Telescopy and astrophotography links

Recent Publications

Secker NH, Chua JPS, Laurie RE, McNoe L, Guy PL, Orlovich DA, Summerfield TC in press. Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand. Journal of Phycology.

Konlechner TM, Orlovich DA, Hilton MJ 2016. Restrictions in the sprouting ability of an invasive coastal plant, Ammophila arenaria, from fragmented rhizomes. Plant Ecology doi:10.1007/s11258-016-0597-6

Anderson TP, Orlovich DA 2016. Cortinarius majestaticus comb. nov.: phylogenetic evidence for the transfer of Descolea majestatica to Cortinarius. Mycological Progress 15, 20. doi: 10.1007/s11557-016-1164-1

Chua JPS, Orlovich DA, Summerfield TC 2014. Cyanobacteria in New Zealand indigenous grasslands. New Zealand Journal of Botany 52, 100–115. doi: 10.1080/0028825X.2013.862554

Wall JM, Wood SA, Orlovich DA, Rhodes LL, Summerfield TC 2014. Characterisation of freshwater and marine cyanobacteria in the Hokianga region, Northland, New Zealand. New Zealand Journal of Marine & Freshwater Research 48, 177–193. doi: 10.1080/00288330.2013.854814

Orlovich DA, Wang XY, Lebel T 2014. Cortinarius beeverorum, a new species of sequestrate Cortinarius from New Zealand. Mycological Progress 13, 915–921. doi: 10.1007/s11557-014-0977-z

Konlechner TM, Hilton MJ, Orlovich DA 2013. Accommodation space limits plant invasion: Ammophila arenaria survival on New Zealand beaches. Journal of Coastal Conservation 17, 463–472. doi: 10.1007/s11852-013-0244-5

Orlovich DA, Draffin SJ, Daly RA, Stephenson SL 2013. Piracy in the high trees: Ectomycorrhizal fungi from an aerial ‘canopy soil’ microhabitat. Mycologia 105, 52–60. doi: 10.3852/11-307

Teasdale SE, Beulke AK, Guy PL, Orlovich DA 2013. Environmental barcoding of the ectomycorrhizal fungal genus Cortinarius. Fungal Diversity 58, 299–310. doi: 10.1007/s13225-012-0218-1

Rees BJ, Midgley DJ, Marchant A, Perkins A, Orlovich DA 2013. Morphological and molecular data for Australian Hebeloma species do not support the generic status of Anamika. Mycologia 105, 1043–1058. doi: 10.3852/12-404

Lord JM, Knight A, Bannister JM, Ludwig LR, Malcolm WM, Orlovich DA 2013. Rediscovery of pycnidia in Thamnolia vermicularis: Implications for chemotype occurrence and distribution. Lichenologist 45, 397–411. doi: 10.1017/S0024282913000017

Lee HJ, Zhang H, Orlovich DA, Fawcett JP 2012. The influence of probiotic treatment on sulfasalazine metabolism in rat. Xenobiotica 42, 791–797. doi: 10.3109/00498254.2012.660508

Lyttle DJ, Orlovich DA, Guy PL 2011. Detection and analysis of endogenous badnaviruses in the New Zealand flora. AoB Plants, plr008. doi: 10.1093/aobpla/plr008

Lee HJ, Waller RD, Stebbings S, Highton J, Orlovich DA, Schmierer D, Fawcett JP 2010. The effects of an orally administered probiotic on sulfasalazine metabolism in individuals with rheumatoid arthritis: A preliminary study. International Journal of Rheumatic Diseases 13, 48–54. doi: 10.1111/j.1756-185X.2009.01449.x

Linder HP, Baeza M, Barker NP, Galley C, Humphreys A, Lloyd KM, Orlovich DA, Pirie MD, Simon BK, Walsh N, Verboom GA 2010. A generic classification of the Danthonioideae (Poaceae). Annals of the Missouri Botanical Garden 97, 306–364. doi: 10.3417/2009006

Roberts AE, Radford IJ, Orlovich DA 2009. Do alterations of arbuscular mycorrhizal fungal communities change interactions between an invader Hieracium lepidulum and two co-occurring species? A glasshouse study. Australasian Mycologist 28, 29–35.

Lee HJ, Orlovich DA, Tagg JR, Fawcett JP 2009. Detection and specific enumeration of multi-strain probiotics in the lumen contents and mucus layers of the rat intestine after oral administration. Probiotics & Antimicrobial Proteins 1, 113–120. doi: 10.1007/s12602-009-9019-6

Rees BJ, Cracknell R, Marchant A, Orlovich DA 2009. A near-fatal case consistent with mushroom poisoning due to Amanita species. Australasian Mycologist 28, 23–28. Download.

Pirie MD, Humphreys AM, Galley C, Barker NP, Verboom GA, Orlovich D, Draffin SJ, Lloyd K, Baeza CM, Negritto M, Ruiz E, Sanchez JH, Reimer E, Linder HP 2008. A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. Molecular Phylogenetics & Evolution 48, 1106–1119. doi: 10.1016/j.ympev.2008.05.030

Lloyd KM, Hunter AM, Orlovich DA, Draffin SJ, Stewart AV, Lee WG 2007. Phylogeny and biogeography of endemic Festuca (Poaceae) from New Zealand based on nuclear (ITS) and chloroplast (trnL–trnF) nucleotide sequences. Aliso 23, 406–419. Download.

Atkinson TJ, Miller AN, Huhndorf SM, Orlovich DA 2007. Unusual new Chaestosphaeria species from New Zealand: Intrafamilial diversity and elucidations of the Chaetosphaeriaceae – Lasiosphaeriaceae relationship (Sordariomycetes, Ascomycotina). New Zealand Journal of Botany 45, 685–706. doi: 10.1080/00288250709509744

Lucas EJ, Belsham SR, Lughadha EMN, Orlovich DA, Sakuragui CM, Chase MW, Wilson PG 2005. Phylogenetic patterns in the fleshy-fruited Myrtaceae: Preliminary molecular evidence. Plant Systematics & Evolution 251, 35–51. doi: 10.1007/s00606-004-0164-9

Hunter AM, Orlovich DA, Lloyd KM, Lee WG, Murphy DJ 2004. The generic position of Austrofestuca littoralis and the reinstatement of Hookerochloa and Festucella (Poaceae) based on evidence from nuclear (ITS) and chloroplast (trnL–trnF) DNA sequences. New Zealand Journal of Botany 42, 253-262. doi: 10.1080/0028825X.2004.9512902

Bagley SJ, Orlovich DA 2004. Genet size and distribution of Amanita muscaria in a suburban park, Dunedin, New Zealand. New Zealand Journal of Botany 42, 939-947. doi: 10.1080/0028825X.2004.9512940

Orlovich DA, Cairney JWG 2004. Ectomycorrhizal fungi in New Zealand: Current perspectives and future directions. New Zealand Journal of Botany 42, 721–738. doi: 10.1080/0028825X.2004.9512926

Belsham SR, Orlovich DA 2003. Development of the hypanthium and androecium in Acmena smithii and Syzygium australe (Acmena alliance, Myrtaceae). Australian Systematic Botany 16, 621–628. doi: 10.1071/SB02036

Orlovich DA, Oliver A-MB 2002. The taxonomic identity of Gymnopilus rubrocastaneus recently described from New Zealand. New Zealand Journal of Botany 40, 481–487. doi: 10.1080/0028825X.2002.9512808

Rees BJ, Zuccarello GC, Orlovich DA 2002. Relationships between Australian and northern hemisphere Gymnopilus species II. A preliminary phylogeny of species of Gymnopilus and related genera based on internal transcribed spacer (ITS) region of ribosomal DNA. Mycotaxon 84, 93–110. Abstract.

qiime-deploy

On Ubuntu 14

sudo apt-get –force-yes -y install python-dev libncurses5-dev libssl-dev libzmq-dev libgsl0-dev openjdk-6-jdk libxml2 libxslt1.1 libxslt1-dev ant git subversion build-essential zlib1g-dev libpng12-dev libfreetype6-dev mpich2 libreadline-dev gfortran unzip libmysqlclient18 libmysqlclient-dev ghc sqlite3 libsqlite3-dev libc6-i386 libbz2-dev

Installing iPython

Under macqiime,
sudo easy_install pip
sudo pip install ipython[all]
git clone --recursive https://github.com/ipython/ipython.git
cd ipython
python setupegg.py develop
git pull
iptest

During iptest it calls xorg so you need to install this if not already.
To install ipython I ran macqiime and installed it under that shell.
sudo easy_install readline
sudo easy_install ipython
sudo easy_install pyreadline
sudo easy_install pyzmq
sudo easy_install tornado

Seems to work

DNA extraction

CTAB method for DNA extraction

  • heat water bath to 65°C (can be 60–74°C).
  • for grinding up the specimens, there are a few options:

A. You can grind the sample dry by putting the sample in an Eppendorf tube, and dipping the end of the tube in liquid nitrogen until the sample freezes (the tube won’t crack, and it takes about 10 seconds for the end of the tube/specimen to freeze) – cool down a pellet pestle as well (see http://www.kontes.com/html/pg-749520-0090.html, catalogue number 749521-1500 or equivalent), then just grind it up while frozen until it’s a fine powder (takes about 10–30 seconds). Then add 500 μL of CTAB extraction buffer, mix, and incubate for 10 minutes at 65°C.

B. Alternatively you can heat up 500 μL of CTAB extraction buffer in a new tube, and then add the sample to the buffer and grind it while it’s hot, then return to the water bath for 10 minutes at 65°C.

C. Third option (which I must admit I usually do) is to just grind the sample in CTAB buffer at room temperature and then put it into the water bath for 10 minutes at 65°C.

  • While incubating, invert the tubes a few times during the ten minutes to mix them. If I’m doing a number of samples (which is most of the time), I grind them up and put them in the water bath, and then once they’re all done I leave them for 10 minutes after the last sample went in. It means that the first sample gets longer in the water bath than the last—I’ve never found this to make any difference.
  • spin at 12000 G for 5 minutes.
  • transfer supernatent to a clean tube and add an equal volume of chloroform and mix (don’t vortex) to emulsify.
  • spin at 12000 G for 5 minutes.
  • transfer aqueous (upper) layer to a clean tube and add another equal volume of chloroform and mix (it’ll be pretty clean at this stage and will settle out quickly).
  • spin at 12000 G for 3–5 minutes.
  • transfer aqueous (upper) layer to a clean tube and add two volumes of 95% ethanol and 1/10 volume of 3 M sodium acetate pH 5.2. (e.g., if you’ve got 400 μL of solution left after the last chloroform extraction, add 800 μL of ethanol and 40 μL of sodium acetate). Tilt the tube back and forth – you might be able to see DNA precipitate out at this stage. Mix it gently until the sodium acetate and ethanol have mixed properly. If you’re brave and you’ve got a decent amount of DNA, you can ‘hook’ the DNA out at this stage and transfer it (using a yellow pipette tip) into a clean tube containing 70% ethanol. Wash it twice in 70% ethanol, dry and re-suspend in 50 μL of TE buffer (I usually leave overnight in the fridge at this stage to ensure the DNA is dissolved).
  • If there’s no obvious DNA (or if there is only a little and you aren’t brave enough to scoop it out, or if you just feel like doing it this way) incubate the tube at room temperature for 30 minutes, then spin at 12000 G for 15 minutes. This almost always gives at least a small pellet, which will contain enough DNA for PCR etc. Wash pellet twice in about 500 μL 70% ethanol, dry, and dissolve in 50 μL TE buffer (again, leave overnight if necessary).

You want to make sure the 70% ethanol really is 70%. If it falls below this (due to evaporation of the ethanol over time), then the DNA might dissolve in the ethanol and you’ll loose it. Some people use 80% ethanol instead, to ensure that the pellet stays solid. The disadvantage of this is that the salt is not quite so efficiently removed – but I’ve used both 70% and 80% and found it works OK both ways.

  • The next morning, add 1 μL RNAase (Roche RNase, DNA-free – Catalogue number 1119915) and incubate at 37°C for 15 minutes. I find this improves PCR success a lot.
  • refrigerate or freeze sample until ready for PCR.

To make CTAB isolation buffer, add:

2.0 g CTAB (hexadecyl-trimethyl-ammonium bromide)

28 mL of 5M NaCl (make this as a stock solution)

4 mL of 0.5M EDTA (make this as a stock solution)

1 g PEG 8000

10 mL of 1M Tris-HCl (make this as a stock solution)

and make to 100 mL volume with water. I usually add most of the water, then dissolve it on a magnetic stirrer for a while (few hours), then transfer to a volumetric flask and make up to 100 mL.

CTAB buffer recipe from:

Carlson JE, Tulsieram LK, Glaubitz JC, Luk VMK, Kauffeldt CRR 1991. Segregation of random amplified DNA markers in F1 progeny of conifers. Theoretical and Applied Genetics 83, 194–200.