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PLoS Biology

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https://www.readbyqxmd.com/read/28328924/scientific-crowdsourcing-in-wildlife-research-and-conservation-tigers-panthera-tigris-as-a-case-study
#1
Özgün Emre Can, Neil D'Cruze, Margaret Balaskas, David W Macdonald
With around 3,200 tigers (Panthera tigris) left in the wild, the governments of 13 tiger range countries recently declared that there is a need for innovation to aid tiger research and conservation. In response to this call, we created the "Think for Tigers" study to explore whether crowdsourcing has the potential to innovate the way researchers and practitioners monitor tigers in the wild. The study demonstrated that the benefits of crowdsourcing are not restricted only to harnessing the time, labor, and funds from the public but can also be used as a tool to harness creative thinking that can contribute to development of new research tools and approaches...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28323828/liquid-handling-lego-robots-and-experiments-for-stem-education-and-research
#2
Lukas C Gerber, Agnes Calasanz-Kaiser, Luke Hyman, Kateryna Voitiuk, Uday Patil, Ingmar H Riedel-Kruse
Liquid-handling robots have many applications for biotechnology and the life sciences, with increasing impact on everyday life. While playful robotics such as Lego Mindstorms significantly support education initiatives in mechatronics and programming, equivalent connections to the life sciences do not currently exist. To close this gap, we developed Lego-based pipetting robots that reliably handle liquid volumes from 1 ml down to the sub-μl range and that operate on standard laboratory plasticware, such as cuvettes and multiwell plates...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28323820/selective-stalling-of-human-translation-through-small-molecule-engagement-of-the-ribosome-nascent-chain
#3
Nathanael G Lintner, Kim F McClure, Donna Petersen, Allyn T Londregan, David W Piotrowski, Liuqing Wei, Jun Xiao, Michael Bolt, Paula M Loria, Bruce Maguire, Kieran F Geoghegan, Austin Huang, Tim Rolph, Spiros Liras, Jennifer A Doudna, Robert G Dullea, Jamie H D Cate
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a key role in regulating the levels of plasma low-density lipoprotein cholesterol (LDL-C). Here, we demonstrate that the compound PF-06446846 inhibits translation of PCSK9 by inducing the ribosome to stall around codon 34, mediated by the sequence of the nascent chain within the exit tunnel. We further show that PF-06446846 reduces plasma PCSK9 and total cholesterol levels in rats following oral dosing. Using ribosome profiling, we demonstrate that PF-06446846 is highly selective for the inhibition of PCSK9 translation...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28323818/teaching-broader-impacts-of-science-with-undergraduate-research
#4
Kenneth C Keiler, Kathy L Jackson, Leslie Jaworski, David Lopatto, Sarah E Ades
Science plays an important role in most aspects of society, and scientists face ethical decisions as a routine part of their work, but science education frequently omits or segregates content related to ethics and broader impacts of science. Undergraduate research experiences have the potential to bridge traditional divides in education and provide a holistic view of science. In practice, these experiences can be inconsistent and may not provide the optimal learning environment. We developed a course that combines seminar and independent research elements to support student learning during undergraduate research, makes ethical and societal impacts of science clear by relating them to the students' own research projects, and develops students' ethical decision-making skills...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28319149/walking-and-talking-the-tree-of-life-why-and-how-to-teach-about-biodiversity
#5
Cissy J Ballen, Harry W Greene
Taxonomic details of diversity are an essential scaffolding for biology education, yet outdated methods for teaching the tree of life (TOL), as implied by textbook content and usage, are still commonly employed. Here, we show that the traditional approach only vaguely represents evolutionary relationships, fails to denote major events in the history of life, and relies heavily on memorizing near-meaningless taxonomic ranks. Conversely, a clade-based strategy-focused on common ancestry, monophyletic groups, and derived functional traits-is explicitly based on Darwin's "descent with modification," provides students with a rational system for organizing the details of biodiversity, and readily lends itself to active learning techniques...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28319115/plos-biology-2016-reviewer-and-editorial-board-thank-you
#6
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28301467/life-is-three-dimensional-and-it-begins-with-molecules
#7
Philip E Bourne
The iconic image of the DNA double helix embodies the central role that three-dimensional structures play in understanding biological processes, which, in turn, impact health and well-being. Here, that role is explored through the eyes of one scientist, who has been lucky enough to have over 150 talented people pass through his laboratory. Each contributed to that understanding. What follows is a small fraction of their story, with an emphasis on basic research outcomes of importance to society at large.
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28301466/genome-editing-bioethics-shows-the-way
#8
Carolyn P Neuhaus, Arthur L Caplan
When some scientists hear the word "bioethics," they break out in intellectual hives. They shouldn't. Good bioethics is about enabling science to move forward. Bioethics pushes scientists to acknowledge that they operate not within a vacuum but within a society in which diverse perspectives and values must be engaged. Bioethicists give voice to those divergent perspectives and provide a framework to facilitate informed and inclusive discussions that spur progress, rather than stall it. The field is needed to advance cutting-edge biomedical research in domains in which the benefits to be had are enormous, such as genome editing, but ethical concerns persist...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28291793/antibiotic-exposure-perturbs-the-gut-microbiota-and-elevates-mortality-in-honeybees
#9
Kasie Raymann, Zack Shaffer, Nancy A Moran
Gut microbiomes play crucial roles in animal health, and shifts in the gut microbial community structure can have detrimental impacts on hosts. Studies with vertebrate models and human subjects suggest that antibiotic treatments greatly perturb the native gut community, thereby facilitating proliferation of pathogens. In fact, persistent infections following antibiotic treatment are a major medical issue. In apiculture, antibiotics are frequently used to prevent bacterial infections of larval bees, but the impact of antibiotic-induced dysbiosis (microbial imbalance) on bee health and susceptibility to disease has not been fully elucidated...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28291791/three-dimensional-preservation-of-cellular-and-subcellular-structures-suggests-1-6-billion-year-old-crown-group-red-algae
#10
Stefan Bengtson, Therese Sallstedt, Veneta Belivanova, Martin Whitehouse
The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28282371/increasing-efficiency-of-preclinical-research-by-group-sequential-designs
#11
Konrad Neumann, Ulrike Grittner, Sophie K Piper, Andre Rex, Oscar Florez-Vargas, George Karystianis, Alice Schneider, Ian Wellwood, Bob Siegerink, John P A Ioannidis, Jonathan Kimmelman, Ulrich Dirnagl
Despite the potential benefits of sequential designs, studies evaluating treatments or experimental manipulations in preclinical experimental biomedicine almost exclusively use classical block designs. Our aim with this article is to bring the existing methodology of group sequential designs to the attention of researchers in the preclinical field and to clearly illustrate its potential utility. Group sequential designs can offer higher efficiency than traditional methods and are increasingly used in clinical trials...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28282370/tor1-and-ck2-kinases-control-a-switch-between-alternative-ribosome-biogenesis-pathways-in-a-growth-dependent-manner
#12
Isabelle C Kos-Braun, Ilona Jung, Martin Koš
Ribosome biogenesis is a major energy-consuming process in the cell that has to be rapidly down-regulated in response to stress or nutrient depletion. The target of rapamycin 1 (Tor1) pathway regulates synthesis of ribosomal RNA (rRNA) at the level of transcription initiation. It remains unclear whether ribosome biogenesis is also controlled directly at the posttranscriptional level. We show that Tor1 and casein kinase 2 (CK2) kinases regulate a rapid switch between a productive and a non-productive pre-rRNA processing pathways in yeast...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28278152/all-biology-is-computational-biology
#13
Florian Markowetz
Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28267757/cubocube-student-creation-of-a-cancer-genetics-e-textbook-using-open-access-software-for-social-learning
#14
Puya Seid-Karbasi, Xin C Ye, Allen W Zhang, Nicole Gladish, Suzanne Y S Cheng, Katharina Rothe, Jessica A Pilsworth, Min A Kang, Natalie Doolittle, Xiaoyan Jiang, Peter C Stirling, Wyeth W Wasserman
Student creation of educational materials has the capacity both to enhance learning and to decrease costs. Three successive honors-style classes of undergraduate students in a cancer genetics class worked with a new software system, CuboCube, to create an e-textbook. CuboCube is an open-source learning materials creation system designed to facilitate e-textbook development, with an ultimate goal of improving the social learning experience for students. Equipped with crowdsourcing capabilities, CuboCube provides intuitive tools for nontechnical and technical authors alike to create content together in a structured manner...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28257456/stochastic-assembly-produces-heterogeneous-communities-in-the-caenorhabditis-elegans-intestine
#15
Nicole M Vega, Jeff Gore
Host-associated bacterial communities vary extensively between individuals, but it can be very difficult to determine the sources of this heterogeneity. Here, we demonstrate that stochastic bacterial community assembly in the Caenorhabditis elegans intestine is sufficient to produce strong interworm heterogeneity in community composition. When worms are fed with two neutrally competing, fluorescently labeled bacterial strains, we observe stochastically driven bimodality in community composition, in which approximately half of the worms are dominated by each bacterial strain...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28257421/the-mechanism-of-sirtuin-2-mediated-exacerbation-of-alpha-synuclein-toxicity-in-models-of-parkinson-disease
#16
Rita Machado de Oliveira, Hugo Vicente Miranda, Laetitia Francelle, Raquel Pinho, Éva M Szegö, Renato Martinho, Francesca Munari, Diana F Lázaro, Sébastien Moniot, Patrícia Guerreiro, Luis Fonseca, Zrinka Marijanovic, Pedro Antas, Ellen Gerhardt, Francisco Javier Enguita, Bruno Fauvet, Deborah Penque, Teresa Faria Pais, Qiang Tong, Stefan Becker, Sebastian Kügler, Hilal Ahmed Lashuel, Clemens Steegborn, Markus Zweckstetter, Tiago Fleming Outeiro
Sirtuin genes have been associated with aging and are known to affect multiple cellular pathways. Sirtuin 2 was previously shown to modulate proteotoxicity associated with age-associated neurodegenerative disorders such as Alzheimer and Parkinson disease (PD). However, the precise molecular mechanisms involved remain unclear. Here, we provide mechanistic insight into the interplay between sirtuin 2 and α-synuclein, the major component of the pathognomonic protein inclusions in PD and other synucleinopathies...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28253258/empirical-assessment-of-published-effect-sizes-and-power-in-the-recent-cognitive-neuroscience-and-psychology-literature
#17
Denes Szucs, John P A Ioannidis
We have empirically assessed the distribution of published effect sizes and estimated power by analyzing 26,841 statistical records from 3,801 cognitive neuroscience and psychology papers published recently. The reported median effect size was D = 0.93 (interquartile range: 0.64-1.46) for nominally statistically significant results and D = 0.24 (0.11-0.42) for nonsignificant results. Median power to detect small, medium, and large effects was 0.12, 0.44, and 0.73, reflecting no improvement through the past half-century...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28253256/a-mechanism-for-the-cortical-computation-of-hierarchical-linguistic-structure
#18
Andrea E Martin, Leonidas A A Doumas
Biological systems often detect species-specific signals in the environment. In humans, speech and language are species-specific signals of fundamental biological importance. To detect the linguistic signal, human brains must form hierarchical representations from a sequence of perceptual inputs distributed in time. What mechanism underlies this ability? One hypothesis is that the brain repurposed an available neurobiological mechanism when hierarchical linguistic representation became an efficient solution to a computational problem posed to the organism...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28249024/health-disparities-and-clinical-trial-recruitment-is-there-a-duty-to-tweet
#19
Arthur Caplan, Phoebe Friesen
While it is well known that the homogeneity of clinical trial participants often threatens the goal of attaining generalizable knowledge, researchers often cite issues with recruitment, including a lack of interest from participants, shortages of resources, or difficulty accessing particular populations, to explain the lack of diversity within sampling. It is proposed that social media might provide an opportunity to overcome these obstacles through affordable, targeted recruitment advertisements or messages...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28248965/pancreas-lineage-allocation-and-specification-are-regulated-by-sphingosine-1-phosphate-signalling
#20
Ioannis Serafimidis, Eva Rodriguez-Aznar, Mathias Lesche, Kazuaki Yoshioka, Yoh Takuwa, Andreas Dahl, Duojia Pan, Anthony Gavalas
During development, progenitor expansion, lineage allocation, and implementation of differentiation programs need to be tightly coordinated so that different cell types are generated in the correct numbers for appropriate tissue size and function. Pancreatic dysfunction results in some of the most debilitating and fatal diseases, including pancreatic cancer and diabetes. Several transcription factors regulating pancreas lineage specification have been identified, and Notch signalling has been implicated in lineage allocation, but it remains unclear how these processes are coordinated...
March 2017: PLoS Biology
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