I saw this news, it is worth to read it.
Ada Lovelace (from wiki)
She is today appreciated as the "first programmer". She also foresaw the capability of computers to go beyond mere calculating or number-crunching while others focused only on these capabilities.
Ada Lovelace Day – celebrating the women of tech
Ada Lovelace
Blog about a woman in science or technology
Ada Lovelace Day - Bringing women in technology to the fore
Read more!
Sunday, March 29, 2009
Despair is the greatest sorrow
I just made a sad decision. I completely give up any effort trying to change this situation. Six years is not a short time and I already tried my best except going down on my knees.
Here is the translation of 哀莫大於心死:
Etymology
Literally: Nothing is more lamentable than a dead heart.
Proverb
Despair is the greatest sorrow; Nothing gives greater cause for sorrow than despair; There is no grief so great as despair; There is no poverty like the poverty of spirit.
Read more!
Here is the translation of 哀莫大於心死:
Etymology
Literally: Nothing is more lamentable than a dead heart.
Proverb
Despair is the greatest sorrow; Nothing gives greater cause for sorrow than despair; There is no grief so great as despair; There is no poverty like the poverty of spirit.
Read more!
Thursday, March 26, 2009
Forensic Science
This is some information for myself.
DNA profiling - Wikipedia, the free encyclopedia
DNA Profiling Techniques - Forensic DNA Analysis
Forensic DNA Analysis: Technology and Application (BP443e)
DNA Forensics
DNA.gov: History of Forensic DNA Analysis
QIAGEN - Genetic Identity and Forensics
Studying Forensic Science in Australia
Griffith University | Programs and courses | Science | Forensic science
FORENSICnetBASE: Forensic Handbooks Online
Read more!
DNA profiling - Wikipedia, the free encyclopedia
DNA Profiling Techniques - Forensic DNA Analysis
Forensic DNA Analysis: Technology and Application (BP443e)
DNA Forensics
DNA.gov: History of Forensic DNA Analysis
QIAGEN - Genetic Identity and Forensics
Studying Forensic Science in Australia
Griffith University | Programs and courses | Science | Forensic science
FORENSICnetBASE: Forensic Handbooks Online
Read more!
Tuesday, March 24, 2009
Maybe or maybe not?
I am just wondering if a person you know does not response to your email many times for a while. Maybe that person does not want to keep contact with you or maybe not?
For example:
Sending an email to that person on Feb 27 to discuss some issues s/he mentioned
No response, sending another email on March 15 to discuss.
No response, sending another email on March 23 with more topics and information to discuss.
Still no response. What would you do?
The worst part is that this similar situation has happened many many times in the past 5 years. It just makes me feel this is a one-way export but not two-way communication. Truly and really frustrated.
Read more!
For example:
Sending an email to that person on Feb 27 to discuss some issues s/he mentioned
No response, sending another email on March 15 to discuss.
No response, sending another email on March 23 with more topics and information to discuss.
Still no response. What would you do?
The worst part is that this similar situation has happened many many times in the past 5 years. It just makes me feel this is a one-way export but not two-way communication. Truly and really frustrated.
Read more!
How can you buy or sell the sky
I still love this speech very much even with a great deal of controversy surrounding Chief Seattle's speech of 1854. Maybe the translation of his speech has changed a lot of what he really said, maybe the so-called translation was created by others. But we all know that indigenous people did not view the land as their own property until we force them.
........
How can you buy or sell the sky, the warmth of the land? The idea is strange to us.
If we do not own the freshness of the air and the sparkle of the water, how can you buy them?
Every part of this earth is sacred to my people. Every shining pine needle, every sandy shore, every mist in the dark woods, every clearing and humming insect is holy in the memory and experience of my people. The sap which courses through the trees carries the memories of the red man.
........
* Chief Seattle's Speech of 1854
* Thus Spoke Chief Seattle: The Story of An Undocumented Speech, by Jerry L. Clark, the National Archives Vol. 18, No. 1 (Spring 1985).
Detailed research calling into question the very existence of the speech, based on the Bureau of Indian Affairs records at the National Archives.
* Chief Seattle on internet, Research by Per-Olof Johansson in Denmark
* Chief Seattle's Thoughts, Two versions of the speech by Duane Bristow
Read more!
........
How can you buy or sell the sky, the warmth of the land? The idea is strange to us.
If we do not own the freshness of the air and the sparkle of the water, how can you buy them?
Every part of this earth is sacred to my people. Every shining pine needle, every sandy shore, every mist in the dark woods, every clearing and humming insect is holy in the memory and experience of my people. The sap which courses through the trees carries the memories of the red man.
........
* Chief Seattle's Speech of 1854
* Thus Spoke Chief Seattle: The Story of An Undocumented Speech, by Jerry L. Clark, the National Archives Vol. 18, No. 1 (Spring 1985).
Detailed research calling into question the very existence of the speech, based on the Bureau of Indian Affairs records at the National Archives.
* Chief Seattle on internet, Research by Per-Olof Johansson in Denmark
* Chief Seattle's Thoughts, Two versions of the speech by Duane Bristow
Read more!
Fire in Lab
Our lab was on fire this afternoon right after I started A-addition experiment around 2 pm.
I smelled something cooking/burning while I transferred Roche HPPP clean up PCR samples from 1.5 mL eppendorf tube to 200 uL PCR tubes around 2:05 pm. Then I heard somebody using fire extinguish to put off the fire. The smell became worse and I decided to take a look what's going on.
Wa! The laminar flow hood was emitting heavy white smoke from its top part, i.e. the filter part. Very thick smoke. School policemen came and everybody went out to lobby/hall around 2:10 pm. Then I heard the fire alarm was ringing from outside the building. I did not hear anything inside the lab. Hmm, this is very strange.
Firemen came in 5-10 minutes. They went inside to check the situation. More firemen with mask came around 2:35 pm and started to broadcast and evacuate the building. I am wondering why we couldn't hear the fire alarm inside the building and why they evacuate people so late? Maybe because too many false alarm?
I hope my A-addition experiment is OK. It supposes to run 20 minutes at 37 oC, then move to ice box for the ligation I intend to do today, and store at -20 oC after that. I guess it has to stay at room temperature for long now. I hope my pGEM-T EZ buffer is OK. I left it in ice box because I plan to do ligation this afternoon. I hope the PCR samples mixed with loading dye which are ready to run gel are OK because I left them on bench at room temperature.
It is 3:45 pm. They said the hood is still burning and we are not allowed to get in. The ice should be melting and I am afraid most samples and reagents in the ice box are exposed to room temperature now. My samples .....
I finally got in at 4:45 pm to put all my samples in freezer.
March 25: My lab still smell really bad. The smell makes many people headache. The detail story about this is:
The lab research assistant accidentally put a burning forceps into EtOH bottle (ps. for tissue culture work, we put forceps in EtOH, take it out and burn it with burner to sterilize the surface). Then fire burst out from the bottle, she got panic and pushed the bottle away, the bottle felt and spread EtOH everywhere in the hood, then the filter of the hood was on fire.
I heard that it will cost 10,000 AUD to fix it. Woop!
Read more!
I smelled something cooking/burning while I transferred Roche HPPP clean up PCR samples from 1.5 mL eppendorf tube to 200 uL PCR tubes around 2:05 pm. Then I heard somebody using fire extinguish to put off the fire. The smell became worse and I decided to take a look what's going on.
Wa! The laminar flow hood was emitting heavy white smoke from its top part, i.e. the filter part. Very thick smoke. School policemen came and everybody went out to lobby/hall around 2:10 pm. Then I heard the fire alarm was ringing from outside the building. I did not hear anything inside the lab. Hmm, this is very strange.
Firemen came in 5-10 minutes. They went inside to check the situation. More firemen with mask came around 2:35 pm and started to broadcast and evacuate the building. I am wondering why we couldn't hear the fire alarm inside the building and why they evacuate people so late? Maybe because too many false alarm?
I hope my A-addition experiment is OK. It supposes to run 20 minutes at 37 oC, then move to ice box for the ligation I intend to do today, and store at -20 oC after that. I guess it has to stay at room temperature for long now. I hope my pGEM-T EZ buffer is OK. I left it in ice box because I plan to do ligation this afternoon. I hope the PCR samples mixed with loading dye which are ready to run gel are OK because I left them on bench at room temperature.
It is 3:45 pm. They said the hood is still burning and we are not allowed to get in. The ice should be melting and I am afraid most samples and reagents in the ice box are exposed to room temperature now. My samples .....
I finally got in at 4:45 pm to put all my samples in freezer.
March 25: My lab still smell really bad. The smell makes many people headache. The detail story about this is:
The lab research assistant accidentally put a burning forceps into EtOH bottle (ps. for tissue culture work, we put forceps in EtOH, take it out and burn it with burner to sterilize the surface). Then fire burst out from the bottle, she got panic and pushed the bottle away, the bottle felt and spread EtOH everywhere in the hood, then the filter of the hood was on fire.
I heard that it will cost 10,000 AUD to fix it. Woop!
Read more!
MADS-box genes
Some references for MADS-box genes
Abascal, F., R. Zardoya, et al. (2005). "ProtTest: selection of best-fit models of protein evolution." Bioinformatics 21(9): 2104-5.
Alvarez-Buylla, E. R., S. J. Liljegren, et al. (2000). "MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes." Plant J 24(4): 457-66.
Alvarez-Buylla, E. R., S. Pelaz, et al. (2000). "An ancestral MADS-box gene duplication occurred before the divergence of plants and animals." Proc Natl Acad Sci U S A 97(10): 5328-33.
Becker, A. and G. Theissen (2003). "The major clades of MADS-box genes and their role in the development and evolution of flowering plants." Mol Phylogenet Evol 29(3): 464-89.
Black, D. L. (2003). "Mechanisms of alternative pre-messenger RNA splicing." Annu Rev Biochem 72: 291-336.
Causier, B., R. Castillo, et al. (2005). "Evolution in action: following function in duplicated floral homeotic genes." Curr Biol 15(16): 1508-12.
Chen, F. C., S. S. Wang, et al. (2007). "Plant gene and alternatively spliced variant annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species." Plant Physiology 143(3): 1086-1095.
Cseke, L. and G. Podila (2004). "MADS-box genes in dioecious aspen II: a review of MADS-box genes from trees and their potential in forest biotechnology." Physiology and Molecular Biology of Plants 10(1): 7-28.
de Folter, S., R. G. Immink, et al. (2005). "Comprehensive interaction map of the Arabidopsis MADS Box transcription factors." Plant Cell 17(5): 1424-33.
Egea-Cortines, M., H. Saedler, et al. (1999). "Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus." Embo J 18(19): 5370-9.
Glazko, G. V. and M. Nei (2003). "Estimation of divergence times for major lineages of primate species." Mol Biol Evol 20(3): 424-34.
Guindon, S. and O. Gascuel (2003). "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood." Syst Biol 52(5): 696-704.
Guindon, S., F. Lethiec, et al. (2005). "PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference." Nucleic Acids Res 33(Web Server issue): W557-9.
Hartmann, U., S. Hohmann, et al. (2000). "Molecular cloning of SVP: a negative regulator of the floral transition in Arabidopsis." Plant J 21(4): 351-60.
Hartwell, L., L. Hood, et al. (2004). Genetics: from genes to genomes, McGraw-Hill Higher Education, Boston.
Hernandez-Hernandez, T., L. P. Martinez-Castilla, et al. (2007). "Functional diversification of B MADS-box homeotic regulators of flower development: Adaptive evolution in protein-protein interaction domains after major gene duplication events." Mol Biol Evol 24(2): 465-81.
Hileman, L. C., J. F. Sundstrom, et al. (2006). "Molecular and phylogenetic analyses of the MADS-box gene family in tomato." Mol Biol Evol 23(11): 2245-58.
Honma, T. and K. Goto (2001). "Complexes of MADS-box proteins are sufficient to convert leaves into floral organs." Nature 409(6819): 525-9.
Irish, V. F. and A. Litt (2005). "Flower development and evolution: gene duplication, diversification and redeployment." Curr Opin Genet Dev 15(4): 454-60.
Katoh, K., K. Kuma, et al. (2005). "MAFFT version 5: improvement in accuracy of multiple sequence alignment." Nucleic Acids Res 33(2): 511-8.
Katoh, K., K. Misawa, et al. (2002). "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform." Nucleic Acids Res 30(14): 3059-66.
Kaufmann, K., R. Melzer, et al. (2005). "MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants." Gene 347(2): 183-98.
Kramer, E. M., M. A. Jaramillo, et al. (2004). "Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms." Genetics 166(2): 1011-23.
Krizek, B. A. and J. C. Fletcher (2005). "Molecular mechanisms of flower development: an armchair guide." Nat Rev Genet 6(9): 688-98.
Litt, A. and V. F. Irish (2003). "Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development." Genetics 165(2): 821-33.
Moore, R. C. and M. D. Purugganan (2005). "The evolutionary dynamics of plant duplicate genes." Curr Opin Plant Biol 8(2): 122-8.
Nam, J., C. W. dePamphilis, et al. (2003). "Antiquity and evolution of the MADS-box gene family controlling flower development in plants." Mol Biol Evol 20(9): 1435-47.
Nam, J., J. Kim, et al. (2004). "Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms." Proc Natl Acad Sci U S A 101(7): 1910-5.
Ng, M. and M. F. Yanofsky (2001). "Function and evolution of the plant MADS-box gene family." Nat Rev Genet 2(3): 186-95.
Parenicova, L., S. de Folter, et al. (2003). "Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world." Plant Cell 15(7): 1538-51.
Posada, D. and T. R. Buckley (2004). "Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests." Syst Biol 53(5): 793-808.
Posada, D. and K. A. Crandall (1998). "MODELTEST: testing the model of DNA substitution." Bioinformatics 14(9): 817-8.
Promega (2005). ImProm-II reverse transcription system.
QIAGEN (2001). RNeasy Mini Handbook, QIAGEN Inc.
Ratcliffe, O. J., R. W. Kumimoto, et al. (2003). "Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold." Plant Cell 15(5): 1159-69.
Reddy, A. S. N. (2007). "Alternative splicing of pre-messenger RNAs in plants in the genomic era." Annual Review of Plant Biology 58: 267-294.
Rijpkema, A. S., T. Gerats, et al. (2007). "Evolutionary complexity of MADS complexes." Curr Opin Plant Biol 10(1): 32-8.
Sablowski, R. W. and E. M. Meyerowitz (1998). "Temperature-sensitive splicing in the floral homeotic mutant apetala3-1." Plant Cell 10(9): 1453-63.
Sheldon, C. C., A. B. Conn, et al. (2002). "Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression." Plant Cell 14(10): 2527-37.
Sheldon, C. C., D. T. Rouse, et al. (2000). "The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC)." Proc Natl Acad Sci U S A 97(7): 3753-8.
Theissen, G. (2001). "Development of floral organ identity: stories from the MADS house." Curr Opin Plant Biol 4(1): 75-85.
Theissen, G., A. Becker, et al. (2000). "A short history of MADS-box genes in plants." Plant Mol Biol 42(1): 115-49.
Theissen, G. and H. Saedler (2001). "Plant biology. Floral quartets." Nature 409(6819): 469-71.
Tuskan, G. A., S. Difazio, et al. (2006). "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)." Science 313(5793): 1596-604.
Tzeng, T. Y., H. C. Liu, et al. (2004). "The C-terminal sequence of LMADS1 is essential for the formation of homodimers for B function proteins." J Biol Chem 279(11): 10747-55.
Vandenbussche, M., G. Theissen, et al. (2003). "Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations." Nucleic Acids Res 31(15): 4401-9.
Wang, B. B. and V. Brendel (2006). "Genomewide comparative analysis of alternative splicing in plants." Proc Natl Acad Sci U S A 103(18): 7175-80.
Wernersson, R. and A. G. Pedersen (2003). "RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences." Nucleic Acids Res 31(13): 3537-9.
Zhu, Q. H., A. Y. Guo, et al. (2007). "DPTF: a database of poplar transcription factors." Bioinformatics 23(10): 1307-8.
Read more!
Abascal, F., R. Zardoya, et al. (2005). "ProtTest: selection of best-fit models of protein evolution." Bioinformatics 21(9): 2104-5.
Alvarez-Buylla, E. R., S. J. Liljegren, et al. (2000). "MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes." Plant J 24(4): 457-66.
Alvarez-Buylla, E. R., S. Pelaz, et al. (2000). "An ancestral MADS-box gene duplication occurred before the divergence of plants and animals." Proc Natl Acad Sci U S A 97(10): 5328-33.
Becker, A. and G. Theissen (2003). "The major clades of MADS-box genes and their role in the development and evolution of flowering plants." Mol Phylogenet Evol 29(3): 464-89.
Black, D. L. (2003). "Mechanisms of alternative pre-messenger RNA splicing." Annu Rev Biochem 72: 291-336.
Causier, B., R. Castillo, et al. (2005). "Evolution in action: following function in duplicated floral homeotic genes." Curr Biol 15(16): 1508-12.
Chen, F. C., S. S. Wang, et al. (2007). "Plant gene and alternatively spliced variant annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species." Plant Physiology 143(3): 1086-1095.
Cseke, L. and G. Podila (2004). "MADS-box genes in dioecious aspen II: a review of MADS-box genes from trees and their potential in forest biotechnology." Physiology and Molecular Biology of Plants 10(1): 7-28.
de Folter, S., R. G. Immink, et al. (2005). "Comprehensive interaction map of the Arabidopsis MADS Box transcription factors." Plant Cell 17(5): 1424-33.
Egea-Cortines, M., H. Saedler, et al. (1999). "Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus." Embo J 18(19): 5370-9.
Glazko, G. V. and M. Nei (2003). "Estimation of divergence times for major lineages of primate species." Mol Biol Evol 20(3): 424-34.
Guindon, S. and O. Gascuel (2003). "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood." Syst Biol 52(5): 696-704.
Guindon, S., F. Lethiec, et al. (2005). "PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference." Nucleic Acids Res 33(Web Server issue): W557-9.
Hartmann, U., S. Hohmann, et al. (2000). "Molecular cloning of SVP: a negative regulator of the floral transition in Arabidopsis." Plant J 21(4): 351-60.
Hartwell, L., L. Hood, et al. (2004). Genetics: from genes to genomes, McGraw-Hill Higher Education, Boston.
Hernandez-Hernandez, T., L. P. Martinez-Castilla, et al. (2007). "Functional diversification of B MADS-box homeotic regulators of flower development: Adaptive evolution in protein-protein interaction domains after major gene duplication events." Mol Biol Evol 24(2): 465-81.
Hileman, L. C., J. F. Sundstrom, et al. (2006). "Molecular and phylogenetic analyses of the MADS-box gene family in tomato." Mol Biol Evol 23(11): 2245-58.
Honma, T. and K. Goto (2001). "Complexes of MADS-box proteins are sufficient to convert leaves into floral organs." Nature 409(6819): 525-9.
Irish, V. F. and A. Litt (2005). "Flower development and evolution: gene duplication, diversification and redeployment." Curr Opin Genet Dev 15(4): 454-60.
Katoh, K., K. Kuma, et al. (2005). "MAFFT version 5: improvement in accuracy of multiple sequence alignment." Nucleic Acids Res 33(2): 511-8.
Katoh, K., K. Misawa, et al. (2002). "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform." Nucleic Acids Res 30(14): 3059-66.
Kaufmann, K., R. Melzer, et al. (2005). "MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants." Gene 347(2): 183-98.
Kramer, E. M., M. A. Jaramillo, et al. (2004). "Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms." Genetics 166(2): 1011-23.
Krizek, B. A. and J. C. Fletcher (2005). "Molecular mechanisms of flower development: an armchair guide." Nat Rev Genet 6(9): 688-98.
Litt, A. and V. F. Irish (2003). "Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development." Genetics 165(2): 821-33.
Moore, R. C. and M. D. Purugganan (2005). "The evolutionary dynamics of plant duplicate genes." Curr Opin Plant Biol 8(2): 122-8.
Nam, J., C. W. dePamphilis, et al. (2003). "Antiquity and evolution of the MADS-box gene family controlling flower development in plants." Mol Biol Evol 20(9): 1435-47.
Nam, J., J. Kim, et al. (2004). "Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms." Proc Natl Acad Sci U S A 101(7): 1910-5.
Ng, M. and M. F. Yanofsky (2001). "Function and evolution of the plant MADS-box gene family." Nat Rev Genet 2(3): 186-95.
Parenicova, L., S. de Folter, et al. (2003). "Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world." Plant Cell 15(7): 1538-51.
Posada, D. and T. R. Buckley (2004). "Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests." Syst Biol 53(5): 793-808.
Posada, D. and K. A. Crandall (1998). "MODELTEST: testing the model of DNA substitution." Bioinformatics 14(9): 817-8.
Promega (2005). ImProm-II reverse transcription system.
QIAGEN (2001). RNeasy Mini Handbook, QIAGEN Inc.
Ratcliffe, O. J., R. W. Kumimoto, et al. (2003). "Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold." Plant Cell 15(5): 1159-69.
Reddy, A. S. N. (2007). "Alternative splicing of pre-messenger RNAs in plants in the genomic era." Annual Review of Plant Biology 58: 267-294.
Rijpkema, A. S., T. Gerats, et al. (2007). "Evolutionary complexity of MADS complexes." Curr Opin Plant Biol 10(1): 32-8.
Sablowski, R. W. and E. M. Meyerowitz (1998). "Temperature-sensitive splicing in the floral homeotic mutant apetala3-1." Plant Cell 10(9): 1453-63.
Sheldon, C. C., A. B. Conn, et al. (2002). "Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression." Plant Cell 14(10): 2527-37.
Sheldon, C. C., D. T. Rouse, et al. (2000). "The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC)." Proc Natl Acad Sci U S A 97(7): 3753-8.
Theissen, G. (2001). "Development of floral organ identity: stories from the MADS house." Curr Opin Plant Biol 4(1): 75-85.
Theissen, G., A. Becker, et al. (2000). "A short history of MADS-box genes in plants." Plant Mol Biol 42(1): 115-49.
Theissen, G. and H. Saedler (2001). "Plant biology. Floral quartets." Nature 409(6819): 469-71.
Tuskan, G. A., S. Difazio, et al. (2006). "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)." Science 313(5793): 1596-604.
Tzeng, T. Y., H. C. Liu, et al. (2004). "The C-terminal sequence of LMADS1 is essential for the formation of homodimers for B function proteins." J Biol Chem 279(11): 10747-55.
Vandenbussche, M., G. Theissen, et al. (2003). "Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations." Nucleic Acids Res 31(15): 4401-9.
Wang, B. B. and V. Brendel (2006). "Genomewide comparative analysis of alternative splicing in plants." Proc Natl Acad Sci U S A 103(18): 7175-80.
Wernersson, R. and A. G. Pedersen (2003). "RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences." Nucleic Acids Res 31(13): 3537-9.
Zhu, Q. H., A. Y. Guo, et al. (2007). "DPTF: a database of poplar transcription factors." Bioinformatics 23(10): 1307-8.
Read more!
Late March 2009 papers
Some interest papers.
Plant cell biology: When autumn falls, Simon Bishop, Nature Reviews Molecular Cell Biology 10:238-239.
Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis, Jin Hee Kim, Hye Ryun Woo, Jeongsik Kim, Pyung Ok Lim, In Chul Lee, Seung Hee Choi, Daehee Hwang, Hong Gil Nam, Science 323:1053–1057 (2009).
Aquaculture: Future fish, Daniel Cressey, Nature 458(7237):398-400 (26 March 2009).
The only way to meet the increasing demand for fish is through aquaculture. Daniel Cressey explores the challenges for fish farmers and what it means for dinner plates in 2030.
Structural biology: Spliceosome subunit revealed, Charles C. Query, Nature 458(7237):418-419 (26 March 2009).
The spliceosome enzyme binds to RNA transcripts at splice sites and removes intron sequences. The crystal structure of a spliceosome subunit shows how the enzyme recognizes one end of the intron.
The ubiquitin system, Nature 458(7237):421–467 (26 March 2009).
The central role of ubiquitin in cell-cycle regulation, DNA repair, cell growth, signalling and immune function is starting to become clear right down to the molecular level. Identifying irregularities in the system has opened up opportunities in drug discovery, and in diagnostics and treatment for a range of disorders, from cancer to neurodegeneration.
Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution, Daniel A. Pomeranz Krummel et al., Nature 458(7237):475-480 (26 March 2009).
In eukaryotes, many genes contain one or more introns — sequences that are transcribed into mRNA, but which are then excised before the mRNA is translated into protein. Multiprotein–RNA complexes called snRNPs are the machinery that clips these introns out. This study presents the structure of the U1 snRNP, which assembles at the 5′ end of the intron; the subunit interactions suggest a model by which the snRNP is assembled and the 5′ splice site is recognized.
PROFILE: JORGE CHAM: Piled Higher and Deeper: The Everyday Life of a Grad Student, Science 323(5922):1668 - 1669 (27 March 2009).
Jorge Cham's comic strip, capturing the trials and tribulations of grad school, became so popular that he left the lab for a career as a cartoonist and lecturer.
CHEMISTRY: Producing Transportation Fuels with Less Work, D. Hildebrandt et al., Science 323(5922):1680 - 1681 (27 March 2009).
New reaction chemistry may reduce the energy input and carbon dioxide emissions from processes that convert coal into liquid fuels.
Conserved intragenic elements were critical for the evolution of the floral C-function, Barry Causier, Desmond Bradley, Holly Cook and Brendan Davies, The Plant Journal 58(1):41 - 52.
Glutaredoxin Functions in Floral Development, Nancy R. Hofmann, Plant Cell 21:363 (2009).
The Future of Science: Food and Water for Life, Nancy A. Eckardt, Eleonora Cominelli, Massimo Galbiati, and Chiara Tonelli, Plant Cell 21:368-372 (2009).
Nuclear Activity of ROXY1, a Glutaredoxin Interacting with TGA Factors, Is Required for Petal Development in Arabidopsis thaliana, Shutian Li, Andrea Lauri, Mark Ziemann, Andrea Busch, Mrinal Bhave, and Sabine Zachgo, Plant Cell 21:429-441 (2009).
A Bacterial-Type ABC Transporter Is Involved in Aluminum Tolerance in Rice, Chao Feng Huang, Naoki Yamaji, Namiki Mitani, Masahiro Yano, Yoshiaki Nagamura, and Jian Feng Ma,
Plant Cell 21:655-667 (2009).
A Novel Plant Leucine-Rich Repeat Receptor Kinase Regulates the Response of Medicago truncatula Roots to Salt Stress, Laura de Lorenzo, Francisco Merchan, Philippe Laporte, Richard Thompson, Jonathan Clarke, Carolina Sousa, and Martin Crespi, Plant Cell 21:668-680 (2009).
Cheap third-generation sequencing, Nicole Rusk, Nature Methods 6(4):244.
By covalently attaching cyclodextrin to a hemolysin nanopore, researchers show single-molecule, label-free sequencing at very high accuracy.
Snapshots of proteins at work, Allison Doerr, Nature Methods 6(4):246.
Two groups extend the boundaries of in-cell nuclear magnetic resonance spectroscopy.
QPCR without the 'P', Irene Kaganman, Nature Methods 6(4):250.
With the addition of a ligand-sensing aptamer sequence, a self-replicating RNA enzyme system enables general molecular detection, analogous to that of quantitative PCR.
Journeys across the membrane, Nathan Blow, Nature Methods 6(4):305-309.
From high-throughput electroporation platforms capable of transfecting thousands of different cells in a day, to nanowires that puncture and deliver DNA to just a single cell, new technology is emerging to help researchers with their changing gene delivery needs.
Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system, Anjali Shah, Nature Methods 6(4).
Chromatin immunoprecipitation (ChIP) is a technique for identifying and characterizing elements in protein-DNA interactions involved in gene regulation or chromatin organization. Microarray platforms provide a method for 'global' ChIP analysis, but direct sequencing of enriched fragments has proven a more effective means for determining locations of DNA-binding proteins along the genome in an unbiased manner. The massively parallel sequencing capacity, high accuracy and flexibility of the SOLiD™ system make it well suited for ChIP-sequencing (ChIP-Seq) applications.
Read more!
Plant cell biology: When autumn falls, Simon Bishop, Nature Reviews Molecular Cell Biology 10:238-239.
Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis, Jin Hee Kim, Hye Ryun Woo, Jeongsik Kim, Pyung Ok Lim, In Chul Lee, Seung Hee Choi, Daehee Hwang, Hong Gil Nam, Science 323:1053–1057 (2009).
Aquaculture: Future fish, Daniel Cressey, Nature 458(7237):398-400 (26 March 2009).
The only way to meet the increasing demand for fish is through aquaculture. Daniel Cressey explores the challenges for fish farmers and what it means for dinner plates in 2030.
Structural biology: Spliceosome subunit revealed, Charles C. Query, Nature 458(7237):418-419 (26 March 2009).
The spliceosome enzyme binds to RNA transcripts at splice sites and removes intron sequences. The crystal structure of a spliceosome subunit shows how the enzyme recognizes one end of the intron.
The ubiquitin system, Nature 458(7237):421–467 (26 March 2009).
The central role of ubiquitin in cell-cycle regulation, DNA repair, cell growth, signalling and immune function is starting to become clear right down to the molecular level. Identifying irregularities in the system has opened up opportunities in drug discovery, and in diagnostics and treatment for a range of disorders, from cancer to neurodegeneration.
Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution, Daniel A. Pomeranz Krummel et al., Nature 458(7237):475-480 (26 March 2009).
In eukaryotes, many genes contain one or more introns — sequences that are transcribed into mRNA, but which are then excised before the mRNA is translated into protein. Multiprotein–RNA complexes called snRNPs are the machinery that clips these introns out. This study presents the structure of the U1 snRNP, which assembles at the 5′ end of the intron; the subunit interactions suggest a model by which the snRNP is assembled and the 5′ splice site is recognized.
PROFILE: JORGE CHAM: Piled Higher and Deeper: The Everyday Life of a Grad Student, Science 323(5922):1668 - 1669 (27 March 2009).
Jorge Cham's comic strip, capturing the trials and tribulations of grad school, became so popular that he left the lab for a career as a cartoonist and lecturer.
CHEMISTRY: Producing Transportation Fuels with Less Work, D. Hildebrandt et al., Science 323(5922):1680 - 1681 (27 March 2009).
New reaction chemistry may reduce the energy input and carbon dioxide emissions from processes that convert coal into liquid fuels.
Conserved intragenic elements were critical for the evolution of the floral C-function, Barry Causier, Desmond Bradley, Holly Cook and Brendan Davies, The Plant Journal 58(1):41 - 52.
Glutaredoxin Functions in Floral Development, Nancy R. Hofmann, Plant Cell 21:363 (2009).
The Future of Science: Food and Water for Life, Nancy A. Eckardt, Eleonora Cominelli, Massimo Galbiati, and Chiara Tonelli, Plant Cell 21:368-372 (2009).
Nuclear Activity of ROXY1, a Glutaredoxin Interacting with TGA Factors, Is Required for Petal Development in Arabidopsis thaliana, Shutian Li, Andrea Lauri, Mark Ziemann, Andrea Busch, Mrinal Bhave, and Sabine Zachgo, Plant Cell 21:429-441 (2009).
A Bacterial-Type ABC Transporter Is Involved in Aluminum Tolerance in Rice, Chao Feng Huang, Naoki Yamaji, Namiki Mitani, Masahiro Yano, Yoshiaki Nagamura, and Jian Feng Ma,
Plant Cell 21:655-667 (2009).
A Novel Plant Leucine-Rich Repeat Receptor Kinase Regulates the Response of Medicago truncatula Roots to Salt Stress, Laura de Lorenzo, Francisco Merchan, Philippe Laporte, Richard Thompson, Jonathan Clarke, Carolina Sousa, and Martin Crespi, Plant Cell 21:668-680 (2009).
Cheap third-generation sequencing, Nicole Rusk, Nature Methods 6(4):244.
By covalently attaching cyclodextrin to a hemolysin nanopore, researchers show single-molecule, label-free sequencing at very high accuracy.
Snapshots of proteins at work, Allison Doerr, Nature Methods 6(4):246.
Two groups extend the boundaries of in-cell nuclear magnetic resonance spectroscopy.
QPCR without the 'P', Irene Kaganman, Nature Methods 6(4):250.
With the addition of a ligand-sensing aptamer sequence, a self-replicating RNA enzyme system enables general molecular detection, analogous to that of quantitative PCR.
Journeys across the membrane, Nathan Blow, Nature Methods 6(4):305-309.
From high-throughput electroporation platforms capable of transfecting thousands of different cells in a day, to nanowires that puncture and deliver DNA to just a single cell, new technology is emerging to help researchers with their changing gene delivery needs.
Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system, Anjali Shah, Nature Methods 6(4).
Chromatin immunoprecipitation (ChIP) is a technique for identifying and characterizing elements in protein-DNA interactions involved in gene regulation or chromatin organization. Microarray platforms provide a method for 'global' ChIP analysis, but direct sequencing of enriched fragments has proven a more effective means for determining locations of DNA-binding proteins along the genome in an unbiased manner. The massively parallel sequencing capacity, high accuracy and flexibility of the SOLiD™ system make it well suited for ChIP-sequencing (ChIP-Seq) applications.
Read more!
Monday, March 23, 2009
Lock Out
We both are writing something now, then we decide to come to school and work in my husband's office during weekends.
After we pour boiling water into Pyrex bowl for instant noodle yesterday noon, we decided to put the teakettle back to lunch room in case if somebody might need to use it. I closed the door right after me, then my husband suddenly said that he did not bring his keys. Gee! We were locked out off his office.
Crying! Our lunch, our work, and every updated files were locked inside his office. We checked everywhere and there was nobody around who could open the door for us. Finally we called the university police for help and they came in 10 minutes to open it for us. Thanks God!
Read more!
After we pour boiling water into Pyrex bowl for instant noodle yesterday noon, we decided to put the teakettle back to lunch room in case if somebody might need to use it. I closed the door right after me, then my husband suddenly said that he did not bring his keys. Gee! We were locked out off his office.
Crying! Our lunch, our work, and every updated files were locked inside his office. We checked everywhere and there was nobody around who could open the door for us. Finally we called the university police for help and they came in 10 minutes to open it for us. Thanks God!
Read more!
Sunday, March 15, 2009
Pie Day
I just learned that yesterday is "Pie Day".
In wiki: Pi Day and Pi Approximation Day are two holidays held to celebrate the mathematical constant π (pi). Pi Day is observed on March 14, 3/14 being the first three digits of pi. It can also be celebrated on March 4 (when 14% of the month of March has elapsed). Pi Approximation Day is observed on July 22, due to π being roughly equal to 22/7.
Pi Minute is also sometimes celebrated on March 14 at 1:59 p.m. If π is truncated to seven decimal places, it becomes 3.1415926, making March 14 at 1:59:26 p.m., Pi Second (or sometimes March 14, 1592 at 6:53:58 a.m.).
(image from wiki)
March 14 is also an interest day. It is Einstein's birthday and it is also White Day in Japan.
Read more!
In wiki: Pi Day and Pi Approximation Day are two holidays held to celebrate the mathematical constant π (pi). Pi Day is observed on March 14, 3/14 being the first three digits of pi. It can also be celebrated on March 4 (when 14% of the month of March has elapsed). Pi Approximation Day is observed on July 22, due to π being roughly equal to 22/7.
Pi Minute is also sometimes celebrated on March 14 at 1:59 p.m. If π is truncated to seven decimal places, it becomes 3.1415926, making March 14 at 1:59:26 p.m., Pi Second (or sometimes March 14, 1592 at 6:53:58 a.m.).
(image from wiki)March 14 is also an interest day. It is Einstein's birthday and it is also White Day in Japan.
Read more!
Friday, March 13, 2009
Mid March 2009 papers
Some interest papers.
RESOURCE POLICY: Wood Energy in America, D. deB. Richter Jr. et al., Science 323(5920):1432 (13 March 2009).
Sustainable wood energy offers recurring economic, social, and environmental benefits.
(note, here are some sentences from first 2 paragraphs of this article. Maybe this is a way out for our energy consumption and CO2 emission?
"....thanks to regrowth of forests and improved technologies, advanced wood combustion (AWC) is being deployed throughout Europe, supplying heat, cooling, and power and reducing greenhouse-gas emissions. ......
More than 1000 AWC facilities have been constructed in Austria, nearly all local community-based; more than 100 combine heat and electric power. .... The facilities emit remarkably low quantities of air pollutants, including greenhouse gases, and have thermal efficiencies across the system approaching 90%.")
A Functional Genomics Approach Reveals CHE as a Component of the Arabidopsis Circadian Clock, J. L. Pruneda-Paz et al., Science 323(5920):1481 - 1485 (13 March 2009).
A transcription factor (CHE) binds the promoter of the clock gene CCA1, adding to the molecular clock circuitry in plants.
Paternal Control of Embryonic Patterning in Arabidopsis thaliana, M. Bayer et al., Science 323(5920):1485 - 1488 (13 March 2009).
Transcripts of a cytoplasmic gene from sperm are translated after fertilization and control asymmetric zygotic division.
Obeying the clock yields benefits for metabolism, Kathryn Moynihan Ramsey and Joseph Bass, PNAS 106(11):4069-4070 (March 17, 2009).
From the Cover: Adverse metabolic and cardiovascular consequences of circadian misalignment, Frank A. J. L. Scheer, Michael F. Hilton, Christos S. Mantzoros, and Steven A. Shea, PNAS 2009 106(11):4453-4458.
The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis, Tara J. Holman, Peter D. Jones, Laurel Russell, Anne Medhurst, Susana Úbeda Tomás, Prabhavathi Talloji, Julietta Marquez, Heike Schmuths, Swee-Ang Tung, Ian Taylor, Steven Footitt, Andreas Bachmair, Frederica L. Theodoulou, and Michael J. Holdsworth, PNAS 2009 106(11):4549-4554.
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice, Yasuyuki Takahashi, Kosuke M. Teshima, Shuji Yokoi, Hideki Innan, and Ko Shimamoto, PNAS 2009 106(11):4555-4560.
Epigenetics: RNAi protects across the generations, Louisa Flintoft, Nature Reviews Genetics 10:220-221 (April 2009).
RNAi is increasingly being recognized as a means of protecting the genome from harmful epigenetic changes. Two new studies in plants describe how RNAi can prevent or reverse the reactivation of transposable elements (TEs), which might otherwise wreak havoc in the genomes of successive generations.
A role for RNAi in the selective correction of DNA methylation defects, Teixeira, F. K. et al., Science 323(5921):1600 - 1604(20 March 2009).
Epigenetic reprogramming and small RNA silencing of transposable elements in pollen, Slotkin, R. K. et al., Cell 136:461–472 (2009)
Epigenetics: Taking a position on regulatory diversity, Louisa Flintoft, Nature Reviews Genetics 10:220-221 (April 2009).
Epigenetic differences between individual cells, populations or species are established contributors to differences in gene expression. Whereas previous work has focused mainly on the contribution of proteins that act in trans to epigenetic differences, studies using yeast now reveal that differences in nucleosome positioning that contribute to variability and divergence in gene expression can be encoded in the genome.
MOLECULAR BIOLOGY: Dynamic DNA Methylation, J. A. Law and S. E. Jacobsen, Science 323(5921):1568 - 1569 (20 March 2009).
The methylation of DNA during plant development is a much more dynamic process than previously assumed.
A Role for RNAi in the Selective Correction of DNA Methylation Defects, F. K. Teixeira et al., Science 323(5921):1600 - 1604 (20 March 2009).
An RNA interference–dependent DNA methylation rescue system helps to preserve a subset of DNA methylation marks in Arabidopsis.
Read more!
RESOURCE POLICY: Wood Energy in America, D. deB. Richter Jr. et al., Science 323(5920):1432 (13 March 2009).
Sustainable wood energy offers recurring economic, social, and environmental benefits.
(note, here are some sentences from first 2 paragraphs of this article. Maybe this is a way out for our energy consumption and CO2 emission?
"....thanks to regrowth of forests and improved technologies, advanced wood combustion (AWC) is being deployed throughout Europe, supplying heat, cooling, and power and reducing greenhouse-gas emissions. ......
More than 1000 AWC facilities have been constructed in Austria, nearly all local community-based; more than 100 combine heat and electric power. .... The facilities emit remarkably low quantities of air pollutants, including greenhouse gases, and have thermal efficiencies across the system approaching 90%.")
A Functional Genomics Approach Reveals CHE as a Component of the Arabidopsis Circadian Clock, J. L. Pruneda-Paz et al., Science 323(5920):1481 - 1485 (13 March 2009).
A transcription factor (CHE) binds the promoter of the clock gene CCA1, adding to the molecular clock circuitry in plants.
Paternal Control of Embryonic Patterning in Arabidopsis thaliana, M. Bayer et al., Science 323(5920):1485 - 1488 (13 March 2009).
Transcripts of a cytoplasmic gene from sperm are translated after fertilization and control asymmetric zygotic division.
Obeying the clock yields benefits for metabolism, Kathryn Moynihan Ramsey and Joseph Bass, PNAS 106(11):4069-4070 (March 17, 2009).
From the Cover: Adverse metabolic and cardiovascular consequences of circadian misalignment, Frank A. J. L. Scheer, Michael F. Hilton, Christos S. Mantzoros, and Steven A. Shea, PNAS 2009 106(11):4453-4458.
The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis, Tara J. Holman, Peter D. Jones, Laurel Russell, Anne Medhurst, Susana Úbeda Tomás, Prabhavathi Talloji, Julietta Marquez, Heike Schmuths, Swee-Ang Tung, Ian Taylor, Steven Footitt, Andreas Bachmair, Frederica L. Theodoulou, and Michael J. Holdsworth, PNAS 2009 106(11):4549-4554.
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice, Yasuyuki Takahashi, Kosuke M. Teshima, Shuji Yokoi, Hideki Innan, and Ko Shimamoto, PNAS 2009 106(11):4555-4560.
Epigenetics: RNAi protects across the generations, Louisa Flintoft, Nature Reviews Genetics 10:220-221 (April 2009).
RNAi is increasingly being recognized as a means of protecting the genome from harmful epigenetic changes. Two new studies in plants describe how RNAi can prevent or reverse the reactivation of transposable elements (TEs), which might otherwise wreak havoc in the genomes of successive generations.
A role for RNAi in the selective correction of DNA methylation defects, Teixeira, F. K. et al., Science 323(5921):1600 - 1604(20 March 2009).
Epigenetic reprogramming and small RNA silencing of transposable elements in pollen, Slotkin, R. K. et al., Cell 136:461–472 (2009)
Epigenetics: Taking a position on regulatory diversity, Louisa Flintoft, Nature Reviews Genetics 10:220-221 (April 2009).
Epigenetic differences between individual cells, populations or species are established contributors to differences in gene expression. Whereas previous work has focused mainly on the contribution of proteins that act in trans to epigenetic differences, studies using yeast now reveal that differences in nucleosome positioning that contribute to variability and divergence in gene expression can be encoded in the genome.
MOLECULAR BIOLOGY: Dynamic DNA Methylation, J. A. Law and S. E. Jacobsen, Science 323(5921):1568 - 1569 (20 March 2009).
The methylation of DNA during plant development is a much more dynamic process than previously assumed.
A Role for RNAi in the Selective Correction of DNA Methylation Defects, F. K. Teixeira et al., Science 323(5921):1600 - 1604 (20 March 2009).
An RNA interference–dependent DNA methylation rescue system helps to preserve a subset of DNA methylation marks in Arabidopsis.
Read more!
Tuesday, March 10, 2009
Aggressive driver
I don't like those aggressive drivers.
Driver's attitude is one way I use to judge the civilization level in a country. I always remember that the suddenly change when I left Taiwan and arrived US. I have to look around in all directions and be careful very much when I tried to cross a road in Taiwan no matter if that is a green light for me to walk. I don't need to pay much attention when I cross a road in US because most drivers will stop and wait for pedestrian to cross.
I thought that Australia might be similar to US, but I am wrong. Well, it is better than Taiwan, but much worse than US. I have to look around and wait for those aggressive drivers to pass through first if I don't want to be run down by them. I have to run through the regular and roundabout pedestrians' crossing several times when those cars run toward me from 100 meters away and passed me at top speed sounding its horn. I did not want to take my chance to see if those drivers will slow down to avoid hitting me because I feel that they don't care.
Read more!
Driver's attitude is one way I use to judge the civilization level in a country. I always remember that the suddenly change when I left Taiwan and arrived US. I have to look around in all directions and be careful very much when I tried to cross a road in Taiwan no matter if that is a green light for me to walk. I don't need to pay much attention when I cross a road in US because most drivers will stop and wait for pedestrian to cross.
I thought that Australia might be similar to US, but I am wrong. Well, it is better than Taiwan, but much worse than US. I have to look around and wait for those aggressive drivers to pass through first if I don't want to be run down by them. I have to run through the regular and roundabout pedestrians' crossing several times when those cars run toward me from 100 meters away and passed me at top speed sounding its horn. I did not want to take my chance to see if those drivers will slow down to avoid hitting me because I feel that they don't care.
Read more!
Parking problem
We have changed our life style for 3 AUD/day.
We used to park on the street in St. Lucia during weekdays when we go to work. It is about 12 minutes walking distance to UQ. Unfortunately, the St. Lucia city council (ps. we are in UQ St. Lucia campus) decided to extend its street parking limitation in March 2009. It means that the area of 2P (2 hours free street parking) and/or 1P (1 hour free street parking) expands now.
If we still want to park on street during weekdays, we have to walk about 20-30 minutes to UQ. We both work in lab and it is very difficult to be able to catch the last bus (6 pm) everyday because some experiments should not be interrupted. We intended to purchase a annual all-day parking permit of UQ (~500 AUD/year) instead of a guarantee all-day parking permit (~900 AUD/year) to solve this problem.
The staff in UQ Transportation and Parking said that they do not offer annual all-day parking permit anymore. If we want to park in parking lot, we have to purchase a guarantee all-day parking permit, otherwise we have to spend 3 AUD/day to park in those causal street parking. The staff also mentioned that those causal parking will fade away in the near future. Hmmm, it is ~10 minutes walking distance from those causal parking space to our offices.
I am not happy about this. If UQ or Queensland government try to encourage people to take public transportation or bike instead of driving a car, they should try to provide better services (park-and-ride, free school shuttle as university in US, safer bike route, better bus/ferry schedule and/or discount ticket for commuter, etc) instead of just punishment.
There is one big street close to UQ (~8 minutes walking distance) is still free of all-day street parking. We decide to park in there. We came to that street at 7:10 am yesterday and only few spaces left. We came to that street at 6:52 am this morning and find more spaces, but many of them were filled up before 7 am.
I think that we will come to school early, then I stay in my husband's office to write or read something. I like this change based on 2 days experiment. I think it is because I fall asleep at night and think more clearly in the morning and the desk and chair in my husband's office is more comfortable for me to use computer.
Ha! I think we will go to bed earlier and wake up around or before 6 am now. Our life style has been changed due to this parking problem and 3 AUD/day. Maybe we will continue this.
March 18, 2009: we still keep this schedule. We get up around 6 am, eat breakfast and prepare our bag, leave home around 6:40 am, arrive that street around 6:52 am, then walk to my husband's office, and study or do some computer work for 2 hours before starting lab work. The only problem is that we fall asleep earlier at night on our sofa.
Read more!
We used to park on the street in St. Lucia during weekdays when we go to work. It is about 12 minutes walking distance to UQ. Unfortunately, the St. Lucia city council (ps. we are in UQ St. Lucia campus) decided to extend its street parking limitation in March 2009. It means that the area of 2P (2 hours free street parking) and/or 1P (1 hour free street parking) expands now.
If we still want to park on street during weekdays, we have to walk about 20-30 minutes to UQ. We both work in lab and it is very difficult to be able to catch the last bus (6 pm) everyday because some experiments should not be interrupted. We intended to purchase a annual all-day parking permit of UQ (~500 AUD/year) instead of a guarantee all-day parking permit (~900 AUD/year) to solve this problem.
The staff in UQ Transportation and Parking said that they do not offer annual all-day parking permit anymore. If we want to park in parking lot, we have to purchase a guarantee all-day parking permit, otherwise we have to spend 3 AUD/day to park in those causal street parking. The staff also mentioned that those causal parking will fade away in the near future. Hmmm, it is ~10 minutes walking distance from those causal parking space to our offices.
I am not happy about this. If UQ or Queensland government try to encourage people to take public transportation or bike instead of driving a car, they should try to provide better services (park-and-ride, free school shuttle as university in US, safer bike route, better bus/ferry schedule and/or discount ticket for commuter, etc) instead of just punishment.
There is one big street close to UQ (~8 minutes walking distance) is still free of all-day street parking. We decide to park in there. We came to that street at 7:10 am yesterday and only few spaces left. We came to that street at 6:52 am this morning and find more spaces, but many of them were filled up before 7 am.
I think that we will come to school early, then I stay in my husband's office to write or read something. I like this change based on 2 days experiment. I think it is because I fall asleep at night and think more clearly in the morning and the desk and chair in my husband's office is more comfortable for me to use computer.
Ha! I think we will go to bed earlier and wake up around or before 6 am now. Our life style has been changed due to this parking problem and 3 AUD/day. Maybe we will continue this.
March 18, 2009: we still keep this schedule. We get up around 6 am, eat breakfast and prepare our bag, leave home around 6:40 am, arrive that street around 6:52 am, then walk to my husband's office, and study or do some computer work for 2 hours before starting lab work. The only problem is that we fall asleep earlier at night on our sofa.
Read more!
Sunday, March 8, 2009
Early March 2009 papers
Here are some interest papers.
Regulation of Carotenoid Composition and Shoot Branching in Arabidopsis by
a Chromatin Modifying Histone Methyltransferase, SDG8, Christopher I. Cazzonelli, Abby J. Cuttriss, Susan B. Cossetto, William Pye, Peter Crisp, Jim Whelan, E. Jean Finnegan, Colin Turnbull, and Barry J. Pogson, Plant Cell 2009;21 39-53
Lutein is a key carotenoid in plant photosynthesis and is also implicated
in limiting age-related macular degeneration of human eyes. The absence of
SET DOMAIN GROUP8 alters methylation of chromatin surrounding the
carotenoid isomerase gene, impairs lutein synthesis, and increases shoot
branching, possibly by limiting synthesis of the carotenoid-derived
branching hormone strigolactone.
Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development, Fabien Mounet, Annick Moing, Virginie Garcia, Johann Petit, Michael Maucourt, Catherine Deborde, Stephane Bernillon, Gwenaelle Le Gall, Ian Colquhoun, Marianne Defernez, Jean-Luc Giraudel, Dominique Rolin, Christophe Rothan, and Martine Lemaire-Chamley, Plant Physiol. 149:1505-1528.
Live cell microscopy analysis of radiation-induced DNA double-strand break motion, B. Jakob, J. Splinter, M. Durante, and G. Taucher-Scholz, PNAS 106(9):3172-3177 (March 3, 2009).
Oceanic acidification affects marine carbon pump and triggers extended marine oxygen holes, Matthias Hofmann and Hans-Joachim Schellnhuber, PNAS 106(9):3017-3022 (March 3, 2009).
PLANT SCIENCE: Anti-Rust Antitrust, D. J. Kliebenstein and H. C. Rowe, Science 323(5919):1301 - 1302 (6 March 2009).
The identification of genes that confer durable, multipathogen resistance may help breeders overcome devastating wheat fungal diseases.
A Kinase-START Gene Confers Temperature-Dependent Resistance to Wheat Stripe Rust, Daolin Fu, Cristobal Uauy, Assaf Distelfeld, Ann Blechl, Lynn Epstein, Xianming Chen, Hanan Sela, Tzion Fahima, Jorge Dubcovsky, Science 323(5919):1357 - 1360.
Several specific genes in wheat confer resistance to common fungal diseases.
A Putative ABC Transporter Confers Durable Resistance to Multiple Fungal Pathogens in Wheat, Simon G. Krattinger, Evans S. Lagudah, Wolfgang Spielmeyer, Ravi P. Singh, Julio Huerta-Espino, Helen McFadden, Eligio Bossolini, Liselotte L. Selter, and Beat Keller, Science 323(5919):1360 (6 March 2009).
Identification of novel meristem factors involved in shoot regeneration through the analysis of temperature-sensitive mutants of Arabidopsis, Hiroaki Tamaki, Mineko Konishi, Yasufumi Daimon, Mitsuhiro Aida, Masao Tasaka, Munetaka Sugiyama, The Plant Journal 57(6):1027 - 1039.
MTP1-dependent Zn sequestration into shoot vacuoles suggests dual roles in Zn tolerance and accumulation in Zn-hyperaccumulating plants, Jeffery L. Gustin, Marcello E. Loureiro, Donggiun Kim, Gunnam Na, Marina Tikhonova, David E. Salt, The Plant Journal 57(6):1116 - 1127.
Green fuels thrust, Victor Bethencourt, Nature Biotechnology 27:216 (2009).
A splicing component adapted to gene silencing, Xavier Roca & Adrian R Krainer, Nature Biotechnology 27:250 - 251 (2009).
U1 adaptors offer an alternative to siRNA for targeted gene knockdown.
Gene silencing by synthetic U1 Adaptors, Rafal Goraczniak, Mark A Behlke & Samuel I Gunderson, Nature Biotechnology 27:257 - 263 (2009).
Goraczniak et al. introduce a gene-silencing method that uses 'U1 adaptors' to block polyadenylation of pre-mRNA in the nucleus. Silencing is stronger when U1 adaptors are combined with siRNAs than when either is used alone.
Read more!
Regulation of Carotenoid Composition and Shoot Branching in Arabidopsis by
a Chromatin Modifying Histone Methyltransferase, SDG8, Christopher I. Cazzonelli, Abby J. Cuttriss, Susan B. Cossetto, William Pye, Peter Crisp, Jim Whelan, E. Jean Finnegan, Colin Turnbull, and Barry J. Pogson, Plant Cell 2009;21 39-53
Lutein is a key carotenoid in plant photosynthesis and is also implicated
in limiting age-related macular degeneration of human eyes. The absence of
SET DOMAIN GROUP8 alters methylation of chromatin surrounding the
carotenoid isomerase gene, impairs lutein synthesis, and increases shoot
branching, possibly by limiting synthesis of the carotenoid-derived
branching hormone strigolactone.
Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development, Fabien Mounet, Annick Moing, Virginie Garcia, Johann Petit, Michael Maucourt, Catherine Deborde, Stephane Bernillon, Gwenaelle Le Gall, Ian Colquhoun, Marianne Defernez, Jean-Luc Giraudel, Dominique Rolin, Christophe Rothan, and Martine Lemaire-Chamley, Plant Physiol. 149:1505-1528.
Live cell microscopy analysis of radiation-induced DNA double-strand break motion, B. Jakob, J. Splinter, M. Durante, and G. Taucher-Scholz, PNAS 106(9):3172-3177 (March 3, 2009).
Oceanic acidification affects marine carbon pump and triggers extended marine oxygen holes, Matthias Hofmann and Hans-Joachim Schellnhuber, PNAS 106(9):3017-3022 (March 3, 2009).
PLANT SCIENCE: Anti-Rust Antitrust, D. J. Kliebenstein and H. C. Rowe, Science 323(5919):1301 - 1302 (6 March 2009).
The identification of genes that confer durable, multipathogen resistance may help breeders overcome devastating wheat fungal diseases.
A Kinase-START Gene Confers Temperature-Dependent Resistance to Wheat Stripe Rust, Daolin Fu, Cristobal Uauy, Assaf Distelfeld, Ann Blechl, Lynn Epstein, Xianming Chen, Hanan Sela, Tzion Fahima, Jorge Dubcovsky, Science 323(5919):1357 - 1360.
Several specific genes in wheat confer resistance to common fungal diseases.
A Putative ABC Transporter Confers Durable Resistance to Multiple Fungal Pathogens in Wheat, Simon G. Krattinger, Evans S. Lagudah, Wolfgang Spielmeyer, Ravi P. Singh, Julio Huerta-Espino, Helen McFadden, Eligio Bossolini, Liselotte L. Selter, and Beat Keller, Science 323(5919):1360 (6 March 2009).
Identification of novel meristem factors involved in shoot regeneration through the analysis of temperature-sensitive mutants of Arabidopsis, Hiroaki Tamaki, Mineko Konishi, Yasufumi Daimon, Mitsuhiro Aida, Masao Tasaka, Munetaka Sugiyama, The Plant Journal 57(6):1027 - 1039.
MTP1-dependent Zn sequestration into shoot vacuoles suggests dual roles in Zn tolerance and accumulation in Zn-hyperaccumulating plants, Jeffery L. Gustin, Marcello E. Loureiro, Donggiun Kim, Gunnam Na, Marina Tikhonova, David E. Salt, The Plant Journal 57(6):1116 - 1127.
Green fuels thrust, Victor Bethencourt, Nature Biotechnology 27:216 (2009).
A splicing component adapted to gene silencing, Xavier Roca & Adrian R Krainer, Nature Biotechnology 27:250 - 251 (2009).
U1 adaptors offer an alternative to siRNA for targeted gene knockdown.
Gene silencing by synthetic U1 Adaptors, Rafal Goraczniak, Mark A Behlke & Samuel I Gunderson, Nature Biotechnology 27:257 - 263 (2009).
Goraczniak et al. introduce a gene-silencing method that uses 'U1 adaptors' to block polyadenylation of pre-mRNA in the nucleus. Silencing is stronger when U1 adaptors are combined with siRNAs than when either is used alone.
Read more!
Subscribe to:
Posts (Atom)