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(What I'm Currently Reading)
(What I'm Currently Reading:)
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Perhaps one of the oldest papers, but also one of the best in terms of examining the basic engineering concepts that the other papers seem to take for granted.  
Perhaps one of the oldest papers, but also one of the best in terms of examining the basic engineering concepts that the other papers seem to take for granted.  
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<br>
<br>
Ohta K, et al. 1991. Genetic Improvement of E. Coli for Ethanol production: chromosomal integration of Z. mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Applied and Env Microbio, 57, 4: 893-900. [http://aem.asm.org.ezp1.harvard.edu/cgi/reprint/57/4/893?view=long&pmid=2059047 full text]<br>
Ohta K, et al. 1991. Genetic Improvement of E. Coli for Ethanol production: chromosomal integration of Z. mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Applied and Env Microbio, 57, 4: 893-900. [http://aem.asm.org.ezp1.harvard.edu/cgi/reprint/57/4/893?view=long&pmid=2059047 full text]<br>
Looks intriguing. Again, relatively old, but I think it will emphasize basic manipulations that have been experimentally performed - which is good if we plan to look into this. I haven't read this one fully yet, but I'll update if I do. <br><br>
Looks intriguing. Again, relatively old, but I think it will emphasize basic manipulations that have been experimentally performed - which is good if we plan to look into this. I haven't read this one fully yet, but I'll update if I do. <br><br>
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Rao K, et al. 2007. Enhanced ethanol fermentation of brewery wastewater using genetically modified strain E. coli KO11.<br>
Rao K, et al. 2007. Enhanced ethanol fermentation of brewery wastewater using genetically modified strain E. coli KO11.<br>
Two major results should be emphasized: yeast consistently produced EtOH more rapidly; commericial enzymes (alpha-amylase and pectinase) enhanced EtOH yields in both yeast and e.coli. As a side note, I'm finding it interesting that most of the newer articles (such as this one) seem to advocate using engineered yeast rather than e.coli, while many earlier studies (early 1990s) seemed to find that E. coli were equally, or more, efficient. I'll keep an eye out for this trend as I continue reading. <br>
Two major results should be emphasized: yeast consistently produced EtOH more rapidly; commericial enzymes (alpha-amylase and pectinase) enhanced EtOH yields in both yeast and e.coli. As a side note, I'm finding it interesting that most of the newer articles (such as this one) seem to advocate using engineered yeast rather than e.coli, while many earlier studies (early 1990s) seemed to find that E. coli were equally, or more, efficient. I'll keep an eye out for this trend as I continue reading. <br>
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<br><br>
<br><br>
<b> Adaptamers</b>
<b> Adaptamers</b>
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<br> <i> Don't get intimidated by this list - I did a lot of this reading last semester for my research course over the period of a few months. The most pertinent ones are the ones that focus on adaptamers - such as the Reid PCR paper - and even those that focus on aptamers, since many of the potential applications parallel those of adaptamers </i>
+
<br> <i> Don't get intimidated by this list - I did a lot of this reading last semester for my research course over the period of a few months. The most pertinent ones are the ones that focus on adaptamers - such as the Reid PCR paper - and even those that focus on aptamers, since many of the potential applications parallel those of adaptamers. </i>
-
<br>
+
<br><br>
-
Postier, et. al, “The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy”. BioMed Central Genomics, 2003; 4:23.  
+
Postier, et. al, “The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy”. BioMed Central Genomics, 2003; 4:23. <br>
-
 
+
Erdeniz, et. al, “Cloning-Free PCR-Based Allele Replacement Methods”. Genome Research, 1997; 7: 1174-1183. <br>
-
Erdeniz, et. al, “Cloning-Free PCR-Based Allele Replacement Methods”. Genome Research, 1997; 7: 1174-1183.
+
Rimmele, Martina, “Nucleic Acid Aptamers as Tools and Drugs: Recent Developments”, ChemBioChem, 4, 963-71. <br>
-
 
+
Smalley and Ley, “L-selectin: Mechanisms and Physiological Significance of Ectodomain Cleavage.” Journal of Cellular and Molecular Medicine, 2005; 9.2: 255-66. <br>
-
Rimmele, Martina, “Nucleic Acid Aptamers as Tools and Drugs: Recent Developments”, ChemBioChem, 4, 963-71.
+
Fors, et. al, “L-Selectin Shedding Is Independent of Its Subsurface Structures and Topographic Distribution”. The Journal of Immunology, 2001; 167: 3642-51. <br>
-
 
+
Hafezi-Moghadam A, et. al., “L-selectin shedding regulates leukocyte recruitment”. Journal of Experimental Medicine 2001; 193: 863-72. <br>
-
Smalley and Ley, “L-selectin: Mechanisms and Physiological Significance of Ectodomain Cleavage.” Journal of Cellular and Molecular Medicine, 2005; 9.2: 255-66.
+
Dong, et.al., “Mechanisms for Induction of L-selectin Loss from T Lymphocytes by a Cryptococcal Polysaccharide, Glucuronoxylomannan”. Infection and Immunity, 1999; 67: 220-9. <br>
-
 
+
Norman KE, et al, “Peptides derived from the lectin domain of selectin adhesion molecules inhibit leukocyte rolling in vivo”. Microcirculation, 1996; 3: 29-38. <br>
-
Fors, et. al, “L-Selectin Shedding Is Independent of Its Subsurface Structures and Topographic Distribution”. The Journal of Immunology, 2001; 167: 3642-51.  
+
Reid, et. al, “Cloning-Free Genome Alterations in Saccharomyces cerevisiae Using Adaptamer-Mediated PCR”. Methods in Enzymology, 2002; 350: 258 -77. <br>
-
 
+
Guo, et. al, “A New Technique for the Isolation and Surface Immobilization of Mesenchymal Stem Cells from Whole Bone Marrow Using High-Specific DNA Aptamers”. Stem Cells, 2006; 24: 2220-31. <br>
-
Hafezi-Moghadam A, et. al., “L-selectin shedding regulates leukocyte recruitment”. Journal of Experimental Medicine 2001; 193: 863-72.
+
Dellaire, et. al, “In situ imaging and isolation of proteins using dsDNA oligonucleotides”. Nucleic Acids Research, 2004; 32: 20. <br>
-
 
+
Harvard iGEM team. http://parts2.mit.edu/wiki/index.php/Harvard_2006 <br>
-
Dong, et.al., “Mechanisms for Induction of L-selectin Loss from T Lymphocytes by a Cryptococcal Polysaccharide, Glucuronoxylomannan”. Infection and Immunity, 1999; 67: 220-9.
+
Spertini, et. al, “ELISA for quantitation of L-selectin shed for leukocytes in vivo”. Journal of Immunological Methods, 1992; 156: 115-23. <br>
-
 
+
Schmuke and Welply, “A Method for Measuring Leukocyte Rolling on the Selectins.” Analytical Biochemistry, 1995; 226: 197-201. <br>
-
Norman KE, et al, “Peptides derived from the lectin domain of selectin adhesion molecules inhibit leukocyte rolling in vivo”. Microcirculation, 1996; 3: 29-38.
+
Ley, et. al, “Lectin-like adhesion molecule 1 mediates leukocyte rolling in mesenteric venules in vivo.” Blood 1991; 77: 2553-55. <br>
-
 
+
Norman KE, et. al, “Peptides derived from the lectin domain of selectin adhesion molecules inhibit leukocyte rolling in vivo.” Microcirculation. 1996; 3: 29-38. <br>
-
Reid, et. al, “Cloning-Free Genome Alterations in Saccharomyces cerevisiae Using Adaptamer-Mediated PCR”. Methods in Enzymology, 2002; 350: 258 -77.  
+
Reid, et. al, “Efficient PCR-based gene disruption in Saccharomyces strains using intergenic primers”. Yeast 2002; 19: 319-28. <br>
-
 
+
-
Guo, et. al, “A New Technique for the Isolation and Surface Immobilization of Mesenchymal Stem Cells from Whole Bone Marrow Using High-Specific DNA Aptamers”. Stem Cells, 2006; 24: 2220-31.  
+
-
 
+
-
Dellaire, et. al, “In situ imaging and isolation of proteins using dsDNA oligonucleotides”. Nucleic Acids Research, 2004; 32: 20.  
+
-
 
+
-
Harvard iGEM team. http://parts2.mit.edu/wiki/index.php/Harvard_2006  
+
-
 
+
-
Spertini, et. al, “ELISA for quantitation of L-selectin shed for leukocytes in vivo”. Journal of Immunological Methods, 1992; 156: 115-23.
+
-
 
+
-
Schmuke and Welply, “A Method for Measuring Leukocyte Rolling on the Selectins.” Analytical Biochemistry, 1995; 226: 197-201.
+
-
 
+
-
Ley, et. al, “Lectin-like adhesion molecule 1 mediates leukocyte rolling in mesenteric venules in vivo.” Blood 1991; 77: 2553-55.  
+
-
 
+
-
Norman KE, et. al, “Peptides derived from the lectin domain of selectin adhesion molecules inhibit leukocyte rolling in vivo.” Microcirculation. 1996; 3: 29-38.  
+
-
 
+
-
Reid, et. al, “Efficient PCR-based gene disruption in Saccharomyces strains using intergenic primers”. Yeast 2002; 19: 319-28.  
+
-
 
+
Reference website: Intergenic Primer Search Page. http://rothsteinlab.hs.columbia.edu/projects/primersearch.html. Rothstein Laboratory of Columbia University. Last Accessed: 22 December 2006.  
Reference website: Intergenic Primer Search Page. http://rothsteinlab.hs.columbia.edu/projects/primersearch.html. Rothstein Laboratory of Columbia University. Last Accessed: 22 December 2006.  
<br><br>
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Revision as of 05:42, 23 April 2007

Stephanie Lo
Harvard College 2010

1885 Harvard Yard Mail Center
Cambridge, MA 02138

I have always had a passion for sciences, particularly chemistry, and hope to pursue a joint concentration in Molecular and Cellular Biology and Economics. Eventually, I plan to apply for an MD/PhD program and specialize in digestive disorders.

Latest news:
I'll be making a presentation at the next iGEM meeting on engineering E.coli to efficiently produce EtOH as well as adaptamers (past studies of, and potential applications of). Adaptamers haven't been at the forefront of discussion lately, but they're great for labs of the iGEM size, and have an array of potential uses.
Presentation Handout


What I'm Currently Reading:


Note: I'm not formatting my citations correctly, I know. If there is any confusion, please let me know. Also, though some of the articles do not have links, they should be readily accessible via PubMed with a Harvard login.

Engineering for EtOH production

Ingram L, et al. 1987. Genetic engineering of ethanol production in E. coli. Applied and Environmental Microbiology. 53, 10: 2420-2425. Full text
Perhaps one of the oldest papers, but also one of the best in terms of examining the basic engineering concepts that the other papers seem to take for granted.
Ohta K, et al. 1991. Genetic Improvement of E. Coli for Ethanol production: chromosomal integration of Z. mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Applied and Env Microbio, 57, 4: 893-900. full text
Looks intriguing. Again, relatively old, but I think it will emphasize basic manipulations that have been experimentally performed - which is good if we plan to look into this. I haven't read this one fully yet, but I'll update if I do.

Rao K, et al. 2007. Enhanced ethanol fermentation of brewery wastewater using genetically modified strain E. coli KO11.
Two major results should be emphasized: yeast consistently produced EtOH more rapidly; commericial enzymes (alpha-amylase and pectinase) enhanced EtOH yields in both yeast and e.coli. As a side note, I'm finding it interesting that most of the newer articles (such as this one) seem to advocate using engineered yeast rather than e.coli, while many earlier studies (early 1990s) seemed to find that E. coli were equally, or more, efficient. I'll keep an eye out for this trend as I continue reading.

Stephanopoulos, G. Challenges in engineering microbes for biofuels production. 2007, Science, 315, 801.
Easily readable, but not extremely pertinent to the engineering of E. coli that we've been considering.

Service, R. CELLULOSIC ETHANOL: Biofuel Researchers Prepare to Reap a New Harvest. Science 16 March 2007. Vol. 315, no 5818, 1488-1491.Full Text; requires login
This paper isn't as mechanism-based as the Aristou paper (cited below), but provides a nice overview of the history of ethanol use, why energy is a concern, etc. It seems to be a nice background for the general public, and provides a nice introduction to the field.

Aristidou, A and M Penttila. Metabolic engineering applications to renewable resource utilization. Science Direct: Current Opinion in Biotechnology 1 April 2000. Vol 11, no 2, 187-198. Full text
This review focuses on the bioconversion of the pentose fractions into ethanol and suggests use of biocatalysts (such as bacteria and yeast) to assist in this slow-step in the conversion of sugars into useful products.

Adaptamers
Don't get intimidated by this list - I did a lot of this reading last semester for my research course over the period of a few months. The most pertinent ones are the ones that focus on adaptamers - such as the Reid PCR paper - and even those that focus on aptamers, since many of the potential applications parallel those of adaptamers.

Postier, et. al, “The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy”. BioMed Central Genomics, 2003; 4:23.
Erdeniz, et. al, “Cloning-Free PCR-Based Allele Replacement Methods”. Genome Research, 1997; 7: 1174-1183.
Rimmele, Martina, “Nucleic Acid Aptamers as Tools and Drugs: Recent Developments”, ChemBioChem, 4, 963-71.
Smalley and Ley, “L-selectin: Mechanisms and Physiological Significance of Ectodomain Cleavage.” Journal of Cellular and Molecular Medicine, 2005; 9.2: 255-66.
Fors, et. al, “L-Selectin Shedding Is Independent of Its Subsurface Structures and Topographic Distribution”. The Journal of Immunology, 2001; 167: 3642-51.
Hafezi-Moghadam A, et. al., “L-selectin shedding regulates leukocyte recruitment”. Journal of Experimental Medicine 2001; 193: 863-72.
Dong, et.al., “Mechanisms for Induction of L-selectin Loss from T Lymphocytes by a Cryptococcal Polysaccharide, Glucuronoxylomannan”. Infection and Immunity, 1999; 67: 220-9.
Norman KE, et al, “Peptides derived from the lectin domain of selectin adhesion molecules inhibit leukocyte rolling in vivo”. Microcirculation, 1996; 3: 29-38.
Reid, et. al, “Cloning-Free Genome Alterations in Saccharomyces cerevisiae Using Adaptamer-Mediated PCR”. Methods in Enzymology, 2002; 350: 258 -77.
Guo, et. al, “A New Technique for the Isolation and Surface Immobilization of Mesenchymal Stem Cells from Whole Bone Marrow Using High-Specific DNA Aptamers”. Stem Cells, 2006; 24: 2220-31.
Dellaire, et. al, “In situ imaging and isolation of proteins using dsDNA oligonucleotides”. Nucleic Acids Research, 2004; 32: 20.
Harvard iGEM team. http://parts2.mit.edu/wiki/index.php/Harvard_2006
Spertini, et. al, “ELISA for quantitation of L-selectin shed for leukocytes in vivo”. Journal of Immunological Methods, 1992; 156: 115-23.
Schmuke and Welply, “A Method for Measuring Leukocyte Rolling on the Selectins.” Analytical Biochemistry, 1995; 226: 197-201.
Ley, et. al, “Lectin-like adhesion molecule 1 mediates leukocyte rolling in mesenteric venules in vivo.” Blood 1991; 77: 2553-55.
Norman KE, et. al, “Peptides derived from the lectin domain of selectin adhesion molecules inhibit leukocyte rolling in vivo.” Microcirculation. 1996; 3: 29-38.
Reid, et. al, “Efficient PCR-based gene disruption in Saccharomyces strains using intergenic primers”. Yeast 2002; 19: 319-28.
Reference website: Intergenic Primer Search Page. http://rothsteinlab.hs.columbia.edu/projects/primersearch.html. Rothstein Laboratory of Columbia University. Last Accessed: 22 December 2006.

General

Current Research Activity in Biosensors. Nakamura et al, 2003, Analytical Bioanalytical Chem.
A really great overview of some potential applications of biosensors, including electrochemical sensors, detergent sensors, acid rain sensors, red tide, cyanide sensors, E. coli used for gas toxicity monitoring (see reference 276 of the paper - I intend to look into this more), and food sensors to detect glucose, sucrose, and lactose.

Harvard iGEM

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