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Deep Sea News
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- August 12, 2011
- 12:15 PM
- 518 views
A great day for a little Traumatic Insemination
by Holly Bik in Deep Sea News
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Sometimes I think that those of us studying ‘minor phyla’ do so in order to prevent from developing some secret (potentially peverse) obsessions. Example: I recently a........ Read more »
COOMANS, A., VERSCHUREN, D., & VANDERHAEGHEN, R. (1988) The demanian system, traumatic insemination and reproductive strategy in Oncholaimus oxyuris Ditlevsen (Nematoda, Oncholaimina). Zoologica Scripta, 17(1), 15-23. DOI: 10.1111/j.1463-6409.1988.tb00083.x
- August 3, 2011
- 08:00 PM
- 520 views
Marine Fungi are Totally Badass
by Holly Bik in Deep Sea News
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That’s right, you heard me—there are mushrooms that live in the sea. OK, well technically a mushroom is a fruiting body of a fungus with a cap, stem and gills, but let........ Read more »
Atalla, MM, Kheiralla, ZH, Hamed, ER, Youssry, AA, & Abeer, AA. (2010) Screening of some marine-derived fungal isolates for lignin degrading enzymes (LDEs) production. Agricultural and Biology Journal of North America, 1(4), 591-599. info:/
Bhadury P, Mohammad BT, & Wright PC. (2006) The current status of natural products from marine fungi and their potential as anti-infective agents. Journal of industrial microbiology , 33(5), 325-37. PMID: 16429315
HOOLEY, P., & WHITEHEAD, M. (2006) The genetics and molecular biology of marine fungi. Mycologist, 20(4), 144-151. DOI: 10.1016/j.mycol.2006.10.002
Jansson, H., & Nordbring-Hertz, B. (1979) Attraction of Nematodes to Living Mycelium of Nematophagous Fungi. Microbiology, 112(1), 89-93. DOI: 10.1099/00221287-112-1-89
Jones, M., Forn, I., Gadelha, C., Egan, M., Bass, D., Massana, R., & Richards, T. (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature, 474(7350), 200-203. DOI: 10.1038/nature09984
Sayre RM. (1973) Theratromyxa weberi, An Amoeba Predatory on Plant-Parasitic Nematodes. Journal of nematology, 5(4), 258-64. PMID: 19319347
- June 14, 2011
- 08:56 AM
- 604 views
The Circle of Life (and how Jellyfish screw it up)
by Holly Bik in Deep Sea News
Mufasa was right. We’re all intertwined. Whether we humans like to admit it or not, every action by a living organism on Earth has repercussions. (And yes, you can lump in viruses and prions because I’m not getting into a philosophical debate about what constitutes ‘living’). Run, Harry! You don't want to catch Irukandji . . . → Read More: The Circle of Life (and how Jellyfish screw it up)... Read more »
Condon, R., Steinberg, D., del Giorgio, P., Bouvier, T., Bronk, D., Graham, W., & Ducklow, H. (2011) Jellyfish blooms result in a major microbial respiratory sink of carbon in marine systems. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1015782108
Richardson, A., Bakun, A., Hays, G., & Gibbons, M. (2009) The jellyfish joyride: causes, consequences and management responses to a more gelatinous future. Trends in Ecology , 24(6), 312-322. DOI: 10.1016/j.tree.2009.01.010
Parsons, T.R., & Lalli, C.M. (2002) Jellyfish population explosions: revisiting a hypothesis of possible causes. La Mer, 111-121. info:/
- May 14, 2011
- 10:19 AM
- 695 views
Predicting Microbial Communities in the Deep-sea
by Holly Bik in Deep Sea News
I recently reported on the awesomeness of high-throughput sequencing technologies, and commented on their huge potential for transforming the way biologists do business. (Seriously, people, its going to be like the renaissance of 21st century science – you heard it here first!) As a follow up to my previous post, I wanted to . . . → Read More: Predicting Microbial Communities in the Deep-sea... Read more »
Brazelton, W., Ludwig, K., Sogin, M., Andreishcheva, E., Kelley, D., Shen, C., Edwards, R., & Baross, J. (2010) Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys. Proceedings of the National Academy of Sciences, 107(4), 1612-1617. DOI: 10.1073/pnas.0905369107
- April 26, 2011
- 07:27 PM
- 768 views
Metagenomics: Transforming our understanding of oceans
by Holly Bik in Deep Sea News
If you’ve ever talked to me in person for more than 5 minutes, I’ve probably mentioned the !#$%*ING AWESOMENESS of high-throughput sequencing. Frankly, I’m a bit obsessed. If my life were an SAT analogy, it would be Dr Bik:Sequencing platforms as Teenage Girls:Twilight. My gorgeous Illumina never sleeps (runs 2 weeks straight for . . . → Read More: Metagenomics: Transforming our understanding of oceans... Read more »
Gilbert, J., & Dupont, C. (2011) Microbial Metagenomics: Beyond the Genome. Annual Review of Marine Science, 3(1), 347-371. DOI: 10.1146/annurev-marine-120709-142811
- March 10, 2011
- 07:13 AM
- 908 views
Deep-sea additions to the Nematode Tree of Life
by Holly Bik in Deep Sea News
Sometimes I am stunned by the vastness of the internet, as well as the brief 15-nanoseconds of fame that go along with most of its content. The other day I discovered the ‘Charlie the Unicorn’ videos on YouTube, after (ironically?) having a conversation with a real three-dimensional human.
I was excited by this hilarity and went . . . → Read More: Deep-sea additions to the Nematode Tree of Life... Read more »
Bik, H., Thomas, W., Lunt, D., & Lambshead, P. (2010) Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida). BMC Evolutionary Biology, 10(1), 389. DOI: 10.1186/1471-2148-10-389
Bik, H., Lambshead, P., Thomas, W., & Lunt, D. (2010) Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades. BMC Evolutionary Biology, 10(1), 353. DOI: 10.1186/1471-2148-10-353
- December 24, 2010
- 12:16 PM
- 1,039 views
Seafood Safety, Part 2a: ‘safe’ criteria, PAHs
by Holly Bik in Deep Sea News
What criteria makes Gulf seafood “safe to eat”?
In part 2, we’re geting down to the nitty gritty: what guidelines and criteria are the FDA and NOAA using to approve the sale and consumption of seafood from the Gulf of Mexico?
The FDA is currently focusing its tests on two separate compounds: PAHs (Polycyclic Aromatic Hydrocarbons) to test . . . → Read More: Seafood Safety, Part 2a: ‘safe’ criteria, PAHs... Read more »
Yader, R., Michel, J., & Lord, C. (2002) Managing Seafood Safety after an Oil Spill. Seattle: Hazardous Materials Response Division, Office of Response and Restoration, National Oceanic and Atmospheric Administration. info:other/http://response.restoration.noaa.gov/book_shelf/963_seafood2.pdf
- December 19, 2010
- 01:15 PM
- 777 views
Sunday Spill Special: Seafood Safety, Part 1
by Holly Bik in Deep Sea News
Everything we do in life presents choices, and every choice presents a risk. Some activities present a high and obvious risk, like skiing a black diamond without a helmet. The inherent risks in more mundane activities may be well-documented, yet so subtle, that we choose to ignore them on a day-to-day basis…like eating seafood.
This week, the . . . → Read More: Sunday Spill Special: Seafood Safety, Part 1... Read more »
Yader, R., Michel, J., & Lord, C. (2002) Managing Seafood Safety after an Oil Spill. Seattle: Hazardous Materials Response Division, Office of Response and Restoration, National Oceanic and Atmospheric Administration. info:other/http://response.restoration.noaa.gov/book_shelf/963_seafood2.pdf
Kingston, P. 1999. (1999) Recovery of the marine environment following the Braer spill, Shetland. Proceed- ings 1999 Oil Spill Conference, Seattle, Washington, March 8-11, 103-109. info:/
Law, R., & Hellou, J. (1999) Contamination of Fish and Shellfish Following Oil Spill Incidents. Environmental Geosciences, 6(2), 90-98. DOI: 10.1046/j.1526-0984.1999.08039.x
- September 6, 2010
- 04:11 PM
- 815 views
Follow Dr. Bik to the Gulf!
by Holly Bik in Deep Sea News
Remember Dr. M’s recent disturbing post about the quelling of independent science in the Gulf? I can now officially announce that my lab was one of the recipients of the rapid response research grants awarded by the National Science Foundation—hurrah! I’m the postdoc assigned to this project, which aims to characterize pre-spill meiofaunal community structure in . . . → Read More: Follow Dr. Bik to the Gulf!... Read more »
De Troch, M.D., et al. (2006) Resource availability and meiofauna in sediment of tropical seagrass beds: Local versus global trends. Marine Environmental Research, 61(1), 59-73. DOI: 10.1016/j.marenvres.2005.05.003
- September 1, 2010
- 08:37 AM
- 660 views
Dispersants! Part III: Do dispersants really promote degradation of oil?
by Holly Bik in Deep Sea News
Promoting microbial degradation of oil has been one of the main arguments in favor of dispersant use. Interestingly, the PWSRCAC review (covering literature from 1997-2008) did not identify any recent study that explicitly found dispersant use enhancing the biodegradation of oil. Actually, ~50% of studies found that chemical additives inhibited microbial degradation and the other half . . . → Read More: Dispersants! Part III: Do dispersants really promote degradation of oil?... Read more »
Venosa AD, & Holder EL. (2007) Biodegradability of dispersed crude oil at two different temperatures. Marine pollution bulletin, 54(5), 545-53. PMID: 17316707
Yoshida A, Nomura H, Toyoda K, Nishino T, Seo Y, Yamada M, Nishimura M, Wada M, Okamoto K, Shibata A.... (2006) Microbial responses using denaturing gradient gel electrophoresis to oil and chemical dispersant in enclosed ecosystems. Marine pollution bulletin, 52(1), 89-95. PMID: 16202430
- August 23, 2010
- 08:35 AM
- 544 views
Dispersants! Part II: Toxicity
by Holly Bik in Deep Sea News
Part II: How toxic are dispersants?
This, I suppose, is the million-dollar question. The EPA has continually insisted that the actual dispersants is less toxic than dispersed oil. Ok, oil is full of some pretty nasty compounds, and the studies do in fact back up this claim. If you spray Corexit on some shrimp, and then spray . . . → Read More: Dispersants! Part II: Toxicity... Read more »
Fingas, M.F. (2008) A Review of Literature Related to Oil Spill Dispersants 1997-2008. Prince William Sound Regional Citizens’ Advisory Council (PWSRCAC) Report. info:/
Khan RA, & Payne JF. (2005) Influence of a crude oil dispersant, Corexit 9527, and dispersed oil on capelin (Mallotus villosus), Atlantic cod (Gadus morhua), longhorn sculpin (Myoxocephalus octodecemspinosus), and cunner (Tautogolabrus adspersus). Bulletin of environmental contamination and toxicology, 75(1), 50-6. PMID: 16228872
- August 21, 2010
- 09:25 AM
- 479 views
Dispersants! A multi-part series to enlighten your brains.
by Holly Bik in Deep Sea News
When I don’t know enough about a subject, I tend to Google and data-mine—obsessively. So it has become with dispersants. In the wake of oil spill, this word has been thrown around, but often without any corresponding depth of information. Kind of like that cousin you always see at family parties but never manage to . . . → Read More: Dispersants! A multi-part series to enlighten your brains.... Read more »
Fingas, M.F. (2008) A Review of Literature Related to Oil Spill Dispersants 1997-2008. Prince William Sound Regional Citizens’ Advisory Council (PWSRCAC) Report. info:/
- July 28, 2010
- 04:13 PM
- 699 views
If I had my way, we’d just sequence everything
by Holly Bik in Deep Sea News
Transcriptomics of any variety is the study of RNA molecules (messenger RNAs, ribosomal RNAs, transcript RNAs and non-coding RNAs) present in a cell at any given time. By sequencing RNA molecules, we can get a snapshot of the genes being expressed in a cell, tissue, organism, or even whole community of organisms at a given place and time. These type of studies used to be carried out in a limited fashion using quantitative PCR (qPCR) or microarrays, but new sequencing technologies (454, Illumin........ Read more »
Gilbert, J., Field, D., Huang, Y., Edwards, R., Li, W., Gilna, P., & Joint, I. (2008) Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities. PLoS ONE, 3(8). DOI: 10.1371/journal.pone.0003042
Hewson, I., Poretsky, R., Beinart, R., White, A., Shi, T., Bench, S., Moisander, P., Paerl, R., Tripp, H., Montoya, J.... (2009) In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii. The ISME Journal, 3(5), 618-631. DOI: 10.1038/ismej.2009.8
Moran, M.A. (2009) Metatranscriptomics: Eavesdropping on complex microbial communities. Microbe, 4(7), 329-335. info:/
Poretsky, R., Hewson, I., Sun, S., Allen, A., Zehr, J., & Moran, M. (2009) Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environmental Microbiology, 11(6), 1358-1375. DOI: 10.1111/j.1462-2920.2008.01863.x
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