The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis.

Cancer initiates as a consequence of genomic mutations and its subsequent progression relies in part on increased production of ribosomes to maintain high levels of protein synthesis for unchecked cell growth. Recently, cytidine deaminases have been uncovered as sources of mutagenesis in cancer. In an attempt to form a connection between these 2 cancer driving processes, we interrogated the cytidine deaminase family of proteins for potential roles in human ribosome biogenesis. We identified and validated APOBEC3A and APOBEC4 as novel ribosome biogenesis factors through our laboratory's established screening platform for the discovery of regulators of nucleolar function in MCF10A cells. Through siRNA depletion experiments, we highlight APOBEC3A's requirement in making ribosomes and specific role within the processing and maturation steps that form the large subunit 5.8S and 28S ribosomal (r)RNAs. We demonstrate that a subset of APOBEC3A resides within the nucleolus and associates with critical ribosome biogenesis factors. Mechanistic insight was revealed by transient overexpression of both wild-type and a catalytically dead mutated APOBEC3A, which both increase cell growth and protein synthesis. Through an innovative nuclear RNA sequencing methodology, we identify only modest predicted APOBEC3A C-to-U target sites on the pre-rRNA and pre-mRNAs. Our work reveals a potential direct role for APOBEC3A in ribosome biogenesis likely independent of its editing function. More broadly, we found an additional function of APOBEC3A in cancer pathology through its function in ribosome biogenesis, expanding its relevance as a target for cancer therapeutics.

Palaeoclimate evidence of vulnerable permafrost during times of low sea ice.

Climate change in the Arctic is occurring rapidly, and projections suggest the complete loss of summer sea ice by the middle of this century1. The sensitivity of permanently frozen ground (permafrost) in the Northern Hemisphere to warming is less clear, and its long-term trends are harder to monitor than those of sea ice. Here we use palaeoclimate data to show that Siberian permafrost is robust to warming when Arctic sea ice is present, but vulnerable when it is absent. Uranium-lead chronology of carbonate deposits (speleothems) in a Siberian cave located at the southern edge of continuous permafrost reveals periods in which the overlying ground was not permanently frozen. The speleothem record starts 1.5 million years ago (Ma), a time when greater equator-to-pole heat transport led to a warmer Northern Hemisphere2. The growth of the speleothems indicates that permafrost at the cave site was absent at that time, becoming more frequent from about 1.35 Ma, as the Northern Hemisphere cooled, and permanent after about 0.4 Ma. This history mirrors that of year-round sea ice in the Arctic Ocean, which was largely absent before about 0.4 Ma (ref. 3), but continuously present since that date. The robustness of permafrost when sea ice is present, as well as the increased permafrost vulnerability when sea ice is absent, can be explained by changes in both heat and moisture transport. Reduced sea ice may contribute to warming of Arctic air4-6, which can lead to warming far inland7. Open Arctic waters also increase the source of moisture and increase autumn snowfall over Siberia, insulating the ground from low winter temperatures8-10. These processes explain the relationship between an ice-free Arctic and permafrost thawing before 0.4 Ma. If these processes continue during modern climate change, future loss of summer Arctic sea ice will accelerate the thawing of Siberian permafrost.

Discovery of novel microRNA mimic repressors of ribosome biogenesis.

While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A (p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We provide evidence that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.

Signal transduction at GPCRs: Allosteric activation of the ERK MAPK by ß-arrestin.

ß-arrestins are multivalent adaptor proteins that bind active phosphorylated G protein-coupled receptors (GPCRs) to inhibit G protein signaling, mediate receptor internalization, and initiate alternative signaling events. ß-arrestins link agonist-stimulated GPCRs to downstream signaling partners, such as the c-Raf-MEK1-ERK1/2 cascade leading to ERK1/2 activation. ß-arrestins have been thought to transduce signals solely via passive scaffolding by facilitating the assembly of multiprotein signaling complexes. Recently, however, ß-arrestin 1 and 2 were shown to activate two downstream signaling effectors, c-Src and c-Raf, allosterically. Over the last two decades, ERK1/2 have been the most intensely studied signaling proteins scaffolded by ß-arrestins. Here, we demonstrate that ß-arrestins play an active role in allosterically modulating ERK kinase activity in vitro and within intact cells. Specifically, we show that ß-arrestins and their GPCR-mediated active states allosterically enhance ERK2 autophosphorylation and phosphorylation of a downstream ERK2 substrate, and we elucidate the mechanism by which ß-arrestins do so. Furthermore, we find that allosteric stimulation of dually phosphorylated ERK2 by active-state ß-arrestin 2 is more robust than by active-state ß-arrestin 1, highlighting differential capacities of ß-arrestin isoforms to regulate effector signaling pathways downstream of GPCRs. In summary, our study provides strong evidence for a new paradigm in which ß-arrestins function as active "catalytic" scaffolds to allosterically unlock the enzymatic activity of signaling components downstream of GPCR activation.

The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22.

The SAGA coactivator complex is essential for eukaryotic transcription and comprises four distinct modules, one of which contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II Ser2 phosphorylation and subsequent transcriptional elongation. In contrast to this H2B-associated role in transcription, we report here that human USP22 contributes to the early stages of stimulus-responsive transcription, where USP22 is required for pre-initiation complex (PIC) stability. Specifically, USP22 maintains long-range enhancer-promoter contacts and controls loading of Mediator tail and general transcription factors (GTFs) onto promoters, with Mediator core recruitment being USP22-independent. In addition, we identify Mediator tail subunits MED16 and MED24 and the Pol II subunit RBP1 as potential non-histone substrates of USP22. Overall, these findings define a role for human SAGA within the earliest steps of transcription.

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae.

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae.

The spiral wave frequency effect in atrial fibrillation.

A spiral wavefront (WF), generated by a cardiac rotor that drifts between surface electrodes during atrial fibrillation, exhibits frequency changes inconsistent with classical Doppler effect (CDE) phenomena. Recent clinical studies reveal three repeatedly observed events--1) side-dependent frequency changes across the path of the rotor, 2) one additional WF strike on the higher frequency side, and 3) a reversal of WF strike sequence--which constitute a diametrical property of spinning WF sources. A linear ray model is first used to reveal and develop the diametrical phenomena. Mathematical models of an Archimedean spiral and a spiral generated by the diffusion equation are developed and compared. Each formulation predicts the diametrical property that CDE does not capture and illuminates the occurrence of a strong side and weak side with respect to the rotor path. Whereas CDE exhibits higher and lower frequencies from approaching and receding sources of WFs, respectively, spiral rotors generate higher and lower frequencies on opposite sides of the migration path. This motivates the reconsideration of mapping and ablation strategies that have traditionally been based on identifying sites of the dominant frequency. While this research aims to characterize the path of a spiral rotor during atrial fibrillation accurately, the results are applicable in other fields of science and engineering in which rotating spiral waves occur.

Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing.

In eukaryotes, the nucleolus is the site of ribosome biosynthesis, an essential process in all cells. While human ribosome assembly is largely evolutionarily conserved, many of the regulatory details underlying its control and function have not yet been well-defined. The nucleolar protein RSL24D1 was originally identified as a factor important for 60S ribosomal subunit biogenesis. In addition, the PeBoW (BOP1-PES1-WDR12) complex has been well-defined as required for pre-28S rRNA processing and cell proliferation. In this study, we show that RSL24D1 depletion impairs both pre-ribosomal RNA (pre-rRNA) transcription and mature 28S rRNA production, leading to decreased protein synthesis and p53 stabilization in human cells. Surprisingly, each of the PeBoW complex members is also required for pre-rRNA transcription. We demonstrate that RSL24D1 and WDR12 co-immunoprecipitate with the RNA polymerase I subunit, RPA194, and regulate its steady state levels. These results uncover the dual role of RSL24D1 and the PeBoW complex in multiple steps of ribosome biogenesis, and provide evidence implicating large ribosomal subunit biogenesis factors in pre-rRNA transcription control.

Biomechanics of biting in loggerhead shrikes: jaw-closing force, velocity and an argument for power.

Differences in the physical and behavioral attributes of prey are likely to impose disparate demands of force and speed on the jaws of a predator. Because of biomechanical trade-offs between force and speed, this presents an interesting conundrum for predators of diverse prey types. Loggerhead shrikes (Lanius ludovicianus) are medium-sized (∼50 g) passeriform birds that dispatch and feed on a variety of arthropod and vertebrate prey, primarily using their beaks. We used high-speed video of shrikes biting a force transducer in lateral view to obtain corresponding measurements of bite force, upper and lower bill linear and angular displacements, and velocities. Our results show that upper bill depression (about the craniofacial hinge) is more highly correlated with bite force, whereas lower bill elevation is more highly correlated with jaw-closing velocity. These results suggest that the upper and lower jaws might play different roles for generating force and speed (respectively) in these and perhaps other birds as well. We hypothesize that a division of labor between the jaws may allow shrikes to capitalize on elements of force and speed without compromising performance. As expected on theoretical grounds, bite force trades-off against jaw-closing velocity during the act of biting, although peak bite force and jaw-closing velocity across individual shrikes show no clear signs of a force-velocity trade-off. As a result, shrikes appear to bite with jaw-closing velocities and forces that maximize biting power, which may be selectively advantageous for predators of diverse prey that require both jaw-closing force and speed.

Reporting of paediatric osteoporotic vertebral fractures in Duchenne muscular dystrophy and potential impact on clinical management: the need for standardised and structured reporting.

BACKGROUND: In boys with Duchenne muscular dystrophy (DMD), initiation of bisphosphonate is recommended upon identification of moderate or severe vertebral fractures, even if asymptomatic. Clear radiological reporting is important for consistency of clinical interpretation and management. OBJECTIVES: To audit radiology reports of spine imaging for vertebral fracture assessment in DMD, and assess potential impact on diagnosis and management. MATERIALS AND METHODS: Lateral thoracolumbar spine imaging (71 lateral spine radiographs and 13 lateral dual energy absorptiometry spine image) in 84 boys with DMD performed across two centres. Anonymised radiology reports by paediatric radiologists were circulated to two neuromuscular clinicians and two endocrinologists. Clinicians determined if there was vertebral fracture, no vertebral fracture, or unclear interpretation. Endocrinologists also determined if bisphosphonate was indicated. A single observer (a clinician with expertise in vertebral fracture assessment) performed vertebral fracture assessment in 37 images and re-reported using a structured format. Structured reports were re-circulated to the four clinicians to re-evaluate the degree of concordance in clinical diagnosis of vertebral fracture and treatment decisions with bisphosphonate. RESULTS: The term "fracture" was used in 25/84 (30%) radiology reports and only in 8/43 (19%) with description of vertebral body abnormalities. Fracture grading was included in 7/43 (16%) radiology reports. Diagnostic concordance by the clinicians was noted in 36/84 (43%). Unclear interpretation was noted in 22% to 51% based on radiology reports. No unclear interpretation was noted with structured reports. Complete diagnostic (37/37, 100%) and treatment (37/37, 100%) concordance was noted with the structured reports, whereas complete diagnostic and treatment concordance was noted in only 16/37 (43%) and 17/37 (46%) of the radiology reports, respectively. CONCLUSION: Only a third of radiology reports of spine imaging in DMD explicitly used the terminology "fracture". Grading was only noted in a small percentage. Variability in diagnostic interpretation by clinicians may lead to differing management plans. As identification of vertebral fracture is a trigger for treatment, developing reporting guidelines for paediatric vertebral fracture assessment will improve care. A structured template should be introduced for radiological reporting of paediatric vertebral fracture assessment.

Prehospital Ultrasound Use to Guide Emergent Pericardiocentesis: A Case Report.

Point-of-care ultrasound (POCUS) has been shown to be a valuable tool in the management of acutely ill patients in the prehospital setting. POCUS not only has utility from a diagnostic perspective but also has been shown to reduce the rate of complications from otherwise traditionally "blind" procedures, such as pericardiocentesis. This case report highlights the utility of POCUS in the prehospital setting to guide emergent pericardiocentesis to treat cardiac tamponade. The applicability of various approaches to ultrasound-guided pericardiocentesis is also discussed.

Prehospital Cardiac Ultrasound to Confirm Mechanical Capture in Emergency Transcutaneous Pacing: A Case Report.

Point-of-care ultrasound (POCUS) is a safe diagnostic tool that clinicians use to rapidly evaluate critically ill patients.1 POCUS has expanded into the prehospital setting and has been demonstrated to be accurate, feasible, and helpful in guiding clinical decision making.2-4 Additionally, the American College of Emergency Physicians recommends the use of echocardiography to evaluate for ventricular activity in the setting of cardiac arrest.5 There is minimal evidence regarding the use of POCUS to confirm mechanical capture in patients undergoing transcutaneous pacing. This case report highlights the use of POCUS in a patient with bradyasystolic cardiac arrest requiring transcutaneous pacing. Despite electrical capture, the patient had absent central pulses; however, POCUS demonstrated ventricular contractions, indicating mechanical capture. This suggests a role for POCUS for the evaluation of mechanical capture in patients undergoing cardiac pacing.

Lonely Individuals Process the World in Idiosyncratic Ways.

Loneliness is detrimental to well-being and is often accompanied by self-reported feelings of not being understood by other people. What contributes to such feelings in lonely people? We used functional MRI of 66 first-year university students to unobtrusively measure the relative alignment of people's mental processing of naturalistic stimuli and tested whether lonely people actually process the world in idiosyncratic ways. We found evidence for such idiosyncrasy: Lonely individuals' neural responses were dissimilar to those of their peers, particularly in regions of the default-mode network in which similar responses have been associated with shared perspectives and subjective understanding. These relationships persisted when we controlled for demographic similarities, objective social isolation, and individuals' friendships with each other. Our findings raise the possibility that being surrounded by people who see the world differently from oneself, even if one is friends with them, may be a risk factor for loneliness.

Development of Cationic Lipid LAH4-L1 siRNA Complexes for Focused Ultrasound Enhanced Tumor Uptake.

RNAi has considerable potential as a cancer therapeutic approach, but effective and efficient delivery of short interfering RNA (siRNA) to tumors remains a major hurdle. It remains a challenge to prepare a functional siRNA complex, target enough dose to the tumor, and stimulate its internalization into tumor cells and its release to the cytoplasm. Here, we show how these key barriers to siRNA delivery can be overcome with a complex─comprising siRNA, cationic lipids, and pH-responsive peptides─that is suited to tumor uptake enhancement via focused ultrasound (FUS). The complex provides effective nucleic acid encapsulation, nuclease protection, and endosomal escape such that gene silencing in cells is substantially more effective than that obtained with either equivalent lipoplexes or commercial reagents. In mice bearing MDA-MB-231 breast cancer xenografts, both lipid and ternary, lipid:peptide:siRNA complexes, prepared with near-infrared fluorescently labeled siRNA, accumulate in tumors following FUS treatments. Therefore, combining a well-designed lipid:peptide:siRNA complex with FUS tumor treatments is a promising route to achieve robust in vivo gene delivery.

Networks of necessity: Simulating COVID-19 mitigation strategies for disabled people and their caregivers.

A major strategy to prevent the spread of COVID-19 is the limiting of in-person contacts. However, limiting contacts is impractical or impossible for the many disabled people who do not live in care facilities but still require caregivers to assist them with activities of daily living. We seek to determine which interventions can best prevent infections of disabled people and their caregivers. To accomplish this, we simulate COVID-19 transmission with a compartmental model that includes susceptible, exposed, asymptomatic, symptomatically ill, hospitalized, and removed/recovered individuals. The networks on which we simulate disease spread incorporate heterogeneity in the risk levels of different types of interactions, time-dependent lockdown and reopening measures, and interaction distributions for four different groups (caregivers, disabled people, essential workers, and the general population). Of these groups, we find that the probability of becoming infected is largest for caregivers and second largest for disabled people. Consistent with this finding, our analysis of network structure illustrates that caregivers have the largest modal eigenvector centrality of the four groups. We find that two interventions-contact-limiting by all groups and mask-wearing by disabled people and caregivers-most reduce the number of infections in disabled and caregiver populations. We also test which group of people spreads COVID-19 most readily by seeding infections in a subset of each group and comparing the total number of infections as the disease spreads. We find that caregivers are the most potent spreaders of COVID-19, particularly to other caregivers and to disabled people. We test where to use limited infection-blocking vaccine doses most effectively and find that (1) vaccinating caregivers better protects disabled people from infection than vaccinating the general population or essential workers and that (2) vaccinating caregivers protects disabled people from infection about as effectively as vaccinating disabled people themselves. Our results highlight the potential effectiveness of mask-wearing, contact-limiting throughout society, and strategic vaccination for limiting the exposure of disabled people and their caregivers to COVID-19.

Soil Bacterial Assemblage Across a Production Landscape: Agriculture Increases Diversity While Revegetation Recovers Community Composition.

Aboveground ecological impacts associated with agricultural land use change are evident as natural plant communities are replaced with managed production systems. These impacts have been extensively studied, unlike those belowground, which remain poorly understood. Soil bacteria are good candidates to monitor belowground ecological dynamics due to their prevalence within the soil system and ability to survive under harsh and changing conditions. Here, we use soil physicochemical assessment and 16S rRNA gene sequencing to investigate the soil physical and bacterial assemblage changes across a mixed-use agricultural landscape. We assess soil from remnant vegetation (Eucalyptus mallee), new and old vineyards, old pasture, and recently revegetated areas. Elevated concentrations of nitrogen (NO3-) and plant-available (Colwell) phosphorus were identified in the managed vineyard systems, highlighting the impact of agricultural inputs on soil nutrition. Alpha diversity comparison revealed a significant difference between the remnant mallee vegetation and the vineyard systems, with vineyards supporting highest bacterial diversity. Bacterial community composition of recently revegetated areas was similar to remnant vegetation systems, suggesting that bacterial communities can respond quickly to aboveground changes, and that actions taken to restore native plant communities may also act to recover natural microbial communities, with implications for soil and plant health. Findings here suggest that agriculture may disrupt the correlation between above- and belowground diversities by altering the natural processes that otherwise govern this relationship (e.g. disturbance, plant production, diversity of inputs), leading to the promotion of belowground microbial diversity in agricultural systems.

Human nucleolar protein 7 (NOL7) is required for early pre-rRNA accumulation and pre-18S rRNA processing.

The main components of the essential cellular process of eukaryotic ribosome biogenesis are highly conserved from yeast to humans. Among these, the U3 Associated Proteins (UTPs) are a small subunit processome subcomplex that coordinate the first two steps of ribosome biogenesis in transcription and pre-18S processing. While we have identified the human counterparts of most of the yeast Utps, the homologs of yeast Utp9 and Bud21 (Utp16) have remained elusive. In this study, we find that NOL7 is the likely ortholog of Bud21. Previously described as a tumour suppressor through regulation of antiangiogenic transcripts, we now show that NOL7 is required for early pre-rRNA accumulation and pre-18S rRNA processing in human cells. These roles lead to decreased protein synthesis and induction of the nucleolar stress response upon NOL7 depletion. Beyond Bud21's nonessential role in yeast, we establish human NOL7 as an essential UTP that is necessary to maintain both early pre-rRNA levels and processing.

Low-dimensional behavior of a Kuramoto model with inertia and Hebbian learning.

We study low-dimensional dynamics in a Kuramoto model with inertia and Hebbian learning. In this model, the coupling strength between oscillators depends on the phase differences between the oscillators and changes according to a Hebbian learning rule. We analyze the special case of two coupled oscillators, which yields a five-dimensional dynamical system that decouples into a two-dimensional longitudinal system and a three-dimensional transverse system. We readily write an exact solution of the longitudinal system, and we then focus our attention on the transverse system. We classify the stability of the transverse system's equilibrium points using linear stability analysis. We show that the transverse system is dissipative and that all of its trajectories are eventually confined to a bounded region. We compute Lyapunov exponents to infer the transverse system's possible limiting behaviors, and we demarcate the parameter regions of three qualitatively different behaviors. Using insights from our analysis of the low-dimensional dynamics, we examine the original high-dimensional system in a situation in which we draw the intrinsic frequencies of the oscillators from Gaussian distributions with different variances.

Recurrence recovery in heterogeneous Fermi-Pasta-Ulam-Tsingou systems.

The computational investigation of Fermi, Pasta, Ulam, and Tsingou (FPUT) of arrays of nonlinearly coupled oscillators has led to a wealth of studies in nonlinear dynamics. Most studies of oscillator arrays have considered homogeneous oscillators, even though there are inherent heterogeneities between individual oscillators in real-world arrays. Well-known FPUT phenomena, such as energy recurrence, can break down in such heterogeneous systems. In this paper, we present an approach-the use of structured heterogeneities-to recover recurrence in FPUT systems in the presence of oscillator heterogeneities. We examine oscillator variabilities in FPUT systems with cubic nonlinearities, and we demonstrate that centrosymmetry in oscillator arrays may be an important source of recurrence.

Tyrosinase Inhibitors: A Perspective.

Due to its integral role in the biosynthesis of melanin in all kingdoms of life, tyrosinase has become an extremely important target for inhibition in several sectors of research including agricultural and cosmetic research. Inhibitors of tyrosinase have made it to the market in the cosmetics industry, but their use has been limited due to conflicting efficacy and potential toxicity, which has led to several small molecules being removed from the market. Undaunted, researchers have continued to pursue tyrosinase inhibitors with varying degrees of success. These pursuits have built an impressive and rich library of research. This review is intended to provide a perspective of the past twenty years (2003-2023) of research on tyrosinase inhibitors by highlighting exemplar molecules and developments.