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Protocol: a beginner's guide to the analysis of RNA-directed DNA methylation in plants.

Plant methods

Zhang H, Tang K, Wang B, Duan CG, Lang Z, Zhu JK.
PMID: 24955108
Plant Methods. 2014 Jun 14;10:18. doi: 10.1186/1746-4811-10-18. eCollection 2014.

BACKGROUND: DNA methylation is a conserved epigenetic mark that controls genome stability, development and environmental responses in many eukaryotes. DNA methylation can be guided by non-coding RNAs that include small interfering RNAs and scaffold RNAs. Although measurement of DNA...

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Zhang H, Tang K, Wang B, et al. Protocol: a beginner's guide to the analysis of RNA-directed DNA methylation in plants. Plant Methods. 2014;10:18doi: 10.1186/1746-4811-10-18.
Zhang, H., Tang, K., Wang, B., Duan, C. G., Lang, Z., & Zhu, J. K. (2014). Protocol: a beginner's guide to the analysis of RNA-directed DNA methylation in plants. Plant methods, 1018. https://doi.org/10.1186/1746-4811-10-18
Zhang, Huiming, et al. "Protocol: a beginner's guide to the analysis of RNA-directed DNA methylation in plants." Plant methods vol. 10 (2014): 18. doi: https://doi.org/10.1186/1746-4811-10-18
Zhang H, Tang K, Wang B, Duan CG, Lang Z, Zhu JK. Protocol: a beginner's guide to the analysis of RNA-directed DNA methylation in plants. Plant Methods. 2014 Jun 14;10:18. doi: 10.1186/1746-4811-10-18. eCollection 2014. PMID: 24955108; PMCID: PMC4065543.
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RNA-Seq Study of Microbially Induced Hemocyte Transcripts from Larval Heliothis virescens (Lepidoptera: Noctuidae).

Insects

Shelby KS, Popham HJ.
PMID: 26466627
Insects. 2012 Aug 14;3(3):743-62. doi: 10.3390/insects3030743.

Larvae of the tobacco budworm are major polyphagous pests throughout the Americas. Development of effective microbial biopesticides for this and related noctuid pests has been stymied by the natural resistance mediated innate immune response. Hemocytes play an early and...

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Shelby KS, Popham HJ. RNA-Seq Study of Microbially Induced Hemocyte Transcripts from Larval Heliothis virescens (Lepidoptera: Noctuidae). Insects. 2012;3(3):743-62doi: 10.3390/insects3030743.
Shelby, K. S., & Popham, H. J. (2012). RNA-Seq Study of Microbially Induced Hemocyte Transcripts from Larval Heliothis virescens (Lepidoptera: Noctuidae). Insects, 3(3), 743-62. https://doi.org/10.3390/insects3030743
Shelby, Kent S, and Popham, Holly J R. "RNA-Seq Study of Microbially Induced Hemocyte Transcripts from Larval Heliothis virescens (Lepidoptera: Noctuidae)." Insects vol. 3,3 (2012): 743-62. doi: https://doi.org/10.3390/insects3030743
Shelby KS, Popham HJ. RNA-Seq Study of Microbially Induced Hemocyte Transcripts from Larval Heliothis virescens (Lepidoptera: Noctuidae). Insects. 2012 Aug 14;3(3):743-62. doi: 10.3390/insects3030743. PMID: 26466627; PMCID: PMC4553588.
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High-energy collision-induced dissociation mass spectrometry of synthetic mannose-6-phosphate oligosaccharides.

Journal of the American Society for Mass Spectrometry

Lipniunas PH, Townsend RR, Burlingame AL, Hindsgaul O.
PMID: 24203240
J Am Soc Mass Spectrom. 1996 Feb;7(2):182-8. doi: 10.1016/1044-0305(95)00635-4.

The high-energy collision-induced dissociation spectra of a series of linear and branched synthetic mannosyl oligosaccharides that contain 6-phosphate substituents on either or both non-reducing terminal or penultimate residues have been studied. These phosphorylated structures were designed to mimic those...

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Lipniunas PH, Townsend RR, Burlingame AL, et al. High-energy collision-induced dissociation mass spectrometry of synthetic mannose-6-phosphate oligosaccharides. J Am Soc Mass Spectrom. 1996;7(2):182-8doi: 10.1016/1044-0305(95)00635-4.
Lipniunas, P. H., Townsend, R. R., Burlingame, A. L., & Hindsgaul, O. (1996). High-energy collision-induced dissociation mass spectrometry of synthetic mannose-6-phosphate oligosaccharides. Journal of the American Society for Mass Spectrometry, 7(2), 182-8. https://doi.org/10.1016/1044-0305(95)00635-4
Lipniunas, P H, et al. "High-energy collision-induced dissociation mass spectrometry of synthetic mannose-6-phosphate oligosaccharides." Journal of the American Society for Mass Spectrometry vol. 7,2 (1996): 182-8. doi: https://doi.org/10.1016/1044-0305(95)00635-4
Lipniunas PH, Townsend RR, Burlingame AL, Hindsgaul O. High-energy collision-induced dissociation mass spectrometry of synthetic mannose-6-phosphate oligosaccharides. J Am Soc Mass Spectrom. 1996 Feb;7(2):182-8. doi: 10.1016/1044-0305(95)00635-4. PMID: 24203240.
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Phenolic Compounds from Olea europaea L. Possess Antioxidant Activity and Inhibit Carbohydrate Metabolizing Enzymes In Vitro.

Evidence-based complementary and alternative medicine : eCAM

Dekdouk N, Malafronte N, Russo D, Faraone I, De Tommasi N, Ameddah S, Severino L, Milella L.
PMID: 26557862
Evid Based Complement Alternat Med. 2015;2015:684925. doi: 10.1155/2015/684925. Epub 2015 Oct 08.

Phenolic composition and biological activities of fruit extracts from Italian and Algerian Olea europaea L. cultivars were studied. Total phenolic and tannin contents were quantified in the extracts. Moreover 14 different phenolic compounds were identified, and their profiles showed...

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Dekdouk N, Malafronte N, Russo D, et al. Phenolic Compounds from Olea europaea L. Possess Antioxidant Activity and Inhibit Carbohydrate Metabolizing Enzymes In Vitro. Evid Based Complement Alternat Med. 2015;2015:684925doi: 10.1155/2015/684925.
Dekdouk, N., Malafronte, N., Russo, D., Faraone, I., De Tommasi, N., Ameddah, S., Severino, L., & Milella, L. (2015). Phenolic Compounds from Olea europaea L. Possess Antioxidant Activity and Inhibit Carbohydrate Metabolizing Enzymes In Vitro. Evidence-based complementary and alternative medicine : eCAM, 2015684925. https://doi.org/10.1155/2015/684925
Dekdouk, Nadia, et al. "Phenolic Compounds from Olea europaea L. Possess Antioxidant Activity and Inhibit Carbohydrate Metabolizing Enzymes In Vitro." Evidence-based complementary and alternative medicine : eCAM vol. 2015 (2015): 684925. doi: https://doi.org/10.1155/2015/684925
Dekdouk N, Malafronte N, Russo D, Faraone I, De Tommasi N, Ameddah S, Severino L, Milella L. Phenolic Compounds from Olea europaea L. Possess Antioxidant Activity and Inhibit Carbohydrate Metabolizing Enzymes In Vitro. Evid Based Complement Alternat Med. 2015;2015:684925. doi: 10.1155/2015/684925. Epub 2015 Oct 08. PMID: 26557862; PMCID: PMC4618337.
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Anti-androgenic effects of flavonols in prostate cancer.

Ecancermedicalscience

Boam T.
PMID: 26557883
Ecancermedicalscience. 2015 Oct 22;9:585. doi: 10.3332/ecancer.2015.585. eCollection 2015.

Dietary-derived agents, such as the flavonoids, are of particular interest for prostate cancer (PCa) chemoprevention as they may offer a favourable safety and side-effect profile. An agent that demonstrates action on the androgen receptor (AR) axis may have value...

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Boam T. Anti-androgenic effects of flavonols in prostate cancer. Ecancermedicalscience. 2015;9:585doi: 10.3332/ecancer.2015.585.
Boam, T. (2015). Anti-androgenic effects of flavonols in prostate cancer. Ecancermedicalscience, 9585. https://doi.org/10.3332/ecancer.2015.585
Boam, Tristan. "Anti-androgenic effects of flavonols in prostate cancer." Ecancermedicalscience vol. 9 (2015): 585. doi: https://doi.org/10.3332/ecancer.2015.585
Boam T. Anti-androgenic effects of flavonols in prostate cancer. Ecancermedicalscience. 2015 Oct 22;9:585. doi: 10.3332/ecancer.2015.585. eCollection 2015. PMID: 26557883; PMCID: PMC4631581.
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Precocious markers of cardiovascular risk and vascular damage in apparently healthy women with previous gestational diabetes.

Diabetology & metabolic syndrome

Zajdenverg L, Rodacki M, Faria JP, Pires ML, Oliveira JE, Halfoun VL.
PMID: 24955136
Diabetol Metab Syndr. 2014 May 26;6:63. doi: 10.1186/1758-5996-6-63. eCollection 2014.

UNLABELLED: Previous gestational diabetes mellitus (pGDM) indicates future risk for type 2 diabetes (T2DM). Insulin resistance (IR) may precede T2DM in many years and is associated with an increased risk for cardiovascular diseases.AIM: This study aims to identify endothelial...

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Zajdenverg L, Rodacki M, Faria JP, et al. Precocious markers of cardiovascular risk and vascular damage in apparently healthy women with previous gestational diabetes. Diabetol Metab Syndr. 2014;6:63doi: 10.1186/1758-5996-6-63.
Zajdenverg, L., Rodacki, M., Faria, J. P., Pires, M. L., Oliveira, J. E., & Halfoun, V. L. (2014). Precocious markers of cardiovascular risk and vascular damage in apparently healthy women with previous gestational diabetes. Diabetology & metabolic syndrome, 663. https://doi.org/10.1186/1758-5996-6-63
Zajdenverg, Lenita, et al. "Precocious markers of cardiovascular risk and vascular damage in apparently healthy women with previous gestational diabetes." Diabetology & metabolic syndrome vol. 6 (2014): 63. doi: https://doi.org/10.1186/1758-5996-6-63
Zajdenverg L, Rodacki M, Faria JP, Pires ML, Oliveira JE, Halfoun VL. Precocious markers of cardiovascular risk and vascular damage in apparently healthy women with previous gestational diabetes. Diabetol Metab Syndr. 2014 May 26;6:63. doi: 10.1186/1758-5996-6-63. eCollection 2014. PMID: 24955136; PMCID: PMC4064263.
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Bacterial co-expression of the α and β protomers of human l-asparaginase-3: Achieving essential N-terminal exposure of a catalytically critical threonine located in the β-subunit.

Protein expression and purification

Karamitros CS, Konrad M.
PMID: 24157738
Protein Expr Purif. 2014 Jan;93:1-10. doi: 10.1016/j.pep.2013.10.007. Epub 2013 Oct 22.

l-asparaginases hydrolyze l-asparagine to l-aspartic acid and ammonia. Enzymes of bacterial origin are used as therapeutic agents for the treatment of acute lymphoblastic leukemia. Recently, the structure of a human homolog, hASNase3, which possesses l-asparaginase activity, was solved setting...

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Karamitros CS, Konrad M. Bacterial co-expression of the α and β protomers of human l-asparaginase-3: Achieving essential N-terminal exposure of a catalytically critical threonine located in the β-subunit. Protein Expr Purif. 2013;93:1-10doi: 10.1016/j.pep.2013.10.007.
Karamitros, C. S., & Konrad, M. (2014). Bacterial co-expression of the α and β protomers of human l-asparaginase-3: Achieving essential N-terminal exposure of a catalytically critical threonine located in the β-subunit. Protein expression and purification, 931-10. https://doi.org/10.1016/j.pep.2013.10.007
Karamitros, Christos S, and Konrad, Manfred. "Bacterial co-expression of the α and β protomers of human l-asparaginase-3: Achieving essential N-terminal exposure of a catalytically critical threonine located in the β-subunit." Protein expression and purification vol. 93 (2014): 1-10. doi: https://doi.org/10.1016/j.pep.2013.10.007
Karamitros CS, Konrad M. Bacterial co-expression of the α and β protomers of human l-asparaginase-3: Achieving essential N-terminal exposure of a catalytically critical threonine located in the β-subunit. Protein Expr Purif. 2014 Jan;93:1-10. doi: 10.1016/j.pep.2013.10.007. Epub 2013 Oct 22. PMID: 24157738.
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Dodonaea viscosa var. angustifolia Inhibits Germ Tube and Biofilm Formation by C. albicans.

Evidence-based complementary and alternative medicine : eCAM

Naicker SD, Patel M.
PMID: 24223612
Evid Based Complement Alternat Med. 2013;2013:261978. doi: 10.1155/2013/261978. Epub 2013 Oct 09.

The virulence factors of Candida albicans are germ tube and biofilm formation, adherence to host tissues, and production of hydrolytic enzymes. This study investigated the effect of Dodonaea viscosa var. angustifolia extract on the germ tube and biofilm formation...

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Naicker SD, Patel M. Dodonaea viscosa var. angustifolia Inhibits Germ Tube and Biofilm Formation by C. albicans. Evid Based Complement Alternat Med. 2013;2013:261978doi: 10.1155/2013/261978.
Naicker, S. D., & Patel, M. (2013). Dodonaea viscosa var. angustifolia Inhibits Germ Tube and Biofilm Formation by C. albicans. Evidence-based complementary and alternative medicine : eCAM, 2013261978. https://doi.org/10.1155/2013/261978
Naicker, Serisha Devi, and Patel, Mrudula. "Dodonaea viscosa var. angustifolia Inhibits Germ Tube and Biofilm Formation by C. albicans." Evidence-based complementary and alternative medicine : eCAM vol. 2013 (2013): 261978. doi: https://doi.org/10.1155/2013/261978
Naicker SD, Patel M. Dodonaea viscosa var. angustifolia Inhibits Germ Tube and Biofilm Formation by C. albicans. Evid Based Complement Alternat Med. 2013;2013:261978. doi: 10.1155/2013/261978. Epub 2013 Oct 09. PMID: 24223612; PMCID: PMC3809598.
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Dichloromethane extracts of propolis protect cell from oxygen-glucose deprivation-induced oxidative stress via reducing apoptosis.

Food & nutrition research

Sun LP, Xu X, Hwang HH, Wang X, Su KY, Chen YL.
PMID: 27329777
Food Nutr Res. 2016 Jun 20;60:30081. doi: 10.3402/fnr.v60.30081. eCollection 2016.

BACKGROUND: Bee propolis, a mixture of the secretion from bee tongue gland and wax gland, was collected from the tree bud and barked by bees. The components were rich in terpenes, phenolics, and flavonoids, and had anti-cancer, anti-bacterial, anti-inflammatory,...

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Sun LP, Xu X, Hwang HH, et al. Dichloromethane extracts of propolis protect cell from oxygen-glucose deprivation-induced oxidative stress via reducing apoptosis. Food Nutr Res. 2016;60:30081doi: 10.3402/fnr.v60.30081.
Sun, L. P., Xu, X., Hwang, H. H., Wang, X., Su, K. Y., & Chen, Y. L. (2016). Dichloromethane extracts of propolis protect cell from oxygen-glucose deprivation-induced oxidative stress via reducing apoptosis. Food & nutrition research, 6030081. https://doi.org/10.3402/fnr.v60.30081
Sun, Li-Ping, et al. "Dichloromethane extracts of propolis protect cell from oxygen-glucose deprivation-induced oxidative stress via reducing apoptosis." Food & nutrition research vol. 60 (2016): 30081. doi: https://doi.org/10.3402/fnr.v60.30081
Sun LP, Xu X, Hwang HH, Wang X, Su KY, Chen YL. Dichloromethane extracts of propolis protect cell from oxygen-glucose deprivation-induced oxidative stress via reducing apoptosis. Food Nutr Res. 2016 Jun 20;60:30081. doi: 10.3402/fnr.v60.30081. eCollection 2016. PMID: 27329777; PMCID: PMC4916261.
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Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India.

Genome announcements

Mukherjee T, Bose S, Sen U, Roy C, Rameez MJ, Ghosh W, Mukhopadhyay SK.
PMID: 27365353
Genome Announc. 2016 Jun 30;4(3). doi: 10.1128/genomeA.00629-16.

Here we report the draft genome sequence of Meiothermus taiwanensis strain RP (MCC 2966), isolated from the Paniphala hot spring of India, which contains genes encoding for enzymes of the methyl erythritol 4-phosphate (MEP) pathway of isoprenoid biosynthesis and...

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Mukherjee T, Bose S, Sen U, et al. Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India. Genome Announc. 2016;4(3)doi: 10.1128/genomeA.00629-16.
Mukherjee, T., Bose, S., Sen, U., Roy, C., Rameez, M. J., Ghosh, W., & Mukhopadhyay, S. K. (2016). Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India. Genome announcements, 4(3), . https://doi.org/10.1128/genomeA.00629-16
Mukherjee, Trinetra, et al. "Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India." Genome announcements vol. 4,3 (2016). doi: https://doi.org/10.1128/genomeA.00629-16
Mukherjee T, Bose S, Sen U, Roy C, Rameez MJ, Ghosh W, Mukhopadhyay SK. Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India. Genome Announc. 2016 Jun 30;4(3). doi: 10.1128/genomeA.00629-16. PMID: 27365353; PMCID: PMC4929516.
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Biotransformation of caffeoyl quinic acids from green coffee extracts by Lactobacillus johnsonii NCC 533.

AMB Express

Bel-Rhlid R, Thapa D, Kraehenbuehl K, Hansen CE, Fischer L.
PMID: 23692950
AMB Express. 2013 May 21;3:28. doi: 10.1186/2191-0855-3-28. eCollection 2013.

The potential of Lactobacillus johnsonii NCC 533 to metabolize chlorogenic acids from green coffee extract was investigated. Two enzymes, an esterase and a hydroxycinnamate decarboxylase (HCD), were involved in this biotransformation. The complete hydrolysis of 5-caffeoylquinic acid (5-CQA) into...

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Bel-Rhlid R, Thapa D, Kraehenbuehl K, et al. Biotransformation of caffeoyl quinic acids from green coffee extracts by Lactobacillus johnsonii NCC 533. AMB Express. 2013;3:28doi: 10.1186/2191-0855-3-28.
Bel-Rhlid, R., Thapa, D., Kraehenbuehl, K., Hansen, C. E., & Fischer, L. (2013). Biotransformation of caffeoyl quinic acids from green coffee extracts by Lactobacillus johnsonii NCC 533. AMB Express, 328. https://doi.org/10.1186/2191-0855-3-28
Bel-Rhlid, Rachid, et al. "Biotransformation of caffeoyl quinic acids from green coffee extracts by Lactobacillus johnsonii NCC 533." AMB Express vol. 3 (2013): 28. doi: https://doi.org/10.1186/2191-0855-3-28
Bel-Rhlid R, Thapa D, Kraehenbuehl K, Hansen CE, Fischer L. Biotransformation of caffeoyl quinic acids from green coffee extracts by Lactobacillus johnsonii NCC 533. AMB Express. 2013 May 21;3:28. doi: 10.1186/2191-0855-3-28. eCollection 2013. PMID: 23692950; PMCID: PMC3679781.
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Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer.

Oncoscience

Shim EH, Sudarshan S.
PMID: 26097881
Oncoscience. 2015 May 15;2(5):483-6. doi: 10.18632/oncoscience.165. eCollection 2015.

Alterations in metabolism are now considered a hallmark of cancer. One of the clearest links between metabolism and malignancy are oncometabolites. To date, several putative oncometabolites with transforming properties have been identified in the context of tumors due to...

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Shim EH, Sudarshan S. Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer. Oncoscience. 2015;2(5):483-6doi: 10.18632/oncoscience.165.
Shim, E. H., & Sudarshan, S. (2015). Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer. Oncoscience, 2(5), 483-6. https://doi.org/10.18632/oncoscience.165
Shim, Eun-Hee, and Sudarshan, Sunil. "Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer." Oncoscience vol. 2,5 (2015): 483-6. doi: https://doi.org/10.18632/oncoscience.165
Shim EH, Sudarshan S. Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer. Oncoscience. 2015 May 15;2(5):483-6. doi: 10.18632/oncoscience.165. eCollection 2015. PMID: 26097881; PMCID: PMC4468334.
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Showing 25 to 36 of 40378 entries