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  • May 12, 2017
  • 07:00 AM
  • 140 views

Friday Fellow: Spreading Earthmoss

by Piter Boll in Earthling Nature

by Piter Kehoma Boll If you still think mosses are uninteresting lifeforms, perhaps you will change your mind after knowing the spreading earthmoss, Physcomitrella patens. Found in temperate regions of the world, except for South America, but more commonly recorded in … Continue reading →... Read more »

Cove, D. (2005) The Moss Physcomitrella patens. Annual Review of Genetics, 39(1), 339-358. DOI: 10.1146/annurev.genet.39.073003.110214  

  • April 24, 2017
  • 04:22 AM
  • 219 views

Promising mouse model for Ngly1 deficiency

by adam phillips in It Ain't Magic

A recent study of Ngly1 deficient mice used a secondary knockout to create double knockouts with symptoms similar to human NGLY1 deficiency.... Read more »

  • February 21, 2017
  • 09:00 PM
  • 310 views

Redrawing Ratite Relationships

by Jente Ottenburghs in Evolutionary Stories

Scientists have sequenced the DNA of two extinct birds: the moa and the elephantbird. Comparison with their living relatives led to some surprising findings.... Read more »

Maderspacher F. (2017) Evolution: Flight of the Ratites. Current biology : CB, 27(3). PMID: 28171755  

Yonezawa T, Segawa T, Mori H, Campos PF, Hongoh Y, Endo H, Akiyoshi A, Kohno N, Nishida S, Wu J.... (2017) Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites. Current biology : CB, 27(1), 68-77. PMID: 27989673  

  • February 8, 2017
  • 05:36 AM
  • 355 views

Sex, alcohol, and structural variants in fission yeast

by Christophe Dessimoz in Open Reading Frame

Our latest study just came out (Jeffares et al., Nature Comm 2017). In it, we carefully catalogued high-confidence structural variants among all known strains of the fission yeast population, and assessed their impact on spore viability, winemaking and other traits. This post gives a summary and the story behind the paper.

Structural variants (SVs) measure genetic variation beyond single nucleotide changes …

Next generation sequencing is enabling the study of genomic diversity on unprec........ Read more »

Jeffares, D., Jolly, C., Hoti, M., Speed, D., Shaw, L., Rallis, C., Balloux, F., Dessimoz, C., Bähler, J., & Sedlazeck, F. (2017) Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature Communications, 14061. DOI: 10.1038/ncomms14061  

Jeffares, D., Rallis, C., Rieux, A., Speed, D., Převorovský, M., Mourier, T., Marsellach, F., Iqbal, Z., Lau, W., Cheng, T.... (2015) The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nature Genetics, 47(3), 235-241. DOI: 10.1038/ng.3215  

  • January 6, 2017
  • 05:00 AM
  • 430 views

Friday Fellow: Conan the Bacterium

by Piter Boll in Earthling Nature

by Piter Kehoma Boll Most people would agree that 2016 was a hard year. So let’s try to make 2017 better by starting this year with a tough Friday Fellow, actually the toughest of them all: Conan the bacterium, or Deinococcus … Continue reading →... Read more »

  • January 2, 2017
  • 04:06 AM
  • 453 views

This Month in Blastocystis Research (DEC 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

2016 is coming to an end, and in the last post of the year, I highlight three of the most important articles on Blastocystis published in 2016.... Read more »

Scanlan PD, Knight R, Song SJ, Ackermann G, & Cotter PD. (2016) Prevalence and genetic diversity of Blastocystis in family units living in the United States. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 95-97. PMID: 27545648  

Kurt Ö, Doğruman Al F, & Tanyüksel M. (2016) Eradication of Blastocystis in humans: Really necessary for all?. Parasitology international, 65(6 Pt B), 797-801. PMID: 26780545  

  • December 30, 2016
  • 06:30 PM
  • 428 views

This Month in Blastocystis Research (DEC 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

2016 is coming to an end, and in the last post of the year, I highlight three of the most important articles on Blastocystis published in 2016.... Read more »

Scanlan PD, Knight R, Song SJ, Ackermann G, & Cotter PD. (2016) Prevalence and genetic diversity of Blastocystis in family units living in the United States. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 95-97. PMID: 27545648  

Kurt Ö, Doğruman Al F, & Tanyüksel M. (2016) Eradication of Blastocystis in humans: Really necessary for all?. Parasitology international, 65(6 Pt B), 797-801. PMID: 26780545  

  • December 11, 2016
  • 02:07 PM
  • 487 views

MS2 mRNA imaging in yeast: more evidence for artefacts

by Gal Haimovich in Green Fluorescent Blog

Previously, on the story of MS2 in yeast: Last year, Roy Parker published a short article, in which he claimed that using the MS2 system in yeast causes the accumulation of 3′ RNA fragments, probably due to inhibition of mRNA … Continue reading →... Read more »

  • December 2, 2016
  • 08:30 PM
  • 442 views

This Month in Blastocystis Research (NOV 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

Lab protocols on Blastocystis culture, cryopreservation, and subtyping are now available in Wiley Online Library.... Read more »

  • November 22, 2016
  • 03:43 AM
  • 416 views

Interview with Rosa Fernández, 2016 OMA Visiting Fellow

by Christophe Dessimoz in Open Reading Frame

Note: We are rebooting our “Life in the Lab” series, which features interviews of interns and visitors. This post is by our inaugural OMA Visiting Fellow Rosa Fernández García, who spent a month with us earlier this year. You can follow Rosa on Twitter at @Rosamygale. —Christophe

 

Please introduce yourself and your research interests.

I received my bachelor’s degree in Biology (major in Zoology) at Complutense University in Madrid, Spain. I got my master’s and PhD at the s........ Read more »

Fernández R, Laumer CE, Vahtera V, Libro S, Kaluziak S, Sharma PP, Pérez-Porro AR, Edgecombe GD, & Giribet G. (2014) Evaluating topological conflict in centipede phylogeny using transcriptomic data sets. Molecular biology and evolution, 31(6), 1500-13. PMID: 24674821  

Novo M, Fernández R, Andrade SC, Marchán DF, Cunha L, & Díaz Cosín DJ. (2016) Phylogenomic analyses of a Mediterranean earthworm family (Annelida: Hormogastridae). Molecular phylogenetics and evolution, 94(Pt B), 473-8. PMID: 26522608  

Sharma, P., Fernandez, R., Esposito, L., Gonzalez-Santillan, E., & Monod, L. (2015) Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal. Proceedings of the Royal Society B: Biological Sciences, 282(1804), 20142953-20142953. DOI: 10.1098/rspb.2014.2953  

  • November 10, 2016
  • 06:14 AM
  • 553 views

This Month in Blatstocystis Research (OCT 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

Highlights of the month include a Special Issue on Blastocystis appearing in Parasitology International, a study of mitochondrial genomes, relationships between gut parasites and gut bacteria, and a announcement of an EMBO anaerobic protist conference next year in the UK.... Read more »

Dogruman-Al F, Stensvold CR, & Yoshikawa H. (2016) Editorial - PAR INT - special issue on Blastocystis. Parasitology international, 65(6 Pt B), 749. PMID: 27742000  

Iebba V, Santangelo F, Totino V, Pantanella F, Monsia A, Di Cristanziano V, Di Cave D, Schippa S, Berrilli F, & D'Alfonso R. (2016) Gut microbiota related to Giardia duodenalis, Entamoeba spp. and Blastocystis hominis infections in humans from Côte d'Ivoire. Journal of infection in developing countries, 10(9), 1035-1041. PMID: 27694739  

  • October 14, 2016
  • 06:20 AM
  • 671 views

Forgetting Earth, forgetting Mars: Dementia, pollution, and space travel

by gdw in FictionalFieldwork

Forgetting Earth Dementia. Few words inspire greater fear in those of us who value (quasi-?) independent thought. The term ‘dementia’ encompasses various brain disorders that all share some scary traits: general decline in cognitive function, decreased ability to speak, and in later stages, being unable to take care of oneself. Unfortunately, as human lifespan increases […]... Read more »

Killin LO, Starr JM, Shiue IJ, & Russ TC. (2016) Environmental risk factors for dementia: a systematic review. BMC geriatrics, 16(1), 175. PMID: 27729011  

Parihar VK, Allen BD, Caressi C, Kwok S, Chu E, Tran KK, Chmielewski NN, Giedzinski E, Acharya MM, Britten RA.... (2016) Cosmic radiation exposure and persistent cognitive dysfunction. Scientific reports, 34774. PMID: 27721383  

  • October 5, 2016
  • 09:06 AM
  • 775 views

Of microbes and men: Evolving as one and terraforming earth

by gdw in FictionalFieldwork

Me and my microbes In the past decade or so, the microbiota, the community of microbes that makes its home in the guts of humans and other animals, has become quite a popular research topic. Quite rightly so, since our little guests seem to affect aspects of our lives that we wouldn’t necessarily consider to […]... Read more »

Faria VG, Martins NE, Magalhães S, Paulo TF, Nolte V, Schlötterer C, Sucena É, & Teixeira L. (2016) Drosophila Adaptation to Viral Infection through Defensive Symbiont Evolution. PLoS genetics, 12(9). PMID: 27684942  

Solé RV, Montañez R, & Duran-Nebreda S. (2015) Synthetic circuit designs for earth terraformation. Biology direct, 37. PMID: 26187273  

  • September 22, 2016
  • 09:27 AM
  • 739 views

Will tardigrades get humanity into space?

by gdw in FictionalFieldwork

The mighty water bear Tardigrades, aka water bears, are tiny animals that can be found just about everywhere on earth, with a slight preference for the moisture in moss. They happily amble along on their four pairs of legs and slurp up plant cells, algae, and even smaller invertebrates that can’t get away fast enough […]... Read more »

Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Nishimura EO, Tintori SC, Li Q, Jones CD, Yandell M.... (2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proceedings of the National Academy of Sciences of the United States of America, 112(52), 15976-81. PMID: 26598659  

Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, & Blaxter M. (2016) No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proceedings of the National Academy of Sciences of the United States of America, 113(18), 5053-8. PMID: 27035985  

Hashimoto T, Horikawa DD, Saito Y, Kuwahara H, Kozuka-Hata H, Shin-I T, Minakuchi Y, Ohishi K, Motoyama A, Aizu T.... (2016) Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nature communications, 12808. PMID: 27649274  

  • September 18, 2016
  • 07:03 AM
  • 669 views

5 Things We Learned This Week | Open-Access Science | Week 37, 2016

by TakFurTheKaffe in Tak Fur The Kaffe

New theories in ocean circulation and acidification, shorter sea ice season in polar bear habitats, and new tools to track bird migrations and hair protein analysis in forensic IDs. Here are five of the latest scientific studies published open-access this week.... Read more »

Stern, H., & Laidre, K. (2016) Sea-ice indicators of polar bear habitat. The Cryosphere, 10(5), 2027-2041. DOI: 10.5194/tc-10-2027-2016  

Shamoun-Baranes, J., Farnsworth, A., Aelterman, B., Alves, J., Azijn, K., Bernstein, G., Branco, S., Desmet, P., Dokter, A., Horton, K.... (2016) Innovative Visualizations Shed Light on Avian Nocturnal Migration. PLOS ONE, 11(8). DOI: 10.1371/journal.pone.0160106  

Parker, G., Leppert, T., Anex, D., Hilmer, J., Matsunami, N., Baird, L., Stevens, J., Parsawar, K., Durbin-Johnson, B., Rocke, D.... (2016) Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome. PLOS ONE, 11(9). DOI: 10.1371/journal.pone.0160653  

  • September 9, 2016
  • 10:00 AM
  • 589 views

Predicting protein function: what’s new?

by Iddo Friedberg in Byte Size Biology

Long time readers of this blog (hi mom!) know that I am working with many other people in an effort called CAFA: the Critical Assessment of protein Function Annotation. This is a challenge that many research groups participate in, and its goal is to determine how well we can predict a protein function from its amino-acid sequence. The first CAFA challenge (CAFA1) was held in 2010-2011 and published in 2013. We learned several things from CAFA1. First, that the top ranking function prediction pro........ Read more »

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A.... (2016) An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome biology, 17(1), 184. PMID: 27604469  

  • September 8, 2016
  • 09:16 AM
  • 684 views

CRISPR on my plate, and some GMO’s on the side

by gdw in FictionalFieldwork

A CRISPR recipe Less than a month ago, the world’s first official CRISPR/Cas9 meal was served. CRISPR/Cas9 is a fairly new technology to edit genomes, and cut and paste genes at will. Well, it’s not exactly that new. It’s actually been around for a long time. CRISPR, or *humhum* Clustered regularly interspaced short palindromic repeats […]... Read more »

Snell C, Bernheim A, Bergé JB, Kuntz M, Pascal G, Paris A, & Ricroch AE. (2012) Assessment of the health impact of GM plant diets in long-term and multigenerational animal feeding trials: a literature review. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 50(3-4), 1134-48. PMID: 22155268  

  • September 2, 2016
  • 10:41 AM
  • 609 views

This Month in Blastocystis Research - AUG

by Christen Rune Stensvold in Blastocystis Parasite Blog

About the factors potentially limiting susceptibility to Blastocystis colonisation/infection.... Read more »

Blessmann, J., Ali, I., Ton Nu, P., Dinh, B., Ngo Viet, T., Le Van, A., Clark, C., & Tannich, E. (2003) Longitudinal Study of Intestinal Entamoeba histolytica Infections in Asymptomatic Adult Carriers. Journal of Clinical Microbiology, 41(10), 4745-4750. DOI: 10.1128/JCM.41.10.4745-4750.2003  

Scanlan PD, Stensvold CR, Rajilić-Stojanović M, Heilig HG, De Vos WM, O'Toole PW, & Cotter PD. (2014) The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. FEMS microbiology ecology, 90(1), 326-30. PMID: 25077936  

  • August 31, 2016
  • 10:58 AM
  • 621 views

Why do we hate coriander?

by Alice Breda in la-Plumeria

In the morning you get up, trudge all the way to the sink, grab a bar of soap and rub it on your face. Sometimes, after you rinsed, you realize that some soap got into your mouth. The taste is nasty, pungent, more in your nose than on your tongue and it persists until you eat or drink something.

This sickening feeling doesn’t hit me only in my brightest mornings, but also every time in an ethnic restaurant or during a trip the cook decides to decorate my tacos or my curry with some chop........ Read more »

  • August 1, 2016
  • 07:36 PM
  • 702 views

This Month in Blastocystis Research - Interactive Edition

by Christen Rune Stensvold in Blastocystis Parasite Blog

What are your thoughts on Blastocystis carriage and age? Please comment!... Read more »

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