Biology

Correction: Brain-Computer Interface-Based Communication in the Completely Locked-In State

PLOS Biology (new articles) - 9 hours 27 min ago

by Ujwal Chaudhary, Bin Xia, Stefano Silvoni, Leonardo G. Cohen, Niels Birbaumer

Categories: Biology, Journals

Integrative network-centric approach reveals signaling pathways associated with plant resistance and susceptibility to <i>Pseudomonas syringae</i>

PLOS Biology (new articles) - 9 hours 27 min ago

by Elizabeth K. Brauer, George V. Popescu, Dharmendra K. Singh, Mauricio Calviño, Kamala Gupta, Bhaskar Gupta, Suma Chakravarthy, Sorina C. Popescu

Plant protein kinases form redundant signaling pathways to perceive microbial pathogens and activate immunity. Bacterial pathogens repress cellular immune responses by secreting effectors, some of which bind and inhibit multiple host kinases. To understand how broadly bacterial effectors may bind protein kinases and the function of these kinase interactors, we first tested kinase–effector (K-E) interactions using the Pseudomonas syringae pv. tomato–tomato pathosystem. We tested interactions between five individual effectors (HopAI1, AvrPto, HopA1, HopM1, and HopAF1) and 279 tomato kinases in tomato cells. Over half of the tested kinases interacted with at least one effector, and 48% of these kinases interacted with more than three effectors, suggesting a role in the defense. Next, we characterized the role of select multi-effector–interacting kinases and revealed their roles in basal resistance, effector-triggered immunity (ETI), or programmed cell death (PCD). The immune function of several of these kinases was only detectable in the presence of effectors, suggesting that these kinases are critical when particular cell functions are perturbed or that their role is typically masked. To visualize the kinase networks underlying the cellular responses, we derived signal-specific networks. A comparison of the networks revealed a limited overlap between ETI and basal immunity networks. In addition, the basal immune network complexity increased when exposed to some of the effectors. The networks were used to successfully predict the role of a new set of kinases in basal immunity. Our work indicates the complexity of the larger kinase-based defense network and demonstrates how virulence- and avirulence-associated bacterial effectors alter sectors of the defense network.
Categories: Biology, Journals

Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity

PLOS Biology (new articles) - 9 hours 27 min ago

by Tadeusz Wróblewski, Laurentiu Spiridon, Eliza Cristina Martin, Andrei-Jose Petrescu, Keri Cavanaugh, Maria Jose-Truco, Huaqin Xu, Dariusz Gozdowski, Krzysztof Pawłowski, Richard W. Michelmore, Frank L.W. Takken

The ability to induce a defense response after pathogen attack is a critical feature of the immune system of any organism. Nucleotide-binding leucine-rich repeat receptors (NLRs) are key players in this process and perceive the occurrence of nonself-activities or foreign molecules. In plants, coevolution with a variety of pests and pathogens has resulted in repertoires of several hundred diverse NLRs in single individuals and many more in populations as a whole. However, the mechanism by which defense signaling is triggered by these NLRs in plants is poorly understood. Here, we show that upon pathogen perception, NLRs use their N-terminal domains to transactivate other receptors. Their N-terminal domains homo- and heterodimerize, suggesting that plant NLRs oligomerize upon activation, similar to the vertebrate NLRs; however, consistent with their large number in plants, the complexes are highly heterometric. Also, in contrast to metazoan NLRs, the N-terminus, rather than their centrally located nucleotide-binding (NB) domain, can mediate initial partner selection. The highly redundant network of NLR interactions in plants is proposed to provide resilience to perturbation by pathogens.
Categories: Biology, Journals

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

PLOS Biology (new articles) - 9 hours 27 min ago

by Eirini M. Kallimasioti-Pazi, Keerthi Thelakkad Chathoth, Gillian C. Taylor, Alison Meynert, Tracy Ballinger, Martijn J. E. Kelder, Sébastien Lalevée, Ildem Sanli, Robert Feil, Andrew J. Wood

Genome editing occurs in the context of chromatin, which is heterogeneous in structure and function across the genome. Chromatin heterogeneity is thought to affect genome editing efficiency, but this has been challenging to quantify due to the presence of confounding variables. Here, we develop a method that exploits the allele-specific chromatin status of imprinted genes in order to address this problem in cycling mouse embryonic stem cells (mESCs). Because maternal and paternal alleles of imprinted genes have identical DNA sequence and are situated in the same nucleus, allele-specific differences in the frequency and spectrum of mutations induced by CRISPR-Cas9 can be unequivocally attributed to epigenetic mechanisms. We found that heterochromatin can impede mutagenesis, but to a degree that depends on other key experimental parameters. Mutagenesis was impeded by up to 7-fold when Cas9 exposure was brief and when intracellular Cas9 expression was low. In contrast, the outcome of mutagenic DNA repair was unaffected by chromatin state, with similar efficiencies of homology-directed repair (HDR) and deletion spectra on maternal and paternal chromosomes. Combined, our data show that heterochromatin imposes a permeable barrier that influences the kinetics, but not the endpoint, of CRISPR-Cas9 genome editing and suggest that therapeutic applications involving low-level Cas9 exposure will be particularly affected by chromatin status.
Categories: Biology, Journals

First direct evidence that later school day really does help teenagers

Genetics - Wed, 2018-12-12 21:00
Since Seattle high schools decided to start an hour later, students have been getting more sleep – and school attendance and grades have improved
Categories: Biology

Australia’s ‘marsupial lion’ was a meat-ripping, tree-climbing terror

Genetics - Wed, 2018-12-12 21:00
First full reconstruction of Thylacoleo carnifex shows it tore apart its prey like a Tasmanian devil, had the bite strength of a lion, and climbed like a koala
Categories: Biology

If you think black holes are strange, white holes will blow your mind

Genetics - Wed, 2018-12-12 20:05
White holes are black ones in reverse, spewing out matter– and they could give us our first glimpse of the quantum source of space-time, says physicist Carlo Rovelli
Categories: Biology

Bitcoin’s price is plummeting – will the cryptocurrency survive?

Genetics - Wed, 2018-12-12 20:00
Bitcoin investors have had a rough ride this year as the price of the cryptocurrency has tumbled, making it less economical to produce the coins
Categories: Biology

Quantum network joins four people together for encrypted messaging

Genetics - Wed, 2018-12-12 20:00
A multi-user quantum network shows that secure quantum links between several people at once could be possible using standard telecommunications equipment
Categories: Biology

Acne study reveals genes for hair follicles are partly to blame

Genetics - Wed, 2018-12-12 15:17
The genes involved in producing hair follicles are partly to blame for acne, according to an analysis of the DNA of over 5000 people with severe acne
Categories: Biology

Endangered relative of the hedgehog may be thriving in Vietnam

Genetics - Wed, 2018-12-12 13:00
The Hainan gymnure is a stinky but spine-free relative of the hedgehog that we thought was rare – a new discovery in northern Vietnam suggests we were wrong
Categories: Biology

How lab-on-a-chip technology is turning smartphones into food sensors

Genetics - Wed, 2018-12-12 12:00
A lab-on-a-chip that fits inside a smartphone is set to change our relationship with food and the chemicals we use to make it
Categories: Biology

When humans are wiped from Earth, the chicken bones will remain

Genetics - Wed, 2018-12-12 02:01
When humans have vanished from Earth, one of the most enduring marks of our impact will be the sudden appearance of copious chicken bones in the fossil record
Categories: Biology

Coral likes to make its ocean home in places with noisy neighbours

Genetics - Wed, 2018-12-12 02:01
As larvae, corals drift around the ocean searching for somewhere to live – and they seem to appreciate a spot in an area full of loud fish
Categories: Biology

Monkeys chill out just from seeing their friends being groomed

Genetics - Wed, 2018-12-12 02:01
Barbary macaques became more relaxed and friendlier after seeing another macaque being groomed – a finding that may help explain ‘head orgasm’ videos
Categories: Biology

Reply to “Far away from the lamppost”

PLOS Biology (new articles) - Wed, 2018-12-12 00:00

by Thomas Stoeger, Martin Gerlach, Richard I. Morimoto, Luís A. Nunes Amaral

In this Formal Comment, the authors of the recent publication "Large-scale investigation of the reasons why potentially important genes are ignored" maintain that it can be read as an opportunity to explore the unknown.
Categories: Biology, Journals

Far away from the lamppost

PLOS Biology (new articles) - Wed, 2018-12-12 00:00

by Tudor I. Oprea, Lily Jan, Gary L. Johnson, Bryan L. Roth, Avi Ma’ayan, Stephan Schürer, Brian K. Shoichet, Larry A. Sklar, Michael T. McManus

This Formal Comment responds to a recent Meta-Research Article by identifying initiatives that are already in place for funding risky exploratory research that illuminate mysteries of the dark genome.
Categories: Biology, Journals

Sex-specific dominance reversal of genetic variation for fitness

PLOS Biology (new articles) - Wed, 2018-12-12 00:00

by Karl Grieshop, Göran Arnqvist

The maintenance of genetic variance in fitness represents one of the most longstanding enigmas in evolutionary biology. Sexually antagonistic (SA) selection may contribute substantially to maintaining genetic variance in fitness by maintaining alternative alleles with opposite fitness effects in the two sexes. This is especially likely if such SA loci exhibit sex-specific dominance reversal (SSDR)—wherein the allele that benefits a given sex is also dominant in that sex—which would generate balancing selection and maintain stable SA polymorphisms for fitness. However, direct empirical tests of SSDR for fitness are currently lacking. Here, we performed a full diallel cross among isogenic strains derived from a natural population of the seed beetle Callosobruchus maculatus that is known to exhibit SA genetic variance in fitness. We measured sex-specific competitive lifetime reproductive success (i.e., fitness) in >500 sex-by-genotype F1 combinations and found that segregating genetic variation in fitness exhibited pronounced contributions from dominance variance and sex-specific dominance variance. A closer inspection of the nature of dominance variance revealed that the fixed allelic variation captured within each strain tended to be dominant in one sex but recessive in the other, revealing genome-wide SSDR for SA polymorphisms underlying fitness. Our findings suggest that SA balancing selection could play an underappreciated role in maintaining fitness variance in natural populations.
Categories: Biology, Journals

Major companies are using AI to decide who you speak to on the phone

Genetics - Tue, 2018-12-11 18:52
When you ring a call centre, an AI could be deciding which person will speak to you, based on their ability to influence your decisions
Categories: Biology

Vibrating crystal made of 10 billion atoms smashes quantum record

Genetics - Tue, 2018-12-11 17:56
Testing increasingly large objects proves that quantum mechanics works at larger scales - a finding that could help build quantum computers
Categories: Biology