Small RNAs include tRNA, snRNA, micro-RNA, tRNA fragments and others that constitute > 90% of RNA copy numbers in a human cell and perform many essential functions. Popular small RNA-seq strategies ...limit the insights into coordinated small RNA response to cellular stress. Small RNA-seq also lacks multiplexing capabilities. Here, we report a multiplex small RNA-seq library preparation method (MSR-seq) to investigate cellular small RNA and mRNA response to heat shock, hydrogen peroxide, and arsenite stress. Comparing stress-induced changes of total cellular RNA and polysome-associated RNA, we identify a coordinated tRNA response that involves polysome-specific tRNA abundance and synergistic N3-methylcytosine (m
C) tRNA modification. Combining tRNA and mRNA response to stress we reveal a mechanism of stress-induced down-regulation in translational elongation. We also find that native tRNA molecules lacking several modifications are biased reservoirs for the biogenesis of tRNA fragments. Our results demonstrate the importance of simultaneous investigation of small RNAs and their modifications in response to varying biological conditions.
TAR-DNA binding protein 43 (TDP-43) is a multifunctional RNA binding protein directly implicated in the etiology of amyotrophic lateral sclerosis (ALS). Previous studies have demonstrated that loss ...of TDP-43 function leads to intracellular accumulation of non-coding repetitive element transcripts and double-stranded RNA (dsRNA). These events could cause immune activation and contribute to the neuroinflammation observed in ALS, but this possibility has not been investigated. Here, we knock down TDP-43 in primary rat astrocytes via siRNA, and we use RNA-seq, immunofluorescence, and immunoblotting to show that this results in: 1) accumulation of repetitive element transcripts and dsRNA; and 2) pro-inflammatory gene and protein expression consistent with innate immune signaling and astrocyte activation. We also show that both chemical inhibition and siRNA knockdown of protein kinase R (PKR), a dsRNA-activated kinase implicated in the innate immune response, block the expression of all activation markers assayed. Based on these findings, we suggest that intracellular accumulation of endogenous dsRNA may be a novel and important mechanism underlying the pathogenesis of ALS (and perhaps other neurodegenerative diseases), and that PKR inhibitors may have the potential to prevent reactive astrocytosis in ALS.
•The RNA binding protein TDP-43 is implicated in amyotrophic lateral sclerosis.•TDP-43 knockdown in astrocytes increases repetitive and double-stranded RNA levels.•Knocking down TDP-43 also causes astrocytes to become reactive/pro-inflammatory.•Inhibition of protein kinase R prevents astrocyte activation with TDP-43 knockdown.
Pornography has become widely accessible in recent years due to its integration with the Internet, generating social scientific and moralistic debate on potential “media effects,” given correlations ...between consumption and various sexual traits and behaviors. One popular public debate (Wilson, 2012) claimed that exposure to Internet pornography has addictive qualities that could impact men’s sexual relationships, underpinned by the “Coolidge effect,” where males are sexually motivated by the presence of novel mates. As claims about Internet and sexual addictions are scientifically controversial, we provide a direct experimental test of his proposal. Adapting a paradigm used to examine “Coolidge-like” effects in men, we examined the extent to which exposure to images of pornographic actresses altered men’s attractiveness ratings of (1) familiar faces/bodies on second viewing and (2) familiar versus novel women’s faces/bodies. Independent of slideshow content (pornographic versus clothed versions of same actress), heterosexual men were less attracted to familiar bodies, and homosexual men were less attracted to familiar women (faces and bodies), suggesting that mere visual exposure to attractive women moderated men’s preferences. However, consistent with one of our preregistered predictions, heterosexual but not homosexual men’s preferences for familiar versus novel women were moderated by slideshow content such that familiar women were less salient on the attractiveness dimension compared to novel women when sexual arousal was greater (pornographic versus clothed slideshows). In sum, our findings demonstrate that visual exposure/sexual arousal moderates attractiveness perceptions, albeit that much greater nuance is required considering earlier claims.
Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in ...the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas in mammals the substrate for Q-modification in tRNA is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing from biological RNA samples. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method periodate-dependent analysis of queuosine and sulfur modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.
Transfer RNA (tRNA) utilizes multiple properties of abundance, modification, and aminoacylation in translational regulation. These properties were typically studied one-by-one; however, recent ...advance in high throughput tRNA sequencing enables their simultaneous assessment in the same sequencing data. How these properties are coordinated at the transcriptome level is an open question. Here, we develop a single-read tRNA analysis pipeline that takes advantage of the pseudo single-molecule nature of tRNA sequencing in NGS libraries. tRNAs are short enough that a single NGS read can represent one tRNA molecule, and can simultaneously report on the status of multiple modifications, aminoacylation, and fragmentation of each molecule. We find correlations among modification-modification, modification-aminoacylation and modification-fragmentation. We identify interdependencies among one of the most common tRNA modifications, m1A58, as coordinators of tissue-specific gene expression. Our method, SingLe-read Analysis of Crosstalks (SLAC), reveals tRNAome-wide networks of modifications, aminoacylation, and fragmentation. We observe changes of these networks under different stresses, and assign a function for tRNA modification in translational regulation and fragment biogenesis. SLAC leverages the richness of the tRNA-seq data and provides new insights on the coordination of tRNA properties.
Extensive efforts have been made to develop novel conjugated polymers that give improved performance in organic photovoltaic devices. The use of polymers based on alternating electron-donating and ...electron-accepting units not only allows the frontier molecular orbitals to be tuned to maximize the open-circuit voltage of the devices but also controls the optical band gap to increase the number of photons absorbed and thus modifies the other critical device parameterthe short circuit current. In fact, varying the nonchromophoric components of a polymer is often secondary to the efforts to adjust the intermolecular aggregates and improve the charge-carrier mobility. Here, we introduce an approach to polymer synthesis that facilitates simultaneous control over both the structural and electronic properties of the polymers. Through the use of a tailored multicomponent acceptor–donor–acceptor (A–D–A) intermediate, polymers with the unique structure A–D1–A–D2 can be prepared. This approach enables variations in the donor fragment substituents such that control over both the polymer regiochemistry and solubility is possible. This control results in improved intermolecular π-stacking interactions and therefore enhanced charge-carrier mobility. Solar cells using the A–D1–A–D2 structural polymer show short-circuit current densities that are twice that of the simple, random analogue while still maintaining an identical open-circuit voltage. The key finding of this work is that polymers with an A–D1–A–D2 structure offer significant performance benefits over both regioregular and random A–D polymers. The chemical synthesis approach that enables the preparation of A–D1–A–D2 polymers therefore represents a promising new route to materials for high-efficiency organic photovoltaic devices.
Although creativity is attractive in a potential mate, it is unclear (i) whether the effects of creativity on attractiveness generalize to other social contexts and (ii) whether creativity has ...equivalent effects on men's and women's attractiveness. As social knowledge of creativity may either enhance or ‘offset’ the appeal of social partners who differ in physical attractiveness, three repeated measures experiments were conducted to directly address these issues. Here, participants rated a series of face–text pairs for attractiveness on trials that differed in one of four combinations of facial attractiveness (attractive and less attractive) and creativity (creative and less creative), rating story-tellers in two experiments (short interpretations of an identical painting) and creative ideas in a further experiment (alternative uses for an everyday object). Regardless of the sex of the judge, creativity and facial attractiveness had independent effects on men's overall attractiveness (initial experiment) and, in further experiments, more substantial effects on the attractiveness of men with less attractive faces than men with attractive faces (when using a different measure of creativity) and specific effects on the attractiveness of individuals with less attractive faces (when using different face stimuli). Collectively, across three experiments, these findings suggest that creativity may compensate for putative cues to lower biological ‘quality’ and that the benefits of creativity to social groups more generally enhance attraction to creative men (in two experiments) and creative men and women (one experiment). More broadly, the data suggest that species can integrate knowledge of cognitive intelligence with visual cues to biological ‘quality’ to facilitate mate and/or ally choice.
While facial cues to body size are a valid guide to health and attractiveness, it is unclear whether the observer’s own condition predicts the salience of (low) size as a cue to female ...attractiveness. The current study examines whether measures related to women’s own attractiveness/appearance predict the extent to which they use facial cues to size to differentiate other women on the attractiveness dimension. Women completed a body mass index (BMI) preference task, where they indicated their preference for high- versus low-BMI versions of the same woman, provided data to calculate their BMI and completed various psychometric measures (self-rated attractiveness/health, dissatisfaction with physical appearance). Here, attractive women and women who were dissatisfied with their own appearance were more likely to associate facial cues to low body size with high attractiveness. These data suggest that psychological factors related to women’s appearance shape their evaluations of other women based on cues to size. Such variation in attractiveness judgements may function to reduce the costs of female competition for resources, for example, by identifying “quality” rivals or excluding others based on cues to size.
Growing evidence supports a key role for inflammation in the onset and progression of tendinopathy. However, the effect of the inflammatory infiltrate on tendon cells is poorly understood.
We ...investigated stromal fibroblast activation signatures in tissues and cells from patients with tendinopathy. Diseased tendons were collected from well-phenotyped patient cohorts with supraspinatus tendinopathy before and after sub-acromial decompression treatment. Healthy tendons were collected from patients undergoing shoulder stabilisation or anterior cruciate ligament repair. Stromal fibroblast activation markers including podoplanin (PDPN), CD106 (VCAM-1) and CD248 were investigated by immunostaining, flow cytometry and RT-qPCR.
PDPN, CD248 and CD106 were increased in diseased compared to healthy tendon tissues. This stromal fibroblast activation signature persisted in tendon biopsies in patients at 2-4 years post treatment. PDPN, CD248 and CD106 were increased in diseased compared to healthy tendon cells. IL-1β treatment induced PDPN and CD106 but not CD248. IL-1β treatment induced NF-κB target genes in healthy cells, which gradually declined following replacement with cytokine-free medium, whilst PDPN and CD106 remained above pre-stimulated levels. IL-1β-treated diseased cells had more profound induction of PDPN and CD106 and sustained expression of IL6 and IL8 mRNA compared to IL-1β-treated healthy cells.
We conclude that stromal fibroblast activation markers are increased and persist in diseased compared to healthy tendon tissues and cells. Diseased tendon cells have distinct stromal fibroblast populations. IL-1β treatment induced persistent stromal fibroblast activation which was more profound in diseased cells. Persistent stromal fibroblast activation may be implicated in the development of chronic inflammation and recurrent tendinopathy. Targeting this stromal fibroblast activation signature is a potential therapeutic strategy.
Positive associations between physical attractiveness and employee reward are well-documented within the organisational literature. Although the impact of facial cues to trustworthiness and dominance ...on a number of social outcomes has been established outside of the workplace, the extent to which they, in addition to attractiveness, affect pay at different managerial levels is yet to be investigated. This paper presents research into this issue using a face payment task for shop floor managers (Retail Managers) and senior managers (Heads of Retail Operations). Evaluations indicated that all three facial cues were positively associated with awarded pay at both managerial levels. Moreover, attractiveness had a significantly stronger link with shop-floor managers' than senior managers' pay, whereas perceived trustworthiness and perceived dominance had significantly stronger links with pay for senior managers than shop-floor managers. It further emerged that women were paid more in this experimental task where pay was awarded solely based on facial features and that the facial features were more predictive of women's than men's pay. Awareness of the role of physical cues in pay awards can be considered by organisations to reduce biases in remuneration.
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