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News for Theoretical sciences

#1

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Name	Rapid emergence of subaerial landmasses and onset of a modern hydrologic cycle 2.5 billion years ago \| Nature
Description	The history of the growth of continental crust is uncertain, and several different models that involve a gradual, decelerating, or stepwise process have been proposed1,2,3,4. Even more uncertain is the timing and the secular trend of the emergence of most landmasses above the sea (subaerial landmasses), with estimates ranging from about one billion to three billion years ago5,6,7. The area of emerged crust influences global climate feedbacks and the supply of nutrients to the oceans8, and therefore connects Earth’s crustal evolution to surface environmental conditions9,10,11. Here we use the triple-oxygen-isotope composition of shales from all continents, spanning 3.7 billion years, to provide constraints on the emergence of continents over time. Our measurements show a stepwise total decrease of 0.08 per mille in the average triple-oxygen-isotope value of shales across the Archaean–Proterozoic boundary. We suggest that our data are best explained by a shift in the nature of water–rock interactions, from near-coastal in the Archaean era to predominantly continental in the Proterozoic, accompanied by a decrease in average surface temperatures. We propose that this shift may have coincided with the onset of a modern hydrological cycle owing to the rapid emergence of continental crust with near-modern average elevation and aerial extent roughly 2.5 billion years ago. #Theoretical sciences
Field	# Theoretical sciences
Updated	23 May 2018

#2

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Name	Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector \| Nature
Description	Ubiquitination is a post-translational modification that regulates many cellular processes in eukaryotes1,2,3,4. The conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein, usually on a lysine side chain1,5. Recent studies of the Legionella pneumophila SidE family of effector proteins revealed a ubiquitination method in which a phosphoribosyl ubiquitin (PR-Ub) is conjugated to a serine residue on substrates via a phosphodiester bond6,7,8. Here we present the crystal structure of a fragment of the SidE family member SdeA that retains ubiquitination activity, and determine the mechanism of this unique post-translational modification. The structure reveals that the catalytic module contains two distinct functional units: a phosphodiesterase domain and a mono-ADP-ribosyltransferase domain. Biochemical analysis shows that the mono-ADP-ribosyltransferase domain-mediated conversion of Ub to ADP-ribosylated Ub (ADPR-Ub) and the phosphodiesterase domain-mediated ligation of PR-Ub to substrates are two independent activities of SdeA. Furthermore, we present two crystal structures of a homologous phosphodiesterase domain from the SidE family member SdeD9 in complexes with Ub and ADPR-Ub. The structures suggest a mechanism for how SdeA processes ADPR-Ub to PR-Ub and AMP, and conjugates PR-Ub to a serine residue in substrates. Our study establishes the molecular mechanism of phosphoribosyl-linked ubiquitination and will enable future studies of this unusual type of ubiquitination in eukaryotes. #Theoretical sciences
Field	# Theoretical sciences
Updated	23 May 2018

#3

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Name	Plasmon propagation pushed to the limit
Description	Excitations called plasmons have the potential to miniaturize photonic devices, but are often short-lived. Microscopy reveals that plasmons in the material graphene can overcome this limitation at low temperatures. #Theoretical sciences
Field	# Theoretical sciences
Updated	23 May 2018

#4

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Name	Stellarator’s plasma results show a triumph of engineering and modeling \| Ars Technica
Description	A possible route to fusion makes a very impressive start. #Theoretical sciences;#Energy
Field	# Theoretical sciences
Updated	23 May 2018

#5

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Name	How you end up sleep-deprived matters \| Ars Technica
Description	There's more than one type of sleep deprivation, and the impacts vary. #Theoretical sciences
Field	# Theoretical sciences
Updated	23 May 2018

#6

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Name	How to fit in when you join a lab abroad
Description	Punam Amratia grew up in Kenya, where she attended a British school. She then completed her bachelor’s degree in statistics and a master’s in epidemiology in the United Kingdom. In both nations, she was accustomed to people being blunt. If teachers didn’t like her work, they were upfront about it. “They told me, ‘It’s crap. Go back and do it again,’” she says. So when Amratia started her PhD in malaria epidemiology in 2014, she did not sugarcoat her own opinions. During her first month at the University of Florida in Gainesville, her laboratory met to discuss a paper that her supervisor was reviewing. Amratia recalls calling the paper “shit” and saying that it should not be published. A US lab mate described the paper’s positive attributes and outlined items that could be improved. Amratia’s colleagues suggested to her that she could be more diplomatic. After the meeting, she tried to temper her directness. But Amratia also faced problems socializing with her PhD-committee members, partly because she didn’t understand US popular-culture references. At a social event, while her colleagues laughed about a popular 1980s TV show, she stayed quiet because she was unfamiliar with it. Such incidents made it hard for her to establish a casual rapport with these faculty members, so she did not feel comfortable asking them for advice during her doctoral programme. Plenty of opportunities exist to study and work abroad. But some early-career scientists might face challenges adapting to different communication styles and different workplace and academic hierarchies. Supervisors and junior researchers can reduce the risk of misunderstandings by actively learning about each other’s cultures and communicating workplace expectations clearly. #Theoretical sciences
Field	# Theoretical sciences
Updated	23 May 2018

#7

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Name	The global south is rich in sustainability lessons that students deserve to hear
Description	In a Bangalore slum, Dhanalakshmi tends six plant pots balanced on a wall. They contain shoots of holy basil (or tulasi, Ocimum tenuiflorum). I asked her why she does this, in a cramped space with an unreliable water supply. She told me that the plants replace her tiny roadside kitchen garden, which she lost when the street was widened. The wind blew the basil seeds into the pots. “How can one turn away a guest, even if they come uninvited?” she said. Dhanalakshmi’s deep, personal connection to nature shapes her actions, even though she lives far from the countryside. Such attachments are shared by many people around the world. They run through centuries of Indian thinking on sustainability: nature offers material benefits; it is part of people’s cultural identities and often viewed as sacred. Protecting nature also confers social merit. A stone inscription from AD 1340 describes the motivation of Chenneya Nayaka, the ruler of a region near Bangalore, for building an irrigation tank: ‘to support animals, cattle, birds, and all other living beings, and the service at all times of (the goddess of water) Ganga Devi’1. In the early twentieth century, Mahatma Gandhi fought poverty and injustice through peaceful civil resistance. He championed local production, education, health care and self-sufficiency. Inspired by Gandhi’s ideas, members of the Chipko and Appiko environmental movements hugged trees in the 1970s and 1980s to prevent them from being felled2. In 2014, after 12 years of campaigning, the Dongria Kondh forest tribe in India’s Odisha state won a lawsuit to stop a bauxite mine from opening and ruining the hillsides that they revered and depended on for food. These strongly rooted local movements have brought sustainability issues into everyday conversations in India. They have inspired generations of activists. Yet most university courses on sustainability omit them. Teachings still have a Western focus, even in India. Most books on sustainability frame the discourse in terms of Earth’s finite resources and rising population. #Theoretical sciences
Field	# Theoretical sciences
Updated	23 May 2018

#8

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Name	Scientists Plan New Project to Search for Particles that Escape from LHC
Description	The Massive Timing Hodoscope for Ultra Stable Neutral Particles (which goes by the inaccurate but much simpler nickname MATHUSLA) will ... #Theoretical sciences
Field	# Theoretical sciences
Updated	23 May 2018

#9

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Name	Nuclear Detectives Hunt Invisible Particles That Escaped the World's Largest Atom Smasher
Description	The Large Hadron Collider hasn't found any new physics since the Higgs boson. A team of outsider physicists think they know why. #Theoretical sciences
Field	# Theoretical sciences
Updated	22 May 2018

#10

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Name	What is the multiverse?
Description	Some scientists say we live in a multiverse, and that the universe we inhabit is just one of many — or perhaps an infinite number — in existence. #Theoretical sciences
Field	# Theoretical sciences
Updated	22 May 2018

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