667 results
Search Results
52. What exactly is ‘N’ in cell culture and animal experiments?
- Author
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Lazic, Stanley E., Clarke-Williams, Charlie J., and Munafò, Marcus R.
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CELL culture ,INFERENTIAL statistics ,MITOCHONDRIA ,MATERNAL health ,PREGNANCY - Abstract
Biologists determine experimental effects by perturbing biological entities or units. When done appropriately, independent replication of the entity–intervention pair contributes to the sample size (N) and forms the basis of statistical inference. If the wrong entity–intervention pair is chosen, an experiment cannot address the question of interest. We surveyed a random sample of published animal experiments from 2011 to 2016 where interventions were applied to parents and effects examined in the offspring, as regulatory authorities provide clear guidelines on replication with such designs. We found that only 22% of studies (95% CI = 17%–29%) replicated the correct entity–intervention pair and thus made valid statistical inferences. Nearly half of the studies (46%, 95% CI = 38%–53%) had pseudoreplication while 32% (95% CI = 26%–39%) provided insufficient information to make a judgement. Pseudoreplication artificially inflates the sample size, and thus the evidence for a scientific claim, resulting in false positives. We argue that distinguishing between biological units, experimental units, and observational units clarifies where replication should occur, describe the criteria for genuine replication, and provide concrete examples of in vitro, ex vivo, and in vivo experimental designs. [ABSTRACT FROM AUTHOR]
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- 2018
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53. Population genetics and GWAS: A primer.
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Gibson, Greg
- Subjects
GENE frequency ,BIOLOGICAL evolution ,GENETICS ,QUANTITATIVE genetics ,DATA ,GENOMES ,HUMAN genetic variation - Abstract
The article focuses on the study of allele frequencies and quantitative genetics. Topics discussed include analysis of data for evaluating the role of evolutionary genetics; analysis of deep sequencing and genome-wide association study on the same; and analysis of genetic variation in heritability estimates.
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- 2018
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54. A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila.
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Verd, Berta, Clark, Erik, Wotton, Karl R., Janssens, Hilde, Jiménez-Guri, Eva, Crombach, Anton, and Jaeger, Johannes
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RED flour beetle ,DROSOPHILA ,INSECTS ,RADIATION ,GENETIC regulation - Abstract
Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, such as the vinegar fly Drosophila melanogaster, determine all segments simultaneously through a hierarchical cascade of gene regulation. Gap genes constitute the first layer of the Drosophila segmentation gene hierarchy, downstream of maternal gradients such as that of Caudal (Cad). We use data-driven mathematical modelling and phase space analysis to show that shifting gap domains in the posterior half of the Drosophila embryo are an emergent property of a robust damped oscillator mechanism, suggesting that the regulatory dynamics underlying long- and short-germband segmentation are much more similar than previously thought. In Tribolium, Cad has been proposed to modulate the frequency of the segmentation oscillator. Surprisingly, our simulations and experiments show that the shift rate of posterior gap domains is independent of maternal Cad levels in Drosophila. Our results suggest a novel evolutionary scenario for the short- to long-germband transition and help explain why this transition occurred convergently multiple times during the radiation of the holometabolan insects. [ABSTRACT FROM AUTHOR]
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- 2018
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55. Sugar industry sponsorship of germ-free rodent studies linking sucrose to hyperlipidemia and cancer: An historical analysis of internal documents.
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Kearns, Cristin E., Apollonio, Dorie, and Glantz, Stanton A.
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MEDICAL research ,FINANCE ,SUCROSE ,GUT microbiome ,HYPERLIPIDEMIA ,CANCER ,SUGAR industry - Abstract
In 1965, the Sugar Research Foundation (SRF) secretly funded a review in the New England Journal of Medicine that discounted evidence linking sucrose consumption to blood lipid levels and hence coronary heart disease (CHD). SRF subsequently funded animal research to evaluate sucrose’s CHD risks. The objective of this study was to examine the planning, funding, and internal evaluation of an SRF-funded research project titled “Project 259: Dietary Carbohydrate and Blood Lipids in Germ-Free Rats,” led by Dr. W.F.R. Pover at the University of Birmingham, Birmingham, United Kingdom, between 1967 and 1971. A narrative case study method was used to assess SRF Project 259 from 1967 to 1971 based on sugar industry internal documents. Project 259 found a statistically significant decrease in serum triglycerides in germ-free rats fed a high sugar diet compared to conventional rats fed a basic PRM diet (a pelleted diet containing cereal meals, soybean meals, whitefish meal, and dried yeast, fortified with a balanced vitamin supplement and trace element mixture). The results suggested to SRF that gut microbiota have a causal role in carbohydrate-induced hypertriglyceridemia. A study comparing conventional rats fed a high-sugar diet to those fed a high-starch diet suggested that sucrose consumption might be associated with elevated levels of beta-glucuronidase, an enzyme previously associated with bladder cancer in humans. SRF terminated Project 259 without publishing the results. The sugar industry did not disclose evidence of harm from animal studies that would have (1) strengthened the case that the CHD risk of sucrose is greater than starch and (2) caused sucrose to be scrutinized as a potential carcinogen. The influence of the gut microbiota in the differential effects of sucrose and starch on blood lipids, as well as the influence of carbohydrate quality on beta-glucuronidase and cancer activity, deserve further scrutiny. [ABSTRACT FROM AUTHOR]
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- 2017
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56. The credibility crisis in research: Can economics tools help?
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Gall, Thomas, Ioannidis, John P. A., and Maniadis, Zacharias
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MEDICAL sciences ,PHARMACEUTICAL research ,DRUG development ,PHARMACOLOGY ,MEDICAL economics - Abstract
The issue of nonreplicable evidence has attracted considerable attention across biomedical and other sciences. This concern is accompanied by an increasing interest in reforming research incentives and practices. How to optimally perform these reforms is a scientific problem in itself, and economics has several scientific methods that can help evaluate research reforms. Here, we review these methods and show their potential. Prominent among them are mathematical modeling and laboratory experiments that constitute affordable ways to approximate the effects of policies with wide-ranging implications. [ABSTRACT FROM AUTHOR]
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- 2017
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57. A Swarm of Bee Research.
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Richardson, Lauren A.
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BEES ,BEE behavior ,ANIMAL social behavior ,OPERANT conditioning ,INSECT communication ,RESPIRATION ,HONEYBEES ,INSECTS - Abstract
The article discusses developments on bee research. A study published in the journal "PLOS Biology" highlighted the capabilities of bees for social learning and cultural transmission. Also discussed are an operant conditioning test for bees, mechanisms used by bees to warn their nestmates of danger, and collective respiratory behavior in Asian giant honeybees.
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- 2017
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58. Current Incentives for Scientists Lead to Underpowered Studies with Erroneous Conclusions.
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Higginson, Andrew D. and Munafò, Marcus R.
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INCENTIVE (Psychology) ,OCCUPATIONAL achievement ,SCIENTISTS ,ADAPTABILITY (Personality) ,CONFIRMATORY factor analysis - Abstract
We can regard the wider incentive structures that operate across science, such as the priority given to novel findings, as an ecosystem within which scientists strive to maximise their fitness (i.e., publication record and career success). Here, we develop an optimality model that predicts the most rational research strategy, in terms of the proportion of research effort spent on seeking novel results rather than on confirmatory studies, and the amount of research effort per exploratory study. We show that, for parameter values derived from the scientific literature, researchers acting to maximise their fitness should spend most of their effort seeking novel results and conduct small studies that have only 10%–40% statistical power. As a result, half of the studies they publish will report erroneous conclusions. Current incentive structures are in conflict with maximising the scientific value of research; we suggest ways that the scientific ecosystem could be improved. [ABSTRACT FROM AUTHOR]
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- 2016
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59. Sex Chromosomes Do It Differently.
- Author
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Richardson, Lauren A.
- Subjects
SEX chromosomes ,GENE expression ,X chromosome ,GENE silencing ,X-linked genetic disorders ,TRANSCRIPTIONAL repressor CTCF - Abstract
The article discusses the difference of heterogametic sex chromosomes in animals and plants which are commonly evolved from ancestral autosomes. Topics include the decrease of gene expression from the germline X chromosome, the addition of the protein-coding genes after the Meiotic Sex Chromosome Inactivation (MSCI) defeated the transcription of X-linked noncoding RNA and the dosage compensation fo X chromosome from the autosome for the transcriptional activation.
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- 2016
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60. Retraction: PER-TIM Interactions with the Photoreceptor Cryptochrome Mediate Circadian Temperature Responses in Drosophila.
- Author
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Kaushik, Rachna, Nawathean, Pipat, Busza, Ania, Murad, Alejandro, Emery, Patrick, and Rosbash, Michael
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CRYPTOCHROMES ,DROSOPHILA ,CIRCADIAN rhythms ,MUTANT proteins ,NEURONS - Abstract
The article discusses the findings on the study concerning the implicated photoreceptor cryptochrome (CRY) which mediates temperature response in the Drosophila circadian system. Topics discussed include the Period (PER) and Timeless (TIM) clock proteins, the CRY expression to rescue mutant phenotype within clock neurons, and the inhibition of per effect caused by the absence of CRY.
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- 2016
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61. Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression.
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Book, Adam J., Lewin, Gina R., McDonald, Bradon R., Takasuka, Taichi E., Wendt-Pienkowski, Evelyn, Doering, Drew T., Suh, Steven, Raffa, Kenneth F., Fox, Brian G., and Currie, Cameron R.
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CELLULOSE ,STREPTOMYCES ,STREPTOMYCETACEAE ,GENE expression ,PLANT biomass ,FUNGI ,BACTERIA - Abstract
The evolution of cellulose degradation was a defining event in the history of life. Without efficient decomposition and recycling, dead plant biomass would quickly accumulate and become inaccessible to terrestrial food webs and the global carbon cycle. On land, the primary drivers of plant biomass deconstruction are fungi and bacteria in the soil or associated with herbivorous eukaryotes. While the ecological importance of plant-decomposing microbes is well established, little is known about the distribution or evolution of cellulolytic activity in any bacterial genus. Here we show that in Streptomyces, a genus of Actinobacteria abundant in soil and symbiotic niches, the ability to rapidly degrade cellulose is largely restricted to two clades of host-associated strains and is not a conserved characteristic of the Streptomyces genus or host-associated strains. Our comparative genomics identify that while plant biomass degrading genes (CAZy) are widespread in Streptomyces, key enzyme families are enriched in highly cellulolytic strains. Transcriptomic analyses demonstrate that cellulolytic strains express a suite of multi-domain CAZy enzymes that are coregulated by the CebR transcriptional regulator. Using targeted gene deletions, we verify the importance of a highly expressed cellulase (GH6 family cellobiohydrolase) and the CebR transcriptional repressor to the cellulolytic phenotype. Evolutionary analyses identify complex genomic modifications that drive plant biomass deconstruction in Streptomyces, including acquisition and selective retention of CAZy genes and transcriptional regulators. Our results suggest that host-associated niches have selected some symbiotic Streptomyces for increased cellulose degrading activity and that symbiotic bacteria are a rich biochemical and enzymatic resource for biotechnology. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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62. Investing in Health Innovation: A Cornerstone to Achieving Global Health Convergence.
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Yamey, Gavin and Morel, Carlos
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MEDICAL innovations ,ECONOMIC convergence ,EMPIRICAL research ,MEDICAL decision making ,PREVENTIVE medicine - Abstract
Gavin Yamey and Carlos Morel, coordinators of a new PLOS collection on the innovations needed to reduce infectious, maternal, and child deaths to universally low levels, highlight the key cross-cutting themes emerging from the collection. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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63. Autophagy and Its Effects: Making Sense of Double-Edged Swords.
- Author
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Thorburn, Andrew
- Subjects
AUTOPHAGY ,LYSOSOMES ,MICROORGANISMS ,HYDROLASES ,MACROMOLECULES - Abstract
: Autophagy delivers cellular material to lysosomes for recycling. This article discusses why both good and bad effects arise because of autophagy and argues that exploiting this knowledge can treat disease. [ABSTRACT FROM AUTHOR]
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- 2014
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64. Creating clear and informative image-based figures for scientific publications
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Helena, Jambor, Alberto, Antonietti, Bradly, Alicea, Tracy L, Audisio, Susann, Auer, Vivek, Bhardwaj, Steven J, Burgess, Iuliia, Ferling, Małgorzata Anna, Gazda, Luke H, Hoeppner, Vinodh, Ilangovan, Hung, Lo, Mischa, Olson, Salem Yousef, Mohamed, Sarvenaz, Sarabipour, Aalok, Varma, Kaivalya, Walavalkar, Erin M, Wissink, and Tracey L, Weissgerber
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Science and Technology Workforce ,Cell Physiology ,Biomedical Research ,Physiology ,Imaging Techniques ,Science Policy ,Writing ,Plant Science ,Research and Analysis Methods ,Careers in Research ,Pictorial Works as Topic ,Diagnostic Radiology ,Diagnostic Medicine ,Fluorescence Imaging ,Ultrasound Imaging ,Medicine and Health Sciences ,Humans ,Publishing ,Communication ,Radiology and Imaging ,Publications ,Biology and Life Sciences ,Cell Biology ,Magnetic Resonance Imaging ,Scholarly Communication ,Professions ,Plant Physiology ,People and Places ,Meta-Research Article ,Scientists ,Population Groupings ,Periodicals as Topic - Abstract
Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.
- Published
- 2020
65. Rogue Sperm Indicate Sexually Antagonistic Coevolution in Nematodes.
- Author
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Ellis, Ronald E. and Schärer, Lukas
- Subjects
- *
COEVOLUTION , *NEMATODES , *ANTAGONISTIC fungi , *SEXUAL intercourse , *SPERMATOZOA - Abstract
: Reproductive competition often continues long after copulation ends. This article reviews the field and introduces a new paper showing that nematode sperm can directly harm the female germ line. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
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66. What’s not in the news headlines or titles of Alzheimer disease articles? #InMice
- Author
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Fabio Castro Gouveia and Marcia Triunfol
- Subjects
0301 basic medicine ,Social Sciences ,Human condition ,Alzheimer's Disease ,Medical Conditions ,0302 clinical medicine ,Sociology ,Medicine and Health Sciences ,Biology (General) ,Mammals ,General Neuroscience ,Publications ,Newspapers as Topic ,Social Communication ,Eukaryota ,Neurodegenerative Diseases ,Cognition ,Animal Models ,Research Assessment ,Test (assessment) ,Neurology ,Experimental Organism Systems ,Social Networks ,Vertebrates ,Meta-Research Article ,Affect (linguistics) ,General Agricultural and Biological Sciences ,Network Analysis ,Computer and Information Sciences ,Scrutiny ,QH301-705.5 ,Twitter ,MEDLINE ,Mice, Transgenic ,Mouse Models ,Biology ,Research and Analysis Methods ,Rodents ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Model Organisms ,Alzheimer Disease ,Mental Health and Psychiatry ,Animals ,Humans ,Animal Models of Disease ,Association (psychology) ,Scientific Publishing ,Altmetrics ,General Immunology and Microbiology ,Organisms ,Media studies ,Biology and Life Sciences ,Communications ,030104 developmental biology ,Amniotes ,Animal Studies ,Dementia ,Social Media ,Zoology ,030217 neurology & neurosurgery - Abstract
There is increasing scrutiny around how science is communicated to the public. For instance, a Twitter account @justsaysinmice (with 70.4K followers in January 2021) was created to call attention to news headlines that omit that mice, not humans, are the ones for whom the study findings apply. This is the case of many headlines reporting on Alzheimer disease (AD) research. AD is characterized by a degeneration of the human brain, loss of cognition, and behavioral changes, for which no treatment is available. Around 200 rodent models have been developed to study AD, even though AD is an exclusively human condition that does not occur naturally in other species and appears impervious to reproduction in artificial animal models, an information not always disclosed. It is not known what prompts writers of news stories to either omit or acknowledge, in the story’s headlines, that the study was done in mice and not in humans. Here, we raised the hypothesis that how science is reported by scientists plays a role on the news reporting. To test this hypothesis, we investigated whether an association exists between articles’ titles and news’ headlines regarding the omission, or not, of mice. To this end, we analyzed a sample of 623 open-access scientific papers indexed in PubMed in 2018 and 2019 that used mice either as models or as the biological source for experimental studies in AD research. We found a significant association (p < 0.01) between articles’ titles and news stories’ headlines, revealing that when authors omit the species in the paper’s title, writers of news stories tend to follow suit. We also found that papers not mentioning mice in their titles are more newsworthy and significantly more tweeted than papers that do. Our study shows that science reporting may affect media reporting and asks for changes in the way we report about findings obtained with animal models used to study human diseases., This study reveals that when scientists omit from the papers’ title that research findings were obtained using mice, as opposed to humans, the media tend to replicate the trend by omitting the use of mice from the news stories headlines that report on these papers, thereby perpetuating the misleading omission.
- Published
- 2021
67. Living Life on a Magnet.
- Author
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Roberts, Roland G.
- Subjects
MAGNETIC fields ,ANIMALS ,BACTERIA ,BIOMINERALIZATION ,NEMATODES - Abstract
The article discusses the use of magnetic fields for animals and bacteria. Topics covered include the magnetosensory skills of some animals, the use of magnetotaxis by bacteria, the way by which magnetotactic bacteria are able to biomineralise iron to make tiny magnetite crystals in compartments called magnetosomes and the use of magnetic cues by nematodes to direct movement in the vertical axis as they burrow through the soil.
- Published
- 2016
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68. Morton, Gould, and Bias: A Comment on “The Mismeasure of Science”.
- Author
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Weisberg, Michael and Paul, Diane B.
- Subjects
RACISM ,GIANT cell arteritis ,MEASUREMENT - Abstract
A closer look at Stephen Jay Gould’s criticisms of Samuel Morton vindicates Gould’s accusations of racial bias in Morton’s cranial measurements. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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69. A standardized citation metrics author database annotated for scientific field
- Author
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John P. A. Ioannidis, Richard Klavans, Jeroen Baas, and Kevin W. Boyack
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Science and Technology Workforce ,Databases, Factual ,Social Sciences ,computer.software_genre ,Careers in Research ,Field (computer science) ,Sociology ,Citation analysis ,Community Page ,Medicine and Health Sciences ,Biology (General) ,Data Curation ,Data Management ,Psychiatry ,Database ,General Neuroscience ,Publications ,Reference Standards ,Research Assessment ,Research Personnel ,Professions ,Benchmarking ,Citation Analysis ,Telecommunications ,Engineering and Technology ,Journal Impact Factor ,General Agricultural and Biological Sciences ,QH301-705.5 ,Science Policy ,Immunology ,MEDLINE ,Scientific field ,Bibliometrics ,Biology ,Research and Analysis Methods ,General Biochemistry, Genetics and Molecular Biology ,Humans ,Scientific Publishing ,Publishing ,General Immunology and Microbiology ,Biology and Life Sciences ,Composite indicator ,Authorship ,Communications ,People and Places ,Scientists ,Population Groupings ,Scientific publishing ,Clinical Medicine ,Citation ,computer - Abstract
Citation metrics are widely used and misused. We have created a publicly available database of 100,000 top scientists that provides standardized information on citations, h-index, coauthorship-adjusted hm-index, citations to papers in different authorship positions, and a composite indicator. Separate data are shown for career-long and single-year impact. Metrics with and without self-citations and ratio of citations to citing papers are given. Scientists are classified into 22 scientific fields and 176 subfields. Field- and subfield-specific percentiles are also provided for all scientists who have published at least five papers. Career-long data are updated to end of 2017 and to end of 2018 for comparison., Citation metrics are widely used and misused. This Community Page article presents a publicly available database that provides standardized information on multiple citation indicators and a composite thereof, annotating each author according to his/her main scientific field(s).
- Published
- 2019
70. Challenges and recommendations to improve the installability and archival stability of omics computational tools
- Author
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Laura E. Grieneisen, Thiago Mosqueiro, Dat Duong, Gargi Dayama, Richard J. Abdill, Brian L. Hill, Benjamin Statz, Serghei Mangul, Ran Blekhman, Varuni Sarwal, Lana S. Martin, Keith Mitchell, Eleazar Eskin, Jaqueline J. Brito, Russell Littman, Jonathan Flint, and Angela Ka Mei Lam
- Subjects
0301 basic medicine ,Computer and Information Sciences ,Biomedical Research ,Databases, Factual ,Process (engineering) ,Bioinformatics ,QH301-705.5 ,Information Storage and Retrieval ,Biology ,Research and Analysis Methods ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Database and Informatics Methods ,0302 clinical medicine ,Resource (project management) ,Software ,Software Design ,Component (UML) ,Genetics ,Humans ,Computer Networks ,Biology (General) ,Internet ,Altmetrics ,General Immunology and Microbiology ,business.industry ,Software Tools ,Information Dissemination ,General Neuroscience ,Software development ,Software Development ,Software Engineering ,Biology and Life Sciences ,Computational Biology ,Genomics ,Research Assessment ,Genome Analysis ,Data science ,030104 developmental biology ,Perspective ,Software design ,Engineering and Technology ,The Internet ,General Agricultural and Biological Sciences ,business ,030217 neurology & neurosurgery - Abstract
Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed “easy to install,” and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software., Developing new software tools for analysis of large-scale biological data involves numerous unique challenges; this Perspective article surveys more than 36,000 software resources, concluding that a rigorous standardized approach is needed to ensure the installability and archival stability of software tools prior to their publication.
- Published
- 2019
71. Rxivist.org: Sorting biology preprints using social media and readership metrics
- Author
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Richard J. Abdill and Ran Blekhman
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0301 basic medicine ,Computer and Information Sciences ,QH301-705.5 ,Download ,Twitter ,Social Sciences ,Biology ,Research and Analysis Methods ,Filter (software) ,General Biochemistry, Genetics and Molecular Biology ,World Wide Web ,03 medical and health sciences ,Database and Informatics Methods ,0302 clinical medicine ,Sociology ,Server ,Community Page ,Social media ,Biology (General) ,Computer Networks ,Database Searching ,Data Management ,Publishing ,Internet ,Metadata ,Altmetrics ,General Immunology and Microbiology ,business.industry ,General Neuroscience ,Data Visualization ,Social Communication ,Biology and Life Sciences ,Research Assessment ,Communications ,Audience measurement ,030104 developmental biology ,Social Networks ,Bibliometrics ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,The Internet ,General Agricultural and Biological Sciences ,business ,Social Media ,030217 neurology & neurosurgery ,Network Analysis - Abstract
Preprints have arrived. In increasing numbers, researchers across the life sciences are embracing the once-niche practice, shaking off decades of reluctance and posting hundreds of papers per week to preprint servers, sharing their findings with the community before embarking on the weary march through peer review. However, there are limited methods for individuals sifting through this avalanche of research to identify the preprints that are most relevant to their interests. Here, we describe Rxivist.org, a website that indexes all preprints posted to bioRxiv.org, the largest preprint server in the life sciences, and allows users to filter and sort papers based on download metrics and Twitter activity over a variety of categories and time periods. In this work, we hope to make it easier for readers to find relevant research on bioRxiv and to improve the visibility of preprints currently being read and discussed online., This Community Page article describes Rxivist.org, a new website that indexes all preprints posted to bioRxiv.org and allows users to filter and sort papers based on download metrics and Twitter activity over a variety of categories and time periods.
- Published
- 2019
72. Nucleic acid purification from plants, animals and microbes in under 30 seconds
- Author
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Conny Turni, Matt Trau, Yiping Zou, Patrick J. Blackall, Yuling Wang, Michael G. Mason, José Ramón Botella, and Eugene J. H. Wee
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0106 biological sciences ,0301 basic medicine ,Leaves ,Arabidopsis ,Oligonucleotides ,Artificial Gene Amplification and Extension ,Plant Science ,Biochemistry ,Polymerase Chain Reaction ,Purification techniques ,01 natural sciences ,Nucleic Acids ,Biology (General) ,DNA extraction ,Organic Compounds ,Plant Anatomy ,General Neuroscience ,Methods and Resources ,Nucleic acid methods ,Eukaryota ,Plants ,Chemistry ,Experimental Organism Systems ,Genetic Techniques ,Physical Sciences ,General Agricultural and Biological Sciences ,Nucleic Acid Amplification Techniques ,DNA purification ,QH301-705.5 ,Arabidopsis Thaliana ,Brassica ,Biology ,Research and Analysis Methods ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Extraction techniques ,Model Organisms ,Plant and Algal Models ,Animals ,Humans ,Molecular Biology Techniques ,Cellulose ,Molecular Biology ,General Immunology and Microbiology ,Bacteria ,Organic Chemistry ,Chemical Compounds ,Organisms ,Biology and Life Sciences ,Correction ,DNA ,RNA extraction ,Plant Leaves ,030104 developmental biology ,Nucleic acid ,RNA ,010606 plant biology & botany - Abstract
Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries., Author summary Nucleic acid amplification has proven to be indispensable in laboratories around the world for a myriad of applications from diagnostics to genotyping. The first step in any application aiming to amplify DNA or RNA is the extraction of nucleic acids from a complex biological sample; a task traditionally requiring specialised equipment, trained technicians, and multiple liquid handling steps. It is this complexity of current nucleic acid isolation methods that limit the use of many DNA amplification technologies outside of the modern laboratory environment. Therefore, in this study, we investigated new materials and approaches to simplify nucleic acid extraction. We found that cellulose-based filter paper can be used to rapidly bind nucleic acids, retain them during a short washing step to remove contaminants, and then elute them directly into the amplification reaction. We then adapted the cellulose filter to create a dipstick that can be used to purify nucleic acids from a wide range of plant, animal, and microbe samples in less than 30 seconds without the need for any specialised equipment. The speed and simplicity of our method makes it ideally suited for nucleic acid amplification-based applications both within and outside the laboratory, including limited resource settings such as remote field sites, developing countries, and teaching institutions.
- Published
- 2018
73. Training in experimental design and statistics is essential: Response to Jordan.
- Author
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Lazic, Stanley E., Clarke-Williams, Charlie J., and Munafò, Marcus R.
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DESIGN ,ANIMAL models in research ,HUMAN behavior - Abstract
This Formal Comment responds to Jordan et al., and stresses that if scientific findings are to be robust, training in experimental design and statistics is critical to ensure that research questions, design considerations, and analyses are aligned. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
74. Empirical assessment of published effect sizes and power in the recent cognitive neuroscience and psychology literature
- Author
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John P. A. Ioannidis and Denes Szucs
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Basic science ,Developmental cognitive neuroscience ,Social Sciences ,Behavioral neuroscience ,Empirical Research ,Behavioral Neuroscience ,0302 clinical medicine ,Empirical research ,Surveys and Questionnaires ,Statistics ,Range (statistics) ,Psychology ,Biology (General) ,Statistic ,Statistical Data ,General Neuroscience ,Applied Mathematics ,Simulation and Modeling ,05 social sciences ,Publications ,Physical Sciences ,Meta-Research Article ,Probability distribution ,General Agricultural and Biological Sciences ,Statistics (Mathematics) ,Algorithms ,Statistical Distributions ,QH301-705.5 ,Imaging Techniques ,Cognitive Neuroscience ,Neuroimaging ,Cognitive neuroscience ,Research and Analysis Methods ,050105 experimental psychology ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Functional neuroimaging ,Replication (statistics) ,Humans ,0501 psychology and cognitive sciences ,p-value ,Probability ,General Immunology and Microbiology ,Correction ,Biology and Life Sciences ,Probability Theory ,Sample size determination ,Cognitive Science ,Null hypothesis ,030217 neurology & neurosurgery ,Mathematics ,Neuroscience - Abstract
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. This is so because sample sizes have remained small. Assuming similar true effect sizes in both disciplines, power was lower in cognitive neuroscience than in psychology. Journal impact factors negatively correlated with power. Assuming a realistic range of prior probabilities for null hypotheses, false report probability is likely to exceed 50% for the whole literature. In light of our findings, the recently reported low replication success in psychology is realistic, and worse performance may be expected for cognitive neuroscience., Author summary Biomedical science, psychology, and many other fields may be suffering from a serious replication crisis. In order to gain insight into some factors behind this crisis, we have analyzed statistical information extracted from thousands of cognitive neuroscience and psychology research papers. We established that the statistical power to discover existing relationships has not improved during the past half century. A consequence of low statistical power is that research studies are likely to report many false positive findings. Using our large dataset, we estimated the probability that a statistically significant finding is false (called false report probability). With some reasonable assumptions about how often researchers come up with correct hypotheses, we conclude that more than 50% of published findings deemed to be statistically significant are likely to be false. We also observed that cognitive neuroscience studies had higher false report probability than psychology studies, due to smaller sample sizes in cognitive neuroscience. In addition, the higher the impact factors of the journals in which the studies were published, the lower was the statistical power. In light of our findings, the recently reported low replication success in psychology is realistic, and worse performance may be expected for cognitive neuroscience.
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- 2017
75. Development of neural specialization for print: Evidence for predictive coding in visual word recognition.
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Zhao, Jing, Maurer, Urs, He, Sheng, and Weng, Xuchu
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NEURAL development ,WORD recognition ,COMPUTATIONAL biology ,NEURAL codes - Abstract
How a child's brain develops specialization for print is poorly understood. One longstanding account is selective neuronal tuning to regularity of visual-orthographic features, which predicts a monotonically increased neural activation for inputs with higher regularity during development. However, we observed a robust interaction between a stimulus' orthographic regularity (bottom-up input) and children's lexical classification ability (top-down prediction): N1 response, which is the first negative component of the event-related potential (ERP) occurring at posterior electrodes, was stronger to lower-regularity stimuli, but only in children who were less efficient in lexically classifying these stimuli (high prediction error). In contrast, N1 responses were reduced to lower-regularity stimuli in children who showed high efficiency of lexical classification (low prediction error). The modulation of children's lexical classification efficiency on their neural responses to orthographic stimuli supports the predictive coding account of neural processes of reading. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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76. Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism.
- Author
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Lee, Karen J. I., Bushell, Claire, Koide, Yohei, Fozard, John A., Piao, Chunlan, Yu, Man, Newman, Jacob, Whitewoods, Christopher, Avondo, Jerome, Kennaway, Richard, Marée, Athanasius F. M., Cui, Minlong, and Coen, Enrico
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CELL morphology ,LEAF development ,BOTANY ,CELL size ,DEVELOPMENTAL biology ,CELL sheets (Biology) - Abstract
Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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77. Waves of prediction.
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Friston, Karl J.
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COGNITIVE neuroscience ,COMPUTATIONAL biology ,PHYSICAL sciences ,CYTOLOGY - Abstract
Predictive processing (e.g., predictive coding) is a predominant paradigm in cognitive neuroscience. This Primer considers the various levels of commitment neuroscientists have to the neuronal process theories that accompany the principles of predictive processing. Specifically, it reviews and contextualises a recent PLOS Biology study of alpha oscillations and travelling waves. We will see that alpha oscillations emerge naturally under the computational architectures implied by predictive coding-and may tell us something profound about recurrent message passing in brain hierarchies. Specifically, the bidirectional nature of forward and backward waves speaks to opportunities to understand attention and how it nuances bottom-up and top-down influences. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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78. Conservation stories from the front lines.
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Gross, Liza, Hettinger, Annaliese, Moore, Jonathan W., and Neeley, Liz
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ENVIRONMENTAL protection ,ENVIRONMENTALISTS ,ENVIRONMENTAL remediation - Abstract
An introduction is presented in which the editor discusses various reports within the issue on topics including the management and preservation of species and the ecosystem, a new approach in freshwater fish conservation and the life trajectory of a jaguar.
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- 2018
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79. Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum.
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Rodriguez, Lauren, Voorhies, Mark, Gilmore, Sarah, Beyhan, Sinem, Myint, Anthony, and Sil, Anita
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FUNGAL gene expression ,MORPHOLOGY ,GENETIC testing ,MESSENGER RNA ,GENE expression ,SYSTEMS biology ,QUORUM sensing - Abstract
Phenotypic switching between 2 opposing cellular states is a fundamental aspect of biology, and fungi provide facile systems to analyze the interactions between regulons that control this type of switch. A long-standing mystery in fungal pathogens of humans is how thermally dimorphic fungi switch their developmental form in response to temperature. These fungi, including the subject of this study, Histoplasma capsulatum, are temperature-responsive organisms that utilize unknown regulatory pathways to couple their cell shape and associated attributes to the temperature of their environment. H. capsulatum grows as a multicellular hypha in the soil that switches to a pathogenic yeast form in response to the temperature of a mammalian host. These states can be triggered in the laboratory simply by growing the fungus either at room temperature (RT; which promotes hyphal growth) or at 37 °C (which promotes yeast-phase growth). Prior worked revealed that 15% to 20% of transcripts are differentially expressed in response to temperature, but it is unclear which transcripts are linked to specific phenotypic changes, such as cell morphology or virulence. To elucidate temperature-responsive regulons, we previously identified 4 transcription factors (required for yeast-phase growth [Ryp]1–4) that are required for yeast-phase growth at 37 °C; in each ryp mutant, the fungus grows constitutively as hyphae regardless of temperature, and the cells fail to express genes that are normally induced in response to growth at 37 °C. Here, we perform the first genetic screen to identify genes required for hyphal growth of H. capsulatum at RT and find that disruption of the signaling mucin MSB2 results in a yeast-locked phenotype. RNA sequencing (RNAseq) experiments reveal that MSB2 is not required for the majority of gene expression changes that occur when cells are shifted to RT. However, a small subset of temperature-responsive genes is dependent on MSB2 for its expression, thereby implicating these genes in the process of filamentation. Disruption or knockdown of an multicopy suppression of a budding defect 2 (Msb2)-dependent mitogen-activated protein (MAP) kinase (HOG2) and an ASM-1/Phd1/StuA/EFG1/SOK2 (APSES) transcription factor (STU1) prevents hyphal growth at RT, validating that the Msb2 regulon contains genes that control filamentation. Notably, the Msb2 regulon shows conserved hyphal-specific expression in other dimorphic fungi, suggesting that this work defines a small set of genes that are likely to be conserved regulators and effectors of filamentation in multiple fungi. In contrast, a few yeast-specific transcripts, including virulence factors that are normally expressed only at 37 °C, are inappropriately expressed at RT in the msb2 mutant, suggesting that expression of these genes is coupled to growth in the yeast form rather than to temperature. Finally, we find that the yeast-promoting transcription factor Ryp3 associates with the MSB2 promoter and inhibits MSB2 transcript expression at 37 °C, whereas Msb2 inhibits accumulation of Ryp transcripts and proteins at RT. These findings indicate that the Ryp and Msb2 circuits antagonize each other in a temperature-dependent manner, thereby allowing temperature to govern cell shape and gene expression in this ubiquitous fungal pathogen of humans. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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80. Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation.
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Sakofsky, Cynthia J., Saini, Natalie, Klimczak, Leszek J., Chan, Kin, Malc, Ewa P., Mieczkowski, Piotr A., Burkholder, Adam B., Fargo, David, and Gordenin, Dmitry A.
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SOMATIC mutation ,APOLIPOPROTEIN B ,DNA damage ,DEAMINASES ,NUCLEIC acids - Abstract
A single cancer genome can harbor thousands of clustered mutations. Mutation signature analyses have revealed that the origin of clusters are lesions in long tracts of single-stranded (ss) DNA damaged by apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases, raising questions about molecular mechanisms that generate long ssDNA vulnerable to hypermutation. Here, we show that ssDNA intermediates formed during the repair of gamma-induced bursts of double-strand breaks (DSBs) in the presence of APOBEC3A in yeast lead to multiple APOBEC-induced clusters similar to cancer. We identified three independent pathways enabling cluster formation associated with repairing bursts of DSBs: 5′ to 3′ bidirectional resection, unidirectional resection, and break-induced replication (BIR). Analysis of millions of mutations in APOBEC-hypermutated cancer genomes revealed that cancer tolerance to formation of hypermutable ssDNA is similar to yeast and that the predominant pattern of clustered mutagenesis is the same as in resection-defective yeast, suggesting that cluster formation in cancers is driven by a BIR-like mechanism. The phenomenon of genome-wide burst of clustered mutagenesis revealed by our study can play an important role in generating somatic hypermutation in cancers as well as in noncancerous cells. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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81. Calreticulin is a Critical Cell Survival Factor in Malignant Neoplasms.
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Han, Arum, Li, Chen, Zahed, Tara, Wong, Michael, Smith, Ian, Hoedel, Karl, Green, Douglas, and Boiko, Alexander D.
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POLY ADP ribose ,CALRETICULIN ,CELL transformation ,CELL death ,CELL physiology - Abstract
Calreticulin (CRT) is a high-capacity Ca
2+ protein whose expression is up-regulated during cellular transformation and is associated with disease progression in multiple types of malignancies. At the same time, CRT has been characterized as an important stress-response protein capable of inducing immunogenic cell death (ICD) when translocated to the cell surface. It remains unclear why CRT expression is preserved by malignant cells during the course of transformation despite its immunogenic properties. In this study, we identify a novel, critical function of CRT as a cell survival factor in multiple types of human solid-tissue malignancies. CRT knockdown activates p53, which mediates cell-death response independent of executioner caspase activity and accompanied full-length poly ADP ribose polymerase (PARP) cleavage. Mechanistically, we show that down-regulation of CRT results in mitochondrial Ca2+ overload and induction of mitochondria permeability transition pore (mPTP)-dependent cell death, which can be significantly rescued by the mPTP inhibitor, Cyclosporin A (CsA). The clinical importance of CRT expression was revealed in the analysis of the large cohort of cancer patients (N = 2,058) to demonstrate that high levels of CRT inversely correlates with patient survival. Our study identifies intracellular CRT as an important therapeutic target for tumors whose survival relies on its expression. [ABSTRACT FROM AUTHOR]- Published
- 2019
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82. Allosteric regulation of a prokaryotic small Ras-like GTPase contributes to cell polarity oscillations in bacterial motility.
- Author
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Baranwal, Jyoti, Lhospice, Sébastien, Kanade, Manil, Chakraborty, Sukanya, Gade, Priyanka Rajendra, Harne, Shrikant, Herrou, Julien, Mignot, Tâm, and Gayathri, Pananghat
- Subjects
ALLOSTERIC regulation ,CELL polarity ,RAS oncogenes ,GUANINE nucleotide exchange factors ,GUANOSINE triphosphatase ,GTPASE-activating protein ,MYXOCOCCUS xanthus - Abstract
Mutual gliding motility A (MglA), a small Ras-like GTPase; Mutual gliding motility B (MglB), its GTPase activating protein (GAP); and Required for Motility Response Regulator (RomR), a protein that contains a response regulator receiver domain, are major components of a GTPase-dependent biochemical oscillator that drives cell polarity reversals in the bacterium Myxococcus xanthus. We report the crystal structure of a complex of M. xanthus MglA and MglB, which reveals that the C-terminal helix (Ct-helix) from one protomer of the dimeric MglB binds to a pocket distal to the active site of MglA. MglB increases the GTPase activity of MglA by reorientation of key catalytic residues of MglA (a GAP function) combined with allosteric regulation of nucleotide exchange by the Ct-helix (a guanine nucleotide exchange factor [GEF] function). The dual GAP-GEF activities of MglB accelerate the rate of GTP hydrolysis over multiple enzymatic cycles. Consistent with its GAP and GEF activities, MglB interacts with MglA bound to either GTP or GDP. The regulation is essential for cell polarity, because deletion of the Ct-helix causes bipolar localization of MglA, MglB, and RomR, thereby causing reversal defects in M. xanthus. A bioinformatics analysis reveals the presence of Ct-helix in homologues of MglB in other bacterial phyla, suggestive of the prevalence of the allosteric mechanism among other prokaryotic small Ras-like GTPases. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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83. Control over single-cell distribution of G1 lengths by WNT governs pluripotency.
- Author
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Jang, Jiwon, Han, Dasol, Golkaram, Mahdi, Audouard, Morgane, Liu, Guojing, Bridges, Daniel, Hellander, Stefan, Chialastri, Alex, Dey, Siddharth S., Petzold, Linda R., and Kosik, Kenneth S.
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HUMAN embryonic stem cells ,EMBRYONIC stem cells ,PLURIPOTENT stem cells ,CELL populations ,STEM cells ,DEVELOPMENTAL biology ,FIBROBLAST growth factors - Abstract
The link between single-cell variation and population-level fate choices lacks a mechanistic explanation despite extensive observations of gene expression and epigenetic variation among individual cells. Here, we found that single human embryonic stem cells (hESCs) have different and biased differentiation potentials toward either neuroectoderm or mesendoderm depending on their G1 lengths before the onset of differentiation. Single-cell variation in G1 length operates in a dynamic equilibrium that establishes a G1 length probability distribution for a population of hESCs and predicts differentiation outcome toward neuroectoderm or mesendoderm lineages. Although sister stem cells generally share G1 lengths, a variable proportion of cells have asymmetric G1 lengths, which maintains the population dispersion. Environmental Wingless-INT (WNT) levels can control the G1 length distribution, apparently as a means of priming the fate of hESC populations once they undergo differentiation. As a downstream mechanism, global 5-hydroxymethylcytosine levels are regulated by G1 length and thereby link G1 length to differentiation outcomes of hESCs. Overall, our findings suggest that intrapopulation heterogeneity in G1 length underlies the pluripotent differentiation potential of stem cell populations. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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84. The evolution of a new cell type was associated with competition for a signaling ligand.
- Author
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Ettensohn, Charles A. and Adomako-Ankomah, Ashrifia
- Subjects
MESODERM ,CELLULAR evolution ,VASCULAR endothelial growth factors ,VASCULAR endothelial growth factor receptors ,SEA urchins - Abstract
There is presently a very limited understanding of the mechanisms that underlie the evolution of new cell types. The skeleton-forming primary mesenchyme cells (PMCs) of euechinoid sea urchins, derived from the micromeres of the 16-cell embryo, are an example of a recently evolved cell type. All adult echinoderms have a calcite-based endoskeleton, a synapomorphy of the Ambulacraria. Only euechinoids have a micromere-PMC lineage, however, which evolved through the co-option of the adult skeletogenic program into the embryo. During normal development, PMCs alone secrete the embryonic skeleton. Other mesoderm cells, known as blastocoelar cells (BCs), have the potential to produce a skeleton, but a PMC-derived signal ordinarily prevents these cells from expressing a skeletogenic fate and directs them into an alternative developmental pathway. Recently, it was shown that vascular endothelial growth factor (VEGF) signaling plays an important role in PMC differentiation and is part of a conserved program of skeletogenesis among echinoderms. Here, we report that VEGF signaling, acting through ectoderm-derived VEGF3 and its cognate receptor, VEGF receptor (VEGFR)-10-Ig, is also essential for the deployment of the skeletogenic program in BCs. This VEGF-dependent program includes the activation of aristaless-like homeobox 1 (alx1), a conserved transcriptional regulator of skeletogenic specification across echinoderms and an example of a “terminal selector” gene that controls cell identity. We show that PMCs control BC fate by sequestering VEGF3, thereby preventing activation of alx1 and the downstream skeletogenic network in BCs. Our findings provide an example of the regulation of early embryonic cell fates by direct competition for a secreted signaling ligand, a developmental mechanism that has not been widely recognized. Moreover, they reveal that a novel cell type evolved by outcompeting other embryonic cell lineages for an essential signaling ligand that regulates the expression of a gene controlling cell identity. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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85. Nystagmus in patients with congenital stationary night blindness (CSNB) originates from synchronously firing retinal ganglion cells.
- Author
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Winkelman, Beerend H. J., Howlett, Marcus H. C., Hölzel, Maj-Britt, Joling, Coen, Fransen, Kathryn H., Pangeni, Gobinda, Kamermans, Sander, Sakuta, Hiraki, Noda, Masaharu, Simonsz, Huibert J., McCall, Maureen A., De Zeeuw, Chris I., and Kamermans, Maarten
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RETINAL ganglion cells ,PHOTORECEPTORS ,NYSTAGMUS ,EYE movements ,FREQUENCIES of oscillating systems ,BIPOLAR cells - Abstract
Congenital nystagmus, involuntary oscillating small eye movements, is commonly thought to originate from aberrant interactions between brainstem nuclei and foveal cortical pathways. Here, we investigated whether nystagmus associated with congenital stationary night blindness (CSNB) results from primary deficits in the retina. We found that CSNB patients as well as an animal model (nob mice), both of which lacked functional nyctalopin protein (NYX, nyx) in ON bipolar cells (BCs) at their synapse with photoreceptors, showed oscillating eye movements at a frequency of 4–7 Hz. nob ON direction-selective ganglion cells (DSGCs), which detect global motion and project to the accessory optic system (AOS), oscillated with the same frequency as their eyes. In the dark, individual ganglion cells (GCs) oscillated asynchronously, but their oscillations became synchronized by light stimulation. Likewise, both patient and nob mice oscillating eye movements were only present in the light when contrast was present. Retinal pharmacological and genetic manipulations that blocked nob GC oscillations also eliminated their oscillating eye movements, and retinal pharmacological manipulations that reduced the oscillation frequency of nob GCs also reduced the oscillation frequency of their eye movements. We conclude that, in nob mice, synchronized oscillations of retinal GCs, most likely the ON-DCGCs, cause nystagmus with properties similar to those associated with CSNB in humans. These results show that the nob mouse is the first animal model for a form of congenital nystagmus, paving the way for development of therapeutic strategies. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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86. V1 interneurons regulate the pattern and frequency of locomotor-like activity in the neonatal mouse spinal cord.
- Author
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Falgairolle, Melanie and O’Donovan, Michael J.
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SPINAL cord ,INTERNEURONS ,CENTRAL pattern generators ,MOTOR neurons ,NERVOUS system ,CYTOLOGY - Abstract
In the mouse spinal cord, V1 interneurons are a heterogeneous population of inhibitory spinal interneurons that have been implicated in regulating the frequency of the locomotor rhythm and in organizing flexor and extensor alternation. By introducing archaerhodopsin into engrailed-1-positive neurons, we demonstrate that the function of V1 neurons in locomotor-like activity is more complex than previously thought. In the whole cord, V1 hyperpolarization increased the rhythmic synaptic drive to flexor and extensor motoneurons, increased the spiking in each cycle, and slowed the locomotor-like rhythm. In the hemicord, V1 hyperpolarization accelerated the rhythm after an initial period of tonic activity, implying that a subset of V1 neurons are active in the hemicord, which was confirmed by calcium imaging. Hyperpolarizing V1 neurons resulted in an equalization of the duty cycle in flexor and extensors from an asymmetrical pattern in control recordings in which the extensor bursts were longer than the flexor bursts. Our results suggest that V1 interneurons are composed of several subsets with different functional roles. Furthermore, during V1 hyperpolarization, the default state of the locomotor central pattern generator (CPG) is symmetrical, with antagonist motoneurons each firing with an approximately 50% duty cycle. We hypothesize that one function of the V1 population is to set the burst durations of muscles to be appropriate to their biomechanical function and to adapt to the environmental demands, such as changes in locomotor speed. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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87. The cat is out of the bag: How parasites know their hosts.
- Author
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English, Elizabeth D. and Striepen, Boris
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TOXOPLASMA gondii ,PARASITE life cycles ,PARASITES ,FELIDAE ,LINOLEIC acid ,CATS - Abstract
Toxoplasma gondii is a remarkably successful protozoan parasite that infects a third of the human population, along with most mammals and birds. However, the sexual portion of the parasite’s life cycle is narrowly limited to cats. How parasites distinguish between hosts has long been a mystery. A new study reveals that Toxoplasma identifies cats based on a single fatty acid, linoleic acid. Experimental manipulation of fatty acid metabolism by drug treatment turns a mouse into a cat in the “eye” of the parasite. This new model enables genetic crosses of an important human pathogen without the use of companion animals and opens the door to future discovery. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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88. Loss of Bardet-Biedl syndrome proteins causes synaptic aberrations in principal neurons.
- Author
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Haq, Naila, Schmidt-Hieber, Christoph, Sialana, Fernando J., Ciani, Lorenza, Heller, Janosch P., Stewart, Michelle, Bentley, Liz, Wells, Sara, Rodenburg, Richard J., Nolan, Patrick M., Forsythe, Elizabeth, Wu, Michael C., Lubec, Gert, Salinas, P., Häusser, Michael, Beales, Philip L., and Christou-Savina, Sofia
- Subjects
LAURENCE-Moon-Biedl syndrome ,DENDRITIC spines ,POSTSYNAPTIC density protein ,NEURONS ,GRANULE cells ,RETINAL degeneration - Abstract
Bardet-Biedl syndrome (BBS), a ciliopathy, is a rare genetic condition characterised by retinal degeneration, obesity, kidney failure, and cognitive impairment. In spite of progress made in our general understanding of BBS aetiology, the molecular and cellular mechanisms underlying cognitive impairment in BBS remain elusive. Here, we report that the loss of BBS proteins causes synaptic dysfunction in principal neurons, providing a possible explanation for the cognitive impairment phenotype observed in BBS patients. Using synaptosomal proteomics and immunocytochemistry, we demonstrate the presence of Bbs proteins in the postsynaptic density (PSD) of hippocampal neurons. Loss of Bbs results in a significant reduction of dendritic spines in principal neurons of Bbs mouse models. Furthermore, we show that spine deficiency correlates with events that destabilise spine architecture, such as impaired spine membrane receptor signalling, known to be involved in the maintenance of dendritic spines. Our findings suggest a role for BBS proteins in dendritic spine homeostasis that may be linked to the cognitive phenotype observed in BBS. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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89. The remote allosteric control of Orai channel gating.
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Zhou, Yandong, Nwokonko, Robert M., Jr.Baraniak, James H., Trebak, Mohamed, Lee, Kenneth P. K., and Gill, Donald L.
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REMOTE control ,ALLOSTERIC regulation ,ION channels ,PHYSICAL sciences ,PROTEIN binding ,CELL membranes ,ENDOPLASMIC reticulum - Abstract
Calcium signals drive an endless array of cellular responses including secretion, contraction, transcription, cell division, and growth. The ubiquitously expressed Orai family of plasma membrane (PM) ion channels mediate Ca
2+ entry signals triggered by the Ca2+ sensor Stromal Interaction Molecule (STIM) proteins of the endoplasmic reticulum (ER). The 2 proteins interact within curiously obscure ER-PM junctions, driving an allosteric gating mechanism for the Orai channel. Although key to Ca2+ signal generation, molecular understanding of this activation process remain obscure. Crystallographic structural analyses reveal much about the exquisite hexameric core structure of Orai channels. But how STIM proteins bind to the channel periphery and remotely control opening of the central pore, has eluded such analysis. Recent studies apply both crystallography and single-particle cryogenic electron microscopy (cryo-EM) analyses to probe the structure of Orai mutants that mimic activation by STIM. The results provide new understanding on the open state of the channel and how STIM proteins may exert remote allosteric control of channel gating. [ABSTRACT FROM AUTHOR]- Published
- 2019
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90. Artificially selecting microbial communities: If we can breed dogs, why not microbiomes?
- Author
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Arias-Sánchez, Flor I., Vessman, Björn, and Mitri, Sara
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BIOTIC communities ,DOG breeding ,ANIMAL sexual behavior ,PLANNED communities ,BREEDING - Abstract
Natural microbial communities perform many functions that are crucial for human well-being. Yet we have very little control over them, and we do not know how to optimize their functioning. One idea is to breed microbial communities as we breed dogs: by comparing a set of microbiomes and allowing the best-performing ones to generate new communities, and so on. Although this idea seems simple, designing such a selection experiment brings with it many decisions with surprising outcomes. Xie and colleagues developed a computational model that reveals this complexity and shows how different experimental design decisions can impact the success of such an experiment. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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91. Targeting oxidative pentose phosphate pathway prevents recurrence in mutant Kras colorectal carcinomas.
- Author
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Gao, WenChao, Xu, YuTing, Chen, Tao, Du, ZunGuo, Liu, XiuJuan, Hu, ZhiQian, Wei, Dong, Gao, ChunFang, Zhang, Wei, and Li, QingQuan
- Subjects
PENTOSE phosphate pathway ,CANCER stem cells ,TRIOSE-phosphate isomerase ,CARCINOMA ,CELL physiology - Abstract
Recurrent tumors originate from cancer stem cells (CSCs) that survive conventional treatments. CSCs consist of heterogeneous subpopulations that display distinct sensitivity to anticancer drugs. Such a heterogeneity presents a significant challenge in preventing tumor recurrence. In the current study, we observed that quiescent CUB-domain–containing protein 1 (CDCP1)+ CSCs are enriched after chemotherapy in mutant Kirsten rat sarcoma viral oncogene homolog (Kras) colorectal carcinomas (CRCs) and serve as a reservoir for recurrence. Mechanistically, glucose catabolism in CDCP1+ CSCs is routed to the oxidative pentose phosphate pathway (PPP); multiple cycling of carbon backbones in the oxidative PPP potentially maximizes NADPH reduction to counteract chemotherapy-induced reactive oxygen species (ROS) formation, thereby allowing CDCP1+ CSCs to survive chemotherapeutic attack. This is dependent on silent mating type information regulation 2 homolog 5 (Sirt5)-mediated inhibition of the glycolytic enzyme triosephosphate isomerase (TPI) through demalonylation of Lys56. Blocking demalonylation of TPI at Lys56 increases chemosensitivity of CDCP1+ CSCSs and delays recurrence of mutant Kras CRCs in vivo. These findings pinpoint a new therapeutic approach for combating mutant Kras CRCs. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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- View/download PDF
92. Perceptual uncertainty.
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Diamond, Mathew E.
- Subjects
TOUCH ,TRP channels ,COMPUTATIONAL biology ,SENSORY perception ,UNCERTAINTY ,PHYSICAL sciences - Abstract
The number of the distinct tactile percepts exceeds the number of receptor types in the skin, signifying that perception cannot be explained by a one-to-one mapping from a single receptor channel to a corresponding percept. The abundance of touch experiences results from multiplexing (the coexistence of multiple codes within a single channel, increasing the available information content of that channel) and from the mixture of receptor channels by divergence and convergence. When a neuronal representation emerges through the combination of receptor channels, perceptual uncertainty can occur—a perceptual judgment is affected by a stimulus feature that would be, ideally, excluded from the task. Though uncertainty seems at first glance to reflect nonoptimality in sensory processing, it is actually a consequence of efficient coding mechanisms that exploit prior knowledge about objects that are touched. Studies that analyze how perceptual judgments are “fooled” by variations in sensory input can reveal the neuronal mechanisms underlying the tactile experience. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
93. Agonist-induced membrane nanodomain clustering drives GLP-1 receptor responses in pancreatic beta cells.
- Author
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Buenaventura, Teresa, Bitsi, Stavroula, Laughlin, William E., Burgoyne, Thomas, Lyu, Zekun, Oqua, Affiong I., Norman, Hannah, McGlone, Emma R., Klymchenko, Andrey S., JrCorrêa, Ivan R., Walker, Abigail, Inoue, Asuka, Hanyaloglu, Aylin, Grimes, Jak, Koszegi, Zsombor, Calebiro, Davide, Rutter, Guy A., Bloom, Stephen R., Jones, Ben, and Tomas, Alejandra
- Subjects
GLUCAGON-like peptide-1 agonists ,PANCREATIC beta cells ,GLUCAGON-like peptide-1 receptor ,G protein coupled receptors ,SMALL molecules ,ALLOSTERIC regulation ,CYTOLOGY - Abstract
The glucagon-like peptide-1 receptor (GLP-1R), a key pharmacological target in type 2 diabetes (T2D) and obesity, undergoes rapid endocytosis after stimulation by endogenous and therapeutic agonists. We have previously highlighted the relevance of this process in fine-tuning GLP-1R responses in pancreatic beta cells to control insulin secretion. In the present study, we demonstrate an important role for the translocation of active GLP-1Rs into liquid-ordered plasma membrane nanodomains, which act as hotspots for optimal coordination of intracellular signaling and clathrin-mediated endocytosis. This process is dynamically regulated by agonist binding through palmitoylation of the GLP-1R at its carboxyl-terminal tail. Biased GLP-1R agonists and small molecule allosteric modulation both influence GLP-1R palmitoylation, clustering, nanodomain signaling, and internalization. Downstream effects on insulin secretion from pancreatic beta cells indicate that these processes are relevant to GLP-1R physiological actions and might be therapeutically targetable. [ABSTRACT FROM AUTHOR]
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- 2019
- Full Text
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94. MDT-15/MED15 permits longevity at low temperature via enhancing lipidostasis and proteostasis.
- Author
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Lee, Dongyeop, An, Seon Woo A., Jung, Yoonji, Yamaoka, Yasuyo, Ryu, Youngjae, Goh, Grace Ying Shyen, Beigi, Arshia, Yang, Jae-Seong, Jung, Gyoo Yeol, Ma, Dengke K., Ha, Chang Man, Taubert, Stefan, Lee, Youngsook, and Lee, Seung-Jae V.
- Subjects
LOW temperatures ,SATURATED fatty acids ,FATTY acid desaturase ,UNSATURATED fatty acids ,MONOUNSATURATED fatty acids ,LONGEVITY ,BODY temperature - Abstract
Low temperatures delay aging and promote longevity in many organisms. However, the metabolic and homeostatic aspects of low-temperature–induced longevity remain poorly understood. Here, we show that lipid homeostasis regulated by Caenorhabditis elegans Mediator 15 (MDT-15 or MED15), a transcriptional coregulator, is essential for low-temperature–induced longevity and proteostasis. We find that inhibition of mdt-15 prevents animals from living long at low temperatures. We show that MDT-15 up-regulates fat-7, a fatty acid desaturase that converts saturated fatty acids (SFAs) to unsaturated fatty acids (UFAs), at low temperatures. We then demonstrate that maintaining a high UFA/SFA ratio is essential for proteostasis at low temperatures. We show that dietary supplementation with a monounsaturated fatty acid, oleic acid (OA), substantially mitigates the short life span and proteotoxicity in mdt-15(-) animals at low temperatures. Thus, lipidostasis regulated by MDT-15 appears to be a limiting factor for proteostasis and longevity at low temperatures. Our findings highlight the crucial roles of lipid regulation in maintaining normal organismal physiology under different environmental conditions. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
95. The parietal operculum preferentially encodes heat pain and not salience.
- Author
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Horing, Björn, Sprenger, Christian, and Büchel, Christian
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FUNCTIONAL magnetic resonance imaging ,GALVANIC skin response ,SENSORY stimulation ,PAIN threshold ,ACOUSTIC stimulation ,PAIN - Abstract
Substantial controversy exists as to which part of brain activity is genuinely attributable to pain-related percepts and which activity is due to general aspects of sensory stimulation, such as its salience, or the accompanying arousal. The challenge posed by this question rests largely in the fact that pain per se exhibits highly intense but unspecific characteristics. These therefore should be matched by potential control conditions. Here, we used a unique combination of functional magnetic resonance imaging (fMRI) and behavioral and autonomic measures to address this longstanding debate in pain research. Subjects rated perceived intensity in a sequence alternating between heat and sound stimuli. Neuronal activity was monitored using fMRI. Either modality was presented in 6 different intensities, 3 of which lay above the pain threshold (for heat) or the unpleasantness threshold (for sound). We performed our analysis on 26 volunteers in which psychophysiological responses (as per skin conductance responses [SCRs]) did not differ between the 2 stimulus modalities. Having thus ascertained a comparable amount of stimulation-related but unspecific activation, we analyzed stimulus-response functions (SRFs) after painful stimulation and contrasted them with those of the matched acoustic control condition. Furthermore, analysis of fMRI data was performed on the brain surface to circumvent blurring issues stemming from the close proximity of several regions of interest located in heavily folded cortical areas. We focused our analyses on insular and peri-insular regions that are strongly involved in processing of painful stimuli. We employed an axiomatic approach to determine areas showing higher activation in painful compared to nonpainful heat and, at the same time, showing a steeper SRF for painful heat compared to unpleasant sound. Intriguingly, an area in the posterior parietal operculum emerged, whose response showed a pain preference after satisfying all axiomatic constraints. This result has important implications for the interpretation of functional imaging findings in pain research, because it clearly demonstrates that there are areas where activity following painful stimulation is not due to general attributes or results of sensory stimulation, such as salience or arousal. Conversely, several areas did not conform to the formulated axioms to rule out general factors as explanations. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
96. The Candida albicans biofilm gene circuit modulated at the chromatin level by a recent molecular histone innovation.
- Author
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Rai, Laxmi Shanker, Singha, Rima, Sanchez, Hiram, Chakraborty, Tanmoy, Chand, Bipin, Bachellier-Bassi, Sophie, Chowdhury, Shantanu, d’Enfert, Christophe, Andes, David R., and Sanyal, Kaustuv
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GENE regulatory networks ,CANDIDA albicans ,BINDING sites ,GENE expression ,CYTOPLASMIC filaments ,UNICELLULAR organisms ,CHROMATIN - Abstract
Histone H3 and its variants regulate gene expression but the latter are absent in most ascomycetous fungi. Here, we report the identification of a variant histone H3, which we have designated H3V
CTG because of its exclusive presence in the CTG clade of ascomycetes, including Candida albicans, a human pathogen. C. albicans grows both as single yeast cells and hyphal filaments in the planktonic mode of growth. It also forms a three-dimensional biofilm structure in the host as well as on human catheter materials under suitable conditions. H3VCTG null (hht1/hht1) cells of C. albicans are viable but produce more robust biofilms than wild-type cells in both in vitro and in vivo conditions. Indeed, a comparative transcriptome analysis of planktonic and biofilm cells reveals that the biofilm circuitry is significantly altered in H3VCTG null cells. H3VCTG binds more efficiently to the promoters of many biofilm-related genes in the planktonic cells than during biofilm growth, whereas the binding of the core canonical histone H3 on the corresponding promoters largely remains unchanged. Furthermore, biofilm defects associated with master regulators, namely, biofilm and cell wall regulator 1 (Bcr1), transposon enhancement control 1 (Tec1), and non-dityrosine 80 (Ndt80), are significantly rescued in cells lacking H3VCTG . The occupancy of the transcription factor Bcr1 at its cognate promoter binding sites was found to be enhanced in the absence of H3VCTG in the planktonic form of growth resulting in enhanced transcription of biofilm-specific genes. Further, we demonstrate that co-occurrence of valine and serine at the 31st and 32nd positions in H3VCTG , respectively, is essential for its function. Taken together, we show that even in a unicellular organism, differential gene expression patterns are modulated by the relative occupancy of the specific histone H3 type at the chromatin level. [ABSTRACT FROM AUTHOR]- Published
- 2019
- Full Text
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97. Tagger—A Swiss army knife for multiomics to dissect cell type–specific mechanisms of gene expression in mice.
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Kaczmarczyk, Lech, Bansal, Vikas, Rajput, Ashish, Rahman, Raza-ur, Krzyżak, Wiesław, Degen, Joachim, Poll, Stefanie, Fuhrmann, Martin, Bonn, Stefan, and Jackson, Walker Scot
- Subjects
GENE expression ,NUCLEIC acids ,MOLECULAR biology ,NUCLEOTIDE sequence ,CYTOLOGY ,AMYLOID plaque - Abstract
A deep understanding of how regulation of the multiple levels of gene expression in mammalian tissues give rise to complex phenotypes has been impeded by cellular diversity. A handful of techniques were developed to tag-select nucleic acids of interest in specific cell types, thereby enabling their capture. We expanded this strategy by developing the Tagger knock-in mouse line bearing a quad-cistronic transgene combining enrichment tools for nuclei, nascent RNA, translating mRNA, and mature microRNA (miRNA). We demonstrate that Tagger can capture the desired nucleic acids, enabling multiple omics approaches to be applied to specific cell types in vivo using a single transgenic mouse line. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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98. Remote reefs and seamounts are the last refuges for marine predators across the Indo-Pacific.
- Author
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Letessier, Tom B., Mouillot, David, Bouchet, Phil J., Vigliola, Laurent, Fernandes, Marjorie C., Thompson, Chris, Boussarie, Germain, Turner, Jemma, Juhel, Jean-Baptiste, Maire, Eva, Caley, M. Julian, Koldewey, Heather J., Friedlander, Alan, Sala, Enric, and Meeuwig, Jessica J.
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CORAL reef conservation ,CORAL reef ecology ,PREDATORY animals - Abstract
Since the 1950s, industrial fisheries have expanded globally, as fishing vessels are required to travel further afield for fishing opportunities. Technological advancements and fishery subsidies have granted ever-increasing access to populations of sharks, tunas, billfishes, and other predators. Wilderness refuges, defined here as areas beyond the detectable range of human influence, are therefore increasingly rare. In order to achieve marine resources sustainability, large no-take marine protected areas (MPAs) with pelagic components are being implemented. However, such conservation efforts require knowledge of the critical habitats for predators, both across shallow reefs and the deeper ocean. Here, we fill this gap in knowledge across the Indo-Pacific by using 1,041 midwater baited videos to survey sharks and other pelagic predators such as rainbow runner (Elagatis bipinnulata), mahi-mahi (Coryphaena hippurus), and black marlin (Istiompax indica). We modeled three key predator community attributes: vertebrate species richness, mean maximum body size, and shark abundance as a function of geomorphology, environmental conditions, and human pressures. All attributes were primarily driven by geomorphology (35%−62% variance explained) and environmental conditions (14%−49%). While human pressures had no influence on species richness, both body size and shark abundance responded strongly to distance to human markets (12%−20%). Refuges were identified at more than 1,250 km from human markets for body size and for shark abundance. These refuges were identified as remote and shallow seabed features, such as seamounts, submerged banks, and reefs. Worryingly, hotpots of large individuals and of shark abundance are presently under-represented within no-take MPAs that aim to effectively protect marine predators, such as the British Indian Ocean Territory. Population recovery of predators is unlikely to occur without strategic placement and effective enforcement of large no-take MPAs in both coastal and remote locations. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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99. Strategic deployment of feature-based attentional gain in primate visual cortex.
- Author
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Kozyrev, Vladislav, Daliri, Mohammad Reza, Schwedhelm, Philipp, and Treue, Stefan
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VISUAL cortex ,PRIMATES - Abstract
Attending to visual stimuli enhances the gain of those neurons in primate visual cortex that preferentially respond to the matching locations and features (on-target gain). Although this is well suited to enhance the neuronal representation of attended stimuli, it is nonoptimal under difficult discrimination conditions, as in the presence of similar distractors. In such cases, directing attention to neighboring neuronal populations (off-target gain) has been shown to be the most efficient strategy, but although such a strategic deployment of attention has been shown behaviorally, its underlying neural mechanisms are unknown. Here, we investigated how attention affects the population responses of neurons in the middle temporal (MT) visual area of rhesus monkeys to bidirectional movement inside the neurons’ receptive field (RF). The monkeys were trained to focus their attention onto the fixation spot or to detect a direction or speed change in one of the motion directions (the “target”), ignoring the distractor motion. Population activity profiles were determined by systematically varying the patterns’ directions while maintaining a constant angle between them. As expected, the response profiles show a peak for each of the 2 motion directions. Switching spatial attention from the fixation spot into the RF enhanced the peak representing the attended stimulus and suppressed the distractor representation. Importantly, the population data show a direction-dependent attentional modulation that does not peak at the target feature but rather along the slopes of the activity profile representing the target direction. Our results show that attentional gains are strategically deployed to optimize the discriminability of target stimuli, in line with an optimal gain mechanism proposed by Navalpakkam and Itti. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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100. Expanding beyond carnivores to improve livestock protection and conservation.
- Author
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Rodriguez, Shari L. and Sampson, Christie
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ELEPHANTS ,CARNIVOROUS animals ,LIVESTOCK ,ANIMALS - Abstract
Promoting human–wildlife coexistence is critical to the long-term conservation of many wild animal species that come into conflict with humans. Loss of livestock to carnivore species (e.g., lions, tigers, wolves) is a well-documented occurrence and the focus of mitigation strategies around the world. One area that has received little research is the impact of noncarnivores on livestock. Both African and Asian elephant species are known to cause livestock injuries and deaths. Livestock owners within elephant ranges perceive elephants as a risk to their livestock, which may reduce their tolerance towards elephants and jeopardize conservation efforts in the area. Though feral hogs may not be of conservation concern, these animals contribute significant losses to farmers’ livelihoods. We advocate for the inclusion of noncarnivore species in policies that promote livestock protection because it will allow for better communication regarding effective strategies and more application in the field. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
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