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
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
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
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 »
Klockmann, M., Mikolajewicz, U., & Marotzke, J. (2016) The effect of greenhouse gas concentrations and ice sheets on the glacial AMOC in a coupled climate model. Climate of the Past, 12(9), 1829-1846. DOI: 10.5194/cp-12-1829-2016
Sutton, A., Sabine, C., Feely, R., Cai, W., Cronin, M., McPhaden, M., Morell, J., Newton, J., Noh, J., Ólafsdóttir, S.... (2016) Using present-day observations to detect when anthropogenic change forces surface ocean carbonate chemistry outside preindustrial bounds. Biogeosciences, 13(17), 5065-5083. DOI: 10.5194/bg-13-5065-2016
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
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
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
Panchin AY, & Tuzhikov AI. (2016) Published GMO studies find no evidence of harm when corrected for multiple comparisons. Critical reviews in biotechnology, 1-5. PMID: 26767435
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
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 »
Eriksson, N., Wu, S., Do, C., Kiefer, A., Tung, J., Mountain, J., Hinds, D., & Francke, U. (2012) A genetic variant near olfactory receptor genes influences cilantro preference. Flavour, 1(1), 22. DOI: 10.1186/2044-7248-1-22
Callaway, E. (2012) Soapy taste of coriander linked to genetic variants. Nature. DOI: 10.1038/nature.2012.11398
by Christen Rune Stensvold in Blastocystis Parasite Blog
What are your thoughts on Blastocystis carriage and age? Please comment!... Read more »
Forsell J, Granlund M, Samuelsson L, Koskiniemi S, Edebro H, & Evengård B. (2016) High occurrence of Blastocystis sp. subtypes 1-3 and Giardia intestinalis assemblage B among patients in Zanzibar, Tanzania. Parasites , 9(1), 370. PMID: 27356981
Poulsen CS, Efunshile AM, Nelson JA, & Stensvold CR. (2016) Epidemiological Aspects of Blastocystis Colonization in Children in Ilero, Nigeria. The American journal of tropical medicine and hygiene, 95(1), 175-9. PMID: 27139454
by gdw in FictionalFieldwork
Water churns. Earth moves. Molecules jostle and chemicals mix. Between heaven and hell, a young planet finds itself in full flux. Developing. Forming. Star stuff rains down and forged elements bubble up. Then it happens. It seems as if it’s just another chemical match-up, another reaction in the vast library of possibilities. But it would […]... Read more »
Scharf C, & Cronin L. (2016) Quantifying the origins of life on a planetary scale. Proceedings of the National Academy of Sciences of the United States of America. PMID: 27382156
by Mark Lasbury in As Many Exceptions As Rules
It is usually animals that are referred to as endotherms or ectotherms – plants can’t regulate their temperature, right? Don’t tell that to a certain philodendron that can spike the temperature of its flowers to more than 113˚F on two nights of the year, just to attract the beetles that will pollinate it.... Read more »
Ito K, & Seymour RS. (2005) Expression of uncoupling protein and alternative oxidase depends on lipid or carbohydrate substrates in thermogenic plants. Biology letters, 1(4), 427-30. PMID: 17148224
Dötterl, S., David, A., Boland, W., Silberbauer-Gottsberger, I., & Gottsberger, G. (2012) Evidence for Behavioral Attractiveness of Methoxylated Aromatics in a Dynastid Scarab Beetle-Pollinated Araceae. Journal of Chemical Ecology, 38(12), 1539-1543. DOI: 10.1007/s10886-012-0210-y
by Piter Boll in Earthling Nature
by Piter Kehoma Boll Freshwater planarians are relatively well-known as those cute arrow-shaped cockeyed animals. Land planarians are far away from having all the fame of their aquatic cousins and most people do not even know that they exist. Maybe … Continue reading →... Read more »
Carbayo, F., Álvarez-Presas, M., Olivares, C., Marques, F., Froehlich, E., & Riutort, M. (2013) Molecular phylogeny of Geoplaninae (Platyhelminthes) challenges current classification: proposal of taxonomic actions. Zoologica Scripta, 42(5), 508-528. DOI: 10.1111/zsc.12019
by Mark Lasbury in As Many Exceptions As Rules
Evolution brings wisdom with age – and bacteria are ancient. Bacteria have evolved defenses ranging from evasion or inhibition of immune systems to protecting crucial functions from environmental injury. New studies have identified spring-loaded spikes that can be assembled and disassembled for puncturing other bacteria and delivering toxins, while other work is focused on using those same toxins to kill antibiotic resistant organisms, with E. coli have been engineered to produce toxins ag........ Read more »
Basler, M., Pilhofer, M., Henderson, G., Jensen, G., & Mekalanos, J. (2012) Type VI secretion requires a dynamic contractile phage tail-like structure. Nature, 483(7388), 182-186. DOI: 10.1038/nature10846
Saeidi, N., Wong, C., Lo, T., Nguyen, H., Ling, H., Leong, S., Poh, C., & Chang, M. (2011) Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Molecular Systems Biology. DOI: 10.1038/msb.2011.55
by Christen Rune Stensvold in Blastocystis Parasite Blog
The May entry of "This Month in Blastocystis Research" focusses especially on the increasing interest in Blastocystis in a gut microbiota context. ... Read more »
Audebert C, Even G, Cian A, Blastocystis Investigation Group, Loywick A, Merlin S, Viscogliosi E, & Chabé M. (2016) Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota. Scientific reports, 25255. PMID: 27147260
Andersen LO, Bonde I, Nielsen HB, & Stensvold CR. (2015) A retrospective metagenomics approach to studying Blastocystis. FEMS microbiology ecology, 91(7). PMID: 26130823
Stensvold CR, & Clark CG. (2016) Current status of Blastocystis: A personal view. Parasitology international. PMID: 27247124
O'Brien Andersen L, Karim AB, Roager HM, Vigsnæs LK, Krogfelt KA, Licht TR, & Stensvold CR. (2016) Associations between common intestinal parasites and bacteria in humans as revealed by qPCR. European journal of clinical microbiology . PMID: 27230509
Ramírez JD, Sánchez A, Hernández C, Flórez C, Bernal MC, Giraldo JC, Reyes P, López MC, García L, Cooper PJ.... (2016) Geographic distribution of human Blastocystis subtypes in South America. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 32-5. PMID: 27034056
by Alice Breda in la-Plumeria
Life on Earth was born in water. Then, about half a billion years ago, the first organisms stare colonizing lands that offered new spaces, less predators and, in time, abundant oxygen and nutrients. Still, the indissoluble bond that living organisms had with water remained, and in order to survive in this new environment plants and animals had to develop anatomical, physiological and behavioral adaptations to better obtain, manage and save water. Plant bodies, as well as ours, are mostly made of........ Read more »
Moore, J., Le, N., Brandt, W., Driouich, A., & Farrant, J. (2009) Towards a systems-based understanding of plant desiccation tolerance. Trends in Plant Science, 14(2), 110-117. DOI: 10.1016/j.tplants.2008.11.007
by Piter Boll in Earthling Nature
by Piter Kehoma Boll In his work “The Hitchhiker’s Guide to the Galaxy”, Douglas Adams defined that the answer to life, the universe and everything is 42. Now a group of scientists measured glucose metabolism in brains in a resting … Continue reading →... Read more »
Stender, J., Mortensen, K., Thibaut, A., Darkner, S., Laureys, S., Gjedde, A., & Kupers, R. (2016) The Minimal Energetic Requirement of Sustained Awareness after Brain Injury. Current Biology. DOI: 10.1016/j.cub.2016.04.024
by Gal Haimovich in Green Fluorescent Blog
Translating the information encoded in mRNAs into proteins is one of the most basic processes in biology. The mechanism requires a machinery (i.e. ribosomes) and components (mRNA template, charged tRNAs, regulatory factors, energy) that are shared by all organisms on … Continue reading →... Read more »
Yan X, Hoek TA, Vale RD, & Tanenbaum ME. (2016) Dynamics of Translation of Single mRNA Molecules In Vivo. Cell, 165(4), 976-89. PMID: 27153498
Wang C, Han B, Zhou R, & Zhuang X. (2016) Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells. Cell, 165(4), 990-1001. PMID: 27153499
Morisaki, T., Lyon, K., DeLuca, K., DeLuca, J., English, B., Zhang, Z., Lavis, L., Grimm, J., Viswanathan, S., Looger, L.... (2016) Real-time quantification of single RNA translation dynamics in living cells. Science. DOI: 10.1126/science.aaf0899
Wu, B., Eliscovich, C., Yoon, Y., & Singer, R. (2016) Translation dynamics of single mRNAs in live cells and neurons. Science. DOI: 10.1126/science.aaf1084
by gdw in FictionalFieldwork
The fight against aging Ever since the ancient Sumerians, men has sought eternal life. We still do. Anti-aging science has become quite an industry. As we dive deeper and deeper into our biological foundations, we’re learning more and more about how and why we age. A lot of mysteries remain, but there’s still talk about […]... Read more »
De Winter, G. (2014) Aging as Disease. Medicine, Health Care and Philosophy, 18(2), 237-243. DOI: 10.1007/s11019-014-9600-y
Biagi E, Franceschi C, Rampelli S, Severgnini M, Ostan R, Turroni S, Consolandi C, Quercia S, Scurti M, Monti D.... (2016) Gut Microbiota and Extreme Longevity. Current biology : CB. PMID: 27185560
by Pranab Chatterjee in Zoonoticus
In a recent paper in the Lancet Infectious Diseases, Pritt et al have identified a new genospecies of Borrelia which is attributed to have caused several cases of Lyme disease, marked by a high degree of spirochetemia. In their research article abstract, they state: Methods At the Mayo clinic, from 2003 to 2014, we tested […]... Read more »
Pritt BS, Mead PS, Johnson DK, Neitzel DF, Respicio-Kingry LB, Davis JP, Schiffman E, Sloan LM, Schriefer ME, Replogle AJ.... (2016) Identification of a novel pathogenic Borrelia species causing Lyme borreliosis with unusually high spirochaetaemia: a descriptive study. The Lancet. Infectious diseases. PMID: 26856777
by thelonevirologist in Virology Tidbits
During the current outbreak of ZIKV in Brazil, ZIKV RNA was detected in amniotic fluid samples of women infected with ZIKV during pregnancy and ZIKV RNA has also been isolated from tissue (brain and CNS) of neonates born with microcephaly, suggesting that ZIKV infection of the mother might be a contributive factor in the observed increase of microcephaly cases in neonates. In addition to microcephaly, miscarriages have also been reported in ZIKV positive pregnant women, especially during the fir........ Read more »
Slavov SN, Otaguiri KK, Kashima S, & Covas DT. (2016) Overview of Zika virus (ZIKV) infection in regards to the Brazilian epidemic. Brazilian journal of medical and biological research , 49(5). PMID: 27143174
Ribeiro GS, & Kitron U. (2016) Zika virus pandemic: a human and public health crisis. Revista da Sociedade Brasileira de Medicina Tropical, 49(1), 1-3. PMID: 27163559
Noronha L, Zanluca C, Azevedo ML, Luz KG, & Santos CN. (2016) Zika virus damages the human placental barrier and presents marked fetal neurotropism. Memorias do Instituto Oswaldo Cruz. PMID: 27143490
Carod-Artal FJ. (2016) Epidemiology and neurological complications of infection by the Zika virus: a new emerging neurotropic virus. Revista de neurologia, 62(7), 317-328. PMID: 26988170
De Carvalho NS, De Carvalho BF, Fugaça CA, Dóris B, & Biscaia ES. (2016) Zika virus infection during pregnancy and microcephaly occurrence: a review of literature and Brazilian data. The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases. PMID: 27102780
Bayer A, Lennemann NJ, Ouyang Y, Bramley JC, Morosky S, Marques ET Jr, Cherry S, Sadovsky Y, & Coyne CB. (2016) Type III Interferons Produced by Human Placental Trophoblasts Confer Protection against Zika Virus Infection. Cell host . PMID: 27066743
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Miner, J., Cao, B., Govero, J., Smith, A., Fernandez, E., Cabrera, O., Garber, C., Noll, M., Klein, R., Noguchi, K.... (2016) Zika Virus Infection during Pregnancy in Mice Causes Placental Damage and Fetal Demise. Cell. DOI: 10.1016/j.cell.2016.05.008
Tang H, Hammack C, Ogden SC, Wen Z, Qian X, Li Y, Yao B, Shin J, Zhang F, Lee EM.... (2016) Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth. Cell stem cell, 18(5), 587-90. PMID: 26952870
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Estornes Y, Toscano F, Virard F, Jacquemin G, Pierrot A, Vanbervliet B, Bonnin M, Lalaoui N, Mercier-Gouy P, Pachéco Y.... (2012) dsRNA induces apoptosis through an atypical death complex associating TLR3 to caspase-8. Cell death and differentiation, 19(9), 1482-94. PMID: 22421964
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Frumence E, Roche M, Krejbich-Trotot P, El-Kalamouni C, Nativel B, Rondeau P, Missé D, Gadea G, Viranaicken W, & Desprès P. (2016) The South Pacific epidemic strain of Zika virus replicates efficiently in human epithelial A549 cells leading to IFN-β production and apoptosis induction. Virology, 217-26. PMID: 27060565
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