K29-linked free polyubiquitin chains affect ribosome biogenesis and direct ribosomal proteins to the intranuclear quality control compartment.

Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs) Ubp2 and Ubp14, and E3 ligases Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the intranuclear quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with ribosomopathies.

K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ).

Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs), Ubp2 and Ubp14, and E3 ligases, Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the Ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the Intranuclear Quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with Ribosomopathies.

Developmental changes in audiotactile event perception.

The fission and fusion illusions provide measures of multisensory integration. The sound-induced tap fission illusion occurs when a tap is paired with two distractor sounds, resulting in the perception of two taps; the sound-induced tap fusion illusion occurs when two taps are paired with a single sound, resulting in the perception of a single tap. Using these illusions, we measured integration in three groups of children (9-, 11-, and 13-year-olds) and compared them with a group of adults. Based on accuracy, we derived a measure of magnitude of illusion and used a signal detection analysis to estimate perceptual discriminability and decisional criterion. All age groups showed a significant fission illusion, whereas only the three groups of children showed a significant fusion illusion. When compared with adults, the 9-year-olds showed larger fission and fusion illusions (i.e., reduced discriminability and greater bias), whereas the 11-year-olds were adult-like for fission but showed some differences for fusion: significantly worse discriminability and marginally greater magnitude and criterion. The 13-year-olds were adult-like on all measures. Based on the pattern of data, we speculate that the developmental trajectories for fission and fusion differ. We discuss these developmental results in the context of three non-mutually exclusive theoretical frameworks: sensory dominance, maximum likelihood estimation, and causal inference.

Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events.

BACKGROUND: The Ccr4-Not complex is mostly known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics has been reported. Typical studies that evaluate translation efficiency rely on soluble extracts obtained after the disruption of cells and ribosome profiling. Yet cellular mRNAs in condensates can be actively translated and may not be present in such extracts. RESULTS: In this work, by analyzing soluble and insoluble mRNA decay intermediates in yeast, we determine that insoluble mRNAs are enriched for ribosomes dwelling at non-optimal codons compared to soluble mRNAs. mRNA decay is higher for soluble RNAs, but the proportion of co-translational degradation relative to the overall mRNA decay is higher for insoluble mRNAs. We show that depletion of Not1 and Not4 inversely impacts mRNA solubilities and, for soluble mRNAs, ribosome dwelling according to codon optimality. Depletion of Not4 solubilizes mRNAs with lower non-optimal codon content and higher expression that are rendered insoluble by Not1 depletion. By contrast, depletion of Not1 solubilizes mitochondrial mRNAs, which are rendered insoluble upon Not4 depletion. CONCLUSIONS: Our results reveal that mRNA solubility defines the dynamics of co-translation events and is oppositely regulated by Not1 and Not4, a mechanism that we additionally determine may already be set by Not1 promoter association in the nucleus.

GPR68 limits the severity of chemical-induced oral epithelial dysplasia.

Head and neck cancer is the sixth most common malignancy, and there is an urgent need to identify physiological processes contributing to tumorigenesis. Extracellular acidification caused by aerobic glycolysis within tumor microenvironments can stimulate proton-sensing receptors. GPR68, or ovarian cancer G protein-coupled receptor 1, responds to extracellular acidity and is highly expressed in head and neck squamous cell carcinoma (HNSCC) as well as normal esophageal tissue. To study the role of GPR68 in oral dysplasia, wild-type and GPR68-/- mice were treated with 4-Nitroquinoline N-oxide (4NQO) in drinking water for 11-13 weeks, followed by normal water for 11-12 weeks. 4NQO treatment resulted in 45 percent of GPR68-/- mice developing severe dysplasia or squamous cell carcinoma compared to only 10.5 percent of GPR68+/+ mice. This correlated with increased frequencies of regulatory T cells in the spleens of male GPR68-/- mice. Dysplastic regions of the tongue had increased CD31 staining compared to normal regions in both GPR68-/- and GPR68+/+ mice, suggesting that angiogenesis was GPR68-independent. RNA knockdown studies using HNSCC cell lines demonstrated no direct effect of GPR68 on survival or growth. Overall, we demonstrate that GPR68-deficiency worsens the severity of chemical-induced oral dysplasia, suggesting a protective role for this gene in tumorigenesis.

The development of audio-visual temporal precision precedes its rapid recalibration.

Through development, multisensory systems reach a balance between stability and flexibility: the systems integrate optimally cross-modal signals from the same events, while remaining adaptive to environmental changes. Is continuous intersensory recalibration required to shape optimal integration mechanisms, or does multisensory integration develop prior to recalibration? Here, we examined the development of multisensory integration and rapid recalibration in the temporal domain by re-analyzing published datasets for audio-visual, audio-tactile, and visual-tactile combinations. Results showed that children reach an adult level of precision in audio-visual simultaneity perception and show the first sign of rapid recalibration at 9 years of age. In contrast, there was very weak rapid recalibration for other cross-modal combinations at all ages, even when adult levels of temporal precision had developed. Thus, the development of audio-visual rapid recalibration appears to require the maturation of temporal precision. It may serve to accommodate distance-dependent travel time differences between light and sound.

Effect of Coronavirus Disease 2019 (Covid-19), a Nationwide Mass Casualty Disaster on Intensive Care Units: Clinical Outcomes and Associated Cost-of-Care.

OBJECTIVE: The COVID-19 pandemic resulted in millions of deaths worldwide and is considered a significant mass-casualty disaster (MCD). The surge of patients and scarcity of resources negatively impacted hospitals, patients and medical practice. We hypothesized ICUs during this MCD had a higher acuity of illness, and subsequently had increased lengths of stay (LOS), complication rates, death rates and costs of care. The purpose of this study was to investigate those outcomes. METHODS: This was a multicenter, retrospective study that compared intensive care admissions in 2020 to those in 2019 to evaluate patient outcomes and cost of care. Data were obtained from the Vizient Clinical Data Base/Resource Manager (Vizient Inc., Irvine, Texas, USA). RESULTS: Data included the number of ICU admissions, patient outcomes, case mix index and summary of cost reports. Quality outcomes were also collected, and a total of 1304981 patients from 333 hospitals were included. For all medical centers, there was a significant increase in LOS index, ICU LOS, complication rate, case mix index, total cost, and direct cost index. CONCLUSION: The MCD caused by COVID-19 was associated with increased adverse outcomes and cost-of-care for ICU patients.

Ribosome biogenesis and the cellular energy economy.

Cell growth relies upon the ability to produce new proteins, which requires energy and chemical precursors, and an adequate supply of the molecular machines for protein synthesis - ribosomes. Although not widely appreciated, ribosomes are remarkably abundant in all cells. For example, in a rapidly growing yeast cell there are ∼2-4 x 105 ribosomes, produced and exported to the cytoplasm at a rate of ∼2,000-4,000 per minute, with ribosomal proteins making up ∼50% of total cellular protein number and ∼30% of cellular protein mass. Even in a typical human cell ribosomal proteins constitute ∼4-6% of total protein mass, and ribosomes are present at ∼107 per cell. We begin this primer by exploring the tight relationship between ribosome production and cell growth, which has important implications not just for the cell's global protein expression profile and maximum growth rate, but also for the molecular composition of the ribosome itself. We then discuss how and to what extent the expression of the RNA and protein components of ribosomes is fine-tuned to match the cell's needs and minimise waste. Finally, we highlight the importance of coordinated ribosomal RNA (rRNA) and ribosomal protein expression in eukaryotes and explore how defects in this process are associated with proteotoxicity and disease. A central underlying question addressed throughout is whether regulation of ribosome biogenesis has evolved to optimise energy efficiency or is instead (or in addition) driven by other goals, such as maximising cell growth rate, promoting adaptation to changing environmental conditions, or maintaining the stability of the cellular proteome.

Lung and extrathoracic cancer incidence among underground uranium miners exposed to radon progeny in the Príbram region of the Czech Republic: a case-cohort study.

OBJECTIVES: Radon is carcinogenic, but more studies are needed to understand relationships with lung cancer and extrathoracic cancers at low exposures. There are few studies evaluating associations with cancer incidence or assessing the modifying effects of smoking. METHODS: We conducted a case-cohort study with 16 434 underground uranium miners in the Czech Republic with cancer incidence follow-up 1977-1996. Associations between radon exposure and lung cancer, and extrathoracic cancer, were estimated with linear excess relative rate (ERR) models. We examined potential modifying effects of smoking, time since exposure and exposure rate. RESULTS: Under a simple ERR model, assuming a 5-year exposure lag, the estimated ERR of lung cancer per 100 working level months (WLM) was 0.54 (95% CI 0.33 to 0.83) and the estimated ERR of extrathoracic cancer per 100 WLM was 0.07 (95% CI -0.17 to 0.72). Most lung cancer cases were observed among smokers (82%), and the estimated ERR of lung cancer per 100 WLM was larger among smokers (ERR/100 WLM=1.35; 95% CI 0.84 to 2.15) than among never smokers (ERR/100 WLM=0.12; 95% CI -0.05 to 0.49). Among smokers, the estimated ERR of lung cancer per 100 WLM decreased with time since exposure from 3.07 (95% CI -0.04 to 10.32) in the period 5-14 years after exposure to 1.05 (95% CI 0.49 to 1.87) in the period 25+ years after exposure. CONCLUSIONS: We observed positive associations between cumulative radon exposure and lung cancer, consistent with prior studies. We observed a positive association between cumulative radon exposure and extrathoracic cancers, although the estimates were small. There was evidence that the association between radon and lung cancer was modified by smoking in a multiplicative or super-multiplicative fashion.

Imagine Your Crossed Hands as Uncrossed: Visual Imagery Impacts the Crossed-Hands Deficit.

Successful interaction with our environment requires accurate tactile localization. Although we seem to localize tactile stimuli effortlessly, the processes underlying this ability are complex. This is evidenced by the crossed-hands deficit, in which tactile localization performance suffers when the hands are crossed. The deficit results from the conflict between an internal reference frame, based in somatotopic coordinates, and an external reference frame, based in external spatial coordinates. Previous evidence in favour of the integration model employed manipulations to the external reference frame (e.g., blindfolding participants), which reduced the deficit by reducing conflict between the two reference frames. The present study extends this finding by asking blindfolded participants to visually imagine their crossed arms as uncrossed. This imagery manipulation further decreased the magnitude of the crossed-hands deficit by bringing information in the two reference frames into alignment. This imagery manipulation differentially affected males and females, which was consistent with the previously observed sex difference in this effect: females tend to show a larger crossed-hands deficit than males and females were more impacted by the imagery manipulation. Results are discussed in terms of the integration model of the crossed-hands deficit.

Herpes Simplex Virus Meningoencephalitis Following Pulse-Dose Methylprednisolone: A Case Report and Literature Review.

BACKGROUND Several cases of herpes simplex virus type 1 meningoencephalitis (HSVE) have been reported in patients receiving steroids, but the exact contribution of steroids to the disorder remains unclear because other risk factors, such as chemotherapy, brain radiation, or surgery, were present in almost all cases. CASE REPORT We report the case of a 76-year-old man who developed HSVE following the administration of pulse-dose steroids. The patient had occupational asbestos exposure and a chronic interstitial lung disease of unclear etiology (sarcoidosis versus hypersensitivity pneumonitis) and was admitted for acute-on-chronic respiratory failure requiring mechanical ventilation. After a negative infectious workup and several days of antibiotics without improvement, pulse-dose steroids were administered. In the following days, the patient developed a fever and worsening encephalopathy. A lumbar puncture showed elevated nucleated cells and positive polymerase chain reaction for herpes simplex virus 1 in the cerebrospinal fluid, confirming the diagnosis of HSVE. Acyclovir treatment was initiated, but the patient later died as a result of persistent severe encephalopathy and respiratory failure with an inability to wean mechanical ventilation. CONCLUSIONS Clinicians should keep in mind that HSVE is a potential complication of steroids and carefully consider the benefit/risk ratio of pulse-dose steroids, taking into account associated factors of immunosuppression. A high level of awareness should be especially maintained in critically ill patients because of associated risk factors (critical illness immune paralysis) and because neurological signs of HSVE may be missed in mechanically ventilated, sedated patients.

Exploring Reference Frame Integration Using Response Demands in a Tactile Temporal-Order Judgement Task.

Exploring the world through touch requires the integration of internal (e.g., anatomical) and external (e.g., spatial) reference frames - you only know what you touch when you know where your hands are in space. The deficit observed in tactile temporal-order judgements when the hands are crossed over the midline provides one tool to explore this integration. We used foot pedals and required participants to focus on either the hand that was stimulated first (an anatomical bias condition) or the location of the hand that was stimulated first (a spatiotopic bias condition). Spatiotopic-based responses produce a larger crossed-hands deficit, presumably by focusing observers on the external reference frame. In contrast, anatomical-based responses focus the observer on the internal reference frame and produce a smaller deficit. This manipulation thus provides evidence that observers can change the relative weight given to each reference frame. We quantify this effect using a probabilistic model that produces a population estimate of the relative weight given to each reference frame. We show that a spatiotopic bias can result in either a larger external weight (Experiment 1) or a smaller internal weight (Experiment 2) and provide an explanation of when each one would occur.

Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals.

Ribosome biogenesis requires prodigious transcriptional output in rapidly growing yeast cells and is highly regulated in response to both growth and stress signals. This minireview focuses on recent developments in our understanding of this regulatory process, with an emphasis on the 138 ribosomal protein genes (RPGs) themselves and a group of >200 ribosome biogenesis (RiBi) genes whose products contribute to assembly but are not part of the ribosome. Expression of most RPGs depends upon Rap1, a pioneer transcription factor (TF) required for the binding of a pair of RPG-specific TFs called Fhl1 and Ifh1. RPG expression is correlated with Ifh1 promoter binding, whereas Rap1 and Fhl1 remain promoter-associated upon stress-induced down regulation. A TF called Sfp1 has also been implicated in RPG regulation, though recent work reveals that its primary function is in activation of RiBi and other growth-related genes. Sfp1 plays an important regulatory role at a small number of RPGs where Rap1-Fhl1-Ifh1 action is subsidiary or non-existent. In addition, nearly half of all RPGs are bound by Hmo1, which either stabilizes or re-configures Fhl1-Ifh1 binding. Recent studies identified the proline rotamase Fpr1, known primarily for its role in rapamycin-mediated inhibition of the TORC1 kinase, as an additional TF at RPG promoters. Fpr1 also affects Fhl1-Ifh1 binding, either independently or in cooperation with Hmo1. Finally, a major recent development was the discovery of a protein homeostasis mechanism driven by unassembled ribosomal proteins, referred to as the Ribosome Assembly Stress Response (RASTR), that controls RPG transcription through the reversible condensation of Ifh1.

Approaching Protein Barriers: Emerging Mechanisms of Replication Pausing in Eukaryotes.

During nuclear DNA replication multiprotein replisome machines have to jointly traverse and duplicate the total length of each chromosome during each cell cycle. At certain genomic locations replisomes encounter tight DNA-protein complexes and slow down. This fork pausing is an active process involving recognition of a protein barrier by the approaching replisome via an evolutionarily conserved Fork Pausing/Protection Complex (FPC). Action of the FPC protects forks from collapse at both programmed and accidental protein barriers, thus promoting genome integrity. In addition, FPC stimulates the DNA replication checkpoint and regulates topological transitions near the replication fork. Eukaryotic cells have been proposed to employ physiological programmed fork pausing for various purposes, such as maintaining copy number at repetitive loci, precluding replication-transcription encounters, regulating kinetochore assembly, or controlling gene conversion events during mating-type switching. Here we review the growing number of approaches used to study replication pausing in vivo and in vitro as well as the characterization of additional factors recently reported to modulate fork pausing in different systems. Specifically, we focus on the positive role of topoisomerases in fork pausing. We describe a model where replisome progression is inherently cautious, which ensures general preservation of fork stability and genome integrity but can also carry out specialized functions at certain loci. Furthermore, we highlight classical and novel outstanding questions in the field and propose venues for addressing them. Given how little is known about replisome pausing at protein barriers in human cells more studies are required to address how conserved these mechanisms are.

Haptic awareness changes when lying down.

Accurate localization of touch requires the integration of two reference frames-an internal (e.g., anatomical) and an external (e.g., spatial). Using a tactile temporal order judgement task with the hands crossed over the midline, we investigated the integration of these two reference frames. We manipulated the reliability of the visual and vestibular information, both of which contribute to the external reference frame. Visual information was manipulated between experiments (Experiment 1 was done with full vision and Experiment 2 was done while wearing a blindfold). Vestibular information was manipulated in both experiments by having the two groups of participants complete the task in both an upright posture and one where they were lying down on their side. Using a Bayesian hierarchical model, we estimated the perceptual weight applied to these reference frames. Lying participants on their side reduced the weight applied to the external reference frame and produced a smaller deficit; blindfolding resulted in similar reductions. These findings reinforce the importance of the visual system when weighting tactile reference frames, and highlight the importance of the vestibular system in this integration.

Mechanisms coordinating ribosomal protein gene transcription in response to stress.

While expression of ribosomal protein genes (RPGs) in the budding yeast has been extensively studied, a longstanding enigma persists regarding their co-regulation under fluctuating growth conditions. Most RPG promoters display one of two distinct arrangements of a core set of transcription factors (TFs) and are further differentiated by the presence or absence of the HMGB protein Hmo1. However, a third group of promoters appears not to be bound by any of these proteins, raising the question of how the whole suite of genes is co-regulated. We demonstrate here that all RPGs are regulated by two distinct, but complementary mechanisms driven by the TFs Ifh1 and Sfp1, both of which are required for maximal expression in optimal conditions and coordinated downregulation upon stress. At the majority of RPG promoters, Ifh1-dependent regulation predominates, whereas Sfp1 plays the major role at all other genes. We also uncovered an unexpected protein homeostasis-dependent binding property of Hmo1 at RPG promoters. Finally, we show that the Ifh1 paralog Crf1, previously described as a transcriptional repressor, can act as a constitutive RPG activator. Our study provides a more complete picture of RPG regulation and may serve as a paradigm for unravelling RPG regulation in multicellular eukaryotes.

Divergence and Convergence of Royalty Determinations between Compulsory Licensing under the TRIPS Agreement and Ongoing Royalties as an Equitable Remedy.

Patent rights are recognized as a property asset with an attendant right to exclude. However, recent policy developments highlight that the right to exclude is not inviolable. This paper explores two rapidly evolving exceptions to patent exclusivity, both of which take the form of compulsory licenses. First, under the international Agreement on Trade-Related Aspects of Intellectual Property Rights ("TRIPS"), national governments can compel patent owners to out-license technology in service of greater good. These egalitarian compulsory licenses improve access to technology but undermine patent value. Second, compulsory licenses are increasingly relied upon as an equitable remedy in U.S. patent litigation. Typically referred to as "ongoing royalties," these court-mandated compulsory licenses are a modern alternative to injunctions against adjudged infringers. TRIPS compulsory licenses and ongoing royalties arise under independent legal frameworks, but necessarily invoke parallel economic considerations. While the wisdom of each has been discussed at length by others, this paper explores principles of royalty determination employed in each context. Considering both frameworks, an analysis of where each succeeds and fails is provided, together with an exploration of optimized royalty frameworks.

Today's Leadership Lesson: Mind the Wildlife and Prepare for Tomorrow's Disruption.

As the world reacts with unprecedented efforts to contain the COVID-19 pandemic, the role of organizational leaders is to embark on a parallel track to keep mission-critical initiatives moving forward. One track includes preparing their organizations for the next "novel" virus. After all, organizations do not hire leaders to maintain the status quo; they are hired to drive the future. As much as death and taxes are inevitable, it is equally predictable that all organizations will sooner or later confront a black swan event. History teaches us that while the order of magnitude may vary, management crises are not entirely novel. This article explores a series of early risk mitigation strategies to prevent the next COVID-19 and prepare leadership to face this inevitable challenge.