Controlling contamination in Chlamydomonas cultures

Figure 1 from Wang et al. 2016.  Effects of bactericide/fungicide cocktails on the removal of microbial contaminants from Chlamydomonas reinhardtii cultures.

Figure 1 from Wang et al. 2016. Effects of bactericide/fungicide cocktails on the removal of microbial contaminants from Chlamydomonas reinhardtii cultures. (A) Control plate. (B) Plate with the One-shot Solution cocktail composed of ampicillin, cefotaxime, and carbendazim. (C) Plate with axoxystrobin and nalidixic acid. (D) Plate with tebuconazole and nalidixic acid. 1: uncontaminated cultures; 2–4: contaminated cultures containing fungi and bacteria.

A new paper in BioTechniques describes an improved antibiotic cocktail for controlling bacterial and fungal contamination of Chlamydomonas cultures. This is a problem that has cost our lab many hours, especially when using media that include acetate.

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Volvox meeting review online early

Fig. 1 from Herron 2016. Examples of volvocine species. (A) Chlamydomonas reinhardtii, (B) Gonium pectorale, (C) Astrephomene gubernaculiferum, (D) Pan- dorina morum, (E) Volvulina compacta, (F) Platydorina caudata, (G) Yamagishiella unicocca, (H) Colemanosphaera charkowiensis, (I) Eudorina elegans, (J) Pleodorina starrii, (K) Volvox barberi, (L) Volvox ovalis, (M) Volvox gigas, (N) Volvox aureus, (O) Volvox carteri. Figure Credit for A and B: Deborah Shelton.

Fig. 1 from Herron 2016. Examples of volvocine species. (A) Chlamydomonas reinhardtii, (B) Gonium pectorale, (C) Astrephomene gubernaculiferum, (D) Pandorina morum, (E) Volvulina compacta, (F) Platydorina caudata, (G) Yamagishiella unicocca, (H) Colemanosphaera charkowiensis, (I) Eudorina elegans, (J) Pleodorina starrii, (K) Volvox barberi, (L) Volvox ovalis, (M) Volvox gigas, (N) Volvox aureus, (O) Volvox carteri. Figure Credit for A and B: Deborah Shelton.

Pretty much what the title says: the meeting review from Volvox 2015 is online early at Molecular Ecology. That only took six months! This is the final, published version. Thanks for a great meeting, and thanks to everyone who read earlier drafts!

On paywalls

Screenshot 2016-03-03 07.58.23

No, you don’t have to pay to read this blog post. Or most scientific articles.

I often blog about peer-reviewed articles, and some of those articles are behind a paywall. There’s a large and growing trend toward open access journals, which charge the authors a publication fee and make their articles available to everyone for free, but this is far from universal. A lot of the big, high-profile journals, such as Science, Nature, PNAS, Ecology Letters, and Current Biology still charge for their articles. And the charges aren’t trivial. A typical scientific paper might cite 50-100 previous articles, and an author might have to read two or three times that many that don’t end up being cited. If you had to pay $38 for each one of those articles, you’d be a lot less inclined to do a thorough literature search.

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Volvox in Highlights Magazine

Highlights_screenshot

This is so cool! The March issue of Highlights Magazine (“Fun with a purpose”) includes a full page on Volvox. Highlights is aimed at kids 6-12 and publishes both print and digital editions:

In every 40-page issue, kids explore new topics, investigate cool subjects and find out about the world. Highlights magazine for kids is filled with stories, games, puzzles, riddles, science experiments, craft projects and interactive entertainment!

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Chlamy postdoc at NASA Ames

Ames

Oana Marcu — you might remember her from the First Volvox Meeting — is looking for a postdoc to do research on Chlamydomonas at NASA Ames Research Center:

This position is for a postdoctoral fellow with experience in Chlamydomonas. The project is part of a larger DOE collaboration focused on approaches to improve biomass and lipid production in microalgae. The work will take place at the NASA Ames Research Center in California and is centered on the molecular and biochemical aspects at the core of the project.

Qualifications: strong experience with Chlamydomonas growth, mutants, biochemistry/molecular biology assays and bioinformatics experience in genomics/transcriptomics. Experience with ICP-MS is desirable. The candidate should be able to pursue independent research while interacting with a large team of scientists of various expertise. The laboratory is at NASA Ames, with local collaborations at Stanford U. and Lawrence Livermore National Labs.

Instructions for applicants are here.

Changing into my old genes: Betül Kaçar’s molecular paleontology

KacarTapeofLife

Betül Kaçar has posted another preprint to bioRxiv describing her work combining molecular paleontology with experimental evolution. I’ve written about Dr. Kaçar’s research, and the Discovery Institute’s bizarre interpretations, before, and I won’t be surprised if the cdesign proponentsists feel compelled to respond again.

The new preprint describes experimental evolution in E. coli bacteria genetically engineered to express an ancient protein in place of its modern counterpart. The gene encoding the protein, Elongation Factor Tu (EF-Tu), exists in two copies in the wild-type E. coli genome. Dr. Kaçar’s team deleted one copy and replaced the other with a gene sequence inferred to be similar to that in E. coli‘s ancestor from 700 million years ago.

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Levels of selection in biofilms: Ellen Clarke on individuality

Pseudomonas biofilm. From Spiers et al. 2013.

Pseudomonas biofilm. From Spiers et al. 2013.

The question of what constitutes a biological individual is intimately entangled with questions about levels of selection. Many authors implicitly or explicitly treat individuals as units of evolution or some variation on this theme. A recent appreciation for the complexity of bacterial biofilms has led to comparisons with multicellular organisms. A recent paper by Ellen Clarke bucks this trend by claiming that multispecies biofilms are not evolutionary individuals.

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