An ultra‐high affinity protein–protein interface displaying sequence‐robustness

Protein–protein interactions are crucial in biology and play roles in for example, the immune system, signaling pathways, and enzyme regulation. Ultra‐high affinity interactions (K _d <0.1 nM) occur in these systems, however, structures and energetics behind stability of ultra‐high affinity protein–protein complexes are not well understood. Regulation of the starch debranching barley limit dextrinase (LD) and its endogenous cereal type inhibitor (LDI) exemplifies an ultra‐high affinity complex (K _d of 42 pM). In this study the LD–LDI complex is investigated to unveil how robust the ultra‐high affinity is to LDI sequence variation at the protein–protein interface and whether alternative sequences can retain the ultra‐high binding affinity. The interface of LD–LDI was engineered using computational protein redesign aiming at identifying LDI variants predicted to retain ultra‐high binding affinity. These variants present a very diverse set of mutations going beyond conservative and alanine substitutions typically used to probe interfaces. Surface plasmon resonance analysis of the LDI variants revealed that high affinity of LD–LDI requires interactions of several residues at the rim of the protein interface, unlike the classical hotspot arrangement where key residues are found at the center of the interface. Notably, substitution of interface residues in LDI, including amino acids with functional groups different from the wild‐type, could occur without loss of affinity. This demonstrates that ultra‐high binding affinity can be conferred without hotspot residues, thus making complexes more robust to mutational drift in evolution. The present mutational analysis also demonstrates how energetic coupling can emerge between residues at large distances at the interface.     

Cryo‐EM reveals the complex architecture of dynactin's shoulder region and pointed end

Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra‐processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled‐coil adaptor. Dynactin consists of an actin‐related filament whose length is defined by its flexible shoulder domain. Despite previous cryo‐EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high‐resolution information in these regions. Here we combine multiple cryo‐EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high‐resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder securely houses the p150 subunit and positions the four identical p50 subunits in different conformations to bind dynactin’s filament. The pointed end map allows us to build the first structure of p62 and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end.     

Dr. Manners

Good manners make a difference—in science and elsewhere. This includes our social media etiquette as researchers. Subject Categories: S&S: History & Philosophy of Science, Methods & Resources, S&S: Ethics

Elbows off the table, please. Don’t chew with your mouth open. Don’t blow your nose at the table. Don’t put your feet up on the chair or table. And please, do not yuck my yum. These are basic table manners that have come up at some of our lab meals, and I have often wondered if it was my job to teach my trainees social graces. A good fellow scientist and friend of mine once told me it was absolutely our place as mentors to teach our trainees not only how to do science well, but also how to be well‐mannered humans. While these Emily Post‐approved table manners might seem old‐fashioned (I’m guessing some readers will have to look up Emily Post), I strongly believe they still hold a place in modern society; being in good company never goes out of style.Speaking of modern society: upon encouragement by several of my scientist friends, I joined Twitter in 2016. My motivation was mainly to hear about pre‐prints and publications, conference announcements and relevant news, science or otherwise. I also follow people who just make me laugh (I highly recommend @ConanOBrien or @dog_rates). I (re)tweet job openings, conference announcements, and interesting new data. Occasionally, I post photos from conferences, or random science‐related art. I also appreciate the sense of community that social media brings to the table. However, social media is a venue where I have also seen manners go to die. Rapidly.It is really shocking to read what some people feel perfectly comfortable tweeting. While most of us can agree that foul language and highly offensive opinions are generally considered distasteful, there are other, subtler but nonetheless equally—if not more—cringe‐worthy offenses online when I am fairly certain these people would never utter such words in real life. In the era of pandemic, the existence of people tweeting about not being able to eat at their favorite restaurant or travel to some destination holiday because of lockdown shows an egregious lack of self‐awareness. Sure it sucks to cancel a wedding due to COVID‐19, but do you need to moan to your followers—most of whom are likely total strangers—about it while other people have lost their jobs? If I had a nickel for every first‐world complaint I have seen on Twitter, I’d have retired a long time ago; although to be honest, I would do science for free. However, these examples pale in comparison with another type of tweeter: Reader, I submit to you, “the Humblebragger.”From the MacMillan Buzzword dictionary (via Google): a humblebrag is “a statement in which you pretend to be modest but which you are really using as a way of telling people about your success or achievements.” I would further translate this definition to indicate that humblebraggers are starved for attention. After joining Twitter, I quickly found many people using social media to announce how “humble and honored” they are for receiving grant or prize X, Y, or Z. In general, these are junior faculty who have perhaps not acquired the self‐awareness more senior scientists have. Perhaps the most off‐putting posts I have seen are from people who post photos of their NIH application priority scores right after study section, or their Notice of Awards (NOA). When did we ever, before social media, send little notes to each other—let alone to complete strangers—announcing our priority scores or NOAs? (Spoiler: NEVER)Some of you reading this opinion piece might have humblebragged at one or time or another, and might not understand why it is distasteful. Please let me explain. For every person who gets a fundable score, there are dozens more people who do not, and they are sad (I speak from many years of experience). While said fundable‐score person might be by someone we like—and I absolutely, positively wish them well—there are many more people who will feel lousy because they did not get funding from the same review round. When has anyone ever felt good about other people getting something that they, too, desire? I think as children, none of us liked the kid on the playground who ran around with the best new Toy of the Season. As adults, do we feel differently? Along these lines, I have never been a fan of “best poster/talk/abstract” prizes. Trainees should not be striving for these fleeting recognitions and should focus on doing the best science for Science’s sake; I really believe this competition process sets people up for life in a negative way—there, I’ve said it.Can your friends and colleagues tweet about your honors? Sure, why not, and by all means please let your well‐wishers honor you, and do thank them and graciously congratulate your trainees or colleagues for helping you to get there. But to post things yourself? Please. Don’t be surprised if you have been muted by many of your followers.It is notable that many of our most decorated scientists are not on Twitter, or at least never tweet about their accomplishments. I do not recall ever seeing a single Nobel laureate announce how humbled and honored they are about their prize. Of course, I might be wrong, but I am willing to bet the numbers are much lower than what I have observed for junior faculty. True humility will never be demonstrated by announcing your achievements to your social media followers, and I believe humblebragging reveals insecurity more than anything. I hope that many more of us can follow the lead of our top scientists both in creativity, rigor, and social media politeness.     

Freelancer

What long‐term changes can we expect, in how academic work is conducted and remunerated, in the post‐pandemic world? Subject Categories: S&S: Economics & Business, S&S: History & Philosophy of Science, S&S: Ethics

Although still two years away, my looming “retirement” from university employment is inevitably going to herald a major change of life. “Of course, you''ll become ‘Emeritus’”, most colleagues have opined. My answer to all of them has been a firm “No. I''ll become a freelancer”. The concept of a freelance scientist is obviously so alien to most of them that they invariably change the subject immediately. However, my gut feeling is that in 20 years or less, almost all of us will be freelancers of some kind.The COVID‐19 pandemic has altered the world of work in very obvious ways. There has been much talk of how the changes are likely to carry over to the future, even if more traditional patterns will probably reassert themselves in the short to medium term. Working from home, conducting meetings remotely, not wasting days travelling between continents for a few precious hours of face‐time and being free to structure workdays around our own priorities: these are the most obvious novelties that many believe will continue long after the effects of the pandemic on health and wealth have faded. But I have a slightly different take.Major disruptive events of worldwide import—world wars, global economic slumps, cataclysmic volcanic eruptions and pandemics—have often been harbingers of profound social change. This is not only due to their direct and immediate effects, but more so because the disruption accelerates and facilitates changes that were already happening. In the case of COVID‐19, one may place in this category the demise of cash, the rise of streaming services in place of live entertainment, online grocery shopping and even virtual dating. Another is paying people to stay home and do nothing, otherwise known as the universal basic income (or, in the USA, “stimulus cheques”).Inefficient practices in academia are equally ripe for change. Why bother with classes for 500 first‐year students when a much better edition of the lecture by an expert communicator is available on the internet? What’s the use of an ageing PhD advisor 20 years away from bench science, who struggles to guide the next generation of experimentalists in the lab, when the expertise of a plethora of specialists can easily be accessed online? What’s the value in published papers that are read by fewer people than wrote them? Or in seminars delivered to a roomful of attentive postdocs and PhD students who lack the courage or the time to address even a single question to the speaker?Yes, there is still great value in small‐group teaching and mentorship, in the creative verve of a close‐knit laboratory team, and in good writing and oratory: but the required skills are already different from those in which we were schooled. Thus, even if I do not hold in my palm the crystal ball to predict exactly which changes will happen and how fast, I believe that our traditional jobs are going to melt away very fast in the post‐pandemic world. Universities and research institutes may still exist, but I expect that their practices will be different, reshaped by rational need more than by tradition. Today’s academic science is already quite unlike that of 1920, but it has evolved so slowly during that century—spanning a much longer time period than the lifetime of a scientific career—that we barely perceive the changes that have occurred. In contrast, the changes now afoot will certainly happen much faster, especially since the funds to support the current “inefficient” model are likely to diminish rapidly.So, I predict that university teaching and science communication in general will be the first to evolve into freelance activities, where universities will invite bids from individuals or their agents and award commissions on a fee‐paying basis rather than using salaried employees. But these are not the only component parts of academia facing such a shake‐up. The practices of laboratory science are also likely to be rebuilt. When discussing with colleagues how research might be undertaken on a freelance basis, they usually raise issues such as bricks and mortar and the complex infrastructure that is needed to sustain cutting‐edge research, especially in the life sciences: how, they ask, could a freelancer access state‐of‐the‐art imaging, mass spectrometry or DNA sequencing? How could their acquisition of such expensive hardware possibly be financed, especially if they had to somehow acquire it personally and set it up in the garage or carry it around with them?But the answers to these questions are already evident in the practices of some major research agencies, most notably in Europe’s pioneering funder of single‐investigator grants for blue‐skies science, the European Research Council (ERC). The ERC already treats its awardees as freelancers, in the sense that it encourages them to shop around for the most attractive venue in which to embed and implement their research project. The quest for the best host institution takes place not only at the preparatory step of an ERC application: it also happens after the grant is awarded, since the grant money is considered inherently portable and can even be moved later on from one institution to another. This encourages potential host universities to compete for providing the best research environment, in which many factors come into play, not just but not least, the quality of its research infrastructure. How well it supports, rather than burdens its staff with administrative tasks, the nature of its recruitment and personnel policies, how it handles relocation issues for incoming researchers and their families, what opportunities it provides for further training in relevant skills and career development: these are just some of the factors in play.In recent years, universities have seen their primary role in this process as encouraging their own tenured or tenure‐track staff to apply for ERC grants. But I foresee the emphasis shifting increasingly to investigators who seek out universities that can make the most appealing offer, whilst universities and government agencies standing behind them will shape their policies so as to remain competitive. Moreover, in such a landscape there is no reason why a scientist cannot operate research projects on multiple sites if this offers the most convenient arrangement. The tools for remote meetings and cloud computing to which we have all become accustomed mean that there is no longer any need for a research group to be located in one building or even in one country, to operate efficiently as a team.At the same time, many of the tasks involved in running a research institute or department can be efficiently outsourced to the most competitive bidder—to be assessed on the basis of value‐for‐money, not just minimum cost. As a society, we should be asking ourselves why we continue to waste the talents of highly specialized scientists on performing admin tasks for which they are neither properly trained nor motivated, instead of just engaging a smart‐software developer. Why should we fund creative thinkers to undertake laboratory projects in host institutions that do not have the required state‐of‐the‐art facilities to perform them? Or allocate budgets that are so pared down that grantholders cannot even afford to purchase such services elsewhere? Why should we expect them to make do with poorly paid trainees instead of a team of professionals? And why should we continue to organize research in pyramid structures where everything depends on commands from the top, where all findings are announced using an institutional slide template, where colleagues elsewhere are considered as untrustworthy “competitors”, and where credit for individual creativity is usurped by seniors who barely know the contents of the papers they “write”?In the “old system”, we have all gotten used to making do with sub‐optimal working arrangements and grumbling about them, whilst considering them an immutable fact of life. But I envisage a time coming soon where we scientists will have the edge in reshaping the market for teaching and research in a way that is much more to our liking and properly aligned with our skills. At the same time, our individual success in accomplishing our professional goals will have a direct effect on our income and job satisfaction, and steer us towards activities where our talents are most effectively deployed. In short, I believe that we, as freelance scientists, will be much more firmly in control of science in the future and that time is not far off.     

Borrowed robes

Should scientists indulge their fantasies by writing fiction? Subject Categories: Careers, Economics, Law & Politics, History & Philosophy of Science

Like a substantial fraction of the literate population, I have a collection of unpublished novels in the drawer. Six of them in fact. Some of them were composed in barely more than a week, and others I have been struggling to complete for over 10 years: so maybe it is more accurate to say five and a half. Anyhow, most of them are good to go, give or take a bit of editorial redlining. Or, as my helpful EMBO editor would say, the removal of thousands of unnecessary adverbs and dubiously positioned commas.What do I write about and why? My style is not unique but rather particular. I write fiction in the style of non‐fiction. My subject matter is somewhere in the general realms of science fiction, alternate history and political drama. Putting these ingredients together, and taking account of my purported day job as a serious scientist, it is easy to see why my fictional work is potentially subversive—which is one reason why I have been rather reluctant thus far to let it out of the drawer. At the very least, I should take pains to conceal my identity, lest it corrupts perceptions of my scientific work. Even if I regularly tell my students not to believe everything they read, it would impose far too great a burden on them if they came to question my peer‐reviewed articles purely on the basis of untrue statements published in my name, spoken by jaded politicians, washed‐up academics or over‐credulous journalists. Even if they are imaginary. Real journalists are theoretically bound by strict rules of conduct. But imaginary ones can do whatever they like.Today, I noticed a passage in one of these unpublished works that is clearly written in the style of a young William Shakespeare, dealing with a subject matter that fits neatly into one of his most famous plays. In fact, the illusion was such that I was sure I must have lifted the passage from the play in question and set about searching for the quote, which I then could and should cite. Yet, all Internet searches failed to find any match. The character in whose mouth I placed the words was depicted as being in a delirious state where the boundaries of fact and fiction in his life were already blurred; borrowed identities being one of the themes of the entire novel and arguably of my entire oeuvre. But am I guilty here of plagiarism or poetry, in adopting the borrowed identity of my national playwright?In another work, I lay great emphasis on the damaging role of mitochondrial reactive oxygen species (ROS) as the cause of biological ageing. I have even grafted this explanation onto a thinly disguised version of one of my most valued colleagues. Although there is some support for such a hypothesis from real science, including some papers that I have myself co‐authored, it is also a dangerously broad generalization that leads easily into wrong turnings and misconstructions—let alone questionable policies and diet advice. But, by advancing this misleading and overly simplistic idea in print, have I potentially damaged not only my own reputation, but that of other scientists whom I respect? Even if the author’s identity remains hidden.In one novel, I fantasize that nuclear weapons, whilst they do undoubtedly exist, have in fact been engineered by their inventors so as never actually to work, thus preventing their possible misuse by vainglorious or lunatic politicians unconcerned with the loss of millions of lives and planetary ruin. But if any insane national leader—of which there are unfortunately far too many—would actually come to believe that my fiction in the style of non‐fiction were true, they might indeed risk the outbreak of nuclear war by starting a conventional one in order to secure their strategic goals.Elsewhere, I vindicate one author of published claims that were manifestly based on falsified data, asserting him to have instead been the victim of a conspiracy launched to protect the family of an otherwise much respected American President. None of which is remotely true. Or at least there is no actual evidence supporting my ridiculous account.I have great fun writing fiction of this kind. It is both liberating and relaxing to be able to ignore facts and the results of real experiments and just invent or distort them to suit an imaginary scenario. In an age when the media and real politicians have no qualms about propagating equally outrageous “alternative facts”, I can at least plead innocent by pointing out that my lies are deliberate and labelled as such, even if people might choose to believe them.In a further twist, the blurb I have written to describe my latest work characterizes it as the “semi‐fictionalized” biography of a real person, who was, in fact, a distant relative of mine. But if it is semi‐fictionalized, which bits are true and which are made up? Maybe almost the whole thing is invented? Or maybe 99% of it is based on demonstrable facts? Maybe the subject himself concocted his own life story and somehow planted it in falsified documents and newspaper articles to give it an air of truth. Or maybe the assertion that the story is semi‐fictionalized is itself a fictional device, that is, a lie. Perhaps the central character never existed at all.It is true (sic) that the most powerful fiction is grounded in fact—if something is plausible, it is all the more demanding of our attention. And, it can point the way to truths that are not revealed by a simple catalogue of factual information, such as in a scientific report.But I have already said too much: if any of my novels ever do find their way into print, and should you chance to read them, I will be instantly unmasked. So maybe I’ll have to slot in something else in place of my pseudo‐Shakespearean verse, mitochondrial ROS hypothesis, defunct weapons of mass destruction and manipulated data manipulation.     

Alcodemia: are we training our students to be great thinkers or great drinkers?

Academia has fostered an unhealthy relationship with alcohol that has an undeniable impact on the health and behaviour of students and staff. Subject Categories: S&S: History & Philosophy of Science, Chemical Biology, S&S: Ethics

University life has a lot to offer. And, for better or worse, much of it goes hand in hand with a bottle. Believe it or not, I was a bit of teetotaler in my undergraduate days but quickly made up for it in graduate school, where each celebration included inebriation. Indeed, my initial tour of the laboratory I eventually worked in included a refreshing visit to the grad club. Orientation week ended with a marathon beer blitz at a nightclub. The semester’s first invited seminar speaker was welcomed with the sounds of loose change, ice buckets and the clickity‐clack of organic microbrews being opened. Our inaugural genome evolution journal club was such a success that we vowed to spill even more red wine onto our notebooks the following week. In hindsight, I should have realized at this early stage in my studies that I was fostering an unhealthy and unsustainable relationship between biology and booze. Unfortunately, my post‐graduate education in alcohol didn’t stop there.Like many keen students, I arrived at my first scientific conference with a belly full of nerves and a fistful of drink tickets, which I quickly put to good use at the poster session. The successful completion of my PhD proposal assessment was met with pats on the back as I was swiftly marched off to a local pub with no chance of escape. My first peer‐reviewed paper literally arrived with a pop as Champagne was generously poured into plastic cups for the entire laboratory group. My failures, too, were greeted with a liberal dose of ethanol. “Sorry you came up short on that scholarship application, Smitty. It’s nothing a little weapons‐grade Chianti won’t cure.” “That experiment failed again! Come on, let me buy you a lunchtime martini to make up for it.” Soon I learnt that every academic event, achievement or ailment, no matter how big or small, could be appropriately paired with beer, wine or spirit. Missing from the menu were two crucial ingredients for any burgeoning researcher: moderation and mindfulness.But it was the older vintages that really inspired me – the legendary drinking escapades of my scientific mentors, advisors and idols. The tale of professor so‐and‐so who at that epic meeting in 1993 polished off an entire magnum of rosé at dinner and then went on to deliver among the greatest keynote lectures on record at 9 am the following morning. That celebrated chaired researcher who kept the single malt next to the pipette tips for quick and easy access. The grizzled evolutionary ecologist who never went into the field without half a dozen cans of high‐end smoked oysters and two hip flaks, which didn’t contain water. And so, when I was told by someone in the know of how the most famous geneticist on campus wrote that monumental Nature paper (the one I’d read ten times!) while locked in his office for twelve hours with a six‐pack, I bought into the romance hook, line and sinker. The result: I’ve been nursing a recurring headache for nearly two decades and I’m still waiting on that Nature paper. Most importantly, I now realize the various dangers of romanticizing the bottle, especially for individuals in mentorship positions.Like my idols before me, I’ve accrued a cask full of well‐oaked academic drinking stories, except that they haven’t aged well. There is that heroic evening of intense scotch‐fueled scientific discussion, which led to me forfeiting two front teeth to the concrete sidewalk (my mother still thinks it was a squash accident). Or that time I commemorated the end of a great conference in Barcelona by throwing up on the front window of a café while the most prominent minds in my field sipped aperitifs inside (thank god this was before Twitter). Even more romantic: me buying a bottle of Cotes de Nuits Burgundy at Calgary airport on route to a job interview, discreetly opening the bottle in‐flight because economy class wine sucks, and then being met by airport security upon landing. Let’s just say I didn’t get the job. To some, these anecdotes might seem light‐hearted or silly, but they are actually rather sad and underscore the seriousness of substance abuse. Many readers will have their own complicated experiences with alcohol in academia and, I believe, will agree that it is high time we asked ourselves: are we training our graduate students to be great thinkers or great drinkers? Moreover, this question does not address the equally if not more serious issue of excessive drinking among undergraduate students.As I sit at my desk writing this, I think to myself: is it normal that within a two‐minute walk of my university office there are three different places on campus that I can have a beer before lunch, not including the minifridge behind my desk? Is it normal that in my department the first thing we do after a student defends their thesis is go to the grad club where they can have any alcoholic drink of their choosing for free from the goblet of knowledge, which is kept on a pedestal behind the bar? Is it normal that before the COVID pandemic when I was visiting a prominent university for an invited talk, one of the professors I met with offered me a glass of expensive Japanese gin at 11 am in the morning? (And, yes, I accepted the drink.)Of course, if you don’t want to drink you can just say no. But we are learning more and more how institutional cultures – “the deeply embedded patterns of organisational behaviour and the shared values, assumptions, beliefs or ideologies that members have about their organisation or its work” (Peterson & Spencer, 1991) – can have powerful effects on behaviour. Excessive alcohol consumption is undeniably an aspect of collegial culture, one that is having major impacts on the health and behaviour of students and staff, and one that I’ve been an active participant in for far too long. I’ll be turning forty in a few months and I have to face the fact that I’ve already drunk enough alcohol for two lifetimes, and not one drop of it has made me a better scientist, teacher or mentor. The question remains: how much more juice can I squeeze into this forty‐year‐old pickled lemon? Well, cheers to that.     

Mismatched expectations

Public funding for basic research rests on a delicate balance between scientists, governments and the public. COVID could further shift this equilibrium towards translation and application.

Keeping a research laboratory well‐funded to pay for salaries, reagents, infrastructure, travel, and publications is surely a challenging task that can consume most of a PI’s time. The risk is that if the funding decreases, the laboratory will have to shrink, which means less publications and a decreased probability of getting new grants. This downward spiral is hard to reverse and can end up with a token research activity and increased teaching instead. Some would see this is as an unwelcome career change. Apart from the personal challenge for PIs to keep the income flowing, there is no guarantee that the overall funding wallet for research will continue to grow and no certainty that the covenant between the funder and the funded will remain unchanged. The COVID‐19 pandemic could in fact accelerate ongoing changes in the way public funding for research is justified and distributed.There are three legs that support the delicate stool of competitive funding. The first is the scientists or, more precisely, the primary investigators. To get to that position, they had be high achievers as they moved from primary degree to PhD to post doc to the Valhalla of their own laboratory. Along the way they showed to be hard‐working, intelligent, competitive, innovative, lucky, and something between a team player and a team leader. The judgment to grant independence is largely based on publications—and given their track record of great papers to get there, most young PIs assume they will continue to get funding. This is not a narcissistic sense of entitlement; it is a logical conclusion of their career progression.They will get started by recruiting a few PhD or higher degree students. Although this is about educating students, a PI of course hopes that their students generate the results needed for the next grant application. The minimum time for a PhD is about three years, which explains that many grants are structured around a 3‐ to 5‐year research project. The endpoints are rarely the finishing line for a group’s overall research program: Hence, the comments in reviews along the line that “this paper raises more questions than it answers and more work will be required…” Work is carried on with a relay of grants edging asymptotically to answer a question raised decades before. I recall a lecturer from my PhD days who said that he would not do an obvious experiment that would prove or disprove his hypothesis, because “If I did that experiment, it would be the end of my career”. Others are less brazen but still continue to search for the mirage of truth when they know deep in their hearts that they are in a barren desert.The funding from the competitive grants is rarely enough to feed the ever‐growing demand for more people and resources and to make provisions for a hiatus in grant income. Eventually, an additional income stream comes from industry attracted by the knowledge and skills in the laboratory. The PI signs a contract for a one‐year period and allocates some resources to deliver the answers required when due. Similarly, some other resources are shepherded to fulfill the demands of a private donor who wants rapid progress on a disease that afflicts a loved one. The research group is doing a marathon run working on their core challenges with occasional sprints to generate deliverables and satisfy funders who require rapid success—a juggling act that demands much intellectual flexibility.State funding is the second leg and governments have multiple reasons for supporting academic research, even if these are not always presented clearly. Idealistically, the public supports research to add to the pool of knowledge and to understand the world in which we live but this is not how public funding started. The first universities began as theological seminars that expanded to include the arts, law, philosophy and medicine. Naturalists and natural scientists found them a serene and welcoming place to ponder important questions, conduct experiments, and discuss with their colleagues. The influence of Wilhelm von Humboldt who championed the concept of combining teaching and research at universities was immense: both became more professional with codified ways of generating and sharing knowledge. Government funding was an inevitable consequence: initially to pay for the education of students, it expanded to provide for research activities.While that rationale for supporting teaching and research remains, additional reasons for funding research emerged, mostly in the wake of World War 2: the military, national economies, and medicine required new products and services enabled by knowledge. It also required new structures and bodies to control and distribute public resources: hence the establishment of research funding agencies to decide which projects deserve public money. The US National Science Foundation was founded in 1950 following the analysis of Vannevar Bush that the country’s economic well‐being and security relied on research. The NIH extramural program started tentatively in the late 1930s. The Deutsche Forschungsgemeinschaft (DFG) was established in 1951. The EU Framework Programmes started in 1984 with the explicit goal to strengthen the economy of the community. It was only in 2007 that the European Research Council (ERC) was established to support excellence in research rather than to look at practical benefits.But the tide is inevitably moving toward linking state research funding with return on investment measured in jobs, economic growth, or improved health. Increasingly, the rationale for government investment is not just generation of knowledge or publications, but more products and services. As science is seen as the driver of innovation and future economic growth, the goal has been to invest 3% or more of a country’s GDP into research—although almost two‐thirds of this money comes from industry in advanced economies. Even nations without a strong industrial base strive to strengthen their economies by investing in brains. This message about government’s economic expectations is not lost on the funding agencies and softly trickles down to selection committees, analysts, and program officers. The idealistic image of the independent scientist pursuing knowledge for knowledge’s sake no longer fits into this bigger picture. They are now cajoled into research collaborations and partnerships and, hooked to the laboratories’ funding habit, willingly promise that the outcome of the work will somehow have practical applications: “This work will help efforts to cure cancer”.The third leg that influences research directions is the public who pay for research through their taxes. Mostly, they do not get overly excited or concerned about those few percentages of the national budget that go to laboratories. However, the COVID‐19 crisis could change that: Now, the people in the white coats are expected to provide rapid solutions to pressing and complex problems. The scientists have so far performed extremely well: understanding SARS‐CoV‐2 pathology, genetics, and impact on the immune system along with diagnostic tests and vaccine candidates came in record time. Vaccine development moved with lightning speed from discovery of the crucial receptor proteins to mass‐producing jabs, employing many new technologies for the first time. 2020 has been a breath‐taking and successful year for scientists who delivered a great return on investment.The public have also seen what a galvanized and cooperative scientific community across disciplines can achieve. “Aha,” they may say, “why don’t you now move on to tackle triple‐negative breast cancer, Alzheimer’s or Parkinson’s?” This is a fair and challenging question. And the increasing involvement of consumers and patients in research, at the behest of funding agencies, will further this expectation until the researchers respond. And respond they will, as they have always done to every hint of what might be needed to obtain funding.The old order is changing. The days of the independent academics getting funding for life to do what they like in the manner they chose will not survive the pressures from government to show a return on investment and from society to provide solutions to their problems. The danger is that early‐stage research—I did not say “basic” as it has joined “academic” as a pejorative term—will be suffocated. Governments appoint the heads of funding agencies, and it is not surprising if the appointees share the dominant philosophy of their employer. Peer‐review committees are being discouraged, subtly, from supporting early‐stage research. Elsewhere, the guidelines for decisions on grant applications give an increasing score for implementation, translation, IP generation, and so on. Those on the panels get the message and bring it back to their institutions that slowly move away from working to understand what we are ignorant about to using our (partial) understanding to develop cures and drugs.As in all areas, balance is needed. Those at the forefront of translating knowledge into outcomes for society have to remind the public as well as the government that the practical today is only possible because of the “impractical” research of yesterday. Industry is well aware of this and has become a strong champion for excellent early‐stage research to lay the groundwork for solving the next set of hard problems in the future. The ERC and its national counterparts have a special role to play in highlighting the benefits of supporting research with excellence as the sole criterion. In the meantime, scientists have to embrace the new task of developing solutions to societal problems without abandoning the hard slog of innovative research that opens up new understanding from which flows translation into practical applications.     

Innate,translation‐dependent silencing of an invasive transposon in Arabidopsis

Co‐evolution between hosts’ and parasites’ genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence degeneration, and, ultimately, loss of autonomy of most transposable elements (TEs). Recognition of newly invasive plant TEs, by contrast, involves an innate antiviral‐like silencing response. To investigate this response’s activation, we studied the single‐copy element EVADÉ (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically reactivated. In Ty1/Copia elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full‐length genomic flGAG‐POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly nuclear flGAG‐POL. During this process, an unusually intense ribosomal stalling event coincides with mRNA breakage yielding unconventional 5’OH RNA fragments that evade RNA quality control. The starting point of sRNA production by RNA‐DEPENDENT‐RNA‐POLYMERASE‐6 (RDR6), exclusively on shGAG, occurs precisely at this breakage point. This hitherto‐unrecognized “translation‐dependent silencing” (TdS) is independent of codon usage or GC content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against EVD de novo invasions that underlies its associated sRNA pattern.     

No evidence for female kin association,indications for extragroup paternity,and sex‐biased dispersal patterns in wild western gorillas

Characterizing animal dispersal patterns and the rational behind individuals’ transfer choices is a long‐standing question of interest in evolutionary biology. In wild western gorillas (Gorilla gorilla), a one‐male polygynous species, previous genetic findings suggested that, when dispersing, females might favor groups with female kin to promote cooperation, resulting in higher‐than‐expected within‐group female relatedness. The extent of male dispersal remains unclear with studies showing conflicting results. To investigate male and female dispersal patterns and extragroup paternity, we analyzed long‐term field observations, including female spatial proximity data, together with genetic data (10 autosomal microsatellites) on individuals from a unique set of four habituated western gorilla groups, and four additional extragroup males (49 individuals in total). The majority of offspring (25 of 27) were sired by the group male. For two offspring, evidence for extragroup paternity was found. Contrarily to previous findings, adult females were not significantly more related within groups than across groups. Consistently, adult female relatedness within groups did not correlate with their spatial proximity inferred from behavioral data. Adult females were similarly related to adult males from their group than from other groups. Using R _ST statistics, we found significant genetic structure and a pattern of isolation by distance, indicating limited dispersal in this species. Comparing relatedness among females and among males revealed that males disperse farer than females, as expected in a polygamous species. Our study on habituated western gorillas shed light on the dispersal dynamics and reproductive behavior of this polygynous species and challenge some of the previous results based on unhabituated groups.     

"Willing to Pay?" Tax Compliance in Britain and Italy: An Experimental Analysis

As shown by the recent crisis, tax evasion poses a significant problem for countries such as Greece, Spain and Italy. While these societies certainly possess weaker fiscal institutions as compared to other EU members, might broader cultural differences between northern and southern Europe also help to explain citizens’ (un)willingness to pay their taxes? To address this question, we conduct laboratory experiments in the UK and Italy, two countries which straddle this North-South divide. Our design allows us to examine citizens’ willingness to contribute to public goods via taxes while holding institutions constant. We report a surprising result: when faced with identical tax institutions, redistribution rules and audit probabilities, Italian participants are significantly more likely to comply than Britons. Overall, our findings cast doubt upon “culturalist” arguments that would attribute cross-country differences in tax compliance to the lack of morality amongst southern European taxpayers.     

Transient characteristics of universal cells on human‐induced pluripotent stem cells and their differentiated cells derived from foetal stem cells with mixed donor sources

IntroductionIt is important to prepare ‘hypoimmunogenic’ or ‘universal’ human pluripotent stem cells (hPSCs) with gene‐editing technology by knocking out or in immune‐related genes, because only a few hypoimmunogenic or universal hPSC lines would be sufficient to store for their off‐the‐shelf use. However, these hypoimmunogenic or universal hPSCs prepared previously were all genetically edited, which makes laborious processes to check and evaluate no abnormal gene editing of hPSCs.MethodsUniversal human‐induced pluripotent stem cells (hiPSCs) were generated without gene editing, which were reprogrammed from foetal stem cells (human amniotic fluid stem cells) with mixing 2‐5 allogenic donors but not with single donor. We evaluated human leucocyte antigen (HLA)‐expressing class Ia and class II of our hiPSCs and their differentiated cells into embryoid bodies, cardiomyocytes and mesenchymal stem cells. We further evaluated immunogenic response of transient universal hiPSCs with allogenic mononuclear cells from survival rate and cytokine production, which were generated by the cells due to immunogenic reactions.ResultsOur universal hiPSCs during passages 10‐25 did not have immunogenic reaction from allogenic mononuclear cells even after differentiation into cardiomyocytes, embryoid bodies and mesenchymal stem cells. Furthermore, the cells including the differentiated cells did not express HLA class Ia and class II. Cardiomyocytes differentiated from transient universal hiPSCs at passage 21‐22 survived and continued beating even after treatment with allogenic mononuclear cells.     

Patterns and correlates of patient‐reported helpfulness of treatment for common mental and substance use disorders in the WHO World Mental Health Surveys

Patient‐reported helpfulness of treatment is an important indicator of quality in patient‐centered care. We examined its pathways and predictors among respondents to household surveys who reported ever receiving treatment for major depression, generalized anxiety disorder, social phobia, specific phobia, post‐traumatic stress disorder, bipolar disorder, or alcohol use disorder. Data came from 30 community epidemiological surveys – 17 in high‐income countries (HICs) and 13 in low‐ and middle‐income countries (LMICs) – carried out as part of the World Health Organization (WHO)’s World Mental Health (WMH) Surveys. Respondents were asked whether treatment of each disorder was ever helpful and, if so, the number of professionals seen before receiving helpful treatment. Across all surveys and diagnostic categories, 26.1% of patients (N=10,035) reported being helped by the very first professional they saw. Persisting to a second professional after a first unhelpful treatment brought the cumulative probability of receiving helpful treatment to 51.2%. If patients persisted with up through eight professionals, the cumulative probability rose to 90.6%. However, only an estimated 22.8% of patients would have persisted in seeing these many professionals after repeatedly receiving treatments they considered not helpful. Although the proportion of individuals with disorders who sought treatment was higher and they were more persistent in HICs than LMICs, proportional helpfulness among treated cases was no different between HICs and LMICs. A wide range of predictors of perceived treatment helpfulness were found, some of them consistent across diagnostic categories and others unique to specific disorders. These results provide novel information about patient evaluations of treatment across diagnoses and countries varying in income level, and suggest that a critical issue in improving the quality of care for mental disorders should be fostering persistence in professional help‐seeking if earlier treatments are not helpful.     

Potential for prediction of psychosis and bipolar disorder in Child and Adolescent Mental Health Services: a longitudinal register study of all people born in Finland in 1987

Current strategies to predict psychosis identify only a small proportion of individuals at risk. Additional strategies are needed to increase capacity for pre­diction and prevention of serious mental illness, ideally during childhood and adolescence. One possible approach would be to investigate systems in which psychosis risk factors are concentrated during childhood. One notable such system is represented by Child and Adolescent Mental Health Services (CAMHS). Although psychotic disorders are uncommon in CAMHS, many risk factors for psychosis are highly prevalent in young people who enter this system. We hypothesized, therefore, that youth attending CAMHS would be a high‐risk group for psychosis if followed into adulthood and, furthermore, that CAMHS systems would capture a substantial proportion of future psychosis cases. We constructed a total population cohort study of all Finns born in 1987 (N=55,875), linking together extensive register data on health care contacts from birth through age 28 years. We identified all individuals diagnosed with a psychotic or bipolar disorder by age 28 (N=1,785). The risk of psychosis/bipolar disorder by age 28 years was 1.8% for individuals who had not attended CAMHS during childhood or adolescence, whereas it was 12.8% for those with a history of any outpatient CAMHS contact (odds ratio, OR=7.9, 95% CI: 7.2‐8.7). Furthermore, the risk of psychosis/bipolar disorder by age 28 years was 2.3% for individuals without a history of inpatient CAMHS admission, whereas it was 24.0% for those with a history of inpatient CAMHS admission (OR=13.3, 95% CI: 11.9‐14.9), and 36.5% for those with a history of inpatient CAMHS admission in adolescence (age 13‐17 years) (OR=24.2, 95% CI: 21.2‐27.6). Individuals who attended CAMHS but received no mental disorder diagnosis had an equally high risk of subsequently developing a psychosis/bipolar disorder as individuals who did receive a diagnosis (OR=0.9, 99.5% CI: 0.7‐1.1). Compared to other CAMHS attendees, individuals who developed psychosis or bipolar disorder were more likely to have had an initial CAMHS diagnosis of depressive or other mood disorder (OR=2.3, 99.5% CI: 1.6‐3.0) and disruptive behaviour disorder (OR=1.7, 99.5% CI: 1.2‐2.5). Of all psychosis/bipolar diagnoses by age 28 years, 50.2% occurred in individuals who had, at some point in childhood or adolescence, attended CAMHS, indicating that CAMHS represent not only a high‐risk but also a high‐capacity system for prediction of psychosis/bipolar disorder. These findings suggest an enormous, untapped potential for large‐scale psychosis/bipolar disorder prediction and prevention research within existing specialist CAMHS.     

Knowledge of HIV Serodiscordance,Transmission, and Prevention among Couples in Durban,South Africa

Objective

Couples’ voluntary HIV counseling and testing (CVCT) significantly decreases HIV transmission within couples, the largest risk group in sub-Saharan Africa, but it is not currently offered in most HIV testing facilities. To roll out such an intervention, understanding locale-specific knowledge barriers is critical. In this study, we measured knowledge of HIV serodiscordance, transmission, and prevention before and after receipt of CVCT services in Durban.

Design

Pre- and post-CVCT knowledge surveys were administered to a selection of individuals seeking CVCT services.

Methods

Changes in knowledge scores were assessed with McNemar Chi-square tests for balanced data and generalized estimating equation methods for unbalanced data.

Results

The survey included 317 heterosexual black couples (634 individuals) who were primarily Zulu (87%), unemployed (47%), and had at least a secondary level education (78%). 28% of couples proved to be discordant. Only 30% of individuals thought serodiscordance between couples was possible pre‐CVCT compared to 95% post-CVCT. One-third thought there was at least one benefit of CVCT pre‐CVCT, increasing to 96% post‐CVCT. Overall, there were positive changes in knowledge about HIV transmission and prevention. However, many respondents thought all HIV positive mothers give birth to babies with AIDS (64% pre-CVCT, 59% post-CVCT) and that male circumcision does not protect negative men against HIV (70% pre-CVCT, 67% post-CVCT).

Conclusions

CVCT was well received and was followed by improvements in understanding of discordance, the benefits of joint testing, and HIV transmission. Country-level health messaging would benefit from targeting gaps in knowledge about serodiscordance, vertical transmission, and male circumcision.     

Population structure of indigenous inhabitants of Arabia

Modern day Saudi Arabia occupies the majority of historical Arabia, which may have contributed to ancient waves of migration out of Africa. This ancient history has left a lasting imprint in the genetics of the region, including the diverse set of tribes that call Saudi Arabia their home. How these tribes relate to each other and to the world’s major populations remains an unanswered question. In an attempt to improve our understanding of the population structure of Saudi Arabia, we conducted genomic profiling of 957 unrelated individuals who self-identify with 28 large tribes in Saudi Arabia. Consistent with the tradition of intra-tribal unions, the subjects showed strong clustering along tribal lines with the distance between clusters correlating with their geographical proximities in Arabia. However, these individuals form a unique cluster when compared to the world’s major populations. The ancient origin of these tribal affiliations is supported by analyses that revealed little evidence of ancestral origin from within the 28 tribes. Our results disclose a granular map of population structure and have important implications for future genetic studies into Mendelian and common diseases in the region.     

Does Size Matter? Scaling of CO2 Emissions and U.S. Urban Areas

Urban areas consume more than 66% of the world’s energy and generate more than 70% of global greenhouse gas emissions. With the world’s population expected to reach 10 billion by 2100, nearly 90% of whom will live in urban areas, a critical question for planetary sustainability is how the size of cities affects energy use and carbon dioxide (CO₂) emissions. Are larger cities more energy and emissions efficient than smaller ones? Do larger cities exhibit gains from economies of scale with regard to emissions? Here we examine the relationship between city size and CO₂ emissions for U.S. metropolitan areas using a production accounting allocation of emissions. We find that for the time period of 1999–2008, CO₂ emissions scale proportionally with urban population size. Contrary to theoretical expectations, larger cities are not more emissions efficient than smaller ones.     

Nucleolar c‐Myc recruitment by a Vibrio T3SS effector promotes host cell proliferation and bacterial virulence

Pathogen type 3 secretion systems (T3SS) manipulate host cell pathways by directly delivering effector proteins into host cells. In Vibrio parahaemolyticus, the leading cause of bacterial seafood‐borne diarrheal disease, we showed that a T3SS effector, VgpA, localizes to the host cell nucleolus where it binds Epstein–Barr virus nuclear antigen 1‐binding protein 2 (EBP2). An amino acid substitution in VgpA (VgpA^L10A) did not alter its translocation to the nucleus but abolished the effector’s capacity to interact with EBP2. VgpA‐EBP2 interaction led to the re‐localization of c‐Myc to the nucleolus and increased cellular rRNA expression and proliferation of cultured cells. The VgpA‐EBP2 interaction elevated EBP2’s affinity for c‐Myc and prolonged the oncoprotein’s half‐life. Studies in infant rabbits demonstrated that VgpA is translocated into intestinal epithelial cells, where it interacts with EBP2 and leads to nucleolar re‐localization of c‐Myc. Moreover, the in vivo VgpA‐EBP2 interaction during infection led to proliferation of intestinal cells and heightened V. parahaemolyticus’ colonization and virulence. These observations suggest that direct effector stimulation of a c‐Myc controlled host cell growth program can contribute to pathogenesis.