To fully understand the regulation of gene expression, it is critical to quantitatively define whether and how RNA-binding proteins (RBPs) discriminate between alternative binding sites in RNAs. ...Here, we describe new methods that measure protein binding to large numbers of RNA variants, and ways to analyse and interpret data obtained by these approaches, including affinity distributions and free energy landscapes. We discuss how the new methodologies and the associated concepts enable the development of inclusive, quantitative models for RNA-protein interactions that transcend the traditional binary classification of RBPs as either specific or nonspecific.
Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in ...metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process.
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•Metabolic pulse-chase labeling of rats identified long-lived proteins in rats•Long-lived proteins include nucleoporins, histone variants, and enzymes•Long-lived proteins cannot be replaced despite their robust translation•Nuclear pores are maintained over the lifespan of the organism
A system-wide identification of proteins with exceptional lifespans in the rat brain suggests that these have a higher propensity for damage. Cells utilize specific mechanisms to ensure that such proteins are maintained in a functional state through aging.
The survival rate for metastatic osteosarcoma has not improved for several decades, since the introduction and refinement of chemotherapy as a treatment in addition to surgery. Over two thirds of ...metastatic osteosarcoma patients, many of whom are children or adolescents, fail to exhibit durable responses and succumb to their disease. Concerted efforts have been made to increase survival rates through identification of candidate therapies via animal studies and early phase trials of novel treatments, but unfortunately, this work has produced negligible improvements to the survival rate for metastatic osteosarcoma patients. This review summarizes data from clinical trials of metastatic osteosarcoma therapies as well as pre-clinical studies that report efficacy of novel drugs against metastatic osteosarcoma in vivo. Considerations regarding the design of animal studies and clinical trials to improve survival outcomes for metastatic osteosarcoma patients are also discussed.
Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be noncoding, including 5′ UTRs and long noncoding RNAs (lncRNAs). Apparent ribosome footprints outside ...of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs). Here, we show hallmarks of translation in these footprints: copurification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. We develop a metric for distinguishing between 80S footprints and nonribosomal sources using footprint size distributions, which validates the vast majority of footprints outside of coding regions. We present evidence for polypeptide production beyond annotated genes, including the induction of immune responses following human cytomegalovirus (HCMV) infection. Translation is pervasive on cytosolic transcripts outside of conserved reading frames, and direct detection of this expanded universe of translated products enables efforts at understanding how cells manage and exploit its consequences.
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•Assembled 80S ribosomes occupy many 5′ UTRs and some lncRNAs•Fragment length metric (FLOSS) identifies true ribosome footprints bioinformatically•Large ribosome subunit pull-down confirms ribosome footprints experimentally•Noncanonical translation produces peptides, including novel antigens
Ribosome profiling, an experimental approach for detecting and quantifying translation, detected apparent ribosome footprints outside of annotated protein-coding genes, including many 5′ UTRs and some lncRNAs. Here, Ingolia et al. verify the presence of assembled 80S ribosomes on these RNAs through computational and experimental approaches. Furthermore, they show that peptides are translated from these regions in human cytomegalovirus (HCMV) and serve as HCMV-specific antigens, suggesting that endogenous human 5′ UTRs and lncRNAs may encode self-antigens and cancer neoantigens as well.
Nations have been questioned as meaningful units for analyzing culture due to their allegedly limited variance-capturing power and large internal heterogeneity. Against this skepticism, we argue that ...culture is by definition a collective phenomenon and focusing on individual differences contradicts the very concept of culture. Through the “miracle of aggregation,” we can eliminate random noise and arbitrary variation at the individual level in order to distill the central cultural tendencies of nations. Accordingly, we depict national culture as a gravitational field that socializes individuals into the orbit of a nation’s central cultural tendency. Even though individuals are also exposed to other gravitational forces, subcultures in turn gravitate within the limited orbit of their national culture. Using data from the World Values Survey, we show that individual values cluster in concentric circles around their nation’s cultural gravity center. We reveal the miracle of aggregation by demonstrating that nations capture the bulk of the variation in the individuals’ cultural values once they are aggregated into lower-level territorial units such as towns and sub-national regions. We visualize the gravitational force of national cultures by plotting various intra-national groups from five large countries that form distinct national clusters. Contrary to many scholars’ intuitions, alternative social aggregates, such as ethnic, linguistic, and religious groups, as well as diverse socio-demographic categories, add negligible explained variance to that already captured by nations.
Acid/base catalysis is an important catalytic strategy used by ribonucleases and ribozymes; however, understanding the number and identity of functional groups involved in proton transfer remains ...challenging. The proton inventory (PI) technique analyzes the dependence of the enzyme reaction rate on the ratio of D2O to H2O and can provide information about the number of exchangeable sites that produce isotope effects and their magnitude. The Gross–Butler (GB) equation is used to evaluate H/D fractionation factors from PI data typically collected under conditions (i.e., a “plateau” in the pH–rate profile) assuming minimal change in active site residue ionization. However, restricting PI analysis to these conditions is problematic for many ribonucleases, ribozymes, and their variants due to ambiguity in the roles of active site residues, the lack of a plateau within the accessible pL range, or cooperative interactions between active site functional groups undergoing ionization. Here, we extend the integration of species distributions for alternative enzyme states in noncooperative models of acid/base catalysis into the GB equation, first used by Bevilacqua and colleagues for the HDV ribozyme, to develop a general population-weighted GB equation that allows simulation and global fitting of the three-dimensional relationship of the D2O ratio (n) versus pL versus kn /k 0. Simulations using the GPW-GB equation of PI results for RNase A, HDVrz, and VSrz illustrate that data obtained at multiple selected pL values across the pL–rate profile can assist in the planning and interpreting of solvent isotope effect experiments to distinguish alternative mechanistic models.
This study examines how a university's research activities are viewed through the priorities of both of the university and the surrounding community. Framed by the notion of anchor institution, the ...study reports the results of a case study of the US regional university within an urban context. The findings demonstrate the lack of consensus around the role of the university, the disconnect related to research priorities between the community and the university, and the role of faculty activities and rewards. The analysis shows the challenges with universities with high research activity serving as anchor institutions, particularly related to social concerns. Implications for universities and researchers are also addressed.
"And I looked, and behold a pale horse: and his name that sat on him was Death, and Hell followed with him. And power was given unto them over the fourth part of the earth, to kill with sword, and ...with hunger, and with death, and with the beasts of the earth. New Testament, Revelation, Chapter 6, verse 8, King James Version"We are social psychologists, variously enmeshed in the havoc occasioned by the last year and beyond that Covid-19 has wrought to the world we each had come to know, to understand, and manage. Malignant, stealthy, elusive, invisible, and highly infectious, this disease rides on the back of normal human sociality, impacting the lives of all humanity, whether directly or indirectly. We each have adapted and continue to adapt to whatever requirements for change we confront in our local and national communities and do so with widely varying psychological effects—personal, interpersonal, and occupational.Societal changes slowly evolve as local containment strategies show variable and sometimes conflicting results, leading public health planners and political authorities to deliver inconsistent guidance over time, confusing and unsettling citizens. Uncertainty about the likely course of the pandemic and its impact on our lives frustrates us, the public, sometimes immobilizing, puzzling, and depressing us. What does our and humanity’s future hold? We might well wonder along with Yeats in his poem, Sailing to Byzantium, “What rough beast, its hour come round at last, slouches towards Bethlehem to be born?”The pandemic that the SARS-COV-2 virus has unleashed in its wake has impacted all our lives, disrupting long established habits and reorganizing our work routines and priorities professionally. As practicing social psychologists, how shall we respond, particularly those of us in Asia? Does our geographical-cultural positioning provide us with distinctive perspectives and emic conceptualizations that we can usefully exploit and share with our colleagues locked into their social realities elsewhere?
As well as being spatial, planning is necessarily also about the future - and yet time has been relatively neglected in the academic, practice and policy literature on planning. Time, in particular ...the need for longer-term thinking, is critical to responding effectively to a range of pressing societal challenges from climate change to an ageing population, poor urban health to sustainable economic development. This makes the relative neglect of time not only a matter of theoretical importance but also increasing practical and political significance.
A Future for Planning is an accessible, wide-ranging book that considers how planning practice and policy have been constrained by short-termism, as well as by a familiar lack of spatial thinking in policy, in response to major social, economic and environmental challenges. It suggests that failures in planning often represent failures to anticipate and shape the future which go well beyond planning systems and practices, rather our failure to plan for the longer-term relates to wider issues in policy-making and governance.
This book traces the rise and fall of long-term planning over the past 80 years or so, but also sets out how planning can take responsibility for twenty-first century challenges. It provides examples of successes and failures of longer-term planning from around the world. In short, the book argues that we need to put time back into planning, and develop forms of planning which serve to promote the sustainability and wellbeing of future generations.
What do pure mathematicians do, and why do they do it? Looking beyond the conventional answers-for the sake of truth, beauty, and practical applications-this book offers an eclectic panorama of the ...lives and values and hopes and fears of mathematicians in the twenty-first century, assembling material from a startlingly diverse assortment of scholarly, journalistic, and pop culture sources.
Drawing on his personal experiences and obsessions as well as the thoughts and opinions of mathematicians from Archimedes and Omar Khayyám to such contemporary giants as Alexander Grothendieck and Robert Langlands, Michael Harris reveals the charisma and romance of mathematics as well as its darker side. In this portrait of mathematics as a community united around a set of common intellectual, ethical, and existential challenges, he touches on a wide variety of questions, such as: Are mathematicians to blame for the 2008 financial crisis? How can we talk about the ideas we were born too soon to understand? And how should you react if you are asked to explain number theory at a dinner party?
Disarmingly candid, relentlessly intelligent, and richly entertaining,Mathematics without Apologiestakes readers on an unapologetic guided tour of the mathematical life, from the philosophy and sociology of mathematics to its reflections in film and popular music, with detours through the mathematical and mystical traditions of Russia, India, medieval Islam, the Bronx, and beyond.
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