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Showing 1 to 12 of 17 entries
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Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation.

Molecular microbiology

Musharova O, Sitnik V, Vlot M, Savitskaya E, Datsenko KA, Krivoy A, Fedorov I, Semenova E, Brouns SJJ, Severinov K.
PMID: 30875129
Mol Microbiol. 2019 Jun;111(6):1558-1570. doi: 10.1111/mmi.14237. Epub 2019 Apr 06.

CRISPR interference occurs when a protospacer recognized by the CRISPR RNA is destroyed by Cas effectors. In Type I CRISPR-Cas systems, protospacer recognition can lead to «primed adaptation» - acquisition of new spacers from in cis located sequences. Type...

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Musharova O, Sitnik V, Vlot M, et al. Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation. Mol Microbiol. 2019;111(6):1558-1570doi: 10.1111/mmi.14237.
Musharova, O., Sitnik, V., Vlot, M., Savitskaya, E., Datsenko, K. A., Krivoy, A., Fedorov, I., Semenova, E., Brouns, S. J. J., & Severinov, K. (2019). Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation. Molecular microbiology, 111(6), 1558-1570. https://doi.org/10.1111/mmi.14237
Musharova, Olga, et al. "Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation." Molecular microbiology vol. 111,6 (2019): 1558-1570. doi: https://doi.org/10.1111/mmi.14237
Musharova O, Sitnik V, Vlot M, Savitskaya E, Datsenko KA, Krivoy A, Fedorov I, Semenova E, Brouns SJJ, Severinov K. Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation. Mol Microbiol. 2019 Jun;111(6):1558-1570. doi: 10.1111/mmi.14237. Epub 2019 Apr 06. PMID: 30875129; PMCID: PMC6568314.
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First Report of Fusarium Wilt of Endive (Cichorium endivia) Caused by Fusarium oxysporum in Italy.

Plant disease

Garibaldi A, Gilardi G, Troisi M, Gullino ML.
PMID: 30754361
Plant Dis. 2009 Oct;93(10):1078. doi: 10.1094/PDIS-93-10-1078C.

In the summer of 2007, a wilt of endive (Cichorium endivia) cv. Myrna plants was observed on several commercial farms near Alessandria in northern Italy. Approximately 40% of the plants on each farm were symptomatic. Affected plants were stunted...

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Garibaldi A, Gilardi G, Troisi M, et al. First Report of Fusarium Wilt of Endive (Cichorium endivia) Caused by Fusarium oxysporum in Italy. Plant Dis. 2009;93(10):1078doi: 10.1094/PDIS-93-10-1078C.
Garibaldi, A., Gilardi, G., Troisi, M., & Gullino, M. L. (2009). First Report of Fusarium Wilt of Endive (Cichorium endivia) Caused by Fusarium oxysporum in Italy. Plant disease, 93(10), 1078. https://doi.org/10.1094/PDIS-93-10-1078C
Garibaldi, A, et al. "First Report of Fusarium Wilt of Endive (Cichorium endivia) Caused by Fusarium oxysporum in Italy." Plant disease vol. 93,10 (2009): 1078. doi: https://doi.org/10.1094/PDIS-93-10-1078C
Garibaldi A, Gilardi G, Troisi M, Gullino ML. First Report of Fusarium Wilt of Endive (Cichorium endivia) Caused by Fusarium oxysporum in Italy. Plant Dis. 2009 Oct;93(10):1078. doi: 10.1094/PDIS-93-10-1078C. PMID: 30754361.
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Molecular insights into the taxonomy of Glyceria (Poaceae: Meliceae) in North America.

American journal of botany

Whipple IG, Barkworth ME, Bushman BS.
PMID: 21636425
Am J Bot. 2007 Apr;94(4):551-7. doi: 10.3732/ajb.94.4.551.

Eighteen Glyceria species grow in the United States and Canada, with 16 being native to the region. We used data from morphology and three chloroplast DNA intergenic regions to address taxonomic questions concerning Glyceria in North America, particularly the...

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Whipple IG, Barkworth ME, Bushman BS. Molecular insights into the taxonomy of Glyceria (Poaceae: Meliceae) in North America. Am J Bot. 2007;94(4):551-7doi: 10.3732/ajb.94.4.551.
Whipple, I. G., Barkworth, M. E., & Bushman, B. S. (2007). Molecular insights into the taxonomy of Glyceria (Poaceae: Meliceae) in North America. American journal of botany, 94(4), 551-7. https://doi.org/10.3732/ajb.94.4.551
Whipple, Ian G, et al. "Molecular insights into the taxonomy of Glyceria (Poaceae: Meliceae) in North America." American journal of botany vol. 94,4 (2007): 551-7. doi: https://doi.org/10.3732/ajb.94.4.551
Whipple IG, Barkworth ME, Bushman BS. Molecular insights into the taxonomy of Glyceria (Poaceae: Meliceae) in North America. Am J Bot. 2007 Apr;94(4):551-7. doi: 10.3732/ajb.94.4.551. PMID: 21636425.
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Comparison of Sequences from the Ribosomal DNA Intergenic Region of Meloidogyne mayaguensis and Other Major Tropical Root-Knot Nematodes.

Journal of nematology

Blok VC, Phillips MS, Fargette M.
PMID: 19274129
J Nematol. 1997 Mar;29(1):16-22.

The unusual arrangement of the 5S ribosomal gene within the intergenic sequence (IGS) of the ribosomal cistron, previously reported for Meloidogyne arenaria, was also found in the ribosomal DNA of two other economically important species of tropical root-knot nematodes,...

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Blok VC, Phillips MS, Fargette M. Comparison of Sequences from the Ribosomal DNA Intergenic Region of Meloidogyne mayaguensis and Other Major Tropical Root-Knot Nematodes. J Nematol. 1997;29(1):16-22
Blok, V. C., Phillips, M. S., & Fargette, M. (1997). Comparison of Sequences from the Ribosomal DNA Intergenic Region of Meloidogyne mayaguensis and Other Major Tropical Root-Knot Nematodes. Journal of nematology, 29(1), 16-22.
Blok, V C, et al. "Comparison of Sequences from the Ribosomal DNA Intergenic Region of Meloidogyne mayaguensis and Other Major Tropical Root-Knot Nematodes." Journal of nematology vol. 29,1 (1997): 16-22.
Blok VC, Phillips MS, Fargette M. Comparison of Sequences from the Ribosomal DNA Intergenic Region of Meloidogyne mayaguensis and Other Major Tropical Root-Knot Nematodes. J Nematol. 1997 Mar;29(1):16-22. PMID: 19274129; PMCID: PMC2619761.
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The divergence pattern of Trichinella spiralis isolates from China revealed by mitochondrial and ribosomal markers.

Tropical biomedicine

Zhang X, Duan JY, Wang H, Qi X, Sun GG, Jiang P, Liu RD, Wang ZQ, Cui J.
PMID: 33579129
Trop Biomed. 2016 Sep 01;33(3):561-569.

Trichinella spiralis is the main etiological agent of human trichinellosis. In China, trichinellosis remains a serious food-borne parasitic zoonosis and poses a serious threat to human health. However, the genetic structure of Chinese T. spiralis population is still little...

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Zhang X, Duan JY, Wang H, et al. The divergence pattern of Trichinella spiralis isolates from China revealed by mitochondrial and ribosomal markers. Trop Biomed. 2016;33(3):561-569
Zhang, X., Duan, J. Y., Wang, H., Qi, X., Sun, G. G., Jiang, P., Liu, R. D., Wang, Z. Q., & Cui, J. (2016). The divergence pattern of Trichinella spiralis isolates from China revealed by mitochondrial and ribosomal markers. Tropical biomedicine, 33(3), 561-569.
Zhang, X, et al. "The divergence pattern of Trichinella spiralis isolates from China revealed by mitochondrial and ribosomal markers." Tropical biomedicine vol. 33,3 (2016): 561-569.
Zhang X, Duan JY, Wang H, Qi X, Sun GG, Jiang P, Liu RD, Wang ZQ, Cui J. The divergence pattern of Trichinella spiralis isolates from China revealed by mitochondrial and ribosomal markers. Trop Biomed. 2016 Sep 01;33(3):561-569. PMID: 33579129.
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Identifying functional annotation for noncoding genomic sequences.

Current protocols in human genetics

Mortlock DP, Pregizer S.
PMID: 22241655
Curr Protoc Hum Genet. 2012 Jan;Unit1.10. doi: 10.1002/0471142905.hg0110s72.

The recent success of genome-wide association studies has generated a trove of biologically significant variants implicated in human disease. However, many, if not most, of these variants fall in noncoding regions that have traditionally lacked much functional annotation. New...

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Mortlock DP, Pregizer S. Identifying functional annotation for noncoding genomic sequences. Curr Protoc Hum Genet. 2012;Unit1.10doi: 10.1002/0471142905.hg0110s72.
Mortlock, D. P., & Pregizer, S. (2012). Identifying functional annotation for noncoding genomic sequences. Current protocols in human genetics, Unit1.10. https://doi.org/10.1002/0471142905.hg0110s72
Mortlock, Douglas P, and Pregizer, Steven. "Identifying functional annotation for noncoding genomic sequences." Current protocols in human genetics vol. (2012): Unit1.10. doi: https://doi.org/10.1002/0471142905.hg0110s72
Mortlock DP, Pregizer S. Identifying functional annotation for noncoding genomic sequences. Curr Protoc Hum Genet. 2012 Jan;Unit1.10. doi: 10.1002/0471142905.hg0110s72. PMID: 22241655.
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Change in ribosomal DNA intergenic spacer-length composition in maize recurrent selection populations. 1. Analysis of BS13, BSSS, and BSCB1.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

Rocheford TR.
PMID: 24186108
Theor Appl Genet. 1994 Jul;88(5):541-7. doi: 10.1007/BF01240916.

Five different ribosomal DNA (rDNA) intergenic spacer-length variants (slvs) were detected among the maize inbreds which were the progenitors of Iowa Stiff Stalk Synthetic (BSSS). One rDNASstI restriction site polymorphism in the 3' region of the 26S gene was...

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Rocheford TR. Change in ribosomal DNA intergenic spacer-length composition in maize recurrent selection populations. 1. Analysis of BS13, BSSS, and BSCB1. Theor Appl Genet. 1994;88(5):541-7doi: 10.1007/BF01240916.
Rocheford, T. R. (1994). Change in ribosomal DNA intergenic spacer-length composition in maize recurrent selection populations. 1. Analysis of BS13, BSSS, and BSCB1. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 88(5), 541-7. https://doi.org/10.1007/BF01240916
Rocheford, T R. "Change in ribosomal DNA intergenic spacer-length composition in maize recurrent selection populations. 1. Analysis of BS13, BSSS, and BSCB1." TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik vol. 88,5 (1994): 541-7. doi: https://doi.org/10.1007/BF01240916
Rocheford TR. Change in ribosomal DNA intergenic spacer-length composition in maize recurrent selection populations. 1. Analysis of BS13, BSSS, and BSCB1. Theor Appl Genet. 1994 Jul;88(5):541-7. doi: 10.1007/BF01240916. PMID: 24186108.
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CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.

BMC bioinformatics

Yao Y, Liu Z, Wei Q, Ramsey SA.
PMID: 30727967
BMC Bioinformatics. 2019 Feb 06;20(1):63. doi: 10.1186/s12859-019-2637-4.

BACKGROUND: We previously reported on CERENKOV, an approach for identifying regulatory single nucleotide polymorphisms (rSNPs) that is based on 246 annotation features. CERENKOV uses the xgboost classifier and is designed to be used to find causal noncoding SNPs in...

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Yao Y, Liu Z, Wei Q, et al. CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. BMC Bioinformatics. 2019;20(1):63doi: 10.1186/s12859-019-2637-4.
Yao, Y., Liu, Z., Wei, Q., & Ramsey, S. A. (2019). CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. BMC bioinformatics, 20(1), 63. https://doi.org/10.1186/s12859-019-2637-4
Yao, Yao, et al. "CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features." BMC bioinformatics vol. 20,1 (2019): 63. doi: https://doi.org/10.1186/s12859-019-2637-4
Yao Y, Liu Z, Wei Q, Ramsey SA. CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. BMC Bioinformatics. 2019 Feb 06;20(1):63. doi: 10.1186/s12859-019-2637-4. PMID: 30727967; PMCID: PMC6364436.
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Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus.

Indian journal of microbiology

Ferri DV, Munhoz CF, Neves PM, Ferracin LM, Sartori D, Vieira ML, Fungaro MH.
PMID: 24293712
Indian J Microbiol. 2012 Dec;52(4):569-74. doi: 10.1007/s12088-012-0292-9. Epub 2012 Aug 01.

The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana crops. The use of the entomopathogenic fungus Beauveria bassiana as a biological control agent for this pest may contribute towards reducing the application...

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Ferri DV, Munhoz CF, Neves PM, et al. Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus. Indian J Microbiol. 2012;52(4):569-74doi: 10.1007/s12088-012-0292-9.
Ferri, D. V., Munhoz, C. F., Neves, P. M., Ferracin, L. M., Sartori, D., Vieira, M. L., & Fungaro, M. H. (2012). Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus. Indian journal of microbiology, 52(4), 569-74. https://doi.org/10.1007/s12088-012-0292-9
Ferri, D V, et al. "Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus." Indian journal of microbiology vol. 52,4 (2012): 569-74. doi: https://doi.org/10.1007/s12088-012-0292-9
Ferri DV, Munhoz CF, Neves PM, Ferracin LM, Sartori D, Vieira ML, Fungaro MH. Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus. Indian J Microbiol. 2012 Dec;52(4):569-74. doi: 10.1007/s12088-012-0292-9. Epub 2012 Aug 01. PMID: 24293712; PMCID: PMC3516667.
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EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements.

BMC bioinformatics

Hartmann T, Bernt M, Middendorf M.
PMID: 29843612
BMC Bioinformatics. 2018 May 30;19(1):192. doi: 10.1186/s12859-018-2170-x.

BACKGROUND: To study the differences between two unichromosomal circular genomes, e.g., mitochondrial genomes, under the tandem duplication random loss (TDRL) rearrangement it is important to consider the whole set of potential TDRL rearrangement events that could have taken place....

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Hartmann T, Bernt M, Middendorf M. EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements. BMC Bioinformatics. 2018;19(1):192doi: 10.1186/s12859-018-2170-x.
Hartmann, T., Bernt, M., & Middendorf, M. (2018). EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements. BMC bioinformatics, 19(1), 192. https://doi.org/10.1186/s12859-018-2170-x
Hartmann, Tom, et al. "EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements." BMC bioinformatics vol. 19,1 (2018): 192. doi: https://doi.org/10.1186/s12859-018-2170-x
Hartmann T, Bernt M, Middendorf M. EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements. BMC Bioinformatics. 2018 May 30;19(1):192. doi: 10.1186/s12859-018-2170-x. PMID: 29843612; PMCID: PMC5975268.
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Development of Polymerase Chain Reaction Primers Highly Specific for Xanthomonas albilineans, the Causal Bacterium of Sugarcane Leaf Scald Disease.

Plant disease

Pan YB, Grisham MP, Burner DM, Legendre BL, Wei Q.
PMID: 30845497
Plant Dis. 1999 Mar;83(3):218-222. doi: 10.1094/PDIS.1999.83.3.218.

New primers were developed that greatly improved the specificity of the polymerase chain reaction (PCR) protocol for Xanthomonas albilineans, the causal agent of sugarcane leaf scald disease. Length-polymorphic PCR products, amplified under the current PCR protocol from the 16S-23S...

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Pan YB, Grisham MP, Burner DM, et al. Development of Polymerase Chain Reaction Primers Highly Specific for Xanthomonas albilineans, the Causal Bacterium of Sugarcane Leaf Scald Disease. Plant Dis. 1999;83(3):218-222doi: 10.1094/PDIS.1999.83.3.218.
Pan, Y. B., Grisham, M. P., Burner, D. M., Legendre, B. L., & Wei, Q. (1999). Development of Polymerase Chain Reaction Primers Highly Specific for Xanthomonas albilineans, the Causal Bacterium of Sugarcane Leaf Scald Disease. Plant disease, 83(3), 218-222. https://doi.org/10.1094/PDIS.1999.83.3.218
Pan, Y-B, et al. "Development of Polymerase Chain Reaction Primers Highly Specific for Xanthomonas albilineans, the Causal Bacterium of Sugarcane Leaf Scald Disease." Plant disease vol. 83,3 (1999): 218-222. doi: https://doi.org/10.1094/PDIS.1999.83.3.218
Pan YB, Grisham MP, Burner DM, Legendre BL, Wei Q. Development of Polymerase Chain Reaction Primers Highly Specific for Xanthomonas albilineans, the Causal Bacterium of Sugarcane Leaf Scald Disease. Plant Dis. 1999 Mar;83(3):218-222. doi: 10.1094/PDIS.1999.83.3.218. PMID: 30845497.
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Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan.

Malaria journal

Mustafa MSEK, Jaal Z, Abu Kashawa S, Mohd Nor SA.
PMID: 34923983
Malar J. 2021 Dec 19;20(1):469. doi: 10.1186/s12936-021-03994-7.

BACKGROUND: Anopheles arabiensis is a member of Anopheles gambiae complex and the main malaria vector in Sudan. There is insufficient population genetics data available on An. arabiensis for an understanding of vector population structure and genetics, which are important...

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Mustafa MSEK, Jaal Z, Abu Kashawa S, et al. Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan. Malar J. 2021;20(1):469doi: 10.1186/s12936-021-03994-7.
Mustafa, M. S. E. K., Jaal, Z., Abu Kashawa, S., & Mohd Nor, S. A. (2021). Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan. Malaria journal, 20(1), 469. https://doi.org/10.1186/s12936-021-03994-7
Mustafa, Mashair Sir El Khatim, et al. "Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan." Malaria journal vol. 20,1 (2021): 469. doi: https://doi.org/10.1186/s12936-021-03994-7
Mustafa MSEK, Jaal Z, Abu Kashawa S, Mohd Nor SA. Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan. Malar J. 2021 Dec 19;20(1):469. doi: 10.1186/s12936-021-03994-7. PMID: 34923983; PMCID: PMC8684682.
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