REgCM4 hyper-MAtrix) experiment. The cyclones were identified using an automated tracking scheme based on minima (cyclonic in Southern Hemisphere) of relative vorticity from the wind at 925 hPa. The threshold of -1.5 x 10-5s-1 was used in the algorithm. All cyclones in RegCM4 and ERA-Interim with relative vorticity lower than this threshold and with lifetime higher or equal 24 hours were included in the climatology. ERA-Interim shows three main cyclogenetic regions near east coast of SA. In general, RegCM4 simulated these same regions but with an underestimation of the number of cyclones. In each of these regions, there is a different season of higher cyclones frequency. Over extreme south of southern Brazil and Uruguay the higher frequency of cyclones occurs in winter, while southeastern Brazil and southeastern Argentina cyclones are most frequent during summer. RegCM4 is able to simulate this observed seasonality.

  12. Pancreatic islet-specific overexpression of Reg3β protein induced the expression of pro-islet genes and protected the mice against streptozotocin-induced diabetes mellitus.

    PubMed

    Xiong, Xiaoquan; Wang, Xiao; Li, Bing; Chowdhury, Subrata; Lu, Yarong; Srikant, Coimbatore B; Ning, Guang; Liu, Jun-Li

    2011-04-01

    Reg family proteins have been implicated in islet β-cell proliferation, survival, and regeneration. The expression of Reg3β (pancreatitis-associated protein) is highly induced in experimental diabetes and acute pancreatitis, but its precise role has not been established. Through knockout studies, this protein was shown to be mitogenic, antiapoptotic, and anti-inflammatory in the liver and pancreatic acinars. To test whether it can promote islet cell growth or survival against experimental damage, we developed β-cell-specific overexpression using rat insulin I promoter, evaluated the changes in normal islet function, gene expression profile, and the response to streptozotocin-induced diabetes. Significant and specific overexpression of Reg3β was achieved in the pancreatic islets of RIP-I/Reg3β mice, which exhibited normal islet histology, β-cell mass, and in vivo and in vitro insulin secretion in response to high glucose yet were slightly hyperglycemic and low in islet GLUT2 level. Upon streptozotocin treatment, in contrast to wild-type littermates that became hyperglycemic in 3 days and lost 15% of their weight, RIP-I/Reg3β mice were significantly protected from hyperglycemia and weight loss. To identify specific targets affected by Reg3β overexpression, a whole genome DNA microarray on islet RNA isolated from the transgenic mice revealed more than 45 genes significantly either up- or downregulated. Among them, islet-protective osteopontin/SPP1 and acute responsive nuclear protein p8/NUPR1 were significantly induced, a result further confirmed by real-time PCR, Western blots, and immunohistochemistry. Our results suggest that Reg3β is unlikely an islet growth factor but a putative protector that prevents streptozotocin-induced damage by inducing the expression of specific genes.

  13. On the ability of RegCM4 regional climate model to simulate surface solar radiation patterns over Europe: an assessment using satellite-based observations

    NASA Astrophysics Data System (ADS)

    Alexandri, G.; Georgoulias, A. K.; Zanis, P.; Katragkou, E.; Tsikerdekis, A.; Kourtidis, K.; Meleti, C.

    2015-07-01

    In this work, we assess the ability of RegCM4 regional climate model to simulate surface solar radiation (SSR) patterns over Europe. A decadal RegCM4 run (2000-2009) was implemented and evaluated against satellite-based observations from the Satellite Application Facility on Climate Monitoring (CM SAF) showing that the model simulates adequately the SSR patterns over the region. The bias between RegCM4 and CM SAF is +1.54 % for MFG (Meteosat First Generation) and +3.34 % for MSG (Meteosat Second Generation) observations. The relative contribution of parameters that determine the transmission of solar radiation within the atmosphere to the deviation appearing between RegCM4 and CM SAF SSR is also examined. Cloud macrophysical and microphysical properties such as cloud fractional cover (CFC), cloud optical thickness (COT) and cloud effective radius (Re) from RegCM4 are evaluated against data from CM SAF. The same procedure is repeated for aerosol optical properties such as aerosol optical depth (AOD), asymmetry factor (ASY) and single scattering albedo (SSA), as well as other parameters including surface broadband albedo (ALB) and water vapor amount (WV) using data from MACv1 aerosol climatology, from CERES satellite sensors and from ERA-Interim reanalysis. It is shown here that the good agreement between RegCM4 and satellite-based SSR observations can be partially attributed to counteracting effects among the above mentioned parameters. The contribution of each parameter to the RegCM4-CM SAF SSR deviations is estimated with the combined use of the aforementioned data and a radiative transfer model (SBDART). CFC, COT and AOD are the major determinants of these deviations; however, the other parameters also play an important role for specific regions and seasons.

  14. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity.

    PubMed

    Nuñez, James K; Lee, Amy S Y; Engelman, Alan; Doudna, Jennifer A

    2015-03-12

    Bacteria and archaea insert spacer sequences acquired from foreign DNAs into CRISPR loci to generate immunological memory. The Escherichia coli Cas1-Cas2 complex mediates spacer acquisition in vivo, but the molecular mechanism of this process is unknown. Here we show that the purified Cas1-Cas2 complex integrates oligonucleotide DNA substrates into acceptor DNA to yield products similar to those generated by retroviral integrases and transposases. Cas1 is the catalytic subunit and Cas2 substantially increases integration activity. Protospacer DNA with free 3'-OH ends and supercoiled target DNA are required, and integration occurs preferentially at the ends of CRISPR repeats and at sequences adjacent to cruciform structures abutting AT-rich regions, similar to the CRISPR leader sequence. Our results demonstrate the Cas1-Cas2 complex to be the minimal machinery that catalyses spacer DNA acquisition and explain the significance of CRISPR repeats in providing sequence and structural specificity for Cas1-Cas2-mediated adaptive immunity.

  15. Evaluation of freshwater sediment quality values including apparent effects thresholds of Hyalella azteca and Microtox{reg_sign}

    SciTech Connect

    Cubbage, J.; Batts, D.

    1995-12-31

    Data from 36 studies in Washington State were merged into a single database to derive Apparent Effects Thresholds (AETS) for freshwater sediments and to evaluate other sediment quality values. Sediments from 235 sites were analyzed for several contaminants, Bioassays tested at 30 or more of these sites included Hyalella azteca, Daphnia magna and Chironomus tentans mortality, Ceriodaphnia dubia reproduction and growth, and Microtox{reg_sign} luminescence reduction. Adequate sample size (n > 50) and wide range of response were available for Hyalella (n = 235) and Microtox{reg_sign} (n = 61) to determine AETs for organic carbon normalized PAHs, pesticides, and PCBs, and dry weight normalized metals, phenols and chlorinated phenols. The ability of these AETs to predict response in any bioassay at the sites in the database was compared with Ontario Ministry Environment and Energy (OMEE) Sediment Quality Guidelines and the Environment Canada (EC) Interim Sediment Quality Values. Measures of sensitivity (number correctly predicted/number impacted) and efficiency (number correctly predicted/number predicted) were compared. The EC Threshold Effects Level (TEL) was the most sensitive (fewest Type 2 errors) at 92%, but the least efficient (most Type 1 errors) at 35%. The lowest AET (LAET) of Hyalella and Microtox{reg_sign}, derived from the current study, was the next most sensitive (77%) and more efficient (44%). The OMEE Severe Effects Level was the least sensitive (59%) and the most efficient (53%). The EC Probable Effects Level (PEL) was 50% efficient and 72% sensitive. Of the four sets of sediment quality values, the OMEE Severe Effects Level had the highest overall reliability (number of correct predictions of effects and non-effects/number of sites examined) in predicting bioassay effects in the Washington State freshwater sediment database.

  16. Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex.

    PubMed

    Numata, Tomoyuki; Inanaga, Hideko; Sato, Chikara; Osawa, Takuo

    2015-01-30

    Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. Here, we show that the Csm1, Csm3, and Csm4 proteins from Methanocaldococcus jannaschii form a stable subcomplex. We also report the crystal structure of the M. jannaschii Csm3-Csm4 subcomplex at 3.1Å resolution. The complex structure revealed the presence of a basic concave surface around their interface, suggesting the RNA and/or DNA binding ability of the complex. A gel retardation analysis showed that the Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Based on bioinformatics, we constructed a model structure of the Csm1-Csm4-Csm3 ternary complex, which provides insights into its role in the Csm interference complex.

  17. Quantitative orientational analysis of a polymeric material (Kevlar{sup {reg_sign}} fibers) with x-ray microspectroscopy

    SciTech Connect

    Smith, A.P.; Ade, H.

    1996-12-01

    It has previously been shown that x-ray linear dichroism microscopy can be utilized to image and determine orientation in a polymeric material at high spatial resolution. We have now expanded on this technique and extracted quantitative information about the orientation of specific functional groups in a polymeric system from submicron areas. This is accomplished by acquiring and analyzing spectral data sets rather than just images at specific energies. It has allowed us to compare the relative lateral orientation of various grades of Kevlar{sup {reg_sign}} fibers. {copyright} {ital 1996 American Institute of Physics.}

  18. Application of CRISPR/Cas9 for biomedical discoveries.

    PubMed

    Riordan, Sean M; Heruth, Daniel P; Zhang, Li Q; Ye, Shui Qing

    2015-01-01

    The Clustered Regions of Interspersed Palindromic Repeats-Cas9 (CRISPR/Cas9), a viral defense system found in bacteria and archaea, has emerged as a tour de force genome editing tool. The CRISPR/Cas9 system is much easier to customize and optimize because the site selection for DNA cleavage is guided by a short sequence of RNA rather than an engineered protein as in the systems of zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN), and meganucleases. Although it still suffers from some off-target effects, the CRISPR/Cas9 system has been broadly and successfully applied for biomedical discoveries in a number of areas. In this review, we present a brief history and development of the CRISPR system and focus on the application of this genome editing technology for biomedical discoveries. We then present concise concluding remarks and future directions for this fast moving field.

  19. Editing plant genomes with CRISPR/Cas9.

    PubMed

    Belhaj, Khaoula; Chaparro-Garcia, Angela; Kamoun, Sophien; Patron, Nicola J; Nekrasov, Vladimir

    2015-04-01

    CRISPR/Cas9 is a rapidly developing genome editing technology that has been successfully applied in many organisms, including model and crop plants. Cas9, an RNA-guided DNA endonuclease, can be targeted to specific genomic sequences by engineering a separately encoded guide RNA with which it forms a complex. As only a short RNA sequence must be synthesized to confer recognition of a new target, CRISPR/Cas9 is a relatively cheap and easy to implement technology that has proven to be extremely versatile. Remarkably, in some plant species, homozygous knockout mutants can be produced in a single generation. Together with other sequence-specific nucleases, CRISPR/Cas9 is a game-changing technology that is poised to revolutionise basic research and plant breeding.

  20. Application of CRISPR/Cas9 to Autophagy Research.

    PubMed

    O'Prey, J; Sakamaki, J; Baudot, A D; New, M; Van Acker, T; Tooze, S A; Long, J S; Ryan, K M

    2017-01-01

    The ability to efficiently modulate autophagy activity is paramount in the study of the field. Conventional broad-range autophagy inhibitors and genetic manipulation using RNA interference (RNAi), although widely used in autophagy research, are often limited in specificity or efficacy. In this chapter, we address the problems of conventional autophagy-modulating tools by exploring the use of three different CRISPR/Cas9 systems to abrogate autophagy in numerous human and mouse cell lines. The first system generates cell lines constitutively deleted of ATG5 or ATG7 whereas the second and third systems express a Tet-On inducible-Cas9 that enables regulated deletion of ATG5 or ATG7. We observed the efficiency of autophagy inhibition using the CRISPR/Cas9 strategy to surpass that of RNAi, and successfully generated cells with complete and sustained autophagy disruption through the CRISPR/Cas9 technology.

  1. CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity.

    PubMed

    Barrangou, Rodolphe; Marraffini, Luciano A

    2014-04-24

    Clustered regularly interspaced short palindromic repeats (CRISPR), and associated proteins (Cas) comprise the CRISPR-Cas system, which confers adaptive immunity against exogenic elements in many bacteria and most archaea. CRISPR-mediated immunization occurs through the uptake of DNA from invasive genetic elements such as plasmids and viruses, followed by its integration into CRISPR loci. These loci are subsequently transcribed and processed into small interfering RNAs that guide nucleases for specific cleavage of complementary sequences. Conceptually, CRISPR-Cas shares functional features with the mammalian adaptive immune system, while also exhibiting characteristics of Lamarckian evolution. Because immune markers spliced from exogenous agents are integrated iteratively in CRISPR loci, they constitute a genetic record of vaccination events and reflect environmental conditions and changes over time. Cas endonucleases, which can be reprogrammed by small guide RNAs have shown unprecedented potential and flexibility for genome editing and can be repurposed for numerous DNA targeting applications including transcriptional control.

  2. 48 CFR 9903.201-1 - CAS applicability.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... following categories of contracts and subcontracts are exempt from all CAS requirements: (1) Sealed bid... subcontracts awarded on the basis of adequate price competition without submission of cost or pricing data....

  3. Engineering the Caenorhabditis elegans genome with CRISPR/Cas9.

    PubMed

    Waaijers, Selma; Boxem, Mike

    2014-08-01

    The development in early 2013 of CRISPR/Cas9-based genome engineering promises to dramatically advance our ability to alter the genomes of model systems at will. A single, easily produced targeting RNA guides the Cas9 endonuclease to a specific DNA sequence where it creates a double strand break. Imprecise repair of the break can yield mutations, while homologous recombination with a repair template can be used to effect specific changes to the genome. The tremendous potential of this system led several groups to independently adapt it for use in Caenorhabditiselegans, where it was successfully used to generate mutations and to create tailored genome changes through homologous recombination. Here, we review the different approaches taken to adapt CRISPR/Cas9 for C. elegans, and provide practical guidelines for CRISPR/Cas9-based genome engineering.

  4. 48 CFR 970.3002-1 - CAS applicability.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SUPPLEMENTARY REGULATIONS DOE MANAGEMENT AND OPERATING CONTRACTS Cost Accounting Standards Administration 970.3002-1 CAS applicability. The provisions of 48 CFR part 30 and 48 CFR chapter 99 (FAR Appendix)...

  5. Potential pitfalls of CRISPR/Cas9-mediated genome editing.

    PubMed

    Peng, Rongxue; Lin, Guigao; Li, Jinming

    2016-04-01

    Recently, a novel technique named the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas)9 system has been rapidly developed. This genome editing tool has improved our ability tremendously with respect to exploring the pathogenesis of diseases and correcting disease mutations, as well as phenotypes. With a short guide RNA, Cas9 can be precisely directed to target sites, and functions as an endonuclease to efficiently produce breaks in DNA double strands. Over the past 30 years, CRISPR has evolved from the 'curious sequences of unknown biological function' into a promising genome editing tool. As a result of the incessant development in the CRISPR/Cas9 system, Cas9 co-expressed with custom guide RNAs has been successfully used in a variety of cells and organisms. This genome editing technology can also be applied to synthetic biology, functional genomic screening, transcriptional modulation and gene therapy. However, although CRISPR/Cas9 has a broad range of action in science, there are several aspects that affect its efficiency and specificity, including Cas9 activity, target site selection and short guide RNA design, delivery methods, off-target effects and the incidence of homology-directed repair. In the present review, we highlight the factors that affect the utilization of CRISPR/Cas9, as well as possible strategies for handling any problems. Addressing these issues will allow us to take better advantage of this technique. In addition, we also review the history and rapid development of the CRISPR/Cas system from the time of its initial discovery in 2012.

  6. Calibrated Ancillary System (CAS) user's guide, volume 7

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Calibrated Ancillary System (CAS) provides real-time calibrated parameters from the orbiter downlink (ancillary data) to the Goddard Space Flight Center (GSFC). This user's guide contains the introduction to the equipment, operation, general procedures, and specific procedures of CAS. Volume 7 describes the data flow engineer (DFE) user mission planning procedures which include instructions for processing the SDT/TDT (shuttle data tape/telemetry descriptor tape).

  7. Calibrated Ancillary System (CAS) user's guide, volume 5

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Calibrated Ancillary System (CAS) provides real-time parameters from the orbiter downlink (ancillary data) to the Goddard Space Flight Center (GSFC). This user's guide contains the introduction to the equipment, operation, general procedures, and specific procedures of CAS. Volume 5 describes the testing user mission planning procedures including the bulletin board system and ancillary products procedures. Instructions for viewing the SDT/TDT (shuttle data tape/telemetry descriptor tape) data base and the file management menu are also given.

  8. Calibrated Ancillary System (CAS) user's guide, volume 6

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Calibrated Ancillary System (CAS) provides real-time calibrated parameters from the orbiter downlink (ancillary data) to the Goddard Space Flight Center (GSFC). This user's guide contains the introduction to the equipment, operation, general procedures, and specific procedures of CAS. Volume 6 describes ancillary products procedures, enhancement menu and processing task procedures for SDT/TDT (shuttle data tape/telemetry descriptor tape), database errors and network data driver (NDD) product menu procedures, and utility menu procedures.

  9. Calibrated Ancillary System (CAS) user's guide, volume 4

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Calibrated Ancillary System (CAS) provides real-time calibrated parameters from the orbiter downlink (ancillary data) to the Goddard Space Flight Center (GSFC). This user's guide contains the introduction to the equipment, operation, general procedures, and specific procedures of the CAS. Volume 4 presents the GSFC user mission planning procedures covering the mission planning main menu, bulletin board system, ancillary products menu, utility menu procedures, and ancillary support files procedures.

  10. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

    PubMed Central

    Ward, Lucas D.; Kellis, Manolis

    2016-01-01

    More than 90% of common variants associated with complex traits do not affect proteins directly, but instead the circuits that control gene expression. This has increased the urgency of understanding the regulatory genome as a key component for translating genetic results into mechanistic insights and ultimately therapeutics. To address this challenge, we developed HaploReg (http://compbio.mit.edu/HaploReg) to aid the functional dissection of genome-wide association study (GWAS) results, the prediction of putative causal variants in haplotype blocks, the prediction of likely cell types of action, and the prediction of candidate target genes by systematic mining of comparative, epigenomic and regulatory annotations. Since first launching the website in 2011, we have greatly expanded HaploReg, increasing the number of chromatin state maps to 127 reference epigenomes from ENCODE 2012 and Roadmap Epigenomics, incorporating regulator binding data, expanding regulatory motif disruption annotations, and integrating expression quantitative trait locus (eQTL) variants and their tissue-specific target genes from GTEx, Geuvadis, and other recent studies. We present these updates as HaploReg v4, and illustrate a use case of HaploReg for attention deficit hyperactivity disorder (ADHD)-associated SNPs with putative brain regulatory mechanisms. PMID:26657631

  11. IL-17 functions through the novel REG3β-JAK2-STAT3 inflammatory pathway to promote the transition from chronic pancreatitis to pancreatic cancer

    PubMed Central

    Loncle, Celine; Bonjoch, Laia; Folch-Puy, Emma; Lopez-Millan, Maria Belen; Lac, Sophie; Molejon, Maria Inés; Chuluyan, Eduardo; Cordelier, Pierre; Dubus, Pierre; Lomberk, Gwen; Urrutia, Raul; Closa, Daniel; Iovanna, Juan L

    2015-01-01

    Pancreatic ductal adenocarcinoma (PDAC) offers an optimal model for discovering “druggable” molecular pathways that participate in inflammation-associated cancer development. Chronic pancreatitis, a common prolonged inflammatory disease, behaves as a well-known premalignant condition that contributes to PDAC development. Although the mechanisms underlying the pancreatitis-to-cancer transition remain to be fully elucidated, emerging evidence supports the hypothesis that the actions of proinflammatory mediators on cells harboring Kras mutations promote neoplastic transformation. Recent elegant studies demonstrated that the IL-17 pathway mediates this phenomenon and can be targeted with antibodies, but the downstream mechanisms by which IL-17 functions during this transition are currently unclear. In this study, we demonstrate that IL-17 induces the expression of REG3β, a well-known mediator of pancreatitis, during acinar-to-ductal metaplasia and in early PanIN lesions. Furthermore, we found that REG3β promotes cell growth and decreases sensitivity to cell death through activation of the gp130-JAK2-STAT3-dependent pathway. Genetic inactivation of REG3β in the context of oncogenic Kras-driven PDAC resulted in reduced PanIN formation, an effect that could be rescued by administration of exogenous REG3β. Taken together, our findings provide mechanistic insight into the pathways underlying inflammation-associated pancreatic cancer, revealing a dual and contextual pathophysiological role for REG3β during pancreatitis and PDAC initiation. PMID:26404002

  12. Rational design of a split-Cas9 enzyme complex

    SciTech Connect

    Wright, Addison V.; Sternberg, Samuel H.; Taylor, David W.; Staahl, Brett T.; Bardales, Jorge A.; Kornfeld, Jack E.; Doudna, Jennifer A.

    2015-02-23

    Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool for genome editing, transcriptional regulation, and cellular imaging applications. Structures of Streptococcus pyogenes Cas9 alone or bound to single-guide RNA (sgRNA) and target DNA revealed a bilobed protein architecture that undergoes major conformational changes upon guide RNA and DNA binding. To investigate the molecular determinants and relevance of the interlobe rearrangement for target recognition and cleavage, we designed a split-Cas9 enzyme in which the nuclease lobe and α-helical lobe are expressed as separate polypeptides. The lobes do not interact on their own, the sgRNA recruits them into a ternary complex that recapitulates the activity of full-length Cas9 and catalyzes site-specific DNA cleavage. The use of a modified sgRNA abrogates split-Cas9 activity by preventing dimerization, allowing for the development of an inducible dimerization system. We propose that split-Cas9 can act as a highly regulatable platform for genome-engineering applications.

  13. Rational design of a split-Cas9 enzyme complex

    DOE PAGES

    Wright, Addison V.; Sternberg, Samuel H.; Taylor, David W.; ...

    2015-02-23

    Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool for genome editing, transcriptional regulation, and cellular imaging applications. Structures of Streptococcus pyogenes Cas9 alone or bound to single-guide RNA (sgRNA) and target DNA revealed a bilobed protein architecture that undergoes major conformational changes upon guide RNA and DNA binding. To investigate the molecular determinants and relevance of the interlobe rearrangement for target recognition and cleavage, we designed a split-Cas9 enzyme in which the nuclease lobe and α-helical lobe are expressed as separate polypeptides. The lobes do not interactmore » on their own, the sgRNA recruits them into a ternary complex that recapitulates the activity of full-length Cas9 and catalyzes site-specific DNA cleavage. The use of a modified sgRNA abrogates split-Cas9 activity by preventing dimerization, allowing for the development of an inducible dimerization system. We propose that split-Cas9 can act as a highly regulatable platform for genome-engineering applications.« less

  14. Rational design of a split-Cas9 enzyme complex.

    PubMed

    Wright, Addison V; Sternberg, Samuel H; Taylor, David W; Staahl, Brett T; Bardales, Jorge A; Kornfeld, Jack E; Doudna, Jennifer A

    2015-03-10

    Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool for genome editing, transcriptional regulation, and cellular imaging applications. Structures of Streptococcus pyogenes Cas9 alone or bound to single-guide RNA (sgRNA) and target DNA revealed a bilobed protein architecture that undergoes major conformational changes upon guide RNA and DNA binding. To investigate the molecular determinants and relevance of the interlobe rearrangement for target recognition and cleavage, we designed a split-Cas9 enzyme in which the nuclease lobe and α-helical lobe are expressed as separate polypeptides. Although the lobes do not interact on their own, the sgRNA recruits them into a ternary complex that recapitulates the activity of full-length Cas9 and catalyzes site-specific DNA cleavage. The use of a modified sgRNA abrogates split-Cas9 activity by preventing dimerization, allowing for the development of an inducible dimerization system. We propose that split-Cas9 can act as a highly regulatable platform for genome-engineering applications.

  15. Genes Specific for the Biosynthesis of Clavam Metabolites Antipodal to Clavulanic Acid Are Clustered with the Gene for Clavaminate Synthase 1 in Streptomyces clavuligerus

    PubMed Central

    Mosher, Roy H.; Paradkar, Ashish S.; Anders, Cecilia; Barton, Barry; Jensen, Susan E.

    1999-01-01

    Portions of the Streptomyces clavuligerus chromosome flanking cas1, which encodes the clavaminate synthase 1 isoenzyme (CAS1), have been cloned and sequenced. Mutants of S. clavuligerus disrupted in cvm1, the open reading frame located immediately upstream of cas1, were constructed by a gene replacement procedure. Similar techniques were used to generate S. clavuligerus mutants carrying a deletion that encompassed portions of the two open reading frames, cvm4 and cvm5, located directly downstream of cas1. Both classes of mutants still produced clavulanic acid and cephamycin C but lost the ability to synthesize the antipodal clavam metabolites clavam-2-carboxylate, 2-hydroxymethyl-clavam, and 2-alanylclavam. These results suggested that cas1 is clustered with genes essential and specific for clavam metabolite biosynthesis. When a cas1 mutant of S. clavuligerus was constructed by gene replacement, it produced lower levels of both clavulanic acid and most of the antipodal clavams except for 2-alanylclavam. However, a double mutant of S. clavuligerus disrupted in both cas1 and cas2 produced neither clavulanic acid nor any of the antipodal clavams, including 2-alanylclavam. This outcome was consistent with the contribution of both CAS1 and CAS2 to a common pool of clavaminic acid that is shunted toward clavulanic acid and clavam metabolite biosynthesis. PMID:10223939

  16. Pipe Crawler{reg_sign} internal piping characterization system - deactivation and decommissioning focus area. Innovative Technology Summary Report

    SciTech Connect

    1998-02-01

    Pipe Crawler{reg_sign} is a pipe surveying system for performing radiological characterization and/or free release surveys of piping systems. The technology employs a family of manually advanced, wheeled platforms, or crawlers, fitted with one or more arrays of thin Geiger Mueller (GM) detectors operated from an external power supply and data processing unit. Survey readings are taken in a step-wise fashion. A video camera and tape recording system are used for video surveys of pipe interiors prior to and during radiological surveys. Pipe Crawler{reg_sign} has potential advantages over the baseline and other technologies in areas of cost, durability, waste minimization, and intrusiveness. Advantages include potentially reduced cost, potential reuse of the pipe system, reduced waste volume, and the ability to manage pipes in place with minimal disturbance to facility operations. Advantages over competing technologies include potentially reduced costs and the ability to perform beta-gamma surveys that are capable of passing regulatory scrutiny for free release of piping systems.

  17. Climate-vegetation interactions in the coupled RegCM4 - CLM4.5 CNDV model

    NASA Astrophysics Data System (ADS)

    Caporaso, Luca; Giuliani, Graziano; Giorgi, Filippo

    2016-04-01

    We use the latest version of International Center for Theoretical Physics (ICTP) regional climate model (RegCM4) coupled with the Community Land Model version 4.5 (CLM4.5) including a dynamic vegetation model to study biogeophysical feedbacks in the climate system related to vegetation composition and structure. Sets of parallel experiments are conducted over the Africa and South America CORDEX domains using the RegCM4-CLM4.5 in its standard configuration and with the CNDV activated (CLM 4.5 with both the Carbon Nitrogen and the Dynamic Vegetation Model activated). The potential role of regional vegetation feedbacks within the climate system and the impact of climate variability and change on the ecosystem dynamics is assessed for both domains. In addition, the sensitivity to initial vegetation conditions and different idealized climate forcings is investigated. Preliminary results show that the changes in the climate forcing can have substantial effects on the dynamics and evolution of different vegetation types over both domains, and that the vegetation coupling can have a substantial effect on the simulated regional climate regimes. Our results thus indicate on the one hand that climate change can have profound effects on the evolution of important ecosystems for the two regions, and on the other that vegetation dynamics can indeed affect the climate response at the regional scale.

  18. Dose response of benzo(a)pyrene-induced mutagenesis using the BigBlue{reg_sign} transgenic mouse assay

    SciTech Connect

    Kotturi, G.; Holcroft, J.; Boer, J. de

    1997-10-01

    To investigate the dose response of benzo(a)pyrene-induced mutagenesis, groups of five BigBlue{reg_sign} transgenic mice were injected with a single intra-peritoneal dose were injected with corn oil containing benzo(a)pyrene to achieve the following concentrations: 0, 62.5, 125, 250, 500 mg/kg. Tissues were harvested after a 14 day expression time and analysed for mutational events. DNA adducts were measured in the liver of mice that were sacrificed 1 day after injection. The mutant frequency in the mouse liver linearly increased from 5.2 to 53.5 x 10{sup -5} in a dose-specific manner from 0 to 500 mg/kg benzo(a)pyrene. Mutants were sequenced to give an estimate of the number of clonal events as a function of benzo(a) pyrene with a total of 20 exposed animals (4 doses and five animals/dose), we established frequently mutated sites or `mutational hotspots` as well as a full mutational spectrum. Various other factors associated with the BigBlue{reg_sign} assay were analysed such as the effect of plating density on the purity of mutant plaques during the phage purification step.

  19. Enhanced bioremediation of anthracene contaminated soil by bioaugmentation and application of non-ionic surfactant -- Fuelbuster{reg_sign}

    SciTech Connect

    Pattanayek, M.; Cobb, G.P.

    1995-12-31

    Surfactants enable the mass transfer of hydrophobic compounds to more hydrophilic phases, thereby increasing bioavailability to microorganisms for degradation. Indigenous soil bacteria was enriched over three months to selectively degrade anthracene. Enhanced soil remediation was determined using radiolabeled anthracene and comparing the end product 14-CO{sub 2} from different treatment and control groups. Bioreactors were engineered, fitted with inflow of air and CO{sub 2} trapping devices. The two treatment groups included were, (1) sterile soil seeded with enriched microorganisms and (2) sterile soil seeded with microorganisms and Fuelbuster{reg_sign} at concentrations below its critical micellar concentrations (determined by surface tension method). The control group had only sterile soil to account for any abiotic degradation. Remediation was monitored over 91 days and the end product was analyzed by liquid scintillation counting. On day 50 of remediation the relative CO{sub 2} evolution was 0.086 : 0.22 : 0.69 for control: Treatment 1: Treatment 2. On day 50 additional Fuelbuster{reg_sign} was injected into Treatment 2, which resulted in a 30% increase in CO{sub 2} evolution when the study was terminated. Binding effect of soil on the bioavailability of anthracene is currently being studied using the same experimental setup, excluding soil from all treatment groups.

  20. iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations.

    PubMed

    Liang, Siqi; Tippens, Nathaniel D; Zhou, Yaoda; Mort, Matthew; Stenson, Peter D; Cooper, David N; Yu, Haiyuan

    2017-01-18

    The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-DNA and chromatin-chromatin interactions for the analysis of both coding and non-coding disease-associated mutations to obtain mechanistic insights into their functional impact. Using iRegNet3D, we find that disease-associated mutations may perturb the regulatory network through diverse mechanisms including chromatin looping. iRegNet3D promises to be an indispensable tool in large-scale sequencing and disease association studies.

  1. Cas9 in Genetically Modified Food Is Unlikely to Cause Food Allergy.

    PubMed

    Nakajima, Osamu; Nishimaki-Mogami, Tomoko; Kondo, Kazunari

    2016-01-01

    Genome editing has undergone rapid development during the last three years. It is anticipated that genetically modified organisms (GMOs) for food purposes will be widely produced using the clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR)/Cas9 system in the near future. However, the Cas9 gene may then enter the genomes of GMOs for food if the breeding process is not strictly managed, which could lead to the Cas9 protein or associated peptides being produced within these organisms. A variety of peptides could theoretically be produced from the Cas9 gene by using open reading frames different from that of Cas9 in the GMOs. In this study, Cas9 and the peptides potentially encoded by Cas9 genes were studied regarding their immunogenicity, in terms of the digestibility of Cas9 and the homology of the peptides to food allergens. First, the digestibility and thermal stability of Cas9 were studied. Digestibility was tested with natural or heat-denatured Cas9 in simulated gastric fluid in vitro. The two types of Cas9 were digested rapidly. Cas9 was also gradually degraded during heat treatment. Second, the peptides potentially encoded by Cas9 genes were examined for their homology to food allergens. Specifically, an 8-mer exact match search and a sliding 80-mer window search were performed using allergen databases. One of the peptides was found to have homology with a food allergen.

  2. Tyrosine phosphorylation within the SH3 domain regulates CAS subcellular localization, cell migration, and invasiveness.

    PubMed

    Janoštiak, Radoslav; Tolde, Ondřej; Brůhová, Zuzana; Novotný, Marian; Hanks, Steven K; Rösel, Daniel; Brábek, Jan

    2011-11-01

    Crk-associated substrate (CAS) is a major tyrosine-phosphorylated protein in cells transformed by v-crk and v-src oncogenes and plays an important role in invasiveness of Src-transformed cells. A novel phosphorylation site on CAS, Tyr-12 (Y12) within the ligand-binding hydrophobic pocket of the CAS SH3 domain, was identified and found to be enriched in Src-transformed cells and invasive human carcinoma cells. To study the biological significance of CAS Y12 phosphorylation, phosphomimicking Y12E and nonphosphorylatable Y12F mutants of CAS were studied. The phosphomimicking mutation decreased interaction of the CAS SH3 domain with focal adhesion kinase (FAK) and PTP-PEST and reduced tyrosine phosphorylation of FAK. Live-cell imaging showed that green fluorescent protein-tagged CAS Y12E mutant is, in contrast to wild-type or Y12F CAS, excluded from focal adhesions but retains its localization to podosome-type adhesions. Expression of CAS-Y12F in cas-/- mouse embryonic fibroblasts resulted in hyperphosphorylation of the CAS substrate domain, and this was associated with slower turnover of focal adhesions and decreased cell migration. Moreover, expression of CAS Y12F in Src-transformed cells greatly decreased invasiveness when compared to wild-type CAS expression. These findings reveal an important role of CAS Y12 phosphorylation in the regulation of focal adhesion assembly, cell migration, and invasiveness of Src-transformed cells.

  3. A non-inheritable maternal Cas9-based multiple-gene editing system in mice.

    PubMed

    Sakurai, Takayuki; Kamiyoshi, Akiko; Kawate, Hisaka; Mori, Chie; Watanabe, Satoshi; Tanaka, Megumu; Uetake, Ryuichi; Sato, Masahiro; Shindo, Takayuki

    2016-01-28

    The CRISPR/Cas9 system is capable of editing multiple genes through one-step zygote injection. The preexisting method is largely based on the co-injection of Cas9 DNA (or mRNA) and guide RNAs (gRNAs); however, it is unclear how many genes can be simultaneously edited by this method, and a reliable means to generate transgenic (Tg) animals with multiple gene editing has yet to be developed. Here, we employed non-inheritable maternal Cas9 (maCas9) protein derived from Tg mice with systemic Cas9 overexpression (Cas9 mice). The maCas9 protein in zygotes derived from mating or in vitro fertilization of Tg/+ oocytes and +/+ sperm could successfully edit the target genome. The efficiency of such maCas9-based genome editing was comparable to that of zygote microinjection-based genome editing widely used at present. Furthermore, we demonstrated a novel approach to create "Cas9 transgene-free" gene-modified mice using non-Tg (+/+) zygotes carrying maCas9. The maCas9 protein in mouse zygotes edited nine target loci simultaneously after injection with nine different gRNAs alone. Cas9 mouse-derived zygotes have the potential to facilitate the creation of genetically modified animals carrying the Cas9 transgene, enabling repeatable genome engineering and the production of Cas9 transgene-free mice.

  4. Microarray-based gene expression profiling reveals genes and pathways involved in the oncogenic function of REG3A on pancreatic cancer cells.

    PubMed

    Xu, Qianqian; Fu, Rong; Yin, Guoxiao; Liu, Xiulan; Liu, Yang; Xiang, Ming

    2016-03-10

    We previously reported that regenerating islet-derived protein 3 alpha (REG3A) exacerbates pancreatic malignancies. The mechanism of this effect has not been clearly elucidated. Here we first identified key differentially expressed genes (DEGs) and signal pathways in the pancreatic cancer cell line SW1990, compared to two control cell lines, by microarray analysis. We then identified key genes and pathways regulated by REG3A or the cytokine IL6 in SW1990 cells. Afterwards, these DEGs induced by REG3A or IL6 were subjected to KEGG pathway enrichment analysis and GO function analysis by the DAVID online tool. Ultimately, we constructed protein-protein interaction networks among the DEGs by Cytoscape. Among the three pancreatic cell lines, SW1990 exhibited highly deterioration with the activation of genes and pathways related to proliferation, survival, angiogenesis, and invasion. As a result, 50 DEGs enriched in 11 pathways were identified in REG3A-treated SW1990 cells, and 28 DEGs enriched in 9 pathways were detected in IL6-treated cells. Overall, results of microarray analysis followed by qRT-PCR and Western blotting suggest that REG3A regulates pancreatic cell growth by increasing the expression of at least 8 genes: JAK1, STAT3, IL10, FOXM1, KRAS, MYC, CyclinD1, and c-fos; and activation of at least 4 signal pathways: TGFβ, PDGF, angiogenesis and RAS. Similar results were obtained with IL6 treatment. Regulation network analysis confirmed the cell growth related DEGs, and further uncovered three transcription factor families with immune functions regulated by REG3A.

  5. Comparative analysis of CRISPR-Cas systems in Klebsiella genomes.

    PubMed

    Shen, Juntao; Lv, Li; Wang, Xudong; Xiu, Zhilong; Chen, Guoqiang

    2017-02-03

    Prokaryotic CRISPR-Cas system provides adaptive immunity against invasive genetic elements. Bacteria of the genus Klebsiella are important nosocomial opportunistic pathogens. However, information of CRISPR-Cas system in Klebsiella remains largely unknown. Here, we analyzed the CRISPR-Cas systems of 68 complete genomes of Klebsiella representing four species. All the elements for CRISPR-Cas system (cas genes, repeats, leader sequences, and PAMs) were characterized. Besides the typical Type I-E and I-F CRISPR-Cas systems, a new Subtype I system located in the ABC transport system-glyoxalase region was found. The conservation of the new subtype CRISPR system between different species showed new evidence for CRISPR horizontal transfer. CRISPR polymorphism was strongly correlated both with species and multilocus sequence types. Some results indicated the function of adaptive immunity: most spacers (112 of 124) matched to prophages and plasmids and no matching housekeeping genes; new spacer acquisition was observed within the same sequence type (ST) and same clonal complex; the identical spacers were observed only in the ancient position (far from the leader) between different STs and clonal complexes. Interestingly, a high ratio of self-targeting spacers (7.5%, 31 of 416) was found in CRISPR-bearing Klebsiella pneumoniae (61%, 11 of 18). In some strains, there even were multiple full matching self-targeting spacers. Some self-targeting spacers were conserved even between different STs. These results indicated that some unknown mechanisms existed to compromise the function of self-targets of CRISPR-Cas systems in K. pneumoniae.

  6. ProReg XL Tool: an easy-to-use computer tool suite for rapidly regrouping a large number of identical electrophoretic profiles.

    PubMed

    Massias, Bastien; Urdaci, Maria C

    2009-05-01

    The ProReg XL Tool (Profile Regrouping Excel Tool) is a new tool suite designed to rapidly regroup a large number of identical electrophoretic profiles. This tool suite is coded in Visual Basic Application for Microsoft Excel, and thus requires this spreadsheet software to operate. It was designed for use with a new screening strategy of clones from an rrs (16S rDNA) clone library, but it may also be helpful in other electrophoretic applications. ProReg XL Tool is organized in different steps where the user has the capability--in addition to regrouping electrophoretic profiles--to control gel quality, determine signal attenuation, and draw pie charts.

  7. Spectroscopic studies of three Cepheids with high positive pulsation period increments: SZ Cas, BY Cas, and RU Sct

    NASA Astrophysics Data System (ADS)

    Usenko, I. A.; Klochkova, V. G.

    2015-07-01

    Three high-resolution spectra have been taken at different times with the 6-m SAO RAS telescope (LYNX and PFES spectrographs) for three Cepheids exhibiting high positive period increments: the small-amplitude (DCEPS) SZ Cas and BY Cas and the classical (DCEP) RU Sct. SZ Cas and RU Sct are members of the Galactic open clusters χ and h Per and Trump 35, respectively. Analysis of the spectra has shown that the interstellar Na I D1 and D2 lines in all objects are considerably stronger than the atmospheric ones and are redshifted in SZ Cas and BY Cas and blushifted in RU Sct. The core of the H α absorption line in BY Cas has an asymmetric knifelike shape, while RU Sct exhibits an intense emission in the blue wing of this line. Such phenomena are observed in long-period Cepheids and bright hypergiants with an extended envelope. In this case, the strong Mg Ib 5183.62 Å and Ba II 5853.67, 6141.713, and 6496.90 Å lines with low χlow in SZ Cas and RU Sct also show characteristic knifelike profiles with an asymmetry in the red region, while the Ba II 4934.095 Å line shows similar profiles in the blue one. The absorption lines of neutral atoms and singly ionized metals with different lowerlevel excitation potentials exhibit different degrees of asymmetry: from a pronounced one with secondary components in BY Cas (similar to those in the small-amplitude Cepheid BG Cru pulsating in the first overtone and having an envelope) to its insignificance or virtual absence in SZ Cas and RU Sct. Analysis of the secular changes in mean T eff determined from photometric color indices and spectra over the last 55 years for these stars has revealed periodic fluctuations of 200 K for SZ Cas and BY Cas and 500 K for RU Sct. For SZ Cas and RU Sct, T eff determined in some years from some color indices show much lower values, which together with the temperature fluctuations can be associated with mass loss and dust formation. Based on these facts, we hypothesize the existence of

  8. Pyo-pneumothorax tuberculeux: à propos de 18 cas

    PubMed Central

    Hicham, Souhi; Hanane, El Ouazzani; Hicham, Janah; Ismaïl, Rhorfi; Ahmed, Abid

    2016-01-01

    Le pyo-pneumothorax tuberculeux est une complication rare mais grave de la tuberculose pulmonaire évolutive. Nous rapportons une série de 18 cas de pyo-pneumothorax tuberculeux colligés au service de Pneumo-Phtisiologie de l'Hôpital Militaire d'Instruction Mohammed V de Rabat entre janvier 2005 et décembre 2009. Il s'agit de 15 hommes et 3 femmes d’âge moyen de 35 ans ±7 ans. 4 patients étaient diabétiques. Le tabagisme était retrouvé chez 9 cas. Le pyo-pneumothorax était du coté droit dans 13 cas. La radiographie thoracique avait montré des lésions cavitaires chez 15 patients et des lésions étendues et bilatérales chez 8 cas. La recherche de BK dans le liquide de tubage gastrique était positive chez 16 cas. Un drainage thoracique associé à un traitement antituberculeux selon le régime 2SRHZ/7RH et une kinésithérapie respiratoire ont été instaurés chez tous les cas. La durée moyenne de drainage pleural était de 4 semaines. Chez 3 cas on avait noté la persistance de la suppuration pleurale ayant nécessité une toilette pleurale sous thoracoscopie avec pleurectomie et exérèse pulmonaire limitée emportant la lésion parenchymateuse tuberculeuse et la persistance d'une volumineuse poche pleurale avec trouble ventilatoire restrictif ayant nécessité une décortication pleurale chirurgicale chez deux cas. L’évolution était favorable avec pachypleurite séquellaire minime chez le reste des cas. Le pyo-pneumothorax tuberculeux est une forme grave, qui est souvent en rapport avec une tuberculose cavitaire active. L’évolution est généralement trainante malgré le traitement antituberculeux et le drainage thoracique, d'où la nécessité d'un diagnostic et un traitement précoce de toute forme de tuberculose. PMID:27583090

  9. Cornerstones of CRISPR-Cas in drug discovery and therapy.

    PubMed

    Fellmann, Christof; Gowen, Benjamin G; Lin, Pei-Chun; Doudna, Jennifer A; Corn, Jacob E

    2017-02-01

    The recent development of CRISPR-Cas systems as easily accessible and programmable tools for genome editing and regulation is spurring a revolution in biology. Paired with the rapid expansion of reference and personalized genomic sequence information, technologies based on CRISPR-Cas are enabling nearly unlimited genetic manipulation, even in previously difficult contexts, including human cells. Although much attention has focused on the potential of CRISPR-Cas to cure Mendelian diseases, the technology also holds promise to transform the development of therapies to treat complex heritable and somatic disorders. In this Review, we discuss how CRISPR-Cas can affect the next generation of drugs by accelerating the identification and validation of high-value targets, uncovering high-confidence biomarkers and developing differentiated breakthrough therapies. We focus on the promises, pitfalls and hurdles of this revolutionary gene-editing technology, discuss key aspects of different CRISPR-Cas screening platforms and offer our perspectives on the best practices in genome engineering.

  10. SD-CAS: Spin Dynamics by Computer Algebra System.

    PubMed

    Filip, Xenia; Filip, Claudiu

    2010-11-01

    A computer algebra tool for describing the Liouville-space quantum evolution of nuclear 1/2-spins is introduced and implemented within a computational framework named Spin Dynamics by Computer Algebra System (SD-CAS). A distinctive feature compared with numerical and previous computer algebra approaches to solving spin dynamics problems results from the fact that no matrix representation for spin operators is used in SD-CAS, which determines a full symbolic character to the performed computations. Spin correlations are stored in SD-CAS as four-entry nested lists of which size increases linearly with the number of spins into the system and are easily mapped into analytical expressions in terms of spin operator products. For the so defined SD-CAS spin correlations a set of specialized functions and procedures is introduced that are essential for implementing basic spin algebra operations, such as the spin operator products, commutators, and scalar products. They provide results in an abstract algebraic form: specific procedures to quantitatively evaluate such symbolic expressions with respect to the involved spin interaction parameters and experimental conditions are also discussed. Although the main focus in the present work is on laying the foundation for spin dynamics symbolic computation in NMR based on a non-matrix formalism, practical aspects are also considered throughout the theoretical development process. In particular, specific SD-CAS routines have been implemented using the YACAS computer algebra package (http://yacas.sourceforge.net), and their functionality was demonstrated on a few illustrative examples.

  11. Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n-Butanol Production in Escherichia coli.

    PubMed

    Heo, Min-Ji; Jung, Hwi-Min; Um, Jaeyong; Lee, Sang-Woo; Oh, Min-Kyu

    2017-02-17

    Genome editing using CRISPR/Cas9 was successfully demonstrated in Esherichia coli to effectively produce n-butanol in a defined medium under microaerobic condition. The butanol synthetic pathway genes including those encoding oxygen-tolerant alcohol dehydrogenase were overexpressed in metabolically engineered E. coli, resulting in 0.82 g/L butanol production. To increase butanol production, carbon flux from acetyl-CoA to citric acid cycle should be redirected to acetoacetyl-CoA. For this purpose, the 5'-untranslated region sequence of gltA encoding citrate synthase was designed using an expression prediction program, UTR designer, and modified using the CRISPR/Cas9 genome editing method to reduce its expression level. E. coli strains with decreased citrate synthase expression produced more butanol and the citrate synthase activity was correlated with butanol production. These results demonstrate that redistributing carbon flux using genome editing is an efficient engineering tool for metabolite overproduction.

  12. [Cardiovascular and renal protection of patients with type 2 diabetes : focus after EMPA-REG OUTCOME and LEADER].

    PubMed

    Scheen, A J; Piérard, L; Krzesinski, J-M; Paquot, N

    2016-09-01

    Type 2 diabetes (T2D), often associated with arterial hypertension, represents a high risk of cardiovascular disease and nephropathy. Two clinical trials demonstrate the superiority versus a placebo of two antidiabetic drugs in patients with T2D and high cardiovascular risk : empagliflozin, an inhibitor of sodium-glucose type 2 (SGLT2) cotransporters, in EMPA-REG OUTCOME and liraglutide, an agonist of glucagon-like peptide-1 (GLP-1) receptors, in LEADER. Both medications showed a significant reduction in major cardiovascular events (-14 and -13 %, respectively), cardiovascular mortality (-38 and -22%), all-cause mortality (-32 and -15 %) and renal events (-39 et -22 %). The underlying protective mechanisms remain controverted. Ongoing studies should allow to decide whether the benefits are specific to each molecule or may be attributed to a class effect.

  13. Diagnosing the strength of soil temperature in the land atmosphere interactions over Asia based on RegCM4 model

    NASA Astrophysics Data System (ADS)

    Liu, Di; Yu, Zhongbo; Zhang, Jianyun

    2015-07-01

    This study aims to investigate the soil temperature atmosphere (ST Atm) coupling strength and their influence on the subsequent climate anomalies over Asia based on a regional climate model RegCM4 with both statistical analysis method and numerical experiments. The major findings are as follows: (1) The soil temperature precipitation (ST P) coupling is quite weak and spatially scattered from both RegCM4 output and GLDAS data in each season with the only obvious signals existing over the north India region in summer season according to the RegCM4 output; the soil temperature 2m air temperature (ST T2m) coupling is strong and spatially continuous with the India (in spring, summer and autumn seasons), South Indochina (in spring and summer seasons) and part of North China (in summer season) standing out as hotspots. (2) The soil temperature evapotranspiration (ST ET) and soil temperature evaporative fraction (ST EF) coupling almost resembles the same spatial patterns and magnitude in each season. Both the ET and EF play an important role in linking ST P coupling in each season, but not in the ST T2m coupling. The hotspots of ST T2m coupling outweigh the areas with strong ST ET and ST EF coupling. Only the India and Indochina in each season are recognized by the RegCM4 while the Indochina and west Asia in spring, north India, Indochina and part of mid-high latitudes in summer season pinpointed by GLDAS data show consistent strong ST T2m coupling with significant ST ET and ST EF coupling. This finding demonstrates the complicated ST Atm coupling. (3) The ST anomalies prescribed at the first step of each season can only persist a short time (within 5 days) over most part of the study area while the fixed one-month anomalies can last longer (approximately 2 months with colder anomalies and 45 days with warmer anomalies in tropical regions). (4) The impact of ST anomalies on subsequent precipitation is quite weak and can be ignored over most part of the study area, while

  14. Assessment of TEES{reg_sign} applications for Wet Industrial Wastes: Energy benefit and economic analysis report

    SciTech Connect

    Elliott, D.C.; Scheer, T.H.

    1992-02-01

    Fundamental work is catalyzed biomass pyrolysis/gasification led to the Thermochemical Environmental Energy System (TEES{reg_sign}) concept, a means of converting moist biomass feedstocks to high-value fuel gases such as methane. A low-temperature (350{degrees}C), pressurized (3100 psig) reaction environment and a nickel catalyst are used to reduce volumes of very high-moisture wastes such as food processing byproducts while producing useful quantities of energy. A study was conducted to assess the economic viability of a range of potential applications of the process. Cases examined included feedstocks of cheese whey, grape pomace, spent grain, and an organic chemical waste stream. The analysis indicated that only the organic chemical waste process is economically attractive in the existing energy/economic environment. However, food processing cases will become attractive as alternative disposal practices are curtailed and energy prices rise.

  15. Recent Climate Trends over the Western Himalayas: An Application of Regional Climate Model (RegT-Band)

    NASA Astrophysics Data System (ADS)

    Tiwari, Pushp Raj; Charan Mohanty, Uma

    2013-04-01

    It is a well-known fact that the present day General Circulation Models (GCMs) are unable to represent various regional scale processes because of their coarser resolution. On the other hand Regional Climate Models (RCMs), which have well established resolvability of sub-grid scale features such as topography and clouds may perform better compare to GCMs. So keeping in mind the edge of RCMs over GCMs an attempt has been made to study the regional climate especially the precipitation and surface air temperature during recent decades over the Western Himalayas (WH), which comes under East Asia CORDEX domain. This region receives its wintertime precipitation mainly in the form of snow, which is the main source of water for most of the Northern Indian Rivers. Recent studies using observational data show the variability of temperature and precipitation over this heterogeneous region for wintertime (December, January, February, DJF). In the present study, performance of tropical band version of regional climate model is examined in representing wintertime circulation and precipitation features (as well as variation in extreme years) during recent decades. Latest version of ICTP Regional Climate Model (RegT-Band) has been integrated for a period of 30 years (1981 - 2011) at a horizontal resolution of 45 km. The model has been integrated for four months i.e. for each winter season separately (Nov 1981-Feb 1982; Nov 1982-Feb 1983;…; Nov 2011-Feb 2012) where first one month is kept for model spin up. In order to understand the large scale circulation pattern as well as mid latitude synoptic systems that influence the climate/weather situation over the study area, the model domain is extended from 30˚S - 55˚N and 30˚E - 120˚E. The initial and lateral boundary conditions in the model are provided from National Centre for Environment Prediction (NCEP) - Department of Energy (DOE) reanalysis 2 data. The geophysical parameters from the United State Geological Survey and

  16. Knockout of leucine aminopeptidase in Toxoplasma gondii using CRISPR/Cas9.

    PubMed

    Zheng, Jun; Jia, Honglin; Zheng, Yonghui

    2015-02-01

    Leucine aminopeptidases of the M17 peptidase family represent ideal drug targets for therapies directed against the pathogens Plasmodium, Babesia and Trypanosoma. Previously, we characterised Toxoplasma gondii leucine aminopeptidase and demonstrated its role in regulating the levels of free amino acids. In this study, we evaluated the potential of T. gondii leucine aminopeptidase as a drug target in T. gondii by a knockout method. Existing knockout methods for T. gondii have many drawbacks; therefore, we developed a new technique that takes advantage of the CRISPR/Cas9 system. We first chose a Cas9 target site in the gene encoding T. gondii leucine aminopeptidase and then constructed a knockout vector containing Cas9 and the single guide RNA. After transfection, single tachyzoites were cloned in 96-well plates by limiting dilution. Two transfected strains derived from a single clone were cultured in Vero cells, and then subjected to expression analysis by western blotting. The phenotypic analysis revealed that knockout of T. gondii leucine aminopeptidase resulted in inhibition of attachment/invasion and replication; both the growth and attachment/invasion capacity of knockout parasites were restored by complementation with a synonymously substituted allele of T. gondii leucine aminopeptidase. Mouse experiments demonstrated that T. gondii leucine aminopeptidase knockout somewhat reduced the pathogenicity of T. gondii. An enzymatic activity assay showed that T. gondii leucine aminopeptidase knockout reduced the processing of a leucine aminopeptidase-specific substrate in T. gondii. The absence of leucine aminopeptidase activity could be slightly compensated for in T. gondii. Overall, T. gondii leucine aminopeptidase knockout influenced the growth of T. gondii, but did not completely block parasite development, virulence or enzymatic activity. Therefore, we conclude that leucine aminopeptidase would be useful only as an adjunctive drug target in T. gondii.

  17. Detecting changes in future precipitation extremes over eight river basins in China using RegCM4 downscaling

    NASA Astrophysics Data System (ADS)

    Qin, Peihua; Xie, Zhenghui

    2016-06-01

    To detect the frequency and intensity of precipitation extremes in China for the middle 21st century, simulations were conducted with the regional climate model RegCM4 forced by the global climate model GFDL_ESM2M under the middle emission scenario (RCP4.5). Compared with observed precipitation extremes for the reference period from 1982 to 2001, RegCM4 generally performed better in most river basins of China relative to GFDL. In the future period 2032-2051, more wet extremes will occur relative to the present period in most study areas, especially in southeast China while significantly less dry extremes will occur in arid and semiarid areas in northwest China. In contrast, areas in northwest China showed an increase in the trend of dry extremes (CDD) and a decrease in the trend of wet extremes (R95p and Rx5day), which might result in more drought in the future. Finally, we discuss in detail the possible reason of these processes, such as zonal wind, vertical wind, and water vapor. In the Huaihe river basin (HU), reduced south winds in summer (June-August) and a decrease of the upward vertical p velocity cause less future precipitation and might lead to changes of extreme events. We also completed correlation analysis between the precipitation extreme indices and the climate factors and found that the precipitation extremes were more sensitive to the annual and seasonal mean precipitation, total water vapor, and upward vertical wind relative to the geopotential height and 2 m temperature over most river basins in China. Perhaps the changes of some wet extremes could be verified partly through changes of annual precipitation due to their high consistence.

  18. A sensitive pressure sensor for diamond anvil cell experiments up to 2 GPa: FluoSpheres[reg

    SciTech Connect

    Picard, Aude; Oger, Phil M.; Daniel, Isabelle; Cardon, Herve; Montagnac, Gilles; Chervin, Jean-Claude

    2006-08-01

    We present an optical pressure sensor suitable for experiments in diamond anvil cell in the 0.1 MPa-2 GPa pressure range, for temperatures between ambient and 323 K. It is based on the pressure-dependent fluorescence spectrum of FluoSpheres[reg], which are commercially available fluorescent microspheres commonly used to measure blood flow in experimental biology. The fluorescence of microspheres is excited by the 514.5 nm line of an Ar{sup +} laser, and the resulting spectrum displays three very intense broad bands at 534, 558, and 598 nm, respectively. The reference wavelength and pressure gauge is that of the first inflection point of the spectrum, located at 525.6{+-}0.2 nm at ambient pressure. It is characterized by an instantaneous and large linear pressure shift of 9.93({+-}0.08) nm/GPa. The fluorescence of the FluoSpheres[reg] has been investigated as a function of pressure (0.1-4 GPa), temperature (295-343 K), pH (3-12), salinity, and pressure transmitting medium. These measurements show that, for pressures comprised between 0.1 MPa and 2 GPa, at temperatures not exceeding 323 K, at any pH, in aqueous pressure transmitting media, pressure can be calculated from the wavelength shift of two to three beads, according to the relation P=0.100 ({+-}0.001) {delta}{lambda}{sub i}(P) with {delta}{lambda}{sub i}(P)={lambda}{sub i}(P)-{lambda}{sub i}(0) and {lambda}{sub i}(P) as the wavelength of the first inflection point of the spectrum at the pressure P. This pressure sensor is approximately thirty times more sensitive than the ruby scale and responds instantaneously to pressure variations.

  19. Sensitivity of the regional climate model RegCM4.2 to planetary boundary layer parameterisation

    NASA Astrophysics Data System (ADS)

    Güttler, Ivan; Branković, Čedo; O'Brien, Travis A.; Coppola, Erika; Grisogono, Branko; Giorgi, Filippo

    2014-10-01

    This study investigates the performance of two planetary boundary layer (PBL) parameterisations in the regional climate model RegCM4.2 with specific focus on the recently implemented prognostic turbulent kinetic energy parameterisation scheme: the University of Washington (UW) scheme. When compared with the default Holtslag scheme, the UW scheme, in the 10-year experiments over the European domain, shows a substantial cooling. It reduces winter warm bias over the north-eastern Europe by 2 °C and reduces summer warm bias over central Europe by 3 °C. A part of the detected cooling is ascribed to a general reduction in lower tropospheric eddy heat diffusivity with the UW scheme. While differences in temperature tendency due to PBL schemes are mostly localized to the lower troposphere, the schemes show a much higher diversity in how vertical turbulent mixing of the water vapour mixing ratio is governed. Differences in the water vapour mixing ratio tendency due to the PBL scheme are present almost throughout the troposphere. However, they alone cannot explain the overall water vapour mixing ratio profiles, suggesting strong interaction between the PBL and other model parameterisations. An additional 18-member ensemble with the UW scheme is made, where two formulations of the master turbulent length scale in unstable conditions are tested and unconstrained parameters associated with (a) the evaporative enhancement of the cloud-top entrainment and (b) the formulation of the master turbulent length scale in stable conditions are systematically perturbed. These experiments suggest that the master turbulent length scale in the UW scheme could be further refined in the current implementation in the RegCM model. It was also found that the UW scheme is less sensitive to the variations of the other two selected unconstrained parameters, supporting the choice of these parameters in the default formulation of the UW scheme.

  20. Simulations of Future Drought Conditions in Central Asia CORDEX Region 8 by Using RegCM4.3.5

    NASA Astrophysics Data System (ADS)

    Ozturk, Tugba; Turp, M. Tufan; Türkeş, Murat; Kurnaz, M. Levent; An, Nazan

    2015-04-01

    In this work, projected future changes in mean surface air temperature and precipitation climatology, inter-annual and seasonal variability and climatic aridity/humidity conditions for the period 2070-2100 over the large Central Asia region with respect to present climate (from 1970 to 2000) were simulated based on the RCP4.5 and RCP8.5 emission scenarios. Regional Climate Model (RegCM4.3.5) of the International Centre for Theoretical Physics (ICTP) was used for projections of future and present climate conditions. HadGEM2 global climate model of the Met Office Hadley Centre and MPI-ESM-MR global climate model of the Max Planck Institute for Meteorology were downscaled to 50 km for the CORDEX Region 8. We investigated the seasonal time-scale performance of RegCM4.3.5 in reproducing observed climatology over the domain of Central Asia by using 2 different global climate model outputs. For the future climatology of the domain, the regional model predicts relatively high warming in the warm season and northern part of the domain at cold season with a decrease in precipitation almost all part of the domain. The results of our study show that surface temperatures in the region will increase from 3 °C up to more than 7 °C on average according to the emission scenarios for the period 2070-2100 with respect to past period 1970-2000. Therefore, the projected warming and decrease in precipitation and also resultant or associated increased aridity and more frequent and severe drought events very likely adversely affect the ecological and socio-economic systems of this region, which is already characterised with mostly arid and semi-arid climate and ecosystems.

  1. Simulations of Future Drought Conditions in Central Asia CORDEX Region 8 by Using RegCM4.3.5

    NASA Astrophysics Data System (ADS)

    Turp, M. T.; Ozturk, T.; An, N.; Türkeş, M.; Kurnaz, L.

    2014-12-01

    In this work, projected future changes in mean surface air temperature and precipitation climatology, inter-annual and seasonal variability and climatic aridity/humidity conditions for the period of 2071-2100 over the large Central Asia region with respect to present climate (1971 to 2000) were simulated based on the RCP 4.5 and RCP 8.5 emission scenarios. Regional Climate Model (RegCM4.3.5) of the International Centre for Theoretical Physics (ICTP) was used for projections of future and present climate conditions. HadGEM2 global climate model of the Met Office Hadley Centre and MPI-ESM-MR global climate model of the Max Planck Institute for Meteorology were downscaled to 50 km for the CORDEX Region 8. We investigated the seasonal time-scale performance of RegCM4.3.5 in reproducing observed climatology over the domain of Central Asia by using two different global climate model outputs. For the future climatology of the domain, the regional model predicts relatively high warming in the warm season and northern part of the domain at cold season with a decrease in precipitation almost all part of the domain. The results of our study show that surface temperatures in the region will increase from 3°C up to more than 7°C on average according to the emission scenarios for the period of 2070-2100 with respect to past period of 1970-2000. Therefore, the projected warming and decrease in precipitation and also resultant or associated increased aridity and more frequent and severe drought events very likely adversely affect the ecological and socio-economic systems of this region, which is already characterised with mostly arid and semi-arid climate and ecosystems.

  2. Validation of the RegCM4-Subgrid module for the high resolution climate simulation over Korea

    NASA Astrophysics Data System (ADS)

    Lee, C.; Im, E.; Chang, K.; Choi, Y.

    2010-12-01

    Given the discernable evidences of climate changes due to human activity, there is a growing demand for the reliable climate change scenario in response to future emission forcing. One of the most significant impacts of climate changes can be that on the hydrological process. Changes in the seasonality and the low and high rainfall extremes can influence the water balance of river basin, with several consequences for societies and ecosystems. In fact, recent studies have reported that East Asia including the Korean peninsula is regarded to be a highly vulnerability region under global warming, especially for water resources. As an attempt to accurately assess the impact of climate change over Korea, we developed the dynamical downscaling system using the RegCM4 with a mosaic-type parameterization of subgrid-scale topography and land use (Sub-BATS). The Sub-BATS system is composed of 20 km coarse-grid cell and 4 km sub-grid cell. Before a full climate change simulation is carried out, we performed the simulation spanning the 19-year periods (1989-2007) with the lateral boundary fields obtained from the ERA-Interim reanalysis. The Korean peninsula is characterized by narrow mountain systems surrounded by ocean, and covered by a relatively dense observational network (approximate 400 stations), which provides an excellent dataset to validate a finescale downscaled results over the region. The evaluation of simulated surface variables (e.g. temperature, precipitation, snow, runoff) shows the usefulness of the RegCM4-Subgrid module as a tool to produce fine scale climate information of surface processes for coupling with hydrological model over the Korean peninsula Acknowledgements This work was supported by the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea government(MEST) (No. 2009-0085533), and by the "Advanced research on industrial meteorology" and " Development of meteorological resources for green growth." of National Institute of

  3. Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity.

    PubMed

    Lee, Ciaran M; Davis, Timothy H; Bao, Gang

    2017-03-16

    The recent adaptation of the CRISPR/Cas9 system for targeted genome engineering has led to its widespread applications in many fields worldwide. In order to better understand the design rules of CRISPR/Cas9 systems, several groups have carried out large library-based screens leading to some insight into sequence preferences among highly active target sites. To facilitate CRISPR/Cas9 design these studies have spawned a plethora of gRNA design tools with algorithms based solely on direct or indirect sequence features. Here we demonstrate that the predictive power of these tools is poor, suggesting that sequence features alone cannot accurately inform the cutting efficiency of a particular CRISPR/Cas9 gRNA design. Furthermore we demonstrate that DNA target site accessibility influences the activity of CRISPR/Cas9. With further optimisation we hypothesise that it will be possible to increase the predictive power of gRNA design tools by including both sequence and target site accessibility metrics. This article is protected by copyright. All rights reserved.

  4. Genome Editing in Human Cells Using CRISPR/Cas Nucleases.

    PubMed

    Wyvekens, Nicolas; Tsai, Shengdar Q; Joung, J Keith

    2015-10-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has been broadly adopted for highly efficient genome editing in a variety of model organisms and human cell types. Unlike previous genome editing technologies such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), CRISPR/Cas technology does not require complex protein engineering and can be utilized by any researcher proficient in basic molecular biology and cell culture techniques. This unit describes protocols for design and cloning of vectors expressing single or multiplex gRNAs, for transient transfection of human cell lines, and for quantitation of mutation frequencies by T7 endonuclease I assay. These protocols also include guidance for using two improvements that increase the specificity of CRISPR/Cas nucleases: truncated gRNAs and dimeric RNA-guided FokI nucleases.

  5. Harnessing CRISPR-Cas systems for bacterial genome editing.

    PubMed

    Selle, Kurt; Barrangou, Rodolphe

    2015-04-01

    Manipulation of genomic sequences facilitates the identification and characterization of key genetic determinants in the investigation of biological processes. Genome editing via clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) constitutes a next-generation method for programmable and high-throughput functional genomics. CRISPR-Cas systems are readily reprogrammed to induce sequence-specific DNA breaks at target loci, resulting in fixed mutations via host-dependent DNA repair mechanisms. Although bacterial genome editing is a relatively unexplored and underrepresented application of CRISPR-Cas systems, recent studies provide valuable insights for the widespread future implementation of this technology. This review summarizes recent progress in bacterial genome editing and identifies fundamental genetic and phenotypic outcomes of CRISPR targeting in bacteria, in the context of tool development, genome homeostasis, and DNA repair.

  6. CRISPR-Cas adaptation: insights into the mechanism of action.

    PubMed

    Amitai, Gil; Sorek, Rotem

    2016-02-01

    Since the first demonstration that CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against phages and plasmids, numerous studies have yielded key insights into the molecular mechanisms governing how these systems attack and degrade foreign DNA. However, the molecular mechanisms underlying the adaptation stage, in which new immunological memory is formed, have until recently represented a major unresolved question. In this Progress article, we discuss recent discoveries that have shown both how foreign DNA is identified by the CRISPR-Cas adaptation machinery and the molecular basis for its integration into the chromosome to form an immunological memory. Furthermore, we describe the roles of each of the specific CRISPR-Cas components that are involved in memory formation, and consider current models for their evolutionary origin.

  7. DNA fragment editing of genomes by CRISPR/Cas9.

    PubMed

    Jinhuan, Li; Jia, Shou; Qiang, Wu

    2015-10-01

    The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system from bacteria and archaea emerged recently as a new powerful technology of genome editing in virtually any organism. Due to its simplicity and cost effectiveness, a revolutionary change of genetics has occurred. Here, we summarize the recent development of DNA fragment editing methods by CRISPR/Cas9 and describe targeted DNA fragment deletions, inversions, duplications, insertions, and translocations. The efficient method of DNA fragment editing provides a powerful tool for studying gene function, regulatory elements, tissue development, and disease progression. Finally, we discuss the prospects of CRISPR/Cas9 system and the potential applications of other types of CRISPR system.

  8. Genome engineering using CRISPR-Cas9 system.

    PubMed

    Cong, Le; Zhang, Feng

    2015-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system is an adaptive immune system that exists in a variety of microbes. It could be engineered to function in eukaryotic cells as a fast, low-cost, efficient, and scalable tool for manipulating genomic sequences. In this chapter, detailed protocols are described for harnessing the CRISPR-Cas9 system from Streptococcus pyogenes to enable RNA-guided genome engineering applications in mammalian cells. We present all relevant methods including the initial site selection, molecular cloning, delivery of guide RNAs (gRNAs) and Cas9 into mammalian cells, verification of target cleavage, and assays for detecting genomic modification including indels and homologous recombination. These tools provide researchers with new instruments that accelerate both forward and reverse genetics efforts.

  9. Targeted heritable mutation and gene conversion by Cas9-CRISPR in Caenorhabditis elegans.

    PubMed

    Katic, Iskra; Großhans, Helge

    2013-11-01

    We have achieved targeted heritable genome modification in Caenorhabditis elegans by injecting mRNA of the nuclease Cas9 and Cas9 guide RNAs. This system rapidly creates precise genomic changes, including knockouts and transgene-instructed gene conversion.

  10. Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization.

    PubMed

    Senturk, Serif; Shirole, Nitin H; Nowak, Dawid G; Corbo, Vincenzo; Pal, Debjani; Vaughan, Alexander; Tuveson, David A; Trotman, Lloyd C; Kinney, Justin B; Sordella, Raffaella

    2017-02-22

    The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and temporal control of gene editing in the presence of an FKBP12 synthetic ligand. This system can be easily adapted to co-express, from the same promoter, DD-Cas9 with any other gene of interest without co-modulation of the latter. In particular, when co-expressed with inducible Cre-ER(T2), our system enables parallel, independent manipulation of alleles targeted by Cas9 and traditional recombinase with single-cell specificity. We anticipate this platform will be used for the systematic characterization and identification of essential genes, as well as the investigation of the interactions between functional genes.

  11. Effects of reducing blood pressure on cardiovascular outcomes and mortality in patients with type 2 diabetes: Focus on SGLT2 inhibitors and EMPA-REG OUTCOME.

    PubMed

    Scheen, André J

    2016-11-01

    Empagliflozin, a sodium-glucose cotransporter type 2 (SGLT2) inhibitor, has shown a remarkable reduction in cardiovascular and all-cause mortality in patients with type 2 diabetes (T2D) and antecedents of cardiovascular disease in the EMPA-REG OUTCOME trial. This effect has been attributed to a hemodynamic rather than a metabolic effect, partly due to the osmotic/diuretic effect of empagliflozin and to the reduction in arterial blood pressure. The present review will: (1) summarize the results of specific studies having tested the blood pressure lowering effects of SGLT2 inhibitors; (2) describe the results of meta-analyses of trials having evaluated the effects on mortality and cardiovascular outcomes of lowering blood pressure in patients with T2D, with a special focus on baseline and target blood pressures; (3) compare the cardiovascular outcome results in EMPA-REG OUTCOME versus other major trials with antihypertensive agents in patients with T2D; and (4) evaluate post-hoc analyses from EMPA-REG OUTCOME, especially subgroups of patients of special interest regarding the blood pressure lowering hypothesis. Although BP reduction associated to empagliflozin therapy may partly contribute to the benefits reported in EMPA-REG OUTCOME, other mechanisms most probably play a greater role in the overall CV protection and reduction in mortality observed in this trial.

  12. Effects of reducing blood pressure on renal outcomes in patients with type 2 diabetes: Focus on SGLT2 inhibitors and EMPA-REG OUTCOME.

    PubMed

    Scheen, A J; Delanaye, P

    2017-01-30

    Empagliflozin, a sodium-glucose cotransporter type 2 (SGLT2) inhibitor, has enabled remarkable reductions in cardiovascular and all-cause mortality as well as in renal outcomes in patients with type 2 diabetes (T2D) and a history of cardiovascular disease in the EMPA-REG OUTCOME. These results have been attributed to haemodynamic rather than metabolic effects, in part due to the osmotic/diuretic action of empagliflozin and the reduction in arterial blood pressure (BP). The present narrative review includes the results of meta-analyses of trials evaluating the effects on renal outcomes of lowering BP in patients with T2D, with a special focus on the influence of baseline and achieved systolic BP, and compares the renal outcome results of the EMPA-REG OUTCOME with those of other major trials with inhibitors of the renin-angiotensin system in patients with T2D and the preliminary findings with other SGLT2 inhibitors, and also evaluates post hoc analyses from the EMPA-REG OUTCOME of special interest as regards the BP-lowering hypothesis and renal function. While systemic BP reduction associated to empagliflozin therapy may have contributed to the renal benefits reported in EMPA-REG OUTCOME, other local mechanisms related to kidney homoeostasis most probably also played a role in the overall protection observed in the trial.

  13. Comparative effects of split Orimulsion{reg_sign}, fuel oil {number_sign}6 and Lago Medio Crude oil over functional variables of an estuarine community

    SciTech Connect

    Quilici, A.; Rodriguez-Grau, J.; Vasquez, P.; Infante, C.; Schiazza, J. La; Briceno, H.; Pereira, N.

    1995-12-31

    This study evaluates the effects, on comparative bases, of three different kinds of hydrocarbon products, on physiological and dynamic parameters of a mangrove community (located East of Venezuela), by experimentally monitoring changes on those parameters using Laguncularia racemosa as a bioindicator mangrove species. Orimulsion{reg_sign} has been introduced recently in the World market; and it is, in essence, an emulsion produced from bitumen mixed with water and stabilized with a surfactant. Results indicate that litter disappearance rate, a parameter directly related to nutrient cycling and dynamics, is not altered by the split Orimulsion{reg_sign}, when compared to controls; while the other hydrocarbon products tested, seem to exert an impact over this parameter. In addition, Orimulsion{reg_sign}, is less retained in mangrove sediments compared with the other two products, as indicated by the remaining percent mean of total hydrocarbon soil content sampled on the same consecutive dates. Nonetheless, the photosynthetic capacity of leaves as well as soil respiratory rates, monitored at treatment and control plots, were not affected by any of the products tested. In conclusion, L. racemosa, in terms of its photosynthetic capacity, is not directly affected by any of the hydrocarbon products tested, nor does there seem to be an effect on soil respiration; however, Orimulsion{reg_sign}, in contrast to the other products, does not seem to be causing an impact with regard to litter dynamics.

  14. Mouse Genome Editing Using the CRISPR/Cas System.

    PubMed

    Harms, Donald W; Quadros, Rolen M; Seruggia, Davide; Ohtsuka, Masato; Takahashi, Gou; Montoliu, Lluis; Gurumurthy, Channabasavaiah B

    2014-10-01

    The availability of techniques to create desired genetic mutations has enabled the laboratory mouse as an extensively used model organism in biomedical research including human genetics. A new addition to this existing technical repertoire is the CRISPR/Cas system. Specifically, this system allows editing of the mouse genome much more quickly than the previously used techniques, and, more importantly, multiple mutations can be created in a single experiment. Here we provide protocols for preparation of CRISPR/Cas reagents and microinjection into one-cell mouse embryos to create knockout or knock-in mouse models.

  15. [CRISPR-Cas system as molecular scissors for gene therapy].

    PubMed

    Heinz, G A; Mashreghi, M-F

    2017-02-01

    Since the discovery of the CRISPR-Cas system as the adaptive immune system of prokaryotes, the underlying mechanism has proven to be a precise molecular tool for the targeted editing of genetic information in various cell types. By using the CRISPR-Cas9 system DNA sequences can be cut out at any site in the genome and changed in a sequence-specific manner. In the long term this provides the opportunity to cure diseases caused by gene mutations.

  16. Mouse Genome Editing using CRISPR/Cas System

    PubMed Central

    Harms, Donald W; Quadros, Rolen M; Seruggia, Davide; Ohtsuka, Masato; Takahashi, Gou

    2015-01-01

    The availability of techniques to create desired genetic mutations has enabled the laboratory mouse as an extensively used model organism in biomedical research including human genetics. A new addition to this existing technical repertoire is the CRISPR/Cas system. Specifically, this system allows editing of the mouse genome much faster than the previously used techniques and more importantly multiple mutations can be created in a single experiment. Here we provide protocols for preparation of CRISPR/Cas reagents and microinjection into one cell mouse embryos to create knockout or knock-in mouse models. PMID:25271839

  17. Les sarcomes des tissus mous: à propos de 33 cas

    PubMed Central

    Abdou, Jiddou; Elkabous, Mustapha; M'rabti, Hind; Errihani, Hassan

    2015-01-01

    L'objectif de cette étude est de rapporter les particularités épidémiologiques, cliniques, histologiques, thérapeutiques et évolutives des sarcomes des tissus mous à l'Institut National d'Oncologie et de définir les facteurs influençant la survie des patients. C'est une étude rétrospective de 33 cas de sarcome des tissus mous, colligés entre janvier 2008 et décembre 2010. Les critères d’éligibilité étaient un âge supérieur à 16 ans, une épreuve histologique d'un sarcome des tissus mous à l'exclusion des tumeurs stromales gastro-intestinales (GIST). Les items recueillis étaient: épidémiologiques, cliniques, histologiques, Radiologiques, et thérapeutiques. Des analyses univariées puis multivariées ont été réalisées à la recherche de facteurs influençant la survie à 2 ans. Il s'agit de 33 cas, 17 Hommes et 16 Femmes, l’âge moyen était de 43,21 ans (Extrêmes= 18-76 ans). La tumeur était localisée aux extrémités dans 24 cas (72,72%). Le type histologique prédominant était le Liposarcome dans 9 cas (27,27%). Le stade tumoral était localisé dans 25 cas (75,8%), métastatique dans 8 cas (24,2%). Vingt-cinq tumeurs ont été traitées chirurgicalement dont 21 cas (84%) de chirurgie conservatrice et 4 cas (16%) de chirurgie radicale. La radiothérapie a été réalisée chez 10 patients (30,3%). La chimiothérapie a été faite chez 20 patients. En analyse univariée les facteurs pronostiques étaient l’âge (p=0,03) et le stade tumoral (p=0,09). L’âge et le stade tumoral sont des facteurs pronostiques influençant la survie des sarcomes des tissus mous. PMID:27022434

  18. Applications of CRISPR-Cas systems in neuroscience

    PubMed Central

    Heidenreich, Matthias; Zhang, Feng

    2016-01-01

    Genome editing tools, and in particular those based on CRISPR-Cas systems, are accelerating the pace of biological research and enabling targeted genetic interrogation in virtually any organism and cell type. These tools have opened the door to the development of new model systems for studying the complexity of the nervous system, including animal and stem cell-derived in vitro models. Precise and efficient gene editing using CRISPR-Cas systems has the potential to advance both basic and translational neuroscience research. PMID:26656253

  19. Expanding the Biologist's Toolkit with CRISPR-Cas9.

    PubMed

    Sternberg, Samuel H; Doudna, Jennifer A

    2015-05-21

    Few discoveries transform a discipline overnight, but biologists today can manipulate cells in ways never possible before, thanks to a peculiar form of prokaryotic adaptive immunity mediated by clustered regularly interspaced short palindromic repeats (CRISPR). From elegant studies that deciphered how these immune systems function in bacteria, researchers quickly uncovered the technological potential of Cas9, an RNA-guided DNA cleaving enzyme, for genome engineering. Here we highlight the recent explosion in visionary applications of CRISPR-Cas9 that promises to usher in a new era of biological understanding and control.

  20. Fusion of SpCas9 to E. coli Rec A protein enhances CRISPR-Cas9 mediated gene knockout in mammalian cells.

    PubMed

    Lin, Lin; Petersen, Trine Skov; Jensen, Kristopher Torp; Bolund, Lars; Kühn, Ralf; Luo, Yonglun

    2017-03-01

    Mammalian cells repair double-strand DNA breaks (DSB) by a range of different pathways following DSB induction by the engineered clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein Cas9. While CRISPR-Cas9 thus enables predesigned modifications of the genome, applications of CRISPR-Cas9-mediated genome-editing are frequently hampered by the unpredictable and varying pathways for DSB repair in mammalian cells. Here we present a strategy of fusing Cas9 to recombinant proteins for fine-tuning of the DSB repair preferences in mammalian cells. By fusing Streptococcus Pyogenes Cas9 (SpCas9) to the recombinant protein A (Rec A, NP_417179.1) from Escherichia coli, we create a recombinant Cas9 protein (rSpCas9) which enhances the generation of indel mutations at DSB sites in mammalian cells, increases the frequency of DSB repair by homology-directed single-strand annealing (SSA), and represses homology-directed gene conversion by approximately 33%. Our study thus proves for the first time that fusing SpCas9 to recombinant proteins can influence the balance between DSB repair pathways in mammalian cells. This approach may form the basis for further investigations of the applications of recombinant Cas9 proteins to fine-tuning DSB repair pathways in eukaryotic cells.

  1. Cas9 gRNA engineering for genome editing, activation and repression

    PubMed Central

    Kiani, Samira; Chavez, Alejandro; Tuttle, Marcelle; Hall, Richard N; Chari, Raj; Ter-Ovanesyan, Dmitry; Qian, Jason; Pruitt, Benjamin W; Beal, Jacob; Vora, Suhani; Buchthal, Joanna; Kowal, Emma J K; Ebrahimkhani, Mohammad R; Collins, James J; Weiss, Ron; Church, George

    2015-01-01

    We demonstrate that by altering the length of Cas9-associated guide RNA(gRNA) we were able to control Cas9 nuclease activity and simultaneously perform genome editing and transcriptional regulation with a single Cas9 protein. We exploited these principles to engineer mammalian synthetic circuits with combined transcriptional regulation and kill functions governed by a single multifunctional Cas9 protein. PMID:26344044

  2. Application of CRISPR-Cas system in gene therapy: Pre-clinical progress in animal model.

    PubMed

    Guan, Lihong; Han, Yawei; Zhu, Shaoyi; Lin, Juntang

    2016-10-01

    The clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated proteins (Cas) belong to the crucial adaptive immune system, which exist in archaea and bacteria. Currently, CRISPR-Cas9 system has been modified and widely used to edit genome. In this review, we summarized the discovery, classification and mechanism of CRISPR-Cas system and further discussed the application of CRISPR-Cas9 in gene therapy, mainly in disease models.

  3. CRISPR-Cas immunity and mobile DNA: a new superfamily of DNA transposons encoding a Cas1 endonuclease.

    PubMed

    Hickman, Alison B; Dyda, Fred

    2014-01-01

    Mobile genetic elements such as DNA transposons are a feature of most genomes. The existence of novel DNA transposons can be inferred when whole genome sequencing reveals the presence of hallmarks of mobile elements such as terminal inverted repeats (TIRs) flanked by target site duplications (TSDs). A recent report describes a new superfamily of DNA transposons in the genomes of a few bacteria and archaea that possess TIRs and TSDs, and encode several conserved genes including a cas1 endonuclease gene, previously associated only with CRISPR-Cas adaptive immune systems. The data strongly suggests that these elements, designated 'casposons', are likely to be bona fide DNA transposons and that their Cas1 nucleases act as transposases and are possibly still active.

  4. The VARL gene family and the evolutionary origins of the master cell-type regulatory gene, regA, in Volvox carteri.

    PubMed

    Duncan, Leonard; Nishii, Ichiro; Harryman, Alexandra; Buckley, Stephanie; Howard, Alicia; Friedman, Nicholas R; Miller, Stephen M

    2007-07-01

    Chlamydomonas reinhardtii, Volvox carteri, and their relatives in the family Volvocaceae provide an excellent opportunity for studying how multicellular organisms with differentiated cell types evolved from unicellular ancestors. While C. reinhardtii is unicellular, V. carteri is multicellular with two cell types, one of which resembles C. reinhardtii cytologically but is terminally differentiated. Maintenance of this "somatic cell" fate is controlled by RegA, a putative transcription factor. We recently showed that RegA shares a conserved region with several predicted V. carteri and C. reinhardtii proteins and that this region, the VARL domain, is likely to include a DNA-binding SAND domain. As the next step toward understanding the evolutionary origins of the regA gene, we analyzed the genome sequences of C. reinhardtii and V. carteri to identify additional genes with the potential to encode VARL domain proteins. Here we report that the VARL gene family, which consists of 12 members in C. reinhardtii and 14 in V. carteri, has experienced a complex evolutionary history in which members of the family have been both gained and lost over time, although several pairs of potentially orthologous genes can still be identified. We find that regA is part of a tandem array of four VARL genes in V. carteri but that a similar array is absent in C. reinhardtii. Most importantly, our phylogenetic analysis suggests that a proto-regA gene was present in a common unicellular ancestor of V. carteri and C. reinhardtii and that this gene was lost in the latter lineage.

  5. Analysis of the present and future winter Pacific-North American teleconnection in the ECHAM5 global and RegCM3 regional climate models

    USGS Publications Warehouse

    Allan, Andrea M.; Hostetler, Steven W.; Alder, Jay R.

    2014-01-01

    We use the NCEP/NCAR Reanalysis (NCEP) and the MPI/ECHAM5 general circulation model to drive the RegCM3 regional climate model to assess the ability of the models to reproduce the spatiotemporal aspects of the Pacific-North American teleconnection (PNA) pattern. Composite anomalies of the NCEP-driven RegCM3 simulations for 1982–2000 indicate that the regional model is capable of accurately simulating the key features (500-hPa heights, surface temperature, and precipitation) of the positive and negative phases of the PNA with little loss of information in the downscaling process. The basic structure of the PNA is captured in both the ECHAM5 global and ECHAM5-driven RegCM3 simulations. The 1950–2000 ECHAM5 simulation displays similar temporal and spatial variability in the PNA index as that of NCEP; however, the magnitudes of the positive and negative phases are weaker than those of NCEP. The RegCM3 simulations clearly differentiate the climatology and associated anomalies of snow water equivalent and soil moisture of the positive and negative PNA phases. In the RegCM3 simulations of the future (2050–2100), changes in the location and extent of the Aleutian low and the continental high over North America alter the dominant flow patterns associated with positive and negative PNA modes. The future projections display a shift in the patterns of the relationship between the PNA and surface climate variables, which suggest the potential for changes in the PNA-related surface hydrology of North America.

  6. Creating Genome Modifications in C. elegans Using the CRISPR/Cas9 System.

    PubMed

    Calarco, John A; Friedland, Ari E

    2015-01-01

    The clustered, regularly interspaced, short, palindromic repeat (CRISPR)-associated (CAS) nuclease Cas9 has been used in many organisms to generate specific mutations and transgene insertions. Here we describe a method using the S. pyogenes Cas9 in C. elegans that provides a convenient and effective approach for making heritable changes to the worm genome.

  7. CAS or Pen-and-Paper: Factors That Influence Students' Choices

    ERIC Educational Resources Information Center

    Cameron, Scott; Ball, Lynda

    2015-01-01

    This paper reports on a study of choices about the use of a computer algebra system (CAS) or pen-and-paper (p&p) by a class of seven Year 11 Mathematical Methods (CAS) students as they completed a calculus worksheet. Factors that influenced students' choices are highlighted by comparing and contrasting the use of CAS and p&p between…

  8. After 16 Years of Publishing Standards, Do CAS Standards Make a Difference?

    ERIC Educational Resources Information Center

    Arminio, Jan; Gochenauer, Patty

    2004-01-01

    Using members of professional associations who are a part of the Council for the Advancement of Standards in Higher Education (CAS) consortia as a sample, this study investigated who uses CAS Standards, how and why they are used, and whether CAS Standards are associated with enhanced student learning. Using a quantitative analysis, this study…

  9. Mismatch Negativity Responses in Children with a Diagnosis of Childhood Apraxia of Speech (CAS)

    ERIC Educational Resources Information Center

    Froud, Karen; Khamis-Dakwar, Reem

    2012-01-01

    Purpose: To evaluate whether a hypothesis suggesting that apraxia of speech results from phonological overspecification could be relevant for childhood apraxia of speech (CAS). Method: High-density EEG was recorded from 5 children with CAS and 5 matched controls, ages 5-8 years, with and without CAS, as they listened to randomized sequences of CV…

  10. Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus.

    PubMed

    Tamulaitis, Gintautas; Kazlauskiene, Migle; Manakova, Elena; Venclovas, Česlovas; Nwokeoji, Alison O; Dickman, Mark J; Horvath, Philippe; Siksnys, Virginijus

    2014-11-20

    Immunity against viruses and plasmids provided by CRISPR-Cas systems relies on a ribonucleoprotein effector complex that triggers the degradation of invasive nucleic acids (NA). Effector complexes of type I (Cascade) and II (Cas9-dual RNA) target foreign DNA. Intriguingly, the genetic evidence suggests that the type III-A Csm complex targets DNA, whereas biochemical data show that the type III-B Cmr complex cleaves RNA. Here we aimed to investigate NA specificity and mechanism of CRISPR interference for the Streptococcus thermophilus Csm (III-A) complex (StCsm). When expressed in Escherichia coli, two complexes of different stoichiometry copurified with 40 and 72 nt crRNA species, respectively. Both complexes targeted RNA and generated multiple cuts at 6 nt intervals. The Csm3 protein, present in multiple copies in both Csm complexes, acts as endoribonuclease. In the heterologous E. coli host, StCsm restricts MS2 RNA phage in a Csm3 nuclease-dependent manner. Thus, our results demonstrate that the type III-A StCsm complex guided by crRNA targets RNA and not DNA.

  11. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No....

  12. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No....

  13. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No....

  14. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No....

  15. 40 CFR 721.650 - 11-Aminoundecanoic acid.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false 11-Aminoundecanoic acid. 721.650... Substances § 721.650 11-Aminoundecanoic acid. (a) Chemical substance and significant new use subject to reporting. (1) The chemical substance 11-ami-no-un-de-ca-noic acid, CAS Number 2432-99-7, is subject...

  16. 40 CFR 704.25 - 11-Aminoundecanoic acid.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false 11-Aminoundecanoic acid. 704.25... § 704.25 11-Aminoundecanoic acid. (a) Definitions—(1) 11-AA means the chemical substance 11-aminoundecanoic acid, CAS Number 2432-99-7. (2) Enclosed process means a process that is designed and operated...

  17. 40 CFR 721.10066 - 1-Hexanesulfonic acid, (dimethylphenyl)-.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false 1-Hexanesulfonic acid, (dimethylphenyl... Specific Chemical Substances § 721.10066 1-Hexanesulfonic acid, (dimethylphenyl)-. (a) Chemical substance...-hexanesulfonic acid, (dimethylphenyl)- (PMN P-04-962; CAS No. 676143-36-5) is subject to reporting under...

  18. 40 CFR 704.25 - 11-Aminoundecanoic acid.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false 11-Aminoundecanoic acid. 704.25... § 704.25 11-Aminoundecanoic acid. (a) Definitions. (1) 11-AA means the chemical substance 11-aminoundecanoic acid, CAS Number 2432-99-7. (2) Enclosed process means a process that is designed and operated...

  19. 40 CFR 704.25 - 11-Aminoundecanoic acid.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false 11-Aminoundecanoic acid. 704.25... § 704.25 11-Aminoundecanoic acid. (a) Definitions. (1) 11-AA means the chemical substance 11-aminoundecanoic acid, CAS Number 2432-99-7. (2) Enclosed process means a process that is designed and operated...

  20. 40 CFR 704.25 - 11-Aminoundecanoic acid.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false 11-Aminoundecanoic acid. 704.25... § 704.25 11-Aminoundecanoic acid. (a) Definitions—(1) 11-AA means the chemical substance 11-aminoundecanoic acid, CAS Number 2432-99-7. (2) Enclosed process means a process that is designed and operated...