Feed aggregator

Analysis validation has been neglected in the Age of Reproducibility

PLOS Biology (new articles) - 10 hours 27 min назад

by Kathleen E. Lotterhos, Jason H. Moore, Ann E. Stapleton

Increasingly complex statistical models are being used for the analysis of biological data. Recent commentary has focused on the ability to compute the same outcome for a given dataset (reproducibility). We argue that a reproducible statistical analysis is not necessarily valid because of unique patterns of nonindependence in every biological dataset. We advocate that analyses should be evaluated with known-truth simulations that capture biological reality, a process we call “analysis validation.” We review the process of validation and suggest criteria that a validation project should meet. We find that different fields of science have historically failed to meet all criteria, and we suggest ways to implement meaningful validation in training and practice.
Категории: Biology, Journals

Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration

PLOS Biology (new articles) - 10 hours 27 min назад

by Catherine D. Robinson, Helena S. Klein, Kyleah D. Murphy, Raghuveer Parthasarathy, Karen Guillemin, Brendan J. M. Bohannan

All animals live in intimate association with microorganisms that profoundly influence their health and development, yet the traits that allow microorganisms to establish and maintain host associations are not well understood. To date, most investigations aimed at identifying traits required for host association have focused on intrahost niches. Consequently, little is known about the relative contribution of extrahost factors such as environmental growth and survival and immigration into hosts from the external environment, as promoters of host association. To address this, we developed a tractable experimental evolution system that investigates both intra- and extrahost factors contributing to bacterial adaptation to the vertebrate gut. We passaged replicate lines of a zebrafish bacterial isolate, Aeromonas veronii, through populations of germ-free larval zebrafish (Danio rerio), each time using gut-associated Aeromonas populations to inoculate the aquatic environment of the next zebrafish population. We observed rapid increased adaptation to the host in all replicate lines. The initial adaptations present in early-evolved isolates did not increase intrahost fitness but rather enhanced both immigration from the environment and interhost transmission. Only in later-evolved isolates did we find evidence for intrahost-specific adaptations, as demonstrated by comparing their competitive fitness in the host genotype to which they evolved to that in a different genotype. Our results show how selection for bacterial transmission between hosts and their environment can shape bacterial-host association. This work illuminates the nature of selective forces present in host–microbe systems and reveals specific mechanisms of increased host association. Furthermore, our findings demonstrate that the entire host–microbe–environment system must be considered when identifying microbial traits that contribute to host adaptation.
Категории: Biology, Journals

Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver

PLOS Biology (new articles) - 10 hours 27 min назад

by Adrija Kalvisa, Majken S. Siersbæk, Stine M. Præstholm, Line J. L. Christensen, Ronni Nielsen, Oliver Stohr, Sabine Vettorazzi, Jan Tuckermann, Morris White, Susanne Mandrup, Lars Grøntved

Hepatic circadian gene transcription is tightly coupled to feeding behavior, which has a profound impact on metabolic disorders associated with diet-induced obesity. Here, we describe a genomics approach to uncover mechanisms controlling hepatic postprandial gene expression. Combined transcriptomic and cistromic analysis identified hundreds of circadian-regulated genes and enhancers controlled by feeding. Postprandial suppression of enhancer activity was associated with reduced glucocorticoid receptor (GR) and Forkhead box O1 (FOXO1) occupancy of chromatin correlating with reduced serum corticosterone levels and increased serum insulin levels. Despite substantial co-occupancy of feeding-regulated enhancers by GR and FOXO1, selective disruption of corticosteroid and/or insulin signaling resulted in dysregulation of specific postprandial regulated gene programs. In combination, these signaling pathways operate a major part of the genes suppressed by feeding. Importantly, the feeding response was disrupted in diet-induced obese animals, which was associated with dysregulation of several corticosteroid- and insulin-regulated genes, providing mechanistic insights to dysregulated circadian gene transcription associated with obesity.
Категории: Biology, Journals

The Great Barrier Reef is fighting back by losing weak species

HIV and AIDS - пн, 2018-12-10 18:00
Australia’s Great Barrier Reef appears to be getting better at coping with heatwaves overall, as stronger species take over where vulnerable ones get wiped out
Категории: Healthcare, Science and society

City living makes urban male frogs far more attractive to females

HIV and AIDS - пн, 2018-12-10 18:00
Urban male túngara frogs have evolved more elaborate mating calls than their rural brothers, which make them much better at attracting a mate
Категории: Healthcare, Science and society

Spray-on gel slows down the regrowth of tumours after cancer surgery

HIV and AIDS - пн, 2018-12-10 18:00
A spray applied to the wound left by cancer surgery encourages the immune system to attack any cancer cells the surgeons left behind, a study in mice has found
Категории: Healthcare, Science and society

The most comfortable running shoes may actually increase injury risk

HIV and AIDS - пн, 2018-12-10 17:30
Shoes with extra padding are meant to prevent impact-related injuries, but they may do the opposite by making our legs stiffer when we run
Категории: Healthcare, Science and society

How to transform Earth’s cities

Genetics - вс, 2018-12-09 16:00
When innovators, entrepreneurs, scientists and policy makers meet next week to discuss the UN's goal of making cities inclusive, safe, resilient and sustainable by 2030, the quality of life for billions of people will be at stake.
Категории: Biology

How to transform Earth’s cities

Genetically modified organisms (GMO) - вс, 2018-12-09 16:00
When innovators, entrepreneurs, scientists and policy makers meet next week to discuss the UN's goal of making cities inclusive, safe, resilient and sustainable by 2030, the quality of life for billions of people will be at stake.
Категории: Science and society

Alan Moore interview: Magic and science feed Middle England Watchman

Genetics - сб, 2018-12-08 12:00
The creator of cult comics Watchmen and Halo Jones is an occultist, but his love of science shows in the way he plays with quantum characters and consciousness
Категории: Biology

Alan Moore interview: Magic and science feed Middle England Watchman

Genetically modified organisms (GMO) - сб, 2018-12-08 12:00
The creator of cult comics Watchmen and Halo Jones is an occultist, but his love of science shows in the way he plays with quantum characters and consciousness
Категории: Science and society

Brain scans reveal why your brain forgets details

HIV and AIDS - пт, 2018-12-07 20:30
The way we store and retrieve memories prioritises abstract context over specific details, which might help us learn general lessons from our experiences
Категории: Healthcare, Science and society

Brain scans reveal why your brain forgets details

Genetics - пт, 2018-12-07 20:30
The way we store and retrieve memories prioritises abstract context over specific details, which might help us learn general lessons from our experiences
Категории: Biology

Brain scans reveal why your brain forgets details

Genetically modified organisms (GMO) - пт, 2018-12-07 20:30
The way we store and retrieve memories prioritises abstract context over specific details, which might help us learn general lessons from our experiences
Категории: Science and society

Interstellar asteroid ‘Oumuamua slipped by NASA space telescope unseen

Genetics - пт, 2018-12-07 16:51
The Spitzer Space Telescope failed to spot ‘Oumuamua, the first interstellar object we’ve ever seen, but we were still able to learn something about this strange space rock
Категории: Biology

Interstellar asteroid ‘Oumuamua slipped by NASA space telescope unseen

Genetically modified organisms (GMO) - пт, 2018-12-07 16:51
The Spitzer Space Telescope failed to spot ‘Oumuamua, the first interstellar object we’ve ever seen, but we were still able to learn something about this strange space rock
Категории: Science and society

Interstellar asteroid ‘Oumuamua slipped by NASA space telescope unseen

HIV and AIDS - пт, 2018-12-07 16:51
The Spitzer Space Telescope failed to spot ‘Oumuamua, the first interstellar object we’ve ever seen, but we were still able to learn something about this strange space rock
Категории: Healthcare, Science and society

We’ve added letters to the genetic code – and the results are amazing

Genetics - пт, 2018-12-07 14:50
The first life forms with a six-letter genetic code are already pumping out drugs and other materials that nature has never seen before
Категории: Biology

We’ve added letters to the genetic code – and the results are amazing

Genetically modified organisms (GMO) - пт, 2018-12-07 14:50
The first life forms with a six-letter genetic code are already pumping out drugs and other materials that nature has never seen before
Категории: Science and society

China is about to launch a mission to explore the far side of the moon

Genetics - пт, 2018-12-07 14:27
The Chang’e 4 mission, launching on 7 December, will place both a lander and a rover on the far side of the moon, where no spacecraft has ever landed before
Категории: Biology