Functional specialization of ribosomes?

Ribosomes are highly conserved macromolecular machines that are responsible for protein synthesis in all living organisms. Work published in the past year has shown that changes to the ribosome core can affect the mechanism of translation initiation that is favored in the cell, which potentially leads to specific changes in the relative efficiencies with which different proteins are made. Here, I examine recent data from expression and proteomic studies that suggest that cells make slightly different ribosomes under different growth conditions, and discuss genetic evidence that such differences are functional. In particular, I argue that eukaryotic cells probably produce ribosomes that lack one or more core ribosomal proteins (RPs) under some conditions, and that core RPs contribute differentially to translation of distinct subpopulations of mRNAs

The Bank of Canada's Senior Loan Officer Survey

The Bank of Canada maintains regular contact with financial institutions as part of the information-gathering process that feeds into the larger set of information used to arrive at its monetary policy decision. Since 1999, the Bank has been conducting a quarterly survey of the business-lending practices of major Canadian financial institutions. Analysis of the information collected shows that it is correlated with future growth in both credit and business investment. This article focuses on how the survey is conducted and describes the construction of the summary statistics, highlighting the key statistical relationships in the historical survey data.

Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling

Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. The anticodon modification mcm[superscript 5]s[superscript 2]U[superscript 34] is required for normal growth and stress resistance in yeast; mutants lacking this modification have numerous phenotypes. Mutations in the homologous human genes are linked to neurological disease. The yeast phenotypes can be ameliorated by overexpression of specific tRNAs, suggesting that the modifications are necessary for efficient translation of specific codons. We determined the in vivo ribosome distributions at single codon resolution in yeast strains lacking mcm[superscript 5]s[superscript 2]U. We found accumulations at AAA, CAA, and GAA codons, suggesting that translation is slow when these codons are in the ribosomal A site, but these changes appeared too small to affect protein output. Instead, we observed activation of the GCN4-mediated stress response by a non-canonical pathway. Thus, loss of mcm[superscript 5]s[superscript 2]U causes global effects on gene expression due to perturbation of cellular signaling.National Institutes of Health (U.S.) (Grant GM081399

The use of portraiture to foster humanistic care

It has been said that a picture says a thousand words, that art should speak for itself. Within the social sciences, there is recognition that images are not merely illustrations, but “texts” that can be read, studied and interpreted in different ways: they are visual narratives. When we look at a work of art, we respond with our own thoughts, feelings and ideas about what it communicates. When we look at a portrait specifically, we are not just looking at a picture of an individual, we are looking at a picture of someone being looked at. It is a visual record of an interaction, as much as a likeness of the person. The artist-sitter relationship has much in common with the doctor patient relationship involving trust, attention, and an openness to ambiguity and creativity. As clinicians that are tired and feeling overwhelmed, we may objectify patients. Engaging with art can help hone our skills to consistently see the whole person. It provides freedom to sit with ambiguity and maintain curiosity and can help us become more flexible in our thinking, to hold multiple possibilities in mind at the same time. Viewing art in a group provides opportunities to understand and appreciate others’ perspectives. Drawing on multiple portraiture projects related to pediatric epilepsy, youth mental health and dementia, this presentation will provide constructive ways in which portraiture can be used to foster humanistic, patient centred care, and to understand the power of distributed cognition

Revisiting ‘resilience’ in light of racism, ‘othering’ and resistance

In this commentary the authors analyse how the concept of resilience can be and has been applied to Black, Asian and minority ethnic families and communities in ways that are biased, stigmatising and pathologising. They argue that current definitions of resilience need to be redefined and reconceptualised, particularly in settings dominated by White middle-class voices that define what ‘positive emotions’, ‘successful traits’ and ‘coping mechanisms’ entail. Here, through racism and flawed perceptions and interpretations of resilience and ‘othering’, members from ethnic minority communities are defined as in need of resilience support, whilst at the same time their experience of structural racism, e.g., in relation to mental health support, social/health care practices and school exclusions, is being erased. Instead, the authors argue that resilience can also mean ‘resistance’, i.e., resisting bad treatment and racism, as well as reflecting agency, identity and ownership of one’s own life and choices within this. Reframing resilience thus means taking account of multifaceted and interactive effects of personal, material, institutional and political factors that impact on behaviour, wellbeing and resilience, as well as acknowledging that the way in which ‘behaviour’ is received is by default flawed, if this is largely informed by an oppressive White middle-class viewpoint

Alternative transcription start site selection leads to large differences in translation activity in yeast

mRNA levels do not accurately predict protein levels in eukaryotic cells. To investigate contributions of 5′ untranslated regions (5′ UTRs) to mRNA-specific differences in translation, we determined the 5′ UTR boundaries of 96 yeast genes for which in vivo translational efficiency varied by 80-fold. A total of 25% of genes showed substantial 5′ UTR heterogeneity. We compared the capacity of these genes' alternative 5′ UTR isoforms for cap-dependent and cap-independent translation using quantitative in vitro and in vivo translation assays. Six out of nine genes showed mRNA isoform-specific translation activity differences of greater than threefold in at least one condition. For three genes, in vivo translation activities of alternative 5′ UTR isoforms differed by more than 100-fold. These results show that changing genes' 5′ UTR boundaries can produce large changes in protein output without changing the overall amount of mRNA. Because transcription start site (TSS) heterogeneity is common, we suggest that TSS choice is greatly under-appreciated as a quantitatively significant mechanism for regulating protein production.National Institutes of Health (U.S.) (NIH grant GM081399

Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs

Translational control of gene expression plays essential roles in cellular stress responses and organismal development by enabling rapid, selective, and localized control of protein production. Translational regulation depends on context-dependent differences in the protein output of mRNAs, but the key mRNA features that distinguish efficiently translated mRNAs are largely unknown. Here, we comprehensively determined the RNA-binding preferences of the eukaryotic initiation factor 4G (eIF4G) to assess whether this core translation initiation factor has intrinsic sequence preferences that may contribute to preferential translation of specific mRNAs. We identified a simple RNA sequence motif-oligo-uridine-that mediates high-affinity binding to eIF4G in vitro. Oligo(U) motifs occur naturally in the transcript leader (TL) of hundreds of yeast genes, and mRNAs with unstructured oligo(U) motifs were enriched in immunoprecipitations against eIF4G. Ribosome profiling following depletion of eIF4G in vivo showed preferentially reduced translation of mRNAs with long TLs, including those that contain oligo(U). Finally, TL oligo(U) elements are enriched in genes with regulatory roles and are conserved between yeast species, consistent with an important cellular function. Taken together, our results demonstrate RNA sequence preferences for a general initiation factor, which cells potentially exploit for translational control of specific mRNAs. Keywords: RNA binding; eIF4G; ribosome footprint profiling; transcript leaders; translation initiationNational Institutes of Health (U.S.) (Grant GM094303)National Institutes of Health (U.S.) (Grant GM081399)National Institutes of Health (U.S.) (Grant T32GM007287

Protein kinase A regulates gene-specific translational adaptation in differentiating yeast

Cellular differentiation is driven by coordinately regulated changes in gene expression. Recent discoveries suggest that translation contributes as much as transcription to regulating protein abundance, but the role of translational regulation in cellular differentiation is largely unexplored. Here we investigate translational reprogramming in yeast during cellular adaptation to the absence of glucose, a stimulus that induces invasive filamentous differentiation. Using ribosome footprint profiling and RNA sequencing to assay gene-specific translation activity genome-wide, we show that prolonged glucose withdrawal is accompanied by gene-specific changes in translational efficiency that significantly affect expression of the majority of genes. Notably, transcripts from a small minority (<5%) of genes make up the majority of translating mRNA in both rapidly dividing and starved differentiating cells, and the identities of these highly translated messages are almost nonoverlapping between conditions. Furthermore, these two groups of messages are subject to condition-dependent translational privilege. Thus the “housekeeping” process of translation does not stay constant during cellular differentiation but is highly adapted to different growth conditions. By comparing glucose starvation to growth-attenuating stresses that do not induce invasive filamentation, we distinguish a glucose-specific translational response mediated through signaling by protein kinase A (PKA). Together, these findings reveal a high degree of growth-state specialization of the translatome and identify PKA as an important regulator of gene-specific translation activity.National Institutes of Health (U.S.) (R01 GM094303

DNA Extraction from Dry Museum Beetles without Conferring External Morphological Damage

BACKGROUND: A large number of dry-preserved insect specimens exist in collections around the world that might be useful for genetic analyses. However, until now, the recovery of nucleic acids from such specimens has involved at least the partial destruction of the specimen. This is clearly undesirable when dealing with rare species or otherwise important specimens, such as type specimens. METHODOLOGY: We describe a method for the extraction of PCR-amplifiable mitochondrial and nuclear DNA from dry insects without causing external morphological damage. Using PCR to amplify ≈220 bp of the mitochondrial gene cytochrome c oxidase I, and 250–345 bp fragments of the multi-copy, nuclear 28s ribosomal DNA gene, we demonstrate the efficacy of this method on beetles collected up to 50 years ago. CONCLUSIONS: This method offers a means of obtaining useful genetic information from rare insects without conferring external morphological damage

An analysis of automatic teller machine usage by older adults : a structured interview approach.

It is often assumed that automatic teller machines (ATMs) are inherently easy to use and require no training. However, there is evidence to suggest that ATM users do experience difficulty when learning to use the system. The purpose of the present study was to conduct an in-depth analysis of ATM usage by older adults. Our approach consisted of telephone interviews followed by structured individual interviews. The goals were to understand the problems encountered by ATM users, to determine how ATMs might be better designed and to assess the training needs of older individuals. The phone interview data provide information about the relationships between age, sex and ATM usage within the adult sample, as well as information about why some people choose not to use ATMs. The structured interview data provide a more in-depth view of the concerns of both users and non-users, and information about training needs. The training and design implications of the results are discussed